caa a22 4500 605512302 CHVBK 20210128100655.0 cr unu---uuuuu 210128e20151001xx s 000 0 eng 10.1007/s00894-015-2812-0 doi (NATIONALLICENCE)springer-10.1007/s00894-015-2812-0 Empirical force field for cisplatin based on quantum dynamics data: case study of new parameterization scheme for coordination compounds [Elektronische Daten] [S. Yesylevskyy, Bruno Cardey, S. Kraszewski, Sarah Foley, Mironel Enescu, Antônio da Silva Jr., Hélio Santos, Christophe Ramseyer] Parameterization of molecular complexes containing a metallic compound, such as cisplatin, is challenging due to the unconventional coordination nature of the bonds which involve platinum atoms. In this work, we develop a new methodology of parameterization for such compounds based on quantum dynamics (QD) calculations. We show that the coordination bonds and angles are more flexible than in normal covalent compounds. The influence of explicit solvent is also shown to be crucial to determine the flexibility of cisplatin in quantum dynamics simulations. Two empirical topologies of cisplatin were produced by fitting its atomic fluctuations against QD in vacuum and QD with explicit first solvation shell of water molecules respectively. A third topology built in a standard way from the static optimized structure was used for comparison. The later one leads to an excessively rigid molecule and exhibits much smaller fluctuations of the bonds and angles than QD reveals. It is shown that accounting for the high flexibility of cisplatin molecule is needed for adequate description of its first hydration shell. MD simulations with flexible QD-based topology also reveal a significant decrease of the barrier of passive diffusion of cisplatin accross the model lipid bilayer. These results confirm that flexibility of organometallic compounds is an important feature to be considered in classical molecular dynamics topologies. Proposed methodology based on QD simulations provides a systematic way of building such topologies. Springer-Verlag Berlin Heidelberg, 2015 Cisplatin nationallicence Coordination compounds nationallicence Molecular dynamics nationallicence Parameterixation nationallicence Quantum dynamics nationallicence Yesylevskyy S. Department of Physics of Biological Systems, Institute of Physics of the National Academy of Sciences of Ukraine, Prospect Nauky 46, 03680, Kiev-28, Ukraine aut Cardey Bruno Laboratoire Chrono Environnement UMR CNRS 6249, Université de Franche-Comté, 16 route de Gray, 25030, Besançon Cedex, France aut Kraszewski S. Department of Biomedical Engineering (W11/K7), Wroclaw University of Technology, Wybrzeze Wyspianskiego 27, 50-370, Wroclaw, Poland aut Foley Sarah Laboratoire Chrono Environnement UMR CNRS 6249, Université de Franche-Comté, 16 route de Gray, 25030, Besançon Cedex, France aut Enescu Mironel Laboratoire Chrono Environnement UMR CNRS 6249, Université de Franche-Comté, 16 route de Gray, 25030, Besançon Cedex, France aut da Silva Jr. Antônio Núcleo de Estudos em Química Computacional, Departamento de Química, ICE, Universidade Federal de Juiz de Fora (UFJF), Campus Universitário, Martelos, 36036-900, Juiz de Fora, MG, Brazil aut Santos Hélio Núcleo de Estudos em Química Computacional, Departamento de Química, ICE, Universidade Federal de Juiz de Fora (UFJF), Campus Universitário, Martelos, 36036-900, Juiz de Fora, MG, Brazil aut Ramseyer Christophe Laboratoire Chrono Environnement UMR CNRS 6249, Université de Franche-Comté, 16 route de Gray, 25030, Besançon Cedex, France aut Journal of Molecular Modeling Springer Berlin Heidelberg 21/10(2015-10-01), 1-9 1610-2940 21:10<1 2015 21 894 https://doi.org/10.1007/s00894-015-2812-0 text/html Onlinezugriff via DOI BK010053 XK010053 XK010000 Metadata rights reserved Springer special CC-BY-NC licence nationallicence 1 research-article jats NATIONALLICENCE NATIONALLICENCE NL-springer NATIONALLICENCE 856 40 https://doi.org/10.1007/s00894-015-2812-0 text/html Onlinezugriff via DOI NATIONALLICENCE 700 1- Yesylevskyy S. Department of Physics of Biological Systems, Institute of Physics of the National Academy of Sciences of Ukraine, Prospect Nauky 46, 03680, Kiev-28, Ukraine aut NATIONALLICENCE 700 1- Cardey Bruno Laboratoire Chrono Environnement UMR CNRS 6249, Université de Franche-Comté, 16 route de Gray, 25030, Besançon Cedex, France aut NATIONALLICENCE 700 1- Kraszewski S. Department of Biomedical Engineering (W11/K7), Wroclaw University of Technology, Wybrzeze Wyspianskiego 27, 50-370, Wroclaw, Poland aut NATIONALLICENCE 700 1- Foley Sarah Laboratoire Chrono Environnement UMR CNRS 6249, Université de Franche-Comté, 16 route de Gray, 25030, Besançon Cedex, France aut NATIONALLICENCE 700 1- Enescu Mironel Laboratoire Chrono Environnement UMR CNRS 6249, Université de Franche-Comté, 16 route de Gray, 25030, Besançon Cedex, France aut NATIONALLICENCE 700 1- da Silva Jr Antônio Núcleo de Estudos em Química Computacional, Departamento de Química, ICE, Universidade Federal de Juiz de Fora (UFJF), Campus Universitário, Martelos, 36036-900, Juiz de Fora, MG, Brazil aut NATIONALLICENCE 700 1- Santos Hélio Núcleo de Estudos em Química Computacional, Departamento de Química, ICE, Universidade Federal de Juiz de Fora (UFJF), Campus Universitário, Martelos, 36036-900, Juiz de Fora, MG, Brazil aut NATIONALLICENCE 700 1- Ramseyer Christophe Laboratoire Chrono Environnement UMR CNRS 6249, Université de Franche-Comté, 16 route de Gray, 25030, Besançon Cedex, France aut NATIONALLICENCE 773 0- Journal of Molecular Modeling Springer Berlin Heidelberg 21/10(2015-10-01), 1-9 1610-2940 21:10<1 2015 21 894