Investigation of the behavior of dioxadet molecules in water by molecular dynamics simulation

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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.

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About the authors

E. A. Yakush

Voevodsky Institute of Chemical Kinetics and Combustion Siberian Branch of the Russian Academy of Sciences; Novosibirsk State University

Email: nikmed@kinetics.nsc.ru
Russian Federation, Novosibirsk; Novosibirsk

A. V. Kim

Voevodsky Institute of Chemical Kinetics and Combustion Siberian Branch of the Russian Academy of Sciences; Novosibirsk State University

Email: nikmed@kinetics.nsc.ru
Russian Federation, Novosibirsk; Novosibirsk

N. N. Medvedev

Voevodsky Institute of Chemical Kinetics and Combustion Siberian Branch of the Russian Academy of Sciences

Author for correspondence.
Email: nikmed@kinetics.nsc.ru
Russian Federation, Novosibirsk

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Supplementary files

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2. Fig. 1. Structure of the dioxade molecule. The numbers indicate the atoms on which the largest partial charges are concentrated.

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3. Fig. 2. Radial distribution function (RDF) of water molecules relative to the surfaces of the nearest atoms of the triazine ring DXT; The RDFs of all models tend to unity at large distances, as for the AmberHF model. The curves for AmberB3LYP, ATB and SwissParam are shifted down for ease of viewing.

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4. Fig. 3. Time dependence of the distance between the centers of mass of two DXT molecules for different models: a - ATB, b - Amber B3LYP, c - Amber HF, d - SwissParam.

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5. Fig. 4. Screenshots showing aggregates of four DXT molecules in water (water molecules not shown) arising in the ATB model.

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Note

Х Международная конференция им. В.В. Воеводского “Физика и химия элементарных химических про­цессов” (сентябрь 2022, Новосибирск, Россия).


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