NMR-SIM Options

Irrespective of the dimension of the experiment the NMR-SIM option dialog box offers the possibility to alter the simulation environment to be as realistic as possible. In addition some options can be toggled on and off depending upon the simulation routine. 

Optimize pulse program Shorn pulse program One column edit  

Normally the experiment parameter dialog box displays the pulse program and a list of parameters with a brief comment beside each parameter. This scroll window can be changed into a more compact form by disabling the options Show pulse program and One column edit. The option Start Win NMR allows either ID WIN-NMR or 2D WIN-NMR to be started automatically as soon as the calculation is completed with the current simulated data loaded into the main display window. 

The Relaxation option becomes important if relaxation effects should be considered either during the pulse program execution or just during the data acquisition period. Set to Acquisition the simulated FID can be processed in a similar manner to experimental data. Although relaxation cannot be excluded in real experiments, NMR-SIM has the option to turn off relaxation effects when analysing a pulse sequence by selecting the None option and so reduce the simulation time. 

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The main window of NMR-SIM is subdivided in the title bar with the program name, the menu bar with the pull-down menu commands File, NMR-Wizard, Edit etc., the rf channel option bar with two accessible rf channel combo boxes and the main status window, see Fig. 1.3. Each command in the menu bar opens a pull-down menu that may contain sub-menus or commands that can be selected and opened/executed. The rf channel option bar uses isotope identifier to assign a specific nucleus and hence NMR frequency to the FI or F2 channel. The main status window is built up in line order and shows the pulse program name, spin system name and other optional files associated with the current simulation. 

Load the configuration file ch3221.cfg (File I Experiment Setup Load from file...)- Open the NMR-Sim settings dialog box (Options I NMR-Sim settings...) and select the option Relaxation Acquisition. Run the simulation (Go I Run experiment). Apply an exponential window function (Window button) but no DC correction. Fourier transform the FID (FT button). (The effects of window functions are explained in section 3.2.3). Save the spectrum (FilelSave) for comparison with the second calculation. For the second simulation select the option Relaxation None and run the simulation saving the file with a new name. Process the data in exactly the same way as for the first simulation (Window and then the FT button) and compare the two spectra using the dual display mode of 1D WIN-NMR (DisplayIDual Display) (see section 3.2.3.4). 

Consequently NMR-SIM has the option to modify the rf pulse behaviour according nucleus being excited and to generate spectra that are close to real experiments. 

Load the configuration file ch3222.cfg. Open the NMR-Sim settings dialog box (Options I NMR-Sim settings...) and disable the Modify RF fields... 

NMR-SIM does not permit such spectrometer imperfections to be simulated so that the DC offset correction is redundant. Indeed this correction must never be applied if a resonance signal is placed directly on-resonance, i.e. a nuclear spin is defined with 5 = 01 ppm (the transmitter frequency). In ID WIN-NMR the DC Correction dialog box opens automatically before processing of the current FID data but for the processing of NMR data generated by NMR-SIM the No option should always be selected. The effect of the DC offset correction is shown in Check it 3.2.3.1 using a data set containing a pseudo DC offset. 

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. 

The setup of experiment parameters can be separated in different categories. The entry of experiment parameters is not just restricted to the dialog box of the Go I Check Experiment Parameters pull-down menu command. The rf channel option bar is an integral part of the NMR-SIM main window whilst the Parameters I... pull-down menu command opens several different dialog boxes. The various different categories of experiment parameters are listed in Table 4.4. 

A job file is a text file containing a number of different configuration files, which are loaded, sequentially into NMR-SIM and the corresponding experiment simulated. As shown in Fig. 4.17, the job file can also contain optional comments. Job files maybe modified by deleting or adding further parameters to the configuration files. 

Using the File I Job... command select the job file Ihexp.job. Modify the spin system (Edit I Spin system) by replacing the existing spin system parameters with those listed on the left-hand side of this Check it. In the Options I NMR-SIM settings... dialog box select the option Output File to User defined. Start the job using the Go I Start Job command. Enter appropriate output file names and process the spectra at the end of the job execution in ID WIN-NMR and respectively 2D WIN-NMR. 

In NMR-SIM replace the spin system by the file ch4213b.ham (FilelSpin system...)- Select F19 for the Obs channel and start the NMR wizard again. In 2D WIN-NMR select the same options as before and process the data. The simulated COSY spectrum should be the same as the spectrum in the resultpdfY e. 

Load the configuration file ch4216a.cfg using the File I Experiment Setup I Load from file... command and in the Options I NMR-SIM settings... 

Load the file ch5214.cfg (File I Experiment setup I Load from file...). Check the pulse lengths of pi 2.5u (90° pulse) and p3 0.5u (4.5° pulse) (Go Check Experiment Parameters). In the Options I NMR-Sim settings... dialog box select the Modify RF field option. To simulate the decoupler pulse calibration, open the parameter optimizer dialog box (Go I Optimize parameter). Select the Show results as 1D series, N 8 and p3 for optimization. Click on the OK button. In the next dialog box enter the start value p3 0.5u and increment size inpO 2.0u. Click on the OK button and enter then the path and name for the calculated and saved files. Run the series of simulations. In 1D WIN-NMR the last simulated FID will be automatically loaded into the spectrum window. Process the FID (zero filling Sl(r+i) 16k, apodization EM, LB 1.0 [Hz]) amd... 

In an SPT experiment one spectral line which belongs to a single transition of the spin system is irradiated and the effects on the spectrum observed. To understand the effect of a SPT experiment the energy levels of the spin system must first be calculated. NMR-SIM has the option to generate an energy level scheme of a spin system and to display the results either as a list or in graphical representation. 

WIN-NMR, USA Bruker Instruments, Inc., Manning Park, Billerica, MA 01821. (Optional modules include NMR-SIM, WIN-DAISY, and WIN-HT.)... 

Before using the Wizard the correct nucleus must first be specified in the Obs channel of the rf channel option bar and the various options in the OptionsINMR-SIM settings dialog box set. The NMR Wizard is started using the Wizard command which opens the dialog box shown in Fig. 4.19. 

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