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COSMOtherm User Manual
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1. DMOL3 DFT with PBE functional and numerical DNP basis set Gaussian98 obsolescent feature DFT with B3 LYP functional and 6 31 G d p basis set DMOL3 obsolescent feature DFT with VWN BP functional and numerical DNP basis set 51 This density functional method and basis set combination is equivalent to the Turbomole method Thus the COSMOtherm parameter set optimized for the according Turbomole DFT method can be used with COSMO files produced by this quantum chemical program package 52 Gaussian M J Frisch et a Gaussian Inc Pittsburgh PA 2011 Please note that only Gaussian09 Revision C 01 of September 2011 and later or Gaussian03 revisions B 01 up to C 01 as released between October 2003 and March 2006 are able to produce COSMO files that can be read by COSMOtherm 53 The PBE DNP COSMO model is available in the 2006 version of DMOL3 as implemented in Accelrys Materials Studio 4 3 as well as in all later versions of DMOL3 and Accelrys Materials Studio 4 Please note that it is not recommended to use COSMO files computed at this level of theory in COSMOtherm This calculation method and the according COSMOtherm parameter file is supported for reasons of downward compatibility only The method and parameter file will not be improved or updated in future versions of COSMOtherm 158 The choice of the correct DFT functional basis set and COSMO options is explained in the user manuals of the different
2. ctd BP_TZVP_C30 1501 ctd cdir CTDATA FILES fdir DATABASE COSMO BP TZVP COSMO efile vpfile Isothermal binary phase diagram of Octane Acetic Acid f octane cosmo f aceticacid cosmo f aceticacid_ dimer half mcos IEI 1 tc 70 0 binary EN IEI 1 1 3 0 0 0 Example 10 b Acetic acid dimer COSMO meta file aceticacid_ dimer half mcos f aceticacid_dimer cosmo W 1111111100000000 213 5 9 lonic Liquids The prediction of thermodynamic properties of ionic liquid IL solutions with COSMOtherm involves a complication that results from the fact that the ionic liquid which in experiment is seen as one species in COSMOtherm should be treated as two individual ions In general any salt liquid or solid can be described via two different definition of the mole fraction The salt either can be described as one substance or as a sum of anion and cation in the ratio of their stoichiometric coefficients While the one substance approach is quite natural for experimental purposes the sum of ions view is more convenient for modeling strategies that take into account the different particle interactions in the mixture One can imagine three approaches for the calculation of properties of ionic liquid mixtures Use the two ions as separate molecules with the equal mole fractions Il Combine the two ions in a meta file Ill Use a cosmo file of an ion pair The third approach does
3. input The vapor pressure of an IL phase is computed from the partial vapor pressure contributions of each of the components of the IL phase in terms of their activity in the overall mixture By default a SIL phase is assumed to show ideal mixing behavior This means that the overall activity of a pure IL phase is one and the vapor pressure of the IL phase is not computed from the activities of the IL phase components but from their relative mixture ratio in the IL phase only Alternatively it is possible to define the IL phase in a way that it shows real mixing behavior via input option ILphase REAL If the ILphase REAL option is activated the vapor pressure of the IL phase is computed from the contribution of the IL phase components with respect to their activities based on the concentrations derived from the ratio of the components stoichiometry as well as to the overall concentrations of all compounds in the given binary phase This means that now the IL components behave like a real stoichiometric mixture of the IL phase s components A composite IL phase with nonzero vapor pressure e g a liquid salt solvent associate thus defined as real phase will have the same partial vapor pressure in the binary SIL system as in a multinary see section 2 3 8 system defined with the same relative and absolute concentrations of the components In addition to the regular VLE phase diagram computation it is also possible
4. m Val l val Lue Lue Lue Lue ue ue Optional for solub computations Define the reference solubility value for a reference solubility calculation of AG The ref _sol_s option assumes that the given reference solubility value is given as the decadic logarithm of the solutes mole fraction log x The ref_sol_x option assumes that the given reference solubility value is given as the solutes mole fraction x so The ref_sol_c option assumes that the given reference solubility value is given as the solutes mass fraction concentration cso The ref _sol_g option assumes that the given reference solubility value is given as the solutes mass based solubility g in g g By default or if the wso12 keyword is given the input as well as the output of the mass based solubility g o is assumed to be the unnormalized mass based solubility of Definition 2 gso W sor2 xp MW 1 xf MWeoivent If the additional keyword wso11 is given the input as well as the output of the mass based solubility g soL is assumed to be the unnormalized mass based solubility of Definition 1 go Wg XP MW MW sovent If the additional keyword wfract is given the input as well as the output of the mass based solubility g is assumed to be the mass fraction i e identical to the input of the ref sol_c option The ref sol m option assumes that the given reference solubility value is given as the solutes mol
5. 69 C Print options for the COSMOtherm output file continued compound contact probability contact or contact i io or ncontact name name gt segment _contact i i sh Optional Compute statistics of the surface contacts between the compounds in this mixture If given in a temperature mixture line of the COSMOtherm input file the contact option is active only for the temperature mixture line where it is given If the option contact is given without argument the contact statistics is printed for all compounds in the mixture If the option contact i i2 is given the contact statistics is printed only for compounds i where i is the number of the compound in the order that is given in the compound section of the COSMOtherm input file If the option ncontact name name is given the contact statistics is printed only for compounds name name where name is the name given in the compound section of the COSMOtherm input file Optional Compute statistics of the surface segment contacts between the compounds in this mixture If given in a temperature mixture line of the COSMOtherm input file the segment contact option is active only for the temperature mixture line where it is given The contact statistics is printed only for compounds i where i is the number of the compound in the order that is given in the compound section of the COSMOtherm input file The molecular surface contacts for all segmen
6. By default the SMC s of all compounds are set to zero unless specified otherwise SMC s can be specified individually for each molecule in the compound option section of the COSMOtherm input file see section 2 2 In general SMC s may be used in two situations 1 If you want to obtain a very good fit for a certain logarithmic partition coefficient for which you have many experimental data In this case you may first take the direct COSMOtherm calculations of the logarithmic partition coefficients for a large set of compounds and then consider the deviations from experimental data as goal property in a linear regression analysis which uses the o moments up to the desired order as descriptors If you divide the coefficients yielded by the regression by RTIn10 i e at room temperature by 1 365 kcal mol you get the required SMCs which you have to use as an input for one of the 2 solvents of your partition problem Please take care about the correct sign Leave out the first c moment in this case in the regression because as long as you only have neutral compounds the first moment is zero and hence the coefficient is not defined 2 If you want to describe a solvent or a matrix which cannot be expected to be properly described by standard COSMOtherm either due to unknown impurities ionization amorphous state or for other reasons and if you have good partition data available for that matrix you may just proceed as in 1 An applicat
7. is 5 It can be increased by the global 1xmx option see section 2 1 The LIQ EX option unlike almost all of the other computation options in COSMO therm can be done in the framework not of relative mole or mass fraction concentrations but of the absolute amounts of substance namely compound mole numbers N or compound masses W Thus the total amount of substances has to be read from the input as a starting point of the phase equilibration The initial concentrations of the two phases can be given in two different ways in the COSMO therm input 1 Give mole numbers N of the compounds in the nphase phases via options N1 N N N and N2 N N7 where N is the mole number of compound in phase and N is 2 N the mole number of compound in phase Il If more than two phases are defined via input of Nphaser all additional phases can be defined accordingly N3 N Ni N N4 N Y N N ete 2 Give masses W of the compounds in the npase phases via options W1 W W W s and W2 W W W where w is the mass g of compound in phase and w4 is the mass g of compound in phase Il If more than two phases are defined via input of npnase all additional phases can be defined accordingly W3 W Ww W s W4 WY WY WY ete For input options N and W the phase equilibrium is computed iteratively with the side condition that the total mole numbers
8. 0 33177236 0 15116381 06 500807 2 07766787 3 13169212 0 82705508 0 09557137 0 044978 0 955022 0 30000 0 70000 0 37161778 0 16900260 94 368163 1 91802739 3 19226333 0 71532039 0 13815009 0 076165 0 923835 0 35000 0 65000 0 40211320 0 18265251 83 514917 1 77771621 3 25988257 0 61101921 0 18859611 0 123697 0 876303 0 40000 0 60000 0 42319354 0 19211964 74 464937 1 65296 48 3 33484059 0 51476831 0 24662537 0 192206 0 807794 0 45000 0 55000 0 43485015 0 19742545 67 583632 1 54129906 3 41754078 0 42685550 0 3119469 6 0 284046 0 715954 0 50000 0 50000 0 43714741 0 19860659 63 069955 1 44100143 3 50850619 0 34746872 0 38419420 0 396388 0 603612 0 55000 0 45000 0 43021576 0 19571400 60 952100 1 35083314 3 60845700 0 27668976 0 46294213 0 519786 0 480214 0 60000 0 40000 0 41426377 0 18881166 61 099584 1 26984189 3 71841420 0 21451602 0 54769920 0 640571 0 359429 0 65000 0 35000 0 38954269 0 17797522 63 247717 1 19724482 3 83990819 0 16083562 0 63795859 0 746361 0 253639 0 70000 0 30000 0 35635613 0 16329027 67 031779 1 13237899 3 97529398 0 11546136 0 73318724 0 830441 0 169559 0 75000 0 25000 0 31504527 0 14485076 72 024711 1 07465991 4 12837868 0 07813623 0 83284625 0 892261 0 107739 0 80000 0 20000 0 26597888 0 12275731 77 714848 1 02355858 4 30574112 0 04854659 0 93640263 0 985113 0 064887 0 85000 0 15000 0 20954394 0 09711543 83 840041 0 97858763 4 51
9. 86 58 0 2408 0000 0564 0000 ooo 8 1 COSMO file propanone cosmo 1257 8251 4292 2210 3015 5091 6328 2969 0798 0008 kcal mol kcal mol kcal mol kcal mol kcal mol kcal mol A 2 A 3 a m u a u 0 0032 47 9057 54 LETO 0 0000 0 0024 4 2408 Debye 36 0270 66 2727 83 0209 126 2395 2 7906 0 9717 0 0000 0 0000 First the atomic weights are given default values of one in this example then the energy of the solvated molecule EF COSMO plus the averaged correction for the dielectric energy dE and the gas phase energy E_gas as read from the input file or estimated by COSMOtherm are given The following lines contain the net energy difference between the ideally screened state and the gas phase E_COSMO E_gas dE the total dielectric energy E_ diel Eq 7 of reference 6 the averaged correction for the dielectric energy dE Eq 15 in reference 3 and the van der Waals energy of this molecule in a continuum Evdw Please note that this Evdw is a purely hypothetical free energy and in contrast to the enthalpy of mixture that is given in the mixture output section H_vdW see below the EvdwW in continuum is not observable or available experimentally The next lines give the total area of the surface segments as computed by the quantum chemical COSMO calculation and if provided in the cosmo file the volume enclosed by this area Below the mol
10. ERROR Stopping COSMOtherm execution You may override this error message with the global AWPS option error 40 ERROR Illegal character found in the input of atomic weights ERROR Only blank spaces are allowed error 41 ERROR Illegal character found in the input of sigma moment coefficients ERROR Only blank spaces are allowed 168 COSMO therm Error Codes continued error 42 error 43 error 44 error 45 error 46 error 47 error 48 error 49 error 50 error 51 error 52 error 55 error 57 error 58 error 59 error 60 error 61 error 62 error 67 error 70 error 71 error 72 error 75 error 76 error 77 error 78 error 79 error 80 error 81 error 82 error 83 error 84 error 85 error 86 error 87 error 90 error 91 error 93 error 94 error 95 error 96 error 97 error 98 error 100 error 101 ERROR ERROR ERROR ERROR ERROR ERROR ERROR ERROR ERROR ERROR ERROR ERROR ERROR ERROR ERROR ERROR ERROR ERROR ERROR ERROR ERROR ERROR ERROR ERROR ERROR ERROR ERROR ERROR ERROR ERROR ERROR ERROR ERROR ERROR ERROR ERROR ERROR ERROR ERROR ERROR ERROR ERROR ERROR ERROR ERROR ERROR ERROR ERROR ERROR ERROR ERROR ERROR Atomic Weigths are all zero for one molecule No atoms found for a molecule Unknown element detected Problem in calculation of molecular volum
11. is used to identify comments in the input file If the hash character is the first character of a line the complete line will be ignored In other positions any text after the hash character will be ignored This holds for the COSMOtherm input file as well as for other files which hold commands that are interpreted by COSMOtherm such as COSMO metafiles vapor pressure files or database list files The COSMOtherm input file has three main areas l Global command line s and comment line II Compound input and options lines III Temperature mixture lines 18 Stewart J J P MOPAC2002 program package Fujitsu Corp 2002 Please cf Fujitsu FQS poland web site for further details http www fqspl com pl linmopac overview html 15 2 1 Global Command and Comment Lines The first or if necessary the first two lines of the COSMOtherm input file are used for global commands and general file handling commands The second or third line is a comment line that is also used as a job identifier in the output file The COSMOtherm program automatically recognizes whether there are one or two lines of global commands i e whether the comment line is the second or the third line of the input file Note that at least one global command line is required in the input even if it is only a dummy line l e if no global commands are given an empty line should be given as first line of the input file Regarding the input of the directories it is
12. system then the equilibrium condition 2 3 19 will have several solutions In this case the SLE search algorithm will pick the correct solution where the SLE point is outside the virtual miscibility gap and start the iterative refinement of the SLE search from this point Both LLE and the resulting SLLE points will be written to the of COSMOtherm output and table file Because COSMOtherm can only calculate compound in a liquid for the solid liquid equilibrium of solid compound with a solvent the Gibbs free energy of fusion of the compound AG has also be taken into account AG can be given in the compound section of the COSMOtherm input file via option DGfus value see section 2 2 1 A temperature dependent free energy of fusion can be calculated from experimental compound data such as enthalpy or entropy of fusion AH or AS respectively and melting temperature T melt T T AG T MH po L ACP ps Tyner T MCP T In oar 2 3 3a melt as t AG T AS ns T pen T ACp ps T pen T ACP pT In 2 3 40 Thus the usage of compounds melting temperatures and enthalpy or entropy and optionally heat capacity of fusion allows the automatic calculation of the compounds solid liquid equilibrium at different temperatures with the binary SLE option AH Or AS can be given in the compound section of the COSMOtherm input file via option DHfus value or DSfus value respectively see section 2 2 1 Optionally the heat
13. 25 VRML the Virtual Reality Modeling Language is a script language allowing interactively the examination of virtual three dimensional objects see http www vrml org VRML files usually identified name wrl can be viewed with COSMOthermx the graphical user interface of COSMOtherm Alternatively they can be viewed within common World Wide Web browsers such as Mozilla Firefox or Microsoft Internet Explorer if an appropriate VRML browser plug in has been installed Such plug ins are available freely e g the Cortona VRML client by Parallel Graphics see http www parallelgraphics com products cortona 37 Control options for the visualization of molecular properties continued wrlmap mapfile namwrl name wrl wrl_min min_ val wrl max max val map_column iso1 Optional Create a VRML file of the molecular COSMO surface property map that is given in file mapfile The wrlmap command is active only for the actual compound and the actual property map mapfile By default for a molecule molecule cosmo a VRML file molecule _map wr1 will be created The property map file mapfile is expected to be in the same format as the surface contact statistics map file name contact that can be created by COSMOtherm via command segment contact see section 5 7 Alternatively the property map file can be read in the format of an uncompressed COSMO file as computed by Turbomole l e it is also possible to visualize a Turbomole COSMO file
14. Options for pseudo ternary phase diagram computations with composite mixture phases ternary i SMIX SMIX or nternary name MIX SMIX Optional for ternary computations Toggle composite mixture pseudo binary phase diagram computation The input of the mixture phase is possible either via the ternary i SMIX SMIX command where i is the number of a solvent phase i e a neutral solvent compounds with number i as given in the sequence of compounds in the compound input section argument i is expected to be a positive integer number and the terms MIX denote the composite mixture phases or alternatively by the nternary name SMIX SMIX command where name is the name of a solvent compound as given in the compound input section and the terms MIX denote the composite mixture phase as defined by the xm or cm options given below Note that any or all of the ternary phases can be defined as MIX phases 132 Suboptions of the binary i MIX or nbinary name MIX options xm X Xo or cm Cy Co MIXphase RI EAL Required for binary or ternary MIX computations Give finite mixture concentration for the MIX composite phase defined in the binary computation input The input of the concentrations is possible either in mole fractions xm or mass fractions cs of the compounds of the mixture as real numbers x and c The arguments are expected as real numbers between zero an
15. n heptane water 2 2 4 trimethylpentane water n hexadecane water olive oil water gas water water cell permeation water skin permeation at 37 C blood brain logBB water plant cuticle tadpole narcosis log 1 C intestinal absorption in enthalpy of solvation in water kj mol aqueous solubility log xs 72 M H Abraham Chem Soc Rev 22 1993 73 M H Abraham H S Chadha G S Whiting R C Mitchell J Pharm Sci 83 1994 1085 M H Abraham H S Chadha J Dixon A J Leo J Phys Org Chem 7 1994 712 M H Abraham G S Whiting W J Shuely R M Doherty Can J Chem 76 1998 703 M H Abraham G S Whiting P W Carr H Ouyang J Chem Soc Perkin Trans 2 1998 1385 M H Abraham J A Platts A Hersey A J Leo R W Taft J Pharm Sci 88 1999 670 M H Abraham J Andonian Haftvan J P Osei Owusu P Sakellariou J S Urieta M C Lopez R Fuchs J Chem Soc Perkin Trans 2 1993 299 M H Abraham F Martins R C Mitchell C J Salter J Pharm Sci 88 1999 241 M H Abraham J Le W E Acree Jr Collect Czechoslov Chem Commun 64 1999 1748 M H Abraham J Le W E Acree Jr P W Carr J Phys Org Chem 12 1999 675 M H Abraham A M Zissimos W E Acree Jr New J Chem 27 2003 1041 M H Abraham A M Zissimos W E Acree Jr Phys Chem Chem Phys 3 2001 3732 197 Abraham parameter QSPR property files for BP SVP AM11 level QSPR property file BP SVP
16. or approximation of the pure compound vapor pressures 3 d PVmin K temp via the vpant vpant1 vpwag or vpexp option is valid If the temperature in a binary ternary or multinary caclulation is lower than argument temp a warning message will be printed to the output file temp is expected in C for the TPVmin option and in K for TPVmin K option respectively a PVmax temp Optional Give a maximum temperature for which the or approximation of the pure compound vapor pressures rPVmax K temp via the vpant vpant1 vpwag or vpexp option is valid If the temperature in a binary ternary or multinary caclulation is higher than argument temp a warning message will be printed to the output file temp is expected in C for the TPVmin option and in K for TPVmin_K option 52 Pure compound boiling point temperature Tsoi input Tboil value or Tboil C value or Tboil K value Tref value or Tref C value or Tref K value or Tref F value pref value or pref Pa value or pref kPa value or pref bar value or pref psia value Optional Input of a compounds experimental boiling point temperature Argument value is the pure compound boiling point temperature value T of the given compound in C for the tboil and tboil C options and in K for the tboil_K option The argument is expected to be a real number The Tso value thus given can be used as a reference point for scal
17. ridft A matrix vers 1 0 cav vers 1 0 ridft b p def TZVP cosmo epsilon infinity nppa 1082 nspa 92 disex 10 0000 rsolv 1 30 routf 0 85 cavity closed amat file amat cosmo phsran 0 0 ampran 0 10E 04 cosmo_data fepsi 1 0000000 disex2 3538 50 nsph 32 nps 136 npsd 228 npspher 92 area 153 77 volume 172 63 coord_rad atom x 1 0 00000070500000 0 00000000000000 0 12717137800000 o 1 72000 2 1 44387771300000 0 00000000000000 1 00928443900000 h 1 30000 3 1 44386652900000 0 00000000000000 1 00929324200000 h 1 30000 screening_charge cosmo 0 012199 correction 0 011725 total 0 000474 cosmo_energy Total energy a u 76 4781152239 Total energy OC corr a u 76 4785388965 Total energy corrected a u 76 4783270602 Note incorrect value contained for downward compatibility Dielectric energy a u 0 0148636263 Diel energy OC corr a u 0 0152872990 segment_information 1 1 2433277990 0 061540093 2 281238018 0 002737924 0 309230275 0 008853997 0 086607271 2 1 0 030670543 2 199288003 2 520246977 0 007124829 0 343589194 0 020736475 0 147729007 3 1 0 527417415 1 061508920 3 153652997 0 006402601 0 343589194 0 018634465 0 149873711 The main information read by COSMOtherm are the info cosmo and cosmo data sections which denote the quantum chemical level basis set and COSMO cavity construction algorithm the COSMO file was created with the coord section w
18. BP TZVP Abra BP TZVP Abra BP TZVP Abra nam nam nam nam nam nam nam nam nam nam nam nam nam nam nam nam nam nam nam nam nam nam nam nam nam nam le for BP TZVP COSMO level LogP Octanol wet Water prop logP Octanol dry Water prop LogP OleylAlcohol Water prop LogP Acetone Water prop LogP PGDP Water prop LogP CH2C12 Water prop LogP CHC13 Water prop LogP CC14 Water prop LogP CS2 Water prop LogP Benzene Water prop LogP Toluene Water prop LogP Cyclohexane Water prop LogP Hexane Water prop LogP Heptane Water prop logP Isooctane Water prop logP Hexadecane Water prop LogP OliveOil Water prop LogP Gas Water prop LogP Cell Water prop LogP Skin Water prop LogP Blood Brain prop LogP PlantCuticle Water prop LogP Tadpole Narcosis prop ntestinal Absorption prop ham Hsolv Water prop logS Water prop LogP Diethylether wet Water prop Partition coefficient wet l octanol water dry 1 octanol water oleyl alcohol water acetone water propylene glycol dipelargonate water wet diethylether water methylenechloride water chloroform water tetrachloromethane water carbon disulfide water benzene water toluene water cyclohexane water n hexane water
19. COSMOlogic Predicting Solutions COSMOtherm Reference Manual Version C3 0 Release 15 01 1999 2014 Frank Eckert COSMOlogic GmbH amp Co KG Imbacher Weg 46 D 51379 Leverkusen Germany cosmotherm cosmologic de Contents COSMOthermM Reference Manu l siniseen iaaiiai iniiai 1 A INCROGUCUOM E teehee teat eee hi E ache heh eels Bethea eve casi ate oh ental pecla Je eetartas tad than 4 Ved TRO ONY n E E se eh ae eo Sete Sea E ode Sede eh he E A 4 12 Practicalt Aspects 42 vcs Rect et aoe ees hates ce eek a hee ae ee Rie Dah A a Bate 11 1 3 Installation in enean ee a ee ee vn es 13 E S Ta E TE cabsacideaddsensnadisenge add cand desegaaiacacgvaga A ET 14 22 a LAO E a E A E E E E E agen teezaetavg alae 15 2 1 Global Command and Comment LineS eecceeeeeeesceeeeeeeeeeeeeeneeeseeesaeeeseeesaeeeaaeeseaeesaeeseaeeesaeensaeeeaaes 16 Zedel FUG HANGINGS e dbs hve a aaa a a a aaa aa aaa a a a aae 16 2 1 2 Print Options for the COSMOtherm Output File cccceceeecceeeceeeceeeeeeeeeeeeeeeaeeeaeeeaeesaeseeeeneeeaes 20 2 1 3 General Program Control and Thresholds ccccssscceeeeeeeeeeeeeeeeeeceneeeescaeeeeeseeeeeecneeeeessneeeessnees 23 2 1 4 Additional Tabulated Output Files ccc eeceeeneeeeeeeeeeeeeeaeeeeaeeeeaeeseaeeeaeeseaeeseaeeeeaeeeeaeeseaeeeeaeess 27 22 COMPOUNG IM PUT isis lt ctsscee cra nest acuywek nedesiaes a steaduaviensaahcsigesnecssaedavahieeas csassdserddaedasilvaldscehiavassasessdauddeedanudis 31 2 2 1
20. DHfus_salt value option AH is expected in kcal mol for the DHfus_salt_SI option AH is expected to be in kJ mol Argument value is expected to be a real number Optional Give the entropy of fusion AS for a salt For the DSfus_salt value option AS is expected in kcal mol for the DSfus_salt_SI option AS is expected to be in kJ mol Argument value is expected to be a real number Optional Give the heat capacity of fusion ACp for a salt For the Dcpfus salt value option ACp is expected in kcal mol for the Dcpfus_ salt SI option ACp is expected to be in kJ mol Argument value is expected to be a real number Optional Give the melting temperature Ter for a salt For the Tmelt_salt temp and Tmelt salt _C temp options Tmer is expected in C for the Tmelt_ salt K temp option Tmer is expected in K Argument temp is expected to be a real number Optional for the input of a temperature dependent salt free energy of fusion via input of enthalpy or entropy of fusion AH OF AS and melting point Ter toggle the approximation of the heat capacity of fusion as ACp AS AH ful Tmen The value of AG 7T thus obtained wil be used to compute the solubility of the salt compound If the dcpfus estimate keyword is given in a salt solubility computation input line the approximation to ACp is valid for the given salt and the given mixture line Optional use alternative mean ionic free en
21. Ln gl Do anc J Intg 0 Intg 2 Ang x 3 ya 2 126 lonic Liquid salt binary and ternary phase diagram computation options binary i SIL or nbinary name SIL ternary i j SIL or ternary name name IL Optional for binary computations Toggle lonic Liquid salt pseudo binary phase diagram computation The input of the lonic Liquid pseudo binary mixture is possible either via the binary i IL command where i is the number of the solvent phase i e a neutral solvent compound with number i as given in the sequence of compounds in the compound input section arguments i is expected to be a positive integer number and the term SIL denotes the IL salt phase or alternatively by the nbinary name IL command where name is the name of the solvent phase compound as given in the compound input section and the term IL denotes the IL salt phase as defined by the IL and IL_n options given below Optional for ternary computations Toggle lonic Liquid pseudo ternary phase diagram computation The input of the lonic Liquid pseudo ternary mixture is possible either via the ternary i j SIL command where i j is the number of the solvent phases i e neutral solvent compound with numbers i j as given in the sequence of compounds in the compound input section arguments i is expected to be a positive integer number and the term SIL denotes the IL salt phase or alternatively b
22. are as described above for the solubility of individual compounds The iterative refinement of the computed solubility value as defined by eq 2 3 2 iterative option is also possible for a salt solubility computation Application and restrictions of the iterative salt solubility compuation are the same as for the neutral compound solubility option above Although it is possible to define a QSPR estimate for the free energy of fusion of salts similar to the QSPR model for neutral compounds currently no parameters are available for this model Thus the default value for the heat of fusion salt solubility computation is zero i e it is assumed that the salt in fact is a ionic liquid It is possible however to provide experimental data which can be used to compute the salt free energy of fusion via eq 2 3 3 or eq 2 3 4 and which subsequently can be used in eq 2 3 1a to compute a solid salts solubility value The input of the required experimental data is similar to the input of the free energy of fusion related data of pure compounds in the pure compound input section see section 2 2 of this manual with the difference that the salt heat of fusion data input has to be done in the same mixture line where the solub salt and salt_n commands are located The net Gibbs free energy of fusion of the salt can be given by options DGfus_salt or DGfus_salt_SI The net enthalpy of fusion of the salt as used in eq 2 3 3 can be given by options DHfu
23. is expected to be in kJ mol Argument value is expected to be a real number Optional Give the heat capacity of fusion ACp for an IL salt For the Dcpfus_salt value option ACp is expected in kcal mol for the Dcpfus_ salt SI option ACp is expected to be in kJ mol Argument value is expected to be a real number Optional Give the melting temperature Ter for an IL salt For the Tmelt_ salt temp and Tmelt salt _C temp options Tmer is expected in C for the Tmelt_ salt K temp option Tey is expected in K Argument temp is expected to be a real number Optional for the input of a temperature dependent compound free energy of fusion via input of enthalpy or entropy of fusion AH or AS and melting point Tren toggle the approximation of the heat capacity of fusion as ACp ASus AM fus Tmex The value of AG 7 thus obtained wil be used to compute the SLE of the given lonic Liquid salt system If the Dcpfus_estimate keyword is given in binary mixture SLE computation input line the approximation to ACP is valid for all compounds including the given lonic Liquid salt in the given mixture line 129 2 3 7 5 Treatment of Composite Phases in Pseudo Binary Ternary Mixture Computations COSMOtherm offers the possibility to compute phase diagrams of binary or ternary mixtures where each of two solvent phases can be defined as a composite with a given mixture concentration This assumes that the composite
24. iz option 1 seg imo1 Lseg latm Lot Latom or latm ino ALL natm inol latom3 tatomi Latom2 Optional Compute statistics of the surface segment contacts between all segments of molecule i as given in the command segment _contact i with segment i of molecule i This option is active only for the temperature mixture line where it is given The contact statistics is printed only for compound i where i is the number of the compound in the order that is given in the compound section of the COSMOtherm input file The molecular surface contacts for all segments of the given compounds are written to the contact statistics file name contact where name is the name of the COSMOtherm input file Optional Compute statistics of the surface segment contacts between all segments of molecule i as given in the command segment _contact i with all of the segments that are associated with atom itom Of molecule inox or if the string ALL is given instead of iatow With all atoms of molecule inoi This option is active only for the temperature mixture line where it is given The contact statistics is printed only for compound imo where i is the number of the compound in the order that is given in the compound section of the COSMOtherm input file The molecular surface contacts for all segments of the given compounds are written to the contact statistics file name contact where name is the na
25. or PROPQSPR_SI C1 C2 Cig prop Optional Toggle the automatic calculation of a o moment QSPR property for all compounds in the input The PROPQSPR command is closely related to the OSPR command of the global command section There are some small differences in that the PROPQSPR command writes its results to the mixture section of the COSMOtherm output file as well as to the COSMOtherm table file but not to the molecules o moment files If no temperature and mixture concentration are given in the same mixture line the PROPQSPR command will toggle the computation of the given QSPR property for all molecules If temperature and mixture concentration are given the PROPQSPR command will toggle the computation of the given QSPR property for all compounds i e if several conformers are present for a given compound the QSPR property will be averaged due to the Boltzmann conformer distribution of the conformers at the given temperature and mixture concentration The PROPQSPR filename option reads the o moment QSPR regression coefficients from file filename while for option PROPQSPR c cy Cig prop coefficients are read from the input For option PROPQSPR_SI the coefficients must be defined in Sl units If the coefficients are to be read from a file the QSPR coefficient file filename is expected to be in the directory that also holds the COSMOtherm parameter file i e in the directory denoted by the environment variable COSMOTHERM
26. phase extraction equilibrium calculation see section 2 3 14 If given in the global input section Ixmx the new maximum number of phases allowed is active for the complete COSMOtherm run i e for all compounds in all of the following temperature mixture lines Argument Ixmx is expected to be a integer number Note that an increase of Ixmx increases the memory requirements of COSMOtherm 2 1 3 General Program Control and Thresholds symmetry usage nosym mus ym Optional for the use of conformers Switch off the usage of symmetry information in the distribution of molecules among conformer sets Details on the use of symmetry in conformer sets are given in section 2 2 4 of this manual Optional Toggle the use of absolute symmetry contributions to the chemical potential If the global musym option is used a symmetry contribution RTIN Nirep Will be added to the liquid and gas phase chemical potential of each molecule present Niep is the symmetry number the number of irreducible representations of the symmetry point group of the molecule By default N ep is determined by COSMOtherm but it is also possible to input a fixed symmetry number or point group in the molecule s COSMO file see section 2 2 1 the molecule s gas phase energy file see section 2 2 2 the compound s vapor pressure property file or in the compound input line see section 2 2 3 25 2 1 3 General Program Control and Thresholds COSMO metafile op
27. respectively The COSMOtherm o potential similarity factor is defined as the sum of the differences between the two pure compound o potentials o and Lio m 0 02 Si EXD gt u c ulon 2 3 21 m 0 02 Thus S will be small if the overlap between the compounds o potentials is small Please see section 5 2 for further information on the definition and use of c potentials As an alternative to the simple and molecular non specific cutoff function of eq 2 3 21 COSMOtherm allows the calculation of a so ute specific o potential similarity p is the o potential similarity for compounds i and j weighted by the o profile p o of compound k As shown in eq 2 3 22 the o profile of a third compound k is used as a weighting function in surface charge density o during the calculation of the o potential difference of compounds i and j m 0 03 2 3 22 Si p exp gt pilon ulon ulen m 0 03 In COSMOtherm this solute specific weighting of the o potential similarity is viable with the simpot i j k Ofnsimpot name name name commands in the mixture input section of the COSMOtherm input file see section 5 2 on o potentials For the simpot i j k option S p is computed for the two compounds with the compound numbers i and j and weighted by the o profile of compound k For the nsimpot name name name option S p is computed for the two compounds with the compound names name
28. solvent in g l Note that the solvdens option only will effect the computation of GS in the molar framework If Gsolv reference is used the solvdens keyword will not have any effect on the computed Go Note If a finite concentration input via options xh or ch is used no arguments need to be given to the henry Or nhenry option 80 2 3 4 Automatic Solubility Calculation The solub i or nsolub name option allows for the automatic computation of the solubility of liquid or solid compounds in solvent i It is also possible to calculate the solubilities for a mixture of solvents at a given finite concentration via the xs x1 x2 or cs cl c2 commands By default this option will compute the chemical potentials 4 of all pure compounds j the chemical potentials 4 of all compounds in water and subsequently the chemical potentials 4 at infinite dilution in compound i If the compound is solid the energy change of a compound from the subcooled liquid state to the ordered solid state has to be taken into account l e the solutes Gibbs free energy of fusion AG or equivalently its Gibbs free energy of crystallization 4G AG has to be either given and computed from experimental data or estimated by COSMOtherm The solubility of a solute j in a solvent or solvent mixture i is calculated via logyo x uP u max 0 AG RT In 10 2 3 1 j j The solubility thus computed is a zero order approximation I
29. water solubility and activity coefficients Prediction Of Soil Sorption Coefficients With A Conductor Like Screening Model For Real Solvents Andreas Klamt Frank Eckert and Michael Diedenhofen Environmental Toxicology and Chemistry 21 2562 2566 2002 This article presents the application of COSMOtherm to the prediction of the soil sorption coefficients logKoc of over 500 compounds of varying chemical functionality COSMOtherm results are compared to correlations of logKoc with experimental octanol water partition coefficients Prediction of Aqueous Solubility of Drugs and Pesticides with COSMO RS Andreas Klamt Frank Eckert Martin Hornig Michael E Beck and Thorsten Burger Journal of Computational Chemistry 23 275 281 2002 DOI 10 1002 jcc 1168 This article presents the application of COSMOtherm to the prediction of the water solubility of drug like substances and pesticides COSMOtherm results are compared to predictions from the HQSAR method Use of COSMO RS for the Prediction of Adsorption Equilibria Carsten Mehler Andreas Klamt and Wolfgang Peukert AICHE Journal 48 1093 1099 2002 This article presents COSMOtherm applications to the correlation and prediction of adsorption equilibria Was darf der Verfahrensingenieur von COSMO RS erwarten Robert Franke J rg Krissmann and Ralf Janowsky Chemie Ingenieur Technik 74 85 89 2002 This article presents a critical evaluation and v
30. 0 000000 0 000000 0 000000 0 000000 0 000000 0 000000 0 000000 0 000000 0 000000 0 000000 0 000000 0 000000 0 000000 0 000000 0 000000 0 000000 0 000000 0 000000 0 000000 0 000000 0 000000 0 000000 0 000000 0 000000 0 000000 0 000000 0 000000 0 000000 0 000000 0 000000 0 000000 0 000000 0 000000 0 000000 0 000000 0 000000 0 000000 0 000000 0 000000 0 000000 0 000000 0 000000 0 000000 0 000000 0 000000 0 000000 0 000000 0 000000 0 000000 0 000000 0 883842 0 082837 0 033321 0 034117 0 428511 0 537372 0 072674 3 009389 3 327705 0 0 0 229239 0 310937 0 0 921458 0 050916 0 027626 0 012776 0 310715 0 676508 0 042644 3 329786 4 321485 Q 0 131927 0 327640 0 0 953647 0 024886 0 021467 0 002871 0 166690 0 830439 0 020638 3 704919 5 826672 0 0 049788 0 0 0 987350 0 000000 0 012650 0 000163 0 000000 0 999837 0 003272 4 370218 8 709337 o 0 000000 0 0 0 000000 0 000000 0 000000 0 000000 0 000000 0 000000 0 000000 0 000000 0 000000 0 000000 0 000000 0 000000 0 964749 0 016339 0 018913 0 001321 0 109551 0 889128 0 014081 3 875224 6 608202 0 459689 0 025135 0 373200 0 0 952312 0 025895 0 021794 0 003090 0 172725 0 824185 0 021472 3 686259 5 752224 0 303452 0 052679 0 354217 0 0 000000 0 000000 0 000000 0 000000 0 000000 0 000000 0 000000 0 000000 0 000000 0 000000 0 000000 0 000000 0 893329 0 074677 0 031994 0 027869 0 403357 0 568774 0 064718 3 082335 3 532710 0 008481 0 204777 0 854586 0 108363 0 037051 0 056527 0 490551 0 452922 0 098699 2 80820
31. 0 30000000 0 26037727 0 42187072 396 223600 4 30254533 2 83401909 2 55397181 1 25078183 0 03478190 0 89233027 0 32819026 0 38927854 0 0 35000000 0 30000000 0 35000000 0 32638745 0 48807074 397 170918 4 28177476 3 01287193 2 38291150 1 12897061 0 04399279 1 00451792 0 33816873 0 2 71 o0 0 40000000 0 20000000 0 40000000 0 40255570 0 55348809 401 935661 4 27317534 3 26842021 2 22309608 1 00882837 0 05157304 1 0 33866411 0 19512215 0 0 45000000 0 10000000 0 45000000 0 49105832 0 61841561 412 449786 4 27381059 3 71117949 2 07196598 089005627 0 05535066 0 32970466 0 09543389 0 57486145 0 50000000 0 00000000 0 50000000 0 59529047 0 68323337 430 872637 4 28233264 0 00000000 1 92799497 0 77142704 0 05322213 0 31144741 0 00000000 0 68855259 0 00000000 0 00000000 1 00000000 0 00000000 0 00000000 152 880249 0 00000000 0 00000000 2 35381411 8 72237465 0 92262422 0 00000000 0 00000000 1 00000000 0 05000000 0 05000000 0 90000000 0 09224136 0 22865739 1452 219564 2 83339059 4 14583605 2 36016199 5 99321 0 07174409 0 0 01377 0 0 10000000 0 10000000 0 80000000 0 15575529 0 35751384 694 781073 3 43001687 3 86357366 2 33331733 3 70790784 o 0 04468670 0 0 15000000 0 15000000 0 70000000 0 20131030 0 43155984 500 138592 3 78037921 3 6971 1SS 2 31336972 2 75693382 0 0 0 20000000 0 20000000 0 60000000 0 23583073 0 47026294 433 162216 3 99816689 3 43226305 059958 2 13015960 0 o o 0 25000000 0 25000000 0 50000000 0 26355197 0 48385713 407 494415 4 141
32. 232 radii 159 surface charges 18 219 COSMObase 155 175 177 COSMO frag 174 COSMOmic 19 60 225 COSMO RS 4 5 12 parameters 5 6 fine tuning 220 gas phase 222 223 hydrogen bonding 221 224 misfit 221 224 symmetry detection 224 van der Waals 222 223 theory 4 5 COSMO therm handling 12 license 14 16 output 17 69 165 parameter file 12 16 160 161 COSMOTHERM HOME 13 14 cr 183 188 cstart 110 111 136 cstep 110 111 136 CT CREATE 155 ctab 20 69 npzero 20 69 ctd 16 CTDATA 12 16 160 161 cw 36 Cwrl 18 37 database 155 index file 16 23 156 157 list file 155 dbas 16 21 156 157 dbco 23 157 dbn 31 155 156 157 dconv 23 Depfus 54 83 122 Depfus_ estimate 24 54 122 125 129 131 134 Depfus_ mix 134 Depfus_ mix SI 134 Depfus_ salt 99 129 Depfus_ salt SI 99 129 Depfus_ SI 54 del 35 177 delgqa 177 density 68 142 181 IL 143 144 IL n 143 144 lonic Liquids 142 143 nIL 143 144 polyprep 181 DFT 158 160 DGA DFT 158 160 161 162 164 DGfus 24 54 83 121 DGfus_ mix 134 DGfus_ mix SI 134 DGfus_salt 24 99 129 DGfus_ salt SI 24 99 129 DGfus_ SI 24 54 dhbset 222 224 DHfus 54 83 121 DHfus mix 134 DHfus mix SI 134 DHfus_ salt 99 129 DHfus_ salt SI 99 129 DHfus SI 54 dipole moment 165 DIPPR equation 51 DMOL3 12 31 158 160 163 DNP 163 DSfus 54 83 121 DSfus_ mix 134 DSfus mix SI 134 DSfus_ salt 99 129 DSfus_ salt SIT 99 129 DSfus SI 54 dvd
33. 4 8 will be printed as 0 4800000000000000E 01 Optional Print complete atomic weight or real weight string to the compound section of the output file If you toggle this option the file line for the atomic weights may become very long Optional Print full compound and or molecule names to all tables in the name tab table output file and the name mom sigma moments file By default the compound molecule names are cropped after 20 characters Optional Print Na Not Available message to the name tab table output file if empty table entries occur By default an empty table entry is filled with blank spaces only Optional Print compound and conformer mixture information to the COSMOtherm table file The ctab keyword toggles the additional tabulation of all mixture information which by default is written to the ouput file only to be printed to the COSMOtherm table file For each temperature mixture as given in the mixture section of the input file a separate table will be created If in addition the wconf keyword is used an additional table with the properties of the calculated COSMOtherm mixture information for each individual conformer is written to the table file By default all concentrations are written to the ctab table headers If the the additional keyword npzero is used only nonzero concentrations are written to the ctab table headers To avoid an extremely large number of tables to be created this option is only active for
34. 87 1991 201 5 7 Surface Contact Statistics 5 7 1 Computation of Contact Statistics COSMOtherm allows the computation of the contact probability of molecules and molecule surface segments in arbitrary mixtures via the contact and the segment contact options respectively The net contact probability P of molecule A with molecule B is given as E bp A A 7 7 je Yer Pca See 5 7 1 A A A total total Where i j are indices of the surface segments of molecule A and B respectively i 1 N Xg is the mole fraction of molecule B in the mixture A A are the segment surface area for surface segments of molecule A and B respectively A is the total surface area of molecule A Avn is the total surface area of all molecules in the mixture 7 y are the segment activity coefficients for surface segments of molecule A and B A A are the segment surface areas for surface segments of molecule A and B respectively and E is the surface segment interaction energy Note that P is not necessarily equal to Ppa If the contact option is given in the global command section of the COSMOtherm input file the contact interactions P of all possible combinations of the given molecules will be computed for all mixtures given in the mixture section of the COSMOtherm input file The values of P will be written to the COSMOtherm output file If given in a temperature mixture line of the COSMOtherm input file the contact
35. COSMO file filenames Chemical Abstracts Registry Numbers CAS RN or trivial names respectively The filenames CAS RN or trivial names in the database list file are then processed as if they were directly given in the COSMOtherm input file It is required that the first column of the database list file either holds COSMO file filenames the CAS RN or the trivial name Additional columns in the database list file separated by blank spaces will also be processed by COSMOtherm and can be used to give additional data for the actual compound for example vapor pressure information conformer identifiers and or gas phase energies Thus a typical database list file might look like this methanol cosmo vpexp 0 10 69 00 10 00 20 40 1000 00 64 20 ethanol cosmo vpexp 0 10 56 00 10 00 7 00 1000 00 78 00 Please note that all additional commands given in the compound input line of the COSMOtherm input file that holds the SDATABASE filename command will be processed for each of the compounds given in the database list file COSMOtherms processing of a list of compounds involves the simultaneous storage of all the COSMO information in the memory of the computer The number of COSMO files to be processed by the SDATABASE filename option is restricted to 200 since larger number of molecules processed simultaneously would unnecessarily lead to a strong increase of COSMOtherms requirements regarding computer memory as well as slo
36. IL compound this is unlike the regular density option for individual compounds which always computes the densities of all compounds present 143 Suboptions of the density option are QSPR_DENS Cymer Crap Optional for density computations Give the generic parameters Cycosmo Cm2 Cwring Co Cm2 2 for the QSPR approach of the corrected molar liquid volume and or density The arguments are expected as real numbers The QSPR_DENS SI Cuymp Cusp parameters are expected to be used with energy values in kcal mol Cycosmo Cm2 Cwring Co Cm2 2 and volumes in A3 For the QSPR_DENS_ SI command parameters are expected to be used with energy values in kJ mol and volumes in nm i e in the Sl unit frame EL PARAM k C area Optional for density computations Give an element specific or surface area parameter for the QSPR approach of the corrected EL PARAM SI k C srea molar liquid volume and density Argument k is the element number and is expected as an integer Argument c is the surface area parameter and is expected as a real number The parameters are expected to be used with surface areas in A2 For the EL PARAM SI command parameters are expected to be used with surface areas in nm i e in the Sl unit frame It is possible to give several EL PARAM inputs in the same mixture line PRINT ELEM Optional for density computations For each compound write the element specific surf
37. IL 123 127 MIX 130 132 ndgf 24 nflatsurf 68 218 ngamma 61 77 nhenry 60 79 80 nirrep 42 44 45 nlogp 62 102 nocompw 20 nohb 23 71 nomix 20 69 nosym 25 57 notempty 20 nothb 23 71 notvdw 23 71 novdw 23 71 Bees Z2Z2224 235 npKa 62 105 107 nreaction 47 62 183 NRTL 113 115 NRTL ALPHA 115 NRTL2 113 115 nsimilarity 64 138 nsimpot 65 138 139 nsms 64 138 nsolub 54 61 81 87 88 89 90 91 95 98 nternary SIL 127 SMIX 130 132 nx pure 59 oclp 9 24 72 odir 17 omrset 223 output 69 atomic weights 20 CAS registry number 21 debug information 21 interaction energy atomic 21 mixtures 166 number format 20 pure compounds 165 symmetry information 21 table 166 trivial name 21 output file 165 parameterization 160 basis 160 recommended 162 partition coefficients automatic calculation 62 102 dissociation correction 103 logD 103 QSPR correlation 194 Abraham descriptors 195 196 blood brain 195 human serum albumin 195 intestinal absorption 195 octanol water 195 soil water 195 228 pdir 17 194 pgroup 42 44 pH 94 104 phase diagram binary 63 108 109 110 113 115 118 121 123 130 azeotrope 108 114 lonic Liquids 123 mixtures 130 isobar 137 multinary 63 108 109 118 120 135 ternary 63 108 109 110 118 120 126 130 lonic Liquids 126 mixtures 130 phase equilibrium 68 146 multi phase 147 pK acid 55 93 103 pK base 55 93 103
38. If the QSPR property file is not found in the CTDATA FILES then as next step a PROP directory below the CTDATA FILES directory will be searched for This default can be overridden by the global pdir command The pdir path option given in the global commands section of the COSMOtherm input file allows to set a separate search path for the QSPR property files which then is independent from the CTDATA FILES directory given by the cdir option Example 8 shows the QSPR coefficient file LogPOW prop which holds the QSPR coefficients from a multilinear regression of COSMOtherm o moments with logarithmic octanol water partition coefficients The first two lines are comment lines indicated by the hash character the following lines hold the coefficients C Cie the property color ranges c Cig values of zero indicate that COSMOtherm is setting the color range automatically and the property name that is used to identify the QSPR property in the COSMOtherm output file It is possible to give several QSPR properties in one QSPR coefficient file If such a multiproperty QSPR coefficient file is used COSMOtherm will print all given QSPR properties to the output and to the moments file s For the QSPR filename and the QSPR c cp Cig name options the coefficients are assumed to be used with o moments in atomic units except for c which is used with c moment M M is equivalent to the molecular surface area and per default is g
39. Klamt A F Eckert M Hornig M E Beck and T Burger Prediction of aqueous solubility of drugs and pesticides with COSMO RS J Comput Chem 23 275 2002 85 The computed values of log x are written to the COSMOtherm output file and to the COSMOtherm table file In addition all of the computed chemical potentials and QSPR descriptors as well as the given or computed AG value are written to the table file For the SLESOL option additional columns with the virtual or apparent liquid liquid phase equilibrium values x and Xx will be written to the solubility results table Moreover the mass based solubility w 9 Q oiution Will be written to the COSMOtherm table file as well as the COSMOtherm output file There are three possible definitions of the mass based solubility where MW and MW Solven are the molecular weights of the solute i and the solvent or solvent mixture 1 By default and or if the keyword wso12 is given in addition to the solub keyword the unnormalized mass based solubility is computed by Definition 2 wer wore XPO MW 1 XPD MW vent Il If the keyword wso11 is given in addition to the solub keyword the unnormalized mass based solubility is computed by Definition 1 we wl x sot MW MW J J i i Please note that although commonly used in pharmaceutical chemistry definition 1 is an olvent approximation derived for small solubilities Thus it s
40. N1 N77 or the total masses w7 W of each compound are conserved over the sum of the all n phases The output of the converged system will return the mole numbers N N and masses W W as well as the mole fractions x x of the compounds in the new equilibrium phases to the COSMO therm table file In addition for each phase equilibrium iteration step the phase equilibrium constants K and the associated equilibrium concentrations x K7 1 K are written to the COSMO therm output file In addition to simple equilibration of the two phases starting from npnase given phase concentrations it is possible to predefine the n n phases as solvent phases and add one or several solutes to the two phases from an external solute reservoir This corresponds to adding a certain amount of an external reservoir to the two phases In practice the additional solute compounds are distributed between the phase Given solvent phases according to their partition coefficient K in the initial solvent phases and thus are fully dissolved in the n nase phases Thus in the following course of the iterative solution of the system the n nase phases will consist of the initial solvent compounds and the added solute compound This option may be helpful if it is not clear in advance which phase will be preferred by a given compound 147 when added to the system In the above example
41. Output File e a pa a eaaa a ae e a A a aaa Ee a eE SEAE ATATA e ka ARa EA aaRS AARE 165 AT Error CodeS neirt e iat e aaae ya aia Noa eVi odin dad e eaa a aee a S 168 5 Advanced Features of COSMOtherm scccscceccceseeeseeeeeseeeeeeeeaeceaecaeecaeecaeeeaeseaeeeaeseaeseaesaeesaneseesaeeeaeenaeees 171 BA O RROTINES surme a tat aesove hetrw a a a a tates 171 5 2eo POLENtlalS 2s oh rete ce entree A Gee ets ae aerate eval aac eens ete ated eet due teers a deoee 171 5 3 Atomic Weights and COSMO Metafiles cccccsssccssecsseecsssecsseecsseeeseeeeseeeeeeeesseeeseeeesseeessaeesseeeeeaes 173 5 31 Difference Ghar Ges csc AAE A A EE dead P EA dss AE EE E A E tees fests E 177 5 3 2 Treatment of Polymers a a a a e a e a E a aaa E Ea 178 5 5 Property Computation via o moment QSPR ssssssssseesrrrsesrrssrirnnstinnserinnstinnntnnnstinnntnnantnnnatnnnnennnnet 193 5 5 IOSMOMEMUS ae a a eaaa aa EN EE sas arr aa cad oaae a Naenae den anrea Aa aKa iNe Takaaki drena 193 Be oE AOE a r AE T E E A A E E A 193 5 5 3 o MOMEnt Correction svscecccctsescaversacceasvacdenessaenseastsenadetaenaeasticnonsdedeaauescgeauatensabsnsccaeaseneasedseaieasaieas 200 5 6 Chemical Potential Gradients ceeeeeseeeeseeeeneeeeaeeeeaeeeeaeeseaeeeeaeeeeaeeeeaeeesaeeeeaeeesaeeeeeeseaeeeseeetsaeeeaaes 201 5 7 Surface Contact Statistics aa ae aTa a aa aa aaa aa Ea Ea aE A A ra hbk lajeadesdeascphusessecdeenehbiageds 202 5 7 1 Computation of Contact Statistics cccccc
42. VE on A In the pseudo binary definition that is used in the COSMOtherm table output the mole fraction of the IL is expressed as a sum over the ion mole fractions while the solute i mole fractions are the ternary ones x This definition is used in the table bodies of the COSMOtherm table output It was introduced to preserve the column structure of the table files ger ae x2 2 yeni 5 9 10 Using eq 5 9 10 the conversion of the sum of ions or ternary mole fraction x to the one substance or laboratory binary x definition reads ee bin Vin x vi 5 9 11 In eq SIT thev values are equal to v the sum of the anions and cations stoichiometries of the given IL if compound j is the IL and equal to one if compound j is a neutral solute compound X is the pseudo binary definition of the mole fraction according to eq 5 9 10 l e x is equal to x for neutral solute compounds If compound jis the IL x is equal to the sum of the the ternary mole fractions of all components of the IL 216 5 10 FlatSurf Surface Activity COSMO RS theory originally was developed to calculate the chemical potential of solutes in homogeneous liquid phases where the residual part of the chemical potential yu of solute compound i in phase S is calculated as aoe gt ahs o 5 10 1 vei Here u o is the o potential of phase S Sometimes it is of interest to estimate the
43. X3 I I T cl c 1 Co C3 II II c2 c 1 Coc k k k ck c Co C3 xthresh xt maxiter imax pr K pr xK pr mu a ich II Required for liq ex computations alternative to N1 or W1 option Give mole fractions x of the compounds initially in phase I x is the mole fraction of compound in phase I Required for liq ex computations alternative to N2 or W2 option Give mole fractions x of the compounds in the phase II x is the mole fraction of compound in phase II Required for 1iq_ex npnase Computations alternative to Nk or Wk option Give mole fractions x of the compounds in the additional phases k where k 3 npnase X is the mole fraction of compound jin phase k Required for liq ex computations alternative to N1 or W1 option Give mass fractions c of the compounds initially in phase I c is the mass fraction of compound in phase I Required for liq ex computations alternative to N2 or W2 option Give mass fractions c of the compounds in the phase Il c77 is the mass fraction of compound in phase II Required for liq _ex npnase Computations alternative to xk option Give mass fractions c of the compounds in the additional phases k where k 3 npnase C is the mole fraction of compound in phase k Optional for liq ex computations Set threshold for the self consistent convergence of the liq_ex computation Argument xt is expected to be a positive real mole fract
44. a table with the results of the LLE searches each started at the concentration grid points given in the upper table The LLE results table holds the two tie point concentrations x i and x i for the three phases i 1 2 3 If no LLE was found the values of x i and x i are set to zero The following columns of the LLE results table hold the logarithm of the activity coefficients at the tie points blank if no LLE was found and the temperature and total pressure at the tie points Note that the second table holds the LLE ouput in the points in the pseudo ternary framework analogue to the ternary LLE computations of neutral compounds meaning that the tie point concentrations x i and x i of an IL phase are the sum of the concentrations of the individual ions the IL phase consists of Finally a table block with the LLE results tie point concentrations x i and x i and activity coefficients as converted to the laboratory ternary framework is printed to the COSMOtherm table file see section 5 9 for details on this conversion A typical table output of a ternary LLE computation with an IL phase is shown below Results for ternary mixture of benzene _cO 1 hexane _cO 2 C4mim PF6 3 at T 298 15 K Job 1 as 12 LLE results for multinary system Job 1 1 2 a 2 L L u LLE results for multinary system converted to laboratory Lx frame IL single compound Job 1 1 2 a G a g Lx 1
45. acceptor and donor moments Musae and Mupdon3 With keyword pr _allmom all COSMO RS derived QSPR descriptors available will be printed to the COSMOtherm table files In addition to the 15 c moment descriptors described above some other molecule compound properties are written to the COSMOtherm table file if the pr_allmom option is used in combination with PROPQSPR In agreement with the descriptors printed to the mom and or momc files the extra properties are molecular Volume V molecular weight MW dielectric energy F the energy gain resulting from the averaging of the molecular surface charges dE the molecular van der Waals energy Eww the topological descriptor E and the chemical potential of the molecule compound in the gas phase w Some of these supplementary descriptors may be useful for the QSPR of complicated or weakly defined thermodynamic properties where the o moments alone are not sufficient for a good fit It is important to note that two of these supplementary descriptors Eu and 4ga may differ considerably if they are computed as properties of compounds i e computed in a mixture at given temperature and concentration conditions compared to them being computed as properties of molecules The reason for this is that in the case of a compound PROPOSPR calculation in a given mixture the compound s actual van der Waals energy Ew and chemical potential in the gas phase as computed by COSMO RS
46. almost all thermodynamic properties of compounds or mixtures such as activity coefficients excess properties or partition coefficients and solubility In addition to the prediction of thermodynamics of liquids COSMO RS is also able to provide a reasonable estimate of a pure compound s chemical potential in the gas phase Gas _ fi i f Hi z Egas Ecosmo E king Ring Gas 1 10 where E sas and E cosmo are the quantum chemical total energies of the molecule in the gas phase and in the COSMO conductor respectively The remaining contributions consist of a correction term for ring shaped molecules with n being the number of ring atoms in the molecule and an adjustable parameter as well as parameter 7 providing the link between the reference states of the system s free energy in the gas phase and in the liquid Using equations 1 6 and 1 10 it is possible to a priori predict vapor pressures of pure compounds Please note that eq 1 10 is an empirical formulation It is not part of the rigorous statistical thermodynamics approach that leads to equations 1 4 to 1 6 thus it is valid for pure compounds only The majority of larger and more complex compounds can be built in more than one conformation which means that they have relevant metastable energy minima in addition to the global energy minimum Fortunately the conformational ambiguity can be disregarded in many cases for the calculation of chemical potentials and phas
47. and 999 where numbers that are larger than 9 are valid only for the name_cx cosmo name convention For details on conformer handling see section 2 2 4 1 Automatic Conformer Search Optional suboption of the autoc command Only use the cosmo ccf or mcos files with numbers i4 iz as conformers in the autoc option where iy iz are expected to be integer numbers between 0 and 9 COSMO files must follow the name convention of conformer COSMO files in COSMObase i e conformer COSMO files are named by subsequent numbers starting with zero name0 cosmo namel cosmo name9 cosmo Optional required input option for the COSMOmic plugin Read micelle definition file name mic The micelle definition file extension mic holds the micelle grid and compound definitions required for a COSMOmic calculation File name mic is expected to be located in the same location as the COSMOtherm input file Please note that this option is available only if the COSMOmic plugin is activated via the COSMOtherm license file For details and handling of the COSMOmic plugin please see section 5 12 of this manual and the COSMOmic documentation that is available from the COSMOthermx graphical user interface Optional for the input of boiling point temperatures globally use the pure compound boiling points TBoil as given in the compound input section or read from a compounds vapor pressure property file as a reference point for scaling the vapor pressu
48. and molecule the computed property value will be written to an additional column of the COSMOtherm table and or moments file and to an additional line of the COSMOtherm output file By default all Abraham parameter coefficients computed will be written to the table file together with the optional Abraham property as last column If the additional keyword noaptab is given in the PROPQSPR mixture line the computed Abraham parameter coefficients will not be printed to the table file Instead only the final property computed from the Abraham coefficients will be listed as results column in the PROPQSPR table Currently COSMOtherm is shipped with a number of QSPR property files holding the QSPR coefficients for the five Abraham parameters and the definition of a thermodynamic partition property via the six Abraham coefficients for both computational COSMO levels BP TZVP and BP SVP AM1 More Abraham 196 coefficients for a vast number of solvent or physiological partitions and related free energy properties can be found in the literature Abraham parameter QSPR property files for BP TZVP COSMO level QSPR property fi BP TZVP Abra BP TZVP Abra BP TZVP Abra BP TZVP Abra BP TZVP Abra BP TZVP Abra BP TZVP Abra BP TZVP Abra BP TZVP Abra BP TZVP Abra BP TZVP Abra BP TZVP Abra BP TZVP Abra BP TZVP Abra BP TZVP Abra BP TZVP Abra BP TZVP Abra BP TZVP Abra BP TZVP Abra BP TZVP Abra BP TZVP Abra BP TZVP Abra BP TZVP Abra BP TZVP Abra
49. are given than there are atoms in the molecule the weights for the remaining atoms are assumed to be one This default can be changed by the command wdfl value If given either in the same compound input line as the weight string or within the meta file see below the value given will override the default weight number of 1 Technical note In the first version of COSMOtherm the atomic weighting was applied to the atoms prior to the ensemble averaging process that produces the o values used in COSMOtherm In some situations this lead to small problems We now starting with COSMOtherm Version C1 0 apply the weighting after the averaging which avoids these errors In addition we now apply a round off of the total screening charge 173 for each molecule This ensures that the effect of an eventually non perfect neutrality of fragments is further reduced The so called COSMO metafiles denoted name mcos are a conceptual extension of the atomic weigthing approach Using COSMO metafiles it is possible to construct large molecules via molecular fragments taken from different cOSMO files The syntax of the metafiles is the same as the syntax of the compound input lines in the COSMOtherm input files Each line of the metafiles represents one molecular fragment which is described by two necessary input commands the COSMO file filename given by the f name cosmo card and the atomic weights input given by the w iii card for integer weights or the rw
50. at the same time thus accounting for several different hydrogen bonding types Third it is possible to scale the hydrogen bonding threshold oyg in an element specific way using the SHBSET iciemen factor command where isiement iS the element number of either the atom to which the hydrogen bonding donor hydrogen atom is attached or the element of the hydrogen bonding acceptor atom This means that the SHBSET option allows for the individual enabling disabling of hydrogen bonds of different Donor H Acceptor bonding types It is possible to provide several SHBSET i ejement factor commands to the global command input lines at the same time Fourth it is possible to scale the hydrogen bonding prefactor Cpg of atomic compounds i e compounds such as the chloride anion Cl in an element specific way using the AHBSET isiement factor command where isiement is the element number of the atomic compound It is possible to provide several AHBSET iciement factor commands to the global command input lines at the same time thus accounting for several different atomic compounds Please note that currently no other element than hydrogen is allowed to be a donor in a hydrogen bonding interaction However sometimes atomic cations i e compounds such as the sodium cation Na are seen as hydrogen like donors as well The usage of atomic cations as hydrogen bond like donor molecule can be enabled with the global SPHCATION c
51. azeo 114 xgrid 110 111 xm 133 Boltzmann weight 8 57 109 symmetry prefactor 8 25 57 BP 163 164 c 59 CAS 31 155 Registry Number 155 cdir 14 17 cend 110 111 136 chbset 221 224 chemical potential combinatorial contribution 7 23 71 160 178 179 free volume 23 71 179 polymers 23 71 179 COSMO therm definition 7 8 166 200 gas phase 8 18 27 43 73 74 108 222 gradient 22 69 201 composition 201 temperature 201 hydrogen bonding contribution 23 71 HB2012 161 163 vacuum 22 69 van der Waals contribution 23 71 cmet 26 35 175 emfset 221 224 combi 7 23 71 178 179 combi ELBRO 23 71 179 180 comp 32 comp acid 93 94 104 comp base 93 94 104 complexation 208 compound name 32 conformer 8 19 24 33 57 72 name convention 58 weight factor 109 weight prefactor 8 25 57 gas phase energy 57 conformer block 57 contact 22 70 202 209 210 211 latm 203 204 1lseg 203 204 natm 203 204 segment contact 22 38 70 202 203 204 206 wlconf 203 contact probability atoms 202 203 204 geometry 208 209 210 211 groups 202 203 204 molecules 22 70 202 segments 22 38 70 202 203 204 206 SSC energy 208 209 210 211 probability 208 209 210 211 COSMO compressed files 12 30 31 40 database 155 difference charges 35 177 files 12 31 FINE 161 163 fine cavity 161 163 FlatSurf surface charges 219 marching tetrahedron cavity 161 163 metafiles 17 26 32 35 173 174
52. can be used to estimate the kinetic constant of the reaction To assess the expectable quality of a COSMOtherm prediction of reaction equilibrium constant reaction Gibbs free energy and reaction enthalpy with eqs 5 4 2 to 5 4 4 it is important to consider the quality of the contributions of which the free energies and enthalpies in COSMOtherm are built a compounds Gibbs free energy G and enthalpy H as computed by COSMOtherm are formed from a COSMOtherm contribution liquid contribution and from a quantum chemical contribution that results from the quantum chemical energy of the compound This has practical consequences for the expectable accuracy the accuracy of the abso ute number of the predicted reaction energy and enthalpy mainly is determined by the accuracy of the underlying quantum chemical calculation Because currently all COSMOtherm parameterizations rely on a density functional theory DFT model the accuracy of the reaction energy basically will be the accuracy of the DFT method which for the DFT functionals and basis sets used may be as bad as 5 kcal mol Thus the quality of the prediction of abso ute reaction energies and enthalpies will be quite low if only the DFT based quantum chemical energies are used in the reaction calculation 182 If it is sufficient just to consider the re ative reaction energies of e g the same reaction in different solvents i e if we are looking at the liquid COSMOtherm contribution
53. columns of the COSMOtherm table file Because COSMOtherm can only calculate compound in a subcooled liquid for the solubility of solid compounds the Gibbs free energy of fusion AG has to be taken into account The definition of Gibbs free energy of fusion in equations 2 3 1 and 2 3 2 assumes that 4G is the energy that is required to form an ordered solid from the random particle distribution in the subcooled liquid Thus a positive value for AG indicates that the solute is solid while zero or negative vales of AG indicate that the solute is liquid at the given temperature condition Please note that this definition of AG is different from the definitions used in the articles published on the solubility topic In these articles the negatively signed definition of the solids free energy i e AGs was used but this property was referred to as AG Thus the definitions of AGs in the COSMOtherm program and in the articles are not consistent but can easily be translated into each other by changing their sign There are two possibilities of incorporating AG in a COSMOtherm calculation either experimental data of the solid liquid phase transition may be introduced into the calculation or COSMOtherm may provide an estimate for AG AG can be given in the compound section of the COSMOtherm input file via option DGfus value see section 2 2 1 Please note that by default only positive values of AG are allowed to be read i
54. command for the symmetry detection of the geometries read from gas phase energy files Please note that the symmetry scaling factors affect the symmetry detection thresholds in a general way i e all the different thresholds present in the symmetry detection are scaled by the same given factor Input options for the fine tuning of COSMOtherm parameters vdwset Global input option element specifically scale van der Waals interaction let mant Je1ament factor parameter Cc with factor The argument iciement and jerement are the element numbers of the atoms undergoing van der Waals interaction They are expected to be integer numbers Argument factor is expected to be a real number wvdwset factor Global input option scale van der Waals temperature dependency parameter w with factor The argument factor is expected to be a real number dvdwset factor Global input option scale van der Waals temperature dependency parameter dw with factor The argument factor is expected to be a real number etaset factor Global input option scale general gas phase parameter nga with factor Argument factor is expected to be a real number omrset factor Global input option scale gas phase ring correction parameter ging with factor Argument factor is expected to be a real number tetset factor Global input option scale general gas phase temperature dependency parameter z with factor Argument factor is expected to be a real number torset f
55. compound as integer numbers i separated by blanks IEI numbers can be IET i4 Ss a used to treat the concentration dependency if a reaction between two or more species in the mixture is taking place e g the dimerization of a organic acids the formation of a charge transfer complex between solute and solvent See section 5 8 Concentration Dependent Reactions for a detailed description of the usage of IEI numbers xw xi Optional Give fixed compound concentrations for this compound The or argument xi and ci is expected to be real number between 0 and 1 For cw ci xw xi the argument is assumed to be a mole fraction concentration for cw ci a mass fraction concentration The fixed compound concentrations are multiplied with all concentrations for compound i given in the temperature mixture input section of the COSMOtherm input file Thus this option allows the simple handling of mixtures of mixtures The usage of interaction energy indices as well as the usage of the optional input of c moment coefficients is explained in section 5 Advanced Features of COSMOtherm 36 Control options for the visualization of molecular properties i e the generation of molecular VRML files Cwrl name wrl Swrl name wrl Pwrl name wrl Wrlres res Optional Create a VRML file of the molecular geometry If given in this section of the COSMOtherm input file the Cwrl command is active only for the actual compound
56. compute thermodynamic properties that are related to the gas phase i e vapor pressure heat of vaporization Gibbs free energy of solvation COSMOtherm requires the free energy of the gaseous phase This can either be approximated or preferably computed on the basis of the quantum chemical energy of molecule in the gas phase i e the the quantum chemical energy of the molecule optimized on the same level as the COSMO file but without the COSMO model COSMOtherm is able to process such a quantum chemical gas phase energy via the input of gas phase energy files denoted by file suffix energy COSMOtherm allows several different procedures of reading gas phase energy files Compound input options continued gas phase energy input e energy or eH energy or eJ energy or eC energy ef filename or efH filename or efJ filename or efC filename e gas min off Optional Give gas phase energy for this compound For keywords e energy and eH energy the energy is expected in atomic units Hartree for eJ energy and eC energy it is expected in kJ and kcal Optional Read gas phase energy for this compound from file filename If no argument is given i e just the ef efH efJ or efC keyword the name of the gas phase energy file is expected to be the name of the according COSMO file with the file extension energy i e for COSMO file name cosmo a gas phase energy file name energy is expected In the ga
57. e g from a different published parameter set because the interdependence with the other parameters is nonlinear and ultimately unknown Any strong modification of single parameters may destroy the method as a whole With the objections raised above it is possible to modify the parameters to get better results for a given compound system It is possible to modify all the microscopic energy contributions E_misfit E_HB and E_vdw as well as the gas phase energy contribution to the vapor pressure All of the parameters involved can be scaled by a factor given in the COSMOtherm input In the COSMOtherm input file these options have to be given in the global command section i e first or second line of the input file The following fine tuning scaling parameters can be given 77 A Klamt F Eckert Fluid Phase Equilibria 260 2007 183 189 doi 10 1016 j fluid 2007 07 055 220 1 The electrostatic misfit energy contribution to COSMO RS is given in equation 5 11 1 Therein o and o are surface charge sigma values a is the effective contact area and a the misfit prefactor is an adjustable parameter Eyr 0 0 ag a 0 5 11 1 The electrostatic misfit term can be modified by its prefactor a via the global CMFSET factor command This will scale the a coefficient in the COSMOtherm parameter set by the given value of factor Please note that any change of the a misfit prefactor using the CMFSET keyword will str
58. equations can be expressed with this equation if the constants are set appropriately e g the regular Antoine equation D E F G 0 the Kirchhoff equation C D F G 0 the Riedel equation C D 0 G 6 or the DIPPR equation C D 0 G 2 Note that the coefficients A G are expected for temperatures 7 in C or in K for VPKantl VPKantl Pa and VPKant1_ kPa keywords respectively and vapor pressures P in mbar or in Pa for the VPantl_Pa and VPKant1_Pa keywords or in kPa for the VPant1_kPa and VPKant1_kPa keywords 27 Reid R C J M Prausnitz and B E Poling The properties of Gases and Liquids 4 ed McGraw Hill New York 1997 51 Pure compound vapor pressure input options continued Il Pexp Pi T p2 T2 p3 T3 a Pexp Pa pi T p2 T2 p3 T3 5 Pexp_kPa p T p2 Tz p3 T3 PKexp p T p2 T2 p3 T3 Optional Give three pairs of vapor pressures temperatures for this compound The values are then used to calculate the Antoine equation s coefficients for this compound Temperatures T are expected in C or in K for VPKexp VPKexp Pa and VPKexp kPa keywords and vapor pressures p in mbar or in Pa for the VPexp_ Pa and VPKexp Pa keywords or in kPa for 5 the VPexp_kPa and VPKexp_ kPa keywords PKexp_Pa p Ti p2 T2 p3 Ts lt 0O lt 0O lt O lt O lt O lt al PKexp_kPa p T p2 Tz p3 T3 5 d PVmin temp Optional Give a minimum temperature for which the
59. exp 4i eam 5 10 3 an The minimum of the free energy of the solute i at the flat interface of S and S u s of eq 5 10 2 and the total free energy of the solute i at the flat interface of S and S G of eq 5 10 3 both can be used as significant and thermodynamically rooted descriptors for the determination of surface activity in a solution 217 Figure 3 Schematic illustration of the FlatSurf option Phase S e g water In COSMOtherm the calculation of the flat surface interaction energy between two solvents is toggled via the flatsurf i j option i and j being the compound numbers in the order of the compounds given in the compound input section or the nflatsurf nam nam option nam and nam being the compound names as given in the compound input section of the COSMOtherm input file Using either of these automatic calculation options COSMOtherm will compute the surface interaction energy at the surface interface of the two solvents for all compounds that are given in the compound input section of the COSMOtherm input file The flat surf option will provide the following descriptors and for each compound i write them to the COSMOtherm output file and in tabulated from to the COSMOtherm table file u25 Gmin the minimum of the free energy of the solute at the flat interface of S and S G gt Gtot the total free energy of the solute j at the flat interface of S and S45 Amean the mean expulsion area of
60. figure a certain amount of acetone is added to the two phase liquid system Now in the LIQ EX computation the acetone is automatically equilibrated and distributed between phase and Il giving the result that acetone prefers the IL phase and that the converged self consistent phase equilibrium finds about 90 of the acetone in the IL rich phase Il The solute phase can be given to the COSMO therm input file via options NO N N N or W0O W wW Ws where N is the mole number of solute compound and w is the total mass of solute compound In addition to the absolute mole number or mass based equilibrium calculation N and w basis COSMO therm offers the possibility of using relative amounts namely mole or mass fractions x or c basis in the LIQ EX computation 3 Give mole fractions x of the compounds in the nphase phases via options x1 x x x 3 I TE and x2 x x x where x is the mole fraction of compound in phase and x is the mole fraction of compound in phase Il If more than two phases are defined via input of Nphaser all additional phases can be defined accordingly x3 x x x7 m x4 x x xs J ete 4 Give mass fractions c of the compounds in the npnase phases via options cl c c c 3 and T where c7 is the mass fraction of compound in phase and c is the efase y Cre 6 mass fraction of compound in phase II I
61. file All current i e Version C30_1501 COSMOtherm parameterization files include the density volume QSPR parameters for room temperature as well as optimized element specific surface area parameters for elements H N C O F S Cl Br and For other elements reasonable guesses for the element specific surface area parameters are provided The parameters were derived from a set of 761 room temperature densities including lonic Liquids and zwitterionic compounds such as amino acids Note that previous version of the COSMOtherm parameter files may not include density QSPR parameters It is also possible to explicitly give the values of the seven density volume QSPR parameters in the COSMOtherm input file via the OSPR_DENS Cyyr Cane Cvcosmo Cm2 Cwring Co Cm2 2 command The 142 element specific surface area parameters can be given with the EL PARAM k c command see below The computed liquid densities and volumes will be written to the mixture section of the COSMOtherm output file and tabulated in the COSMOtherm table file In addition for each compound the density and volume QSPR descriptors will be written to the table file By default the element specific surface areas are not written to the COSMOtherm table file However this can be done optionally using the PRINT ELEM keyword The computation of density of a pure lonic Liquid IL compound is feasible from the individual ions that form the specific IL
62. finite portion of compound j according to x and from that calculate the partial pressure of the compound pj according to eq 2 3 23 This process is repeated until the difference of the computed partial vapor pressure p and the given reference pressure p is less than a given threshold By default this threshold is 0 1 mbar It can be changed with the pthresh thresh input option see below The computation of a gas solubility requires the knowledge of the vapor pressure of the pure compound p at a given temperature For each compound there are several possibilities to calculate or approximate this property In order of increasing accuracy you might a Use the COSMOtherm approximation of the vapor pressure using the approximated gas phase energy of the compound This is the default and requires no additional input b Use the COSMOtherm approximation of the vapor pressure using the exact gas phase energy of the compound given via the e energy or ef filename command in the compound input and options section of the input file or the efile command in the global options section of the input file c Use the Wagner DIPPR or Antoine equation In p A B T C to compute the vapor pressure at the given temperature see section 2 2 1 The Antoine equations coefficients either can be given directly in the compound input and options section of the input file via the vpant command or they can be calculated from three temperature vapor pressure p
63. fraction conversion 97 98 SLE 82 87 sphcation 221 224 Spot 27 Spotc 27 Sprf 27 ssc_ang 208 211 ssc_ions 211 ssc_name 208 211 ssc probability 208 209 210 ssc_strength 208 209 210 ssc_weak 208 211 surface charges 18 219 SVP 164 Swrl 18 37 symcset 223 224 symgset 223 224 symmetry 25 42 44 57 chemical potential 25 SYMMETRY 45 tboil 53 thoil Cc 53 tboil K 53 tc 59 73 137 temperature dependency hydrogen bonding 71 van der Waals 71 ternary 53 63 108 109 110 111 112 118 120 126 130 137 IL 126 127 MIX 130 132 cgrid 110 111 cm 133 confweight 109 HE SPLIT 109 IL n 126 pr pp 109 qgrid 110 111 xgrid 110 111 xm 133 tetset 223 tf 59 73 137 tk 59 73 137 Tmelt 54 83 84 122 Tmelt C 54 Tmelt K 54 Tmelt mix 134 Tmelt mix C 134 Tmelt mix K 134 Tmelt salt 99 129 Tmelt_salt_c 99 129 Tmelt salt K 99 129 torset 223 tref 53 tref bar 53 tref C 53 tref F 53 tref K 53 238 tref kPa 53 tref psia 53 Turbomole 12 31 161 162 163 164 TZVP 162 163 164 UNIQUAC Q1 55 116 117 UNIQUAC 02 116 117 UNIQUAC R1 116 117 UNIQUAC R2 55 116 117 UNIQUAC2 113 115 UNIQUAC4 113 115 117 UNIT 22 167 BRITISH 22 SI 22 167 uqme 24 47 184 uqme OFF 184 uqmg 24 47 184 ugmg OFF 184 use tboil 19 53 108 112 usec 19 33 58 vapor pressure partial 109 vapor pressure automatic calculation 60 73 files 18 input 18 43 50 108 iterative calculatio
64. free energy gain of a molecule at a surface or interface between two different liquid phases S and S Under the idealized assumption of a flat interface we can calculate this energy gain relative to the free energy in phase S in the following way For a given position i e distance z of the solute center from the interface and orientation T described by the orientation of a fixed solute axis with respect to the surface normal direction of the solute relative to the interface a certain part of the surface segments will be imbedded in phase S and the rest in phase S Thus for fixed z and T we can calculate the chemical potential as uS zT Ya pus o gt a Ms o 5 10 2 velinS velins By sampling all relevant positions and orientations we can find the minimum of the free energy of the solute j at the flat interface of S and S see Figure 3 Taking into account the free energy difference between different conformations of i the search for the optimal association of i at the interface can be extended to conformationally flexible molecules if required Assuming that the free combinatorial part of the free energy stays essentially unchanged and subtracting the residual chemical potential in bulk phase S we yield the maximum free energy gain of i at the S S interface In addition to the maximum free energy gain we can try to calculate a total free energy gain from the interface partition sum S S res S res GSS RT In S
65. handle macromolecules Of the numerous free volume terms that were published in the chemical engineering literature it was found that the free volume method of Elbro et al is particular useful in combination with COSMO RS If dealing with macromolecules in an absolute and quantitative way it is therefore recommended to switch on the free volume combinatorial contribution of Elbro et a using the combi ELBRO command which either can be given locally in a temperature mixture line or generally in a global command line of the COSMOtherm input file Unlike the default combinatorial contribution of COSMOtherm which accounts for shape and size effects of molecules in terms of their molecular hard core i e COSMO cavity volumes and areas see section 1 1 the free volume method of Elbro et al also allows for the handling of compounds that do not have a well defined surface area or volume in particular macromolecules such as polymers The combinatorial contribution to the excess free energy of the Elbro free volume FV term closely resembles the Flory Huggins combinatorial contribution X L o Go RT x n 5 3 5 i Wherein gf is the free volume fraction of compound i with molecule fraction x 5 3 6 5 Loschen C Klamt A Ind Eng Chem Res 53 11478 2014 s Elbro H S Fredenslund A Rasmussen P A Macromolecules 23 4707 1990 179 The free volume V V r is defined as the difference be
66. ionic species The quantum chemical method of choice for such a problem is a full Turbomole BP RI DFT or Gaussian03 DGA1 BP86 DFT COSMO optimization of the molecular geometry using the large TZVP basis set Alternatively COSMO files created by the PQS Molpro or ORCA program at the same level of theory and basis set can be used with the same COSMOtherm parameter set The appropriate COSMOtherm parameterization for this quantum chemistry level is the BP_TZVP_C30_1501 ctd parameterization Recommended for the computation of ionic species Program Package DFT functional Basis Set COSMOtherm Parameterization Turbomole BP RI DFT TZVP BP_TZVP_C30_1501 ctd 164 4 The COSMOtherm Output File The structure of the COSMOtherm output file filename out closely resembles that of the input file as described in section 2 After some header lines that include the job identifier as well as the date time stamp of the COSMOtherm run the calculated information for the pure compounds are listed Example 3 shows the pure compound output for propanone Example 3 Compound Information for molecule 1111111111 Atomic weights E_COSMO dE E gas E_COSMO E_gas dE E diel Averaging corr dE EvdW in continuum Area Volume olecular Weight Total COSMO charge Sigma moments 1 6 H bond moments donor Dipole moment t x y Z H bond moments accept 121263 21256 6 8 0 3 102
67. known to be liquid at the given temperature conditions i e if T gt T en the QSPR derived Gibbs free of fusion AG for this compound will be set to zero If possible the five QSPR parameters are read from the CTDATA file Currently the parameterization for single point DFT COSMO calculations upon semiempirically optimized MOPAC AM1 COSMO geometries namely BP_SVP_AM1_C30_1501 ctd and the parameterizations for fully relaxed Turbomole or DMOL3 DFT COSMO calculations with the larger TZVP basis set namely BP _TZVP_C30_1501 ctd and DMOL3_PBE_C30_1501 ctd include solubility parameters that were derived from a set of solubility data of 150 solid compounds A closer description of the fitting procedure used to gain the solubility parameters is given in references 32 and 33 It is also possible to explicitly give the values of the QSPR parameters in the COSMOtherm input file using the solQSPR c c2 C3 C4 C5 command The solubility of liquid compounds also can be calculated with the solub option If the keyword liquid is given in addition to the solub keyword the heats of fusion of all compounds AG are assumed to be zero In this case no additional input of AG or QSPR parameters is necessary 31 Duffy E M and W L Jorgensen J Am Chem Soc 122 2878 2000 32 Klamt A F Eckert and M Hornig COSMO RS A novel view to physiological solvation and partition questions J Computer Aided Mol Design 15 355 2001 33
68. license file is not part of the COSMOtherm release distribution It is delivered separate from the program installer 14 2 Input Structure In this section the commands to be included in the COSMOtherm input file filename inp are described The syntax of the COSMOtherm commands closely resembles the MOPAC input concept All commands are given in the form command argument or command argumentl argument2 argument3 i e if several arguments are given for a command the arguments have to be included into curved brackets and separated by blank spaces Note that only blanks are allowed as delimiter inside the curved brackets The usage of commas or similar will result in an error message There is however no limitation in the number of blanks that are set between the commands and arguments spare spaces are ignored The commands do not need to be given in a special order except for their affiliation to one of the three main areas of the input file described below Commands are not case sensitive Note however that filenames given as arguments of the commands possibly will be case sensitive for example if COSMOtherm is run on a UNIX system Also note that unknown commands do not lead to an error message they plainly will be ignored The input of real numbers is of free format i e arguments like 1 0 0 5d 4 l e 2 500 are valid However the latter format input of a real number as an integer is not recommended The hash character
69. mutually exclusive If the SLESOL keyword is used COSMOtherm attempts to solve the actual solid liquid SLE and if present liquid liquid LLE or solid liquid liquid SLLE equilibrium conditions for each solute with the given solvent or solvent mixture The equilibrium conditions that are solved for are described in section 2 3 7 2 and 2 3 7 3 The use of the SLESOL option has several implications the most important one being computational time the explicit solution of the phase equilibrium conditions requires a considerably higher number of COSMOtherm function evaluations than the simple recursive algorithmic solution of the iterative option Typically with the SLESOL option computational time will increase by a factor of 10 or more compared to the iterative option Unlike the latter there is no ambiguity in the results of the SLESOL option The solubilities thus computed are actual solutions of the systems phase equilibrium conditions Unlike the iterative case complex phase situations like the SLLE case mentioned above can be resolved correctly by the SLESOL option Some care has to be taken in the interpretation of the results of the two options While the iterative solubility does not distinguish between liquid and solid solubility in terms of the given results the SLESOL option does both the results of the solid liquid equilibrium and the liquid liquid equilibrium conditions are written to the solubility table Th
70. o potentials of the four solvents water acetone chloroform and hexane respectively Of these hexane is the least polar compound This is reflected in the narrow distribution of the charge densities around zero in Figure 1 The two peaks can be assigned to the carbon atoms for positive o and to the hydrogen atoms for negative o values please keep in mind that negative partial charges of atoms cause positive screening charge densities and vice versa The corresponding o potential which is a measure for the affinity of the solvent to a molecular surface of polarity o is a simple parabola centered at o 0 see Figure 2 Such a shape arises from misfit contributions only no hydrogen bonding and is equivalent to purely dielectric behavior The other extreme is represented by the o profile of water It is very broad and the probability for o is almost zero at the center of the o profile The broad peak around 0 015 e A arises from the two very polar hydrogen atoms whereas the peak around 0 015 e A results from the lone pairs of the oxygen This reflects the excellent ability of water to act as a donor as well as an acceptor for hydrogen bonding In addition such a symmetric shape of the o profile indicates a favorable electrostatic interaction of water with itself explaining its high boiling point and surface tension The corresponding o potential has a much higher value around zero reflecting an unfavorable interaction with nonpolar surface This is re
71. of this compound The given free volume will be used in the polymer specific Elbro combinatorial contribution described in section 5 3 2 Argument V is expected to be a real number larger than zero For the expmolvol option argument V is expected to be in A and for the expdensity SI option in nm respectively Optional Provide the polymer molecular weight MWpoiymer Of this compound The given polymer weight will be used in the polymer specific Elbro combinatorial contribution described in section 5 3 2 Argument MWpoiymer In g mol is expected as a real number larger than zero Optional Identify compound as polymer This flag will be used in the polymer specific Elbro combinatorial contribution described in section 5 3 2 56 2 2 4 Conformer Input Different conformers of one compound have to be given in a so called Conformer Block denoted by square brackets and All molecules found inside the square brackets are assigned as conformers of one compound If no compound name is given via the comp name command the name of the first molecule in the Conformer Block will be used Note that the square brackets have to be in the same lines as the compound molecule input lines The conformers will be weighted internally by COSMOtherm using their COSMO energy and chemical potential In addition a conformer weight prefactor accounting for degeneracy or symmetry of conformer distributions is taken into account the conformer wei
72. on o potentials For the simpot i j option S is computed for the two compounds with the compound numbers i and j in the order of compounds given in the compound input section For the nsimpot name name option is computed for the two compounds with the compound names name and name as given in the compound input section of the COSMOtherm input file In case of the o potential similarity it is not only possible to compute the similarity of two given compounds but also the similarity of two compound mixture phases This is possible if in the input file the mixture concentrations are given for the two phases between which the sigma potential similarity coefficient shall be computed The input of the concentrations of the two phases is possible either in mole fractions xsl x x xS2 x X2 or mass fractions csl c co cs2 cj C2 Of the compounds of the mixture where x are mole fractions and c are mass fraction concentrations The computed similarity factor S is printed to the mixture output section of the COSMOtherm output file S is printed below the compound output block of the first compound given in the similarity command i e compound i or name At a given temperature the n simpot option will 47 Thormann M Klamt A Hornig M Almstetter M J Chem Inf Model 46 2006 1040 1053 138 toggle two COSMOtherm computations of the o potentials 4 c and y o for the pure compounds i and j
73. only the prediction quality is much better When looking only at the re ative differences between the reaction energies of a reaction in different solvents these differences will be predicted with the usual expectable quality of COSMOtherm for properties of liquids which is about 0 5 kcal mol The large absolute number error resulting from the underlying DFT method is cancelled out in this case If however high accuracy for abso ute predictions of the reaction energy or enthalpy is required this can be achieved by introducing external energy data for the compounds from high quality quantum chemistry calculations into the calculation of the compounds G and H values This can be achieved most conveniently by separating the COSMOtherm and the quantum chemical QM contributions 2 to G and H by means of the compounds Gibbs free energy of solvation AGS and enthalpy of vaporization AH which describe the the change of the compounds total free energy and energy when going from gas phase the reference state of the quantum chemical calculation to the liquid phase the state of COSMOtherm Thus AGS and AH describe the change of the free energy and enthalpy which occurs if compound is dissoluted from the gas phase into the liquid phase G EM AGE 5 4 5 H EM AH 5 4 6 The AGS and AH terms describe the transition from gas to liquid state The terms are computed by Gas COSMOtherm from the chemical pote
74. option is active only for the temperature mixture line where it is given If the option contact is given without argument P is printed for all compounds in the mixture If the option contact i iz is given the contact statistics is printed only for compounds i where i is the number of the compound in the order that is given in the compound section of the COSMOtherm input file If the option ncontact name name is given the contact statistics is printed only for compounds name name where name is the name given in the compound section of the COSMOtherm input file If conformers of compounds are used the contact statistics will be averaged over conformer weights as computed for the given temperature and mixture condition If detailed conformer information output is requested by the global or mixture section keyword wconf see section 2 1 the individual contact probabilities of all given conformers with nonzero concentration in the given mixture will be printed to the molecule conformer section in the output file in addition to the conformer properties and weight factors It is also possible to calculate a more detailed contact interaction statistics of all segments of molecule A with the molecule B This can be achieved with the command segment_contact i i2 in a temperature mixture line of the COSMOtherm input file This command is active only in the temperature mixture line where it is given If this option is given a detai
75. or CSTEP Npoints or qstep Nypoints Optional for binary and ternary computations Change default concentration grid of the VLE LLE or SLE calculation to mole fraction xgrid default mass fraction cgrid or surface fraction qgrid concentrations Optional for binary and ternary computations Mole fraction concentration grid input of initial mole fraction xstart mass fraction cstart or surface fraction qstart concentration vector of the compounds of the binary or ternary mixture as real numbers x cand q The arguments are expected as real numbers between zero and one If the values do not add up to one COSMOtherm will normalize them If less concentration values than defined phases are given the missing ones will be assumed zero If a negative number is given the concentration for this component will be inserted automatically using the normalization of the sum of the remaining concentrations Only one negative number is allowed per concentration input Optional for binary and ternary computations Mole fraction concentration grid input of final mole fraction xstart mass fraction cstart or surface fraction qstart concentration vector of the compounds of the binary or ternary mixture as real numbers x c and q Properties of the xend cend and qend commands are the same as described for the xstart cstart and qstart keywords Optional for binary and ternary computations Input of the number of grid poin
76. output and table file by CAS Registry Numbers RN To be active this option requires that a database index file has been read in via the dbas option use cosmo database index file If wcas is used the compounds CAS RN associated with the given compound as read from the database index file will be printed to output and table files instead of the compound name Optional Replace compound names in the output and table file by COSMO database trivial names To be active this option requires that a database index file has been read in via the dbas option use cosmo database index file If wdbn is used the compounds trivial name associated with the given compound as read from the database index file will be printed to output and table files instead of the compound name 21 2 1 2 Print Options for the COSMOtherm Output File continued UNIT SI UNIT BRITISH contact segment contact grad pvac Optional UNIT SI in the global command section triggers the output of all values in the out tab mom moma prf pot files to be in Sl units l e energies in kJ mol pressures in kPa areas and volumes in nm and nm atomic masses in g mol temperatures in K charges in C mol surface charges o in e nm c potentials u in kJ mol nm Antoine constants in the kPa K frame and solubility parameters in the kJ nm frame Optional UNIT BRITISH in the global command section triggers the output of all values in
77. parameterizations will not be enhanced or updated for future releases of COSMOtherm In addition COSMObase the database of COSMO files will not be shipped for such quantum chemical levels There are three main areas of application which require different proceeding regarding quantum chemistry 3 3 1 High quality prediction of thermophysical data for chemical engineering The application of COSMOtherm in chemical and engineering thermodynamics e g prediction of binary VLE or LLE data activity coefficients in solution or vapor pressures typically requires high quality of the predictions of the properties of mixtures of small to medium sized molecules up to 25 non Hydrogen atoms The quantum chemical method of choice for such a problem is a full Turbomole BP RI DFT COSMO optimization of the molecules geometry using the large TZVP basis set Alternatively COSMO files created by the PQS Molpro or ORCA program at the same level of theory and basis set can be used with the same COSMOtherm parameter set Starting with version Gaussian03 it is also possible to use the Gaussian program package DGA1 DFT with BP86 B88 VWN P86 functional and Ahlrichs TZVP basis set Although the charge surfaces of COSMO files produced by Gaussian and Turbomole are not identical the charge surface of Gaussian COSMO files can be converted into a charge surface that is equivalent to the charge surface produced by Turbomole using a molecule of the same geometry
78. phase diagram computations pr_pp Optional for binary ternary or multinary computations in the binary ternary or multinary phase diagram table replace the default output of the compound mole fraction in the gas phase y with the compounds partial vapor pressure p HE SPLIT Optional for binary ternary or multinary computations print the three contributions to the total excess enthalpy to the COSMOtherm table and output files confweight Optional for binary ternary or multinary computations print as additional columns the Boltzmann weight factors of molecular conformers to the binary ternary or multinary phase diagram table 109 If no additional phase diagram calculation suboptions are given in the mixture input i e if a simple vapor liquid equilibrium VLE calculation is performed the binary and ternary options will compute a default grid of 29 and 231 mole fraction concentration points respectively The default grid values span the complete concentration range of the two and three dimensional binary and ternary phase space The concentrations of the VLE default grid are defined in mole fractions which are unevenly spaced the concentrations steps in the grid are becoming smaller if a compound approaches infinite dilution This specific grid accounts for the fact that properties such as activity coefficients y or concentrations in the vapor phase y typically show their strongest changes at low x concentrations Thus b
79. phases between which the FlatSurf properties shall be computed cf l c1 Cz The input of the concentrations is possible either in mole fractions xf1 and or xf2 or mass fractions cf1 cf2 of the compounds of the xf 2 x X2 mixture as real numbers x and c The arguments are expected as real or numbers between zero and one in the same sequence of compounds as given cf 2 c Cp in the second input area If the values do not add up to one COSMOtherm will normalize them If less mole fractions concentrations than compounds are given the missing ones will be assumed zero If a negative number is given the concentration for this compound will be inserted automatically using the normalization of the sum of mole fractions Only one negative number is allowed per mixture input line ift value Optional for FlatSurf computations Give the interfacial tension IFT of the two phases between which the FlatSurf properties shall be computed The argument value is expected to be in dyne cm Fwrl Optional for FlatSurf computations Create VRML files of the molecular COSMO surface charges at the FlatSurf interface A VRML file name_flat wrl will be created for each molecule name cosmo that is given in the compound input section The usage of the Fwrl command and the created VRML files are identical to the sigma charge surface VRML files created by the Swrl command cf the Swrl keyword in the compound input s
80. possibilities to calculate or approximate this property In order of increasing accuracy you might 1 Use the COSMOtherm approximation of the vapor pressure using the approximated gas phase energy of the compound This is the default and requires no additional input 2 Use the COSMOtherm approximation of the vapor pressure using the exact gas phase energy of the compound given via the e energy or ef filename command in the compound input and options section of the input file 3 Use COSMOtherm approximation of the vapor pressure in combination with an experimental boiling point value either normal boiling point T at 1 atm or a reference boiling temperature T ef at a given reference pressure P via the via the use_tboil option 4 Use a vapor pressure correlation equation such as Wagner DIPPR or Antoine equation to compute the vapor pressure at the given temperature The vapor pressure equation coefficients either can be given directly in the compound input section of the input file they can be read from a vapor pressure property file vap file or they can be calculated from three temperature vapor pressure pairs given via the vpexp command see section 2 2 3 5 Give the exact value of the vapor pressure for this temperature via the vpinp command in the compound input and options section of the input file The given sequence of the vapor pressure estimates also indicates the hierarchy in which the vapor pressure estimates a
81. r r r3 card for real number weights Alternatively for the iwl n n n _ option all weights are zero by default and only the atoms with the numbers n n n explicitly given with this option are set to one The input otions aw n w no w awu n iW N2 W2 and awz n w no w gt provide a more flexible alternative to the iw1 option in that real number weights w can be given for atom with number n For option aw the default weight of the atoms not explicitly given as argument of the keyword are all one or w as given by wdf1 w keyword For option awu the default weight is one and for option awz the default weight is zero Thus the iw1 and the aw awu and awz options allow for a simple cutout of a small area e g an active site in a large molecule e g a protein Example 6 shows a COSMO metafile for 1 octanol constructed from 1 pentanol and n pentane having zeroed out the terminal CH groups Example 6 f 1l pentanol cosmo w 111110011111111100 f pentane cosmo w 11110111111111000 10 Another possibility of constructing the same molecule would be the use of the 1 heptanol COSMO file as a basis file and weighting one of the middle CH groups doubly Some general precautions have to be taken if molecules shall be constructed via metafiles First the quality of the COSMOtherm results critically depends on a chemically reasonable choice of the fragments For example functional groups should no
82. section 2 2 3 EPSILONO EST g Input of the molecule s dielectric constant s This input will overwrite the default dielectric constant estimate computed by COSMOtherm but it will be overwritten by the dielectric constant input from a vapor pressure property file or from a compound line input see section 2 2 3 SYMMETRY Nirrep or nirrep Nirrep Input of a fixed symmetry number N number of irreducible representations to be used in conformer equilibrium computations or as addition to the chemical potential of a compound via global option musym see section 2 1 3 replacing the symmetry computed from the COSMO file geometry Note that for the SYMMETRY N rrep and the nirrep N keywords no blanks are allowed between and N srep pgroup I Input of a fixed point group H where I is the point group symbol e g II cs c2v D4h to be used in conformer equilibrium computations or as addition to the chemical potential of a compound via global option musym see section 2 1 3 replacing the symmetry point group computed from the COSMO file geometry Note that for the pgroup keyword no blank spaces are allowed between and II The given point group symbol IT will be used to determine the fixed symmetry number number of irreducible representations N Of the molecule and replace the Nirrep NUMber computed by COSMOtherm 42 2 2 2 Gas Phase Energy Input To be able to
83. solubility w7 to Definition 1 which is w Xa MWacl MWsoivent Optional for solub computations Change the output of the mass based solubility w 7 to Definition 2 which is w Xoo MWacl 1 xP MW vent Optional for solub computations Change the output of the mass based solubility w 7 to normalized mass fraction output which is w x 0 MW xa MW 1 Xa MW sonent Optional for solub computations of salts Change the output of the mole fraction solubility x to pseudo binary framework where the salts anions and cations are considered to be independent species default output of x is the laboratory binary framework where the salt is considered to be one single compound see section 5 9 for details of the conversion 98 Salt heat of fusion crystallization input DGfus_salt value or DGfus_ salt STI value DHfus_salt value or DHfus_ salt SI value DSfus_salt value or DSfus_ salt _SI value Dcpfus_ salt value or Dcpfus_ salt SI value Tmelt_salt temp or Tmelt_ salt _C temp or Tmelt salt _K temp dcpfus_ estimate DGfmean Optional Give the free enthalpy of fusion AG for a salt For the DGfus_salt value option AG is expected in kcal mol for the DGfus_ salt SI option AG is expected to be in kJ mol Argument value is expected to be a real number Optional Give the enthalpy of fusion AH for a salt For the
84. statistics file that was created by COSMOtherm via command segment contact the 6 real number column holds the contact interaction statistics see section 5 7 The map_ column command allows the visualization of other properties in file mapfile For example the surface potential on the COSMO surface that is given in the 7 column of a surface contact statistics file created by COSMOtherm can be visualized via map_column 7 206 Control options for the visualization of surface contact statistics map files continued absconwrl absconscale relconscale wrl_min min val wrl max max val Optional suboption of the wrlmap mapfile command Visualize contact statistics that are not scaled by the apparent surface area This option is only valid if segment contact statistics are visualized from a contact file i e if the default visualization is used or if map_column 6 is given Optional suboption of the wrlmap mapfile command Use absolute coloring scheme scaled by surface concentration ratio of the contacting molecules This option is only valid if segment contact statistics are visualized from a contact file i e if the default visualization is used or if map_column 6 is given Optional suboption of the wrlmap mapfile command Use absolute coloring scheme scaled by the apparent overall contact probability of the contacting molecules This option is only valid if segment contact statistics are visualized from a contac
85. that the concentration of the dissociated species in the solution is negligible If this assumption breaks down i e if the system dissociates strongly at the given pH conditions the Henderson Hasselbalch correction term will become erroneous In such a case equations 2 3 4 2 or 2 3 4 3 should be applied instead Accordingly equations 2 3 4 2 and 2 3 4 3 are used by default if a dissocation corrected solubility calculation is toggled in COSMOtherm using the solub option The Henderson Hasselbalch equations 2 3 4 4 and 2 3 4 5 can be used optionally by means of the keyword use_hh Note that eqations 2 3 4 1 2 3 4 5 are based on the implicit assumption that the dissociated species are completely dissolvable in the solvent phase As this assumption may not hold any more for nonaqueous solvents the DC correction of solubility calculations currently is restricted to solvent pure water The automatic solubility solub option of COSMOtherm will apply the dissociation correction to any solute of which the pK value is given or estimated The solubility value thus computed will be written to the COSMOtherm output file as well as to an additional column in the table output of the solub option in the COSMOtherm table file In addition the pK acid or pK base value used in the dissociation correction calculation is printed to the output and table files The dissociation corrected solubility values are identified by a DC Dissociation Corrected ta
86. the compounds initially in phase I N is the mole number of compound in phase l Required for liq ex computations Give mole numbers N of the compounds in the phase II N is the mole number of compound in phase Il Required for liq _ex n nase Computations Give mole numbers N of the compounds in the additional phases k where k 3 ngnase N is the mole number of compound in phase k Required for liq ex computations alternative to N1 option Give absolute masses wW of the compounds initially in phase I w7 is the mass of compound in phase I Required for lig ex computations alternative to N2 option Give absolute masses wW of the compounds in the phase II w77 is the mass of compound in phase II Required for liq _ex npnase Computations alternative to Wk option Give masses W of the compounds in the additional phases k where k 3 Npnase W is the mass of compound in phase k Optional for liq ex computations using mole numbers N or absolute masses W Give mole numbers N of compounds present in an additional solute phase 0 N is the mole number of compound in phase 0 Optional for liq ex computations using mole numbers N or absolute masses W Give absolute masses W of compounds present in an additional solute phase 0 w is the mass of compound in phase 0 152 Suboptions of the 1iq_ex option continued I E I xl X 1 Xo X3 n II Il X2 X 1 X gt X k k k xk x X
87. the COSMOtherm input file the grad option is active only for the temperature mixture line where it is given See also section 5 6 Chemical Potential Gradients for further information pvac Optional Print the value of the the chemical potential of vacuum for the given mixture to the output file wtln Optional Print full compound and or molecule names to all tables in the name tab table output file and the name mom sigma moments file By default the compound molecule names are cropped after 20 characters ctab Optional Print compound and conformer mixture information to the COSMOtherm table file The ctab keyword toggles the additional tabulation of all mixture information which by default is written to the ouput file only to be printed to the COSMOtherm table file For each temperature mixture as given in the mixture section of the input file a separate table will be created If in addition the wconf keyword is used an additional table with the properties of the calculated COSMOtherm mixture information for each individual conformer is written to the table file By default all concentrations are written to the ctab table headers If the the additional keyword npzero is used only nonzero concentrations are written to the ctab table headers To avoid an extremely large number of tables to be created this option is only active for the plain Temperature and Mixture input using x or x pure as described in section 2 3 A above
88. the ab initio quantum chemistry program GAMESS US Treatment of outlying charge in continuum solvation models Andreas Klamt and Volker Jonas J Chem Phys 105 9972 9980 1996 Presents some methodological refinements of COSMO increasing the accuracy and reliability of this model Incorporation of solvent effects into density functional calculations of molecular energies and geometries Jan Andzelm Christoph K lmel and Andreas Klamt J Chem Phys 103 9312 9320 1995 Implementation of COSMO into the Density Functional program DMOL3 COSMO A New Approach to Dielectric Screening in Solvents with Explicit Expressions for the Screening Energy and its Gradient A Klamt and G Sch rmann J Chem Soc Perkin Trans II 799 805 1993 The original presentation of the Conductor like Screening Model COSMO and its first implementation into the semiempirical quantumchemistry program package MOPAC 230 COSMO Applications and Related Articles Calculation of UV Vis Spectra in Solution Andreas Klamt J Phys Chem 100 3349 3353 1996 Application of the COSMO MOPAC model to the theoretical calculation of UV Vis spectra Prediction of Phase Equilibria for Binary Mixtures by Molecular Modeling Maurizio Fermeglia and Sabrina Pricl AIChE Journal 47 2371 2382 2001 A combination of the COSMO model with an equation of state EOS is applied to the prediction of binary phase diagrams Compari
89. the contact of two different SCDs The specific interaction energy per unit area resulting from this misfit of SCDs is given by 1 Eyp O 0 ay soto 1 1 8 Andzelm J C K lmel and A Klamt J Chem Phys 103 9312 1995 B Delley J Phys Chem A 110 13632 2006 Gaussian 09 M J Frisch et al Gaussian Inc Pittsburgh PA 2011 10 Baldridge K and A Klamt J Chem Phys 106 66622 1997 11 PQS P Pulay J Baker K Wolinski Paralell Quantum Solutions Fayetteville AR 2003 12 MOLPRO a package of ab initio programs designed by H J Werner and P J Knowles version 2004 1 R D Amos A Bernhardsson A Berning P Celani D L Cooper M J O Deegan A J Dobbyn F Eckert C Hampel G Hetzer P J Knowles T Korona R Lindh A W Lloyd S J McNicholas F R Manby W Meyer M E Mura A Nicklass P Palmieri R Pitzer G Rauhut M Sch tz U Schumann H Stoll A J Stone R Tarroni T Thorsteinsson 2004 13 COLUMBUS an ab initio electronic structure program release 6 by H Lischka R Shepard I Shavitt R M Pitzer M Dallos Th M ller P G Szalay F B Brown R Ahlrichs H J B hm A Chang D C Comeau R Gdanitz H Dachsel C Ehrhardt M Ernzerhof P H chtl S Irle G Kedziora T Kovar V Parasuk M J M Pepper P Scharf H Schiffer M Schindler M Sch ler M Seth E A Stahlberg J G Zhao S Yabushita and Z Zhang 2003 14 ORCA large sca
90. the lonic Liquid defined by the ions as given by the IL i j or nIL name name command The stoichiometry factors vi v are expected to be positive integer numbers ILphase REAL Optional for binary or ternary IL computations Define the lonic Liquid salt complex phase as real mixture with respect to activity and vapor pressure of the phase The argument of the ILphase option is expected to be upcase 128 Suboptions of the SLE and binary i SIL ornbinary name IL option are DGfus_salt value or DGfus_ salt STI value DHfus_salt value or DHfus_ salt SI value DSfus_salt value or DSfus_ salt _SI value Dcpfus_ salt value or Dcpfus_ salt SI value Tmelt_ salt temp or Tmelt salt _C temp or Tmelt salt _K temp Depfus_ estimate Optional Give the free enthalpy of fusion AG for an IL salt For the DGfus_salt value option AG is expected in kcal mol for the DGfus_salt_ SI option AG is expected to be in kJ mol Argument value is expected to be a real number Optional Give the enthalpy of fusion AH for an IL salt For the DHfus_salt value option AH is expected in kcal mol for the DHfus_ salt SI option AH is expected to be in kJ mol Argument value is expected to be a real number Optional Give the entropy of fusion AS for an IL salt For the DSfus_salt value option AS is expected in kcal mol for the DSfus_ salt SI option AS
91. the number of secondary or tertiary aliphatic amino groups in the compound The NAmine descriptor and its coefficient c 2 5 kcal mol is needed only if the solvent in which the solubility is calculated is water For any other solvent c is zero An approximate temperature 30 Hildebrand J H Prausnitz J M and Scott R L Regular and Related Solutions Van Nostrand Reinhold Co New York 1970 84 dependency for the AG term of the solubility QSPR is used This term uses Walden s Rule claiming that the temperature dependency of the free energy of fusion of nonsymmetric organic molecules can be approximated by AS 0 0135 kcal mol K Note that the ACp estimate described above toggled by the keyword dcpfus_estimate may also be used in combination with QSPR AG and Walden s rule The precautions noted above apply in this case too Quite frequently a compounds melting temperature Ter is known experimentally but none of its enthalpy of fusion AH entropy of fusion AS or heat capacity of fusion ACp data In such a case AG has to be estimated by the QSPR approach of equation 2 3 5 If available for a given compound COSMOtherm will use the melting temperature information T melt to determine if the compound is a solid at the given conditions of the solubility computation This information will be written to additional columns in the table output of the solub computation table output In addition if the compound is
92. the reference solubility value for a reference solubility calculation of AG The ref _sol_s option assumes that the given reference solubility value is given as the decadic logarithm of the solutes mole fraction log x The ref_sol_x option assumes that the given reference solubility value is given as the solutes mole fraction x so The ref_sol_c option assumes that the given reference solubility value is given as the solutes mass fraction concentration cso The ref _sol_g option assumes that the given reference solubility value is given as the solutes mass based solubility g in g g By default or if the wso12 keyword is given the input as well as the output of the mass based solubility g o is assumed to be the unnormalized mass based solubility of Definition 2 gso W sorz xp MW 1 xf MWeoivent If the additional keyword wsoll1 is given the input as well as the output of the mass based solubility g 4 is assumed to be the unnormalized mass based solubility of Definition 1 gso Wg XP MW MW sovent If the additional keyword wfract is given the input as well as the output of the mass based solubility g is assumed to be the mass fraction i e identical to the input of the ref sol_c option The ref sol m option assumes that the given reference solubility value is given as the solutes molar concentration M o in mol l Please note that the input of a molar reference solubility requires
93. the solvent phase volume quotient VQ V V will be estimated from solvent densities p and o If VQ is not given in the input COSMOtherm will try estimate the solvents volumes with the liquid density volume QSPR method as described in section 2 3 12 Please note that for solvent mixtures the density estimate is a linear interpolation between the pure compounds densities where excess density volume is neglected If no density estimate is available the solvent phase volume quotient will be estimated from the COSMO Volumes of the given solvent compounds However it is also possible to read VQ from the input file using the vq value command see below The input of VQ will be necessary if the densities of the two solvent phases differ substantially and thus the estimate from the QSPR densities or COSMO volumes based on the assumption of an incompressible liquid will be poor In addition it is possible to give finite concentrations at which the chemical potentials p of the compounds are computed via the xl1 x1 x2 and cll cl c2 commands for the first solvent and x12 xl x2 and cl2 cl c2 commands for the second solvent This will be necessary if the two solvent phases are partially soluble in each other e g as for the case of octanol water where the octanol rich phase contains about 0 274 mole fractions of water Suboptions of the logp or nlogp command are x1l1l xl x2 Optional for logp computations Give fi
94. to the solub keyword the decadic logarithm of the molar solubility of the solute in the solvent logio Sac Mol logig x e Veoivent Will be written to the COSMOtherm table file 97 Salt lonic Liquid solubility computation suboptions to the solub or nsolub command salt i j or nsalt name name salt_n vi v wsoll wsol2 wfract pr_ILtern a we eh Optional for solub computations Define the salt composition from individual anion and cation compounds The input of the salt composition is possible either via their compound number salt i j command where i j are the numbers of the ion compounds numbers as given in the sequence of compounds in the compound input section The arguments i j are expected to be positive integer numbers or via their compound name nsalt name name command where name name are the names of the ion compounds as given in the compound input section Optional for solub computations Define the salt stoichiometry from individual anion and cation compounds The input of the salt stoichiometry factors vi v is possible via the salt_n v vj command where v v are the j stoichiometry numbers of the salt compound defined by the ions as given by the salt i j or nsalt name name command The stoichiometry factors vi vj are expected to be positive integer numbers Optional for solub computations Change the output of the mass based
95. weight is used to compute the contact statistics map of the given compound If however the detailed conformer information output is requested by the global or mixture section keyword wconf see section 2 1 then the individual contact probabilities of all given conformers with nonzero concentration in the given mixture will be computed and written to the contact statistics map file In addition to the default of the segment contact option where the contacts of the segments of a molecule A with the complete molecule B are computed it is also possible to compute site specific contact probabilities i e the contacts of the segments of a molecule A with specific sites on molecule B The sites on molecule B can be defined as single surface segments single atoms or groups of atoms Using the additional command 1seg ino iseg in combination with the segment _contact i i command the detailed contact interaction statistics of all individual segments of compound A i e molecule i as given in the segment_contact i i command with one single segment i g of molecule B molecule i o1 as given in the 1seg imo1 ise Option are computed The resulting contact interaction map thus quantitatively describes the probabilities that segments j se of molecule A will have contact with the given segment i e of molecule B Using the additional command latm ino iatom in combination with the segment contact i i command the detailed contact intera
96. wet Water prop Partition coefficient wet l octanol water dry l octanol water oleyl alcohol water acetone water propylene glycol dipelargonate water wet diethylether water methylenechloride water chloroform water tetrachloromethane water carbon disulfide water benzene water toluene water cyclohexane water n hexane water n heptane water 2 2 4 trimethylpentane water n hexadecane water olive oil water gas water water cell permeation water skin permeation at 37 C blood brain logBB water plant cuticle tadpole narcosis log 1 C intestinal absorption in enthalpy of solvation in water kj mol aqueous solubility log xs 198 The global OSPR option will write the computed property of each molecule to the compound output section of the COSMOtherm output file If the smom file mom option is used to create an additional tabulated file with the molecular c moments the computed QSPR property will also be written to an additional column of that file The mixture option PROPQSPR will write the computed property of each molecule to the compound output section of the COSMOtherm output file and to the COSMOtherm table file If no temperature and no mixture concentrations are given in the mixture input line the PROPQSPR command will toggle the computation of the given QSPR property for all molecules Conformers are treated as individual molecules in this case I
97. will also be computed and written to COSMOtherm output and table files In addition to the Henry law constant it is possible to compute the closely related Gibbs free energy of solvation G for all compounds This is possible with the keyword Gsolv There are two possible reference framwork that G can be computed in 1 By default i e if Gsolv is given without argument G7 of all compounds is computed in the molar framework i e G5 is the free energy of transfer of a solute molecule i from an ideal gas at molar 1 mol l concentration to an ideal solution at the same solute concentration The reference state of this calculation is 1 of ideal gas and 1 of liquid solvent In this reference state the free energy of solvation is computed as GJ u ul RT In ps Vig MW where 4 S is 5 is the infinite dilution the chemical potential of the compound in the ideal gas phase 4 chemical potential of the compound in solution MW is the molecular weight of the solvent Vg is the molar volume of the ideal gas and p is the density of the solvent or solvent mixture The density of the solvent or solvent mixture p can be provided to COSMOtherm via the the solvdens keyword If p is not given in the input COSMOtherm will estimate the solvents density with the liquid density volume QSPR method as described in section 2 3 12 Please note that for solvent mixtures the density estimate is a linear interpolation b
98. zero in the COSMO meta file The second step in the description of a reaction is the assignment of the interaction energy in the mixture part of the COSMOtherm input file This is done with the en_IEI i i2 c_H c_S option i and i are the IEI numbers of the reacting compound as given in the compound input section The two parameters c Handc S are parameters for the enthalpic and entropic contribution to the interaction energy of the two IEI numbered compounds c_H and c_S are kcal mol and kcal mol K respectively The interaction Gibbs free energy between the two IEI numbers is calculated from equation 5 8 1 G ii i 2A e H Tec S 5 8 1 A is the energy different between the first conformer A and the second conformer meta file A B The value of A automatically is calculated by COSMOtherm It is possible to give several en _IETI entries in one compound input line for the treatment of several different reactions Example 10 shows the according en_IEI entry for the dimerization reaction of acetic acid The only interaction that has to be taken into account for this reaction is that of IEI number 1 with itself because only species A acetic acid with IEI number 1 are involved in the reaction This is the simplest case of a concentration dependent reaction in solution The interaction energy of this reaction is determined from eq 5 8 1 using c_H 3 kcal mol while c_S is zero Example 10 a COSMOtherm input
99. 00 0 35000000 0 27146677 0 44974618 396 777606 2 94021437 2 46058849 1 299 92 0 0 88 601 0 21703 0 0 0 20000000 0 40000000 0 40000000 0 15460050 0 37444353 402 066707 2 90436831 2 53133874 1 78474129 0 0 63 40 62 0 0 10000000 0 45000000 0 45000000 0 00330668 0 25286222 405 2 83018829 2 60867576 2 47607805 s 0 40169193 0 Oy 0 0 00000000 0 50000000 0 50000000 0 18803413 0 07075771 286 6 0 00000000 2 67948163 2 69104320 3 52849562 0 05225085 0 16808653 0 00000000 0 68450147 0 0 00000000 1 00000000 0 00000000 0 00000000 0 00000000 372 0 00000000 2 26785511 0 00000000 2 01608701 0 00000000 0 29232938 0 00000000 1 00000000 0 00000000 0 05000000 0 90000000 0 05000000 0 03104505 0 07354543 387 686277 5 04525166 2 33481735 4 03111466 1 88615867 0 00110131 0 38420045 0 10552977 0 86551699 0 02895323 0 10000000 0 80000000 0 10000000 0 06647283 0 14579248 395 777338 4 68338969 2 40840281 3 52501758 1 75642515 0 00431289 0 47903884 0 18159001 0 75604449 0 06 0 0 15000000 0 70000000 0 15000000 0 10637407 0 21671244 398 817949 4 50573809 2 49077272 3 20161080 1 62756092 0 00959557 0 57711325 0 23762625 0 65997255 0 0 20000000 0 60000000 0 20000000 0 15151163 0 28631977 398 736913 4 40282246 2 58518168 2 95165906 1 50011694 001675292 0 67860228 0 27898008 0 56986992 0 0 25000000 0 50000000 0 25000000 0 20247834 0 35467159 397 307575 4 34023126 2 69674008 2 74084888 1 37442695 0 02537971 0 78368701 0 30864293 0 48072937 0 0 30000000 0 40000000
100. 09231 33070173 1 68448331 Qs 0 41031490 0 0 30000000 0 30000000 0 40000000 0 28787586 0 47838555 398 303793 4 23872893 2 38135022 1 35014299 0 87341741 0 36058163 0 0 35000000 0 35000000 0 30000000 o 0 45769206 396 383149 4 30760981 2 47662712 1 08874583 1 01275479 0 8149 0 0 40000000 0 40000000 0 20000000 Qs 0 42433748 397 726219 4 35740424 2 64941961 0 87768525 0 19944020 1 14918458 0 30018346 0 0 45000000 0 45000000 0 10000000 o 0 38006404 400 348943 4 39402775 3 00742737 0 70287996 032659140 1 28491904 0 28168767 0 58029108 0 50000000 0 50000000 0 00000000 0 0 32603774 403 145695 4 42138735 0 00000000 0 55492095 0 46035080 1 42291825 0 26806753 0 73193247 LLE results for multinary system x 2 xD xD 2 B An gle D Ang x 2 An g x 3 An g x D Ang x 2 An g x 3 yQ Qs 0 000000 0 000000 0 000000 0 000000 0 000000 Oo 0 000000 0 000000 0 000000 0 000000 0 000000 Qs 0 000000 0 000000 0 000000 0 000000 0 000000 o 0 076257 0 032263 0 029035 0 408412 0 562553 0 066250 3 067761 3 491315 0 3 Gs 0 084031 0 033511 0 035085 0 431947 0 532968 0 073856 2 999099 3 299431 0 o 0 089361 0 034332 0 039467 0 446604 0 513929 0 079167 2 954405 3 180000 0 Oo 0 093224 0 034907 0 042753 0 456560 0 500687 0 083059 2 923134 3 098830 0 0 0 096559 0 035500 0 045172 0 463704 0 491124 0 086560 2 896059 3 041669 0 Oo 0 098898 0 035845 0 047213 0 469140 0 483647 0 088967 2 877908 2 996761 0 0 000000 0 000000 0 000000 0 000000
101. 2 avsaltmu 150 154 c1 148 153 c2 148 153 gaseous 150 154 maxiter 153 NO 148 152 N1 147 152 N2 147 152 pr_k 148 153 pr_mu 148 153 pr_xk 148 153 pref 151 154 salt phase 149 150 154 solid 148 149 154 salt 149 vmol 151 154 vref 151 154 W0 148 152 W1 147 152 W2 147 152 x1 148 153 x2 148 153 xthresh 153 liq _ex n 147 152 liquid liquid equilibrium 82 87 110 112 118 lonic Liquids 124 maxiter 112 threshold 112 LE 110 112 optimization 112 LLE fine grid 112 LLE 118 LLE 118 LLE fine grid 118 LLE binodal 118 LLE spinodal 118 LLE fine grid 118 LLE 118 LLE optimization 118 LLE fine grid 118 LLE tangent plane criterion 120 LE 124 LLE lonic Liquids 124 LE NEW conf dx 112 maxiter dx 112 110 112 118 118 118 LE NEW 124 logD 10 logp 55 62 102 cli 102 c12 102 vq 102 xl1 102 x12 102 logPVAP 75 long 20 lxmx 25 147 map column 38 206 mass fraction 59 mcse 26 35 176 mdir 17 32 melting temperature 54 83 84 122 mixture 134 salt 99 129 metafile 26 35 173 misfit correction 164 mole fraction 59 molecular structure file Brookhaven pdb 29 39 MDL SIS mol 29 39 MDLIISIS sdf 29 39 MsSl car 29 39 Sybyl mol2 29 39 XMol xyz 29 39 209 211 MOPAC 12 31 85 160 164 230 231 multinary 53 63 108 109 112 118 120 135 136 137 confweight 109 HE SPLIT 109 pr pp 109 musym 25 42 45 223 n2 55 namwrl 38 206 nbinary
102. 2 3 1a can be considered a mean ionic solubility a definition that is similar to the mean ionic activity coefficient of Debye Huckel theory but has a different reference state whereas the mean ionic activity coefficient uses the infinite dilution of the salt in the solvent as reference state for the ions the solubility option uses the pure salt as reference state which is the stoichiometric mix of the anions and cations The salt solubility as computed from eq 2 3 1a assumes that the free energy of fusion value which describes the transfer of the salt from the subcooled liquid state to the crystalline solid state is defined as bulk free energy of fusion of the salt AG which implies that the salt is one unified compound and fusi not made of individual ions This is the most common definition of a salts free energy of fusion Most experimental AG data for salts is defined this way By default COSMOtherm uses this salt free energy of fusion AG in combination with equation 2 3 1 a to compute salt solubilities However in some cases the free energy of fusion is defined in an alternative way as a mean ionic free energy of fusion AG Using this definition of the solid phase equation 2 3 1a has to be reformulated as soL _ 0 i AC log x52 u2 z Hac y V ot max 0 AG ji RT In 10 2 3 1 b Thus the mean salt free energy of fusion and the bulk salt free energy of fusion are related simply as AG COS
103. 2 energy Compound Input 2 f toluene cosmo f toluene energy Compound Input 3 tc 0 multinary xstart 0 1 0 xend 0 5 0 0 5 xstep 5 MULTINARY Computation toluene propanone methylene 46 Note that the automatic computation of thermodynamic properties as done in binary ternary and multinary computations requires the additional calculation of the chemical potentials of the pure substance of all of the compounds involved These additional calculations automatically are done by COSMOtherm They will not be printed into the tabulated results file only into the long COSMOtherm output file 135 The additional input required for the mult inary option in the same line of the input file is xstart x X2 or cstart c co or qstart q q2 xend x X2 or cend c co or gend qi q2 xstep npoints or CStep npoints or qstep Nyoints Required for multinary computations Custom concentration grid start vector mole fraction xstart mass fraction cstart or surface fraction qstart concentrations of the compounds of a multinary mixture as real numbers x ci or q The arguments are expected to be real numbers between zero and one in the same sequence of compounds as given in the second input area If the values do not add up to one COSMOtherm will normalize them If less mole fractions concentrations than compounds are given the missing ones will be assumed zero If a negative number is given the
104. 2 jcc 20309 Prediction of Halocarbon Thermodynamics with COSMO RS Frank Eckert and Andreas Klamt Fluid Phase Equilibria 210 117 141 2003 DOI 10 1016 S0378 3812 03 00166 3 This article presents COSMOtherm applications to the prediction of thermodynamic properties of hydrofluoro hydrochloro and mixed halocarbon compounds 227 Prediction of Infinite Dilution Activity Coefficients Using COSMO RS R Putnam R Taylor A Klamt F Eckert and M Schiller Industrial and Engineering Chemistry Research 42 3635 3641 2003 DOI 10 1021 ie020974v This article presents COSMOtherm prediction of infinite dilution activity coefficients of organic compounds in variuos solvents and compares the results to UNIFAC predictions A detailed analysis of the COSMO RS and UNIFAC results is given Prediction of Infinite Dilution Activity Coefficients of Organic Compounds in lonic Liquids Using COSMO RS Michael Diedenhofen Frank Eckert and Andreas Klamt Journal of Chemical and Engineering Data 48 475 479 2003 DOI 10 1021 je025626e This article presents COSMOtherm applications to the prediction of organic compound properties in ionic liquid solvents Prediction of the mutual solubility of hydrocarbons and water with COSMO RS Andreas Klamt Fluid Phase Equilibria 206 223 235 2003 DOI 10 1016 S0378 3812 02 00322 9 This article presents COSMOtherm applications to the prediction and analysis of hydrocarbon
105. 21263 72041 kcal mol Total mean interaction energy in the mix H_int 4 74018 kcal mol Misfit interaction energy in the mix H MF 2 47774 kcal mol H Bond interaction energy in the mix H_HB 0 00000 kcal mol VdW interaction energy in the mix H_vdW 7 21792 kcal mol Ring correction 0 00000 kcal mol The first line gives the chemical potential of the compound in the mixture i e the converged value of u of Eq 1 6 Below the common logarithm of the fugacity partial vapor pressure x of the compound is given Next is the total free energy of the compound G i e E COSMO dE of the pure compound plus the chemical potential in the mix u The closing lines contain the mean interaction enthalpy of the compound with its surrounding H_int i e the interaction enthalpy of the compound which can be used to derive heats of mixing and heats of vaporization Finally this interaction enthalpy is separated into different contributions arising from electrostatic misfit H_MF hydrogen bonding H_HB van der Waals interactions H_vdw and a lt contribution resulting from rings in molecules Ring correction compare section 1 1 Please note that if conformers are used H_ int is not the sum of the misfit hydrogen bond and van der Waals enthalpy contributions because it contains an additional energy contribution resulting from conformational excitation H_ conf which is not written to the output file If the automatic calculation o
106. 2767 b XYZ geometry file format The gas phase energy file is expected to contain the gas phase energy as well as the compounds gas phase geometry in Cartesian xyz xmol format which consists of the number of atoms n in the first line a comment line as second line followed by n atom coordinate lines which hold the atom elements followed by their Cartesian x y and z coordinates in Angstrom The second line which is a info comment line in the xmol xyz format is used to pass over the gas phase energy information to COSMOtherm It is organized the following way the info line can contain several information fields separated by colons There is one required field holding the gas phase energy of the compound which is identified by the keyword ENERGY Several other information fields and optional keywords may follow E g ethanol0 energy from the COSMOtherm release database holds 9 ERGY 155 10644832767 METHOD b p BASIS def TZVP 1G 0 015981329 1 282788176 0 256363746 H 0 848236555 1 354251576 0 936194247 C 0 032393182 0 002051837 0 563717745 H 0 932167610 1 323654004 0 862141107 H 0 007353355 2 167141078 0 399090004 H 0 827867695 0 054160155 1 246142506 H 0 946500407 0 021482131 1 187552880 O 0 058541905 1 187809328 0 241635127 H 0 691607816 1 176916222 0 861486484 Therein the ENERGY 155 1064483276 is the required gas phase energy in Hartree The following two fields METHOD an
107. 4 Solubility of Salts Complexes and Cocrystals The prediction of salt solubility involves a few complications First in COSMOtherm a salt Av Cv is treated by means of its anion A and cation C with stoichiometries v and va respectively To obtain a salts solubility the chemical potentials have to be determined for the individual anion A and cation C and and the heat of fusion of the salt AG has to be known The salt solubility x is computed from the mean chemical potentials and the heat of fusion of the salt sor log olie uE u8 max 0 AG3 v RT In 10 2 3 1a where vio Va Vc is the sum of the ion stoichiometries The chemical potential of the pure salt sz is the stoichiometric sum of the chemical potentials of anion A and cation C This means the chemical potential of the pure salt is the sum of the chemical potentials of anion 4 and cation ue determined in an stoichiometric mix of anion A and cation C x va Vio XO Ve Vio Mae Va Ma Ve u The chemical potential of the salt in solution uc is the stoichiometric sum of the chemical potentials of the anion A and cation C computed in infinite dilution in solvent s This means the chemical potentials of the soluted salt is the stoichiometric sum of the chemical potentials of anion uw and cation u determined in pure solvent s tac Va Ha ve uc The salt or if AG 0 ionic liquid solubility x 2 as calculated by equation
108. 5 10 11 20 21 22 23 24 29 26 30 31 32 33 35 36 37 38 39 40 41 45 46 50 5l 52 53 54 60 61 62 63 64 65 66 ERROR ERROR ERROR ERROR ERROR ERROR ERROR ERROR ERROR ERROR ERROR ERROR ERROR ERROR ERROR ERROR ERROR ERROR ERROR ERROR ERROR ERROR ERROR ERROR ERROR ERROR ERROR ERROR ERROR ERROR ERROR ERROR ERROR ERROR ERROR ERROR ERROR ERROR ERROR ERROR ERROR ERROR ERROR ERROR The pKa LFER parameters in the parameter file were determined for a specific solvent These parameter values are not valid for solvents or solvent mixtures other than the given one PKA calculation not possible At this temperature the vapor pressure can not be extrapolated from the WAGNER coefficients Please use a different method for the estimation of the pure compound vapor pressure Illegal input in contact interaction computation Illegal input in contact interaction computation The compound for contacts is required to have a finite concentration in the given mixture Concentration input XM CM missing or damaged in BINARY TERNARY MIX input BINARY TERNARY computation not possible MIX components are overlapping BINARY TERNARY computation not possible MIX and IL options can not be mixed Automatic computation of the thermodynamics of a BINARY TERNARY MULTINARY system not possible Number of processed compounds is to
109. 5 138 xsl 65 138 xs2 65 138 SLE 110 113 121 125 131 lonic Liquids 125 liquid 122 maxiter SLE 121 122 mixture 131 SLE iter thresh 121 122 SLLE 82 121 Smc 36 Smom 27 sms 64 138 solgas 61 140 cs 140 141 max iter 141 nsolvent 141 pthresh 140 141 237 solvent 141 xs 140 141 solid liquid equilibrium 82 87 110 113 121 lonic Liquids 125 solvent mixture 131 solid liquid liquid equilibrium 82 121 solub 54 61 81 87 88 89 90 91 95 98 amino corr 89 cs 81 88 dcpfus_estimate 84 85 89 96 99 dgfmean 95 96 99 100 iterative 81 85 87 liquid 87 max iterations 87 ndgf 83 nsalt 95 98 nsolute 84 91 100 pr_ILtern 98 pr_ILTERN 97 100 pr_ni 81 87 pr_rs 82 87 ref sol c 90 101 ref sol _g 90 101 ref sol 1 90 101 ref sol m 90 101 ref sol_s 84 90 101 ref sol x 90 101 salt 95 98 salt_n 98 slesol 82 86 87 solQSPR 87 solQSPR_SI 87 solute 84 91 100 solvdens 86 88 90 97 101 use HH 93 94 wfract 86 88 90 97 98 101 wsoll 86 88 90 97 98 101 wsol2 86 88 90 97 98 101 xs 81 88 solubility Abraham descriptors 195 196 automatic calculation 61 81 dissociation correction 92 Henderson Hasselbalch 92 93 gas 61 140 lonic Liquids 95 iterative refinement 81 85 87 liquid 87 LLE 82 87 mass based 86 88 90 97 98 101 mass fraction 86 88 90 97 101 molar 86 88 90 97 101 polymers 178 179 reference solubility 90 101 relative 82 87 salts 81 95 98 mole
110. 5 2 815162 0 040676 0 305120 0 786134 0 169290 0 044576 0 121382 0 566460 0 312158 0 167867 2 430614 2 035423 0 043339 0 484007 0 000000 0 000000 0 000000 0 000000 0 000000 0 000000 0 000000 0 000000 0 000000 0 000000 0 000000 0 000000 If the phase space considered in an LLE search has three or more dimension i e if the LLE option is used within a ternary computation or with a multinary computation where n gt 2 then it is possible that several different phase separations take place in the phase space spanned by the compound concentrations Each of the pairs of LLE tie points found by solving equation 2 3 17 correspond to a minimum in the total Gibbs free energy of the system Dependent on the starting concentration it is possible that the solution of eq 2 3 17 leads to a local minimum for systems with more than two components and more than two phases Now while all solutions of eq 2 3 17 correspond to actual LLE phase separations these may not be the most stable phases that are possible in the system The overall most stable phase separation corresponds to the global minimum of the system Gibbs free energy It is possible to assess the LLE points found by eq 2 3 17 using the method of tangent plane analysis which claims that a phase specified at a given temperature pressure and starting composition x is unstable if the Gibbs free energy of mixing falls below a hyperplane tangent to the phase space hypersurface at the start compo
111. 50 Pure compound vapor pressure input options continued Pant A B C 5 Pant Pa A B C 5 Pant kPa A B C Ss PKant A B C 5 PKant_Pa A B C 5 PKant_kPa A B C lt Q lt 0O lt 0O lt 0 lt O lt O0 lt PTCant A B C r Pantl Pa A BCDE r Pantl kPa A B C D PKantl A BCDEF r PKantl Pa A BC D r V o V o V or V o V o V PKantl kPa A B C D Pantl A B C DE F G F G E F G G E F G E F G Optional Give the coefficients of the Antoine equation In pf A B T C to be used in the calculation of the vapor pressure p of compound i Antoine coefficients for many substances are tabulated in the book of Reid et al Note that the coefficients A B and C are expected for temperatures T in C or in K for VPKant VPKant_Pa and VPKant_kPa keywords respectively and vapor pressures P in mbar or in Pa for the VPant_Pa and VPKant_Pa keywords or in kPa for the vPant_kPa and VPKant_kPa keywords For the VPTCant keyword the coefficients are expected to compute logi0 P with vapor pressures P in Torr mmHg and temperatures T in C Optional Give the coefficients of the extended Antoine equation In p A B T C DT E In T FT to be used in the calculation of the vapor pressure p of compound ji This extended Antoine equation is equivalent to the ANT1 equation of the IK CAPE standard Several other vapor pressure
112. 74 76 pvap pressure 60 74 76 thresh pp 74 76 thresh pvap 74 76 Pwrl 18 37 gend 110 111 136 QSPR 18 28 86 193 194 Abraham coefficients 196 197 Abraham descriptors 195 196 density 68 142 181 viscosity 68 145 QSPR_DENS 142 144 QSPR_DENS SI 144 QSPR SI 28 194 QSPR_VISC 145 QSPR_VISC_SI 145 qstart 110 111 136 qstep 110 111 136 reaction 47 62 183 186 concentration dependence 36 72 212 cr 62 183 188 energy 24 47 182 enthalpy 24 47 182 equilibrium constant 62 182 activity 186 188 Ka 186 188 Kgamma 186 188 Kx 186 reference 186 188 K activity 186 188 nprod 184 187 nreact 184 187 pref 184 188 pressure 183 184 188 prod 184 187 prod eqm 184 190 prod_Gsol 185 192 prod _Hvap 185 192 prod_n 184 187 prod zpe 184 190 react 184 187 react _eqm 184 189 react Gsol 185 191 react Hvap 185 191 react_n 184 187 react zpe 184 189 stoichiometry 182 184 xr 62 183 188 RI DFT 158 160 162 163 164 Riedel equation 51 rmic 19 60 225 rn 31 155 156 157 RN 31 155 rw 34 174 180 Satm 27 search path prop files 17 194 COSMO files 17 32 COSMO metafiles 17 32 CTDATA files 17 license files 17 QSPR coefficient files 17 194 shbset 221 224 similarity 64 138 compound o potential similarity 65 138 139 solute specific 65 139 molecule o profile match similarity 64 138 molecule o profile similarity 64 138 SMS 64 138 simpot 65 138 139 csl 65 138 cs2 6
113. 8_ parameterization files as well as for pre 2008 DMOL3 parameterization files i e parameter file DMOL3_C21_0107 ctd and previous ones These files were parameterized on old and inferior COSMO cavity versions as implemented in old program versions of Gaussian Gaussian98 and DMOL3 DMOL3 in Accelrys Materials Studio 4 1 and previous in addition a different DFT functional VWN BP instead of PBE was used there respectively and they are kept for downward compatibility reasons only The G98_ and old DMOL3 parameterization files are not updated or enhanced any more and thus do not support the full current COSMOtherm functionality 3 3 Recommended Parameterizations The choice of the appropriate quantum chemistry method and basis set level and thus also the choice of the appropriate parameter set of COSMOtherm generally depends upon the required quality and the later application of the predictions For a given problem setting the optimal results and fastest computation times are achieved if an appropriate combination of quantum chemistry method and COSMOtherm parameterization is used as recommended below Please note that parameterizations for quantum chemical methods other than the recommended ones e g B3 LYP or DMOL3 VWN BP parameterizations will still be shipped with this and future COSMOtherm releases l e it is still possible to use the COSMO files computed at these levels of quantum chemical theory within COSMOtherm However these
114. 997583 0 02633515 1 04333887 0 963548 0 036452 0 90000 0 10000 0 14613711 0 06803426 89 815534 093929328 4 79972053 0 01111374 1 15316084 0 981789 0 018211 0 95000 0 05000 0 07615738 0 03562506 95 354357 0 90525056 5 23695929 0 00247458 1 26540332 0 993148 0 006852 0 98000 0 02000 0 03117929 0 01462873 98 349825 0 88717868 5 77149875 0 00027694 1 33372919 0 997682 0 002318 0 99000 0 01000 0 01570698 0 00737689 99 282550 0 88152858 6 16024457 0 00002189 1 35664812 0 998903 0 001097 0 99900 0 00100 0 00158117 0 00074329 100 091720 0 87659917 7 42152638 0 00000821 1 37733214 0 999896 0 000104 0 99999 0 00001 0 00001583 0 00000744 100 178931 0 87606584 9 92286860 0 00000009 1 37961058 0 999999 0 000001 1 00000 0 00000 0 00000002 0 00000001 100 179810 0 87606047 13 67303899 0 00000000 1 37963358 1 000000 0 000000 Note that the chemical potential p as given by COSMOtherm is the pseudo chemical potential as defined by Ben Naim In order to obtain the partial free energy i e the experimentally available chemical potential an entropic term RTIn x has to be added to the COSMOtherm qp see section 1 1 This entropic correction to p is done in the table file whereas the COSMOtherm output file always contains the uncorrected pi 167 4 1 Error Codes If COSMOtherm discovers an unrecoverable error in the input file or during the course of the COSMOtherm run it will write a text mes
115. AM BP SVP AM BP SVP AM BP SVP AM BP SVP AM BP SVP AM BP SVP AM BP SVP AM BP SVP AM BP SVP AM BP SVP AM BP SVP AM BP SVP AM BP SVP AM BP SVP AM BP SVP AM BP SVP AM BP SVP AM BP SVP AM BP SVP AM BP SVP AM BP SVP AM BP SVP AM BP SVP AM BP SVP AM BP SVP AM BP SVP AM Abra Abra Abra Abra Abra Abra Abra Abra Abra Abra Abra Abra Abra Abra Abra Abra Abra Abra Abra Abra Abra Abra Abra Abra Abra Abra Abra nam nam nam nam nam nam nam nam nam nam nam nam nam nam nam nam nam nam nam nam nam nam nam nam nam for BP SVP AM1 COSMO level LogP Octanol wet Water prop LogP Octanol dry Water prop LogP OleylAlcohol Water prop LogP Acetone Water prop LogP PGDP Water prop LogP CH2C12 Water prop LogP CHC13 Water prop LogP CC14 Water prop LogP CS2 Water prop LogP Benzene Water prop LogP Toluene Water prop LogP Cyclohexane Water prop LogP Hexane Water prop LogP Heptane Water prop LogP Isooctane Water prop LogP Hexadecane Water prop LogP OliveOil Water prop LogP Gas Water prop LogP Cell Water prop LogP Skin Water prop LogP Blood Brain prop LogP PlantCuticle Water prop LogP Tadpole Narcosis prop ntestinal Absorption prop ham Hsolv Water prop nam LogS Water prop LogP Diethylether
116. Appendix A Publications A 1 COSMO RS COSMOtherm related publications Review Articles COSMO RS From Quantum Chemistry to Fluid Phase Thermodynamics and Drug Design Andreas Klamt Elsevier Science Ltd Amsterdam The Netherlands 2005 ISBN 0 444 51994 7 This book provides an extensive and detailed overview over the COSMO RS COSMOtherm methodology and its various fields of application Fast Solvent Screening via Quantum Chemistry The COSMO RS approach Frank Eckert and and Andreas Klamt AIChE Journal 48 369 385 2002 This article aimed especially at the chemical engineering audience presents an introduction to the COSMO RS COSMOtherm methodology and compares it to other methods used in that field i e group contribution methods such as UNIFAC In addition a number of typical applications of industrial relevance is presented This review article is possibly the best starting point for interested readers from the chemical engineering industrial chemistry community COSMO RS A novel way from Quantum Chemistry to Free Energy Solubility and General QSAR Descriptors for Partitioning Andreas Klamt and Frank Eckert book chapter in Rational Approaches to Drug Design H D H ltje and W Sippl Editors Prous Science S A Barcelona 2001 pp 195 205 This article aimed especially at the life science and molecular modeling audience presents an introduction to the COSMO RS COSMOtherm methodology and comp
117. Binary or Ternary Phase Diagrams The binary and ternary options allows for the automatic computation of phase diagrams of two and three component mixtures respectively Phase diagrams of higher dimensionsonality can be computed with the multinary phase diagram option which is described in section 2 3 8 below If one of the binary ternary Or multinary options is applied no mole x or mass c fraction input is required Instead the program automatically computes a list of concentrations covering the whole range of possible mole fractions of the binary or ternary mixture Then for a given temperature COSMOtherm automatically calculates the excess properties the phase diagram as well as other useful information like azeotropic points The total pressures used in the computation of a phase diagram are obtained from Prot SPAN 2 3 7a The p are the pure compound vapor pressures for compounds i i 1 2 for binary and i 1 2 3 for ternary computations respectively x are the mole fractions of the compounds in the liquid and y are the activity coefficients of the compounds as predicted by COSMOtherm Ideal behaviour of the gas phase is assumed Vapor mole fractions y are obtained from the ratio of partial and total vapor pressures Thus the computation of phase diagrams requires the knowledge of the vapor pressures of the pure Y P XY I Por 2 3 7b compounds p at a given temperature For each compound there are several
118. By default for a molecule molecule cosmo a VRML file molecule mol wrl will be created If the command Cwrl name wrl is given with an argument a VRML file name wr1 will be created Optional Create a VRML file of the molecular COSMO surface charge If given in this section of the COSMOtherm input file the Swr1l command is active only for the actual compound By default for a molecule molecule cosmo a VRML file molecule _sig wrl will be created If the command Swrl name wrl is given with an argument a VRML file name wrl will be created Optional Create a VRML file of the molecular QSPR property surface If given in this section of the COSMOtherm input file the Pwr1 command is active only for the actual compound By default for a molecule molecule cosmo a VRML file molecule prop wrl will be created If the command Pwrl name wrl is given with an argument a VRML file name wr1 will be created This option is valid only if the OSPR or QSPR_SI option is given in the global command section see section 5 5 The properties calculated by the QSPR formula of the COSMOtherm o moments will be color coded and mapped to the COSMO surface of the molecule Optional Set the graphical resolution of the VRML files of molecular COSMO surface charges and molecular QSPR property surfaces If given in this section of the COSMOtherm input file the wrlres command is active only for the actual compound The argument res is expected as a real number gt 0 2
119. C mpo nd and GoNFormMerINPUts seieseissseigy desccesasheciend a a a a iE 31 2 2 2 G s Phase En rgy ADUT c2iciiinssddiciecdeads sadadovavedesenwtdeddishadeabeestinaidseaneasdiaasadasdaveacbeaiandaaceteaacedaasdacaie 43 2 2 3 Vapor Pressure Property Mp UT a a a araa aaraa aaa Ea aar aaea a a a e Eak 49 2 2 4 Conf rmer INPUT zese eea aV E E e aE T E a aE a 57 2 3 Temperature Mixture INDUt cccccessecceessseeeeeesensenesconeesesceeeeessaseeensenseseeseeesasseceesaseesesseneeeeseneeeeness 59 2 3 1 Automatic Vapor Pressure Calculation cccccscccceseseeeeeeeeeesseeeeeeecneeeescaeeeseseeeeescnseeeeseneeeessaness 73 2 3 2 Automatic Activity Coefficient Calculation ccccccsccssscsssecssseeesseessneeesseesseeesseesseesseessneeesaeess 77 2 3 3 Automatic Henry Law Coefficient Calculation ccccccccceceseceeeeceeeeeeeceeeceeeeaeeeaeeeaeeeaeeeaeeneeseneeaes 79 2 3 4 Automatic Solubility Calculation eeccececceeeeeeeeeeeeeeeeceaeeeeaeeseaeeeeaeeseaeeeeaeeseaeeeeaeeseaeeseaeeseaeeeeaeess 81 2 3 5 Automatic Partition Coefficient Calculation cccceeccesecececeeececeeeeeaeeeaeeeaesenecenesaeeeaeeeaeenaeees 102 2 3 6 Automatic pK Acidity Basicity Calculation cceeceeeeeeeseeeeeeeeeeeeeseaeeeseeeseaeeeseeeseaeeeneeessaeeeaes 105 2 3 7 Automatic Calculation of Binary or Ternary Phase Diagrams cssccesceteeeeeeeeeeereeteeeeees 108 2 3 8 Automatic Computation of n Dimensional Multinary Ph
120. COSMOtherm i e ensemble averaging over molecular surface segments see section 1 1 such a representation of symmetry equivalent parts of molecules is no approximation in the framework of the COSMOtherm theory However if the saturation group is not chosen properly the replacement of symmetry equivalent groups might introduce errors in the quantum chemical calculation thus also introducing errors into COSMOtherm In some cases it even can be useful to virtually elongate an alkane chain in a molecule by weighting one middle CH group by an appropriate replication factor in order to mimic a molecule with a longer chain in COSMOtherm For example it is not necessary to calculate an octadecane explicitly One could as well take a decane and weight one of the middle CH groups by a factor 9 in order to get the correct number of CH groups Such an approximation normally will not have any significant effect on the outcomes of the COSMOtherm calculation For example 1 nonanol can be constructed from a 1 octanol COSMO file by double weighting of a central CH group f l pentanol cosmo w 112111111122111111 S Se a a an F 9 Obviously if you can afford the calculation for the entire molecule it is best to use that and work without explicit atomic weights in order to avoid any artefacts which may arise if the saturation is not realistic By default all weight strings are assumed to be one This means if in the weight string less weight numbers
121. COSMOtherm automatically does this conversion if COSMO files produced by Gaussian are used Thus the same COSMOtherm parameter set can be used for COSMO files of the two program packages If the vapor pressure of the compound also has to be predicted by COSMOtherm a full optimization of the molecular geometry in the gas phase i e without the COSMO option is also strongly recommended in order to obtain the gas phase energy of the molecule which then can be utilized by COSMOtherm to obtain a reasonable prediction of the compounds vapor pressure Based on such quantum chemical COSMO and gas phase calculations the best quality of the COSMOtherm prediction can be achieved with the BP_TZVP_C30_1501 ctd parameterization A 162 similar quality can be reached with the DMOL3 program package using full COSMO and gas phase geometry optimization with the PBE DFT functional and the numerical DNP basis set on the quantum chemistry level and the DMOL3_PBE_C30_1501 ctd parameterization in COSMOtherm Recommended for high quality predictions of thermophysical data for chemical engineering purposes Program Package DFT functional Basis Set COSMOtherm Parameterization Turbomole BP RI DFT TZVP BP_TZVP_C30_1501 ctd DMOL3 PBE DNP DMOL3_PBE_C30_1501 ctd In 2012 a new quantum chemical calulation level BP TZVPD FINE was introduced to COSMOtherm and TURBOMOLE This method is based on a Turbomole BP RI DFT COSMO single point calculation with TZVPD ba
122. E properties are calculated from the solid liquid phase equilibrium condition eq 2 3 19 Give Gees uP AG p T ppotion RT In x 2 3 19 Please note that the SLE search using eq 2 3 19 assumes that there is a simple eutectic point in the binary mixture Complicated systems with several phase transitions in the solid state can not be predicted by the SLE option The SLE search algorithm will solve the solid liquid equilibrium condition of eq 2 3 19 on a grid of 325 mixture concentrations points of the binary system it is the same grid that is used for the binary lle new option described in the previous section If the equilibrium condition 2 3 19 was met on the concentration grid then COSMOtherm will perform an additional iterative refinement of the SLE points By default the iterative refinement will compute the SLE points up to an accuracy threshold of x 10 mole fractions within a maximum number of 150 iterations These defaults can be changed by options SLE iter thresh value for the accuracy threshold value and maxiter SLE value for the maximum number of iterations Please note that in addition to the solution of eq 2 3 19 the binary grid is checked for the presence of a solid liquid liquid thermodynamic equilibrium SLLE which means that the virtual system of supercooled liquids of the given compounds shows a miscibility gap at the given conditions If such a virtual LLE miscibility gap is present in a SLLE
123. FER parameters is toggled with the WATER BASE suboption of the pKa igoivent ineutrar ron Command Alternatively the pKaLFER c c command may be used to give the aqueous base pK LFER parameters in the COSMOtherm input Note For secondary and tertiary aliphatic amines COSMOtherm systematically underestimates the base pK This underestimation is the result of a well known problem of continuum solvation models like COSMO with aliphatic amines and amino cations in polar solvents Because the error is systematic it can be accounted for by a simple correction term The pK prediction of tertiary aliphatic amines should be corrected pK pK P 2 0 The pK prediction of secondary aliphatic amines should be corrected pK pK P 1 0 The given corrections are valid for COSMOtherm version C2 1 revision 01 07 to 01 11 If you use an older version of COSMOtherm amine pK correction values of 3 8 for tertiary aliphatic amines and 1 7 for secondary aliphatic amines should be applied For COSMOtherm version C3 0 revision 12 01 and later no correction is necessary Please keep in mind that the systematic amine error only occurs for secondary and tertiary aliphatic amines that are not constrained geometrically For aromatic amines or aliphatic amines that are sterically hindered such as tertiary bridge nitrogens in bicyclic rings the error does not occur and thus the COSMOtherm pK prediction is applicable without correction COSMOther
124. For example the CTDATA file for Turbomole COSMO files with BP functional and Ahlrichs SVP basis set shipped with COSMOtherm Version C3 0 Release 15 01 is denoted BP SVP C30 1501 ctd The parameterizations based on single point DFT calculations upon semiempirically optimized geometries are denoted by the additional shorthand index am e g BP SVP _AM1 C30 1501 ctd Note that it is still possible to use the older pre Version C1 1 COSMOtherm parameterization file format files which are named crsdata_ However the old parameterizations will not be updated or enhanced in future releases Parameterizations shipped with COSMOtherm Version C3 0 Release 15 01 BP _TZVP_C30_1501 ctd Use with quantum chemical COSMO calculations Turbomole GAMESS PQS Molpro Columbus ORCA or Q Chem RI DFT with BP functional and def TZVP basis set or Gaussian03 09 DGA1 DFT with BP86 functional and Ahlrichs TZVP basis set based on fully optimized geometries BP_SVP_AM1_C30_1501 ctd Use with quantum chemical single point COSMO calculations Turbomole RI DFT with BP functional and def SVP basis set or Gaussian03 09 DGA1 DFT with BP86 functional and Ahlrichs SVP basis set based on geometries optimized by MOPAC AM1 COSMO BP_TZVPD_FINE_C30_1501 ctd Quantum chemical level BP TZVPD FINE parameter set with a novel Hydrogen Bond interaction term HB2012 term and a novel van der Waals dispersion te
125. HOME or in a directory denoted by the cdir command For the definition of the QSPR coefficients and the format of the QSPR coefficient file see section 5 5 If the coefficients are read from the input file via the QSPR c co Cig prop command the coefficients c are expected as real numbers separated by blank spaces If less than 18 coefficients are given the missing ones are assumed to be zero The property name prop is expected to be a string of up to 9 characters For a further description of the c moment QSPR property computation see section 5 5 66 B Property calculation options continued QSPR property calculation options noaptab pr_mom pr_allmom smomc file momc Optional for PROPQSPR computations print option do not print the computed Abraham parameter coefficients to the table file Instead only the final property computed from the Abraham coefficients will be listed as results column in the PROPQSPR table Optional for PROPQSPR computations print option print the most important QSPR descriptors to the table file Optional for PROPQSPR computations print option print all possible QSPR descriptors to the table file Optional for PROPQSPR computations print option with given temperature and mixture conditions print averaged compound QSPR descriptors and the averaged compound QSPR properties to an additional c moments file with the extension momc If no argument is given the momc file
126. IX commands are located The net Gibbs free energy of fusion of the mixture can be given by options DGfus_mix or DGfus_mix SI The net enthalpy of fusion of the mixture as used in eq 2 3 18 can be given by options DHfus_ mix or DHfus_ mix SI The net entropy of fusion of the mixture as used in eq 2 3 19 can be given by options DSfus_mix or DSfus_mix_ SI The net heat capacity of fusion of the mixture as used in equation 2 3 18 or 2 3 19 can be given by options Depfus_mix or Dcpfus_mix_ SI The net melting temperature of the mixture as used in equation 2 3 18 or 2 3 19 can be given by options Tmelt_mix Tmelt_mix_C or Tmelt_mix_K see below for details The ACp estimate described in the solubility section 2 3 4 keyword Dcpfus_ estimate may also be used in binary mixture SLE computations However following the considerations taken in section 2 3 4 the ACp estimate should be used with great caution if ions are involved in the mixture All of these input options expect net mixture data values that are defined for the whole of the mixture as defined in composition by the xm or cm commands Thus no individual heat of fusion data of the mixture components can be used for SLE MIX computations An example for a SLE computation with a composite phase is given below The pseudo binary system consists of one single compound phase of aspirin 1 and a composite MIX phase 2 which is an equimolar mixture of chloroform and acetone l e the
127. If two MIX phases are requested COSMOtherm expects two entries of the mixture phase concentration input xm or cm which will be assigned to the MIX phases simply by the sequence at which they are given in the mixture input line The treatment of ternary phases diagrams is equivalent if one two or three MIX identifiers are given within the ternary i j j MIX options COSMOtherm expects to find the mixture concentrations of the composite MIX phases to be in the same line as the ternary MIX input in the SMIX or nternary name nam order in which they are given in the ternary input option Please note that the mixtures of the composite phases are not allowed to overlap neither with another pure compound phase nor with another composite mixture phase The vapor pressure of a mixture phase is computed from the partial vapor pressure contributions of each of the components of the IL phase in terms of their activity in the overall mixture The mixture phase by default is assumed to show ideal mixing behavior This means that the overall activity of a pure MIX phase is one and the vapor pressure of the mixture phase is not computed from the activities of the mixture components but from their relative mixture ratio in the mixture phase only Alternatively it is possible to define the MIX phase in a way that it shows real mixing behavior via input option MIXphase REAL If the MIXphase REAL option is activated the vapor pres
128. Indices IEI numbers The reacting compounds have to be treated as pseudo conformers in the compound input section COSMOtherm input file For an equilibrium reaction A B A B the first conformer of compound A is the free compound A The second conformer for compound A is a COSMO metafile of the reaction product A B wherein all atoms of the reaction partner B are set to zero by atomic weights see section 5 3 for COSMO meta files and the handling of atomic weights Thus the second conformer describes the behaviour of compound A after the reaction not the behaviour of the reaction product A B Compound B is constructed similarly i e one conformer is pure compound B and the second conformer is a meta file of A B with all atomic weights of A set to zero The conformer built from the COSMO meta file has to be identified by a unique interaction energy index IEI number This is done with the IEI i command in the same line where the compound is given It is also possible to assign more than 212 one IEI number to a compound using the command IEI i i i the latter is required only if the compound is able to undergo several reactions with different products Example 10 shows the simple case of the dimerization reaction of acetic acid in a binary mixture with octane i e the equilibrium A A e A A One conformer of the reactive species is monomeric acetic acid and the second conformer is the acetic acid dimer where one half of the dimer is set to
129. LLE NEW option is only possible for isothermal binary computations If given for an isobaric system or for a system with more that two phases COSMOtherm will use the regular LLE search procedure instead The thermodynamic properties of the additional mixtures are written to the COSMOtherm output file and in tabulated form to the COSMOtherm table file Subsequently COSMOtherm will search the computed mixtures for possible points of liquid phase separation and if found writes them to the COSMOtherm output file If the commands LLE or LLE NEW are given in the same line as the binary command COSMOtherm will compute the thermodynamic properties of the binary mixture on a grid the coarse 29 point grid is used for option LLE and the fine 325 point grid is used for the LLE NEW option and afterwards refine the value of the binodal LLE miscibility gap found on the grid with an iterative optimization procedure The iteratively optimized binodal LLE value will be written to output and table files and replaces the value found on the grid If the LLE option is used with the ternary or multinary option additional tabulated output with the LLE tie points and related information will be printed to the COSMOtherm table file In the case of the ternary option a different default grid will be used if the LLE search is toggled Instead of the irregular grid of 231 concentrations in the ternary phase space that is used
130. MOtherm Currently definition 2 3 1a is used by default while use of 2 3 1b can be toggled by keyword dgfmean keyword see below AG Vto Both definitions of AG as used in equations 2 3 1a and 2 3 1b are available in fus A special suboption to the solub or nsolub option allows for the automatic computation of the solubility of a salt or ionic liquid compound in a given solvent or mixture The composition of the salt has to be defined in the input This can be done with the salt i j command where i j are the numbers of the ion compounds numbers as given in the sequence of compounds in the compound input section or the nsalt name name command where name name are the names of the ion compounds as given in the compound input section In addition the salt stoichiometry has to be defined for the individual anion and cation compounds The input of the salt stoichiometry factors v v is possible via the salt_n v vj command where v vj are the stoichiometry numbers of the salt compound defined by the ions as given by the salt i j or nsalt name name command For example the salt sodiumsulfate Na SO would be defined by the combination of the option nsalt na so4 defining the salt composition from sodium cation na cosmo and sulfate dianion so4 cosmo and the option salt _n 2 1 defining the stoichiometry of the salt i e two sodium ions one sulfate ion The definition of the salt is no
131. MOtherm It needs to be activated via the COSMOtherm license file license ctd Within a COSMOtherm input file the COSMOmic plugin has to be called in two steps First a micelle definition file needs to be read in the global input section via command rmic name mic see section 2 1 of this manual The micelle definition file file extension mic holds all relevant information about the micelle i e the compound information cosmo filenames and file paths of the components that the micelle consists of and tabulated grid information about the layers that form the micelle Note that only one micelle definition file can be read in a COSMOtherm input file i e only one micelle definition can be used per input file Micelle definition file can be created by the COSMOthermxX graphical user interface A recipe for the micelle import procedure in COSMOthermX is given in the COSMOmic documentation Because all information about the micelle including cosmo file and search path information of the components the micelle is built of is in the micelle definition file all additional compounds that are read in the compound input section of the COSMOtherm input file are considered as solutes in the framework of the COSMOmic calculation The second piece of input required for a COSMOmic calculation is the actual call of the micelle as a pseudo solvent for the given solutes This call is done with the x pure MICELLE keyword in the temperature mixtur
132. OSMOtherm activity coefficients in a least squares procedure and subsequently are written to the COSMOtherm output file below the output of the binary option If the NRTL2 option is used only the binary interaction parameters t and t are fitted Factor a is held at a constant value By default a 0 3 is used for the NRTL2 option However it is also possible to give the value of a in the COSMOtherm input via option NRTL_ALPHA value Reasonable values of a are a 0 3 for common organic mixtures a 0 2 for mixtures that show a miscibility gap and a 0 46 for associating systems that show strong interactions between the two compounds Suboptions of the binary NRTL2 option are NRTL_ ALPHA value Optional for binary NRTL2 computations Give NRTL parameter a Argument value is expected as a real number If the WILSON command is given the COSMOtherm activity coefficients are adjusted in a least squares procedure to Wilson s equation Ai Ay 2 3 9 Xp X Ayy xX X A In y ln x A ox x The two adjustable parameters of Wilson s equation A and A are written to the COSMOtherm output file below the output of the binary option Note that for both models the expression for In y can are obtained from the equations for In y by interchanging the subscripts 1 and 2 If the UNIQUAC2 or the UNIQUAC4 command is given the COSMOtherm activity coefficients are adjusted in a least squares ln y In y In y 41 Renon H a
133. P COSMO wemn efile UQME Computation of a reaction equilibrium constant in solution f 5 methyl 4 nitrobenzofuroxane EQMH 732 7436522 EZPC 79 68 f 7 methyl 4 nitrobenzofuroxane EQMH 732 7493550 EZPC 79 64 f h2o f propanone f hexane tc 25 reaction 3 REACT 1 REACT N 1 PROD 2 PROD N 1 tc 25 reaction 4 REACT 1 REACT N 1 PROD 2 PROD N 1 tc 25 reaction 5 REACT 1 REACT N 1 PROD 2 PROD N 1 tc 25 reaction 1 REACT 1 REACT N 1 PROD 2 PROD N 1 In Example 7 the vome EQMH and EZPC keywords are used to read in external high level quantum chemistry gas phase energies and zero point vibrational energies to compute the reaction equilibrium constant Kreacr and reaction energy AGgeac for the isomerization reaction unimolecular Boulton Katritzky rearrangement of 5 methyl 4 nitrobenzofuroxane compound 1 reactant v 1 to 7 methyl 4 nitrobenzofuroxane compound 2 product v 1 in different solvents water acetone and hexane as well as in bulk reactant which is assumed to be liquid BS Eckert F Rauhut G Steele P J Katritzky A R J Am Chem Soc 121 1999 6700 185 The equilibrium constant K react that is computed by the reaction option according to equations 5 4 2 5 4 4 is the mole fraction based apparent equilibrium constant K The apparent equilibrium constant K varies with the chosen solvent pressure and mixture conditions The solvent independent activity equilibri
134. Thus a IL is pieced together from its anion s and cation s the composition of the IL has to be defined in the input This is possible with the IL i j command where i j are the numbers of the ion compounds numbers as given in the sequence of compounds in the compound input section or the nIL name name command where name name are the names of the ion compounds as given in the compound input section In addition the IL s stoichiometry has to be defined for the individual anion and cation compounds The input of the IL stoichiometry factors v v is possible via the IL_n v vj command where vj v are the stoichiometry numbers of the IL defined by the ions as given by the IL i j Or nIL name name command For example the IL bmim BF would be defined by the combination of the option nIL 1 butyl 3 methyl imidazolium0 bf4 defining the IL composition from bmim cation 1 butyl 3 methyl imidazolium0 cosmo and tetrafluoroborate anion b 4 cosmo and the option IL n 1 1 defining the stoichiometry of the salt i e simple binary IL with one bmim and one BF If these options are given as additional input to an automatic density computation density input line COSMOtherm will compute the density of the IL of the given composition and stoichiometry via eqs 2 3 25 and write the result to the COSMOtherm output and table file If the IL option is used COSMOtherm only will compute the density of the given
135. VWN P86 and Ahlrichs TZVP basis set Gaussian03 09 DGA1 DFT with BP86 B88 VWN P86 functional and Ahlrichs TZVP basis set gt Gaussian98 obsolescent feature DFT with B3 LYP functional and 6 31 G d p basis set DMOL3 obsolescent feature DFT with VWN BP functional and numerical DNP basis set All of these parameterizations are based on geometries quantum chemically optimized at the given method basis set level For large molecules where a full optimization of the geometry is too expensive at DFT COSMO level there are two additional parameterization available which are based on single point energy calculations at DFT COSMO level upon geometries optimized at semi empirical MOPAC AM1 COSMO level Turbomole RI DFT with BP B88 VWN P86 functional and def SVP basis set GAMESS PQS Molpro Columbus ORCA Q Chem B88 VWN P86 and Ahlrichs SVP basis set Gaussian03 09 DGA1 DFT with BP86 B88 VWN P86 functional and Ahlrichs SVP basis set Starting with Version C1 2 the COSMOtherm program includes a new generic expression for the combinatorial contribution to the chemical potential see section 1 1 The new parameterizations of COSMOtherm that use the new generic combinatorial contribution replace all older parameterizations based on the old generic combinatorial term or the Stavermann Guggenheim term In addition also the special parameterizations for ionic species are obsole
136. X input Could not find compound given in pure compound computation Illegal compound number given in pure compound computation wrong argument for X_PURE input X_PURE argument needs to be a compound number or MICELLE if COSMOmic is used Concentrations and pure compound input can not be mixed Concentrations and mole fractions can not be mixed Illegal concentration input Invalid COSMOtherm license COSMOtherm license expired COSMOtherm license file nodelock ctd is empty COSMOtherm license file nodelock ctd is damaged COSMOtherm license does not allow this type of calculation The COSMOtherm license does not include COSMObase The given COSMObase cosmo file can not be used COSMOtherm license does not include COSMOmic COSMOtherm license Illegal compound file in RESTRICTED operating mode Education Demo No LFER parameters found for pKa computation PKA option will be ignored The charge difference between molecules A and B used in pKa computation is not one PKA computation not possible 169 COSMO therm Error Codes continued error 102 error error error error error error error error error error error error error error error error error error error error error error error error error error errors error error error error error error error error 0
137. a COSMO metafile via the expmw command the charge neutrality warning may occur quite regularly if no special care is taken in the preparation of the molecular fragment However this large charge mismatch and the resulting neutrality issues and according warning message typically are relevant only if the resulting polymer is used as a solute in the COSMOtherm calculation If the scaled up polymer is used as a solvent i e if the predicted properties of the polymer itself are not looked at but only the properties of other molecular compounds dissoluted in the polymer the neutrality faults are not as relevant as in the solute case and the neutrality warning may be ignored as a start It should be kept in mind however that if the charge mismatches are blown out of proportion the prediction quality of the COSMOtherm calculation may suffer even if the polymer is used as solvent only If no expmw is given COSMOtherm will use the molecular weight of the molecular fragment i e the monomeric repeat unit as MW oiymer Value 7 Kouskoumvekaki I A Michelsen M L Kontogeorgis G M Fluid Phase Equilib 202 325 2002 180 The free volume of a compound polymer or molecule can be entered in several different ways In the compound input section of the COSMOtherm input file or the compound vapor pressure property file it is possible to give the free volume V itself with the freevol value or freevol_SI value options which expect as argument the
138. a weight of 1 for all atoms However if we consider very large molecules like polymer chains it may be impossible to do a single quantum chemical calculation for the entire molecule Instead it is useful to compose the large molecule out of molecular fragments which are calculated independently but which have to be sufficiently saturated by e g one or more monomeric units at all sites where the fragment is cut Hence the COSMO file of such a compound will contain atoms of the saturation region which should not be taken into account in the COSMOtherm calculation This can be achieved by setting the weight of these atoms to zero while the weight of the atoms of the fragment itself are kept one Another possible application of the explicit modification of the atomic weight factors is the case of large symmetric molecules In order to speed up the quantum chemistry calculation the symmetry equivalent parts of the molecule might be replaced by a suitable smaller saturation fragment e g in a metal ligand complex replace three of the large ligands by smaller saturation groups such as hydrogens The original untruncated molecule then can be re established in the COSMOtherm calculation by weighting the atoms of the symmetry equivalent part of the molecule with the number of symmetry equivalent groups i e four in the above example the unique atoms with one and the atoms of the saturation groups with zero Note that due to the basic principle of
139. ace areas to the COSMOtherm table file In the table file the areas are given in the range H N C O F S Cl Br If other elements are present in a compound the areas accordings to these elements will be tabulated in additional columns in the table file using the order of their element number IL i j Optional for density computations Define a lonic Liquid from or individual anion and cation compounds The input of the Ionic nIL name name Liquid composition is possible either via their compound number IL i j command where i j are the numbers of the ion compounds numbers as given in the sequence of compounds in the compound input section the arguments i j are expected to be positive integer numbers or via their compound number nIL name name command where name name are the names of the ion compounds as given in the compound input section IL n vy Vj Optional for density computations Define the lonic Liquid stoichiometry from individual anion and cation compounds The input of the lonic Liquid stoichiometry factors v vj is possible via the IL n v vj command where vi vj are the stoichiometry numbers of the lonic Liquid defined by the ions as given by the IL i j of nIL name name command The stoichiometry factors v v are expected to be positive janes integer numbers 144 2 3 13 Computation of the liquid viscosity of pure compounds The VISCOSITY op
140. acl xac MWac 1 Xp MW sonent Please note that if at the given conditions a compound is miscible with the solvent i e if the logarithm of the mole fraction solubility is zero the mass based solubility is not well defined and thus it will not be printed to output and table file If the density of the solvent and solute is known or can be estimated the decadic logarithm of the molar solubility of the salt in the solution logjo Sac Mol I logio Xa Volution will be written to an additional column in the COSMOtherm table file The molar volume of the solution V Psolution MW Salin is calculated from the molar masses and densities of the given solvent Poent and salt 4c according to the salt solubility x computed The density of the solvent or solvent mixture olution Psovent Can be provided to COSMOtherm via the the solvdens keyword If sovent is NOt given in the input COSMOtherm will try to estimate the solvents density with the liquid density volume QSPR method as described in section 2 3 12 If no density estimate is available the molar solubility of the solute in the solvent will not be computed The density of the salt p is estimated from the molecular COSMO volume of the individual ion components of the salt This estimate which is somewhat poorer than the liquid density volume QSPR is used because the liquid density volume QSPR is not applicable to solid salt compounds If the wso11 keyword is given in addition
141. actions cr of the compounds of the mixture as real numbers x and c The arguments are expected as real numbers between zero and one in the same sequence of compounds as given in the second input area If the values do not add up to one COSMOtherm will normalize them If less mole fractions concentrations than compounds are given the missing ones will be assumed zero If a negative number is given the concentration for this compound will be inserted automatically using the normalization of the sum of mole fractions Only one negative number is allowed per mixture input line Optional for reaction computations use given reference pressure p for the computation of the reaction equilibrium The input of the reference pressure p is possible via the pref p keyword where p is the pressure value that will be used to compute the reaction equilibrium The pressure p is expected to be positive real number For the keyword pref the given pressure are expected to be in mbar for the keyword pref_Pa it is expected to be in Pa for the keyword pref kPa it is expected to be in kPa for the keyword pref psia it is expected to be in psia and for the keyword pref bar it is expected to be in bar respectively Optional for reaction computations compute the solvent independent activity equilibrium constant K K activity and the nonideality factor K K gamma Optional for reaction computations input of a reference activity equilibr
142. actor Global input option scale gas phase ring correction temperature dependency parameter z with factor Argument factor is expected to be a real number 223 Input options for the fine tuning of COSMOtherm parameters continued cmfset factor chbset factor xhbset icement factor shbset isiement Factor ahbset iciement factor sphcation whbset factor dhbset factor symcset factor symgset factor Global input option scale misfit prefactor a with factor The argument factor is expected to be a real number Global input option scale hydrogen bonding global prefactor c with factor The argument factor is expected to be a real number Global input option element specifically scale hydrogen bonding global prefactor c with factor The argument isiement is the element number of the atom to which the hydrogen bonding donor hydrogen atom is attached It is expected to be an integer number Argument factor is expected to be a real number Global input option element specifically scale hydrogen bonding threshold parameter o with factor The argument ieiemenr is the element number of either the atom to which the hydrogen bonding donor hydrogen atom is attached or of the hydrogen bond acceptor atom It is expected to be an integer number Argument factor is expected to be a real number Global input option scale the hydrogen bonding prefactor Cyg of atomic compounds The argument isiement iS the element numbe
143. airs given via the vpexp command d Give the exact value of the vapor pressure for this temperature via the vpinp command in the compound input and options section of the input file see section 2 2 1 If the solgas keyword is given the reference pressure p is expected to be a positive real number pressure in mbar If the solgas_ Pa keyword is given the reference pressure p is expected to be a positive real number pressure in Pa If the solgas_kPa keyword is given the reference pressure p is expected to be a positive real number pressure in kPa If the solgas_ bar keyword is given the reference pressure p is expected to be a positive real number pressure in bar If the solgas psia keyword is given the reference pressure p is expected to be a positive real number pressure in psia If the solgas keyword is given and the solvent is set correctly see below for a given temperature COSMOtherm automatically calculates the mole fraction x of all compounds in the given solvent or solvent mixture at which the partial pressure according to eq 2 3 23 is equal to the reference pressure The decadic logarithm of the optimized mole fractions log x is written to the output as well as to the table file In addition the natural logarithms of the activity coefficients In y at the optimized solute concentrations x will be printed to the output and table files for all compounds j Please note that the iterative gas solubility computation is ambiguo
144. alidation of the COSMOtherm method by a research group independent from COSMOlogic GmbH amp Co KG Applications to vapor liquid equilibria and liquid liquid equilibria of industrial relevance are presented Note Article is in german language 228 Validation of the COSMO RS method Six Binary Systems Frank Eckert and Andreas Klamt Industrial and Engineering Chemistry Research 40 2371 2378 2001 DOI 10 1021 ie0009132 This article presents COSMOtherm applications to vapor liquid equilibria VLE and liquid liquid equilibria LLE of industrial relevance and compares them to the results obtained with the group contribution method UNIFAC COSMO RS a novel view to physiological solvation and partition questions Andreas Klamt Frank Eckert and Martin Hornig Journal of Computer Aided Molecular Design 15 355 365 2001 Presents applications of COSMO RS to problems of biochemistry life science COSMO RS a novel and efficient method for the a priori prediction of thermophysical data of liquids Andreas Klamt and Frank Eckert Fluid Phase Equilibria 172 43 72 2000 This article presents COSMO RS theory and does a methodological comparison of the COSMO RS theory to group contribution method UNIFAC In addition some applications are presented Refinement and Parameterization of COSMO RS Andreas Klamt Volker Jonas Thorsten Burger and John C W Lohrenz J Phys Chem A 102 5074 5085 1998 Pr
145. alue of higher states of ionization In this case the neutral and single ionic species iyeuers and izon have to be replaced by higher ionized species For example the first pK of phosphoric acid is calculated from the free energy difference of G H3PO G H PO while the second pK of phosphoric acid results from the free energy difference of G H PO G HPO and the third pK from the free energy difference of G HPO G PO The pK LFER denoted in eq 2 3 6 does include a temperature dependency term which implies that it is valid for the temperature of the LFER fit i e room temperature only By default LFER parameters c and c for acidic solutes in solvent water at room temperature are read from the COSMOtherm parameter file However it is also possible to read the LFER parameters from the COSMOtherm input file via the pKaLFER c c or pKaLFER SI co c commands see below The input of of the LFER paramaters will be necessary if solvents other than water or temperatures other than room temperature are used In addition it is possible to give finite concentrations of a solvent mixture where the free energies Gyeutrai and Gon are computed This is possible via the commands xp x x2 OF cp Ccz C2 m Suboptions of the pKa or npKa command are xp X1 X2 Optional for pKa computations Give finite mixture concentrations for the or solvent phase in which the pK value shall be computed The input of the Cp te
146. ame i j xyz and anion name i j xyz where name is the molecule conformer name of the anion and cation created respectively while i and j are the number of the molecule conformer contacts i and j are given in the order that is given in the compound section of the COSMOtherm input file Please note that the surface contact complex XYZ geometry files of subsequent contact runs will be overwritten Optional for the ssc strength ssc probability or ssc_ions option Force the creation of additional weak surface contact complex XYZ geometry files Optional Give the stepsize of the dihedral angle used in the creation of cluster geometries by the ssc strength or ssc probability options Thus for a given dihedral angle stepsize angle which has to be given as integer degree between 1 and 359 default angle 45 surface contact complex geometry files complex ij angle xyz or complex namei namej_angl xyz if the ssc_name option is used will be written for the range of dihedral angles between 0 and 360 with the given stepsize angle 211 5 8 Concentration Dependent Reactions The prediction of thermodynamic mixture properties with COSMOtherm sometimes involves the additional complication that in solution and dependent on the solute concentration reactions between solute and solvent or solute and solute occur Examples for such reactions are the concentration dependent dimerization of small organic acids solute solute reaction or
147. an be written to a file filename prf detailed information about theo moments and hydrogen bonding moments can be written to a file filename mom molecular information or filename moma molecular information divided further into atomic information and the o potentials of all mixtures calculated in the COSMOtherm job can be written to a file filename pot The o profiles moments potentials are written in a format readable by all common spreadsheet programs or by scientific graph visualization programs like GNUplot For the physical significance and practical use of o profiles c moments and o potentials cf Section 5 and the original 12 COSMO RS COSMOtherm articles In the special case of the automatic calculation of phase diagrams for binary ternary or multinary mixtures and for automatic computation of activity coefficients or partition coefficients see below an additional file filename tab is produced which presents the evaluated information condensed to a single table 1 3 Installation COSMOtherm release comes in one single installation form A self extracting COSMOthermX program installer which includes the Java based graphical user interface GUI COSMOthermX as well as the command line version of COSMOtherm a Windows COSMOthermX C30 1501 Installer Win32 exe b Linux COSMOthermX C30 1501 Installer Linux32 sh The self extracting installer files automatically install all components of COSMOtherm and its graphical user int
148. and name and weighted by the o profile of the compound with the name name The computed similarity factor is printed to the mixture output section of the COSMOtherm output file 5S p is printed below the compound output block of the first compound given in the similarity command i e compound i or name At a given temperature the solute specific n simpot option will toggle three COSMOtherm computations for pure compounds i j and k respectively 139 2 3 11 Computation of gas solubility in a solvent The solgas p option allows for the automatic computation of the solubility of a gas with partial pressure p in a given solvent For a given pure solvent solvent i or nsolvent name options see below or solvent mixture xs and cs options see below the solgas option will compute the gas solubility of all compounds j in the given solvent or solvent mixture using an iterative procedure For each compound j the mole fraction x is varied until the partial pressure of the compound which is calculated from eq 2 3 23 is equal to the given reference pressure p Pit py 2 3 23 The p are the pure compound vapor pressures for compounds j x are the mole fractions of the compounds in the liquid and y are the activity coefficients of the compounds as predicted by COSMOtherm Ideal behaviour of the gas phase is assumed In each iteration step COSMOtherm will vary x compute y in the given solvent or solvent mixture with a
149. and parameters are expected to be used with energy values in kJ mol and areas in nm i e in the Sl unit frame 145 2 3 14 Multi Component Multi Phase Extraction Equilibria The LIQ_EX option allows for the automatic computation of a multi component multi phase liquid liquid extraction equilibrium If toggled in a temperature mixture line of the COSMO therm input file the LIQ_EX option will compute the mole or mass based equilibrium partition of an arbitrary number of compounds between a given number of liquid phases and optional solid precipitation and gaseous evaporation phases The functionality of the option two liquid phases and five compounds is described in the figure below There are two predefined phases and II both of which may be mixtures of compounds including lonic Liquids or dissolved salts Phases and Il are assumed to be immiscible and to separate in thermodynamic equilibrium Using a given starting concentration in the two phases and Il for each compound neutral as well as ions COSMO therm will compute the affinity of each compound to each of the two phases i e the impetus of the compound to stay in the phase where it is or to move to the opposite phase by means of the thermodynamic equilibrium partition constant K K exp u u VRT 2 3 27 In this expression u7 and 4 are the chemical potentials of compound in phase and phase II respectively Now each individual compound is allowe
150. ar concentration Mso in mol l Please note that the input of a molar reference solubility requires the input of the solvent density solvdens option above If no solvent density is given the conversion of the molar solubility to mole fraction can only be done in an approximative way The ref sol 1 option assumes that the given reference solubility value is given as the solutes mass volume concentration L so in g l Please note that the mass volume concentration units also requires the input of the solvent density Along the lines of the mass based solubility input the mass volume concentration input assumes that L is given by mass Definition 2 as noted above unless the wsoll or wfract keywords are used in which case the input of L o is assumed to be a Definition 1 mass solubility or a mass fraction respectively 101 2 3 5 Automatic Partition Coefficient Calculation The logp i i2 or nlogp name name option allows for the automatic computation of partition coefficients between compounds i and i gt By default this option will compute the chemical potentials 4 of all compounds j in infinite dilution in pure compound i and subsequently the chemical potentials u at infinite dilution in pure compound i The partition coefficients are then calculated as log P j logio exp y 4 RT V V and written to the COSMOtherm output file and to the COSMOtherm table file By default
151. are set to values larger than one the labels of the corresponding atoms will be marked yellow in the molecular VRML file Surface parts corresponding to atoms zeroed out via atomic weights will not be shown in COSMO charge or property surface VRML files name_sig wrl and name_prop wrl Atomic weights larger than one are represented in the corresponding surface areas of the charge or property VRML files via a lighter color which is the lighter the higher the atomic weight factor The same holds also if COSMO metafiles are used In this case COSMOtherm will write individual VRML files for all of the compounds given in the COSMO metafile Such VRML files of COSMO files fragments from COSMO metafiles are denoted name meta _mol wrl for the molecular geometry files and name meta sig wrl or name_meta_prop wrl for the molecular charge and property surface files respectively It is possible to use several COSMO metafiles together to form a conformer block the same way it is done for regular COSMO files However putting together COSMO metafiles in a conformer block has a severe pitfall the quantum chemical COSMO energy unlike all the other properties that are pieced together with 175 the metafile methodology is not additive linearly The quantum chemical COSMO energy of the meta compound defined by the metafile is not the sum of the COSMO energies of the fragment COSMO files The relative weight factor of the individual conformers however is deter
152. ares it to other methods used in that field i e QSAR QSPR MM MD methods The article concentrates on the prediction of properties relevant to industrial life science applications such as solubility and other QSAR QSPR descriptors This review article is possibly the best starting point for interested readers from the biochemistry life science or environmental chemistry community 3 An updated list of publications related to COSMO and COSMOtherm can be found on the COSMOlogic website at http www cosmologic de publications html 226 COSMO RS COSMOtherm Theory and Application Prediction of acidity in acetonitrile solution with COSMO RS Frank Eckert Ivo Leito Ivari Kaljurand Agnes K tt Andreas Klamt Michael Diedenhofen Journal of Computational Chemistry 30 799 810 2009 Presents COSMOtherm methodology for the prediction of acid pK dissociation constants in nonaqueous solvent acetonitrile Article DOI 10 1002 jcc 21103 A Klamt BJ Smith in Molecular Drug Properties Measurement and Prediction Methods and Principles in Medicinal Chemistry R Mannhold H Kubinyi G Folkers Series Editors Wiley 2008 This book chapter describes the theory and the inherent problems of drug solubility prediction It is shown that COSMO RS has a systematic advantage in predicting the non linearity in drug solubility but that other aspects as the unresolved problem of the prediction of AGfus are giving rise to a substant
153. ase Computations Define phase k of the liq_ex computation as gaseous vaporization phase Argument k is expected to be a positive integer number between 1 and ngnase Optional for liq _ex n nase computations with defined gaseous k phase use given reference pressure p for the computation of the vapor liquid liquid equilibrium The input of the reference pressure p is possible via the pref p keyword where p is the pressure value that will be used to compute the equilibrium The pressure p is expected to be a positive real number For the keyword pref the given pressure are expected to be in mbar for the keyword pref Pa it is expected to be in Pa for the keyword pref kPa it is expected to be in kPa for the keyword pref _ psia it is expected to be in psia and for the keyword pref bar it is expected to be in bar respectively Optional for 1iq_ex npnase computations with defined gaseous k phase use given molar reference volume V for the computation of the vapor liquid liquid equilibrium Argument vV is the molar volume value that will be used to compute the equilibrium pressure of the gaseous phase V o is expected to be a positive real number volume in I mol Optional for 1iq_ex npnase computations with defined gaseous k phase use given reference volume V for the computation of the vapor liquid liquid equilibrium Argument V lt is the absolute volume value that will be used to compute the equilibrium pressure of the g
154. ase Diagrams ccceseeeees 135 2 3 9 Automatic Computation of Isobaric Phase Diagrams cecccecceeceeeeeeeeeeeeeeeeseneseeeeeeeaeeneeees 137 2 3 10 Computation of a similarity factor between two COMPOUNGCGL cesccseseeeetseeseeesssesseeeees 138 2 3 11 Computation of gas solubility in a solvent ccecccssscceseeesseeeesseessaeeeseeessseeeseeessneessatessaeessaes 140 2 3 12 Computation of the liquid density Of pure COMPOUNGAS ccesccsesceestseeseeesetessneessetessaeesaes 142 2 3 13 Computation of the liquid viscosity of pure compounds ceccceceeeeeeeeeeteeeteeeteeeeaeeeeeeeeeees 145 2 3 14 Multi Component Multi Phase Extraction Equilibria eceeeceseseeesceeeeneeeseeeseaeeeseeeesaeeeeaes 146 2 4 The COSMO Databases ieia ernaia aea hues eat a aa a aa aaa a a na aaa 155 2 4 1 Creating COSMO files with a quantum chemistry PrOGraM cscccescccssscssseesseesseessstessneeeaes 158 3 The COSMOtherm Parameter File cescccesceeeseecesceeeseeseaeeeeaeeseaeeeaeessaeeesaeeeeaaeeeseeeeaaeseaaeeeeeeeseeeteeeneaaes 160 3 1 Parameterization Of COSMOtherm ceccccccecceececeseeeeeeenecenecaeeeaeeeaeeaecaeesaeeeaeeeaeeeaeeneeseeesaeesaeseaeeeatens 160 3 2 Parameterization Usage icc sicccsieg a a e aa bbe aa aa oa ea e a aaa aa Eaa 161 3 3 Recommended Parameterizations ccscccesceceseeeeneeeeeeeeeeeeeeeeeeaeeeseeeeeaeeesaeeeeaeeeeaeeeeseeseeeseeeeeaeeea 162 4 Th amp ecCOSMOth rm
155. aseous phase Vz is expected to be a positive real number volume in I Optional for liq ex nphase computations with salt compounds Use the average chemical potential of the salt to compute the phase equilibrium constants of the salt s components 154 2 4 The COSMO Database COSMOtherm allows for simple and efficient processing of large numbers of compounds i e a database of molecular COSMO files e g the COSMObase database One aspect of the easy processing of large datasets is the use of the auxiliary program CT_CREATE that is shipped with COSMOtherm CT_CREATE is a simple tool that is able to automatically create COSMOtherm input files over a dataset of COSMO files run these COSMOtherm jobs and scan their output for the required data For further information cf the CT_CREATE user s manual The second possibility to process large datasets of COSMO files is the SDATABASE filename command which can be used in the compound input section of the COSMOtherm input file This option reads in a database list file of the name filename which can be used in connection with the f filename cosmo command which then is replaced by f SDATABASE listfile the rn aaaaaa bb c command RN which then is replaced by rn SDATABASE 1istfile or the dbn name command which then is replaced by dbn SDATABASE listfile Basically the database list file that is read in with this option is a simple text file holding a list of
156. at are read in by COSMOtherm The COSMO file information will be written in a compressed and encoded binary format that is only about 6 the size of the conventional COSMO files ASCII text files The compressed COSMO files are identified by the extension ccf and can be read in by COSMOtherm just like conventional COSMO files Cf also the Wccf keyword in the compound input section of the COSMOtherm input file see section 2 2 Optional Write converted COSMO file for all of the COSMO files computed with the Gaussian program that are read in by COSMOtherm The charge surface of the Gaussian COSMO files are converted into a charge surfaces that are equivalent to the charge surfaces produced by Turbomole with a molecule of the same geometry Thus the COSMO files produced by this option can be used by COSMOtherm in combination with a COSMOtherm parameterization that was optimized for Turbomole i e BP_TZVP or BP_SVP_AM1 see section 3 3 Cf also the Wgauss keyword in the compound input section of the COSMOtherm input file see section 2 2 30 2 2 Compound Input The fourth and following lines of the COSMOtherm input file are used to provide the program with the information about the compounds which shall be used in the following COSMOtherm calculation Each line represents the information given for one compound l e all commands and options for this compound have to be given in this one line 2 2 1 Compound and Conformer Input The compoun
157. ate keyword is given in the global input section the approximation to ACp is valid for all compounds and all mixture computations Optional for the input of gas phase energies switch off the usage of gas phase minimum conformer energies in single conformer calculations see section 2 2 gas phase energy files 24 2 1 3 General Program Control continued awps accc ilxmx 1xmx Optional Allow Wrong Parameter Set i e allow the usage of a parameter set that does not match the computation level of the COSMO files used By default such a combination would cause COSMOtherm to stop with an error message Please note that COSMOtherm predictions typically will not be reasonable any more if parameterization and quantum chemical computation level do not match Hence awps is an expert option that should be used with the greatest caution Optional Allow mixture of CCF and COSMO files in Conformer block i e allow the usage of compressed and uncompressed COSMO files in the same conformer block By default such a combination would cause COSMOtherm to stop with an error message Please note that mixing compressed and uncompressed COSMO files can lead to inconsistent conformer energies Hence a slight bias on the conformer distribution might be introduced into the COSMOtherm predictions Thus accc is an expert option that should be used with some caution Optional increase the number of phases allowed in a multi componen multi
158. ature conditions of a vapor pressure prediction are out of the temperature range where typical organic compounds are liquid below 150K or over 550 K the computed total vapor pressures will be written to the COSMOtherm table file in square brackets e g T and PVtot column look like this 723 15000 0 12801479E 06 in the graphical user interface COSMOthermxX such entries are marked red indicating that the values were computed outside the core region of COSMOtherm applicability and thus may show a higher than usual error If the compounds melting point Tmer iS Known i e if it is read from the compound input lines or the compounds vap file see section 2 2 1 the predicted total vapor pressures will be written to the COSMOtherm table file in round brackets e g T and Pvtot column look like this 173 15000 0 51704579E 07 in the graphical user interface COSMOthermxX such entries are marked blue if the temperature of the computation is below the melting point temperature of the given compound or if the vapor pressure of a mixture is computed below the melting point of one of the components of the mixture indicating that the vapor pressure thus computed corresponds to the vapor pressure of a subcooled melt If three or more temperature points were calculated in a vapor pressure curve the total vapor pressure will be fitted to Antoine s vapor pressure equation In p A B C T where T is the temperature in K and A B an
159. bar phase diagram requires three additional COSMOtherm calculations per mixture If the temperature thus optimized is outside the range of the three computed temperatures i e if the scheme was used to extrapolate rather than to interpolate the temperature extrapolation errors might be introduced into the resulting temperature However such errors can be minimized using the iterative thresh sub option of the isobar option If the iterative option is given the interpolated or extrapolated temperature is refined iteratively The optimized temperature is used as new starting guess for the temperature Again COSMOtherm will compute the mixture properties at that temperature plus at additional two temperature values above and below that temperature and interpolate a new guess for the optimized temperature from the vapor pressures computed at these three temperatures This procedure is repeated until the change in the guess of the optimized temperature is below a certain threshold thresh default thresh 0 2 K The syntax of the isobar option is isobar pressure Optional for binary ternary or multinary computations or Compute phase diagram at fixed pressure given in mbar and in isobar Pa pressure Pa for the isobar Pa command or in kPa for the isobar kPa or command The argument pressure is expected to be a positive real isobar _kPa pressure number Suboptions of the isobar option are iterative thresh Optional for binary ternary or
160. ber MW Formula Alternative Name Conformerl Name Conformerl Alternative Name Conf2 Name f Conf2_AltName Conf3 Name j Conf3 AltName Conf4 Name Conf4 AltName l e the additional conformers are attached to the database index list shown above as additional entries with two additional fields for each conformer first the conformers COSMO filename without extension and then separated by a comma the For a given CAS RN and its corresponding compound name name COSMOtherm will search for the file name cosmo in the COSMO file directory i e the current working directory or the directory given with the fdir command in the global command section If no name cosmo could be found COSMOtherm will search for name cos MOPAC COSMO format If such a file also cannot be found COSMOtherm will search for a COSMO metafile of the corresponding name name mcos If none of the three file types were found for the compound name COSMOtherm will terminate and return an error message 156 conformers trivial name Up to nine additional conformers can be processed For example the compound valine that consists of two conformers is given in the database index file as VALINEO 000072 18 4 117 1474 C5H11NO2 L VALINE conformer 0 VALINE1 L VALINE By default only the first conformer is read in if the rn xxxxxx xx x or dbn trivialname options are used However it is also possible to automatically process all c
161. bility option the LIQ EX calculation allows the definitions of several salts If several salt definitions are to be given these definitions simply can be given subsequently in a row in the same LIQ EX input line By default all salts will precipitate into the phase k that is defined as solid via the solid k command Alternatively each salt can be forced to precipitate into its own separate salt phase k This can be toggled by the salt phase k command where argument k is the phase presumed to be the container for the precipitation of salt compound The salt_phase k keyword has to be given within a salt input block i e subsequent to the salts component definition stoichiometry and AG information A salt thus defined will precipitate exclusively into its denoted salt phase k No other compound can precipitate into a defined salt phase 149 If ionic species are considered in the phase equilibrium in terms of dissoluted salts or ionic liquid IL compounds the convergence of the algorithm that conducts the phase equilibration may be compromised if the individual ions that form the salt or IL have strongly different affinities with respect to the different phases This is quite common for e g aprotic IL s where typical IL anions such as aorganic sulfates or sulfonylimides are polar and thus tend towards polar solvent or mixture phases while typical IL cations such as alkylimidazolium compounds are quite unipolar and tend t
162. capacity of fusion ACp can also be used to decribe the temperature dependency of the Gibbs free energy of fusion ACp can be given in the compound section of the COSMOtherm input 121 file with option Dcpfus value see section 2 2 1 If no Dcpfus value is given it is assumed zero A compounds melting temperature Ter can be given in the compound section of the COSMOtherm input file via option Tmelt temp see section 2 2 1 The ACp estimate described in the solubility section 2 3 4 keyword Dcpfus_ estimate may also be used in binary SLE computations However following the considerations taken in section 2 3 4 the ACp estimate should only be used the prerequisites described there are met As an alternative to the definition of the free energy of fusion described above the binary SLE option also allows the classification of one or both binary phases as liquid This can be done with the liquid 1 keyword given in the compound line of the binary SLE option where argument 1 is the identifier of the binary phase i e 1 can be 1 or 2 the first or the second phase given in the binary option If no argument is given both phases are considered to be liquid In this case only the LLE s can be found in a possible SLLE equilibrium For a phase thus designated as liquid AG is defined as zero at any temperature This slightly artificial definition in reality AG always will be zero at some low temperature serves the purpose of a s
163. cations resulting from use of this program must acknowledge the following F Eckert and A Klamt COSMOtherm Version C3 0 Release 15 01 COSMO ogic GmbH amp Co KG Leverkusen Germany 2014 In addition reference 1 should be cited 1 1 Theory The COSMOtherm program is based on COSMO RS theory of interacting molecular surface charges 3 COSMO RS is a theory of interacting molecular surfaces as computed by quantum chemical methods QM COSMO RS combines an electrostatic theory of locally interacting molecular surface descriptors which are available from QM calculations with a statistical thermodynamics methodology The quantum chemical basis of COSMO RS is COSMO the Conductor like Screening Model which belongs to the class of QM continuum solvation models CSMs In general basic quantum chemical methodology describes isolated molecules at a temperature of T 0 K allowing a realistic description only for molecules in vacuum or in the gas phase CSMs are an extension of the basic QM methods towards the description of liquid phases CSMs describe a molecule in solution through a quantum chemical calculation of the solute molecule with an approximate representation of the surrounding solvent as a continuum Either by solution of the dielectric boundary condition or by solution of the Poisson Boltzmann equation the solute is treated as if embedded in a dielectric medium via a molecular surface or cavity that is constructed around
164. ck has to be terminated by the Send entry The order of the data blocks is arbitrary It is expected that all data given in the data blocks is on the quantum chemical level as defined by METHOD and BASTS fields as defined above It is possible to give comments in the keyword lines equivalently to the COSMOtherm input using a character Note that comments are allowed in the data block part of the energy file only Please also note that the data blocks are intended to hold accessory information which can not be edited by COSMOtherm and COSMOthermxX In COSMOtherm the entries for fixed symmetry number symmetry and zero point vibrational energy zpe of the molecule in the gas phase are read with lower priority than the entries in the second line the xyz comment line E g if no EZP value entry for zero point vibrational energy is given in the the xyz comment line then COSMOtherm will look for a zpe entry in the accessory data block and if present read the zpe value given in Hartree atomic units from there Same holds for the entry of a fixed symmetry number Any other entries in the accessory data blocks will be ignored by COSMOtherm 46 Compound input options continued External Quantum Mechanical energy input eqm E Optional input of a molecules external quantum chemical gas phase or energy E Argument E is expected to be a real number For the keywords eqmH E eqm and eqmH the
165. coefficient for ions and the mean ionic activity coefficient of a salt anion plus cation will be one at infinite dilution of the salt It is possible to override the defaults for the reference state by explicitly fiving a reference state concentration to COSMOtherm This is possible with the xref x x Or cref c Cc suboptions of gamma see table below The explicit reference state given in the input will be applied to all compounds in the mix and override the defaults for neutral and charged compounds The activity coefficients are calculated as In y 4 p RT and written to the COSMOtherm output file and to the COSMOtherm table file It is also possible to calculate the activity coefficients at a given finite mixture concentration via the xg x x OF cg c c2 commands see table below Suboptions of the gamma i and the ngamma name option xg X X2 Optional for gamma computations Give finite mixture concentration at or which the activity coefficient shall be computed The input of the cg c Co s concentrations is possible either in mole fractions xg or mass fractions cg of the compounds of the mixture as real numbers x and c The arguments are expected as real numbers between zero and one in the same sequence of compounds as given in the second input area If the values do not add up to one they will be normalized by COSMOtherm If less mole fractions concentrations than compounds are gi
166. combi name name the combinatorial contribution is switched off for all compounds in the mixture If the option combi i iz is given the combinatorial contribution is switched off only for compounds i where i is the number of the compound in the order that is given in the compound section of the COSMOtherm input file If the option ncombi name name is given the combinatorial contribution is switched off only for compounds compounds name name where name is the name given in the compound section of the COSMOtherm input file combi ELBRO Optional Switch on special free volume combinatorial contribution to the chemical potential If given in a temperature mixture line the combi ELBRO command is active for the given mixture job option only The free volume term by Elbro et al is recommended for the computation of macromolecules see section 5 3 2 71 D Program control options continued IEI en_I or en_I oclp EI i ip c H c S EI SI i ip cH c S Optional Give the interaction energy parameters c_H enthalpic contribution and c_S entropic contribution of the interaction of two compounds identified by interaction energy indices IEI numbers i and iz i and i are expected as integer numbers the two parameters c H enthalpic contribution and c s entropic contribution are expected to be real numbers in kcal mol and kcal mol K respectively If the en_IEI_SI opti
167. compound s free volume V in units A3 and nm3 respectively Alternatively the experimental molar volume V can be given via the expmolvol value or expmolvol_SI value keywords which expect as argument the compound s molar volume J in units A3 and nm respectively The free volume of compound i is computed from the input molar volume V as V V ri Moreover it is possible to use the experimental density of compound as input via keywords expdensity value expdensity SI value or expdensity_ Brit value which expect as argument the compound density in units g ml g cm and lbm ft respectively The experimental density p thus given is converted into the molar volume V MW N p which serves to compute the free volume as VF V r In order to be thermodynamically consistent the combi ELBRO term has to be applied to all compounds in the given system This implies that the free volume or alternatively the experimental molar volume or density has to be known and greater than zero for all compounds that are present in a given COSMOtherm calculation The direct input of free volume molar volume or density for all of the compounds present in the COSMOtherm calculation may not be convenient or even possible at certain situations For this case COSMOtherm offers the additional possibility to do an estimate of the free volumes This estimation method is a two step procedure which utilizes the room temperature QSPR de
168. computes the partition coefficients between the compounds of the names name and name By default the common logarithms of the partition coefficients log P are calculated for pure compounds i and i gt It is also possible to calculate logP at finite concentration of the two solvent phases using the xli or cli commands see section 2 3 5 If such a finite concentration input is used for both solvent phases the arguments i or name need not be given to the logp or nlogp option Optional Toggle the automatic calculation of the pK value of the acidity basicity of a compound in solvent S which normally is water The pKa isoivent ineutrar tron Option computes the pK value from the free energy difference of the neutral compound iyeutra and the ionic compound izon in solvent isoivent Where i are the compound numbers in the range given in the compound input section The npKa namegoivent NAMENeutrar NAaMezo Option computes the pK value from the free energy difference of the neutral compound nNameyeutra and the ionic compound name in solvent namesoivents where name are the names of the compounds as given in the compound input section By default the pK is calculated for pure Solvent isoivent However it is also possible to calculate pK in a solvent mixture using the xp or cp commands see section 2 3 6 Optional Toggle a reaction equilibrium calculation in given solvent see section 5 4 If the reaction keyword i
169. concentration definition of the start and end concentration vectors given Any possible combination of xstep cstep or qstep keywords with xstart cstart or qstart and xend cenad or qend is allowed 136 2 3 9 Automatic Computation of Isobaric Phase Diagrams The binary ternary multinary options by default compute phase diagrams at a fixed given temperature It is also possible to compute phase diagrams at a given fixed pressure with variable temperatures via the isobar command If this sub option of the binary ternary multinary options is used for each given concentration COSMOtherm will compute the mixture properties at the temperature given in the input file plus at additional two temperature values above and below the given initial temperature Thus a starting guess for the temperature is necessary for any isobar computation By default room temperature 298 15 K is used as starting guess Alternatively it is possible to override this default and read the first guess for the exact temperature from the input This is done with the usual temperature input commands tk temp K tc temp C or tf temp F The vapor pressures computed at the three temperature values are then used to interpolate the temperature value at the given pressure In the fourth step all the thermodynamic properties of the mixture are calculated at this optimized interpolated temperature Thus compared to the isothermal case the automatic computation of iso
170. concentration for this compound will be inserted automatically using the normalization of the sum of mole fractions Only one negative number is allowed per mixture input line Required for multinary computations Custom concentration grid end vector mole fraction xend mass fraction cend or surface fraction qend concentrations of the compounds of a multinary mixture as real numbers x c Or qi The attributes of the xena cend and qend commands are the same as described for the xstart cstart and qstart keywords above Please note that is possible to leave out this definition of a concentration grid end vector in the input In such a case only one grid point as defined by the xstart cstart or qstart keywords above will be computed Optional for multinary computations Number of points to be calculated in custom concentration grid of a multinary mixture computation Argument n ints is expected to be an integer number between 2 and 235 Default is npoints 10 If xstep is used evenly spaced mole fraction concentration grid points will be set between the given start and end concentration vectors If cstep is used evenly spaced mass fraction concentration grid points will be set between the given start and end concentration vectors If qstep is used evenly spaced surface fraction concentration grid points will be set between the given start and end concentration vectors The xstep cstep or qstep options are independent
171. cosmo conformer from the database and one metafile that includes the 1 butanoll cosmo conformer from the COSMO database Both metafiles need to have the same fragmentation pattern and it is important that the actual fragmentation does not take place in any group that is substantial for the difference between two conformations in the case of 1 butanol0 cosmo and 1 butanoll cosmo you may safely cut off the terminating CH group of the conformer it is essentially the same in the conformers but not the hydroxy group it is exactly in the hydroxy group where these conformers differ Given these conditions it is safe to assume that the value of the quantum chemical COSMO energy of the metafile can be approximated by the sum of fragment molecule energies because in the Boltzmann conformer equilibrium we are looking at the energies only in a relative way i e only the difference between the conformer energies is accounted for The usage of the sum of the fragment COSMO energies instead of the default zero in determination of the the total free energy of the metafile conformers is toggled by the mese Metafile Conformer Sum of Energy command which can be used as a global command or as local command in the compound input lines of the COSMOtherm input file Please be aware that the usage of the mcse command only makes sense if all the conditions given above are met If this is not the case then the COSMO energies of the fragments that are summed up will not be c
172. cs 27 1995 447 448 102 Dissociation Corrections to Partition Coefficients Distribution Coefficient logD In partition coefficient calculations of systems with one aqueous phase most prominently for the 1 octanol water system logPow it is possible that acidic or basic solutes dissociate in the water phase The dissociated species typically have partition properties different from the partition property of the undissociated compound thus affecting the apparent partition coefficient of the compound The effect of the dissociated compound approximatively can be taken into account by applying a dissociation correction to the partition coefficient Following the assumption that the dissociated solute species will not migrate into the organic solvent phase the fraction of the dissociated solute species in the aqueous phase solely is detemined by the solutes aqueous dissociation constant pK and the pH of the aqueous phase The resulting dissociation corrected partition coefficient is denoted as distribution coefficient logD If the solute is an acid HA showing the dissociation reaction HA H O A H 0 the correction term to partition coefficient logP can be approximated by equation 2 3 5 1 employing the acids dissociation constant pK acid and the pH of the aqueous phase log D log P log 1 10024 PK acid 2 3 5 1 If the solute is an base B showing the dissociation reaction B H O BH OH the correction term to parti
173. ction see section 5 5 The properties calculated by the QSPR formula for the COSMOtherm o moments will be color coded and mapped to the COSMO surface of the molecule Cf also the Pwrl name wrl1 keyword in the compound input section of the COSMOtherm input file section 2 2 Optional Set the graphical resolution of the VRML files of molecular COSMO surface charges and molecular QSPR property surfaces If given in this section of the COSMOtherm input file the given resolution will be used for all VRML files of all compounds The argument res is expected as a real number gt 0 2 18 2 1 1 File Handling continued autoc maxautoc usec i io rmic name mic use _tboil use pvapt Optional Use all cosmo ccf or mcos files that are found in the directory as specified by the fdir command as conformers The COSMO file filenames must follow the name convention of conformer COSMO files in COSMObase i e conformer COSMO files are named by subsequent numbers starting with zero name0 cosmo namel cosmo name _9 cosmo Or name_c0 cosmo name_cl cosmo name _c9 cosmo By default conformer numbers ranging from 0 to 9 are considered The optional argument maxautoc assigns the maximum number of conformers that are searched for meaning that COSMOtherm will read all cosmo files with numbers 0 to maxautoc that are present within the given conformation s name convention Note that maxautoc has to be integer number between 1
174. ction statistics of all individual segments of compound A i e molecule i as given in the segment _contact i iz command with one given atom itom Of molecule B molecule imo1 as given in the latm inoy tatom option are computed The resulting contact interaction map thus quantitatively describes the probabilities that segments jse of molecule A will have contact with the all of the segment that are associated with atom itom Of molecule B If you substitute the atom number itom by the string ALL e g latm inos ALL then the contact statitics with all atoms of the given molecule i is computed and printed to the contact file In addition an atom atom contact matrix is printed to COSMOtherm table file Using the additional command natm ino atom Latom2 Latom3 in combination with the segment contact i iy command the detailed contact interaction statistics of all individual segments of compound A i e molecule i as given in the segment _contact i i command with the functional group defined by the atoms istomtatomaLatom3 Of molecule B molecule i as given in the natm inor atomi Latome option are computed The resulting contact interaction map thus quantitatively describes the probabilities that segments j e of molecule A will have contact with the all of the segment that are associated with the functional group defined by the given atoms istom Of molecule B 203 Suboptions of the segment _contact i
175. cured in reading of COSMO file error 17 ERROR Cannot write uncompressed COSMO file for compound Molecule is too large error 18 ERROR Problems in creating VRML file for ISOCAV surface of this molecule ERROR Please check your cosmo file error 20 ERROR Illegal file format of compressed cosmo ccf file error 21 ERROR Cannot use compressed COSMO file with used COSMOtherm parameter set ERROR Please use COSMOtherm parameter set for Turbomole COSMO file COSMOtherm Revision C12_0702 or later error 22 ERROR CCF files are limited to less atoms error 23 ERROR This option can not be used with secure ccf file error 25 ERROR COSMO Metafile empty or damaged error 26 ERROR Metafile damaged COSMO filename missing error 27 ERROR Could not find compound input file ERROR This file is required by metafile error 28 ERROR COSMO metafile is not charge neutral error 30 ERROR The DBAS RN DBN input can not be combined with the explicit conformer block input error 31 ERROR More than one conformer block identifier was found error 32 ERROR Conformer block close identifier was found but the block was never opened error 35 ERROR QM computation level found in a molecule differs from QM level of the parameter set ERROR Stopping COSMOtherm execution You may override this error message with the global AWPS option error 36 ERROR The QM method in the QSPR file does not match with the parameter set used
176. d However if a second temperature is given via the tk2 T tc2 Tz or tf2 T commands the vapor pressures are calculated over the range of temperatures spanned by the two values By default the vapor pressure then will be calculated at 10 temperature values evenly spaced between T and T The number of temperature points to be calculated in the temperature range can be changed via the tstep npoints command npoints is restricted to 101 Alternatively the temperature points in the interval of T and T can be determined by a given temperature stepsize via the tstepsize AT command At each temperature for each compound i in the mixture S the partial vapor pressures p 1 bar exp 48 ue RT the chemical potential of the compound in the gas phase u and its enthalpy of vaporization are written to the COSMOtherm output file The tota vapor pressure of the mixture is written to the COSMOtherm table file in tabulated form pyap vs T If the keyword pr_pp is given the partial vapor pressures of all compounds in the mixture will be written to additional columns in the COSMOtherm table file In addition the total chemical potentials of the liquid 11 and of the gas phase u 5 as well as the heat of vaporization of the mixture AHy p are written to the COSMOtherm table file Please note that in the case of mixtures the given AHy p value of the mixture is the sum of the partial AH values of the contributing compounds If the temper
177. d BASIS are information lines created by Turbomole They can be used to identify and check the method and basis set that were applied in the quantum chemical calculation that created the energy file it should be the same method and basis set that were used to create the associated cosmo file There are several additional keywords and information fields that can be stored in the xyz format gas phase energy file The info comment line of the xyz format may hold the gas phase energy conformer minimum energy E_GAS MIN option external quantum chemical energies and zero point vibrational energies EQM and EZP options and symmetry information in terms of the molecules point group or number of irreducible representations PGROUP SYMMETRY and NIRREP options Please note that the keywords in the xyz info comment line are case sensitive The keywords have to be separated and terminated by semicolons No blanks are allowed between the equal sign and the argument of the keyword 44 Currently the following information fields can be read from the info comment line of a xyz formatted gas phase energy file E GAS MIN E_ GAS min Input of the gas phase energy conformer minimum energy E GAS min Gas phase energy conformer minimum energy E_GAS MIN option If present the E_GAS_ MIN information will be used in single conformer computations of conformers with a gas phase energy that is higher than the minimum gas phase energy thus r
178. d C are the coefficients of Antoine s equation The resulting coefficients are written to COSMOtherm output file and also to the COSMOtherm table file If available i e if given in the input or read from a vapor pressure property file see section 2 2 experimental vapor pressures will be printed to the table file This allows for the direct comparison of the calculated vapor pressures with experimental data However the output of experimental data is restricted to pure compounds i e it is printed only if pure compounds vapor pressures are predicted not for mixtures Furthermore the experimental values are printed only if we are inside the interpolative region of the given vapor pressure equation Otherwise the experimental data field will be left blank If the given temperature is below a compounds melting point the automatic vapor pressure computation option pvap by default will compute the partial and total vapor pressure of the subcooled melt However if experimental data on a compounds solid state properties are available in terms of the compounds melting point T and free energy of fusion data AG T as read from the compound input lines or the compounds vapor pressure and property vap file see section 2 2 1 Vapor Pressure Property Input COSMOtherm will compute the compounds partial sublimation pressures Psu 1 bar exp 1 54 pp AG RT and write the computed partial sublimation pressures and the according ent
179. d as given in the compound input section and 1L denotes the IL or salt phase If the IL keyword is given in the binary or nbinary input denoting a IL or salt phase to be present in the pseudo binary phase equilibrium it is necessary to define the IL or salt phase via the individual ions that form the specific IL or salt The IL or salt is pieced together from its anion s and cation s and thus its composition has to be defined in the input This is possible with the IL i j command where i j are the numbers of the ion compounds numbers as given in the sequence of compounds in the compound input section or the nIL name name command where name name are the names of the ion J compounds as given in the compound input section In addition the IL s or salts stoichiometry has to be defined for the individual anion and cation compounds The input of the IL stoichiometry factors v v is possible via the IL_n v v command where v i v are the stoichiometry numbers of the IL 3 defined by the ions as given by the IL i j OrnIL name name command For example the IL bmim BF would be defined by the combination of the option nIL 1 butyl 3 methyl imidazoliumO bf4 defining the IL composition from bmim cation 1 butyl 3 methyl imidazolium0 cosmo and tetrafluoroborate anion b 4 cosmo and the option IL_n 1 1 defining the stoichiometry of the IL or salt a simple equimolar two com
180. d for a specific temperature only because the viscosity QSPR model does not include a temperature dependency term If several conformers are present for a given compound COSMOtherm will compute the viscosity descriptors of all individual conformers and subsequently do a thermodynamic average of the conformer descriptors at the given temperature condition from which the averaged viscosity of the compound is predicted If possible the five viscosity QSPR parameters are read from the COSMOtherm parameterization file CTDATA file All current parameterizations sets of version C30_1501 include the QSPR parameters for room temperature viscosity prediction The parameters were derived from a set of 175 room temperature viscosities of organic liquids It is also possible to explicitly give the values of the five viscosity QSPR parameters in the COSMOtherm input file via the QSPR_VISC Carea Cm2 Cnring Crs Co command see below The computed liquid viscosities will be written to the mixture section of the COSMOtherm output file and tabulated in the COSMOtherm table file Suboptions of the viscosity option are QSPR_VISC Optional for viscosity computations Give the generic parameters Carea Cm2 Curing Crs Co for the QSPR approach of the liquid viscosity The arguments are or expected as real numbers The parameters are expected to be used QSPR_VISC_SI with energy values in kcal mol and areas in A2 For the Carea Cm2 Curing Crs Co QSPR_VISC_SI comm
181. d input lines might contain the following commands f name Required Give the filename of the results file of the quantum chemical or COSMO calculation for a molecule COSMO file ccf file cos file or f name cosmo mcos file The file extension cosmo identifies a COSMO file from a DMOL3 or Gaussian or Turbomole calculation whereas the extension cos identifies a f name cos COSMO file from a Mopac calculation The file extension ccf identifies or compressed COSMO file in binary format The file extension mcos identifies a f name ccf so called COSMO metafile see section 5 3 If none of these file extension are or given COSMOtherm will try to replenish the extension and search for COSMO f name mcos files or COSMO metafiles in the following order 1 Search for a file name without extension The file format i e regular COSMO file or COSMO metafile of files without extension is recognized automatically 2 Search for a file name cosmo DMOL3 Gaussian or Turbomole COSMO file 3 Search for a file name cos Mopac COSMO file 4 Search for a file name ccf compressed COSMO file 5 Search for a file name mcos COSMO metafile Note that the filename of the COSMO file must not contain blank spaces unless it is given in quotes e g f name 0 cosmo rn aaaaaa bb c Optional replaces the f name cosmo command Instead of a COSMO file filename read in a Chemical Abstracts Registry Number CAS RN The CAS RN will b
182. d one in the same sequence of compounds as given in the second input area If the values do not add up to one COSMOtherm will normalize them If less mole fractions concentrations than compounds are given the missing ones will be assumed zero Optional for binary or ternary MIX computations Define the mixture phase as real mixture with respect to activity and vapor pressure of the phase The argument of the MIXphase option is expected to be upcase 133 Suboptions of the SLE and binary i MIX or nbinary name MIX options DGfus_mix value or DGfus_mix SI value DHfus_mix value or DHfus_mix SI value DSfus_mix value or DSfus_mix SI value Dcepfus_mix value or Dcepfus_mix SI value Tmelt_mix temp or Tmelt_mix C temp or Tmelt_ mix K temp Depfus_estimate Optional Give the free enthalpy of fusion AGs for mixture composite For the DGfus_mix value option AG is expected in kcal mol for the DGfus_ mix SI option AG is expected to be in kJ mol Argument value is expected to be a real number Optional Give the enthalpy of fusion AH for mixture composite For the DHfus_mix value option AH is expected in kcal mol for the DHfus_mix SI option AH is expected to be in kJ mol Argument value is expected to be a real number Optional Give the entropy of fusion AS for mixture composite For the DSfus_mix value option AS is expected in kcal mol for the DSfus_
183. d to move between the phases according to its computed affinity to each of the phases with the side conditions that the sum over the two phases of the mass or mole numbers of the compounds stays the same mass conservation and that both phases are charge neutral neutrality condition In the example depicted above phase is the water rich phase consisting of mainly water while phase II is a lonic Liquid IL phase consisting of mainly bmim cation and PF anion Both phases contain a small amount of methanol Now if the thermodynamic equilibrium partition constants K are computed and the new equilbrium concentrations of the two phases are computed it can be seen that the majority of the water will stay in phase and only a small amount of water will move to the IL phase The same holds for the IL phase which mainly stays stable and minor portions of bmim cation and PF anion move to the water phase The polar methanol will prefer the most polar phase that allows for hydrogen bonding and thus mainly move to water rich phase i e in this example the methanol is extracted from the IL phase by the water phase At this point the two phases now consist of different 146 compound concentrations than at the start Thus the chemical potentials of the compounds in the phases will change and consequently the equilibrium partition constants K will be different Thus the computation of K has to be repeated at the new concentrations of both phases The comp
184. e No segments found in COSMO file Maximum number of segments exceeded Extreme sigma charge area values found in a molecule COSMO file of this molecule may be damaged Cannot run COSMOtherm calculation with this molecule Something went wrong in cavity construction for vdw calculation Unreasonable gas phase energy read Unreasonable COSMO or gasphase energy for a conformer of one compound was detected Please check your COSMO files Unreasonable COSMO energy for a conformer of one compound was detected Please check your COSMO files Total number of processed compounds is too large Out of memory Boundarys exceeded Memory allocation fault Memory deallocation fault The computation of analytic gradients is not possible if conformers are used The computation of analytic gradients is not possible for COSMOtherm parameter set Could not reach self consistency in chemical potential calculation Multiple compound input errors found Too many mixture options in a single mixture line The mixture is not charge neutral It is possible to override this error break with the IGNORE_CHARGE keyword All concentrations are zero Invalid temperature input Ambiguous temperature input Missing argument for temperature input Temperature is less or equal to zero Kelvin Temperature T is unreasonable for a COSMOtherm computation No concentrations or mole fractions found Missing argument for pure compound
185. e default p e 1 bar can be given by optional input keyword pref p where p is the reactions reference pressure in mbar It is also possible to give the reaction pressure in Pa pref_Pa p option in kPa pref_kPa p option in psia pref_psia p option or in bar pref_bar p option Optionally external values for 2 can be read from the input file Thus it is possible to introduce high level quantum chemistry gas phase energies to be used in eqs 5 4 5 and 5 4 6 to compute the compounds free energies and enthalpies and finally the reaction energy and enthalpy and equilibrium constant The external quantum chemical energies of the reactant compounds can be given with the keyword react_eqm E E where E are quantum chemical energies in atomic units for the reactant compounds ij iz It is also possible to give the reaction energies in atomic units Hartree react_eqm E Ej and react_eqmH E Ei option in kcal mol react_eqmC E Eiz option in kJ mol react_eqmJ E E option or in eV react_eqmV E Eiz option Equivalently the external quantum chemical energies of the product compounds can be given with the keyword prod_eqm E Ej or its variants for different energy units prod_eqmH E E52 Hartree p
186. e equilibria with COSMOtherm This is the case if the o profiles of the different conformations are very similar as for bond rotation conformations in alkane chains In such cases the thermodynamic equilibria are unaffected by the conformational ambiguity and the compound can be well described by its minimum energy conformation If however the polarity of the conformations is very different in particular if intramolecular hydrogen bond is possible in the molecule the free energy difference may change strongly between a polar solvent such as water and a non polar solvent or the gas phase In this case different molecular conformations have to be taken into account in COSMOtherm A compound j can be represented by a set of COSMO files for the conformers Input and processing of conformers is decribed in sections 2 2 and 2 4 The population of a conformer j in solvent S is calculated according to the Boltzmann distribution between states of different free energy Gf Elcosmo u equation 1 11 The multiplicity w will be assigned to each conformer by COSMOtherm based on J molecular symmetry considerations or can be given explicitly Elom E Can Yaa ns 1 11 Ecosmo Hk w exp L0 r gt i kT If the compound i is a part of the system S i e if it is present at finite dilution in S the chemical potentials u themselves depend on the conformational population Therefore equation 1 11 has to be iterated to self consistency
187. e filename inp is the COSMOtherm input file and contains a batch of commands controlling the COSMOtherm calculation It is recommended to use an input file of the form filename inp i e with a file extension inp In this case it is possible to leave out the file extension inp when invoking the COSMOtherm program However any other names and file extensions are also valid The format of and commands to be used in the input file are described in the second section The second file indispensable for the correct performance of the COSMOtherm program is the COSMOtherm parameter file COSMOtherm parameter files are identified by the extension ctd By default a parameter file of the name CTDATA ctd is read in by the program However it is possible to use COSMOtherm parameter files of any other name which can be assigned in the COSMOtherm input file see section 2 A detailed description of the COSMOtherm parameter file is given in section 3 cf also the original COSMO RS articles Note that previously COSMOtherm has been introduced as COSMO RS i e the Conductor like Screening Model for Real Solvents However since then the underlying physical model has been refined and largely extended cf reference 1 and forthcoming articles to the representation of all kinds of thermodynamics in solution Thus the program has been renamed COSMOtherm In addition the COSMOtherm program requires the so called COSMO files which are result files from qua
188. e input lines of the COSMOtherm input file see section 2 3 of this manual Thus a COSMOmic input closely resembles a simple mixture input with a pure compound solvent only temperature tc tk or tf and x pure keywords are required with the difference that the H E definition that was read in by argument of x_pure does not point to a given solvent but to the MICEL the rmic name mic option It is possible to run several COSMOmic jobs in one COSMOtherm input file e g COSMOmic jobs at different temperatures It is also possible to run other COSMOtherm jobs in the same COSMOtherm input file where the COSMOmic input is given As noted above the only restriction is that only one micelle definition per input file can be used An example input for COSMOmic is given in Example 12 keywords relevant to COSMOmic are highlighted Further information on this topic can be found in the separate COSMOmic manual Example 12 COSMOmic input with DMPC micelle and solute methanol ctd BP_TZVP_C30_1501 ctd cdir CTDATA FILES ldir licensefiles RMIC COSMOmic dmpc mic COSMOmic with DMPC micelle f methanol_c0 fdir DATABASE COSMO BP TZVP COSMO Compound input methanol tc 25 00 x pure 1 CTAB Mixture computation in solvent compound 1 methanol tc 25 00 x pure MICELLE COSMOmic computation with solvent DMPC micelle 79 A Klamt U Huniar S Spycher and J Keldenich J Phys Chem B 112 2008 12148 12157 225
189. e mapped to the according filename name cosmo or cos or ccf by COSMOtherm The use of this option requires the input of a COSMO database index file see section 2 4 dbn name Optional replaces the f name cosmo command Instead of a COSMO file filename read in a trivial name The trivial name name will be mapped to the according COSMO file filename name cosmo or cos or ccf if the trivial name is listed somewhere in the COSMO database index file This option is case insensitive The use of this option requires the input of a COSMO database index file see section 2 4 31 By default the cosmo files as requested with the f rns or don command are searched for in the current working directory or in the directory given by the global or local fdir keyword see section 2 1 A and below In addition if the requested cosmo file is not found in the given file directory COSMOtherm will search for the file in the subdirectory defined by the first character of given cosmo file filename e g given fdir home DATABASE COSMO BP TZVP COSMO and f methanol cosmo COSMOtherm first will try to open the file home DATABASE COSMO BP TZVP COSMO methanol cosmo and if this is not found subsequently try to open home DATABASE COSMO BP TZVP COSMO m methanol cosmo This additional automatic search allows the the user to store all cosmo related files in the subdirectories defined by the first character of the filenam
190. e moma Sprf name prf Spot name pot Spotc Optional Write the o moments of all processed compounds in tabulated form to file name mom If no argument is given the c moments will be written to filename mom where filename is the name of the input file In addition some other molecular information will be written to the moments file name mom including volume V molecular weight dielectric energy Egiey average energy correction dE van der Waals energy in continuum E ring vdw correction energy E and the standard chemical potential of the molecule in ring the gas phase with respect to the ideally screened state 2 Ecosmo Esas dE E aw Eng Neas Please note that 12 is not identical to the ugas as ring computed by eq 1 10 It is a simplified and temperature independent term intended for the use as additional descriptor of sigma moment QSPR For further details on sigma moments and QSPR please refer to section 5 5 Optional Write the atomic c moments of all processed compounds to file name moma If no argument is given the o moments will be written to filename moma where filename is the name of the input file If this option is used o moments will be calculated for each atom of the compounds By default the molecular c moments are written to the output file only Optional Write the o profiles of all processed compounds to file name prf If no argument is given the o profiles will be written
191. e of the solute compounds melting temperature for neutral compounds from the compound vap file or as given in the compound input section via the Tmelt temp option see section 2 2 1 above or for salts from the mixture input section see below COSMOtherm also will compute the enthalpy of fusion AH of the solute compound and print it together with the melting temperature into additional columns of the solubility table in the COSMOtherm table file The AG and AH values thus computed can be used in subsequent solubility computations for this solute compound as is taken advantage of by the solubility screening panel of COSMOtherm graphical user interface COSMOthermxX Alternatively AG can be estimated by COSMOtherm This is possible via a QSPR approach The free energy of fusion can be approximated from the following COSMOtherm descriptors using AGs E c N e V c 2 3 5 c to c are the QSPR parameters for the free energy of fusion 1 is the chemical potential of solute j in water N 9 is the number of ring atoms in compound j andV is the Volume of the compound Please note that this QSPR approach is valid only for the estimation of heats of fusion at room temperatures i e T 25 C Please note that due to a known systematic error of COSMO and COSMO RS methods for secondary and tertiary aliphatic amines it is necessary to correct the chemical potential of such compounds by a value of about 2 5 kcal mol times N A
192. e written in MDL ISIS mol format Cf also the Wmol keyword in the compound input section of the COSMOtherm input file see section 2 2 Optional Write the geometries of all processed compounds name cosmo to molecular structure files name xyz The molecular geometry will be written in Cartesian Xmol xyz format Cf also the wxyz keyword in the compound input section of the COSMOtherm input file see section 2 2 Optional Write the geometries of all processed compounds name cosmo to molecular structure files name pdb The molecular geometry will be written in Brookhaven database pdb format Cartesian coordinates Cf also the Wpdb keyword in the compound input section of the COSMOtherm input file see section 2 2 19 MSI car format see Accelrys ACCL http www accelrys com 2 Tripos mol2 format http www tripos com custResources mol2Files 21 MDL ISIS sdf format htt 22 MDL ISIS sdf format htt 23 Xmol xyz format see e g 24 Brookhaven Database pdb http www rcsb org pd p www mdli com downloads literature ctfile pdf p www mdli com downloads literature ctfile pdf http staff csc fi laaksone gopenmol help xmol_file html format The detailed definition of the pdb model can be found on the Brookhave web site b docs format pdbguide2 2 guide2 2_ frame html 29 2 1 4 3 Output of COSMO files Wecf Wgauss Optional Write compressed COSMO files for all of the compounds th
193. eccceceeeeeeeeseeeseceeeceeeceesaeeeaeseaeseeesaeeeseeeaeesaeseaeeeeeeaes 202 5 7 2 Visualization of Contact Statistics cccceccceccceceeeceeceseeeaeeeeeceeeceeeeaeeeaeceaeseeeeseeeseeeaeeeaeeeaeeeeeeaes 205 5 7 3 Creation of Cluster and lon Geometries based on Contact Statistics cccceeeeeeeeseeereeees 208 5 8 Concentration Dependent Reactions ccccecescceeeeneeeeseeeeeeeeeeeeeeseneeeeceeeeeseceeeeeseaeeeseeeesensuneeeesas 212 5 9lonic LAG UIGS 5 a teese ca veaeay Senedd th a Sohal hasta aa a a Ea a bdigbushe cad a aa aE e 214 5 10 FlatSuirt Surtace Activity haters wien beeen nou Shen T r a e E E 217 5 11 Fine Tuning of COSMO RS parameters ceccescceecceeceseeeeeceseceneceeeeaeeeaeceaeeaeeseeeseeeeaeeeaeesaeseneeeeetaes 220 Be 12 COSMONUC aa Ea a a a a a aa 225 Appendix A Pu lica OSa arana aa Ea re a a aa aa aa Ta a Ea a a a Ae aaa a Eaa Aai a ERa 226 A 1 COSMO RS COSMOtherm related Publications ecceeseeeeeeeeeeeeeeeeteaeeeeaeeeeaeeeeaeeseaeeesaeeseeeenaeess 226 A 2 COSMO related PUublications cccccccceseseeeeseceeeeeseeeeesaneeeesneeeeccaeesescaeesescaeeeeesaueeesseeeeessseeeesseess 230 WAG K atone Faved Batons has A A A E A A E AE A E A E eM toed 232 1 Introduction COSMOtherm is a program that computes thermophysical data of liquids COSMOtherm is based on COSMO RS theory A list of COSMO and COSMO RS COSMOtherm related publications can be found in Appendix A Publications All publi
194. econd table converted to the laboratory ternary framework of concentrations see sections 2 3 7 4 and 5 9 In the case of the multinary option first the regular n dimensional phase diagram information according to the multinary phase vector input is printed to a table block in the table file Each of the concentration points of the multinary phase vector given in the input will be used as starting point for an LLE search Thus for k given concentrations steps along the multinary phase vector COSMOtherm will perform k LLE searches and compute k possible LLE tie points The LLE tie points then will be printed to a second table block below the multinary VLE table For details on the computation of n dimensional phase diagrams with the multinary option see section 2 3 8 A typical ternary or multinary LLE computation output is shown below First the regular VLE output table with the mole fraction concentrations of the grid points and all computed themrdynamic properties such as HE GE pt at the grid points is printed followed by a table with the results of the LLE searches each started at the concentration grid points given in the upper table The LLE results table holds the two tie point concentrations x i and x i for the three phases i 1 2 3 If no LLE was found the values of x i and x i are set to zero The following columns of the LLE results table hold the logarithm of the activity coefficients at the tie points blank
195. ection of the COSMOtherm input file section 2 2 of this manual with the small difference that the Fwrl command is only possible in combination with a FlatSurf calculation and that the FlatSurf immersion depth between the two phases is shown on the charge surface in the form of a black and white ring where the black part of the ring points towards FlatSurf solvent phase 1 and the smaller white part of the ring point towards FlatSurf solvent phase 2 l e the ring shows how the solute molecule is immersed in the two phases 76 Lide R D Ed CRC Handbook of Chemistry and Physics CRC Press 2000 219 5 11 Fine Tuning of COSMO RS parameters It is possible to adjust the COSMO RS method to achieve better predictions for a specific system This is decribed further in the article Prediction fine tuning and temperature extrapolation of a vapor liquid equilibrium using COSMOtherm Fluid Phase Equilibria 260 2007 183 There are two principal approaches to the task of trying to obtain optimal results with respect to given reference data for a specific molecule system and a specific prediction property Both approaches are somewhat complimentary and can be used together in COSMOtherm 1 from the viewpoint of the molecule or compound it is possible to modify the COSMO charge surface of a molecule thus accounting for the deficits of the quantum chemical DFT COSMO calculations for the specific molecule used In practice such a modificat
196. ecular weight and the total screening charge of this molecule are given followed by the molecules dipole moment the four numbers are first the total sum of the dipole moment and then the x y and z components of the dipole moment vector all given in Debye The last lines of the pure compound output contain the o moments M for this molecule cf Section 5 5 as well as the corresponding sigma moments resulting from the ability of the molecule to be an acceptor or donor of hydrogen bond The value of 0 0564 for propanone in the above example indicates a slight hydrogen bonding acceptor capacity as can be expected for a molecule with a carbonyl group 165 The third part of the output file contains the information about the mixed compounds For each mixture ratio and temperatures given in the input file the information for all compounds in the mixture and optionally if the compound consists of several conformers and the wconf command is given for all of the individual molecules in the mix Example 4 shows the results for propanone in a mixture with methylene chloride at 273 0 K Example 4 Results for mixture 1 Temperature 273 000 K Compound Nr 3 1 2 Compound propanone ch2cl2 Mole Fraction 1 000 0 000 Compound 1 propanone Chemical potential of the compound in the mixture 0 89620 kcal mol Log10 partial pressure mbar x 2 08578 Free energy of molecule in mix E_COSMO dE Mu 1
197. ecule ccf will be created If the command Wecf is given with an argument Wccf name ccf a compressed COSMO file name ccf will be created The compressed COSMO files are identified by the extension ccf and can be read in by COSMOtherm just like conventional COSMO files If given in this section of the COSMOtherm input file the Wccf command is active only for the actual compound Wgauss nam cosmo Optional Write converted COSMO file for all of the COSMO files computed with the Gaussian program that are read in by COSMOtherm The charge surface of the Gaussian COSMO files are converted into a charge surfaces that are equivalent to the charge surfaces produced by Turbomole with a molecule of the same geometry Thus the COSMO files produced by this option can be used by COSMOtherm in combination with a COSMOtherm parameterization that was optimized for Turbomole i e BP_TZVP or BP_SVP_AM1 see section 3 3 By default for a molecule molecule cosmo a converted COSMO file molecule cosmo will be created If the command Wgauss is given with an argument Wgauss name cosmo a converted COSMO file name cosmo will be created If given in this section of the COSMOtherm input file the wccf command is active only for the actual compound 40 COSMO and CCF files contain all of the relevant quantum chemical information that is required for a COSMOtherm calculation of liquid thermodynamic properties A typical COSMO file looks like this info current prog
198. ed by quantum chemistry Thus a compromise between computational demands of quantum chemistry and quality of the COSMOtherm predictions has to be made A very good compromise is the optimization of molecular geometry on the computationally very cheap semiempirical MOPAC AM1 COSMO level with a subsequent single point COSMO calculation on Turbomole BP RI DFT or Gaussian03 DGA1 BP86 DFT COSMO level using the small SVP basis set Alternatively COSMO files created by the PQS Molpro or ORCA program at the same level of theory and basis set can be used with the same COSMOtherm parameter set Based on such quantum chemical COSMO calculations the best quality of the COSMOtherm prediction can be achieved with the BP_SVP_AM1 C30_1501 ctd parameterization This parameterizations also includes the optimized QSPR parameters that can be utilized by COSMOtherm to predict solids solubilities in arbitrary solvents Recommended for the screening of a large number of compounds using COSMOtherm Program Package Quantum Chemical Method COSMOtherm Parameterization MOPAC Turbomole AM1 opt BP RI DFT SVP single BP_SVP_AM1_C30_1501 ctd 3 3 3 lonic Species The treatment of ionic species does not require any special COSMOtherm parameterization The standard parameterizations can be used Although it should be noted that a high quality quantum chemistry method in combination with a large basis set is required to capture the strong polarity of the
199. eing uneven the default VLE grid tries to cover the phase space of the computed properties as comprehensive and effective as possible If a liquid liquid equilibrium LLE calculation is performed using the LLE or LLE NEW options see below section 2 3 7 2 for a closer description of these options the default grid values are modified The default VLE grid of 29 concentrations is used for binary calculations with the LLE option The iterative LLE search algorithm see below section 2 3 7 2 for details on the LLE algorithms starts from an initial guess derived from the coarse VLE default grid If the binary calculation is performed with the LLE NEW option a considerably finer default grid of 323 evenly spaced mole fraction concentrations is used The iterative LLE NEW algorithm starts from an initial guess derived from this fine grid A ternary calculation with LLE search option behaves slightly different If no other concentration options are given the ternary LLE option will compute a default grid of 33 mole fraction concentration which strides across the ternary phase space in three evenly spaced grids which all follow the same slicing pattern the phase space is crossed from one of the pure compounds towards an even 1 1 mixture of the remaining two components of the ternary phase space Unlike the binary LLE options which only perform one LLE search per binary calculation the ternar
200. elow The starting point is always a QM COSMO calculation However the time consuming QM COSMO calculations have to be done only once for each compound The results of the QM COSMO calculations i e the charge distribution on the molecular surface can be stored in a database COSMO RS then can be run from a database of stored QM COSMO calculations Thus COSMO RS is well suited for the task of screening large numbers of solvents or solutes if an appropriate database of QM COSMO calculations is available compare section 2 4 10 Flow chart of a COSMOtherm calculation Water Acetone Chloroform o potential of the mixture Fast Statistical Thermodynamics 28 8 SHbeMoRME gog rey noos eA Results Mixture Equilibrium Data Chemical potentials of all compounds Vapor pressures Solubilities Activity coefficients Partition coefficients Excess energies enthalpies Phase diagrams 80 F Liquid 55 F 50 45 F 40 35 30 25 Pyap kPa w4uayiOWSOD 11 1 2 Practical Aspects In the current implementation COSMOtherm is a command line file driven program which is run directly from a UNIX LINUX terminal window or in Microsoft Windows systems from a DOS shell cmd exe or the Windows PowerShell powershel1 exe respectively In a UNIX LINUX or DOS window COSMOtherm is invoked via cosmotherm filename inp The fil
201. en by the react i i2 Of nreact name name commands The energies E are expected to be real numbers For the keywords react Hvap and react HvapH the given energies are expected to be in atomic units Hartree for the keyword react HvapC energies are expected to be in kcal mol for the keyword react HvapJ energies are expected to be in kJ mol and for the keyword react _HvapV energies are expected to be in eV 191 Suboptions of the reaction option continued vap Hj Hy2 prod_Gsol or prod_GsolH or prod_GsolC or prod_GsolJ or prod_GsolV prod_H or prod_HvapH or prod_HvapC or prod HvapJ or prod HvapV G51 Gji ji JI H51 jl L G51 G32 see G32 os Gs e j2 j2 jpe j2 Optional for reaction computations provide external free energy of solvation energies for the product compounds The input of the product AG G is possible via the prod _Gsol G G5 _ command where Gji Gjo are the free energy of solvation values that will be used for the product compounds defined by the compound numbers or names as given by the react 3 j2 or nreact name name commands The arguments G are expected to be real numbers For the keywords prod Gsol and prod_GsolH the given energies are expected to be in atomic units Hartree for the keyword prod _GsolC energies are expected to be in kcal mol for the keyword
202. energy is expected to be in atomic units Hartree for the or keyword eqmc the energy is expected to be in kcal mol for the keyword eqmC E eqmJ the energy is expected to be in kJ mol and for the keyword eqmv the or energy is expected to be in eV eqmJ E or eqmV E eZp EZP Optional input of a molecules vibrational zero point energy E Argument or EZP is expected to be a real number For the keywords ezp and ezpH the ezpH EZP energy is expected to be in atomic units Hartree for the keyword ezpc the or energy is expected to be in kcal mol for the keyword ezpJ the energy is ezpC EZP expected to be in kJ mol and for the keyword ezpv the energy is expected or to be in eV ezpJ EZP or ezpV EZP In combination with the global uqme or uqmg Use external QM energies keywords the external gas phase molecular quantum chemical energies E and vibrational zero point energies E7 as given in the compound input section with the eqm and ezp option can be used for two purposes 1 Toggle Boltzmann weighing of conformers with the given external molecular 2 EZ energies overriding the default use of molecular COSMO file energies E in conformer equilibrium a The uqme keyword toggles the computation of conformer equilibria using E E EZE u dE i e the external QM energy contributions 2 7 plus the chemical potential in the given mixture 4 and the dielectric energy correcti
203. ent from experimental data one can apply both definitions of the mole fraction P 5 9 3 te 0 Airi i Because the pressure in eq 5 9 3 is a measured value the experimentally determined activity coefficient is dependent on the view on the system i e the definition of the mole fraction The calculated value is dependent on the interactions in the system only Because both definitions describe the same system on the molecular level it is independent of the definition of the mole fraction If x is used to obtain the experimental data the resulting activity coefficients can be compared directly with COSMOtherm predictions of y However if the x Y definition is used for the determination of the experimental data one has to apply a factor to the COSMOtherm predictions to account for the different macroscopic reference systems binary and ternary system The activity coefficient y for a system that is defined as binary system experimentally but calculated as a ternary system in COSMOtherm as done in Example 11 is defined as ternary ternary ternary __ i binary 5 9 4 i i ternary ternary 4 i x l lon Eq 5 9 4 leads to conversion equation 5 9 5 that translates the ternary COSMOtherm calculated activity coefficients to binary experimentally measured activity coefficients binary _ L l l lon a i 4 aien 5 9 5 For the calculation of an activity coefficient in infinite dilution in an IL this reduces t
204. ents file Currently COSMOtherm is shipped with the the following multi property QSPR coefficient files ADME prop A collection of the three ADME properties logK logPs and logK for BP SVP AM1 COSMO Abraham BP SVP AM1 prop Abraham linear free energy descriptors V hydrophobicity B hydrogen bond acidity S polarity polarizability A hydrogen bond acidity and E excess molar refraction for BP SVP AM1 COSMO Abraham BP TZVP prop Abraham linear free energy descriptors V hydrophobicity B hydrogen bond acidity S polarity polarizability A hydrogen bond acidity and E excess molar refraction for BP TZVP COSMO 70 Klamt A Eckert F Diedenhofen M Environmental Toxicology and Chemistry 21 2562 2566 2002 71 Zissimos A M Abraham M H Klamt A Eckert F Wood J J Chem Inf Comput Sci 42 1320 2002 195 The computation of the five Abraham linear free energy descriptors V hydrophobicity BX hydrogen bond acidity S polarity polarizability A hydrogen bond acidity and E excess molar refraction for a compound X from the according QSPR property file allows the additional possibility of directly calculating a thermodynamic property using the computed five descriptors and Abraham s linear free energy relationships for processes within condensed phases equation 5 5 3 log Pyy cy V cg BX c S Cy AX c E Cy 5 5 3 Thus the solubility or partition pro
205. ents which are assumed to be unity in COSMOtherm If a KP value is passed into the reaction option input via the K_activity K option the reference data K will be used to compute a scaling factor f K K which in return is used to scale the apparent solvent dependent equilibrium constant Kx 186 Suboptions of the reaction option react i is or nreact name name gt react _n Vi1 Viz prod j1 jz 4 or nprod name name gt prod n vVi1 Vig Required for reaction computations Define the reactant composition from compound COSMO files The input of the reactant composition is possible either via their compound numbers react i i gt command where i i gt are the numbers of the compounds as given in the sequence of compounds in the compound input section The arguments i are expected to be positive integer numbers or via their compound name nreact name name command where name name are the names of the compounds as given in the compound input section Required for reaction computations Define the reactants stoichiometry The input of the reactant stoichiometry factors vii viz is possible via the react n vi vi2 command where vii Viz are the stoichiometry numbers of the reactant compounds defined by the compound numbers or names as given by the react i ip or nreact name name commands The stoichiometr
206. eplacing the energy read from the ENERGY field This default can be disabled by the global or compound line input option E GAS MIN OFF Pt EQM Eou and E7 P E ZP Input of external quantum chemical energy and zero point vibrational energy See below for more details on the EQM and EZP options SYMMETRY N rrep or NIRREP N rrep Input of a fixed symmetry number Nirrep number of irreducible representations to be used in conformer equilibrium computations or as addition to the chemical potential of a compound via global option musym see section 2 1 3 replacing the symmetry computed from the COSMO file geometry PGROUP IT Input of a fixed point group H where I is the point group symbol e g II cs c2v D4h to be used in conformer equilibrium computations or as addition to the chemical potential of a compound via global option musym see section 2 1 3 replacing the symmetry point group computed from the COSMO file geometry The given point group symbol TI will be used to determine the fixed symmetry number number of irreducible representations N of the molecule and replace the Nirrep number computed by COSMOtherm 45 Using the xyz format the COSMOtherm energy file allows the storage of further quantum chemistry calculation results data Currently this information is not processed by COSMOtherm or COSMOthermxX Accessory data of this kind such as charges vibrational fr
207. equencies or gas phase dipole moments may be added below the xyz geometry coordinate block separated by one empty line ENERGY METHOD b p BAST S def TZVP BQMH EZP E GAS MIN SYMMETRY 0 454248850 1 237812268 0 000098685 0 044033599 0 080935387 0 000377161 1 441015399 0 260196871 0 000034548 0 893703277 0 997075240 0 000415213 H 0 558769498 1 952457654 0 000524451 H 1 894542884 0 827226585 0 000850507 H 1 653497874 1 337692988 0 011012317 H 1 903200971 0 184834546 0 890965416 H 1 908222659 0 204516002 0 877963952 Scharge formal charge of the molecule in a u 0 s2 S2 expectation value 0 Sdipole dipole moment in a u abs x y z 1 5163 0 1957 1 5036 0 00127 Ssymmetry molecular symmetry number of irreducible representations ji zpe zero point vibrational energy in a u 0 0711859 Svibration vibrational frequencies in 1 cm 10 entries per lin 17 50 220 80 417 34 510 94 526 72 651 44 815 25 945 71 1017 71 1081 92 1299 67 1350 57 1428 44 1445 31 1570 72 1712 74 2983 25 3060 46 3063 24 3495 12 3632 20 Send end of data blocks The entries in this optional accessory data block have to be separated by keyword entries which are denoted by a Dollar sign as first character The line s below the keyword entry are intended to hold the actual data It is possible to give several data blocks in a row The final data blo
208. erar It is possible to give up tO Neomp total number of compounds comp acid and comp base input fields in one logp mixture input line pH value Optional for logp computations Input of the logarithmic acidity basicity pH of the water phase for a logD distribution coefficient computation Argument value is the pH value of the water solvent phase It is expected to be a real number If no pH value is given it is assumed that the aqueous phase is neutral pH 7 104 2 3 6 Automatic pK Acidity Basicity Calculation The pKa igoivent ineutrar ron OF npKa namegoivent MAMEyeutrar Namezo Option allows for the automatic computation of the pK value of acidity basicity for a compound in a solvent isoiyent where isoivent Normally is water By default this option will compute the free energy Gyeytra Of compound ixeutra1 and the free energyG of compound izon in the solvent isoivent at infinite dilution of iyeuera and iton Subsequently the pK value is estimated from the linear free energy relationship LFER pK c a AGE AG 2 3 6 Neutral Ion The pK value is written to the COSMOtherm output file and to the COSMOtherm table file Thus to obtain a pK value it is necessary to do a quantum chemical COSMO calculation of a molecule in its neutral state and as an ion The neutral and the ionic compounds both have to be given in the input of the pK option AS ineutra ANd iron It is also possible to estimate the pK v
209. ere are three situations where the results of the SLESOL and iterative option may differ First if the solubility of a liquid is computed i e if the Gibbs free energy of fusion of the solute 4G 0 the iterative option will provide just that the liquid solubility log x In contrast the log x solubility value predicted by SLESOL option will be zero because solid liquid equilibrium SLE conditions can not be solved for if there is no solid phase Instead the liquid liquid equilibrium x and x values will be written to additional columns of the solubility table output Second if the given solute is solid with a finite Gibbs free energy of fusion AGs and the solute s virtual liquid shows a phase separation with the liquid solvent i e the SLLE case described above as noted before the iterative option may show ambiguous or undetermined results The SLESOL option will solve such a system correctly solving the solid liquid phase equilibrium conditions with the boundary condition of the virtual liquid liquid phase equilibrium If this is the case the solubility table output will show finite numbers for both the solid s log x solubility output as well as for the virtual liquid s x and x values Third in cases where the solubility is very high the iterative option may fail to converge properly or converge to miscibility where predicted log x 0 The SLESOL option may still be able to resol
210. ered to a specific value most often to a value of pH 7 4 which is the pH of blood serum and thus of significance in physiological partition Suboptions of the logp or nlogp option are pKacid Optional for Logp computations Input of experimental aqueous dissociation isolute Value constants for acidic pKacid option or basic pKbase option solutes for a or logD distribution coefficient computation Argument isoiute is the compound pkKbase number of the solute It is expected to be an integer number designating a iso1ute value compound in the sequence of the compound input Argument value is the pK acid pKacid option or pK base pKbase option value for solute isciute It is expected to be a real number It is possible to give up to Noon total number of compounds pKacid and pKbase input fields in one logp mixture input line comp _acid Optional for Logp computations Input of experimental aqueous dissociation fieiras Laon constants for acidic pKacid option or basic pKbase option solutes for a or logD distribution coefficient computation Argument jineuira is the comp base compound number of the solute It is expected to be an integer number ineutrar leation designating a compound in the sequence of the compound input Argument ianion for the pKacid option or ication for the pKbase option are the compound numbers of the ionic compounds that result from the acidic or basic dissociation reaction of the given solute iyeu
211. erface COSMOthermX The only additional step required is to copy the COSMOtherm license file into the appropriate directory see section 1 4 On first execution of the installed COSMOthermX you will be prompted for the license file which will be copied into the correct location by COSMOthermX The self extracting installer files automatically install all components of COSMOtherm The only additional step on first execution of COSMOthermX is to copy the COSMOtherm license file into the appropriate directory see section 1 4 By default the search path for the COSMOtherm license files is the directory of the COSMOtherm parameterization i e the CTDATA FILES directory The CTDATA FILES directory can be set via a keyword cdir in the COSMOtherm input file see section 2 Alternatively COSMOtherm can read the cdir location from the environment variable COSMOTHERM_HOME In a Linux environment if using sh or kshell add to your profile if using bash add to your bashrc file or using bash on Apple Mac OS add to your bash_profile export COSMOTHERM HOME yoursoftwaredir COSMOlogic10 COSMOtherm CTDATA FILES In a Windows 7 Vista XP or 2000 environment the paths can be added interactively using the System Information program If you launch the System Information program from the START menu the paths can be added in the Environment Variables section of the Software Environment
212. ergy of fusion definition for the given AGy of a salt If the DGfmean option is given equation 2 3 1b will be used to calculate the salt solubility instead of equation 2 3 1a i e the given AG data is not scaled by the salts overall stoichiometry number 99 In addition to the input of salt heat of fusion crystallization data in terms of experimental melting point and free energy enthalpy entropy or heat capacity of fusion data it is possible to compute a salts Gibbs or AG solubility value for the salt The input and processing of reference solubility is equivalent to the reference free energy of fusion AG us fu aS defined in eqs 2 3 1a and 2 3 1b from a given reference solubility input of the neutral compound solubility computation option described above Please note however that there are two complications if the solute is a salt compound consisting of several individual ion components First the input of reference mole fraction solubilities depends on the salts mole fraction definition as described above and in section 5 9 By default COSMOtherm assumes that the given reference mole fraction of the salt is given in the laboratory binary or IL binary framework where the salt is considered to be one single compound This value is converted to COSMOtherm s internal multicomponent framework where the salt is considered to consist of independent anion and cation components If the keyword pr_ILTERN is gi
213. erty calculation options continued molecular similarity calculation options similarity i j or nsimilarity nam nam sms i j or nsms nam nam Optional Toggle the automatic calculation of the molecular c profile similarity of two compounds see section 2 3 10 For the similarity i j option the similarity factor is computed for the two compounds with the compound numbers i and j in the order of compounds given in the compound input section For the nsimilarity nam nam option the similarity factor is computed for the two compounds with the compound names nam and nam as J given in the compound input section of the COSMOtherm input file i e either the names of the COSMO files without extension or the name given via the comp name option Optional Toggle the automatic calculation of the molecular o profile match similarity of two compounds see section 2 3 10 For the sms i j option the similarity factor is computed for the two compounds with the compound numbers i and j in the order of compounds given in the compound input section For the nsms nam nam option the similarity factor is computed for the two compounds with the compound names nam and nam as given in the compound input section of the COSMOtherm input file i e either the names of the COSMO files without extension or the name given via the comp name option 64 B Property calculation options continued molecular similari
214. es to avoid having to put a large number of files into one single directory which may cause trouble in old 32bit Linux systems Compound input options continued compound list and file directory input f SDATABASE 1st or rn DATABASE 1 st or dbn DATABASE 1st fdir directory mdir directory comp name Optional replaces the f name cosmo command Instead of a filename read in a database list file called 1st which holds a list of COSMO filenames for the SDATABASE 1st command or a list of Chemical Abstracts Registry Numbers CAS RN for the rn SDATABASE 1 st command or a list trivial names for the dbn SDATABASE 1st command COSMOtherm will then proceed with the filenames CAS RN or trivial names given in the database list file as if they were given in the input file A detailed description of this option is given in section 2 4 Optional Locally sets the directory where to search for the cosmo cos ccf or mcos files of the quantum chemical COSMO calculation for the compound in this compound input line Given in this section of the COSMOtherm input file the dir command is overwrites any fdir command given in the global input section It is active only for the compound input line where it is given The directory name must not contain blank spaces unless it is given in quotes e g fdir C Program Files COSMOtherm DATABASE COSMO BP TZVP COSMO Optional Locally sets the director
215. es of subsequent contact runs will be overwritten 209 Suboptions of the contact i i2 option creation of cluster and ion geometry files continued ssc_probability C n n2 ssc_strength C n no Optional Create geometry files of the most probable surface segment contacts SSC for all compounds given in the contact option with all other compounds in the mixture This option behaves similar to the ssc _ probability option described above with the difference that generation of the interaction complexes is restricted to the boundary conditions given by the arguments C n no where C is a single character that may be A or E and n and nz are integer numbers There are two possible usages of the option 1 If the character A is given the integer numbers n and n will be interpreted as atom numbers of the two compounds l e the generation of the interaction complexes is restricted to the contacts between atom n of molecule 1 and atom n of molecule 2 only Thus via the ssc probability A n n2 option complexes with specific atom atom interaction patterns can be created 2 If the character E is given the integer numbers n and n will be interpreted as element numbers e g 1 for hydrogen 8 for oxygen l e the generation of the interaction complexes is restricted to the contacts between elements n and n only Thus via the ssc _probability E n nz option complexes with s
216. es the processing of a COSMO database index file which maps the CAS RN and the compounds trivial names to the name of the according COSMO file In COSMO therm Version C21 Revision 0109 and later the database index file is searched for in a hierachical manner with highest priority the database index file is read from a directory that is one branch above the global COSMO file directory as given by the fdir command this matches the database handling of COSMO thermx the graphical user interface of COSMO therm which expects the database index file to be located one directory above the actual COSMO file directory if it is not found there it is looked for in the directory of the COSMOtherm parameter files given via the cdir command or read from the environment variable COSMOTHERM HOME if neither found above fdir nor in cdir it is searched for directly in fdir and if not found there either in the current working directory For all older versions of COSMO therm the COSMO database index file is expected to be in the directory of the COSMOtherm parameter files i e the current working directory or the directory given via the cdir command or read from the environment variable COSMOTHERM HOME By default COSMOtherm expects a COSMO database index file of the name DATABASE COSMO csv However this filename can be changed via the dbas filename command in the global command section of the COSMOtherm input file The COSMO database
217. es to a cavity format that is compliant with the COSMO construction form generally used in COSMOtherm This conversion is done automatically by COSMOtherm if a Gaussian COSMO file is detected Because this conversion is somewhat time consuming COSMOtherm offers the possibility to create a COSMO file converted to the general COSMO file format created by other quamtum chemistry programs which is read in quickly This can be accomplished by the Wgauss name cosmo keyword where the optional argument name cosmo is the name of the converted COSMO file In addition to reading of plain text COSMO files COSMOtherm allows the processing i e reading and writing of Compressed COSMO files CCF files which are identified by file suffix ccf The size of CCF files is about one ninth of plain text COSMO files thus allowing for strong savings in disc space for large databases of molecules COSMOtherm can create CCF files with the Wccf name ccf keyword where the optional argument name ccf is the name of the target CCF file Control options for the output of COSMO files and compressed COSMO files cc f files Wecf name ccf Optional Write the compound information for the processed compound to a compressed COSMO file The COSMO file information will be written in a compressed and encoded binary format that is only about 6 the size of the conventional COSMO file ASCII text file By default for a molecule molecule cosmo a compressed COSMO file mol
218. esents an older version of COSMO RS theory and shows some applications COSMO and COSMO RS Andreas Klamt in Encyclopedia of Computational Chemistry P v R Schleyer and L Allinger Editors Wiley New York 1998 pp 604 615 This book chapter in the critically acclaimed Encyclopedia of Computational Chemistry presents an overview of the COSMO and COSMO RS COSMOtherm methods and an older implementation of the method into a quantum chemistry program Conductor like Screening Model for Real Solvents A New Approach to the Quantitative Calculation of Solvation Phenomena Andreas Klamt J Phys Chem 99 2224 2235 1995 Presents the original COSMO RS approach and gives a first glimpse of its accuracy and wide applicability to chemical problems in solution 229 A 2 COSMO related publications COSMO Theory COSMO Implementation in TURBOMOLE Extension of an efficient quantum chemical code towards liquid systems Ansgar Schafer Andreas Klamt Diana Sattel John C W Lohrenz and Frank Eckert Phys Chem Chem Phys 2 2187 2193 2000 Presents the implementation of the refined COSMO into the TURBOMOLE ab initio quantum chemistry program and demonstrates its capabilities on some applications First principles implementation of solvent effects without outlying charge error Kim Baldridge and Andreas Klamt J Chem Phys 106 66622 66633 1997 Presents the implementation of the refined COSMO into
219. esults are quite poor if a COSMO file is used that was computed on such a quantum chemical level e g Turbomole BP or DMOL3 PBE Difference charges can be used to correct such defects For example the difference charge for DMSO in sequence of atoms of the COSMO file of the COSMObase database of COSMO files is del 0 03 0 023 0 023 0 023 0 085 0 007 0 030 0 023 0 023 0 023 delga Fortunately the number of molecules where DFT quantum chemical methods show such defects is small the most prominent cases being DMSO the molecular class of secondary amides and a few phosphorous containing compounds like hexamethylphosphoramide HMPT Another field of application of the difference charge concept is fragmentation of complicated molecules using COSMO metafiles For example inductive and electronic effects of substituents on aromatic rings can be simulated with the help of difference charges Thus complicated systems of substituted heterocyclic rings might be replaced by much simpler fragments that are equipped with the according difference charges 177 5 3 2 Treatment of Polymers For large molecules like polymer chains it is currently not possible to do a single quantum chemical calculation of the entire molecule Instead it is useful to compose the large molecule from smaller fragments which are calculated indepently The molecules from which the fragments are taken have to be chosen such that the fragments direct environments c
220. etween the pure compounds densities where excess density volume is neglected If no density estimate is possible a default value the liquid density of water about 997 g l is used If the solvent used as given by the henry i or nhenry name option is pure water i e if the Gibbs free energy of hydration is calculated COSMOtherm automatically will fill in the exact density of the water Thus if the Gibbs free energy of hydration is calculated it is not necessary to give the solvent density via the input 2 If Gsolv is given with argument Gsolv bar mol or Gsolv reference G of all compounds is computed in the theoretical COSMO RS reference framework i e reference state of the calculation is 1 bar of ideal gas and 1 mol of liquid solvent via GS 45 u where uf is the chemical potential of the compound in the ideal gas phase and 4 is the infinite dilution chemical potential of the compound in solution 79 Suboptions of the henry i and the nhenry name option are xh xl x2 or ch cl c2 logH Gsolv refstate solvdens value Optional for henry computations Give finite mixture concentration at which the activity coefficient shall be computed The input of the concentrations is possible either in mole fractions xh or mass fractions ch of the compounds of the mixture as real numbers xi and ci The arguments are expected as real numbers between zero and one in the same sequence o
221. example input computes the SLE solubility of aspirin in a mixed solvent consisting of chloroform and acetone Please note that the heat of fusion data input for the single pure phase aspirin 1 is given in the compound input section or vap file as usual while the input of the heat of fusion data of the composite phase 2 is given in the temperature mixture line input f aspirin c0 tmelt_k 408 1500 DHfus 2 755 f chcl3_c0 f propanone_ c0 tc 25 sle binary 1 SMIX xm 0 0 5 0 5 tmelt_mix K 180 dhfus_mix si 5 7 131 Options for pseudo binary phase diagram computations with composite mixture phases binary i MIX or nbinary name SMIX Optional for binary computations Toggle composite mixture pseudo binary phase diagram computation The input of the mixture phase is possible either via the binary i MIX command where i is the number of the solvent phase i e a neutral solvent compound with number i as given in the sequence of compounds in the compound input section argument i is expected to be a positive integer number and the term MIX denotes the composite mixture phase or alternatively by the nbinary name MIX command where name is the name of the solvent phase compound as given in the compound input section and the term MIX denotes the composite mixture phase as defined by the xm or cm options given below Note that any or both of the binary phases can be defined as MIX phases
222. eyword is a suboption of the density option and it does two things it triggers the conversion of the computed densities p to molar volumes V MW N p and ultimately free volumes VF V ri In addition the free volumes thus computed will be stored in way that they can be used by all property computation that follow later in the input and involve the combi ELBRO keyword Note that the free volume estimate thus computed has a lower priority than any input of experimental free volumes molar volumes or densities given in the compound input line or vapor pressure property file I e no experimental data will be overwritten by this step It s only purpose is to fill the gaps of the missing free volume data Now in a second step the actual polymer property computation is done In this example an activity coefficient gamma calculation is done wherein the given PDMS polymer serves as solvent The special polymer combinatorial contribution is toggled with the combi ELBRO keyword 181 5 4 Chemical Equilibrium and Reactions The equilibrium of a chemical reaction in solution can be decribed in terms of the reaction free energy of the system For an example reaction WVA B gt YC HD 5 4 1 the Gibbs free energy of reaction is defined as difference of the total free energies of the product compounds and the reactant compounds which for the example reaction 5 4 1 reads AGreacr VeGe Vp Gp Va Ga Ve Ge 5 4 2 w
223. f compounds are won from the statistical averaging in the ensemble of interacting surface pieces To describe the composition of the surface segment ensemble with respect to the interactions which depend on o only only the probability distribution of o has to be known for all compounds X Such probability distributions p o are called o profiles The o profile of the whole system mixture p o is just a sum of the o profiles of the components X weighted with their mole fraction in the mixture x o profiles give a detailed and vivid description of molecules polarity properties Some examples for the usage and interpretation of o profiles are given in section 5 2 A comprehensive overview over the properties and usage of o profiles is given in references 1 and 2 5 2 o Potentials The chemical potential o of a surface segment with screening charge density SCD o in an ensemble described by normalized distribution function p c is a measure for the affinity of the system S to a surface of polarity o It is a characteristic function of each system and is called o potential A comprehensive overview over the properties and usage of o potentials is given in references 1 and 2 The COSMO RS representations of molecular interactions namely the o profiles and o potentials of compounds and mixtures respectively contain valuable information qualitatively as well as quantitatively Figures 1 and 2 show the o profiles and the room temperature
224. f an oscillating behavior is detected in the iterations of the solubility concentrations COSMOtherm applies a sequence of techniques to force the convergence If such a forced convergence is used it will be noted in the table and output files In addition the noniterative solubility value printed to the COSMOtherm table file will be enclosed by parentheses In most cases the forced solubility value thus computed will be the correct solubility However there is one situation where the forced convergence 81 value might not be correct if at a given temperature the system shows SLLE behavior i e there is simultaneous phase separation in the liquid and precipitation of the solute to the solid phase The iterative solubility option can not resolve this behavior and in rare cases a false solubility value at the may be optimized although the error thus made should be quite small only a few percent of the solubility in general Thus to account for this special kind of phase behavior a SLE and or LLE calculation should be done for the compound SLE LLE calculations either can be performed with the binary phase diagram option see section 2 3 7 or in combination with the automatic solubility computation option solub The computation of a SLE LLE calculation as part of a solubility computation is toggled with the keyword SLESOL which is a sub option of the solub or nsolub option The SLESOL and the iterative solubility options are
225. f binary or ternary mixtures is toggled binary or ternary keywords additional output is produced The initial two three mixtures produced by the binary or ternary options are mixtures consisting of only one of the concerned compounds The output for these mixtures does not differ from the usual as described above However the outputs for the following mixtures differ For each compound i two more output lines are given The activity coefficient y and the partial pressure of this compound in the gas phase p in mbar In addition for each mixture the excess enthalpy H kcal mol and excess free energy G kcal mol as well as the composition of the mixture in the gas phase mole fractions y are given This information is also written to the file filename tab in condensed tabulated form which then can directly be visualized by a spreadsheet program Example 5 shows the table file of the binary system propanone methylene chloride at 0 C The table file lists the mole fractions of both E kcal mol the total vapor gt compounds xi the excess enthalpy and excess free energy H E G pressure above the mixture ptot mbar the partial free energies of the compounds in the mixture 166 mui RT1n xi kcal mol the logarithm of the activity coefficient 1n gammai and the mole fraction of the compound in the gas phase yi Note If not stated otherwise all energies in the COSMOtherm output or table files are
226. f compounds as given in the second input area If the values do not add up to one they will be normalized by COSMOtherm If less mole fractions concentrations than compounds are given the missing ones will be assumed zero If a negative number is given the concentration for this compound will be inserted automatically using the normalization of the sum of mole fractions Only one negative number is allowed per mixture input line Optional for henry computations Output of the Henry law constant in the table file will be written in log pressure units if the additional keyword logH is given or if the logHenry keyword is given instead of the henry keyword Optional for henry computations Output of the Gibbs free energy of solvation G as additional column in the table file If Gsolv is given without argument or if it is given with arguments Gsolv 1 1 or Gsolv molar Gj of all compounds is computed in the molar framework i e reference state of the calculation is 1 of ideal gas and 1 of liquid solvent If Gsolv is given with argument Gsolv bar mol or Gsolv reference G of all compounds is computed in the COSMO RS reference framework i e reference state of the calculation is 1 bar of ideal gas and 1 mol of liquid solvent Optional for henry Gsolv computations Optional input of the solvent density as used in the computation of the molar Gibbs free energy of solvation The argument value is expected to be the density value of the
227. f however a temperature and a mixture concentration are given the PROPQSPR command will toggle the computation of the given QSPR property for all compounds This means that if several conformers are present for a given compound the computed values of QSPR properties of the conformers will be averaged due to the Boltzmann distribution of the conformer s total free energy at the given temperature and mixture conditions The averaged compound QSPR properties thus computed are written to the COSMOtherm output and table files If the keyword smomc file momc option is used in combination with the PROPQSPR mixture option an additional tabulated file with the averaged compound QSPR properties and the averaged o moments will be written to an additional compound o moments file which is identified by the file extension momc The filename of the momc file can be given as argument of the smomc keyword If no argument is given the momc file will obtain the name of the current COSMOtherm input file By default the PROPQSPR mixture option only writes the molecule or compound QSPR properties to the COSMOtherm table file With keyword pr_mom an additional five QSPR descriptors will be printed to the COSMOtherm table file The five descriptors printed are the ones that have proven to be most significant for c moment QSPR applications They are the molecular surface area A the second and third c moment MX and M as well as the third hydrogen bonding
228. f more than two phases are defined via input of npnase all additional phases can be defined accordingly c3 x t ct ci wu c4 s c c 05 ud etc Clearly if the input of relative amounts of substance in a phase i e mole or mass fractions x or c is used there is no mole number or mass conservation Consequently the addition of solute compound is not possible for the mole or mass fraction based LIQ EX computations The converged relative concentration of the compounds in the npnase Phases is based on the thermodynamic equilibrium and phase neutrality only Only the relative amount of compound in a phase is defining the system This is equivalent to the free equlibration that is used in solubility or LLE phase diagram calculations In fact a LIQ EX computation in mole or mass fractions x or c basis of two compounds that show phase separation will converge to the LLE miscibility gap of this system The output of the converged system computed in the mole or mass fraction basis will return the mole fractions x x of the compounds in the new equilibrium phases and II to the COSMO therm table file In addition for each phase equilibrium iteration step the phase equilibrium constants K and the associated equilibrium concentrations x K7 1 K are written to the COSMO therm output file Optionally the converged phase equilibrium constants K7 the associated phase equilibrium concentrations x and the chemical poten
229. f the COSMOtherm input file with option Dcpfus value see section 2 2 1 If no Dcpfus value is given it is assumed zero Because ACp us is a property that is not readily available by experiment but at same time quite often a non neglible property it has been proposed that the estimation of ACp AS 5 AHius Ter is closer to the physical reality for 28 Prigogine l R Defay R Chemical Thermodynamics Longmans Greeen London 1953 29 Neau S H Bhandarkar S V and Hellmuth E W Pharm Res 14 601 1997 83 nonspherical and neutral molecules than the assumption that ACp 0 Please note that the ACp estimate shows unphysical behavior if the absolute zero point temperature is approached Thus we recommend to use the ACp estimate only if two prerequisites are met 1 the solute compounds are neutral and nonspherical and 2 the temperature is over 150 K In COSMOtherm the ACp estimate is toggled by the keyword dcpfus_estimate which can be given either in the global input lines see section 2 1 or for specific compounds in the compound input line see section 2 2 1 or in the mixture input line where the solubility calculation is defined A different pathway to the determination of AG from experimental data is the computation of reference solubility if the experimental solubility of a given solute in a given solvent or mixture at a given temperature is known this reference solubility x can be used to deter
230. f the solute is a base B x x showing the dissociation reaction B H O BH OH in water the concentration of the dissociated ionic species Xp X 4 is computed by equation 2 3 4 3 employing the base s aqueous dissociation constant pK base and the pH of the aqueous phase Coys Ly olen pkw 1 1oCrH 2rKw 4 cs 10 base pK 2 3 4 3 Equations 2 3 4 2 and 2 3 4 3 were derived from the law of mass action of a dissociating system in a buffered solution using the self dissociation constant of water pKy 14 By default COSMOtherm will apply eq 2 3 4 2 to all solutes denoted as acids whose aqueous pK acid is given and eq 2 3 4 3 to all solutes denoted as bases whose aqueous pK base is given Equations 2 3 4 2 and 2 3 4 3 can be simplified using the additional assumption of an unbuffered solution i e the initial concentration of the dissociated water H O0 and OH is zero which leads to the well known Henderson Hasselbalch equation which for an acids dissociation reaction HA H O A H 0 holds C Cg 10 PH PKo acid 2 3 4 4 34 Henderson L J Am J Physiol 21 1908 173 Hasselbalch K A Biochemische Zeitschrift 78 1917 112 92 For a base B showing the dissociation reaction B HO BH OH the Henderson Hasselbalch correction term holds Ce E C5 10 K base pH BH 2 3 4 5 Please note that the Henderson Hasselbalch equations 2 3 4 4 and 2 3 4 5 are based upon the side condition
231. f the solutes have to be taken into account and the selectivity is defined as Sif x 1 X PP YIPP Y 5 3 4 The relative polymer solubility calculation method thus sketched typically is not sufficient to provide absolute or quantitative predictions of the solubility in polymers However with sufficient experimental data available a regression analysis can be done outside COSMOtherm e g a empirical regression of computed 1 y with experimental x data which then can be used to predict quasi absolute solubilities for a given polymer solvent Computation of absolute solubility in a polymer In addition to the relative or with the help of external data regression semi quantitative prediction polymer solubilities presented above COSMOtherm also offers an absolute and quantitative prediction method for polymer properties The absolute prediction of systems that contain polymers involves two modifications of the COSMO RS theory First because in COSMOtherm the polymer is represented by a small molecular fragment e g by a monomeric repeat unit of the polymer chain the absolute prediction of the polymer properties needs to take into account the apparent molecular weight of the polymer MW ome Second the combinatorial contribution to the chemical potential which was derived from molecular size and shape considerations see section 1 1 has to be replaced by a special combinatorial term that accounts for free volume effects and thus can
232. fferent phases As a consequence LIQ EX performance may be sped up in austere cases It is also possible to define one of the given phases as a gaseous vaporization phase This can be done with the GASEOUS k command where argument k is the phase presumed to be the container for the evaporation of the volatile compounds The functionality of the gas container is described in the figure below It describes the vapor liquid liquid equilibrium of two separated liquid phases a water phase and a wet octanol phase with an additional vaporization container This system can be described by a three phase LIQ EX 3 calculation where phase Ill is defined as vaporization phase via input option GASEOUS 3 The final distribution of the compounds between the three phases corresponds to the vapor liquid liquid equilibrium VLLE of the octanol water system The phase equilibrium constants K of the transition between a liquid phase and the gaseous vaporization phase are computed according to the gas phase free energy of the compound at the given mixture concentrations i e 44 48 Thus the chemical potential of the compound in the gas phase is computed in this case The chemical potential in the gas phase is 45 is computed in accordance with the pure compound vapor pressure estimate used i e it is either computed from a given experimental pure compound vapor pressure value or if no experimental data is available for the compound estimated by COSMO
233. flected the much stronger hydrophilicity of water in comparison to hexane The shape of the outer regions of the o potential is due to hydrogen bonding If a hydrogen bond donor in another compound has a SCD that is greater than 0 01 e A or if a hydrogen bond acceptor has a SCD that is below 0 01 e A it can build hydrogen bonds with water The o profile of acetone is not symmetric The peak at 0 012 e A resulting 171 from the carbonyl oxygen indicates hydrogen bonding acceptor capacity However unlike water there is no corresponding peak in the hydrogen bonding donor area Therefore the interaction of acetone with itself is very unfavorable explaining its relatively low boiling point and surface tension This is also reflected in the o potential While on the positive side it shows almost parabolic behavior no hydrogen bonding donor capacity on the negative side it quickly becomes strongly negative Compared to water the hydrogen bonding acceptor capacity of acetone is stronger which is reflected in the smaller o values at which the o potential becomes negative The o profile of chloroform shows three peaks in the region around zero that derive from the chlorine atoms The peak at 0 013 e A correspond to an acidic hydrogen atom But due to quite small area of this peak no significant hydrogen bonding donor capacity can be expected from this hydrogen atom This is clearly visible from the o potential which is not getting negative in the re
234. for VLE calculations the LLE search uses a grid of 3 11 concentrations scanning the three dimensional phase space along the concentration vectors that lead from each pure compound to an equimolar mix of the two other compounds respectively Each of the concentration points of the ternary phase vector given in the input will be used as starting point for an LLE search Thus by default COSMOtherm will perform 33 LLE searches and compute 33 possible LLE 43 Prausnitz J M Lichtenthaler R M and Azevedo E G Molecular Thermodynamics of Fluid Phase Equilibria 3 ed Prentice Hall PTR Upper Saddle River NJ 1999 118 tie points As an alternative it is possible to compute the LLE tie points on a given grid of concentration points along a concentratin vector The input format of this is the same as for the multinary option and is described in section 2 3 8 The ternary computation in combination with the LLE option will produce two table blocks in the COSMOtherm table file first the regular multinary VLE table for 33 default or the given concentrations Second a table with the LLE tie points and related properties It is possible to use one or more lonic Liquids phases in a ternary computation see section 2 3 7 4 If one or more lonic Liquids phases are defined in the input then in addition to the VLE and LLE table blocks a third table block will printed to the table file This third table holds the information of the LLE tie points of the s
235. g A solutes aqueous dissociation constant pK acid or pK base value may either be given to COSMOtherm as additional input in the vap file compound input line or logp option mixture input line or it may be estimated by COSMOtherm using the pK prediction methodology described in section 2 3 6 of this manual There are three possibilities to enter a compounds aqueous dissociation constant pK acid or pK base specify the pK value in the compounds vapor pressure property vap file using the pK_acid value or pK_base value option see section 2 2 specify the pK value in the compound input line using the pK_acid value or pK_base value option see section 2 2 specify the solute compound and the pK value in the solub option mixture input line using the pKacid isoiute value or pKbase igoiute value options where igoiute is the number of the solute compound as given in the collating sequence of compounds in the compound input see below As an alternative to the input of the solute pK values COSMOtherm may also compute an estimate of a solutes pK acid or pK base using the Linear Free Energy Relationship pK LFER described in section 2 3 6 In the framework of solubility calculations the pK estimate for acidic and basic solutes is toggled by the comp_acid iyeutra1 ianion and comp_base inyeutrar ication Options given in the solub option mixture input line Therein iyeutrar is the number of the solute compound as
236. ge of the sum of the COSMO charges of the fragments given in the mcos file i e a neutral mcos file will be neutralized to charge 0 a single cation s mcos file to charge 1 or by the atom weights of a given compound respectively If the compound cmet option is given with the optional argument q the meta compound defined by the mcos file or the compound s atom weights will be neutralized to match the given charge q The argument neutralization charge q is expected to be an integer charge number in atomic units a u If a real number charge q is given it will be rounded to the nearest integer number By default i e if no cmet keyword is given all COSMO metafiles and atom weighted compounds will be neutralized to neutrality i e q 0 a u The usage of atomic weights COSMO metafiles and difference charges is explained in section 5 3 Atomic Weights and COSMO Metafiles 35 Compound input options continued miscellaneous options SMC c co Optional Give o moment coefficients for this compound as real numbers c separated by blanks See section 5 5 for a detailed description of the usage of o moment coefficients If less than seven or nine compare section 5 5 coefficients are given the missing ones are assumed zero If more than seven nine coefficients are given the superfluous ones will be ignored IEI i Optional Give one or several interaction energy indices IEI numbers for this or
237. ght prefactor accounts for cases where it is possible to form a conformer in several different ways The conformer weight prefactor is determined automatically via comparison of the symmetry properties of all conformer geometries found in a conformer block The automatic use of symmetry for determining the weight prefactor of the conformer distribution can be disabled by the global nosym option see section 2 1 3 Note that for COSMOtherm parameter sets C30 1501 and later the symmetry prefactors to conformer distribution are switched off by default Alternatively it is possible to give a conformer weight factor in the input using the we value command overriding the default derived from symmetry considerations The gas phase energy confortmers can be weighted independently using the wg value command It is possible to use zero as argument of the wc or wg command which means that the cosmo or gas phase energy conformer of the compound input line where the wc or wg command is given will not be used in the conformer equilibrium As an example of an explicit choice of the conformer weight prefactor the input lines for a mixture of the two compounds glycerol composed of three conformers with zero one and two internal hydrogen bonds and water are shown in Example 1 Example 1 ctd BP TZVP_C30 1501 ctd 15 Global command line wcmn wconf 2 Global command line Glycerol conformer equilibrium in Water Comment line f h2o0 cosmo co
238. gion of large positive o values As for the acetone the asymmetric shape of the o profile indicates an unfavorable interaction of chloroform with itself again resulting in a relatively low boiling point It should be noted that the o profiles of acetone and chloroform are almost complementary in the region of misfit interactions i e for o values between 0 008 and 0 008 e A This means that they should mix quite favorably This is in fact the case as can be seen from the strongly negative excess enthalpy of acetone chloroform mixtures see also section 3 1 To sum up one can say that o profiles and o potentials can be used to qualitatively interpret the interactions in a compound or a mixture e g to assert a certain solvent or co solvent which has a certain effect on the activities in a solution or mixture Figure 1 o profile water acetone chloroform hexane 0 025 0 02 0 015 0 01 0 005 0 0 005 0 01 0 015 0 02 0 025 o elA Figure 2 o potential p o kcal mol A water acetone chloroform hexane 0 025 0 02 0 015 0 01 0 005 0 0 005 0 01 0 015 0 02 0 025 o elA 172 5 3 Atomic Weights and COSMO Metafiles In most of its typical applications COSMOtherm is intended to treat complete molecules as one entity In such a case obviously all atoms of the compound have to be taken into account in the calculation of the sigma profile This corresponds to
239. given in kcal mol and in kJ mol if UNIT STI is used All pressures are given in mbar and in kPa All temperatures are in K Example 5 Results for binary mixture of propanme 1 ch2cl2 2 at T 273 15 K energies are in kcal mol temperature is in K pressure is in mbar x1 x2 HE GE ptot mul RTin xl m2 RTIn x2 1n gamma 1n gamma2 yl y2 0 00000 1 00000 0 00000002 0 00000002 64 178922 11 68211827 2 92362731 1 48397517 0 00000002 0 000000 1 000000 0 00001 0 99999 0 00001739 0 00000808 64 177329 7 93194468 2 92363274 1 483 4630 0 00000004 0 000000 1 000000 0 00100 0 99900 0 00173772 0 00080556 64 019027 5 43028662 2 92417195 1 48108609 0 00000276 0 000032 0 999968 0 01000 0 99000 0 01723917 0 00798484 62 540353 4 16615949 2 92916929 1 45516100 0 00015797 0 000336 0 999664 0 02000 0 98000 0 03416940 0 01581217 60 815493 3 77430768 2 93492503 1 42652086 0 00060761 0 000718 0 999282 0 05000 0 95000 0 08307495 0 03834306 55 153272 3 23081039 2 95349855 1 34169474 0 00372928 0 002206 0 997794 0 10000 0 90000 0 15810329 0 07268951 44 297902 2 11913120 2 98896557 1 20400624 0 01499196 0 006248 0 993752 0 15000 0 85000 0 22478782 0 10297503 32 148097 2 48800367 3 03029611 1 07206410 0 03396402 0 013324 0 986676 0 20000 0 80000 0 28277002 0 12914633 19 323528 2 26350429 3 07777919 0 94622045 0 06080277 0 025305 0 974695 0 25000 0 75000
240. given in the collating sequence of compounds in the compound input and ianion ANd ication are the compound numbers of the anion and cation compounds that are formed on acidic and basic dissociation of the solute compound respectively Please note that the pK LFER estimate of pK acid or pK base values requires the presence 2 Po Henry N Senozan N M J Chem Educ 78 2001 1499 93 of COSMO files of the dissociated species A or BH which form from solute via the acidic or basic dissociation reaction For more details on the pK LFER methodology see section 2 3 6 The pH of the aqueous phase is assumed to be 7 0 This value can be changed by the input option pH value Please note that for measurements of solubility of drugs the pH of the aqueous phase is buffered to a specific value most often to a value of pH 7 4 which is the pH of blood serum and thus of significance in physiological partition Dissociation correction DC suboptions of the solub or nsolub option pKacid isoiute value or pKbase solute value comp acid yeutral lanion or comp _base ineutral ication pH value use_HH Optional for solub computations Input of experimental aqueous dissociation constants for acidic pKacid option or basic pKbase option solutes for a logD distribution coefficient computation Argument isoiute is the compound number of the solute It is expected to be an integer number desi
241. gnating a compound in the sequence of the compound input Argument value is the pK acid pKacid option or pK base pKbase option value for solute isoiute It is expected to be a real number It is possible to give up tO Neomp total number of compounds pKacid and pKbase input fields in one logp mixture input line Optional for solub computations Input of experimental aqueous dissociation constants for acidic pKacid option or basic pKbase option solutes for a logD distribution coefficient computation Argument iyeutra1 S the compound number of the solute It is expected to be an integer number designating a compound in the sequence of the compound input Argument ianion for the pKacid option or ication for the pKbase option are the compound numbers of the ionic compounds that result from the acidic or basic dissociation reaction of the given solute iyeuerai It is possible to give up tO Neomp total number of compounds comp acid and comp base input fields in one logp mixture input line Optional for solub computations Input of the logarithmic acidity basicity pH of the water phase for a logD distribution coefficient computation Argument value is the pH value of the water solvent phase It is expected to be a real number If no pH value is given it is assumed that the aqueous phase is neutral pH 7 Optional for solub computations Use Henderson Hasselbalch dissociation correction instead of default buffered solution term 9
242. h for the cosmo cos or ccf files of the quantum chemical COSMO calculations Default is to search in the current working directory The directory name must not contain blank spaces unless it is given in quotes e g fdir C Program Files COSMOtherm DATABASE COSMO BP TZVP COSMO Optional Sets the directory where to search for the cosmo or ccf files of the quantum chemical COSMO calculations that are requested from COSMO metafiles See section 5 3 for details Default is to search in the current working directory or if given in the directory set by the fdir command The directory name must not contain blank spaces unless it is given in quotes e g mdir C Program Files COSMOtherm DATABASE COSMO BP TZVP COSMO Optional Sets the directory for COSMOtherm output file Default is to use the current working directory The odir option also redirects the output of all other output and table files i e c profile potential and name tab files The directory name must not contain blank spaces unless it is given in quotes e g odir C Program Files COSMOtherm Output Optional Sets the directory where to search for L moment QSPR coefficient name prop files By default the CDTATA FILES directory as given by the cdir command or as read from the UNIX or Windows environment variable COSMOTHERM_HOME is used for PDIR Note that the pdir command in the input file overrides this default The directory name must not contai
243. halpies of sublimation to the COSMOtherm output file In addition the total sublimation pressure of the mixture 73 and the total enthalpy of sublimation are written to additional columns of the py p vs T table in the COSMOtherm table file The pvap pressure mbar or pvap_SI pressure kPa options allow for the iterative optimization of the temperature for a given vapor pressure The temperature of the system is varied until difference of the COSMOtherm prediction of the total vapor pressure and the given value of pressure is below a certain accuracy threshold Thus the iterative pvap pressure option allows the automatic calculation of a compounds boiling point at a given pressure The default value for the accuracy threshold of the vapor pressure prediction is 10 mbar It is possible to change this value using the thresh pvap Ap mbar or thresh pvap SI Ap kPa options Alternatively it is possible to use a relative accuracy threshold thresh_pp p which sets the accuracy of the iterative pressure optimization to p percent of the given reference pressure During the optimization of the temperature for each temperature and for each compound in the mixture the partia vapor pressures the chemical potential of the compound in the gas phase and its enthalpy of vaporization are written to the COSMOtherm output file If convergence is reached i e if the required accuracy threshold is met the tota vapor pressure of the mixture is written
244. he solubility section 2 3 4 keyword Dcpfus_ estimate may also be used in binary salt SLE computations However following the considerations taken in section 2 3 4 the ACp estimate should be used with great caution if salts or lonic Liquids are involved All of these input options expect net salt data values that are defined for the salt as defined in composition and stoichiometry by the IL and IL_n commands Thus no individual ion heat of fusion data can be used for SLE computations Please note that similar to considerations on salt solubility or lonic Liquid activity coefficient calculations see sections 2 3 4 and 5 9 of this manual respectively for IL SLE computations some care has to be taken in the interpretation of the COSMOtherm results for the computed SLE mole fraction To compare the computed salt mole fraction with experimental data depending on the reference state of the SLE measurement it may be necessary to convert the computed SLE mole fraction value along the guidelines given in section 5 9 lonic Liquids of this manual 125 What has been noted above for binary IL computations also holds for ternary IL computations with a few important differences however the ternary option does not allow solid liquid equilibrium computations SLE option nor is it possible to search for spinodal liquid liquid equilibrium points lle new option The regular binodal liquid liquid equilibrium search LLE option see sect
245. here v are the stoichiometry indices of the reacting compounds and G are the total Gibbs free energies of the reacting compounds in the given solution Please note that the total Gibbs free energy G contains an entropic ideal mixture contribution of RTIn x if compound k is present in the mixture at a finite concentration In a similar way the enthalpy of reaction is defined as difference of the liquid enthalpies of the product compounds and the reactant compounds which for the example reaction 5 4 1 reads AHpeact VeHe VpHp vH Vg He 5 4 3 where w are the stoichiometry indices of the reacting compounds and H are the liquid enthalpies of the reacting compounds in the given solution The equilibrium constant of the reaction can be computed from the Gibbs free energy of reaction Kpreact XP AGgeacr RT 5 4 4 Using eqs 5 4 1 to 5 4 4 it is also possible to estimate reaction barriers and kinetic constants of reactions To do this a pseudo reaction has to be defined wherein the reactions transition state A B is the product compound y A vgB va A B Thus the transition state geometry of the reacting compounds has to be optimized on quantum chemical cosmo and gas phase level and the transition state s COSMO file has to be used used as the product compound of this pseudo reaction The reaction Gibbs free energy as computed by eq 5 4 2 then corresponds to reaction barrier height which via Arrhenius equation
246. herm will do this conversion automatically and print the mole fraction of the LLE as additional lines to the output and table file LLE point found at x 1 0 20067648 x 2 0 79932352 and x 1 0 99707420 x 2 0 00292580 T 298 15 K LLE IL BINARY x 1 0 33427236 x 2 0 66572764 and x 1 0 99853496 x 2 0 00146504 T 298 15 K Spinodal LLE point x 1 0 51250000 x 2 0 48750000 and x 1 0 97250000 x 2 0 02750000 T 298 15 K Spinodal IL BINARY x 1 0 67768595 x 2 0 32231405 and x 1 0 01394170 x 2 0 98605830 T 298 15 K The first and third lines are describing the binodal and spinodal LLE points in the pseudo binary framework in analogy to the LLE computations of neutral compounds The second and fourth lines denoted by the phrase IL BINARY are the additional output lines that are given only for IL LLE computations They contain the binodal and spinodal LLE points converted to the laboratory binary framework respectively Please note that this conversion between pseudo binary and laboratory binary framework is done for the values of the binodal and spinodal mole fractions of the miscibility gap only The body of the binary phase diagram table uses the pseudo binary definition throughout 124 It is also possible to compute solid liquid phase equilibria SLE for pseudo binary solutions with an lonic Liquid or salt phase An IL SLE co
247. hich holds the molecular geometry the cosmo_energy section which holds the quantum chemical energy and the segment information section which holds the molecules sigma surface In addition to these mandatory fields it is possible to pass over some accessory compound information in a COSMO file in the cosmo_info section of the COSMO file The cosmo_info section may include the CAS registry number the sum formula or the molecular weight of the given molecule Moreover the cosmo info section can also be used to provide COSMOtherm with information specific to the given molecular conformation or specific to the COSMO file of the molecule Please note that all of entries in the Scosmo_info field of the COSMO file are fixed format and case sensitive l e they have to given in the COSMO file in the exact formats described in the list below 41 Currently the following COSMO file information fields can be processed and used by COSMOtherm Single point energy a u E_GAS SP Input of a gas phase single point energy E_GAS SP which will be used as fallback value if no gas phase energy file see section 2 2 2 is read in the COSMOtherm input N 2 EST n Input of the molecules squared refraction index n This input will overwrite the default refraction index estimate computed by COSMOtherm but it will be overwritten by the refraction index input from a vapor pressure property file or from a compound line input see
248. hould be used only if the solubility is expected to be small log io x gt lt 3 Ill If the keyword wfract is given in addition to the solub keyword the normalized mass fraction solubility is computed W L waT SOL MW xO MW 1 x5 MWoivent Please note that if at the given conditions a compound is miscible with the solvent i e if the logarithm of the mole fraction solubility is zero the mass based solubility is not well defined and thus it will not be printed to output and table file Finally if the density of the solvent and solute is known or can be estimated the decadic logarithm of the molar solubility of the solute in the solution log S mol I logig xpO Veoiution Will be written to an additional column in the COSMOtherm table file The molar volume of the solution Vsoiution Psotution MW solution according to the solubility x6 computed The density of the solvent or solvent mixture soven Can be provided to COSMOtherm via the the solvdens keyword If sovent Is NOt given in the input COSMOtherm is calculated from the molar masses and densities of the given solvent Pyoyen aNd solute p will try to estimate the solvents density with the liquid density volume QSPR method as described in section 2 3 12 Please note that for solvent mixtures the density estimate is a linear interpolation between the pure compounds densities where excess density volume is neglected The density of the solute p also
249. ial noise level Prediction fine tuning and temperature extrapolation of a vapor liquid equilibrium using COSMOtherm Andreas Klamt and Frank Eckert Fluid Phase Equilibria 260 183 189 2007 Presents a novel approach for fine tuning and adjustment of COSMOtherm predictions to experimental data Article DOI 10 1016 j fluid 2007 07 055 Prediction of Solubility with COSMO RS Frank Eckert in Developments and Applications in Solubility Trevor Letcher Ed The Royal Society of Chemistry UK 2006 ISBN 0 85404 372 1 ISBN 13 978 0 85404 372 9 This book chapter presents the COSMOtherm methodology for and application of the prediction of the solubility of neutral compounds and organic salts in water and non aqueous solvents Prediction of Blood Brain Partitioning and Human Serum Albumin Binding Based on COSMO RS Moments Karin Wichmann Michael Diedenhofen and Andreas Klamt Journal of Chemical Information and Modeling 47 228 233 2007 Presents QSPR models for blood brain partitioning logBB and human serum albumin binding logK HSA of neutral molecules on the basis of COSMO RS sigma moment descriptors Article DOI 10 102 1 ci600385w Accurate prediction of basicity in aqueous solution with COSMO RS Frank Eckert and Andreas Klamt Journal of Computational Chemistry 27 11 19 2006 Presents COSMOtherm methodology for and application of the prediction of pK basicity Abstract Article DOI 10 100
250. if no LLE was found and the temperature and total pressure at the tie points Results for ternary mixture of toluene 1 methanol 2 h2o 3 at T 323 15 K energies are in kcal mol pressure is in mbar molecular weights 1 92 1390 2 32 0420 3 18 0153 xl x2 x3 H E GE ptot 1 RTIn x1 mu2 RT1n x2 mu3 RTIn x3 1n gamma1 1n gamma2 1n gamma3 yl y2 y3 1 00000000 0 00000000 0 00000000 0 00000000 0 00000000 124 090099 4 33260921 0 00000000 0 00000000 0 00000000 3 32577236 5 02134966 1 00000000 0 00000000 0 00000000 0 90000000 0 05000000 0 05000000 0 27242388 0 19096273 396 373839 4 36078897 3 09222698 2 26912402 006148506 1 9762 3 12759347 0 29962447 0 26031442 0 0 80000000 0 10000000 0 10000000 0 38101410 0 31831547 420 747541 4 37147457 2 99987182 0 16263078 1 16284605 49223192 0 27761005 0 o 0 70000000 0 15000000 0 15000000 043011566 040736255 420 018346 4 37267678 2 97338048 0 29429035 0 79862755 2 05640003 0 27757196 0 o 0 60000000 0 20000000 0 20000000 0 43836032 0 46433389 412 557200 4 36462003 2 96533601 2 29026807 0 46098526 0 52347060 1 70837814 0 28615910 0 0 40910653 0 50000000 0 25000000 0 25000000 0 41304220 0 49105619 404 190128 4 34608203 2 96205170 2 33956024 0 67217020 0 30544068 1 40848742 0 30063618 0 0 38672656 0 40000000 0 30000000 0 30000000 0 35721649 0 48701850 398 068980 2 95605881 2 39662038 0 94337073 0 1 1 13732409 0 32028713 0 o 0 30000000 0 350000
251. ighted with their mole fraction in the mixture x xp o ies 1 4 Using e 6 0 E qylo 0 Eyglo 0 Em0 0 a et the chemical potential of a surface segment with SCD o in an ensemble described by normalized distribution function p o is given by plo Fm f p lo en Sa a ela o lo as 16 Abrams D S and J M Prausnitz AIChE Journal 21 116 1975 Us c is a measure for the affinity of the system S to a surface of polarity o It is a characteristic function of each system and is called o potential Eq 1 5 is an implicit equation It must be solved iteratively This is done in milliseconds on any PC A detailed description and a rationale of this statistical averaging procedure are given in reference The COSMO RS representations of molecular interactions namely the o profiles and o potentials of compounds and mixtures respectively contain valuable information qualitatively as well as quantitatively A detailed description of these features is given in sections 5 1 and 5 2 The chemical potential the partial Gibbs free energy of compound i in system S is readily available from integration of the c potential over the surface of i expressed in terms of the unnormalized o profile po wo u f p o u odo 1 6 ui is a combinatorial contribution to the chemical potential Starting with Version C1 2 the COSMOtherm program includes a generic expression for the combinatorial contribution to the chemical
252. ilibrium of the goven binary VLE for Azeotropes using an iterative self consistent algorithm which computes additional mixture concentrations points azeo iter thresh valu Optional for binary computations with iterative azeotrope search give the accuracy threshold for the iterative refinement of the azeotropic point calculation Argument value is expected to be a nonzero positive real number Default is azeo iter thresh 1 0E 5 maxiter azeo value Optional for binary computations with iterative azeotrope search give the maximum number of iterations for the iterative refinement of the azeotropic point calculation Argument value is expected to be a nonzero positive integer number Default is maxiter azeo 500 114 2 3 7 1 Activity Coefficient Model Computation for Binary Mixtures If using the binary option COSMOtherm offers the possibility to correlate the evaluated data with activity coefficient models such as the non random two liquid NRTL model Wilson s equation and the UNIQUAC model simply by giving the keywords NRTL WILSON UNIQUAC2 or UNIQUAC4 in combination with the binary command If the NRTL command is used selected activity coefficients of the binary computation are fitted to the NRTL equation 2 G T G In y x ral 21 12712 2 3 8 Xi XG X X G G exp at G exp ar The three adjustable parameters of the NRTL equation tiz T23 and a are fitted to the C
253. imple shortcut for solvents e g if only one side of the SLE is looked at and the other side is considered a liquid solvent with unknown AG In addition to the SLE computation of two neutral compounds the binary SLE option allows for the definition of a multicomponent phase i e one of the phase is defined as a ionic liquid a salt or a cocrystal This requires the additional input of two types of data the definiton of the multicomponent phase and the input of the multicomponent phase free energy of fusion The definition of the multicomponent phase is identical to the input of a ionic liquid phase in a binary VLE phase diagram which is described in section 2 3 7 4 The input of the multicomponent phase free energy of fusion is identical to the input of a salt free energy of fusion described in section 2 3 4 Suboptions to binary SLE computations Depfus_ estimate Optional for the input of a temperature dependent compound free energy of fusion via input of enthalpy or entropy of fusion AH or ASus and melting point T toggle the approximation of the heat capacity of fusion as ACpy AS AHiy Time The value of AG 7 thus obtained wil be used to compute the SLE of the binary system If the Depfus_ estimate keyword is given in binary mixture SLE computation input line the approximation to ACp is valid for all compounds and the given mixture line SLE iter thresh valu Optional for a SLE computation give
254. index file is expected as a plain ASCII text file in the comma separated file CSV format i e all entries are separated by commas The CSV format can be written by all common spreadsheet programs such as Microsoft Excel or Lotus 123 The first entry in the index file has to be the compound name followed by the CAS RN the molecular weight the sum formula and a trivial name 1 butanol 000071 36 3 74 1224 C4H100 BUTANOL 2 butanol 000078 92 2 74 1224 C4H100 S BUTANOL The CAS RN is expected in the form aaaaaa bb c and must not exceed 11 digits including the separators The leading zeroes of the CAS RN might be left out i e it is possible to give 79 09 4 instead of 000079 09 4 This also holds for the rn registry number command in the COSMOtherm input file Please also note that the trivial name in the last field of the database index file must not contain any blank spaces This also holds for the trivial name given by the dbn name option Thus if the above COSMO database index file is processed the compound input expression f 1 butanol cosmo in the COSMOtherm input file can be replaced by the term rn 71 36 3 or by the term dbn butanol Please note that the dbn name command is case insensitive Starting with Version C1 2 Revision 01 03 COSMOtherm is able to read in additional information about different conformers of one compound in the database index file This new database index file has the format COSMO Name CAS Num
255. ing the vapor pressure prediction of the pvap or the binary ternary or multinary phase diagram options via the use_tboil keyword cf sections 2 3 1 and 2 3 7 Optional Input of a compounds experimental boiling point reference temperature This option is valid only in combination with the input of a boiling point reference pressure pref option see below Argument value is the pure compound boiling point reference temperature value T of the given compound It is expected to be given as real number T is expected to be in C for the tref and tref_C options in K for the tref_K option and in F for the tref F option The T value thus given can be used as a reference point for scaling the vapor pressure prediction of the pvap or the binary ternary Or multinary phase diagram options via the use_tboil keyword cf section 2 3 1 and 2 3 7 Optional Input of a compounds experimental boiling point reference pressure This option is valid only in combination with the input of a boiling point reference temperature tref option above Argument value is the pure compound boiling point reference pressure value p e of the given compound It is expected to be given as real number larger than zero p e is expected to be in mbar for the pref option in Pa for the pref Pa option in kPa for the pref KPA option in bar for the pref bar option and in psia for the pref psia option The pr value thus given can be used as a reference poi
256. inte value options where isolute is the number of the solute compound as given in the collating sequence of compounds in the compound input see below In addition to the use of experimental aqueous dissociation constants COSMOtherm is able to provide an estimate of a solutes pK acid or pK base using the Linear Free Energy Relationship pK LFER decribed 38 Leo A Hansch C Elkins D Chem Rev 71 1971 525 103 in section 2 3 6 In the framework of partition coefficient calculations the pK estimate for acidic and basic solutes is toggled by the comp_acid ineutra1 ianion aNd comp_base iyeutra ication Options given in the logp option mixture input line Therein iyeutrar is the number of the solute compound as given in the collating sequence of compounds in the compound input and ianion ANd ication are the compound numbers of the anion and cation compounds that are formed on acidic and basic dissociation of the solute compound respectively Please note that the pK LFER estimate of pK acid or pK base values requires the presence of COSMO files of the dissociated species A or BH which form from solute via the acidic or basic dissociation reaction For more details on the pk LFER methodology please see section 2 3 6 The pH of the aqueous phase is assumed to be 7 0 This value can be changed by the input option pH value Please note that for measurements of distribution coefficient the pH of the aqueous phase is buff
257. ion creation of cluster and ion geometry files continued ssc_ions ssc_name ssc_weak ssc_ang angle Optional Create molecular structures of ions by dissociating a cluster geometry created by the ssc strength or ssc_probability option The ion geometry files will be written to the current working directory in Cartesian Xmol XYZ format The surface contact complex geometry files will be named ionA i j xyz and ionB i_j xyz where i is the number of the molecule conformer in the order that is given in the compound section of the COSMOtherm input file j is the number of the partner molecule conformer in the order that is given in the compound section of the COSMOtherm input file and angle is the dihedral angle orientation of two molecules in the complex Please note that the surface contact complex XYZ geometry files of subsequent contact runs will be overwritten Optional Write named files with molecular contact cluster or ion geometry created by the ssc strength ssc probability or ssc_ions option The geometry files will be written to the current working directory in Cartesian Xmol XYZ format The surface contact complex geometry files will be named complex name name angle xyz where name and name are the molecule conformer names of the contacting compounds and angle is the dihedral angle orientation of two molecules in the complex The ion geometry files created by the ssc_ions option will be named cation n
258. ion 2 3 7 2 however is possible in combination with the ternary option for lonic Liquids For the ternary option it is possible to define up to three separate IL phases in one ternary computation In the COSMOtherm ternary input up to three SIL descriptors denoting IL phases may be given E g input of the ternary SIL i IL command describes a system with two IL phases and one neutral solvent phase where i is the number of the solvent compound i e a neutral solvent compound with number i as given in the sequence of compounds in the compound input section If more than one IL phase is given via SIL keys in the ternary i j k Ornternary name name name option the IL phases have to be defined by subsequent groups of IL i j Or nIL name name and IL n v vj keys The first IL IL_n group found in the ternary mixture input line is assigned to the first SIL key in the Input ternary input the second IL IL_n group found in the input line is assigned to the second IL key in the ternary input and so on If the liquid liquid equilibrium search LLE option see section 2 3 7 2 is combined with the ternary option for lonic Liquids three table blocks will be printed to the COSMOtherm table file First the regular VLE output table with the mole fraction concentrations of the grid points and all computed themrdynamic properties such as H GF p t at the grid points is printed followed by
259. ion number A liq_ex computation will be considered converged if the changes of all compound mole fractions in all phases are below this threshold default xt 10 5 Optional for liq ex computations Set maximum number of iterations in the self consistent convergence of the liq_ex computation Argument imax is expected to be a positive integer number default imax 500 Optional for liq ex computations Print the converged phase equilibrium constants K to the LIQ EX table in the COSMO therm table file Optional for liq ex computations Print the converged phase equilibrium concentrations x to the LIQ EX table in the COSMO therm table file Optional for Liq ex computations Print lt the chemical potentials of all compounds in all phases in converged phase equilibrium to the LIQ_EX table in the COSMO therm table file 153 Suboptions of the Liq_ex option continued solid k Salt_phase kgait gaseous k pref p or pref Pa p or pref kPa p or pref psia p or pref bar p vm01 Vno1 vref Vrer avsaltmu Optional for liq_ex npnase Computations Define phase k of the liq _ex computation as solid phase Argument k is expected to be a positive integer number between 1 and npnase Optional for 1iq_ex npnase computations Define phase k of the liq ex computation as salt precipitation phase Argument ksar is expected to be a positive integer number between 1 and ngnase Optional for liq_ex npn
260. ion of COSMO charges can be done with the technique of difference charges which is described in section 5 3 1 of this manual ll from the viewpoint of the thermodynamic interaction energy contribution i e from the viewpoint of the interacting system of compounds it is possible to modify the microscopic COSMO RS interaction energy contributions in the COSMOtherm program to adjust the COSMOtherm predictions to match certain given thermodynamic property data However before changing any COSMO RS parameters it is important to be aware of the sometimes severe ramifications of the parameter modification All parameters in the COSMO RS model are dependent upon each other in a non linear way This means that any modification reduces the predictive capabilities of the COSMO RS as a whole E g if the parameters are modified in a way that alkanes are predicted well then inevitably polar molecules like ethanol will be predicted much much worse Thus any modified parameter COSMO RS will not be general any more It will not be applicable any more to compounds with a different chemical functionality any modification of a single parameter indirectly via the computed segment contact statistics that results from the solution of the COSMO RS equation 1 5 affects all other parameters Thus if one predicted property may get better by modifying a parameter other may get worse it does not make sense to change absolute numbers to a given value
261. ion of the SMC method to the prediction of thermal adsorption equilibria is given in ref 73 73 Mehler C Klamt A and Peukert W AICHE Journal 48 1093 2002 200 5 6 Chemical Potential Gradients Composition and temperature derivatives of the chemical potential or activity coefficient are important properties for process simulations COSMOtherm allows the computation of analytic temperature and composition derivatives of the chemical potential The computation of the analytic gradients is triggered by the grad option either in the global command section or the temperature mixture section of the COSMOtherm input file In the first case the analytic temperature and composition gradients of all compounds are printed into the output file for all mixtures that are computed In the latter case the gradients are printed only for the mixture where the grad command is given Example 9 shows the output of the analytic temperature and composition gradients of propanone and water in an equimolar mixture of the two compounds at room temperature Example 9 Compound 1 propanone Chemical potential of the compound in the mixture 0 72644 kcal mol Chemical potential gradient dmu RT 1 dT 0 02804 kcal mol Chemical potential gradient dmu RT 1 dn 1 0 45656 kcal mol Chemical potential gradient dmu RT 1 dn 2 0 45656 kcal mol Compound 2 h2o0 Chemical potential of the compound in the mixture 2 16937 kcal mol Che
262. iquid liquid extraction equilibrium If toggled in a temperature mixture line of the COSMO therm input file the LIQ Ex option will compute the mole or mass based equilibrium partition of an arbitrary number of compounds between to given liquid phases see section 2 3 14 68 C Print options for the COSMOtherm output file nomix Optional Do not write the mixture information to the output file weomp i ip Optional Write to the COSMOtherm output file the evaluated information only for compounds i i where i is the number of the compound as given in the compound section of the COSMOtherm input file The wcomp option can help to shorten the output file if not all evaluated information is required by the user The wcomp option is active only for the temperature mixture line where it is given wonly name name gt Optional Write to the COSMOtherm output file the evaluated information only for compounds name name where name is the name given in the compound section of the COSMOtherm input file i e it is either the name of the COSMO file without extension or the name given via the comp name option The wonly command has the same effect as the wcomp command It is active only for the temperature mixture line where it is given Grad Optional Print the values of the temperature and composition derivatives of the chemical potentials of all compounds If given in a temperature mixture line of
263. is estimated by the liquid density volume QSPR If no density estimate is available the molar solubility of the solute in the solvent will not be computed If the wso11 keyword is given in addition to the solub keyword see above the decadic logarithm of the molar solubility of the solute in the solvent log S mol I 10910x Psoivent MWeoivent Will be written to the COSMOtherm table file 86 Suboptions of the solub i or nsolub name command are liquid iterative thresh_solub SLESOL proni pr rs max iterations i SOLQSPR C1 C2 C3 C4 C5 or SOLQSPR SI c C2 C3 C4 C5 Optional for solub computations Computed liquid solubilities only Heats of fusion for all compounds are assumed to be zero Optional for solub computations Refine the computed solubilities iteratively i e iterate the mixture computations for each compound until the difference of the computed solubility log x of the compound differs less than threshold value thresh_solub from log x of the last iteration If no argument is given with the iterative command COSMOtherm will use the default value of thresh _solub 1 0d 5 i e of 10 log x units The optional argument thresh _solub is expected as a real number larger than zero Optional for solub computations solve the solid liquid SLE and or liquid liquid LLE equilibrium conditions to obtain the solubility value The SLESOL option can be used as an alternative to the iterat
264. is given the concentration for this compound will be inserted automatically using the normalization of the sum of mole fractions Only one negative number is allowed per mixture input line Note that the mole or mass fraction input is not required if only one compound is given in the compound input section or if the binary the ternary the multinary or one of the property calculation options gamma logp solub henry or pKa see below is used Optional replaces x x x andc c c2 input Compute properties of pure compound i If the x pure i command is used the mole fraction concentration of compound i where i is the compound number in the range given in the compound input section is set to 1 all other compound concentrations are set to zero If the nx pure namei option is used the mole fraction concentration for the compound of the name namei is set to 1 all other compound concentrations are set to zero Note that the mole fraction input is not required if only one compound is given in the compound input section or if the binary the ternary the multinary or one of the property calculation options gamma logp solub henry or pKa see below is used 59 A Temperature and mixture input continued x pure MICELLE Optional Trigger a COSMOmic computation Please note that this option is available only if the COSMOmic plugin is activated via the COSMOtherm license file and if a micelle definition file has bee
265. ium constant K for the purpose of scaling the apparent equilibrium constant K K react 188 Suboptions of the reaction option continued react_eqm or react _eqmH or react_eqmC or react_eqmJ or react_eqmV react_zpe or react_zpeH or react _zpeC or react_zpeJ or react _zpeV F TA il il T EAN 42 se i2 i2 s HD ses i2 E ZP x N pd T N rail x N rail esd w ZP 2 e E j 2e E j2 Ei Qee E j2 Optional for reaction computations provide external quantum chemistry energies for the reactant compounds The input of the reactant energies E is possible via the react eqm E Ey command where F Eiz are the energies values that will be used ilr for the reactant compounds defined by the compound numbers or names as given by the react i i Of nreact name name commands The energies E are expected to be negative real numbers For the keywords react _eqm and react _eqmH the given energies are expected to be in atomic units Hartree for the keyword react _eqmC energies are expected to be in kcal mol for the keyword react _eqmd energies are expected to be in kJ mol and for the keyword react _eqmv energies are expected to be in eV Optional for reaction computations provide e
266. ive refinement option Both options are mutually exclusive Optional for solub computations with iterative refinement or SLESOL In addition to the iteratively refined solubilities print the noniterative zero order guess solubility values to additional columns of the table file Optional for solub computations without iterative refinement In addition to regular absolute solubilities print the re ative solubility values to additional columns of the table file Optional for iterative solub computations Give the maximum number of iterations i that are used in the iterative refinement procedure for the solubility Default value of max iterations is 999 Argument i is expected as an integer number larger than one Optional for solub computations Give the parameters for the QSPR approach for the free energy of fusion The arguments are expected as real numbers The parameters are expected to be used with energy values in kcal mol and volumes in A For the solOSPR_SI command they are expected to be used with energy values in kJ mol and volumes in nm i e in the Sl unit frame 87 Suboptions of the solub i or nsolub name command continued xs xl x2 or cs cl c2 wsoll wsol2 wfract solvdens value Optional for solub computations Give finite solvent mixture concentration at which the solubility shall be computed The input of the concentrations is possible either in mole fractions xs or
267. iven in A If the QSPR coefficients have been determined for c moments in Sl units i e M in nm and all other MX in atomic units the QSPR_SI filename and the OSPR SI C C2 Cig name have to be used to read in the parameters 194 Example 8 logPOW prop logP Octanol Water QSPR parameters for Turbomole BP SVP AM1 COSMO files Regression 210 compounds r 2 0 94 rmse 0 34 0 02948233 0 area 0 1 charge 0 0432569 2 0 036411 3 0 4 0 5 0 6 0 HBaccl 0 HBacc2 0 0578499 HBacc3 0 HBacc4 0 HBdonl 0 HBdon2 0 00520617 HBdon3 0 HBdon4 0 6681521 Constant 0 inimum of property 0 aximum of property log Pow Property name Currently COSMOtherm is shipped with QSPR coefficient file for the following properties logPOW prop Octanol water partition coefficients logPow for BP SVP AM1 COSMO logKOC prop Soil Water partition coefficients logKoc for BP SVP AM1 COSMO logKOC BP TZVP prop Soil Water partition coefficients logKoc for BP TZVP COSMO COSMO logBB prop Blood Brain partition coefficients logP for BP SVP AM1 COSMO logKIA prop Intestinal absorption coefficients logK for BP SVP AM1 COSMO logKHSA prop Human Serum Albumin partition logK for BP SVP AM1 COSMO It is possible to give several QSPR properties in one QSPR coefficient file If such a multiproperty QSPR coefficient file is used COSMOtherm will print all given QSPR properties to the table output and mom
268. iven in both the compound input line and the vap file or the energy file the input line has highest priority followed by vap file and the energy file Thus if eqm is present both in the input and in the vap file the value from the input file will be used 48 2 2 3 Vapor Pressure Property Input Several automatic computation options of COSMOtherm utilize experimental pure compound data E g binary ternary or multinary computations see section 2 3 8 are able to use pure compound vapor pressures the solub option for the solubility prediction of solid compounds can process experimental free energy of fusion data and the dissociation correction to the partition coefficient calculation option Logp utilizes experimental dissociation constants COSMOtherm allows several ways of reading in such compound specific experimental data The data either can be given in the compound input line in the compound section of the COSMOtherm input file or alternative theycan be read from a vapor pressure property file filename vap using either the global vPfile option see section 2 1 or the local vPf filename option VPf filename Optional Read the vapor pressure property input for this compound from file filename If no argument is given i e only the vP keyword the name of the vapor pressure property file is expected to be the name of the according COSMO file with the file extension vap i e for COSMO file name cosmo a vapor pressure proper
269. iven in equation 2 3 1b is used to compute the salt solubility 36 Prediction of Solubility with COSMO RS Frank Eckert in Developments and Applications in Solubility Trevor Letcher Ed The Royal Society of Chemistry UK 2007 96 Please note that for salt solubilities similar to considerations taken on ionic liquids systems some care has to be taken in the interpretation of the COSMOtherm results for the computed salt solubility mole fractions x To be able to compare the computed salt mole fraction with experimental data depending on the reference state of the salt solubility measurement it may be necessary to convert the computed salt mole fraction value along the guidelines given in section 5 9 of this manual COSMOtherm by default will convert the mole fraction based salt solubility results from the computed multicomponent framework where the salt is considered to consist of independent anion and cation components to the laboratory binary or IL binary framework see section 5 9 where the salt is considered to be one single compound Because experimental solubility measurements of salt solubilities typically are done in the laboratory binary framework the multicomponent mole fraction soluilities are converted to the laboratory binary framework by COSMOtherm by default and printed to the salt solubility table accordingly It is possible to print the multicomponent pseudo binary or IL ternary mole fraction
270. l the parameters which are required by COSMOtherm in order to produce reliable high quality calculations of physicochemical data The original set of parameters is described in detail in references 1 and 3 These parameters are partly intrinsic parameters of COSMOtherm as well as element specific parameters In addition a few numerical thresholds are set in the CTDATA files Each CTDATA file has a header line in which the properties of the parameterization are listed The body of the file is not intended to be modified by the user Therefore we do not give a detailed explanation of the numbers here 3 1 Parameterization of COSMOtherm Because the quality accuracy and systematic errors of the electrostatics resulting from the underlying quantum chemical COSMO calculations depend on the quantum chemical method e g DFT functional or SCF MP2 or semi empirical Hamiltonians as well as on the basis set COSMOtherm needs a special parameterization for each of these method basis set combinations Currently COSMOtherm Version C3 0 Release 15 01 parameterizations for the following program packages and method basis set combinations are available Turbomole RI DFT with BP B88 VWN P86 functional and def TZVP basis set Turbomole RI DFT with BP functional def2 TZVPD basis set and novel fine grid cavity DMOL3 DFT with PBE functional and numerical DNP basis set GAMESS PQS Molpro Columbus ORCA Q Chem B88
271. le electronic structure package F Neese Max Planck Institut f r Bioanorganische Chemie M lheim Germany 2005 1 Q Chem Version 4 0 Q Chem Inc 2012 where a y is the effective contact area between two surface segments and a is an adjustable parameter The basic assumption of eq 1 1 which is the same as in other surface pair models like UNIQUAC is that residual non steric interactions can be described by pairs of geometrically independent surface segments Thus the size of the surface segments a has to be chosen in a way that it effectively corresponds to a thermodynamically independent entity There is no simple way to define a from first principles and it must be considered to be an adjustable parameter Obviously if o equals o the misfit energy of a surface contact will vanish Hydrogen bonding HB can also be described by the two adjacent SCDs HB donors have a strongly negative SCD whereas HB acceptors have strongly positive SCDs Generally a HB interaction can be expected if two sufficiently polar pieces of surface of opposite polarity are in contact Such a behavior can be described by a functional of the form Eup O 0 AjyCyz MIN min 0 min 0 O tonor O up max 0 O acceptor O HB 1 2 wherein cy and Opg are adjustable parameters In addition to electrostatic misfit and HB interaction COSMO RS also takes into account van der Waals vdW interactions between surface segments via Ew Oo aof a
272. led contact statistics is computed which gives the contact interaction probability of all individual segments of compound A with the complete molecule B In addition the contact interaction probabilities of all atoms of compound A with the complete molecule B are computed The detailed contact statistics will be written to an additional output file the contact statistics map file called name contact where name is the name of the COSMOtherm input file The detailed contact statistics file can be renamed by input option namcont yourname contact which overrides the default name contact The contact statistics are written only for compounds i where i is the number of the compound in the order that is given in the compound section of the COSMOtherm input file If the segment_contact option is given without argument the detailed contact statistics map will be written for all possible contacts of all compounds that are present in the given mixture at a finite concentration If certain compounds consist of several conformers by default only one contact statistics map per compound and contact is printed to the contact statistics map file If no other input is given the 202 first conformer as given in the input section is used for the contact statistics map If the additional keyword wlconf is given the contact statistics maps of the conformer with the lowest free energy in the given mixture or equivalently the conformer with the highest conformer
273. lubility calculation The argument n is expected to be a positive integer number The default value is max_iter 1000 141 2 3 12 Computation of the liquid density of pure compounds The DENSITY option allows for the automatic computation of the pure compound liquid density of a given substance If toggled in a temperature mixture line of the COSMOtherm input file the density option will compute the liquid densities of all compounds that are given in the compound input section at the given temperature The liquid density p of a pure compound i is computed from the corrected molar liquid volume of the compound MW is the molecular weight of the compound N is Avogadros constant red 2 3 24 VNa The corrected molar liquid volume V is computed from a Quantitative Structure Property Relationship QSPR Elements Ring 2 3 25 vy MF HB COSMO k Y Coup Hi CHyp Hi C cosmo Vi T Cm M2 CNRing Ni Ca Ai The descriptors for the corrected molar liquid volume are the pure compounds misfit interaction enthalpy HF the pure compounds hydrogen bonding enthalpy H the COSMO Volume of the compound as given in the compounds COSMO file V the second c moment of the compound M the number of ring atoms in the compound Nf and the areas of surface in a given compound that belong to atoms of the same element type A where k is the element number Thus the QSPR model for the corrected molar liquid volume and density con
274. m a number of additional computation steps in which the vapor pressures of the individual compounds are adjusted to their given boiling points data Of course this adjustment is only possible if an experimental boiling point temperature was provided for the compound either in the compound input line or in its vapor pressure property file In addition to the use of boling points as reference pressures COSMOtherm the possibility to use the compound s experimental vapor pressure as reference point The compound s temperature 74 dependent vapor pressure as read from the compound input line or from the vapor pressure property file see section 2 2 in terms of pairs of experimental p T or Antoine extended Antoine or Wagner equation coefficients directly can be used as reference pressures Pref P s T The usage of temperature dependent pure compound vapor pressures is toggled by the keyword use_pvapt which either can be given in the pvap mixture line where it is active for this mixture only or in the global input lines where it will be active for all pvap computations given Suboptions of the pvap command tk2 1 or tc2 1 or p tf2 1 2 tstep npoints tstepsize AT tstepsize F AT LogPVAP use tboil use pvapt pr_pp Optional for pvap computations Give a second temperature which together with the temperature from the tk T tc T or tf T command defines the temperature range for the automatic vap
275. m input file Vapor pressures are compound specific properties thus they have to be given in the compound section of the input file COSMOtherm allows several ways of reading in a compounds vapor pressure Pure compound vapor pressure input options VPinp pressure Optional Give the vapor pressure of this compound It is or expected in mBar for the VPinp command in Pa for VPinp Pa pressure the VPinp Pa command in kPa for the VPinp kPa or command and in psia for the VPinp psia command VPinp kPa pressure respectively or VPinp psia pressure VPwag A B CDE F Optional Give the coefficients of the Wagner equation or In o In A 1 1 1 Ct Dt Ev Fr wherein t 1 VPwag Pa A B C D E F T B to be used in the calculation of the vapor pressure or p of compound i Coefficients A and B correspond to the VPwag_kPa A B C D E F compounds critical pressure p and critical temperature T respectively Wagner equation coefficients for many substances are tabulated in databases such as KDB7 Note that the coefficients B C D E and F are expected for temperatures T in K Coefficient A is defined as vapor pressure P in mbar or in Pa for the VPwag_Pa or in kPa for the VPwag_kPa keywords respectively 76 Kang J W K P Yoo H Y Kim H Lee D R Yang and C S Lee Korea Thermophysical Properties Databank KDB Department of Chemical Engineering Korea University Seoul Korea 2000
276. m molecular vap files EQM and EZP option see section 2 2 Compound Input In combination with the global UQME or UOMG Use external QM energies keyword the energies thus read in during compound input will be used as 2 and values in the reaction computation If conformers are present the conformer molecules of a compound will be weighted according to their external 2 E energies and not their cosmo energies as is the default Note that the react_ prod_ input in the reaction mixture line overrides the EQM and EZP input of the compound input section The global usage of the external QM energies and ZPE toggled by the global UQME or UQMG keyword and read in in the compound input section or from a vap or gas phase energy file can be switched off locally i e for a given reaction computation by using the local command UQME OFF and UQMG OFF options in the mixture line of the reaction input 184 In addition to the external values for 2 and 7 it is also possible to provide external values for AG SOY and AH to COSMOtherm which then will be used in eqs 5 4 5 and 5 4 6 to compute the compounds free energies andenthalpies overriding the COSMOtherm predictions for these properties For the reactant compounds AG can be given with the keyword react_Gsol G Giz where G are free energies of solvation in atomic units for the reactant compounds i i
277. m pK predictions are not restricted to solvent water It is also possible to compute an acid or base pK for nonaqueous solvents This requires a reparameterization of the pK LFER parameters The pK LFER parameters can be passed over to COSMOtherm with the pKaLFER c c For some common pK solvents the LFER parameters are shipped within the COSMOtherm parameter files and can be used by a simple keyword of the form SOLVENT ACID or SOLVENT BASE Currently pK LFER parameters for acids in the solvents dimethylsulfoxide and acetonitrile are available from the COSMOtherm parameter files The LFER parameters for acids pK at room temperature in solvent dimethylsulfoxide DMSO are shipped within COSMOtherm parameter files BP_TZVP_C30_1501 ctd and BP_SVP_AM1 C30 _1501 ctd The usage of the DMSO acid pK LFER parameters is toggled with the DMSO ACID suboption of the PKa isoivent ineutrar ron Command Note that the solvent isoivent OF NAMEgojyent that is used in the pKa or npKa command is required to be dimethylsulfoxide if the DMSO ACID keyword is used The LFER parameters for acids pK at room temperature in solvent acetonitrile MeCN are shipped within COSMOtherm parameter files BP_TZVP_C30_1501 ctd and BP_SVP_AM1 C30_1501 ctd The usage of the acetonitrile acid pK LFER parameters is toggled with the ACETONITRILE ACID suboption of the PKa isoivent ineutrar ron Command Note that the solvent isoivent OF NAMEgojyent that is
278. mapfile is a surface contact statistics file that was created by COSMOtherm via command segment contact the 6 real number column holds the contact interaction statistics see section 5 7 The map column command allows the visualization of other properties in file mapfile For example the surface potential on the COSMO surface that is given in the 7 column of a surface contact statistics file created by COSMOtherm can be visualized via map column 7 38 Control options for the output of molecular geometry i e the generation of molecular structure files Wcar Wm12 Wsdf Wsdf Wxyz Wpdb Optional Write the geometry of the processed compound name cosmo to molecular structure file name car The molecular geometry will be written in MSI CAR format surface If given in this section of the COSMOtherm input file the Wcar command is active only for the actual compound Optional Write the geometries of the processed compound name cosmo to molecular structure file name m12 The molecular geometry will be written in Tripos Sybyl mol2 format If given in this section of the COSMOtherm input file the Wm12 command is active only for the actual compound Optional Write the geometries of the processed compound name cosmo to molecular structure file name sdf The molecular geometry will be written in MDL ISIS sdf format If given in this section of the COSMOtherm input file the Wsdf command is active only for the actual com
279. mass fractions cs of the compounds of the mixture as real numbers xi and ci The arguments are expected as real numbers between zero and one in the same sequence of compounds as given in the second input area If the values do not add up to one COSMOtherm will normalize them If less mole fractions concentrations than compounds are given the missing ones will be assumed zero If a negative number is given the concentration for this compound will be inserted automatically using the normalization of the sum of mole fractions Only one negative number is allowed per mixture input line Optional for solub computations Change the output of the mass based solubility w to Definition 1 which is w7 x MW MWesoivent Optional for solub computations Change the output of the mass based solubility w to Definition 2 which is w7 x MW 1 1 xP MWooivent Optional for solub computations Change the output of the mass based solubility w to normalized mass fraction output which is w x5 MW xO MW 1 x9 MWoivent Optional for solub computations Optional input of the solvent density as used in the computation of the molar solubility The argument value is expected to be the density value of the solvent in g l Note that the solvdens option only will effect the computation of the molar solubility The mole fraction solubility and the mass based solubility will not be changed Note If a finite conce
280. me option the binary phase diagram is computed for the two compounds with the compound names name and name as given in the compound section of the COSMOtherm input file i e either the names of the COSMO files without extension or the name given via the comp name option Optional Toggle the automatic calculation of the phase diagram and the excess properties of a ternary three compound mixture see section 2 3 7 This option is valid only if the total number of compounds is three Optional Toggle the automatic calculation of the phase diagram and the excess properties of a ternary three compound mixture see section 2 3 7 This option is applicable if the total number of compounds is larger than two For the ternary i j k option the ternary phase diagram is computed for the three compounds with the compound numbers i j and k in the order of compounds given in the compound input section For the nternary name name name option the ternary phase diagram is computed for the three compounds with the compound names name name and name as given in the compound section of the COSMOtherm input file i e either the names of the COSMO files without extension or the name given via the comp name option Optional Toggle the automatic calculation of the phase diagram and the excess properties of a multinary n compound mixture Note that the multinary option requires additional input see section 2 3 8 63 B Prop
281. me of the COSMOtherm input file Optional Compute statistics of the surface segment contacts between all segments of molecule i as given in the command segment _contact i with all of the segments that are associated with the group of atoms iatomk Of molecule inoi This option is active only for the temperature mixture line where it is given The contact statistics is printed only for compound i where i is the number of the compound in the order that is given in the compound section of the COSMOtherm input file The molecular surface contacts for all segments of the given compounds are written to the contact statistics file name contact where name is the name of the COSMOtherm input file 204 5 7 2 Visualization of Contact Statistics COSMOtherm is able to visualize the detailed segment contact interaction maps name contact that were created by the segment_contact i i option as a VRML file COSMOtherm can read in a contact statistics map file name contact that has been created with the segment contact option via the command wrlmap name contact in the compound input section of the COSMOtherm input file Via the wrlmap command COSMOtherm will create a VRML file molec _map wrl that visualizes the contact interaction probability as given in file name contact on the molecular COSMO surface of molecule molec The filename of the VRML file to be created can be given by the namwrl mapname wrl command which overrides the defa
282. menu If you use an older Windows version such as Windows95 98 ME or NT the environment variables have to be added to your Windows autoexec bat file which is located in the systems root directory set COSMOTHERM HOME C yoursoftwaredir COSMOlogic10 COSMOtherm CTDATA FILES The search path for the COSMOtherm license files can be set to a directory different from the cdir directory using the 1dir command in the COSMOtherm input file see section 1 4 below 13 1 4 License The COSMOtherm distribution also requires a valid license file which is necessary for the correct execution of COSMOtherm The license file is named license ctd It is checked every time COSMOtherm is executed It is expected to be in the directory that also holds the COSMOtherm parameter files i e in the directory denoted by the environment variable COSMOTHERM HOME see above or in a directory denoted by the cdir command in the COSMOtherm input file see section 2 1 Alternatively the location of the license file can be appointed to a different directory using the 1dir command in the COSMOtherm input file see section 2 1 Please note that the graphical user interface COSMOthermxX on first execution will ask for the license file and copy it into the licensefiles directory which is located in the installation directory COSMOlLogic10 where all current COSMOlogic products are installed Please also note that the COSMOtherm
283. mer COSMO files with the exact numbers i4 iz will be used as conformers in the autoc option ij iz are integer numbers between 0 and 9 or maxautoc 58 2 3 Temperature Mixture Input Following the input of the different compounds COSMOtherm expects information about the temperature and mixture ratio of these compounds in the third area of the input file The temperature mixture lines are processed subsequently There is no limitation of the number of mixtures to be processed by COSMOtherm The temperature mixture input line can contain the following commands A Temperature and mixture input tk temp or tc temp or tf temp X X X2 or C C1 Co x pure i or nx pure namei Required Temperature of the mixture in Kelvin K tk temp or degrees Celsius C tc temp K C 273 15 or degrees Fahrenheit F tf temp K F 459 67 1 8 Note that the temperature input is not required if an isobar VLE computation is done see section 2 3 9 Required mole fractions x or mass fraction concentrations c of the compounds in this mixture as real numbers x or c The arguments are expected as real numbers between zero and one in the same sequence of compounds as given in the second input area If the values do not add up to one COSMOtherm will normalize them If less mole fractions concentrations than compounds are given the missing ones will be assumed zero If a negative number
284. mic micelle file could not be read ERROR Could not find COSMOmic file COSMOmic micelle file could not be read ERROR Could not open COSMOmic file COSMOmic missing argument in micelle file COSMOmic micelle file corrupted COSMOmic concentrations of all compounds are zero in at least one layer COSMOmic memory problem real weights not possible COSMOmic micelle file could not be read COSMomic number of layers is too large A more detailed description of the actual error can be found at the bottom of the COSMOtherm output file of the crashed COSMOtherm job 170 5 Advanced Features of COSMOtherm 5 1 o Profiles In COSMO RS theory which is the basis of COSMOtherm all molecular interactions consist of local pair wise interactions of segments of molecular COSMO surfaces Basically quantum chemical COSMO calculations provide a discrete surface around a molecule embedded in a virtual conductor Of this surface each segment is characterized by its area a and the screening charge density SCD o on this segment which takes into account the electrostatic screening of the solute molecule by its surrounding which in a virtual conductor is perfect screening and the back polarization of the solute molecule In addition the total energy of the ideally screened molecule Ecosmo is provided Within COSMO RS theory a liquid is now considered an ensemble of closely packed ideally screened molecules Thermodynamic properties o
285. mical potential gradient dmu RT 2 dT 0 05106 kcal mol Chemical potential gradient dmu RT 2 dn 1 0 45956 kcal mol Chemical potential gradient dmu RT 2 dn 2 0 45956 kcal mol As is visible from Example 9 not the derivatives of the chemical potential 4 but the derivatives of property u RT In y i e the derivatives of the activity coefficient are computed by COSMOtherm because In y is a property that is more commonly used in chemical process simulations Please note that COSMOtherm computes the unconstrained derivatives of property 4 RT with regard to the temperature T i e 0 u RT 0T and composition number n i e A u RT On To obtain the constrained normalized derivatives of In y with respect to the temperature T the unconstrained temperature derivatives at composition x have to be subtracted from the unconstrained temperature derivatives of the pure compounds at the given temperature see equation 5 6 1 z Sev Hes et oT oT OT 5 6 1 To obtain the normalized derivatives of In y with respect to the composition x the unconstrained composition derivatives with respect to n have to be subtracted from the unconstrained composition derivative with respect to n as is given in equation 5 6 2 for a binary system olny Ou T x RT _ u T x RT Ox On On i T Xj 2 T nj rn 5 6 2 74 Taylor R and Kooijman H A Chem Eng Comm 102
286. mine the compounds free energy of fusion at these conditions by solving equation 2 3 2 for AG In the COSMOtherm input the reference solubility log x 5 can be read in by the ref_sol_s value keyword COSMOtherm offers several alternative unit systems for the input of the reference solubility see Suboptions of the solub option Tables below In addition to the reference solubility the reference solute has to be defined which is possible via the solute j or nsolute name keywords which define the solute compound of number j or name name as given in the compound section respectively Please note that the reference solubility calculation of AG also is possible for salt solubility calculations see below To be effective in the salt solubility option the arguments of the solute j or nsolute name keywords may point to any of the salt components or alternatively the expression nsolute SALT can be used If both reference solute and solubility value are given correctly COSMOtherm will compute AG of the given solute compound and print the computed value to the DG fus column of the solubility table output row of the reference solute compound Any other sources of AG will be overridden by this option Thus the solubility computation using the value of AG thus computed will reproduce the given solutes reference solubility unless noted otherwise by eventual warning messages that is If there is available an experimental valu
287. mined from the Boltzmann distribution of the compounds total free energy which is the sum of the COSMO energy of the compound Ecosmo its chemical potential in the mixture 4 and its dielectric energy correction dE Now because the quantum chemical COSMO energy of a COSMO metafile can not be known its value by default is set to zero if COSMO metafiles are used assuming that the quantum chemical COSMO energy is the same for all metafile conformers Thus strictly speaking the usage of COSMO metafiles as conformers can only be done consistently if the conformers that are defined by the different metafiles would all have nearly the same quantum chemical COSMO energy This is a very serious restriction that should never be forgotten when using metafiles as conformers Otherwise errors are introduced into the Boltzmann distribution of the metafile conformers However there are special cases where the quantum chemical COSMO energy of the fragments can be considered as closely related to the unknown quantum chemical COSMO energy of the metafile if you have a compound that is built from several conformeric metafiles where all of the conformer metafiles show the same fragmentation patterns and atomic weight patterns but are built from related fragment files where the fragment files used are different conformers of a compound E g if you have a target compound that includes a fragment of 1 butanol you may create two COSMO metafiles that include 1 butanol0
288. mix SI option AS is expected to be in kJ mol Argument value is expected to be a real number Optional Give the heat capacity of fusion ACp for a mixture composite For the Dcpfus_mix value option ACpy is expected in kcal mol for the Dcpfus mix SI option ACp is expected to be in kJ mol Argument value is expected to be a real number Optional Give the melting temperature T for a mixture composite For the Tmelt mix temp and Tmelt mix C temp options Trex is expected in C for the Tmelt_ mix K temp option T melt is expected in K Argument temp is expected to be a real number Optional for the input of a temperature dependent compound free energy of fusion via input of enthalpy or entropy of fusion AH or AS and melting point Tren toggle the approximation of the heat capacity of fusion as ACpy AS AHusdTmen The value of AG T thus obtained wil be used to compute the SLE of the given lonic Liquid salt system If the Dcpfus_estimate keyword is given in binary mixture SLE computation input line the approximation to ACp is valid for all compounds including the given lonic Liquid salt in the given mixture line 134 2 3 8 Automatic Computation of n Dimensional Multinary Phase Diagrams The multinary option is a generalization of the binary ternary concept to n dimensions It allows for the automatic computation of the thermodynamic properties of n dimensional multi component mi
289. modify the default grids with the options xgrid cgrid and qgrid These option will change the basis of the binary or ternary VLE LLE or SLE concentration grid into mole fraction concentrations xgrid keyword default into mass fraction concentrations cgrid keyword or into surface fraction concentrations qgrid keyword respectively Second it is possible to define a custom concentration grid via the definition of a start concentration vector an end concentration vector and the number of grid points to be computed between the two concentration vectors The custom grid definition is possible in mole fractions using options xstart xend and xstep in mass fractions using options cstart cend and cstep and in surface fractions using options qstart qend and qstep respectively The concept of custom grids is described to further detail in section 2 3 8 below Please note that the conversion of the grid concentrations via x c qjgrid or the custom grid options x c q start x c q end and x c q step will not change the units of the concentrations in the output and table files of COSMOtherm On output all concentrations by default will be converted into mole fractions x 110 Optional concentration grid input for the binary and ternary options xgrid or cgrid or qgrid xstart x X2 x3 or cstart c co c3 or qstart q q2 qs xend x X2 x3 or cend c c2 c3 or gend qi q2 q3 XSTEP Npoints
290. mp Water Water input no conformers f glycerol0 cosmo comp Glycerol Glycerol 1 conformer f glyceroll cosmo wc 2 Glycerol 2 conformer f glycerol2 cosmo Glycerol 3 conformer The first compound input line of the example contains the file input for the first compound h2o which is renamed by the comp Water command which will be used to identify this compound in the output file The following line identifies the start of a conformer block via the command In addition the cosmo file for the first conformer and the name Glycerol is given The next line contains the second conformer of this compound which is weighted by a degeneracy factor of two via the wc 2 command The next line holds the third conformer and the end of conformer block identifier 57 2 2 4 1 Automatic Conformer Search As an alternative and or supplement to the input of conformers with the conformer block concept it is possible to use all COSMO files that are found in the directory as specified by the fdir command as conformers with the global or local compound line command autoc If autoc is given either in the global command line or in a local compound input line of the input file COSMOtherm automatically will search for conformer cosmo ccf or mcos files of a given COSMO filename in the fdir directory and if found use these COSMO files as conformers of the given compound To be able to do this it is necessary that the COSMO filenames m
291. mputation is toggled with the keyword SLE the same way it is done for binary mixtures of non ionic compounds see section 2 3 7 3 Solid Liquid Equilibrium Computation for Binary Mixtures To do an IL SLE computation it is necessary to provide experimental data that can be used to compute the free energy of fusion of the IL salt phase via eq 2 3 18 or eq 2 3 19 and which subsequently can be used in eq 2 3 17 to compute the SLE The input of the required experimental data is equivalent to the input of the salt free energy of fusion used for the computation of solid salt solubilities see section 2 3 4 Automatic Solubility Calculation of this manual the IL salt heat of fusion data input has to be done in the same mixture line where the SLE salt and salt_n commands are located The net Gibbs free energy of fusion of the salt can be given by options DGfus_salt or DGfus_salt_SI The net enthalpy of fusion of the salt as used in eq 2 3 18 can be given by options DHfus_ salt or DHfus_salt_ SI The net entropy of fusion of the salt as used in eq 2 3 19 can be given by options DSfus_salt or DSfus_ SALT SI The net heat capacity of fusion of the salt as used in equation 2 3 18 or 2 3 19 can be given by options Dcpfus_salt or Dcpfus_ SALT SI The net melting temperature of the salt as used in equation 2 3 18 or 2 3 19 can be given by options Tmelt salt Tmelt salt _C or Tmelt salt kK see below for details The ACp estimate described in t
292. multinary computations with the isobar option Iteratively refine the interpolated temperature to achieve a higher quality of the isobar phase diagram The optional argument thresh is the accuracy of the temperature to be reached by the iterative process The iterative procedure is repeated until the change in energy is below the threshold value thresh If no argument is given a default accuracy of thresh 0 2 K is used The optional argument thresh is expected to be a positive real number 137 2 3 10 Computation of a similarity factor between two compounds COSMOtherm allows the automatic calculation of the molecular o profile similarity S of two compounds i and j using the similarity i j or nsimilarity name name options in the mixture input section of the COSMOtherm input file see section 5 1 on o profiles For the similarity i j option S is computed for the two compounds with the compound numbers i and j in the order of compounds given in the compound input section For the nsimilarity name name option is computed for the two compounds with the compound names name and name as given in the compound input section of the COSMOtherm input file The computed similarity factor S is printed to the mixture output section of the COSMOtherm output file 5 is printed below the compound output block of the first compound given in the similarity command i e compound i or name If several conformers are present for either comp
293. n 60 74 phase diagram 108 scaling 74 sublimation pressure 73 vdwset 222 223 viscosity 68 145 volume quotient 102 vpant 51 140 vpant_kPa 51 vpant_ Pa 51 vpantl 51 vpantl_ kPa 51 vpantl Pa 51 vpexp 52 108 140 vpexp_ kPa 52 vpexp Pa 52 vpf 49 vpfile 18 48 vpinp 50 108 140 vpinp kPa 50 vpinp Pa 50 vpinp psia 50 vpKant 51 vpKant_kPa 51 vpKant_ Pa 51 vpKantl1 51 vpKant1 kPa 51 vpKant1 Pa 51 vpKexp 52 vpKexp_ kPa 52 vpKexp Pa 52 vpTCant 51 vpwag 50 vpwag_kPa 50 vpwag_ Pa 50 VRML 18 37 175 205 w 34 174 Wagner equation 50 we 57 Wear 29 39 weas 21 wccf 30 40 wemn 20 wcomp 69 weonf 20 21 69 109 166 202 203 wdbn 21 wdfl 34 173 174 wg 57 Wgauss 30 40 whbset 222 224 WILSON 113 115 Wm12 29 39 Wmol 29 39 wonly 69 Wpdb 29 39 wrl max 38 206 207 wrl min 38 206 207 wrlmap 38 205 206 207 absconscale 205 206 207 absconwrl 205 206 207 relconscale 205 206 207 Wrlres 18 37 Wsdf 29 39 wtin 20 69 wvdwset 222 223 Wxyz 29 39 x 59 69 x pure 59 69 micelle 60 225 xend 110 111 136 xhbset 221 224 xstart 110 111 118 136 xstep 110 111 136 xw 36 ZPE 45 46 47 183 184 185 o moment correction 36 193 200 o moments 18 27 165 193 200 o potentials 7 27 65 138 139 171 o profiles 6 27 64 138 171 239
294. n a molecule Please also note that the absconwrl absconscale and relconscale options are mutually exclusive All of the contact coloring options including the default min max scheme may be overridden by the explicit input of the minimum and maximum of the color scheme by the wrl_min and wrl_max keywords Control options for the visualization of surface contact statistics map files wrlmap mapfile namwrl name wrl map _column igg1 Optional Create a VRML file of the molecular COSMO surface property map that is given in file mapfile The wrlmap command is active only for the actual compound and the actual property map mapfile The property map file mapfile is expected to be in the same format as the surface contact statistics map file name contact that can be created by COSMOtherm via command segment contact The mapfile is expected to be found in the directory where the COSMOtherm input file is Optional Suboption of the wrlmap mapfile command Give the name of the VRML visualization file of the property map given by the wrlmap mapfile command name wrl overrides the default VRML visualization file name molec _map wrl Optional Suboption of the wrlmap mapfile command Choose column io of the COSMO surface property map mapfile that shall be visualized on the COSMO surface By default the 6 real number column of mapfile is expected to hold the property that should be visualized If property map file mapfile is a surface contact
295. n an as is state Nevertheless COSMOtherm users should feel encouraged to use this level it probably fits their special demands in property prediction better than the recommended standard levels BP TZVP COSMO and DMOL3 PBE in particular if the mentioned compound classes are involved Recommended for best quality predictions of thermophysical data for chemical engineering purposes Program Package DFT functional Basis Set COSMOtherm Parameterization Turbomole BP RI DFT FINE TZVPD BP_TZVPD_FINE_C30_1501 ctd 61 As an alternative to Turbomole the COSMO files for this level of theory and basis set can be calculated with the Gaussian03 Gaussian09 PQS Molpro GAMESS US10 Q Chem Columbus or ORCA quantum chemistry programs 62 The BP TZVPD FINE methodology is available in TURBOMOLE release 6 4 Spring 2012 and later versions 163 3 3 2 High Throughput Screening The application of COSMOtherm for the purpose of screening a large number of compounds e g prediction of solubility of compound in various solvents or prediction of solvent partition coefficients like logPocanol water fOr a large number of solutes as often are demanded in life science applications such as agent drug design typically requires a predictive quality that is somewhat lower than for typical chemical engineering applications However the molecules involved are often larger gt 100 atoms and an overall large number of compounds has to be comput
296. n blank spaces unless it is given in quotes e g pdir C Program Files COSMOtherm CTDATA FILES PROP Optional Sets the directory where to search for the COSMOtherm license files license ctd By default the CDTATA FILES directory as given by the cdir command or as read from the environment variable COSMOTHERM_HOME is used as LDIR The Idir command in the input file overrides this default The directory name must not contain blank spaces unless it is given in quotes e g Idir C Program Files COSMOlogic LICENSES 17 2 1 1 File Handling continued Efile or EHfile or EJfile or ECfile VPfile Cwrl Swrl Pwrl Wrlres res Optional If this keyword is used COSMOtherm automatically searches for the gas phase energy files for all molecules given in the compound input section The gas phase energy files are expected to be of the form name energy where name is the name from the according COSMO file name cosmo as given in the compound input section A description of the format of the energy file can be found in section 2 2 compound input of this manual For the commands Efile and EHfile the energy is expected in atomic units Hartree for EJf ile it is expected in kJ mol and for ECfile it is expected kcal mol By default the current working directory is searched if the fdir command is used the according path given by fdir is searched cf also the ef filename keyword in the compound in
297. n from the input In addition the free energy of fusion is used with a max 0 AG function in equations 2 3 1 and 2 3 2 Although unphysical it might be eligible to allow negative AG values in certain situations The use of negative 4G values can be forced by the global ndgf option see section 2 1 A temperature dependent heat of fusion can be calculated from the Schr der van Laar equation if the compounds enthalpy or entropy of fusion AH or AS respectively and melting temperature T are known T AG ns T AH psl 1 Aa ACP jus T pen T ACP just In ae 2 3 3 melt T nen AG p T AS ps T pen z T ACP us Ea rs T T ACP just In Ji 2 3 4 Thus the combination of a compounds experimental melting temperatures and enthalpy or entropy and optionally heat capacity of fusion eqs 2 3 3 or 2 3 4 used in eq 2 3 1 and 2 3 2 allows the automatic calculation of the compounds solid solubility at different temperatures with the solub or nsolub option AH Or AS can be given in the compound section of the COSMOtherm input file via option DHfus value or DSfus value respectively see section 2 2 1 A compounds melting temperature Ter can be given in the compound section of the COSMOtherm input file via option Tmelt temp see section 2 2 1 Optionally the heat capacity of fusion ACp can also be used to decribe the temperature dependency of the Gibbs free energy of fusion ACp can be given in the compound section o
298. n read in the global input section via command rmic name mic For details and handling of the COSMOmic plugin please see section 5 12 of this manual and the COSMOmic documentation that is available from the COSMOthermxX graphical user interface B Property calculation options vapor pressure boiling point Henry law coefficient pvap pvap pressure or pvap_SI pressure henry i or nhenry name Optional Toggle the automatic calculation of the total vapor pressure of the system at a given temperature and concentration It is also possible to compute the vapor pressures for a given temperature range via the tk2 temp or tc2 temp commands see section 2 3 1 Optional Toggle the iterative calculation of the vapor pressure of a given mixture The given pressure is expected as a real number in mbar for the pvap pressure option and in kPa for pvap_SI pressure option The temperature of the mixture will be varied iteratively until the given value of pressure is met see section 2 3 1 Optional Toggle the automatic calculation of the Henry law coefficients of all compounds in the ith compound where i is the compound number in the range given in the compound input section The nhenry name option computes the Henry law coefficients in the compound of the name name By default the Henry law coefficients H are calculated at infinite dilution in compound i It is also possible to calculate H at finite concentrations using the xh
299. nce temperature Tke and pressure Pre The argument of the use pref value option is expected to be a real number temperature which is expected to be in mbar for keyword use pref in Pa for keyword use tref Pa in kPa for keyword use tref_ kPa in bar for keyword use _tref_ bar and in psia for keyword use tref psia Suboptions of the pvap pressure and the pvap SI pressure commands thresh _pvap Ap or thresh pvap_SI Ap thresh _pp Ppy Optional for pvap pressure computations Give the absolute accuracy threshold for the iterative vapor pressure computation The thresh pvap Ap and the thresh pvap SI Ap commands expect as argument a pressure value Ap in mbar and in kPa respectively Optional for pvap pressure computations Give a relative accuracy threshold for the iterative vapor pressure computation The thresh_pp p command expects as argument a relative pressure p in 76 2 3 2 Automatic Activity Coefficient Calculation The gamma i or ngamma name option allows for the automatic computation of the activity coefficients in compound i By default this option will compute the chemical potentials 1 of all pure compounds j and subsequently the chemical potentials at infinite dilution in compound i For ionic species j the reference state for the activity coefficient is not the pure compound yu but infinite dilution of the ionic species in the solvent i Thus according to Debye HUuckel limiting law the activity
300. nd J M Prausnitz AIChE Journal 14 135 1968 42 Wilson G M J Am Chem Soc 86 127 1964 115 procedure to the UNIQUAC equation The activity coefficient of a species in a mixture is built from two contributions The first term the combinatorial contribution In y accounts for the size and shape differen 2 3 10 compounds 2 3 11 OD O ON i i i lny In a 5q Ea l X 3 xl and are the normalized volume and surface area fraction of species i in the mixture Each species i is characterized by its mole fraction concentration in the mixture x its volume r and its surface area q XE 0 S _ 2 3 12a Dn J o Ali 2 3 13 Ds es J L 5 r q r 1 2 3 12c The remaining contribution to the activity coefficient the residual contribution In yf describes the interaction between the different compounds in the mixture R Y 7 lny q 1 In AF Us j j KU The UNIQUAC interaction parameters t can be expressed by an average interaction energy a for a species i species j interaction 2 3 14 ai RT Thus for binary mixtures the UNIQUAC model contains only two adjustable parameters t and t3 Int If the UNIQUAC2 option is used within the framework of a binary calculation only the two UNIQUAC interaction parameters t and t are adjusted to match the activity coefficient data computed by COSMOtherm By default the compound specific UNIQUAC volume and s
301. ndency 85 heat capacity 54 83 122 heat capacity estimate 24 54 84 85 89 96 99 122 125 129 131 134 mixtures 134 mixturess 134 reference solubility 84 89 90 91 100 reference solute 84 salts 99 129 Schr der van Laar 83 Walden s Rule 85 henry 60 79 80 ch 79 80 Gsolv 79 80 logH 80 solvdens 79 80 xh 79 80 Henry law coefficients automatic calculation 60 79 polymers 178 179 high throughput screening 164 IEI 36 72 212 ierror 168 input Antoine coefficients 51 extended 51 boiling point reference pressure 53 boiling point reference temperature 53 boiling point temperature 19 53 74 112 CAS RN 31 155 compound 31 34 35 36 43 47 49 50 51 52 conformers 19 33 57 name convention 58 COSMO file 31 database 16 23 155 DIPPR coefficients 51 fixed mixture ratio 36 global 16 Kirchhoff coefficients 51 mixture 59 reference pressure 19 74 75 76 reference temperature 74 75 76 Riedel coefficients 51 temperature 59 73 75 temperature range 75 temperature stepsize 73 75 trivial name 31 155 vapor pressure 18 50 Wagner coefficients 50 interaction energy index 36 72 212 lonic Liquids 123 126 142 214 ions 164 activity coefficient 77 78 geometry creation 211 solubility 81 isobar 59 137 isobar kPa 137 isobar Pa 137 ispolymer 56 180 iterative 137 iwl 34 174 Kirchhoff equation 51 ldir 17 LICENSE 16 license file 14 license ctd 14 16 234 liq ex 68 146 15
302. ng that COSMOtherm will read all cosmo files with numbers 0 to maxautoc that are present within the given conformation s name convention Note that maxautoc has to be integer number between 1 and 999 where numbers that are larger than 9 are valid only for the name_ex cosmo name convention For details on conformer handling see section 2 2 4 1 Automatic Conformer Search Optional suboption of the autoc command Only use the cosmo ccf or mcos files with numbers i4 iz as conformers in the autoc option where iy iz are expected to be integer numbers between 0 and 9 COSMO files must follow the name convention of conformer COSMO files in COSMObase i e conformer COSMO files are named by subsequent numbers starting with zero name0 cosmo namel cosmo name9 cosmo 33 Compound input options continued atomic weights options w 0 011 Sc rw 0 1 1 d2 iwl n n2 aw n iw uot awu Nn1 W1 we awz n iw we wdfl wo n3 awn Ng W2 Ng W2 Noi Wo N3 W3 N3 W3 N3 W3 Optional Give weights for the atoms of this compound Weights are integer numbers 0 to 9 and are expected in the sequence of the geometry read from the cosmo cos or ccf file By default weights for all atoms are 1 Note in order to shorten the input for large molecules it is possible to leave out the blanks between the weights i e give w 0011 See also section 5 3 Optional Give real numbe
303. nite mixture concentrations for the or two phases between which the partition coefficient shall be computed The cll cl c2 input of the concentrations is possible either in mole fractions x11 and or x12 or mass fractions cll cl2 of the compounds of the x12 xl x2 mixture as real numbers xi and ci The arguments are expected as real or numbers between zero and one in the same sequence of compounds as given cl2 cl c2 in the second input area If the values do not add up to one COSMOtherm will normalize them If less mole fractions concentrations than compounds are given the missing ones will be assumed zero If a negative number is given the concentration for this compound will be inserted automatically using the normalization of the sum of mole fractions Only one negative number is allowed per mixture input line vq value Optional for logp computations Give the volume quotient VQ V V between the two phases for which the partition coefficient shall be computed The argument is expected as a non negative non zero real number Note If a finite concentration input via options x11 or cll and x12 or c12 is given for both solvent phases no arguments need to be given to the logp or nlogp option 37 The recommended value for the volume quotient of the wet 1 octanol water system with 0 274 mole fractions of water in the octanol rich phase is VQ 0 1505 cf A Dallos J Liszi 4 Chem Thermodynami
304. not describe a molten salt very well because the relative orientation of anion and cation is fixed in this picture The system consists of ion pairs with the same structure only The second approach combines the surface charge o the area and the volume of the two ions and takes into account interactions with two distinct ions But the entropic term of the whole IL is used thus leading to errors in the chemical potential if the IL is present at a finite concentration in the mixture We recommend the first approach because the picture of two distinct ions should be closer to reality However approach I requires a careful look at the definitions and reference states of the computed thermodynamic property In the COSMOtherm input file the two IL components are given as individual compounds see Example 11 Example 11 COSMOtherm input for Ionic Liquid ctd BP_TZVP_C30 1501 ctd cdir CTDATA FILES fdir DATABASE COSMO BP TZVP COSMO Compute activity coefficient of hexane in an IL f f BF4 cosmo 4 methyl n butylpyridinium cosmo IL cation IL anion f hexane cosmo Solute tk 314 gamma 1 xg 0 5 0 5 Activity coefficient computation In Example 11 the ionic liquid is used as a solvent for a third compound present in infinite dilution For the calculation one has to take care that anion and cation have the same mole fraction In this example the activity coefficient of all substances in a mixture of 50 4 methyl N butylp
305. not necessary to distinguish if COSMOtherm is run on UNIX or Windows based computers On DOS Windows systems COSMOtherm can use the UNIX format for directories for example C cosmotherm work as well as the V DOS format for directory input i e C cosmotherm work The following optional commands are valid in the global command line s 2 1 1 File Handling LICENSE name Optional Give the name of the COSMOtherm license file Default license file name license ctd ctd name ctd Optional Use the file name ctd as COSMOtherm parameter file default name CTDATA ctd dbas name csv Optional Use the file name csv as COSMO database index file default name DATABASE COSMO csv For purpose and description of the COSMO database index file see section 2 4 16 2 1 1 File Handling continued cdir directory fdir directory mdir directory odir directory pdir directory ldir directory Optional Sets the directory where to search for the COSMOtherm parameter file Default is to search in the current working directory Alternatively CDIR can be read from the UNIX or Windows environment variable COSMOTHERM HOME Note that the cdir command in the input file overrides the latter option The directory name must not contain blank spaces unless it is given in quotes e g cdir C Program Files COSMOtherm CTDATA FILES Optional Sets the directory where to searc
306. ns Only one negative number is allowed per mixture input line 78 2 3 3 Automatic Henry Law Coefficient Calculation The henry i or nhenry name option allows for the automatic computation of the Henry law coefficients H in compound i It is also possible to calculate the Henry law coefficients at a given finite concentration for example in a mixture of solvents via the xh x1 x2 orf ch cl c2 commands By default this option will compute the chemical potentials yu of all pure compounds j and subsequently the chemical potentials at infinite dilution in compound i In addition the vapor pressures of the pure compounds are calculated The Henry law coefficients H for all compounds j are then calculated from the activity coefficients and the vapor pressures of the compounds and written to the COSMOtherm output file and to the COSMOtherm table file For a given solute compound the Henry law coefficient H is computed from the compounds chemical potential difference between the ideal gas phase and the infinite dilution state in the given solvent or solvent mixture H exp 4 4 RT which for an incompressible liquid state is equivalent to the expression H 75 p S If possible i e if experimental pure component vapor pressure data is available from a vap file or given in the compound input section of the input file the Henry law coefficient as computed with the experimental vapor pressure Hs pv exp 7 Pi
307. nsity estimate for neutral compounds as described in section 2 3 12 of this manual The course of action is demonstrated in the example input below ctd BP_TZVP_C30_1501 ctd cdir CTDATA FILES ldir licensefiles Global command line 1 fdir DATABASE COSMO BP TZVP COSMO UNIT SI sprf se Global command line 2 Automatic activity coefficient calculation for a polymer Comment line f pdms mcos ispolymer ExpDensity 0 97 ExpMW 6800 comp pdms polymer Compound input polymer f ethane _c0 cosmo Compound input solute f propane_c0 cosmo Compound input solute f butane_c0 cosmo Compound input solute tc 25 density polyprep Prepare for polymer computation compute free volumes of solutes tc 25 ngamma pdms polymer COMBI ELBRO Automatic activity coeffcient calculation in polymer solvent In the example input shown the activity coefficients of three gaseous solutes in the polymer PDMS polydimethylsiloxane are computed Experimental density and molecular weight values are provided for the polymer compound only For the solute compounds no experimental free volumes or densities are given in the input Hence they have to be estimated which is done in a two step procedure As a first initialization step a regular density calculation is done for all compounds in the input The densities and molar volumes thus computed are stored for later use with the combi ELBRO combinatorial term using the keyword polyprep The polyprep k
308. nt for scaling the vapor pressure prediction of the pvap or the binary ternary or multinary phase diagram options via the use_tboil keyword cf section 2 3 1 and 2 3 7 53 COSMOtherm allows the processing of several other compound specific properties that can be read in the compound section of the COSMOtherm input file Pure compounds heat of fusion crystallization input DGfus value or DGfus_ SI value DHfus value or DHfus SI value DSfus value or DSfus_ SI value Depfus value or Depfus_ SI value Tmelt temp or Tmelt C temp or Tmelt_K temp Depfus_estimate Optional Give the free enthalpy of fusion AG for this compound For the DGfus value option AG is expected in kcal mol for the DGfus_ SI option AG is expected to be in kJ mol Argument value is expected to be a real number The value of AG thus given can be used to compute the solubility of solid compounds via the SOLUB or NSOLUB option see section 2 3 4 Optional Give the enthalpy of fusion AH for this compound For the DHfus value option AH is expected in kcal mol for the DHfus SI option AH is expected to be in kJ mol Argument value is expected to be a real number The value of AH thus given can be used in combination with a given melting point 7 melt to compute the solubility of solid compounds via the SOLUB or NSOLUB option see section 2 3 4 Optional Give the entropy of fusion AS for this compo
309. ntial difference between the gas phase and liquid 4 cf equation 1 10 in the Theory section 1 1 of this manual If available it is also possible to use experimental data for AG 5 and AH to compute the reaction energy and enthalpy Further quantitative improvement of the total free energy or enthalpy value can be achieved if the zero point vibrational energy is included for each compound G EM EZE AG SOV 5 4 5a H EM EZE AH 5 4 6a If the reactant or product compounds are present in the mixture at a finite concentration with a mole fraction x e g if the reaction takes places in bulk reactant liquid an entropic contribution RTIn x of the compound is added to the compounds free energy G By default the reaction is assumed to occur at the COSMOtherm standard reference pressure of 1 bar in the ideal gas phase Different reference pressures for the reaction can be taken into account by utilizing the pressure dependency of the free energy of solvation AG SOY Pre AG SY 1 bar RTIn p 1 bar 5 4 7 For a given temperature the computation of a chemical equilibrium is toggled by the keyword reaction The solvent liquid wherein the reaction takes place can be defined with the reaction i or the nreaction name keywords where i is the compound number of the solvent and name is the compound name respectively Alternatively a solvent or compound mixture can be defined where the reacti
310. ntly are isothermal This means that if one of the reference pressure molar volume or volume options is used the system can only try to match the given reference pressure or volume of the gaseous phase by variation of the compound concentrations in the phases The reference pressure or volume can not be matched through variation of the temperature which is not adegree of freedom in isothermal calculations This implies that the reference pressure molar volume or volume options typically will converge only if the phase equilibration is run at a temperature and concentration range that is inbetween the systems dew and bubble point curves It is only at these conditions that a variation of concentrations alone can yield the given reference pressure or volume 151 Temperature mixture line input that toggles the liquid extraction calculations JIQ EX I QE X Nphase Suboptions of the liq_ex option N1 N N N II N2 N N7 N Nk N N N5 2 W1 W _W W s II W2 W W W Wk W We W s NO N N N 3 0 0 0 wo we W wes II 3 II 3 Toggles a multi component two phase liquid liquid extraction equilibrium calculation Toggles a multi component multi phase liquid liquid extraction equilibrium calculation in n nase phases Argument nphase can be any integer number between 2 and 5 Required for liq ex computations Give mole numbers N of
311. ntration input via options xs or cs is used no arguments need to be given to the solub or nsolub option 88 Suboptions of the solub i or nsolub name command continued dcpfus_ estimate amino corr Optional for the input of a temperature dependent compound free energy of fusion via input of enthalpy or entropy of fusion AH or AS and melting point T 4 toggle the approximation of the heat capacity of fusion as ACpy AS AH yudTmen The value of AG 7 thus obtained wil be used to compute the solubility of the compounds If the Depfus_ estimate keyword is given in a solubility computation input line the approximation to ACp is valid for all compounds and the given mixture line Optional for solub computations Toggle correction term for secondary and tertiary amino groups for the computation of aqueous solubility By default the amino correction is used only if a solids solubility in pure water is computed using the QSPR estimate to the free energy of fusion The amino corr command overrides this default and forces the solub option to use the amino correction term with the side condition that the solvent is water 89 Suboptions of the solub i or nsolub name command continued input of reference solubility ref sol or ref sol or ref_ sol or ref solz or ref sol or ref_sol m Val l val Lue Lue Lue Lue ue ue Optional for solub computations Define
312. ntum chemical COSMO calculations of the compound to be processed COSMOtherm is extracts all the relevant information for a COSMOtherm calculation directly from the COSMO files from quantum chemical COSMO calculations COSMO files are identified by the extension cosmo if they were computed by the quantum chemical program packages Turbomole DMOL3 Gaussian and others or by the extension cos if they were computed by the semi empirical program package MOPAC see section 2 for details To save disk space COSMOtherm also allows the processing of compressed COSMO files that are identified by the extension ccf In such compressed COSMO files all of the information relevant to COSMOtherm is stored in a extremely packed binary format thus using only about 6 of the disk space of a conventional COSMO file In practice the handling of the compressed COSMO files is completely equivalent to the handling of conventional COSMO files It is also possible to simply give the Chemical Abstracts Registry Number CAS RN or a short trivial name in order to identify a compound s COSMO file In this case an additional index file called the COSMO database index file which maps the CAS RN and the trivial names to the filenames of the compound COSMO files has to be read in by COSMOtherm see section 2 for details By default COSMOtherm produces one file of output The COSMOtherm output file filename out Optionally the o profiles of the processed compounds c
313. o 1 pens 5 9 6 Because now we have the same reference framework of the IL composition for the experimental and calculated system the COSMOtherm prediction of the vapor pressures according to eq 5 9 3 directly can be compared with the experimental data If however activity coefficients y and properties derived from activity coefficients are considered it is crucial to stay within the same definition Thus typically activity coefficients computed with COSMOtherm in the sum of ions or ternary framework need to be converted to the one substance or laboratory binary framework to be comparable to values derived from experiment A general expression for the conversion between the two frameworks is given below 13 Historically this term has been coined for mixtures of one IL and one solute Although it might be a bit misleading we will continue with this expression even for mixtures with more than three components 215 In COSMOtherm three types of mole fraction definitions are used For ILs with stoichiometry Vinin and Vestion and vg E Vien Vanion Veation the mole numbers are the same for all definitions Nion Nation Nanion ny 5 9 7 In the one substance or laboratory binary the mole fraction of a solute is given as n b X 5 9 8 Yin n i In the sum of ions or ternary gt framework the mole fraction of a solute is given as tern X 5 5 9 9 i UM
314. o slightly depends on the choice of the molecular fragment i e an insensible choice of the fragments will also lead to a bad volume estimate Third if complex compounds are built up from several molecular fragments or if large polymer compounds are represented by a monomeric repeat unit represented by an atom weighted cut out of a monomer COSMO file there may occur a certain amount of charge mismatch of the COSMO charges at the cutting edges of the molecular fragments If a COSMO metafile is built up from a large number of fragments or if a single cut out repeat unit is weighted up by a large atom weight factor the usually small partial cutting charges of the fragment s may add up to a considerable overall fault cutting charge of the meta compound as a whole Such faulty cutting charges will be reneutralized by COSMOtherm to guarantee the overall exact neutrality of the given meta compound By default all meta compounds i e COSMO metafiles and atom weighted COSMO files will be reneutralized to neutrality to a charge of g 0 a u This holds even if the cutting charges of the COSMO metafile or the atom weighted COSMO file add up to more than 0 5 a u Hence even if the meta compound would be formally a charged due to fault cutting charges it will by default be reneutralized by COSMOtherm to exact neutrality This behavior can be changed by the cmet q option this options allows the use of charged meta compounds and optionally se
315. o small or too large MULTINARY concentration vector missing IL input not consistent BINARY VLE LLE computation not possible BINARY computation not possible IL components overlapping in SLE computation No parameters found for automatic solubility computation of solids SOLUB option will be ignored Automatic solubility computation via QSPR requires compound water in the compound input section Please add water in the compound input section SOLUB option will be ignored Illegal reference solubility value log x Ref Ambiguous input of mass based solubility definitions Missing SOLVENT for gas solubility computation Could not find compound required for automatic gas solubility computation Illegal compound number found for automatic gas solubility computation Illegal solvent concentration found for automatic gas solubility computation Missing pressure for gas solubility computation Invalid pressure argument in gas solubility computation Illegal pressure found for automatic gas solubility computation Missing QSPR parameters for density calculation Missing QSPR parameters for viscosity calculation Missing starting concentration in LIQ EX computation Illegal starting concentration in LIQ EX computation Illegal solute concentration in LIQ EX computation In LIQ EX computation phase numbers for GASEOUS phase and SOLID phase cannot be the same Too many compounds in LIQ EX computation COSMO
316. of the salt where x is defined as the stoichiometric sum of the ion mole fractions x xX X to the salt solubility table using the keyword pr_ILTERN in the salt solubility mixture input line Both IL binary and IL ternary definition of the salt solubility mole fractions will be printed to the by COSMOtherm output file In addition to the mole fraction output the salt solubility option will print the mass based solubility w dacGsolution to the output and table file There are three possible definitions of the mass based solubility where MW c and MWsovenr are the molecular weights of the salt solute and the solvent or solvent mixture olven 1 By default and or if the keyword wsol2 is given in addition to the solub keyword the unnormalized mass based solubility is computed by Definition 2 Wad Wa xac MWacl 1 xac MW sonent Il If the keyword wso11 is given in addition to the solub keyword the unnormalized mass based solubility is computed by Definition 1 Wad Wa xac MW MW soren Please note that although commonly used in pharmaceutical chemistry definition 1 is an approximation derived for small solubilities Thus it should be used only if the solubility is expected to be small log 9 x lt 3 Ill If the keyword wfract is given in addition to the solub keyword the normalized mass fraction solubility is computed SOL _ FRACT _ y SOL SOL SOL Wac Wac Xa MW
317. of the solute in the polymer can be approximated by the inverse activity coefficient we 5 3 2 Thus the polymer solubilities of gaseous and liquid compounds are obtained from an activity coefficient cf section 2 3 2 or Henry law coefficient ky py cf section 2 3 3 calculation rather than a solubility calculation In addition the iterative procedure for the calculation of solubility should not be used with polymers since this procedure treats the polymer like a liquid Instead the activity coefficient at infinite dilution can be used as a reasonable approximation for polymers at low solute load l e the solute s solubility in the polymer is approximated from an infinite dilution activity or Henry law coefficient of the solute compound in a given monomeric repeat unit of the polymer Obviously this approximative procedure does not allow for the calculation of absolute or quantitative solubility values of gaseous or liquid solutes in the polymer But the solubility thus computed can provide qualitative or relative information about the solubility of different solutes in the polymer e g in terms of a relative solubility ranking of the solutes or in terms of the relative selectivity Se the ratio of two relative solubilities or absorption coefficients between two solutes For example the selectivity of two liquid solutes can be calculated as Sif XIE I Yi 5 3 3 178 In the case of gaseous solutes the partial pressures o
318. ols by create produce geometry files that are indexed by the molecule numbers in the order as given in the input Sometimes it is more convenient to have the created geometry files named by the actual molecule names This can be done with the SSC_NAME keyword 208 Suboptions of the contact i i2 option creation of cluster and ion geometry files ssc_probability ssc_strength Optional Create geometry files of the most probable surface segment contacts SSC for all compounds given in the contact option with all other compounds in the mixture Molecular surface contact complex geometry files will be written for the contacts of all conformers of the compounds that are given in the contact i i command with all conformers of the other compounds j that are present in the mixture No complex geometry file will be written for molecules that are present at infinite dilution only Moreover no complex geometry file will be written if the contact between the two molecules is hindered by unfavourable van der Waals interaction The surface contact complex geometry files will be written to the current working directory in Cartesian Xmol XYZ format The surface contact complex geometry files will be named complex ij angle xyz where i is the number of the molecule conformer in the order that is given in the compound section of the COSMOtherm input file j is the number of the partner molecule conformer in the order that is given in the comp
319. oment M is correlated with screening charge of the compound system and the third second c moment M is a measure for the skewness of the sigma profile of the compound COSMOtherm allows for a maximum number of 6 i e for a total of 7 SMC s However usually co moments of orders up to 3 or 4 will be sufficient for a correct description of the o potential For compounds or systems that include Hydrogen Bonding donors and or acceptors Hydrogen Bonding moments M 48 can be defined In COSMO therm the first Hydrogen Bonding moment is defined as 0 lt HB Mii p O f uml do with him e if toso oto if to gt om 5 5 1 2 Where subscript defines either a Hydrogen Bonding donor aon or an Hydrogen Bonding acceptor acc and oy is COSMO therm s Hydrogen Bonding threshold an adjustable parameter defined in equation 1 2 of section 1 1 of this manual The higher Hydrogen Bonding moments are defined similarly however using fixed threshold values Mie p 0 oO fi ipl o do 5 5 1 3 AA 0 if o lt 0 6 0 21 with 4B 0 Abs a 0 6 0 21 if gt 0 6 0 21 Wherein 2 3 4 Note that via definitions 5 5 1 2 and 5 5 1 3 the first Hydrogen Bonding moments for HB acceptor and donors M 8 have the sign of the Hydrogen Bonding screening charge values while the higher Hydrogen Bonding moments M 5 are positive absolute values 5 5 2 o moments QSPR The c moments M computed b
320. ommand If thus enabled the hydrogen bonding donor strength of the atomic cations can be scaled by the AHBSET isjement factor command In COSMOtherm the hydrogen 221 bonding prefactor Cyg is considered to be temperature dependent The temperature dependence of Cyg is accounted for in the functional form of eq 5 11 3 T In w s exp dip RT Wp 1 Troom Wes exp dup RT goon Was 1 Cup T Cug 5 11 3 This functional form is derived from a plausible physical assumption about the energy gain and the entropy loss during the formation of a hydrogen bond It holds two parameters w and dyg which can be scaled via the WHBSET factor and DHBSET factor commands 3 The van der Waals vdW energy contribution to COSMO RS is given in equation 5 11 4 Therein aey is the effective contact area Caw and z are element specific adjustable parameters E aw OnO Ve Caw c 0 Ge are i Taw j 5 11 4 The vdW energy is dependent only on the element type of the atoms that are involved in surface contact The vdW energy contribution can be modified in terms of scaling the element element interaction vdW energy parameter Cw This is possible with the VDWSET ierement Jelement factor command where derement and jeiement are the element numbers of the atoms that are having a vdW contact This means that the VDWSET option allows for the individual scaling of the interaction energy of s
321. on d This option assumes that the external QM energy was computed at the ideally screened state i e that E 2 is a COSMO file energy b The uqmg keword toggles the computation of conformer equilibria using E E 2 EZE AGS i e the external QM energy contributions 2 7 plus the free energy of solvation AG of the compound in the given mixture This option assumes that the external QM energy was computed for the isolated molecule without screening i e that E 2 is a Gas Phase Energy 2 Compute reaction equilibria with the reaction ornreaction computation option see section 5 4 of this manual Note that either of the uqme or the uqmg keywords can be used to toggle the usage of the external energies for reaction computations They both have the same effect 47 Please note that 2 and 7 F external energies via eqm and ezp options can be read either from the compound input lines of the COSMOtherm input file from the molecules vapor pressure and property file molecule vap if the automatic vap file reading option VPfile option is triggered see section 2 1 or if the local vPf filename option is used or from the comment line second line of the molecules gas phase energy file molecule energy if the automatic energy file reading option Efile option is triggered see section 2 1 or if the local Ef filename option is used If several values are given i e if eqm and ezp options are g
322. on equilibrium computation option see section 5 4 of this manual Optional for the input of compound free energy of fusion Allow negative values of AG in the DGfus DGfus_ SI DGfus_salt or DGfus salt SI input The value of AG thus given can be used to compute the solubility of solid compounds or salts see section 2 3 4 Optional for the use of conformers Use the old conformer equilibration algorithm Starting with version C21 0111 COSMOtherm by default uses a novel conformer equilibration algorithm which significantly improves computation time if conformers are present Because the resulting conformer equilibrium may differ by a few typically lt 2 percent from the two algorithms the oclp option offers the possibility to use the old slow algorithm to be able to exactly reproduce old COSMOtherm calculations If given in the global command section the oclp command is active for the complete COSMOtherm run i e for all following temperature mixture lines Optional for the input of a temperature dependent compound free energy of fusion via input of enthalpy or entropy of fusion AH or AS and melting point Tmer toggle the approximation of the heat capacity of fusion as ACp AS tus AH ul Tmer The value of AG 7 thus obtained can be used to compute the solubility of solid compounds or salts as well as solid liquid equilibria SLE calculations See sections 2 3 4 for solubility and 2 3 7 3 for SLE If the Depfus estim
323. on is used c H and c_S are expected to be real numbers in kJ mol and kJ mol K respectively It is possible to give several en IEI entries in one compound input line The IEI formalism can be used to treat the concentration dependency if a reaction between two or more species in the mixture is taking place e g the dimerization of a organic acids the formation of a charge transfer complex between solute and solvent See section 5 8 for a detailed description of the IEI method Optional for the use of conformers and IEI computations Use the old conformer equilibration algorithm Starting with version C21 0111 COSMOtherm by default uses a novel conformer equilibration algorithm which significantly improves computation time if conformers are present Because the resulting conformer equilibrium may differ by a few typically lt 2 percent from the two algorithms the oclp option offers the possibility to use the old slow algorithm to be able to exactly reproduce old COSMOtherm calculations If used in this section of the input file the oclp command is active only for the temperature mixture line where it is given 72 2 3 1 Automatic Vapor Pressure Calculation The pvap option allows for the automatic computation of vapor pressures over a given temperature range and fixed mixture concentration If no other input is given the vapor pressure will be calculated only for the temperature given with the tk T tc T or tf T comman
324. on takes place via input of the mixture concentration mole fractions x with the keyword xr x x2 or via input of the mixture concentration mass fractions c with the keyword cr c cz The reactant compounds either can be given by their numbers i as given in the sequence of the compound 183 input using the keyword react i i or they can be given by their compound names name using the keyword nreact name name The product compounds either can be given by their numbers jx as given in the sequence of the compound input using the keyword prod 4j j2 or they can be given by their compound names name using the keyword nprod name name The stoichiometry numbers w of the reactant and product compounds can be given with the keyword react_n v 1 viz and prod_n v Vj2 respectively If the reaction is set up this way i e defining solvent concentration reactant and product compounds and stoichiometry the reactions Gibbs free energy AGgracz enthalpy AHgeacn and equilbrium constant Kgeacr are computed using the quantum chemical energies as read from the compounds cosmo and gas phase energy files i e DFT quality energies which means that 2 as used in eqs 5 4 5 and 5 4 6 is equivalent to the 2 the gas phase energy that is read from the energy file or if no energy file is available estimated from the compounds cosmo energy A reference pressure for the reaction that is different from th
325. onformers of a compound that are given in the database index file of the new format This is toggled by the command dbco given in the global command section of the COSMOtherm input file Starting with Version C3 0 Revision 14 01 COSMOtherm is able to read an alternative file format of the COSMO database index file which is created by the COSMObase Editor functionality of COSMOthermx Database index files created by the COSMObase Editor functionality are written in the extensible markup language XML format They are recognized by the extension xml The dbas filename xml input allows a COSMO file handling that is fully equivalent to the usage of a database index file in CSV format the dbco dbn and rn commands can be used the same way as for a csv database index file The main difference of the xml and the csv index files is that the latter is restricted to 10 conformers while for the XML format index file there is no such restriction 157 2 4 1 Creating COSMO files with a quantum chemistry program COSMOtherm Version C3 0 Release 15 01 is able to read COSMO information created by the following program packages and method basis set combinations Turbomole RI DFT with BP B88 VWN P86 functional and def TZVP basis set GAMESS PQS Molpro Columbus ORCA Q Chem B88 VWN P86 and Ahlrichs TZVP basis set Gaussian03 09 DGA1 DFT with BP86 B88 VWN P86 functional and Ahlrichs TZVP basis set
326. ongly affect the overall outcome of COSMOtherm This option should be used with greatest care 2 The hydrogen bonding energy contribution to COSMO RS is given in equation 5 11 2 Therein agg is the effective contact area Ogonor aNd Cacceptor are Surface charge values of hydrogen bonding donor and acceptor sites respectively while c and o are adjustable parameters Eyp O 0 ag Cup min 0 min 0 6 jono O up max 0 0 seepi O yg 5 11 2 The hydrogen bonding energy contribution can be modified in four different ways first the general hydrogen bonding prefactor Cys can be scaled via option CHBSET factor command The scaling of the cy coefficient by the given factor value globally will affect the hydrogen bonding energy All microscopic hydrogen bonding energy contributions will be scaled by this factor Second it is possible to scale the hydrogen bonding prefactor Cs in an element specific way using the XHBSET ieiement factor command where isiement is the element number of the atom to which the HB donor hydrogen atom is attached This means that the XHBSET option allows for the individual scaling of hydrogen bonds of different bonding type e g C H Acceptor type hydrogen bonds which typically are weaker than O H Acceptor type hydrogen bonds can be scaled independently using the XHBSET option It is possible to provide several XHBSET icjement factor commands to the global command input lines
327. onsistent and thus may lead to severe errors in the Boltzmann distribution of the conformers 176 5 3 1 Difference Charges In addition to atomic weights it is also possible to give a number of atomic difference charges in the compound lines of a COSMO metafile or the COSMOtherm input file via command del q q2 The difference charges q must be given in the same sequence as the atoms in the corresponding COSMO file of the compound The difference charges can be used to do an atom wise correction of the charges in the COSMO file as they were computed by quantum chemistry Please note that in the COSMOtherm version C21_0110 and older COSMOtherm versions the numbers given with the del option were interpreted as surface charges o q a not as charges q This has been corrected in COSMOtherm version C30_1201 and following versions Now by default the numbers given in the del option are interpreted as charges q If you want the numbers to be interpreted as surface charges o this can ba achieved with the additional keyword delga The a posteriori correction of atomic charges can be useful mainly in two cases First if the surface charges of the given compound can not be calculated properly by the quantum chemical COSMO level that is used An example for this case is compound dimethylsulfoxide DMSO the charges of which are not represented very well if density functional theory is used as quantum chemical method Thus also the COSMOtherm r
328. or mixture phases consist of a mixture of compounds that are present at a given and fixed mixture ratio Implicitly this approach also assumes that the physical and thermodynamic properties of the given mixture phases are additive with respect to the contributions of the mixtures components Using mixture phases thus defined COSMOtherm can perform a pseudo binary or pseudo ternary multicomponent phase diagram computation This means that within COSMOtherm the mixture phase is treated by means of its individual components at the given mixture ratio but on output the results of the individual compound properties are combined to form a single mixture phase It is possible to include neutral components as well as ions into such a composite phase if it is assured that the resulting mixture is charge neutral A composite mixture phase in a binary VLE LLE or SLE calculation ora ternary VLE or LLE calculation is denoted by the placeholder keyword MIX Each or any of the binary or ternary phases can be defined as mixture phases by the MIX placeholder If one or two MIX identifiers are given within the binary i MIX or nbinary name MIX options COSMOtherm expects to find the mixture concentrations of the composite SMIx phase to be in the same line as the binary MIX input The mixture concentrations can be given via keywords xm x x2 x3 in mole fraction concentrations or cm C C2 C3 in mass fraction concentrations
329. or ch command see section 2 3 3 If such a finite concentration input is used arguments i or name need not be given to the henry or nhenry option 60 B Property calculation options continued solid liquid gas solubility activity coefficient gamma i or ngamma name solub i or nsolub name sol or sol or Sol or sol or SOL as p gas_Pa p gas_kPa p gas_bar p gas_psia p Optional Toggle the automatic calculation of the activity coefficients of all compounds in the ith compound where i is the compound number in the range given in the compound input section The ngamma name option computes the activity coefficients in the compound of the name name By default the natural logarithms of the activity coefficients In y are calculated at infinite dilution in compound i It is also possible to calculate y at finite concentrations using the xg or cg command see section 2 3 2 If such a finite concentration input is used arguments i or name need not be given to the gamma or ngamma option Optional Toggle the automatic calculation of the solubility of all compounds in the ith compound where i is the compound number in the range given in the compound input section The nsolub name option computes the solubilities in the compound of the name name By default the common logarithms of the mole fractions of the solutes log o x are calculated at infinite dilution in compo
330. or pressure computation The tk2 T the tc2 T and the tf2 T command expect as argument a temperature T in K in C and in F respectively Optional for pvap computations Give the number of temperature values to be computed in the given temperature range The argument npoints is expected as an integer number between 1 and 101 Default value is npoints 10 Optional for pvap computations Give a temperature step value AT to be computed in the given temperature range Argument AT the temperature stepsize is expected as a positive real number in K for option tstepsize and in F for option tstepsize F respectively Note that option tstepsize overrides the tstep option If the given temperature stepsize AT is larger than the given temperature interval or if the given temperature stepsize AT is too small to fill up the the given temperature interval with the maximum number of allowed steps the tstepsize option will be disabled and the tstep default will be used instead Optional for pvap computations Output of the pressure in the table file will be written in decadic logarithmic log olp units if the additional keyword logPVAP is given or if the logPVAP keyword is given instead of the pvap keyword Optional for pvap computations Use the pure compound boiling points Toi as given in the compound input section or read from a compounds vapor pressure property file cf section 2 2 as a reference point for scaling the vapor pressu
331. or the awz atom numbered weights with default zero option default weights for all atoms are 0 Optional Give new default value for weight strings By default all weight strings are assumed to be one The wdfl w option changes this default to Wo Argument wy is expected to be a positive integer or real number See also section 5 3 34 Compound input options continued atomic weights options del q q2 mcse cmet q Optional Give difference charges for this compound as real numbers q separated by blanks The difference charges q are expected to be in the same order as the atoms in the COSMO file of the given compound See section 5 3 Atomic Weights and COSMO Metafiles for a detailed description of the usage of difference charges If the number of q thus given is lower than the number of atoms in the compound the missing ones are assumed zero If more q values are given the superfluous ones will be ignored Optional for the use of COSMO metafiles or atomic weights Use the sum of the fragment COSMO file energies in the calculation of the total free energy by default a zero value is used Optional for the use of COSMO metafiles or atomic weights Allow charged metafile and optionally set its neutralization charge If the cmet option is given locally in a compound input line the given COSMO metafile mcos file or atom weighted compound will be neutralized to match the exact integer char
332. orrespond to the environment in the untruncated molecule For instance for the calculation of silicon we use a O Si CH fragment saturated by a Si CH group and a OSi CH group In a COSMOtherm calculation a fragment of a molecule can be defined by atom weight factors The atom weight for atoms which should be taken into account must be set to one while the weights of the atoms which should not be taken into account must be set to zero The chemical potential of the polymer is calculated from a monomer or larger repeat unit and hence the corresponding solvent area and volume do not reflect the real surface area and volume of the polymer It is therefore recommended to switch off the combinatorial contribution to the chemical potential with the combi command in a global command line of the COSMOtherm input file COSMOtherm allows for the calculation of solubilities of gaseous and liquid compounds in polymers if the polymer is treated as a liquid solvent of monomeric or larger repeat units This appoximation is only valid for non crystalline polymers Furthermore polymer swelling cannot be taken into account because the employed relations are valid only for low solute load Computation of relative solubility in a polymer The solubility of a gaseous compound in a polymer can be calculated from its partial vapor pressure and activity coefficient Pi 1 Pi PPX and Xi 5 3 1 Pi Yi For a liquid compound the mole fraction
333. ound section of the COSMOtherm input file and angle is the dihedral angle orientation of two molecules in the complex Please note that the surface contact complex XYZ geometry files of subsequent contact runs will be overwritten Optional Create geometry files of the lowest energy surface segment contacts SSC for all compounds given in the contact option with all other compounds in the mixture Molecular surface contact complex geometry files will be written for the contacts of all conformers of the compounds that are given in the contact i i command with all conformers of the other compounds j that are present in the mixture No complex geometry file will be written for molecules that are present at infinite dilution only Moreover no complex geometry file will be written if the contact between the two molecules is hindered by unfavourable van der Waals interaction The surface contact complex geometry files will be written to the current working directory in Cartesian Xmol XYZ format The surface contact complex geometry files will be named complex ij angle xyz where i is the number of the molecule conformer in the order that is given in the compound section of the COSMOtherm input file j is the number of the partner molecule conformer in the order that is given in the compound section of the COSMOtherm input file and angle is the dihedral angle orientation of two molecules in the complex Note that the complex XYZ geometry fil
334. ounds again are distributed between the two phases due to their computed K values giving again new compositions of phase and II This procedure is repeated until the concentrations of the two phases do not change any more Thus the thermodynamic equilibrium the mass balance and if ions are present the charge neutrality condition as a boundary condition of the mass balance of the two phases are solved simultaneously in an iterative selfconsistent manner until the system converges to a thermodynamic and mass equilibrium of two neutral phases The converged system thus provides two new phases and II with all compounds distributed between the two phases according to their thermodynamic equilibrium partition In this viewpoint there are no explicit solvents or solutes Each compound including individual ions can move freely according to its affinity to each of the two phases with the side conditions of charge neutrality and mass conservation This corresponds to the solution of the liquid liquid extraction equilibrium in this system Please note that the model is restricted to the equilibrium calculation of liquid phases that are assumed to be immiscible i e show a liquid liquid phase separation By default if the LIQ EX option is given without argument it is assumed that there are two liquid phases present Nphase 2 Using the LIQ EX ngnase Option it is possible to define n phase phases where 2 lt Noghase S lam The default value for 1
335. owards nonpolar solvent or mixture phases In such a case the boundary condition of phase neutrality may become the dominating force in the phase equilibration which can slow down the convergence of the LIQ_ EX option considerably It may even lead to divergence in severe cases If this kind of behavior happens during a LIQ EX calculation with charged components it can be helpful to define solid or liquid salts as a salt input block in terms of the salts component definition stoichiometry and AG information as described above To define a liquid salt i e an IL or a salt that is completely dissoluted in the solvent phases the Gibbs free energy of fusion AG t should be set to zero in the salt input block Now given a proper and complete salt definition the LIQ EX option can be forced to use the average chemical potential of the salt components instead of the individual chemical potentials of the salt s ion components This option is toggled automatically for solid salts if a separate salt precipitation phase is defined with the salt_phase k command If no solid or salt phase is defined the use of the average salt chemical potential for the salt s components can be toggled with the avsaltmu command By means of using the salt s average chemical potential for all of it s ionic components possible converge problems are avoided which can be caused by individual ion s chemical potentials that show a tendency towards di
336. pKa 62 105 106 107 acetonitrile 106 acids 106 107 bases 106 107 ACETONITRILE ACID 106 107 ACETONITRILE BASE 106 107 acidity 105 107 aqueous 105 107 automatic calculation 62 93 103 105 basicity 106 107 cp 105 DMSO 106 acids 106 107 DMSO ACID 106 107 heptane 107 acids 107 HEPTANE ACID 107 linear free energy relationship 93 103 105 106 nonaqueous 106 107 pKaLFER 105 106 pKaLFER SI 105 thf 107 bases 107 THF BASE 107 THF BASE 107 water acids 55 93 103 105 107 bases 55 93 103 106 107 WATER ACID 105 107 WATER BASE 106 107 xp 105 pKacid 93 94 103 104 pKbase 93 94 103 104 polymers 7 173 178 180 pr_w 20 pref 53 pref Pa 53 pril 21 pri2 21 print options 20 21 22 69 print elem 143 144 program control 23 24 25 26 71 PROPQSPR 66 194 noaptab 67 196 pr_allmom 67 199 pr_mom 67 199 smomc 67 199 PROPQSPR_ SI 66 194 pure compound concentration 59 pvac 22 69 pvap 19 53 60 73 75 76 logPVAP 75 pr _ pp 73 75 te 75 236 tc2 73 75 tf 75 t 2 73 75 tk 75 tk2 73 75 tstep 73 75 tstepsize 73 75 tstepsize F 75 use pref 74 76 use pref bar 74 use pref kPa 74 use pref Pa 74 use pref psia 74 use pvapt 19 75 use tboil 74 75 use tref 74 76 use_tref bar 76 use tref C 74 76 use tref F 74 76 use tref K 74 76 use tref kPa 76 use_tref Pa 76 use tref psia 76 pvap SI pressure 60 74 76 thresh pp 74 76 thresh pvap SI
337. pecific element element interaction patterns e g hydrogen to oxygen can be created Optional Create geometry files of the lowest energy surface segment contacts SSC for all compounds given in the contact option with all other compounds in the mixture This option behaves similar to the ssc_ strength option described above with the difference that generation of the interaction complexes is restricted to the boundary conditions given by the arguments C n no where C is a single character that may be A or E and n and nz are integer numbers There are two possible usages of the option 1 If the character A is given the integer numbers n and n will be interpreted as atom numbers of the two compounds l e the generation of the interaction complexes is restricted to the contacts between atom n of molecule 1 and atom n of molecule 2 only Thus via the ssc probability A n n2 option complexes with specific atom atom interaction patterns can be created 2 If the character E is given the integer numbers n and n will be interpreted as element numbers e g 1 for hydrogen 8 for oxygen l e the generation of the interaction complexes is restricted to the contacts between elements n and n only Thus via the ssc _probability E n n option complexes with specific element element interaction patterns e g hydrogen to oxygen can be created 210 Suboptions of the contact i iz opt
338. pecific element element vdW contacts It is possible to provide several VDWSET iejement Jelement factor commands to the global command input lines at the same time thus accounting for several different vdW interaction types In COSMOtherm the van der Waals parameter C w is considered to be temperature dependent too The temperature dependence of Cyw is accounted for in the functional form of eq 5 11 5 T In w aw exp daw IRT Wyaw ag 1 5 11 5 Cyaw T Caw 5 11 5 T room Waw exp daw 1 RT poom Wray 1 This functional form is derived from a plausible physical assumption about the energy gain and the entropy loss during the formation of a van der Waals contact It holds two parameters Waw and d aw which can be scaled via the WVDWSET factor and DVDWSET factor commands 4 The chemical potential of the ideal gas phase i a as used in the vapor pressure related property predictions of COSMOtherm is given in equation 5 11 6 where E sas and E cosmo are the quantum chemical energies of the molecule in the gas phase and in the COSMO conductor The remaining contributions consist of a correction term for ring shaped molecules with n being the number of ring atoms in the molecule and g g an adjustable parameter as well as parameter 7 providing the link between the reference states of the system s free energy in the gas phase and in the liquid thus describing the entropy loss that occurs in the t
339. perty Input A compound can be flagged as polymer using the ispolymer term Please note that the ispolymer flag does not affect the results of the COSMOtherm calculation It simply is used as an identifier which allows COSMOtherm to refer to the given compound as a polymer in the output and in potential warning or error messages The apparent molecular weight of a polymer MW oiyme can be given with the expmw value option The argument MW ome will be used by COSMOtherm to scale up the molecular weight of the given molecular fragment to match the actual apparent polymer weight using the atomic weights concept explained in this section directly above The concept of real number weights similar to the rw option that can be used in a compound input line and in COSMO metafiles is used to blow up the molecular fragment or monomeric repeat unit that is given in the COSMO file or COSMO metafile in order to match the input MW polymer value Please note that this scaling procedure implies that the caveats described for the construction of the molecular fragments in COSMO metafiles above also hold if the expmw option is used If the scaling procedure results in a large charge mismatch and thus in a nonzero neutralization charge as described in section 5 3 above COSMOtherm will produce a warning message This implies that for a typical polymer case where a large macromolecule is scaled up from a monomeric and thus very small repeat unit in
340. perty is defined by its five Abraham coefficients Cy Cg Cer Ca Cg and a shift parameter c These six parameters can be read in by COSMOtherm from the QSPR property file if they are given with the command ABRAHAM COEFF cy Cg Cs Ca Cg Co given in a comment line i e following a character The name of the property that is defined by these six coefficients can be read from the same line of the QSPR property file using the ABRAHAM PROP Name command For example in Abrahams formulation the decadic logarithm of the partition between water and wet octanol is given by eq 5 5 3 using the coefficient values cy 3 814 c 3 460 c 1 054 c 0 034 c 0 562 and c 0 088 The input of these coefficients and the Abraham property name in a QSPR property files looks like this example QSPR property file BP TZVP Abraham logP Octanol wet Water prop Turbomole BP TZVP ABRAHAM COEFF 3 814 3 460 1 054 0 034 0 562 0 088 ABRAHAM PROP logP Octanol wet Water Coefficient roma cB oS cA cE c 0 Abraham coefficients for the computation of the decadic logarithm of the partition coefficient between solvents water and 1 octanol wet When reading a QSPR property file COSMOtherm automatically detects if Abraham coefficients are given If that is the case COSMOtherm automatically will compute the thermodynamic property defined by the given Abraham coefficients and the computed Abraham descriptors using eq 5 5 3 For each compound
341. phase The dissociated species typically have solution properties different from the solubility of the undissociated compound thus affecting the apparent solubility of the compound The effect of the dissociated compound approximatively can be taken into account by applying a dissociation correction to the solubility of the neutral compound Using the assumption that the dissociation reaction is independent from the solution process and further assuming that the dissociation process is described solely by the solutes dissociation constant pK and the given pH of the solvent phase a dissociation correction term can be derived from the law of mass action The dissociation corrected mole fraction solubility x is computed from the solubility of the undissociated species x as computed with the regular solub option and a correction term derived from the mole fraction concentration of the dissociated ionic species x 2 3 4 1 log x c log x log 2 2 2 S If the solute is an acid HA x Xa showing the dissociation reaction HA H O A H O in water the concentration of the dissociated ionic species x x is computed from eq 2 3 4 2 employing the acids aqueous dissociation constant pK acid and the pH of the aqueous phase 2 3 4 2 c ljo 4 1 gH e 107 PKa acid A 4 S Molar concentrations c relate to mole fraction concentration via x c MW p o where MW o is solvent molar weight and p is solvent density I
342. ponent IL with one bmim cation and one BF anion in this case If these options are given as additional input to an automatic binary VLE computation binary i SIL or nbinary name IL input line COSMOtherm will compute the pseudo binary phase diagram of the IL phase of the given composition and stoichiometry with the given solvent phase via eqs 2 3 7a and 2 3 7b and write the result to the COSMOtherm output and table file Note that the computed properties of the IL or salt compounds will be written output file by means of their individual ion properties while the table file will contain the mixture property table in its usual binary form where the properties of the ions are summed up to a single IL or salt phase property It is possible to define up to two separate IL phases in one binary computation In the COSMOtherm binary input up to two SIL descriptors denoting IL phases may be given E g input of the binary SIL SIL command describes a system with two IL phases If more than one IL phase is given via SIL keys in the binary i j Of nbinary name name options the IL phases have to be defined by subsequent 123 groups of IL k 1 or nIL name name and IL n v v input keys The first IL IL n group found in the ternary mixture input line is assigned to the first IL key in the binary input the second IL IL_n group found in the input line is assigned to the second IL key in the binary
343. possible via the QSPR filename or the QSPR c Co Cig name commands in the global command section of the COSMOtherm input file or the PROPQSPR filename or the PROPQSPR c C2 Cig name commands in the mixture section of the COSMOtherm input file The QSPR filename and PROPQSPR filename commands attempt to read the coefficients from a file called filename while the QSPR c Cz Cig name and PROPQSPR c cp Cig name read the coefficients directly from the input file In the latter case the coefficients given inside the curved brackets are expected as real number separated by blank spaces The first 16 numbers are the QSPR coefficients c _c as used in the QSPR formula above with c being a constant shift The remaining two parameters are used only in connection with the PWRL option see section 2 2 and give the minimum and maximum of the property color scale in the property VRML file Values of c 0 12 and c 0 03 usually are sufficient The last optional entry is the name of the property to be computed This name will be used in the output of the computed property which by default is in the compound section of the COSMOtherm output file The structure of QSPR coefficient file read in with the QSPR filename option is explained in Example 8 The default search path for the QSPR property files as given with the OSPR filename prop or PROPQSPR filename prop commands is the CTDATA FILES directory as given by the global cdir command
344. potential This combinatorial contribution results from the derivation of the combinatorial free energy expression GS Gy RT Ay 4 92 x In 7 In SAh 4 x lnq 4 1n gt x4 1 7 The combinatorial contribution to the chemical potential of compound j is G l ua eRT nnn 41 2 r i Ox l Jes j 4 in 1 8 q q In eq 1 8 r is the dimensionless molecular volume and q is the dimensionless molecular area of compound i The total volume and area of all compounds in the mixture are defined r xr 1 9a q 2x4 a The combinatorial contribution eq 1 8 contains three adjustable parameters o and A gt Please note that the COSMOtherm software allows to switch off the combinatorial contribution to the chemical potential 4 either individually for any of the given compounds or globally for all compounds combi option see sections 2 1 and 2 3 with the effect that 1 of eq 1 8 is set to zero This option is useful if compounds are used in COSMOtherm which do not have a well defined surface area and volume such as polymers or amorphous phases The handling of polymers and macromolecules within COSMOtherm is explained to further detail in section 5 3 Please note that the chemical potential of eq 1 6 is a pseudo chemical potential which is the standard chemical potential minus RT In x The chemical potential 4 of eq 1 6 allows for the prediction of
345. pound Optional Write the geometries of the processed compound name cosmo to molecular structure file name mo1 The molecular geometry will be written in MDL ISIS mol format If given in this section of the COSMOtherm input file the Wmol command is active only for the actual compound Optional Write the geometries of the processed compound name cosmo to molecular structure file name xyz The molecular geometry will be written in Cartesian Xmol xyz format If given in this section of the COSMOtherm input file the Wxyz command is active only for the actual compound Optional Write the geometries of the processed compound name cosmo to molecular structure file name pdb The molecular geometry will be written in Brookhaven database pdb format Cartesian coordinates If given in this section of the COSMOtherm input file the Wodb command is active only for the actual compound 39 2 2 1 1 COSMO Files and Compressed COSMO Files CCF Files Currently COSMOtherm is able to process COSMO files created by a number of different quantum chemistry packages see section 2 4 1 The majority of these COSMO files can be used directly as produced from the given quantum chemistry program However the COSMO charge surface as produced by the Gaussian program is based on a somewhat different COSMO cavity constrcution algorithm for more details on Gaussian COSMO files please see section 2 4 1 which requires COSMOtherm to convert all Gaussian COSMO fil
346. prod _GsolJ energies are expected to be in kJ mol and for the keyword prod _GsolV energies are expected to be in eV Optional for reaction computations provide enthalpies of vaporization for the product compounds The input of the product AH Hj is possible via the prod_Hvap Hj Hj2 command where H Hj are the zero pontenergies values that will be used for the product compounds defined by the compound numbers or names as given by the react j j2 Of nreact name name commands The energies Ej are expected to be real numbers For the keywords prod _Hvap and prod HvapH the given energies are expected to be in atomic units Hartree for the keyword prod HvapC energies are expected to be in kcal mol for the keyword prod _Hvapd energies are expected to be in kJ mol and for the keyword prod_HvapvV energies are expected to be in eV 192 5 5 Property Computation via co moment QSPR 5 5 1 o moments As already noted in first COSMO RS paper the c potential eq 1 5 of a given liquid pure compound or mixture S can be represented by a Taylor series with respect to o us o ies with Mx p o o do 5 5 1 1 l The c are o moment coefficients SMC s describing the liquid system S and Mx are the o moments of solute X The zero order c moment M is the molecular area of the compound or system the first o moment M is the negative of the total charge of the compound or system the second c m
347. put section 2 2 Optional If this keyword is used COSMOtherm automatically searches for the vapor pressure property files for all molecules given in the compound input section The vapor pressure property files are expected to be of the form name vap where name is the name derived from the according COSMO file name cosmo as given in the compound input section Cf also the VPf name keyword in the compound input section of the COSMOtherm input file see section 2 2 Optional Create VRML files of the molecular geometry of all molecules that are read in the compound input section If this option is used for all molecules name cosmo a VRML file name_mol wrl will be created Cf also the Cwrl name wrl keyword in the compound input section of the COSMOtherm input file see section 2 2 Optional Create VRML files of the molecular COSMO surface charges of all molecules that are read in the compound input section If this option is used for all molecules name cosmo a VRML file name_sig wrl will be created Cf also the Swrl name wrl keyword in the compound input section of the COSMOtherm input file see section 2 2 Optional Create VRML files of the molecular QSPR property surface of all molecules that are read in the compound input section If this option is used for all molecules name cosmo a VRML file name_prop wrl will be created This option is valid only if the OSPR or QSPR_SI option is given in the global command se
348. pvap option Input of a reference temperature Tke is possible via keywords use_tref use tref_C use _tref K or use _tref F processing reference temperature values in units degree Celsius for the first two keywords Kelvin and Fahrenheit respectively Input of reference pressure Pres is possible via keywords use_pref use pref Pa use pref kPa use pref bar oruse pref psia processing reference pressure values in units millibar Pascal kiloPascal bar and psia respectively Further for pure compound and mixture vapor pressure predictions there is the possibility to use the compound s experimental normal boiling point temperature as reference point s The compound s boiling point temperature as read from the compound input line or from the vapor pressure property file see section 2 2 is used as reference temperature Tret Tsoi assuming normal boiling point conditions thus the reference pressure used is PretlTRet 1 atm 1013 25 mbar The usage of pure compound boiling points in a pure compounds vapor pressure prediction is toggled by the keyword use_tboil which either can be given in the pvap mixture line where it is active for this mixture only or in the global input lines where it will be active for all pvap computations given The adjustment of the vapor pressure prediction with the given boiling point data is possible for pure compound vapor pressure computations as well as for mixtures In the latter case COSMOtherm will perfor
349. qm Ej Ej command where 51 E 2 are the energies values that will be used for the reactant compounds defined by the compound numbers or names as given by the prod j j2 Of nprod name name commands The energies E are expected to be negative real numbers For the keywords prod eqm and prod _eqmH the given energies are expected to be in atomic units Hartree for the keyword prod _eqmC energies are expected to be in kcal mol for the keyword prod _eqmJ energies are expected to be in kJ mol and for the keyword prod_eqmvV energies are expected to be in eV Optional for reaction computations provide external zero point energies for the product compounds The input of the product zero point energies EZP is possible via the prod _zpe EZP EZP 2 command where EZP EZP 2 are the zero pontenergies values that will be used for the reactant compounds defined by the compound numbers or names as given by the prod j j2 or nprod name name commands The energies E are expected to be real numbers For the keywords prod_zpe and prod_zpeH the given energies are expected to be in atomic units Hartree for the keyword prod_zpeC energies are expected to be in kcal mol for the keyword prod_zped energies are expected to be in kJ mol and for the keyword prod_zpevV energies are expected to be in eV 190 Suboptions of the reaction op
350. quantum chemistry programs However there is a general set of element specific descriptors that are required for the construction of the COSMO surfaces by the quantum chemistry programs The COSMO radii We recommend to use the following optimized COSMO radii A for elements 2 Element Ycosmo H T300 B 2 048 2 000 N 1 830 O L120 F L120 Al 24 153 Si 2 200 P 2 106 S 2 160 C1 2 050 Zn 1 626 Ge 2 700 As 2390 Se 2 200 Br 2 160 Sn 2 550 I 25320 Pb 2 360 If there is no optimized COSMO radius for a certain element the radius parameter can be estimated reasonably from ryaw the elements van der Waals radius rcosmo Evaw 1 17 Recommended values for van der Waals radii of the elements can be found in the review article of Bondi and Mantina et al For elements that are used as atomic ions only i e no covalent bonding the same estimate rcosmo fyaw 1 17 can be used However in this case we recommend the covalent radii ryan as provided by Sutton Atom Ions Xcosmo Li 1 570 Na 1 800 K 2 290 gt Bondi A J Phys Chem 68 441 1964 gt 6Mantina M Chamberlin A C Valero R Cramer C J and Truhlar D G J Phys Chem A 113 5806 2009 Sutton L Ed Tables of Interatomic Distances andConfiguration in Molecules and lons 18 Spec Publ London 1965 159 3 The COSMOtherm Parameter File The COSMOtherm Parameter files CTDATA files discernible by the ending ctd contain al
351. r of the atomic compound It is expected to be an integer number Argument factor is expected to be a real number Global input option Allow hydrogen bonding donor capacity for atomic cation compounds Global input option scale hydrogen bonding temperature dependency parameter Wy with factor The argument factor is expected to be a real number Global input option scale hydrogen bonding temperature dependency parameter d with factor The argument factor is expected to be a real number Global input option scale COSMO file symmetry detection thresholds with factor The argument factor is expected to be a real number larger than zero Global input option scale gas phase energy file symmetry detection thresholds with factor The argument factor is expected to be a real number larger than zero 224 5 12 COSMOmic COSMOnmiic is a plugin option of COSMOtherm and its graphical user interface COSMOthermxX COSMOmic models surfactant micelles or bio membranes as inhomogeneous layered liquids allowing the calculation of membrane partition coefficients and free energy profiles of solutes in a micelle or a membrane Details of the methodology are described in Ref Further particulars of the methodology as well as as some practical guidelines for the use of COSMOmic can be found in the COSMOmic documentation that is available in the COSMOthermX graphical user interface Please note that the COSMOmic plugin is not available in default COS
352. r salt have a fixed ratio according to the IL salt stoichiometry This means that within COSMOtherm the IL salt is treated by means of the individual ions but on output the results of the individual ion s properties are combined to form a single IL or salt phase Please note that is also possible to include neutral components into the definition of the IL or salt phase Thus molecular complexes and related multicomponent associates where two or more distinct molecular components are assumed to be tied together e g salts like gypsum CaSO 2H O where the ionic components are associated with one or several solvent molecules can be treated with the binary and ternary IL option as well In such a case i e if a salt like gypsum is dissoluted in solvent water which also is a component of its salt stoichiometry COSMOtherm will solve the thermodynamic equilibrium condition for this system and notify this in the output table of the solubility In practice a binary VLE LLE or SLE computation containing an IL or salt phase is toggled by the command binary i IL command where i is the number of the solvent phase i e a neutral solvent compound with number i as given in the sequence of compounds in the compound input section and IL denotes the IL or salt phase as defined by the IL and IL_n input options below Alternatively the nbinary name IL command can be used where name is the name of the solvent phase compoun
353. r weights for the atoms of this compound Weights are arbitrary real numbers divided by blank spaces and are expected in the sequence of the geometry read from the cosmo cos or ccf file By default weights for all atoms are 1 See also section 5 3 Optional Give weights for the atoms of this compound For the iw1 option by default weights for all atoms are 0 For atoms with the numbers n nz n weights are set to 1 Numbers n n na are the atom numbers in the sequence of the geometry read from the cosmo cos or ccf file See also section 5 3 Optional Give weights for the atoms of this compound For the aw atom numbered weights option default weights for all atoms are 1 or as given by the wdfl w option see below This default is overwritten by the weights that are given as arguments of the aw n w n2 W2 n3 W3 option weights have to be given in the format n w i e separated by a colon where n is the atom number in the sequence of the geometry read from the cosmo cos or ccf file and w is the atomic weight integer or real number All n w entries have to be separated by blanks Optional Give weights for the atoms of this compound Input Syntax is the same as for the aw option above For the awu atom numbered weights with default unity option default weights for all atoms are 1 Optional Give weights for the atoms of this compound Input Syntax is the same as for the aw option above F
354. rameters is toggled with the THF BASE suboption of the PKa isorvent ineutrar ron Command Note that the solvent isojyent OF NAMEgojyent that is used in the pKa or npKa command is required to be n tetrahydrofuran if the THF BASE keyword is used Suboptions of the pKa or npKa command are WATER ACID Default for pKa computations Use aqueous acid pK LFER parameters c and c from the COSMOtherm parameter file This is the default setting for pKa computations WATER BASE Optional for pKa computations Use aqueous base pK LFER parameters c and c from the COSMOtherm parameter file DMSO ACID Optional for pKa computations Use dimethylsulfoxide DMSO acid pK LFER parameters c and c from the COSMOtherm parameter file ACETONITRILE ACID Optional for pKa computations Use acetonitrile MeCN acid pK LFER parameters co and c from the COSMOtherm parameter file ACETONITRILE BASE Optional for pKa computations Use acetonitrile MeCN base pK LFER parameters co and c from the COSMOtherm parameter file HEPTANE ACID Optional for pKa computations Use n heptane HEPTANE acid pK LFER parameters c and c from the COSMOtherm parameter file THF BASI Optional for pKa computations Use tetrahydrofuran THF base pK LFER BI parameters co and c from the COSMOtherm parameter file 40 Frank Eckert Ivo Leito to be published 107 2 3 7 Automatic Calculation of
355. ransition from gas to liquid state Gas i i i Hi Egas E cosmo ring Ring cas 5 11 6 78 A Klamt COSMO RS From Quantum Chemistry to Fluid Phase Thermodynamics and Drug Design Elsevier Science Ltd Amsterdam The Netherlands 2005 ISBN 0 444 51994 7 222 The gas phase chemical potential related parameters can be modified in terms of scaling the general gas phase parameter ngas This is possible with the ETASET factor command which globally scales 7 by the factor value In addition the entropic ring contribution parameter pj can be modified with the OMRSET factor command which globally scales wp by the factor value Note that modification of neas OF ping ONly affect the gas phase related properties such as vapor pressure Henry law constant and heat of solvation but not the liquid state properties such as activity coefficient The temperature dependence of Of Msas ANA Oring is accounted for in the simple functional form of eq 5 11 7 CGas T CGas T WA k Z A Tr CG oom 5 11 7 The temperature dependency parameters t and 7 can be scaled via the TETSET factor and TORSET factor commands 5 Miscellaneous options The thresholds of the symmetry detection as used in the conformer equilibration and the musym option can be modified with the SYMCSET factor command for the symmetry detection of the geometries read from COSMO files and with the SYMGSET factor
356. rcs keywords Required for solgas computations alternative to solvent option Give finite solvent mixture concentration at which the gas solubility shall be computed The input of the concentrations is possible either in mole fractions xs or mass fractions cs of the compounds of the mixture as real numbers x and c The arguments are expected as real numbers between zero and one in the same sequence of compounds as given in the second input area If the values do not add up to one COSMOtherm will normalize them If less mole fractions concentrations than compounds are given the missing ones will be assumed zero If a negative number is given the concentration for this compound will be inserted automatically using the normalization of the sum of mole fractions Only one negative number is allowed per mixture input line Note an alternative definition of the solvent in the solgas option is possible with the solvent ornsolvent keywords Optional for solgas computations Give the pressure accuracy threshold for the iterative gas solubility calculation The gas solubility value will be optimized iteratively until the difference of the predicted partial vapor pressure p and the given reference pressure p is less than thresh The argument thresh is expected to be a positive real number The default value is pthresh 0 1 mbar Optional for solgas computations Give the maximum number of iteration that shall be done in the iterative gas so
357. re prediction The use tboil option is valid for pure compound and mixture vapor pressure predictions Optional for pvap computations Use the temperature dependent experimental pure compound vapor pressure p T as given in the compound input section or read from a compounds vapor pressure property file cf section 2 2 as a reference point for scaling the vapor pressure prediction The use pvapt option is valid for pure compound and mixture vapor pressure predictions Optional for pvap computations of mixtures Print partial pressures of the compounds in the mixture to the results table 75 Suboptions of the pvap command continued use_tref value or use_tref C valu or use _tref K valu or use _tref F valu use pref value or use pref Pa valu or use tref kPa valu or use tref bar valu or use _tref psia valu Optional for pvap computations Input of reference temperature Tres for the purpose of scaling the vapor pressure prediction to match a pair of given reference temperature Tke and pressure Pre The argument of the use _tref value option is expected to be a real number temperature which is expected to be in C for keywords use _tref and use tref C in K for keyword use_tref_K and in F for keyword use tref F Optional for pvap computations Input of reference pressure Pres for the purpose of scaling the vapor pressure prediction to match a pair of given refere
358. re prediction of the pvap option see section 2 3 1 Optional for the input of experimental pure compound vapor pressures Use the temperature dependent experimental pure compound vapor pressure P t T as given in the compound input section or read from a compounds vapor pressure property file as a reference point for scaling the vapor pressure prediction of the pvap option see section 2 3 1 19 2 1 2 Print Options for the COSMOtherm Output File wemn wconf nocompw nomix long wtln notempty ctab Optional Write the compound mixture number to the right side of the output file This information can be used to efficiently process the output file e g via the UNIX command grep Optional If a compound input consists of several conformers see next section the wconf option toggles the output of the calculated COSMOtherm mixture information for each individual conformer By default only the results for the compound are written to the output file Optional Do not write the pure compound information to the output file Only notes warnings or error messages will be printed to the compound section of the output file Optional Do not write the mixture information to the output file Only notes warnings or error messages will be printed to the mixture section of the output file Optional In the output file print all real numbers in scientific exponent number format with 15 significant digits e g real number
359. re processed in COSMOtherm l e if several options are used simultaneously a vpinp input value for the vapor pressure will override any vapor pressure equation data given which itself overrides the use_tboil option which overrides COSMOtherm s native vapor pressure estimates 108 By default the mole fractions of the compounds in the gas phase y are written to the output and the table file for each mixture The computed partial pressures of compounds p y Pt by default are written to the output file only The additional keyword pr_pp given in the same line as the binary ternary or multinary option toggles the printing of the partial pressures of compounds p to the COSMOtherm table file replacing the entries for mole fractions of the compounds in the gas phase y By default the excess Gibbs free energy Gf and the excess enthalpy Hf are written to the output and the table file for each mixture The additional keyword HE SPLIT given in the same line as the binary or ternary command toggles the printing of the three contributions to the total excess enthalpy to the COSMOtherm table and output files The three contributions to HF are the misfit excess enthalpy H MF a contribution from hydrogen bonding H HB and a contribution from van der Waals interactions H vdW If several conformers are present for a given compound the computed values of the phase diagram properties of the conformers will be averaged due to the Boltzmann dist
360. recipitation phase are computed according to the solid state free energy of the compound i e s4 4P AG Thus for a LIQ EX calculation with solid phase the Gibbs free energy of fusion AG has to be taken into account for all compounds that are assumed to be solid The solid compounds Gibbs free energy of fusion can be given in the compound input lines or read from the compounds vapor pressure property files vap files The input and processing of the Gibbs free energy of fusion data is fully equivalent to the input and processing guidelines described in section 2 3 4 Automatic Solubility Calculation of this manual For further particulars on input and computation of Gibbs free energies of fusion we refer you to this section In addition to the definition of individual neutral compounds as solids by means of the compounds AG it is also possible to define solid salts by means of a salts AG To define possible salt precipitation into the solid phase k the solid salt has to be given by means of the salts composition i e the ions of which it is made of its stoichiometry and the Gibbs free energy of fusion of the salt AG The input of the salt composition stoichiometry and heat of fusion is fully equivalent to the input of these properties in the Salt Solubility option See subsection Solubility of Salts Complexes and Cocrystals of section 2 3 4 of this manual for further details Note that in contrast to the salt solu
361. results for the decadic logarithm of x o the chemical potential of the solute in the initial solvent ui the mass based solubility w g g and if possible the molar solubility Sin mol l for definition of the latter two see below will be printed to additional columns of the COSMOtherm table file Please note that the iterative solubility computation is ambiguous and physically ill defined if the solute is part of the solvent mixture e g if you want to compute the iterative solubility of water in a given mixture of 0 9 mole fractions of octanol and 0 1 mole fractions of water In such a case COSMOtherm will assume that the solute concentration in the solvent is zero and compute the iterative solubility in the resulting solvent mixture in the given example COSMOtherm will compute the iterative solubility of the water in the pure octanol The additional solubility unit conversions mass based solubility and molar solubility see below will be done using the original solvent concentrations however In general there is no guarantee that the iterative solubility option will converge to a refined solubility value If the convergence of iterative refinement of the solubility fails the noniterative solubility value will be printed to the COSMOtherm table file and a warning message will be printed to the table and output files In addition the noniterative solubility value printed to the COSMOtherm table file will be enclosed by square brackets I
362. ribution of the conformers total free energies at the given temperature and mixture concentration see section 2 2 2 By default only the average property of the compound is printed to the output and table file The global keyword wconf see section 2 1 toggles the printing of all conformer thermodynamic properties as well as conformer weights for all temperatures and mixtures to the output file For the often large number of temperature and mixture state points that are computed in the course of an automatic phase diagram calculation it might be difficult to extract the conformer information from the output file Thus an additional suboption has been introduced into the automatic phase diagram calculation options which allows the printing of the conformer weight factors to the phase diagram table in the COSMOtherm table file The keyword confweight given in the same line as the binary ternary or multinary command toggles the printing of the conformer weights to the binary ternary or multinary phase diagram table output For each of the conformers of the given compounds or all compounds in the case of a multinary computation there will be added a column with the conformers Boltzmann weight factor added to the phase diagram table If no conformers are present for a compound only one additional column will be written and the conformer weight factors in this column will all be equal to one General printing suboptions of the binary ternary or multinary
363. rm based on the D3 method of Grimme et a This parameter set is considered to be the best quality set currently offered by COSMOlogic Use it with quantum chemical COSMO calculations based on Turbomole BP86 functional and def2 TZVPD basis set single point calculations with the novel fine grid marching tetrahedron cavity FINE COSMO based upon geometries optimized with BP86 functional and TZVP basis set DMOL3_PBE_C30_1501 ctd Use with quantum chemical COSMO calculations DMOL3 PBE functional DNP basis set on fully optimized geometries 5a Mohr P J Taylor B N Newell D B CODATA Recommended Values of the Fundamental Physical Constants 2010 National Institute of Standards and Technology Gaithersburg Maryland 20899 8420 USA Web physics nist gov constants 59 Reinisch J Klamt A Eckert F A Comprehensive Description of the Current State of COSMO RS and its Hydrogen Bond Expression in preparation for J Comp Chem 2015 60 Grimme S Antony J Ehrlich S Krieg H J Chem Phys 132 154104 2010 161 The COSMOtherm program is fully downward compatible to older parameterizations Nevertheless it is strongly recommended to use only the new parameterizations shipped with Version C3 0 Release 15 01 of the COSMOtherm program Moreover please note that the use of older parameterization versions may lead to a reduced functionality and or prediction quality in COSMOtherm This is the case for all G9
364. rming molecules This can be achieved by adding an argument bracket to SSC option i e SSC_PROBABILITY c n n2 Or SSC_STRENGTH c n nz see suboptions table below These special SSC options may be helpful if a specific cluster complex geometry is sought that is not the geometry of the most probable contact or lowest interaction energy obtained from the SSC PROBABILITY and SSC_STRENGTH options as given without argument In addition to searching the segments on the molecular surfaces of the two compounds that have the most probable contact or the lowest interaction energy the SSC options will probe several orientations of the two molecules in the complex and create the complex geometries of the most favourable orientations By default the dihedral angle between the two contacting molecules in the cluster is varied with a stepsize of 45 This stepsize can be changed using the keyword ssc_ang angle Apart from cluster complex geometries it is possible to create ionic structures using the SSC_IONS suboption of the SSC_PROBABILITY or SSC_STRENGTH options If this keyword is given COSMOtherm will create two additional geometry xyz files for each cluster The ions are built are created by shifting the hydrogen atom that is doing the contact interaction from one cluster compound to the other one thus simulating the dissociation reaction of the interacting compounds The SSC options i e the contact cluster complex and ion geometry generation to
365. rod_eqmC E E kcal mol prod_eqmJ E E kJ mol prod_eqmV E Ejo eV Optionally the zero point vibrational energies as used in eqs 5 4 5a and 5 4 6a can be given by the keyword react_zpe EZP EZP where EZP are zero point vibrational energies in atomic units for the reactant compounds i iz It is also possible to give the zero point vibrational energies in atomic units Hartree react_zpe EZP Ej and react_zpeH EZP EZPj option in kcal mol react_zpeC EZP EZPj gt option in kJ mol react_zpeJ EZP EZPj option or in eV react_zpeV EZP EZP option Equivalently the zero point vibrational energies of the product compounds can be given with the keyword prod_zpe EZP EZP or its variants for different energy units prod_zpeH EZP EZP gt Hartree prod_zpeC EZP EZP kcal mol prod zpeJ EZP EZP kJ mol prod_zpeV EZP EZP eV All of the react_ prod_ options for the input of external QM or ZPE energies assume that the given energies are compound energies which already are averaged over conformers if there are any Alternatively the external QM or ZPE energies can be read individually for compounds conformers in the molecule input of the compound input section or fro
366. s given the argument i is expected to be a positive integer number which is the compound number in the sequence that was given in the compound input section The nreaction name option computes the reaction equilibrium in the compound of the name name By default the reaction equilibrium is calculated at infinite dilution in compound i name It is also possible to calculate the reaction in a solvent mixture using the mixture concentration input xr or cr command see section 5 4 If such a finite concentration input is used arguments i or name need not be given to the reaction or nreaction option 62 B Property calculation options continued VLE calculation binary binary i j or nbinary name name ternary ternary i j k or nternary name name name multinary Optional Toggle the automatic calculation of the phase diagram and the excess properties of a binary two compound mixture see section 2 3 7 This option is valid only if the total number of compounds is two Optional Toggle the automatic calculation of the phase diagram and the excess properties of a binary two compound mixture see section 2 3 7 This option is applicable if the total number of compounds is larger than two For the binary i j option the binary phase diagram is computed for the two compounds with the compound numbers i and j in the order of compounds given in the compound input section For the nbinary name na
367. s in that it integrates concepts from quantum chemistry dielectric continuum models electrostatic surface interactions and statistical thermodynamics Still COSMO RS is based upon the information that is evaluated by QM COSMO calculations Basically QM COSMO calculations provide a discrete surface around a molecule embedded in a virtual conductor Of this surface each segment i is characterized by its area a and the screening charge density SCD o on this segment which takes into account the electrostatic screening of the solute molecule by its surrounding which in a virtual conductor is perfect screening and the back polarization of the solute molecule In addition the total energy of the ideally screened molecule Ecosmo is provided Within COSMO RS theory a liquid is now considered an ensemble of closely packed ideally screened molecules In order to achieve this close packing the system has to be compressed and thus the cavities of the molecules get slightly deformed although the volume of the individual cavities does not change significantly Each piece of the molecular surface is in close contact with another one Assuming that there still is a conducting surface between the molecules i e that each molecule still is enclosed by a virtual conductor in a contact area the surface segments of both molecules have net SCDs o and o In reality there is no conductor between the surface contact areas Thus an electrostatic interaction arises from
368. s nam and nam as given in the compound input section of the COSMOtherm input file i e either the names of the COSMO files without extension or the name given via the comp name option The o potential similarity will be weighted by the o profile of the compound with the name nam If the third argument k or nam is not given the unweighted non solute specific o potential similarity as defined above is computed Optional for simpot or nsimpot computations Give finite mixture concentrations for the two phases between which the sigma potential similarity coefficient shall be computed The input of the concentrations is possible either in mole fractions xs1 xs2 or mass fractions cs1 cs2 of the compounds of the mixture as real numbers x and c The arguments are expected as real numbers between zero and one in the same sequence of compounds as given in the second input area If the values do not add up to one COSMOtherm will normalize them If less mole fractions concentrations than compounds are given the missing ones will be assumed zero If a negative number is given the concentration for this compound will be inserted automatically using the normalization of the sum of mole fractions Only one negative number is allowed per mixture input line 65 B Property calculation options continued QSPR property calculation options PROPQSPR filename or PROPQSPR C1 Cz Cig prop or PROPQSPR_SI filename
369. s obtained can be used to compute the solubility of solid compounds or salts as well as solid liquid equilibria SLE calculations See sections 2 3 4 and 2 3 7 3 If the Dcpfus_ estimate keyword is given in the compound input section the approximation to ACp is valid for the given compound in all mixture computations 54 Pure compound aqueous dissociation constant pK input pK_acid value or pK_base value Optional Input of experimental aqueous dissociation constants for acidic pK_acid keyword or basic pK_base keyword solutes Argument value is the aqueous pK acid pK_acid option or pK base pK base option value of the given compound The argument is expected to be a real number The pK values thus given can be used to obtain a dissociation correction to partition coefficent calculations with the logp option i e distribution coefficient logD Pure compound UNIQUAC parameter input options UNIQUAC_RI ri UNIQUAC_QI qi Optional Give UNIQUAC volume parameter r for this compound The given r value will be used in the fitting of UNIQUAC2 parameters for binary VLE see section 2 3 7 1 Argument ri is expected as a real number larger than zero Optional Give UNIQUAC surface area parameter for this compound The given q value will be used in the fitting of UNIQUAC2 parameters for binary VLE see section 2 3 7 1 Argument qi is expected as a real number larger than zero Compound dielectric constan
370. s phase energy file the energy should be given as a single number free format without any further text or other control characters For keywords ef and efH the energy is expected in atomic units Hartree for efJ and efc it is expected in kJ mol or kcal mol COSMOtherm will search the actual working directory or if specified the directory given by the fdir command for the gas phase energy files Note that it is also possible to automatically search for the gas phase energy files for all of the molecules given in the compound input section via the global command Efile or its variants EHfile EJfile or ECfile see section 2 1 The filename of the energy file must not contain blank spaces unless it is given in quotes e g ef name 0 energy Optional for the input of gas phase energies switch off the usage of gas phase minimum conformer energies in single conformer calculations see below 43 If the gas phase energy is read from a gas phase energy file name energy the COSMOtherm file name and file format conventions have to be met The energy files have to follow the name of the cosmo file they are associated with e g ethanol0 energy is appendant to ethanol0 cosmo The energy file itself can be provided in two alternative formats a Plain energy format The gas phase energy file is expected to contain the gas phase energy as a single number in the first line of the file E g ethanol0 energy holds 155 1064483
371. s_ salt or DHfus_salt_SI The net entropy of fusion of the salt as used in eq 2 3 4 can be given by options DSfus_ salt or DSfus SALT SI The net heat capacity of fusion of the salt as used in eq 2 3 3 or 2 3 4 can be given by options Dcpfus_ salt or Depfus_ SALT SI The net melting temperature of the salt as used in eq 2 3 3 or 2 3 4 can be given by options Tmelt_ salt Tmelt_salt_C orTmelt_salt_K see below for details All of these input options expect net salt data values that are defined for the salt as defined in composition and stoichiometry by the salt and salt_n commands Thus no individual ion heat of fusion data can be used for salts The ACp estimate described above for neutral compounds solubility toggled by the keyword Depfus_ estimate may also be used in combination with salts However following the considerations taken above the ACp estimate should only be used with great caution when it comes to the computation of salt solubilities Please note the ambiguity in the definition and use of given free energy of fusion data described above by default the definition 2 3 1a is used which means that the free energy of fusion computed from experimental heat of fusion data or given explicitly in the input will be used as is in equation 2 3 1a If the keyword dgfmean is given in the same line as the salt solubility and salt heat of fusion data input the alternative definition of the mean ionic free energy of fusion as g
372. sage to the bottom of the COSMOtherm output file and stop execution In addition an error code ierror will be sent to the command line shell window or if the graphical user interface COSMOthermx is used a separate message window with the error code will pop up The following error codes can be given by COSMOtherm COSMO therm Error Codes error 1 ERROR Input file missing Usage cosmotherm file inp error 2 ERROR COSMOTHERM input file not found error 3 ERROR COSMOTHERM input file is damaged or empty error 4 ERROR COSMOtherm parameter file not found error 5 ERROR COSMOtherm license file not found error 6 ERROR COSMOtherm database file not found error 7 ERROR Maximum number of DATABASE entries exceeded error 8 ERROR Parameter file version is newer than program version ERROR Please use appropriate parameter file error 9 ERROR Parameter file has a wrong format ERROR Please use appropriate parameter file error 10 ERROR Compound not found in database index file error 11 ERROR Missing argument for given compound input error 12 ERROR Could not find cosmo cos ccf or mcos file for given compound input error 13 ERROR Cannot read file ERROR Unknown Illegal COSMO file format error 14 ERROR No AUTOC conformers found within the number range requested by USEC command ERROR Exiting with FILE NOT FOUND error Error 15 error 15 ERROR Could not find file error 16 ERROR Problem oc
373. shold 1 0E 5 maxiter value Optional for binary ternary or multinary computations with iterative LLE search give the maximum number of iterations for the iterative LLE point calculation Argument value is expected to be a nonzero positive integer number Default is maxiter 1000 LLE NEW Optional for binary computations Search the computed binary mixture for points of phase separation liquid liquid equilibria This option is searching the LLE on a fine grid using additional mixture concentrations points In addition to the binodal LLE found by the regular LLE option the LLE_NEW option also computes the spinodal miscibility gap see section 2 3 7 2 conf dx value Optional for binary computations with LLE NEW search give the accuracy threshold for the iterative refinement of the LLE NEW calculation Argument value is expected to be a nonzero positive real number Default is conf_dx 1 0E 5 maxiter dx value Optional for binary computations with LLE NEW search give the maximum number of iterations for the iterative LLE NEW point calculation Argument value is expected to be a nonzero positive integer number Default is maxiter_dx 400 Other general control options of the binary ternary and multinary options use tboil Optional for the input of boiling point temperatures use the pure compound boiling points Tzv or a pair of reference pressure and temperature P
374. sis set on top of an optimized BP TZVP COSMO geometry The COSMO single point calculation is using the large TZVPD basis set with additional diffuse basis functions and a novel type of molecular surface cavity construction fine grid marching tetrahedron cavity FINE which creates a COSMO surface whose segments are more uniform and evenly distributed compared to the standard COSMO cavity The gas phase energy files of this level are optimized on Turbomole BP RI DFT level with TZVP basis set followed by a single point BP RI DFT calculation with larger TZVPD basis set The associated BP_TZVPD_ FINE _C30_1501 ctd parameter set additionally incorporates a novel hydrogen bonding term HB2012 and a novel van der Waals dispersion term based on the D3 method of Grimme et al which shows improved thermodynamic property prediction results for compound classes where the classical COSMO RS hydrogen bonding term showed weaknesses e g with secondary and tertiary aliphatic amines and polyether compounds In addition the wider realm of organic liquid and gas phase thermodynamics is predicted with the same quality or slightly better than the standard BP TZVP COSMO and DMOL3_PBE methods Hence the BP TZVPD FINE level in combination with the BP_TZVPD_FINE C30 _1501 ctd parameterization is considered to be best quality calculation method that we currently offer Until further experience is gained this level of theory and parameterization are provided i
375. sition vector For a given start concentration x and the LLE tie points x found via eq 2 3 17 the tangent plane criterion tm can be defined as tm yx fin x In x y 2 3 18 i This number is printed to COSMOtherm output file for all ternary and multinary computation where n gt 2 Actually tm is a measure of the steepness of the tangent between the LLE point the Gibbs free energy minimum and the starting point It may be useful in two situations First if tm is negative the stationary LLE point that was found is not the global minimum of the free energy Second if COSMOtherm detects a discontinuity during the course of a LLE search when stepping from one grid starting point to the next i e if we have the case that the LLE tie points optimized belong to two different phase separations in the system which is noted by a warning message in the COSMOtherm ouput and table files If this is the case the tm values may help to assess the nature of the LLE points found a large tm value implies a steep descent to the Gibbs free energy minimum and thus more likely the global minimum Now if in combination with the COSMOtherm warning message one LLE point yields a large value of tm while the value for the next LLE point in the grid is considerably smaller this suggests that the LLE point with the smaller tm might be a local Gibbs minimum and thus not a stable point of phase separation In both situations noted above it is strongly
376. sons with results from COSMOtherm calculations are also given C J Cramer and D G Truhlar Chemical Reviews 99 2161 2200 1999 Review article on continuum solvation models including COSMO A methodological comparison as well as a large number of applications are presented C J Cramer and D G Truhlar in Reviews in Computational Chemistry Volume IV K B Lipkowitz and D Boyd Editors VCH New York 1995 pp 1 72 Older review article on continuum solvation models including COSMO A methodological comparison as well as a some applications are presented 231 Index conformer block start 57 conformer block end 57 accc 25 activity coefficient 113 automatic computation 61 77 phase diagram 108 140 reference state 77 activity coefficient model NRTL 113 115 UNIQUAC 113 115 Wilson 113 115 ahbset 221 224 amorphous phases 7 200 Antoine equation 51 73 108 140 extended 51 atomic weights 26 34 35 165 173 autoc 19 33 58 aw 34 174 awps 25 awu 34 174 awz 34 174 azeotrope 108 114 B3 LYP 158 160 B88 VWN 163 basis set 158 160 6 31 G d p 158 160 163 DNP 163 SVP 164 TZVP 162 163 164 binary 53 63 108 109 110 111 112 113 115 118 130 137 STL 123 127 ILphase REAL 124 128 SMIX 130 132 MIXphase REAL 130 133 cgrid 110 111 cm 133 confweight 109 HE SPLIT 109 IL 123 128 IL n 123 124 128 nIL 123 128 pr_pp 109 qgrid 110 111 search azeotrope 114 azeo iter thresh 114 maxiter
377. ssing ones are assumed to be zero The property name prop is expected to be a string of up to 20 characters For a further description of the o moment QSPR property computation see section 5 5 Optional Read the o moment QSPR regression coefficients for o moments in Sl units from file filename or directly from the input Syntax see OSPR filename and QSPR c C2 Cig prop option 28 2 1 4 2 Output of molecular geometry files Wcar Wm12 Wsdf Wmol Wxyz Wpdb Optional Write the geometries of all processed compounds name cosmo to molecular structure files name car The molecular geometry will be written in MSI CAR format Cf also the Wcar keyword in the compound input section of the COSMOtherm input file see section 2 2 Optional Write the geometries of all processed compounds name cosmo to molecular structure files name m12 The molecular geometry will be written in Tripos Sybyl mol2 format Cf also the wm12 keyword in the compound input section of the COSMOtherm input file see section 2 2 Optional Write the geometries of all processed compounds name cosmo to molecular structure files name sdf The molecular geometry will be written in MDL ISIS sdf format Cf also the Wsdf keyword in the compound input section of the COSMOtherm input file see section 2 2 Optional Write the geometries of all processed compounds name cosmo to molecular structure files name mol The molecular geometry will b
378. starting from an initial population guess based on u 0 This additional self consistency cycle on top of the COSMO RS equation self consistency results in a somewhat higher COSMOtherm 17 Ben Naim A Solvation Thermodynamics Plenum Press New York and London 1987 computation time if conformers are involved However starting with version C21 0111 COSMOtherm uses a novel conformer equilibration algorithm which significantly improves computation time of the conformer s self consistency This new algorithm is used by default now The old algorithm is still available and can be toggled by a keyword oclp option see sections 2 1 and 2 3 COSMO RS depends on an extremely small number of adjustable parameters the seven basic parameters of eq 1 1 1 3 1 8 and 1 10 plus nine Taw values some of which are physically predetermined COSMO RS parameters are not specific of functional groups or molecule types The parameters have to be adjusted for the QM COSMO method that is used as a basis for the COSMO RS calculations only Thus the resulting parameterization is completely general and can be used to predict the properties of almost any imaginable compound mixture or system All parameters necessary for COSMO RS computations with the COSMOtherm are given in the COSMOtherm parameter files CTDATA files see section 4 that are shipped with each release of COSMOtherm The course of a COSMO RS calculation is illustrated in the flow chart b
379. suggested to rerun the LLE searches using different starting concentrations e g use a finer grid of starting concentrations in the ternary or multinary computation or try starting a new LLE search from inside the LLE points that have been found in the initial run This way ultimately the global Gibbs minima the stable phase separations may be found u Michelsen M L and Mollerup J M Thermodynamic Models Fundamentals and Computational Aspects 2 ed Tie Line Publications Denmark 2007 3 Michelsen M L Fluid Phase Equilib 9 1 1982 Michelsen M L Fluid Phase Equilib 9 21 1982 Baker L E Pierce A C Luks K D Soc Pet Eng J 731 1982 120 2 3 7 3 Solid Liquid Equilibrium Computation for Binary Mixtures For the binary option COSMOtherm also offers the possibility to automatically search for points of solid liquid equilibrium SLE via the keyword SLE If this command is given in the same line as the binary command COSMOtherm will search the computed mixtures for possible concentrations of solidification and if found writes them to the COSMOtherm output file If this option is used COSMOtherm will compute the thermodynamic properties of the binary mixture at 325 additional mixture concentrations that are distributed on an even spaced grid The thermodynamic properties of the additional mixtures are written to the COSMOtherm output file and in tabulated form to the COSMOtherm table file The SL
380. sure of the mixture phase is computed from the contribution of the mixture phase components with respect to their activities based on the concentrations derived from the ratio of the components stoichiometry as well as to the overall concentrations of all compounds in the given binary or ternary phase Hence a mixture phase thus defined as real phase will show the same partial vapor pressure in the binary or ternary MIX system as in a multinary see section 2 3 8 system defined with the same relative and absolute concentrations of the components 130 It is also possible to compute solid liquid phase equilibria SLE for pseudo binary solutions with composite phases A binary MIX SLE computation is toggled with the keyword SLE the same way it is done for binary mixtures of pure compounds see section 2 3 7 3 Solid Liquid Equilibrium Computation for Binary Mixtures To perform a SMIX SLE computation it is necessary to provide experimental data that can be used to compute the free energy of fusion of the composite mixture phase via eq 2 3 18 or eq 2 3 19 and which subsequently can be used in eq 2 3 17 to compute the SLE The input of the required experimental data is equivalent to the input of the salt free energy of fusion used for the computation of lonic Liquid salt SLE see section 2 3 7 4 above the composite mixture phase heat of fusion data input has to be done in the same mixture line where the SLE and M
381. t and refraction index n input options epsilon s Optional Provide the dielectric constant s of this compound Argument s is expected as a real number larger than zero Optional Provide the square of the refraction index n of this compound Argument n is expected as a real number larger than zero 55 Compound density volume and polymer molecular weight input options expdensity p or expdensity SI p or expdensity Brit p expmolvol V or expmolvol SI V freevol VF or freevol st VF expmw MWpolymer ispolymer Optional Provide the experimental density p of this compound The given density will be utilized to calculate the free volume as used in the polymer specific Elbro combinatorial contribution described in section 5 3 2 Argument p is expected as a real number larger than zero For the expdensity option argument p is expected to be in g ml for the expdensity_SI option in g cm and for the expdensity Brit option in lbm ft respectively Optional Provide the experimental molar volume V of this compound The given molar volume will be utilized to calculate the free volume as used in the polymer specific Elbro combinatorial contribution described in section 5 3 2 Argument V is expected to be a real number larger than zero For the expmolvol option argument V is expected to be in A and for the expdensity_ SI option in nm respectively Optional Provide the free volume V
382. t be cut in between In addition COSMOtherm results are vastly improved if complete groups the CH groups in the above example and not only single atoms for example single H atoms are weighted or zeroed out Currently at COSMOlogic a program COSMOquick COSMOfrag is available which is able to automatically construct metafiles that are reasonable in this respect The COSMO metafile generation in the COSMOquick COSMOfrag program is based upon a very large database of molecular fragments CFDB Second the weights provided in the COSMO metafiles depend on the sequence of atoms in the underlying COSMO files l e a COSMO metafile is not necessarily transferable between different sources of COSMO files for example if a molecule was optimized using different starting geometries at different levels of quantum chemical theory the sequence of atoms in the resulting COSMO files might differ However in 64 Loschen C Klamt A COSMOquick COSMOlogic GmbH amp Co KG 2014 174 COSMObase the database of COSMO files provided by COSMOlogic the metafiles are fully transferable between the COSMO files of all the quantum chemical methods In addition it should be noted that the molecular volume of molecules constructed via COSMO metafiles or atomic weights can only be determined approximately However the volume is usually approximated within lt 10 deviation from the exact COSMO volume Note that the quality of the approximated volume als
383. t corresponds to the approximation that xol Iye This zero order solubility is valid only for small concentrations of the solute i e if the solubility itself is small If the solubility of the solute in the solvent is large x o gt 0 1 x lt o is a poor approximation However Xso can be refined iteratively If the zero order x o is re substituted into the solubility calculation a better approximation for Xso is achieved logy o x5 uP Ww x8 max 0 AG RT In 10 2 3 2 j j l e the solubility now is calculated in a mixture of the solvent with solute j in a mole fraction concentration x The x lt 9 value thus computed can again be re substituted into the solubility equation and again a better guess for x can be achieved This procedure can be iterated until the computed value of Xo is constant In practice the iterations are done until the difference of Ix X sol is below a given threshold In COSMOtherm this iterative procedure is toggled with the keyword iterative which is a sub option of the solub or nsolub option To avoid long calculation times it is possible to limit the maximum number of iterations in an iterative solubility calculation using the keyword max_iterations If the iterative solubility computation is used it is possible to print the noniterative results to the table output file as well using the pr_ni print noniterative results keyword If pr ni is given the noniterative
384. t file i e if the default visualization is used or if map_column 6 is given Optional suboption of the wrlmap mapfile command Set the minimum value min val for the property visualization of a COSMO surface property map mapfile By default this value is determined automatically from the smallest value of the property given in the property column of mapfile If the wrl min command is used the color management for the COSMO surface property map is adjusted according to the given min val Optional suboption of the wrlmap mapfile command Set the maximum value max val for the property visualization of a COSMO surface property map mapfile By default this value is determined automatically from the largest value of the property given in the property column of mapfile If the wrl max command is used the color management for the COSMO surface property map is adjusted according to the given max val 207 5 7 3 Creation of Cluster and lon Geometries based on Contact Statistics Using the SSC_PROBABILITY or SSC_STRENGTH option it is possible to create geometry files of the most probable surface segment contacts SSC of any two molecules in a given mixture These options may be helpful to visualize and thus better understand the actual contact interactions between any two molecules that are present in a given mixture Moreover these options may be used to find the most probable structures of the molecular complexes or clusters built or not built b
385. t phase and the xf2 x x Or C 2 c Co commands for the second solvent phase 218 COSMOtherm can use the experimental interfacial tension of the two solvent phases to improve the computed FlatSurf energies This is possible with the IFT value keyword The value of the interfacial tension is expected to be in dyne cm Values for interfacial tensions of various solvent solvent or air solvent combinations can be found e g in the CRC Handbook of Chemistry and Physics Please note that the IFT option considerably increases the computational time of a FlatSurf calculation The immersion and geometric partition of a solute in the two phases can be visualized with the Fwrl command This keyword either can be given in the global command section or in the mixture input section It is only active if a FlatSurf calculation is done The Fwr1 command provides a graphical representation of the immersion depth z of a solute between the two solvent phases The immersion in the phase is shown on the charge surface in the form of a black and white ring where the black part of the ring points towards FlatSurf solvent phase 1 and the smaller white part of the ring point towards FlatSurf solvent phase 2 Thus the ring indicates how the solute molecule is immersed in each of the two phases Suboptions of the FlatSurf or nFlatSurf commands are xf1 x X Optional for FlatSurf computations Give finite mixture concentrations for or the two
386. t restricted to simple binary salts with ionic components It is also possible to 95 include neutral components into the definition of the salt compound Thus complexated salts salt compound that include one or several molecules of a solvent in their crystal lattice e g gypsum CaSO 2H O and even cocrystals two or more distinct molecular components within the crystal lattice that are assumed to crystallize together can be treated with the salt solubility option as well In such a case i e if a salt like gypsum is dissoluted in solvent water which also is a component of its salt stoichiometry COSMOtherm will solve the thermodynamic equilibrium condition for this system and notify this in the output table of the solubility If the salt and salt_n options are given as additional input to an automatic solubility computation solub option input line COSMOtherm will compute the solubility of the salt of the given composition and stoichiometry via eq 2 3 1a and write the results to the COSMOtherm output and table files If the salt option is used COSMOtherm only will compute the solubility of the given solute salt or cocrystal compound this is unlike the simple solub option for individual neutral compounds which always computes the solubilities of all compounds as given in the compound input The options for the choice of the solvent solub i or nsolub name options or a solvent mixture xs x x2 OF CS C X2 options
387. tains 6 generic parameters plus one additional parameter for each element Starting with release version C21_0110 of COSMOtherm the density QSPR model of eq 2 3 25 has been expanded by one additional descriptor namely M7 the square of the compounds second o moment leading to a sum of 7 generic descriptors and parameters in the model This additional nonlinear descriptor improves the prediction for the core chemistry of neutral liquid compounds and in addition it widens the application range of the model towards ionic species namely lonic Liquids and zwitterionic compounds which now can be predited with the same QSPR model and at the same quality as simple neutral compounds The QSPR coefficients in eq 2 3 25 are valid for a specific temperature only because the density volume QSPR model does not include a temperature dependency term If several conformers are present for a given compound COSMOtherm will compute the density descriptors of all individual conformers and subsequently do a thermodynamic average of the conformer descriptors at the given temperature condition from which the averaged density of the compound is predicted Please note that due to its major importance water is treated as a special case in that the experimental value of the density and volume are given by the density option If possible the six generic QSPR parameters and the element specific surface area parameters are read from the COSMOtherm parameterization file CTDATA
388. te with Version C1 2 of COSMOtherm Thus there is only one COSMOtherm parameterization for each quantum chemical level of theory and basis set Please note that it is still possible to use any of the older parameterizations The COSMOtherm program is fully downward compatible to older parameterizations Nevertheless it is strongly recommended to use the new C30 1501 parameterizations shipped with Version C3 0 Release 15 01 of the COSMOtherm program 160 Please note that starting with version C3 0 Release 15 01 of the COSMOtherm program the unit conversions and fundamental physical constants used in the COSMOtherm parameterizations Avogadro constant N Boltzmann constant k Elementary charge e Electron mass m Planck constant h and Electric constant e were updated according to the latest NIST CODATA recommendations In older parameterization files the original values of the physical constants and unit conversions have been retained to ensure downward compatibility of the predictions with these parameter sets 3 2 Parameterization Usage All COSMOtherm parameter files CTDATA files name ctd are identified by the quantum chemical calculation method they were parameterized for plus eventually the basis set of the quantum chemical calculation Additionally they are denoted by the program version and release number of the COSMOtherm version they are shipped with Thus any CTDATA file is identified METHOD BASIS VERSION RELEASE ctd
389. ten to the COSMOtherm table file In addition the binary property table will be modified according to any LLE that has been detected Within the points of LLE the vapor pressures or for isobar calculations the temperatures and the mole fractions in the gas phase y will be replaced by the values of the LLE points In practice any miscibility gap as found by COSMOtherm will be visible as a straight horizontal line in the x y and xy pio phase diagram The iterative LLE search for binary systems by defaults starts at the LLE points eventually found on the binary concentration grid However it is also possible to give an explicit starting concentration via the xstart keyword see section 2 3 8 If the command LLE_NEW is given in the same line as the binary command COSMOtherm will compute the thermodynamic properties of the binary mixture at 325 additional mixture concentrations that are distributed on an even spaced grid In addition to the binoda LLE defined by equation 2 3 17 COSMOtherm also computes the spinodal LLE points which distinguish the unstable region of a liquid mixture 0 AG 0x lt 0 from the metastable region 6 AG Ox gt 0 If the mole fraction of the binary mixture falls within the unstable region spontaneous phase separation occurs when going from the one phase to the two phase region For an LLE thus found the points of spinodal phase separation are also written to the COSMOtherm output file The
390. th the keyword absconwrl The color scheme of the contacts visualized by default is determined from the minimum and maximum values of the given contacts This automatic assignment of the color scheme according to the property minimum and maximum has the advantage of building a stable framework for the coloring of the VRML file which always remains within the typical color scheme that is used for surface charge visualization It has the disadvantage that the contact probabilities of different molecules can not be compared visually because the color scheme of the contact surface visualized is determined individually for each molecule s contact surface due to it s contacts minimum and maximum values Moreover this kind of color designation may lead to visual artifacts if the absolute values of the scaled contacts are very similar i e if the difference between the minimum and maximum contact area is small In such a case the color scheme may be blown out of proportion and exaggerate minimal differences or even numerical noise To avoid the kind of ambiguity that is caused by a min max value based coloring scheme COSMOtherm offers two additional color schemes for the visualization of contacts namely the options absconscale and relconscale Both options provide an absolute color scheme that is independent of the individual numerical distribution of the contact values in a contact file thus allowing the direct visual comparison of the contact s
391. the out tab mom moma prf pot files to be in British units l e energies in kcal mol pressures in psia 1 psia 6 89467 kPa areas and volumes in A2 and A2 atomic masses in g mol temperatures in K charges in a u surface charges o in e o potentials u in kcal mol A 2 Antoine constants in the psia K frame and solubility parameters in the kcal 3 frame Optional Print statistics of the molecular surface contacts for all compounds in all mixtures to the output file See section 5 7 for details Optional Print statistics of the molecular surface contacts for all segments of all compounds in all mixtures to the output file to the contact statistics table file name contact See section 5 7 for details Optional Print the values of the temperature and composition derivatives of the chemical potentials of all compounds in all mixtures to the output file See section 5 6 Chemical Potential Gradients for further information Optional Print the value of the the chemical potential of vacuum in all mixtures to the output file 22 2 1 3 General Program Control and Thresholds dconv value combi combi ELBRO dbco nothb notvdw nohb novdw Optional Change threshold for the iterative self consistency cycle for the determination of the chemical potential A smaller value of dconv leads to higher accuracy of the COSMOtherm results but also to a longer computational time d
392. the accuracy threshold for the iterative refinement of the SLE point calculation Argument value is expected to be a nonzero positive real number Default is SLE iter thresh 1 0E 5 maxiter SLE value Optional for a SLE computation give the maximum number of iterations for the iterative refinement of the SLE point calculation Argument value is expected to be a nonzero positive integer number Default is maxiter SLE 150 liquid 1 Optional for a SLE computation Define one or both binary phase s as liquid phases with AG 1 0 If no argument is given both phases are defined as liquid The value of argument 1 is defined as the binary phase number i e it can be 1 or 2 where 1 defines the first phase i given in the binary i j option as liquid whereas 2 defines the second phase j given in the binary i j option as liquid 122 2 3 7 4 Treatment of lonic Liquids Salts and Complexes in Binary and Ternary Mixture Computations COSMOtherm also offers the possibility to compute phase diagrams of binary or ternary mixtures of a lonic Liquid IL phase with additional solvent phases Because in COSMO RS theory any lonic Liquid or dissoluted salt phase has to be treated by means of the individual ions forming the IL or salt a binary phase diagram computation has to be conducted in the form of a pseudo binary multicomponent phase diagram with the boundary condition of the anion and cation concentrations forming the IL o
393. the formation of charge transfer complexes between solute and solvent In experimental property measurements normally the influence of such a reaction on the measured property is not separated from the other effect of the solutes interactions polar interaction hydrogen bonding Example 10 shows the activity coefficient plot of the binary system octane 1 acetic acid 2 at 343 K This binary system shows a concentration dependent dimerization of acetic acid At high concentrations of acetic acid mostly the acids dimer can be expected whereas at low concentration the monomer is more probable Clearly the steep ascent of the activity coefficient of acetic acid on the side of low acid concentration in Example 10 is due to the fact that at low acid concentration the formation of the dimer is unlikely Thus the activity coefficient is dominated by the monomeric acetic acid which is much more polar than the dimer and thus also its activity coefficient in the unpolar octane is larger Thus the overall activity coefficient of acetic acid in the mixture with octane rises strongly if the concentration dependent dimerization reaction is pushed to the side of the monomer which is the case at low acid concentrations if x octane gt 0 95 Example 10 5 0 Octane 1 Acetic Acid 2 4 5 em Octane 3 5 em Acetic Acid COSMOtherm is able to treat such concentration dependent reactions with the concept of Interaction Energy
394. the input of the solvent density solvdens option above If no solvent density is given the conversion of the molar solubility to mole fraction can only be done in an approximative way The ref sol 1 option assumes that the given reference solubility value is given as the solutes mass volume concentration L so in g l Please note that the mass volume concentration input also requires the solvent density Along the lines of the mass based solubility input the mass volume concentration input assumes that L is given by mass Definition 2 as noted above unless the wsoll or wfract keywords are used in which case the input of L is assumed to be a Definition 1 mass solubility or a mass fraction respectively 90 Suboptions of the solub i or nsolub name command continued input of reference solubility solute j or nsolute name Optional for solub computations Define the solute compound for a reference solubility calculation of AG The solute j option computes defines the reference solute compound j which is the compound number in the collating sequence of the compound input section The nsolute name option computes the reference solubility for the solute compound of the name name 91 Dissociation Corrections to the Solubility of Neutral Compounds In solubility calculations of compounds solvent in protic solvent water it is possible that acidic or basic solutes dissociate in the aqueous solvent
395. the molecule Hereby normally the macroscopic dielectric constant of the solvent is used COSMO is a quite popular model based on a slight approximation which in comparison to other CSMs achieves superior efficiency and robustness of the computational methodology The COSMO model is available in several quantum chemistry program packages Turbomole DMOL3 Gaussian GAMESS US PQS 1 Eckert F and A Klamt AIChE Journal 48 369 2002 2 Klamt A and F Eckert Fluid Phase Equilibria 172 43 2000 3 Klamt A V Jonas T Burger and J C W Lohrenz J Phys Chem A 102 5074 1998 4 Klamt A J Phys Chem 99 2224 1995 5 Klamt A and G Sch rmann J Chem Soc Perkin Trans II 799 1993 6 Klamt A COSMO and COSMO RS in Encyclopedia of Computational Chemistry Schleyer P v R and L Allinger Editors Wiley New York 1998 pages 604 615 7 Schafer A A Klamt D Sattel J C W Lohrenz and F Eckert Phys Chem Chem Phys 2 2187 2000 Molpro Columbus ORCA and Q Chem If combined with accurate QM CSMs have been proven to produce reasonable results for properties like Henry law constants or partition coefficients However as has been shown elsewhere the continuum description of CSMs is based on an erroneous physical concept In addition concepts of temperature and mixture are missing in CSMs COSMO RS the COSMO theory for real solvents goes far beyond simple CSM
396. the plain Temperature and Mixture input see section 2 3 A Temperature Mixture Input below 20 2 1 2 Print Options for the COSMOtherm Output File continued pril pri2 wcas wdbn Optional Print additional debug information to the output file Currently this option toggles the printing of the following additional information 1 Molecular symmetry point groups 2 Molecule principal moments of inertia 3 Zwitterion information 4 If additional keyword wconf is given the conformer weight prefactors are printed to the mixture conformer output 5 If the dbas option use cosmo database index file is used the database entries for CAS number and compound trivialname are printed to compound output Optional Print additional debug information to the output file second level Currently this option toggles the printing of the following additional information 1 All debug information as produced by option pril 2 in combination with the wconf keyword for each molecule the atom wise contributions to the interaction energy terms chemical potential u total mean interaction energy Hw misfit interaction energy H H Bond interaction energy Hy and van der Waals interaction energy Haw are printed to the conformer mixture section of the output file 3 Molecule principal moments of inertia eigenvectors 4 Number of irreducible representations of molecular symmetry point groups Optional Replace compound names in the
397. the solute i at the flat interface a Amin the contact area of the solute i with phase S at the free energy minimum a A the initial area of the COSMO surface of solute z Depth the distance of the center of solute i from the interface at the free energy minimum k K the number of orientations that were use to determine the surface interaction energy minimum of solute i If several conformers were used to compute a compounds surface interaction energy COSMOtherm will always write the name of the specific conformer to the table output which was able to achieve the lowest value of u Gmin Thus from the list of all conformers of a given compound the one with lowest of all minimum free energy values at the flat interface of S and S will be listed In contrast G gt Gtot the total free energy gain of the solute j at the flat interface always is the thermodynamic average according to the interface partition sum of all conformers if several conformers are present in one compound In addition to FlatSurf in pure solvent phases as described above it is possible to compute the FlatSurf properties in phases of mixed solvents e g compute the surface chemical potential of a solute between one phase water and another phase consisting of an alkane mixture For this the concentrations of the compounds in the two phases have to be given in the input This is possible via the xf1 x x2 or cfl c cy commands for the first solven
398. therm please see section 2 2 1 2 2 2 and 2 3 1 of this manual for details on the computation estimation of compounds chemical potential in the gas phase 4 75 and vapor pressure 150 Phase III GASEOUS 1 octanol H20 By default it is assumed that each gaseous compound in the gas container can reach an individual pure compound pressure of 1 bar l e the chemical potentials of the 15 of all compounds are computed due to their partial pressure above the liquid phase that is contacting the gas container Alternatively it is possible to define a reference pressure for the whole of the gas container If such a reference total pressure of the gaseous container protar is given the chemical potentials of the gas phase 4 of all compounds are computed with respect to this reference pressure of the gas container as a whole i e all 46 values are varied in order to reproduce the given reference py tai The reference pressure of the gaseous container may be given with the PREF P ota1 mbar keyword or by one of its pressure unit variants pref Pa piotai Pa pref kPa p kPa pref _psia p psia and pref bar p bar respectively Alternatively the molar Volume can be given via keyword VMOL V I mol which is converted to prota via ideal gas equation of state Piota RT Vmo In addition it is possible to give an absolute reference Volume of the gaseous container using VREF Vne I Please note that liq ex calculations curre
399. thermodynamics at the given temperature mixture conditions are used as descriptors while in the case of a molecular PROPQSPR calculation without given temperature and concentrations approximate temperature and mixture independent estimates are used for these two descriptors properties 199 5 5 3 o moment correction As noted above the o potentials of pure compounds and liquid mixtures and other more complex disordered matrices can be represented by a Taylor series with respect to o In the same sense we may assume that for a given solvent system S there is a correction function Su c which corrects the c potential of uu as calculated by COSMOtherm and that this function can be expressed by a Taylor series of low order In such situation the chemical potential of a solute X in solvent S as calculated by COSMOtherm has to be corrected by a term X lt l X jux a 5 5 4 where the c are o moment coefficients SMC s describing the specific corrections required for matrix S The Mx are the o moments of solute X The program allows for m lax 6 i e for a total of 7 SMC s However usually c moments of orders up to 3 or 4 will be sufficient for a correct description of chemical potentials Although in principle acting on solvents SMC s are considered as compound specific in COSMOtherm SMC s for mixtures are handled by weighting SMC s of the compounds by their relative contribution to the total o profile of the mixture
400. tials of the compounds at phase equilibrium 4 may be printed to the LIQ_Ex table in the COSMO therm table file This is toggled by the keywords pr_K K pr_xK x and pr_mu 4 respectively By default all n phases in a LIQ EX calculation are assumed to be liquid phases It is however possible to define one of the given phases as a solid precipitation phase This is possible with the SOLID k command where argument k is the phase presumed to be the container for the precipitation of solid compounds The functionality of the solid container is described in the figure below It describes the dissolution partition of a solid solute between two separated liquid phases This requires a three phase LIQ EX 3 calculation where phase III is defined as solid precipitation phase via input option SOLID 3 In this example the solid compound aspirin is dissoluted into two liquid phases consisting of a water rich phase and a wet octanol phase consisting of 1 octanol and water Because the aspirin solute barely is soluble in water and only moderately soluble in wet octanol the solid cannot be dissoluted fully in both of the phases Thus some aspirin remains in the solid phase Ill The final distribution of the aspirin between the three phases corresponds to the solid liquid liquid equilibrium SLLE of the aspirin 148 Aspirin Phase III SOLID The phase equilibrium constants K of the transition between a liquid phase and the solid p
401. tion continued react Gso l or react GsolH or react_GsolC or react_GsolJ or react_GsolV react or react or react or react or react vap Hi His vapH vapC vapJ vapV Lid il Mid il l Gi1 Gio see li Qe Hi2 Fipe lj 2s Optional for reaction computations provide external free energy of solvation energies for the reactant compounds The input of the reactant AG 5 Giy is possible via the react Gsol Gi Giz command where Gi Giz are the free energy of solvation values that will be used for the reactant compounds defined by the compound numbers or names as given by the react i i or nreact name name commands The arguments G are expected to be real numbers For the keywords react Gsol and react _GsolH the given energies are expected to be in atomic units Hartree for the keyword react _GsolC energies are expected to be in kcal mol for the keyword react_GsolJ energies are expected to be in kJ mol and for the keyword react GsolV energies are expected to be in eV Optional for reaction computations provide enthalpies of vaporization for the reactant compounds The input of the reactant AH Hix is possible via the react Hvap H Hiz command where H Hiz are the zero pontenergies values that will be used for the reactant compounds defined by the compound numbers or names as giv
402. tion allows for the automatic computation of the pure compound liquid viscosity of a given substance If toggled in a temperature mixture line of the COSMOtherm input file the viscosity option will compute the liquid viscosities of all compounds that are given in the compound input section at the given temperature The liquid viscosity 4 of a pure compound ji is computed from a Quantitative Structure Property Relationship QSPR In C Area Ai y M CN py Noo CTS Co 2 3 26 The descriptors for the liquid viscosity are the compounds surface area as read from its COSMO file A the second c moment of the compound M the number of ring atoms in the compound N 9 and the pure compounds entropy times temperature TS which is computed from the difference of the total enthalpy of mixture of the pure compound H and the chemical potential of the pure compound yy TS H 4 This definition implies that the TS descriptor used in the viscosity QSPR model is in fact the negative entropy times temperature contribution i e it is the entropic part TS of the Gibbs free energy G H TS Altogether the QSPR model for the liquid viscosity contains five generic parameters The viscosity QSPR model eq 2 3 26 was determined for neutral organic compounds If it is used outside of this application range e g for salts zwitterionic compounds or metals the predictive quality may degrade substantially The QSPR coefficients in eq 2 3 26 are vali
403. tion coefficient logP can be approximated by equation 2 3 5 2 employing the base dissociation constant pK base and the pH of the aqueous phase log D log P log 1 100 609 27 5 The automatic partition coefficient prediction logp option of COSMOtherm will apply the dissociation correction to any solute of which the pK value is given or estimated The logD value thus computed will be written to the COSMOtherm output file as well as to an additional column in the table output of the logp option in the COSMOtherm table file In addition the pK acid or pK base value used in the logD calculation is printed to the output and table files A solutes aqueous dissociation constant pK acid or pK base value may either be given to COSMOtherm as additional input in the vap file compound input line or logp option mixture input line or it may be estimated by COSMOtherm using the pK prediction methodology described in section 2 3 6 of this manual There are three possibilities to enter a compounds aqueous dissociation constant pK acid or pK base specify the pK value in the compounds vapor pressure property vap file using the pK_acid value or pK_base value option see section 2 2 specify the pK value in the compound input line using the pK_acid value or pK_base value option see section 2 2 specify the solute compound and the pK value in the logp option mixture input line using the pPKacid igointe value or pKbase igg
404. tion is used within the framework of a binary calculation the two UNIQUAC interaction parameters t and t are adjusted to match the activity coefficient data computed by COSMOtherm In addition the compound specific UNIQUAC volume and surface area parameters are adjusted to optimally match the activity coefficient data computed by COSMOtherm This is achieved by introducing an additional compound specific scaling factor s to the computation of the UNIQUAC volume and area F VCE 130 Gasca 40 parameters 2 3 16a 2 3 16b Thus for binary mixture computations the UNIQUAC4 option depends upon four adjustable parameters 1 5 Toy S aN sz 117 2 3 7 2 Liquid Liquid Equilibrium Computation for Binary Mixtures For the binary ternary and multinary computation options COSMOtherm offers the possibility to detect miscibility gaps i e points of liquid liquid equilibrium LLE phase separation via the keyword LLE If this command is given in the same line as the binary ternary or multinary command COSMOtherm will search the computed mixtures for possible points of separation and if found writes them to the COSMOtherm output and table file The LLE properties are calculated from the liquid phase equilibrium condition eq 2 3 17 where indices and denote the two liquid phases and denotes the compound XV X y forall s 2 3 17 If the LLE option is used with the binary option the LLE tie points will be writ
405. tions mcse cmet q Optional for the use of COSMO metafiles or atomic weights Use the sum of the fragment COSMO file energies in the calculation of the total free energy by default a zero value is used instead Details on the usage of atomic weights and COSMO metafiles are given explained in section 5 3 of this manual Optional for the use of COSMO metafiles or atomic weights Allow charged metafiles If the global cmet option is given all COSMO metafiles mcos files and atom weighted compounds will be neutralized to match the exact integer charge of the sum of the COSMO charges of the metafile fragments i e neutral metafiles will be neutralized to charge 0 singly charged cation s metafile to charge 1 or atom weighted compounds respectively If the global cmet option is given with the optional argument q all given mcos files and atom weighted compounds will be neutralized to match the given charge g The argument neutralization charge q is expected to be an integer charge number in atomic units a u If a real number charge q is given it will be rounded to the nearest integer number By default i e if no cmet keyword is given all COSMO metafiles and atom weighted compounds will be neutralized to neutrality i e q 0 a u Details on the usage of atomic weights and COSMO metafiles are given in section 5 3 of this manual 26 2 1 4 Additional Tabulated Output Files Smom name mom Satm nam
406. to the COSMOtherm table file in tabulated form py p vs T In addition the total chemical potentials of the liquid piou and of the gas phase jg as well as the heat of vaporization of the mixture AHyap are written to the COSMOtherm table file A characteristic trait of COSMOtherm s vapor pressure prediction is that the absolute quantitative prediction of the vapor pressure at a given temperature point shows a certain error but that the temperature dependency of the vapor pressure i e the qualitative shape of the p T curve is predicted very well Thus it is possible to predict a py p T vapor pressure curve to a very high accuracy if the predicted vapor pressure is adjusted to match a given experimental reference pressure Pz at a given reference temperature Tze In practice the pressure difference between the COSMOtherm vapor pressure prediction p ATrep and the given reference pressure PpelTrep is used to determine a correction term to chemical potential in the gas phase 07 which subsequently is used to scale the vapor pressure prediction yielding a corrected vapor pressure value p gt 1 bar exp p p 59 pd XRT J which replaces the regular prediction value p COSMOtherm offers several possibilities to include a reference pressure and temperature into the pvap prediction option it is possible to use a reference temperature Tze and pressure Pret Pair which can be given in the mixture input line together with the
407. to compute liquid liquid phase equilibrium LLE i e phase separation miscibility gaps for pseudo binary solutions with a lonic Liquid or salt phase An IL LLE computation is toggled with the keywords 11e or 1le_new the same way it is done for binary mixtures of non ionic compounds see section 2 3 7 2 Liquid Liquid Equilibrium Computation for Binary Mixtures Please note however that for IL LLE s some care has to be taken in the interpretation of the COSMOtherm results for the computed miscibility gap mole fractions To compare the computed IL or salt mole fraction with experimental data depending on the reference state of the miscibility gap measurement it may be necessary to convert the computed mole fractions along the guidelines given in section 5 9 lonic Liquids of this manual The pseudo binary definition of the mole fraction where x is defined as the sum of the ions mole fractions x gt xf is different from the laboratory binary definition where the lonic Liquid is considered to be one single compound This means that for a AC IL 1 mol of the IL AC in the laboratory binary framework corresponds to 1 mol A and 1 mol C in the pseudo binary framework The conversion between the pseudo binary framework as used by COSMOtherm and the laboratory binary framework is explained in section 5 9 If an LLE is computed with the LLE or LLE_NEW option and one phase is defined as lonic Liquid COSMOt
408. to filename prf where filename is the name of the input file A summary of the o profiles will be written in tabulated form to the table file filename tab Optional Write the o potentials of all calculated mixtures to file name pot If no argument is given the o potentials will be written to filename pot where filename is the name of the input file A summary of the o potential information will be written in tabulated form to the table file filename tab Optional suboption of spot In addition to the c potentials also write the o potential coefficients of all calculated mixtures to file name pot 27 2 1 4 1 o moment QSPR Coefficient Input and Output QSPR filename or QSPR C Co Cig prop QSPR_SI filename or QSPR_SI cj C2 Cig prop Optional Read the o moment QSPR regression coefficients from file filename or directly from the input If the coefficients are to be read from a file the QSPR coefficient file ilename is expected to be in the directory that also holds the COSMOtherm parameter file i e in the directory denoted by the environment variable COSMOTHERM HOME or in a directory denoted by the cdir command For the format of the QSPR coefficient file see section 5 5 If the coefficients are to be read from the input file via the QSPR c cy Cig prop command the coefficients c are expected as real numbers separated by blank spaces If less than 18 coefficients are given the mi
409. ts it s neutralization charge The cmet q keyword can be given either in a global input line where it will be active for all given COSMO metafiles and atom weighted compounds see section 2 1 3 in a compound input line where it will be active for the actual given meta compound only see section 2 2 1 or it can be given inside the COSMO metafile where it will be active for this specific COSMO metafile If the cmet option is given without argument the meta compound will be neutralized to the nearest integer charge of the sum of the fragment charges given in the COSMO metafile or by the atom weights E g a supposedly neutral meta compound with cutting charges of 0 4 a u would still be neutralized to a neutral meta compound of charge 0 but a meta compound with cutting charges of 0 9 a u now would be neutralized to charge 1 a u If the cmet q keyword is given with an argument q the meta compound will be neutralized to match the given charge q The argument neutralization charge q is expected to be an integer charge in atomic units a u Thus the cmet q keyword can be used to force the processing of meta compounds of a given specific charge Atomic weights will also be identified in any VRML file of the molecular structure or the COSMO and property surface created by COSMOtherm If atomic weights are set to zero the corresponding atomic labels will be marked red in the molecular VRML file name_mol wrl If atomic weights
410. ts of the given compounds are written to the contact statistics file name contact where name is the name of the COSMOtherm input file See section 5 7 for details 70 D Program control options nohb Optional Switch off hydrogen bonding HB contribution to the chemical potential If used in this section of the input file the nohb command is active only for the temperature mixture line where it is given novdw Optional Switch off van der Waals vdW contribution to the chemical potential If used in this section of the input file the novdw command is active only for the temperature mixture line where it is given nothb Optional Switch off temperature dependency of the hydrogen bond contribution to the total interaction energy of the compound If used in this section of the input file the nothb command is active only for the temperature mixture line where it is given notvdw Optional Switch off temperature dependency of the van der Waals contribution to the total interaction energy of the compound If used in this section of the input file the not vdw command is active only for the temperature mixture line where it is given combi Optional Switch off combinatorial contribution to the chemical or potentials If given in the mixture section of the COSMOtherm input combi i io file the combi command is active only for the temperature mixture or line where it is given If the option combi is given without argument n
411. ts to be calculated in the concentration grid computation Argument n ints is expected to be an integer number between 2 and 235 Default is n in 10 If xstep is used the concentration grid points will be chosen evenly spaced between the given start and end concentration vectors in the frame of mole fraction concentrations If cstep is used the points will be chosen evenly spaced in the frame of mass fraction concentrations If qstep is used the points will be chosen evenly spaced in the frame of surface fraction concentrations The xstep cstep or qstep options are independent of the surface mass or mole fraction frame of the start and end concentration vectors i e any combination of xstep cstep or qstep with xstart cstart or qgstart and xend cend or gend is possible 111 In addition to the general print options it is possible to toggle an automatic search for Liquid Liquid equilibria LLE s for binary ternary or multidimensional mixtures LLE Optional for binary ternary or multinary computations Search for points of phase separation liquid liquid equilibria This option is searching the LLE with an iterative optimization procedure See section 2 3 7 2 threshold value Optional for binary ternary or multinary computations with iterative LLE search give the accuracy threshold for the iterative refinement of the LLE calculation Argument value is expected to be a nonzero positive real number Default is thre
412. tween the molar volume J as derived from the compound or polymer density and the molecular hard core volume r which can be approximated very well by the molecule s COSMO volume Using the free volume fraction of thus defined the free volume contribution to the chemical potential of compound reads Hy ae FV FV RT In 41 2 5 3 7 Ox Xx x l l l Please note that the value of x used in equations 5 3 5 to 5 3 7 is the mole fraction with respect to the polymer chain not the molecular fragment repeat unit This implies that in a COSMOtherm calculation that utilizes the combi ELBRO term and the input of the polymer s molecular weight MW omer all mole fractions x are converted to the polymer framework with the help of the given MW value Hence in polymer practice the absolute prediction of solubilities and related properties in polymer solvents requires the input or assessment of the molecular weight of the polymer MW oiymer aS Well as the input or estimation of the free volumes V of all compounds involved including the molecular species such as the solutes or other non macromolecular solvents The input of all polymer related properties is done in the compound input section i e the polymer definitions and properties can be given either in the compound input line of the COSMOtherm input file or in the vapor pressure property name vap file of the compound see section 2 2 3 Vapor Pressure Pro
413. ty calculation options simpot i j or nsimpot nam nam simpot i j k or nsimpot nam nam nam xsl or csl and o xs2 or cs2 X C X1 C Ko ow CQ a5 XQ s Co we Optional Toggle the automatic calculation of the pure compound o potential similarity of two compounds see section 2 3 10 For the simpot i j option the similarity factor is computed for the two compounds with the compound numbers i and j in the order of compounds given in the compound input section For the nsimpot nam nam option the similarity factor is computed for the two compounds with the compound names nam and nam as given in the compound input section of the COSMOtherm input file i e either the names of the COSMO files without extension or the name given via the comp name option Optional Toggle the automatic calculation of the pure compound o potential similarity of two compounds weighted by the o profile of a third compound Thus the computed similarity is a solute specific o potential similarity see section 2 3 10 For the simpot i j k option the similarity factor is computed for the two compounds with the compound numbers i and j in the order of compounds given in the compound input section The o potential similarity will be weighted by the o profile of compound k For the nsimpot nam nam nam option the similarity factor is computed for the two compounds with the compound name
414. ty file name vap is expected The syntax of the vapor pressure property file is identical to the syntax of the vapor pressure input in the compound input line i e it is possible to use the VPinp Vpexp VPant and other commands as described above COSMOtherm will search the actual working directory or if specified the directory given by the fdir command for the vapor pressure property files Note that it is also possible to automatically search for the vapor pressure property files for all of the molecules given in the compound input section via the global command vPfile see section 2 1 The filename of the vap file must not contain blank spaces unless it is given in quotes e g VPf name 0 vap The syntax of the pure compound data input is the same in the compound input line and in the vapor pressure property vap file Please note however that if data is given in both the compound input line and in the vapor pressure property vap file then the former input will be treated with higher priority i e if both vap file and compound line input are read in the compound line input finally will be used The different pure compound data input options are listed below 49 The automatic computation of phase diagrams with COSMOtherm using the binary ternary or multinary keyword see section 2 3 8 requires the knowledge of the pure compounds vapor pressures These can either be estimated by COSMOtherm or given in the COSMOther
415. ue to an increasing number of iterations Default value dconv 10 Optional Switch off combinatorial contribution to the chemical potential If given in the global command section the combi command is active for the complete COSMOtherm run i e for all compounds in all of the following temperature mixture lines Optional Switch on special free volume combinatorial contribution to the chemical potential If given in the global command section the combi ELBRO command is active for the complete COSMOtherm run i e for all compounds in all of the following temperature mixture lines The free volume term by Elbro et al is recommended for the computation of macromolecules see section 5 3 2 Optional Use all given conformer information if using a COSMO database index file to identify compound COSMO files with the RN CAS or DBN Trivialname commands For purpose and description of this command and the COSMO database index file see section 2 4 Optional Switch off temperature dependency of the hydrogen bond contribution to the total interaction energy of the compound If given in the global command section the nothb command is active for the complete COSMOtherm run i e for all following temperature mixture lines Optional Switch off temperature dependency of the van der Waals contribution to the total interaction energy of the compound If given in the global command section the notvdw command is active for the complete COSMOtherm r
416. ult name molec _map wrl If the name contact file contains more than one segment contact map a cascade of VRML files will be created for each of segment map entries in the name contact file The VRML files created will be named by additional numbers according to the entries in the name contact file molec _mapl wrl molec _map2 wrl molec _map3 wrl will be created for the first second third entry in the name contact file If the output name of the VRML files id given with the namwrl mapname wrl command then the VRML files will be numbered on the basis of the given name mapnamel wrl mapname2 wrl mapname3 wrl will be created for the first second third entry in the name contact file The visualization of a contact map file can be done either in the compound input section or in the mixture input section either in the same input line where the contact file was created or in a subsequent mixture line Please see section 2 2 for details on the VRML file creation procedure Please note that the contact probabilities visualized as VRML surfaces are scaled by the apparent surface area i e not the absolute contact numbers as given in the contact file are visualized but the relative contact strengths per surface area contact area which is in direct analogy to the visualization of a COSMO file surface charges in terms in terms of surface o charge area It is possible to force the visualization of the area dependent contact probabilities wi
417. um constant K K activity also called thermodynamic or effective equilibrium constant is related to the apparent equilibrium constant K via the nonideality factor K K gamma also called activity coefficient equilibrium constant K K K 5 4 8 The nonideality factor K according to example reaction scheme 5 4 1 is defined as the stoichiometry weighted ratio of the reactants and products activity coefficients y K Ys Yp yaa Yg 5 4 9 The computation of the activity equilibrium constant K is toggled by the keyword K_activity If this keyword is given as a suboption of the reaction option COSMOtherm will compute the activity coefficents of all species in the given reaction and from these will compute K and K which will be written both to the COSMOtherm table output and the output file In addition the activity coeffcients y will be tabulated in additional column of the reaction table output If for a given reaction the activity equilibrium constant K is known experimentally it can be passed into the reaction option of COSMOtherm as a reference activity equilibrium constant KR The solvent independent reference equilibrium constant K then can be used to scale the solvent dependent apparent equilibrium constant K This can be done using the option K_activity K Using an experimental K f the reaction system can be accounted for e g nonideality in the gas phase thus avoiding explicit use of fugacity coeffici
418. un i e for all following temperature mixture lines Optional Switch off hydrogen bonding HB contribution to the chemical potential If given in the global command section the nohb command is active for the complete COSMOtherm run i e for all compounds in all of the following temperature mixture lines Optional Switch off van der Waals vdW interaction energy contribution to the chemical potential If given in the global command section the novdw command is active for the complete COSMOtherm run i e for all compounds in all of the following temperature mixture lines 23 2 1 3 General Program Control and Thresholds continued uqme uqmg ndgf oclp Depfus_estimate E gas_min off Optional for the input of external quantum chemical energies and vibrational zero point energies Use the external quantum chemical QM energies and vibrational zero point energies EZP as given in the compound input section eqm and ezp options for the Boltzmann weighing of conformers see section 2 2 of this manual and in the reaction equilibrium computation option see section 5 4 of this manual Optional for the input of external quantum chemical energies and vibrational zero point energies Use the external quantum chemical QM energies and vibrational zero point energies EZP as given in the compound input section eqm and ezp options for the Boltzmann weighing of conformers see section 2 2 of this manual and in the reacti
419. und For the DSfus value option AS is expected in kcal mol K for the DSfus_ SI option AS is expected to be in kJ mol K Argument value is expected to be a real number The value of AS thus given can be used in combination with a given melting point T melt to compute the solubility of solid compounds via the SOLUB or NSOLUB option see section 2 3 4 Optional Give the heat capacity of fusion ACp for this compound For the Depfus value option ACp is expected in kcal mol K for the Dcpfus_ SI option ACp is expected to be in kJ mol K Argument value is expected to be a real number The value of ACp thus given can be used to compute the solubility of solid compounds via the SOLUB or NSOLUB option see section 2 3 4 Optional Give the melting temperature Tmer for this compound For the Tmelt temp and Tmelt C temp options T is expected in C for the Tmelt K temp option Tmer is expected in K Argument temp is expected to be a real number The value of T ey thus given can be used in combination with a given enthalpy or entropy of fusion AH or AS to compute the solubility of solid compounds via the SOLUB or NSOLUB option see section 2 3 4 Optional for the input of a temperature dependent compound free energy of fusion via input of AH or AS and melting point Tren toggle the approximation of the heat capacity of fusion as ACp AS AHtusdT mei The value of AG T thu
420. und i It is also possible to calculate x7 at finite concentrations using the xs or cs command see section 2 3 4 If such a finite concentration input is used arguments i or name need not be given to the solub or nsolub option Optional Toggle the automatic calculation of the gas solubility of all compounds at the given partial pressure p in a given solvent see section 2 3 11 If the solgas keyword is given the argument p is expected to be a positive real number pressure in mbar If the solgas Pa keyword is given the argument p is expected to be a positive real number pressure in Pa If the solgas_kPa keyword is given the argument p is expected to be a positive real number pressure in kPa If the solgas_bar keyword is given the argument p is expected to be a positive real number pressure in bar If the solgas_psia keyword is given the argument p is expected to be a positive real number pressure in psia 61 B Property calculation options continued partition coefficient dissociation constant reaction energy logp i1 i2 or nlogP name name gt pKa solvent Lneutral Lion or npKa NaM solvent nam neutral name ton reaction i or nreaction name Optional Toggle the automatic calculation of the partition coefficients of all compounds between the compounds i and iz where i are compound numbers in the range given in the compound input section The nlogp name name option
421. und ji or j the similarity factor will be computed for all possible combinations of the given conformers and the overall compound similarity factor is averaged from the computed conformer similarity factors The COSMOtherm o profile similarity factor S j is defined as the normalized overlap integral of the o profiles p c and po of the two compounds i and j p o p o do 2 3 20 Se AA Thus 5 will be small if the overlap between the compounds o profiles is small Please see section 5 1 for further information on the definition and use of o profiles In addition the similarity factor given by eq 2 3 20 is corrected by a factor S taking into account the difference in the apparent hydrogen bonding donor and acceptor capacities of the two compounds and by a factor taking into account size differences between the two compounds i and j Alternatively COSMOtherm allows the calculation of a molecular o profile similarity by the Sigma Match Similarity SMS algorithm The similarity factor SMS of two compounds i and j can be computed using the sms i j or nsms name name options in the mixture input section of the COSMOtherm input file see section 5 1 on o profiles In addition COSMOtherm allows the calculation of a molecular o potential similarity S of two compounds i and j using the simpot i j ornsimpot name name options in the mixture input section of the COSMOtherm input file see section 5 2
422. urface area parameters are approximated by scaled volumes and areas of the compounds COSMO surface r V 30 2 3 15a q AS 40 2 3 15b Alternatively the UNIQUAC volume and area parameters r and q can be given in the input file using the options UNIQUAC_R1 rl1 UNIQUAC_R2 r2 UNIQUAC_Q1 ql and UNIQUAC_Q2 q2 or in the compound input section the options UNIQUAC_RI ri and UNIQUAC QI qi 116 Suboptions of the binary UNIQUAC2 option are UNIQUAC_R1 r1l UNIQUAC_R2 r2 UNIQUAC_Q1 q1 UNIQUAC_Q2 q2 Optional for binary UNIQUAC2 computations Give UNIQUAC volume parameter for compound 1 Argument r1 is expected as a real number larger than zero Optional for binary UNIQUAC2 computations Give UNIQUAC volume parameter for compound 2 Argument r2 is expected as a real number larger than zero Optional for binary UNIQUAC2 computations Give UNIQUAC surface area parameter for compound 1 Argument q1 is expected as a real number larger than zero Optional for binary UNIQUAC2 computations Give UNIQUAC surface area parameter for compound 2 Argument q2 is expected as a real number larger than zero Please note that the input of UNIQUAC volume and surface parameters in the mixture section of the COSMOtherm input file i e as a sub option of the the binary UNIQUAC2 command overrides any values given in the compound input section of the COSMOtherm input file via UNIQUAC_RI and UNIQUAC QI If the UNIQUAC4 op
423. urfaces of different molecules or conformers in a qualitative to semi quantitative manner For both of the absolute color schemes colors are assigned in a way that a typical color distribution in direct analogy to the surface o charge area color scheme is achieved l e the average contact is green while stronger than average contacts with increasing contact strength will settle in the color range of yellow orange red and brown Weaker than average contacts with decreasing contact strength will settle in the color range between turquoise blue and purple In each case the color reference is the contact map of the compound with itself i e a surface that is completely green The two absolute color schemes differ in the way the color distribution is spread with respect to the contact strength relative to the reference state for option absconscale the contact s color distribution is scaled by the ideal contact strength which is just the surface concentration ratio of the contacting molecules whereas for option relconscale it is scaled 205 by the apparent contact strength which is the sum of the contacts in this molecule Thus typically the absconscale option will show a somewhat weaker color spread than the relconscale option Due to their absolute nature which is calibrated to best visualize typical contact strengths of neutral molecules both color schemes may overshoot if extreme contact strengths are present i
424. us and physically ill defined if the gaseous solute is part of the solvent mixture e g if you want to compute the gas solubility of CO in heptane solvent mix with 0 1 mole fractions of CO In such a case COSMOtherm will assume that the solute concentration in the solvent mixture is zero and compute the gas solubility in the resulting solvent mixture in the given example COSMOtherm will compute the gas solubility of the CO in the pure heptane 140 Suboptions of the solgas option are solvent i or nsolvent name XS X X2 or CS C1 Cp pthresh thresh max iter n Required for solgas computations Use pure compound i as solvent for gas solubility calculation If the solvent or nsolvent keyword is used the gas solubility computation will be done in pure solvent i for all compounds that are given in the compound input section l e the activity coefficient calculations for eq 2 3 23 will be done in solvent i If the solvent i keyword is given the i compound as given in order of the compound input section will be used as solvent Argument i is expected as integer number between one and the number of compounds given in the compound input section If the nsolvent name keyword is given the compound with the name name as given in the compound input section will be used as solvent Argument name is expected as character string Note an alternative definition of the solvent in the solgas option is possible with the xs o
425. used in the pKa or npKa command is required to be acetonitrile if the ACETONITRILE ACID keyword is used The usage of the acetonitrile base pK LFER parameters is toggled with the ACETONITRILE BASE suboption of the PKa isoivent ineutrar ron Command Note that the solvent isojyent OF NAMEgojyent that is used in the pKa or npKa command is required to be acetonitrile if the ACETONITRILE BASE keyword is used 39 Frank Eckert Ivo Leito Ivari Kaljurand Agnes Kutt Andreas Klamt Michael Diedenhofen Journal of Computational Chemistry 30 799 810 2009 Please note that the ACETONITRILE ACID LFER as given in the COSMO therm parameterization corresponds to the complete fit eq 4 of the cited article 106 The LFER parameters for acids pK at room temperature in solvent n heptane HEPTANE are shipped within COSMOtherm parameter files BP_TZVP_C21_0109 ctd and BP_SVP_AM1 C21 0109 ctd The usage of the n heptane acid pK LFER parameters is toggled with the HEPTANE ACID suboption of the PKa isoivent ineutrar ron Command Note that the solvent isoivent OF NAMEgojyent that is used in the pKa or npKa command is required to be n heptane if the HEPTANE ACID keyword is used The LFER parameters for base pK at room temperature in solvent tetrahydrofuran THF are shipped within COSMOtherm parameter files BP_TZVP_C21_0109 ctd and BP_SVP_AM1 C21 0109 ctd The usage of the tetrahydrofuran acid pK LFER pa
426. ust follow the name convention of conformer COSMO files in COSMObase i e for a given base filename name cosmo the conformer COSMO files have to be named by the base filename with subsequent numbers starting with zero name0Q cosmo namel cosmo name9 cosmo In addition the autoc command also recognizes files for the alternative the name convention of conformer COSMO files in COSMObase which claims that for a given base filename name cosmo the conformer COSMO files have to be named by the base filename with a _c conformer identifier followed by subsequent numbers starting with zero name_c0 cosmo name_cl cosmo name_c9 cosmo By default the autoc command urges COSMOtherm to use all conformers of numbers 0 to 9 plus the given base filename COSMO file if they are found in the given COSMO file directory If the autoc maxautoc keyword is given with the optional argument maxautoc COSMOtherm will use all conformers with conformer numbers between 0 and maxautoc plus the given base filename COSMO file The value of the maximum number of conformers that will be searched for is 0 lt maxautoc lt 10 for the namex cosmo name convention and 0 lt maxautoc lt 1000 for the name _cxxx cosmo name convention The number of conformers to be used automatically with the autoc command additionally can be restricted with the global or local compound line suboption usec i i If given only the confor
427. ve such cases and predict a finite solubility value log x In addition to the absolute solubility predictions defined by eq 2 3 1 and 2 3 2 it is possible to compute relative solubility values using the pr_rs print relative solubility keyword The relative solubility Xp is defined as Xgs 44 RT It is important to realize that the value of the predicted x does not make sense as a single absolute number It only reasonably can be used in comparison with other relative solubility numbers e g comparing the xg values of a given solute in several different solvents This opens up the possibility to compare relative solubilities in cases where the absolute values can not be compared any more e g if the solvent is predicted to be fully miscible with the solvent by the absolute solubility prediction in this case the relative solubility xp can provide qualitative and even quantitative information about the solubility behavior of the given solute in a set of solvents In addition please note that a relative solubility computation only makes sense for noniterative solubility calculations and thus the pr rs 82 keyword is inactive if the the iterative refinement of the solubility computation is switched on If the pr_rs keyword is given the decadic logarithm of Xps the mass based relative solubility wgs g g and if possible the molar solubility 5 in mol l for definition of the latter two see below will be printed to additional
428. ven the missing ones will be assumed zero If a negative number is given the concentration for this compound will be inserted automatically using the normalization of the sum of mole fractions Only one negative number is allowed per mixture input line Note If a finite concentration input via options xg or cg is used no arguments need to be given to the gamma or ngamma option 77 Suboptions of the gamma i and the ngamma name option continued xref x X2 or cref c Co Optional for gamma computations Give finite mixture concentration of the reference state of the activity coefficient computation This option overrides the default reference states i e the pure compound for neutral species and infinite dilution in the solvent for ionic species and is used for all compounds in the mixture The input of the reference state concentrations is possible either in mole fractions xref or mass fractions cref of the compounds of the mixture as real numbers x and c The arguments are expected as real numbers between zero and one in the same sequence of compounds as given in the second input area If the values do not add up to one they will be normalized by COSMOtherm If less mole fractions concentrations than compounds are given the missing ones will be assumed zero If a negative number is given the concentration for this compound will be inserted automatically using the normalization of the sum of mole fractio
429. ven in the salt solubility mixture input line it is assumed that the reference mole fraction of the salt is given in the multicomponent pseudo binary or IL ternary framework where SOL Xac energy of fusion as computed by the reference solubility option by default is assumed to be AG as is defined as the stoichiometric sum of the ion mole fractions x X4 Xc Second the Gibbs free defined in equation 2 3 1a l e by default equation 2 3 1a will be used to compute AG from the reference solubility If the keyword DGfmean is given in the same line as the reference salt solubility input the alternative definition of the mean ionic free energy of fusion AG will be computed from equation 2 3 1b Reference salt solubility input solute j Optional for solub computations Define the solute compound or for a reference solubility calculation of AG The solute j nsolute name option computes defines the given salt as reference solute or compound where j may be the compound number of any of nsolute SALT the salt components in the collating sequence of the compound input section The nsolute name or nsolute SALT options define the given salt as reference compound for the salt solubility computation where name may be the name of any of the salt components 100 Reference salt solubility input continued ref sol or ref sol or ref_ sol or ref solz or ref sol or ref_sol
430. via the wrlmap name cosmo command The mapfile is expected to be found in the directory where the COSMOtherm input file is Optional Suboption of the wrlmap mapfile command Give the name of the VRML visualization file of the property map given by the wrlmap mapfile command name wrl overrides the default VRML visualization file name molec _map wrl Optional Suboption of the wrlmap mapfile command Set the minimum value min_val for the property visualization of a COSMO surface property map mapfile By default this value is determined automatically from the smallest value of the property given in the property column of mapfile If the wrl min command is used the color management for the COSMO surface property map is adjusted according to the given min val Optional Suboption of the wrlmap mapfile command Set the maximum value max val for the property visualization of a COSMO surface property map mapfile By default this value is determined automatically from the largest value of the property given in the property column of mapfile If the wrl max command is used the color management for the COSMO surface property map is adjusted according to the given max val Optional Suboption of the wrlmap mapfile command Choose column io of the COSMO surface property map mapfile that shall be visualized on the COSMO surface By default the 6 real number column of mapfile is expected to hold the property that should be visualized If property map file
431. w down the performance of COSMOtherm If larger amount of compounds shall be processed it is much more efficient to use the auxiliary program CT CREATE see above COSMOtherm additionally allows the usage of Chemical Abstracts Registry Numbers CAS RN to identify compounds via the rn registry number command RN in the compound input section It also allows the usage of trivial names to identify compounds via the dbn name command in the compound input section 48 COSMObase is a database of molecular COSMO files available from COSMOlogic GmbH amp Co KG Currently COSMObase consists of over 2000 compounds including a large number of industrial solvents plus a wide variety of common organic compounds All compounds in COSMObase are indexed by their Chemical Abstracts Registry Number CAS RN by a trivial name and additionally by their sum formula and molecular weight allowing a simple identification of the compounds Currently COSMObase is available for the following quantum chemical methods and basis sets Turbomole BP TZVP Turbomole BP SVP AM1 49 Eckert F CT_CREATE Users Manual Version C3 0 Release 15 01 COSMOlogic GmbH amp Co KG 2014 155 If the rn command is used COSMOtherm will assign a compound name to the given CAS RN and read in the corresponding molecular COSMO file Trivial names given by the dbn name command are processed similarly In any case the use of the rn registry number or the dbn name option requir
432. will get the name of the current input file Alternatively the filename of the momc file can be given as argument of the smomc keyword 67 B Property calculation options continued surface activity density viscosity and Liquid extraction FlatSurf i j or NFlatSurf nam nam density viscosity liq ex Optional Toggle the automatic calculation of the flat surface interaction energy between two solvents see section 5 10 For the flatsurf i j option for all compounds the surface interaction energy is computed at the surface interface of the two solvents with the compound numbers i and j i and j being the compound numbers in the order given in the compound input section For the nflatsurf nam nam option for all compounds the surface interaction energy is computed at the surface interface of the two solvents with the compound names nam and nam as given in the compound input section of the COSMOtherm input file Optional Toggle the automatic calculation of the density p This option computes the pure compound liquid density p for all given compounds For details on the density calculation option see section 2 3 12 Optional Toggle the automatic calculation of the viscosity 7 This option computes the pure compound liquid viscosity 7 cp for all given compounds For details on the viscosity calculation option see section 2 3 13 Optional Toggle the automatic calculation of a multi component two phase l
433. with the UNIQUAC model The two binary interaction parameters t and t are fitted to the computed activity coefficient data The compounds volumes and surfaces r and q are not fitted See section 2 3 7 1 SLE Optional for binary computations Search the computed binary mixture for points of solid phase separation solid liquid equilibria This option is searching the LLE on a fine grid using additional mixture concentrations points See section 2 3 7 3 113 In binary phase diagrams COSMOtherm also looks for possible azeotropes If an azeotrope is found the mole fraction concentration of the azeotropic point will be written to the COSMOtherm output and table files By default the azeotrope concentration as found on the given concentration grid is used With the keyword search azeotrope COSMOtherm will perform an additional iterative refinement of the azeotropic point s found By default the iterative refinement will compute the azeotropc points up to an accuracy threshold of x 10 mole fractions within a maximum number of 500 iterations These defaults can be changed by options azeo iter thresh value for the accuracy threshold value and maxiter azeo value for the maximum number of iterations Azeotrope related suboptions specific to the binary option search azeotrope Optional for binary computations Toggle iterative refinement of the azeotropic point s in the computed binary mix This option solves the thermodamic equ
434. wset 222 223 e 43 108 E GAS MIN 44 45 e gas_min off 43 e gas_min off 24 E GAS MIN OFF 45 eC 43 ECfile 18 43 ef 43 108 efc 43 efH 43 efile 48 Efile 18 43 efJ 43 H 43 Hfile 18 43 J 43 Jfile 18 43 PARAM 143 144 EL PARAM SI 144 en IEI 36 72 212 energy gas phase external 183 quantum chemical 24 45 47 184 zero point vibrational 24 45 46 47 183 184 185 ZPE 183 epsilon 55 eqm 24 44 45 47 184 equilibrium chemical 24 62 182 reaction 24 62 182 error code 168 etaset 223 excess enthalpy contributions 109 expdensity 56 181 Hook o 233 expdensity Brit 56 181 expdensity SI 56 181 expmolvol 56 181 expmolvol SI 56 181 expmw 56 180 extraction 68 146 liquid 68 146 ezp 24 44 45 46 47 184 f 31 f SDATABASE 32 155 fdir 17 19 32 33 58 file handling 16 flatsurf 68 218 219 cf1 218 219 cf2 218 219 Fwrl 219 ift 219 xf1 218 219 xf2 218 219 FlatSurf 68 217 218 freevol 56 181 freevol SI 56 181 gamma cg 77 cref 77 xg 77 xref 77 gamma 61 77 gamma xg 77 gamma cg 77 gamma xref 78 gamma cref 78 gas phase energy 18 43 108 file 18 43 44 Gaussian 12 30 31 40 158 160 161 162 163 164 Gibbs free energy hydration 79 solvation 79 80 grad 22 69 201 heat of fusion enthalpy 54 83 84 121 entropy 54 83 121 Gibbs free energy 24 54 83 84 89 99 121 122 129 134 149 QSPR estimate 84 85 87 salt 149 150 Temperature Depe
435. xternal zero point energies for the reactant compounds The input of the reactant zero point energies EZP is possible via the react _ zpe EZP EZPip _ command where EZPi1 EZPi gt are the zero pontenergies values that will be used for the reactant compounds defined by the compound numbers or names as given by the react i i or nreact name name commands The energies F are expected to be real numbers For the keywords react_zpe and react _zpeH the given energies are expected to be in atomic units Hartree for the keyword react _zpeC energies are expected to be in kcal mol for the keyword react _zped energies are expected to be in kJ mol and for the keyword react _zpeV energies are expected to be in eV 189 Suboptions of the reaction option continued prod_eqm E or prod_eqmH or prod_eqmC E or prod_eqmJ or prod_eqmV E prod_zpe or prod_zpeH E or prod_zpeC E or prod_zpeJ E or prod_zpeV E B51 jl B51 ji jl Bj2 P32 we Bj e Dj2 e BJR e ii ZPj1 m ZP 32 ove P52 e E2 ee P52 e P52 e Optional for reaction computations provide external quantum chemistry energies for the product compounds The input of the product energies E is possible via the prod_e
436. xtures similar to the way done in the binary ternary options described in section 2 3 7 The multinary option performs an automatic calculation of a slice of the n dimensional phase space The section of the phase space to be computed is defined in terms of of a custom concentration grid This requires the input of start and end concentration vectors of mole mass or surface fraction concentrations plus the number of points to be calculated between these vectors The multinary calculation moves along these coordinates using equidistant concentration steps The start and end vectors are defined as the first and last point in phase space Example 2 shows the input file for the multinary computation of a section of a three component system The section computed is also shown graphically in the ternary diagram of this system The vapor pressures of the pure compounds which are used in the computation of the thermodynamic properties are handled as described above for the binary ternary options i e they can be approximated by COSMOtherm or given in the molecular section of the COSMOtherm input file The maximum number of compounds that can be handled by a multinary computation is 235 Example 2 ctd BP TZVP_C30 _ 1501 ctd Global Commands 1 cdir COSMOTHERM CTDATA FILES Global Commands 2 aceton methylene chloride toluene MULTINARY Comment Line f propanone cosmo ef propanone energy Compound Input 1 f ch2c12 cosmo ef ch2c1
437. y COSMOtherm can be used to compute certain molecular properties via a Quantitative Structure Property Relationship QSPR approach i e COSMOtherms o moments can be correlated with certain molecular properties such as lipophilicity biological or environmental partition behavior like the octanol water or soil water partition the partition of a compound between the blood brain barrier or the CaCo2 cell permeability The coefficients for a certain property can be determined from 6 Klamt A and F Eckert COSMO RS A Novel Way from Quantum Chemistry to Free Energy Solubility and General QSAR Descriptors for Partitioning in Rational Approaches to Drug Design H ltje H D and Sippl W Editors Prous Science Barcelona 2001 pages 195 205 193 a multinlinear regression of the oc moments with a sufficient number of experimental data For a compound X a property og P is calculated via log P c M c M c MX c4 M cs M c M Co M Ca Mugar Co Mygac Cio Minpaces C11 Minwacca C12 Myjpdont C13 Mygdonz C1a Mygdon3 Cis Mugdong Cis 5 5 2 where MZ is the i o moment of compound X and Mpsac and Mygaon are the i hydrogen bonding acceptor and donor moments of compound X Thus 16 coefficients are required to do the o moment QSPR calculation of a molecular property Such a calculation can be done automatically by COSMOtherm if the coefficients c are given to the program This is
438. y LLE option will perform LLE searches for each grid point l e each of the 33 grid concentrations is used as individual starting point for a LLE search If a solid liquid equilibrium SLE calculation is performed via the SLE option see below section 2 3 7 3 for a closer description of SLE calculations the default grid is modified If a binary calculation is performed with the SLE option a considerably finer default grid of 323 evenly spaced mole fraction concentrations same as for the LLE_NEW option above is used The iterative SLE algorithm will initiate from a first guess that is derived from this fine grid The default binary and ternary VLE LLE and SLE concentration grids are given in mole fraction concentrations x This may not always be the best choice for an optimal coverage of the phase space with as little grid points as possible If the compounds used show large differences in their size or shape it may be better if the grid concentrations are scaled in a way that reflects these size or shape differences Such can be achieved by defining the grid point concentration in terms of mass fraction concentrations c or surface area fraction concentrations q both of which somehow reflect apparent size and shape differences of the compounds involved COSMOtherm offers two possibilities to modify the grid concentrations in the framework of the binary and ternary calculation options First it is possible to
439. y factors Vi are expected to be positive integer numbers Required for reaction computations Define the product composition from compound COSMO files The input of the product composition is possible either via their compound numbers prod 3 j2 Command where j j2 are the numbers of the compounds as given in the sequence of compounds in the compound input section The arguments j are expected to be positive integer numbers or via their compound name nprod name name command where name name are the names of the compounds as given in the compound input section Required for reaction computations Define the products stoichiometry The input of the product stoichiometry factors v51 v5 is possible via the prod _n v5 v5 command where vj v52 are the stoichiometry numbers of the reactant compounds defined by the compound numbers or names as given by the prod 3 j2 or n prod name name gt commands The stoichiometry factors vx are expected to be positive integer numbers 187 Suboptions of the reaction option continued Xr X X2 or Cr C Co pref p or pref Pa p or pref kPa p or pref psia p or pref bar p K_activity K_activity K Optional for reaction computations Give finite solvent mixture concentration at which the reaction equilibrium properties shall be computed The input of the concentrations is possible either in mole fractions xr or mass fr
440. y the nternary name name IL command where name and name are the names of the solvent phase compounds as given in the compound input section and the term IL denotes the IL salt phases as defined by the IL and IL n options given below All three neutral solvent phases i j k or name name name may be replaced by a lonc Liquid phase definition denoted by the IL command 127 Suboptions of the binary i IL or nbinary name IL and the ternary i j SIL or nternary name name IL options j IL i 3 a Required for binary or ternary IL computations Define a or lonic Liquid salt from individual anion and cation compounds The nIL name name input of the lonic Liquid composition is possible either via their compound number IL i j command where i j are the numbers of the ion compounds numbers as given in the sequence of compounds in the compound input section the arguments i j are expected to be positive integer numbers or via their compound number niL name name command where name name are the names of the ion compounds as given in the compound input section IL n vji Vj Required for binary or ternary IL computations Define the lonic Liquid salt stoichiometry from individual anion and cation compounds The input of the lonic Liquid stoichiometry factors v v is possible via the IL n v v command where vi v are the stoichiometry numbers of
441. y two given compounds e g binary complexes bound by intermolecular hydrogen bonds or by charge transfer complexation and provide reasonable initial geometries of such complexes which in the following may be optimized by a quantum chemical method Only complexes that are not hindered sterically or by van der Waals interactions will be created Thus by default not all possible complexes actually will be created You may force the creation of additional complexes using the keyword SSC_ WEAK which forces the creation of complexes with weak contacts Option SSC_PROBABILITY will create geometries of complexes based on the criterion of highest contact probabilities between two molecules while option SSC_STRENGTH will create geometries of complexes based on the criterion of lowest interaction energy between the surface segments of two molecules Please note that the SSC_PROBABILITY segment contact criterion is somewhat more strict and tends to create a lower number of complex geometry files only complexes with strong interactions such as intermolecular hydrogen bonds will be created while the SSC_STRENGTH interaction energy criterion is less tight and will also create complexes of unpolar molecules which can not build intermolecular hydrogen bonds or charge transfer complexes For the complex formation options SSC_PROBABILITY and SSC_STRENGTH it is possible to force the contact of two molecules at specific sites within the two complex fo
442. y where to search for the cosmo files of the quantum chemical COSMO calculation that are requested from a COSMO metafile compound mcos given in this compound input line See section 5 3 for details Default is to search in the current working directory or if set in the directory given by the fdir command Given in this section of the COSMOtherm input file the mdir command is overwrites any mdir command given in the global input section It is active only for the compound input line where it is given The directory name must not contain blank spaces unless it is given in quotes e g mdir C Program Files COSMOtherm DATABASE COSMO BP TZVP COSMO Optional change name of the compound to name for output By default the filename argument of the f name command is used 32 Compound input options continued automatic conformer input autoc maxautoc usec i io Optional Use all cosmo ccf or mcos files that are found in the directory as specified by the fdir command as conformers The COSMO file filenames must follow the name convention of conformer COSMO files in COSMObase i e conformer COSMO files are named by subsequent numbers starting with zero name0 cosmo namel cosmo name_9 cosmo Or name_c0 cosmo name_cl cosmo name _c9 cosmo By default conformer numbers ranging from 0 to 9 are considered The optional argument maxautoc assigns the maximum number of conformers that are searched for meani
443. yocs 3 concentrations is possible either in mole fractions xp x x or mass fractions cp c c2 of the compounds of the mixture as real numbers x and c The arguments are expected as real numbers between zero and one in the same sequence of compounds as given in the second input area If the values do not add up to one COSMOtherm will normalize them If less mole fractions concentrations than compounds are given the missing ones will be assumed zero If a negative number is given the concentration for this compound will be inserted automatically using the normalization of the sum of mole fractions Only one negative number is allowed per mixture input line pKaLFER cy C1 Optional for pKa computations Give the LFER parameters cy and c required or in the pK computation The arguments c and c are expected as real pKaLFER_SI co C1 numbers If the pKaLFER cy c option is used the LFER parameters are expected in kcal mol If the pkKaLFER_SI cy c option is used the LFER parameters are expected in kJ mol 105 COSMOtherm pK prediction is not restricted to acid pK It is also possible to compute aqueous base pK However base pK prediction requires a reparameterization of the pK LFER parameters The LFER parameters for aqueous base pK at room temperature are shipped within COSMOtherm parameter files BP_TZVP_C30_1501 ctd and BP_SVP_AM1 C30_1501 ctd The usage of the aqueous base pK L
444. yor Tref aS given in the compound input section or read from a compounds vapor pressure property file see section 2 2 3 as a reference point for scaling the vapor pressure prediction of the binary ternary or multinary option 112 The binary option allows further automatic post processing of the computed properties such as fitting of the computed activity coefficients to activity coefficient models special LLE search and solid liquid equilibrium SLE detection Suboptions specific to the binary option are NRTL Optional for binary computations Correlate the computed activity coefficients with the three parameter NRTL model See section 2 3 7 1 NRTL2 Optional for binary computations Correlate the computed activity coefficients with the two parameter NRTL2 model Only the two binary interaction parameters t and t are fitted to the computed activity coefficient data Factor a is held at a constant value See section 2 3 7 1 WILSON Optional for binary computations Correlate the computed activity coefficients with the WILSON model See section 2 3 7 1 UNIQUAC4 Optional for binary computations Correlate the computed activity coefficients with the UNIQUAC model The two binary interaction parameters t and t and the compound volume and surface parameters r and q are fitted to the computed activity coefficient data See section 2 3 7 1 UNIQUAC2 Optional for binary computations Correlate the computed activity coefficients
445. yridinium cation and 50 borontetrafluoride anion is calculated Other properties can be calculated in the same way Some care has to be taken in the interpretation of the COSMOtherm results for the computed thermodynamic properties One has to be aware of the different definitions of the mole fraction in an IL system Considering example 11 the COSMOtherm calculation in the sum of ions view is a ternary mixture calculation cation anion and solute i with the boundary condition that the molar amount of anion equals the molar amount of cation in the mixture Nj Nanion cation ternary _ n S n 2n ton 5 9 1 On the other hand the experimental determination of IL thermodynamic properties in the one substance view is based on the assumption of a binary system consisting of the IL and the solute n binary __ i n ny 5 9 2 214 These two definitions are just different views on the same system Therefore any calculated value corresponds to both definitions of the mole fraction The calculated chemical potentials are dependent on only the temperature and the composition of the system on the molecular level Nevertheless the two definitions may lead to different values if the mole fraction is used explicitly for the determination of experimental real world or laboratory binary data Example In a given ionic liquid mixture x and x belong to same composition To obtain the activity coeffici
446. yt Taw T ae 1 3 wherein zy and Taw are element specific adjustable parameters The vdW energy is dependent only on the element type of the atoms that are involved in surface contact It is spatially non specific E jy is an additional term to the energy of the reference state in solution Currently nine of the vdW parameters for elements H C N O F S Cl Br and I have been optimized For the majority of the remaining elements reasonable guesses are available The link between the microscopic surface interaction energies and the macroscopic thermodynamic properties of a liquid is provided by statistical thermodynamics Since in the COSMO RS view all molecular interactions consist of local pair wise interactions of surface segments the statistical averaging can be done in the ensemble of interacting surface pieces Such an ensemble averaging is computationally efficient especially in comparison to the computationally very demanding molecular dynamics or Monte Carlo approaches which require averaging over an ensemble of all possible different arrangements of all molecules in a liquid To describe the composition of the surface segment ensemble with respect to the interactions which depend on o only only the probability distribution of o has to be known for all compounds i Such probability distributions pc are called o profiles The o profile of the whole system mixture p c is just a sum of the o profiles of the components i we
447. z It is possible to give AG 5 in atomic units Hartree react_Gsol G Gip and react_GsolH G Gip option in kcal mol react_GsolC G Gi2 option in kJ mol react_GsolJ G Gj option or in eV react_GsolV G Gip option Equivalently external AG for the product compounds can be given with the keyword prod _Gsol G Gj or its variants for different energy units prod_GsolH G G Hartree prod_GsolcC G G kcal mol prod_GsolJ G Gjo kJ mol prod_GsolV G Gj eV The reactants AH can be given with the keyword react _Hvap H Hip where H are free energies of solvation in atomic units for the reactant compounds ij iz It is possible to give AH S Y in atomic units Hartree react_Hvap and react _HvapH option in kcal mol react_HvapC option in kJ mol react_HvapJ option or in eV react_HvapV option Equivalently external AH for the product compounds can be given with the keyword prod Hvap H H or its variants for different energy units prod_HvapH Hartree prod_HvapC kcal mol prod_Hvapd kJ mol prod_Hvapv eV An example of the usage of the reaction option can be found in the input file REACTION inp in the EXAMPLE INPUTS directory of the COSMOtherm installation Example 7 REACTION inp ctd BP_TZVP_C30 1501 ctd cdir CTDATA FILES fdir DATABASE COSMO BP TZV
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