Granted Patent B2

US 12,254,963 · App. 17/793,218 · Granted Mar 18, 2025

Inventors: Markus Zweckstetter (Göttingen, DE); Nina Alexandra Klama (Göttingen, DE); Alain Ibanez De Opakua Lopez De Abi (Göttingen, DE)

Assignees: MAX-PLACK-GESELLSCHAFT ZUR FORDERUNG DER WISSENSCHAFTEN E.V.; DEUTSCHES ZENTRUM FUR NEURODEGENRATIVE ERKANKUNG

G16C20/20G01N24/087G16C20/30G16C20/50

Abstract

Claims (21)

1. A method for determination of molecular parameters for a configuration of a known single organic molecule embedded in an anisotropic environment generated by alignment media, said known single organic molecule comprising particles, comprising:

a) defining a three-dimensional grid that is aligned with a known atomic structure of an alignment medium;

b) placing the particles of the known single organic molecule on respective grid points of a three-dimensional grid in relation to at least one assigned atom of the alignment medium;

c) determining an interaction between the particles of the single organic molecule and the alignment medium for a set of orientations and a plurality of configurations of the particles; and

d) calculating anisotropic parameters, obtainable by measuring with nuclear magnetic resonance (NMR) spectroscopy, by use of the determined interactions for each of the plurality of configurations of the single organic molecule.

2. The method according to claim 1 , wherein the determination of the interaction between the particles of the organic molecule and the alignment medium in step c) comprises evaluating steric effects and/or evaluating van der Waals forces and/or evaluating electrostatic forces acting between a respective organic molecule and the alignment medium.

3. The method according to claim 1 , further comprising

e) comparing anisotropic parameters measured for the organic molecules embedded in the alignment medium with nuclear magnetic resonance (NMR) spectroscopy with each of the anisotropic parameters determined for each of the plurality of configurations of the organic molecule, and

f) determining a configuration of the organic molecule.

4. The method according to claim 3 wherein the step of comparing comprises calculating a quality parameter (RQ) with a term comprising the Pearson correlation coefficient (R) and a scaled quality factor, wherein the scaled quality factor is calculated with residual dipolar couplings (RDCs) scaled with a slope of the fitting (Qs), wherein the configuration related to the highest quality parameter is determined as the configuration of the organic molecule.

5. The method according to claim 4 , wherein the quality parameter (RQ) is calculated by a formula (R+1) 2 /Qs, wherein R is the Pearson correlation coefficient of a linear fitting of observed residual dipolar couplings (RDCs) measured by nuclear magnetic resonance (NMR) spectroscopy (D exp ) versus a calculated residual dipolar couplings (RDCs) obtained by simulation (D calc ), and wherein the scaled quality factor Qs is calculated by a slope of the fitting for a quality factor Q=rms(D exp −D calc )/rms(D exp ), with rms indicating the root-mean-square.

6. The method according to claim 1 wherein the determination of the interaction in step c) comprises determining potential energies between the organic molecule and related atoms of the alignment medium by calculating a respective equation of steric obstruction and/or van der Waals interaction and/or continuum electrostatics.

7. The method according to claim 1 further comprising converting potential energies determined in step c) into probabilities for orientation of the respective organic molecule in front of a related atom of the alignment medium by use of the Boltzmann equation.

8. The method according to claim 1 further comprising placing a simulated organic molecule in step b) outside a radius defined by the van der Waals force of a related atom of the alignment medium in its three-dimensional atomic structure for determining interaction of the organic molecule and the related atom of the known alignment medium in step c).

9. The method according to claim 1 further comprising calculating alignment tensors of the organic molecule for the respective points of the three-dimensional grid by use of the probabilities for orientation.

10. The method according to claim 9 further comprising comparing of anisotropic NMR parameters calculated from alignment tensors with anisotropic NMR parameters measured by NMR spectroscopy.

11. The method according to claim 10 wherein the step of comparing comprises calculating a quality parameter (RQ) with a term comprising the Pearson correlation coefficient (R) and a scaled quality factor, wherein the scaled quality factor is calculated with residual dipolar couplings (RDCs) scaled with a slope of the fitting (Qs), wherein the configuration related to the highest quality parameter is determined as the configuration of the organic molecule.

12. The method according to claim 11 , wherein the quality parameter (RQ) is calculated by a formula (R+1) 2 /Qs, wherein R is the Pearson correlation coefficient of a linear fitting of the observed residual dipolar couplings (RDCs) measured by nuclear magnetic resonance (NMR) spectroscopy (D exp ) versus a calculated residual dipolar couplings (RDCs) obtained by simulation (D calc ), and wherein the scaled quality factor Qs is calculated by a slope of the fitting for a quality factor Q=rms(D exp −D calc )/rms(D exp ), with rms indicating the root-mean-square.

13. A data processing apparatus comprising means for carrying out the steps of claim 1 .

14. A computer program product comprising instructions for a computer program encoded on a non-transient computer readable storage medium which, when the computer program is executed by a computer, cause the computer to carry out the steps of claim 1 .

15. A non-transient computer readable storage medium comprising instructions for a computer program which, when executed by a computer, cause a computer to carry out the method of claim 1 .

Assignments (1)

Priority Claims (1)

Continuity (1)

References Cited (13)