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1. Connect moving the divider between them If you make see l the space for the structure very small the E structure pane will be hidden use the Include Structure Show command to bring it back If a you have not imported a structure but still Split Show Folded Delete Atoms Labels gt want to use the structure pane to enter data use Sructure Create to create a default structure This is just a list of the atoms in the spin system arranged vertically but you can edit it into a real structure if you want see below If you want to remove the structure but keep the spin system use Structure Delete The structure drawing can be copied to the clipboard using the Sructure Copy command This is just a Windows graphic so you cannot paste it back into a structure drawing program However it contains enough embedded information that you can paste it as a complete molecule into another gN MR Molecule window The structure cannot be printed separately but choosing File Print Molecule section 3 3 will include the structure drawing in the printout Document Molecule 1 a Q Options Spectrum In the structure the labels for nuclei included in the spin system are shown in anormal font labels for nuclei excluded from the 58 Entering data Chapter 3 simulation are shown in italic If several nuclei have been folded into a single equivalence group only one of them will
2. A single molecule can be copied to the clipboard in a plain text format using the Edit Copy Molecule command The text can then be copied into a word processor document The copy contains enough information that you can paste it back into another gN MR Molecule window using the Edit Paste Molecule command Any structure in a Molecule window is not copied in this way you need the Stucture Copy command for that With a Molecule window at the front the File Print Molec ule command prints the current molecule including the structure if present The data are not printed WYSIWYG but as plain text in tabular form they will contain a title and date 3 4 Entering data without a structure The Molecule window is a kind of molecule spreadsheet In it you enter the relevant data for each spin group in the system a spin group is a group of magnetically equivalent nuclei The current program version accepts up to 49 spin groups in the Molecule window Each spin group occupies two rows in the Molecule window Figure 23 The first of these rows contains the actual data nucleus name chemical shift etc The second row can be used to assign variable names to some of these data Variable names are more important to Entering data 47 Figure 23 Molecule window and Nucleus name dialog Chapter 3 iterative calculations than to normal simulation and will be discussed later Chapter 5 If you want to enter data in a certain field y
3. References 10 11 12 13 A Steigel M echanistic studies of Rearrangements and Exchange Reactions by Dynamic N MR Spectroscopy in N MR Basic Principles and Progress P Diehl E Fluck and R Kosfeld eds vol 15 Springer Verlag Berlin 1978 p 1 Lybrics file format definition University of Wisconsin Madison 1987 D Ziessow On line Rechner in der Chemie Walter de Gruyter Berlin 1966 H Barkhuijsen R de Beer W M M J Bov e and D van Ormondt J Magn Res 61 1985 465 C F Tirendi and J F Martin J Magn Res 85 1989 162 H Barkhuijsen R de Beer and D van Ormondt J Magn Res 73 1987 553 M Fedrigo G Esposito S Cattarinussi P Viglino and F Fogolari J Magn Res A 121 1996 97 F Montigny J Brondeau and D Canet Chem Phys Lett 170 1990 175 M A Dasuc F Ni and G C Levy J Magn Res 73 1987 548 G Zhu and A Bax J Magn Res 100 1992 202 W H Press B P Flannery S A Teukolsky and W T Vetterling Numerical Recipes in C Cambridge University Press Cambridge 1988 J A Pople W G Schneider and H J Bernstein High Resolution Nuclear Magnetic Resonance McGraw Hill New York 1959 A Jones Comp J 13 1970 301 D S Stephenson and G Binsch J Magn Res 32 1978 145 G Binsch J Am Chem Soc 91 1969 1304 D S Stephenson and G Binsch J Magn Res 30 1978 625 gNMR 233 References 15 E Pretsch J Seibl W Simon and T Clerc Tabellen zur
4. lt PgDn gt lt Ctrl l gt lt I gt lt PgUp gt lt Ctrl T gt lt Ctrl End gt lt Ctrl H ome gt next cell down or to top of next column one field right or to start of next row one field left or to end of previous row one field right or down one page right to end of row one field left or up one page left to start of row one field down or right one page down to bottom of column one field up or left one page up to top of column to last field of grid to first field of grid Installation Chapter 1 Within a grid some keys can have special meanings lt gt usually copies a value from the field above it lt gt from the field to the left of it where appropriate In some contexts lt gt initiates a special operation like adding a new row created a linked value rate intensity or completing a permutation In Molecule and Exchange windows structures can be displayed in aseparate pane The divider between the structure and data panes can be moved by dragging Moving it far to the left hides the structure completely use the Struc ture Show command to redisplay it 1 4 About this manual This manual describes how to use gN MR for simulation It assumes you already know what you want to accomplish For more background on the use of simulation see the separate booklet Simulation of one dimensional NMR spectra a Companion to the gNMR User Manual Chapter 2 is a tutorial
5. ee eeeeeceeeeeceeeeeeeeeeeaeeeseeeeesaeeateeaeeeees 74 gNMR vii Contents 4 5 Markers integral regions cecececsseeseeeeeeceeeeeteeeeeeteeaeeeees 75 4 6 Links between Spectrum Molecule and Exchange windows77 4 7 Print copy and paste ssssssssssssisesrersrsrnsrsrssnsnnnnnsnsnsrersrsrns 79 5 Assignment iteration sssssssssssssnsusannnnannnnnnnanunnnnnnannnnannnnannnnanan nanna 83 SE MtrOG UCU ON 222 00 keidi eevee dee 83 5 2 Iteration variables oo ccceeseeeeeeeeeeeeeeeneeeetsesaeeateestesaeeaeens 83 5 3 MOUSE ASSIGNMENHS 0 eeeeeeeeteeteeeeeeeeeeeeeeeeseeetaetateateetetaetatees 85 5 4 Numerical assignMents ceeseeceeeseeeeeeeeeeateeeeeeeteetaeeateetees 87 5 5 Settings affecting the iteration 0 0 eee eseeeeeeeeeeeeteees 90 5 6 Starting assignment iteration ee eeeeeeece cess ceeteeeteeetees 93 5 7 Inspecting the reSults ceceeeeeseeeeeeeeeeeeeeeeaeeeeeeeeseetaeeateetees 94 5 8 Checking the solution oe ee eeeeeeeeeeeeeeeeeeeeeeeeeseeeteetaeeateetees 95 6 Full lineshape iteration ssssssssusonnusunnnnunnnnunnnnnnnunanannnnannnnnnannnnannnna 97 GL nthoduction ci 2o Aae see he eee T 97 6 2 Iteration variables oo eee eeeeeeeeeeeeeeeeeeeetsetaeteseestetaeeatens 97 6 3 Iteration data ieaiaia i eee ene 99 6 4 Starting and steering the iteration s 100 6 5 Searching for more than one solution sses 102 6 6 When not to use full lineshape analysis 00 0 eee 103 6 7 If th
6. Four exercises take you through common tasks of setting up a simulation with or without a structure an iteration and an exchange calculation Examples of some special operations are also provided Chapter 3 describes entering data shifts coupling constants etc and using molecular structures for setting up a simulation Chapter 4 explains how to display the resulting spectra and compare them with experimental spectra Chapters 5 and 6 discuss the use of iteration for optimizing NMR parameters Chapter 7 deals with chemical exchange calculations Chapter 8 describes the role of symmetry in gNMR Installation 5 Chapter 1 Chapter 9 discusses the use of approximate methods to simulate large systems gt 12 nuclei Chapter 10 explains the use of databases with the gN MR programs Chapter 11 deals with import of experimental spectra from various sources Chapter 12 introduces gSPG the spectrum processing utility provided with gNMR Appendix A lists all options available for customizing gN MR Appendix B deals with some common questions from gN MR users 6 Installation Chapter 2 2 Tutorial 2 1 Introduction This tutorial illustrates common steps in setting up simulations N ot everything is explained in detail the rest of the manual provides a more comprehensive description of all topics covered here The first four sections of this tutorial are step by step descriptions of basic tasks e Setting up a
7. Full lineshape iteration 99 Chapter 6 out it tends to stay out and the final results may not be very good To prevent this kind of accident we recommend that you use iteration windows with reasonable margins of empty space on both sides experience suggests 20 empty 60 multiplets 20 empty is Suitable Another source of problems is the use of very narrow lines The fit procedure used in gN MR tends to become numerically unstable if the linewidths are very small compared to the width of the iteration window say less than 1 1000 If you want to do a fit on such a spectrum first do a full lineshape iteration on a set of experimental data having a larger linewidth then do only the final cycle of the iteration on the narrow line spectrum Generally it is wise to start the iteration with initial linewidths set slightly larger than the experimental ones 6 4 Starting and steering the iteration Since full lineshape iteration is both more time consuming and more unpredictable than assignment iteration gN MR provides you with a few settings that you can change to influence the iteration process these are the flattening parameter Cs and the factor C by which it is changed on going from one cycle to the next A value of Cs very close to zero implies complete flattening loss of detail values of Cs close to 1 or 1 imply little flattening Negative values for Cs use a bi exponential flattening function recommended positive val
8. Let us start with the experimental spectrum A high quality experimental spectrum is essential for a successful iteration In particular there should be no impurity peaks the baseline should not contain any hidden intensity and the relative areas of the various multiplets should be correct You can do some limited spectral editing using gSPG see Chapter 12 but in principle the experimental spectrum should be good enough before you convert it to gN MR format The reason that baseline errors and impurity peaks are so troublesome is that in the first few cycles gN MR tries to create the correct intensity distribution over the spectrum without bothering about agreements between individual peaks You can see this quite clearly if you monitor the progress of an iteration on screen chemical shifts and large coupling constants are determined rather quickly but the finer details giving rise to characteristic splitting patterns appear much later in the iteration If you havea hump in the baseline gN MR will try to match it possibly by generating one or more ridiculously large coupling constants If you try to prevent this by fixing coupling constants it will move the multiplets to an intermediate position between the hump and the real multiplet you are interested in Impurity peaks have a similar effect If you see something like this happening itis a 104 Full lineshape iteration Chapter 6 sign that gN MR cannot reproduce the experime
9. So if you try to simulate the spectrum of 1 chloro 2 bromo ethane which is an AA BB system by using an A2Bz type spin system you will never get the right parameters Your calculated spectrum may still look quite reasonable sometimes it is simply impossible to determine the nature of the spin system with certainty from the experimental spectrum 94 Assignment iteration Chapter 5 e You may not have supplied enough data to completely determine all parameters of the system For example if you want to use the X part of an AA X spectrum to determine the relevant parameters x Ada Jax Jax Jaa from peak positions only the final error analysis will show that one linear combination of parameters is undetermined The X spectrum consists of 6 peaks but is always symmetric Thus there are only 4 independent frequency data the center of the multiplet and three distances to the center Clearly this is insufficient to determine 5 parameters Inclusion of intensity data can be sufficient to determine all parameters e You may have made some errors in the assignments If you have interchanged say 2 out of 20 assignments the least squares iteration will usually still produce a reasonable solution because the 18 correct assignments dominate The spectrum display will not show any large discrepancies but the numerical assignment list will show a few large deviations that will stand out from the generally good agreement and if you dis
10. So you would enter 27 in the intensity fields of peaks 29 and 30 As a short cut you can type a lt gt to specify that you want to add the current peak to the group immediately above it in the example above assuming you are skipping peak 28 you could first enter 0 13 in the field of peak 27 and then lt gt in the fields of peaks 29 and 30 If you have an open Spectrum window containing an experimental spectrum and you have checked Show Assignments in the Settings Spectrum dialog box see next section the assignments visible there Figure 40 will be adjusted when you enter new data in the Assignments window If you have checked Highlight Assignments in the Settings File dialog Assignments section the peak being assigned will be highlighted in all Soectrum windows Assignment iteration 89 Figure 39 Assignments section of Settings File dialog Chapter 5 regardless of whether you have an experimental spectrum This helps you keep track of your position 5 5 Settings affecting the iteration The Assignment section of the Settings File dialog Figure 39 contains several parameters that affect assignment iteration File Settings Ea Assignments Assignment Thresh 2 Ue 02 M Group Assignments Grouping Threshold p 00e 02 Assignment Order Ascending l Highlight Assignments Iteration Assignment Threshold If there are only a few peaks in the spectrum all of them will always
11. files Varian VNMR does not normally store transformed spectra in its data files Instead it transforms the spectrum only on request and discards all transformed data after a session You can of course import the FID let gCVT do the FFT and phase the spectrum in gSPG However the following trick will allow you to pick up the transformed spectrum as well e Transform and phase your spectrum in VNMR using the usual file load process weight transform etc menu choices 156 File conversion General Electric GE SUN JEOL GX Chapter 11 e Moveto another VN MR experiment menu choices MainMenu Workspace expn and display some data there this forces VNMR to write the previously transformed data in the original experiment to disk e Start up a separate UN IX session without quitting VN MR Move to the experiment directory containing the temporary transformed data you are interested in The VN MR directories for the different experiments are usually called exp1 exp9 and are located in a directory vnmrsys their full path names will vary from system to system Copy the temporary transformed data file datdir phasefile On the GE SUN use the command export gefile exportfile to create a binary NMR data file with a text header and transfer this file to your PC in binary form Normally GE SUN files contain the name of the observe nucleus in the f 1_nucleus parameter and gCVT will use that name Sometimes the name of t
12. installing the database support will take another 8 30 Mb of disk space gN MR will simulate systems of up to 49 NM R active nuclei For systems up to 11 nuclei with the default settings exact simulation is used Above this limit the program switches to an approximate scheme Simulations of molecules larger than 10 nuclei will takea significant amount of memory and computer time A very fast but much less accurate approximate method is also available section 9 3 Exchange calculations are always much more expensive than normal simulations gN MR will do exchange calculations on molecules containing up to 5 or 6 nuclei 1 2 Installing the program Insert the gN MR CD run Setup exe and follow the instructions on screen The installer will always install the main program files ca 14 Mb In addition you can choose to install the following sets of files Tutorial ca 1 Mb Several files that are required by the tutorial Chapter 2 These files will be installed in the subdirectory Tutorial Import examples 32M b max Experimental spectra in various formats to illustrate import into gN MR The complete set will take up to 32MB of hard disk space We suggest that you install only those examples corresponding to your NMR instrumenation These files will be stored in the directory Import 2 Installation Chapter 1 Script samples and utilities ca 2 3 M b Texts of the structure and spectrum import scripts Appendix D cop
13. l Hide non Top files M Show Windows list ao Cancel Defaults Help The Spectrometer frequency Scale units Lineshape Isotropic and Include Quadrupoles items correspond to items in the gNMR Settings File dialog section 3 2 Undo level sets the maximum number of actions that can be undonein gNMR and gSPG Set this to 0 to disable Undo Redo Remembering actions for undo costs memory and time so we do not recommend using values larger than 20 Undo in gNMR is fairly coarse grained for example all editing in a single Molecule window constitutes a single action that can be undone In contrast gSPG undo is fine grained allowing Undo Redo of a single marker placement Start gNMR Determines how gN MR starts up There are four possible values 186 Customizing gNMR Appendix A Welcome dialog 9N MR starts with the Welcome dialog Figure 19 which has the choices of creating an empty file importing or pasting a structure or opening an existing gN MR file Settings File Creates a new empty file single molecule with 1H at 0 ppm and displays the Settings File dialog for it This can be useful to remind you to fill in a title and spectrometer frequency Empty Molecule Creates a new empty file single molecule with 1H at 0 ppm No new file gN MR will start up without creating a file or displaying a dialog Click selects whole field In several windows and dialogs data is entered or modified ina grid If this
14. Data are either peak positions for Tutorial 15 Defining variable names Figure 6 Molecule window with variables names Mouse assignment Chapter 2 assignment iteration or the datapoints of an experimental spectrum for full lineshape iteration Open the file ODCBDATA dta created in the first section of the tutorial or the file ODCB1 dta inthe Tutorial directory In the Molecule window click on the gray field below the first chemical shift This field is to contain the name used for the chemical shift of the A nuclei in the AA BB system So type an a and press lt gt to move to the name for the second chemical shift Type the remaining shift names b lt I gt b lt gt a lt gt In the empty row at the bottom press lt gt again to move to the next column and lt gt to move to the first coupling constant column Then type names for the coupling constants ab lt I gt ab lt J gt aa lt I gt lt J gt bb lt 1 gt ab lt gt lt 1 gt ab The window should now look like Figure 6 Alternatively you could have used the Molec ule Show Symmetry command to let gN MR assign names automatically as described at the end of the previous section Save the result for use in the next section as ODCBVars dta Options Spectrum To start the assignment procedure select iterate Assignments Window 1 1H from the menu bar The Spectrum window will appear as usual but now you can
15. FID and so it could be used immediately as an experimental spectrum in gN MR However here we will transform it with a line broadening of 1 Hz Select the AD window and then AD WFT The WFTdialog appears Near the top from the Function Type pulldown select Lorentz An edit field appears below this enter the line broadening 1 here Click on Update now to see the resulting weighting function and weighted FID Now click on the WFTbutton The FID is transformed the Spec tum window is updated but the WFTdialog remains You could keep on selecting other weighting functions and transforming until you are satisfied with the results Click on the Done button to dismiss the dialog The newly transformed spectrum is not phased correctly To phase it first move to the Spectrum window and then select Spectrum Phase The Phase dialog appears This contains three sliders corresponding to left phase pivot phase and right phase The pivot is initially at the highest peak but you can move it by clicking anywhere in the Spectrum window Moving the pivot slider applies a uniform phase correction to the spectrum moving the left or right slider changes the phase at that end but leaves the phase at the pivot intact so the phase at the other end is also adjusted In the present case a uniform correction i e using the middle slider of about 80 is nearly correct Getting the last bit right by hand is awkward so when the spectrum looks nearly right
16. FID from the peak list and then transforms it Direct uses the peak list to directly calculate the 182 Spectrum processing Chapter 12 spectrum using Lorentzians The two options differ slightly in how they handle phase shifts over the spectrum range 12 12 Print copy and paste Asin gN MR spectrum and FID output will never contain markers and a baseline Printouts and clipboard copies are always in black and white even if the screen display uses colors File Print Spectrum prints the spectrum If the spectrum is larger than the window so scroll bars are visible File Print Visible Part prints only the part that is currently displayed in the window If you have selected a subrange and then choose the Selection radiobutton in the Print dialog only the subrange part will be printed Edit Copy Spectrum copies the spectrum to the clipboard for pasting in eg a word processor or drawing program File data is not included in the copy by default but you can use the Settings Spectrum dialog Hardcopy section Include Data in Copy item to change this You can also keep the Shift key depressed while making the copy to use the opposite of the current Include Data in Copy setting this may result in very large copies File Export As WMF creates a placeable Windows metafile representing the spectrum or FID File Export As EPSF creates an embedded PostScript picture File Export As ASCII generates a text only list of y values for i
17. Open in gSPG gNMR checkbox at the bottom of the dialog before clicking Go 11 3 Getting spectra to your PC Nowadays most PC s and spectrometers are connected to networks Therefore you will usually move spectrum files to your PC using some kind of network transfer The most important issue here is that of file translation Text files are represented differently on PC s Macintoshes and UNIX systems On aPC a line of text is terminated by a CR LF File conversion 151 File names Chapter 11 combination OD 0A the Macintosh uses a single CR OD character and UNIX uses a single LF 0A character Therefore file transfer programs like ftp can do translations of text files to compensate for system differences This keeps text files readable but unfortunately translating a binary file produces nonsense Some ftp programs try to be smart about translation inspecting the first line s of a file to test for text files Since some file types may contain both text and binary sections this may result in inappropriate translations gCVT will accept text files whether they have been translated or not Binary files should never be translated If you use a program like ftp to transfer your files we recommend that you always specify the kind of translation you need TEXT or BINARY explicitly If you need to be able to read transferred text files yourself use TEXT translation for them and BINARY for the rest If you only want t
18. Strukturaufklarung organischer Verbindungen mit spektroskopischen M ethoden 294 ed Springer Verlag Berlin 1981 234 gNMR Index A Abbreviations 54 Anisotropic spectra 44 Approximate calculations 131 Aromaticity 54 ASCII 155 Assignments and symmetry 92 group 90 91 mouse 85 numerical 87 threshold 90 Baseline 74 correction 164 Baseline parameters 98 Baseline Fourier command 164 Baseline Linear command 164 Baseline Remove N oise command 166 Baseline Spline command 165 Baseline Truncate below command 164 C Chemical shift 50 Chunking 132 Concentration 45 97 gNMR Index Coupling constant 51 D DISN MR 155 Edit Auto Variables command 85 Edit Fix Variable command 85 Edit Free Variable command 85 Edit Variables command 84 Expanding spectra 205 Experimental spectra 71 local copy 72 F FID WFT command 171 File formats 221 File transfer 151 binary 152 text 151 Full lineshape iteration 97 G GE SUN 157 H Hz units 50 l Intensities 235 normalization 89 Isotopomers 49 restrictions 51 Iterate Assignments command 85 Iterate Continue command 102 Iterate Go command 93 101 Iterate Last Cycle command 102 Iterate Next Cycle command 102 Iterate Solutions command 103 Iteration assignments 83 intensities 87 marking parameters 83 97 peak positions 83 J JCAMP 156 L Lineshape 45 Linewidth indivi
19. Table C 3 Isotope mixture names recognized by gNMR Appendix C Name Name Name Name Name Name Name He 3 S 33 Cu 63 Sr 87 Sn 119 Eu 151 Re 187 Li 7 Cl 35 Zn 67 Zr 91 Sb 121 Gd 157 Os 187 B 11 K 39 Ga 69 Mo 95 Te 125 Dy 163 Ir 193 C 13 Ca 43 Ge 73 Ru 101 Xe 129 Er 167 Pt 195 N 15 Ti 47 Se 77 Pd 105 Ba 137 Yb 171 Hg 199 O 17 Cr 53 Br 79 Ag 107 Ce 140 Lu 175 TI 205 Ne 21 Fe 57 Kr 83 Cd 111 Nd 143 Hf 177 Pb 207 Mg 25 Ni 61 Rb 87 In 115 Sm 147 W 183 U 235 Si 29 C 2 Modifying the nucleus list Under certain circumstances you might not be satisfied with the standard list of nuclei used by gN MR In that case you can construct your own nucleus list as described below You should however be very cautious with this Existing gNMR data and spectrum files have been constructed based on data in the default list and the data in these files might not be valid in combination with any custom list you create this may lead to unpredictable results Therefore you should make sure never to use a data or spectrum file together with a nucleus list other than the one it was created with However just changing the display color for a specific nucleus is completely harmless The remainder of this section describes how to createa custom list On startup all gNMR programs will try to read a custom nucleus list from a file called gNMR41 iso in your Windows directory or in the gN MR director
20. a smaller distance since the two small peaks are closer together in the experimental spectrum than in the calculated spectrum When you are at the second peak click the mouse again The calculated line will now be positioned at the right flank of the first large peak in the calculated spectrum M ove the observed line to a similar position and click again This time the Tutorial 17 Chapter 2 calculated line will hardly move this large peak actually consists of two components and we want to assign both of them You can click the mouse immediately or first try to position the observed line just a bit better This is not too important in this case the accuracy of mouse assignment is limited by the screen resolution so you can hardly expect to do better than a 1 pixel error in the assignments Do the rest of the assignments in a similar manner there are 24 peaks in all but a few may coincide After you have assigned the last one you will hear a beep and the calculated line will move back to the first peak of the spectrum With the assignments complete press lt Esc gt to return to the normal spectrum display Save the data File Save As aS ODCBMoul dta You are now ready to start the iteration choose Iterate Go A small iterate window will appear in which you can see the progress of the iteration the point number and a sum of squares error will be displayed The Log window will also become visible iteration progress in
21. as shown in Figure 1 this can be used to enter data for a single molecule E Document Molecule 1 OF Xx eee eee f Nucleus wW J ppm Hz 1 Sie ooo O Oo ee Options Spectrum The Molecule window is similar to a spreadsheet it has columns for types of nuclei shifts coupling constants etc Every nucleus is represented by two lines the first is for actual data the second can be used to enter variable names covered in the next section Initially the data window contains only a single row of data representing a 1H nucleus at 0 ppm Directly below it is an empty row If you enter any non zero data in this empty row you will see that the spreadsheet expands a new nucleus is inserted in place of the empty row and anew empty row is added You can delete a row by entering a 0 in the number of nuclei column for that row Alternatively you can press the lt gt or lt gt key in the number of nuclei column to add or delete a nucleus 8 Tutorial Chapter 2 Before entering the data for a molecule it is a good Hy idea to analyze the system on paper e g to establish CI H2 a numbering scheme for the spins in the system In the case of o dichlorobenzene ODCB we have Cl Hs decided to number the nuclei as shown This gives Hy three ortho coupling constants J12 J 34 and J 23 of approximately 8 Hz two meta couplings J13 J24 of around 2 Hz and a single para coupling J14 estimate
22. back into gN MR since most drawing programs interpret the clipboard data and throw away any embedded extra information Four other spectrum output options may be useful File Export As SPG creates a spectrum spg file corresponding to the calculated spectrum File Export As ASCII creates a text representation of the calculated spectrum data straight series of y values one per line which could eg be imported in a spreadsheet Displaying spectra 79 Chapter 4 File Export As WMF creates a placeable Windows metafile representing the spectrum File Export As EPSF creates an embedded PostScript picture of the spectrum This always uses a H elvetica font for all texts even if you have selected other fonts for texts in gNMR Appendix A The Hardcopy section of the Settings Spectrum dialog Figure 35 contains several items relevant to hardcopies and clipboard copies Figure 35 Settings Tapie Hardcopy Spectrum dialog E Hardcopy section Line thickness 1 72 IT Print Nucl Ranges in M Include all data in copies Iteration Ake Baseline Cancel Apply Help Line thickness can be used to set the line thickness in units of 1 72 The default is 0 25 which produces good quality output on most laser printers If you need to reduce the size of the spectrum so much that the line thickness drops below 1 pixel on the printer you may want to use a slightly larger line thickness Include a
23. by an arrow as shown in the Figure You can click and Shift click on the same nucleus to indicate that it doesn t move in the reaction After specifying all nuclei that do move you can also press lt gt to complete the current permutation by letting all remaining nuclei stay in place After Chemical exchange 115 Chapter 7 specifying the permutation with mouse clicks you will of course still have to enter a rate to create a valid reaction Figu re 43 E J ExchTestStr Exchange Exchange window H4 SH ee gt showing a structure ee n H a Ii a Clear All Spectrum If you click on a nucleus for which a destination has already been set this indicates that you want to specify anew destination within the same reaction To start on a new reaction first click on any field in the empty rightmost column of the window and then start clicking in the structure again Of course you can also mix mouse and keyboard entry when creating permutations If you have imported a structure chances are that gN MR has folded nuclei it thinks are equivalent e g the protons of a methyl group into an equivalence group This is usually OK but sometimes you may want to exchange just one nucleus of such a group with another nucleus for an example see section 7 6 In that case you may have to split the equivalence group within its Molecule window see section 3 7 before starting to enter the permutation 7 5 Marking rate
24. can use Spectrun Regions Auto Integrate to let gNMR find interesting regions of the spectrum automatically You are left in integral break mode so that it is easy to add or delete breaks afterwards To clear all integral regions at once use the Spectum Regions Clear All command If you havea calculated and an experimental spectrum integrals are always displayed in both spectra simultaneously and the same breaks are used for both 4 6 Links between Spectrum Molecule and Exchange windows Sometimes it is easy to lose track of which multiplet in a spectrum corresponds to which nucleus in a molecule gN MR can help you here If Show Nucl Ranges in the Settings Spectrum dialog is checked this is the default the spectrum will show range indicators for each nucleus above the multiplets in the spectrum If you select an atom in a structure or a single nucleus field like a chemical shift in a Molecule window the corresponding indicator in the Spec trum window s will be highlighted If you double click the atom or chemical shift a Spectrum window containing that nucleus will come to the front and the range of that nucleus is selected as a subrange see section 4 2 If you double click on a multiplet in the calculated spectrum you will be moved to the corresponding chemical shift field in the Molecule window If there is more than one nucleus that could correspond to your double click a popup menu will appear from which you can choose the
25. column 2 row 3 of this matrix corresponds to J 3 the coupling between spin groups 2 and 3 Since couplings are symmetric that is Jij Jji only the lower half of the matrix is normally shown If you are calculating anisotropic partially oriented spectra however the full matrix is shown the area below the diagonal is used to hold the indirect couplings Jij and the area above the diagonal will contain the direct dipolar couplings Dj For quadrupolar nuclei or spin groups containing more than a single nucleus self couplings Di on the diagonal are also needed 3 5 Isotopomer mixtures The use of isotopomer mixtures introduces a few complications not encountered in normal molecules Entering data 51 52 Chapter 3 Coupling constants will be different for each isotope in the mixture Therefore you will have to enter them for a certain agreed upon isotope called the main isotope This is why gN MR uses notations like Pt 195 which means use the natural abundance mixture but assume that all supplied coupling constants refer to the main isotope 1 Pt Conversion to values for the other isotopes if necessary will be done automatically isotope shifts are ignored by default but see below If some of the NMR active isotopes of an isotope mixture name have spin 2and some havea higher nuclear spin the treatment of the higher spin isotopes depends on the setting of the filewide Include Quadrupoles parameter see sectio
26. desired nucleus During simulation you will often want to see how the spectrum depends on a particular parameter eg a shift or coupling constant One way of doing this is by repeatedly entering a new value and recalculating the spectrum A less repetitive alternative is to select the Displaying spectra 77 Figure 34 Edit Interactive dialog Chapter 4 field of that parameter in a Molecule window and then choose Edit Interactive xx where xx represents the parameter e g Delta l1 A dialog appears Figure 34 that contains a vertical slider moving the slider changes the parameter value When you release the slider the spectrum is recalculated If you want quicker feedback check the Quick box which causes the spectrum to be recalculated immediately after any slider movement You can also type a new value and click the Apply button To change the sensitivity of the slider click the 10 or 10 button When you are done click the Done button to accept the new value or the Cancel button to return to the old values Interactive x Deltaf1 11 194 Sensitivity j 10 10 3 194 F Quick i Cancel ees Help This method for interactively changing parameters can also be used for individual linewidths isotope shifts section 3 5 exchange rates in the Exchange window click on a rate field and select Edit Interactive K x and whole spectrum linewidths in a Spectrum window select
27. dialog section 4 2 You can also toggle marker display on or off with the Spectrum Markers Hide Spectrum Markers Show commands and delete all markers from a spectrum with the Spectrum Markers Clear Markers command The Spectrum Markers Marker Info command can be used to display the positions of markers In the dialog Figure 33 you can select two markers from pulldown menus The rest of the dialog will then display their positions difference and average in both ppm and H2 Markers will never appear in hardcopies or clipboard copies From E 7 135 ppm 2140 56 Hz To 2 7 365 ppm 2209 54 Hz Average 7 250 ppm 2175 05 Hz Difference 0 230 ppm 68 97 Hz ve In a Spectrum window you can display the integral of the calculated and experimental spectrum Integral display can be toggled with the Spectrum Regions Show Integral Spectrum Regions Hide Integral command Integrals are normally displayed only within 76 Displaying spectra Chapter 4 specific integral regions which are separated by breaks the integral will be alternatingly visible and invisible after breaks If you turn integral display on with Spectrum Regions Show Integral or Spec trun Regions Set Integral Regions the cursor shape changes to a broken integral Clicking in the spectrum adds a break Ctrl clicking removes a break You leave integral break mode by pressing lt Esc gt Instead of manually defining the integral regions you
28. distribution disk to your harddisk We recommend installing it in the Database Access Subdirectory of your gNMR directory Start the ODBC administrator this is located in the Control Panel and is usually called ODBC or 32bit ODBC Click on the tab User DSN and then on the Add button In the dialog that appears select the Microsoft Access Driver and click on Finish This will produce the Access Setup dialog Click on the Select button and browse to the gNMR41 mdb file Fill in a Data Source Name eg gNMR Tutorial 29 Figure 14 ODBC Administrator window after definition of an Access data source Chapter 2 Access and optionally a Description sample gNMR Access database Then click on OK The ODBC Administrator window should now display the newly defined database Figure 14 Click on OKagain to leave the ODBC Administrator ODBC Data Source Administrator xi User DSN System DSN File DSN ODBC Drivers Tracing About User Data Sources Add Microsoft Excel Driver xIs Remove Microsoft Access Driver mdb Microsoft Access Driver mdb Configure MS Access 7 0 Database Microsoft Access Driver mdb the indicated data provider 4 User data source is only visible to you and can only be used on the current machine An ODBC User data source stores information about how to connect to Start the BDE administrator program BDEadmin and click on the Databases tab This should a
29. even if all exact factorizations S2 and Sz for each type of nucleus molecular symmetry are exploited Therefore one rapidly reaches the limit computers can handle 10 spins can be done on a PC or Macintosh but 15 spins is impossible even on a Cray The problem size grows so quickly because all interactions between spins are treated equally This is necessary for a system where every spin couples strongly to every other spin but in practice such a situation is rarely encountered It is often possible to divide the system into regions which are only connected by weak couplings This can be exploited by the use of perturbation theory the sub systems are solved separately and the weak interactions between them are then added as a correction gNMR automatically detects the presence of such weakly coupled regions and divides the system accordingly The use of perturbation theory does not make NMR simulation much faster but as in the symmetry case the memory requirements are reduced so you can handle larger systems gNMR only employs perturbation theory if it is safe to do so a spectrum calculated using perturbation theory should never differ significantly from an exact calculation Neither symmetry nor perturbation theory actually reduces the number of states that are involved in the NMR calculation both methods just divide the problem into smaller parts that can be solved one by one treating fewer states at a time However the number of
30. files Use File New to start on a new empty gN MR file This will initially contain a single ae a molecule having a 1H nucleus at 0 ppm P Close File Open opens an existing file You can rosal a also choose from the list of recently used files Save Ctrl S under File Recent When you open afile its geas Molecule and if applicable Exc hange Print Setup windows will be opened immediately the Print Spectrum thP Log window will be shown in minimized Print gt state Save EPSF Save WMF Save SPG File Close doses the current file if i Exit AlF4 necessary you will be prompted to save Get Info your changes first File Close All closes all a open files File Save and File Save As save the currently open file File Revert reverts to the last saved file contents You can also use the Edit menu Undo and Redo commands to move backwards and forwards in a sequence of changes File wide parameters can be set through the Settings File dialog The dialog Figure 20 has several sections of which only the one labeled General is relevant here Assignments is discussed in section 5 5 Iteration in section 6 4 and Symmetry and Approximations in chapter 8 Entering data 43 Figure 20 Settings File dialog General section Chapter 3 File Settings Ea Topic General File title Benzene anisotropic amp Spectrometer Frequency Symmetr
31. for this specify all four permutations to ensure that they keep the same rates link the rates see section 7 2 e lt Ghethical exchange Figure 45 Simultaneous methyl rotation and proton exchange processes Chapter 7 Sometimes you might encounter exchange involving apart of a group of equivalent nuclei such as the intramolecular exchange of a single proton with a methyl group You cannot enter such a reaction directly since gN MR will not accept an exchange between groups containing 1 and 3 equivalent nuclei This is reasonable what actually happens is exchange of a single hydrogen combined with rapid rotation of the methyl group This suggests the way to simulate the problem enter the methyl groups as three separate hydrogens 1 2 and 3 with identical shifts and coupling constants add the extra hydrogen 4 and then define two permutations as illustrated in Figure 45 The first is the methyl rotation which will havea very high rate say 10 to ensure equivalencing of the methyl protons the corresponding permutation would be 2314 The second permutation is the reaction you are really interested in Enter a realistic rate for this and a permutation which causes exchange with a single methyl proton eg 4231 methyl rotation proton exchange i Hs 4 Hp Hp H4 HZ Hj gt H 152 134 233 2 gt 2 31 333 44 4 gt 1 or or 2314 4231 Chemical exchange 119 Chapter 8 8 Symmetry 8 1 Symmetry an
32. gN MR is a program for simulation of one dimensional NMR spectra Included in the package are separate programs for importing foreign spectra gCVT and for processing such spectra gSPG Simulation of spectra of arbitrary nuclei Mixtures of up to 10 components Automatic handling of isotope mixtures Use of structures created in chemistry drawing programs Chemical exchange calculations Iterative optimization of shifts coupling constants exchange rates etc Anisotropic spectra Simulation of larger systems using symmetry and or various approximate methods Store spectra and data in databases You can store your own data and spectrum files in dBase Paradox and ODBC databases This may be a more convenient way of organizing your data than keeping individual files around Also you can search these databases for specific properties filename title nucleus etc Chapter 10 Improved parameter prediction using databases Data you store in databases will be used to improve parameter prediction for new structures you import Chapter 10 Installation 1 Limitations and requirements Chapter 1 M ore spectrum processing options Inverse transform reference deconvolution linear prediction Chapter 12 gN MR V4 1 requires a 80486 or higher CPU It runs under Win32 and therefore requires Windows 95 98 or Windows NT A Pentium or higher at least 16 Mb of memory The minimum installation requires about 8 Mb of disk space
33. gt button and Spectrum Horz 2 p4 button double and halve the horizontal size while leaving the display limits intact Spec trun Vert 2 button and Spectrum Vert 2 X button double and halve the vertical size Spec tum Expand Selection expands the current subrange see above to fill the window Spectrum Resize with Window toggles the coupling between window size and spectrum size on or off If Resize with Window is checked resizing any Spectrum window will result in the resizing of the spectrum inside it so that the spectrum including texts and axes exactly fits in the window If the menu item is not checked window size and spectrum size are unrelated If you then resize the window to a smaller size than the spectrum inside it scroll bars will appear Settings xx units or the lt Ctrl U gt shortcut can be used to toggle between Hz and ppm axes units The Dimensions section of the Settings Spectrum dialog Figure 28 controls spectrum content and size 66 Displaying spectra Figure 28 Settings Spectrum dialog Dimensions section Chapter 4 Spectrum Settings Ea Topic Dimensions fiH gt 0 20 13 884 Nucleus Linewidth Hz Scale Hz cm From ppm 7 036 0 pane To ppm 7 475 9 23 9 47 Vert Size cm T Absolute Scaling Hor Size cm po Cancel Apply Help Iteration Aus Baseline Nucleus This pulldown menu allows you to select a di
34. in a single directory To configure a Paradox or dBase database start the BDE administrator program BDEadmin Click on the Databases tab select Object New and in the small dialog that appears select STANDARD for the Database Driver Name This will produce a new entry in the list of databases Change the name of the new entry in the left pane of the window from STANDARD1 to aname of your choice e g gNMR PDox In the right pane which has a single tab Definition fill in the name of the directory containing the Paradox database files under the PATH variable if you click in the empty field to the right of the PATH label a button labeled will appear which you can click to browse for the directory 140 Databases Initializing a database Opening a database in gNMR Setting the default database Chapter 10 Select Object Apply to save the new settings and then Object Exit The database is now available for use by gN MR If you create a new database following either of the above procedures it will be completely empty gN MR can only use it if it contains definitions for tables and indexes The gBase utility can be used to create these Start gBase and choose the Database Select Database command In the dialog that appears select the newly created database from the pulldown and click on OK Then choose Database Create Tables After the command has completed quit gBase 10 4 Using databases with gNMR The simpl
35. involving low intensity transitions are then dropped The criterion for this is that the intensity of the transition is lower than the default peak neglect criterion and lower than 10 of the most intense transition divided by the exchange rate For per nucleus calculations the intensity contributions of the target nucleus to each peak are calculated see F 2 and then are used both for matrix reduction and partial exchange calculation F 8 Chemical shift prediction Chemical shift prediction in gNMR is mostly based on additivity rules given by Pretsch gt The file gNMR41 abr contains a list of standard group abbreviations like Et Ph COOH that can be expanded on structure import The file gNMR41 frg contains base molecules and fragment increments used to predict shifts In cases where gN MR cannot find an increment for a fragment it will usually just ignore the fragment which may result in some odd predictions The following differences from standard increment calculation should be noted e gNMR does not try to distinguish between cis and trans increments at double bonds e The base molecule list is longer than the list of molecules for which substituent increments are available Where applicable gN MR will try to combine the base shift of a complicated molecule with increments for a simpler system Also increments for carbocycles will be used where increments for nitrogen containing aromatics are not available 230 Technical
36. issues D atabase prediction Appendix F e For calculation of 1H shifts of aliphatic hydrogens gN MR uses a modified list of two bond distant substituent increments and then adds a correction for three bond distant substituents The 1H shift calculation is not completely additive e A non additivity correction factor is used for the calculation of unsymmetrically substituted phosphines phosphinoxides etc For fragment recognition gNMR constructs environments for a nucleus including from 1 up to 5 bonds away from that nucleus These are then matched against the database The largest fragment match i e for as many bonds as possible is used but only a complete match for the same number of bonds in all directions is accepted Bond orders and cyclic structures are included in the encoded environment For every bond path gNMR generates two encodings one including only the atoms on the bond path and one also including all atoms one bond away from this path Bond orders and cis trans information is used in the path if possible Substituents are encoded like atom environments except that the base fragment they are attached to is excluded from the encoding gN MR will accept a substituent prediction if it can find a match for all substituents the match for different substituents may have different numbers of matching bonds including 0 bonds only a match for the first atom of the substituent Technical issues 231 References
37. may want to fix or free a set of linked parameters You could do this manually by adding or removing a leading character from the name of each parameter A quicker way is to select Edit Free Variable or Edit Fix Variable and let gN MR do the task automatically The Edit Auto Variables menu choice automatically assigns variable names to all parameters of the current molecule based on the permutation symmetry of the system 5 3 Mouse assignments To use mouse assignments you must have prepared at least one Spectrum window showing an experimental spectrum see section 4 3 for details gN MR allows you to display the connections between observed and calculated peaks in the Spectrum window see sections 4 2 and 5 5 if you do this before starting mouse assignment you will see the connections change during the procedure which can be helpful Once you have prepared a Spectrum window select Iterate Assignments from the menu bar In the submenu that appears you can select the correct Spectrum window each entry will show both the window number and the nucleus name For example Window 1 1H means that window 1 contains an experimental 1H spectrum that could be used for mouse assignments Assignment iteration 85 Figure 37 Spectrum window during mouse assignments with status bar showing frequencies Chapter 5 If you select one of these Spectrum windows it will be shown with a vertical line in the calculated spectrum A
38. multiplication by zero would remove all noise Spectrum processing 167 Figure 56 gSPG Spectrum Regions Modify dialog Chapter 12 Modify Integrals Ea From Method 0 942 1 088 1 891 2 110 2 913 3 059 Multiply Multiply Multiply You move between the items with the usual lt gt lt Tab gt lt Shift Tab gt and vertical arrow keys or with the mouse The adjustment method fields are all small pop up menus with just two choices each When you have entered your changes click Apply to start the modification or Cancel to abort Spectrum Regions Peak List Analyzes the integral regions to generate peak lists The peaks in the list are obtained by least squares fitting to the transformed spectrum and a single linewidth is also fitted per region Overlapping peaks are handled correctly This option should only be used for high quality spectra with not too many peaks per region To set an amplitude threshold for peak list generation press the Shift key before choosing Spectrum Regions Peak List This will result in a horizontal line in the spectrum Use the mouse to move the line to the desired height above the baseline and then click to set the threshold This does not set an absolute threshold but rather the height by which a peak must extend above the surrounding datapoints to be recognized Peaks being detected will be numbered more information about them can be
39. next peak lt S gt lt Space gt Moves to the next peak without doing any new assignment for the current peak N gt lt gt Moves one peak to the left and changes the processing order to right to left P gt lt gt Moves one peak to the right and changes the processing order to left to right lt gt Home gt Restarts assignments starting from the rightmost first peak in the spectrum lt L gt lt End gt Restarts assignments starting from the leftmost last peak in the spectrum lt Esc gt Terminates the assignment procedure and returns to the normal spectrum display 5 4 Numerical assignments The numerical assignment procedure allows you to enter assigned frequencies and or intensities for calculated peaks You need not enter observed data for all peaks but you should at least try to supply data for all major peaks in the spectrum The frequency ordering of calculated and observed peaks need not be the same if in doubt it is best to try an order which already has a reasonable agreement in both frequencies and intensities even if you are not going to iterate on intensities Intensity data are a special problem in iterative calculations gNMR expects them to be normalized that is to add up to the correct number of nuclei times the molecule concentrations if appropriate Even if some intensities are missing from the list the program assumes that the rest are on the correct absolute scale A second
40. optimized are scaled versions of these constants with the scale factors chosen to ensure that all parameters have a similar influence on the appearance of the spectrum Jones spiral algorithm with corrections noted by Binsch 3 is used for the minimization To avoid problems with ill determined parameters the Taylor series condition o Aj41 A B is solved using singular value decomposition with a singular value cutoff threshold which is decreased in successive points of the minimization Technical issues 227 Appendix F All derivatives needed for assignment iteration are determined analytically The frequency derivatives are calculated from the usual energy level derivative expression En a Glai P OP Calculation of intensity derivatives is more complicated and has not been described before for this particular case The basic expression is TBa Sie a 2 Alay TO Op Op OP p The wavefunction derivatives needed in this equation are given by perturbation theory as Q Q ani am _y P OP Izm Em This expression causes difficulties in cases of near degeneracy Since assignment problems occur in such cases anyway the perturbation summand is replaced by e E j oH os E o m 1 for len el lt E thresh E thresh thresh 0 p j This modified term goes smoothly to zero if and m become degenerate F 6 Full lineshape iteration Direct least squares fitting of observed and
41. peak in the Spec trum window plus space needed for titles range indicators axes and labels If you have enabled absolute scaling see below Vert size represents the vertical size of a peak corresponding to a single nucleus with a 1 Hz linewidth Absolute scaling Normally you use the Vert size parameter see above to set the vertical size of the calculated spectrum In some cases however you might want to use an absolute vertical scale for example to have a consistent scaling for different Spectrum windows In that case you can check Absolute box and then set the desired absolute size above You have to do this for every window for which you want to use absolute scaling Fixed Exp Scale Check this if you want to havea fixed ratio of calculated and experimental vertical scales irrespective of the spectrum areas in the selected region A field will appear where you can enter this ratio If the option is unchecked the default gN MR will always scale the experimental spectrum to have the same area as the calculated spectrum The Display section Figure 29 controls display of individual spectrum elements 68 Displaying spectra Figure 29 Settings Spectrum dialog Display section Chapter 4 Spectrum Settings Ea Topic vale 2 a Dimensions V Show Info l Show Assignments Display M Show Integral V Show Markers Number gt M Show Nucl Ranges I Messages to Log file Ite
42. r Non linear least squares rror M Rotate Unfilter Baseline Corr 0 l 150 50 1 0e 04 Analysis l Remove lt noise F Remove lines gt F Reset linewidths to r Remove out of phase pe F Reset all phases to 0 1 000 100 000 0 100 iki i aks Transform Spectrum size Via FFT C Direct 16384 Cancel Help Chapter 12 The LP dialog is invoked by the AD Linear Prediction command The first set of options select the algorithms to be used in the LP procedure Method This specifies the basic LP algorithm Choices are Std SVD standard SVD the original LP SVD approach TLS total least squares 5 and Sel SVD selective SVD similar to the H ankel SVD approach Selective SVD appears to be the more stable algorithm but it also is the most expensive one for high degree prediction Total least squares appears to be preferable to Standard SVD in most cases although the differences are generally not dramatic Spectrum processing 179 Chapter 12 Use conelation function The LP algorithm can either be applied directly to first part of the raw FID data or if this option is checked to a correlation function calculated over the whole FID In our experience the use of a correlation function generally gives better results and is only marginally more expensive Non linear least squares The LP procedure first determines frequencies and li
43. simulation Section 2 2 e Iteration section 2 3 e Exchange calculations section 2 4 e Installing and using a sample database with gN MR section e Spectrum transformation and phasing section 2 6 The last section of this chapter introduces a few special topics using sample files provided on the distribution disks The sections on data entry and exchange start with examples that do not use a molecular structure only after this do they show how the same results could be obtained with a structure You may well find that using structures to set up simulations is more convenient Nevertheless it is important to realize that the data shifts couplings entered determine the results of a simulation The structure is only a way to facilitate entering the same data gN MR tries to predict NMR parameters from structures but the prediction is not very accurate So if you use a structure always check whether the shifts and coupling constants generated for it make sense Tutorial 7 o Dichloro benzene without a structure Figure 1 Empty Molecule window Chapter 2 2 2 Data entry and simulation This section covers e Data entry without a structure e Comparing with an experimental spectrum e Data entry with a structure Start the gN MR program by double clicking the gN MR program icon The Welcome dialog appears choose the top option Start with an empty molecule by clicking on its button An empty Molecule window appears
44. spectrum data However phasing next section requires both components of the spectrum The AD Reconstuct Imaginary and Spectrum Transform Reconstruct Imaginary commands let you reconstruct the imaginary parts of an FID and a transformed spectrum respectively There are no further parameters to set If you don t need the imaginary component of an FID or spectrum any longer you can discard it using the AD Discard Imaginary or Spectrum Transform Discard Imaginary commands Sometimes an experimental spectrum has a strongly non ideal lineshape This may for example be due to poor shimming Obviously it would be desirable to rerecord such a spectrum with more careful shimming but this may not always be possible If the spectrum is relatively noise free it is possible to correct it by reference deconvolution a reference peak is selected and inverse transformed a correction filter is constructed from this transform and that of an ideal lineshape the whole spectrum is inverse transformed multiplied by the correction filter and re transformed The new lineshape should not be set to a much smaller value than the original lineshape else the deconvolution will result in strong amplification of noise To carry out a reference deconvolution first select a reference peak by dragging the mouse The peak should be fairly well isolated from other peaks and the region selected to enclose it should not be too narrow Then select Spec tum Transf
45. states also grows exponentially with the number of spins in the system no method that does not reduce the number of states can help for really large molecules Clearly larger systems require some kind of approximate treatment This chapter describes two Approximation calculations 131 Chapter 9 approximate methods that can be used for static systems and some approximations available with exchanging systems 9 2 Chunking gN MR uses an experimental scheme for approximate calculations The idea is that to simulate the part of the spectrum that is duetoa single nucleus A we only need to include a limited number of other nuclei certainly those coupling directly to A and possibly a few more some of which could be handled as X nuclei The spectrum of this chunk can easily be calculated but of course the parts of it not due to A will probably be inaccurate Therefore we only retain the part that is really due to A If we repeat this procedure for every atom in the molecule and then add the resulting subspectra we eventually end up with a complete spectrum This method scales linearly in the number of chunks and thus in the number of atoms as long as the chunk sizes are limited By default gN MR switches to the use of chunking if the system becomes larger than 11 spins it then uses a maximum chunk size of 9 atoms You can change these defaults section 9 5 In our experience the default settings give satisfactory results unle
46. symmetry by gN MR In general you do not need to worry about how gN MR uses symmetry The appearance of a calculated spectrum is completely determined by its collection of shifts and coupling constants and Symmetry 121 Determining the symmetry of an existing molecule Creating a symmetric molecule Symbolic systems Chapter 8 should be the same whether the simulation program uses symmetry or not In case of doubt you can disable symmetry usage section 8 3 8 2 Entering symmetric systems If you have already entered a complete molecule including shifts and coupling constants gN MR will be able to determine and use the symmetry present in the system for simulations However if you change a single value in the system its symmetry related values will not be updated automatically so the symmetry will be lost The Molecule Show Symmetry command section 3 3 lets you determine the current symmetry if you click the Enforce button in the resulting dialog gNMR will add variable names to ensure that the symmetry will be preserved Choosing Edit Auto Variables is equivalent to Molecule Show Symmetry plus Enforce The purpose of using symmetry input is that you can be certain that your molecule gets and keeps the correct symmetry regardless of the numeric values you supply for shifts and coupling constants This is ensured by the use of variable names Two gNMR symmetry input facilities can help you set up the names see eg
47. that you can change to let gNMR use first order calculations Simulation can be set to Nomal uses exact or chunking calculation unless the system size exceeds the Approx Method Threshold size see below Approximate uses first order simulation including thatch effects regardless of system size First order uses first order simulation including only simple splittings i e not even thatch effects regardless of system size Approximate Method Threshold spin systems larger than this threshold size are treated by the approximate first order method unless the Chunk size threshold has been passed first Set to 0 or a very large value to disable approximate first order treatment With the default setting of 15 first order methods will never be used since chunking previous section kicks in first Approximation calculations 133 Chapter 9 9 4 Approximate exchange calculations The size of an exchange calculation scales even more dramatically with the number of spins than that of a static calculation Therefore an exchange calculation may easily run out of memory or take forever for molecules containing only 6 or 7 spins None of the techniques described earlier in this chapter can be used to simplify exchange calculations We have incorporated two methods in gNMR which can under certain conditions enable calculation of slightly larger systems Both are based on the use of an eigenfunction basis for the exchange ma
48. the permutation The top row of the Exchange window will contain the rates one for each reaction A B Clear All Spectrum Clear All Spectrum 24 Tutorial Exchange in dialkyl formamides Chapter 2 To start the data entry type a value of 300 in the topmost field of the first empty column Below this field you will see the text Inc ompl This field is used to indicate the status of the reaction you are entering It will show the text Inc ompl as long as the reaction is incomplete or incorrect As soon as you have completed entry of the reaction rate and permutation it will change see below For now we can ignore this field press lt gt to move over the indicator to the first field of the permutation This is going to contain the destination of the first nucleus Since our reaction is a simple exchange of two nuclei the destination of the first nucleus is 2 and the of the second is 1 So type 2 lt gt followed by 1 lt gt You will see that the Incompl below the rate changes to a pop up menu with the setting Fixed indicating that you have entered a complete and correct reaction A new column will also appear allowing you to enter a second permutation but you can ignore this The completed Exchange window is shown in Figure 11B To finally see the results click Recalculate a spectrum showing a broadened singlet will appear in the Spectrum window You can recalculate the spectrum for different rate
49. the results A Spectrum window will appear showing the calculated spectrum Figure 3 10 Tutorial Figure 3 Spectrum window for ODCB Comparing with an experimental spectrum Chapter 2 Document Spectrum 1 ioj x Fri Sep 19 20 38 19 1997 ODCEB tutorial example W1 1H Axis ppm Scale 16 58 Hz cm 14 23 rma 7 450 7 400 7 350 7 300 7 250 7 200 7 150 7 100 7 050 After inspecting a simulated spectrum you may wish to compare it with an experimental result If you have installed the tutorial files your Tutorial folder will contain an experimental 300 MHz ODCB spectrum which we will use to illustrate this With the Spec trum window still in front select Settings Spectrum This controls various display settings which are grouped into separate topics for convenience Select a topic by clicking its icon from the list at the left and enter values in the pane displayed at the right of the box To display the experimental spectrum click the Iteration icon then click the File button and select the file oDCB spg using the standard file dialog The item Display will become visible and is set to Both Up indicating that both calculated and experimental spectra are available Click OK a double trace appears with the experimental spectrum drawn above the calculated one Figure 4 Tutorial 11 Figure 4 Spectrum window with calculated and experimental spectrum Chapter 2 YZ Document S
50. there is one completely undetermined linear combination the difference between the two Jpc s Tutorial 37 Figure 17 Observed spectrum and peak list for an AX X system Approximate simulation Chapter 2 ppm Hz Intensity 1 136 635 9275 97 0 021 2 136 818 9288 41 0 643 2 137 025 9302 47 1 188 4 137 232 9316 59 0 691 R 137 401 9328 01 0 013 mananan WW Mirena 138 000 137 500 137 000 136 500 136 000 Systems larger than ca 12 spins the precise limit depends on system symmetry and other factors cannot be simulated in an exact manner the required amount of computer time and storage would be prohibitive However most real molecules are larger than this If a molecule gets too large for normal exact simulation gN MR switches automatically to an approximate method called chunking Though not exact this method normally gives rather accurate results Itis not very fast but its time and memory requirements do not increase very steeply with system size allowing it to be used for fairly large molecules Asan example let us simulate the spectrumof gt OF vinyl 4 hydroxy 5 chloro 6 phenyl 7 methyl cycloheptene This is a 19 spin system far beyond the reach of exact simulation Import the tutorial file 7ring cwg into anew gNMR file using File Import ChemWindow the shifts and couplings predicted by gNMR may not be accurate but that is not the point of this exercise Calculate th
51. to the situation before the start of the iteration define the necessary variable name see sections 5 2 and 6 2 and try again 208 Questions and answers Appendix C C Nuclei recognized by gNMR C 1 Standard nuclei The following three Tables list all nuclei recognized by gNMR Table C 1 contains NM R active isotopes with their spin resonance frequency relative to 1H 100 000 MHz and natural abundance in Table C 2 contains NMR inactive isotopes and Table C 3 contains the isotope mixture names which will generate isotopomer mixture spectra when used in gNMR TableC 1 NMR Name Spin Freq Abund Name Spin Freq Abund active nuclei recognized by gNMR Nuclei recognized by gNMR 209 Appendix C Table C 1 cont Name Spin Freq Abund Name Spin Freq Abund 210 Nuclei recognized by gNMR Table C 1 cont TableC 2 NM R inactive nucle recognized by gNMR Name Spin Freq Abund 57 149 57 708 20 921 203T 205T 207Pb 1 5 1 5 1 5 Name Abund 29 50 70 50 22 60 Name Abund Nuclei recognized by gNMR gt 5 Tia 209Bi 235U 16 069 1 790 Name Abund Appendix C Name Spin Freq Abund 100 00 0 72 211 Appendix C Table C 2 cont 176Hf 178Hf 180H f 180Ta 180W 182W 184W 186W 1840s 1860s 1880s 1900s 1920s 190Pt 192Pt 194Pt 196Pt 198Pt 196H g 198Hg 200H g 202H g 204H g 204Pb 206Pb 208Pb 238U 212 Nuclei recognized by gNMR
52. were in the drawing program Numbers Atoms will be labeled by numbers indicating their position in the spin system Molecule window Entering data 59 Chapter 3 Nuc Names Atoms will be labeled by their full gN MR isotope names Nrs Niames Atom labels will consist of their position in the spin system plus the full isotope name Shifts Atoms will be labeled by their chemical shifts Hements Atoms will be labeled by their element names only 3 8 Modifying structures gN MR is not a structure drawing program Normally you will use your favorite drawing program to create structures and only import the final structure into gNMR Occasionally you might want to modify a structure lightly after importing it gN MR offers some possibilities for that You can move atoms by Ctrl dragging If you Ctrl drag on an atom not previously selected only that atom will move If you Ctrl drag on one atom of a selected set all selected atoms will move You can delete a set of selected atoms with the Stucture Delete Atoms command These atoms will of course also be removed from the spin system N ew atoms can be added by adding new nuclei to the spin system they will appear below the rest of the structure not connected to other atoms 60 Entering data A bond between two selected atoms can be removed using the Struc ture Detach command Two selected atoms can be connected with the Stucture Connect command You can also choose a spec
53. you need not worry about the effect of couplings to other nuclei on a weak coupling separation Theoretically with a given J A the perturbation theory peak positions will bein error by J A8 3 and intensities will have relative errors of J A5 2 Experience suggests that the default setting of 0 1 will never introduce significant errors due to perturbation treatment You can disable perturbation treatment by setting the threshold to 0 Approximation calculations Databases for file organization Chapter 10 10 Databases and NMR parameter prediction 10 1 Introduction The first part of this chapter discusses the use of databases with gN MR gN MR V4 1 allows you to store data and spectrum files in databases Organizing data in databases may be more convenient than keeping individual files around Databases may be searched for title nucleus parameters etc Data stored in databases can also be used by gNMR for NMR parameter prediction Parameter prediction is discussed in the second part of this chapter Even in the absence of database data gN MR will try to predict some NMR parameters based on simple rules However the use of database data can improve the quality of predictions considerably gN MR comes with a sample database that can be used as a basis for improved parameter prediction 10 2 About databases and gNMR gN MR allows you to store any data or spectrum file in a database The file need not contain a structure
54. 00 0 7 100 The iterate window displays the cycle number the point number within the cycle the modified sum of squares residual and the phase of the calculation function value or gradient calculation As before the Molecule and Spectrum windows are updated at each new point Full lineshape iteration takes much longer than assignment iteration the present example takes about 25 seconds on a 100M Hz Pentium machine The iteration procedure consists of a fixed number of cycles 5 by default All but the last are generalized least squares fits only the last is a normal least squares fit In every cycle the program tries to minimize a residual comparable to the normal sum of squares fit criterion if this minimization has converged the next cycle is started Within a cycle convergence is usually slower than with assignment iteration a single cycle often takes a number of points equal to 2 4 22 Tutorial Chapter 2 times the number of independent variables in the system Linewidths are not optimized in preliminary cycles but only in the final true least squares cycle At the start of the iteration you will see that the centres of the two multiplets quickly move to the correct position but the correct pattern of peaks within each multiplet takes a while to emerge When the optimization has converged you will hear a beep and the status window disappears Save the new data as ODCBFul2 dta In the Spectrum window you will see a r
55. 870s gt 1870s and Entering data Chapter 3 187Qs 9 isotopomers since 1870s is the only spin 42isotopomer of Os However if Include Quadrupoles were set gN MR would also try to generate isotopomers containing the spin 7 2 isotope 1890s like 1870s 1890s and would then refuse to do the calculation as in the silver example Even if gNMR accepts your specification of for example 4 equivalent Pt 195 nuclei you may not get the results you expected gN MR assumes that there will be only a single isotopomer for each generated number of NMR active nuclei and that in each of the isotopomers all these N M R active nuclei are still equivalent These assumptions will hold for a tetrahedral arrangement of four platinum atoms but not for a square planar structure In the latter case the 195Pt 3 isotopomer will contain two inequivalent types of 15Pt nuclei inner and outer and there will be two different 1 Pt 2 isotopomers cis and trans Be careful with groups of equivalent isotope mixture nuclei As mentioned above gN MR does not automatically take isotope shifts into account But it is possible to use explicit isotope shifts in gN MR The Molecule Isotope Shifts command changes the normal coupling constant display to the display of a rectangular matrix of isotope shifts all zero initially Here you can enter isotope shifts i e the effect that a unit change in mass number of one nucleus has on the chemical s
56. 888 257 6652 28364 So Western Ave Suite 491 gnmr usa cherwell com Rancho Palos Verdes CA 90275 USA Cherwell Scientific Ltd oCHEM Tal 069 970841 11 Research GmbH Fax 069 970841 41 Hamburger Allee 26 28 gnmr d cherwell com 60486 Frankfurt Germany If you need to contact Cherwell Scientific for support it would help if you have the following information to hand e Your serial number e Theversion of gNMR you are using e Theversions of the system software you are using and the amount of memory available e A detailed description of what happened when the problem occurred e Other relevant information e g the type of printer for a printing problem e If possible have gN MR up and running and a copy of this user manual with you Visit Cherwell Scientific s web site for the latest information on new products FAQs and technical support http www cherwell com iv gNMR gNMR 1995 1999 IvorySoft All rights in this product are reserved by Cherwell Scientific Limited the Publisher This end user license agreement describes the rights and warranty granted to its customers by the Publisher By using the enclosed disk you the customer are agreeing to be bound by the terms of this agreement which includes the software license software limited warranty and hardware limited warranty 1 License The Publisher grants the customer and the customer accepts a perpetual non exclusive and non transferable lice
57. About tab This will show the versions of all components If they are labeled 3 0 or newer you need not install ODBC from the oN MR distribution disk To install ODBC first uncompress the package if necessary and then double click setup exe and follow the instructions on the screen Once the necessary software has been installed you need to configure a database for use with gN MR We recommend that you install the Paradox version since that is faster But you may have other reasons to prefer the Access database First make sure the example Paradox database has been installed on your system It is only installed when you select the Database option during gN MR installation You can also install the database manually by simply copying all files from the Dat abase Paradox directory on the gN MR distribution disk to your hard disk We recommend installing it in the Dat abase Paradox subdirectory of your gN MR directory Start the BDE administrator program BDEadmin Click on the Databases tab select Object New and in the small dialog that appears select STANDARD for the Database Driver Name This will produce a new entry in the list of databases Change the name of the new entry in the left pane of the window to gNMR PDox In the right pane which has a single tab Definition fill in the name of the directory containing the Paradox database under the PATH variable if you click in the empty field to the right of the PATH label a butto
58. Axial groups Sn Cn Cnh Cay Dn Dah Dna If Dnd you choose one of these gN MR will ask you al for the order n of the highest rotation axis Th Td e Other groups Ci C T Th Ty O Op After the space group has been selected a dialog box appears showing all special positions of the group Figure 48 you should fill in their contents Each position is labeled by the number of times an atom in such a position will occur in the expanded group followed by an indication of the symmetry element A list of special positions for each of the above groups is given in the online help Spacegroup Ea Contents CA General _ Cancel Help Subgroup The contents of a special position can bea simple list of nucleus names separated by spaces the names follow the same rules as for the Molec ule window see section 3 4 If you want to choose nuclei 124 Symmetry Chapter 8 from a menu just press lt gt A group of magnetically equivalent nuclei is indicated by a number before the nucleus name eg 3 h note the space between the 3 and h 3h would indicate tritium You can also specify more complex arrangements The formal syntax for the input is given in the online help but here are some examples 1 1 3 1 h isequivalentto 1H 1H 3 1H 1H and means e asingle hydrogen e another single hydrogen e agroup of three equivalent hydrogens e afinal single hydrogen 2 h isequivalentto 1H 19F 1H 19F and means e on
59. Chapter 12 The Spectrum Baseline submenu contains a number of baseline correction options If the Linear Fourier whole spectrum is displayed the correction will Spline affect the whole spectrum If only part of the Truncate below Remove Noise spectrum is displayed the correction will be applied to the visible part only and linear corrections will be used for the invisible parts to prevent discontinuities at the display limits One action related to baseline correction the removal of impurity peaks from a spectrum will be discussed later Spec trun Baseline Linear Selects a linear correction which always uses the outer 4 2 on each end of the spectrum This will give very poor results if there are peaks at either end of the spectrum so take care that the display limits are wide enough before you use this option Spectrum Baseline Fourier Uses a Fourier series of the form Xo B x a ha sin 2x j aa b co s 2m j a to fit the points belonging to the baseline you will be prompted for the Fourier order n to be used Fourier corrections are good for fitting wavy baselines Using a large order can be very time consuming moreover you may end up with spikes replacing your waves Values in the range 3 10 are recommended Before the actual Fourier fit starts gSPG determines the set of points belonging to the baseline using an iterative algorithm you will see this on the screen as two horizontal lines that
60. Edit Interactive Width 78 Displaying spectra Chapter 4 4 7 Print copy and paste gN MR spectrum output is not completely WYSIWYG Out of range indicators markers the baseline and assignments are never shown in clipboard copies or printouts The display of nuclear ranges in printouts can be disabled separately from its display in screen output see below Printouts and clipboard copies are always in black and white even if the screen display uses colors If a Spectrum window is topmost File Print Spectrum prints the spectrum If the spectrum is larger than the window so scroll bars are visible File Print Visible Part prints only the part that is currently displayed in the window If you have selected a subrange see section 4 2 and then choose the Selection radiobutton in the Print dialog only the subrange part will be printed Edit Copy Spectrum copies the spectrum to the clipboard for pasting in e g a word processor or drawing program By default see below enough data is included in the copy to reconstruct the file later if you paste the spectrum from the word processor back into gN MR the Edit Paste File menu choice will be present and enabled For large data sets this may increase the size of the clipboard data considerably if you don t want to include the data keep the Shift key depressed while copying the data to the clipboard The embedded data will usually not survive pasting into a drawing program and then
61. ID Offset 50 46 H Data points 16384 Sweep Width 2408 46 Hz W Bruker FID Cancel Help There are separate sweep width and offset settings for the spectrum and the FID This is because some operations result in a reduced spectrum range but of course the range corresponding to the FID will remain unchanged If you do a Fourier transformation the range settings of the FID will be copied to the new transformed spectrum since the new spectrum range will correspond to the FID range 12 4 Displaying a spectrum or FID Display operations common to FID and spectrum windows can be found in the Display menu The Full Spectrum and horizontal and vertical expansion choices and their button bar equivalents work as the corresponding Spectrum menu choices in gN MR Selections can be made using the Selection miniwindow or directly by dragging in the spectrum just like in gN MR The link between spectrum or FID size and window size can be toggled with the Display Resize with Window menu choice The Display Imaginary command can be used to turn display of the imaginary spectrum or FID component on or off On screen the 162 Spectrum processing Chapter 12 imaginary component will be displayed in a different color Hardcopies including the imaginary component are rarely useful Axis units for spectra can be switched between Hz and ppm with the Spectrum xx units lt Ctrl U gt command The axis units for FID s are always sec
62. If checked gNMR will try to expand simple abbreviations Me Et Ph CHO to real structure elements Add hydrogens If checked gNMR will try to satisfy all carbon valences by adding hydrogens where necessary it will also expand notations like NH 2 to generate individual hydrogen atoms You can import complete or incomplete structures without using structure completion However shift prediction see below will only work satisfactorily if you use complete structures so itis recommended that you leave these options checked The next four options determine which atoms gN MR will actually include in the spin system The remaining atoms will also be read in but they will not be included in the spin system i e they will be treated as NMR inactive you can always add or delete atoms from the spin system afterwards Atoms in the molecule are divided into four groups hydrogens carbons abundant spin 2 heteroatoms and Entering data 55 Chapter 3 all other atoms For each of these groups you can select one of the following import options Include all All of these atoms will be included in the spin system Exclude all None of these atoms will be included in the spin system Explicit only Only the atoms bearing a full gNMR isotope name will be included in the spin system The default is to include all hydrogens and abundant heteroatoms and none of the carbons or rare heteroatoms If during the import gN MR encounters seve
63. NMR will no longer be able to locate it If you want to make sure that the spectrum stays with the simulation check the Make Copy checkbox in the standard file dialog This tells gNMR to make a local copy of the spectrum file and include it in the simulation file Of course the oN MR file will become larger if you do this Once your file contains one of more of such local copies clicking the Local button in the Settings File dialog brings up a popup menu of these local spectra Thus you can select the same local copy for display in several Spectrum windows If you are storing spectra in a database Chapter 10 you can link to a stored spectrum by clicking the DBase button This brings up the database query dialog and after that the database browser Move to 72 Displaying spectra Chapter 4 the record you want then right click it and select Use This Rec ord from the popup that appears One an experimental spectrum has been selected for display with the calculated spectrum you can control the way the two are displayed with the Display pulldown Calculated only Show only the calculated spectrum and ignore any experimental spectrum specified Both Up Display both spectra the experimental one on top in parallel traces Back to Back Show the experimental spectrum pointing upwards and the calculated one pointing downwards from a common horizontal axis This is the most popular format for journal publications Over
64. R sesse 138 10 4 Using databases with QN MR cesssseeeeeeeteeeeeeeeeeeeeeaes 141 10 5 Database related COMMANGCS seeeceeeteeeeeeeeeteeeeeeeaes 142 10 6 NMR parameter prediction cceceeeeeeeeeeteeeeeeeees 145 10 7 Settings affecting prediction ceeeeseeeseseeeeeeeeeteeeteees 147 11 File conversion USING GQCVT ssssssssssusannnnunnnnunannunnnnnnnnnannnnnnanana 149 11 1 Kangoo Ule no n Eea E hain tees 149 11 2 Converting between different gN MR versions 150 11 3 Getting spectra to your PC ssssssssssssssisisisisrsrsrsrrsrernrssnen 151 11 4 Converting data to gSPG format 153 11 5 Notes on individual conversions sssrin 154 12 Spectrum processing using gSPG wns 159 12 1 Introd di ON We eh iea ioia eles eit 159 12 2 Files and WINdOWS s ssssssssssesisrsisisrsrsrnersrsnsnnnrnennsnsrsrsnsns 160 12 3 Filewide SELINGS eseessssseeseersrsrsrsrnsrestnrnnnrnrnsnsnnnsrsrsrns 161 12 4 Displaying a spectrum or FID sssssssssssssssssssrsrersrsrerrsrsrsrss 162 12 5 Manipulating the SO CtrUM s ssssssssssrssssssssrisrsrennrrnssrsns 163 12 6 Adding and subtracting spectra s 166 12 7 Regions integrals and multiplets 167 12 8 Markers and calibration ssssssesssssssisesssnsisrsnnrnersrssrsns 171 12 9 Fourier transformation sssssssseseesrsrssssnsrsrsnrnrirnsisrsnss 171 gNMR ix Contents 1210 Phasing n pede eee le eden ioan 176 12 11 Linear Prediction ee eeeeeceeeceeeeeeee
65. Ungroup Descending Clear 88 Assignment iteration Chapter 5 To enter frequency assignments fill in the values in the Frequency Obs column You need not supply values for all peaks just leave blank fields for peaks you do not want to assign To remove an assignment clear the corresponding field To duplicate an observed frequency from the field above it press lt gt to enter an observed frequency exactly equal to the calculated frequency press lt gt Entering intensity assignments is similar simply type the data in the Intensity Obs column Before starting this however you should make sure that your observed intensities are normalized so that they will add up to the correct number of nuclei in the system Also remember that intensities reoresent integrals not peak heights If you have a separate intensity for each peak you can enter the data as described above possibly using lt gt to duplicate values and lt gt to set observed values equal to calculated ones Often however you will want to supply only a total intensity for a group of peaks For example let us suppose that we have an integrated intensity of 0 13 for peaks 27 29 and 30 together You start by entering the total intensity 0 13 in the field for one of the peaks say peak 27 which we will call the base peak For the remaining peaks you do not enter an intensity but instead the negative of the number of the base peak
66. adding a new structure to the prediction database If you want to add a parameter which happens to be nearly zero set it to some small value e g 0 01 Hz before adding the structure to the database This method is similar to the more primitive built in additivity rules described earlier It tries to identify atoms as part of a known fragment e g a benzene ring and then tries to match all substituents attached to the fragment to substituents in the database This method is more reliable to the fragment matching described in the previous paragraphs because it can see further 146 Databases Chapter 10 Take for example the para hydrogen of aniline Fragment matching will not see further than the aniline nitrogen 5 bonds away and will thus give the same prediction for this compound and for the para hydrogen of nitrobenzene Moreover fragment prediction works poorly for polysubstituted arenes because it only accepts a match if the complete environment matches up to a certain number of bonds In contrast substituent prediction sees the complete amine or nitro substituent in the para position Because it inspects the substituents individually it can also combine arbitrary contributions to arrive at a prediction Substituent contributions are calculated from statistical analysis of a large number of chemical shifts At present gNMR cannot calculate new contributions based on compounds you add to a database Therefore new comp
67. alog and select gNMR Access from the pulldown Default Data Source list Then quit gNMR Once either of the above databases has been installed it will be used automatically in parameter prediction you don t have to take any special action for that To add a single data or spectrum file to the database open the file in gN MR or gSPG and then select File Database Add data to xxx or File Database Add spectrum to xxx where xxx stands for the name of the selected database Try adding the ODCB spectrum from within gSPG in this way If you want to add a number of files it is probably easier to use the gBase utility As an example we are going to add all data files from the tutorial Start gBase dismiss any Selection dialog that appears if necessary and select Database Add Data Browse to the Tutorial directory click on one of the gN MR Data ata files and check the Tutorial 31 Importing a spectrum Chapter 2 All DTA box Then click on Open This will add the specified file and all other dta files in the same directory To open afile stored in a database you need to search for it first For example let s open the ODCB spectrum just added to the database Start gSPG open the database if necessary and select File Database Query In the dialog that appears select Spectra from the Search pulldown and All Records from the For pulldown Then click on the Search button A dialog appears that will show only one record Ri
68. alog are discussed separately in the following sections 4 3 Using experimental spectra You can display experimental spectra and calculated spectra together on the screen to facilitate comparing the two The relevant options are located in the Iteration section of the Settings File dialog Figure 41 the end of this section describes an alternative method for selecting an experimental spectrum Displaying spectra 71 Figure 31 Settings Spectrum dialog Iteration section Chapter 4 Spectrum Settings Ea Topic ey Dimensions Iteration Spectrum File EXOBJ ODCB SPG i Be pease Local Display Both Up ry W Full lineshape iteration nym Display N Iterate on Linewidth i dots I Iterate on Baseline Iteration Nu Cancel Apply Help Baseline x The top of the dialog section shows the text Spectrum with below it a space to hold a filename and below that three buttons labeled File DBase and Local To supply a file click the File button and select the desired file using the standard file dialog When you have selected a file its name will be filled in and several other dialog items will appear which are described below and in Chapter 6 Selecting a file in this way only establishes a link to the spectrum file but does not include the spectrum file in the gN MR file Therefore if you later move rename or delete the spectrum file g
69. also maintains a separate Log file where important changes are tracked like the progress of iteration results A Log window displays the contents of the most recent entries into the Log file the Log window is initially minimized Old data may be lost from the top of the window as new information is added but the Installation 3 Table 1 Keyboard navigation of grids Chapter 1 Log file never loses data It is a plain text file that you can open in any editor or word processor Several gNMR windows contain grids for data entry Moving between cells of a grid can be done by clicking the mouse or with various keyboard keys see Table 1 You can select a single cell or a collection of cells for copy amp paste To select a whole row or column at atime click the left or top header cell of the row or column Shift click and Ctrl click modify the selection in the usual manner A copy of acell range can be pasted into a spreadsheet or word processor If you paste a cell range back into gN MR the selected target cell range must be the same size as the cell range being pasted This method of copying pastes cell contents without any interpretation so it is possible to paste shifts in a linewidth column There are separate operations for copying whole molecules and structures in an intelligent fashion lt Return gt lt Tab gt lt Shift Tab gt lt gt lt Ctrl PgDn gt lt End gt lt gt lt Ctrl PgU p gt lt Home gt lt gt
70. although obviously files without structures will not help to improve prediction But there can be other reasons to organize your files in a database instead of in separate disk files e You hard disk becomes less cluttered because instead of hundreds of individual data and spectrum files there will be only one or a few databases e Moving asingle database file is more convenient than moving a lot of separate files e You can search for spectrum and data files in a database using criteria like original file name title spectrometer frequency nucleus molecular formula etc Databases 137 Your system must be configured Chapter 10 Within gNMR and gSPG you can use a database contained file just as you would use a normal file This includes referencing a spectrum file from within a gN MR Spectrum window Database contained files can also be updated saved after modification just like disk files In addition a special utility gBase is provided for bulk moves importing sets of files into the database or exporting them back to disk 9N MR offers a lot of flexibility when it comes to the choice of database This allows you to use your favourite database driver in most cases You can choose one of the many drivers included with ODBC or with the BDE see below This flexibility comes at a price you will have to configure your system for a particular driver and database This is done using the ODBC and BDE configuration utili
71. aming convention to let gCVT recognize files automatically The acquisition and processing parameter files can be in the original DISN MR format a binary format these files start with File conversion 155 Bruker Aspect JCAMP DX Varian VNMR Chapter 11 the characters A 000 or in the newer JCAMP format a text format these files start with the characters On some spectrometers the observe nucleus is not filled in in the acquisition parameter file so you can specify it yourself in the Convert dialog The spectrum and FID files are binary files containing straight sets of single precision 4 byte floating point values This is an older format used by the dedicated Bruker Aspect computers All data is combined in a single binary file nucleus and offset information is usually missing JCAMP DxX is a general spectrometer format gCVT will recognize JCAMP files as produced by Bruker WinNMR A JCAMP fileis a text file in which the spectrum data can be written out in full or compressed form Each file contains either a spectrum or an FID Varian VNMR runs on several platforms We have only tested conversion from the Sun OpenWindows version The names of the files you need are as follows Contents PC name VNMR name acquisition fn pre fn fid procpar parameters real spectrum fn spc see text FID fn fid fn fid fid comments fn txt fn fid text Use the PC naming convention in the table to let gCVT recognize the
72. ample database comes in both Paradox and Access formats install the Paradox version if you want to avoid use of ODBC ODBC version 3 5is provided on the gN MR distribution disk However a newer version may already be installed on your system as ODBC comes bundled with a large number of software packages To install ODBC run Setup from the install CD again choosing Custom install and selecting the install ODBC option Alternatively choosing to install the sample Access database will automatically install ODBC We recommend you install the newest version supplied 2s BDE5 01 You can also download a recent version from Inprise http www borland com bde To install the BDE first uncompress the package if necessary and then double click setup exe and follow the instructions on the screen Start the ODBC administrator this is located in the Control Panel and is usually called ODBC or 32bit ODBC Click on the tab User DSN and then on the Add button In the dialog that appears select eg the Microsoft Access Driver and click on Finish This will produce the Access Setup dialog e Tosetup an existing database click on the Select button and browse to the desired database file Fill ina Data Source Name g JNMR Access this is the name the user will see later in the BDE and in gNMR and optionally a Description sample gNMR Access database Then click on OK e Toset up anew database click on the Create button browse to th
73. an be used to get information on these peaks A part from calculating averages and differences you can also specify a new value for the shift of a peak in either ppm or Hz This is interpreted as a recalibration once you press the Calibrate button the horizontal scale is adjusted so that the selected peak has the specified shift Alternatively you can click the Solvent button and select a solvent shift from the list that appears to set a standard solvent shift for the selected peak You may not agree with the default solvent shifts provided with gN MR in that case adjust to gNMR41 s1v solvent shift file to your liking 12 9 Fourier transformation The AD WFT command is used to start a Fourier transform The WFT dialog appears Figure 59 which you can use to specify a weighting function gSPG lets you specify up to three weighting functions which will be multiplied to generate the final FID weighting Spectrum processing 171 Figure 59 gSPG FID WEFT dialog Chapter 12 Weight Transform x Apodization Function h H Function Type Lorentz Gauss gt LB Hz 3 GB Hz Po Data Exclude initial points r Reconstruct using LP Use FID points 16384 Fill to 16384 r Reconstruct using LP l Bruker FT I Mirror M Rotate Unfilter M Baseline Corr M Show Weighted FID Update Now WFT Done Cancel Help The following windowing functions are available None No weighti
74. and then complete the reaction Chapter 7 To be valid a permutation has to satisfy these rules e All destinations must exist and must be different e The source and destination of each nucleus must have the same nucleus name and the same number of nuclei field e lsotope mixture nuclei must not move in any permutation e You should not include the identity permutation i e onein which every nucleus stays in place Sometimes you may have to enter sets of symmetry related permutations as discussed in the previous section There are however a few cases where you should never enter related permutations e You do not have to enter the reverse of any reaction separately gN MR always averages between forward and backward reactions e You do not have to enter repeated applications of the same permutation So if you have entered a permutation 2341 you do not have to enter its repeat 8412 separately unless you want to distinguish between the four step 2341 8412 4123 1234 and two step 8412 1234 processes 7 4 Entering reactions using structures If you are using structures for all molecules in a file you can also use them to enter your permutations When you move to the Exchange window a separate pane containing all structures will be displayed Figure 43 For every nucleus that moves in a reaction first click on the position it moves from then Shift click on the position it moves to The nucleus movement will be indicated
75. ast squares cycle will do if you are already quite close to the final solution To use full lineshape iteration for this purpose select iterate Last Cycle instead of terate Go Paradoxically full lineshape iteration tends to work poorly for simple first order systems The reason for this may be that the algorithm is forced to make a choice for a particular local minimum at a stage when it cannot yet see enough detail to make the right choice The moral is that if you can solve the spectrum with a ruler and some thinking doing a full lineshape analysis is not very useful You Full lineshape iteration 103 Chapter 6 might however still want to do the analysis to optimize linewidths and obtain error limits and of course to get a nice looking fit for a publication Performing only the final least squares cycle suffices for this terate Last Cycle 6 7 If the iteration fails Sometimes full lineshape analysis just will not give a reasonable fit It seems to fiddle around in the first few cycles changing parameters alot but not drastically improving the resemblance of calculated and experimental spectra if you included linewidth parameters in the iteration the final cycle produces very broad lines Apparently gN MR cannot find the right set of parameters There are many possible reasons for this but they can be divided into two categories problems with the experimental spectrum and problems with your preparation of the iteration
76. ather nice similarity between the experimental and calculated spectra Figure 10B The two traces even appear to have the same height because the linewidth was optimized Of course full lineshape iteration doesn t always give you the right answer If it fails it often fails soectacularly producing a calculated spectrum that appears to be totally unrelated to the experimental one 2 4 Chemical exchange This section covers e Setting up exchange calculations without a structure e Setting up exchange calculations with a structure To do a dynamic or chemical exchange calculation we first have to set up the corresponding static calculation which is the low temperature or slow exchange limit of the dynamic system After that we have to define the chemical reaction that is responsible for the dynamic behavior of the system The reactions studied by dynamic NMR spectroscopy are always closed that is the number and type of the nuclei involved does not change Individual nuclei move about in the reaction but for every nucleus that leaves a certain position another takes its place so the net chemical composition does not change Therefore we can characterize a reaction by a permutation scheme that lists for every nucleus in the system the place it moves to in the reaction Once you have set up the molecules Tutorial 23 Exchange in DMF Figure 11 Exchange window before A and after B entry of the permutation Chapte
77. be displayed for assignment If there are many peaks only those that have an intensity higher than the Threshold fraction of the highest peak will be shown The default threshold is 0 02 Group Assignments If unchecked all individual peaks will be displayed separately Often this results in many peaks having the same or nearly the same frequency If checked the default such peaks will be displayed and assigned as a group You can also group and ungroup peaks in the Assignments window by clicking the appropriate button 90 Assignment iteration Chapter 5 Grouping Threshold Peaks closer than this threshold default 0 01 Hz will be grouped if you check Group Assignments or if you click on the Group button in the Assignments window Assignment Order Can be set to either Ascending low to high frequencies or Descending high to low frequencies select the choice that corresponds to the peak listings produced by your spectrometer You can also click the corresponding button in the Assignments window to toggle the peak ordering Highlight Assignments If checked the peak currently being assigned will be indicated by a colored vertical linein all Spectrum windows If you have an experimental spectrum available it may be a good idea to make your assignments visible To do so move to the Spectrum window select the Display topic of the Settings Spectrum dialog and check the Show Assignments box see section 4 2 and Figure 40 Ver
78. be shown ina normal font the rest will bein italic After selecting a single nucleus see below you can use the Structure Show Folded command to see which nuclei are folded with the selected one Clicking on an atom in the structure moves you to the corresponding chemical shift field in the spreadsheet pane Shift clicking on a second atom then moves you to the field for the coupling constant between the two Of course this works only if the nuclei are included in the spin system You can sdect a single atom by clicking on it or a set of atoms by dragging all atoms in the rectangular drag area will be selected Shift clicking and Shift dragging can be used to add to delete from the selection A set of selected nuclei can be folded into a single equivalence group with the Structure Fold command Similarly one or more equivalence groups can be split by selecting their atoms and choosing Structure Split A set of selected atoms can be added to the spin system by choosing Structure Include or excluded from it with Structure Exclude By default atom labels in the structure are displayed as they werein the drawing program None Original except that any hydrogens that were added are Numbers shown explicitly But you can choose from NucNames P Nrs Names several other labeling styles using the cra Stucture Labels command Elements None Does not display any atom labels Original Atoms will be labeled as they
79. c acid molecule would be indicated by 1 2 meaning molecule M 1 position 2 H4 i pare 1 0 H4 4 yA 2 Cl H4 2 Ho 4 M1 M2 M1 M2 With this convention the exchange reaction becomes 1 1 gt 1 1 1252 1 2 1 gt 1 2 A single chemical reaction can involve several molecules at a time In practice most reactions are either unimolecular A B or bimolecular A B lt gt CorA Be C D Moreover dynamic Chemical exchange 111 Chapter 7 NMR is primarily useful in the study of simple rearrangement processes A lt gt A or A lt gt B or degenerate exchange processes A B lt A B So most exchange reactions you will encounter involve either one or two molecules Occasionally there might be more than one dynamic process in a molecule gNMR accepts up to 6 different permutations each of which can have its own rate you can mix intra and inter molecular permutations 7 2 Reaction rates The number that is most relevant to a chemical exchange calculation is the pseudo first order rate constant which is the absolute rate divided by the concentration of the exchanging species If there are several species contributing to a single reaction each may have its own concentration and therefore its own rate constant but there will only bea single absolute rate To simplify the input gN MR requires you to enter rates not rate constants for exchange calculations gNMR then calculates the required rate constants u
80. calculated lineshapes though possible in theory does not yield very satisfactory results in practice because of the negligible overlap between corresponding peaks in observed and calculated lineshapes To overcome this problem Binsch 3 devised a generalization of the least squares 228 Technical issues Appendix F formalism Instead of directly minimizing Oobs 9calc Mobs Ocalc he repeatedly solved the minimization of ops Ocalc W Mobs Ocalc Where the correlation matrix W is used to smooth the least squares surface Binsch argued that W should have the form Wij F li j In the first cycle Wij is chosen as a very flat function of i j in later cycles W is changed gradually in the direction of the identity matrix Wij 6 Binsch proposed two forms of W an exponential form WE exp ali j and a Lorentzian form WE 148 i j 2 1 Binsch also noted that evaluation of the product Oobs Ocalc W Oobs Ocalc often became a bottleneck and some threshold and grouping strategies were proposed to cope with this problem For the special case of an exponential correlation however it turns out that the correlated vector W dops Ocaic can be evaluated very efficiently for a vector of length n only 2n multiplications and 4n additions are needed Binsch demonstrated that a Lorentzian correlation has a better chance of finding the global minimum because of its zero slope at the origin Lorentzian correlations cannot be computed v
81. can first use the Settings Spectrum dialog box to set the correct display limits and dimensions see section 4 2 and then choose File Print Peaks that should have the same height do not If you generate spectra with very small linewidths peaks may sometimes fall between datapoints gN MR takes special precautions to ensure that integrated peak intensities will always come out correct Nevertheless you may occasionally see noticeable distortions in the peak heights up to a factor of 2 depending on whether the intensities of very narrow peaks are concentrated in a single datapoint or shared between two datapoints gNMR uses approximately 2000 datapoints for each spectrum it displays so you can expect significant distortions when using linewidths smaller than ca 1 soo of the window width am trying to do mouse assignments for a fairly large system but nothing seems to happen when try to assign a peak There are probably many coincident peaks at the position you are looking at this may happen if there are many zero couplings in the system You are actually assigning a lot of peaks at the same position Just keep on assigning you will eventually get to the next real peak where the same thing may happen To avoid having to do this you can select Group Assignments see section 5 5 to assign such groups of peaks as single peaks When How do use intensity data in assignment iteration First a note assignment i
82. center spike at the transmitter frequency Exclude initial points This specifies the number of initial points of the FID to be ignored in the LP calculation Generally the first few 1 3 points are contaminated and should be excluded For digitally filtered FIDs it may be necessary to exclude more points Unlike in normal Fourier transformation excluding initial points does not result in a spurious phase shift here Use AD points This specifies the number of FID points or correlated points to be used in the LP procedure Values in the range of 200 400 can easily be handled on a modern PC Max peaks This is the LP prediction order or the maximum number of peaks that will be detected by the LP procedure The actual number of peaks will generally be smaller than this in the LP procedure spurious peaks will be eliminated based on various criteria listed below We recommend that Max peaks be set to 0 3 0 5 times the value of the Use AD points mentioned above Always specify at least 2 3 times the number of real peaks you expect in the spectrum SVD cutoff This sets the threshold below which singular vectors will be discarded as a fraction of the most significant vector The following options determine which LP peaks will be retained for further processing For selective SVD and total least squares a pre selection and refinement will be done based of the combination of forward and backward LP SVD results with roots hav
83. click on the Autophase button This takes some time but the results are probably better than you could by moving the sliders manually Click Done to dismiss the dialog 2 7 Special topics This section covers e Approximate and first order simulation e Symbolic systems Tutorial 33 Symbolic systems Individual linewidths Chapter 2 e individual linewidths and decoupling e Isotopomer mixtures and isotope shifts e Anisotropic spectra e Using intensity data in assignment iteration e Approximate simulation e First order simulation gN MR comes with a few predefined spin systems like AA BB and it is easy to add your own see section 8 2 for details H ere we just show how your could have entered ODCB as an explicit AA BB system Select Molec ule Symbolic AA BB and in the resulting dialog dick OKto accept the 1H nucleus for the system This will give a spin system with the correct links between parameters but with all shifts and couplings initially zero Enter the unique parameters 51 a 7 1 83 b 7 4 Jaz aa 1 J13 ab 8 J14 ab 2 and J34 bb 8 Then click on Spectrum to see the by now familiar spectrum The advantage of this method of setting up the system is that you do not have to worry about keeping symmetry related values equal Using a single linewidth for a whole system is often NH2 appropriate Sometimes however some nuclei have Cl noticeably broader lines Nearby quadrupolar nuclei ma
84. ction can be defined as a permutation of nuclei we will work through some examples to illustrate this It is recommended that you always work out the permutation on paper before entering it ingNMR Let us start with the inversion of a primary amine RNH gt 2 In the equilibrium structure the nitrogen atom is pyramidal if the group R is chiral the two hydrogen atoms will be inequivalent diastereotopic However inversion of the nitrogen atom which is usually rapid at room temperature exchanges the hydrogens Hp inversion iy Hy rotation R N H2 Y Hy Hy H If we labe the hydrogen atoms with the numbers 1 and 2 the rather simple permutation scheme becomes 152 2 gt 1 where the arrow should be read as moves to the position of Asaslightly more complicated example we will take the one pair fluorine exchange reaction in SF4 One possibility for this reaction is the exchange of Fj and F4 the other two nuclei remain in place Chemical exchange 109 Chapter 7 Fax F4 F I F sv 4 Sv 1 INF T NF 2 2 The permutation could be written as 1 4 2 gt 2 33 451 There are three alternative one pair exchanges which are symmetry related to the Fy F4 exchange Fic F3 Foo F3 Foo Fa 1 gt 3 1 1 151 2 gt 2 2 gt 3 2 4 31 352 353 4 gt 4 4 gt 4 4 gt 2 In practice the four exchange processes would always occur with the same rates In the rest of this chapter we will often indicate per
85. d Items not listed here are always drawn in black The dialog displays samples of all colors to change a color click on its Change button Imaginary Used for display of imaginary component for the calculated spectrum if spectra are displayed overlapping Integral Used for display of integral and weighting function Connections Used for display of assigned peaks connecting peaks in calculated and experimental spectra Highlighted Peak Used to highlight the peak currently being assigned and the nucleus range corresponding to the currently selected nucleus Highlighted Area Used for display of unassigned peaks Spare Color Used for any of the above items that would otherwise have the same color as the spectrum The bottom part of this topic allows you to customize nucleus colors Click on the button displaying a nucleus name to select the nucleus you want then click on Change to select a new color If you check Use nucleus colors everywhere the nucleus specific colors will also be used in the appropriate row of Molecule and Exchange windows and in structure displays Customizing gNMR 201 Precision section Appendix A Preferences Ea Topic Precision and Field Widths Import Dec places ppm values ike Dec places Hz values l2 H Editing Max Shift ppm 9999 RiT Max Shift Hz 99999 WFT Max Coupling Hz 3999 z PerLP Max Linewidth Hz 999 x Tn Precision Hz 1 0e 01 Color
86. d at 1 Hz H2 and H3 will probably resonate at higher field than H and H4 let us guess the chemical shifts 52 53 as 7 1 ppm and 81 64 as 7 4 ppm We are ready to enter the data The first column of the Molecule window contains the names of the nuclei in the system We need 1H which is already there so press lt gt to move to the next column The second column contains the number of magnetically equivalent nuclei in a group In the present case we have no magnetic equivalence only chemical equivalence so there will be only 1 sin this column Press lt gt to skip this column as well The third column is to contain the chemical shifts these we really need The top of the column contains an indicator showing whether the current chemical shift unit is ppm parts per million or Hz Herz the default is ppm you can use lt Ctrl U gt to toggle between the two To enter the chemical shift for nucleus 1 type 7 4 and press lt 1 gt note that this takes you to the empty bottom row of the spreadsheet Type 7 1 52 and press lt 14 gt Now you will see that the spreadsheet has expanded the second row also contains a 1H nucleus and you have moved to the third row Enter the shifts of nuclei 3and 4 7 1 lt gt 7 4 lt gt in the same way You end up in the empty fifth row There are no more nuclei so press lt 1 gt again this moves you to the top of the next column The fourth column can contain an individual linew
87. d simulation In NMR symmetry has several important roles e The presence of symmetry in a molecule influences the appearance of a spectrum Thus it is frequently possible to deduce from an experimental spectrum the presence or absence of certain symmetry elements this can be a great help in elucidating molecular structures e If a molecule has symmetry there will be a number of symmetry related shifts and coupling constants This means that a complete interpretation of the spectrum requires the determination of fewer spectral parameters than would otherwise be required e gNMR can exploit the presence of symmetry to reduce the size of acalculation making it possible to handle systems that would be too large in the absence of symmetry As far as NMR is concerned the symmetry of a molecule is completely unrelated to the three dimensional structure of the molecule The symmetry elements that are important in NMR are permutations of nuclei that leave the set of NMR parameters unchanged Thus this symmetry is determined by the pattern of equal shifts and coupling constants in the molecule gN MR is able to deduce this symmetry without any assistance and useitina calculation so you need never tell the program the symmetry of your system However entering a highly symmetric system is not always trivial and gN MR offers a few options that can help you set up such systems section 8 2 This chapter also discusses some aspects of the use of
88. ding athumbnail sketch if available at the bottom of the dialog Previews are only available under Windows 95 98 and NT 4 0 or higher Symmetry and Approximations oe Symmetry and Approximations section Abundance Threshold M Use Symmetry l Symmetry with Assignments Perturbation Threshold p 00e 01 Calculation Method Normal z Chunk Size ro Polymer Chunk Size 8 Approx Method Threshold 15 Mo Cancel Defaults Help These settings correspond to the Symmetry and Approximation sections of the gN MR Settings File dialog chapters 8 and 9 188 Customizing gNMR Dimensions section Appendix A Preferences Ea Topic Dimensions Length Units cm Horizontal Size Vertical Size 8 00 Absolute Size 10 00 I Absolute Scaling V Resize with Window Auto Subselect Prompt Pts Spectrum 2000 al ao Cancel Defaults Help The Horizontal size Vertical size Absolute size and Absolute scaling items correspond to items in the Settings Spectrum dialog section 4 2 Length Units Sets the unit of length to be used when defining spectrum dimensions within gNMR or gSPG and can be set to cm or inch The Horizontal size Vertical size and Absolute size items in the Preferences dialog however are always in cm Resize with Window Corresponds to the gN MR Spectrum Resize with Window and gSPG Display Resize with Window menu choices If this is checked resizing a w
89. dition is limited to the purchase price paid by the customer The Publisher shall have no liability whatsoever arising out of any defect error or omission or breach of warranty or condition unless the customer shall have returned the defective material to the Publisher within 90 days of the date of purchase In that event the Publisher shall as requested by the customer either replace the defective material without charge or refund the purchase price paid by the customer in respect of the defective material The Publisher shall have no further or other liability induding without limitation in respect of damage to other property or in respect of any economic or consequential loss of whatever nature arising out of or in connection with the product or any part thereof or its use or application Should you have any questions concerning this license or this limited warranty or if you want to contact Cherwell Scientific Ltd for any reason please write to Cherwell Scientific Limited The Magdalen Centre The Oxford Science Park Oxford OX4 4GA gNMR v Contents Table of Contents Table of Contents css vii 1 Installation ov ssi 1 Lid ABOutgN MRi aaa e aiaia iaia 1 1 2 Installing the program sssssssssssssssrsisiersrsrnsnsrsrsnsnnnnnsnnnsnersrsnsns 2 1 3 Theuser interface ssssssesesssesssssrsnsnrsninsnesnsnstnsnensnenenennennnnennn 3 1 4 Aboutthis manual ssssssssssssssssssssnsrsrnsnsnesisistnsnsnsnensnenensnsnsene
90. dths from their center and displaced downwards so that the truncation points exactly touch the baseline This produces slight discontinuities in the derivative but avoids the spiking caused by a straightforward truncation As an alternative to the normal Lorentzian lineshape two other lineshape functions are available The Gaussian lineshape function is given by 2x a 21 m2 li W r or for narrow lines J ex era eid Mex a W W 2A It has much less tailing than a Lorentzian and is sometimes more appropriate for spectra obtained by artificial line narrowing Tailing is completely absent in the triangular lineshape function Es max 01 1 W W For calculation of out of phase spectra we also need dispersion components The dispersion component corresponding to a Lorentzian is 226 Technical issues Appendix F The theoretical lineshape for a Gaussian dispersion component is intractable The function we use is rina fRe 22 ele W m W Finally for the dispersion component of a triangular lineshape function we use 0 for x lt W a for Wapen WU W 2 ae for Newer Ww 2 a 1 4 for lt x lt W wl W 0 for x gt W F 5 Assignment iteration In assignment iteration the least squares sum 3 freq i i X Wipe P Freg Freq Wt Int Int Wheeq 1 Wt 50 all frequencies in Hz freq is minimized as a function of the chemical shifts and coupling constants The parameters actually
91. dual 51 whole spectrum 67 98 Linking parameters 83 Lorentzian 45 Lybrics 158 M Magnetic equivalence 50 and import 56 Markers 75 236 Index Molecule Exchange command 112 Mouse assignments 85 Nucleus names 49 209 Number of nuclei 50 Numerical assignments 87 P Permutations 109 114 Perturbation theory 131 Phase 74 ppm units 50 R Rate 113 iterating on 116 Rate constants 98 Reduce Compress command 163 Reduce Smooth command 163 Reduce Subspectrum command 163 Regions Modify command 167 Regions Modify dialog 167 Regions Multiplets command 169 Regions Peak List command 168 Regions Solutions command 170 gNMR S Settings File command 101 Solutions random 102 sign combinations 102 Spectrometer frequency 44 Spectrum A utophase command 178 Spectrum Phase command 176 U Units Hz 50 gNMR Index ppm 50 V Variable names 83 VNMR 156 W Window Exchange 113 Spectrum 63 WinN MR 155 237
92. e directory where you want to create the file and fill in the database filename e g NewAcs mdb Fill in a Data Source Name e g New Access this is the name the user will see later Databases 139 Defining a direct BDE data source Chapter 10 in the BDE and in gNMR and optionally a Description Then click on OK In either case the ODBC Administrator window should now display the newly defined database Click on OK again to leave the ODBC Administrator Now that the new data source has been defined it must be registered with the BDE Start the BDE administrator program BDEadmin and Click on the Databases tab and expand the list of databases in the left pane if necessary This should already show the newly defined database indicated by the Data Source Name entered in the ODBC administrator However we need to tell the BDE to save configuration info for the database else gN MR will not be able to retrieve it So click on the database a list of settings appears in the right pane Change one of the options on the right and change it back to its original value we suggest using Enable BCD Then select Object Apply and confirm to save the changes As mentioned earlier the BDE can access DBase or Paradox databases directly without going through ODBC Defining such a database is the same whether you are configuring a new or an existing database A Paradox or dBase database actually consists of anumber of files kept together
93. e iteration fails ee ceee cece ceeeeeeaeeeeeeteetetetateetee 104 6 8 Checking the solution oo eeeeeeeeeeeeeeeeeeeeeteeteetaeeaeeetieeees 106 7 Chemical exchange calculationS sssssssssssnsrusasnnnnnnnnnnnannnnnnnnnnnnnn 109 7 1 Describing a reaction as a permutation s es 109 7 2 REAN rates iniiaiee airaa aiaia aiaa 112 7 3 Entering reactions without Structures esssereeseeeereern 114 7 4 Entering reactions using Structures essesesesereresrreerrrrrn 115 7 5 Marking rates for optimization ssssssesssessseerersrersssrsrsrsrsnen 116 7 6 More than a single permutation ssseseseseseseseererereerrersrsrsrsrnn 117 8 SYM MAY eens 121 8 1 Symmetry and simulation 00 eee ee eee eeteeeeteteeeeettetetateetaes 121 8 2 Entering symmetric SYStCMS eeeeeeseeeeeeeeeteeeteeteetetateetees 122 Contents 8 3 Settings affecting symmetry handling in gNMR 4 126 9 Approximate methods s ee 131 OL Introductions ashen hae eh es de tee 131 9 2 CHUNKING isni eine aian 132 9 3 First order calculationS sesssesesseseersrersrnsrsrerensnrnnrisrsrsnss 133 9 4 Approximate exchange calculations 134 9 5 Other settings affecting approximate calculations 135 10 Databases and NMR parameter prediction 137 10 1 IMEPOMUCTION inkara ce ta cetecie dieses tees 137 10 2 About databases and gNMR eseceeceseeeeeeeeteeteeeetsetaseeeateeees 137 10 3 Configuring databases for use with g9N M
94. e spectrum by clicking on the Spectrum button This may take some time at the start of the calculation you may see a warning in the status bar about Cl 38 Tutorial Figure 18 Spectrum of a substituted cycloheptene simulated using chunking A and fast first order approximation B First Order simulation Chapter 2 the use of an approximate method The result should look like Figure 18A L J T g bo0 7 500 7 000 6 500 6 bo0 5 500 5 000 4 500 4 000 3 500 3 000 2 500 2 000 1 500 1 000 0 500 MW 8 000 7 500 7 000 6 500 6 000 5 500 5 000 4 500 4 000 3 500 3 000 2 500 2 000 1 500 1 000 0 500 r Even though you can simulate a system of this size with gN MR the simulation takes so long that you would not want to play a lot with shifts and coupling constants to see what happens For such cases gN MR offers an alternative much faster but less accurate approximate method Continuing with the previous cycloheptene example select Settings File and move to the Approx topic Change the Simulation Method pulldown from Normal to Approximate and recalculate the spectrum This will now be almost instantaneous the result should look like Figure 18B There are clear differences between the fast method and the more accurate chunking method because there are a number of strong couplings in this example In general splittings tend to be too sharp with the fast method N evert
95. ear none WinNMR imaginary spectrum Browse Clear gt fone WinNMR FID file Browse oea none Nucleus 1H age File Browse none Version gNMR 4 0 gt l Save as Float M Open in gSPG gNMR Cancel Help The top item is a pulldown showing the current conversion use this to select a different conversion if needed Below that in the Source group you will see a set of entries for filenames The number of entries depends on the conversion There may be separate entries for parameter files FID file transformed data etc Select a file by clicking on the Browse button clear an entry if necessary by clicking on the Clear button If you select a file in one of the entries gCVT will try to find files with the same name but different extensions to fill subsequent entries Below the set of file entries you may depending on the conversion see dialog items for nucleus spectrometer frequency sweep width and offset These dialog items are shown because the corresponding values are Sometimes absent from the N MR data files supplied For example not all WinN MR acquisition parameter files contain the name of the observe nucleus You can add this information yourself File conversion 153 Chapter 11 if there turns out to be a value for the item in the source files after all the file value will override the value entered in the dialog Below the Source group is the Targe
96. ectrum into gSPG format The gCVT conversion utility provides conversions from a number of popular spectrum formats It is also extensible adding a new conversion or updating an existing one is as simple as dropping a new conversion script see Appendix D in the gN MR directory gCVT can also be used to convert between different versions of gN MR V3 0 V4 1 as described in the next section To generate a gSPG file from spectrometer data gCVT needs at least the following pieces of information e A set of values representing the real part of the transformed spectrum Alternatively a real or complex FID can be supplied in which case gCVT does a default FFT e The name of the observe nucleus e The spectrometer frequency e Thesweep width e The offset in the gSPG format this is the frequency of the high field end of the spectrum These three items are optional e A spectrum title e Theimaginary component of the spectrum File conversion 149 Automatic conversion Chapter 11 e Thereal or complex FID Depending on the source of your spectrum data a part or all of this information will be present in one of more data files To carry out a conversion you first transfer the necessary files to your PC section 11 3 discussed file translation which may be relevant to this file transfer Then you select the desired conversion point gCVT at the data files supply any missing information in the conversion dialog and sta
97. ed from dta files The query results can be combined with the results of the previous query to create a new selection and you can also specify the ordering of the results When you click OK the query is executed and alist displaying the search results appears The Database Show selection command can be used to redisplay the most recent query results Many commands that modify the 142 Databases Settings Spectrum dialog Settings Preferences dialog Chapter 10 database will clear the result set and therefore disable this command While a result set is displayed right clicking in a row brings up a menu of common operations on that record Open Opens the record in gN MR or gSPG Details Displays some more details about the record Data Spectra Stuctures Switches to a selection of data spectrum or structure records that are associated with the current record If a query is displayed from a gN MR spectrum window there will also be a choice to display that spectrum as an experimental spectrum together with the calculated spectrum The two Database Switch to commands can be used to switch between e g a set of spectrum records and all the data files referring to them or between structures and the files containing those structures The Database Open selection command can be used to open all selected records at once In the Spectrum window you can select an experimental spectrum to be displayed together wit
98. ed immediately and data in this database will now be used for prediction 10 5 Database related commands Most database commands are grouped in the Database menu The Database Select DB command allows you to open a different database A dialog appears from which you can select a different database You can also select none to close the current database without opening a new one This selection is only temporary after you exit the program and restart it the default database will be opened again To change the default database use the Preferences dialog The Database Add data to command can be used to store an open file into the current database the command will show the name of the database This can be a data file in gN MR or aspectrum file in gSPG The command corresponds to the regular File Save As command If you open a record in the database and then select Add data to anew copy will be added to the database If you only want to update the existing record use File Save which works for both open files and open records If you store a data dt a file in a database any spectrum spg files it refers to in Spectrum windows will also be stored The Database Query command lets you select a set of records based on search criteria like filename title spectrometer frequency etc You can select Data records stored dta files Spectrum records stored spg files or Structures molecular structures extract
99. eeeeteeseeeseesetaeeateeees 178 12 12 Print copy and PASC eee cece eeeeeeeeeeeeeeteetatetateaeeeees 183 A Customizing ON MR sssssssssussnnnsnnnunannnnunnnnnunannnnanunannnnannnnanannanann nnna 185 B Questions And aANSWErfS sssssssssnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnan 205 C Nuclei recognized by gN MR sees 209 C 1 Standard nucle s iieo i ei aaia 209 C 2 Modifying the nucleus liSt sessessseseeererernsrersrerersrsnnn 213 D Using scripts for structure and spectrum import e 217 E File formats sssusa eee 221 F Technical ISSUeS sssssusususnsnnnnnnnnnnnnnnnnnnnnnananannnannnnnnnnnnnnannnnnnannnnan an 223 Flo P sASD CtS mean miaa iara a ia aaea 223 F 2 Spectrum evaluation ssssssssssssssssssrnrssnsntrnnrsrnrnnnnnnnnns 223 F 3 Individual linewidths ssssssssssssssssssnsrsrnsnsnsrsnererensnrnnsnenes 225 F4 LineshapeSn irasai iaiia ii iaia 225 F 5 Assignment iteration s s ssssssesesssssssisnnsinsntnrnerersrsrsnnnnnnns 227 F 6 Full limeshape iteration ssssessessrsssesnsrsrsrnrrsrsrerersrsrsrsrsnns 228 F 7 Chemical exchange calculations ssssesssesrsrerererrersrees 230 F 8 Chemical shift prediction ssssssesesesesrersrersnsnsrsrsnnnrrersrsnss 230 References sense eee 233 NAdEX ssssssnnnnnnnnnanannnnnnnnnnnannnananannnnnnananannnnananannanananananannananananannanananannanananan 235 gNMR Features New in V4 1 1 Chapter 1 Installation 1 1 About gNMR
100. ehydrogen e one fluorine e asecond independent hydrogen e asecond independent fluorine C2 1 p 2 h indicates the presence of a locally C2 symmetric sub fragment with e asingle phosphorus atom on the twofold axis position 1 e asymmetry repeated hydrogen in a general position position mp Subgroups can be entered manually as in the last example shown above but it is easier to let gN MR do the work Move to the position where you want to insert the subgroup and select the subgroup from the Subgroup pulldown to start a second symmetry input dialog Symmetry 125 Chapter 8 When you select OKin the subgroup dialog box gNMR will insert a textual representation of the subgroup in the correct place Once the contents of the special positions are completed click the OK button to let gNMR generate the molecule this will reolace your original molecule in the Molecule window If you hear a beep and the dialog box does not disappear gN MR has detected an error in your input the cursor will usually be positioned at the offending position You can correct the mistake and try OKagain or click Cancel to abort symmetry input gN MR constructs a molecule from your input from the inside out that is innermost expansions are performed first This may help you keep track of the different images of each atom in the final molecule the variable names generated by gN MR a1 J13 are not very helpful For very complicated s
101. em with the mouse mouse assignment or by typing in the values numerical assignment 5 2 Iteration variables You can use names to link shifts linewidths and coupling constants and to mark them for iteration Linking parameters is a way of telling QN MR that two or more parameters should actually be considered as asingle numeric value any change to one set of linked parameters will change every value in the set You can use linking to enforce symmetry restrictions For example after you have linked the shifts of two nuclei they will always have the same shift Variable names can be up to 8 characters long Leading and trailing spaces are ignored but names should not contain embedded spaces a is OK but a b is not There are no other restrictions To link parameters you must use exactly the same case J and j are considered different You can only link parameters of the same type a shift can only be linked to other shifts a coupling to other couplings etc Even if you use the same name for a shift and a coupling they will be treated as distinct variables the error analysis will show the same name twice which can be confusing You can link parameters of different Assignment iteration 83 Chapter 5 molecules which can be useful if you are simulating mixtures of closely related species e g isotopomers entered as separate molecules In addition to linking parameters variable names are also used to mark paramete
102. er ppm in degrees Height Is the baseline height in absolute spectrum units which should in general be considered as arbitrary units Tit Is the baseline tilt that is a linear baseline correction It is zero in the middle of the spectrum Sin 1 Cos 1 Sin 2 Cos 2 Arethe first four Fourier expansion corrections that can be added to the baseline 4 5 Markers integral regions gN MR allows you to place markers in a spectrum and perform some simple calculations on them Markers are displayed as vertical arrows carrying numbers starting at 1 After selecting Spectum Markers Define you place and change markers by clicking in the spectrum display area in various ways During marker placement the cursor has a vertical arrow shape To exit marker placement mode press lt Esc gt If you place markers very close Displaying spectra 75 Table 3 M arker placement operations Figure 33 Spectrum Marker Marker Info dialog Integrals Chapter 4 together they can easily obscure each other The marker placement options are listed in Table 3 Action M arker operation Click Place a marker at the cursor position Shift Click Move the nearest marker to the cursor position Ctrl Click Remove nearest marker Alt Click Place a marker at the nearest peak Alt Shift Click Move the nearest marker to the nearest peak Esc Stop marker placement Marker display can be controlled through the Settings Spectrum
103. eration Results as well as the assignment data File Print Assignments and the final iterated parameters File Print Spin system data When you look at the final list of frequencies and intensities you may occasionally see that the order of numbering of the list differs from the one you started with This is because due to changes in parameter values energy levels and peak positions can move past each other and peaks can gain or loose intensity gN MR does not keep a fixed order of assigned peaks but instead tries to track energy levels and peaks during the iteration phase This tracking may sometimes fail especially if there are many zero coupling constants in the system but usually it works quite well 5 8 Checking the solution The final question to be asked of any iteration is did obtain the right solution This is partly a philosophical question there may not be a way to determine whether you have the right solution or there may not even bea right solution From a mathematical point of view the right solution is the one that gives the best agreement between observed and calculated data but this solution is not necessarily very close to the real set of shifts and coupling constants These are some ways in which an iteration can produce wrong results e Themost serious error is onein the spin system gNMR always assumes that you have supplied the correct spin system and will never try to change that during an iteration
104. erical parameters used in these rules are collected in the file gNMR41 frg installed as part of the samples installation option It is possible to adjust the values or add new substituents but we do not recommend this When gN MR is asked to predict parameter values for any molecule it examines the environment of each nucleus in turn and tries to match that to fragments stored in the database Initially it tries to find a match for up to 5 bonds away from the target nucleus but it will reduce this down to 1 bond if necessary until a match is found The stored shift corresponding to that fragment is then used as prediction If there are several matches for the same distance in the database the weighted average is used Coupling constant prediction is donein a similar way An encoding of all atoms along the bond path connecting the two target nuclei is matched against previously stored bond paths A more elaborate bond path encoding including all atoms one bond away from the path is also tested for a match If there are several bond paths of the same length connecting the atoms predicted values for these are averaged If the user stores new structures in the prediction database environment and bond path encodings are also stored so they will contribute to future predictions Only non zero values for shifts and coupling constants will be stored Therefore you should set to zero any shifts and couplings you consider unreliable before
105. ery efficiently but a correlation using the bi exponential W amp 4 2 exp ai j exp 2o i j which has a shape resembling a Lorentzian can be evaluated nearly as efficiently as the pure exponential WE Therefore gN MR uses either WE or WE2 The values of used for successive cycles are determined by the parameters Conelation Start Cs and Corelation Increase C in the Iteration section of the Settings File dialog The first cycle uses a Cs and either WE for Cs gt 0 or WE2 for Cs lt 0 After each cycleis completed amp is increased by a factor C as soon as it gets 1 the correlation is dropped altogether and a final pure least squares cycleis performed In full lineshape iteration all derivatives are calculated by finite difference The Jones spiral algorithm is used for minimization as described in the previous section the SVD modification discussed there has a damping effect on the first few points of each cycle and often prevents good starting values from being scrambled immediately Technical issues 229 Built in rules Appendix F F 7 Chemical exchange calculations gN MR uses the standard Liouville representation of quantum mechanics to evaluate dynamic spectra as described by Binsch 14 This formalism easily lends itself to treatment of general inter and intra molecular permutations of nuclei For approximate calculations the exchange matrix is constructed in an eigenfunction basis Rows and columns
106. est way to open a database is using the File Database Select DB command of gN MR and gSPG or the Database Select Database command of gBase The program scans the available databases this might take some time and then displays a dialog in which you can select the database you want from a pulldown list Databases are identified by their aliases as displayed in the BDE Configuration utility not by their original filenames After you have selected a database most of the remaining Database commands become enabled After you close a database record it will appear in the File Recentlist among the normal disk files indicated by database alias and record number as in gNMR fragment s 1 and you can open this directly without going through the database selection dialog Going through the database selection dialog every time you want to use a database quickly becomes annoying Therefore you may want to define a default database which will be opened every time you start gN MR gSPG or gBase gN MR will always use this default database for parameter prediction To define a default database start gNMR and select Settings Preferences M ove to the Database topic and select the database you want to use from the Default Data Source pulldown Check Use database for prediction if necessary Then click on OK Databases 141 The Database menu Chapter 10 to dismiss the dialog exit gNMR and restart it The default database will be open
107. fferent nucleus for the spectrum if there is more than one N M R active nucleus in the system Linewidth Allows you to specify a single linewidth in Hz to be used for the whole spectrum in the current Spectrum window you can have different linewidths for different windows If you are using individual linewidths for the nucleus in the current window this option will be disabled Scale Allows you to specify a scale in Hz cm or H2 inch for the spectrum you are looking at If you change this the display limits remain the same so the horizontal spectrum size has to change see below Fom Is used to specify a new start high field limit for the spectrum display If you change the start frequency of the display the end frequency below will be shifted by the same amount to preserve the current values of the horizontal size and scale If this results in Displaying spectra 67 Chapter 4 the display limits failing to enclose any peaks of the current spectrum the full spectrum will be displayed To Is used to specify the end low field limit of the spectrum display Changing this parameter leaves the start of the display and the scale unchanged so it will generally change the horizontal size Again the full spectrum will be generated if the calculated spectrum falls completely outside the new display limits Vert Size Specifies the vertical size of the printout in cm or inches Normally this is the size of the highest
108. formation is written to it For each new point the spectrum will be redisplayed in the Spectrum window When the iteration has converged the Iterate window disappears and the Molecule and Spectrum windows will correspond to the optimized data One of the best and quickest ways to check the results is to move to the Spectrum window select Settings Spectrum move to the Display topic and check the Show Assignments box This displays all connections between calculated and observed peaks Figure 8 if the iteration results are good these connections should all be vertical straight lines without any crossings Finally save your iteration results as ODCBMou2 dta 18 Tutorial Figure 8 Spectrum window showing assignments after iteration Numerical assignment Chapter 2 2 odcb2 Spectrum 1 OF x oe Fri Sep 19 21 28 33 1997 ODCB tutorial example ODCB 300 MHz smoothed and compressed W1 1H Axis ppm Scale 15 24 Hz cm I li 7 500 7 450 7 400 7 350 7 300 7 250 7 200 7 150 7 100 7 050 7 150 7 100 7 050 i ala Hs CO 7 350 7 300 72 200 Numeric assignments are an alternative to the mouse assignment procedure described above Instead of pointing out peaks with the mouse you enter numeric values for the observed peak positions corresponding to calculated peak positions Typing numbers is more cumbersome than pointing with the mouse However it is also more accurate and you do
109. fts A The easiest way is to select all fields of the shift column of the Molecule window then choose Edit Copy switch to Hz units lt Ctrl U gt and choose Edit Paste You can also use this trick if you happened to have entered shift values in Hz for the wrong spectrometer frequency Q Whenever select a part of a calculated spectrum using the dragging or the Selection miniwindow gN MR starts recalculating the spectrum which takes an annoying amount of time A If you select a subspectrum gN MR recalculates that part using maximum precision If you just want to have a quick look at details but do not need maximum precision use the Spec trun Vert 2 and Spectrum Horz 2 choices or their and 4 gt button bar equivalents to expand without recalculation If the spectrum becomes too large for its enclosing window you can use the scroll bars to move through it Q I am looking at a small window containing a part of a spectrum When select File Print get several pages containing a much larger part A File Print always prints a spectrum that corresponds to the Settings Spectrum dialog box settings range is set by the From and To items size is given by the Hor Size and Vert Size items Even if only a part of this spectrum is visible in the window all of Questions and answers 205 Appendix B it will print To print only the part you are interested in choose File Print Visible Part Alternatively you
110. gNMR version 4 1 Cherwell Scientific Limited The Magdalen Centre Oxford Science Park Oxford OX4 4GA United Kingdom gNMR Copyright Disclaimer Trademarks Author Publisher 1995 1999 IvorySoft All rights reserved No part of this manual and the associated software may be reproduced transmitted transcribed stored in any retrieval system or translated into any language or computer language in any form or by any means electronic mechanical magnetic optical chemical biological manual or otherwise without written permission from Cherwell Scientific Cherwell Scientific make no representations or warranties with respect to the contents hereof and specifically disclaims any implied warranties of merchantability or fitness for any particular purpose All trademarks and registered trademarks are the property of their respective companies The gN MR software and documentation are written by Peter H M Budzelaar oN MR is published by Cherwell Scientific Limited The Magdalen Centre Oxford Science Park Oxford OX4 4GA ISBN 0 9518236 3 9 gN MR User M anual gNMR iii Cherwell Scientific web site For information and customer support contact Cherwell Scientific Publishing at the following addresses Cherwell Scientific Ltd The Tel 44 0 1865 784800 Magdalen Centre Fax 44 0 1865 784801 Oxford Science Park gnmr cherwell com Oxford OX4 4GA United Kingdom Cherwell Scientific Inc Tel Fax
111. ght click on it and select Open from the pop up menu that appears That will open the file within the database Recently opened database records will appear among regular disk files in the File Recentlist where they are indicated by the database name and record number e g gNMRDat a 1 Opening a record this way may be faster than going through a query 2 6 Transforming and phasing spectra This section covers e Importing a spectrum and FID e Weighting and transformation e Phasing and autophasing The Tutorial directory contains a set of files called VNMRtest fid prc spc txt that have been obtained from a Varian spectrometer using the procedure described in section 11 5 of this manual We will first convert them to a gN MR experimental spectrum format using the gCVT program Start gCVT and in the dialog that appears in the pulldown labeled Convert From select VNMR Then to the right of Parameter File click on the Browse button and select the file VNMRtest prc The three other file names below it will be filled in automatically Click on the Go button gCVT will ask for a name to save the file use VNMRt est spg and then start the conversion It will convert the real spectrum imaginary 32 Tutorial Fourier transformation Phasing Chapter 2 spectrum and real and imaginary parts of the FID in turn Then gSPG will start and open the newly converted file The converted file contains both a spectrum and an
112. ght phase amp byte double Spectrum 516 datapoints series of 8 byte doubles or 518 datapoints series of 4 byte floats The spectrometer frequency should bein MHz for 1H not for the observe nucleus The datapoints must be ordered from high to low field i e the reverse of the order used on most spectrometers 222 File formats Appendix F F Technical issues F 1 PC Aspects gN MR V4 1 was written in C with Borland s C C compiler and is based on OWL Many of the algorithms used in gN MR are based on Numerical Recipes in C 10 F 2 Spectrum evaluation Simulation of static NMR spectra is based on general NMR theory see e g Pople magnetic equivalence factorization has been incorporated using the composite particle formalism Perturbation theory is fairly simple for NMR Consider the nearly blocked Hamiltonian H H zy da _ 11 21 H H H 3 Panes where the coupling H 1 between the subblocks is small compared to H If weletk run over the eigenfunctions of H 11 and i over those of H 22 we have 0 0 yi T hy i 9 a 0 Wy 0 0 Y i E 7E i Since H only mixes functions from different sub blocks all odd order energy corrections vanish Bo y Jz wi 0 y ja yO y 0 i EP yi zw 3 eOe E PPO P EPPP Wi 0 Technical issues 223 Appendix F The second order correction term Egl is of order J2 AS and the lowest order remai
113. gradually enclose the baseline noise from above and below Only points between the two lines will be used for the fit If you are not content with this choice of baseline points it may help to first do a Spline correction see below Spec trun Baseline Truncate below Can be used to remove spikes that extend below the baseline 164 Spectrum processing Chapter 12 noise Such negative peaks can give problems in iteration so it may be a good idea to remove them The truncation is not done directly at the baseline level itself but at the negative of the baseline noise level This is important if all negative noise would be removed the remaining uncompensated positive noise would result in intensity throughout the spectrum which would give problems in iteration Truncation below the baseline noise level only removes the large negative artifacts while retaining the normal negative noise The baseline noise amplitude is determined as described above Spectrum Baseline Spline Is the most interactive method of baseline correction You will be prompted for the number of points to be used normal values are 5 40 After you enter this number the spectrum will be displayed with a number of square drag handles on a dotted curve representing the baseline You should move the squares in such a way that they follow what you think is the true baseline gSPG will then calculate a spline through these points and use that for baseline correction T
114. h the calculated spectrum To usea spectrum disk file you would select Settings Spectrum move to the Iteration topic and click the File button as described in section If you want to use a database record instead click on the Database button in the same topic and select the record you want As described in the previous section the Database topic in the Settings Preferences dialog can be used to define the default database which will be opened every time you start gNMR gSPG or gBase If you find that opening the database on startup takes too much time uncheck the Open database on startup option gNMR Databases 143 The gBase utility Chapter 10 will then still use the database for prediction but will not open it immediately on startup Two checkboxes in that topic also let you specify whether you want to use database data for parameter prediction on by default and whether the results from database prediction should be merged with rule based prediction off by default database results take precedence over rule based results The program gBase is mainly intended to do bulk transfers of file sets into and out of databases A part from that it can be used to initialize databases for use with gN MR All of the important commands are located in its Database menu The Select Query Show selection and Open selection commands work as in gNMR The Database Create Tables command creates a set of new empty tables and indexes
115. han peak position only iteration In most cases however the iteration itself will only take a fraction of the time needed for preparation When the iteration has converged you will hear a beep and see the status window disappear Save the results immediately before doing anything else 5 7 Inspecting the results You can inspect the iteration results in a number of ways The fastest Way is visually just look at the resulting Spectrum windows If you have a Spectrum window showing both experimental and calculated traces visual inspection is usually sufficient to decide whether the results make sense particularly if you have enabled the display of assignments See section 5 5 In some cases you may have to adjust the linewidth and or the lineshape function to get a really good agreement but wayward results are nearly always obvious If your experimental spectrum is only available on paper you may wish to make a printout of the calculated spectrum and compare the two using alight box If you havea list of peak positions you can select iterate Assignments again to look at the final calculated frequencies and or intensities Even if you have not assigned any intensities you Assignment iteration 93 Chapter 5 should still make sure that the pattern of calculated intensities roughly matches that of the observed intensities Finally especially after large iterative calculations you may wish to print the error analysis File Print It
116. han to peak heights Establishing the degree of uniqueness is an entirely different question No solution is really unique sign inversion of all coupling constants leaves the spectrum unchanged so there are always at least two solutions In the ODCB case discussed in many parts of this manual interchanging the A and B nuclei does not affect the spectrum and neither does the exchange of Jab and Jap or of Jaq and Jbp SO you should always try to find out how many equivalent solutions exist for your system For the particular case of different sign combinations gN MR offers the option to do a systematic search of all possibilities and collect them in a list See section 6 5 The results are ordered for increasing residual and since equivalent combinations should produce the same spectrum and hence the same residual inspecting the top few of the list should give you all equivalent best combinations As an added bonus you may find better combinations than those identified so far Special care should be taken when iterating on the spectrum for a single nucleus in a molecule containing several NMR active nuclei for example the 31P spectrum of a rhodium phosphine complex or the 3C spectrum of a diphosphine Obviously you cannot determine all spectral parameters from such partial information for example you cannot determine the chemical shift of a rhodium atom from the 31P spectrum of the phosphorus it is bound to However some parameter
117. hape analysis gN MR attempts to fit a calculated to an experimental spectrum using the full set of observed datapoints As a consequence any parameter that affects the appearance of the spectrum can in principle be optimized A part from this full lineshape iteration is similar to assignment iteration you set up a normal simulation mark parameters for optimization and tell gNMR which spectra to use in the iteration Then you start the iteration and wait for the results You never tell gN MR explicitly what kind of iteration to use If you have defined any assignments gN MR will always use assignment iteration If there are no assignments but you have selected one or more experimental spectra for iteration gNMR will use full lineshape iteration In all other cases you will hear a beep or see an error message Full lineshape iteration is much slower than assignment iteration If you find that calculating a single spectrum already takes along time full lineshape iteration may have to be done overnight 6 2 Iteration variables As mentioned in the previous section any parameter that affects the appearance of the spectrum can be optimized in a full lineshape analysis This includes not only shifts and coupling constants but also linewidths concentrations and rate constants Marking shifts and coupling constants for optimization has already been described in the previous Chapter section 5 2 for full lineshape iteration you can also
118. has not been tested extensively Lybrics is a general purpose spectrum file format 2 NMR spectra in Lybrics format are produced by the UWNMR program UWNMR uses the Lybrics format for both FID and transformed spectrum data All data is combined in a single binary file The observe nucleus name and the spectrum offset are missing from the file and have to be entered in the dialog Galactic NUTS Felix and Mestre C conversions are also provided 158 File conversion Chapter 12 12 Spectrum processing using gSPG 12 1 Introduction gN MR uses experimental spectra for comparison with simulated spectra on screen and on paper and for assignment and full lineshape iteration The experimental spectra are usually obtained by conversion from some proprietary spectrometer file format see chapter 11 Whenever possible the spectra should be transformed and phased carefully using the spectrometer NMR software or other dedicated processing software so that you can use the spectrum imported by gCVT directly in a simulation Sometimes however you may need to manipulate the spectrum after it has been converted to gSPG format Some possible reasons are e You want to do something your processing software doesn t do like removing a peak from the spectrum e You don t have access to the original spectrum or processing software any more e Your processing software does not support export of a transformed spectrum so you must import the FID
119. hase changes are applied when you release a slider If you want more immediate feedback check the Quick box The spectrum display will be drawn in a coarser manner but feedback is almost instantaneous C Quick phasing Instead of adjusting the phase manually you can also click the AutoPhase button to let gSPG generate a phase correction automatically This may be time consuming and will only work if the Spectrum processing 177 Chapter 12 phasing is reasonable to begin with You can also choose Spectrum Autophase to apply automatic phase correction directly to the spectrum without going through the Phasing dialog Again this is only recommended if the phasing is already reasonable to begin with 12 11 Linear prediction Linear prediction can be used to extract peak lists directly from the FID without intermediate Fourier transformation In principle it can give more accurate and reliable results than FT followed by peak picking since it makes direct use of the raw observed data In practice it requires considerable experience with the LP parameters to get anything useful out of it The current implementation of linear prediction in gSPG should not be considered definitive 178 Spectrum processing Figure 61 gSPG Linear Prediction dialog Linear Prediction Lx Data Method Mv Use Correlation function l Bruker FID M Mi Exclude initial points Use FID points Max peaks SVD Cutoff Sel SVD Z
120. he spectrum will be included in the gN MR file as a local copy 4 4 Baseline parameters gN MR allows you to modify the phasing and the baseline of the calculated spectrum This is most often used in combination with full lineshape iteration to fit imperfect experimental spectra but you can also use the feature without iteration The baseline parameters are located in the Baseline section of the Settings Spectrum dialog Figure 32 to activate any of them simply fill in a non zero value You can remove the effect of a parameter by clearing its field or setting it to zero All except the phase parameters will also be cleared when you change the display limits Spectrum Settings Ea Topic Phasing and Baseline Phase 0 0 1 Dimensions Phase 1 0 05 Height 0 003 Tilt Sin 1 Cos 1 Sin 2 Iteration ule 1 o Cancel A pply Help Baseline M 74 Displaying spectra Markers Chapter 4 On most NMR spectrometers the phase at a given point x of the spectrum is given by a gt 0 x Q x 9 x where xg and x are the spectral limits and g and are the phases at these limits Such a definition would not be practical in gNMR since changing the display limits would then change the phasing Instead we use the phase at 0 ppm and the phase change per ppm as parameters Phase 0 Is the phase at 0 ppm in degrees Phase 1 Is the phase change p
121. he parameter is left empty in that case gCVT will try to deduce the nucleus from the ratio of the observe frequency 1_freq parameter and spectrometer frequency c _base parameter Since this may produce the wrong result or no result at all resulting in an error message it is advisable to ensure that the 1_nucleus parameter is set correctly If thereisa parameter sample in the header its contents will be used as a file title for the converted file Occasionally you may find that the origin of the converted spectrum is incorrect You can adjust this within gSPG select Settings File and enter the correct value for the Offset parameter high field limit of the spectrum see section 12 3 TheJEOL EX GX format has separate parameter and data files File conversion 157 JEOL Alpha and Lambda MacFID Lybrics Other formats Chapter 11 Contents PC name acquisition fn gxp parameters spectrum FID fn gxd The offset is sometimes missing and can be supplied in the dialog TheJEOL Alpha and Lambda formats have acquisition parameters and data combined in a single binary file By convention the extension nmf indicates a FID and nmd a transformed spectrum The offset is sometimes missing and can be supplied in the dialog The MacFID 1D program stores all data in a single binary file The observe nucleus name and the spectrum offset are missing from the file and have to be entered in the dialog This conversion
122. heless the fast approximate method may be useful for obtaining a quick impression of what the spectrum of a large molecule should look like Tutorial 39 Chapter 3 3 Entering data 3 1 Introduction In gN MR a file corresponds to a combination of a sample and a spectrometer The sample can consist of up to 10 component molecules and you can generate several spectra from it eg for different nuclei However the file can have only a single spectrometer frequency since this is a property of the spectrometer not of an individual spectrum Data for individual components in the sample are entered in Molecule windows section 3 3 and further Spectrometer settings can be changed through the Settings File dialog next section When you have prepared both you can look at one or more spectra in Spectrum windows next chapter If you do nontrivial simulations or work with several open files the gN MR parent window C oNMR i GB Ab can become cluttered with open child windows O Molecule 1 gN MR tries to keep windows belonging to a ay Spectum 1 single file together if you activate one of them i d Benzene the others also move to the front The E Molecule 1 Windows amp Files miniwindow which appears ay Specii when there are many open windows may help you navigate between them if you don t like this feature turn it off with Settings Preferences You might also want to check Window Minimize Inactive which ensu
123. hift of another nucleus Each isotope shift should be entered in the row of the nucleus feeling the shift and in the column of the nucleus causing the shift Thus isotope shifts modifying the chemical shift of a nucleus are always in the same row as the base chemical shift of that same nucleus If you are finished entering isotope shifts you can switch back to normal coupling constant display with the Molecule Coupling Constants command 3 6 Importing chemical structures gN MR can import structures created in several popular chemistry drawing programs and use these for data entry Programs supported include ChemDraw V3 and V4 Isis Draw V1 and V2 ChemWindow V2 V5 and Chemintosh V3 You can import a Entering data 53 Chapter 3 structure from file or from the clipboard To create a structure for import follow these rules e Label all atoms except carbon by their element names If you want to use a specific isotope for a certain atom use the full gN MR isotope name case sensitive 195PT will not be recognized e gNMR recognizes some simple abbreviations Me Et Ph CHO but in general it is advisable to draw all bonds between non hydrogen atoms explicitly You can omit hydrogens bound to carbon but all other hydrogens should either be drawn explicitly or included in the label of the atom e g NH2 for a primary amino group e Usesingle double and triple bonds where necessary gN MR will try to recognize aromaticit
124. his will take you back to corresponding shift field in the Molecule window Move the Molecule window so it doesn t overlap too much with the Spectrum window Now choose Edit Interactive Delta 2 A dialog appears containing a vertical slider Move the slider a small distance and release it New values appear for 52 and 53in the Molecule window and the Spectrum window is updated The slider is very sensitive to reduce sensitivity click once on the 10 button If you want to get quicker feedback check the Quick checkbox to let gNMR recalculate the spectrum continually whenever you move the slider Click on Done when you are satisfied with the results It is essential here to use the symmetry linking described above before using the slider feature else the slider would change only a single chemical shift 2 3 Iteration This section covers e Iteration on peak positions e Full lineshape iteration Iteration or iterative optimization is the least squares determination of a set of parameters from a collection of data To carry out the iteration you must tell the program what parameters you are trying to determine and supply the necessary data Parameters are things like shifts and coupling constants You can tell oN MR that a certain parameter is to be optimized by giving ita name Names are entered right below the corresponding values in the Molecule window Two parameters having the same name will be kept the same during iteration
125. his option is handy for removing broad humps below large multiplets It is also useful in situations where the automatic baseline methods Fourier Truncate Below fail to recognize the baseline because it undulates throughout the spectrum Once you have removed most of the baseline features using the spline procedure the automatic methods will probably work well The drag handles only move vertically even if you move the mouse horizontally When you are satisfied with the baseline press lt 1 gt to carry out the actual correction You can also press lt Esc gt to abort the process and retain the old baseline The spline correction though very versatile is rather inaccurate you are limited by the vertical screen resolution and the baseline noise is often only a few pixels in amplitude This inaccuracy may inadvertently introduce intensity positive or negative in empty regions of the spectrum which may interfere in full lineshape Spectrum processing 165 Removing peaks Chapter 12 iteration Therefore it is recommended that you always follow a spline correction with a Fourier correction Spectun Baseline Remove Noise Is avery crude and radical way to remove noise If you select this option a horizontal line will appear in the spectrum You can position this line using the mouse When you then press lt gt all datapoints below this line will be reset to zero Since a large part of the intensity of most peaks is in the
126. idth for each nucleus in the system H ere we only need a single linewidth for the whole spectrum press lt gt to move to the next column Tutorial 9 Figure 2 Molecule window with ODCB data Chapter 2 The remainder of the Molecule window is the matrix of coupling constants For example row 3 column 2 of this matrix will contain J23 the coupling constant between nuclei 2 and 3 Since coupling constants are symmetric J 23 32 only the lower part is shown The actions described above should have left you in the J12 position of the matrix So type 8 and press lt gt to move to J 73 type 2 and press lt 1 gt again to move to J14 type 1 and press lt gt to move to the empty row As before simply press lt gt without typing any data to move to the top of the next column in this case to J 3 Enter the values 8 2 nothing 8 The completed Molecule window should look like Figure 2 Before looking at the spectrum let us change the spectrometer frequency The gN MR default is 100 MHz but we have a sample experimental spectrum recorded at 300 MHz and we are going to compare the two So select Settings File In the dialog box that appears you will see the item Spectrometer Frequency Type a new value of 300 0 and click OK to confirm Documenti Molecule 1 O1 x Options Spectrum You are now ready to look at the spectrum dick on the Spec trum button to display
127. ies of the gNMR nucleus list Appendix C fragment list and abbreviations list and the groups database generator utility gGRP Section 8 3 With the exception of gGRP these files will be stored in the directory Samples so they will not override the built in scripts and lists Database support BDE support ODBC support and two sample databases The databases are Microsoft Access and Borland Paradox versions of the same database so you need to install only one of them The database s will be installed in the directory Database BDE and ODBC must be installed separately see Chapter 10 for details 1 3 The user interface gN MR is designed to function similar to other Windows programs It supports clipboard copying but not Object Linking and Embedding OLE A gNMR document or file contains all spectrometer and sample data required for a simulation A single document can have several open windows corresponding to components in a mixture exchange reactions calculated spectra etc There are several links between the different kinds of windows If you click on an atom in a structure the data grid editor moves to that chemical shift field and a range indicator will be highlighted in all open Spectrum windows Double clicking on an atom or a shift field moves you to a Spectrum window and selects the corresponding multiplet Double clicking on a multiplet moves you to the corresponding field in a Molecule window For every file gNMR
128. ific bond type from the Stucture Bond Type submenu For directional bonds wedges arrows Structure Bond Type Reverse can be used to reverse the direction of the bond Each atom in the structure can correspond to a nucleus in the spin system i e to a shift and a set of coupling constants this constitutes an assignment of the atom Sometimes you may come to the conclusion that an assignment was Chapter 3 Single Double Triple Quadruple Inside Bold Wedge Dash Hash Hashed Wedge Zigzag Bold Inside Dash Inside Open Wedge Arrow Double Arrow Reverse incorrect usually because two assignments have to be switched This can be done by exchanging all numerical data shifts coupling constants for the two nuclei but that takes a lot of typing The Struc ture Switch Assignments command lets you quickly switch the assignments of two atoms in a structure by simply switching their links to nuclei in the spin system Entering data 61 Chapter 4 4 Displaying Spectra 4 1 Spectrum windows gN MR uses a number of Spectrum windows to display the NMR spectra of a given species or mixture of species in a number of ways Nine windows labeled Spectrum 1 Spectrum 9 are available Each window can have its own collection of display parameters which include plot dimensions frequency limits linewidth and the nucleus you are looking at There are several ways to create a new Spectrum Spectrum window clic
129. ill only contain a single default font independent of the font preferences Static Text This is the font used for static texts in dialogs non editable fields in grids and text on buttons in input windows Molecule Exchange Assignments Customizing gNMR 199 Appendix A Edit Text This is the font used for editable fields in grids and dialogs Plot Text This is the font used for texts in spectra and structures italic Text This is the font used for italic text in eg structures We recommend that you use the same font size for the Plot Text and italic Textfonts Log Text This is the font used for the Log window It should normally bea fixed pitch font so that tabular data will display correctly Colors section Topic Spectrum Part Colors Iteration Imaginary Q Integral is Connections a Change Editing Highlighted Peak a Change byt Highlighted Area m Change WFT help Spare Color Change we Lin Pred Element Colors Element H E Change M Use element colors everywhere Cancel Defaults Help QNMR uses a set of six colors for display of different items in spectra One of these is a spare color The color used for the spectrum itself is determined from values in the nucleus list Appendix C if this Database 200 Customizing gNMR Appendix A conflicts with that of another item in the spectrum the spare color is used for that other item instea
130. in a database This in effect prepares the database for use with gN MR or gSPG No NMR data can be stored in anew database unless it has been initialized with this command If you use this command on an existing database any gN MR data tables will be deleted first The Database Add Data and Database Add Spectra commands let you add data and spectrum files to the database Sel ect one or more data or spectrum files in the usual manner If you check the All DTA or All SPG checkbox in the file dialog all other files from the same directory will also be added The Database List Data Database List Spectra and Database List Sruc tures commands summarize the contents of the corresponding records in the database This is only useful for small databases If you have created a selection using the Query command discussed earlier the Database Restore Data and Database Restore Spectra commands allow you to restore these records as disk files You will be prompted for a directory to store the files in Files will be restored with their original filenames wherever possible If this is not 144 Databases Built in rules Chapter 10 possible or if the write would overwrite a newer file an artificial filename will be generated The Database Clear Tables command can be used to remove all tables needed by gN MR This makes the database useless to gN MR Depending on the database driver this command may or may not shrink the size of the da
131. indow will also resize the spectrum inside it If the option is unchecked resizing the window does not affect the spectrum and you have to use the Settings Spectrum dialog to change the spectrum size Customizing gNMR 189 Appendix A Auto Subselect gN MR uses a fixed number of datapoints to calculate a simulated spectrum see below If you expand a region of a spectrum strongly using Spectrum Horz 2 or the 4b button you may start to see individual points instead of a smooth spectrum Subselection of only the expanded portion would result in a better display since the full number of datapoints would then be used for only that subrange Of course the necessary recalculation might take some time particularly for exchange spectra There are three settings Always Automatically subselects the expanded region in case of strong expansions Never Never subselects automatically Prompt Prompts in case of strong expansion Pts Spec trum Sets the number of datapoints to be used for every simulated spectrum default 2000 190 Customizing gNMR Appendix A Display section Topic Display V Show Info I Messages to Log file l Show Assignments M Show Nucl Ranges l Show Imaginary M Show Integral F Show Markers Number M Thumbnail Spectrum V Out of range Indicators Biot Cancel Defaults Help These settings correspond to the Display section of
132. ing a negative linewidth in at least one of the two calculations being discarded Spectrum processing 181 Chapter 12 Remove lt noise Check this and specify a signal to noise ratio to discard all peaks with an amplitude less than the given fraction of the background noise Values in the range of 0 5 2 are reasonable Remove lines gt Check this and specify a linewidth to eliminate all lines wider than the given threshold in Hz For non exchanging systems 100 is generally a safe value since lines wider than that usually represent baseline artifacts Do not use this option for exchanging systems Remove out of phase peaks This attempts to find a linear phase correction for the spectrum and then delete all peaks that deviate too much from that line on the assumption that they must be artifacts This option may well eliminate real peaks and is not recommended for general use The remaining options specify how the resulting peak list is converted into a spectrum Reset linewidths to Check this option and specify a linewidth to discard all fitted linewidths and use the specified linewidth instead Reset all phases to 0 Check this option to discard all fitted phase information and use a phase of 0 for all peaks Spectum size Specify the number of data points to be used for calculating the transformed spectrum Via FFT Direct Specifies how the spectrum is calculated from the final peak list Via FFT generates a synthesized
133. ion 1 00000 l iterate on Concentration Repeat Units 0 Av bond length 1 72 20 00 Atom Labeling Origina F Apply Cancel Help The Molec ule Show Symmetry command determines and displays the permutation symmetry of the molecule as deduced from the values of shifts and couplings it does not use the structure drawing This need not correspond to the actual point group symmetry of the molecule For example the permutation symmetry will be identical for C Ci and C2 symmetric molecules as these point groups are isomorphous Also nuclei that are in the molecule but not included in the spin system are ignored If you have several accidentally identical shifts and or couplings gNMR may find asymmetry that is too high if the system has a lot of symmetry gN MR may fail to identify the symmetry group The symmetry dialog Figure 22 shows a button labeled Enforce which you can click to let gN MR automatically link symmetry related shifts and couplings equivalent to the Edit Auto Variables command This ensures that when you change one value of a set the others will also change see section 5 2 46 Entering data Chapter 3 Figure 2 Molec ule Show This indicates spin system symmetry as used by Symmetry dialog gNMR NOT molecular symmetry Symmetry Detected From Values a C2 Order 2 Enforce AA From Values and Names SUES no useful symmetry detected pen
134. ion works and keeps on working under all circumstances If you encounter a problem converting a spectrum send Cherwell Scientific a sample data file and we will try to solve the problem 154 File conversion ASCII ASCII FID Bruker WinNMR Chapter 11 ASCII can be considered as the lowest common denominator for data exchange gCVT will accept data files containing a straight series of intensity values in plain ASCII with blanks commas carriage return CR and linefeed LF characters separating the numbers Values of the missing parameters nucleus spectrometer frequency sweep width and offset may be entered in the dialog but you may also put them in the input file before the first spectrum value in statements of the form Nucleus 1H SFreq 200 013 SweepWidth 2400 Offset 200 Asan alternative a header of the form produced by Bruker WinN MR ASCII export is also accepted Spectrum values should be ordered from low to high field This expects a straight series of pairs of numbers representing complex points of the FID Specify missing parameters as in ASCII conversion The Bruker WinNMR and XWinN MR programs use at least five files per spectrum to store their data Contents WinNMR name XWinNMR name acquisition fn acqu text binary parameters processing fn pdata 1 proc text binary parameters real spectrum fn pdata 1 1r binary imaginary fn pdata 1 1i binary spectrum FID fn fid binary Use the WinNMR n
135. ists the possible choices gN MR recognizes two types of names single isotope names of the form 195Pt and natural abundance isotope mixture names of the form Pt 195 Using a single isotope name is straightforward If you use an isotope mixture name gNMR will generate a mixture of isotopomers for your molecule For example Pt 195 will generate a mixture containing 33 8 195Pt and 66 2 of species without this nucleus You can combine several isotope mixture names in a single molecule lsotopomer mixtures are discussed in more detail later in this chapter You don t always have to enter the full name of a nucleus If you just enter the element name eg Pt or P NMR will expand it to either an isotope mixture name Pt 195 or if this is a mono isotopic element to the single isotope name 31P Case is not important pt and PT are both recognized If you want to duplicate the name of the row above typea lt gt If you prefer to choose names from a list rather than typing them yourself type a lt gt and make your choice from the Nucleus name dialog that appears as shown in Figure 23 If you type aname gN MR does not recognize the same dialog appears As long as you editing the nucleus name field you can bring up the Settings Nucleus dialog Figure 24 This allows you to change some settings on a per nucleus basis or for all nuclei of the same type Nucleus Clicking on this button brings up the Nucleus Name dia
136. k the Spectrum at button in a Molecule or Exchange Eon ta window select Spectrum Recalculate v Resize with Window Ctrl R All move to a specific window using the ee Oe Expand Selection Spectum New command or copy the Horz 2 Ctrl settings from an existing window to a new Horz 2 Ctrl one using Spectrum Copy To Once one Me ie or more Spectrum windows have been Seep ARTO SE Delete created you can move between them pies gt using the Spec trum Go To command Regions gt shortcuts lt Ctrl 1 gt to lt Ctrl 9 gt or by 5 ecalcul en simply clicking on the desired window If system data has been changed to make the contents of a Spectrum window invalid the spectrum will be recalculated whenever you move to it Alternatively you can force updates of all spectra using the Spectrum Recalculate All command or by clicking on the Recalculate buttons in Molecule and Exchange windows Recalculate All Unlike Molecule windows Spectrum windows can be closed the parameters belonging to the spectrum will be renembered in case you want to redisplay the spectrum later on Use the Spec trun Delete command to completely remove a spectrum definition Displaying spectra 63 Figure 27 Spectrum window showing integral markers and axes Chapter 4 The calculated spectrum in a Spectrum window is normally used only within a simulation However you may wish to treat it as if it were an experimental spectrum The File Expo
137. lapping Show both traces through one another using the same horizontal axis This is not too useful on black and white printers but can be very revealing on the screen especially for spectra with broad lines Different colors will be used for the two traces if possible On monochrome screens the two spectra are offset vertically by a few pixels The remaining items in this dialog section are only used in full lineshape iteration are explained in section 6 2 If you select an experimental spectrum that has a different spectrometer frequency from the one used in your current simulation gNMR will offer to adjust the spectrometer frequency automatically of course changing the spectrometer frequency in this way may affect other Spectrum windows The range of the calculated spectrum is also extended automatically to encompass that of the experimental spectrum Similarly gNMR may recalculate the Displaying spectra 73 Figure 32 Settings Spectrum dialog Baseline section Chapter 4 spectrum for a different nucleus if the nuclei of calculated and experimental spectrum do not match You can also add an experimental spectrum by copying it from gSPG To do this you will have to include gSPG file data in the clipboard copy this may require using lt Shift Ctrl C gt or lt Shift Ctrl Ins gt in gSPG instead of the normal lt Ctrl C gt or lt Ctrl Ins gt shortcuts see section 12 12 for details In gN MR select Edit Paste Spectrum t
138. ling constants The program has to make a choice at some point between at least two sets of signs and your starting values determine this choice If you start all couplings at 0 both choices are always equally poor and the choice will never be made There are also situations where two couplings play an equivalent role in determining the spectrum In the ODCB system for example interchanging Jab and Jab does not affect the spectrum If you start the iteration with equal values for these parameters the program will never be able to decide which of the two should be the larger and it will always keep them equal So it is best to start the iteration with different starting values for all shifts and coupling constants that are not related by symmetry If you get tired of typing new sets of starting values you can ask Full lineshape iteration 105 Chapter 6 gN MR to generate them for you in a pseudo random fashion as described in section 6 5 6 8 Checking the solution Let us suppose that you have just completed a full lineshape iteration and the results look at least reasonable The question is do you have the right solution This question can really be divided in two parts e Do the parameters obtained adequately explain the experimental spectrum e Isthesolution you have obtained unique We will discuss these two questions separately Full lineshape analysis can produce a very accurate fit between calculated and experimental s
139. ll data in copies If checked a complete gN MR data file will be embedded in spectrum clipboard copies This will enable you to paste the spectrum from a word processor back into gNMR but may increase the size of the copy considerably Uncheck this option if you don t need paste back anyway If you keep the Shift key 80 Displaying spectra Chapter 4 depressed while making a copy gNMR will use the opposite of the current Include all data in copies setting Print Nuc Ranges If this option is checked and Show Nucl Ranges is checked in the Display section nuclear range indicators shown onscreen will also be printed If the option is unchecked they are never printed regardless of the screen display Displaying spectra 81 Chapter 5 5 Assignment iteration 5 1 Introduction Assignment iteration is a least squares procedure that optimizes shifts and coupling constants to produce a fit between observed and calculated peak positions and possibly intensities To set up an assignment iteration first set up anormal simulation as described in the previous chapter After this mark some or all shifts and coupling constants for optimization by assigning names to them and supply observed peak positions corresponding to some or all of the calculated peaks Your initial guess of NMR parameters needs to be fairly good or it will be impossible to establish these correspondences Peak positions can be supplied in two ways by pointing at th
140. log mentioned earlier Include Quadrupoles Overrides the file wide Include Quadrupoles setting section 3 2 for this nucleus Entering data 49 Figure 24 Settings Nucleus dialog Number of nuclei Chemical shift Chapter 3 Decouple Check this if you want to temporarily decouple this nucleus Decoupled nuclei remain visible in the Molecule window but their names will be displayed in italic Apply to Lets you apply the new settings either to the current nucleus only or to all nuclei of the same type e g all 1H in the molecule Nucleus Settings Ea Nucleus I Include Quadrupoles M Decouple Apply To ___ _ This nucleus C AIL 1H in molecule In the column labeled n you can indicate the number of magnetically equivalent nuclei in the spin group For example you would put a 3 here to indicate the three equivalent nuclei of a methyl group a single group can contain up to 9 equivalent nuclei You can enter a o or clear the field to delete a row of the spin system the row will then be deleted when you leave the field Alternatively you can press lt gt to immediately delete a row or lt gt to immediately duplicate the current row For single isotope nuclei the meaning of this field is straightforward For isotope mixture names there are some special considerations which are discussed later on In this field you enter the chemical shift for each spin group Values can be en
141. lready show the newly defined database gNMR Access However weneed to tell the BDE to save configuration info for the database else gN MR will not be able to retrieve it So click on the database gNMR Access and then change one of the options on the right and change it back to its original value we suggest using Enable BCD Then select Object Apply and confirm to save the changes Figure 15 Leave BDE administrator program Object Exit 30 Tutorial Figure 15 BDE dialog for definition of an Access data source Using the database Chapter 2 2 BDE Administrator g Borland Common Files BDE IDAPI CFG Object Edit View Options Help All Database Aliases Definition of NMR Access Definition Databases Configuration a Databases 5 Excel Files GE ONMR Access Type Microsoft Access Driver mdb BATCH COUNT 200 BLOB SIZE 32 BLOBS TO CACHE 64 DATABASE NAME ENABLE BCD FALSE ENABLE SCHEMA CACHE FALSE LANGDRIVER MAX ROWS 1 ODBC DSN gNMRA Access OPEN MODE READ WRITE ROWSET SIZE 20 SCHEMA CACHE DIR SCHEMA CACHE SIZE 8 SCHEMA CACHE TIME 1 5 NMA Data 84 oNMR PDox 5 MS Access 7 0 Database GE The database is now available for use by gN MR To make sure it will be used in parameter prediction you have to define it as the default database Start gN MR select Settings Preferences move to the Database topic this is the last topic of the di
142. mark individual linewidths section 5 2 in the same way The other optimizable parameters are marked as follows Concentrations can be marked by moving to the Molecule window selecting Full lineshape iteration 97 Chapter 6 Settings Molecule and checking the Iterate on concentation box in the dialog box that appears see section 3 3 This only marks the concentration of the current molecule if you want to iterate on the concentrations of several molecules you should set this flag for each of these molecules by moving to its Molecule window To prevent numerical problems you should always leave at least one concentration fixed Whole spectrum linewidths can be marked for iteration by moving to the Spectrum window then selecting Settings Spectrum and checking the Iterate on Linewidth box see section 4 2 This option is only enabled if the Full lineshape iteration box is already checked If you are using individual linewidths for the current nucleus this item will be disabled Rate constants can be marked for iteration by setting their type to Variable as described in the next chapter section 7 5 Baseline parameters in the Baseline topic of the Settings Spectrum dialog section 4 4 fill in non zero values for the baseline parameters you want to optimize then check the Iterate on Baseline box in the iteration topic It is possible to iterate on every parameter in sight but should you do so Some parameters simply ca
143. molecule the contents of which are displayed a i in a Molecule window Molecules are cou te gt numbered Molecule 1 Molecule 10 To Isotope Shifts l Paramet create a mixture add new molecules using IA tee Variable the Molecule New command or copy Auto Variables existing molecules to new ones using the nee lear Molecule Copy To command The Exchange ChE Molec ule Go To command can be used to Symbolic gt move between existing molecules but of Abia Show Symmetry course you can also move to a molecule by clicking on its window Molecule windows can be minimized but they cannot be closed individually Any attempt to close a Molecule window will close the whole file You can delete a molecule from a mixture using the Molecule Delete command and this will also delete its window Molecule Clear reverts a molecule to the default 1H at 0 ppm The Settings Molecule dialog Figure 21 displays settings for a single molecule Concentation is the concentration of the molecule in the mixture iterate on concentration check this to optimize the concentration in full lineshape iteration section 6 2 Entering data 45 Figure 21 Settings Molecule dialog Chapter 3 Bond length is the bond length in units of 1 7 to be used for displaying molecular structures see section 3 7 Atom labeling sets the label type for atoms in molecular structures see section 3 7 Molecule Settings Ea Concentrat
144. mport in eg a spreadsheet Spectrum processing 183 Appendix A A Customizing gNMR The gN MR programs can be customized extensively using the Settings Preferences dialog This dialog is the same in all gNMR programs since some of the settings affect more than one program After you have created new settings click OKto store them they will be used the next time you start the program To revert to the factory defaults click the Defaults button gN MR preferences are stored in the Windows registry under HKEY_CURRENT_USER Software Cherwell Scientific gNMR 4 1 Window locations and lists of most recently used files are also stored there Most gNMR preferences correspond to default values for items found in various gN MR and gSPG dialogs The descriptions given below will simply refer to the relevant manual section for such items There are also several items that control the way the gN MR interface works and these are discussed in more detail in this Appendix Customizing gNMR 185 General section Appendix A Preferences Ea Topic General Spectrometer Frequency in MHz for 1H Scale Units ppm Lineshape Lorentzian M Isotropic General Symmetry gt Dimensions T Include Quadrupoles nyo Display Undo Level 6 AA Start gNMR Welcome Dialog v Wiii W Click selects whole field R MV Move cell w Arrows T Recalculate moves to Spectrum
145. mutations using an abbreviated notation in which the starting positions and arrows are omitted Since the starting positions are the same for all possible permutations they are redundant in the above extended notation In the abbreviated notation the first one pair exchange process can be written as 4231 and the three symmetry related alternatives are then 8214 1324 and 1432 In the examples shown above the reaction was a simple exchange of two nuclei the forward and backward reactions are identical in such cases It is also possible to have more complicated movements as in the rotation of the o bound cyclopentadieny group of x Cs5H5 Fe CO 2 6 CsH 5 70 Ghethical exchange Chapter 7 He H4 C Hy H5 Fe Fe OC OC MH a 4 He Hs This reaction can be characterized by the following permutation 1 2 2 gt 3 34 455 5 gt 1 abbreviated as 23451 As you can easily check this permutation needs to be repeated five times to get back to the initial state For an example of an intermolecular reaction let us look at the proton exchange between formic acid and hydrochloric acid It is possible to number all nuclei in the system consecutively but it is usually clearer and more in line with the gNMR notation to usea separate numbering scheme for each molecule If we do so we will have to denote each position in the system by a combination of molecule number and nucleus number For example the OH proton of the formi
146. n labeled will appear which you can click to browse for the 28 Tutorial Figure 13 BDE dialog for definition of a Paradox data source Configuring the example Access database Chapter 2 directory The window should look more or less like Figure 13 Select Object Apply to save the new settings and then Object Exit BDE Administrator g Borland Common Files BDE IDAPI CFG Object Edit View Options Help eK oo All Database Aliases Definition of NMR PDox Databases Configuration gt amp Databases 8 DIVEPLAN Definition Type STANDARD DEFAULT DRIVER PARADOX g Excel Files ENABLE BCD FALSE g fragments PATH G gNMR Database Parado H 5 ONMR Data Se oNMA PDox 5 MS Access 7 0 Database acs Database Location The database is now available for use by gN MR To make sure it will be used in parameter prediction you have to define it as the default database Start gN MR select Settings Preferences move to the Database topic this is the last topic of the dialog and select gNMR PDox from the pulldown Default Data Source list Then quit gNMR First make sure the example A ccess database has been installed on your system It is only installed when you select the Database option during gN MR installation You can also install the database manually by simply copying the gNMR41 mdb file from the Database Access directory on the gN MR
147. n 3 2 or the individual nucleus settings Section 3 4 With Include Quadrupoles set the quadrupolar isotopes will be explicitly included and you will see coupling to these isotopes in the normal way With the option not set such isotopes will be treated as NMR inactive and you will only see coupling to the spin 2 isotopes of the isotope mixture The use of magnetically equivalent isotope mixture nuclei i e with the number of nuclei field greater than 1 often gives problems Using a set of 2 equivalent Pt 195 nuclei is allowed gN MR will generate 29Pt 2 195Pt and 19Pt p isotopomers But if you were to enter two equivalent Ag 109 nuclei the program would try to generate a mixture of 109A g 2 107A g 2 and 109A g 297A g isotopomers The latter isotopomer has a larger spin system than the original molecule you entered and you would need a place to put the 109A g 197A g coupling constant The two silver atoms are certainly not equivalent in this isotopomer even though you specified 2 equivalent silver nuclei gN MR refuses to generate isotope mixtures for such a case you can only havea number of nuclei field larger than 1 for either single isotope names or mixture names generating just a single NMR active nucleus Note that the effect of this restriction may depend on the setting of the Include Quadrupoles parameter If this were not set and you specified a group of two equivalent Os 187 nuclei gN MR would just generate 1
148. n happens you do not have the peak positions for all peaks because peaks are overlapping or because you cannot recognize some of the smaller peaks you can leave some fields empty If you have entered all values save your data in file ODCBNuml1 dta 20 Tutorial Table 2 Peak listing for ODCB Full lineshape iteration Chapter 2 Fobs lobs Fobs lobs 0 0401 0 0438 0 2904 0 2875 0 2243 0 2241 0 2062 0 2083 0 2141 0 2125 0 0257 0 0229 1 2 3 4 5 6 7 8 9 Start the iteration by selecting terate Go as described above After it has converged first save your results in ODCBNum2 dta Select Iterate Assignments 1H again to examine the results there should be errors in the last decimal places of the frequencies only Itis possible to enter intensity data as well but in the present case they are not needed and would not improve the results Full lineshape iteration is a generalized least squares fitting of the calculated to the experimental spectrum It can be used to optimize not only shifts and coupling constants but also linewidths exchange rates etc Setting up a full lineshape analysis is even simpler than preparing an assignment iteration Using the ODCB example again we will now determine the linewidth as well as the shifts and couplings Start with the set of variable definitions prepared earlier file oDCBVars dta or usefile ODCB2 dtaintheTutorial directory Move to the Spectrum wind
149. n t need a spectrum in electronic form for it It is important to realize that mouse assignments and numeric assignments are not two separate iteration procedures They are just two separate ways of preparing the input for the same iteration procedure You can mix the two assignment methods first do mouse assignments and then check and correct the numeric values or vice versa Begin the numeric assignment procedure with the file ODCBVars dta prepared in the previous section or with ODCB2 dta inthe Tutorial directory Select Iterate Assignments 1H The Assignments window will appear Figure 9 that shows a list of calculated frequencies and intensities and empty columns for observed frequencies and intensities The frequencies can be in either ppm or Hz depending on the global units flag You will initially be positioned at the topmost observed frequency field which corresponds to the highest field calculated Tutorial 19 Figure 9 Assignments window for ODCB Chapter 2 peak You can click the button labeled Descending to invert the peak ordering tw Odcb2 Assignments for 1H OLX Frequency calc obs Intensity calc obs rae 0 0153 Cna 00232 7 182 0 2089 r oze ras i om ra O o2 0 0398 A list of 24 observed peaks for the spectrum is shown in Table 2 Enter the frequency values in the given order pressing lt 4 gt after each one If as ofte
150. ndix B for a discussion One case where intensity data really needs to be included in the iteration is theA part of an AXxX system Suppose you have a 15C resonance of a diphosphine with the observed spectrum and peak list of Figure 17 Setting up the spin system and peak position data is straightforward see the tutorial file Axx_ints dta After opening it choose Iterate Assignments Nucleus 13C to move to the Assignments window Peak positions have already been filled in the only new point is figuring out how to enter the intensities The sum of the observed intensities is 2 466 Since we have only a single BC nucleus the intensities should be normalized to 1 Dividing everything by 2 466 we get the intensities 0085 and 2608 for the first two peaks The third intensity belongs to two calculated peaks Type the value 4818 in the field for the third peak and then type a lt gt in the field below gN MR will use the given intensity value for both peaks together Then enter the intensities 2437 and 0053 for the fifth and sixth peak and choose Kerate Go After a few iterations the iteration converges The Log window will show the error analysis Even though there are large errors associated with the two Jpc coupling constants actually only with their difference you do get well determined values at least the error analysis doesn t complain If you try the same iteration without the intensity data the error analysis will show that
151. newidths by aroot finding procedure and then the corresponding amplitudes and phases by linear least squares If the Non linear least squares option is checked this will be followed by around of simultaneous least squares fitting of all parameters 8 This option can be very time consuming but should in principle give the most accurate results The next few options specify the FID type determine which part of the FID to use and how many peaks will be extracted from it Bruker FT Check this if the FID was of the time proportional phase increment TPPI type often used with Bruker instruments In TPPI spectra real and imaginary components have been measured at interleaved points in time The default for gSPG is simultaneous where the real and imaginary components of each FID point correspond to the same point in time Mirror Check this if the transformed spectrum appears to have its high and low field ends reversed This may happen if during spectrum import the real and imaginary components were interchanged for some reason Rotate Unfilter Check this if the spectrum was or may have been digitally filtered gSPG will left shift the spectrum until the first point has a high amplitude before attempting the transformation This is correct only for sharp digital filters 180 Spectrum processing Chapter 12 Baseline Corr Check this to correct for any DC offset in the FID before transformation This should eliminate the sharp
152. ng Lorentzian Exponential multiplication using the specified positive line broadening h t e Gaussian Gaussian multiplication using the specified positive line broadening _ nw h t e In2 Lorentz Gauss Multiplication by a Lorentzian and a Gaussian The Lorentzian 172 Spectrum processing Chapter 12 linewidth can be negative to improve resolution but the Gaussian linewidth must be positive m nw ee h t e In2 Sinebell mtt h t sin tae Cosine A t Tt cos n Hanning h t l I a g 2 Aa Taas Hamming Tt h t 0 54 gaagos Kaiser 2 t I TO f TO A t where lg is the zero order modified Bessel function and typical values of 6 are 0 5 2 5 If you click the Update button in the dialog the current weighting function and weighted FID will be displayed in the AD window Spectrum processing 173 Chapter 12 Apart from the weighting function s you can specify the part of the FID to be used for transformation Exclude initial points Specifies the number of initial points of the spectrum that should not be included in the transform For normal FIDs this should be set to zero If you have reason to suspect that these first few points are contaminated set this to some small value typically 1 3 Reconstruct using LP Excluding initial points from the transformation will lead to baseline artifacts To prevent this you can check this option to rec
153. ning error E 4 is of order J4 A8 3 Letting yk denote the lower and j the upper level of a transition normalized the first order corrected transition moment is simply yo WO oe P Ire P Ire which allows separate evaluation of the contributions from the upper and lower levels of each transition errors in the corrected intensities are J AS The chunking method for approximate spectrum evaluation contains two important steps not present in normal spectrum evaluation e Selection for each atom of the correct chunk to obtain a reasonable subspectrum e Extraction of this subspectrum from the total spectrum of the chunk The protocol for chunk selection is described briefly in section 9 2 For subspectrum extraction a form of population analysis is used for transitions Consider a transition ya wp 4 where the superscripts 1 and u indicate lower and upper levels of the transition We can expand both sets of eigenfunctions wy into linear combinations of basisfunctions 9 DFe W SR COAN C Yi Lc Qi y LG 9 t J with corresponding transition moments T jj Each non zero transition moment corresponds to a single spin flip and can therefore be associated with a single nucleus n we can write T LT where at most one of the Tijn is non zero Using this property we can divide the total intensity U a into contributions from each nucleus 224 Technical issues Appendix F and then retain only
154. nnot be determined reliably from a spectrum If you have a linewidth of 2 Hz it is probably not worthwhile to optimize those long range coupling constants which you know are smaller than 0 5 Hz If you have transformed your experimental spectrum with a large line broadening all linewidths will be dominated by this and optimizing individual linewidths will not be sensible And if you are fitting exchange broadened spectra it is often best to vary only the rate constant and possibly some chemical shifts if they are very temperature dependent the other parameters cannot be determined reliably from the exchange broadened spectra and should be fixed at their low temperature 98 Full lineshape iteration Chapter 6 values In general do not try to optimize what cannot be determined from the spectrum you will get anumber which is not meaningful Try to find out which parameters are really important and let the program optimize all of these Do not fix any important parameters like shifts or large coupling constants if you make even a small error in these the fit procedure will try to use the remaining spectral parameters to compensate which will usually give wayward results 6 3 Iteration data To enable full lineshape iteration you must have marked at least one Spectrum window for iteration You do this by first selecting an experimental spectrum file see section 4 3 and then checking the Full lineshape iteration box You can mark se
155. nse to use the gN MR software software so long as the customer complies with the terms of this Agreement 2 Copies The Publisher grants the customer the right to make copies of the software for back up purposes only The customer agrees to reproduce and incorporate the copyright notice on any copies It is expressly understood that such copies will not be used for any purpose except to substitute for the initial copy in the event that it is unusable 3 Use In addition the license granted herein includes the right to move the software from one computer to another provided that the software is used on only one computer at a time and that two people will not use the program at the same time on different computers 4 Security The customer agrees to secure and protect each disk the documentation and copies thereof from copying except as permitted above or from modification and shall ensure that its enployees or consultants do not copy or modify the product 5 Ownership The Publisher represents that it has the right to grant the licenses herein granted 6 Limited Warranty Whilst all reasonable efforts have been made to test the software and user manual prior to first publication the Publisher welcomes corrections and suggestions for improvement The liability of the Publisher in respect of any defect error or omission in the disk user manual or software defective material and in respect of any breach of warranty or con
156. nt ranges and producea new spectrum that encompasses both ranges it is probably best to create a new empty spectrum using File New and then add the two 166 Spectrum processing Chapter 12 existing spectra in turn using Spectrum Add Be sure to use enough data points for the new spectrum to prevent loss of accuracy in the addition This is probably the only use within gSPG for the File New command 12 7 Regions integrals and multiplets With the Spectrum Regions submenu choices you can turn integral display on and off and ion define regions just likein gNMR In addition Auto Define Ctrl gSPG allows you to change the areas of integral Clear All Ctrl Modify regions and to perform analyses on peaks in Peak Lists these regions Muttiplets Solutions Spectrum Regions Modify Displays a dialog box Figure 56 listing all integral regions and lets you edit their areas gSPG tries to find a sensible scaling for the regions to get near integer relative areas You can adjust these areas for example to round them to exact integer values for the multiplets or zero for the empty regions You can also specify the method to be used for the adjustment of each region Multiply Multiplies the region by the correct factor to give the desired relative area This is appropriate for modifying the area of multiplets Move Displaces the region vertically to give the desired area This is appropriate for empty areas where
157. ntal intensity distribution A part from the obvious causes like impurities and baseline waviness it is also possible that you are trying to use the wrong spin system for the simulation see below The presence of impurity peaks and or baseline errors is much less of a problem in later cycles of the refinement since the algorithm then has a more local view of the spectrum it is fitting So if you only want to doa final cycle of pure least squares iteration you need not worry much about impurities and baseline errors Another source of trouble may bein your preparation of the iteration The most obvious error would be to simulate a spectrum with the wrong spin system For example if you use a A2BX spin system to simulate something that is really a A2BCX system with B and C nearly coincident the program will never get the correct intensity distribution between theA and B C parts of the multiplet You will end up with poor fits and unrealistic coupling constants Errors of this kind are not as unlikely as they might seem so if nothing seems to work think carefully whether you are really sure of the spin system Lack of success can also be due to poor starting values for the spectral parameters Full lineshape iteration is less sensitive to starting values than assignment iteration but you will certainly not get the correct result for every set of values For example spectra are always invariant under a simultaneous sign change of all coup
158. o feed the files to gCVT you might as well use BINARY for all files thus reducing the risk of accidentally translating a binary file If you use a file sharing protocol any copying or moving you do will probably be binary This is fine for gCVT conversion the only problem is that you yourself may not be able to read any text files you supply to gCVT All file conversions allow you to use arbitrary filenames for any of the files supplied to gCVT However it is more convenient to use a systematic naming convention when supplying the files If for a single conversion all files you supply reside in the same directory have the same file name and standard extensions listed in section 11 5 you only need to supply the first one to gCVT the rest will then be recognized automatically If you use another naming convention or have source files spread over different directories you have to point gCVT at each of them in turn 11 4 Converting data to gSPG format When you start gCVT it comes up with the Convert dialog The appearance of the dialog depends on the conversion selected Figure 53 shows the dialog for WinN MR conversion 152 File conversion Figure53 gCVT Convert dialog for WinNMR conversion Chapter 11 Convert From Sa roo _ _ WinNMR aquisition parameter file Browse Gear be none WinNMR processing parameter file Browse Clear none WinNMR spectrum file Browse Cl
159. obtained from the Marker dialog next section 168 Spectrum processing Chapter 12 Spectrum Regions Multiplets Attempts to do an automatic analysis of multiplet structure If necessary regions and peak lists are generated first Then a dialog appears Figure 57 in which you can set the type of analysis desired for each region possibilities are None No analysis for this region First Order Analyze this region as if it were a first order multiplet i e try to interpret all peaks as caused by simple splittings AB Try to interpret this region as an AB system There must be 4 lines in the region for this to work AA X Try to interpret the region as the A part of an AA X spectrum This requires 8 lines but some of them may overlap If the multiplet is indeed an AA X system there are always at least 2 solutions AXX Try to interpret the region as the A part of an AXX spectrum This normally requires 6 lines but gSPG will handle several cases of overlapping lines AA XX Try to interpret the region as the A part of an AA XX spectrum This requires 12 lines which should not overlap Spectrum processing 169 Figure57 gSPG Spectrum Regions Multiplets dialog Chapter 12 Analyze Multiplets Ea Nuclei Pose 1 000 E ion emo 3 Analysis lst Order d ist Order fd 1st Order hd Set All None M Find connections No x You can set the type of analysis for each mul
160. og Approximations section Chapter 9 approximation will be invoked N ote that this may still result in a system which is too large A reasonable value would be 100 set to 0 default to disable per nucleus exchange calculations 9 5 Other settings affecting approximate calculations All settings relevant to approximate calculations are concentrated in the Approximations section of the Settings File dialog Figure 51 Settings specifically relevant to chunking first order methods and exchange calculations have been discussed in the previous two sections There are two other settings more generally relevant to approximation File Settings Ea Topic Approximations Simulation Normal Abundance Thresh 1 p0e 02 Perturbation Thresh p 00e 01 Chunk Size 3 Polymer Chunk Size 8 Approx Method Thresh 15 Assignments dheas wien Iteration Cancel Help Abundance Threshold In isotopomer mixtures isotopomers with and abundance less than this fraction of the most abundant isotopomer will not be included in the calculation With the default setting of 0 015 13C satellites will usually not be visible in calculated spectra Perturbation Threshold This is the J A6 criterion that will be used to select regions in the molecule for perturbation theory treatment gN MR always assumes a worst case scenario when testing for this criterion so Approximation calculations 135 136 Chapter 9
161. ompl indicator will change to Fixed Click Spectrum to inspect the results Asin the previous example you can vary the rate to get an impression of the dynamic behavior This demonstrates the input of intermolecular exchange reaction between methanol and an acid HCI using structures Close all open files and select File Import ChemWindow Choose the file MeOH cwg accept the default Import settings N ow create a second molecule Molecule New Molecule 2 Select File Import ChemWindow and choose HC1 cwg in the same way Press lt Ctrl E gt to move to the Exchange window This will now show the structures of methanol and HCI in aseparate pane on the left Type a rate of 5 in the rate field Click once on the hydroxyl proton of methanol to select it then Shift click on the HCI proton An arrow appears that connects the two Press lt gt to let gNMR complete the reaction The window should now look like Figure 12 Click on Spectrum to inspect the results 26 Tutorial Figure 12 Exchange window showing structures for methanol acid exchange You need the BDE You may need ODBC Chapter 2 MeOH_HCI Exchange olx Fixed Ef Mcomp ooa o e 2 1 1 2 Clear All Spectrum 2 5 Installing a sample database for use with gNMR gN MR can use one or more databases to store data and or spectrum files and to improve prediction of shifts and coupling constants The two sample databases pr
162. onds s The Settings Spectrum and Settings AD dialogs provide a more precise control over the display of spectrum and FID They are used in the same way as the gN MR Settings Spectrum dialog but contain fewer options 12 5 Manipulating the spectrum The Spectrum Reduce submenu contains commands for smoothing and compression If your spectrum is very noisy you can use the Spectrum Reduce Smooth option to smooth it a bit gSPG will prompt you for a smooth order n and then calculate new spectrum data using a formula due to Ziessow 3 Smooth Compress Subspectrum 3Z 3n 3n 1 5 LE w Y W W 0 a 2 Yis I 2n 3 2n 1 2n 1 0 Large values of the smooth order lead to loss of detail reasonable values are 2 6 You can also apply a small value several times in succession If your spectrum has a large number of datapoints per Hz you may want to smooth the spectrum and reduce the number of datapoints at the same time You can do this with the Spectum Reduce Compress option it uses the same smoothing formula given above but only retains one out of every n datapoints afterwards Reasonable values for the compress order are 2 4 Another way of reducing the number of datapoints is to throw away unwanted portions of the spectrum By using Spec trun Reduce Subspectrum you throw away the parts that are not currently on the screen retaining only the selected part Spectrum processing 163
163. onstruct these initial points from later points using linear prediction Use AD points Specify the number of points of the FID to use in the transformation Normally this would be all of the FID Fill to Specify to how many points the FID should be zero filled before transformation This will always be a power of 2 and is typically twice the size of the FID Reconstruct using LP Attempts to reconstruct the truncated zero filled part of the FID by linear prediction The LP coefficients are generated from the start of the FID but the tail of the FID is used as start values for the extrapolation This may be useful if a very short acquisition time was used resulted in a strongly truncated FID The remaining options affect the transformation algorithm Bruker FT Check this if the FID was of the time proportional phase increment TPPI type often used with Bruker instruments In TPPI spectra real and imaginary components have been 174 Spectrum processing Inverse transformation Chapter 12 measured at interleaved points in time The default for gSPG is simultaneous where the real and imaginary components of each FID point correspond to the same point in time Mirror Check this if the transformed spectrum appears to have its high and low field ends reversed This may happen if during spectrum import the real and imaginary components were interchanged for some reason Rotate Unfilter Check this if the spectrum was o
164. option is checked the default a single click in anew field selects the whole field If you uncheck this option a click will put the edit insertion point at the position of the mouse click Move cell w Arnows If this option is checked the default the lt and arrows will move to the previous or next field If you uncheck the option these arrow keys will move the insertion point within the field Recalculate moves to Spectum If this is checked the default one of the buttons in the Molecule and Exchange window will always be labeled Spectrum and clicking it will move you to a Spectrum window If the option is unchecked and a spectrum is already visible the button will be labeled Recalculate and clicking it will recalculate the spectrum but leave you in the Molecule or Exchange window Hide non Top files If you check this option the Window Minimize inactive menu Customizing gNMR 187 Appendix A choice will be checked and windows not belonging to the topmost file will always be shown minimized Show Windows list If this is checked the default the Windows amp Files miniwindow section 3 1 will appear if you have more than a single open file or more than one open Molecule or Spectrum window If you uncheck this option the miniwindow is never shown Spectum Previews If this is checked File Open dialogs for spectrum and data files will display some information about a selected spectrum or data file inclu
165. orm Deconvolution and enter the new value of the linewidth a sensible default width will be provided Press Enter to start the deconvolution 12 10 Phasing After transformation you will probably have to phase the spectrum The Phasing dialog Figure 60 is invoked by choosing Spectrum Phase This shows three vertical sliders The left one 176 Spectrum processing Figure 60 gSPG Phasing dialog Chapter 12 corresponds to the phase at the left low field end of the spectrum the right one to the right end high field phase and the center one to the phase at the pivot position The pivot position is initially the position of the largest peak in the spectrum but you can click anywhere in the spectrum to set a new pivot position Changing the pivot slider applies a uniform phase correction to the spectrum Changing either the left or right slider applies a linear phase correction that leaves the phase at the pivot position unchanged which means that the phase at the other end of the spectrum has to change You can also click on the Hide Pivot button to remove the pivot slider In that case the left and right sliders adjust the phase at their end of the spectrum while leaving that at the other end unchanged Left phase Pivot phase Right phase 1T 2 1 5 _ Apply _ Apply _ Apply 210 10 10 Ea A0 10 Remove pivot Taa Method _AutoPhase Normal phasing nen Normally p
166. ose Iterate Last Cycle 6 5 Searching for more than one solution Full lineshape analysis does not always find the right solution gN MR normally optimizes a single solution and then stops but you can instruct it to look for and optimize a series of solutions in two different ways If you have no good idea what the solution should look like you can set the Random Restarts parameter in the Settings File dialog iterate section see Figure 41 to a non zero value This instructs gN MR to try several full lineshape iterations using different starting values The first trial will use the starting parameters you supplied for subsequent trials up to the number of restarts you entered the coupling constants will first be randomized using a distribution function with a width equal to the starting value you supplied If you have a reasonable looking set of shifts and coupling constants but you think that maybe some sign combinations of coupling constants might give an even better fit you can check the Try sign changes box also in the Settings File dialog This causes gN MR to do asystematic search of all sign combinations of coupling constants Since most sign changes result in only minor changes to the spectrum you may want to set the initial flattening parameter Cs to 101 or so to save time 102 Full lineshape iteration Chapter 6 In either case gN MR will generate a set of solutions A fter completion of all iterations you the
167. ou can always use the mouse to select the field and then type the data If you want to enter a lot of data itis probably more convenient to start at the top and work your way down using only the keyboard If you do so you will see that when moving vertically you always move two fields at a time either between data fields or between variable name fields You can switch between the two by using the mouse or by selecting Edit Parameters or Edit Variables single nucleus data coupling constants of nuclei shifts linewidths E S a a ee 4 mm too Pt Caso aro sox ak S SSS are DEn ToS 1 The molecule spreadsheet consists of two parts The left hand part contains in each row data for a single spin group the nucleus name the number of nuclei in the spin group the chemical shift and if desired an individual linewidth The right hand part is a matrix containing the coupling constants between groups its width and height are dependent on the number of nuclei in the system The bottom row of the spreadsheet is always empty As soon as you enter any non zero data in this row the spreadsheet expands the row in 48 Entering data Nucleus names Nucleus settings Chapter 3 which you entered the new field will be filled with aspin group and anew empty row will be appended The different data items are discussed individually below Here you fill in the name of the nucleus Appendix C l
168. ould generate a smaller groups database to speed gN MR startup and conserve memory On the other hand you can also create a larger database to include higher order axes or the icosahedral groups To construct a new database start gGRP and then fill in values for the highest rotation order for axial groups and permutation group size for the special groups in the dialog box that appears Figure 50 the permutation order can be 0 no tetrahedral or higher groups 4 tetrahedral and octahedral groups or 5 up to icosahedral groups Then click OKand select an output file name gGRP will start creating the groups and writing them to the database The filename must be gNMR41 sgp for the file to be recognized by gN MR but you could also create several files and rename them when appropriate The groups database file must be located in the gNMR directory Exchanging gN MR data files created with other databases containing non standard symmetry groups may lead to problems since the data files refer tsymmetry o groups unique to a particular database Database Options Ea Rotation groups up to a Permutation groups up to 4 Cancel Help 128 Symmetry Chapter 8 Symmetry 129 Chapter 9 9 Approximate methods 9 1 Introduction The traditional way of simulating an NMR spectrum is by doing a complete diagonalization of the full Hamiltonian The size of such a calculation increases exponentially with the number of spins in the system
169. ounds you add will only be used for the less accurate fragment prediction 10 7 Settings affecting prediction If you have no prediction database installed gN MR prediction can only use the built in rules If a prediction database is installed as set in the Settings Preferences Database item Default Data Source two further Preferences settings determine how prediction is done Use database for prediction If this is checked gNMR will attempt to use database data for shift and coupling constant prediction Substituent prediction takes precedence but if the target atom is not part of a known fragment or if substituents cannot be matched fragment prediction is used Built in rules are only used as a last resort If this option is not checked the database is ignored for prediction and only the built in rules are used Merge with rule based prediction If this is checked the results of database prediction are merged with those of the built in rules to arrive at some weighted average This is not recommended in general It might be useful if Databases 147 Chapter 10 you have added some very exotic compounds to the database and start getting extreme predictions 148 Databases Chapter 11 11 File conversion using gCVT 11 1 Introduction gN MR understands only its own gSPG spectrum file format filename extension spg Since no spectrometer software produces gSPG files you need some kind of conversion program to get a sp
170. oupling constants would not come back To delete it temporarily move to its Nucleus Name field and select Settings Nucleus then check the Decouple box Dismiss the dialog by clicking OK The nucleus name will now be shown in italic It is still there but will be ignored in the calculation when you click the Spectrum Recalculate button Try doing this with one of the aromatic protons of o chloro aniline Suppose we are interested in the 34P spectrum of a diphosphine coordinated to platinum This would show an AB pattern with platinum satellites due to coupling with 1 Pt The gN MR Molecule window corresponding to this system would look like Figure 16 The nucleus name Pt 195 in it means use the natural abundance isotopomer mixture but interpret all couplings as given for 1 Pt Inspect the sample file Pt Diphos dta and verify that simulation indeed produces the satellites Tutorial 35 Figure 16 M olecule window for PtP 2 isotopomer calculation Isotope shifts Anisotropic spectra Chapter 2 m Hz 1 2 EEC BENEAT PE Options Spectrum The standard isotopomer mixture calculation assumes that chemi cal shifts for corresponding nuclei in isotopomers are all identical However this is not always the case Thus the main 31P resonances of the above example need not coincide with the centers of the 1 Pt satellites Also the different NMR inactive Pt isotopes would induce small isotope shifts on the phospho
171. ovided with gNMR contain parameter prediction data We recommend you install one of them both as an exercise and to improve parameter prediction This section describes installation of both gN MR requires the BDE Borland Database Engine for database access M ake sure this has been installed on your system before trying to use a gN MR database Several versions of the BDE are provided on the gNMR ia distribution disk We recommend you install the newest version supplied BDE5 0 You can also download a recent version from the borland com web site http www borland com bdg To install the BDE first uncompress the package if necessary and then double click setup exe and follow the on screen instructions If you want to use any database type other than dBase or Paradox eg Microsoft Access you also need to have Microsoft ODBC Open Database Connectivity installed on your system Tutorial 27 Configuring the example Paradox database Chapter 2 Version 3 0 service pack 1 is provided on the gNMR distribution disk However a newer version may already be installed on your system as ODBC comes bundled with a large number of software packages To check for the presence of ODBC open your Control Panel folder and look for the ODBC icon shown to the right and usually labeled ODBC or 32bit ODBC If itis absent proceed with ODBC installation see below If it is present double click on it and click on the
172. ow by selecting Spectrum Go to Spec tum1 choose Settings Spectrum and move to the Iteration topic Below the name of the experimental spectrum you will see two checkboxes labeled Full lineshape iteration and iterate on Linewidth both currently unchecked The first flag specifies whether the current Spectrum window should be used for full lineshape iteration check it The next item iterate on Linewidth can be used Tutorial 21 Figure 10 ODCB spectrum before A and after B full lineshape iteration Chapter 2 to enable or disable optimization of the linewidth for the current spectrum check this box too To demonstrate the power of full lineshape iteration we will make the problem harder for gNMR Click on the Molecule window enter new values for ab 15 Hz and aa 3 HZ and click Recalculate to see the resulting spectrum The new calculated spectrum bears little resemblance to the experimental ODCB spectrum Figure 10A and you might have difficulty picking out the right peaks for assignment iteration Full lineshape iteration however avoids this problem Save the current data as ODCBFul1 dta and start the iteration with Iterate Go The Iterate status window and the Log window appear and the iteration begins M U Wa 7 00 7 400 7300 7 2007 7400 7 500 7 400 7300 7 200 0 7 100 Al WW 7 500 7 400 7 300 7200 7100 T 75o 7400 0 7 500 72
173. pectra especially if you indude linewidths in the iteration So if you see any significant differences e g in intensity patterns between the two spectra these area sure sign that something is wrong Of course what is significant remains subjective One problem is that the human eye is very sensitive to certain details which the computer thinks are rather irrelevant An example of such a detail is the depth of the dip between two lines that are very close together This dip depends strongly on linewidth lineshape function and the placement of data points within the experimental spectrum even though a discrepancy in such a detail may be obvious to the eye it is not necessarily significant Another detail is the difference in height between components of a multiplet M ultiplet components due to combination lines sometimes have significantly larger linewidths than the normal components and may therefore seem to be too low in the experimental spectrum For example in the 6 line pattern for the X nucleus of an AA X spectrum the two components of intensity at positions 8x l JaxHa x almost always have a smaller linewidth than the other four components gNMR cannot adequately model such linewidth 106 Full lineshape iteration Chapter 6 differences but they should not be considered significant unless the integrated intensities also show a serious disagreement Unfortunately the eye is much less sensitive to linewidths or integrals t
174. pectrum 1 j ioj xi gg gt gt Fri Sep 19 20 41 25 1997 ODCB tutorial example ODCB 300 MHz smoothed and compressed W1 1H Axis ppm Scale 17 78 Hz cm 7 500 7 400 7 300 7 200 7 100 14 23 7 400 7 300 7 200 As you can see the agreement between the two spectra is not perfect The most obvious discrepancy is that the high field multiplet which we have put at 7 1 ppm should be closer to 7 2 ppm To change this double click on the multiplet This takes you back to the shift field for H2 in the Molecule window Enter the new value of 7 2 for both H2 and H3 and then click Recalculate a spectrum corresponding to the new parameter values will be calculated and displayed showing a much better agreement with the experimental spectrum Save your results at this stage as ODCBDATA dta for usein the iteration tutorial by selecting File Save As To finish this exercise we will change some of the display parameters of the spectrum Expand the spectrum horizontally by selecting Spectrum Horz 2 once or twice or click the equivalent 4 button in the button bar The spectrum will now be too large to fit in its window and you can use the horizontal scroll bars to move through it Contract the spectrum again Spectrum Horz 2 or click the p4 button until it is completely visible in its window To recalculate a part of the spectrum with greater accuracy select that part by dragging in the spectrum When you have done so two ve
175. play the assignments in the Spectrum window see section 5 5 some crossings will immediately be obvious Correcting these few assignments and restarting the iteration will then produce a new solution with a much smaller residual for relatively minor changes in the parameter values If there have been many incorrect assignments however the iteration result will often not look much better than the starting values e One of the most insidious errors is that caused by a wrong sign in the starting values for one or more of the coupling constants This may often produce a spectrum quite close to the observed one and iteration may even get the peak positions exactly right However the pattern of intensities is often subtly different for different sign combinations and a close inspection of intensities may help you pick out the correct solution N ote that it is not enough to change a few coupling constant signs and retry the iteration because of the peak tracking feature of gNMR you will also have to redo the assignments Assignment iteration 95 96 Chapter 5 The intention of the above discussion is to make you wary of trusting iteration results You should always ask yourself a few questions and maybe try a few variations before believing the parameters produced by the program No program can replace thinking and careful analysis Assignment iteration Chapter 6 6 Full lineshape iteration 6 1 Introduction In full lines
176. problem with intensity data occurs for overlapping peaks Overlapping peaks do not give a problem for peak positions you can simply use the same assigned frequency for each component For Assignment iteration 87 Figure 38 N umerical assignments window Chapter 5 intensities however you cannot determine the contributions of the individual components only a total intensity gN MR therefore allows you to supply total intensities for such groups it will then iterate on the group intensity instead of on individual intensities To start the numerical assignment procedure select iterate Assignments In the submenu that appears choose the name of the nucleus for which you want to do the assignments The Assignments window will appear Figure 38 showing a list of peak positions and intensities You can use the Edit xxx units menu choice to toggle between Hz and ppm units in the usual way The dialog box contains a Clear button which can be used to remove all assignments for the current nucleus and a button labeled Group or Ungroup which can be used to group or ungroup sets of close lying peaks see next section The peak ordering button toggles between Ascending and Descending tw odcb1 Assignments for 1H ioj x Frequency Intensity calc obs calc zose ES 0 0106 7 082 7 188 0 2224 zoss 7 200 0 2205 7 102 7 208 0 2296 a28 7 233 0 0333 P7369 Soos Pare raa Soera zana narr
177. r if not used in earlier gN MR versions 214 Nuclei recognized by gNMR Appendix C Colors can be specified as RGB values but we recommend the use of the following symbolic names BLACK DARKGRAY LIGHTGRAY WHITE RED LIGHTRED YELLOW BROWN GREEN LIGHTGREEN BLUE LIGHTBLUE CYAN LIGHTCYAN MAGENTA LIGHTMAGENTA The following example shows the relevant lines for carbon C BLACK 6 CATS 12 021 2 50 4 112 12C 0 0 0 0 0 98892 12 000000 Lae L 25 1440 0 0 0 01108 13003355 8 Nuclei recognized by gNMR 215 Appendix D D Using scripts for structure and spectrum import gN MR imports molecular structures from chemistry drawing programs via a file or the clipboard gCVT imports NMR spectra from files produced by other NMR processing software In both cases conversion from a foreign file format is needed In earlier versions of the gN MR package these conversions were hardcoded This meant that when a new format had to be supported a whole new program version was required As the number of supported formats increases this becomes impractical Therefore gN MR now uses scripts to direct the conversion A script fileisa plain ASCII file that describes the file format and contains instructions for extracting the necessary items e g atomic coordinates or spectral parameters These instructions are in an interpreted language somewhat similar to C When gN MR starts up it inspects the gNMR directory for the pre
178. r 2 involved in the reaction as described earlier in this tutorial use the Exchange window to enter the permutation The 1H spectrum of DMF at low temperatureshows H ak two separate methyl resonances at 2 7 and 2 9 ppm gt C N on raising the temperature they coalesce to a singlet 6 Nch There is no significant coupling between the two methyl groups or to other nuclei in the molecule To define the system we should use two complete methyl groups we will cheat a little here and just use two single 1H nuclei The calculation will bea bit faster that way chemical exchange calculations are always much slower than static calculations and since there are no couplings the results will be the same To start the problem define a system of two 1H nuclei at 2 7 and 2 9 ppm with a zero coupling Click Spectrum to see the spectrum two singlets as you would expect Select Molecule Exchange this brings up the Exchange window as shown in Figure 11A The leftmost part of the window lists all nuclei in all molecules indicated by molecule number and number of the nucleus in its molecule This column represents the start positions of the nuclei for the permutations To the right of this area is an empty column where you define the reaction For each nucleus you will have to specify a destination of the form m n where m is the molecule number and n is the nucleus number of the destination The contents of this column will be the destinations of
179. r may have been digitally filtered gSPG will left shift the spectrum until the first point has a high amplitude before attempting the transformation This is correct only for sharp digital filters Baseline Corr Check this to correct for any DC offset in the FID before transformation This should eliminate the sharp center spike at the transmitter frequency If you click the WFTbutton the FID will be transformed using the current weighting function and the newly transformed spectrum will be displayed in the Spectrum window When you are satisfied with the result click the Done button to dismiss the dialog It is also possible to reconstruct an FID from a transformed spectrum this is called an inverse transform It is only recommended if you don t have the original FID any more since most transformed spectra have been obtained using some kind of weighting function inverse transformation results in an FID with alower information content than the original To do an inverse transform simply select Spectrum Transfom Inverse Transform there are no weighting functions to select Inverse transformation will overwrite any existing FID Spectrum processing 175 Reconstruction of imaginary components Discarding imaginary components Reference deconvolution Chapter 12 For most purposes one only needs the real part of a transformed spectrum Therefore the imaginary part is sometimes thrown away or lost during transfer of
180. r the spectrum appearance H owever there are several other ways of controlling spectrum display which are often quicker and more convenient to use Dragging in the spectrum selects a subrange which will be delimited by two vertical dotted lines Clicking once inside the subrange expands that range to fill the whole window equivalent to the Spec tun Expand Selection command clicking outside the range cancels the subrange selection If a subrange is defined Edit Copy Spectrum copies only the subrange not the whole visible spectrum Whenever the topmost window is a Spectrum window you will also see a floating miniwindow labeled Selection that contains a thumbnail sketch of the full stick spectrum The part of the spectrum that is between the currently selected display limits is shown light on a dark background or whatever color combination Windows is using to represent highlighted text the remainder is shown black on white Displaying spectra 65 Menu choices Settings Spectrum dialog Chapter 4 You can select a part of the spectrum by dragging in the spectrum representation of the miniwindow Clicking the Full button reselects the full spectrum range equivalent to the Spectrun Full command Clicking lt gt doubles the current range gt lt halves the current range and gt gt and lt lt movethe current range to the right and left Spectrum Full reselects the full spectrum range Spectrum Horz 2 4
181. ral hydrogens or fluorines bound to the same heavy atom it imports them as a set of magnetically equivalent atoms if there is at most one other bond from the heavy atom to the rest of the molecule In that case you will find that only one of the hydrogens is actually included in the spin system and that it will have a number of nuclei field greater than 1 This may not always be correct eg the hydrogens of a terminal PH2 group may be diastereotopic and hence nonequivalent but you can correct this afterwards If several hydrogens are bound to a heavy atom which is in turn bound to at least two other heavy atoms the hydrogens are always imported as non equivalent Again you may wish to change this later gN MR will only import nuclei whose label it recognizes as an element name it will assume a carbon if there is no label If you use other labels these nuclei will not be included in the spin system more importantly shift prediction will probably fail The next set of two options govern prediction of NMR parameters Predict shifts If checked default gN MR will try to predict chemical shifts for all hydrogen carbon and phosphorus nuclei in the molecule 56 Entering data Chapter 3 Predict couplings If checked default gNMR will try to predict couplings between hydrogens carbons and phosphorus atoms If you uncheck either option the corresponding parameters will simply be set to zero The algorithms gN MR uses to predic
182. rate is so small that it cannot possibly affect the spectrum To delete an entire exchange definition column clear the field of its rate To remove all exchange reactions click the Clear All button at the bottom of the Exchange window 7 3 Entering reactions without structures You fill in the permutations in columns directly below the reaction rates You have to supply destinations for all nuclei in your system even for those that are not involved in the reaction as a shortcut you can press lt gt in any destination field for a nucleus that stays in place If you have entered all nuclei that move in a reaction you can press lt gt to let gN MR complete the permutation A full destination consists of a molecule number and a nucleus number within the molecule For example 4 3 means molecule 4 nucleus 3 If a nucleus stays within its own molecule you can omit the molecule number and the hyphen The indicator Incompl below the rate shows that you are busy with an incomplete exchange definition The indicator will change to either Fixed or Variable as soon as you have completed the definition of the permutation i e pressed lt 1 gt lt after filling in the last destination field If the permutation you entered was incorrect see below the indicator will keep on showing Incompl Any incorrect or incomplete permutation will be lost when you leave the Exchange window so you cannot fill in part of a reaction do something else
183. ration Ns qo Cancel Apply Help Baseline Show Title If checked shows the run title and if present the experimental spectrum title in the spectrum display If this option is not set the out of range indicators and will also be suppressed Show Info Is only enabled if Show Title above is checked If set this causes some date and scaling information to be included in the spectrum display Show Assignments If checked this allows you to display connections between calculated and observed peaks see next Chapter Show Integral Turns integral display on or off To see an integral you also need to define integral regions section 4 5 Show Markers Turns display of markers on or off To see any markers you need to define them first see section 4 5 Markers are never included in hardcopy or clipboard copies The pulldown menu following this option allows a choice of different marker labels Number Frequency or Height Displaying spectra 69 Chapter 4 Show Nucl Ranges Toggles display of the range indicators for multiplets in the spectrum These indicators show which multiplet corresponds to which nucleus If their display is enabled double clicking in the spectrum moves you to the corresponding nucleus in a Molecule window See section 4 6 for details Messages to Log file If checked this causes all relevant parameters to be written to the Log file whenever a spectrum is printed or copied to
184. res that all windows not belonging to the topmost file will be minimized gN MR can be customized extensively There are default settings for things like startup action linewidths fonts precision of numbers etc Most of these can be changed using the Settings Preferences dialog for more details see A ppendix A In this manual we will assume default Preferences settings Entering data 41 Figure 19 gN M R Welcome dialog Chapter 3 Welcome to gNMR Ea h Start with an empty molecule Import a structure ChemWindow gt ie Paste a Molecule or File Open a gNMR file Cancel Help When you start gN MR by double clicking on its icon it normally comes up with the Welcome dialog Figure 19 which offers a choice of common actions Start with an empty molecule This is equivalent to File New It creates a file with a single molecule having a 1H at 0 ppm Importa structure This is equivalent to choosing File Import see section 3 6 First select the file type you want to import from the pulldown list then click the button Paste a stucture This is equivalent to Edit Paste xxx see section 3 6 and is only enabled if there is a readable structure on the clipboard the dialog text will show the format Open an existing gNMR file This is equivalent to File Open If you cancel the dialog gN MR starts up without an open file 42 Entering data Chapter 3 3 2 Opening and closing
185. rs for optimization The rule is simple variable names starting with as the first non blank character are not optimized during iteration all other named variables will be optimized Linewidths can only be optimized in full lineshape iteration shifts and coupling constants can always be optimized Entering and changing variable names is similar to entering and changing data You first move to a Molecule window and then to the field of a variable name using either the mouse or the Edit Variables command Each name belongs to the parameter value immediately above it If you enter aname and then leave the field the resulting link will be established immediately if there is another parameter bearing the same name its value will be copied to the current parameter value field Once you have linked a set of parameters when you enter a new value for any of the set you will see the values for all the others change simultaneously You can remove links by clearing the variable names a single in a field is the same as an unlinked or empty name Figure 36 shows a Molecule window with variables names filled in the name a assigned to the first two chemical shifts ensures that whenever one of them changes the other will change with it 84 Assignment iteration Figure 36 Molecule window with variable names filled in Chapter 5 odcb1 Molecule 1 Bil Eg Options Spectrum Sometimes you
186. rt As SPG command saves the current calculated spectrum as a gSPG format spg experimental spectrum file 2 Odcb Spectrum 1 OO x we Mon Sep 08 21 35 07 1997 ODCB spin system and variables definition ODCB 300 MHz smoothed and compressed W1 1H Axis ppm Scale 13 88 Hz cm jll 2 1 l l 7 450 7 400 7 350 7 300 7 250 7 200 7 150 7 100 x cI ee 7 450 7 400 7 350 7 300 7 250 7 200 7 150 7 100 2 L A Spectrum window can contain a number of elements see Figure 27 e Out of range indicators which are only visible if there are peaks in the calculated spectrum that fall outside the current display limits N ote that these lines might have a very low intensity so that you would not see them even if you selected a much larger range e Date gNMR title spectrum title and some display range information e Rangeindicators showing the correspondences between Spectrum window multiplets and Molecule window nuclei 64 Displaying spectra Spectrum window Selection miniwindow Chapter 4 e Anexperimental spectrum e A calculated spectrum e Axes and axes labels e Integrals e Markers arrows bearing numbers e Assignments not shown in Figure 27 see chapter 5 for details You can control the display of most of these items as described in the next sections 4 2 Display parameters The Settings Spectrum dialog discussed below gives you detailed control ove
187. rt the conversion as described in section 11 4 The last part of this chapter contains notes on individual conversions 11 2 Converting between different gNMR versions QN MR V4 1 does not immediately understand files created by earlier versions The gCVT utility can be used to convert both data dt a and spectrum spg files between different gN MR versions from V3 0 to V4 1 Normally you do not need to use gCVT for this since both gN MR and gSPG will automatically invoke gCVT to doa conversion if they encounter a file created with a different version of the package see below However explicit conversion may be useful if you want to exchange a file with a colleague who has an older version of gN MR Some data are represented in a fundamentally different way in different versions of gNMR and cannot be converted For example assignments will always be lost in the conversion and definitions of molecules beyond the first one will be lost in conversions to V3 2 or earlier which did not support multiple molecules Basic data spin system Spec tum window definitions will always be converted Whenever gN MR or gSPG is asked to open a file created with a different version of gNMR you will see the automatic conversion dialog Figure 52 This gives you a choice between canceling the action converting the file in place this overwrites the original data or creating a new file to hold the converted data leaving the original intact If
188. rtical dotted lines are visible around the selection Click once between them and the selected part will fill the whole window You can also subselect parts of a spectrum in the floating miniwindow labeled 12 Tutorial o Dichloro benzene with a structure Chapter 2 Selection that appears whenever the frontmost window isa Spectrum window To change the linewidth of the spectrum select Settings Spec trum from the menu bar The item at the top of the Dimensions section is labeled Linewidth Hz Change the value to 1 0 and click OK the spectrum will be recalculated with the new linewidth You will see that the observed spectrum is now truncated gN MR scales experimental and calculated spectra to have the same integral and the calculated spectrum is scaled to fit exactly in its window This means that if the observed spectrum has much narrower lines these narrow lines will run off the display area The Settings Spectrum dialog also lets you control the dimensions of the plot and include or exclude axes and texts Asan alternative to the matrix method of entering NMR parameters gNMR can use molecular structures drawn in other programs ChemWindow ChemlIntosh ChemDraw Isis Draw for data entry We will again demonstrate this using ODCB If you still have gN MR open close any open gN MR files and select File Import ChemWindow If you are just starting a new session start gN MR and in the Welcome dialog under Importa s
189. rus resonances To simulate this move to the Molecule window and select Molecule Isotope shifts The area previously used for coupling constants will now be rectangular instead of triangular and is available for entering isotope shifts enter each shift in the row for the nucleus feeling it and in the column for the nucleus causing it Thus enter values of 1 and 3 ppm in the last column of rows one and two to let the two phosphorus atoms feel isotope shifts of 1 and 3 ppm per mass unit change of the Pt isotope this is of course a ridiculously large shift If you recalculate the spectrum you will see a multitude of lines one AB for each Pt isotope except 1Pt and the centers of the 15pt satellites will not coincide with any of the other AB halves You can switch back to normal coupling constant editing using Molecule Coupling Constants but of course the isotope shifts will remain This example is also stored in filePt IsoShf dta In the General topic of the Settings File dialog you can select Anisotropic spectra If you do this the upper triangle of the Molecule window will also become editable and dipolar couplings can be entered there Look at the example file Benzene dta for an example 36 Tutorial Using intensity data in assignment iteration Chapter 2 Assignment iteration is normally done using peak positions only It is possible to use intensities as well but this is rarely necessary see the Q amp A list in Appe
190. s 0 0011 l Precision Cancel Defaults Help gN MR uses a fixed number of places before and after the decimal point to display numbers entered in Hz or ppm The defaults might not be good enough for you For example you might regularly encounter shifts up to 30 000 ppm or linewidths of 30 kHz or you may want an accuracy of 5 decimal places You can use the settings below to modify the display of numeric values The widths of fields in eg Molecule windows will be adjusted for this so if you select many places before and after the decimal point only a few grid fields will fit on a screen Decimal places ppm values Sets the number of decimal places used for values in ppm The default is 3 if you select a higher number you should probably also changes the Precision below Decimal places Hz values Sets the number of decimal places used for values in Hz default 202 Customizing gNMR Appendix A is 2 This should normally be 1 or 2 less than the number of decimal places for ppm values Max Shift ppm Sets the maximum ppm shift value that will fit into a field Max Shift Hz Sets the maximum Hz shift value that will fit into a field Max Coupling Hz Sets the maximum coupling constant in Hz value that will fit into afield Max Linewidth Hz Sets the maximum linewidth in Hz value that will fit into a field Precision Hz Sets the precision used to compare values input by the user e g when de
191. s 5 2 Tutorial eenaa annainne nanasan nee 7 2A dniroducti N eiieeii ei eias 7 2 2 Data entry and simulation sseseesssssssssrsrsrrrnrrrirrrsrsrsnnnnnn 8 2 3 terati Orain i ae aei aiei dee 15 2 4 Chemical exchange s ssssssesesesisrsrsrsrsrrsrsrsrsienrnnensnsnsnsnnnnnnn 23 2 5 Installing a sample database for use with gN MR sesse 27 2 6 Transforming and phasing spe tra ssseseseseereresrsrsrrerssn 32 27 Special topi rende ii a iea 33 3 Entering d ta ssssscsssssscsseesssssessssseseessessessnnecoeeseesoessonssesenesenanss 41 3d Inthoduction 23 3 a Setest an See ee 41 3 2 Opening and Closing files eee eee eseeeeeeeeeeeeeeteetaeteteeeseees 43 3 3 Molecule WING OWS eeeeeeeeeeeteeseeeeeeeeseeeeeeaetaeeaeeeseenetsetaeeatns 45 3 4 Entering data without a structure uu eeeeeeeteseeeeeeeeeeeteeees 47 3 5 ISOLOPOMEL MIXTUMES ee eee eee eceteeeeeeeeeae cee eaeeateeeetaetasaetateetaes 52 3 6 Importing chemical StrUCtUres ceeseeeeeteteeeeeeetteeeeeeees 54 3 7 Using structures to enter data eee cseeeeceeieteeeeeeeeeeeees 58 3 8 Modifying StrUCtures e ee eeeceseeeeeeeeeseeeeeeeaseeeeessetasetateetaes 60 4 Displaying Spectra 63 4 1 Spectrum WINKOWS eeeeeeccceeeeeeeeeeeeeeeeceeeeetaetaseeteeseetateetaeeaee 63 4 2 Display Parameters ecceeeeeeseeeeeeeeceeeeeeetaeeeseeseesteetaeeate 65 4 3 Using experimental Spectra ececceeeseeeeeceeeeeeeeeeeeteeeeeteees 71 4 4 Baseine parameters 0
192. s by typing new rate values in the Exchange window and clicking the Spectrum button Alternatively you can click on the rate field and then select Edit Interactive K 1 to get a slider for changing the rate This example requirestheuse H Ry EG fe of two different molecules one ee N C __N with Rj cis to oxygen and one Ro O Ry with Rj trans to oxygen Each will have only a single N MR active nucleus the carbonyl 8C We will assume that the cis trans ratio is 10 90 Start gN MR and enter a single 13c nucleus at 170 ppm Then select Settings Molecule and enter a concentration of 0 9 click OK to confirm Next open a second molecule Molec ule New Molecule 2 and enter a single 13c nucleus at 175 ppm Select Settings Molecule and enter a concentration of 0 1 again dick OK Tutorial 25 Methanol acid exchange using structures Chapter 2 to confirm Now select Molecule Exchange to move to the Exchange window The chemical reaction we are interested in interchanges nucleus 1 of molecule 1 and nucleus 1 of molecule 2 and can therefore be specified by the following permutation 1152 1 21511 Since the exchange involves different molecules it is necessary to include the molecule numbers in the permutation First enter the rate 100 0 and press lt gt Type the destination of the first nucleus 2 1 and press lt 1 gt again Fill in the destination of the second nucleus 1 1 and press lt gt the Inc
193. s first consider the one pair and two pair exchanges of Me2NPF4 The atoms are numbered P4 F2 and F3 apical and F4 and Fs equatorial all reasonable permutations are shown in Figure 44 Chemical exchange 117 Chapter 7 Figure 44 One and two pair exchange two pair exchange Fv Es mechanisms for D N Pare Fs eae o Fe Pree Fs M N P F4 MeN D MeN P 3 re 151 151 2755 2754 334 335 4 gt 3 4 gt 2 532 533 or or 15432 14523 one pair exchange Fy aa Fy Fo Me N li Me N P fannie F5 Me N P Sirians F5 Me N P finial F5 z OEF eee Fs Fs pet Fs 11 171 11 171 275 252 2754 252 333 3754 333 335 434 4353 4 gt 2 434 532 535 535 533 or or or or 15342 12435 14325 12543 The two pair exchange reaction exchanges both apical fluorines with the equatorial fluorines This can be done in two ways represented by the permutations 15432 and 14523 These are each others reverse so you need to supply only one of them to gN MR The one pair exchange can occur in four ways 15342 12435 14325 and 12543 If you specified only one of these four say the first one 15342 the high temperature limit would not have four equivalent fluorines the rapid exchange between F2 and Fs would lead to anew set of two equivalent fluorines but F3 and F4 would remain different The fast exchange limit would be an ABC2X system instead of the expected A4X system which is probably not what you intended To correct
194. s for optimization Once you have completed the definition of a permutation the indicator below the rate field changes to a pop up menu with a choice between Fixed and Variable The setting Fixed means that the rate will be held fixed in any full lineshape analysis you perform Variable means that it will be optimized The setting of the pop up menu can be changed in the usual way Full lineshape analysis of an exchanging system is always time consuming regardless of whether you also optimize any rates In 16 Ghemical exchange Chapter 7 normal circumstances you would determine all other constants from the low temperature limiting spectrum and then fix them in the simulation of the exchange broadened spectra Sometimes some chemical shifts show a significant temperature dependence and have to be included in the full lineshape iteration on the dynamic spectra Linewidths however should never be optimized simultaneously with reaction rates gN MR will not complain but dependence between the parameters will most likely make the results meaningless The initial guesses for the parameters you want to optimize will usually be very good and you can save a lot of computer time by setting the Correlation Start parameter section 6 4 to 107 or 0 before starting the full lineshape iteration 7 6 More than a single permutation The following two examples illustrate the use of several permutations to define a single reaction Let u
195. s involving only the unobserved nuclei may affect the spectrum you are looking at both Jpp and Adpp can affect the 3c spectrum of a 3CPP system and can therefore be determined from it If in doubt try varying such parameters manually to see whether they have any influence if they do include them in the iteration The error analysis at the end of the iteration can tell you which combinations of parameters are really determined In the example of the 13CPP case you could have included both 5p and 5p separately in the iteration you would then find that the difference Adpp was Full lineshape iteration 107 Chapter 6 determined but the sum was not This is obvious since moving both phosphorus nuclei simultaneously cannot affect the BC spectrum You could also have fixed dp at an arbitrary value and just optimized dp The error analysis would then show that dp was well determined which is misleading since only the distance to the fixed dp has actually been determined 108 Full lineshape iteration Chapter 7 7 Chemical exchange calculations 7 1 Describing a reaction as a permutation Setting up a chemical exchange calculation consists of two steps entering the molecule s involved in the exchange and defining how nuclei move during the actual exchange reaction Setting up the individual molecules has been covered in chapter 3 we will now concentrate on defining and entering the exchange reaction itself The exchange rea
196. s of the group to indicate to gN MR that they should be treated as a single peak as far as intensities are concerned You do not need to enter intensities for all peaks am simulating a platinum phosphorus spectrum and am looking at the 31P spectrum How do get to see the 1 5Pt spectrum Select Settings Spectrum in the dialog box that appears choose 195Pt from the nucleus pop up menu in the Dimensions topic see section 4 2 want to do a full lineshape iteration have prepared a window with an experimental spectrum but when try to start the iteration Iterate Go gN MR refuses to do anything or complains that it lacks data or variables The most probable cause of this problem is that you have forgotten to check the Full lineshape iteration box in the Settings Spectrum dialog box for the Spectrum window containing the observed spectrum see section 6 3 gNMR only Questions and answers 207 Appendix B iterates on windows which have this flag set It may also be that you have forgotten to mark any parameters for optimization see sections 5 2 and 6 2 Q I try to do a full lineshape iteration but gN MR immediately produces a very broad spectrum A The most probable reason is that you have checked Iterate on linewidth but not defined any other variables for iteration gN MR then tries to do a fit by adjusting only the linewidth and the best fit usually is for very broad lines Use Edit Undo to revert
197. s soon as you move the mouse over the display area you will see a second vertical line in the experimental spectrum and the status bar will show a message listing the frequencies of the two lines Figure 37 2 odcb1 Spectrum 1 olx han S UOO Cc Le OS ee ee ee ee Pee aa a S A T SUS et A i T ee S 2 T z500 7450 7 400 7350 7 300 7 250 7 200 7150 7 100 7 050 7 000 Le SS 7 500 7 450 7 400 7 350 7 300 7 250 7 200 7 150 7 100 7 050 7 000 7188ppm calc7 082ppm notassigned tt titi You should now move the experimental line in turn to the peaks corresponding to every peak indicated by the calculated line By default peaks are processed from high field right to low field left but you can change this order If you arrive at either end of the window you will hear a beep and the procedure will restart at the other end During the assignment process certain keys have special functions as shown in Table 4 If you don t want to process the peaks in order you can also click on a peak in the calculated spectrum to continue assignments for that peak 86 Assignment iteration Table 4 Special keys during mouse assignments Chapter 5 Operation lt A gt lt Enter gt Assigns the current observed cursor frequency to the lt Return gt current calculated peak and then moves to the next peak Mouse click lt D gt De assigns any observed frequency from the current calculated peak then moves to the
198. scripts for import Table D 3 Built in spectrum file import scripts Appendix D Import from Override name gNMR gNMR cvt Bruker WinNMR XWinNMR WinNMR cvt Bruker Aspect Aspect cvt Lybrics Lybrics cvt JCAMP DX JCAMP cvt Varian VNMR VNMR cvt GE Sun GESun cvt JEOL Alpha JeolAlph cvt JEOL Lambda JeolLamb cvt JEOL EX GX JeolGX cvt MacFID 1D MacFID cvt ASCII spectrum ASCII cvt ASCII FID ASCIIFID cvt MacNMR MacNMR cvt Felix Felix cvt Galactic Galactic cvt NUTS NUTS cvt Mestre C Spectrum MestreCS cvt Mestre C FID MestreCS cvt Among the distribution files you will find texts of all built in scripts for structure and spectrum import they are not copied to your system by the default installation You are free to change them as you like and if you achieve a significant improvement you are invited to send your modification to Cherwell so that others can share the benefits However Cherwell cannot provide support on the development of scripts A full description of all features of script files would be beyond the scope of this manual The gN MR distribution disk contains an online description Using scripts for import 219 Appendix E E File formats All files used by the gNMR package start with a text string terminated by a Linefeed hex OA character for binary files or CR LF combination for text files This header serves to identify the 9N MR version and the file type For text files e g the iso
199. section 5 2 After that has been done you should take care when changing these names In particular if you want to fix a parameter to prevent it from being optimized in full lineshape iteration use the Edit Fix Variable or Edit Free Variable command instead of changing the names by hand if you forgot to change one name the molecule could lose its symmetry In the NMR literature you often see notations like AA BB which refer to a particular spin system symmetry In the Molec ule Symbolic submenu you will find a few of these it is easy to add new ones see below If you select any of these gNMR will create a spin system with the correct relations between symmetry related shifts and couplings in place Of course you will still have to enter values for these parameters yourself 122 Symmetry Figure 46 N ucleus type query for symbolic systems Creating your own symbolics Chapter 8 When you chose one of the symbolic systems gN MR needs to know the nucleus types in the system Different letters in the abbreviation symbolic name indicate inequivalent nuclei non contiguous letters indicate different nucleus types So if you choose an AA BB system gN MR will ask you for the A nucleus B will be the same but in the case of an AA XX system gNMR will ask for both A and X nucleus types Figure 46 For every nucleus type you want to change simply click the button naming the nucleus and choose a new nucleus from
200. see a dotted vertical line in the calculated part of the spectrum marked A in Figure 7 if you move the cursor over the experimental spectrum you will see asecond vertical line appear there B For each peak in 16 Tutorial Figure 7 Spectrum window during mouse assignments Chapter 2 the calculated spectrum gNMR now expects you to point out the corresponding peak in the experimental spectrum Initially the calculated line will be positioned at the lowest frequency calculated peak in the spectrum Use the mouse to move the corresponding observed line when you are satisfied with the location of the line click the mouse to make the assignment and move to the next peak You can also press the space bar to skip the current peak Other keys allow you to change the assignment direction remove assignments etc see section 5 3 for details 2 odcb1 Spectrum 1 Lolk i oa Se 7 500 7450 7400 7350 7300 7250 7200 7150 7100 7 050 7 000 I MRR ER ee er ns E E R E E 7 500 7450 7400 7 350 7300 7 250 7200 7150 7100 7 050 7 000 paniaananniannnaanennanniann ninanasa 7 188 ppm calc 7 082 ppm not assigned For our ODCB example the order of the peaks happens to be the same in the calculated and experimental spectra So move the observed line to the first small peak in the spectrum and click the mouse The calculated line will jump to the next peak this time you have to move the experimental line
201. sence of structure import scripts extension imo for file import ime for clipboard import Any script files found are scanned and stored and will be available for structure import via the clipboard Edit Paste xx or from file File Import There are a number of built in scripts see tables below but any file in the gN MR directory with the correct name overrides a built in script Thus adding anew conversion or updating an existing one is as simple as dropping a script file in the gN MR directory Similarly gCVT on startup looks for spectrum conversion scripts having the cvt extension Again any file with the correct name can override a built in script The following Tables list the override names for built in scripts Using scripts for import 217 Table D 1 Built in structure file import scripts Table D 2 Built in clipboard import scripts Import from ChemWindow Version V2 V5 Chemlntosh V3 ChemWindow V2V5 Chemlntosh ChemDraw V2V4 V1V2 V1V2 Isis Draw Isis Draw ACD Sketch V2 218 Import from ChemWindow ChemDraw Isis Draw ACD Sketch File types cw2 FCaS eset Cnty skec mol osk2 Version V2V3 V4V5 V3 V4 V1 V2 V2 Appendix D Override name CWg ChemWin imo ChemInts imo SftShScf imo cdx ChemDraw imo MDLSkc imo MDLMol imo ACDsk2 imo Override name ChemWin imc ChemWin4 imc ChemDraw imc Isis imce ACDsk2 imc Using
202. sing the concentrations you supplied so itis important that you enter the correct concentrations Before you can enter any exchange data you have to prepare a complete definition of the static non exchanging spin system as described in Chapter 3 If you change the spin system all exchange definitions will be lost so good preparation for this type of calculation is important Once you have completed entry of the static system including the molecule concentrations select Molecule Exchange to define the chemical exchange process you are interested in Chapter 7 F igu re 42 The rate incomplete Exc hange window optimize flag indicator A before and B ExchTest Exchange Pel ES id ExchTest Exchanje after entry of a permutation Clear All Spectrum Spectrum A sources destinations B The Exc hange window that appears Figure 42A will initially have a text column on the left and an empty column on the right The text column represents all nuclei in all molecules The empty column is where you enter the reaction rate and permutation see next section As soon as you have filled in a valid rate and permutation the window will expand to allow you to enter additional rates and permutations Figure 42B gNMR will accept up to 6 different exchange definitions To enter a reaction rate just type the value in the top field of the empty column Rates are always entered in Hz If yo
203. ss you havea single nucleus which couples to 10 or more different atoms in a molecule A calculation on e g a 22 spin system is feasible but still takes a fair amount of time and memory You might want to experiment with smaller chunk sizes e g 6 which result in faster simulation at the expense of a reduction in accuracy The Chunk size parameter in the Approximations section of the Settings File dialog Figure 51 can be used to set the maximum chunk size As soon as a particular spin system gets larger than 1 3 times this size it will be partitioned into chunks not larger than the maximum chunk size Setting this parameter to 0 or to a large value disables chunking 132 Approximation calculations Chapter 9 9 3 First order calculations Normally a simulation should be exact or at least very accurate But sometimes you may find that speed is more important than precision In that case you may want to switch to the very fast but rather inaccurate method of first order simulation This takes into account the splittings caused by J couplings and depending on some settings the thatch effects of intermediate coupling but no other higher order effects The resulting simulation is fast even for eg 22 spin systems First order simulation is not used by default since it can easily produce inaccurate spectra when used indiscriminately In the Approximations section of the Settings File dialog Figure 51 there are two parameters
204. symmetry in combination with assignments as long as you do not destroy or change the symmetry by changing parameters In gN MR this can be ensured by linking symmetry related parameters If you want to use symmetry in combination with assignments check both Use Symmetry and Symmetry with Assignments in the Settings File dialog see section 8 3 Please note that with these settings any change you make to a variable name affects the symmetry of the system and therefore clears all assignments 92 Assignment iteration Chapter 5 5 6 Starting assignment iteration After you have entered your variable definitions and peak assignments you are ready to start the iteration It is recommended that you always save your data first This will allow you to compare the results before and after iteration To start the iteration select Iterate Go from terate the menu bar The Iterate status window will monde 08 appear as the front window the Log window ennie appears behind it and the iteration starts For Next Cycle each new point the Iterate window will A display the point number and residual the Molecule windows will show the new parameter values and the Spectrum windows will show the resulting spectra Assignment iteration converges quite rapidly typically needing 3 10 points The time taken for each point depends mainly on your computer and the size of the spin system Iteration using intensity data is significantly slower t
205. t NMR parameters are crude and mainly based on simple additivity rules see A ppendix F for some details There are several programs that make more accurate and reliable predictions but having some kind of initial guess is usually better than starting with all zeroes You should probably leave both options checked unless you already have more accurate values for your system The last set of two radio buttons will only be enabled if there already was a nontrivial molecule in the Molecule window you are importing into It gives you a choice between matching the new structure to the existing spin system or first deleting the existing contents and then creating a whole new spin system If you select to match the structure to the molecule gN MR tries to work out which atoms in the structure could correspond to atoms already present in the spin system and sets up the links between them the remaining atoms in the structure will not be added to the spin system even if they qualify under the above mentioned include flag settings The matching algorithm is fairly primitive and will only work satisfactorily in simple cases Entering data 57 Figure 26 Molecule window with a structure Chapter 3 3 7 Using structures to enter data Once a structure has been imported into a z x Delete Molecule window it will appear ina separate TEE pane left of the molecule spreadsheet Figure Copy 26 You can change the sizes of the panes by Structure
206. t group in which you can select a target file and version for the conversion the default target version is of course V4 1 After doing this click on Go to start the conversion If you are converting an FID without a transformed spectrum gCVT will display a message and then perform a default FFT because a gSPG file must always contain a transformed spectrum The result will probably not be phased correctly and you will have to use gSPG for phasing gCVT may sometimes produce a message stating that the integrated intensity is negative The most likely cause of this is that the spectrum was not phased correctly other possible reasons are baseline problems conversion of an FID as if it were a spectrum or a completely incorrect conversion This will be evident for the spectrum display in gSPG By default gCVT will start gSPG to display the conversion result To prevent this you can uncheck the Open in gSPG gNMR checkbox at the bottom of the dialog before clicking Go gCVT normally stores data in 8 byte double precision format This may result in rather large files If you are pressed for disk space you may check the Save as Hoat box to save all data in 4 byte single precision format with some loss of precision 11 5 Notes on individual conversions Producers of NMR spectrometers are continually updating their hardware and software Therefore spectrometer file formats change and it is impossible to guarantee that every convers
207. tabase file to recover unused space The Database Deleted Selected command can be used to delete all currently selected records from the database 10 6 NMR parameter prediction gN MR can use three different types of NMR parameter prediction The simplest of these uses a number of built in additivity rules with fixed contributions for a variety of substituents This method does not require any databases and is the method used by earlier versions of gNMR The second method tries to predict shifts by matching the environment of a nucleus to a set of fragments environments stored in adatabase A variation of this method matches a coupling path between two nuclei to paths stored in a database The third method recognizes the fragment i e a benzene ring that a nucleus belongs to and then retrieves substituent corrections for all substituents attached to the fragment from the database Obviously the second and third method can only be used if database support for gN MR is installed as described in the first part of this chapter gN MR has a number of built in rules for prediction of 1H 3C and 31P shifts and couplings These rules are fairly primitive and cannot be expected to produce very accurate results They are primarily intended to give something more useful than an all zero shift and coupling constant matrix after importing a structure Databases 145 Fragment prediction Substituent prediction Chapter 10 All num
208. tails close to the baseline this scheme will often distort relative intensities and you may have to use the integral modification scheme see next section to correct for this You can remove a peak from the spectrum by selecting an area around it with Ctrl dragging After you do so a dialog box appears prompting you for the method to be used for the peak removal the choices are Truncation and Interpolation Truncation simply replaces all datapoints in the enclosed region by zeroes which is appropriate for peaks well separated from other peaks Interpolation uses a few points near the beginning and end of the region to fit a straight line and then replaces the enclosed region with this line which is more appropriate for narrow peaks on the flanks of much broader ones It may be advantageous to first expand the region containing the impurity to allow more accurate selection of the peak 12 6 Adding and subtracting spectra To add two spectra first open one the old file with File Open and then choose Spectrum Add and select the second spectrum the new one If both spectra have nonzero intensity you will be prompted for the area ratio new old to be used for the addition The FID if any will be deleted since it would no longer correspond to the spectrum The resulting spectrum will have the same range as the original old spectrum even if the spectrum being added had a larger range If you want to add two spectra with differe
209. terate Solutions submenu will show a list of these solutions ordered for increasing residuals You can retrieve and inspect each of them in turn usually only the top ones are interesting because they gave the best fits The final least squares residual of each solution will be added to the title for the run 6 6 When not to use full lineshape analysis In the previous sections we have concentrated on how to aspects of full lineshape analysis Now we will focus more on the why aspect Full lineshape iteration is ideal for determining parameters of strongly coupled systems in which second order effects have distorted the spectrum so strongly that the basic coupling patterns can no longer be recognized Typical examples are aromatic regions of the 1H spectra of mono and di substituted benzenes and 31P spectra of transition metal pol yphosphine complexes containing trans coordinated phosphines For such systems the procedure may yield asolution you would never have guessed by trial and error simulation because it is not obvious what parameters you should change to get certain spectral features Full lineshape iteration is also useful when you need to optimize linewidths or rate constants Assignment iteration cannot help you here trial and error simulation not only takes longer but also does not produce any error estimates For such applications however you do not always need the full generalized least squares procedure a pure le
210. teration select Iterate Go If there BESS are no Spectrum windows marked for M iteration gN MR will refuse to start the Pras iteration If there are no parameters marked for Next Cycle Last Cycle iteration you will see a warning eas When the iteration starts the Iterate dialog and Log window appear and the results for successive points are displayed on the screen Some wild oscillations and seemingly random spectral changes are normal especially during the first few cycles Sometimes however you may see that the procedure has run away so completely that it will never come back In that case you can interrupt the iteration by clicking the Interrupt button If you are sure that you want to throw away the iteration results click Abort to restore the original parameters If you are sure that the current Full lineshape iteration 101 Chapter 6 iteration cycle is not going to do further useful work you can click the Next Cycle button to proceed to the next cycle If you have interrupted an iteration you can continue where you left off by selecting Iterate Continue You can skip to the next cycle without bothering to complete the current one by selecting Hterate Next Cycle if you chose Iterate Go iteration would start again at the first cycle instead of continuing with the current one If you are very close to the correct solution and only want to do a pure least squares refinement without any flattening cho
211. teration is normally done using peak positions only It is possible to use intensities as well but it is rarely necessary since the shifts and couplings of a system can often be determined unambiguously from peak positions only Including intensity data can even be disadvantageous since the errors on observed intensities are usually much larger than those in peak positions resulting in larger error margins in the 206 Questions and answers Appendix B optimized parameters Sometimes there are a few discrete sets of NMR parameters that give rise to the same sets of peak positions but with different intensities In such cases the best procedure is to determine every set from peak positions only and then compare the calculated intensities with the observed ones to select the true solution H owever there are cases where intensity data really need to be included in the iteration one example is given in the tutorial section 2 7 The most important thing to renember is that intensities should be normalized that is their sum should be equal to the number of nuclei in the spectrum range being assigned Intensity data can only be entered in the Assignments window not in the mouse assignment procedure Often several peaks are so close together you only havea single intensity for the group In that case enter the total intensity in the field for the first peak of the group and type a lt gt in the intensity fields for the remaining peak
212. tered in either ppm or Hz units an indicator at the top of the column indicates which unit is in effect Internally gNMR stores all shift values in ppm If you want to enter data in Hz be sure to set the spectrometer frequency first see section 3 2 since this determines the conversion factor between ppm and Hz If you enter 50 Entering data Individual linewidths Coupling constants Chapter 3 values in Hz and then change the spectrometer frequency you will see all shift values change by the appropriate factor they will remain the samein ppm You use this field only if you want to specify a separate linewidth for each nucleus if a single linewidth for the whole spectrum suffices see section 4 2 you can leave this field blank If you specify individual linewidths you have to supply them for all nuclei of a given type you cannot give a separate linewidth for one 1H nucleus and let the others have the default whole spectrum linewidth To remove all individual linewidths for a certain nucleus just clear the entry for one of them the others will be removed automatically Linewidth means the width at half height of a peak regardless of its shape Lorentzian Gaussian or Triangular Linewidths are always expressed in Hz and are related to transverse relaxation times in seconds by the equation TxWy 4 5 The rightmost part of the molecule spreadsheet is a matrix of coupling constants in Hz For example the entry at
213. termining equivalence and molecular symmetry This should be comparable in magnitude to the last decimal place displayed in ppm and Hz values see above Customizing gNMR 203 Database section Appendix A Topic Database Usage Iteration A x Default Data Source Import gNMRdata E Editing M Open database on startup KT V Use database for prediction WFT F Merge with rule based prediction beP Tha Lin Pred Fy Gx Fonts Colors 0 0011 Precision Cancel Defaults Help When you select the Database topic gN MR queries your system for available BDE and ODCB databases This may take some time Default Data Source allows you to select a database that gN MR should use for parameter prediction This database is automatically opened on gN MR startup If you don t want to open a database on startup specify none here but then gNMR will not do any database prediction The remaining two options set the defaults for parameter prediction see section 10 7 204 Customizing gNMR Appendix B B Questions and answers This section contains a list of common gNMR questions and answers If you have suggestions for additional entries please contact Cherwell Scientific Q I have entered my shifts in Hz and then discovered that gNMR was expecting data in ppm Switching to ppm units doesn t help since gN MR then tries to convert the data How do correct this without retyping all shi
214. the clipboard The Axes section Figure 30 controls display of spectrum axes Figure 30 Settings Topic Axes and Baseline Spectrum dialog wallets Axes section cy M Show Axes Dimensions Small Ticks per Large a Large Tick sep cm 2 00 M Show Labels l Show Baseline Iteration Nu Cancel Apply Help Baseline x Show Axes If checked causes axes to be drawn with the spectrum The default axes have a minor tick mark approximately every 0 5 cm and one major tick mark for every four minor tick marks Small Ticks per Large This controls the number of minor tickmarks separating the major tickmarks Set to 0 if you only want major tickmarks If axes labeling is enabled below labels are only drawn at major tickmarks 70 Displaying spectra Chapter 4 Large Tick sep Sets the target separation in cm or inch between major tickmarks The actual separation will differ from this because gN MR attempts to use round values at the major tickmarks Show labels Is only enabled if Show Axes above is checked If set this causes labels to be drawn with major tickmarks in the spectrum Labels may be suppressed at some tickmarks if they would overlap with other labels Show Baseline If checked this causes a dotted baseline to be displayed in calculated and experimental spectra The baseline is never shown in printouts or clipboard copies The remaining sections of this Settings File di
215. the contribution of the nucleus we are interested in 2 up e Coj A U w J U abn U ab 2 nau T ci Oyj ij F 3 Individual linewidths Most NMR simulation programs use a single linewidth for the evaluation of a spectrum This is often unsatisfactory However a rigorous treatment of relaxation is not only cumbersome from a computational point of view but also requires a detailed knowledge of all important relaxation processes Since such knowledge is usually lacking and often irrelevant we have opted to incorporate a more empirical scheme in gNMR This scheme allows the specification of an individual natural linewidth for each nucleus in the system Using the population analysis for peaks described above we calculate the linewidth of a peak as the weighted average of the linewidths for the contributing nuclei 2 n u U Ea Coj Ta W abn _ in Wp ig U W Fi I 2 n ab DM nes ai bj ij y F 4 Lineshapes By default a Lorentzian lineshape is assumed for spectrum evaluation If the linewidth is small relative to the grid spacing the normal Lorentzian intensity function Wese i a i ey x 2 is replaced by the integrated intensity Technical issues 225 Appendix F 1 W Idz I WA z atan 7 7 E T E yA ee 4 4 x 2 2 2 which avoids the intensity distortions caused by peaks falling between datapoints Peaks are truncated at a fixed number of linewi
216. the dialog that appears Symbolic System Nuclei Ea AAO 1H 2 Eea Adding new entries to the Molec ule Symbolic submenu is easy Just copy the sample file gNMR41 sps to your gN MR directory and add the systems you need the next time you start gN MR the newly added systems will appear in the menu You can use a plain text editor like notepad or the DOS edit program to do your editing If you want to use a word processor be sure to save the file as a plain ASCII text file Each entry in the gNMR41 sps file is terminated by a blank line The first line of each entry is the name of the system as it will appear in the menu enclosed in square brackets The second line lists the nuclei the user will be queried for Below these title lines comes a partial molecule listing with one row per nucleus The first item of each line is asymbolic name for the chemical shift the remainder are names for the coupling constants As in the Molecule window equal names indicate symmetry related parameters Figure 47 shows the listing for an AA BB system as an example Symmetry 123 Figure 47 Listing for the AA BB system in gNMR41 sps Using space groups Figure 48 Molec ule Symmetry dialog Chapter 8 AA BB A a a aa b ab ab b ab ab bb To enter a system with a more complicated symmetry you can use the Molec ule Symmetry submenu The menu contains the space groups recognized by Sn Cnh gNMR ER Dn e
217. the gN MR and gSPG Settings Spectrum dialogs sections 4 2 and 12 4 Customizing gNMR 191 Appendix A Axes section Topic Pee M Show Axes Small Ticks per Large Large Tick spacing 2 00 M Show Axis Labels I Show gNMR Baseline M Show gSPG Baseline oe Cancel Defaults Help These settings correspond to the Axes section of the gN MR and gSPG Settings Spectrum dialogs sections 4 2 and 12 4 192 Customizing gNMR Hardcopy section Appendix A Preferences xi Topic dalag S General amp Symmetry Hardcopy gt Line thickness 1 72 Dimensions nm Display T Print Nucl Ranges MV gNMR data in clipboard copies I gSPG data in clipboard copies qo Cancel Defaults Help Customizing gNMR These settings correspond to the Hardcopy section of the gN MR and gSPG Settings Spectrum dialogs sections 4 7 and 12 12 193 Iteration section Due Iterate I Try Sign Changes Dimensions Display aa M Group Assignments I Highlight Assignments Correlation Start Ei te 04 Correlation Increase 10 0 Random Restarts 0 Peak Ordering Ascending Assignment Threshold 2 00e 02 Grouping Threshold j 00e 02 oo Cancel Defaults Help Appendix A These items correspond to the Assignments and Iteration sections of the gN MR Settings File dialog sections 5 5 and 6 4 194 00 C
218. tical bars in both spectra will show relative peak heights and lines will be displayed that connect the observed and calculated peaks This shows you at a glance if there are any improbable assignments it is also a convenient way to judge the quality of iteration results If you have enabled the display of assignments the mouse assignment procedure will also display these connections Assignment iteration 91 Chapter 5 Figure 40 z odcb1 Spectrum 1 OF x Spectrum window with assignments displayed Assignments have only been entered for the high field fen AA multiplet 7 500 7 450 7400 7 350 7 300 7 250 h7 7 050 pt 7 500 7450 7400 7350 7 300 7 250 7200 7150 7 100 7050 7 000 gN MR provides several methods to reduce the size of a calculation symmetry perturbation theory and a new approximate method However these cannot be used easily in combination with assignment iteration The reason for this is that assignment iteration needs an unambiguous and consistent way of labeling transitions Each of the above methods changes the peak labeling because it affects the order in which energy levels and transitions are calculated Moreover changes in shifts and or coupling constants can result in a different partitioning of the system for perturbation theory or approximate calculations Therefore the latter two methods cannot be used at all in combination with assignments It is possible to use
219. ties As long as you have not done this gN MR will run with all database facilities disabled gN MR accesses databases through the BDE Borland Database Engine Therefore the BDE must be always be installed for gNMR database usage The BDE can access Paradox and dBase databases directly For other databases like Microsoft Access it has to go through ODBC Open Database Connectivity which then also has to be installed on your system When using an ODBC database you first set up the ODBC data source then let the BDE recognize this source A new gN MR database needs tables to store its data it needs to be initialized Once the database has been configured using ODBC and the BDE you can use the gBase utility to create these tables Table creation is not necessary for the sample database provided with gNMR since this has already been intialized 10 3 Configuring databases for use with gNMR The procedures below describe how to install ODBC and the BDE and then explain in general terms the steps needed to configure an existing or new database for use with gN MR The tutorial Chapter 2 and online gives a more specific and detailed description of the configuration of the sample databases and new databases 138 Databases Install ODBC Install the BDE Defining an ODBC data source Chapter 10 As mentioned above ODBC installation is only necessary if you plan to use database types other than dBase or Paradox with gNMR The s
220. tiplet individually or for all at once using the Set All pulldown If you check the Find Connections checkbox gSPG will try to connect the multiplets by finding equal coupling constants between them You can also set the maximum number of X nuclei allowed to which non matching couplings will be attributed If you click OK gSPG starts the analysis This will usually result in one or more solutions i e collections of shifts and coupling constants that would explain the observed spectrum Once these have been obtained you can use the Spectrum Regions Solutions dialog Figure 58 to save a solution to a gN MR data file or copy it to the clipboard Opening the filein gN MR or pasting the clipboard contents will give you a simulation corresponding to the solution found by gSPG 170 Spectrum processing Figure 58 gSPG Spectrum Regions Solutions dialog Fourier transformation Chapter 12 Solution IIE ENIF lt Nucleus 1H cor Cancel Help This automatic analysis is still under development and currently only works for high quality spectra with little or no overlap between peaks 12 8 Markers and calibration You can label peaks in the spectrum by clicking the mouse at or near them just as in gN MR section 4 5 You can also use the Spectrum Regions Peak List command previous section for automatic peak detection In either case once some peaks are labeled the Spectrum Markers Marker Info command c
221. topes list and the fragment list this is immediately followed by the actual data For binary files the header is followed by four bytes that tell gN MR the byte order of the data that follows e 02010000 for littleendian PC files e 01020000 for little endian M acintosh UNIX files gN MR can read both little endian and big endian files the byte order flag just serves to tell the program how to interpret the rest of the file The header is followed by a series of records of the form meaning integer 2 bytes record type long 4 bytes record length excluding type and length fields length bytes variable record contents The file is normally terminated by a record with type 1 and length 0 We will not discuss the record types in detail since most of them are not intended to be read or written by other programs H owever you may wish to generate your own gSPG files from other programs In that case use the file header geNMR V4 1 Spectrum File and include at least the following records File formats 221 Appendix E contents description format title CR or LF terminated string Main data 513 nucleus name CR or LF terminated string spectrometer 8 byte double frequency ppm units flag byte 0 FA LSE float save flag byte 0 FA LSE Spectrum 514 of datapoints 4 byte integer parameters high field end of 8 byte double spectrum Hz low field end of 8 byte double spectrum Hz left phase 8 byte double ri
222. trix see ref 1 In the simplest approach rows and columns involving low intensity transitions are simply dropped from the matrix This usually results in a modest increase in speed up to 50 In amore drastic approximation intensities are calculated on a per nucleus basis Only those rows and columns are retained which havea significant contribution of the nucleus in question The results for all nuclei are then added This approach may result in a significant speed increase particularly for nearly first order systems The intensity criterion for dropping rows and columns of the matrix depends on the exchange rate Therefore approximate exchange calculations will become slower and more memory demanding for higher rates At very high rates the eigenfunction approach becomes identical with the exact full matrix approach and the per nucleus approximation become more expensive The two settings affecting approximate exchange calculations are located in the Approximations section of the Settings File dialog Figure 51 Approx Exchange Calculations If this is checked gN MR will use the eigenfunction based approximation method if this results in significant savings Max Exchange Matrix If approximations are allowed previous option and the size of an exchange matrix in the eigenfunction approximation would still grow above the limit set by this option the per nucleus 134 Approximation calculations Figure51 Settings File dial
223. tructure first select ChemWindow from the pulldown and then click the button to the left of it In either case use the file dialog to select the file ODCB cwg gN MR takes some time to interpret the structure and then the Import dialog appears We don t want anything special just dick OK You can also import a structure via the clipboard Open ODCB cwg or one of the other structure drawing files ODCB cw2 ODCB skc ODCB chm ODCB cdx with its drawing program select the structure and copy it to the clipboard Then in gN MR select Edit Paste ChemWindow or similar gN MR will try to predict the shifts and couplings one by one When import and prediction are complete a Molecule window will be Tutorial 13 Figure 5 Molecule window showing ODCB structure Chapter 2 shown containing a structure drawing in a separate left pane Figure 5 The atom numbering may differ from the one used in the earlier example in structure import gN MR assigns atom numbers arbitrarily and you cannot change them To enter anew chemical shift for the topmost hydrogen atom of the structure click on it this moves you to the corresponding shift field in the right pane Type a new value 7 4 and then also enter the same value for the bottom hydrogen To enter a new para coupling constant click on the top hydrogen and Shift click on the bottom hydrogen this moves you to the field of the coupling between them Documentz2 Molecule 1 MEE N
224. ttings correspond to the gSPG AD WFTdialog section 12 9 197 Appendix A Linear Prediction section Topic Weighting and Transformation Function fi gt Function Type None gt Kaiser window Le 00 Gaussian LB Hz 0 00 Lorentzian LB H2 0 00 MV Show Weighted FID Lin Pred Beo Cancel Defaults Help These settings correspond to the gSPG AD Linear prediction dialog section 12 11 198 Customizing gNMR Fonts section Appendix A Preferences Ea Topic Iteration S 5 ann Static Text Sample Change ite Small Static Sample Change Editing Edit Text Sample Change FEEFEE FT Pa Tensame kT Plot Text Sample Change WIT Hate Text Sanpke Change Peri P Hu Log Text Sample Change Lin Pred Colors 0 0011 Cancel Defaults Help _ H gN MR uses several fonts for fields in grids items in dialogs texts in spectra etc You can select fonts for some of these items separately gN MR uses separate fonts for editable and static non editable text items This is convenient in grids because you can see at a glance which field can be edited and which cannot By default gN MR uses the same set of two fonts inside dialogs but you can suppress that Substitute dialog fonts If this is checked the default gN MR will use the Static Text and Edit Text fonts below inside dialogs If you uncheck this option dialogs w
225. turbation theory and it is used for the individual chunks of approximate calculations where appropriate see section 9 2 The Symmetry section of the Settings File dialog Figure 49 determines how gN MR uses symmetry File Settings Ea Topic dalag ar General Symmetry l Symmetry with Assignments Iteration Cancel Help Use symmetry If checked the default symmetry usage is enabled Symmetries included in the internal or external database will be used in simulations If you uncheck this option all use of symmetry is disabled Symmetry with assignments If unchecked the default symmetry is never used in combination with assignments If you check this option assignment calculations may be slightly faster but any change to the system that could change the symmetry including a change in any variable names will clear all assignments In assignment Symmetry 127 Creating a custom groups database Figure50 gGRP database generation dialog Chapter 8 calculations gNMR determines symmetry from variable names not from numerical parameter values so a symmetric system without any variable names will always be treated as unsymmetric The utility gGRP can be used to create a customized groups database The default database contains axial groups with up to 6 fold axes and the tetrahedral and octahedral groups If you are certain you are never going to use very high symmetries you c
226. u are working with the second or subsequent reactions you can also press lt gt to indicate that you want to duplicate the rate value from the previous column This duplication is temporary the values are created equal but you can change them independently afterwards Sometimes you are dealing with a system where there are several equivalent elementary reactions which are related by symmetry You have to enter separate definitions for them but of course you then want the rates to start equal and remain equal In this case you only supply a rate value for the first of them For subsequent definitions enter the negative of the number of the first definition For example to link the rates of definitions 3 and 4 to that of 2 enter a real rate e g 100 0 for 2 then enter 2 for definitions 3 and 4 You can also type a lt gt to indicate a link to the previous definition If you link rates in this way remember that each of them will have the rate you entered for the first reaction so the total rate will be larger Chemical exchange 113 Chapter 7 Itis permissible to enter a reaction rate of 0 If you do this the exchange process will be ignored for spectrum evaluation so the calculation will be as fast as a normal static calculation This allows you to define and store an exchanging system without actually doing any exchange calculations For any non zero value of the rate however the exchange formalism will be used even if the
227. ucleus cama Options Spectrum In ODCB several parameters are not independent since they are related by symmetry Therefore if you want to change the meta coupling you have to enter two new values else the symmetry would be lost It is easy to forget this when doing lots of simulations but there is a way to make symmetry related values stay the same Choose Molecule Show Symmetry The dialog that appears says the C2 symmetry was detected the actual molecular symmetry is higher in this case but the remaining symmetry is not relevant to NMR here Now click the Enforce button This defines variable names for the NMR parameters parameters having equal names will be forced to keep equal values Calculate the spectrum by clicking on the Spectrum button Then use the Settings Spectrum dialog to include the experimental spectrum ODCB spg in the display as described in the previous section We had not yet adjusted the spectrometer frequency to 300 MHz so this time gN MR will ask if it is OK to do that automatically click on OK 14 Tutorial Chapter 2 in that dialog and then on OKin the Settings Spectrum dialog to see the spectra displayed above each other As described in the first exercise you can do trial and error simulation by typing new values in the Molecule window and clicking on the Spectrum button for recalculation However there is amore convenient way Double click on the rightmost multiplet T
228. ues use a simple exponential which can be useful if you want to prevent large changes in parameters Reasonable starting values for Cs are 104 to 10 or 104 to 106 The value of C determines how quickly you move from maximum flattening the starting Cs value to no flattening at all after each cycle Cs is multiplied by C when it passes 1 or 1 the flattening is disabled to make the last cycle a pure least squares cycle If you do this too quickly you are unlikely to converge to the right solution If you do it too slowly you may waste a lot of computer time Experience shows that 4 6 cycles are usually reasonable The default values for Cs 10 4 and C 10 result in a total of 5 cycles 10 103 100 Full lineshape iteration Figure 41 iterate section of Settings File dialog Chapter 6 102 101 and the final least squares cycle If you are in a hurry you could use Cs 104 and C 100 3 cycles in all if you have time you could use Cs 10 and C 10 7 cycles You can set the values of Cs and C in the dialog box that appears when you select Settings File dialog iterate section they are labeled Correlation Start Cs and Correlation Increase C see Figure 41 File Settings Ea Fullineshape Iteration Corr Start Corr Increase 10 0 l Try Sign Changes iA IN l Random Restarts Approx Symmetry Assignments h daha Iteration Cancel Help To start the i
229. using gCVT and then transform and phase the spectrum using gSPG gSPG offers the basic options needed for spectrum processing transformation phasing and some baseline correction options In addition it offers a few spectrum manipulation and analysis options specifically geared to preparing spectra for full lineshape analysis and direct interpretation of multiplet structures Finally it has display and hardcopy functionalities similar to those of gNMR Spectrum processing 159 Chapter 12 12 2 Files and Windows On startup gSPG displays the File Open dialog since you will rarely create a new file a zs from within gSPG File Open opens a new Close file File Close closes the current file and _ GoseAl File Close All closes all open files Save Ctrl S File Save as saves the current file a File Save As saves it under a new name and File Revertreverts to the most recently T a saved file contents You can also use Print Visible Part Edit Undo and Edit Redo to move Save EPSF backwards and forwards in a series of slats alin ase changes The File Recentsubmenu liststhe FH AIFS most recently used files Get Info Recent gt Every open file can have at most three open windows e The Spectum window which displays the transformed spectrum Figure 54 e The AD window which displays the raw FID e TheLog window where operations on the spectrum and FID are logged this is initially displayed minimi
230. ustomizing gNMR Import section Preferences Ea Topic Import V Expand Abbreviations V Add Hydrogens M Predict Shifts M Predict Couplings WET Wer P bal Colors Hydrogens JIncludeall gt Carbons JExcludeall gt Editing Abundant Isotopes Jincludeall gt err T Rare Isotopes Explicitonly gt She Av Bond Length nT Lin Pred Atom Labeling Numbers 0 0011 al Cancel Defaults Help Appendix A These settings correspond to the gNMR Import dialog section 3 6 and Settings Molecule dialog sections 3 3 and 3 7 Customizing gNMR 195 Editing section Appendix A Topic Editing dasa F Iteration A Peak Removal Truncation z n 4 Import Smooth Order E Compress Order 4 Fourier Order 10 20 berT Number of Spline Points Aa l Store Spectra as 4 byte Reals WFT I Use Quick Phasing beP Hu Lin Pred Colors 0 0011 Boo Cancel Defaults Help This sets defaults for some common gSPG operations smoothing baseline corrections phasing 196 Customizing gNMR Weighting and Transformation section Appendix A Preferences Ea Topic Weighting and Transformation Function fi gt Function Type None gt Kaiser window Le 00 Gaussian LB Hz 0 00 Lorentzian LB H2 0 00 MV Show Weighted FID Lin Pred Beo Cancel Defaults Help Customizing gNMR These se
231. veral Spectrum windows for iteration if you like they will all be used simultaneously with weights equal to the number of nuclei in each window The windows can be for the same or different nuclei and the same or different experimental spectrum files they are allowed to overlap Careful spectrum preparation is essential for a successful iteration we will return to this later in the Chapter If there are humps or impurity peaks in the spectrum or if you havea noisy baseline you will probably not get a reasonable fit You can use gSPG for some limited spectral editing see Chapter 12 If you only havea single multiplet or if your peaks are spread more or less evenly over the whole spectrum using a single window for iteration is usually satisfactory If there are large empty areas between the multiplets it is often a good idea to define separate Spectrum windows for each multiplet and mark each of these for iteration It may be useful to also keep a whole spectrum window not marked for iteration to check that nothing strange is happening During the first few steps of the iteration peaks sometimes drift out of the iteration windows If you are iterating on a single window containing all peaks of the spectrum gNMR will try to pull them back in by adding a penalty function to the least squares residual In other cases gNMR cannot be sure that the peaks should be pulled back in and will not try to do so However once a peak has drifted
232. y A sample file corresponding to the standard nucleus list is supplied on one of the distribution disks You can copy it and use it as an example or starting point for modification In general it is recommended that you modify the supplied list rather than create your own from scratch The isotopes list is a plain text file which can be edited using any editor or word processor Each line contains information on a single element or isotope each element is followed by a list of isotopes belonging to it in order of increasing isotope mass Nuclei recognized by gNMR 213 Appendix C Each line for an element contains in order separated by blanks or commas e Atomic symbol e Color to use when displaying spectra see below e Atomic number in periodic table e Main isotope may bea single isotope name or isotope mixture name e Average atomic weight e Electronegativity e Main valence 0 if there is no standard valence e Number in isotope list of previous gN MR version or if not used in earlier gNMR versions Each line for a single isotope contains in order separated by blanks or commas e Nucleus name e Nuclear spin 2 eg 3 for spin 3 gt e Resonance frequency at 2 3488 T corresponding to 1H 100 MHz e Nuclear quadrupole moment 0 for spin Oor Y 2 e Natural abundance as a fraction e g 0 0632 for 6 32 e Exact mass of isotope e Number in isotope list of previous gN MR version o
233. y but if your drawing program has an explicit method of specifying aromaticity the aromatic rings of Chemintosh and ChemWindow we recommend that you use it e Itis best to draw complete molecules for import into gN MR If you draw only a fragment of a molecule you can still import it and use it for data entry but the shift prediction will probably produce wildly inaccurate results You normally import a structure into an existing Molecule window If there was no open file gNMR will create a new file and Molecule window first To import a clipboard copy choose the appropriate Edit menu command e g Edit Paste ChemWindow To importa structure from file use the File Import command e g File Import ChemWindow and select the file you want to import gN MR will interpret the structure this may take some time depending on the size of the molecule and the file type Then the Import dialog appears Figure 25 this has anumber of options that tell gN MR what to do with the structure just read in 54 Entering data Figure 25 Import dialog Chapter 3 Import Structure Ea M Add hydrogens Hydrogen atoms include All Carbon atoms Exclude All gt Abundant isotopes include All Rare isotopes Explicit Only gt MV Predict shifts N Predict couplings _ Match to Current Molecule Replace Current Molecule The first two options pertain to structure completion Expand abbreviations
234. y for 1H in MHz 100 000 KS C ppm Units HzUnits Approx C Isotropic Anisotropic Llau F Include coupling to gt 1 2 isotopes Assignments nesh L tzi ineshape orentzian dhas au Iteration Cancel Help Title Specify a new title for the current file Spectrometer Frequency 1H Set the spectrometer frequency in MHz for 1H gNMR uses it to calculate the observe frequencies for all nuclei Units Can be set to ppm or Hz This setting can also be changed with the menu command Settings xx units of the lt Ctrl U gt shortcut Spectrum Type gN MR can calculate anisotropic partially oriented spectra as well as the more usual isotropic spectra Include coupling to S gt 72 isotopes quadrupoles With this checkbox checked for isotope mixture nuclei generating both spin 12 and quadrupolar isotopes the quadrupolar isotopes will beincluded in the spin system If this box is unchecked such quadrupolar isotopes will be treated as N M R inactive the fast relaxation limit which is valid for most nuclei except 2H and symmetrically surrounded quadrupoles 44 Entering data Chapter 3 Lineshape Function Ideally NMR signals have a Lorentzian lineshape However alternative lineshapes sometimes give a more accurate description of experimental spectra gN MR offers a choice between Lorentzian Gaussian and Triangular lineshapes 3 3 Molecule windows Each open filein gNMR contains at leastone AG
235. y cause rapid relaxation or a residual coupling Or exchange processes may lead to selective broadening As an example consider the molecule of o chloro aniline The NH 2 resonance will probably be broad but all other peaks should have a similar linewidth To simulate this first import the file ocLAnil cwg using File Import ChemWindow Click on one of the aromatic protons and enter a linewidth of 0 5 for it in the column labeled W Hz to the right of the chemical shifts When you leave this field the new linewidth will also be applied to all other hydrogens in the system Now click on one of the amino protons click on the linewidth field and enter a linewidth of 8 there you don t have to 34 Tutorial Decoupling Isotopomer mixtures Chapter 2 click on the protons first but doing so makes it easier to see in which row of the Molecule window the linewidth for a particular nucleus should be entered Click on the Spectrum button to see the simulated spectrum with sharp aromatic multiplets and a broad resonance at 4 7 ppm for the amino group On occasion you may want to remove a nucleus from the system You could permanently delete the atom from the molecule and the structure by selecting it and then choosing Structure Delete Atoms You could remove it from the calculation but keep it in the structure by choosing Stucture Exclude the disadvantage of this is that if you wish to add it again the associated shifts and c
236. you select either Convertor Converta Copy gCVT will be launched if it was not active already and will be switched to the foreground It will convert the file and the original program gSPG 150 File conversion Figure 52 Automatic file conversion dialog Explicit conversion Moving files Chapter 11 or gN MR will return to the foreground Normally gCVT will then quit If you are going to open several files from different versions check the Keep gC VTactive checkbox in the conversion dialog box this will prevent gCVT from quitting when it is done The file EXOBJ Abc_ 36 spg will be converted using gCVT and the converted file will then be opened Convert a copy Cancel Help l Keep gCVT active after conversion gN MR and gSPG always try to use the version of gCVT in the same gN MR directory for automatic conversion If you want to use a gCVT program located somewhere else you will have to do your conversions manually that is by explicitly launching gCVT and telling it which files to convert To converta dta or spg file to a different version start gCVT and at the top of the Convert dialog Figure 53 select the gNMR Int Convert From from the pulldown list Then specify a source file target file and target version and click the Go button to start the conversion If you convert to V4 1 format gSPG or gNMR will be launched automatically to display the result you can prevent this by unchecking the
237. ystems you may have to consult the online help to see the order in which the images of each atom are generated Symmetry input has a few limitations Firstly the final molecule must not contain more than 49 atoms since gN MR cannot handle larger molecules Secondly the textual representation of the complete system group name names and contents of special positions plus separators should not exceed 255 characters this is unlikely to happen Finally icosahedral groups are not yet supported 8 3 Settings affecting symmetry handling in gNMR To use molecular symmetry in simulations gNMR needs a symmetry groups database gN MR comes with an internal database but if it finds a file named gNMR41 sgp in the program directory it will try to use that instead You can use the auxiliary program gGRP see below to construct a customized database With gNMR symmetry is an all or nothing proposition If gNMR detects a symmetry for which it has no data in its groups database it will ignore that symmetry completely it will not use a lower subsymmetry 126 Symmetry Figure 49 Settings File dialog Symmetry section Chapter 8 Symmetry can be used in combination with chemical exchange and is even more useful here than for normal calculations since there is more to gain However only those symmetry elements permutations are used that are not affected by the exchange reactions Symmetry can also be used in combination with per
238. zed You cannot close a Spectrum or AD window individually doing either will close the whole file If you have more than a single open file the Windows amp Files miniwindow will appear to help you keep track of windows You may also want to check the Window Minimize Inactive choice which ensures that all windows not belonging to the topmost file will remain minimized 160 Spectrum processing Figure 54 Sample gSPG Spectum window Chapter 12 IMA Odcb Spectrum OU x gg 22 gt ODCB 300 MHz smoothed and compressed 1H Axis ppm Scale 15 43 Hz cm Senne a N A EERE En TEER ER RR AEA 7 550 7 500 7 450 7 400 7 350 7 300 7 250 7 200 7 150 7 100 12 3 File wide settings The Settings File dialog Figure 55 allows you to change some file wide settings like observe nucleus and spectrometer frequency Be careful here since these settings are things that normally should never be changed If you change the sweep width or offset of a spectrum you do not select a subrange but redefine the meaning of the current spectrum Spectrum processing 161 Figure55 gSPG Settings File dialog Chapter 12 File _ 5 Name EX0BJ 100100 spg Title Spectrum converted from WinNMR Spectrometer Frequency 200 130 MHz Observe Nucleus 1H Observe Frequency 200 130 MHz Spectrum Offset 50 46 Hz Data points 32768 Sweep Width 2408 46 Hz z 7 F

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