- PII
- 10.31857/S0207401X24020084-1
- DOI
- 10.31857/S0207401X24020084
- Publication type
- Article
- Status
- Published
- Authors
- Volume/ Edition
- Volume 43 / Issue number 2
- Pages
- 73-80
- Abstract
- The behaviour of dioxadet molecules in water is studied by the molecular dynamics simulation. This substance has anti-cancer properties and is used in clinical practice. However, its properties have not yet studied at the molecular level. This paper presents the first attempt of such investigation. Parametrization of dioxadet molecule was carried out using different available services: ATB, SwissParam as well as AmberTools in a standard form and with the use of additional quantum-chemical calculations. The obtained models are compared with each other. The number of hydrogen bonds of the molecule with water was calculated, the analysis of hydrated water was carried out. It was shown that the dioxadet molecules in water tend to associate. All the models obtained show similar properties, but the quantitative characteristics differ noticeably. Further research is needed to select the best model. Molecule topology files are available for use.
- Keywords
- молекулярно-динамическое моделирование диоксадэт параметризация молекулы водный раствор
- Date of publication
- 14.09.2025
- Year of publication
- 2025
- Number of purchasers
- 0
- Views
- 6
References
- 1. Bespalov V.G., Kireeva G.S., Belyaeva O.A. et al. // J. Chemotherapy. 2016. V. 28. № 3. P. 203; https://doi.org/10.1179/1973947815Y.0000000040
- 2. Gershanovich M.L., Filov V.A., Kotova D.G. et al. // Vopr. Onkol. 1998. V. 44. №. 2. P. 216;
- 3. Zhikhoreva A.A., Belashov A.V., Bespalov V.G. et al. // Biomed. Opt. Express. 2018. V. 9. №. 11. P. 5817; https://doi.org/10.1364/BOE.9.005817
- 4. Fábián B., Sega M., Voloshin V.P., Medvedev N.N., Jedlovszky P. // J. Phys. Chem. B. 2017. V. 121. №. 13. P. 2814; https://doi.org/10.1021/acs.jpcb.7b00990
- 5. Hummer G. // New J. Phys. 2005. V. 7. №. 1. P. 34; https://doi.org/10.1088/1367-2630/7/1/034
- 6. Torrie G.M., Valleau J.P. // J. Comput. Phys. 1977. V. 23. №. 2. P. 187; https://doi.org/10.1016/0021-9991 (77)90121-8
- 7. Kim A.V., Shelepova E.A., Selyutina O.Y. et al. // Mol. Pharm. 2019. V. 16. №. 7. P. 3188; https://doi.org/10.1021/acs.molpharmaceut.9b00390
- 8. Kim A.V., Shelepova E.A., Evseenko V.I. et al. // J. Mol. Liq. 2021. V. 344. P. 117759; https://doi.org/10.1016/j.molliq.2021.117759
- 9. Зеликман В.А., Ким А.В., Медведев Н.Н. // Журн. структ. хим. 2016, Т. 57, №5, С. 978; https://doi.org/10.15372/JSC20160513
- 10. Зеликман М.В., Ким А.В., Медведев Н.Н., Селютина О.В., Поляков Н.Э. // ЖСХ. 2015. Т. 56. № 1. С. 73; http://doi.org/10.1134/S0022476615010102
- 11. PubChem https://pubchem.ncbi.nlm.nih.gov/compound/Dioxadet
- 12. Malde A.K., Zuo L., Breeze M. et al. // J. Chem. Theory Comput. 2011. V. 7. № 12, P. 4026; https://doi.org/10.1021/ct200196m
- 13. Zoete V., Cuendet M.A., Grosdidier A., Michielin O. // J. Comput. Chem. 2011. V. 32. № 11. P. 2359; https://doi.org/10.1002/jcc.21816
- 14. Case D.A., Cheatham III T.E., Darden T. et al. // Ibid. 2005. V. 26. №. 16. P. 1668; https://doi.org/10.1002/jcc.20290
- 15. Berendsen H.J.C., Postma J.P., van Gunsteren W.F., Hermans J. // Dordrecht: Springer, 1981. P. 331; https://doi.org/10.1007/978-94-015-7658-1_21
- 16. Abraham M.J., Murtola T., Schulz R. et al. // SoftwareX. 2015. V. 1. P. 19; https://doi.org/10.1016/j.softx.2015.06.001
- 17. Bussi G., Donadio D., Parrinello M. // J. Chem. Phys. 2007. V. 126. № 1. P. 014101; https://doi.org/10.1063/1.2408420
- 18. Nosé S. // J. Chem. Phys. 1984. V. 81. №. 1. P. 511; https://doi.org/10.1063/1.447334
- 19. Волошин В.П., Медведев Н.Н. // ЖСХ. 2021. Т. 62. № 5. С. 745; https://doi.org/10.26902/JSC_id72868
- 20. Shelepova E.A., Ludwig R., Paschek D., Medvedev N.N. // J. Mol. Liq. 2021. V. 329. P. 115589; https://doi.org/10.1016/j.molliq.2021.115589
