Structures Controlled by Entropy: The Flexibility of Strychnine as Example
To study the flexibility of strychnine, we performed molecular dynamics simulations with orientational tensorial constraints (MDOC). Tensorial constraints are derived from nuclear magnetic resonance (NMR) interaction tensors, for instance, from residual dipolar couplings (RDCs). Used as orientationa...
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| Format: | Article |
| Language: | English |
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MDPI AG
2022-11-01
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| Series: | Molecules |
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| Online Access: | https://www.mdpi.com/1420-3049/27/22/7987 |
| _version_ | 1797464416595214336 |
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| author | Ulrich Sternberg Raiker Witter |
| author_facet | Ulrich Sternberg Raiker Witter |
| author_sort | Ulrich Sternberg |
| collection | DOAJ |
| description | To study the flexibility of strychnine, we performed molecular dynamics simulations with orientational tensorial constraints (MDOC). Tensorial constraints are derived from nuclear magnetic resonance (NMR) interaction tensors, for instance, from residual dipolar couplings (RDCs). Used as orientational constraints, they rotate the whole molecule and molecular parts with low rotational barriers. Since the NMR parameters are measured at ambient temperatures, orientational constraints generate conformers that populate the whole landscape of Gibbs free energy. In MDOC, structures are populated that are not only controlled by energy but by the entropy term <i>TΔS</i> of the Gibbs free energy. In the case of strychnine, it is shown that ring conformers are populated, which has not been discussed in former investigations. These conformer populations are not only in accordance with RDCs but fulfill nuclear Overhauser effect (NOE)-derived distance constraints and <sup>3</sup>J<sub>HH</sub> couplings as well. |
| first_indexed | 2024-03-09T18:06:51Z |
| format | Article |
| id | doaj.art-5364f666de21452e9a562e67eb055697 |
| institution | Directory Open Access Journal |
| issn | 1420-3049 |
| language | English |
| last_indexed | 2024-03-09T18:06:51Z |
| publishDate | 2022-11-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Molecules |
| spelling | doaj.art-5364f666de21452e9a562e67eb0556972023-11-24T09:24:30ZengMDPI AGMolecules1420-30492022-11-012722798710.3390/molecules27227987Structures Controlled by Entropy: The Flexibility of Strychnine as ExampleUlrich Sternberg0Raiker Witter1Research Partner of the Institute of Nanotechnology, Karlsruhe Institute of Technology (KIT), POB 3640, 76021 Karlsruhe, GermanyInstitute of Quantum Optics, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, GermanyTo study the flexibility of strychnine, we performed molecular dynamics simulations with orientational tensorial constraints (MDOC). Tensorial constraints are derived from nuclear magnetic resonance (NMR) interaction tensors, for instance, from residual dipolar couplings (RDCs). Used as orientational constraints, they rotate the whole molecule and molecular parts with low rotational barriers. Since the NMR parameters are measured at ambient temperatures, orientational constraints generate conformers that populate the whole landscape of Gibbs free energy. In MDOC, structures are populated that are not only controlled by energy but by the entropy term <i>TΔS</i> of the Gibbs free energy. In the case of strychnine, it is shown that ring conformers are populated, which has not been discussed in former investigations. These conformer populations are not only in accordance with RDCs but fulfill nuclear Overhauser effect (NOE)-derived distance constraints and <sup>3</sup>J<sub>HH</sub> couplings as well.https://www.mdpi.com/1420-3049/27/22/7987molecular dynamics MDOCconformersRDCNOE distances3J couplings |
| spellingShingle | Ulrich Sternberg Raiker Witter Structures Controlled by Entropy: The Flexibility of Strychnine as Example Molecules molecular dynamics MDOC conformers RDC NOE distances 3J couplings |
| title | Structures Controlled by Entropy: The Flexibility of Strychnine as Example |
| title_full | Structures Controlled by Entropy: The Flexibility of Strychnine as Example |
| title_fullStr | Structures Controlled by Entropy: The Flexibility of Strychnine as Example |
| title_full_unstemmed | Structures Controlled by Entropy: The Flexibility of Strychnine as Example |
| title_short | Structures Controlled by Entropy: The Flexibility of Strychnine as Example |
| title_sort | structures controlled by entropy the flexibility of strychnine as example |
| topic | molecular dynamics MDOC conformers RDC NOE distances 3J couplings |
| url | https://www.mdpi.com/1420-3049/27/22/7987 |
| work_keys_str_mv | AT ulrichsternberg structurescontrolledbyentropytheflexibilityofstrychnineasexample AT raikerwitter structurescontrolledbyentropytheflexibilityofstrychnineasexample |