Help
Introduction
The NMRKITCHEN is a user-friendly program for simulating spin-system evolution during pulse sequences.
Theoretically, it is possible, using a pen and paper, to calculate analytically evolution of any spin-system during any complicated pulse sequences. You just need time and have be patient and attentive. But practically you can solve a problem for 2-3 spins and a pulse sequence of 2 or 3 pulses, not more. NMRKITCHEN provides a solution for any spin system and pulse sequence even with phase cycling and pulse gradients. Push the button and relax.
The program can consider:
Nuclei (spin ½) 1H,13C and 15N
Hamiltonian includes J-coupling, chemical shift, H0 gradient, noise, cross-relaxation, pseudo-relaxation, chemical exchange
Number of spins up to 10
Number of RF pulses up to 64
Shaped pulses yes
Number of channels 4 (3- RF, 1- Z gradient)
Phase cycling yes
Array delay, RF pulse, gradient pulse…
Graphics Pulse sequence, 1D, 2D, 2D traces, components of product operators
Weighting functions Gaussian, Exponential
Detection Phase sensitively in both dimensions.
Nuclei abundance variable.
This program is distributed in hope that it will be useful for experienced NMR users as well as for students who have a “lucky” chance to study NMR. Authors will be thankful to everybody who will help them to find any bugs, which unfortunately are inevitable in software like these. Authors are ready to expand these program for solving any other interesting NMR tasks. Any comments, questions and suggestions regarding this program can be directed to idiat001@tc.umn.edu or support@nmr-relaxation.com .
Installation
THIS PROGRAM DOES NOT CREATE OR CHANGE ANY SYSTEM FILES. The NMRKITCHEN.exe is executable from any directory. Double click on this file will start the program. During the first start the program will create a new directory NMR_Kitchen\ in the directory located NMRKITCHEN.exe and two files NMRKITCHEN.ini and NMRKITCHEN.psw. This directory will be your working directory for storing created files. The working directory can be changed from Menu/Options.
File Samples.zip contains several examples of pulse sequences, spin-systems and library of shaped pulses. These files should be extracted to working directory.
Uninstall
Delete NMRKITCHEN.exe. THIS PROGRAM DOES NOT CREATE OR CHANGE ANY SYSTEM FILES.
Starting
After selection of the working directory it is a good idea to start doing something. The best way to learn is method of “try and test”. Move a mouse, click everywhere and look what will happen.As an example you can see COSY sequence for 2-coupled protons and 1-carbon coupled to one of protons. After pushing on Menu/Start_2D you will receive 2D correlated spectrum. It is a good idea to change something like pulse widths, delays, phases, spectral width etc. Look at the results to learn more about NMR.
Spin systems
Clicking on spin position will open a window “Nuclei parameters ”. Change any parameter on this window and see changes in the spin system. For adding new spin click on blank spin and set type of nucleus “H,C or N”. This window will disappear when mouse will move out of the window.
Pulse sequences
Clicking on different position of a pulse sequence will activate the different step of the sequence. To change the parameters for given activated step use controls in the “Parameters” section.Clicking buttons “Del” and “Ins” will delete current step of sequence or insert new step to the sequence.
Phase cycling
Phases can be fixed (x. y. -x, -y) as well as variables (f4-f9). Values of variable phases are changed with changing of number of cycles according to tables on “Phase cycles” section.Phases can be also changed for phase- sensitive detection in second dimension.
Cycling part of sequence
Click on the position of first cycling step of sequence and then click on the red button “{“Click on the with red button“}” for setting last step of sequence. For setting the number of cycles use the red text box.
1D experiment
Clicking on Menu/Start will start arrayed (or not) 1D experiments. As arrayed parameter can be used delay, RF pulse or gradient pulse duration. Ni is number of arrayed spectra. The button “Add”-“Mult” sets the method of array to adding or multiplying, respectively. After the experiment, the program plots 1D spectra of detectable signals for all channels. The spectra can be plotted separately or altogether by using “ON”-“OFF” button.
2D experiment
Clicking on Menu/Start_2D will start 2D experiment. To obtain 2D spectra the arrayed parameter must be some delay (dX) and every following scan should has 90-degree phase shift for realization of phase-sensitivity detection. Parameter “Detection (t2)” sets receiver channel of nuclear of interest. After the experiment the program plots 1D spectra of detectable signals for all channels and 2D spectrum.
Save
You can separately save files containing spin-system configuration (*.mol) and created pulse sequence (*.psq) in Menu/File/Save. Don’t forget to create new name for files.
Open
You can separately open files with spin-system configuration and pulse sequence from Menu/File/Open.
Plotting of product operators
After finishing calculations the list box on the bottom left corner will be refreshed and the list of the names of nonzero operators at the end of the sequence step marked by “point” will appear. Clicking within the list will select a spin-order and will plot the dependence of the spin-order values on the arrayed parameter.