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-
- *******************
- gNMR GUIDED TOUR
- *******************
-
-
- Welcome to the gNMR GUIDED TOUR. We hope you will find it useful
- in finding your way around the gNMR demo v 3.6.5.
-
-
-
- NMR Simulation for Windows and Macintosh
- ****************************************
-
- If you need a versatile software package to speed up your analysis of spectral
- data, then take a look at gNMR! This short guided tour of the program takes you
- through several examples and lets you see how easy it is to use.
-
-
- Terminology
- ***********
-
- This guide covers the use of both Macintosh and Windows versions. Where there is
- a difference in the command or filename, written, the Macintosh instructions are
- in brackets immediately after the Windows instructions.
-
- The use of various symbols has also been made to indicate keyboard presses:
-
- <Tab> = Tab key
- <Ctrl>+ = Hold Control key (Windows) or Command key (Mac) while pressing
- additional key
-
-
- Limitations of the demo
- ***********************
-
- This demo contains a fully functional version of the gNMR main simulation
- program, with only the following two differences:
-
- * You cannot save files
-
- * Printed output, clipboard copies, and sometimes screen displays of spectra will
- have the word "DEMO" in big letters over it.
-
- The full gNMR package contains several auxiliary programs for importing and
- editing spectra. With it, you will receive a manual that not only documents gNMR
- itself but also explains in detail how to use simulation to interpret NMR
- spectra.
-
- The size of systems gNMR can handle is determined mainly by the amount of RAM in
- your system. A system of 10 inequivalent nuclei is usually the limit. See Step 8
- on Simulatating Large Molecules for more details.
-
-
- NMR simulation - an introduction
- ********************************
-
- gNMR has been designed to help the simulation process right from the start of
- entering information through to the data processing and actual simulation. gNMR
- places particular emphasis on the analysis of second-order effects and allows the
- direct comparison between experimentally acquired NMR data and simulated spectra.
- gNMR can also help distinguish between reaction mechanisms of rearrangements via
- inter- and intramolecular exchange processes.
-
- Exact calculation of higher-order spectra for larger molecules can take a lot of
- time and memory. gNMR will typically handle systems with up to 10 or 11 nuclei
- (chemical-exchange calculations are limited to even smaller systems). In the
- presence of symmetry or magnetic equivalence, you may be able to handle slightly
- larger systems. If you try to do a simulation of a molecule that is too large for
- gNMR, you may see a warning message suggesting that you save your data first (we
- recommend that you do so). It is particularly easy to enter too-large systems
- when you use structure import (Step 4 of this demo) and Step 8 gives some hints
- for doing simulation of larger molecules. Simulation can be a process of trial
- and error in an attempt to achieve the best fit between experimental and
- simulated data, the process of assignment and full-lineshape iteration (see Step
- 7) will help match simulated data to your experimental results.
-
- ***************************************************************
- * Step 1: Simulating a simple first-order spectrum of ethanol *
- ***************************************************************
-
- Getting started
- ***************
-
- Double-click on the gNMR program icon in your gNMR working directory to start
- gNMR. It will start with the File Options dialog, in which you can set various
- parameters including spectrometer frequency. Click on OK to accept the default
- settings. The Molecule window will appear, in which you can enter shifts,
- coupling constants etc. for a single molecule.
-
-
- Entering data
- *************
-
- Let us first simulate the spectrum of very pure ethanol. Press <Tab> to move to
- the column labelled Group #n (number of nuclei). Enter a "3" (the CH2 group, 3
- equivalent hydrogens) and press <enter> to move to the next row. Enter a "2" (the
- methylene group), press <enter>, and enter a "1" for the OH group. Now we have
- the nuclei we need we will enter their chemical shifts. Press <enter> twice to
- move to the top of the next column, and then type "1.3",<enter>, "3.7", <enter>,
- "5.0". The next column contains linewidths, which we don't need now. Press
- <(enter>, <enter>, <Tab> (to skip to the next column) and enter the coupling
- constants: "7.5", <Tab>, "6.0".
-
- These are all the data we need: now click on the Recalculate button to calculate
- the spectrum . A new window will appear containing the spectrum.
-
- Once you have a spectrum on the screen, you can change its appearance in a number
- of ways.
-
- Clicking the arrow button-bar buttons (or choosing their menu equivalents) lets
- you expand or contract the spectrum. Dragging in the empty area immediately above
- the spectrum lets you move the spectrum; by Shift-dragging in the same area you
- can select a subspectrum. To return to the full spectrum choose Plot|Full
- Spectrum.
-
- The Plot|Options dialog gives more precise control over many aspects of your
- spectrum display. You can also copy or print the spectrum (it will have the text
- DEMO over it).
-
- **********************************************
- * Step 2: Simulating a second order spectrum *
- **********************************************
-
- Now, change the chemical shift of the CH3 group to "3.3" by clicking on the
- number "1.3" in the Molecule window and entering the new value; click on
- Recalculate to calculate the new spectrum. Click on the Spectrum window to bring
- it to the front. This will look much more complicated: the close proximity of the
- CH3 and CH2 groups results in strong second-order effects. Now change the shift
- value back to "1.3" , Recalculate and move to the spectrum window.
-
-
- ********************************************
- * Step 3: Adding chemical exchange effects *
- ********************************************
-
- Usually, ethanol contains some acidic impurities that exchange with the hydroxyl
- proton and cause loss of the CH2-OH coupling. Let us try to simulate this (this
- exchange calculation will take a while on a slow system, it takes 20 seconds on a
- Pentium 90, 3 minutes on a Quadra 650 running the FPU version, or 35 seconds on a
- PowerMac 8100). Select Molecule|Go To|Molecule 2 to add a second molecule to this
- "sample". Set its chemical shift to 9.5 ppm (it is acidic after all). Click on
- the Options button of this window, set the concentration to "1e-5" and click OK.
-
- If you recalculate the spectrum now (Plot|Go To Window|Window 1), a larger range
- is shown (to include the peak at 9.5 ppm, which is too small to show), but
- otherwise the spectrum would be unchanged.
- Now select Molecule|Exchange. Enter a rate ("10") and then press <enter>, "=",
- <enter>(, "=", <enter>, "2-1", <enter>, "1-3".
-
- What you have entered are the positions that each nucleus moves to in the
- exchange reaction. From the ethanol molecule, nuclei 1 and 2 do not move ("="),
- but the third one moves to the position of Molecule 2 - nucleus 1 ("2-1") and
- vice-versa ("1-3").
-
- All done? Press <Ctrl>+1(on the Mac :command key - 1) (equivalent to Plot|Go To
- Window|Window 1) to recalculate the spectrum.
-
- This example has also been prepared: ethanol.dta
- (on the Mac : ethanol exchange).
-
- This may take some time: exchange calculations, especially intermolecular ones,
- take much longer than normal simulations.
-
- Play a bit with the rate to see which value gives the strongest broadening and
- what rate you need to see the fast-exchange limit.
-
- **************************************************
- * Step 4: Importing data via chemical structures *
- **************************************************
-
- Pasting in structures
- *********************
-
- gNMR can import chemical structures drawn with a number of chemical drawing
- packages. Among the DEMO files, you will see ChemDraw, ChemIntosh and ISIS/Draw
- files for o-chloro-aniline; we will show how to import these in gNMR. Now import
- a structure file by choosing File|Import Molecule and selecting either
- oca.cd2 (on the Mac : o-Chloro-Aniline (ChemDraw)),
- oca.cw2 (on the Mac : o-Chloro-Aniline (ChemIntosh)) or oca.mol file (ISIS/Draw
- for Windows only).
-
- Note: If you have one of these programs, you can also open the file from
- within its creator program, copy the molecule to the clipboard, and then paste it
- into an empty gNMR Molecule window using Edit|Paste Molecule.
-
- A dialog will appear. Click on OK to use the defaults. gNMR will now take some
- time to read in the structure and try to predict shifts and coupling constants.
- This procedure uses a fragment list to help predict the shifts and coupling
- constants and the predicted values provide a good starting point for the
- simulation process.
-
- After this, the Structure window appears, showing the molecular structure and
- fields to enter parameters. Click on the aromatic proton to the left of the NH2
- group and then enter a value for its linewidth (L.W.) field ("0.5"). Then click
- on one of the NH2 protons (the one that results in a display of parameter values)
- and enter a much larger linewidth ("10"). Finally click on the Recalculate button
- to compute the spectrum. If you want to change parameters, you can do so via the
- Structure window and/or the Molecule window used in the previous example.
-
- ************************************************
- * Step 5: Dealing with other NMR-active nuclei *
- ************************************************
-
- Other nuclei
- ************
-
- Chlorine consists of a mixture of 35Cl and 37Cl, both with spin 3/2. Normally,
- you don't see any coupling to Cl in NMR because relaxation is rapid. But in a
- simulation you can change this. Click on the Cl atom and then on the Add button.
- Then Shift-click on the hydrogen next to the chlorine, and enter a value of 40 in
- the Jij field. The molecule will now contain an NMR-active chlorine atom with a
- coupling constant of 40 Hz between 35Cl and 1H(and approx 33 Hz between 37CL and
- 1H). Click on the Recalculate button: the Plot Options dialog appears, allowing
- you to choose between 1H, 35Cl and 37Cl nuclei. Press <enter> to accept the
- default 1H.
-
-
- *****************************************************
- * Step 6: Chemical exchange and reaction mechanisms *
- *****************************************************
-
- NMR can not only be used to understand the static structure of a compound, but
- also (in favourable cases) to distinguish between reaction mechanisms of
- rearrangements. As an example, we will consider two possible mechanisms for the
- fluorine scrambling in Me2NPF4. They are called the "one-pair" and "two-pair"
- mechanisms.
-
-
- Low temperature simulation
- **************************
-
- To save you some time, the input files for both systems have already
- been prepared for you.
-
- me2npf41.dta (on the Mac: Me2NPF4 one-pair exchange),
- me2npf42.dta (on the Mac: Me2NPF4 two-pair exchange)
-
- In each mechanism, there are several equivalent ways in which the nuclei can
- move; these will of course have the same rates. You have to tell gNMR about this,
- which makes the Exchange windows more complicated than in the ethanol exchange
- example of Step 3. For both cases, you can simulate the slow-exchange (static)
- spectrum by entering a rate of 0: the results will be identical (triplet of
- triplets). At very high rates (say, 10E5), both systems will give identical
- quintets (try this out!). But at intermediate exchange rates (around 300) you
- will see that the broadening of the centre line compared to the outer lines is
- more pronounced in the one-pair mechanism; there are also distinctive differences
- in the behaviour of the other lines. The best way to see this is to open both
- files simultaneously (gNMR allows you to have several open files) and display the
- calculated spectra side by side in separate Plot windows. The differences are
- clear enough that a comparison with experimental
- data has been used to prove the two-pair exchange mechanism for this compound.
-
-
- Dealing with other NMR active nuclei
- ************************************
-
- gNMR can also simulate the 19F spectrum of Me2NPF4 and this can be displayed
- using Plot|Options and changing from 31P to 19F and the new spectrum is
- displayed. The 19F spectrum is also rate-dependent and shows similar exchange
- processes to the 31P spectrum. Why not try this out?
-
-
- *********************
- * Step 7: Iteration *
- *********************
-
- Helping spectra assignment
- **************************
-
- Calculating a spectrum and playing with the effects of changing shifts and
- couplings can be interesting. But often, you have a measured spectrum, and you
- want to know whether you can reproduce it by a simulation. This may be to see
- whether your idea about the structure of the compound is correct, or it may be to
- extract accurate shifts and couplings. In either case, you will not be satisfied
- by trial-and-error methods: you want to have some kind of "best fit".
-
- In NMR, there are two ways to do this. You can try to fit the positions of all
- peaks in the spectrum by entering positions (and possibly intensities) obtained
- from a measured spectrum; this is called "assignment iteration". Or
- alternatively, you can try to fit on the whole spectrum; this is called
- "full-lineshape iteration". The former procedure is much faster but also requires
- more understanding and a better initial guess by the user; the second method
- requires a measured spectrum in electronic form. It would take too much space
- here to explain how to set up such calculations; this demo contains two
- ready-to-go examples for the rather simple example of o-dichlorobenzene.
-
-
- Assignment iteration
- ********************
-
- For the assignment iteration example, open the file odcbex1.dta (on the Mac :
- Assignment Iteration) in the gNMR working directory. The Molecule window will
- show not only shifts and coupling constants, but also a set of "names" ("a",
- "aa'", etc.) indicating which spectral parameters are to be optimized; equal
- names mean that the parameters will be kept equal. Select Plot|Go To
- Window|Window 1 to see the calculated and observed spectra together.
-
- Observed spectra can be read in from external files created by a wide variety of
- spectrometers eg Bruker and Varian. A conversion utility (gCVT, see later on) for
- these files is provided in the full release of gNMR. Example files are already
- prepared for this demo version.
-
- If you want to inspect the list of calculated and observed peak positions, choose
- Iterate|Assignments, and select 1H from the Nucleus pop-up in the dialog that
- appears. Press OK and the log window will fill with data. To start the iteration,
- select Iterate|Go. After a few short cycles, the procedure has converged: the
- calculated and observed spectra will now be rather similar. If you again select
- Iterate|Assignments|1H,(ensure that the Molecule or Spectrum window is active)
- you will see a much closer match between the observed and calculated positions.
-
-
- Full-lineshape iteration
- ************************
-
- Full-lineshape iteration does not require the user to enter a list of peak
- positions. To start this example, open the file odcbex2.dta (on the Mac:
- Full-lineshape Iteration) file. The Molecule window will show the same set of
- "names" as in the previous example. Display the calculated and observed spectra
- by selecting Plot|Go To Window|Window 1. You will see that the match between
- observed and calculated spectra is much worse than in the assignment iteration
- example: we have made this example more difficult by choosing poorer starting
- values for the shifts and coupling constants. In the Plot|Options dialog section
- Experimental, the items Full-lineshape Iteration and Iterate on Linewidth have
- been checked to tell gNMR to use this window for iteration. To start this
- calculation, again choose Iterate|Go and sit back (this takes about 2 minutes on
- a 486 66, 40 seconds on a Pentium 90, 5 minutes on a Quadra 650 and 50 seconds on
- a PowerMac 8100). The results illustrate clearly that near
- -perfect fits are possible. For a more spectacular example, you might want to run
- the example.dta (on the Mac : Large Iteration Example) file. For best results,
- open Plot windows 1 and 2 before starting the iteration. This should take up to 5
- minutes on a Pentium 90 and 6 minutes on a 8100 Power Mac.
-
-
- **************************************
- * Step 8: Simulating large molecules *
- **************************************
-
- The first thing to do when you want to simulate a large molecule is to make sure
- that gNMR has enough available memory and disk space. Allocating up to 10 Mb of
- both can be useful; if a simulation requires even more, gNMR will run into other
- limitations before then or the simulation will take unacceptably long anyway.
-
- Let's suppose you want to simulate a molecule containing about 20 nuclei. Doing a
- full and exact calculation on such a molecule is currently impossible on any
- computer. The best way to approach this problem is to break it up into pieces. If
- this can be done in such a way that there are no couplings between the pieces,
- you will still get the correct result. In gNMR, you can put the pieces in
- separate "molecule" windows. The file largamin.dta (on the Mac: Large Amine)
- shows how this can be done: the full molecule 1, file largamin.cw2 (on the Mac:
- Large Amine - ChemIntosh) was pasted in three Molecule windows of the same file,
- and two rings in every molecule window were then excluded from the simulation.
- Simulation of this 17-spin system then runs without problems. Depending on a
- number of settings, gNMR may do such a reduction internally, so the simulation of
- the full molecule may also succeed if you do not break it up yourself.
-
- For cases where such a division of the molecule is not possible, gNMR has a new
- method ("chunking") for doing approximate calculations. Basically, this
- calculates spectra piecemeal by including, for each nucleus, only its relevant
- environment in the calculation. As long as there are no nuclei in the system that
- couple to nearly every other nucleus, this method can work well. Because it is
- still considered experimental, this method is disabled by default, but you can
- enable it by setting the Chunking Method in the File/Options dialog (Symmetry
- section) to Fine (most accurate variation; recommended) or "Coarse".
-
- If you want to test this (only recommended for 486 or higher and PPC systems),
- open the file vrylarge.dta (on the Mac: Very Large System), which contains
- molecule 2 (a 12-spin system) with chunking enabled.
-
- Simulation (click on the Recalculate button) is no problem here, although it will
- take a fair amount of computer time. Provided you have allocated enough memory to
- gNMR, this spectrum can also be calculated exactly (set "Chunking Method" to
- "None"). If you do this and compare it with the approximate result, you will see
- that the differences are very small. For a more extreme example, open the file
- toolarge.dta (on the Mac: Too Large System) corresponding to 16-spin molecule 3.
- This still runs because chunking has been enabled, but if you disable it and try
- to recalculate the spectrum the program will exit with the message "System Too
- Large".
-
-
- gNMR's other features include:
- ******************************
-
- * Simulate spectra of mixtures containing up to 10 different compounds
-
- * One-dimensional polymer simulation
-
- * Baseline and phasing parameters
-
- * Anisotropy
-
- * Quadrupoles and more.
-
- There are options for creating PostScript in clipboard copies (Mac) and .PS
- files(Windows), customizing the appearance of spectra, and changing the defaults
- for nearly all gNMR settings. This demo version supports all the features of the
- commercially available full version of gNMR, except the saving of files and
- utilities to convert and edit measured NMR spectra.
-
-
- What you get with gNMR
- **********************
-
- The full gNMR package also includes gCVT (conversion of many spectrum formats to
- gNMR format), gSPG (editing spectra, baseline correction, etc.) and a utility for
- constructing symmetry databases for gNMR. The comprehensive gNMR manual explains
- all of these, and also gives a critical overview of the use of simulation for
- interpreting NMR spectra.
-
-
- The gCVT File Conversion Program
- ********************************
-
- The gCVT file conversion program can be used to import experimental spectra from
- a number of 'foreign' file formats: Bruker Win-NMR, Bruker Aspect, Lybrics,
- General Electric GE-SUN and Varian VNMR. As the most general-purpose exchange
- format, plain ASCII import is also available. In addition, gCVT can be used to
- move gNMR data and spectrum files between different versions of gNMR (both
- Windows and Macintosh). This is useful if you want to exchange data with
- colleagues who use a different version of gNMR.
-
-
- gSPG Spectral Editor
- ********************
-
- Experimental spectra are seldom perfect: they show noise, baseline drift,
- impurity peaks, imperfect phasing, etc. This can be annoying, especially if you
- need a good picture for a paper. And if you want to use the spectrum for a
- full-lineshape iteration, such imperfections are often fatal. Obviously, the
- first remedy to this problem is to obtain high-quality experimental data.
- Sometimes, however, you just have to make do with a given spectrum. Even for
- imperfect spectra, it pays to spend time on careful phasing and baseline
- corrections; you may also want to try adjusting various weighting functions to
- enhance the quality of the spectrum.
-
- If you have done your best to obtain a good spectrum, but the iteration still
- doesn't produce reasonable results, the most probable causes are baseline errors
- and impurity peaks in the experimental spectrum: you can use the gSPG
- spectrum-editing utility to do primitive baseline corrections and remove impurity
- peaks.
-
-
- How to order gNMR
- *****************
-
- You can order a full version of gNMR for evaluation on our risk-free 30-day
- money-back guarantee. Order today and it could be on your desk in just a few
- days. Ask about our special prices for multiple copies. Show gNMR to your
- colleagues and we're sure they'll be grateful.
-
- Call, fax or e-mail your nearest Cherwell Scientific office or your local
- reseller to place your order, or visit our web site at
- http://www.cherwell.com
-
- Cherwell Scientific Publishing
- The Magdalen Centre
- Oxford Science Park
- Oxford OX4 4GA
-
- Tel: +44 (0) 1865 784800
- Fax: +44 (0) 1865 784801
- e-mail: csp@cherwell.com
-
- Cherwell Scientific Publishing
- c/o CHEM Research GmbH
- Hamburger Allee 26-28
- D-60486 Frankfurt
-
- Tel: 069 970841-11
- Fax: 069 970841-41
- e-mail: csp.d@cherwell.com
-
- Cherwell Scientific Publishing Inc
- 744 San Antonio Road
- Palo Alto, Ca 94303
- USA
-
- Tel: (415) 852 0720
- Fax: (415) 852 0723
- e-mail: csp.usa@cherwell.com
-
- We look forward to receiving your order.
-