The Check Its

Each NMR-SIM simulation creates a number of different files in a single subdirectory. The number and format of these files are similar to those obtained when converting experimental data from a BRUKER spectrometer into WIN-NMR format. Table 1.2 lists some of the file extensions used by WIN-NMR. For copyright protection the data sets created by NMR-SIM are encoded and can only be processed by the teaching version of the ID WIN-NMR or 2D WIN-NMR processing software. 

Processed Data - Real Processed Data - Imaginary 

In all the books in the series Spectroscopic Techniques An Interactive Course the emphasis is on the interactive method of learning and this volume follows the same approach. The remaining chapters in this book all have a similar format, a short written introduction and number of Check its for the reader to complete. Before each Check it is a short introduction which may include the discussion of new concepts or the advantage or disadvantage of a particular pulse sequence etc. The Check its are then used to illustrate the points being discussed either by displaying the processed data in ID WIN-NMR or 2D WIN-NMR or in the case of the Bloch simulator in a spherical or other display modes. 

Each Check it is usually based on a configuration file which contains the complete experimental set-up (Fig. 1.6). After starting the simulation the reader will be prompted to define the output file to which the calculated data is stored. If no configuration file exists the pulse program, rf channels, spin system, acquisition and processing parameters have to be chosen by the reader before the simulation is run (Fig. 1.6 left hand side). 

In each Check it the reader has to perform a series of tasks in the correct order. To reduce the text part of each Check it to the minimum and to stop being repetitive these operations and commands will be described in more detail here. The three main tasks are  

---

Start the WINDOWS Explorer and check there is 150-200 MBytes of space available on one of your hard disk(s). Follow one of the standard procedures for copying files from one to another directory. Consult the WINDOWS manual, or first study the Check it instructions for copying a file or directory given in the next section (2.5.6), if necessary. Select in your CD-ROM the directory NMRDATA or any of its subdirectories and copy it to disk D on your PC. The directory NMRDATA GLUCOSE 1D H and a few auxiliary directories therein (see 2.5.4) have already been created during installation of ID WIN-NMR. Answer the corresponding question for overwriting all files stored under the same name with yes. Use the WINDOWS Explorer) to inspect the newly created NMR data directory NMRDATA on your hard disk. Click on several items in this directory and familiarise yourself with the directory structure. 

Should there be any leakage from the dow nstream line through the check, it w ill flow harmlessly out through the relief valve, thereby giving a visual indication that a backflow or backsiphonage condition exists. 

The configuration files used in the Check its can be used with the full version of NMR-SIM but the experimental data can only be processed using the full version of ID... 

Fig. 1.2 shows the directory structure generated by the software installation using the recommended directory. The main TEACH directory contains the program subdirectories Getfile, NMR-Sim, Win ID and Win2D plus the data subdirectory Nmrdata. The subdirectories Manuals and Results contain the software documentation for the programs and the additional information and results for most of the Check its. 

In the following discussion it is assumed that the default pathways have been used during the installation process. If different pathways have been selected during the installation this must be taken into account when using the Check its and other references in this book. 

The loading of a configuration file (cfg files) is done using the Load from file... command in the File pull-down menu. In the Check its this operation is described by the short hand notation File Experiment setup Load from file. A left-hand mouse button click on the command field opens a standard Windows file list box. In this file list box it is possible to select a specific cfg file either directly from the keyboard or by using the mouse it is also possible to change the directory and/or disk drive if necessary. 

Simulations are started using either the Run Experiment or Check Parameters Go commands in the Go pull-down menu. The Check Parameters Go command opens the Experiment parameter dialog box to enable the parameters to be checked before the simulation is started. By default the configuration file used in the Check its require the output filename must to be entered prior to the calculation starting (Fig. 1.9). 

It is recommended that the output files are named systematically with the entry fields User, Name and Exp No. derived from the Check it number. Thus the User field consists of the letters "ch" combined with the number of the Check it excluding the last... 

Bold letters, words and expressions refer to commands and controls, particularly in the Check its and simulation examples. 

In Check its 2.33.7 and 2.3.3.8 a phase-cycled COSY magnitude spectrum is converted into a gradient selected COSY spectrum. The Check its also show how the choice of either the n- or p-type CT pathways influences the frequency display in the fl dimension. 

The FIDs simulated using NMR-SIM should always be processed using the zero filling and apodization parameters shown in Table 3.1. This table also lists the abbreviations used for these parameters in the Check its. Occasionally parameters different from the recommended values may be used in a Check it this is particularly true in simulations where the relaxation option is disabled, the values of the parameters are chosen to improve the spectrum appearance by minimizing line distortions. The Check it may contain the phrase "use zero filling and an apodization (EM, LB 2.0 Hz)" implying zero filling of SI(r+i) 2 TD and an exponential apodization with a LB factor of 2.0. 

NMR-SIM simulation is that the zero- and first-order phase distortions can be investigated separately in contrast to experimental spectra where both errors occur simultaneously. In the first part of Check it 3.2.3.4 the zero-order phase distortion is simulated using a 40° phase shift difference between the excitation pulse and the receiver phase, in the second part the first-order phase distortion is simulated using a delay dlO before the data acquisition. The spin system used in the Check it consists of a number of singlets evenly spaced over a frequency range of 3200 Hz. 

In many of the Check its in this book different spectra are compared using the Dual and Multiple Display modes which are selected from the Display pull-down menu. This pull-down menu contains a number of different options for changing colours, fonts and miscellaneous display parameters, most are mostly self explanatory [3.2]. Although in the dialog boxes associated with both display modes it is possible to toggle the selection between FID and Spectrum, in the following discussion it is assumed that only spectra are to be displayed. 

Open the pulse program ppexaml.seq created in the Check it 4.1.2.6(a) using the Edit I Pulse program command. Add the two phase program lines after the lines for d1 and (p1 ph1) f1. Using the FiielSave As... command save the file with the new name ppexam2.seq. 

Load the configuration file st13cde.cfg (File I Experiment Setup I Load from file...) and replace the spin system file either with the file examS.ham previously created in Check it 4.1.1.3 or the file exam3p.ham delivered with the program. Load the pulse program ppexam/.seq from the Check it 4.1.2.8(c). Run a simulation (GolRun Spectrum) and process the FID with zero filling (Sl(r+i) = 32k) and an exponential window function (LB value of 2 Hz). Phase the spectrum as shown in the result file. 

Table 5.9 categories the different types of J-resolved experiment used by the Check its in this section. The choice of experiment in each Check it has been chosen deliberately to illustrate a specific point how coupling constants may be determined, how different type of artefacts arise and how these artefacts may be suppressed. 

Modify the pulse sequence in the Check it 5.3.1.9 for the schemes shown below saving each modified sequence with a suitable new name e.g. bnp121.seq. Calculate the excitation profile for all three sequences and process the FIDs (no zero filling, wdw EM, LB 2.0 [Hz]). Use the Multiple Display option to compare the magnitude calculated profiles (Process 1 Magnitude Calculation) as a function of pulse train length. 

The TQF IR COSY enhances the cross peak structure, but again reduces the intensity of diagonal peaks such that even doublet diagonal peaks might decrease to a very low intensity. The TQF is achieved by using an extended phase cycling program as shown in the Check it 5.4.1.4(b). 

The advantages of the TOCSY experiment have led to the implementation of spinlock sequences in heteronuclear correlation experiments to detect additional homonuclear coupling interaction. In the l C, IR TOCSY-HMQC experiment in addition to cross peaks from one-bond connectivities between a DC and a IR nucleus there are correlation peaks to protons which are coupled to the primary proton by homonuclear H, H coupling. The advantage of this method is that it allows the differentiate between overlapped iR signals of different spin systems provided that the spin systems differ by the carbon shift of at least one carbon atom. This approach is shown by the simulations in the Check it 5.4.2.4. 

To simulate the 2D [13C, 1H] CIGAR-HMBC spectrum for the spin system used in the Check its 5.S.2.3 and 5.5.2A, load the file ch5525.cfg. Process the data in 2D WIN-NMR. To examine the signal modulation in f1 by the 1H- >H coupling, run a series of simulations using different values of id23 starting with the current Jscale value of 8 [Hz]. 

The OSHA regulation does not specify who is to conduct the check. It would be advisable to contact the OSHA local area office for guidance on the qualifications needed. Also, the manufacturer s instructions should be followed. 

---