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WSolids1 User Manual - Institut für Anorganische Chemie

1. 92 49 FPolarAngles unseren a a a 92 400 Euler Al caca a ee a 93 4101 Rotation Malie acc dar a a rw 94 4102 Determining Euler Angles eoc i a e a a ES 95 4 11 Electric Field Gradient Tensor o o o 96 4 12 Central Transition CT and Satellite Transitions ST 96 4 13 Variable Angle Spinning Angle oo oooooocooo ooo oo 97 4 14 Spinning Frequency o ooo o 97 4 15 Speedy Calculation 02 0600 cee HH nr ee eke anne 97 436 INI File Settings lt concer ee 97 4 16 1 Portable or Non Portable Format portable 2 22222 ooo 97 4 16 2 Default Output File Format OutFile c 00 2 5 98 4 16 3 Number of Triangular Intersections POWDER NT 2 2 2220 98 4 164 Number of Decimal Digits digits tore s aos sani Di aan anne 99 July 30 2015 Chapter 4 Spin System Parameters 4 1 Relative Intensity The relative intensity of each site determines the relative area this site contributes to the total line shape Allowed values are 0 100 but there is no check whether the relative intensities of all sites sum up to 100 Considered as a mere scaling factor To exclude a site momentarily from a calculation without deleting it set the relative intensity of this site to Zero 4 2 Tie to previous site This feature allows to tie the parameters of a site to the parameters of the previous site using
2. Also when saving spectra p 22 in TopSpin format it is advisable to scale up the calculated spec trum The dialog displays the minimum and maximum intensities of the available spectra and sug gests a scaling factor If you agree with the suggested factor press the Accept button to update the value in the field Multiply spectrum by After hitting the OK button the selected spectrum will be multiplied by this value The Cancel button quits this dialog without performing any changes Scale Spectrum C Experimental Calculated Multiply spectrum by 0 461 Experimental Maximum intensity 300772 500 Minimum intensity 5427 320 Calculated Maximum intensity 652165 000 Minimum intensity 3118 397 Factor 0 461 MES 2 4 6 Add Constant This option available from the Tools Add constant menu enables one to add a constant value to an existing spectrum basically a constant base line correction 2 4 7 Reverse Spectrum This option available from the Tools Reverse spectrum menu enables one to reverse the frequency direction of the spectrum Physically for a spectrum consisting of n points this exchanges the intensity of the first and n th point the second and n 1 th point and so on Some versions of WinNMR do not provide such a functionality to swap the high and low frequency halves of the spectrum although some Bruker spectrometers produce d spectra for which this is was necessary 2 4 8 Absol
3. Inquiries about the use of this program or reports of problems can be directed via e mail to Klaus Eichele uni tuebingen de Also you may address correspondence via snail mail to Dr Klaus Eichele Institut fuer Anorganische Chemie Universitaet Tuebingen Auf der Morgenstelle 18 D 72076 Tuebingen Germany July 30 2015 Chapter 1 Getting Started 1 2 Overview The overview provided here is aimed at giving an outline of the steps required to achieve a particular task Following a question in the left column links to the relevant topics are provided After catching up on any specific topic use the Back feature of your reader to return to this screen How do I start Create a new spectrum window p 17 Read an experimental spectrum p 18 Create a new spin system p 35 Define convolution parameters p 32 Calculate p 38 Repeat as required p 38 using the cycle fea ture Save the results p 22 SG 006O00OO How do I work efficiently Use keyboard accelerators p 14 Use the cycle feature p 38 July 30 2015 Chapter 1 Getting Started 1 3 Revision History This page describes changes made to the WSolids1 program versus previous versions and provides a summary of new features 1 3 1 Version 1 21 3 30 07 2015 new feature added a dialog Settings p 40 to change some program settings either temporar ily or permanently new feature added the direct calculation of spinning sideban
4. 10 1063 1 440136 2 J Mason Solid State Nucl Magn Reson 1993 2 285 DOI 10 1016 0926 2040 93 90010 K 4 3 3 Haeberlen Convention b Principal Components zz Sisol 2 dxx disol gt Oy gt iso Oiso Isotropic Value iso 611 622 633 3 Reduced Anisotropy 0 bzz bigo Anisotropy Ar 02 xx dyy 2 Ao 35 2 Asymmetry Syy a xx 0 lt 7 lt 1 July 30 2015 Chapter 4 Spin System Parameters The Haeberlen Mehring 1 2 convention uses different combinations of the principal components to describe the line shape This convention requires that the principal components are ordered accord ing to their separation from the isotropic value The center of gravity of the line shape is described by the isotropic value which is the average value of the principal components The anisotropy and reduced anisotropy describe the largest separation from the center of gravity The term reduced anisotropy is not used in the literature but we introduce it here in order to be able to distinguish between and Ac The sign of the anisotropy indicates on which side of the isotropic value one can find the largest separation The asymmetry parameter indicates by how much the line shape deviates from that of an axially symmetric tensor In the case of an axially symmetric tensor b dyy xx will be zero and hence y 0 The Haeberlen Mehring convention is related to the Standard conventio
5. 17 New Document p 17 Closes and removes existing spectrum windows or spin systems Open p 18 Opens a submenu to retrieve an experimental p 18 or calculated p 22 spectrum or a WSolids1 document p 22 or spin system p 22 Save p 22 Opens a submenu to save a spectrum p 22 or a WSolids1 document p 23 or spin system p 23 Report p 24 Opens to help file explaining how to generate reports Exit p 27 Exits WSolids1 2 1 1 New Document The New document item of the File p 17 pop up menu closes all spectrum windows and removes all spin systems in order to create a new starting point 2 1 2 New Window The New window item of the File p 17 pop up menu creates a new spectrum window in the MDI client area of WSolids1 A spectrum window is required to display experimental and calculated spectra All actions are usu ally performed for the currently active spectrum window For example retrieving a spectrum file from hard disk automatically replaces the experimental spectrum of the currently active spectrum window Some actions automatically generate a new window if they require a spectrum window in order to succeed and no active window exists For example retrieving a spectrum file will automatically load the spectrum into a new window if no window has the input focus However if a spectrum window has the focus WSolids1 will load and display the spectrum in this window 17 July 30 2015 Chapt
6. 2015 Chapter 2 Menus 2 1 10 Report Quick guide to generate a report copy or write your WSolids1 XML document into the directory contain ing the style sheets e open this copy of your XML file in your web browser WSolids1 does not have a feature to create fancy resports Instead this menu option opens the help file at the current section Here I am explaining the steps required to generate a report from your WSolids1 XML document On first sight it may seem complicated but once everything is in place it is not too hard Depending on the version of WSolids1 that you are using it may have shipped with all the necessary style files otherwise you can download the required files from the WSolids1 home page http anorganik uni tuebingen de klaus soft The WSolids1i XML Document Extensible Markup Language XML http www w3 org TR 2006 REC xm111 20060816 is a text file format that can be used to represent data in a structured way It is human readable in contrast to binary files and in many cases human understandable However although the file itself is readable it doesn t make for good reading But there are tools available that help to present the data in a more convenient way For example your favorite web browser should be able to deal with a XML file The following steps explain the procedure The excerpt from a WSolids1 XML document shown below illustrates the concept of human readabil ity but you ma
7. 88 MAS freq p 97 Convention p 88 Delta 11 Delta 22 Delta 33 p 88 Delta iso Span Skew p 88 Delta iso Anisotropy Asym metry p 88 LB p 32 Background In addition to the chemical shift anisotropy CSA the spectrum of a spin in a powder sample under magic angle spinning will depend on the spinning frequency if the spinning frequency is lower than the width of the chemical shift powder pattern In this case the isotropic peak center peak is flanked by spinning sidebands spaced at integer multiples of the spinning frequency The intensities of the spinning sidebands are intimately related to the principal components of the chemical shift tensor For efficiency reasons WSolids1 uses look up tables of precomputed spinning sideband intensities Relative intensity of this site in percent Ties parameters to those of the previous site Spinning frequency in Hz Convention used for chemical shift tensor components Principal components of chemical shift tensor stan dard convention in ppm Principal components of chemical shift tensor Herzfeld Berger convention Principal components of chemical shift tensor Hae berlen convention Provides access to the convolution parameters for the current site To have individual convolution pa rameters for each site specify this in the Spectrum Default Parameters p 28 box July 30 2015 Chapter 3 Spin Systems according to the method of Herzfeld
8. Chapter 2 Menus 2 2 Simulation Menu The Simulation pop up menu consists of the following items WSolids1 File MEA Options Tools Wir M Default parameters New site N Edit sites E Calculate v Active window only Cycle through Enter Cycle options Item Purpose Default parameters p 28 Invokes a dialog box to retrieve parameters for the calculated spectrum New site p 35 Allocates and adds a new site to the calcula tional model Edit sites p 37 Manage sites modify parameters etc P 8 P Calculate p 38 Performs a calculation using the currently se lected simulation models and parameters Active window only p 38 Perform calculation for currently active spec trum window only or for all spectrum windows Cycle through p 38 Calls the next step in the Input Calculate Display cycle Cycle options p 38 Customize the cycle steps 2 2 1 Spectrum Default Parameters The Default parameters item of the Simulation p 28 popup menu invokes the Spectrum Default Parameters dialog box The default parameters characterize the appearance of the calculated spec trum they apply to all sites Spectrum Default Parameters upon closing dialog get parameters from experimental spectrum F 81 03300 MHz Hz ppm S Nucleus P 31 hd 25000 00000 Hz Sk 1024 Pts 25000 00000 Hz VW Use relative threshold value Derivative Mode l Site dependent broadening No C 1
9. document windows have a title bar a sizing border a system menu bitmap Minimize Maximize buttons scroll bars Because document windows always have Minimize and Maximize buttons they can be minimized and maximized When minimized they are represented as icons and displayed in the workspace of the frame window When maximized document windows are sized to fill the entire workspace of the frame window not the entire Windows desktop The title bar of a maximized document window disappears and its caption text is appended to the caption text in the frame window s title bar In addition the system menu bitmap of the document window becomes the first item in the menu bar of the frame window and the button to restore the document window to normal size is positioned at the far right of the frame window s menu bar 1 4 2 Menu Management The frame window s menu bar has a popup menu bar item called Window near the right end of the menu just left of the Help item The Window popup menu contains items related to the arrange ment of document windows within the workspace These options include tiling and cascading of windows and arranging icons at the bottom of the workspace 12 July 30 2015 Chapter 1 Getting Started 1 4 3 Keyboard Interface The Windows MDI has its own keyboard interface that augments the keyboard interface for non MDI applications The MDI key sequences allow users to easily navigate between and mani
10. p 65 Fixed a memory problem bug in model MAS Spin 1 2 Spin S Stick p 70 and modified processing Changed the handling of spectrum files WSolids1 now uses the NMRFILES dynamic link library developed for WSolids2 which allows for a greater variety of file formats Fixed another error in model MAS Spin 1 2 Spin S Diag p 67 cup 1 for sth 0 Modified processing in model MAS Spin 1 2 Spin S Shape p 74 Added Tools Scale spectrum p 44 to allow scaling of spectrum Modified enabling disabling of controls in convolution parameter box changed layout of dia log box 1 3 18 Version 1 16 Fixed cycle feature Actually not really fixed one problem created a new one Fixed MDI accelerators Processing modified for the following dialog boxes default parameters convolution param eters model selection static chemical shift anisotropy static dipolar chemical shift A2 AX static dipolar chemical shift AB static quadrupolar nucleus MAS chemical shift anisotropy HB MAS spin 1 2 spin S Diag About Open file Save file Edit sites 10 July 30 2015 Chapter 1 Getting Started Fixed errors in model Static Dipolar chemical shift A2 AX p 52 and VAS Dipolar chemical shift A2 AX p 76 for A2 system J is neglected now Fixed two errors in model MAS Spin 1 2 Spin S Diag p 67 sign error in sbsf term cet 1 for cth 1 Fixed update of BF1 in AQS file Fixed
11. see be low On first call the matrix is initialized according to the expressions given below LB p 32 Provides access to the convolution parameters for the current site To have individual convolution pa rameters for each site specify this in the Spectrum Default Parameters p 28 box Background Implementation Details The implementation of this spin system is based on the approach summarized by Abragam 1 but instead of working with one complex complex matrix A in Abragam 1 the different parameters are separated into different matrices following Whitesides 2 I w Re w A 1 3 4 1 A Q R K 3 5 Tig where W arow vector with components proportional to the a priori probabilities of the 2S 1 spin states of the nucleus in most papers all are equal to 1 W 1 1 however here we set the elements to 25 1 following Kempgens 3 1 a 2S 1 unit column vector Q a 25 1 x 25 1 diagonal complex matrix with elements corresponding to shifts and couplings ordered in terms of increasing ms S S 1 3m S 25 _ 1 d Om mr Onm i wo Ww m27J 27 K a diagonal matrix whose elements determine the line widths of spin I in absence of contri butions from relaxation of spin S Kam 1 R Abragam 1 and other authors neglect this contribution the only author that uses this separate matrix is Whitesides 2 In WSolids1 this matrix is currently not used be
12. the performance of the interpolation routine for the powder averaging or the convolution routine depends on the digital resolution Valid values for the spectrum size are positive integers greater than or equal to 16 Additionally the letter K can be used to indicate Kilo points 1K 1024 points ppm Hz The two mutually exclusive radio buttons ppm and Hz in the Spectrum Default Parameter p 28 box allow to toggle the input between frequency Hz or chemical shift ppm units In order to perform the conversion the value presently selected for the spectrometer frequency p 29 is used Spectrum Limits 150 100 50 0 50 100 150 ppm lt 8 B The spectrum limits are specified by the high frequency limit in conventional NMR the left limit F1 and the low frequency limit F2 in the Spectrum Default Parameter p 28 box Dependent on July 30 2015 Chapter 2 Menus the state of the radio buttons ppm Hz p 30 the input is taken in units of ppm or Hz To perform the conversion between ppm and Hz the current value of SF p 29 is taken In combination with SI p 30 these parameters determine the digital resolution Use Relative Threshold Value In the Spectrum Default Parameter p 28 box the status of the checkbox for using relative threshold values determines the time required to do a convolution Checkbox Meaning status a The mixed Gaussian Lorentzian line shape used
13. the spectrum width If your spectrum default parameters are such that part of the line shape of a July 30 2015 Chapter 3 Spin Systems spinning sideband is outside the spectrum window you may receive a warning message about con tributions outside the spectrum window Consider increasing the width of the spectrum Also the relative intensities of the sites might be represented erroneously if significant spinning sidebands are outside the calculated spectrum width because the scaling is based on the integral of the spectrum Figure 3 11 shows an example for the succesful simulation of a spectrum arising from the combined effect of chemical shift anisotropy and heteronuclear indirect and dipolar coupling in a powder sample under fast variable angle spinning It is the 31P NMR spectrum of a cadmium phosphine complex A Ele Simulation Tools Window Help VAS Dipolar Chemical Shift Spin Pair lalxi Site 1 Rel Intensity LAJIA l He to previous site Convention STANDARD VAS angle 65 390 Delta 11 49 600 Delta 22 26 500 Delta 33 7 600 ppm ppm Coupled to NAS Cd 113 Spin 1 2 25 000 _ Homonuclear D J Delta J Alpha Beta 250 000 2340 000 Hz Hz Hz deg eg u Figure 3 11 Experimental and calculated 31p VAS NMR spectra of a cadmium phosphine
14. typically quadrupolar nuclei Actually one could also calculate solution H 1 NMR spectra of gt 10 protons coupled to each other when the spectra are purely first order The break down of the high field approximation is taken into account using first order perturbation theory where the quadrupolar interaction is the perturbation Each coupling interaction can be described by an indirect spin spin coupling constant J and a field dependent residual dipolar coupling d as well as the number of nuclei coupled and their respective spins The program calculates the frequency of each transition and puts some intensity a stick into the corresponding bin of the spectrum array One may want to use a higher resolution for the calculated spectrum than for the experimental spectrum e g increase the number of points and decrease the spectral width as the center position of each peak is quantized according to the digital resolution Parameter Purpose Rel Intensity p 88 Relative intensity of this site in percent Tie to previous site p 88 Ties parameters to those of the previous site Ex cept for relative intensity and the spins of the cou pled nuclei all other parameters are affected by the setting of this flag Always have the site with the most coupled nuclei as first site followed by de creasing numbers Otherwise the result will be unpredictable Delta iso p 88 Isotropic chemical shift in ppm Reference SF The re
15. 1 2 nucleus that is coupled to a quadrupolar nucleus in a powder sample It is the C MAS NMR spectrum of a chloroketosulfone where carbon is coupled to C1 35 and Cl 37 and the results have been published in The Influence of Chlorine Carbon Dipolar and Indirect Spin Spin Interactions on High Resolution Carbon 13 NMR Spectra of Chloroketosulfones in the Solid State K Eichele R E Wasylishen J S Grossert A C Olivieri J Phys Chem 1995 99 10110 10113 DOI 10 1021 j100025a010 July 30 2015 Chapter 3 Spin Systems MAS Spin 1 2 Coupled to Quadrupolar Hucleus Diag Figure 3 8 Experimental and calculated 1 C MAS NMR spectra of a carbon coupled to 97C1 This picture also illustrates the workings of the Tie to previous site feature the parameters of the C 13 C1 37 isotopologue are tied to those of the C 13 C1 35 isotopologue by using the ratios of the magnetogyric ratios and nuclear quadrupole moments as factors July 30 2015 Chapter 3 Spin Systems 3 10 MAS Spin 1 2 Spin S Stick MAS Spin 1 2 Coupled to Quadrupolar Nucleus Stick Site 2 Delta iso 0 000 ppm Rel Intensity ULNA Reference SF 100 000 MHz _ Tie to previous site d 100 000 10 000 100 000 10 000 100 000 10 000 Calculates the centerband i e high spinning frequency limit in the MAS spectrum of a powder sam ple containing a spin 1 2 nucleus spin spin coupled to several heteronuclei
16. 2 nucleus in a powder sample It is the Mo NMR MAS spectrum of pentacarbonyl 5 methyldibenzophosphole molybdenum 0 Mo CO 5 MeDBP and the results have been published in Solid State Mo NMR Studies of Some Prototypal Molybdenum Compounds Sodium Molybdate Dihydrate Hexacarbonylmolybdenum and Pentacarbonyl Phosphine Molybdenum 0 Complexes K Eichele R E Wasylishen J H Nelson J Phys Chem A 1997 101 5463 5468 DOI 10 1021 jp9712415 References 1 The second order expression is taken from Amoureux s treatment which follows Taulelle Amoureux Fernandez Granger In Multinuclear Magnetic Resonance in Liquids and Solids Chem ical Applications Granger Harris eds Kluwer Academic Publishers 1990 Ch 22 p 409 July 30 2015 Chapter 3 Spin Systems 3 9 MAS Spin 1 2 Spin S Diag MAS Spin 1 2 Coupled to Quadrupolar Nucleus Diag Site 2 Coupled to N A _ Tie to previous site EXE _ Speedy calculation 100 000 Spin 3 2 Delta iso 0 000 E 510 000 Alpha D Beta D 0 000 deg J 20 000 0 000 deg Delta J 0 000 Chi Spectrum of a powder sample under magic angle spinning containing a spin 1 2 nucleus dipolar and indirect coupled to a quadrupolar nucleus The expectation values for the spin states of the quadrupolar nucleus are evaluated using full matrix diagonalization Only the center peak in the 73 000 MHz Eta 0 000 spectrum is calcul
17. After a successful calculation the calculated spectrum will be displayed If there is no spectrum window currently active this procedure also opens a spectrum window and asks for default spectrum parameters The detailed calculation mode depends on the state of the Active only p 38 menu item 2 2 8 Active Only The item Active only of the Simulation p 28 popup menu determines if a calculation is performed for the currently active window only or for all available spectrum windows 2 2 9 Cycle The item Cycle of the Simulation p 28 popup menu automatically initiates the next step in the generation of a calculated spectrum to refine the agreement between experimental and theoretical spectra The detailed course of the cycle feature depends on the selections made under Cycle options p 38 Note The Enter key is the accelerator key for this action 2 2 10 Cycle Options Cycle Options Cycle through V Default parameters V Site parameters M Convolution parameters V Calculation 7 de P The item Cycle options of the Simulation p 28 popup menu allows to customize the detailed course of the Cycle p 38 feature This cycle consists of Selection Action Windows After all other cycle steps were performed for a win dow switch to the next spectrum window July 30 2015 Chapter 2 Menus Default parameters Site parameters Convolution parameters Calculation 2 3 Options Menu Ed
18. In the case of frequency domain convolution the subroutine uses a threshold p 31 value 0 00001 of the maximum intensity to reduce computation times This however can create funny artefacts therefore you can disable this threshold value Gaussian Convolution GB In the Convolution Parameters p 32 dialog box the value of GB in Hz specifies the full width at half maximum height of a Gaussian peak This line shape will be employed in the convolution of spectra July 30 2015 Chapter 2 Menus The intensity at a given frequency is given by the following expression for an absorption mode Gaus sian 41n 2 v vo GB fv A exp where A peak maximum amplitude vo peak centre frequency GB full width at half maximum height In order to preserve the relative areas of sites with different line broadening parameters the con volution procedure takes into account that the area of a Gaussian peak can be approximated by vr 4ln2 x A x GB 1 064467 x A x GB Lorentzian Convolution In the Convolution Parameters p 32 dialog box the value of LB in Hz specifies the full width at half maximum height of a Lorentzian peak This line shape will be employed in the convolution of spectra The intensity at a given frequency is given by the following expression for an absorption mode Lorentzian A 1 fo where A peak maximum amplitude vo peak ce
19. N 14 nuclei The results and several other examples have been published in Ref 5 July 30 2015 Chapter 3 Spin Systems References 1 Olivieri A C Frydman L Diaz L E J Magn Reson 1987 75 50 62 2 Olivieri A Frydman L Grasselli M Diaz L Magn Reson Chem 1988 26 615 618 3 Olivieri A C J Magn Reson 1989 81 201 205 DOL 10 1016 0022 2364 89 90281 3 4 Harris R K Olivieri A C Progr NMR Spectrosc 1992 24 435 456 DOI 10 1016 0079 6565 92 80004 Y 5 K Eichele R E Wasylishen Inorg Chem 1994 33 2766 2773 DOI 10 1021 ic00091a017 July 30 2015 Chapter 3 Spin Systems 3 11 MAS Spin 1 2 Spin S Shape Spectrum of a powder sample under magic angle spinning containing a spin 1 2 nucleus spin spin coupled to a quadrupolar nucleus The expectation values for the spin states of the quadrupolar nucleus are evaluated using first order perturbation theory where the quadrupolar interaction is the perturbation Only the center peak in the spectrum is calculated i e high spinning limit Note Don t forget to define the observed nucleus this is re quired to evaluate the Larmor frequency of the quadrupolar nu cleus Note For a nucleus with a nuclear spin of 3 a warning will ap pear that the spectrum contains a single line subspectrum Ac cording to the line shape equation this will generally be true of two transitions and independent of the parame
20. PUEVICUS ENE us EE tyta m nenn irn en 88 CORREO oa od oe OR A A A AAA ee e E 88 43 Standard Convene 2 44 0 ee a ed we E E 88 232 Herzteld Berger Convention 0s cag as ea ah a 89 433 Haeberlen Convention lt p ooo osas 8s eee ee eed ede wean 89 4 3 4 Chemical Shift and Magnetic Shielding oo ss cco creca creo tano 90 Coupled le o ces ana nenn en ee an a a ds 91 Natural Abundance noi neha eA aa a A nis 91 Dipolar Coupling Constant seps su ew ek GA anne Eee nn 91 austin are 2220 kee ae ers rain trace eee 92 Anisotropy in Indirect Spin Spin Coupling Delta 22 22 2222 92 POT NS 92 Euler Anglos o na ek un Phebe eee nen nike in 93 2101 ROTON kennen nenne nass oe a ee 94 iv July 30 2015 Contents 212 Determining Euler Angles co resaca Seen a we a E e a 95 4 11 Electric Field Gradient Tensor ocur a a ee KG 96 4 12 Central Transition CT and Satellite Transitions ST 96 4 14 Vasiable Angle Spinning Angle 22 2224 32 sa eee RSA ernannt 97 4 14 Spite Peter cda ran ri nen an BEIDE an 97 4 15 Speedy Calkukton 2 232 a era RES ERA A PR RES 97 2 16 INI Pile Settings cocos ra eee ee eee was 97 4 16 1 Portable or Non Portable Format portable lt oo o 97 4 16 2 Default Output File Format OutFile o o 98 4 16 3 Number of Triangular Intersections POWDERIENT 98 4 16 4 Number of Decimal Digits digits o oo
21. Version 1 17 22 17 03 1999 Fixed a bug related to the relative intensities of several sites when using the model MAS Quadrupolar nucleus p 65 Made changes to the POWDER subroutine to deal with single line lineshapes better previ ously no intensity got added 1 3 16 Version 1 17 21 09 10 1998 Changed the meaning of SF p 29 spectrometer frequency this parameter corresponds now to the frequency of the chemical shift standard Fixed a bug in model MAS Spin 1 2 Spin S Stick p 70 the factor dealing with reference SF and different Larmor frequencies worked in the opposite sense of the intended direction Added Tools Add constant p 45 to allow for a very simple baseline correction Added Tools Absolute value p 45 to generate the absolute value representation Added Tools Reverse spectrum p 45 to reverse the sense of a spectrum Problems with the cycle feature p 38 got probably fixed now Introduced an option in the convolution of spectra to switch off the use of a threshold value p 31 Different sites calculated with the model MAS Chemical Shift Anisotropy HB p 62 should have the proper relative intensities now Added functions to read experimental spectra in Chemagnetics SpinSight p 20 format Added functions to read WinNMR ASCII p 20 spectra directly without the need to convert them into SOLIDS format 1 3 17 Version 1 17 Added a new calculation model MAS Quadrupolar nucleus
22. adobe com devnet svg adobe svg viewer download area html Location of Required Files For security reasons the XML file and the required XSL and CSS helper files need to reside in the same directory New distributions of WSolids1 will bundle these helper files in a subdirectory report of the WSolids1 program directory If you cannot write to this subdirectory because of limited access rights maybe you can copy them to a location where you have write access or you can download the helper files from the WSolids1 home page and install them there My recommendation is to create a WSolids subdirectory in your Own documents place and store all data there With all the files at the same place simply drag the XML file into your browser or open it from the browser s file menu Creating HTML Files Permanently Note There is no point in saving the displayed report from your browser because this will save the original XML file rather than the generated HTML version To permanently generate an HTML version you need an XSL processor e g xsltproc Alternatively SeaMonkey will give you the HTML version if you select File Edit Page There could be reasons for wanting a permanent HTML version of the report e g to import and modify it with word processing software unfortunately they will not display the graphics Unless you are using SeaMonkey as browser anyway you will need additional software such as an XSL processor to ac
23. collected by Pekka Pyykk 3 e the merece ratios of Sn 119 and Sn 117 could be 3 less than the accepted value 2 i e 9 997559x10 rad s T and 9 552955x 107 rad s T instead of 10 021x107 rad s T and 9 589x 107 rad s T71 e Nd 145 apparently has a spin of 7 2 instead of 5 2 4 5 Similarly U 235 has a spin of 7 2 instead of 5 2 4 5 U 233 has been added to the tables 4 5 References 1 Joan Mason Multinuclear NMR Plenum Press New York 1987 2 A Laaksonen and R Wasylishen J Am Chem Soc 1995 117 392 400 DOI 10 1021 ja00106a044 3 P Pyykk Mol Phys 2001 99 1617 1629 DOI 10 1080 00268970110069010 4 Quantities Units and Symbols in Physical Chemistry IUPAC 5 CRC Handbook of Chemistry and Physics 6 R K Harris E D Becker S M Cabral de Menezes R Goodfellow P Granger July 30 2015 Chapter 2 Menus Pure Appl Chem 2001 73 1795 1818 DOI 10 1351 pac200173111795 Solid State Nucl Magn Reson 2002 22 458 483 DOI 10 1006 snmr 2002 0063 Angew Chem 2004 116 2070 2083 DOI 10 1002 ange 200380015 2 4 3 Periodic System of Elements Periodic System of Elements xj Name Hydrogen rs 4 H 3 8 008 1 2 213 458 Magnetic Field T 4 700000 y Me This dialog box accessible from the Tools Periodic table menu item displays a periodic system of elements with information relevant to NMR By setting the magneti
24. eee 99 5 Acknowledgements 101 A oO a a ee ds 101 52 Trademark Acknowleisements 24 20 saw su au ana a a a 102 oo Copyrichtinfetviaten e e ace eee enana da a A en 102 54 Disclaimer st Waranty 224 480 de bed ee einen nen 104 Index 105 vo July 30 2015 July 30 2015 1 Getting Started en Contents 11 Tntroducho ae a let ea ia as e 3 133 Purpose ole Programi oo ec soos lr eee ed 3 LL Features oc Ro Se Reb mee a a e e G 4 LS RER coca a a Res aa OG aw a Ge a A a da Ace de 4 LA Doble ie soa e ey ee we cae a a a a ee ee ee 5 L2 o E 6 1 3 Revision History o ooo e 7 Rok version LALA COOL add e ed a Bb 7 13 2 Version 1202 06 08 2014 a ana 7 Ls Version 10220 reo ar AAA ae 7 134 Version 120 18 SL OL 2012 ooeec ara da e or e E e S 8 133 MEIDEN costra A 8 136 Version 1204 15062010 55 eee ea eae Se Re ee Re 8 137 Version 120304062010 2 4 2 2 24 RRR eh eR A AR 8 138 Version 1 202 25 052010 2 05 4 i Shen 9 1S9 Version TEEN ren ORG Ree ew RE S 9 13 20 Versi n 119 12 2005 2009 o Oe ae ee PRP es 9 1311 Version 1 19 10 GOL 2000 2 4 2 24 daa Barked WEE Rae a a 9 13 2 Version 1 19 2 21 08 2008 4 4 4 4 Ks su aha ter ge dadas 9 1323 Version LIA ALSO DUI cocos RO ek ahnt 9 1314 Version 1 1728 27092000 a cia aa ad a a indes 9 1315 Version 11722 17 03 1999 c c soci aw sra nern 10 1316 Version 11721 09 10 1998 cocos ao a a nt Re 10 Lod Version LI
25. implemented a general approach that sets up the Hamiltonian on the fly there are no restrictions on the spin anymore bug fix setting site dependent convolution parameters when reading XML documents bug fix reading JCAMP DX p 21 files 1 3 6 Version 1 20 4 15 06 2010 Fixed reading spin 1 2 nuclei in MAS Spin 1 2 Spin S Stick p 70 WSolids documents 1 3 7 Version 1 20 3 04 06 2010 Fixed a bug in model MAS Spin 1 2 Spin S Stick p 70 when reading WSolids documents July 30 2015 Chapter 1 Getting Started 1 3 8 Version 1 20 2 25 05 2010 e added saving of all data in XML format as WSolids document 1 3 9 Version 1 19 15 02 10 2009 e fixed a bug in adding spectra from several sites e fixed a bug in calculating MAS spectra of spin 1 2 coupled to quadrupolar nucleus stick approach 1 3 10 Version 1 19 12 20 05 2009 e The Tools Scale spectrum p 44 dialog now presents a scaling suggestion 1 3 11 Version 1 19 10 06 01 2009 e Can read a second spectrum p 22 into the memory assigned as calculated spectrum for dual display with the experimental spectrum 1 3 12 Version 1 19 2 21 08 2008 e This is the first 32 bit release Internally Wsolids1 underwent some serious changes that will not be apparent to the user e Added reading of TopSpin XWinNMR p 19 JCAMP DX p 21 and Simpson p 22 files removed handling of Antiope NMRLAB and CC2X files e In addition to WinNMR f
26. in the convolu tion process is used until the intensity of the wings reaches zero This is the more lengthy process but may be required if weak peaks are to be displayed in the presence of very strong peaks vl The mixed Gaussian Lorentzian line shape used in the convo lution process is used until the intensity of the wings reaches 1 10000 of the greatest spectral intensity This reduces calcula tion time but may produce funny looking line shapes for weak peaks Site Dependent Broadening In the Spectrum Default Parameter p 28 box the status of the checkbox for site dependent broad ening determines whether each site requires its own set of convolution parameters p 32 Because the Gaussian Lorentzian peaks used for convolution are normalized the relative areas of each site are approximately preserved Checkbox Meaning status Usually the selection of no site dependent broadening will do y P 8 In this case only one set of convolution parameters will be nec essary The convolution routine is activated only once after all site specific spectra have been calculated vl In this case each site requires its own set of line broadening pa rameters Also the convolution routine is invoked each time af ter a site specific spectrum has been generated July 30 2015 Chapter 2 Menus GB 0 GB 200 GB 1000 LB 2000 25 20 15 10 5 0 5 10 15 20 25 30 kHz Note Although the convolution paramet
27. into Hz and vice versa For the direct observation of quadrupolar nuclei its magnitude relative to the quadrupolar coupling constant is important for the observed line shape Valid values for the spectrometer frequency are any positive non zero floating point numbers Note All calculations assume that the Zeeman interaction is the domi nant interaction high field approximaton For example calculation of a Pake doublet with a dipolar coupling constant of 1 kHz and a spec trometer frequency of 100 Hz will not give the proper result The high field approximation is slightly relaxed in cases involving quadrupolar nuclei but one should always be aware of the approximations behind any type of calculation Spectrum Size The spectrum size SI defines the size of the calculated spectrum in points and is set in the Spectrum Default Parameter p 28 box Traditionally its values are multiples of two but it is not limited to these numbers If an experimental spectrum is available this parameter is set by default Together with the high and low frequency limits F1 p 30 and F2 p 30 the spectrum size de termines the spectral resolution Often it is sufficient to use the same spectral resolution as the experimental spectrum However in cases involving stick approaches a higher digital resolution for the calulated spectrum is advisable The spectrum size affects the time required for calculating a spectrum i e
28. of the peaks in the first derivative line shape indicates the natural line width a parameter which can be employed in the convolution of the calculated spectrum References e T G Oas C J Hartzell T J McMahon G P Drobny F W Dahlquist J Am Chem Soc 1987 109 5956 DOI 10 1021 ja00254a010 e T G Oas C J Hartzell F W Dahlquist G P Drobny J Am Chem Soc 1987 109 5962 DOI 10 1021 ja00254a011 e C J Hartzell M Whitfield T G Oas G P Drobny J Am Chem Soc 1987 109 5966 DOI 10 1021 ja00254a012 2 2 4 New Site A site is an independent part of a spectrum with a line shape uniquely defined by parameters e g chemical shifts couplings etc specific to the calculational model selected for this site The feature New Site of the Simulation p 28 popup menu adds a new site to the calculation model It calls the Select Calculation Model p 36 dialog box and requests the user to select a model Afterwards it initiates the input of the appropriate site specific parameters July 30 2015 Chapter 2 Menus 2 2 5 Select Calculation Model Select Calculation Model Dipolar chemical shift 42 AX Dipolar chemical shift AB Quadrupolar nucleus Chemical shift anisotropy HB Quadrupolar nucleus Spin 1 2 Spin S Diag Spin 1 2 Spin S Stick ZJ Xn te The Select Calculation Model dialog box available from the New Site p 35 item of the Simulation
29. order Additionally chemical shift anisotropy dipolar and indirect coupling to a heteronucleus can be added note quadrupolar interaction if any is neglected for the coupled heteronucleus Parameter Convention 0 000 0 000 0 000 0 000 0 000 0 000 STANDARD y Coupled to B 11 y ppm N A 100 000 ppm Spin 3 2 ppm D 3500 000 deg y 0 000 deg Alpha 0 000 CO deg Beta 0 000 CO Purpose Rel Intensity p 88 Tie to previous site p 88 Convention p 88 Delta 11 Delta 22 Delta 33 p 88 Delta iso Span Skew p 88 Delta iso Anisotropy Asym metry p 88 Alpha Beta Gamma p 93 Chi p 96 Eta p 96 CTST p 96 Relative intensity of this site in percent Ties parameters to those of the previous site Convention used for chemical shift tensor components Principal components of chemical shift tensor stan dard convention in ppm Principal components of chemical shift tensor Herzfeld Berger convention Principal components of chemical shift tensor Hae berlen convention Euler angles in degrees for going from the electric field gradient tensor frame to the principal axis sys tem of the chemical shift tensor Quadrupolar coupling constant in MHz Asymmetry parameter of the electric field gradient tensor 0 lt eta lt 1 Select central transition CT or satellite transitions ST July 30 2015 Chapter 3 Spin System
30. ratio In these cases it might appear that the quadrupolar coupling constant has the opposite sign There is no quick fix right now contact me if you need more information July 30 2015 3 Spin Systems Contents 3 1 Static Chemical Shift Anisotropy o 50 a ARE 50 Implementation Detalls s o ci a re eh 51 3 2 Static Dipolar Chemical Shift A2 AX o oooooo ooo o 52 PACHO oai o cad A eae 53 Implementation Details o ocas eaa a e a A AAA A 53 3 3 Static Dipolar Chemical Shift AB o ooooooo oo o 55 Backend IA 56 Implementation Details s soc a oe ee aa rara A 56 3 4 Static Quadrupolar Nucleus ooo oooocooooo o o o 58 Background cocinada RAR RR ERR A O 59 Implementation Details u r 24 k need aaa 59 e A E a O O dr tay a O Ie I eR Are oh 60 3 5 Static Three Spin System AMX o o ooooooooo ee ee ee ooo 61 3 6 MAS Chemical Shift Anisotropy HB lt oo oo ooo o 62 Backend econo 52446 ann anne 62 3 7 MAS Dipolar Chemical Shift A2 AX o o oooooo ooo 64 3 8 MAS Quadrupolar Nucleus o ooo ooo 65 Background coca dr A eR ED 65 Implementation Details u r 5 2 04H ns 66 PT A ee aa ee San et Dal a a Ae Rea ee 6 oe 66 3 9 MAS Spin 1 2 Spin S Diag lt lt ooo 67 Background cocoa coria A A nenne 68 Implementation Details 2c ie aw debe a de
31. shielding 90 absolute value 45 absorption 34 abundance 91 accelerators 14 acknowledgements 101 alpha 92 anisotropy in indirect coupling 92 apodization 32 34 AX 76 beginner 1 beta 92 Bruker 19 20 bugs 48 calculation 28 38 central transition 96 changes 7 Chemagnetics 20 chemical shift 90 chemical shift anisotropy 50 52 55 58 62 chi 96 colors 39 convention 88 90 convolution 31 34 44 copyright 102 coupling 91 92 credits 101 cycle 38 D 41 91 default parameters 29 derivative 34 dipolar 52 55 dipolar coupling 91 dipolar coupling constant 41 disclaimer 104 document 17 22 24 dual display 22 edit site 37 electric field gradient 96 elements 44 eta 96 Euler angles 93 95 exit 27 F1 30 F2 30 features 3 files 17 22 FireFox 24 gamma 42 Gaussian 33 Haeberlen 88 help 47 Herzfeld Berger 62 88 heteronuclear 52 58 64 65 67 70 74 76 history 7 homonuclear 52 55 58 64 76 78 Hz 30 indirect coupling 92 intensity 88 Internet 24 introduction 3 6 isotopic labelling 91 J 92 JCAMP DX 21 keyboard 14 Larmor frequency 29 license 3 line broadening 32 34 Lorentzian 33 34 MAS 62 64 65 67 70 74 97 MDI 12 menus 15 model 36 multiple documents 12 multiple spectra 12 natural abundance 42 91 nuclear properties 42 nuclei 44 nucleus 29 offset 45 options 39 overview 6 per
32. transformation files and style sheets new feature added a tool to reference p 45 spectra new feature added a checkbox to the Spectrum Default Parameter p 28 box to re initialize p 29 the parameters of the calculated spectrum new feature there is an ini file parameter OutFile p 98 to set the spectrum output default format new feature there is an ini file parameter NT p 98 to set the number of triangular intersec tions of the POWDER space tiling and interpolation algorithm new feature there is an ini file parameter Digits p 99 to fine tune the number of digits displayed in dialog boxes for floating point numbers new feature added support for other PDF viewers to display context sensitive help p 47 added handling of PDF XChange Viewer by Tracker Software Products Ltd http www tracker software com currently my prefered PDF viewer and Sumatra PDF Viewer http blog kowalczyk info software sumatrapdf also deal with the new Adobe Reader X p 47 new feature added a new spin system that actually is a high resolution solution system HR Spin 1 2 Coupled to Quadrupolar Nucleus Relaxation p 80 this calculation has not been verified yet use at your own risk new feature added a new spin system consisting of three spins Static Three Spin System AMX p 61 this calculation has not been verified yet use at your own risk new feature for the MAS Spin 1 2 Spin S Diag p 67 spin system
33. would this look like without an experimental spectrum is not possible MDI as implemented in WSolids1 allows to calculate spectra for different external magnetic fields different derivative modes or different experimental conditions simultane ously using the same spin system parameters This could help to answer a question like does it make sense to go to a higher field Spin systems and spectra are allocated dynamically One may have as many spectra and spin systems as the memory resources of the computer allow In each case the spectrum and spin system parameters are filled with sensible default values This should allow for easy familiar ization WSolids1 has no build in features to support iterative fitting In order to make the refinement of a calculated spectrum less painful a so called Cycle p 38 feature was implemented De pending on the context and the selected Cycle options pressing the Enter key will perform specific actions such as requesting spectrometer settings requesting spin system parameters requesting convolution parameters performing a calculation or switching to the next spectrum window For several menu commands accelerator keys p 14 have been defined for example press ing C starts a calculation Also holding down the ALT key and pressing any character key activates the corresponding menu item edit control list box button etc for which the corre sponding character is underlined Som
34. 0 0 00000 213 449677 213 449554 4 He 3 172 20 38016 0 0001 0 00000 152 449341 152 445724 5 Li 6 1 do oca 7 5900 0 00081 29 451149 29 448952 6 Li 3 2 10 39770 92 4100 0 04010 77 777740 77 771904 7 Be 9 372 3 75967 100 0000 0 05288 28 123362 28 119648 8 B 10 3 2 87468 19 9000 0 08459 21 503407 21 499565 9 B 11 372 8 58470 80 1000 0 04059 64 216011 64 204529 10 C 13 172 6 72828 1 0700 0 00000 50 329460 50 318707 11 N 14 1 1 93378 99 6320 0 02044 14 465214 14 460873 12 N 15 1 2 2 71262 0 3680 0 00000 20 291149 20 285091 13 0 17 572 3 62808 0 0380 0 02558 27 139061 27 128370 14 F 19 172 25 18148 100 0000 0 00000 188 364578 188 295303 15 Ne 21 372 2 11308 0 2700 0 10155 15 806435 15 797593 Sort for No y Magnetic Field T 4 790008 y Me This dialog box accessible from the Tools Nuclear properties menu item lists nuclear properties for many of the known NMR active nuclei The Properties nuclear spin quantum number magnetogyric ratio y Gamma in units of 10 rad s T natural abundance N A in nuclear electric quadrupole moment Q in units of 10728 m Larmor frequency in MHz of that nucleus at the selected magnetic field strength according to Y VL an frequency in MHz of the reference compound for that nucleus i e chemical shift reference secondary standard at the selected magnetic field strength according to Bo 2 348661 o vou using the absolute freq
35. 1 241 Dipolar Coupling Constant se os rpa sans naar as 41 24 2 Table of Nuclear Properties oa io sanies ia a eh a ss sen nenne 42 24 3 PeriodieSsystem of Elements pe ocras aae aden i sms en 44 PAS Corwohlle ook estas a en K 44 243 CU PE N o A a a db A eier 44 240 Add CONBHNE 22 03 es wa au een a a 45 247 Reverse OPE rr le ana una u 45 248 Absolute Value a csser trpi amat Benin dasa aa arg 45 249 Beferanee Spectrum o ci ook ne bo er 45 Window Menu e a ia ae 22 24 2 224 220 wa ae EE ana ana 46 IBS MEN e cos a e aara ren hehe ur 47 Know Probleme o cocos tasa a a EK AS 48 Systems 49 Static Chemical Shift Anisotispy cn ecek p ee ae ann 50 Static Dipolar Chemical Shift AL AX 664 seo he PES ee wa de ew Pes 52 State Dipolar Chemical Shift AB o e ge a Re We a 55 Static Q uadrupolar Nucleus s sree ey sd e nenne 58 State Three Spm System AMA naar ne nee 61 MAS Chemical Shift Anisotropy FIB ce co rss sn ns ner an tra nitk 62 MAS Dipolar Chemical Suit AL AX 224 22 oe een na nen 64 MAS Duadnipolar Nucleus o ooo 2 200 a een eh nn 65 Mas Spiel 2 Spin DIA gt in aa a rear sera in 67 MAS Spinel 2 SPpir LODO 2 ve be DE Ew a dt e A EER 70 MAS opel 2 Spin Shape dls o a be 74 VAS Dipolar Chemical Shi AL AA oca a na en en 76 VAS Dipolar Chemical SIA oe eed poe ee boa ne ae ee 78 HR Spin 1 2 Coupled to Quadrupolar Nucleus Relaxation 80 System Parameters 87 DES IES ga a E A A A e 88 Teto
36. 1 2 8 1 3 1 g 5 0 0 4 2 44 2 4 0010 3 5 B Bp 3 0 1 0 0 g 2 1 3 4 5 2 Oe 0o 0 4 1 4 3 3 0 0 0 0 33 3 July 30 2015 Chapter 3 Spin Systems Som Moda SF lol le s Options elp 91 x ABLE ej 3 24 3 Site 1 Rel Intensity EERE F Tie to previous site Delta iso 65 000000 ppm Coupled to v 51 v J 615 000000 Hz Spin 7 2 D 0 000000 Hz Tig 0 000330 s Reference SF 100 000000 MHz I modify transition probabilities a EJ x me qAAA gt 5 55 AA A E EE AA DAA E A AD E AE E AR AE A E S LE A T 50 0 70 80 30 100 110 120 al Figure 3 13 Experimental and calculated high resolution solution Sn NMR spectra of tin coupled to a IV nucleus showing the effect of relaxation s 7 2 3 3 3 3 3 2 gt 7 wm 0 0 0 0 0 3 8 f o o o o 301 3 2 0 o 0 4 0 3 140 2 0 0 3 0 0 2 0 4 4 5 0 gt 0 0 0 2 3 5 w 3 jo o o o 3 4 z o o o o 0 ff 4 These are the matrix elements that can be modified if the item modify transition probabilities is checked in the parameter input dialog box compare the elements of the matrix shown in the table for S 7 2 above to the second dialog shown for this calculation model p 80 On first call the elements are initialized using eqs 3 6 and 3 7 and can be modified by the user e g to accomodate deviations from the extreme narrowing limit or
37. 2 m 2100000 0 700000 0 000000 0 000000 0 000000 0 000000 0 000000 ps a T e meer ram T TA Tram ame PE E o a aa e o ae o A A A eee ee ee ds a ea fe e ee a a aL rn en Sa eee el ee E a a a are a nD e SS es ee ee This model is actually intended for the calculation of the solution spectrum HR high resolution solution of a spin 1 2 nucleus spin I in the following coupled to a quadrupolar nucleus S where the spin lattice relaxation of the quadrupolar nucleus affects the spectrum of the spin 1 2 nucleus A few modifications were introduced to accomodate the simulation of solid state spectra in limited cases where first order perturbation theory is valid model MAS Spin 1 2 Spin S Stick p 70 If necessary the individual elements of the transfer probabilities matrix see below can be modified Some example spectra are illustrated below for the following spin system P coupled to gt V I 7 2 with JC 1V IP 500 Hz an LB of 40 Hz and the V spin lattice relaxation times T indicated in the figure At intermediate T s the apparent unequal intensities within the non binomial octet are the result of the different life times of the associated V spin states causing different line widths and hence different peak heights but equal integrals July 30 2015 Chapter 3 Spin Systems Note For each point in t
38. 2 Settings Default Settings 3 xi Default output format TANTA No of digits 6 NT 32 FT Save all values as defaults CONE This dialog allows to modify either temporarily or permanently some program settings that are retrieved from the ini file p 97 upon program start plate Default output format the default output format p 98 for saving spectra p 22 e no of digits the number of decimal digits p 99 to be displayed in edit controls e NT the number of triangular intersections p 98 e Save values as default if checked the changes will be saved in the INI file p 97 otherwise they affect the program only temporarily July 30 2015 Chapter 2 Menus 2 4 Tools Menu The Tools pop up menu consists of the following items Item Dipolar coupling stant p 41 WSolids1 File Simulation Options Window Help coupling constant ru SF 81 033 MHz Convolute Reverse spectrum Purpose con Invokes a dialog box to calculate dipolar coupling constants Nuclear properties p 42 Displays a table of nuclear properties Periodic table p 44 Displays a periodic system of elements relevant to Convolute p 44 NMR Performs an additional convolution of experimental or theoretical spectra Scale spectrum p 44 Scale a spectrum by a given factor Add constant p 45 Adds the specified value to the intensity of the spec
39. 3 Viso 011 022 033 3 In what we shall call the standard convention 1 3 the principal components of the chemical shift tensor 911 622 and 633 are labeled according to the IUPAC rules 2 They follow the high frequency positive order Thus 411 corresponds to the direction of least shielding 011 with the highest fre quency while 633 corresponds to the direction of highest shielding 033 with the lowest frequency The isotropic values dis Or Ciso are the average values of the principal components and correspond to the center of gravity of the line shape In many cases the spectrum or calculation will not depend on any given order and the values can be entered in any order However in some cases where the orientation of the tensors is also important the assignment of values to the principal axes will affect the spectrum References July 30 2015 Chapter 4 Spin System Parameters 1 J Mason Solid State Nucl Magn Reson 1993 2 285 DOI 10 1016 0926 2040 93 90010 K 2 R N Jones A R H Cole E A Miller M A Elyash vich T F rster A Hadni Y Morino N Sheppard E Fluck E R Lippincott R C Lord S Nagakura J Pliv Sir H Thompson D W Turner G Herzberg T Urbanski Pure Appl Chem 1972 29 625 628 DOI 10 1351 pac197229040625 3 R K Harris E D Becker S M Cabral de Menezes P Granger R E Hoffman K W Zilm Pure Appl Chem 2008 80 59 84 DOI 10 1351 pac2008
40. 3 10 Experimental and calculated C MAS NMR spectra showing coupling to 4N Background The quadrupolar interaction at a quadrupolar nucleus causes its axis of quantization to be tilted away from the direction of the external magnetic field This also modifies the spatial dependence of the dipolar interaction so that magic angle spinning is not able to suppress the heteronuclear dipolar coupling in the spectrum of the spin 1 2 nucleus resulting in splittings and broadenings Similar ef fects can be transmitted through the indirect spin spin coupling If the nuclear quadrupolar coupling constant is on the same order of magnitude as the Larmor frequency of the quadrupolar nucleus the combined Zeeman quadrupolar Hamiltonian must be diagonalized at each orientation and averaged over a rotor period to calculate a theoretical spectrum However if the quadrupolar coupling is rela tively small this so called breakdown of the high field approximation causes lineshapes that can be simulated using first order perturbation theory If the broadening is small such lineshapes can also be analyzed using a stick approach Figure 3 10 shows an example for the succesful simulation of a MAS spectrum of a spin 1 2 nucleus that is coupled to several quadrupolar nuclei in a powder sample It is the C MAS NMR spectrum of NH4 SeCN where carbon is coupled to a N 14 nucleus and the results have been published in Nuclear Magnetic Shielding Tensors for the Carb
41. 3 8 MAS Quadrupolar Nucleus MAS Quadrupolar Nucleus 2nd order Site 6 Rel Intensity LAUK Tie to previous site pa 0 120 0 000 0 000 Chi Eta MHz Delta iso Coupled to B 11 7 Spin 3 2 N A 100 000 a J 0 000 Hz Calculates powder MAS spectrum of the central transition of a quadrupolar nucleus considering the quadrupolar interaction to second order Additionally indirect coupling to a heteronucleus can be added note quadrupolar interaction if any is neglected for the coupled heteronucleus Parameter Purpose Rel Intensity p 88 Relative intensity of this site in percent Tie to previous site p 88 Ties parameters to those of the previous site Delta iso p 88 Chi p 96 Eta p 96 Isotropic chemical shift in ppm Quadrupolar coupling constant in MHz Asymmetry parameter of the electric field gradient tensor 0 lt eta lt 1 Coupled to p 91 Specifies the nucleus the observed nucleus is cou pled to Only heteronuclear coupling will be considered N A p 91 Natural abundance in percent of the coupled nu cleus If smaller than 100 WSolids1 automatically includes calculation of the spectrum of the uncou pled spin species J p 92 LB p 32 Indirect spin spin coupling constant in Hz Provides access to the convolution parameters for the current site To have individual convolution pa rameters for each site specify th
42. 4 k of 511 999 996 k free lt DIR gt 14 03 2013 14 27 INES tests lt DIR gt 14 03 2013 1231 lt DIR gt 09 12 2011 16 36 lt DIR gt 27 04 2012 16 29 333 378 09 09 2011 18 42 a 986 26 01 2011 18 44 a lt DIR gt 27 04 2012 16 29 conv 1 9 2win322ip 1 320 616 27 04 2012 11 55 a 2 736 611 27 04 2012 11 56 a 945 27 01 2011 23 21 a 1 370 475 26 01 2011 22 44 a izlib 1 2 5win32 zip 41 650 02 11 2012 18 49 a Icon file C windows system32 shell32 dll gt gt 1 625 18 11 2011 20 48 a g 3 300 26 01 2011 22 37 a zn u Ss 850 14 03 2013 1232 a gt x20M ex 4 340 12 09 2012 22 17 a a gt Cancel 4 113 02 11 2012 18 18 a 4 340 12 09 2012 22 17 a Tooti ue 6 122 06 12 2011 22 36 a Ok 4 852k in 0 6filefs 0k 2 053k in 0 13file s 0 3 dirfs e wsolids Veport gt Y F3 View F4 Edt F5 Copy F6 Move F7 NewFolder F8 Delete AFA Bat Now you can select the XML file you want to convert and hit your custom button Links to the software mentioned xsltproc http xmlsoft org XSLT libxml http www zlatkovic com libxml en html SeaMonkey http www seamonkey project org TotalCommander http www ghisler com 2 1 11 Exit The Exit item of the File p 17 pop up menu quits WSolids1 All existing data will be lost if not saved prior to selecting Exit July 30 2015
43. 6 S0926 2040 97 00023 4 Olivieri A C Solid State Nucl Magn Reson 1998 11 181 187 DOI 10 1016 S0926 2040 98 00035 6 We learned a lot from A C Olivieri s BASIC program ANYCHI to calculate the MAS spectrum of a spin 1 2 nucleus coupled to a spin 3 2 nucleus S H Alarcon A C Olivieri R K Harris Solid State Nucl Magn Reson 1993 2 325 We are grateful to Alejandro C Olivieri for making his program available The design of WSolids1 received some ideas gained by working with the program ANTIOPE We are grateful to John S Waugh for making a copy of this program available to us F S de Bouregas J S Waugh J Magn Reson 1992 96 280 Thanks are due to Jim Frye and Glenn Sullivan both Chemagnetics Varian NMR for their help with the implementation of the SpinSight file import We are grateful to Dr Hans F rster Bruker for providing information on the WinNMR format We acknowledge the notes by W M Westler and F Abildgaard posted on the internet on DMX Digital Filters and Non Bruker Offline Processing The algorithms for bicubic spline interpolation and Marquardt Levenberg non linear least squares procedures are adopted and adapted from 101 July 30 2015 Chapter 5 Acknowledgements W H Press S A Teukolsky W T Vetterling B P Flannery Numerical Recipes in C Cambridge University Press Cambridge 1992 Microsoft for providing Visual C 2008 Express Edition for free Jordan
44. 80010059 4 3 2 Herzfeld Berger Convention a Isotropic Value diso 611 622 933 3 1 da Span O 1 8 0 gt 0 Skew K 3 d22 iso Q 1 lt K lt 1 In the Herzfeld Berger notation 1 a tensor is described by three parameters which are combina tions of the principal components in the standard notation The isotropic value i e the center of gravity is the average value of the principal components The span describes the maximum width of the powder pattern The skew of the tensor is a measure of the amount and orientation of the asymmetry of the tensor As indicated x is given by 3a Q where a 622 digo Depending on the position of 522 with respect to diso the sign is either positive or negative If d22 equals digo a and the skew are zero In the case of an axially symmetric tensor 62 equals either 911 or 933 and a 2 3 Hence the skew is 1 The parameter u used with the Herzfeld Berger tables is related to the span of a tensor by u Q SF spinning rate The parameter p used with the Herzfeld Berger tables corresponds to the skew of a tensor described here For historical reasons we used p throughout this manual but generally we prefer x 2 The Herzfeld Berger convention is related to the Standard convention via 922 digo K QO 3 033 3 diso 622 0 2 611 3 iso 622 933 References 1 J Herzfeld A E Berger J Chem Phys 1980 73 6021 6030 DOI
45. Berger HB The tables used by WSolids1 have been extended compared to the original Herzfeld Berger publication from u 15 to u 30 and includes 15 spinning sidedands instead of 5 for the definition of u see Herzfeld Berger Convention p 89 Roughly corresponds to the number of significant spinning sidebands visible in the spectrum The current extent of the Herzfeld Berger tables is often good enough for the analysis of spinning sideband intensities to retrieve chemical shift tensor components see my program HBA but for great values of y some spinning sidebands might be missing in a simulation Therefore WSolids1 uses a different approach to calculate spinning sideband intensities if 1 exceeds a certain limit 20 currently The calculation is done in the frequency domain as outlined in the Herzfeld Berger paper each spinning sideband is calculated individually More information will be available in the section VAS Dipolar Chemical Shift A2 AX p 76 If the angle of the spinning axis deviates from the magic angle you should use that model to simulate pure chemical shift anisotropy cases despite the name of the model indicating spin pairs Figure 3 5 shows an example for the succesful simulation of a spectrum arising from chemical shift anisotropy in a powder sample under magic angle spinning It is the 9P CP MAS NMR spectrum of a phosphinidene ruthenium cluster nido Ru CO 13 u3 PPh and the results have been published in Ph
46. DF viewer to display context sensitive help p 47 new feature and bug fix the HR Spin 1 2 Coupled to Quadrupolar Nucleus Relaxation p 80 model got a few options added to enable some calculations of solid state NMR spectra the calculations erroneously had a factor of 2 so that the real T should be half of that reported 1 3 2 Version 1 20 22 06 03 2014 new feature added spin system MAS Dipolar Chemical Shift A2 AX p 64 new feature new document p 17 menu item 1 3 3 Version 1 20 21 15 03 2013 Basically a face lift new feature proportional scroll bars with additional accelerator keys Pos1 End Page Up Page Down new feature added mouse zooming and scrolling new feature the report p 24 feature has added support for SVG display in Internet Explorer 9 y July 30 2015 Chapter 1 Getting Started 1 3 4 Version 1 20 18 31 01 2012 new feature after reading or writing a WSolids document the main window title shows the name of the document new feature the report p 24 includes a graphical representation of spectra bug fix for reading from or writing to XML documents the MAS Spin 1 2 Spin S Diag p 67 spin system deal properly with the relative intensity and the speedy flag 1 3 5 Version 1 20 15 25 02 2011 new feature allow to read p 22 or write p 23 spin system only new feature information on creating reports p 24 from the WSolids1 XML document using XSL
47. DOI 10 1063 1 450211 4 16 4 Number of Decimal Digits digits Document Digits 5 In order to fine tune the number of digits displayed in dialog boxes for floating point numbers you can use the parameter Digits in the DOCUMENT section of the INI file Note that Digits only affects the display not the actual number of decimal digits evaluated when entering floating point numbers Le the accuracy is not affected by Digits July 30 2015 100 July 30 2015 5 Acknowledgements Contents 51 Credits occ ieee a 8 A a OE SOS a 101 5 2 Trademark Acknowledgements 1 2 ee eee eee eee eee ene 102 5 3 Copyright Information se eee ee eee eetet eneren enee 102 5 4 Disclaimer of Warranty c sosen soe e ee e ee E e e a o o 104 5 1 Credits Some of the early FORTRAN modules were written by William P Power dipolar chemical shift NMR quadrupolar powder patterns QUADPOW and SECQUAD Gang Wu dipolar chemical shift NMR of homonuclear spin pairs This program contains for space tiling and interpolation purposes the POWDER routine We are grateful to D W Alderman for a copy of the routine in FORTRAN D W Alderman M S Solum D M Grant J Chem Phys 1986 84 3717 DOI 10 1063 1 450211 Dr Alejandro C Olivieri kindly provided BASIC programs that taught me how to calculate spinning sidebands in the frequency domain Olivieri A C Solid State Nucl Magn Reson 1997 10 19 24 DOI 10 101
48. Relative intensity of this site in percent Ties parameters to those of the previous site Convention used for chemical shift components tensor Principal components of chemical shift tensor stan dard convention in ppm Principal components of chemical shift tensor Herzfeld Berger convention Principal components of chemical shift tensor Hae berlen convention Specifies the nucleus the observed nucleus is cou pled to If this is the same isotope as the ob served nucleus the checkbox homonuclear be comes checked Natural abundance in percent of the coupled nu cleus If smaller than 100 WSolids1 automatically includes calculation of the spectrum of the uncou pled spin species Direct dipole dipole coupling constant in Hz Indirect spin spin coupling constant in Hz Anisotropy of the indirect spin spin coupling in Hz July 30 2015 Chapter 3 Spin Systems Alpha p 92 Azimuth angle in degrees of the internuclear vec tor in the principal axis system of the chemical shift tensor Beta p 92 Polar angle in degrees of the internuclear vector in the principal axis system of the chemical shift tensor LB p 32 Provides access to the convolution parameters for the current site To have individual convolution pa rameters for each site specify this in the Spectrum Default Parameters p 28 box Background In addition to the chemical shift anisotropy CSA the spectrum of a spin pair will also depe
49. Russell for making Inno Setup available http www jrsoftware org Jochen Kalmbach for demonstrating how to statically link against the Microsoft CRT and thus get rid of VCREDIST_X86 EXE http blog kalmbach software de chicks for demonstrating in his pdfp PDF tools how to establish Dynamic Data Exchange DDE with Adobe Acrobat Reader http www esnips com web PDFTools This manual has been produced using the MiKTEX http www miktex org distribution of IATFX in combination with the TeXstudio editor http texstudio sourceforge net or TeXnicCenter editor http www ToolsCenter org initially Irfan Skiljan s IrfanView http www irfanview com has been used to process bitmapped images and Inkscape www inkscape org for dealing with vector graphics The routines for complex matrix inversion are based on the code examples by PMD from MIT shown for the Santa Barbara Channel Experiment SBCX My prefered PDF viewer is the free PDF XChange Editor by Tracker Software Products Ltd http www tracker software com more powerful and reliable than the Adobe Acrobat Reader Thanks to Guy Bernard University of Alberta for pointing out a bug in my jcamp input I am grateful to Kirk Marat University of Manitoba for his help making the JCAMP Dx files produced by WSolids1 palatable to SpinWorks 5 2 Trademark Acknowledgements Microsoft MS is a registered trademark and MS DOS MS Word and MS Window
50. Spin System Parameters Le changing the portability parameter in the master INI file makes WSolids1 portable or non portable 4 16 2 Default Output File Format OutFile FILES DutFile 1 The parameter OutFile in the FILES section of the INI file preselects the standard output format of spectra Currently the value of OutFile an integer will correspond to the following file formats see Save Spectrum p 22 for details OutFile Format 1 WinNMR 2 Topspin 3 Solids 4 ASCII file 5 JCAMP DX format 4 16 3 Number of Triangular Intersections POWDER NT Document NT 32 The parameter NT in the DOCUMENT section of the INI file determines the number of triangular intersec tions on the face of an octahedron shown in the figure below for NT 4 In the POWDER algorithm by Alderman Solum and Grant the frequencies and intensities are calculated at triangular intersec tions For a given value of NT there are 2NT 1 different orientations Usually NT 32 is a good compromise between speed of calculation and accuracy The figure below illustrates the effect of changing NT from 8 top to 32 middle to 256 bottom Note that for NT 32 there are small ripples at the low frequency side of 22 and also close to 911 and 633 while the spectrum for NT 256 is very smooth July 30 2015 Chapter 4 Spin System Parameters 5 150 ppm D W Alderman M S Solum D M Grant J Chem Phys 1986 84 3717
51. WSolids1 Solid State NMR Simulations USER MANUAL Klaus Eichele July 30 2015 July 30 2015 Contents 1 Getting Started 1 IL a A NN 3 li Purpose oh ihe fh coca ca aa a ar 3 LLZ Besten cir a AA 4 Asse Liges o a wire ah ee ed na ee a i 4 e Ml A ERA 5 A EAN 6 I3 Royin RUSOS lt a a A A be ee ees a 7 LL Toron Lee Faller 2 een Ro ra A 7 132 Version 12022 06032014 oa ne ee eh ewe eh hee e ae 7 ToS Verion 1202 BIENEN zur 0 ee pe ee PR ER ee ee we PO EE 7 134 Version 12013 LOL 2012 so ee ie ee ee a de 8 doo Versor LAOS SUZ 20 UE ois stu ca ak Pa ER pee oe 8 lea verion LeU SB QUI on to a ce a kannt na 8 13 Version 1203102082010 u ee Od ae eae oo RE oa 8 lan VEO LA ULLOA Ra ee Se ene ES 9 Las Version LIQ IS 02102009 0 cee Ee PEE EN dede eRe EES 9 1340 Version 1 19 12 QUISO urn a id ie 9 LS IL Version LISO WOLA ana oot ee ee aa an a ae a Oe 9 13 12 Version 1192 PIUSE oo ok ce ee a ee ee he ed BE e 9 Lada version LAU US 2 2 at ea oO ee RA Gee oe ee a 9 LATE version 17ER 2er a eae bo Oe oe a 9 ala verion ly aa TUIO rennen au ES 10 1 3 6 Version 1 1721 GOR oo eee Ee BEE dede eae ES 10 e A en ee ne RE RR eb eee ae 10 LAO Vello DIG secre 2 oe ae A ee eee a ar ae EO 10 14 Multiple Document Interface MDI 2 2 2 ee 12 14 1 The Multiple Document Interface o qc ecca 24842 cama osas 12 142 Menu Management s zz cocos cons bee ran a 12 Ua Keyboard ai nce ee een nen Pa pa aa eee ee
52. X Y plane Finally y is the angle between the y axis and the line of nodes 4 11 Electric Field Gradient Tensor A quadrupolar nucleus S with nuclear spin S gt 1 2 is subject to an interaction of the nuclear quadrupole moment eQ with the component of the electric field gradient EFG along a particular direction V egj The Laplace equation requires that the trace of the EFG tensor is zero In addi tion the EFG tensor is symmetric hence consists only of 5 independent components In its principal axis system PAS XYZ the EFG tensor is diagonal and can be characterized by the three principal components Vxx Vyy Vzz In nuclear quadrupole resonance NQR the principal components are labelled according to this convention Vzz gt Vvy gt Vxxl Because of the trace of zero only two independent parameters are required to characterize the mag nitudes of the principal components and these are usually chosen to be Vzz and the dimensionless asymmetry parameter 7 The product of Vzz and the nuclear quadrupole moment is known as the quadrupolar coupling constant x eVzzQ _ egzzQ h h Vxx Wy Vzz Thus 7 is constrained to values between 0 and 1 The quadrupolar coupling constant should not be mixed up with the quadrupolar frequency observed in NOR experiments 4 12 Central Transition CT and Satellite Transitions ST For a quadrupolar nucleus with a nuclear spin greater than 1 2 as observed nucleus one can sele
53. Z oaaae Has ar e e SEES EELS 10 ESA A 10 1 4 Multiple Document Interface MDI oo ooooocooococoo oo 12 141 The Multiple Document Interface o ooa ee a e 12 2 1 July 30 2015 Chapter 1 Getting Started 142 Menu Management o o aa a a Di 4 143 Keyboard Interface 2 2 2222 Hau san ana namen a ai 1 5 Keyboard Accelerators 2 July 30 2015 Chapter 1 Getting Started 1 1 Introduction 1 1 1 Purpose of the Program WSolids1 is a program for the visualization and analysis of processed one dimensional solid state NMR data It is a simulation package initially developed at the Department of Chemistry p 3 Dalhousie University p 4 Halifax Canada in order to deal with the multitude of interactions observed in NMR spectra of static or spinning solid samples The initial versions have been written in C using Borland C 4 5 However in spring 2008 the developments or the lack of such at Borland made me change my programming tools to Microsoft Visual C 2008 Express Edition Not that this development environment has everything that I would need to work efficiently but it is for free it s like they give you a free car without a seat for the driver it s workable but a bit bumpy at times WSolids1 succeeds its earlier FORTRAN version Solids Although there are several general purpose programs or libraries available to calculate many in teractions and for many different experiments the
54. a 13 19 Keyboard Accelerators 2 223 2 2 bee See de ira 14 2 Menus 15 21 MIME 222 ida a Ras irre 17 211 New Dosumentke 44 002 244 Loe dy Pee de ne Se ieee enon eae 17 LLL DE VEO Rs PES ee Be MaRS oS er 17 2 13 pen Pec u se a war bea ee hee ee eet a ede DA a 18 214 Openas Calculated Spectrum c o ecne ie ass ea in 22 LLS Open Woolies Document at eesi sen Shee ea een 22 2 16 pen Woolde Spindystem osos cack san HR a nn 22 ZT CARO SOCEM 2 2 205 a idas ne Bhd ee ee a es 22 218 Save Woolids Document p e e oep ce ann e en ae 23 LLO Save Woolids Spit System 2 2 ccs 0 e A eo Oe OE a 23 Sle Repel ce a ee na EE ERS OS a Ee eS 24 AA A eed a Gee a eS erent e Sw 27 po tl Mena a 4 04 26444 ede ee eae eee Chee es ara ag 28 22 1 Spectrum Default Parameters 4564 cb sew eb ee ee eee as 28 22 2 O lia e u ee II 32 iii July 30 2015 Contents 2 3 2 4 4 4 4 5 4 6 4 7 4 8 4 9 4 10 223 DIES Mode seess a a en pe en eg 34 Da NA E dr R ga aa re E e N a ia ee 35 220 Select Calculation Medel eras cs 2 ewe e EH e ee ee 36 Pee EO EE e u pt e re eS ee TE ee Wee De ia 37 227 Kalculale ocios 2 aaa a ad a a aa A 38 228 Ally serien nenn 38 DE CPE ae a en ee are 4 38 2 240 Cycle Opon sess dbest ne nasse hen ie 38 VPlenebiant a aa ke Gye eek kL ORE Pee ee be eee een an 39 23 DOGS cono RES a POSER RS nee 39 Oe OWNER 6 aw tad eee a dele Teoh mene ad he ae As 40 Tools MENA 2 2 4 au i da ene a eee eas 4
55. acqu procs acqus 1r ti or Zrr fid or ser outd pulseprogram title Those parts of the path name written in red letters are fixed names that are required by TopSpin XWinNMR A data set of name lt name gt consists of one or more spectra each characterized by its experiment number lt expno gt an integer Each spectrum can have different processed data stored in the pdata subdirectory under a specific processing number lt procno gt an integer that is usually 1 In order to be recognized by WSolids as TopSpin XWinNMR file the data files need to adhere to the following format e 1rin binary floating point format needs to be present e procs needs to be present in the same directory and acqus two levels higher both are ASCII parameter files of variable record length and start with JCAMP DX format the acqus file contains the parameters SFO1 SW_h 01 AQ mod BYTORDA TD DECIM DSPFVS NC NUCLEUS and procs contains OFFSET SI XDIM BYTORDP NC proc Bruker WINNMR Generic This was the file format used by BRUKER s WIN NMR version 4 0 1D version and is still produced by Bruker s GetFile utility if conversion of Aspect files is selected basically the parameter files are in binary format In order to be recognized by WSolids1 as a generic WINNMR file the data files need to adhere to the following format where eee stands for the three digit experiment number and ppp for the three digit processing number each zero
56. ally we use the following conventions e the NOR notation is used for labelling the axes of the EFG tensor Vzz gt Vyy gt Vxx e the orientation of the field is given by the polar angle beta wrt Vzz and the azimuth alpha the angle between the projection of By into the Vxx Vyy plane and Vxx cf Abragam e direction cosines of the shielding tensor with respect to the EFG frame are obtained via the Euler angles following Arfken s convention with the initial alignment 11 XX 22 YY 33 ZZ Figure 3 4 shows an example for the successful simulation of a spectrum of a quadrupolar nucleus that shows the combined effect of chemical shift anisotropy and quadrupolar interaction in a powder sample It is the 133Cg NMR spectrum of cesium cadmium thiocyanate CsCd SCN 3 and the results have been published in Cesium 133 NMR Study of CsCd SCN 3 Relative Orientation of the Chemical Shift and Electric Field Gra dient Tensors S Kroeker K Eichele R E Wasylishen J F Britten J Phys Chem B 1997 101 3727 3733 DOI 10 1021 jp970043a July 30 2015 Chapter 3 Spin Systems References 1 The first order expression is taken from Amoureux s treatment which follows Abragam and Taulelle Amoureux Fernandez Granger In Multinuclear Magnetic Resonance in Liquids and Solids Chem ical Applications Granger Harris eds Kluwer Academic Publishers 1990 Ch 22 p 409 2 The second order expression is taken from G H St
57. at abund 14 05 because 14 05 of 87 25 corresponds to 12 26 in total Implementation Details For an introduction see for example the following reference and the literature quoted there in K Eichele R E Wasylishen J Magn Reson A 106 1994 46 56 DOI 10 1006 jmra 1994 1005 Furthermore this article describes the technique of analyzing spectra using the dipolar splitting ratio method and outlines the background behind the program DSR This model employs the POWDER space tiling and interpolation procedure Figure 3 2 shows an example of the succesful simulation of a spectrum arising from the combined effect of chemical shift anisotropy and homonuclear dipolar coupling in a powder sample It is the 31P NMR spectrum of tetraethyl diphosphine disulfide shown as absorption and first derivative spectrum and the results have been published in Phosphorus 31 NMR Studies of Solid Tetraethyldiphosphine Disulfide A Reinvestigation of the 91B41P Spin Spin Coupling Tensor K Eichele G Wu R E Wasylishen J E Britten J Phys Chem 1995 99 1030 1037 DOI 10 1021 j100003a028 July 30 2015 Chapter 3 Spin Systems Dipolar Chemical Shift A2 AX a ele amp s al 3 S S gt o 7 Figure 3 2 Experimental and calculated 91P NMR spectra of a static powder sample of tetraethyl diphosphine disulfide 54 July 30 2015 Chapter 3 Spin Systems 3 3 Static Dipolar Chemica
58. ated i e high spinning frequency limit cleus Note Don t forget to define the observed nucleus this is re quired to evaluate the Larmor frequency of the quadrupolar nu Note There can be a negative magnetogyric ratio a problem p 48 if the observed nucleus has Parameter Purpose Coupled to p 91 N A p 91 Tie to previous site p 88 Speedy calculation p 97 Delta iso p 88 Alpha p 92 Beta p 92 D p 91 J p 92 Specifies the quadrupolar nucleus the observed nu cleus is coupled to Only heteronuclear coupling will be considered Natural abundance in percent of the coupled nucleus Ties parameters to those of the previous site If checked less crystallite orientations are included into the calculation also the averaging over one ro tor period is done in 10 steps rather than 5 steps Isotropic chemical shift in ppm Azimuth angle in degrees of the internuclear vec tor in the principal axis system of the electric field gradient tensor Polar angle in degrees of the internuclear vector in the principal axis system of the electric field gradi ent tensor Direct dipole dipole coupling constant in Hz Indirect spin spin coupling constant in Hz July 30 2015 Chapter 3 Spin Systems Delta J p 92 Anisotropy of the indirect spin spin coupling in Hz Chi p 96 Quadrupolar coupling constant in MHz Eta p 96 Asymmetry parameter o
59. ated spectrum should have the same size and limits this option will be useful Also changing the referencing p 45 of the experimental spectrum could also necessitate this reinitialization Observed Nucleus The kind of observed nucleus is selected in the Spectrum Default Parameter p 28 box In many cases the actual selection here is not important Exceptions are for example e Observation of a quadrupolar nucleus here the nuclear spin quantum number is important e If a quadrupolar nucleus is coupled to the observed nucleus the ratio of magnetogyric ratios of both nuclei is used to calculate the Larmor frequency of the quadrupolar nucleus Spectrometer Frequency The parameter SF defines the spectrometer or Larmor frequency in MHz and is set in the Spectrum Default Parameter p 28 box Actually this value corresponds to the frequency of the chemical shift reference compound and thus not to SFO1 as used in Bruker parameter files On newer versions of TopSpin BFO1 should cor respond to this value if the IUPAC 2001 recommendations of relative frequencies have been imple July 30 2015 Chapter 2 Menus mented If your experimental spectrum has been re referenced use SF of the processing parameters note that the DisMSL DISNMR acquisition parameter SF has a different meaning If an experimental spectrum is available this parameter is set by default and should not be changed This value is used in the conversion of ppm
60. auss J Chem Phys 1964 40 1988 DOI 10 1063 1 1725432 3 Related papers K Narita J I Umeda H Kusumoto J Chem Phys 1966 44 2719 DOI 10 1063 1 1727118 J F Baugher P C Taylor T Oja P J Bray J Chem Phys 1969 50 4914 DOI 10 1063 1 1670988 lolx File Simulation Tools Window Help Alsr s2asommz ES Static Quadrupolar Nucleus CSA Coupling 2nd order Site 1 Chi MHz Rel Intensity A Eta _ He to previous site Y CT ST Convention STANDARD Coupled to Delta 22 ppm Spin 12 Delta 33 ppm p Hz ES Alpha deg J Hz HAH Beta deg Alpha deg Gamma deg Beta deg Figure 3 4 Experimental and calculated Cs NMR spectra of a static powder sample of cesium cad mium thiocyanate July 30 2015 Chapter 3 Spin Systems 3 5 Static Three Spin System AMX this calculation has not been verified yet use at your own risk 61 July 30 2015 Chapter 3 Spin Systems 3 6 MAS Chemical Shift Anisotropy HB Chemical Shift Anisotropy Site 5 Rel Intensity LUKN l Tie to previous site Convention STANDARD v MAS freq Delta 11 Delta 22 Delta 33 This model calculates the spectrum of a powder sample spinning at the magic angle showing chem ical shift anisotropy only Parameter 1000 000 100 000 ppm 50 000 ppm 100 000 ppm Purpose Rel Intensity p 88 Tie to previous site p
61. c field induction strength Bo to a specific value in Tesla this dialog box calcu lates the corresponding frequency of the reference compound for the isotopes of the selected element The default value causes the H 1 peak of TMS to have a resonance frequency of 100 00 MHz The default value of the magnetic field is retrieved from the INI file and can be changed there If there is no INI file or no corresponding entry in the INI file the default value is 2 348661 T For information on the source of the nuclear data refer to Table of Nuclear Properties p 42 2 4 4 Convolute This option available from the Tools Convolute menu enables one to apply additional Convolution p 32 to experimental or calculated spectra For example if a calculation takes a long time it is advisable not to include any convolution into the calculation itself but to save the calculated spectrum to a file and apply convolution separately afterwards 2 4 5 Scale Spectrum This option available from the Tools Scale spectrum menu enables one to multiply a specific spec trum by a given factor For example if one exports a spectrum from WinNMR as ASCII file the spectrum may look jagged because WinNMR converts the intensities into integers and the spectrum did not take advantage of AA July 30 2015 Chapter 2 Menus the full dynamic range This digitization loss can be circumvented by scaling the intensities up by some factor
62. cause it would only allow for Lorentzian line shapes Instead the line shape is convoluted after the actual calculation July 30 2015 Chapter 3 Spin Systems a matrix describing the rates of transfer of magnetization between sites corresponding to different values of mg Usually the matrix also includes Tig but here we put it in front of the matrix in order to be able to deal with the transition probabilities Rj more easily in case they deviate from the value derived from the expressions below The diagonal elements of R Rm m are the appropriate row sums 1 2 89 25 3 gt 1 14 Ta WFP ur 2m 1 S m 1 SF m Rin mt1 3 6 in 2 25 1 2S 3 3 6 S m S m 1 S m 1 Stm 2 R 7 Br 2 25 1 2S 3 67 mim Rinm e L Rinm 3 8 mi where according to Tig Rm 1 Tn this element is related to the average life time Tn of state m E g for different spins this matrix is S 3 2 2 1 1 3 S 1 1 0 4 Bo Der 3 1 1 1 s 2 4 2 o a u 10 10 10 E 1 1 0 1 o 2 2 2 2 2 2 10 10 10 1 1 de 4 1 w u 2 2 2 3 1 1 3 0 z 3 7 5 3 1 1 3 5 S 5 2 3 2 23 2 2 2 5 120 80 40 2 64 64 64 0 0 0 23 80 184 32 72 0 0 2 64 64 64 64 1 40 32 144 0 72 0 2 64 64 64 64 1 0 72 0 144 32 40 2 64 64 64 64 3 0 0 72 32 184 80 2 64 64 64 64 5 40 80 120 2 0 0 0 64 64 64 Ss 3 3 2 1 0 1 2 3 7 5 2 ale 3 2 0o 0o o0 0 5 4 2 3 4 1 1 4 0 0 2 5
63. complex July 30 2015 a Chapter 3 Spin Systems 3 13 VAS Dipolar Chemical Shift AB VAS Homonuclear Two Spin System AB Site 3 1500 00 Hz Rel Intensity 60 000 Hz _ Tie to previous site Delta J 0 000 Hz Convention STANDARD y Alpha 10 000 deg VAS angle 60 000 deg Beta 40 000 deg Nucleus A Nucleus B Delta 11 100 000 ppm Delta 11 100 000 ppm Delta 22 50 000 ppm Delta 22 50 000 ppm Delta 33 100 000 ppm Delta 33 100 000 ppm Alpha 0 000 deg Alpha 0 000 deg Beta 20 000 deg Beta 20 000 deg Gamma 0 000 80 deg Gamma 0 000 deg Spectrum of a powder sample under variable angle spinning containing a homonuclear spin pair using AB equation Background In addition to the chemical shift anisotropy CSA the spectrum of a spin pair will also depend on the direct dipolar coupling and potentially the indirect spin spin coupling between both nuclei Because both the CSA and dipolar interaction are tensorial interactions the actual line shape also depends on their relative orientation Spinning the powder sample rapidly about an axis that forms an angle different from the magic angle with respect to the external magnetic field the resulting lineshape will look like that of a static powder sample but scaled by a factor that depends on the spinning angle This scaling factor ranges from 1 0 for spinning parallel to the field to 0 5 for spinning perpend
64. cross terms Figure 3 13 shows an example of the simulation of a Sn spectrum arising from coupling of tin to vanadium the small feature in the center was produced by considering just for fun not only V but also V In order to convert the necessary parameters for one isotope to those of the other isotope for use with the Tie to previous site p 88 feature I have used e for the spin spin coupling constant y V 50 y v 51 J V 51 0 379 x J V 51 July 30 2015 Chapter 3 Spin Systems e for the relaxation rate the rate of quadrupolar relaxation is given by 1 3127 28 3 Tio 40 S2 2S 1 where see electric field gradient p 96 eVzzQ _ egzzQ h h In molecules which differ only in having different isotopes of the same element the electric field gradient at that elements nuclei eqzz will be close to identical for the isotopes while the rotational correlation time for molecular motion will scarcely be altered by the substitution at least for heavy isotopes where the relative differences between the masses of the isotopologues will be small The equation can thus be simplified to 1 Ta OF S 1Q where f S Sen values of S and corresponding values of f S are 3 5 7 9 f S 5 133 032 0 2 0 136 0 074 0 0379 Hence the value of S is extremely important when comparing the relaxation behaviour of nuclei of different S an increase in S having the opposite effect to an increase i
65. ct calculation of the central transition 1 2 1 2 spectrum only CT of the satellite transition m m 1 with m 4 1 2 spectrum only ST or of all transitions CT ST Action July 30 2015 Chapter 4 Spin System Parameters IN IS Calculates the total spectrum consistin of central transition and satellite transitions N Calculates spectrum only including the central transition Note that quadrupolar nuclei of integral spin don t have a central tran sition IS Calculates spectrum only including the satellite transitions This wouldn t calculate anything therefore the default action is to calculate the central transition 4 13 Variable Angle Spinning Angle The VAS angle specifies the angle between the direction of the external static magnetic field and the spinning axis 4 14 Spinning Frequency The spinning frequency is required in Hz Although the sense of rotation does not affect the spec trum valid values are limited to postive numbers WSolids1 allows to have different spinning fre quencies for different sites although this doesn t make sense physically This design flaw has been remedied in WSolids2 4 15 Speedy Calculation Some calculations are quite time consuming In such cases it is possible to select Speedy calculation in which case only 1 16 of the orientations will be included This is usually sufficient to reproduce the gross features of the line shape but this gai
66. der series of products a mechanism called Dynamic Data Exchange DDE to open a PDF file at a specific position For ages the name of the DDE server has been acroview However with the introduction of Acrobat Reader X this tradition has been broken on purpose breaking many applications that rely on this mechanism WSolids1 should be able to work with older versions of the Acrobat Reader as well as with the acroviewR10 DDE server of Adobe Reader X Because I have been quite dissatisfied with the Adobe products from Reader 5 onwards I am using a different PDF viewer and will not always check whether Acrobat is still working My prefered PDF viewer is the free PDF XChange Editor the successor of PDF XChange Viewer by Tracker Software Products Ltd http www tracker software com more powerful and reliable than the Acrobat Reader The opening of a PDF file at a specific position is achieved via command line parameters Another viewer used by people working with IATEX is the Sumatra PDF Viewer http blog kowalczyk info software sumatrapdf also supported by WSolids1 Other PDF viewers such as FoxIt or NitroPDF do not support DDE or command line parame ters as far as I know July 30 2015 Chapter 2 Menus 2 7 Known Problems Usually I will try to keep the content of this page as small as possible e There is a problem in the MAS Spin 1 2 Spin S Diag p 67 model when the observed nucleus has a negative magnetogyric
67. ds this allows the simulation of MAS spectra in the MAS Chemical Shift Anisotropy HB p 62 and MAS Dipolar Chemical Shift A2 AX p 64 models at slower spinning speeds where the number of spinning side bands exceeds the limits of the Herzfeld Berger tables This functionality was also added to the VAS Dipolar Chemical Shift A2 AX p 76 model that used to calculate spectra in the high spinning speed limit only new feature the title of the spectrum window can be longer than 30 characters in the Display Options p 39 dialog new feature the spectrum window remembers the file type if a spectrum has been read previ ously and sets this as default extension for the current session new feature added export p 22 of spectra in ASCII and JCAMP DX format new feature the location of the INI file p 97 has changed in the pograms directory for the portable version or in the user s documents directory new feature Table of Nuclear Properties p 42 lists Larmor frequency and frequency of the chemical shift reference compound Periodic System of Elements p 44 lists the frequency of the chemical shift reference compound the sign of Larmor frequency and reference frequency reflect the sign of y the form field for entering BO is now a combo box that allows entering a field or selecting one from a list new feature added support for PDF XChange Editor by Tracker Software Products Ltd http www tracker software com as P
68. e For an A2 spin system the isotropic part of the indirect spin spin cou pling p 92 does not contribute to the spectrum but the anisotropy of the indirect spin spin coupling does 4 9 Polar Angles 033 YIs 022 a 011 Polar angles are used to define the orientation of a vector in a three dimensional Cartesian coordinate system x y z as shown in this figure describing the orientation of the internuclear vector r in the July 30 2015 Chapter 4 Spin System Parameters principal axis system of the chemical shift tensor The azimuthal angle alpha is the angle between the x axis d11 and the projection of the vector into the x y plane d11 d22 equatorial plane The polar angle beta is the angle between the vector and the z axis d33 pole The polar angles are closely related to the type of Euler angles p 93 used by WSolids1 Because the dipolar interaction is axially symmetric the two polar angles are sufficient to describe the relative orientations of chemical shift and dipolar interaction For more general cases the set of three Euler angles is required 4 10 Euler Angles The triplet of Euler angles a y is useful to describe rotations or relative orientations of orthogonal coordinate systems Unfortunately their definition is not unique and in the literature there are as many different conventions as authors The convention employed here is one of the more common ones All ro
69. e a A AA A ELMO ANEP AAA E 4 23 Options Menu i ses e lt lt 0 0 0 e a en ea a Zod DispleyOptine coca ee a o RPh eee DA AAN a a o Wag ae A hen eee ee a ee 24 Tools M mu cis a hk a a Ee el oe EN A ee 241 Dipoler Coupling Constant soos Haare bee ee eee 242 Iableof Nuclear Properties lt 64404440508 ph babe uds dS 243 Periodic System tt Elements co p na an ee ee te ee 244 Comvolite e kee 8 van au aan ea 220 SEAN IAN 246 AddConstant aae una nn nn nn nn 247 Beyeissspeiinin a a a ae rain 248 Absolute Value ss am 254055 ce Gea ne Pee ana heran ss 249 Referentin occ ic na BR ee ee eaa 25 Window Meni serena sama oo we ae ee eee OE ehe 26 Help NIA IA OS See MG ae end 2 7 Known Problems lt o oe ee ee eee le eee le ce cece lee 8 et The menu system of WSolids1 consists of the following pop up menus WSolids1 File Simulation Options Tools Window Help Mes elste File p 17 File and document management Simulation p 28 Simulation models and parameters management Options p 39 Change appearance set title Tools p 41 Calculational and processing tools Window p 46 Multiple document management Help p 47 Help and program version information 16 July 30 2015 Chapter 2 Menus 2 1 File Menu The File pop up menu consists of the following items WSolids1 File Simulation Options Tools Window New Spectrum Window Opens a new spectrum window p
70. e of the description of features has already been formulated in the early nineties Nowadays with gigantic office software suites the user is certainly more accustomed to multiple documents etc but I guess it doesn t hurt to keep this description Also the look of WSolids1 is now archaic but remember I am a one man company and not making any money out of this software that I develop and maintain in the evening hours 1 1 3 License This program package can be used without any fee However if you find this program useful and publish results obtained by using WSolids1 we would appreciate a citation or acknowledgment of this program similar to WSolids1 ver 1 21 3 K Eichele Universit t T bingen 2015 Before reading on you may also want to have a look at our credits statement p 101 trademark acknowledgment p 102 copyright message p 102 and obligatory disclaimer p 104 4 July 30 2015 Chapter 1 Getting Started 1 1 4 Trouble Although WSolids1 has been tested and used both in house and by others it is always possible that errors exist Some errors may become apparent after detailed use on the wide variety of chemical systems It is the responsibility of the user to determine the correctness of the results If errors are noticed please notify us of your problems and the prescribed or suggested corrections so that others may benefit from the improved code Also suggestions for improvements are welcome
71. ecord length and start with JC AMP DX format the AOS file contains the parameters SFO1 SW_h O1 and FOS contains OFFSET Bruker WINNMR ASCII WinNMR is able to export spectra in ASCII format depending on the version of WinNMR slight differences arise The file starts with some parameters one on each line and is then followed by pure intensity data each point on its own line Here is the beginning of such a file Data file D NMR ASP3000 KOPOPH3 101001 TXT Starting Point 0 Ending Point 4095 Point Count 4096 Real Data SFO1 81 018000 MHz SF 81 023633 MHz Offset 444 735199 ppm Decim 0 Dspfvs O FW 100000 000000 Hz Sweep Width 83333 333332 Hz Hz Pt 20 345052 First Point 36034 061368 Hz Last Point 47299 271964 Hz First Point 444 735199 PPM Last Point 583 771308 PPM AQmod 2 5759 1961 Chemagnetics SpinSight The Spinsight data format consists of several component files all contained within one directory In order to be recognized by WSolids as SpinSight file the data files need to adhere to the following format e data this is a binary file which contains the actual NMR data The storage order is all real values followed by all imaginary values i e the data are unshuffled No formating end of row or end of file characters are present in this file e acq this is a text file describing the acquisition parameters used in acquiring the data file These parameters can also be used for a pre
72. enus frequency domain convolution with a Lorentzian peak requires N x N 1 multiplications unless a threshold p 31 value is specified Although considered part of the spectrum parameters rather than of the spin system access to con volution parameters is gained by editing the spin system Convolution also depends on the setting of the site dependent convolution p 31 check box in the Spectrum Default Parameter p 28 box Parameter Purpose GB LB mixing p 33 The GB LB mixing in percent determines the amount of Gaussian Lorentzian character of the convolution function 0 pure Gaussian 100 pure Lorentzian GB p 33 Gaussian broadening in Hz LB p 34 Lorentzian broadening in Hz Gaussian Lorentzian Mixing In the Convolution Parameters p 32 dialog box the Gaussian Lorentzian mixing determines the weighting of Gaussian and Lorentzian line shapes in the convolution subroutine A value of 0 corresponds to a pure Gaussian line shape a value of 100 yields a pure Lorentzian line shape In the case of mixed line shapes both Gaussian broadening GB p 33 and Lorentzian broadening LB p 34 must be specified but can be different Note If calculations are performed in the frequency domain Lorentzian line shapes require considerably longer computation times because their wings extend much farther than those of Gaussian peaks For time domain convolution both line shapes require the same time
73. er 2 Menus 2 1 3 Open Spectrum Open Spectrum Suchen in KOOPH2BU Om J 8 001001 F10 Zuletzt 002001 1R verwendete D 3 002001 F10 3 E 002001 TxT s E 003001 1R Desktop 003001 F1D E 004001 1R 3 004001 FID 005001 1R 3 005001 FID 999399 1r Eigene Dateien gs Arbeitsplatz Netzwerkumgeb Dateiname Dateityp The Open Spectrum item of the File p 17 pop up menu retrieves an experimental spectrum into 001001 1R Abbrechen X v Bruker 18 FID SER RR TXT the Spectrum Window p 17 having the focus If the currently active spectrum window already contains an experimental spectrum itis replaced by the new one If no active spectrum window exists a new spectrum window is created automatically Reading an experimental spectrum automatically changes the default parameters p 28 for the theoretical spectrum of course they can be modified afterwards Various formats of experimental spectra are recognized automatically by WSolids1 Please note that the file type option only determines which files are listed in the selection window and does not affect the way the selected file is treated WSolids1 will always rely on its own strategy to determine the file type Thus in order to be recognized the spectrum needs to follow a certain pattern as detailed below for each file format These are the file formats recognized by WSolids S
74. erm archival and exchange of spectroscopic data The main features 1 are e first non binary approach ever e vendor independent JCAMP is not owned by anybody e printable characters only important for e mail etc e reasonable compression rates long before LHARC etc did show up e extendable and open definitions to allow further improvements In my opinion this was a good idea in principle However in practice the standard is too unclear in several aspects thus writing an import filter for such data is a royal pain The advantage however is that WSolids1 using the JCAMP DX route can use any file format that Kirk Marat s SpinWorks ftp davinci chem umanitoba ca pub marat SpinWorks can process WSolids1 checks for the following parameters TITLE JCAMP DX with values of 4 24 5 00 or 5 01 DATA TYPE NPOINTS OBSERVE FREQUENCY FIRSTX LASTX XFACTOR DATA CLASS Currently only XY DATA are supported References 1 posting by Dr Michael Grzonka in the newsgroup bionet structural nmr Subject The JCAMP standard of spectroscopic data transfer a summary on 29 January 1996 2 McDonald Wilks Appl Spectrosc 1988 42 151 3 Davies Lampen Appl Spectrosc 1993 47 1093 4 Lampen Lambert Lancashire McDonald McIntyre Rutledge Fr hlich Davies Pure Appl Chem 1999 71 1549 DOI 10 1351 pac199971081549 Ij July 30 2015 Chapter 2 Menus Simpson SIMPSON A General Simulation Prog
75. ers belong to the spectrum window spectra at different spectrometer frequencies will require different broaden ing the actual parameters are accessible via the spin system 2 2 2 Convolution Parameters Convolution Parameters Site independent convolution parameters GB LB 0 Gaussian GB LB 100 Lorentzian GB LB mixing 0 000 GB 50 000 Hz LB 50 000 Hz amp MESES The convolution parameters determine the amount of line broadening added to the calculated spectrum The convolution parameters should not be mixed up with the LB GB parameters used in apodiza tion functions applied to experimental spectra Here they take into account the sum of all line broadening effects intrinsic to the sample and the spectrometer and processing Such effects can be inhomogeneity of the external magnetic field homonuclear dipolar couplings unresolved indirect couplings interactions with quadrupolar nuclei degree of crystallinity chemical shift dispersion insufficient decoupling power temperature gradients etc etc and finally the actual window func tion applied to the experimental data In short the convolution parameters represent all these effects in a phenomenological manner Convolution is done in the frequency domain rather than in the time domain Exponential multi plication in time domain requires for N points N multiplications in contrast the equivalent in the July 30 2015 Chapter 2 M
76. f the electric field gradient tensor 0 lt eta lt 1 LB p 32 Provides access to the convolution parameters for the current site To have individual convolution pa rameters for each site specify this in the Spectrum Default Parameters p 28 box Background The quadrupolar interaction at a quadrupolar nucleus causes its axis of quantization to be tilted away from the direction of the external magnetic field This also modifies the spatial dependence of the dipolar interaction so that magic angle spinning is not able to suppress the heteronuclear dipolar coupling in the spectrum of the spin 1 2 nucleus resulting in splittings and broadenings Similar effects can be transmitted through the indirect spin spin coupling If the nuclear quadrupolar coupling constant is on the same order of magnitude as the Larmor frequency of the quadrupolar nucleus the combined Zeeman quadrupolar Hamiltonian must be diagonalized at each orientation and averaged over a rotor period to calculate a theoretical spectrum The figure below illustrates the effect a speedy calculation spectrum at bottom has on the calculated spectrum 200 150 100 50 0 50 400 150 200 250 300 Hz Implementation Details Specifically we use the following conventions the NOR notation is used for labelling the axes of the EFG tensor VZZ gt VYY gt VXX Figure 3 8 shows an example for the succesful simulation of a MAS spectrum of a spin
77. file handling functions to use WinAPI exclusively should allow to create and read more files July 30 2015 Chapter 1 Getting Started 1 4 Multiple Document Interface MDI This topic provides some information about the Multiple Document Interface in general and its im plementation in WSolids1 Managing multiple documents is one of the key issues 1 4 1 The Multiple Document Interface The multiple document interface MDI has been designed for applications that need to simultane ously manage e more than one data set e more than one view of a data set In MDI there are two fundamentally different type of windows e The main window of an MDI application is called a frame window Frame windows usually have a title bar a menu a system menu a sizing border Minimize Maximize buttons The non client area of the frame window surrounds a portion of something called the applica tion workspace The workspace can be larger than the frame window s client area because a user can use scroll bars to scroll different portions of the workspace into view e An MDI applications workspace can contain zero or more child windows which are referred to as documents document windows or MDI children In the case of WSolids1 a doc ument window usually corresponds to a window with dual display of an experimental and a calculated spectrum We shall call such a document window a spectrum window In general
78. fixed factors Such a feature is useful if the spectrum is made up of a variety of different isotopologues and the site specific parameters differ only by ratios of nuclear constants Because such cases are rather rare the implementation here does not offer a high degree of sophistication There are a few points to keep in mind e More than one site needs to be available and this feature will not be available for the first site obviously e The simulation models for the sites tied together should be the same This is not checked Tying together different models may produce unexpected results e Once sites are tied together one cannot change the convention used for tensor components e Parameters not affected by the state of the Tie check box are grouped together with this check box in one shaded area all parameters outside this area depend on the state of the check box exceptions are e g spin quantum numbers 4 3 Convention Unfortunately there are many different conventions around in the literature for labeling the principal components of chemical shift tensors Most of the conventions have advantages for certain situations but drawbacks in others Often it is not obvious which convention has been chosen The collection given here attempts to summarize some of the most frequently used conventions 4 3 1 Standard Convention Principal Components 011 gt 077 gt 633 011 lt 022 lt 033 Isotropic Value diso 511 022 633
79. gn Reson A 106 1994 46 56 DOI 10 1006 jmra 1994 1005 This model employs the POWDER space tiling and interpolation procedure Figure 3 3 shows an example of the succesful simulation of a spectrum arising from the combined effect of chemical shift anisotropy and homonuclear dipolar coupling in a powder sample It is the 31P NMR spectrum of pentacarbonyl molybdenum bis diphenylphosphino methane shown as absorption and first derivative spectrum and the results have been published in Phosphorus 31 Solid State NMR Studies of Homonuclear Spin Pairs in Molybdenum Phosphine Complexes Single Crystal Dipolar Chemical Shift Rotational Resonance and 2D Spin Echo NMR Experiments K Eichele G Ossenkamp R E Wasylishen T S Cameron J F Britten Inorg Chem 1999 38 639 651 DOI 10 1021 ic9806232 July 30 2015 Chapter 3 Spin Systems Homonuclear Two Spin System AB QT m Figure 3 3 Experimental and calculated 3tP NMR spectra of a static powder sample of Mo CO dppm 57 July 30 2015 Chapter 3 Spin Systems 3 4 Static Quadrupolar Nucleus Static Quadrupolar Nucleus CSA Coupling 2nd order Site 4 Rel Intensity 0 120 100 000 0 000 _ Tie to previous site viCT viST Delta 11 Delta 22 Delta 33 Alpha Beta Gamma Calculates the static powder spectrum of a quadrupolar nucleus considering the quadrupolar in teraction up to second
80. he spectrum the chemical shift matrix is constructed and added to the relaxation matrix the result is inverted and the probabilities evaluated This is a time consum ing process therefore limit the spectrum limits to the region of interest and only use as many spectrum points SI as necessary Parameter Purpose Rel Intensity p 88 Relative intensity of this site in percent Tie to previous site p 88 Ties parameters to those of the previous site Coupled to p 91 Specifies the quadrupolar nucleus the observed nu Delta is J p 92 d cleus is coupled to Only heteronuclear coupling will be considered o p 88 Isotropic chemical shift in ppm Indirect spin spin coupling constant in Hz Residual dipolar coupling in Hz see model MAS Spin 1 2 Spin S Stick p 70 81 July 30 2015 Chapter 3 Spin Systems Reference SF The residual dipolar coupling is field dependent The value entered for d in the edit box is for the spec trometer frequency entered as reference frequency of the observed nucleus in MHz Spectra at dif ferent fields can be calculated from the same set of parameters based on different observe frequencies Tiq The spin lattice relaxation time in seconds of the coupled nucleus due to the quadrupolar interaction at the coupled nucleus modify transition proba Provides access to the individual matrix elements bilities Rjx representing the transition probabilities
81. hieve this In combination with such an excellent file manager as TotalCommander shareware well worth the money the conversion is as easy as hitting a custom button on a toolbar This section will describe one way to achieve this First download a Windows version of the 1ibxm1 package xs1tproc mentioned above is part of this download In particular you will need the following libraries 1ibxm12 libxslt iconv zlib In principle you can unpack the files in any location you need the files in the bin folders of the zip archives If you have administrator rights program files libxml could be a good place for these files otherwise own documents libxml For some reason xsltproc gobbles up the HTML output if the Mozilla version of the XSL file is used with the IE9 version the resulting HTML works with the Mozilla browsers and IE9 Using the command line you could perform conversions like this c Program Files x86 libxml xsltproc exe output mydocument htm mydocument xml July 30 2015 Chapter 2 Menus Secondly if you want to use Totalcommander you can add a custom button to the toolbar Place the mouse pointer on the toolbar hit the right mouse button and select change Enter the information as shown below adjusting the path to xs1tproc exe to your installation Total Commander x64 8 01 Klaus Eichele E Files Mark Commands Net Show Configuration Start 2 82 Ow Ss o Ba BS Hs 8 a 0148 afa ee 821 58
82. ian files would involve the implementation of all the nec essary processing steps Because there is already nice processing software available freely namely Kirk Marat s SpinWorks see information on JCAMP DX p 21 my efforts will be reduced to en suring that users of SpinWorks will be able to read the JCAMP DX files exported in SpinWorks into WSolids1 2 1 4 Open as Calculated Spectrum Besides reading an experimental spectrum this feature allows to read a second spectrum into the memory reserved for the calculated spectrum for the purpose of dual display Carrying out a calcu lation will replace this spectrum by the calculated spectrum in memory not on disk 2 1 5 Open WSolids Document The WSolids document is a self contained document providing experimental and calculated spectra as well as spin systems with their required parameters 2 1 6 Open WSolids Spin System This menu action retrieves only the spin system part from a WSolids1 XML document You have the choice of discarding all already existing spin systems or of adding to them 2 1 7 Save Spectrum The Save Spectrum item of the File p 17 pop up menu saves a spectrum from the active Spectrum Window p 17 If the spectrum window contains only an experimental spectrum the experimental spectrum is saved If there is a calculated spectrum available the calculated spectrum is always saved July 30 2015 Chapter 2 Menus There are several output formats availab
83. icular to the magnetic field Figure 3 12 shows an example for the succesful simulation of a spectrum arising from the combined effect of chemical shift anisotropy and homonuclear indirect and dipolar coupling in a powder sam ple under fast variable angle spinning It is the 9P NMR spectrum of fac OC 3 7 phen Mo y Ph2P PPh2 and the results have been published in Phosphorus 31 Solid State NMR Studies of Homonuclear Spin Pairs in Molybdenum Phosphine Complexes Single Crystal Dipolar Chemical Shift Rotational Resonance and 2D Spin Echo NMR Experiments K Eichele G Ossenkamp R E Wasylishen T S Cameron J F Britten Inorg Chem 1999 38 639 651 DOF 10 1021 ic9806232 July 30 2015 Chapter 3 Spin Systems VAS Homonuclear Two Spin System AB 1650 000 293 000 Herzfeld Berger Figure 3 12 Experimental and calculated 91P VAS NMR spectra of a molybdenum phosphine com plex July 30 2015 Chapter 3 Spin Systems 3 14 HR Spin 1 2 Coupled to Quadrupolar Nucleus Relaxation HR Spin 1 2 Coupled to Quadrupolar Nucleus Relaxation x Site 1 Rel Intensity 00 000000 F Tie to previous site Delta iso 0 000000 ppm Coupled to v 51 y 500 000000 Hz Spin 712 0 000000 Hz Tiq 0 010000 s Reference SF fl 00 000000 MHz I modify transition probabilities w te Rates of Magnetization Transfer Transition Probabilities M2 512 312 1 2 1 2 3 2 5 2 7
84. ins un affected The rotation matrix to describe this operation is given by cosy siny 0 R y siny cosy 0 0 0 1 The combined effect of these three rotations is given by this transformation matrix cos amp cos Bcos y sin sin y sin cos cos y cosesiny sinfcosy Rz Y Ry B Rz a cosacos Bsin y sinacos y sinacos Bsiny cosacos y sin siny cos sin B sina sin f cos B Note This type of rotation about sequentially newly generated axes produces the same result as rota tions by the same angles about the fixed original axes if the order of angles is reversed Rz a Ry B Rz y cf Mehring s book appendix 1 References 1 M Mehring Principles of High Resolution NMR in Solids 2nd ed Springer Verlag Berlin 1983 4 10 2 Determining Euler Angles Given the relative orientations of two coordinate systems how does one go about determining the Euler angles relating them First one needs to decide which coordinate system to take as the reference coordinate system X Y Z and which one as derived coordinate system x y z Because the Euler transformations allow to switch between coordinate systems easily it does not matter which one is selected July 30 2015 Chapter 4 Spin System Parameters The angle is simply the angle between the z axes of both coordinate systems The angle is the angle between the X axis of the reference coordinate system and the projection of z into the
85. iodic system 44 polar angles 92 105 July 30 2015 Index ppm 30 XWINNMR 20 problems 48 XWinN MR 19 program version 47 Q 42 quadrupolar 58 61 65 67 70 74 80 R 41 referencing 45 reinitialize 29 relaxation 80 report 24 reverse spectrum 45 revision 7 rotations 93 95 satellite transition 96 scaling 44 SeaMonkey 24 settings 40 SEF 29 shielding 90 shift 90 SI 30 Simpson 22 simulation 28 site 35 37 SOLIDS 21 spectrometer frequency 29 spectrum 17 18 22 28 30 44 45 spectrum size 30 spectrum window 18 22 spin 42 spin pair 52 55 58 64 65 67 70 74 76 78 spin system 22 23 35 36 spinning 97 spinning angle 97 SpinSight 20 standard 88 SVG 24 tie 88 tools 41 TopSpin 19 trademarks 102 trouble 3 Varian 22 VAS 76 78 97 warranty 104 window 46 window title 39 WinNMR 19 20 22 x axis units 39 XML 22 24 XSL 24 106 July 30 2015
86. is in the Spectrum Default Parameters p 28 box Background If the nuclear quadrupolar coupling for a quadrupolar nucleus is sufficiently large MAS cannot remove its effect on the line shape of the central transition and causes second order broadening with characteristic lineshapes as well as a second order shift In order to obtain correct chemical shifts July 30 2015 Chapter 3 Spin Systems By E e Simulation Tools Window Help lej xj MAS Quadrupolar Hucleus 2nd order x Site 1 Rel Intensity AMI R LB _ Te to previaus she MHz Chi Eta Delta iso Coupled to P 31 id Spin 1 2 N A T gt gt N e nN gt o i b 3 y a ml wi Figure 3 7 Experimental and calculated Mo MAS NMR spectra of a powder sample of a molybde num phosphine complex for the quadrupolar nucleus simulation of the spectra is required Optionally indirect coupling to a heteronucleus can be added note quadrupolar interaction if any is neglected for the coupled heteronucleus Implementation Details Specifically we use the following convention e the NOR notation is used for labelling the axes of the EFG tensor VZZ gt VYY gt VXX Figure 3 7 shows an example for the succesful simulation of a MAS spectrum of a quadrupolar nucleus that shows the combined effect of quadrupolar interaction and spin spin coupling to a spin 1
87. it the spectrum default parameters for the cur rently active spectrum window Edit the site specific parameters for each available site Edit the convolution parameters Perform calculation of a theoretical spectrum and display the result The Options pop up menu consists of the following items WSolids1 File Simulation Options Tools Window Help AS Display options Settings SF 81 033 MHz Item Purpose Display Options p 39 Settings p 40 2 3 1 Display Options Invokes a dialog box with parameters that deter mine the properties of the spectrum window Invokes a dialog box with some program settings x Axis Y Scaling absolute units Hz ppm simulation balanced pts C sec Colours Window title max 200 defined point SF 81 033 MHz Controls Background Select Select Exp spectrum Ei Select Calc spectrum I Select ea July 30 2015 Chapter 2 Menus This dialog contains parameters to adjust the spectrum window properties e X Axis this group allows to switch between the X axis units displayed underneath the spectra Hz ppm points sec is only available for FIDs e Y Scaling right now only one option simulation e Window title some text to identify the spectrum window the default settings is to display SF p 29 e the colours of several spectrum items 2 3
88. l Shift AB Homonuclear Two Spin System AB Site 3 730 000 Hz Rel Intensity LU E 0 000 Hz Delta J 0 000 Hz _ Tie to previous site Alpha 0 000 deg Convention STANDARD T Beta 0 000 deg Nucleus A Nucleus B Delta 11 269 000 Delta 11 269 000 ppm Delta 22 114 000 Delta 22 114 000 ppm Delta 33 39 000 Delta 33 39 000 ppm Alpha 0 000 deg Alpha 0 000 deg Beta 90 000 deg Beta 90 000 deg Gamma 25 000 deg Gamma 25 000 deg Calculates the spectrum of a static powder sample containing an isolated spin pair of homonuclear spin 1 2 nuclei considering chemical shift anisotropy direct dipole dipole coupling and indirect spin spin coupling including second order effects It is assumed that the dipolar and indirect cou pling tensors are colinear and axially symmetric Parameter Purpose Rel Intensity p 88 Relative intensity of this site in percent Tie to previous site p 88 Ties parameters to those of the previous site Convention p 88 Convention used for chemical shift tensor components Delta 11 Delta 22 Delta 33 Principal components of chemical shift tensor stan p 88 dard convention in ppm Delta iso Span Skew p 88 Principal components of chemical shift tensor Herzfeld Berger convention Delta iso Anisotropy Asym Principal components of chemical shift tensor Hae metry p 88 berlen convention Alpha Beta Gamma p 93 Euler angles in degrees for g
89. le 1 aWinNMR p 20 file with UNIX type ASCII parameter files in TopSpin XWinNMR p 19 format in Solids p 21 format in ASCII format as rows of frequency intensity data in JCAMP DX p 21 format only as uncompressed XYDATA in X Y Y format When writing WinNMR files the file name should adhere to the eeeppp p 19 convention 2 3 4 5 When writing Topspin files please consider that the dialog was written initially for WinNMR There fore if you want to create the file d u data nmrguest nmr simulation 11 pdata 20 1r you should point the path to the simulation subdirectory and enter the file name 011020 file type Topspin WSolids1 extracts from this file name the corresponding experiment and processing numbers Also because Topspin data are stored as integers you should scale up p 44 the calculated spectrum before saving Note When displaying experimental spectra and spectra calcu lated by WSolids1 in WinNMR and the calculated spectrum has not been scaled p 44 to match the amplitude of the experimen tal spectrum use the relative intensities scaling mode of the dual multiple display window 2 1 8 Save WSolids Document The WSolids document is a self contained document providing experimental and calculated spectra as well as spin systems with their required parameters 2 1 9 Save WSolids Spin System Saves the spin system only as a WSolids XML document file July 30
90. le Crystal 9P NMR and X ray Diffraction Study of a Molybdenum Phosphine Complex 5 Methyl dibenzophosphole pentacarbonylmolybdenum 0 K Eichele R E Wasylishen K Maitra J H Nelson J F Britten Inorg Chem 1997 36 3539 3544 DOI 10 1021 jp9712415 51 July 30 2015 Chapter 3 Spin Systems 3 2 Static Dipolar Chemical Shift A2 AX Dipolar Chemical Shift A2 AX Site 2 Si 29 5 Spin 1 2 Homonuclear Coupled to Rel Intensity ULNA _ Tie to previous site Convention 100 000 STANDARD gt B 1650 000 Hz E 0 000 Hz Delta 11 Delta 22 Delta 33 Parameter 150 000 50 000 100 000 Calculates the spectrum of a static powder sample containing an isolated spin pair considering chem ical shift anisotropy direct dipole dipole coupling and indirect spin spin coupling The spin pair can be a homonuclear pair of magnetically equivalent spin 1 2 nuclei or a heteronuclear pair A2 or AX approximation Itis assumed that the dipolar interaction and the anisotropy are both collinear and axially symmetric Delta J Alpha Beta ppm ppm ppm 0 000 Hz 72 000 deg 98 000 deg Purpose Rel Intensity p 88 Tie to previous site p 88 Convention p 88 Delta 11 Delta 22 Delta 33 p 88 Delta iso Span Skew p 88 Delta iso Anisotropy Asym metry p 88 Coupled to p 91 N A p 91 D p 91 J p 92 Delta J p 92
91. lear pair of nuclei i e AB approxi mation under variable angle spinning Considers a spectrum in solution HR high resolution of a spin 1 2 coupled to a quadrupolar nucleus showing the effect of relaxation Chemical shift anisotrop Chemical shift anisotropy te The item Edit Sites of the Simulation p 28 popup menu allows to manage the sites constituting the calculational model A dialog box provides a list of currently available sites Selection Action Edit Highlight the desired site in the list box using mouse or keyboard and select the Edit button to obtain access to the parameters for this site You can also double click on the desired site to trigger this action Add Select the Add button to add a new site to the calculational model July 30 2015 Chapter 2 Menus Delete Select the Delete button to delete the site highlighted in the list box A dialog box requesting confirmation pops up before the site gets actually deleted There is no Undo function Note Access to editing the parameters of a spin system might be easier by using the cycle p 38 feature i e hitting the Enter key the appro priate number of times 2 2 7 Calculate The item Calculate of the Simulation p 28 popup menu starts calculation of a theoretical spectrum using the selected calculation models and site specific parameters If not all parameters were initial ized it calls the appropriate parameter dialog boxes
92. lids Document 2 0 0264 055 anna han a 23 219 Save WeolideSpinSystem oo i os bebe bebe ba ede werd e adee aged 23 PONG II BRE Se RE ORS ee te in a ae 24 The WSolidsl XML Document 2 2 055 65 65 20 2 ee ee ee 24 The XSLT Transformation 24 Stalable Vector Graphis ios a eae AES 25 Location ot Required Files es iiaia o ir atara Pee OP ee a 26 Creating HTML Files Permanently 2 62424 44044 e a eS 26 PA MERA sees es ee II a II 27 2 2 Simulation Menu 2 0 0 eo ee 28 221 Spectrum Default Patameters csa sos oca ee aa 28 Upon Closing Get Parameters From Experimental Spectrum 29 Observed Nucleus oe o 2 ee 29 Specttnneler Frequency 6 oe pE ot Eor een 29 SPOON SZE 2 o u se ana SHAR BE ERE Ree Raga deo eG ke 30 DPS TAZ o cc SRE ee eG Pee tho eh be Beare ae ba els 30 Spec LMS e s ee e i bw ae PE eo ew a eee ve gia 30 Use Relative Threshold Value 2 2 2 0 00 cee eee ee ee ee 31 15 July 30 2015 Chapter 2 Menus Site Dependent Broadening oi eee ea a he A 222 Convolution Parameters 2 24 2 22 2 565 an aa ab ne aa Gaussianf Lorentzian MIDE oo lt ac ee he Bede eee Ge GES ES E e o s a ee Re a ee Lorentzian Convolution lt lt lt o e eee 000 00H aa aaa ana 229 De yvya ve Mode ocio da a eh 224 INGW SIE cc a a eh 225 Select Calculation Model oes ee sae RR HH Ha 220 EOS eo eo o ESS a A A ee ae OS DIT CAE e u a a a e a a a isa aan DE ACEO o e a A pa ME S aaa a
93. lly all July 30 2015 Chapter 3 Spin Systems By Eile Simulation Tools Window Help Chemical Shift Anisotropy x Site 1 Rel Intensity LLAI _ Re to previous site Convention Herzfeld Berger sl RRS Kil E z Figure 3 1 Experimental and calculated P NMR spectra of a static powder sample of a molybdenum phosphine complex orientations of the molecule with respect to the magnetic field are present will consist of a broad line shape with three distinct features corresponding to the principal components However note that for a powder sample there is generally no information about the orientation of the principal components in the molecular frame of reference Exceptions are cases where crystallographic or local symmetry put restrictions on the orientation or if a second interaction e g the dipolar interaction see Static Dipolar Chemical Shift A2 AX p 52 Implementation Details For an introduction see for example the following reference and the literature quoted there in K Eichele R E Wasylishen J Magn Reson A 106 1994 46 56 DOI 10 1006 jmra 1994 1005 This model employs the POWDER space tiling and interpolation procedure Figure 3 1 shows an example of the succesful simulation of a spectrum arising from the chemical shift anisotropy of a powder sample It is the 9P NMR spectrum of a molybdenum phosphine complex and the results have been published in Sing
94. magnitude and geometry In solution NMR studies the magnitude of this interaction is simply called the spin spin coupling constant J reported in Hz In solid state NMR it is more adequately referred to as isotropic spin spin coupling constant as itis in principle anisotropic p 92 in nature 4 8 Anisotropy in Indirect Spin Spin Coupling Delta J The indirect spin spin coupling between the magnetic moments of nuclei is mediated by interven ing electrons This interaction is in principle anisotropic in nature Assuming axial symmetry the anisotropy of the indirect spin spin coupling is defined as the difference between the unique compo nent and the perpendicular components AJ fy Ja In solution NMR spectra the anisotropy of the indirect spin spin coupling does not lead to splittings although it could provide a mechanism for relaxation Physically the anisotropy of the indirect spin spin coupling behaves exactly the same way as the direct dipole dipole coupling Therefore one cannot determine both interactions separately in an experiment only an effective dipolar coupling constant AJ Dep e a However one could calculate the dipolar coupling constant p 91 from known internuclear sepa rations cf Calculate Dipolar Coupling Constant p 41 For an AX spin system the prefactor of the equation above equals one x 1 while for a pair of magnetically equivalent spins this factor corresponds to 3 2 x 1 5 Not
95. n eQ Therefore a FS 5 2 X 7 v 51 0 220 x T V 51 Q V50 f S 6 Actually in Fig 3 13 I have used a T factor somewhat smaller than calculated above 0 1 instead of 0 22 to make the V feature a little sharper Here I just wanted to demonstrate how to deal with isotopologues T V 50 References 1 A Abragam The Principles of Nuclear Magnetism Clarendon Press Oxford 1961 2 G M Whitesides H L Mitchell J Am Chem Soc 1969 91 2245 2250 DOI 10 1021 ja01037a011 3 P Kempgens J Hirschinger K Elbayed J Raya P Granger J Ros J Phys Chem 1996 100 2045 2052 DOI 10 1021 jp9524486 July 30 2015 July 30 2015 4 Spin System Parameters Contents 4 1 Relative Intensity oo e 88 4 2 Tieto previous Site o o e 88 43 CONVENTO u ae a a dt ta wo Sa be ek a 88 431 Standard Convention i 4 4 2 2 anda a aaa aaa ee ale 88 43 2 Herzield Berser Convention os cs cordet ia di hia tiai Deda 89 4 3 3 Haeberlen Convention 89 4 3 4 Chemical Shift and Magnetic Shielding aooaa o 90 aA Coupled To oe 66 si oe dnus wa gaa a sa SE E AA ann 91 45 Natural Abundance 2220er 91 4 6 Dipolar Coupling ConstantD _ oooooooo ooo corno oo 91 4 7 Indirect Spin Spin Coupling o oo ooooo ooo oo 92 4 8 Anisotropy in Indirect Spin Spin Coupling DeltaJ
96. n in speed is bought at the expense of accuracy In any Case a final calculation with Speedy Calculation disabled should be performed to verify the parameters 4 16 INI File Settings There are some settings in the WSolids1 INI file that might be of interest to the user However please make sure that you know what you are doing From WSolids1 version 1 21 onwards you can use the Settings p 40 dialog to change some of them temporarily or permanently The WSolids1 program will use one or two INI files to determine some default settings There will always be one INI file in the same subdirectory as the executable the master INI file For non portable versions of WSolids1 there will also be an INI file in the user s My Documents subdirectory For more detailed information see the next section 4 16 1 Portable or Non Portable Format portable DOCUMENTS portable 1 There is one entry that will be checked at every start of WSolids1 the value of portable in the Document section If portable is set to 1 WSolids1 will consider itself as portable version and peruses the master INI file for all other default settings If portable equals 0 WSolids1 expects per user settings and from now on peruses the INI file in the user s documents directory sub directory WSolids If this file does not exist yet because the current user has not started WSolids1 previously the master INI file will be copied to this location July 30 2015 Chapter 4
97. n via for gt 0 i e dz 011 for lt 0 i e dz 933 911 diso 633 diso 622 digo 6 1 4 2 629 diso 1 4 2 633 digo 1 4 2 11 diso 1 4 2 References 1 U Haeberlen In Advances in Magnetic esonance Suppl 1 J S Waugh Ed Academic Press New York 1976 2 M Mehring Principles of High Resolution NMR in Solids 2nd ed Springer Verlag Berlin 1983 4 3 4 Chemical Shift and Magnetic Shielding It is recommended that the IUPAC conventions 1 are obeyed e The nuclear magnetic shielding absolute shielding 7 in ppm is the difference in shielding between the frequency of the bare nucleus v uc and the frequency of the same nucleus in the species under investigation vs o ppm 1e06 Unucl Vs Ynucl e The chemical shift is the difference in shielding between the nucleus in the species under investigation os and the shielding of the same nucleus in a reference compound jeg ppm ref Os 1 Orer Because oyer is often a small number compared to 1 frequently the following approximation is used Shifts commonly used in solution and solid state NMR studies are thus positive to high frequency Absolute shieldings are positive to low frequency and are only accessible via theoretical calculations The establishment of a correspondence between a chemical shift scale and a chemical shielding scale is not a trivial task and
98. nd on the direct dipolar coupling and potentially the indirect spin spin coupling between both nuclei Because both the CSA and dipolar interaction are tensorial interactions the actual line shape also depends on their relative orientation For historical reasons this model works slightly different from the other models Via the parameters relative intensity and natural abundance one can calculate coupled and uncoupled spectra directly without defining a separate spin system for each This is ok for spin systems where the observed nucleus is coupled to an NMR active isotope and an NMR passive isotope However to deal with situations where the observed nucleus is coupled to an NMR passive isotope and several different NMR active isotopes the generation of several spin systems is required Example P 31 coupled to cadmium Cd 111 12 75 Cd 113 12 26 passive 74 99 e One could use three different sites with the relative intensity reflecting the natural abundancies of each isotope and tying the parameters of the sites together while the natural abundance parameter is set to 100 except for the passive site where this parameter should be zero e Or one could use two different sites The first site should correspond to coupling with one of the active cadmium isotopes say Cd 111 rel intensity 12 75 nat abund 100 The second site reflects both coupling to Cd 113 as well as the passive cadmium thus rel intensity 87 25 n
99. ngle showing chemical shift anisotropy Chemical shift anisotropy direct dipole dipole cou pling and indirect spin spin coupling for a homonu clear pair of equivalent spin 1 2 nuclei or a het eronuclear spin pair in a static powder sample A2 or AX approximation July 30 2015 Chapter 2 Menus MAS Quadrupolar nu cleus p 65 MAS Spin 1 2 Spin S Diag p 67 MAS Spin 1 2 Spin S Stick p 70 MAS Spin 1 2 Spin S Shape p 74 VAS Dipolar chemical shift A2 AX p 76 VAS Dipolar chemical shift AB p 78 HR Spin 1 2 Coupled to Quadrupolar Nucleus Relaxation p 80 2 2 6 Edit Sites Edit Sites Static Static Spectrum of central transition of a quadrupolar nu cleus in a powder sample spinning fast at the magic angle Considers spin spin interactions with a quadrupo lar nucleus under magic angle spinning using full matrix diagonalization Considers spin spin interactions with quadrupo lar nuclei under magic angle spinning using first order perturbation theory and stick approach Considers spin spin interactions with a quadrupo lar nucleus under magic angle spinning using first order perturbation theory to calculate line shape Considers chemical shift and spin spin interac tions for a homo or heteronuclear pair of nuclei i e Az or AX approximation under variable angle spinning Considers chemical shift and spin spin interactions for a homonuc
100. ntre frequency LB full width at half maximum height In order to preserve the relative areas of sites with different line broadening parameters the con volution procedure takes into account that the area of a Lorentzian peak can be approximated by 7 2 x A x LB 1 570796 x A x LB 2 2 3 Derivative Mode In the Spectrum Default Parameter p 28 box the status of the mutually exclusive radio buttons Derivative No lst 2nd determine whether the calculated spectrum will be displayed in normal absorption mode or as the first or second derivative July 30 2015 Chapter 2 Menus Note The experimental spectrum remains unaffected by this setting Use your favourite NMR processing program to manipulate the experi mental spectrum Taking the derivative of a spectrum dramatically de creases the signal to noise ratio Modern processing software has usu ally some sort of digital filtering e g Savitzky Golay implemented for generating derivatives of spectra For calculated spectra one can get away with a much simpler procedure Da There are certain advantages in fitting the line shape in one of the derivative modes In this mode the frequencies of the singularities can be determined more accurately As indicated in the picture the points of inflection e g 61 and 633 correspond to peaks in the first derivative while the discon tinuities e g 622 reveal themselves as peaks in the second derivative The width
101. oing from the crystal frame to the principal axis system of the chemical shift tensors D p 91 Direct dipole dipole coupling constant in Hz J p 92 Indirect spin spin coupling constant in Hz Delta J p 92 Anisotropy of the indirect spin spin coupling in Hz Alpha p 92 Azimuth angle in degrees of the internuclear vec tor in the principal axis system of the chemical shift tensor July 30 2015 Chapter 3 Spin Systems Beta p 92 Polar angle in degrees of the internuclear vector in the principal axis system of the chemical shift tensor LB p 32 Provides access to the convolution parameters for the current site To have individual convolution pa rameters for each site specify this in the Spectrum Default Parameters p 28 box Background In addition to the chemical shift anisotropy CSA the spectrum of a spin pair will also depend on the direct dipolar coupling and potentially the indirect spin spin coupling between both nuclei Because both the CSA and dipolar interaction are tensorial interactions the actual line shape also depends on their relative orientation In contrast to the Az and AX first order spin systems the line shape of a general homonuclear AB spin system may also depend on the relative orientations of the two chemical shift tensors Implementation Details For an introduction see for example the following reference and the literature quoted there in K Eichele R E Wasylishen J Ma
102. on Nitrogen and Selenium Nuclei of Selenocyanates A Combined Experimental and Theoretical Approach G M Bernard K Eichele G Wu C Kirby R E Wasylishen Can J Chem 2000 78 614 625 DOI 10 1139 v00 046 July 30 2015 Chapter 3 Spin Systems 3 12 VAS Dipolar Chemical Shift A2 AX VAS Dipolar Chemical Shift Spin Pair xj Site 1 Coupled to Pt 195 gi Rel Intensity Spin 1 2 34 000 F Tie to previous site N A l Speedy calculation I Homenuclear Convention STANDARD v 1500 000 Hz VAS angle 60 000 deg 60 000 Hz VAS freq iD 000 000 Hz Delta J 0 000 Hz Delta 11 fl 00 000 ppm Alpha 0 000 deg Delta 22 50 000 ppm Beta 20 000 deg Delta 33 100 000 ppm Av NES RE Spectrum of a powder sample under variable angle spinning containing a spin pair where AX or A approximation is valid Most parameters are described in the section on the static case Static Dipolar Chemical Shift A2 AX p 52 In addition the following parameters need to be specified I gt ID Parameter Purpose VAS angle p 97 The angle of the spinning axis with respect to the external magnetic field Bo VAS rate p 97 The spinning frequency in Hz Specify a rate greater than the spectrum width to calculate the high spinning speed limit Background In addition to the chemical shift anisotropy CSA the spectrum of a spin pair will also depend on the direct dipola
103. ons or transformations from one coordinate system into another are conveniently described by the triplet of Euler angles p 93 a P y Using the Euler angles this three dimensional problem can be dissected into a sequence of two dimensional rotations whereby in each rotation one axis remains invariant Here all rotations are counter clockwise right handed mathematically positive sense 2D Analogy dimensional rotation 1 x xcosp ysing Y xsinp ycosqQ or in matrix notation cosp sing R p Start Coincidence Now transferred to a three dimensional problem the goal will be to describe the coordinates in a final rotated system x y z which is related to some initial coordinate system X Y Z by the Euler angles The final system is developed in three steps each step involving a rotation described by one Euler angle At the start both coordinate systems X Y Z and x 1 y 1 z 1 shall be coincident First Rotation operation is given by sing coso cos amp R a sin July 30 2015 0 X x 1 The first rotation involves the Euler angle a z 1 axis system is rotated about the Z axis through an angle a counterclockwise relative to X Y Z to give the new system x 2 y 2 z 2 It is clear from the figure that this rotation mixes the coordinates along X and Y completely analogous to the two dimensional rotation described above while the coordinate along Z remains unaffec
104. ormat spectra can also be saved as TopSpin or Solids files Incorporated the IUPAC Recommendations 2001 for the NMR properties of NMR active iso topes the new Q values from Pyykk fixed spin of Nd 145 and U 235 and added U 233 e MAS Spin 1 2 Spin S Diag p 67 added handling of general spin 5 2 case any chi any eta any orientation and made some modifications to the spin 3 2 part also 1 3 13 Version 1 17 30 23 05 2001 e Included new Herzfeld Berger tables that are more accurate at higher values of y The tables were calculated using a home made dedicated program on a Pentium 400 MHz PC and re quired almost a week of computer time 1 3 14 Version 1 17 28 27 09 2000 e Changed the use of the Relative intensity p 88 parameter it is now introduced after the calculation for that specific site has been carried out sites using different calculational models should now have relative areas corresponding to their relative intensities This also fixed bugs for some of the models where the relative intensity was not handled properly Modified the model Static Quadrupolar Nucleus p 58 to allow a homonuclear A2 spin sys tem itis up to the user to decide if the result makes sense A division by zero for not initialized spectrometer frequency gets caught now Modified the POWDER routine by Alderman previously the interpolation did not cover the half sphere completely July 30 2015 Chapter 1 Getting Started 1 3 15
105. osphorus 31 Chemical Shift Tensors of Phosphinidene Ligands in Ruthenium Carbonyl Cluster Compounds A IP Single Crystal and CP MAS NMR Study K Eichele R E Wasylishen J F Corrigan N J Taylor A J Carty J Am Chem Soc 1995 117 6961 6969 DOI 10 1021 ja00131a019 ioj x WG File Simulation Tools Window Help l x Chemical Shift Anisotropy x Site 1 Rel Intensity LLAU _ Re to previous site Convention STANDARD E Delta 22 294 000 ppm PERE Delta 33 60 000 ppm IU DAA AA A Sale bag 1 RY W og aft e eet Y y Figure 3 5 Experimental and calculated P MAS NMR spectra of a powder sample of a phos phinidene ruthenium cluster July 30 2015 Chapter 3 Spin Systems 3 7 MAS Dipolar Chemical Shift A2 AX MAS Dipolar Chemical Shift A2 AX xi Site 1 Rel Intensity 100 00000 I Tie to previous site Convention N STANDARD AR MAS freq 1000 00000 Delta 11 150 000 Delta 22 50 00000 Delta 33 100 00000 Delta J ppm Alpha ppm Beta ppm Spin Y Homonuclear ro0 00000 9 1650 00 Hz 0 0000 He 0 0000 Hz 72 00000 deg 98 00000 deg Coupled to P 31 132 ESO Calculates the spectrum of a powder sample containing an isolated spin pair and spinning at the magic angle considering chemical shift anisotropy direct dipole dipole cou
106. oupling constant x e7Qqzz h the asymmetry parameter of the EFG tensor Y xx 9yy q22 with principal values qzz gt qyy gt qxx and the Larmor frequency Z ys 3 cos BP 1 y sin BP cos 2a 3 2 2 71 July 30 2015 Chapter 3 Spin Systems 5 x File Simulation Tools Window Help 5 x er a eee i att nnn Nat nl MAS Spin 1 2 Coupled to Quadrupolar Nucleus Stick Delta iso 175 370 ppm Rel Intensity LULURUUY 175 370 _ 144 380 _ Te to previaus shte Reference SF MHz Site 1 117 000 6 200 117 000 6 200 67 000 4 000 67 000 4 000 Figure 3 9 Experimental and calculated Cd MAS NMR spectra showing coupling to N Bo 27 of the S nucleus The dipolar coupling constant D is given by PO Ys N and the azimuthal and polar angles P and P define the orientation of the dipolar vector rys with respect to the principal axis system of the EFG tensor In systems where anisotropy in J has to be considered the parameter D in Eq 3 2 is replaced by an effective dipolar coupling constant D D AJ 3 with AJ J J1 and J J 2J 1 3 assuming axial symmetry for J and J parallel to rys Figure 3 9 shows an example for the succesful simulation of a MAS spectrum of a spin 1 2 nucleus that is coupled to several quadrupolar nuclei in a powder sample It is the Cd MAS NMR spectrum of NMe4 Cd SCN 4 where the octahedral cadmium is coupled to four
107. p 28 popup menu allows the user to select a calculational model from a list of available models Each model is in its performance tailored to a specific situation Currently the following models are supported Model Characteristics Static Chemical shift anisotropy p 50 Static Dipolar chemical shift A2 AX p 52 Static Dipolar Chemical Shift AB p 55 Static Quadrupolar Nu cleus p 58 Static Three Spin System AMX p 61 MAS Chemical shift anisotropy HB p 62 MAS Dipolar Chemical Shift A2 AX p 64 Spectrum of a static powder sample showing chem ical shift anisotropy powder pattern Chemical shift anisotropy direct dipole dipole cou pling and indirect spin spin coupling for a homonu clear pair of equivalent spin 1 2 nuclei or a het eronuclear spin pair in a static powder sample A2 or AX approximation Chemical shift anisotropy direct dipole dipole cou pling and indirect spin spin coupling for a homonu clear pair of spin 1 2 nuclei including second order effects in a static powder sample AB Quadrupolar interaction up to second order for the observed nucleus including chemical shift anisotropy for a static powder sample Optionally dipolar and indirect coupling to a heteronucleus can be added note quadrupolar interaction if any is neglected for the coupled heteronucleus not tested yet Spectrum of a powder sample spinning at the magic a
108. padded if necessary Thus an experiment number of 2 and a processing number of 1 would result in the file name 002001 WSolids1 itself doesn t care about the eeeppp format eeeppp 1R or eeeppp FID in binary floating point format need to be present currently WSolids1 does not read FID s e eeeppp AQS and eeeppp FOS need to be present in the same directory these parameter files are in binary format of fixed record length and start with A000 the AQS file contains the parame ters SFO1 SW_h Ol and FOS contains SR 19 July 30 2015 Chapter 2 Menus Bruker WINNMR UNIX This file format is similar to the generic WIN NMR p 19 file format however the parameter files are of ASCII type and correspond to those generated by UXNMR and XWin NMR WSolids1 uses this file format itself to store calculated spectra if the output format WIN N MR is selected In order to be recognized by WSolids as UNIX type WINNMR file the data files need to adhere to the following format e eeeppp 1R or eeeppp FID in binary floating point format need to be present Note that generic UXNMR files have these data stored as long integers potentially if coming from an SGI the Endianness could also be different If such a file is read WSolids1 attempts to detect and convert them automatically currently WSolids1 does not read FID s eeeppp AQS and eeeppp FQS need to be present in the same directory they are ASCII parameter files of variable r
109. pectrum format TopSpin XWinNMR p 19 WINNMR generic p 19 WINNMR UNIX p 20 WINNMR ASCI p 20 Spinsight p 20 SOLIDS p 21 JCAMP DX p 21 Characteristics Requires an 1r file in floating point or integer format and the parameter files acqus and procs in JCAMP DX format Requires an 1R or FID file in floating point format and the parameter files aqs and fqs in binary format Requires an 1R or FID file in floating point format and the parameter files AQS and FOS in ASCII format Reads a spectrum file in ASCH format generated by Bruker s WinN MK version 5 1 or later it requires a sin gle file usually with the extension TXT Reads a Chemagnetics Spinsight file requires an ASCII file with header followed by inten sity data preferred extension dat requires an ASCII file that follows the JCAMP DX stan dard preferred extension dx 18 July 30 2015 Chapter 2 Menus Simpson p 22 requires an ASCII file in Simpson format Varian p 22 some notes on how to deal with Varian datasets Bruker TopSpin XWinNMR Spectra stored in Bruker s TopSpin or XWinNMR file format consist of a series of files stored in a convoluted directory structure as indicated in this figure user directory e g C u e g e g e g e g nmrguest 4ok01ehm 20 4 lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt pdata proc
110. pen spectrum windows Tile Arrange all open spectrum windows so that each has the same area Arrange Icons Arrange the icons of minimized spectrum windows Close All Close all spectrum windows 46 July 30 2015 Chapter 2 Menus 2 6 Help Menu The Help menu allows access to a variety of information It consists of the following items WSolids1 File Simulation Options Tools Window AE As El e 94 1 Index Content About Item Action Help file Opens the WSolids1 help file on its front page Index Opens the WSolids1 help file at its index page Content Opens the WSolids1 help file at its table of contents page About Displays information about the current version and build number of WSolids1 Initially WSolids1 used for help and documentation the Windows Help program Since version 1 19 4 I switched to the PDF format because it is suitable for both online viewing as well as printing To view or print this documentation any PDF viewer should work Also most viewers should be able to deal with the hyperlinks that cross link topics in this help file However opening a PDF file at a specified position is more complicated Therefore not every PDF viewer will work with WSolids1 to display context sensitive help This matter is aggravated by the fact that every viewer has its own mechanism Currently context sensitive help should work with the following PDF viewers Adobe uses with its Acrobat Rea
111. pling and indirect spin spin coupling The spin pair can be a homonuclear pair of magnetically equivalent spin 1 2 nuclei or a heteronuclear pair A2 or AX approximation Itis assumed that the dipolar interaction and the anisotropy are both collinear and axially symmetric This model uses the same parameters as the Static Dipolar Chemical Shift A2 AX p 52 model In addition the parameter MAS freq p 97 as spinning frequency in Hz is required Similar to the MAS Chemical Shift Anisotropy HB p 62 model this model uses Herzfeld Berger tables to look up spinning sideband intensities if the range of these tables allows so see MAS Chem ical Shift Anisotropy HB p 62 for more details E wsolids wsolids1 doc 20140213 dipcsa_tests 04_TEPS teps_p31_1960 xml WSolids1 SF ric lation Options Tools Window Help ef 3 1 MAS Dipolar Chemical Shift A2 AX ite 1 Convention Rel Intensity F Tie to previous site STANDARD y MAS freq 1960 00000 Delta 11 108 00000 ppm Delta 22 98 00000 ppm Delta 33 54 00000 ppm Coupled to P 31 bal Spin 1 2 M Homonuclear 100 00000 1650 00000 0 00000 fo 00000 72 00000 115 00000 ES ES Figure 3 6 Experimental and calculated P MAS NMR spectra of a powder sample of tetraethyl diphosphine disulfide TEPS 64 July 30 2015 Chapter 3 Spin Systems
112. pulate docu ment windows within an MDI application just as they can navigate between and manipulate appli cations on the Windows desktop see also the section on keyboard accelerators p 14 in WSolids1 e CTRL F4 closes the currently active document window ALT F4 closes an application s main window e CTRL F6 or CTRL TAB switches among document windows in the MDI application s workspace ALT TAB switches among applications on the Windows desktop e ALT HYPHEN invokes the system menu of the active document window ALT SPACEBAR invokes the system menu of the active application s main window B July 30 2015 Chapter 1 Getting Started 1 5 Keyboard Accelerators ALT F4 closes an application s main window ALT HYPHEN ALT SPACEBAR _ invokes the system menu of the active applications main window invokes the system menu of the active document window ALT TAB switches among applications on the Windows desktop CTRL F4 closes the currently active document window CTRL F6 switches among document windows in the MDI applications workspace CTRL TAB switches among document windows in the MDI applications workspace ENTER perform the next step of the cycle feature Calculate E Edit sites N New Site CTRL gt zoom in spectrum window horizontally CTRL zoom out spectrum window horizontally CTRL T zoom in spectrum window vertically CTRL zoom out spectrum window vertically gt sc
113. r coupling and potentially the indirect spin spin coupling between both nuclei Because both the CSA and dipolar interaction are tensorial interactions the actual line shape also depends on their relative orientation Spinning the powder sample rapidly about an axis that forms an angle different from the magic angle with respect to the external magnetic field the resulting lineshape will look like that of a static powder sample but scaled by a factor that depends on the spinning angle This scaling factor ranges from 1 0 for spinning parallel to the field to 0 5 for spinning perpendicular to the magnetic field In versions of WSolids1 before 1 21 this model would calculate the line shape of the isotropic peak in the so called high spinning speed limit where no spinning sidebands play a role Experimentally this can be achieved by adding the line shapes of the spinning sidebands to that of the isotropic peak or by rotor synchronized sampling Note that this high spinning speed limit is sometimes called the infinite spinning speed limit incorrectly Here we are still assuming that the Zeeman interaction is the greatest interaction and hence the Larmor frequency greater than the spinning speed Infinite spinning would require modification of the theory In versions of WSolids1 1 21 and onward the calculation of spinning sidebands was included If you still want to use the high spinning speed limit enter a spinning frequency that is wider than
114. ram for Solid State NMR Spectroscopy was the title of the paper that introduced SIMPSON Its output is an ASCII text file usually with extension SPE WSolids1 requires the parameters SIMP NP SW and in newer versions REF The Simpson spectrum file format does not contain sufficient information for proper referencing in older versions not even the measurement frequency therefore WSolids1 asks you for SF newer ver sions of Simpson produce an output file that contains the REF parameter Anyway this information is not sufficient I will think about a solution to this problem but honestly it is a problem caused by Simpson Also the spectrum produced by Simpson is reversed unless you use the statement conjugate fid false in the par section of your Simpson input file To flip your spectrum around you can use WSolids1 Tools reverse spectrum Currently I would suggest the following procedure 1 read the Simpson spectrum into WSolids1 specify sfol of your experimental spectrum 2 reverse the spectrum 3 save in TopSpin format 4 use TopSpin to change the referencing Reference e M Bak J T Rasmussen N C Nielsen J Magn Reson 2000 147 296 DOI 10 1006 mre 2000 2179 Varian Reading of Varian files has been planned but discarded after reading the Varian documentation The reason is that Varian actually does not save the processed spectrum only the processing instructions to get there Therefore the reading of Var
115. re is still room for programs with specially de signed specific calculation models The main reason is efficiency A routine designed for one partic ular purpose will always be more efficient than a general purpose routine Progress in computing power continually decreases the gap However calculation of a static powder pattern of an iso lated spin pair using a general purpose program still requires several hours as compared to the few seconds using the less general implementation in WSolids the several hours was written in the mid end nineties in 2015 this difference has dwindled The advantage for the user is convenience rather than power not every user has the knowledge to feel comfortable with for example Simpson http www bionmr chem au dk bionmr software simpson php Figure 1 1 The Department of Chemistry at Dalhousie University Halifax Canada July 30 2015 Chapter 1 Getting Started Figure 1 2 The logo of Dalhousie University Halifax Canada 1 1 2 Features This section lists some of the features of WSolids1 the knowledge of which should enable the user to work more efficiently with WSolids1 e WSolids1 uses the Multiple Document Interface p 12 MDI specification The user should familiarize himself with this specification Often the vendors of NMR spectrometers provide some means of analyzing or simulating experimental spectra but often a mere simulation to answer a question like how
116. requires both careful theoretical calculations and experimental measurements 2 The nuclear magnetic shielding absolute shielding is the molecular electronic property The chem ical shift is a quantity that we experimentalists have defined and use because of our inability to directly measure the absolute magnetic shielding This inability results from our inability to know July 30 2015 Chapter 4 Spin System Parameters the magnitude of the magnetic field to an accuracy on the order of parts per billion independent of the resonance experiment 3 Comments The symbol o should only be used for absolute shieldings Often however authors use a pseudo shielding scale where the shielding is obtained by simply reversing the sign of the chemical shift In our opinion this adds only to the confusion without providing any additional insight Note that the exact formulation of the span p 88 Q contains the factor 1 oe B O 011 633 1 Oref References 1 Pure Appl Chem 1972 29 627 1976 45 217 2 Some examples for established shielding scales Carbon A K Jameson C J Jameson Chem Phys Lett 1987 134 461 W T Raynes R McVay S J Wright J Chem Soc Faraday Trans 2 1989 85 759 Silicon C J Jameson A K Jameson Chem Phys Lett 1988 149 300 Phosphorus C J Jameson A De Dios A K Jameson Chem Phys Lett 1990 167 575 Tin A Laaksonen R E Wasyli
117. roll spectrum window horizontally to display lower frequencies scroll spectrum window horizontally to display higher frequencies T scroll spectrum window vertically to display higher intensities Page Up scroll spectrum window vertically in greater steps to display higher inten sities Pos1 scroll spectrum window vertically to the top to display highest intensities l scroll spectrum window vertically to display lower intensities Page Down scroll spectrum window vertically in greater steps to display lower inten sities End scroll spectrum window vertically to the bottom to display lowest intensi ties j July 30 2015 2 Menus Contents 21 Ele Mena 0 02 0 05 0 Ge 17 211 New Doce ccoo hao a a a e Bare a 17 212 New Wind occacosasopo oda 17 ala EP E o al ee a oS oo A en ee ee 18 Bruker TopSpin fAMHNMR oso co 2 19 Bruker WINNMR Generic 19 Bruker WINNMR UNIX gt 22 24 442 ne er 20 Bruker WINNMRASEL o oso 22 4 dae ne er ea 20 Chemagnetios SPORE coco nee are 20 E A tere hs de Redes Pe eS keg E EE hates ey cee pe es Sh pe ae See gt 21 ICAMPDA cusco ke be eee a PS Ea eo ee wg ee 21 PARSON ad oh odd hw Gi dss a a ws A ee 22 o EEE 22 214 Open as Caloulated Spechum oo ae ee eee os Danat nn 22 215 Open WSolids Document 2 0 0 4 5 eR ES 22 216 Open Woolids Spin Systemi c oc soco oe cdd escap ra Ba da ES 22 DIE ACA y a a a nario Bare tee a een eee ee ee de 22 21 8 Save WSo
118. s Coupled to p 91 Specifies the nucleus the observed nucleus is cou pled to Only heteronuclear coupling will be considered N A p 91 Natural abundance in percent of the coupled nu cleus If smaller than 100 WSolids1 automatically includes calculation of the spectrum of the uncou pled spin species D p 91 Direct dipole dipole coupling constant in Hz Tip 92 Indirect spin spin coupling constant in Hz Delta J p 92 Anisotropy of the indirect spin spin coupling in Hz Alpha p 92 Azimuth angle in degrees of the internuclear vec tor in the principal axis system of the electric field gradient tensor Beta p 92 Polar angle in degrees of the internuclear vector in the principal axis system of the electric field gradi ent tensor LB p 32 Provides access to the convolution parameters for the current site To have individual convolution pa rameters for each site specify this in the Spectrum Default Parameters p 28 box Background In addition to the chemical shift anisotropy CSA the spectrum of a quadrupolar nucleus will also depend on the nuclear quadrupolar interaction and the relative orientation of both interactions The quadrupolar interaction is considered up to second order for the observed nucleus Optionally dipo lar and indirect coupling to a heteronucleus can be added note quadrupolar interaction if any is neglected for the coupled heteronucleus Implementation Details Specific
119. s about problems may be directed via e mail to 2 Klaus Eichele uni tuebingen de 103 July 30 2015 Chapter 5 Acknowledgements 5 4 Disclaimer of Warranty Because this software package is licensed free of charge there is no warranty to the extent per mitted by applicable law This package is provided as is without warranty of any kind either expressed or implied including but not limited to the implied warranties of merchantability and fitness for a particular purpose the entire risk as to the quality and performance of the contents of this package is with you should this package prove defective you assume the cost of all nec essary servicing repair or correction in no event unless required by applicable law or agreed to in writing will any copyright holder or any other party who may modify and or redistribute this package as permitted in the license be liable to you for damages including any general special incidental or consequential damages arising out of the use or inability to use the package including but not limited to loss of data or data being rendered inaccurate or losses sustained by you or third parties even if such holder or other party has been advised of the possibility of such damages In any case liability will be limited to the amount of money that the copyright holder received from you for the use of this program 104 July 30 2015 Index A2 76 AB 78 absolute
120. s are trade marks of Microsoft Corporation WordPerfect and WordPerfect Presentations were products of WordPerfect Corporation intermit tently by Novell now by Corel WIN NMR XWIN NMR and TopSpin are products of Bruker Biospin GmbH Spinsight is a product of Chemagnetics Hewlett Packard Company HPGL Other brand and or product names are used for identification purposes only and are trade marks registered trademarks or copyrights of their respective owners 5 3 Copyright Information Copyright C 1994 2015 Klaus Eichele All rights reserved This program executable help file and related files may be distributed freely and may be used with out fee by any individual for non commercial use and by any government organization Although the copyright holder retains all rights to this document and the software package you are allowed to copy and distribute verbatim copies of them as you received them in any medium provided that you conspicuously and appropriately publish on each copy an appropriate copyright notice and disclaimer of warranty keep intact all the notices that refer to this license and to the absence of any warranty and distribute a copy of this license along with it This package may not be distributed as a part of any commercial package You are expressly not allowed to sell or license this package 102 July 30 2015 Chapter 5 Acknowledgements Inquiries about the use of this program or report
121. s contained in the file with the extension css cascading style sheets and the result should look like this July 30 2015 Chapter 2 Menus Wsolids1 1 20 12 Document type expe si 4096 td 4096 sf 44 391041 fi 17362 884766 f2 494 257813 file J archives klaus NACD SCN 3 001001 1R plot A WEREIERGENEENEENS type calc si 4096 ltd 4096 sf 44 391041 ft 17362 884766 f2 494 257813 plot relative intensity 100 000000 tied to previous site no model Multi Spin WSolids1 model MAS Spin 1 2 Spin S Stick Scalable Vector Graphics This report demonstrates that XSL is also able to generate graphics from XML data Here I am using XSL to turn the data into Scalable Vector Graphics SVG The SVG format is supported natively by the Mozilla family of browsers FireFox and SeaMonkey SeaMonkey is my favorite web browser be cause I have been using Netscape Communicator for ages and SeaMonkey follows the Communica tors philosophy of integrating browser email newsreader and HTML editor Other web browsers such as Microsoft Internet Explorer before version 9 may require a plugin to be able to display SVG graphics e g the Adobe SVG viewer plugin Internet Explorer 9 also supports SVG but of course in a way different from other browsers Therefore I am providing two flavours of those XSL files that generate the SVG o
122. scription on how to acquire NMR data The meaning of the acquisition parameters depends on the definitions used in the associated pulse program WSolids1 is mainly interested in SF and SW July 30 2015 Chapter 2 Menus e proc this is a text file containing parameters which describe the current state of the data file and the previous operations that have been performed on the data since it was acquired WSolids1 is mainly interested in datatype domain current_sizel rmp1 rmv1 rmvunits1 SOLIDS This type of file format is produced by Solids the FORTRAN predecessor of WSolids1 and was created to allow a slightly more general interface in terms of file formats ASCII files created by WIN NMR require only minor editing of the file header in order to conform to this format the text and some lines need to be deleted In order to be recognized by WSolids1 as SOLIDS file the ASCII data file need to adhere to the following format where each parameter is on a separate row e number of points SI e spectrometer frequency in MHz SF e digital resolution in Hz per point F1 F2 SI e highest frequency i e frequency of first point in Hz F1 e lowest frequency i e frequency of last point in Hz F2 e intensity data as integers or floating point numbers each in a separate row JCAMP DX The JCAMP DX Joint Committee on Atomic and Molecular Physical Data Exchange format has been initiated by IUPAC to achive better long t
123. se Gas 68 3 10 MAS Spin 1 2 Spin S Stick o oooooooo eee 70 pa oe a eee ee ee Ew ee aaa Bk 71 Implementation Details 2 2 2 6 48455 a RR RAG we ee ES 71 References 1 add eaa haai aaia na daua 73 3 11 MAS Spin 1 2 Spin S Shape oooooocoooo ee o o ooo 74 pia oe a er a Gee we Se ar er ee Ya 75 3 12 VAS Dipolar Chemical Shift A2 AX 2 2 2 ee ee 76 Backend ocio dedo a a a a G 76 3 13 VAS Dipolar Chemical Shift AB o ooooocoooooo romo 78 Packoround gt a a a ee hae Gig 78 3 14 HR Spin 1 2 Coupled to Quadrupolar Nucleus Relaxation 80 pc 2 he be ba EA edad De oea o e 82 Implementation Details o e oa ean a AS rien ine 82 Relerences ol eS PS Pee Ba ee ook 85 49 July 30 2015 Chapter 3 Spin Systems 3 1 Static Chemical Shift Anisotropy Chemical Shift Anisotropy Site 1 Rel Intensity MUAL _ Me ts previous sue Convention STANDARD v Delta 11 100 000 ppm Delta 22 50 000 ppm Delta 33 100 000 ppm This model calculates the spectrum of a static powder sample showing only chemical shift anisotropy powder pattern Parameter Purpose Rel Intensity p 88 Relative intensity of this site in percent Tie to previous site p 88 Ties parameters to those of the previous site Convention p 88 Convention used for chemical shift tensor components Delta 11 Delta 22 Delta 33 Principal components of chemical shif
124. shen J Am Chem Soc 1995 117 392 3 C J Jameson Solid State Nucl Magn Reson 1998 11 265 4 4 Coupled To In some models the observed nucleus is coupled to another nucleus via indirect spin spin or direct dipole dipole coupling The coupled nucleus can be selected from a list of available isotopes In some cases this also updates an entry with the natural abundance p 91 of the selected isotope as well as the spin of this nucleus 4 5 Natural Abundance By default this parameter is set to the natural abundance of an isotope in percent This parameter can however be changed to reflect isotopic enrichment 4 6 Dipolar Coupling Constant D The direct dipole dipole coupling is the through space interaction between the magnetic moments of nuclei The magnitude of this interaction is characterized by the Dipolar Coupling Constant given in Hz It depends on the inverse cube of the distance between the interacting nuclei besides some natural and nuclear constants Mo Y ysl 3 An 2n ris In contrast the indirect spin spin coupling p 92 between nuclear magnetic moments is mediated by intervening electrons 9 July 30 2015 Chapter 4 Spin System Parameters 4 7 Indirect Spin Spin Coupling J The indirect spin spin coupling between the magnetic moments of nuclei is mediated by intervening electrons In contrast to the direct dipole dipole coupling p 91 there is no simple relationship between its
125. sidual dipolar coupling is field dependent The value entered for d in the edit box is for the spec trometer frequency entered as reference frequency of the observed nucleus in MHz Spectra at dif ferent fields can be calculated from the same set of parameters based on different observe frequencies July 30 2015 Chapter 3 Spin Systems Coupled nuclei In the edit box enter parameters for each coupled nucleus on a separate line The parameters spin J and d should be separated by blank spaces To check for proper format use the Parse button to see the result of how WSolidslinterprets the input Spin Nuclear spin of the coupled nucleus This parame ter is not affected by the state of the Tie to previous site flag J Indirect spin spin coupling constant in Hz d Residual dipolar coupling in Hz LB p 32 Provides access to the convolution parameters for the current site To have individual convolution pa rameters for each site specify this in the Spectrum Default Parameters p 28 box Parse Use this button to check if the parameters for the coupled nuclei have been entered correctly Background The quadrupolar interaction at a quadrupolar nucleus causes its axis of quantization to be tilted away from the direction of the external magnetic field This also modifies the spatial dependence of the dipolar interaction so that magic angle spinning is not able to suppress the heteronuclear dipolar coupling in the spec
126. st C 2nd COMES July 30 2015 Chapter 2 Menus The default parameters define Parameter Purpose Nucleus p 29 Observed nucleus SF p 29 Spectrometer frequency Larmor frequency in MHz SI p 30 Size of calculated spectrum in points ppm Hz p 30 Toggles input for F1 F2 between Hz or ppm F1 p 30 High frequency limit of calculated spectrum F2 p 30 Low frequency limit of calculated spectrum Use relative threshold Toggle between use of a threshold value in the convo value p 31 lution or doing the full convolution Site dependent broaden Individual or global line broadening ing p 31 Derivative Mode p 34 Absorption or derivative display Get Experimental Param Upon Closing Get Parameters From Experimental eters p 29 Spectrum Upon Closing Get Parameters From Experimental Spectrum If this checkbox is activated WSolids1 will retrieve SF F1 F2 and SI from the experimental spectrum and update the parameters of the calculated spectrum accordingly This will invalidate the content of the calculated spectrum and require a new calculation When reading an experimental spectrum its parameters will be used to initialize the calculated spec trum However you are free to modify those of the calculated spectrum any time In fact for some calculation models it is advisable to narrow down the limits of the calculated spectrum to the region of interest If however for some reason experimental and calcul
127. t tensor stan p 88 dard convention in ppm Delta iso Span Skew p 88 Principal components of chemical shift tensor Herzfeld Berger convention Delta iso Anisotropy Asym Principal components of chemical shift tensor Hae metry p 88 berlen convention LB p 32 Provides access to the convolution parameters for the current site To have individual convolution pa rameters for each site specify this in the Spectrum Default Parameters p 28 box Background Depending on the local symmetry at the nuclear site the magnitude of the chemical shift will vary as a function of the orientation of the molecule with respect to the external magnetic field This orientation dependence of the chemical shift is referred to as chemical shift anisotropy CSA Math ematically the chemical shift anisotropy is described by a second rank tensor a 3 by 3 matrix which in the case of the symmetric part of the chemical shift CS tensor consists of six independent com ponents Generally one is able to express the chemical shift tensor in a coordinate frame where all off diagonal elements vanish In this principal axis system the chemical shift tensor is fully described by the three diagonal elements the principal components and the three eigenvectors or Euler angles describing the orientation of the principal axes with respect to an arbitrary frame Due to the chemical shift anisotropy the spectrum of a static powder sample where statistica
128. tations are in a counter clockwise fashion right handed mathematically positive sense The Euler angles x 6 y relate two orthogonal coordinate systems having a common origin The transition from one coordinate system to the other is achieved by a series of two dimensional rota tions The rotations are performed about coordinate system axes generated by the previous rotation step the step by step procedure is illustrated in the topic Rotation Matrices p 94 The convention used here is that is a rotation about the Z axis of the initial coordinate system About the y axis of this newly generated coordinate system a rotation by f is performed followed by a rotation by y about the new z axis Given the Euler angles the step by step procedure illustrates how to move from one coordinate system to the other However given the two coordinate systems how can one determine the Euler angles relating them This is described in topic Determining Euler Angles p 95 The usual ranges for a p y are 0 lt a lt 360 0 lt p lt 180 0 lt y lt 360 References 1 G Arfken Mathematical Methods for Physicists 3rd ed Academic Press New York 1985 2 M E Rose Elementary Theory of Angular Momentum Wiley New York 1957 3 K Schmidt Rohr and H W Spiess Multidimensional Solid State NMR and Polymers Academic Press London 1994 July 30 2015 Chapter 4 Spin System Parameters 4 10 1 Rotation Matrices Rotati
129. ted The rotation matrix to describe this sina 0 cosa 0 0 1 z 1 In order to simplify the problem let us start with a two Suppose the coordinates x y of a point in the two dimensional XY system are known but we are actually in terested in knowing the coordinates of this point in another coordinate system X Y which is related to the XY system by a counter clockwise rotation by an angle 9 As the figure indicates the coordinates of the given point in the new coordinate system will be yd The x 1 y Chapter 4 Spin System Parameters Second Rotation The second rotation involves the Euler angle 6 The x 2 y 2 z 2 axis system is rotated about the y 2 axis through an angle counterclockwise to generate the new coordinate system x 3 y 3 z 3 Analogously to the first Euler rotation this mixes the coordinates along x 2 and z 2 while the coordinate along y 2 remains unaffected This operation also generates a line of nodes parallel to the direction of y 2 The rotation matrix to describe this operation is given by cosB 0 sin Ry B o 1 0 sinf 0 cos Third Rotation The last rotation involves the Euler angle y The x 3 y 3 zB axis system is rotated about the z 3 axis through an angle y counterclockwise to generate the final coordinate system x y Z Analogously to the first Euler rotation this mixes the coordinates along x 3 and y 3 while the coordinate along z 3 rema
130. ters used Parameter Purpose Coupled to p 91 Specifies the quadrupolar nucleus the observed nu cleus is coupled to Only heteronuclear coupling will be considered N A p 91 Natural abundance in percent of the coupled nucleus Tie to previous site p 88 Ties parameters to those of the previous site Delta iso p 88 Isotropic chemical shift in ppm Alpha p 92 Azimuth angle in degrees of the internuclear vec tor in the principal axis system of the electric field gradient tensor Beta p 92 Polar angle in degrees of the internuclear vector in the principal axis system of the electric field gradi ent tensor D p 91 Direct dipole dipole coupling constant in Hz J p 92 Indirect spin spin coupling constant in Hz Delta J p 92 Anisotropy of the indirect spin spin coupling in Hz Chi p 96 Quadrupolar coupling constant in MHz Eta p 96 Asymmetry parameter of the electric field gradient tensor 0 lt eta lt 1 LB p 32 Provides access to the convolution parameters for the current site To have individual convolution pa rameters for each site specify this in the Spectrum Default Parameters p 28 box July 30 2015 Chapter 3 Spin Systems MA Elle Simulation Tools Window Help laj x MAS Spin 1 2 Spin S Shape Ria E Spin 1 _ Re te previous she Dette ppm D Hz Alpha D deg Hz Delta J 0 000 Hz AD Figure
131. trum Reverse spectrum p 45 Reverses the frequency direction of the spectrum Absolute value p 45 Generates the absolute value representation of the spectrum Reference spectrum p Add a shift to the experimental or calculated spec 45 trum 2 4 1 Dipolar Coupling Constant Calculate Dipolar Coupling Constant Nucleus 1 Distance A H 1 1 888 Nucleus 2 Dipolar Coupling H 1 128123 453 Hz do Me 2l July 30 2015 Chapter 2 Menus Selection of the Tools Dipolar coupling constant menu item invokes this dialog box To calculate the dipolar coupling constant follow these steps Select from the two list boxes Nucleus 1 and Nucleus 2 the two nuclei constituting the spin pair use mouse arrow keys or first letter of nucleus Enter the internuclear separation in Angstrom Hit Enter to display the calculated dipolar coupling constant If required copy the result to the clipboard by pushing the Copy button or ALT O This can be used to paste typically CTRL V or SHIFT INSERT the result into appropriate edit controls Exit the dialog by selecting Quit or ESC For information on the source of the nuclear data refer to Table of Nuclear Properties p 42 2 4 2 Table of Nuclear Properties x No Nucleus Spin Gamma 1E0 N A Q 1E 28 Larmor MHz Shift Reference MHz 1 H 1 1 2 26 75221 99 9880 0 00000 200 114090 200 114014 2 H 2 1 4 10663 0 0115 0 00286 30 718735 30 718719 3 H 3 1 2 28 53498 0 000
132. trum of the spin 1 2 nucleus resulting in splittings and broadenings Similar effects can be transmitted through the indirect spin spin coupling If the nuclear quadrupo lar coupling constant is on the same order of magnitude as the Larmor frequency of the quadrupolar nucleus the combined Zeeman quadrupolar Hamiltonian must be diagonalized at each orientation and averaged over a rotor period to calculate a theoretical spectrum However if the quadrupolar and dipolar coupling are small relative to the indirect spin spin coupling this so called breakdown of the high field approximation causes no significant broadening of the individual peaks only unequal spacings between the peaks of the multiplet Such spectra can be simulated using first order pertur bation theory with a stick approach where the patterns are characterized by an indirect spin spin coupling constant J and a residual dipolar coupling d Implementation Details If the contribution of the residual dipolar coupling to the actual line shape is small the resonance fre quencies in the MAS NMR spectrum of a spin 1 2 nucleus coupled to a quadrupolar spin S nucleus are given by 3 S S 1 3m 5105 1 d 3 1 Vm Viso m where Viso is the frequency of the uncoupled I nucleus m is the z component of the angular momen tum of the m gt state of nucleus S i e m S S 1 S The residual dipolar coupling d is given by 3xD 20Z with the quadrupolar c
133. uency ratio amp as defined by IUPAC 6 42 July 30 2015 Chapter 2 Menus Sorting By default the nuclei are listed according to their position in the periodic table of elements i e for increasing mass number Using the Sort for list box the display can be sorted alphabetically for the labels of the nuclei the spin the magnetogyric ratio Gamma the natural abundance or the nuclear electric quadrupole moment Magnetic Field The strength of the magnetic field affects the frequency of the reference compound The following values produce the given values of the H NMR frequency of TMS Bo T 1H frequency of TMS MHz 2 348661 100 00 4 700374 200 13 5 874703 250 13 7 049034 300 13 9 397695 400 13 11 746354 500 13 14 0950140 600 13 16 443674 700 13 18 792334 800 13 21 140994071 900 13 22 3153239 950 13 Copying Data Note that it is possible to high light parts of the table and to copy the highlighted parts to the clip board using standard Windows editing techniques CTRL INSERT or CTRL C to copy the selected part Modifications Most nuclear data have originated from Mason s extremely useful book on Multinuclear NMR 1 The current version of R has been updated according to data from the IUPAC Recommendations 2001 6 The following data differ from those in reference 1 all magnetogyric ratios are according to 6 e the nuclear quadrupole moment values are from the Year 2001 Q Values
134. ute Value This option available from the Tools Absolute value menu enables one to generate the absolute value representation of the spectrum 2 4 9 Reference Spectrum This feature available from the Tools Reference spectrum menu is not intended to be some fancy referencing tool but to shift the experimental or calculated spectrum by adding a specified shift to the spectrum Such a feature could be helpful when simulating simultaneously spectra at different magnetic fields or different spinning angles and small adjustments in referencing are necessary July 30 2015 Chapter 2 Menus 2 5 Window Menu The Window menu allows management of spectrum windows and select display regions It consists of the following items WSolids1 File Simulation Tools Mi Expand spectrum Ctrl gt Compress spectrum Ctrl lt Multiply Ctrl Up rrow Divide Ctrl Down rrow Reset display Ctrl R Cascade Tile Arrange Icons Close All Item Action Expand spectrum Horizontally expand spectra frequency scale in the currently active spectrum window Compress spectrum Horizontally contract spectra frequency scale in the currently active spectrum window Multiply Scale up the intensities of spectra in the currently active spectrum window Divide Scale down the intensities of spectra in the currently active spectrum window Reset display Resets the display limits such that the spectra are fully visible Cascade Cascade all o
135. utput one version for IE 9 usolids display ie9 xs1 and another version for all other browsers wsolids display_moz xs1 Depending on the browser that you want to use copy either wsolids_display_ie9 xsl or wsolids_display_moz xsl to wsolids_display xsl The default installation will be for non IE9 users The advantage of SVG is that it prints rather well compared to bitmapped pictures e g JPEG GIF or PNG You can verify this if you zoom in on the graphics shown in the report above many spectra shown in publications will look worse In case you don t want the SVG graphics to be included in the report either because your browser does not support this or you don t want to wait the time required by the browser to process the graphics you can disable them Open the file wsolids_display xslin your text editor of choice 25 July 30 2015 Chapter 2 Menus lt xml version 1 0 encoding iso 8859 1 gt lt xsl stylesheet version 1 0 xmlns xsl http www w3 org 1999 XSL Transform xmlns svg http www w3 org 2000 svg gt lt xsl param name UseSVG select 1 gt lt xsl template match display gt lt xsl apply templates gt lt xsl template gt and change in the line printed in red the 1 to a 0 lt xs1 param name UseSVG select 0 gt Links to the software mentioned e FireFox http www mozilla org en US e SeaMonkey http www seamonkey project org e Adobe SVG viewer plugin http www
136. y also notice that the content is not always understandable If your web browser does not know how to deal with the XML file this will actually be the way it will display the WSolids1 document to you lt xml version 1 0 encoding IS0 8859 1 gt lt xml stylesheet type text xsl href wsolids xsl gt lt wsolids gt lt creator gt Wsolids1 lt creator gt lt creatorversion gt 1 20 12 lt creatorversion gt lt display gt lt count gt 1 lt count gt lt window gt lt id gt 1 lt id gt lt type gt dual lt type gt lt spectrum gt The XSLT Transformation What is required is a way to tell the browser how to deal with the document i e how to translate the data This objective is achieved by using so called Extensible Stylesheet Language transformation XSLT Versions of WSolids1 of 1 20 15 and above write a reference to the necessary XSL file as second line of the XML file If this line is not present you need to add it manually use a text editor such as the Windows Editor Notepad or similar and not a word processing software such as office or other desktop publishing software and you can copy and paste the line displayed in red in the figure above The XSL file will help the browser to turn the XML entries into something that it is used to present i e HTML data In principle this is sufficient but to make the result more fancy we can use a style sheet to tell the browser how to format things This information i

WSolids1 User Manual - Institut für Anorganische Chemie

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WSolids1 User Manual - Institut f&uuml;r Anorganische Chemie

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WSolids1 User Manual - Institut für Anorganische Chemie