DNMR3 for Windows

The DNMR3 plot on the right is a good simulation of an NMR spectrum at room temperature which we obtained.  It is clearly of a molecule undergoing chemical exchange.  The high frequency multiplet, when expanded, appeared as shown below on the left, whereas it might have been expected to be the simple doublet of doublets shown below that.  The compound was P3Se4I, which was made by Prof. R. Blachnik's group at the University of Osnabrueck, and which he sent to the present author as the first of a series of related compounds for NMR analysis.
		In the chemical exchange, in solution in CS2, the iodine substituent migrates from PB to PA, as Sed becomes connected to PB instead of to PA.  The result is that PA and PB exchange their roles, while PC maintains its role, and the product is the enantiomer of the structure shown here.  Because PC maintains its role, its chemical shift does not change, and peaks in its multiplet which are separated by a sum of coupling constants which does not change, remain sharp, as shown above on the left.
The appearance of dynamic NMR spectra depends on the chemical shifts and couplings constants of the molecule(s), and on the first-order rate constant(s) of the process at the temperature at which the spectrum is measured.  The first step in analysis is usually to measure another spectrum, at as low a temperature as is safely accessible for the accumulation of good quality data.  In favourable cases, the exchange may then be slowed down to the point at which the spectrum resembles that of a static system, and may be fitted, e.g. by NUMARIT, to obtain the chemical shifts and coupling constants.  In the present case, we reached 240 K, when the PC , PB and PA multiplets appeared as on the right. It then remains to find the rate constant(s) for each temperature at which the spectrum can be measured, when the enthalpy and entropy of activation, and hence something about what mechanism is taking place, may be found by fitting the rate constants and temperatures to Eyring's equation. In cases where there are only broad peaks, for nuclei which change their roles in the exchange process, as for PB and PA in the room temperature spectrum at the top of this page, peak shape fitting software may be used to obtain rate constants, but it is still quite difficult to produce accurate results.  In contrast, in cases such as the present, where there is a 'spectator' nucleus (PC) it is quite easy to obtain good results by calculating simulations for a series of rate constants and then interpolating the observed multiplet structure.  For this, DNMR3 is ideal, as explained in the Introduction below.
		In the present case, further data may be obtained by simulating the 77Se satellite spectra in the 31P NMR.  In the exchange reaction, when PA exchanges roles with PB, Sea exchanges its role with Seb.  There is a about a 15% chance that either Sea or Seb will be 77Se (with spin 1/2) while the other will be NMR-inactive selenium.  The reaction will interconvert isotopomer a (with 77Se as Sea) and isotopomer b.  This is a non-mutual exchange, since a different isomer is produced, whereas the main 31P spectrum is for a mutual exchange, since an enantiomer indistinguishable by NMR is produced.  A satellite spectrum for the (isotopomer a / isotopomer b) pair is observed for the PC atom, in which there are changes with temperature additional to the those for  the main spectrum multiplet.  A DNMR3 simulation of this satellite spectrum at 285 K is shown on the left. Sec and Sed do not change their roles in the exchange, and multiplets may be observed for them in the 77Se NMR spectrum at room temperature, and simulated using DNMR3.  Even though Sed is switching its connection between PA and PB, it has the same role in either enantiomer.

Preface
Installation
Introduction
Using DNM3RUN
.nm3 Input Files for DNM3RUN
Using N3PLOT
Setup
History

Preface

While other dynamic NMR simulation and fitting programs are available, some of them as freeware, including at least one implementation of DNMR3 itself, the present suite of Windows programs has been created entirely by the present author to reflect his preferences and experiences with DNMR3, as a practising synthetic chemist and spectroscopist.

The package includes a folder of examples, provided both as input files for DNMR3 and as input files of plots for the new plotting program N3PLOT for Windows, drawn from the present author's experience of ³¹P and ^77Se NMR and of teaching NMR analysis as a practical subject to university chemistry undergraduates.

A file  inputfmt.htm is included in the package, giving the present author's explanation of the format required in making up input files for DNMR3.  The original authors' documentation was a masterpiece of both accuracy and brevity, but was aimed at users with an understanding both of dynamic NMR and of Fortran programming.

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 dnm3runw.exe and n3plotw.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 dnm3we.zip.  This is the distribution file for Programmer's File Editor, which you may wish to use for editing input files for DNMR3.  See .nm3 Input Files for DNM3RUN  .  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
Using DNM3RUN
.nm3 Input Files for DNM3RUN
Using N3PLOT
Setup
History

DNMR3 for Windows

Introduction

DNMR3 simulates dynamic high-resolution NMR spectra of spin systems with up to four chemical shifts in each of two exchanging configurations, or up to three chemical shifts when exchanging between three configurations.

• Unlike DNMR5, DNMR3 lacks an iterative peak shape fitting ability, and is purely a simulation program
• It is useful for producing simulations of known systems for teaching purposes, but in research it is really useful in cases where one or more spin-1/2 nuclei do not change their structural role in the chemical exchange, but couple to nuclei which do change their role
• The multiplet due to the 'spectator' nucleus will then contain some sharp lines and some broadened by the exchange
• If this multiplet is simulated for a series of rate constants, and the ratio of the height of a sharp peak to that of a broad peak is measured in each case, a calibration graph may be constructed relating rate constant to this ratio. The corresponding ratios, measured in a set of experimental spectra, may then be interpolated and hence experimental rate constants may be found for the temperatures of the experiments
• Judging the position of the baseline for the experimental multiplet and allowing for any transitions from other spin systems, e.g. from isotopomers, which overlay the peaks to be measured, are the only serious sources of error, and good Eyring plots and correspondingly accurate enthalpies and entropies of activation may be obtained
• N3PLOT was designed to make it easy to select peaks using the mouse, and to display their heights

• DNM3RUN to run the calculations
• N3PLOT to display the resulting plots of regions of the simulated spectra, and optionally to print them or export them to other programs

• Frequency scales for plots can be specified for DNMR3 and, providing they will fit onto A4 paper, N3PLOT will produce printouts at these scales, so that they may be compared exactly with plots of experimental spectra

See History

Using DNM3RUN
.nm3 Input Files for DNM3RUN
Using N3PLOT
Setup
History

History

The present author translated DNMR3 into Fortran 77, and compiled it as a DOS program for use in PCs in 1991

• Only the minimum of alterations of were made, to handle character data using character variables, and to attach files from within the program
• The format of the plot specification line in the input was changed to resemble that of NUMARIT, with the same ability to name the plot region, and the same method of specifying maximum height of the plot
• The plotting routine was altered to write data to a text file, NM3PLTS.EXT which was read by a separate program to produce the plots
• 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 N3PLOT, which has remained in use until now. When DNMR3 was ported to DOS in 1991, output in the same standard text file format was retained, so that all plotting was done via N3PLOT
• N3PLOT for DOS allowed the measurement of relative peak heights, using the mouse, greatly facilitating the use of the program to obtain experimental rate constants for certain kinds of exchanging systems (see Introduction)
• A version of N3PLOT for DOS with output in HP Graphics Language allowed output to Hewlett Packard pen plotters and later to laser printers, thus providing hard copy

• In 2007 it was decided to rewrite N3PLOT as a Windows application, while retaining the same file format (and naming) for transfer of data from DNMR3. N3PLOT 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 DNM3RUN is simply a shell to call the practically unchanged program dnmr3.exe
• In Version 2, the provided dnmr3.exe has been compiled in MinGW Fortran, so that it will run in 64-bit Windows 7 or in Windows XP
• A second copy of dnmr3.exe is provided as dnmr34.exe, as well as the 16-bit dnmr32.exe provided with Version 1 of DNM3RUN
• The MinGW Fortran compilation dnmr34.exe will not run in Windows 95 nor Windows 98
• In Windows XP or earlier, the user may choose to use dnmr32.exe for the calculations, as in Version 1, by copying dnmr32.exe to dnmr3.exe. To return to using dnmr34.exe, which will run in Windows 7, dnmr34.exe may be copied to dnmr3.exe
• The rounding errors in dnmr34.exe are slightly different to those in dnmr32.exe, as a result of the compiler used, even though no changes were made to the source code for the calculation, between the two versions. As far as the present author has tested the program, these rounding errors are insignificant. They are not seen in the graphical output produced by N3PLOT, and do not change the peak frequencies or peak heights reported by N3PLOT in Measure mode. Dnmr34.exe produces identical results when it is run in Windows XP as when it is run in 64-bit Windows 7
• The present Windows implementation is published by permission of EPSRC, the successors to SERC, the publishers of the original version
• DNM3RUN and N3PLOT for Windows are written in Salford ClearWin+ Fortran 90

Using DNM3RUN

• Input files for DNMR3 have the file name extension .nm3
• Some .nm3 files are provided with the programs as examples
• For the information on preparing .nm3 files, see .nm3 Input Files for DNM3RUN
• Click the Calculate from File button. A standard Windows file open dialogue box appears, allowing you to select the .nm3 file required. The DNMR3 run starts immediately
• The file open box opens on the startup folder specified in the shortcut you use to run DNM3RUN, but you can navigate to other folders in the usual way. If you do so, beware that the temporary file created and destroyed by DNM3RUN, and its output files, will still be created in the startup folder, so it is important to set that up appropriately (see Setup)
• Because DNMR3 is run by a DOS .bat file, you may have time to see a DOS window with the message DNMR3 IS CALCULATING ... but this disappears when the calculation is complete
• The full textual output from DNMR3, complete with a few IBM printer carriage control characters, is written to the file NM3PRINT.TXT in the startup folder, which is copied to a scrollable window in DNM3RUN when the DNMR3 run ends, so that you can see the results immediately, without leaving DNM3RUN
• This is overwritten each time DNMR3 is run by DNM3RUN.
• In the output window in DNM3RUN, text may blocked using the mouse, and copied to the clipboard using ctrl-C or the Edit Copy menu item.
• Plot data will be written by DNMR3 to the text file NM3PLTS.EXT in the startup folder, replacing any previous version. In DNM3RUN, the Display Plots button will be ungreyed, if N3PLOT for Windows has been installed in the same program files folder as DNM3RUN (see Setup)
• Click the Display Plots button to view the plots using N3PLOT
• The NM3PLTS.EXT file may be saved as an .en3 file from the File Save Plot File As... menu item in N3PLOT, so that these plots can be viewed later without having to set up and run DNMR3 again
• Plots may be printed from N3PLOT, or copied as bitmaps to other Windows applications, e.g. Word

.nm3 Input Files for DNM3RUN

• 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.
• 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
• For a full description of the format of the files, see  inputfmt.htm
• The format of the files is as described in the documentation for the original DNMR3 program, except for the plot line ("Item 7"), which is as follows
• Columns 1-2

No. of (sets of) rate constants, right justified
• Columns 11-20

Left frequency limit in Hz, with decimal point
• Columns 21-30

Right frequency limit, with decimal point
• Columns 31-40

Frequency scale in Hz per cm, with decimal point
• Columns 41-50

Height of the tallest peak in the plot, as a fraction of 25 cm. Values up to 0.6, i.e. 15 cm, are allowed by N3PLOT, with larger values being reduced to this to allow plotting on A4 landscape paper
• Columns 51-62

(Optional) title for the plot region, for use in the title bar of N3PLOT windows
• If several plot regions are required (for several rate constants), the .nm3 file should contain the corresponding number of copies of the input data, one after the other with no blank lines in between them, one for each plot region desired, but with the plot line differing in each
• Each of these 'runs' should produce plots for the desired number of rate constants, though this may be different for different plot regions
• The maximum number of plots which can be handled by N3PLOT for Windows is 20, so the sum of the number of (sets of) rate constants over the number of plot regions should be 20 or less. If this causes a difficulty, the whole task should be spread over more than one .nm3 file and use of DNM3RUN and N3PLOT
• Where several runs for a single chemical system are to be concatenated in an .nm3 file, the "run number" in columns 1-3 of the first line of each copy of the data may be the same

Using N3PLOT

• N3PLOT reads the fixed-name file NM3PLTS.EXT from its startup folder. This is a text file written by DNMR3
• The Read Plot File button will appear greyed if NM3PLTS.EXT is not present in the startup folder
• To read NM3PLTS.EXT, click the Read Plot File button
• A window to the right of the screen, headed 'Contents of plot file calculated by DNMR3' is filled with the data from the file, in a format for reading by the user.
• It includes the job title for each job in the original .nm3 file which has a different 'run number'
• For each such job it lists, for each plot region, the plot region name (if supplied in the .nm3 file), the frequency range and scale of the plot, and the value of T2 used (i.e. 1/(pi * (width at half height)) for a single-transition peak not broadened by the exchange)
• N3PLOT creates a graphical plot window for each plot requested from DNMR3 (maximum of 20)
• The titles (frequency range and rate constant(s)) 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
• 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 DNMR3, as a separate plot, than to use the blow up facility in N3PLOT to an extreme extent
• 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
• Measure mode is used conveniently to find the heights of peak tops above the baseline for a multiplet
• 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 heights in different multiplets
• Measurements appear in a permanent window, where they remain for comparison until another measurement is made
• They may be selected individually with the mouse and copied to the clipboard using ctrl-C

This is useful for tabulating peak heights in order to make a calibration graph of a peak ratio versus log(kr)
• 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 N3PLOT 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 N3PLOT 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 N3PLOT always reads the file NM3PLTS.EXT, stored plot files may be copied to NM3PLTS.EXT, replacing it, by means of the File Open Plot File menu item
• Stored N3PLOT plot files have the file name extension .en3
• A standard Windows file open dialogue box appears, allowing you to select the .en3 file required. N3PLOT copies the file to NM3PLTS.EXT and reads it immediately
• The file open box opens on the startup folder specified in the shortcut you use to run N3PLOT (or DNM3RUN, 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 NM3PLTS.EXT in the startup folder in use
• When N3PLOT is called directly by DNM3RUN, it immediately reads the NM3PLTS.EXT most recently produced
• To save this as an .en3 file, use the menu item 'File' 'Save Plot File As...'
• A standard Windows save dialogue box appears, showing any .en3 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 .en3 file name extension, which will be added by N3PLOT. N3PLOT copies NM3PLTS.EXT to the file

Setup

• This software will run in Windows95, Windows XP or 64-bit Windows 7 environments
• As received, it will run in Windows XP or Windows 7.  It must be modified to make it run in Windows 95 or Windows 98
• To do this, copy the provided file dnmr32.exe to dnmr3.exe, thus replacing the provided version of dnmr3.exe.  After this modification, the software will run also in Windows XP, but not in 64-bit Windows 7
• To reverse the modification, copy the provided file dnmr34.exe to dnmr3.exe
• 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 DNM3RUNW.EXE and N3PLOTW.EXE are stored. These libraries are commercial products, but you are permitted to take copies of them without charge
• The provided files DNM3RUN.BAT, N3PRUN.BAT and DNMR3.EXE *** must *** be in the same programs folder as DNM3RUNW.EXE.   See Warning about Folder Names for Installation for advice on naming the folder
• If DNM3RUN is to call N3PLOT, the file N3PLOTW.EXE must also be in the same programs folder
• DNM3RUN deletes all files with the extension .$$$ in its startup folder and creates the files NM3PRINT.TXT and NM3PLTS.EXT in its startup folder, overwriting any previous versions of these
• *** IT IS ESSENTIAL *** that you start DNM3RUNW.EXE in a folder which does NOT contain any files which you wish to keep, which have either the name extension .$$$, or which have either of the names NM3PRINT.TXT or NM3PLTS.EXT
• Conveniently, the startup folders for DNM3RUN and N3PLOT should be the same NMR simulation data folder, in which you will keep the .nm3 and .en3 files used by the programs
• See Warning about Folder Names for Installation for advice on naming the startup folder
• To set the startup folders, drag shortcuts for DNM3RUNW.EXE and N3PLOTW.EXE from Windows Explorer onto your desktop, and rename them DNMR3 and N3PLOT respectively. Create a suitable data folder. Right click on each of the two shortcuts in turn, click Properties and alter the Start in: folder to be your data folder. Apply and OK
• Under Windows XP, DNM3RUN alternatively may be started by dragging and dropping a .nm3 file from Windows Explorer onto DNM3RUN's icon. The calculation will start immediately and the output files will be written to the startup folder specified in the shortcut
• If you leave the shortcut to N3PLOTW.EXE with just the program file name in the target field, N3PLOT started from this shortcut will not allow printing of plots from the program. This is for use in classroom situations where extensive printing may not be desirable
• To start N3PLOT 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
• 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
• A typical target field would be

... N3PLOTW.EXE P=600
• DNM3RUN calls N3PLOT via the batch file N3PRUN.BAT so as to provide you with a mechanism for setting up your use of a printer with N3PLOT
• As it is downloaded, N3PRUN.BAT will call N3PLOT with no possibility of printing plots (except by copying and pasting to other programs)
• If you wish to be able to print plots from N3PLOT called from DNM3RUN, use Notepad to modify N3PRUN.BAT, following the instructions contained within it

• DNM3RUN.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 .nm3 file to be used for input
• DNMR3.EXE reads the input file INPTONM3.$$$, and writes its textual output to RAWP.$$$ and its plot data to NM3PLTS.EXT, all in the folder in which DNMR3.EXE is started

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 DNM3RUN
.nm3 Input Files for DNM3RUN
Using N3PLOT
History