NMR Spectroscopic Data Processing

Modern NMR identification uses a range of techniques to provide connectivity and stereochemical information about molecules. In this tutorial, a range of datasets deriving from these techniques are stored on a network file server. This tutorial illustrates how this data can be processed using appropriate software to provide structural information.

Procedure

Part I. Processing of Spectrometer Data

Data from two principle sources is available for processing, the Bruker spectrometers and the Jeol system. The latter is used for running all Student (1D) NMR samples, the former for more complex (often 2D) data sets. If you are following these instructions to process your laboratory acquired data, use the Jeol option. If you are following these instructions using the tutorial data for the structure shown below, use the Bruker option .

Various programs are available for processing NMR data:

Mestrec1D (filename mestrecXY.exe, where XY is the current version number)

Mestrec2D (filename mestrecnd.exe)

SpecNMR (filename spexnmr.exe)

To access these programs, proceed as follows:

All the relevant programs are available on the Windows systems located in the Teaching computer room, with shortcuts either as icons on the desktop, or in the start menu. You should also see an NMR Service file server icon, where the data files will be. If you are not using one of these computers, Run Programs/Accessories/Communications/Remote Desktop (Windows 2000/XP only) and specify chas.ch.ic.ac.uk as the remote application server. If the icon to the left is shown, use this shortcut instead. You must remember to log out of these servers when you finish: do not leave yourself logged in, or just quit the remote desktop program without so logging out.

On MacOS X, run the Remote Desktop connection program (found in Applications or the Dock, icon same as above) and specify chas.ch.ic.ac.uk as the remote application servers. You will enter a standard Windows environment, and Mestre-C, SpecNMR and NMR Service icons should be seen on the desktop or from the Start menu. You must remember to log out of these servers when you finish: do not leave yourself logged in, or just quit the remote desktop program without so logging out.

Ia. Tutorial Data set (Bruker Spectrometers)

The Bruker tutorial datasets for the compound shown at the left are located on the local in a folder called NMR_Data, which contains the following subfolders:

1H is the 400 MHz 1H spectrum

13C is the corresponding 13C data

COSY-2D is the 1H/1H correlated 2D data

H-C-2D is the 1H/13C correlated 2D data

NOE is the 1H NOE experiments

The 1D datasets should be opened with the MestreC23 program, the 2D datasets with the MestrecND program (both located on C:\Mestrec or D:\Mestrec). Proceed as follows

From the 1H sub-folder of NMR_Data, browse to the file called FID. Note that for this file, you should select a Bruker UXNMR file type.

From process, select Fourier transform

View/Set limits to view spectrum between predefined values of the chemical shift.

Use Tools/Reference and Tools/Integrate, followed by a dragging out of the area of spectrum to be integrated.

Use +/- from the toolbar to change height of spectrum

There are numerous other options, which you should explore yourself. The results look akin to this;

Repeat for the folder NOE/4-17/pdata/2/1r to see various nOe experiments. The different spectra relate to different pre-irradiations at selected frequencies, and show the difference spectrum resulting.

For the 2D plots, proceed as follows;

Using MestrecND, go to eg COSY-2D and open the file ser.

Process/Fourier transform/Apodise/SineBell/Apply along t2. You should now see a display comprising a series of vertical stripes. From the menu, change the size to four times its initial value (zero filling eg 256 to 1k) and Apply along t1. The result will be a 2D spectrum. Hit + a few times to increase the size of the contours. Use Tools/Reference F1 and Reference F2 to set the chemical shift to known values, ie TMS. Proton COSY spectra usually look better if symmetrised (Process menu) and forced to be square.

Go to H-C-2D and do the same. In each case the 1H/1H or 1H/13C spectrum is displayed along one frequency axis. The interpretation is that cross peaks in 1H/1H correlation indicate 1H-1H coupling and likewise for 1H/13C.

When you have a spectrum to your liking, Copy data to the clipboard and paste into Microsoft Word or other word processor for inclusion in your report. Do not attempt direct printing, there are no printers provided for the purpose.

Ib. Laboratory Data sets (Jeol spectrometers)

The Jeol datasets derived from samples run as part of laboratory experiments are located in a network drive called 270teaching, subdirectory data on "chnmr3" in the domain CH1. You may find this folder mounted on the "Resonance" network drive (270teaching on 'Chnmr3' (R:) The spectra should appear there after the sample has been run. Note carefully the spectrum code assigned to you.

Run the SpecNMR program located in D:\SpecNMR (there should be a shortcut on the desktop). Invoke File/Open, select Jeol Delta Format as the file type (Important!) and click on Drives and browse to R:\Data\...appropriate sub-folders, Click OK/finish. A list of available files listed in the file dialog box appears. Select the one you want.

The screen should shown an FID (Free induction decay). Select Process/FT+Phase/OK. An (unphased) spectrum appears.

From the Phase floating pane and P0 set, move the slider labelled degrees until the marked peak appears properly phased. Then select P1 and again move the slider until the rest of the spectrum looks properly phased. Finish with Apply.

The spectrum can be expanded by dragging out a box for expansion.

Analyse/Integrate. Hold the right mouse button down (on a Mac, Control/Shift) and pull out a region on the spectrum to integrate. Repeat as often as necessary.

Process/Calibrate to set the reference. Right click to set the point on the spectrum whose chemical shift you know (i.e. TMS) and click OK. If you cannot find a peak whose position you know, enter 8096 (assuming your FID is a 16k one) into the data box and 5.00ppm into the chemical shift box and click OK. The result should be fairly accurate. The spectrum should look similar to:

Edit/copy to clipboard and Paste into Word. Save the Word file either to a removable device (e.g. Pendrive) or to your Network H: drive.

Part II. Simulation of Spectra (optional)

The tutorial relates the following compound, but you should apply the procedure to your own data.

1. Given the structure above, you can simulate the anticipated ¹H NMR Spectrum using either:
   • gNMR and ChemDraw
   • ACDLABS software.
   With the latter, you will have to log into the Application server, and use the built in molecule drawing program, but the operation is fairly self-evident. The results look something like this;
   

Part III. The Wintorg Tutorials (Optional)

Part IV. What is the future?