1

**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?

Thanks.

Ronghui

Thanks.

Ronghui

SpinDynamica v2.14.3 released - now compatible with Mathematica 11.

see SpinDynamica section.

This section allows you to view all posts made by this member. Note that you can only see posts made in areas you currently have access to.

Pages: [**1**] 2

1

Is there an example for 1H simulation considering the coupling from P-31?

Thanks.

Ronghui

Thanks.

Ronghui

2

http://mathematica.stackexchange.com/questions/5714/flipping-axis-on-a-plot

This turns out to be very helpful. Thanks.

This turns out to be very helpful. Thanks.

3

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?

Thanks.

Ronghui

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?

Thanks.

Ronghui

4

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?

Thanks.

Ronghui

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

Thanks.

Ronghui

5

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.

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.

6

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 (http://pubs.acs.org/doi/abs/10.1021/ja066313x

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.

I would like to simulate if there is any NOE effect among the protons in the molecule acrylic acid. See the literature (http://pubs.acs.org/doi/abs/10.1021/ja066313x

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.

7

Is there an example for simualting nuclear overhauser effect? Thanks.

8

Thank you very much.

9

Thank you very much.

10

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

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

11

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.

Thanks.

Ronghui

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

Thanks.

Ronghui

12

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.

Ronghui

Ronghui

13

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.

Ronghui

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.

Ronghui

14

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.

Ronghui

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.

Ronghui

15

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.

http://pubs.rsc.org/en/content/articlehtml/2009/cp/b914188j#tab1

Para-hydrogen induced polarization in multi-spin systems studied at variable magnetic field

Thanks.

Ronghui

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.

http://pubs.rsc.org/en/content/articlehtml/2009/cp/b914188j#tab1

Para-hydrogen induced polarization in multi-spin systems studied at variable magnetic field

Thanks.

Ronghui

Pages: [**1**] 2