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Messages - Ronghui

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Simulations / 1H-31P Coupling
« on: November 18, 2013, 03:13:58 AM »
Is there an example for 1H simulation considering the coupling from P-31?


General Discussion / Re: Plotting NMR spectrum in Mathematica
« on: January 13, 2013, 03:25:30 PM »

General Discussion / Re: Plotting NMR spectrum in Mathematica
« on: January 13, 2013, 02:54:53 PM »
Dr. Kuprov,

Thanks for your reply. Yes I am aware of the Matlab method to reverse the axis. I was wondering if Mathematica has a similar function.

I converted Bruker data into a list which can be read into Mathematica for plotting, and tried to plot the chemical shift scale as well.

Do you have a way to convert Bruker/Varian data into Matlab recognizable form?



General Discussion / Plotting NMR spectrum in Mathematica
« on: January 13, 2013, 03:51:48 AM »
I am trying to plot NMR spectrum (with a list of data points) in Mathematica, but it gave me reverse ordered spectrum where 0 ppm is shown on the left, and higher value like 10 ppm is on the right side.

How to plot the spectrum with descending x-axis, like having 10 ppm on the left and 0 ppm on the right side?



Spinach feature requests / Re: video lectures on Spinach programming
« on: September 28, 2012, 02:42:34 PM »
The Spinach package seems to be very sophisticated.

One request in my mind is to simulate a liq. NMR like the one in Lecture 20, but using Spinach instead. This may be a good starting point to get familiar and understand the functions in Spinach.

Thank you very much.

Simulations / Re: Nuclear overhauser effect
« on: September 28, 2012, 02:34:13 PM »
Exactly! I am interested in 1D selective saturation NOE at the moment.

I would like to simulate if there is any NOE effect among the protons in the molecule acrylic acid. See the literature (
About Long-Lived Nuclear Spin States Involved in Para-Hydrogenated Molecules
J. Am. Chem. Soc., 2007, 129 (5), pp 1445–1449)

Even more, I want to simulate the polarization transfer/redistribution among spins. There are two mechanisms suggested, one is coherence pathway through scalar coupling, the other is the NOE effect. So it will be great if we can see the contributions from those mechanisms.

Thank you very much.

Simulations / Nuclear overhauser effect
« on: September 28, 2012, 01:58:48 AM »
Is there an example for simualting nuclear overhauser effect? Thanks.

Thank you very much.

Spinach feature requests / Re: Function explanation and help
« on: September 23, 2012, 01:08:53 PM »
Thank you very much.

Spinach feature requests / video lectures on Spinach programming
« on: September 23, 2012, 01:07:48 PM »
Those video lectures on simulation design and coding are very helpful. Hope to see a set of video lectures on Spinach.

Spin Dynamics - Lecture 20 - Simulation design and coding, part II

Spinach feature requests / Function explanation and help
« on: September 09, 2012, 04:05:39 AM »
I found it is very easy to find the explanation for any function in SpinDynamica, like in Mathematica, just by typing "?***" in the .nb file.

I hope Spinach can also offer such easy way. It is difficult to locate and find the explanation for functions in the package.



General Discussion / how to convert density matrix into density operator?
« on: September 09, 2012, 04:01:05 AM »
If I have the density matrix for para-Hydrogen as 1/2 {{0,0,0,0},....}, how can I convert it into Bra and Ket form? Thanks.


Dr. Levitt,

I am trying to expand the spin system to 3 spins for the calculation of parahydrogenation of propiolic acid to acrylic acid. The chemical shifts and J-coupling constants are taken from literature. Spin-1 and 2 are from parahydrogen.

Something is wrong, and especially I am not confident about the initial density operator.

I have attached the notebook here and I wonder if you could give me some suggestions.

Thank you very much.


Dr. Levitt,

Thanks for your suggestions.

I have been learning both Spinach and SpinDynamica. I like the easiness of finding the explanation of functions by just typing "?***" in SpinDynamica very much. And our group is much more familiar with Mathematica and  SpinDynamica as well. So it seems to be easier using SpinDanamica to familiarize myself with density matrix simulation as a beginner.

By the way, I am a graduate student working with Dr. Russ Bowers.


Dr. Levitt,

Thank you very much for the examples.

I wonder if there is any limit on the size of spin system in this case? I guess I saw you stated somewhere it is not good for more than 5 spins.

I would like to include other spins in the substrate to simulate the magnetization/hyperpolarization transfer to coupled spins, and this will give me more than 5 spins in total.

For instance, in the following paper, they saw slight polarization of aromatic region during the para-hydrogenation of styrene.
Para-hydrogen induced polarization in multi-spin systems studied at variable magnetic field


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