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| Main Authors: | , , |
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| Format: | Preprint |
| Published: |
2025
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| Subjects: | |
| Online Access: | https://arxiv.org/abs/2509.17959 |
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| _version_ | 1866916961036795904 |
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| author | Deshchenya, Vladimir Gerke, Kirill Kondratyuk, Nikolay |
| author_facet | Deshchenya, Vladimir Gerke, Kirill Kondratyuk, Nikolay |
| contents | Molecular dynamics methods have proven their applicability for the reproduction and prediction of molecular conformations during the last decades. However, most of works considered dilute solutions and relatively short trajectories that limit insights into conformational dynamics. In this study, we investigate the conformational dynamics of sucrose in aqueous solution using microsecond-scale molecular dynamics simulations. For the most of the calculations we use the OPLS-AA/1.14*CM1A-LBCC force field, but we also utilize OPLS-AA/1.14*CM1A and GLYCAM06 for the comparison. We focused on the glycosidic linkage conformers and their lifetimes, glucopyranose and fructofuranose ring puckering. Our findings indicate that the $^1\mathrm{C}_4$ glucopyranose ring conformation can stabilize the sucrose conformer, appeared only in the GLYCAM06 and OPLS-AA/1.14*CM1A force fields. All the results are strengthened by comparison with the available experimental data on NMR J-coupling constants and ultrasonic spectra. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2509_17959 |
| institution | arXiv |
| publishDate | 2025 |
| record_format | arxiv |
| spellingShingle | Microsecond-scale sucrose conformational dynamics in aqueous solution via molecular dynamics methods Deshchenya, Vladimir Gerke, Kirill Kondratyuk, Nikolay Soft Condensed Matter Molecular dynamics methods have proven their applicability for the reproduction and prediction of molecular conformations during the last decades. However, most of works considered dilute solutions and relatively short trajectories that limit insights into conformational dynamics. In this study, we investigate the conformational dynamics of sucrose in aqueous solution using microsecond-scale molecular dynamics simulations. For the most of the calculations we use the OPLS-AA/1.14*CM1A-LBCC force field, but we also utilize OPLS-AA/1.14*CM1A and GLYCAM06 for the comparison. We focused on the glycosidic linkage conformers and their lifetimes, glucopyranose and fructofuranose ring puckering. Our findings indicate that the $^1\mathrm{C}_4$ glucopyranose ring conformation can stabilize the sucrose conformer, appeared only in the GLYCAM06 and OPLS-AA/1.14*CM1A force fields. All the results are strengthened by comparison with the available experimental data on NMR J-coupling constants and ultrasonic spectra. |
| title | Microsecond-scale sucrose conformational dynamics in aqueous solution via molecular dynamics methods |
| topic | Soft Condensed Matter |
| url | https://arxiv.org/abs/2509.17959 |