NUMARIT for Windows

Preface
Installation
Introduction
Setup
Using NUMARIN
Using NUMTRUN
Using NMPLOT
Using NMMIX
History

Preface

While other static NMR simulation and fitting programs are available, some of them as freeware, including at least one implementation of NUMARIT itself, the present suite of Windows programs has been created entirely by the present author to reflect his preferences and experiences with NUMARIT, as a practising synthetic chemist and spectroscopist.

The package includes a folder of 15 examples, provided both as input files for NUMARIT and as input files of plots for the new plotting program NMPLOT for Windows, drawn from the present author's experience of ³¹P NMR and of teaching NMR analysis as a practical subject to university chemistry undergraduates.

The package includes Word .doc and .pdf files of an introductory undergraduate drylab course in subspectral analysis, which are also available at
 http://www.staff.ncl.ac.uk/bruce.tattershall/teaching/drylabs/nfodrylb.html .  The skills taught are useful in hand analysis of observed spectra, up to the point at which NUMARIT can be brought into use.

Platforms

Availability

Built-in Help

Installation

Leave all the .exe, .dll and .bat files in the same program folder, and do not rename them.  Create a separate startup folder, to contain data files created and used by the suite of programs.  Make shortcuts to the executable files nminw.exe, numtrunw.exe, nmplotw.exe and nmmixw.exe, as described in Setup.  You should read and understand the whole of Setup before attempting to try out the software, because it does contain some warnings about the automatic deletion of files in the startup folder.

No further installation under Windows is required.  The software may be uninstalled simply by deleting the .exe, .dll and .bat files.

The file pfe101i.zip is included within numtwe.zip.  This is the distribution file for Programmer's File Editor, which you may wish to use for editing input files for NUMARIT for iterative use.  See Converting .num Files to Iterative Use .  While the present author recommends this freeware from Lancaster University, he can take no responsibility for it.  See README.TXT within pfe101i.zip for information about installation and use of Programmer's File Editor.

Introduction
Setup
Using NUMARIN
Using NUMTRUN
Using NMPLOT
Using NMMIX
History
 

Introduction

This version of NUMARIT simulates static high-resolution NMR spectra of spin systems with up to seven chemical shifts, and performs iterative fitting of coupling constants and chemical shifts to observed peak frequencies

NUMARIT makes no assumptions as to whether a spin system is first order or not, and chemically equivalent but magnetically non-equivalent pairs in a molecule with twofold symmetry, e.g. the AA'BB' system, are particularly provided for

The present version for Windows is a suite of four programs:

• NUMARIN to prepare the input files for simulation runs of NUMARIT
• NUMTRUN to run these calculations using NUMARIT, and display the essential parts of the textual output
• NMPLOT to display the resulting plots of regions of the simulated spectra, and optionally to print them or export them to other programs
• NMMIX to mix together plot data files stored by NMPLOT

• NUMARIN is restricted to preparing input for simulations, but the resulting files may be altered, using a separate editor, to add observed frequencies to make input for iterative runs of NUMARIT
• NUMTRUN and NMPLOT can handle either kind of job
• Frequency scales for plots can be specified in NUMARIN and, providing they will fit onto A4 paper, NMPLOT will produce printouts at these scales, so that they may be compared exactly with plots of experimental spectra

 
• NMMIX is intended as a research tool to combine simulations of parts of the spectra of several compounds in a single plot, instead of viewing printouts stacked on a lightbox, or trying to align copies of plots in other software, for use in publications
• NMMIX will similarly produce printouts which may be compared exactly with experimental spectra, and the plots may be exported to other programs
• Plot regions and scales for a mixture of compounds are specified within NMMIX, along with peak widths for each compound in the region being simulated, rather than using those set up for NMPLOT, making it easier to change the simulation of the mixture experimentally
• Possible applications are to simulate spectra of mixtures of diastereomers, or spectra in which an observed nuclear species is coupled to two or more medium-abundance isotopes of another element

See History
 

Setup
Using NUMARIN
Using NUMTRUN
Using NMPLOT
Using NMMIX
History
 

Setup

• This software will run in Windows95, Windows2000, Windows XP or 64-bit Windows 7 environments
• The screen resolution should be set to at least 800 by 600 pixels in Settings, Control Panel, Display. At 800 by 600 pixels, the windows will just fit on the screen. They do so with space to spare at 1024 by 768 pixels. If the windows run off the bottom of your screen, you probably have the resolution set to 640 by 480
• The library files SALFLIBC.DLL and FTN90.DLL need to be in the windows path or in the programs folders in which NMINW.EXE, NUMTRUNW.EXE, NMPLOTW.EXE and NMMIXW.EXE are stored. These libraries are commercial products, but you are permitted to take copies of them without charge
• The programs MLTIPLET for Windows, PAT for Windows, and ORBITAL for Windows all use the same versions of the .dll files, so if you have them in your system, the .exe files MLTPLTW.EXE, PATW.EXE and ORBTALW.EXE may all be kept conveniently in the same programs folder as NMINW.EXE, NUMTRUNW.EXE, NMPLOTW.EXE and NMMIXW.EXE .  See Warning about Folder Names for Installation for advice on naming the folder.
• The provided files NUMTRUN.BAT, NMPRUN.BAT, NUMARIT.EXE, PLUSCC.EXE and NUMPRNED.EXE *** must *** be in the same programs folder as NUMTRUNW.EXE
• If NUMARIN is to be used to call NUMTRUN, and NUMTRUN is to call NMPLOT, the files NMINW.EXE and NMPLOTW.EXE must also be in the same programs folder

• NUMARIT creates a number of files with the file name extension .$$$ and NUMTRUN deletes all files with the extension .$$$ in its startup folder
• NUMTRUN creates the files IBMPRINT.TXT, NUMPRINT.TXT and NUMPLTS.EXT in its startup folder, overwriting any previous versions of these
• *** IT IS ESSENTIAL *** that you start NUMTRUNW.EXE in a folder which does NOT contain any files which you wish to keep, which have either the name extension .$$$, or which have any of the names IBMPRINT.TXT, NUMPRINT.TXT or NUMPLTS.EXT
• Conveniently, the startup folders for NUMTRUN, NUMARIN, NMPLOT and NMMIX should all be the same NMR simulation data folder, in which you will keep the .num and .enm files used by the programs, and possibly .txt files which have been renamed from NUMPRINT.TXT (though they can easily be regenerated if you keep the .num files)
• See Warning about Folder Names for Installation for advice on naming the startup folder
• To set the startup folders, drag shortcuts for NMINW.EXE, NUMTRUNW.EXE, NMPLOTW.EXE and NMMIXW.EXE from Windows Explorer onto your desktop, and rename them Numarin, Numarit, Nmplot and Nmmix respectively. Create a suitable data folder. Right click on each of the four shortcuts in turn, click Properties and alter the Start in: folder to be your data folder. Apply and OK

 

 

Printing from NMPLOT

• If you leave the shortcut to NMPLOTW.EXE with just the program file name in the target field, NMPLOT started from this shortcut will not allow printing of plots from the program, nor copying of the textual output to Notepad. This is for use in classroom situations where extensive printing may not be desirable.
• To start NMPLOT with printing enabled, alter the target field of the shortcut to it to have a letter P after a space after the .exe file name
• If the printer to be used has the (common) 300 dots per inch resolution, it should then work at the correct scale
• If the printer has a different resolution to 300 dpi, follow the letter P immediately (no spaces) by = and the number of dpi, e.g. P=600
• The author notes that his HP Laser Jet 1022 printer has a default print quality called FastRes 1200, but this works correctly with a setting of P=600 for NMPLOT
• NMPLOT plots lines which are only one pixel wide, so true 1200 dpi printing, as with the HP setting called ProRes 1200, produces lines which are too faint to be useful
• Try a plot requested to be less than 25 cm wide, and check that it is superimposable on an expansion plot from your NMR spectrometer with the no. of Hz per cm which you requested. If there is a small error, either in the scale output by the spectrometer, or in the real resolution of the printer, you can adjust the P=number parameter in steps of 1, to cure the problem. At 300 dpi you can adjust in steps of 0.033 mm per cm
• To be able to copy the textual listing to Notepad, add the letter L separated by spaces to the target field of the shortcut
• A typical target field would be

... nmplotw.exe L P=600
• NUMTRUN calls NMPLOT via the batch file NMPRUN.BAT so as to provide you with a mechanism for setting up your use of a printer with NMPLOT
• As it is downloaded, NMPRUN.BAT will call NMPLOT with no possibility of printing plots (except by copying and pasting to other programs)
• If you wish to be able to print plots from NMPLOT called from NUMTRUN, use Notepad to modify NMPRUN.BAT, following the instructions contained within it
• Typically you will modify NMPRUN.BAT so as to correspond to the printer setting you set up in your shortcut to NMPLOT


Printing from NMMIX

• The default for NMMIX is to be able to print at 300 dpi, so if your printer has this resolution, no modification to the target field of the shortcut is necessary
• For other printer resolutions, use the same format as for NMPLOT, above, e.g. P=600
• Whatever you have successfully set up for printer resolution for NMPLOT should also work for NMMIX, since they use the same output routine
• There is no .bat file to modify in the NMMIX case


Starting NUMTRUN

• Normally NUMTRUN is started from its shortcut and input files are selected within it, or it is called by NUMARIN which passes the name of an input file to it, but, under Windows XP, NUMTRUN alternatively may be started by dragging and dropping a .num file from Windows Explorer onto NUMTRUN's icon. The calculation will start immediately and the output files will be written to the startup folder specified in the shortcut

• NUMTRUN.BAT takes two parameters, separated by spaces: the first is the path to the programs folder, and the second is the full name (including path if it is not in the startup folder) of the .num file to be used for input
• NUMARIT.EXE reads the input file INPTONUM.$$$, writes and rereads several temporary files with file name extension .$$$, and writes its textual output to RAWP.$$$ and its plot data to NUMPLTS.EXT, all in the folder in which NUMARIT.EXE is started
• The present author's DOS program PLUSCC.EXE overlays lines beginning with IBM carriage control + onto the previous line. It reads from standard input and writes to standard output. The + carriage control method is used by NUMARIT to superimpose particular items of output onto more general output lines
• The present author's DOS program NUMPRNED.EXE selects from NUMARIT textual output what, in his opinion, are the important parts to keep or print as a record of a successful simulation or fit. It reads from standard input and writes to standard output.

Disclaimer

The author makes no commitment to remedy reported bugs or make suggested improvements, but nevertheless would welcome comments from users.
  They should be sent to:
  Bruce.Tattershall@ncl.ac.uk

Introduction
Using NUMARIN
Using NUMTRUN
Using NMPLOT
Using NMMIX
History
 

Using NUMARIN

• Input files for NUMARIT have the file name extension .num
• NUMARIN can start a completely new .num file, and in a new run of the program, the screens of its wizard will contain default values or items which must be altered by the user before the user can proceed to the next screen
• If, after completing this file, the user starts a second new .num file within the same run of the program, the previous data will remain filled in as defaults for the new, making it easy to produce related files, e.g. for different isotopomers of a compound
• The user has the option of making a completely fresh start by clicking 'Clear All Data' in the first wizard screen
• To start the wizard to compose a new .num file, click 'Create New File'
• A standard Windows Save dialogue box appears, showing any .num files you have in the startup folder already
• Either select one of these to replace, or enter the name for a new file, but without the .num file name extension, which will be added by NUMARIN
• To use an existing .num file as a starting point, click the menu item 'File' 'Read Old File'
• A standard Windows Open dialogue box appears, showing the .num files in the startup folder
• You can navigate to other folders in the usual way
• Because of the variety of possible contents of a .num file set up for an iterative run of NUMARIT, NUMARIN will read only .num files which are set up for simulation runs, and it will compose only simulation .num files. If there is any chance that you will wish to start another simulation of similar data using NUMARIN, after altering a .num file for iterative use, it is best to keep a copy of the original file before alteration, to use as a starting point

(See Iterative Use in Help on NUMTRUN)
• On clicking Open the Open dialogue box will close, and a Save dialogue box, as for Create New File above, will open
• You may select the same file if you wish to replace it with the new version, so this gives a method of editing a file after running NUMARIT (using NUMTRUN) and NMPLOT
• As the new file is not opened for writing until the wizard finishes, you can experiment with the wizard without damaging an existing file, providing you do not click the Finish button at the end
• In each of the wizard screens which opens, although no edit menu is provided, you may use the standard Windows hotkeys of ctrl-C to copy data to, and ctrl-V to paste data from, the clipboard, in any of the data entry boxes. This allows e.g. the final parameters from a fit to be copied to the initial parameters for a new simulation, e.g. of the spectrum of a different isotopomer

 

 
 
 
 
 
 
 
 
 
 
 

Isotopic species screen

• You must enter a title of some sort
• In this screen, first set the 'Number of different isotopic species...', e.g. in a spin system consisting of phosphorus-31, selenium-77 and protons, this would be set to 3
• The limit for the number of species, set by NUMARIT, is 5, which is in excess of anything the author has ever used in real research
• The selected number of lines of the table change from grey to green, as they become active
• For each of these lines, use the drop-down list under Symbol to select the species. Most common, and some uncommon, isotopic species met with in practical high resolution solution NMR are included
• The name of the species appears under 'Isotopic species'
• The box under 'Transition listing required?' is ticked by default. If you do not require a transition listing for this species in the textual output from NUMARIT, perhaps because you do not have a well-resolved measured spectrum for this nucleus, click on the box to untick it. You will need a listing for any species for which you intend to fit an observed spectrum
• You must have species selected for all the green lines of the table before you can go on to the next screen
• If you set the number of species too high, you can reduce it again, when the unwanted lines of the table will be greyed
• Click the Next button to go to the chemical shifts screen

 

 
 
 
 
 
 
 
 
 
 
 

Chemical shifts screen

• In this screen, first set the 'Number of chemical shifts...' to the total number of different shifts for the spin system, including all of the isotopic species involved, if there is more than one
• The minimum setting is the number of species, i.e. you must have at least one chemical shift for each species, or 2 if there is only one species, since there would be nothing to couple if there were only one shift
• Include as separate shifts any which are equal by accident rather than symmetry
• For systems with twofold symmetry, e.g. AA'BB', count the AA' pair (and each other pair) as a single shift. (You may count them separately, and use up more chemical shifts from the 7 allowed, but this tends to lead to more confusion. NUMARIT has an excellent mechanism for dealing with twofold symmetry pairs, which you are recommended to use. There is no corresponding provision for C₃ symmetry, so the maximum spin system in that case is AA'A''BB'B''M, as in P₇I₃, which uses the maximum capability of NUMARIT)
• The selected number of lines of the table become green and active
• The first species in the table of the species screen becomes the default for the first two active chemical shift lines, but if you change the number of selected lines to more than two, the remaining selected lines have the last specified species as their default. This seemed the best compromise to cover the common cases of one or two species
• Use the drop down lists under 'Isotopic species', which offer only those species selected in the first screen, to change species for the chemical shift lines as necessary
• For each, enter the chemical shift in Hz for the operating frequency of the spectrum to be simulated
• The order of the chemical shift lines, in terms of which isotopic species they are for, does not matter. NUMARIN will sort them out as required according to species, but within a species it will retain the order of shifts used in this table, when presenting them to NUMARIT
• If there is only one chemical shift for an isotopic species, and you do not intend to fit transitions for it, e.g. the unobserved ¹⁹⁵Pt in a ³¹P-¹⁹⁵Pt system, you may leave its shift at the default value of zero. NUMARIT knows that different species have absorption frequencies 'an infinity' apart, even if they have the same chemical shift of zero
• Under 'No. of mag. equiv. nuclei' enter the number of nuclei in one magnetically equivalent group at this chemical shift, e.g. 3 for a freely rotating CH₃ group, or 2 for a pair of nuclei related by a molecular mirror plane which includes all nuclei coupled to them
• Leave the number as 1 for the A chemical shift of an AA'BB' spin system, because A and A' are not magnetically equivalent to each other
• If the nucleus, or magnetically equivalent group of nuclei, is one half of a twofold symmetry pair, such as the AA' pair above, tick the box under 'Mag. nonequiv. pair?'

 

 
 
 
 
 
 
 
 
 
 
 

Plots required screen

• NUMARIT does not have to produce plots of the simulated spectrum, so you may leave the 'No. of plot regions required' as zero, and proceed to the next screen
• For plots, set the 'Number of plot regions...' to the total number of plots required, including all of the isotopic species involved, if there is more than one. A maximum of 7 plots altogether is allowed per run of NUMARIT
• The drop-down lists under 'Isotopic species' are initially blank in this screen, so that, when you select a species, default peak widths may be set up
• Because relaxation times and hence peak widths for single transitions vary widely, even for the same isotopic species within the same molecule, no attempt has been made to tailor default peak widths to each isotopic species in NUMARIN's internal table. However, proton line widths, measured in 5 mm tubes in dilute solutions, tend to be considerably narrower than those for most other isotopic species, so a default half width at half height of 0.15 Hz is set for protons, and of 1.5 Hz for all other species. In the author's work in ³¹P and ⁷⁷Se NMR, using 10 mm tubes to study reaction mixtures, 3 Hz width at half height has been found ideal, with greater widths being set to account for scalar coupling relaxation, e.g. by ¹⁴N
• NUMARIT allows different widths for the left and right halves of peaks, to allow for skewed peaks caused by poor tuning, which was more common, using iron-cored magnets and CW acquisition, at the time NUMARIT was written. For modern spectra, the two half widths are usually set to be the same
• Set the widths under 'Left half width' and 'Right half width' to be half the measured width at half height of a single transition peak in the multiplet to be simulated, if there is one
• If paper plots of a measured spectrum at particular scales, e.g. 50 Hz/cm, are to be simulated, and at this scale a multiplet fits within a 25 cm width, then enter the required scale under 'Horizontal scale', and enter 'Left limit' and 'Right limit' to bracket the frequency of the centre of the multiplet. E.g. at 50 Hz/cm, a 24 cm plot allows 600 Hz above and 600 Hz below the centre of a multiplet
• If a particular scale is not required, the horizontal scale may be left at 0.0, when the plot will be scaled so that the requested left and right limits exactly fit
• If left and right limits are also left at 0.0, an overall plot of the spectrum for the isotopic species specified will be produced, but beware that in a widely spaced spectrum, the outermost peaks, while legible, may be very near to the edge of the plot. It is better, for an overall plot, to set the left and right limits to allow a sensible margin. Clearly, if the separation of chemical shifts is very large compared with couplings, as in some 31P spectra, there will be a problem of resolution in a an overall plot of a simulation, as there is in such a plot of a measured spectrum
• For a conventional NMR spectrum, the 'Left limit' will be more positive (or less negative) than the 'Right limit', but NUMARIT and NMPLOT can accommodate spectra with reversed scales, if necessary
• The vertical scale is the height of the tallest peak for this spin system in this plot region. The default is 15 cm, which is the maximum height which will be reproduced, and any larger number will be treated as if it were 15. A smaller vertical scale will result in peaks being shorter relative to the width of the plot
• A 'Region title' of up to 12 characters may be given, to help identify the plot window in NMPLOT, which otherwise will show only the isotopic species and the frequency range

 

 
 
 
 
 
 
 
 
 
 
 

Coupling constants screen

• This table shows entry boxes with default values of 0.0, for all the couplings required
• The rows and columns are labelled with the isotopic species and the chemical shifts of the nuclei which the coupling is to
• If chemically equivalent but magnetically non-equivalent pairs are present, a pair will occur in both a row label and in a column heading, though only the column heading will be marked as 'Pair'
• Couplings with the same label for both their row and their column are symmetric couplings, e.g. J(AA'), and are coloured blue in NUMARIN
• The two couplings between two pairs are coloured green and red respectively, so as to help the user keep track of which side of the molecule is which. The intended convention is that the in an AA'BB' system, J(AB) is coloured green while J(AB') is coloured red


Exit from the wizard

• Until you click the Finish button in the Coupling constants screen, you may use the Back buttons to go back to previous screens, and alter anything, or even to leave the wizard completely without writing the data to the file you have specified. Always use the Back button if it is desired to return to a previous screen: do not click on the title bar of a previous wizard screen to bring it to the top, if it becomes visible by accident, otherwise proper processing of the data will be bypassed
• Click Finish to write the data to the file
• In NUMARIN, the 'Run NUMARIT' button will be ungreyed, if NUMTRUN has been installed in the same program files folder as NUMARIN (see Setup)
• Click the Run NUMARIT button to run a calculation using the .num file you have just created
• Alternatively, .num files saved previously from NUMARIN may be selected from within NUMTRUN

Using NUMTRUN

• Input files for NUMARIT have the file name extension .num
• Click the Calculate from File button. A standard Windows file open dialogue box appears, allowing you to select the .num file required. The NUMARIT run starts immediately
• The file open box opens on the startup folder specified in the shortcut you use to run NUMTRUN (or NUMARIN, if you are coming from there), but you can navigate to other folders in the usual way. If you do so, beware that the temporary files created and destroyed by NUMTRUN, and its output files, will still be created in the startup folder, so it is important to set that up appropriately (see Setup)
• If NUMTRUN is called from NUMARIN, the last .num file to be written by NUMARIN is run automatically
• Because NUMARIT is run by a DOS .bat file, you may have time to see a DOS window with the message NUMARIT IS CALCULATING ... but this disappears when the calculation is complete
• The full textual output from NUMARIT, complete with IBM printer carriage control characters, is written to the file IBMPRINT.TXT in the startup folder. This is overwritten each time NUMARIT is run by NUMTRUN. You may need to examine it using Notepad if something goes wrong in the run, or if you want to look at each stage of an iterative fitting run. Beware that you will need to scroll the Notepad window horizontally to see the full width of the output correctly
• The most important parts of this textual output, without the carriage control characters, are written to the file NUMPRINT.TXT in the startup folder. This is overwritten each time NUMARIT is run by NUMTRUN, so you should use File Save As... in Notepad to save it with a different name, if you wish to keep it
• NUMPRINT.TXT includes the job title, the spin system, the starting chemical shifts and coupling constants, and if the job was iterative, the final RMS deviation and the final chemical shifts and coupling constants. This is followed by the calculated transition frequencies and intensities, against their NUMARIT transition numbers
• You may print NUMPRINT.TXT from Notepad. Although a few lines are longer than can be printed on A4 paper in portrait orientation in this way, the essential information for fitting an NMR spectrum all fits on the visible page
• The data in NUMPRINT.TXT are also copied to a scrollable window in NUMTRUN when the NUMARIT run ends, so that you can see the results immediately, without leaving NUMTRUN
• In the output window in NUMTRUN, text may blocked using the mouse, and copied to the clipboard using ctrl-C or the Edit Copy menu item. In this way, specific data may be copied and pasted, e.g. back into NUMARIN for Windows for the setup for another run. To copy all the output to the clipboard, it is easier to use Notepad to read NUMPRINT.TXT
• If plots have been requested in the .num file used, plot data will be written by NUMARIT to the text file NUMPLTS.EXT in the startup folder, replacing any previous version. In NUMTRUN, the Display Plots button will be ungreyed, if NMPLOT for Windows has been installed in the same program files folder as NUMTRUN (see Setup)
• Click the Display Plots button to view the plots using NMPLOT
• The NUMPLTS.EXT file may be saved as an .enm file from the File Save Plot File As... menu item in NMPLOT, so that these plots can be viewed later without having to set up and run NUMARIT again
• Plots may be printed from NMPLOT, or copied as bitmaps to other Windows applications, e.g. Word

Converting .num Files to Iterative Use

 The present author uses a Newcastle University column-oriented text editor which is now unsupported and not available for distribution, but he suggests Programmer's File Editor from Lancaster University, which appears to be eminently suitable freeware, currently available from:
http://www.lancs.ac.uk/staff/steveb/cpaap/pfe
A copy of the distribution .zip file from this web site is included with the present software.

Here is what needs to be done:

• In the first line of the .num file, change space to I in column 4 (immediately after the F)
• In the species line (i.e. the one giving the species name, e.g. Proton or Phosphorus) for each species for which you have observed peak frequencies to fit, change space to I in column 6 (immediately after the P if you have requested plot(s) for the species)
• After the chemical shift lines and any plot lines for this species (each such set ends in a line with an L in column 1), introduce a new line in which to start a table of your observed peak frequencies
• For each peak to be assigned, you need a line with the NUMARIT transition number (taken from the NUMPRINT.TXT output of a previous simulation or fit run for the system) right justified in columns 6-8 (i.e. a two digit transition number goes into columns 7 and 8) and the observed frequency, with a decimal point, left justified starting in column 21
• The items on the line are separated by space characters, NOT by TAB characters. If you are using Programmer's File Editor, set it to use 'Soft tabs' every 5 characters. This will enable you easily to reach columns 6 and 21 from the beginning of a fresh line
• Where there are several transitions close together in frequency, you may need to add several lines, with different transition numbers, but the same observed peak frequency
• The last transition line must have an L in column 1
• It is normal to try a fit with slightly more observed transitions than are needed to define the number of chemical shifts and coupling constants in the spin system, examine the textual output from NUMARIT, and then add further observations to the .num file if the observed frequencies are close to the predicted ones, and run the revised fit again. Scientific judgement and honesty have to be used to justify including or excluding observed peaks. Usually, the reason for inclusion is that the peak fits the simulation, both in frequency and in relative intensity. The reason for exclusion is that there is clear evidence that the measured peak position is being influenced by overlap of transitions, either within the spectrum of the observed molecule, or by peaks from observable impurities. In any case, you will usually wish to insert and remove some lines on a trial-and-error basis. These can conveniently be parked after a blank line at the end of the .num file, ready for possible future reinclusion
• Transition file lines do not have to be in order either of transition number or of frequency, but it is easiest to keep them in order of decreasing frequency
• If you do not supply enough appropriate observed transitions to define one of the coupling constants or chemical shifts, you must overwrite with spaces its parameter number, in columns 7-8 of the coupling constant line (line 2 of file onwards) or of the chemical shift line, and renumber any following parameters so that they remain sequential
• If you have more than one isotopic species in the spin system, but do not have observed peak frequencies for one of them, you need to space over the parameter number(s) of its chemical shift(s), as above

Using NMPLOT

• NMPLOT reads the fixed-name file NUMPLTS.EXT from its startup folder. This is a text file written by NUMARIT
• The Read Plot File button will appear greyed if NUMPLTS.EXT is not present in the startup folder
• To read NUMPLTS.EXT, click the Read Plot File button
• A window to the right of the screen, headed 'Contents of plot file calculated by NUMARIT' is filled with the data from the file, in a format for reading by the user.
• It includes the job title, the spin system, a list of chemical shifts labelled numerically, and a list of coupling constants between the nuclei at these chemical shifts
• Normally in the label for a coupling, the second chemical shift number is greater than the first
• Couplings labelled in the form 1-1 are symmetric couplings between chemically equivalent but magnetically non-equivalent groups in a spin system with twofold symmetry, e.g. the J(AA') coupling in AA'BB'
• (Note that in a pure AA'BB' system, there is no way, except by analogy of shifts and couplings with a similar unsymmetrical system, of telling which coupling is J(AA'), and which is J(BB'))
• In a twofold symmetry system, there will be one coupling with the second chemical shift number greater than the first, and a corresponding one in which the first is greater than the second, e.g. 1-2 and 2-1 These, respectively, are the J(AB) coupling and the J(AB') coupling
• The shifts and coupling constants are followed in the window by the name of an isotopic species, e.g. Proton or Phosphorus, and then by list of its calculated transition frequencies (in Hz) and relative intensities
• If there was more than one isotopic species in the spin system, and plot(s) for it was requested from NUMARIT, then another species name and a list of its transitions will follow
• The window will be left scrolled to the end of the data. In the language environment used for writing these Windows programs, there appears to be no provision for moving the scroll bar under program control in this kind of window, so the user should use the mouse to drag the scroll button up, so as to see the beginning of the data
• If, for any reason, it is desired to copy any of the text in this window to another program, it may be selected with the mouse and copied to the clipboard with ctrl-C or Edit Copy Text
• If NMPLOT is set up appropriately (see Setup) the whole contents of the listing window may be copied to Notepad by means of the 'File' 'Copy parameters to Notepad' menu item. Using Notepad's File menu, they may be printed or saved as some other file name, for storage, though this is not usually necessary, since they can be more easily regenerated by another run of NMPLOT using the same, much more compact, plot file. Similarly, large amounts of the data may be copied to the clipboard from Notepad
• NMPLOT creates a graphical plot window for each plot requested from NUMARIT (maximum of 7 per NUMARIT job)
• The titles (species name and frequency range) of the plots are added to a drop-down list at the right of the textual tool bar. If the screen becomes crowded, this may be used to select a different plot from the one currently selected (although it may not be used to come back from the listing window or blow up window to the currently selected plot: if it does not work, click a different plot in the list and then the one you want)
• On each plot window, there are 'Blow up mode' and 'Measure mode' radio buttons
• To blow up a region of a plot, click the Blow up button, then with the mouse, left drag a rectangular box to enclose the desired region. On releasing the mouse button, a Blow up plot window appears
• A blow up plot cannot be blown up further, but it does still have a 'Measure mode' button, and may be useful when peaks in a closely spaced group are to be measured
• Blow up plots cannot be sent to the printer (because the plot has to be recalculated from data in the file for this), but they can be copied and pasted as bitmaps to other programs
• When part of a plot is blown up, the aspect ratio of the selection box is retained. This means that if you select an area that uses most of the height of the window, very little magnification will result, because the blow up plot size will still be limited by the same vertical measurement. Selecting a smaller height of the plot, as well as less width, will result in more magnification.
• Generally, it is better to request a smaller frequency range and fewer Hz per cm from NUMARIT, as a separate plot, than to use the blow up facility in NMPLOT to an extreme extent. This can be done very easily on a trial and error basis if NMPLOT is called from NUMTRUN which in turn was called from NUMARIN, since NUMARIN will remember the original plot requests. The resolution in the blow up plot window is the same as in its parent window, limiting the precision of peak frequencies obtained in Measure mode, whereas a plot requested with fewer Hz per cm will have a higher resolution
• We have found that the limit of 7 plots per job imposed by NUMARIT (and hence by NUMARIN) is more than adequate for our need for expansions, but NMPLOT itself is configured for up to 20 plots. It is possible therefore, if it is required to have more expansions than 7 viewable at once, to introduce more plot requests into NUMPLTS.EXT, using a text editor, by copying and altering existing parts of the file. Each plot requires three file lines, inserted after the transition listing for the isotopic species concerned. All data must be in the correct columns exactly. Be careful not to introduce a blank line at the end of the file, as this will cause NMPLOT to crash
• Measure mode is used conveniently to find the frequency of a peak containing several transitions, for comparison with a measured spectrum, since only the transition frequencies are given in the NUMARIT listing
• To use Measure mode, click its radio button in the required plot window
• Measure mode stays selected only for a single measurement, so if several measurements are to be made, you need to click the button before each. This means that you can swap between windows at will when making measurements, e.g. when comparing peak separations in different multiplets
• Measurements appear in a permanent window, where they remain for comparison until another measurement is made
• To make a measurement, click on the plot with either the left or the right mouse button. A target will be written temporarily on the plot, showing the position which has been measured
• If you click with the left mouse button, the target will go to the nearest frequency on the plot to the point at which you click
• Generally much more usefully, if you click with the right mouse button, the target will go to the nearest point vertically on the spectrum. This means that if you right click moderately accurately above a peak, the target will drop onto the peak top, giving you a measurement of its position
• After each measurement click the Continue button which appears, to remove the target
• If NMPLOT is set up appropriately (see Setup) plots may be sent to a Windows printer, by means of the File Print Plot menu item
• A standard Print dialogue box opens, allowing the selection of a printer, or of Print to file, and, on clicking the Print button, the whole of the currently selected plot is printed
• If the requested plot is 25 cm or less wide, the hard plot should have exactly the Hz per cm scale requested. Wider plots will be scaled to an arbitrary scale, so that they fit
• The maximum peak height is 15 cm in the hard plot. If a greater height is requested, it will be reduced to 15 cm
• Whenever there are plot windows on the NMPLOT screen, the currently selected plot may be copied as a bitmap to the clipboard using the Edit Copy Plot menu item. From there it may be pasted into Word or Powerpoint
• While NMPLOT always reads the file NUMPLTS.EXT, stored plot files may be copied to NUMPLTS.EXT, replacing it, by means of the File Open Plot File menu item
• Stored NMPLOT plot files have the file name extension .enm
• A standard Windows file open dialogue box appears, allowing you to select the .enm file required. NMPLOT copies the file to NUMPLTS.EXT and reads it immediately
• The file open box opens on the startup folder specified in the shortcut you use to run NMPLOT (or NUMTRUN or NUMARIN, if you are coming from there), but you can navigate to other folders in the usual way
• Files copied from other folders will be copied to NUMPLTS.EXT in the startup folder in use
• When NMPLOT is called directly by NUMTRUN, it immediately reads the NUMPLTS.EXT most recently produced
• To save this as an .enm file, use the menu item 'File' 'Save Plot File As...'
• A standard Windows save dialogue box appears, showing any .enm files you have already in the startup folder
• Either select one of these to replace, or enter the name for a new file, but without the .enm file name extension, which will be added by NMPLOT. NMPLOT copies NUMPLTS.EXT to the file

Using NMMIX

Before running NMMIX
• NMMIX reads transition frequencies and relative intensities from the plot data files created by NUMARIT and saved as .enm files by NMPLOT
• Simulate, or preferably fit, the spectrum of each compound to be mixed
• In setting up the input files for NUMARIT, using NUMARIN or by hand using a text editor, request plots only for the isotopic species for which you require the mixed plots, or make this the first isotopic species in each input file
• NMMIX reads each plot data file only as far as the first plot request, and discards the rest
• The transition data it uses are for the isotopic species to which this plot request refers
• Except in locating the correct transition data for each compound, NMMIX does not use the plot ranges, linewidths etc. which you set up in the NUMARIT input files, because the overall plot range for the mixture is specified within NMMIX and linewidths are specified separately for each compound and for each spectral region at that stage
• You may like to specify the correct plot ranges, however, so that you could have NMPLOT and NMMIX running at the same time, enabling you to compare the spectra of single compounds with that of the mixture
• From the File menu in NMPLOT, save the plot data file for each compound as a .enm file

 

 
 
 

Running NMMIX

• On entry to NMMIX you will see, below the toolbar, two captive windows: a Control Panel and a Plot window
• Once you have generated a mixed plot, the Plot window will come to the front, but part of the Control Panel is always visible, so that you may activate it to change any of the mixture parameters, before generating a modified mixed plot

 

 
 
 

Define Compounds

• On entry, the default number of compounds is 2. You may increase this, to generate the spectrum of a mixture of up to five species
• You may also reduce the number of compounds to one, so as to view the spectum of one of the components, in the plot range you set up in NMMIX, but beware that when you reduce the number of compounds, any data that you have entered in NMMIX for compounds beyond that number, will need to be reentered if you increase the number again
• When you have set the appropriate number of compounds, that number of lines of the table will appear in green (instead of greyed out)
• For each green line, use the Browse button to find the .enm plot data file which you have stored for the compound
• A standard Windows file open dialogue box appears, allowing you to select the .enm file required.
• The file open box opens on the startup folder specified in the shortcut you use to run NMMIX, but you can navigate to other folders in the usual way
• If you know the relative integral of each compound, either by integrating a clearer region of the spectrum, or because you are dealing with coupling to isotopes so that relative abundance is known, enter it
• Note that the relative integral is not the same as relative peak height, even for non-overlapping peaks representing the same number of nuclei, unless the peak widths are the same. NMMIX takes account of peak width in calculating the heights of peaks from the relative integrals
• You may enter relative integrals on whatever scale is convenient, e.g. all as percentages or all as numbers less than one. Their sum need not be 100 or 1.0 respectively
• Enter the peak width at half height for each compound
• Note that this is the whole width of a single-transition peak, i.e. 1/(pi * T2) not half the width at half height as used in NUMARIT
• If there are no clear peaks visible for measurement in this multiplet of the compound, it may be necessary to guess a width and refine it experimentally in NMMIX
• NMMIX uses the same peak width for a compound for the whole plot region you specify, but you may alter it for different plot regions
• This may be a problem for AB spin systems etc., where one of the two nuclei close in chemical shift has a very different relaxation time from the other, e.g. because of scalar coupling relaxation by an atom directly bonded to one of them


Define Plot Region

• The left frequency limit must be set to a different value to the right frequency limit
• Horizontal scale may be left at zero, in which case the scale will be set to accommodate in 25 cm the frequency range specified
• Normally, horizontal scale should be set, so that printed plots will be on the same scale as paper plots from the spectrometer
• If the horizontal scale implies a plot wider than 25 cm, the specified frequency range will take precedence, and a non-intended scale will result
• The vertical scale of the plot is specified as the height of the tallest peak after combining overlapping transitions and mixing the spectra of the compounds
• The maximum allowed value is 15 cm to allow the plot to be printed on A4 paper in landscape orientation

 

 
 
 

Generate the plot

• Click the Mix plots button at the lower right of the Control Panel
• If you have provided file names for each of the number of compounds you have selected, and you have specified a non-zero frequency range for the plot, a plot of the mixture should be produced

 

 
 
 

The resulting plot

• If NMMIX is set up appropriately (see Setup) plots may be sent to a Windows printer, by means of the Print Plot button
• A standard Print dialogue box opens, allowing the selection of a printer, or of Print to file, and, on clicking the Print button, the whole of the currently selected plot is printed
• If the requested plot is 25 cm or less wide, the hard plot should have exactly the Hz per cm scale requested
• The maximum peak height is 15 cm in the hard plot
• The plot may be copied as a bitmap to the clipboard using the Copy Plot button. From there it may be pasted into Word or Powerpoint

History

The present author translated NUMARIT into Fortran 77, and compiled it as a DOS program for use in PCs in 1991

• The Fortran 77 translation was tested extensively by comparison of output with that from the original Fortran IV version, which was in all cases found to be identical
• The DOS version has been used by many research workers at the University of Newcastle, England, over a period of 15 years, in the identification of new phosphorus compounds by full analysis of their NMR spectra, and the results published, so this version has been very thoroughly validated against experiment
• The calculation parts of NUMARIT have not gone out of date because the computational errors in simulating an NMR spectrum are much less than the errors in measuring an NMR spectrum using a real NMR spectrometer, however modern. Simulations are almost instantaneous, and the numerical fitting method runs in a very satisfactorily short time, on a modern PC

• However, NUMARIT was written in the days of mainframe computers and punched card input, with wide-bed lineprinter output and roll-paper pen plotters as the only means of viewing the results
• A first priority was to develop a program to display graphical output on a microcomputer screen, instead of waiting for hard plots to be delivered by the mainframe service. This became the DOS version of NMPLOT, which has remained in use until now. When NUMARIT was ported to DOS in 1990-91, output in the same standard text file format was retained, so that all plotting was done via NMPLOT
• The alternative simulation and fitting program LAOCOON was translated and provided with a plot output routine to produce data in the same format as NUMARIT, so that it could also be read by NMPLOT (though in fact the author has done nearly all his research in phosphorus chemistry using NUMARIT rather than LAOCOON)
• A version of NMPLOT for DOS with output in HP Graphics Language allowed output to Hewlett Packard pen plotters and later to laser printers, thus providing hard copy
• Editing input files for NUMARIT using a screen editor is perfectly possible, but the formatting of an exactly determined order of lines, keeping data in exactly the right columns (as for a punched card system) was error-prone and frustrating in the hands of inexperienced research students, so the original, conversational DOS version of NUMARIN was written, and even the present author found it easier to use it for his personal research work, than to compose the input files from the beginning using a screen editor. It also has remained in use until the present.
• Making up NUMARIT input involves making a series of decisions, each of which depends on those made previously. Thus, conversational NUMARIN asked the user how many isotopic species were involved in the spin system, and then for each it asked what its name was, how many different chemical shifts there were for it, etc.
• Conversational NUMARIN protected the user from most kinds of typographical input errors, and suggested useful default replies, but if an inexperienced user misunderstood what was being done, and gave a possible but incorrect reply, there was no way of backtracking through the conversation. The program had to be restarted, or the resultant file had to be altered with a text editor

• It was decided in 2007 to rewrite NMPLOT and NUMARIN as Windows applications, while retaining the same file formats (and naming) for transfer of data from and to NUMARIT.

• The Windows equivalent of a structured conversation is a wizard with several screens, the content of each depending on those which have gone before.  Users are permitted to go to the next screen only when they have made all necessary decisions in the previous one.  NUMARIN for Windows uses this wizard method
• NUMARIN for Windows allows users to go back to previous screens and change previous decisions, in contrast to its conversational predecessor, but because all decisions update data in memory used to initialise the screens of the wizard, the user is presented, on going forward again to the next screen, with the results of their earlier decisions there as defaults for a new attempt
• Free movement forwards and backwards through the screens of a wizard allows simulation data to be tailored easily, and existing NUMARIT simulation input files may be read in and altered, as well as new ones set up

• NMPLOT for Windows allows free movement between all of the plots generated by a job, as well as blow-up and peak measurement facilities. Use of Windows graphical output facilities avoids the use specifically of HPGL, and plots can be copied as bitmaps directly to other applications, e.g. Word.

• The present Windows program NUMTRUN is simply a shell to call the practically unchanged program numarit.exe

• In Version 2, the provided numarit.exe has been compiled in Salford ClearWin+ Fortran 90, so that it will run in 64-bit Windows 7 as well as behaving as a DOS program in earlier Windows versions, from Windows 95 to Windows XP
• A second copy of numarit.exe is provided as numarit3.exe, as well as the 16-bit numarit2.exe provided in Version 1 of NUMTRUN
• In Windows XP or earlier, the user may choose to use numarit2.exe for the calculations, as in Version 1, by copying numarit2.exe to numarit.exe. To return to using numarit3.exe, which will run also in Windows 7, numarit3.exe may copied to numarit.exe
• While numarit2.exe reproduced exactly the results from the Numarit of the original authors, the rounding errors are slightly different in numarit3.exe. This is seen in some predicted transition frequencies and fitted chemical shifts and sometimes in the predicted intensities of transitions. Only seven significant digit precision is available in Numarit, whereas the output of frequencies shows eight digits, so the third decimal place is unreliable for high (or very negative) frequencies. These are met for species other than 1H, when the calculated standard deviations of fitted transitions show clearly that the third decimal place must be neglected, so the rounding errors do not in fact constitute a practical problem

• NMMIX for Windows was added later, purely as a Windows application. It was conceived in response to a colleague who was simulating non-first order spectra of observed nuclei which also showed couplings to boron. Besides the known relative abundances of the two boron isotopes, it was necessary to experiment with different linewidths caused by scalar coupling relaxation
• By taking data on transitions from the data transmission text files used and stored by NMPLOT, NMMIX was able to use much of the code written for NMPLOT. Case data such as chemical shifts and coupling constants, which are contained in the NMPLOT files and displayed by it, are discarded by NMMIX as it reads the files for successive compounds, so it is unable to rewrite a combined plot file in the same format. However, as little data is input to NMMIX, it is easy to rerun it if alterations are required. The resulting plots may be printed or copied just as in NMPLOT. The present version does not allow on-screen blowup or peak measurement

• The present Windows implementation of the NUMARIT suite is published by permission of EPSRC, the successors to SERC, the publishers of the original version
• NUMARIN, NUMTRUN, NMPLOT and NMMIX for Windows are written in Salford ClearWin+ Fortran 90

Introduction
Setup
Using NUMARIN
Using NUMTRUN
Using NMPLOT
Using NMMIX