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1. 31 Test Calculations for SMXGAUSS aan ans dont dantinanasmetiirena 33 SCRE SUNG Mes Cais ooien e oan aea ana s eaaa a eaaa aaa a EE a aE ee 45 Density Functional Methods Recommended for use with CM4 and SM6 in SMXGAUSS 46 Available Solvents in the solvent txt file eeeseeeeeessesssseressssreessssrerssseresrssreessssrressseres 47 PU TOMIDTS SHOOTS na a Nora 52 Plattorms ns air Ba Resale 54 Revision History Mal eaae aa a aa E ea essen OaE O aAA 55 Executive Summary SMXGAUSS is a program that carries out liquid phase calculations by solvation models 5 42 5 43 6 and 6 with temperature dependence SM5 42 SM5 43 SM6 and SM6T which are quantum mechanical free energy calculations based on the self consistent reaction field SCRF method augmented by atomic surface tensions SMXGAUSS can be used to carry out a single point calculation in the liquid phase a geometry optimization in the liquid phase to a minimum or to a transition state or a Hessian calculation in the liquid phase SMXGAUSS can run in two basic modes In mode 1 all calculations are performed using the intrinsic supplied code for Hartree Fock HF density functional theory DFT hybrid DFT generalized Born analytic surface area calculations geometry optimizations and Hessian calculations In this mode no other electronic structure software is required The program running in this mode has been designed however to take as input a GAUSSIAN output file
2. Li G D Hawkins T Zhu Y Volobuev M Dupuis D Rinaldi D A Liotard C J Cramer and D G Truhlar This version of SMXGAUSS is based on version 4 7 of HONDOPLUS Parameter sets for the SM6 solvation model were added Parameters were added for DFT MIDI 6D DFT 6 31G d DFT 6 31 G d and DFT 6 31 G d p where X can take on any value between 0 and 99 9 All of the SMx models can use up to 99 9 for X instead of the previous upper limit that was set to 60 6 Atomic radii are now available for all elements on the periodic table 56 SMXGAUSS version 3 0 1 October 2005 Authors C P Kelly J D Thompson B J Lynch J D Xidos J Li G D Hawkins T Zhu Y Volobuev M Dupuis D Rinaldi D A Liotard C J Cramer and D G Truhlar This version of SMXGAUSS is based on version 4 7 of HONDOPLUS In SMXGAUSS version 3 0 a bug in the file named procinput lib caused the program to stop when liquid phase Hessian calculations were attempted This bug has been fixed in SMXGAUSS version 3 0 1 SMXGAUSS version 3 1 November 2005 Authors C P Kelly J D Thompson B J Lynch J D Xidos J Li G D Hawkins T Zhu Y Volobuev M Dupuis D Rinaldi D A Liotard C J Cramer and D G Truhlar This version of SMXGAUSS is based on version 4 9 of HONDOPLUS This version of SMXGAUSS has been tested on more platforms than previous versions A new test suite has been developed that includes test jobs that test
3. 1 pgf77 version 5 2 4 gnu g77 version 3 2 3 gnu g77 version 3 2 3 MIPSPro version 7 4 1 gnu g77 version 3 2 3 Sun ONE Studio version 7 1 gnu g77 version 3 3 1 gnu g77 version 3 5 0 install ibm csh install ibm csh install ibm csh install linux csh install linux g77 csh install ia64 csh install irix csh install irix g77 csh install sun csh install irix g77 csh install darwin csh Revision History SMXGAUSS version 1 0 April 2004 Authors J D Thompson B J Lynch J D Xidos J Li G D Hawkins T Zhu Y Volobuev M Dupuis D Rinaldi D A Liotard C J Cramer and D G Truhlar This version of SMXGAUSS is based on version 4 5 of HONDOPLUS This is the first version of SMXGAUSS SMXGAUSS can be used to carry out SM5 42 and SM5 43 calculations using the appropriate wave functions specified in the Executive Summary SMXGAUSS version 2 0 October 2004 Authors J D Thompson B J Lynch J D Xidos J Li G D Hawkins T Zhu Y Volobuev M Dupuis D Rinaldi D A Liotard C J Cramer and D G Truhlar This version of SMXGAUSS is based on version 4 6 of HONDOPLUS Additional parameter sets for the SM5 43 solvation model were added In particular the parameters for MPWX MIDI MPWX MIDI 6D MPWX 6 31G d MPWX 6 31 G d and MPWX 6 31 G d p where X can take on any value between O and 60 6 were added SMXGAUSS version 3 0 July 2005 Authors C P Kelly J D Thompson B J Lynch J D Xidos J
4. CalcFCGas and CalcFCSol keywords are used in the same calculation see test case test6 inp below In some cases e g in cases where the user knows that the input geometry is very close to a stationary point or in cases where very little structural relaxation is expected to occur in the liquid phase using the CalcFCGas and CalcFCSol keywords may not be required in order for the transition state geometry optimization to run successfully For an example of a transition state geometry optimization that converges without using either of these keywords see test case test5 inp below Special note to users running SMXGAUSS in mode 2 SMXGAUSS can be used to optimize transition state geometries with or without first performing Hessian calculations regardless of whether the program is being run in mode 1 or mode 2 For users running SMXGAUSS in mode 2 it is useful to point out that some versions of GAUSSIANO3 do not allow the user to perform transition state geometry optimizations via the Opt TS keyword without first calculating or reading in via the input file force constants generated from an initial Hessian calculation While testing SMXGAUSS we discovered that this is true for GAUSSIANO3 revision C 01 Several earlier versions of GAUSSIANO3 that were also tested revision B 01 and B 05 do not have this limitation i e transition state optimizations can be performed without an initial set of force constants However regardless of the GAUSSIANO3
5. G D Cramer C J Truhlar D G Density Functional Solvation Model Based on CM2 Atomic Charges J Chem Phys 1998 109 9117 Li J Hawkins G D Cramer C J Truhlar D G Universal Reaction Field Model Based on Ab Initio Hartree Fock Theory Chem Phys Lett 1998 288 293 Li J Zhu T Hawkins G D Winget P Liotard D A Cramer C J Truhlar D G Extension of the Platform of Applicability of the SM5 42R Universal Solvation Model Theor Chem Acc 1999 103 9 Winget P Thompson J D Cramer C J Truhlar D G Parameterization of a Universal Solvation Model for Molecules Containing Silicon J Phys Chem B 2002 106 5160 Analytic Free Energy Gradients Zhu T Li J Liotard D A Cramer C J Truhlar D G Analytical Gradients of a Self Consistent Reaction Field Solvation Model Based on CM2 Atomic Charges J Chem Phys 1999 110 5503 Application of SM5 42 Chuang Y Y Radhakrishnan M L Fast P L Cramer C J Truhlar D G Direct Dynamics for Free Radical Kinetics in Solution Solvent Effect on the Rate Constant for the Reaction of Methanol with Atomic Hydrogen J Phys Chem A 1999 103 4893 SM5 43 Thompson J D Cramer C J Truhlar D G New Universal Solvation Model and Comparison of the Accuracy of the SM5 42R SM5 43R C PCM D PCM and IEF PCM Continuum Solvation Models for Aqueous and Organic Solvation Free Energies and for Vapor Pressures
6. J Phys Chem A 2004 108 6532 Thompson J D Cramer C J Truhlar D G Density Functional and Hybrid DFT SMS5 43R Continuum Solvation Models for Aqueous and Organic Solvents Theor Chem Acc 2005 113 107 SM6 Kelly C P Cramer C J Truhlar D G SM6 A Density Functional Theory Continuum Solvation Model for Predicting Aqueous Solvation Free Energies of Neutrals Ions and Solute Water Clusters J Chem Theory and Comput 2005 1 1133 SM6T Chamberlin A C Cramer C J Truhlar D G Predicting Aqueous Free Energies of Solvation as Functions of Temperature J Phys Chem B in press Basis Set References The following list gives the references for all basis sets supported by SMXGAUSS e MIDI for H Tatewaki H Huzinaga S J Comput Chem 1980 1 205 e MIDI for Li Tatewaki H Huzinaga S J Comput Chem 1980 1 205 Thompson J D Winget P Truhlar D G PhysChemComm 2001 4 4116 e MIDI for C F Tatewaki H Huzinaga S J Comput Chem 1980 1 205 Easton R E Giesen D J Welch A Cramer C J Truhlar D G Theor Chim Acta 1996 93 281 e MIDI for Si Huzinaga S Andzelm J Klobukowski M Radzio Audzelm E Sakai Y Tatewaki H Gaussian basis sets for molecular calculations Huzinaga S Ed Elsevier Amsterdam 1984 Li J Cramer C J Truhlar D G Theor Chem Acc 1998 99 192 e MIDI for P Cl Huzinaga S Andzelm J Klobukowski M Rad
7. MIDI MIDIX MIDIXS5D or MIDI SD or cc pVDZ are used they can only be used for single point calculations Error message Both Solvent and Solvent_Descriptors keywords were found in the input Use only one of them to specify the solvent for your calculation Explanation Specify the solvent only once using either the Solvent keyword or the Solvent_Descriptors keyword Error message Neither the Solvent nor the Solvent_Descriptors were found in the input file Explanation You must specify the solvent with either the Solvent keyword or the Solvent_Descriptors keyword Platforms SMXGAUSS version 3 3 has been tested on the following platforms Machine Operating System Compiler s Install File IBM SP WinterHawk nodes IBM SP NightHawk nodes IBM pSeries 690 and pSeries 655 Netfinitiy Linux cluster SGI Altix Itanium 2 SGI Origin 2000 SunBlade 2000 UltraSparc III Mac G5 OS X version 10 4 3 SMXGAUSS version 3 4 1 has been tested in mode 2 with the following versions of GAUSSIANO3 AIX version 5 1 AIX version 5 1 AIX version 5 2 Red Hat Linux 2 4 21 Red Hat Linux 2 4 21 IRIX version 6 5 Solaris 9 Darwin 7 9 0 e GAUSSIANO3 Revision C 01 e GAUSSIANO3 Revision D O1 Prior versions of SMXGAUSS have also been tested in mode 2 with the following versions of GAUSSIANO3 e GAUSSIANO3 Revision B 01 e GAUSSIANO3 Revision B 05 XL Fortran version 9 1 XL Fortran version 9 1 XL Fortran version 9
8. MIDIX6D 6 31G d can also be specified as 6 31G 6 31 G d can also be specified as 6 31 G cc pVDZ DZVP 13 Note Not all of the methods listed above are compliant with SM5 42 SM5 43 and SM6 See the section entitled Allowed Combinations of Solvation Model Electronic Structure Method and Basis Set for more details Allowed Combinations of Solvation Model Electronic Structure Method and Basis Set The SMx x 5 42 5 43 and 6 solvation models are parameterized models where the parameters are determined for particular combinations of an electronic structure method and basis set Allowed combinations are given in the tables below Any other combinations will result in an error message For SM5 42 single point calculations electronic structure method basis set HF MIDI HF MIDI 6D HF 6 31G d HF 6 31 G d HF cc pVDZ BPW91 MIDI BPW91 MIDI 6D BPW91 6 31G d BPW91 DZVP B3LYP MIDI For SM5 42 liquid phase geometry optimizations and Hessian calculations electronic structure method basis set HF MIDI 6D HF 6 31G d HF 6 31 G d BPW91 MIDI 6D BPW91 6 31G d BPW91 DZVP For SM5 43 single point calculations electronic structure method basis set HF 6 31G d B3LYP 6 31G d mPWPW91 MIDI mPWPW91 MIDI 6D mPWPW91 6 31G d mPWPW91 6 31 G d mPWPW91 6 31 G d p mPWI1PW91 MIDI mPW1PW91 MIDI 6D mPW1PW91 6 31G d mPW1PW91 6 31 G d mPW1PW91 6 31 G d p MPWIK MIDI MPWIK MIDI 6D
9. MPWIPW91 or C Adamo and V Barone J Chem Phys MPW250 108 664 1998 MPWIS 0 060 MPWO060 B J Lynch Y Zhao and D G Truhlar J Phys Chem A 107 1384 2003 MPWIN 0 406 MPW406 B L Kormos and C J Cramer J Phys Org Chem 15 712 2002 MPWIK 0 428 MPW428 B J Lynch P L Fast M Harris and D G Truhlar J Phys Chem A 104 4811 2000 MPWX 0 000 0 999 MPW 000 999 Available Solvents in the solvent txt file Below is a list of the solvents available in the file solvent txt A pdf version of this file can be found at http comp chem umn edu solvation mnsddb pdf Note that each solvent should appear in the SMXGAUSS input exactly as it appears below except for case since the input is case insensitive If the solvent of interest is not listed either the Solvent_Descriptors keyword needs to be used or the solvent name and its descriptors should be added to the solvent txt file which is in tab delimited format 1 1 1 trichloroethane 1 1 2 trichloroethane 1 1 dichloroethane 1 2 4 trimethylbenzene 1 4 dioxane 1 bromo 2 methylpropane 1 bromopentane 1 bromopropane 1 butanol 1 chloropentane 1 chloropropane 1 decanol 1 fluorooctane 1 heptanol 1 hexanol 1 hexene 1 hexyne 1 iodobutane 1 iodopentene 1 iodopropane 1 nitropropane 1 nonanol l octanol 1 pentanol 1 pentene 1 pentyne 1 propanol 2 2 2 trifluoroethanol 2 2 4 trimethylpentane 2 4 dimethylpentane 2 4 dimeth
10. Phi p where p is the solvent s carbon aromaticity parameter Psi s where s is the solvent s electronegative halogenicity parameter 19 Example Request toluene solvent with the Solvent_Descriptors keyword The seven solvent descriptors for toluene are n 1 496 2 37 a 0 0 B 0 14 y 41 4 p 0 86 and y 0 0 The Solvent_Descriptors keyword would be Solvent_Descriptors n 1 496 Alpha 0 0 Beta 0 14 Gamma 41 4 Phi 0 86 Psi 0 0 Dielectric 2 37 Specification of the Solvent Temperature Computation of solute thermodynamic properties at a given temperature using SM6T can be requested using the SolK keyword In test7a test7b test7c and test7d the SolK keyword is tested for water in water at temperatures 273 298 348 and 373 K respectively The SolK keyword is currently only applicable to the aqueous solutions in the temperature range 273 to 373 K a request for anything outside this range or the use of non aqueous solvents will produce an error Additionally the model SM6T is currently restricted to H C and O containing compounds use of compounds containing atoms other than H C or O will not produce an error however the results should be used with caution Additionally this method does not yet have gradients it can only be used to compute single point energies 20 Specification of the Type of Calculation There are three types of calculations that can be performed with SMXGAUSS a liquid phase single po
11. the CalcFCGas CalcFCSol and TS keywords SMXGAUSS version 3 2 December 2005 Authors C P Kelly J D Thompson B J Lynch J D Xidos J Li G D Hawkins T Zhu Y Volobuev M Dupuis D Rinaldi D A Liotard C J Cramer and D G Truhlar If SMXGAUSS is installed under mode 1 the executable is now named smxgl pl If installed under mode 2 the executable is named smxg2 pl The mode used to run SMXGAUSS either model or mode2 is printed to the output file The ISCRF option via the override keyword is no longer supported A warning message is printed and the calculation ends if geometry optimizations with either the MIDI or cc pVTZ basis sets are attempted 57 SMXGAUSS version 3 3 January 2006 Authors C P Kelly J D Thompson B J Lynch J D Xidos J Li G D Hawkins T Zhu Y Volobuev M Dupuis D Rinaldi D A Liotard C J Cramer and D G Truhlar Earlier versions running under mode 1 did not read the charge and multiplicity from punch files This bug has been fixed in version 3 3 This version has been tested on a Mac mini G4 SMXGAUSS version 3 4 February 2006 Authors A C Chamberlin C P Kelly J D Thompson B J Lynch J D Xidos J Li G D Hawkins T Zhu Y Volobuev M Dupuis D Rinaldi D A Liotard C J Cramer and D G Truhlar The parameters for the temperature dependent version of SM6 were included The additional keyword SolK was included Four addition
12. 000 H 0 880669 1 705800 0 000000 ht Summary of SMxGauss calculation Gas phase energy at MPW1K 6 31 G D G S liq free energy of system at MPW1K 6 31 G D Standard state free energy of solvation Free energy of cavity dispersion solvent structure Free energy of polarization Electronic Nuclear distortion energy Description of Output FEAE FE FE FE AE AE AE E FE FE FE AEE AF 152 193401 a u 152 344243 a u 94 654 kcal mol 7 152 kcal mol 89 888 kcal mol 2 386 kcal mol 39 The optimized geometry of the water hydroxide transition state structure in both the gas and liquid phases is printed to output The standard state free energy of solvation for the liquid phase structure is calculated to be 94 654 kcal mol 40 test6 inp Input SM6 Opt CalcFCGas TS CalcFCSol MPW1K 6 31 G d Solvent water Coordinates h2o0 oh xyz SM6 MPW1K 6 31 G d optimization of the H20 OH transition state CS in water force constants are calculated in both the gas and liquid phase to facilitate geometry optimization Summary of Output Gas phase optimized coordinates H 0 941716 1 413254 0 000000 O 0 000416 1 242997 0 000000 H 0 047323 0 159670 0 000000 O 0 000416 1 243533 0 000000 H 0 901049 1 568632 0 000000 Liquid phase optimized coordinates H 0 930741 1 545884 0 000000 O 0 002026 al 29
13. 31 G SM6 B3LYP 6 31G SM6 B3LYP 6 31 G SM6 BPW91 6 31G SM6 BPW91 6 31 G SM6 B3PW91 6 31G SM6 B3PW91 6 31 G SM6 MPWX 6 31G SM6 MPWX 6 31 G SM6T BLYP 6 31G SM6T BLYP 6 31 G SM6T B3LYP 6 31G SM6T B3LYP 6 31 G SM6T BPW91 6 31G SM6T BPW91 6 31 G SM6T B3PW91 6 31G SM6T B3PW91 6 31 G SM6T MPWX 6 31G SM6T MPWX 6 3 1 G where X in MPWX is the fraction of Hartree Fock exchange in the modified version of Perdew and Wang s exchange functional allowed values of X can be between 0 and 99 9 e Liquid phase geometry optimizations liquid phase Hessian calculations and single point liquid phase free energy calculations at arbitrary geometries may be carried out by the following methods SM5 42 HF MIDI 6D SM5 42 BPW91 MIDI 6D SM5 42 HF 6 31G d SM5 42 BPW91 6 31G d SM5 42 HF 6 31 G d SM5 42 BPW91 DZVP SM5 43 HF 6 31G d SM5 43 B3LYP 6 31G d SM5 43 MPWX MIDI 6D SM5 43 MPWX 6 31G d SM5 43 MPWX 6 31 G d SM5 43 MPWX 6 31 G d p SM6 BLYP MIDI 6D SM6 BLYP 6 31G SM6 BLYP 6 31 G SM6 BLYP 6 31 G SM6 B3LYP MIDI 6D SM6 B3LYP 6 31G SM6 B3LYP 6 31 G SM6 B3LYP 6 31 G SM6 BPW91 MIDI 6D SM6 BPW91 6 31G SM6 BPW91 6 31 G SM6 BPW91 6 31 G SM6 B3PW91 MIDI 6D SM6 B3PW91 6 31G SM6 B3PW91 6 31 G SM6 B3PW91 6 31 G SM6 MPWX MIDI 6D SM6 MPWX 6 31G SM6 MPWX 6 31 G SM6 MPWX 6 31 G Background References Below are the references for the solvation models available in SMXGAUSS SM5 42 Zhu T Li J Hawkins
14. 5199 0 000000 H 0 016390 0 288973 0 000000 O 0 002026 1 312185 0 000000 H 0 881937 1 703418 0 000000 ht Summary of SMxGauss calculation HEEEEE EEE EEE EEE HEHE HF Gas phase energy at MPW1K 6 31 G D 152 193401 a u G S liq free energy of system at MPW1K 6 31 G D 152 344242 a u Standard state free energy of solvation 94 655 kcal mo Free energy of cavity dispersion solvent structure 7 152 kcal mol Free energy of polarization 89 902 kcal mol Electronic Nuclear distortion energy 2 399 kcal mol Description of Output The optimized geometry of the water hydroxide transition state structure in both the gas and liquid phases is printed to output The standard state free energy of solvation for the liquid phase structure is calculated to be 94 655 kcal mol test7a inp Input SM6 B3LYP 6 31 G d p SolK 273 Solvent water Coordinates h20 xyz SM6T B3LYP 6 31 G d p calculation of the aqueous solvation free energy of water at 273 K experimental value 4 46 kcal mol Summary of Output HHHHHHHHHHHPHHHEHE Summary of SMxGauss calculation at 273 K H HHHHHHHHPHHHSE Gas phase energy at B3LYP 6 31 G D P 76 433989 a u G S liq free energy of system at B3LYP 6 31 G D P 76 449145 a u Standard state free energy of solvation 9 511 kcal mol Free energy of cavity dispersion solvent structure 3 900 kcal mo Free energy of polarization 5 845 kcal mol Electroni
15. 8 03000 2 H X 00000 56062 00000 00000 Y 57679 00000 49143 822711 Z 02153 00000 290792 47579 3 H x 00000 56062 00000 00000 x 57674 00000 49142 52268 Z 02025 00000 50793 47575 NORM 1 00000 00000 00000 00000 91 63 00000 03222 00000 00000 51114 48806 00000 51117 48806 NKXNKXNKX NORM 1 00000 Description of Output The three vibrational frequencies of hydrogen sulfide in wave numbers are 2769 2749 and 1247 Below each frequency is the corresponding normal mode The last six frequencies listed correspond to rotational and translational modes 36 test3 inp Input SM6 Opt CalcFCGas Solvent water B3PW91 MIDIX6D Coordinates h2s xyz SM6 B3PW91 MIDIX6D optimization of hydrogen sulfide in water force constants calculated at initial gas phase geometry to facilitate geometry optimization in the liquid phase Summary of Output HH Summary of SMxGauss calculation HHEFHEEHEEEEE HEE EH HH HEH Gas phase energy at B3PW91 MIDIX6D 397 475673 a u G S liq free energy of system at B3PW91 MIDIX6D 397 477643 a u Standard state free energy of solvation 1 236 kcal mol Free energy of cavity dispersion solvent structure 0 360 kcal mol Free energy of polarization 0 994 kcal mol Electronic Nuclear distortion energy 0 118 kcal mol Description of Output The standard state free energy of solvation is calcu
16. Chem Theory Comput 2005 1 1133 In mode 2 SMXGAUSS input files also have the same format as GAUSSIAN input files and the charge multiplicity and geometry can be specified in the SMXGAUSS input file by the same methods as they are in GAUSSIAN e g the geometry can be specified with Cartesian coordinates Z matrix coordinates a combination of Cartesian and Z matrix coordinates etc or they can be read from a GAUSSIAN output file or from an SMXGAUSS summary file created from a previous SMXGAUSS calculation SMXGAUSS version 3 4 1 has the following capabilities e Single point liquid phase free energy calculations based on gas phase geometries are available by the following methods SM5 42 HF MIDI SM5 42 HF MIDI 6D SM5 42 HF 6 31G d SM5 42 HF 6 31 G d SM5 42 HF cc pVDZ SM5 43 HF 6 31G d SM5 43 MPWX MIDI SM5 43 MPWX 6 31G d SM5 43 MWPX 6 31 G d p SM6 BLYP MIDI 6D SM6 BLYP 6 31 G SM6 B3LYP MIDI 6D SM6 B3LYP 6 31 G SM6 BPW91 MIDI 6D SM6 BPW91 6 31 G SM6 B3PW91 MIDI 6D SM6 B3PW91 6 31 G SM6 MPWX MIDI 6D SM6 MPWX 6 31 G SM6T BLYP MIDI 6D SM6T BLYP 6 31 G SM6T B3LYP MIDI 6D SM6T B3LYP 6 31 G SM6T BPW91 MIDI 6D SM6T BPW91 6 31 G SM6T B3PW91 MIDI 6D SM6T B3PW91 6 31 G SM6T MPWX MIDI 6D SM6T MPWX 6 31 G SM5 42 BPW91 MIDI SM5 42 BPW91 MIDI 6D SM5 42 BPW91 6 31G d SM5 42 BPW91 DZVP SM5 42 B3LYP MIDI SM5 43 B3LYP 6 31G d SM5 43 MPW X MIDI 6D SM5 43 MPWX 6 31 G d SM6 BLYP 6 31G SM6 BLYP 6
17. MPWIK 6 31G d MPWIK 6 314 G d MPWIK 6 31 G d p MPWIKK MIDI MPWIKK MIDI 6D MPWIKK 6 31G d MPWIKK 6 31 G d MPWIKK 6 31 G d p MPWX MIDI MPWX MIDI 6D MPWX 6 31G d MPWX 6 314 G d MPWX 6 31 G d p For SM5 43 liquid phase geometry optimizations and Hessian calculations electronic structure method basis set HF 6 31G d B3LYP 6 31G d mPWPW91 MIDI 6D mPWPW91 6 31G d mPWPW91 6 31 G d mPWPW91 6 31 G d p mPWI1PW91 MIDI 6D mPW1PW91 6 31G d mPWI1PW91 6 31 G d mPW1PW91 6 31 G d p MPWIK MIDI 6D MPWIK 6 31G d MPWIK 6 31 G d MPWIK 6 31 G d p MPWIKK MIDI 6D MPWIKK 6 31G d MPWIKK 6 31 G d MPWIKK 6 31 G d p MPWX MIDI 6D MPWX 6 31G d MPWX 6 31 G d MPWX 6 31 G d p 15 For SM6 and SM6T single point calculations electronic structure method basis set BLYP MIDI 6D BLYP 6 31G d BLYP 6 31 G d BLYP 6 31 G d p B3LYP MIDI 6D B3LYP 6 31G d B3LYP 6 31 G d B3LYP 6 31 G d p BPW91 MIDI 6D BPW91 6 31G d BPW91 6 31 G d BPW91 6 31 G d p B3PW91 MIDI 6D B3PW91 6 31G d B3PW91 6 31 G d B3PW91 6 31 G d p mPWPW91 MIDI 6D mPWPW91 6 31G d mPWPW91 6 31 G d mPWPW91 6 31 G d p mPW1PW91 MIDI 6D mPW1PW91 6 31G d mPW1PW91 6 31 G d mPWI1PW91 6 31 G d p MPWIK MIDI 6D MPWIK 6 31G d MPWIK 6 31 G d MPWIK 6 31 G d p MPWIKK MIDI 6D MPWIKK 6 31G d MPWIKK 6 31 G d MPWIKK 6 31 G d p MPWX MIDI 6D MPWX 6 31G d MPWX 6 314 G d MPWX 6 31 G d p 17 For SM6 liquid phase geometry opti
18. SMXGAUSS User s Manual version 3 4 2 date of finalization of software August 23 2007 date of finalization of this document August 23 2007 Jason D Thompson Casey P Kelly Adam C Chamberlin Benjamin J Lynch James D Xidos Jiabo Li Gregory D Hawkins d Tianhai Zhu Yuri Volobuev Michel Dupuis f Daniel Rinaldi Daniel A Liotard Christopher J Cramer and Donald G Truhlar Department of Chemistry and Supercomputer Institute University of Minnesota Minneapolis MN 55455 0431 Current address Mayo Clinic Rochester MN Current address Accelrys San Diego CA dCurrent address SAP America Inc Minneapolis MN eCurrent address IBM Austin TX Environmental Molecular Sciences Laboratory Pacific Northwest National Laboratory Richland WA 8Laboratoire de Chimie Theorique Universite de Nancy I Vandoeuvre Nancy 54506 France hLaboratoire de Physico Chimie Th orique Universit de Bordeaux 1 351 Cours de la Liberation 33405 Talence Cedex France Distribution Site http comp chem umn edu smxgauss Contents Executive ULTIMA Vass Sos ore ecco eras seas pd cad en r E E E ERE T 3 Background Relerenees ar I 5 SMS en neun AA einander euer 5 Analytic Free Energy Gr dients a ana eshure 6 Application of SMS 2 a wi eas a Reese 6 SVE ata cece sa E AT TIEF ERTRTENTERITIHUEREHTRUENRIE ER ties puss yt hin teck 6 SMG sca wuitowa wale alien en in 6 SMOD ran eer ere ete neice error ert
19. YP or mPWX X PW91 1PW91 1K 1KK or fraction HF exchange 1000 Explanation The solvation models in SMXGAUSS are used in conjunction with any of the above electronic structure methods so one of them needs to be specified in the input file See the section entitled Basic Keywords above for appropriate combinations of solvation model electronic structure method and basis set Error message Basis set not found in input You must specify MIDI MIDI 6D 6 31G d 6 31 G d cc pVDZ or DZVP Explanation The solvation models in SMXGAUSS are used in conjunction with any of the above basis sets so one of them needs to be specified in the input file See the section entitled Basic Keywords above for appropriate combinations of solvation model electronic structure method and basis set Error message SMx x 5 42 5 43 or 6 parameters do not exist for Level Basis See the SMXGAUSS manual for a listing of methods for which SMx x 5 42 5 43 6 exist Explanation The choice of solvation model electronic structure method and basis set are inconsistent See the section entitled Basic Keywords for a listing of allowed combinations Error message You have requested a calculation that requires analytical gradients but they are not available for basis sets with spherical harmonic d and f functions 53 Explanation The solvation models in SMXGAUSS only have analytic free energy gradients for basis sets with Cartesian d and f So whenever
20. agnitude will almost always correspond to rotational and translational modes For nonlinear molecules the six frequencies that are smallest in magnitude will correspond to these modes The translational and rotational frequencies are printed last after the vibrational frequencies Note that when all vibrational frequencies excluding the five or six from translations and rotations are real numbers i e when they are all positive the structure corresponds to a minimum and when one or more of the vibrational frequencies is imaginary they will be printed as negative numbers the structure corresponds to a transition state 33 Test Calculations for SmMxGAUSS This section contains eight test calculations for SMXGAUSS which are located in the tests directory of the SMXGAUSS distribution These test jobs are described below testl inp Input SM6 B3LYP 6 31 G d p Solvent water Coordinates h2s xyz SM6 B3LYP 6 31 G d p calculation of the aqueous solvation free energy of hydrogen sulfide experimental value 0 7 kcal mol Summary of Output HH Summary of SMxGauss Calculation HHEEEEEE THEE HEHEHE HHH Gas phase energy at B3LYP 6 31 G D P 399 393411 a u G S liq free energy of system at B3LYP 6 31 G D P 399 394703 a u Standard state free energy of solvation 0 811 kcal mol Free energy of cavity dispersion solvent structure 0 020 kcal mol Free energy of polarization 0 918 kcal mol El
21. ained with this package should give the following reference plus one or more of the background references given in the previous section for whatever method is used Chamberlin A C Kelly C P Thompson J D Lynch B J Xidos J D Li J Hawkins G D Zhu T Volobuev Y Dupuis M Rinaldi D Liotard D A Cramer C J Truhlar D G SUXGAUSS version 3 3 University of Minnesota Minneapolis MN 55455 2004 In addition of course if the GAUSSIAN program is also used to supply GAUSSIAN output files for SMXGAUSS calculations and or to utilize the External option provided by the GAUSSIANO3 executable one should give any references required by GAUSSIAN 11 SMXGAUSS Input and Keywords The format and syntax of an SMXGAUSS input file is similar to the format and syntax of a GAUSSIAN input file see the Gaussian Input section of the GAUSSIAN manual In particular the route section is specified first currently Link 0 commands such as chk rwf subst etc are not allowed The route section is initiated with the symbol can be on multiple lines and is terminated with a blank line After the route section the title section is specified which can also be on more than one line and is terminated with a blank line When the program is run in mode a GAUSSIANO3 executable is not required to run SMXGAUSS When the program is run in mode 2 i e you do have a GAUSSIANO3 executable and wish to use it for geometr
22. al tests for SolK were included in the test suite test7a test7b test7c and test7d The Gau_External script was modified to allow SMXGAUSS to work with versions D01 and D02 of Gaussian 03 SMXGAUSS version 3 4 1 October 2006 Authors A C Chamberlin C P Kelly J D Thompson B J Lynch J D Xidos J Li G D Hawkins T Zhu Y Volobuev M Dupuis D Rinaldi D A Liotard C J Cramer and D G Truhlar In SMXGAUSS version 3 4 a bug in the file named intstaller temp caused the installation to hang up if the user requested to compile the code using mode 2 SMXGAUSS version 3 4 2 August 2007 Authors A C Chamberlin C P Kelly J D Thompson B J Lynch J D Xidos J Li G D Hawkins T Zhu Y Volobuev M Dupuis D Rinaldi D A Liotard C J Cramer and D G Truhlar In prior versions of SMXGAUSS there was a bug that caused the program to compute incorrect gradients for gas phase and liquid phase molecules this bug has been fixed In prior versions of SMXGAUSS there was a bug that caused the program to compute incorrect energies of solvation during geometry optimizations when the ISCRF 2 option was set This error has been corrected
23. c Nuclear distortion energy 0 234 kcal mol Description of Output 41 test7b inp Input SM6 B3LYP 6 31 G d p SolK 298 Solvent water Coordinates h20 xyz SM6T B3LYP 6 31 G d p calculation of the aqueous solvation free energy of water at 298 K experimental value 3 94 kcal mol Summary of Output HHHHHHHPHHPHEHHEHE Summary of SMxGauss calculation at 298 K H HEHHHPEEPEEPEESH Gas phase energy at B3LYP 6 31 G D P T 6a G S liq free energy of system at B3LYP 6 31 G D P 76 Standard state free energy of solvation Free energy of cavity dispersion solvent structure Free energy of polarization Electronic Nuclear distortion energy Description of Output 433989 448478 9 092 3 489 5 836 0 233 1 mo1 1 mo1 1 mo 1 mo1 test7c inp Input SM6 B3LYP 6 31 G d p SolK 348 Solvent water Coordinates h20 xyz SM6T B3LYP 6 31 G d p calculation of the aqueous solvation free energy of water at 348 K experimental value 2 98 kcal mol Summary of Output Harte Summary of SMxGauss calculation at 348 K H H HHEHEEPEEHEHH Gas phase energy at B3LYP 6 31 G D P T 6a G S liq free energy of system at B3LYP 6 31 G D P 76 Standard state free energy of solvation Free energy of cavity dispersion solvent structure Free energy of polarization Electronic Nuclear distortion energy Descripti
24. e energies to calculate partition coefficients is Giesen D J Hawkins G D Liotard D A Cramer C J Truhlar D G Theor Chem Acc 1997 98 85 A general reference for the use of solvation free energies to calculate vapor pressures is Winget P Hawkins G D Cramer C J Truhlar D G J Phys Chem B 2000 104 4726 10 A general reference for the use of solvation free energies to calculate solubilities is Thompson J D Cramer C J Truhlar D G J Chem Phys 2003 119 1661 General references for the use of solvation free energies to calculate rate constants are Chuang Y Y Cramer C J Truhlar D G Int J Quantum Chem 1998 70 887 Chuang Y Y Radhakrishnan M L Fast P L Cramer C J Truhlar D G J Phys Chem A 1999 103 4893 In addition to solvation free energies another quantity available in the output is class IV partial atomic charges which may be used for calculating electrostatic interactions General references are Storer J W Giesen D J Cramer C J Truhlar D G J Comput Aid Mol Des 1995 9 87 Barrows S E Cramer C J Truhlar D G Elovitz M S Weber E J Environ Sci Technol 1996 30 3028 Winget P Thompson J D Xidos J D Cramer C J Truhlar D G J Phys Chem A 2002 106 10707 Kelly C P Cramer C J Truhlar D G Theor Chem Acc 2005 113 133 Required Citations Publications based on results obt
25. ectronic Nuclear distortion energy 0 087 kcal mol Description of Output The standard state free energy of solvation is calculated to be 0 811 kcal mol This output reports the following i the expectation value of the energy using the gas phase optimized wave function which is 399 393411 hartrees ii the free energy in solution which is 399 394703 hartrees iii the nonbulk electrostatic contribution to the free energy of solvation This value is calculated to be 0 020 kcal mol iv the expectation value of the polarization energy which is calculated by the generalized Born method using the liquid phase wave function This value is calculated to be 0 918 kcal mol v the distortion energy which is the change in the energy of the solute upon solvation i e the difference between the liquid phase energy and the gas phase energy This value is calculated to be 0 087 kcal mol 34 test2a inp Input SM6 Opt MPW1PW91 6 31G d Solvent water Coordinates h2s xyz SM6 MPW1PW91 6 31G d optimization of hydrogen sulfide in water Summary of Output The gas phase geometry optimization has completed successfully Gas phase optimized coordinates S 0 000000 0 000000 0 102881 H 0 000000 0 973724 0 823047 H 0 000000 0 973724 0 823047 Liquid phase optimized coordinates S 0 000000 0 000000 0 103118 H 0 000000 0 972303 0 824948 H 0 000000 0 972303 0 824948 HH Summary of SMxGau
26. ed with SMXGAUSS Currently install files exist for a number of combinations of machine operating system and compiler for example the install file install sun g77 csh is intended for installation on a Sun machine with the gnu g77 compiler If you are unsure which install file to use refer to the section entitled Platforms near the end of this manual for a list of platforms that SMXGAUSS has been tested on Once the proper install script has been chosen and executed with the above command this script will ask you if you have GAUSSIANO3 installed and where the g03 executable is located Answer no press enter and then wait for the source code to compile This may take some time depending on the system To finish installing SMXGAUSS for mode 2 the External option in GAUSSIANO3 will be used 4 Unload GAUSSIANO3 as well as any previous versions of GAUSSIAN module unload g03 5 Add the absolute path of the location of the SMXGAUSS distribution to your PATH variable For example if you untar and unzip the SMXGAUSS distribution in home thompson then use the command set path path home thompson SMxGauss v3 4 1 24 6 Load GAUSSIANO3 module load g03 7 Verify that the absolute path of the location of the SMXGAUSS distribution to your PATH variable is listed before the absolute path of the location of GAUSSIANO3 by typing echo path If the absolute path of the location of the SMXGAUSS distribution is NOT li
27. ent in hartree bohr default is 0 005 This option is only available if you do not have GAUSSIANO3 installed If you have GAUSSIANO3 then the convergence criteria used in GAUSSIANO3 is used CalcFCGas Requests a calculation of the gas phase Hessian at the initial set of gas phase coordinates see the section entitled Using a Hessian Matrix for Geometry Optimizations CalcFCSol Requests a calculation of the liquid phase Hessian at the initial set of liquid phase coordinates see the section entitled Using a Hessian Matrix for Geometry Optimizations Requests a liquid phase Hessian calculation followed by a vibrational frequency analysis This keyword can be used to characterize stationary points as minima or transition states see the section entitled dentifying Minima and Transition States with a Hessian Calculation Note that the Opt and Freq cannot be used in the same calculation 21 Specification of the Charge Multiplicity and Geometry The charge multiplicity and coordinates for an SMXGAUSS calculation can be taken from a GAUSSIAN output file or from an SMXGAUSS summary file created from a previous SMXGAUSS calculation This file is specified with the Coordinates keyword in the route section of the SMXGAUSS input file Coordinates file where file is a GAUSSIANX X 94 98 or 03 output file or an SMXGAUSS summary file created from a previous SMXGAUSS calculation For users who do not have a GAUSSIANO3 executable speci
28. es h2s xyz 1 Use the command Executable_Path smxgX pl h2s inp h2s out where X is either 1 or 2 The gas phase geometry will optimize within two steps but not the liquid phase geometry so the calculation will need to be restarted 2 Search h2s out for the string Maximum number of geometry optimization steps has been exceeded to verify that the geometry is not yet optimized 3 Create a new input file named h2s_2 inp containing the following keywords HF MIDI 6D Opt sm5 42 solvent water coordinates h2s pun 4 Use the command Executable_Path smxgX pl h2s_2 inp h2s_2 out where X is either 1 or 2 The program will find the latest set of liquid phase coordinates from the previous calculation so it will skip the geometry optimization in the gas phase 5 Search h2s_2 out for the string Liquid phase optimized coordinates to verify that the geometry has optimized in the liquid phase 28 Using a Hessian Matrix for Geometry Optimizations To facilitate geometry optimizations in the liquid phase a Hessian calculated at the geometry of the solute in the liquid phase can be used Example Optimize the geometry of hydrogen sulfide in water solvent using SM5 42 and HF MIDI 6D The name of the input file is calcfc inp which contains HF MIDI 6D Opt CalcFCSol sm5 42 solvent water coordinates h2s xyz 1 Use the command Executable_Path smxgX pl calcfc inp calcfc out where X is either 1 or 2 Thi
29. esche and H Eschrig Akademie Verlag Berlin 1991 11 J P Perdew J A Chevary S H Vosko K A Jackson M R Pederson D J Singh and C Fiolhais Phys Rev B46 1992 J P Perdew J A Chevary S H Vosko K A Jackson M R Pederson D J Singh and C Fiolhais Phys Rev B48 1993 J P Perdew K Burke and Y Wang Phys Rev B 54 16533 1996 mPWPW91 MPW000 C Adamo and V Barone J Chem Phys 108 664 1998 K Burke J P Perdew and Y Wang in Electronic Density Functional Theory Recent Progress and New Directions Ed J F Dobson G Vignale and M P Das Plenum 1998 J P Perdew in Electronic Structure of Solids 91 Ed P Ziesche and H Eschrig Akademie Verlag Berlin 1991 11 J P Perdew J A Chevary S H Vosko K A Jackson M R Pederson D J Singh and C Fiolhais Phys Rev B 46 1992 J P Perdew J A Chevary S H Vosko K A Jackson M R Pederson D J Singh and C Fiolhais Phys Rev B 48 1993 J P Perdew K Burke and Y Wang Phys Rev B 54 16533 1996 47 Hybrid DFT functionals recommended for use with CM4 and SM6 in SMXGAUSS Method Fraction HFE SMXGAUSS Keyword Reference s B3LYP 0 200 B3LYP P J Stephens F J Devlin C F Chabalowski and M J Frisch J Phys Chem 98 11623 1994 B3PW91 0 200 B3PW91 A D Becke J Chem Phys 98 5648 1993 mPWIPW91 0 250
30. fication of the Coordinates keyword is required For users who have a GAUSSIANO3 executable the geometry can be specified either with the Coordinates keyword or in the molecular specifications section of the input file In the latter case the coordinates can be specified in the usual GAUSSIAN formats i e by using Cartesian coordinates a Z matrix a combination of Cartesian coordinates and Z matrix coordinates etc The SMXGAUSS summary file is useful for restarting geometry optimizations using accurate Hessians to facilitate geometry optimizations and for characterizing optimized geometries as minima or transition states For examples of these types of calculations see the sections entitled Restarting Geometry Optimizations Using a Hessian Matrix for Geometry Optimizations and Identifying Minima and Transition States with a Hessian Calculation below 22 Advanced Keywords Every attempt has been made to assign reasonable default values to all numerical parameters Therefore the hope is that this section is not needed Nevertheless below are available keywords in SMXGAUSS that can be used to change some of the options used to override some of the normal defaults that are used in the SCF portion of SMx x 5 42 5 43 and 6 calculations SCF Changes some of the default options used to converge the SCF This keyword has the following options MaxCylces n where n is an integer number specifying the maximum number of SCF cycles a
31. gas phase Mayer bond order matrix instead of the liquid phase elements In SMXGAUSS Scheme II is automatically used for SM5 42 HF cc pVDZ and all methods that use basis sets containing diffuse functions In general both schemes yield very similar results However Scheme I does not always converge the SCF for methods using larger basis sets such as cc pVDZ or basis sets with diffuse functions but Scheme II almost always does Note that geometry optimizations or Hessian calculations cannot be carried out using the MIDI 5D also called MIDI or MIDIX or cc pVDZ basis sets because analytical free energy gradients are not available for basis sets using spherical harmonic d and f functions or functions of higher angular momentum than f 46 Density Functional Methods Recommended for use with CM4 and SM6 in SMXGAUSS Pure DFT functionals recommended for use with CM4 and SM6 in SMXGAUSS Method SMXGAUSS Keyword Reference s BLYP BLYP A D Becke Phys Rev A 38 3098 1988 C Lee W Yang and R G Parr Phys Rev B 37 785 1988 B Miehlich A Savin H Stoll and H Preuss Chem Phys Lett 157 200 1989 BPW91 BPW91 A D Becke Phys Rev A 38 3098 1988 K Burke J P Perdew and Y Wang in Electronic Density Functional Theory Recent Progress and New Directions Ed J F Dobson G Vignale and M P Das Plenum 1998 J P Perdew in Electronic Structure of Solids 91 Ed P Zi
32. h time a new session is started it is recommended that step 5 be added to the user s cshrc file or any initialization file read in during the login process Keep in mind that step 5 must always be executed when GAUSSIANO3 is unloaded in order for SMXGAUSS to run in mode 2 25 Setting up the Location of the smxGAuss Scratch Directory SMXGAUSS creates and uses several scratch files during a given calculation which are deleted after the calculation has finished Because the length of the path to the scratch directory cannot exceed 80 characters it is highly recommended that the user set the location of the scratch directory before running SMXGAUSS By default SMXGAUSS creates a directory named input where input is the name of the input file for the calculation and is arandom number in the same directory in which the calculation is run If the path containing this default directory name is more than 80 characters in length the SMXGAUSS calculation will not run properly The location of input can be changed from this default by defining the environment variable SCRPATH Example Set the scratch directory to be located in scratch smxgauss Use the command setenv SCRPATH scratch smxgauss Be sure that the directory to which SCRPATH is set exists Running SMXGAUSS To run an SMXGAUSS calculation use the command Executable_Path smxgX pl input output where Executable_Path is the location of the SMXGAUSS program and X i
33. ide n heptane n hexadecane n hexane n methylaniline n octane n pentane nitrobenzene nitroethane nitromethane n nonane o chlorotoluene o cresol o dichlorobenzene o nitrotoluene o xylene p xylene pentadecane pentanal pentanoic acid pentyl ethanoate pentylamine perfluorobenzene phenyl ether propanal propanoic acid 50 propanone propanonitrile propyl ethanoate propylamine pyridine pyrrolidine sec butanol tbutylbenzene tetrachloroethene tetrahydrofuran tetrahyrothiophenedioxide tetralin thiophene thiophenol toluene trans decalin tribromomethane tributylphosphate trichloroethene trichloromethane triethylamine undecane Z 1 2 dichloroethene 51 52 Troubleshooting Below is a listing of some error messages generated by SMXGAUSS and a brief explanation of why they are printed by the program Error message system mopac failed 1 at usr local g03 g03 c01 g03 bsd Gau_External line 53 lt INF gt line 4 Explanation SMXGAUSS was not installed properly mode 2 and must be reinstalled The absolute path of the location of the smxgauss distribution is not listed before the absolute path of the location of GAUSSIANO3 Error message SM5 42 SM5 43 or SM6 was not found in input You must specify one of these options Explanation The keyword SM5 42 SM5 43 or SM6 must be specified in the SMXGAUSS input file Error message Electronic structure method not found in input You must specify HF BPW91 B3L
34. int calculation on the geometry provided in the input file a GAUSSIAN output file or an SMXGAUSS summary file a liquid phase geometry optimization to a minimum or to a transition state or a liquid phase Hessian calculation For single point calculations no further input other than the specification of the electronic structure method basis set solvent and when applicable the Coordinates keyword described below is required in the route section To carry out geometry optimizations in the liquid phase the Opt keyword is used and to carry out frequency or Hessian calculations the Freq keyword is used The usage of these two keywords is as follows Opt Freq Requests a geometry optimization When this keyword is specified a gas phase geometry optimization is first performed using the input geometry as an initial guess Once the gas phase geometry optimization is complete a liquid phase geometry optimization is then carried out using the gas phase optimized geometry as an initial guess This keyword has the following options but note that using this keyword alone will request a geometry optimization to a minimum with reasonable defaults TS Requests a liquid phase geometry optimization to a transition state MaxCycles n where n is an integer number that specifies the maximum number of geometry optimization steps allowed default is 100 Converge c where c specifies the convergence threshold on the maximum gradient compon
35. lated to be 1 236 kcal mol 38 test4 inp Input SM6 opt CalcFCsol Solvent water B3PW91 MIDIX6D Coordinates h2s xyz SM6 B3PW91 MIDIX6D optimization of hydrogen sulfide in water liquid phase force constants calculated for the optimized gas phase geometry to facilitate geometry optimization in the liquid phase Summary of Output HH Summary of SMxGauss Calculation HHEEEEEE THEE HEHEHE HHH Gas phase energy at B3PW91 MIDIX6D 397 475677 a u G S liq free energy of system at B3PW91 MIDIX6D 397 477643 a u Standard state free energy of solvation 1 234 kcal mol Free energy of cavity dispersion solvent structure 0 361 kcal mol Free energy of polarization 0 995 kcal mo Electronic Nuclear distortion energy 0 122 kcal mol Description of Output The standard state free energy of solvation is calculated to be 1 234 kcal mol test5 inp Input SM6 Opt TS MPW1K 6 31 G d Solvent water Coordinates h2o oh xyz SM6 MPW1K 6 31 G d optimization of the H20 OH transition state CS in water Summary of Output Gas phase optimized coordinates H 0 941703 1 413748 0 000000 O 0 000420 1 242876 0 000000 H 0 047155 0 159683 0 000000 O 0 000420 1 243564 0 000000 H 0 901275 1 567924 0 000000 Liquid phase optimized coordinates H 0 930986 1 544716 0 000000 O 0 002049 1 295690 0 000000 H 0 017537 0 288646 0 000000 O 0 002049 1 311635 0 000
36. llowed default is 300 Acurcy x where x is the convergence criterion for the SCF default is 0 0000001 This criterion applies to the density matrix Conventional Requests a conventional SCF calculation i e store two electron integrals on disk this is the default Semi Direct Specifies that some of the two electron integrals are stored on disk and that some of them are calculated as needed depending on the available memory This option is currently only available for HF Direct Specifies that all two electron integrals are calculated as needed and none are stored on disk This option is currently only available for HF 23 Installing SMXGAUSS A working version of PERL is required to install and run SMxGAUss To run in mode 2 a GAUSSIANO3 executable is required SMXGAUSS is distributed as a tarred and gzipped file named smxgaussv3 4 1 tar gz To install SMXGAUSS 1 Unzip the file smxgaussv3 4 1 tar gz which creates a tar file named smxgaussv3 4 tar gunzip smxgaussv3 4 1 tar gz 2 Untar the file smxgaussv3 4 tar which creates a directory named SMxGauss v3 4 1 tar xvf smxgaussv3 4 1 tar 3 Change into the directory SMxGauss v3 4 1 cd SMxGauss v3 4 1 To finish installing SMXGAUSS for mode 1 the External option in GAUSSIANO3 will NOT be used no GAUSSIAN executables are needed 4 Execute the c shell script named install csh bin csh install x csh where x is one of the install files distribut
37. mizations and Hessian calculations electronic structure method basis set BLYP MIDI 6D BLYP 6 31G d BLYP 6 31 G d BLYP 6 31 G d p B3LYP MIDI 6D B3LYP 6 31G d B3LYP 6 31 G d B3LYP 6 31 G d p BPW91 MIDI 6D BPW91 6 31G d BPW91 6 31 G d BPW91 6 31 G d p B3PW91 MIDI 6D B3PW91 6 31G d B3PW91 6 31 G d B3PW91 6 31 G d p mPWPW91 MIDI 6D mPWPW91 6 31G d mPWPW91 6 31 G d mPWPW91 6 31 G d p mPW1PW91 MIDI 6D mPW1PW91 6 31G d mPWI1PW91 6 31 G d mPW1PW91 6 31 G d p MPWIK MIDI 6D MPWIK 6 31G d MPWIK 6 31 G d MPWIK 6 31 G d p MPWIKK MIDI 6D MPWIKK 6 31G d MPWIKK 6 31 G d MPWIKK 6 31 G d p MPWX MIDI 6D MPWX 6 31G d MPWX 6 31 G d MPWX 6 31 G d p 18 Specification of the Solvent The SM5x x 42 and 43 solvation models are universal they are defined for water and any organic solvent that has known values for a set of seven solvent descriptors currently SM6 calculations can only be performed in aqueous solution a universal model for SM6 will be available in future implementations of SMXGAUSS The seven solvent descriptors are the bulk dielectric constant the refractive index at the wavelength of the Na D line n Abraham s hydrogen bond acidity parameter which Abraham denotes as X av Abraham s hydrogen bond basicity parameter which Abraham denotes as X the reduced surface tension y which equals y y where Y m is the macroscopic surface tension at a liquid air inte
38. n the gas phase and the corresponding optimized Cartesian coordinates from both the gas and liquid phases are printed to the SMXGAUSS output and summary files You can determine whether or not the geometry has successfully been optimized in the gas phase by searching for the string Gas phase optimized coordinates and in the liquid phase by searching for the string Liquid phase optimized coordinates in the SMXGAUSS output file When the geometry in the liquid phase does not optimize within the number of steps allotted to the calculation which is specified by the MaxCycles option to the Opt keyword the calculation terminates and the latest set of liquid phase Cartesian coordinates is printed to the SMXGAUSS summary file You can determine whether or not the geometry optimization exceeded the number of steps allotted to the calculation by searching for the string Maximum number of geometry optimization steps has been exceeded in the SMXGAUSS output file To restart failed geometry optimizations use the Coordinates input pun where input pun is the name of the SMXGAUSS summary file created from the previous SMXGAUSS calculation see Running SMXGAUSS above and run the calculation again 27 Example Optimize the geometry of hydrogen sulfide in water solvent using SM5 42 and HF MIDI 6D Create an SMXGAUSS input file called h2s inp containing the following keywords HF MIDI 6D Opt MaxCycles 2 sm5 42 solvent water coordinat
39. nt rey ork rect T E eerste the ene errr eee Teer ents rete 6 Basis Set References nes ee 7 Free Energy Vapor Pressure Solubility Kinetics and Electrostatics 9 Reg ired E ALALIONS a esios naear aaa aaor a a A ea a E aa eaa aE oaa E ea asin 10 SMXGAUSS Input and Keywords uuuesenasenais es uns 11 MS ASTOR VW OLCS ats Facet onenari o E E A a E aetna naan N 12 Specification of the Solvation Model ccssccccccceeeeeeeennneeeeeeeeeeeeeennneeeeeeeeeeeeeees 12 Specification of the Electronic Structure Method and Basis Set 12 Allowed Combinations of Solvation Model Electronic Structure Method and Basis Oe TER ee ET Gea MEME Te inte PPM IE re erence OME A UA SUR A Perce 13 Specification of the Solvent Temperature eisen 19 Specification of the Charge Multiplicity and Geometry sssssseessseesssssseerreeesse 21 Advanc d Keywords eostin resset ee ana E A AA E EAE aea 22 Installing SMXGAUSS nnn EE E ARE E E E NE E TEE E RE 23 Setting up the Location of the SMXGAUSS Scratch Directory eennnseessennneessennnner nenne 23 FRUIT SMXGAUSS ee A N hela 25 Restarting Geometry OptimiiZanonsis cat scat aden acne eee RA Oe w ene 26 Using a Hessian Matrix for Geometry Optimizations eeeeeeeeeeeeeeeeeeeeeeeeeenteeeeeeeeees 28 Performing Geometry Optimizations on Transition States ce eeeeeeessneeeeeeeneeeeeees 30 Identifying Minima and Transition States with a Hessian Calculation
40. ohnson B G Robb M A Cheeseman J R Keith T Peterson G A Montgomery J A Raghavachari K Al Laham M A Zakszewski V G Ortiz J V Foresman J B Peng C Y Ayala P Y Chen W Wong M W Andres J L Replogle E S Gomperts R Martin R L Fox D J Binkley J S DeFrees D J Baker J Stewart J J P Head Gordon M Gonzalez C Pople J A Gaussian Inc Pittsburgh 1995 6 31G d for I MIDI 6D is used e sp diffuse for 6 31G for I MIDI 6D augmented with a set of sp functions with an orbital exponent of 0 03 is used e cc pVDZ for H Li C N O and F Dunning T H Jr J Chem Phys 1989 90 1007 e cc pVDZ for Si P S and Cl Woon D E Dunning T H Jr J Chem Phys 1993 98 1358 e cc pVDZ for Br and I MIDI is used e DZVP Godbout N Salahub D R Andzelm J Wimmer E Can J Chem 1992 70 560 Free Energy Vapor Pressure Solubility Kinetics and Electrostatics The basic output of an SMXGAUSS calculation is a free energy of solvation Free energies of solvation may be used to calculate Henry s law constants partition coefficients chemical potentials solubilities and other thermodynamic properties A general reference is Cramer C J Truhlar D G in Free Energy Calculations in Rational Drug Design Reddy M R and Erion M D Eds Kluwer Academic Plenum New York 2001 pp 63 95 A general reference for the use of solvation fre
41. on of Output 433989 447269 8 334 2 750 5 85 0231 1 mo1 1 mol 1 mo 1 mo test7d inp Input SM6 B3LYP 6 31 G d p SolK 373 Solvent water Coordinates h20 xyz SM6T B3LYP 6 31 G d p calculation of the aqueous solvation free energy of water at 373 K experimental value 2 53 kcal mol Summary of Output Harte Summary of SMxGauss calculation at 373 K tHHHEHEEPEEPEEH Gas phase energy at B3LYP 6 31 G D P T 6a G S liq free energy of system at B3LYP 6 31 G D P 76 Standard state free energy of solvation Free energy of cavity dispersion solvent structure Free energy of polarization Electronic Nuclear distortion energy Description of Output 433989 446721 7 989 2 417 5 803 0 231 1 mo1 1 mo1 1 mo 1 mo SCRF Schemes The keyword ISCRF determines which SCRF scheme is used for a given calculation The value of ISCRF is automatically set by SMXGAUSS based on which basis set is used Currently ISCRF is set to either 1 or 2 When ISCRF is set to 1 SCRF scheme I is used This scheme uses the current solution phase elements of the Mayer bond order matrix at every step of the SCF iterations In SMXGAUSS Scheme I is automatically used for all methods that do not use diffuse basis functions except for SM5 42 HF cc pVDZ The other SCRE scheme used in SMXGAUSS is called Scheme II ISCRF 2 This scheme uses elements of the
42. revision that is used to run SMXGAUSS in mode 2 SMXGAUSS does not have this limitation see test5 smxgauss User s interested in learning more about how SMxGAUSS avoids this limitation should see the file mkgauss lib that is contained in the distribution of SMXGAUSS 31 Identifying Minima and Transition States with a Hessian Calculation Hessian calculations can also be used to characterize stationary points as minima or transition states Example Optimize the geometry of hydrogen sulfide in water solvent using SM5 42 and HF MIDI 6D and then characterize it as a minimum via vibrational frequency analysis The name of the first SMXGAUSS file is h2s_opt inp the contents of which are HF MIDI 6D Opt sm5 42 solvent water coordinates h2s xyz 1 Use the command Executable_Path smxgX pl h2s_opt inp h2s_opt out where X is either 1 or 2 Search the output file for the string Liquid phase optimized coordinates to verify that the geometry has been optimized in the liquid phase 2 Create a new input file named freq inp containing HF MIDI 6D Freq SM5 42 Solvent Water Coordinates h2s_opt pun 32 3 Use the command Executable_Path smxgX pl freq inp freq out where X is either 1 or 2 Locate the vibrational frequencies and their corresponding normal modes by searching for the string Vibrational frequencies CM 1 and normal modes in freq out For linear molecules the five frequencies that are smallest in m
43. rface at 298 K and y is I cal mol A 2 the fraction of nonhydrogenic solvent atoms that are aromatic carbon atoms carbon aromaticity and the fraction of nonhydrogenic solvent atoms that are F Cl or Br electronegative halogenicity w When the solvent is water it is specified with the keyword Solvent Water Organic solvents can be specified with one of two keywords Solvent Solvent_Name where Solvent_Name is the name of the solvent given in a file named solvent txt This file is provided in the SMXGAUSS distribution and contains the seven required solvent descriptors for 175 organic solvents The user can add additional solvents to this file The solvent txt file is tab delimited and the descriptors for a particular solvent in this file appear in this order n a B y d and w A list of available solvents is given in the section entitled Available Solvents in the solvent txt File below If the solvent of interest is not provided in the solvent txt file then the Solvent_Descriptors keyword must be used The seven descriptors are specified as options to the Solvent_Descriptors keyword The options are Dielectric d where d is the solvent s bulk dielectric constant also called the relative permittivity N n where nis the solvent s index of refraction Alpha a where a is Abraham s acidity parameter Beta b where b is Abraham s basicity parameter Gamma g where g is the macroscopic surface tension coefficient
44. s calculation first optimizes the structure in the gas phase at the HF MIDI 6D level carries out a liquid phase Hessian calculation on the gas phase optimized geometry and then optimizes the geometry in the liquid phase beginning from the gas phase optimized geometry and the initial Hessian calculated at this geometry The CalcFCSol option can also be used when restarting liquid phase geometry optimizations In this case the Hessian calculation is carried out on the latest set of liquid phase coordinates found in the file specified by the Coordinates keyword Example Optimize the geometry of hydrogen sulfide in water solvent using SM5 42 and HF MIDI 6D The name of the first SMXGAUSS input file is h2s inp the contents of which are HF MIDI 6D Opt MaxCycles 2 sm5 42 solvent water coordinates h2s xyz 1 Use the command Executable_Path smxgX pl h2s inp h2s out where X is either 1 or 2 The geometry will optimize in the gas phase within two steps but not in the liquid phase Search the output file for the string Exceeded number of allowed steps in geometry optimization to verify that the geometry is not optimized in the liquid phase yet 29 2 Create a new input file named h2s_restart inp containing HF MIDI 6D Opt CalcFCSol SMS 42 Solvent Water Coordinates h2s pun water 1 Use the command Executable_Path smxgX pl h2s_restart inp h2s_restart out where X is either 1 or 2 The latest set of Cartesian coordina
45. s either 1 if SMXGAUSS was installed under mode 1 or 2 if SMXGAUSS was installed under mode 2 input is the name of the SMXGAUSS input file and output is the name of the SMXGAUSS output file The output file contains intermediate and final results of the SCRF calculation and of the geometry optimization steps and a summary of the solvation calculation including the predicted standard state free energy of solvation see the sample output below In addition to the output file SMXGAUSS also creates a summary file named input pun This file contains useful information for restarting liquid phase single point calculations liquid phase geometry optimizations see the section entitled Restarting Geometry Optimizations and Using a Hessian Matrix for Geometry Optimizations below and for characterizing liquid phase optimized structures via vibrational frequency analysis see the section entitled Identifying Minima and Transition States with Hessian a Calculation below Because input pun is a text file it is transferable to other machines 26 Restarting Geometry Optimizations In general a liquid phase geometry optimization with SMXGAUSS is an automated two step procedure In the first step the geometry of the solute is optimized in the gas phase with the electronic structure method and basis set specified in the SMXGAUSS input file In the second step this gas phase geometry is optimized in the liquid phase at the same level of theory used i
46. sic keywords Note that the defaults set by SMXGAUSS have been tested on a large test set of calculations in water and organic solvents about 2200 calculations so these defaults should work in most cases Although keywords are given in the recommended combination of capital letters and lower case letters SMXGAUSS is actually case insensitive for all input 12 Basic Keywords Below are descriptions of the basic keywords available in SMXGAUSS Specification of the Solvation Model There are three solvation models available in SMXGAUSS SM5 42 Requests a calculation using the SM5 42 solvation model SM5 43 Requests a calculation using the SM5 43 solvation model SM6 Requests a calculation using the SM6 solvation model Specification of the Electronic Structure Method and Basis Set The following electronic structure methods are available in SMXGAUSS where their names also indicate their keywords HF BLYP B3LYP BPW91 B3PW91 mPWPW91 mPWI1PW91 MPWIK MPWX where X is the fraction of Hartee Fock exchange 1000 in the modified version of Perdew and Wang s exchange functional The value X must only be three significant figures Example to specify a fraction of Hartree Fock exchange of 0 428 the correct keyword would be MPW428 The following basis sets are available in SMXGAUSS where their names also indicate their keywords MIDI can also be specified as MIDIX MIDIXSD or MIDI SD MIDI 6D can also be specified as
47. ss Calculation H H tHHH THEE HEHEHE HHH Gas phase energy at MPW1PW91 6 31G D 399 384306 a u G S liq free energy of system at MPW1PW91 6 31G D 399 386383 a u Standard state free energy of solvation 1 303 kcal mol Free energy of cavity dispersion solvent structure 0 334 kcal mol Free energy of polarization 1 084 kcal mol Electronic Nuclear distortion energy 0 115 kcal mol Description of Output Both the gas and liquid phase optimized coordinates are printed to output The standard state free energy of solvation for the liquid phase optimized geometry is calculated to be 1 303 kcal mol test2b inp Input SM6 Freq Solvent water MPW1PW91 6 31G d Coordinates test2a pun Numerical frequency evaluation liquid phase for the liquid phase optimized geometry obtained from test2a inp Summary of Output Sasse Vibrational frequencies CM 1 and normal modes 2769 48 2748 97 1246 76 10 24 A A A A 1 S X 00000 04097 00000 00000 Y 02970 00000 00000 02108 Z 00029 00000 00000 57722 2 H X 00000 70651 70711 00000 47233 00000 00000 01787 Zr 92609 00000 00000 57395 3 H X 00000 70651 70711 00000 Y 47234 00000 00000 01864 Z 52549 00000 00000 57990 NORM 1 00000 00000 00000 00000 5 6 7 8 8 30 14 49 28 14 23 94 07 A A A A 1 S X 00000 60943 00000 00000 Y 57739 00000 00000 00000 Z 02092 00000 0319
48. sted before the absolute path of the location of GAUSSIANO3 steps 4 7 must be repeated 8 Use the command which g03 to determine the location of the GAUSSIANO3 executable on your system Copy or write down this absolute path as it will be used in step 9 9 Execute the c shell script named install x csh bin csh install x csh where x is one of the install files distributed with SMxGAUss Currently install files exist for a number of combinations of machine operating system and compiler for example the install file install sun g77 csh is intended for installation on a Sun machine with the gnu g77 compiler If you are unsure which install file to use refer to the section entitled Platforms near the end of this manual for a list of platforms that SMXGAUSS has been tested on Once the proper install script has chosen and executed with the above command this script will ask you if you have GAUSSIANO3 Answer yes and press enter The script will then ask you for the absolute path to the g03 executable Give the absolute path from step 8 press enter Finally the script will ask you whether you have version DO1 or later of Gaussian 03 This information should be available in the Gaussian users manual or from your system administrator Then wait for the source code to compile This may take some time depending on the system Important note for running in mode 2 Because running SMXGAUSS in model 2 requires executing step 5 eac
49. tes in the liquid phase is located on the file h2s pun and these coordinates are the initial coordinates used in this calculation Because the CalcFCSol option is specified a Hessian calculation in the liquid phase at these coordinates is carried out first Then a geometry optimization in the liquid phase is carried out beginning with these coordinates and using the initial liquid phase Hessian The CalcFCGas keyword is used in a similar fashion to CalcFCSol but it is used to aid geometry optimizations in the gas phase CalcFCGas and CalcFCSol can be used in the same calculation 30 Performing Geometry Optimizations on Transition States As mentioned above a liquid phase geometry optimization with SMXGAUSS is an automated two step procedure In the first step the geometry of the solute is optimized in the gas phase with the electronic structure method and basis set specified in the SMXGAUSS input file In the second step this gas phase geometry is optimized in the liquid phase at the same level of theory used in the gas phase and the corresponding optimized Cartesian coordinates from both the gas and liquid phases are printed to the SMXGAUSS output and summary files For transition state geometry optimizations it is often recommended that a Hessian calculation be performed on the initial gas phase geometry using CalcFCGas as well as on the optimized gas phase geometry using CalcFCSol For an example of a calculation in which both the
50. to obtain the charge multiplicity and geometry Thus for example one can optionally begin by optimizing a geometry in the gas phase using GAUSSIAN then use the output file from this calculation and an SMXGAUSS input file to carry out a liquid phase free energy calculation either at the gas phase geometry or with re optimization in the liquid phase Because SMXGAUSS input files have the same format as GAUSSIAN input files the program is especially user friendly to GAUSSIAN users and it provides a way for them to add SMx liquid phase free energy calculations to their research SMXGAUSS running in mode can also read an SMXGAUSS summary file which is created from a previous SMXGAUSS calculation This file contains the charge multiplicity and the Cartesian coordinates and can be used to restart calculations this is explained in more detail below In mode 2 one requires a GAUSSIANO3 executable GAUSSIAN source code is not required In mode 2 the intrinsic Hartree Fock HF density functional theory DFT hybrid DFT generalized Born and analytic surface area capabilities of SMXGAUSS are used in conjunction with the External option of GAUSSIANO3 This allows GAUSSIANO3 to be the driver and to carry out geometry optimizations with the powerful GAUSSIAN optimizers but using the SMXGAUSS liquid phase free energy routines which are more accurate than those in GAUSSIAN cf Thompson et al J Phys Chem A 2004 108 6532 and Kelly et al J
51. y optimization with the External option the charge multiplicity and geometry can be specified in the molecular specifications section in the input file this section follows the title section In addition the charge multiplicity and geometry can be taken from a GAUSSIAN output file or from an SMXGAUSS summary file created from a previous SMXGAUSS calculation The route section is comprised of keywords and options to keywords These keywords are used to specify the electronic structure method basis set solvation model solvent type of calculation to carry out i e a single point calculation in the liquid phase a geometry optimization in the liquid phase to a minimum or transition state or a Hessian calculation in the liquid phase and several other optional keywords and options This input can be on multiple lines but the specification of an individual keyword must be all on one line See the sample runs below for examples of multiple line input Options to keywords are specified in a similar fashion as they are in GAUSSIAN e g keyword option keyword option or keyword option1 option2 There are two types of keywords in SMXGAUSS 1 basic keywords which specify the electronic structure method basis set solvation model solvent and several other simple options and ii advanced keywords which are used to override several defaults automatically set by SMXGAUSS Most users will only need to be familiar with the ba
52. ylpyridine 2 6 dimethylpyridine 2 bromopropane 2 chlorobutane 2 heptanone 2 hexanone 2 methyl 2propanol 2 methylpentane 2 methylpyridine 2 nitropropane 2 octanone 2 pentanone 2 propanol 2 propen 1 ol 3 methylpyridine 3 pentanone 4 heptanone 4 methyl 2 pentanone 4 methylpyridine 5 nonanone alpha chlorotoluene acetonitrile aniline anisole benzaldehyde benzene benzonitrile benzyl alcohol bromobenzene bromoethane 48 bromooctane butanal butanoic acid butanone butanonitrile butyl ethanoate butylamine butylbenzene carbon disulfide carbon tetrachloride chlorobenzene cis 1 2 dimethylcyclohexane cis decalin cyclohexane cyclohexanone cyclopentane cyclopentanol cyclopentanone decane dibromomethane dibutyl ether dichloromethane diethyl ether diethyl sulfide diethylamine diiodomethane dimethyl disulfide dimethylacetamide dimethylformamide dimethylpyridine dimethylsulfoxide dipropylamine dodecane E 1 2 dichloroethene E 2 pentene ethanethiol ethanoic acid ethanol ethyl ethanoate ethyl methanoate ethyl phenyl ether ethylbenzene ethylene glycol fluorobenzene formamide formic acid 49 hexadecyl iodide hexanoic acid iodobenzene iodoethane iodomethane isobutanol isopropyl ether isopropylbenzene isopropyltoluene m cresol m xylene mesitylene methanol methyl benzoate methyl ethanoate methyl methanoate methyl phenyl ketone methyl propanoate methylbutanoate methylcyclohexane methylformam
53. zio Audzelm E Sakai Y Tatewaki H Gaussian basis sets for molecular calculations Huzinaga S Ed Elsevier Amsterdam 1984 Easton R E Giesen D J Welch A Cramer C J Truhlar D G Theor Chim Acta 1996 93 281 e MIDI for Br and I Dobbs K D Hehre W J J Comput Chem 1986 7 359 Li J Cramer C J Truhlar D G Theor Chem Acc 1998 99 192 e 6 31G for H Ditchfield R Hehre W J Pople J A J Chem Phys 1971 54 724 6 31G for Li Dill J D Pople J A J Chem Phys 1975 62 2921 6 31G for C N O and F Hehre W J Ditchfield R Pople J A J Chem Phys 1972 56 2257 6 31G for Si P S and Cl Francl M M Petro W J Hehre W J Binkley J S Gordon M S DeFrees D J Pople J A J Chem Phys 1982 77 3654 d polarization for 6 31G for Li Dill J D Pople J A J Chem Phys 1975 62 2921 d polarization for 6 31G for C N O and F Hairharan P C Pople J A Theor Chim Acta 1973 28 213 d polarization for 6 31G for Si P S and Cl Francl M M Petro W J Hehre W J Binkley J S Gordon M S DeFrees D J Pople J A J Chem Phys 1982 77 3654 sp diffuse for 6 31G for Li C N O F Si P S and Cl Clark T Chandrasekhar J Spitznagel G W Schleyer P v R J Comput Chem 1983 4 294 6 31G d and 6 31 G d for Br GAUSSIAN94 Frisch M J Trucks G W Schlegel H B Gill P M W J

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