Rigid-Body Molecular Dynamics of Fullerene-Based Nanocars on Metallic Surfaces.

Autor:	Konyukhov SS; Department of Chemistry, M.V. Lomonosov Moscow State University, Leninskie Gory 1/3, Moscow 119991, and N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, ul. Kosygina 4, Moscow 119994, Russian Federation, and Department of Chemistry, Rice University, Houston, Texas 77005., Kupchenko IV; Department of Chemistry, M.V. Lomonosov Moscow State University, Leninskie Gory 1/3, Moscow 119991, and N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, ul. Kosygina 4, Moscow 119994, Russian Federation, and Department of Chemistry, Rice University, Houston, Texas 77005., Moskovsky AA; Department of Chemistry, M.V. Lomonosov Moscow State University, Leninskie Gory 1/3, Moscow 119991, and N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, ul. Kosygina 4, Moscow 119994, Russian Federation, and Department of Chemistry, Rice University, Houston, Texas 77005., Nemukhin AV; Department of Chemistry, M.V. Lomonosov Moscow State University, Leninskie Gory 1/3, Moscow 119991, and N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, ul. Kosygina 4, Moscow 119994, Russian Federation, and Department of Chemistry, Rice University, Houston, Texas 77005., Akimov AV; Department of Chemistry, M.V. Lomonosov Moscow State University, Leninskie Gory 1/3, Moscow 119991, and N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, ul. Kosygina 4, Moscow 119994, Russian Federation, and Department of Chemistry, Rice University, Houston, Texas 77005., Kolomeisky AB; Department of Chemistry, M.V. Lomonosov Moscow State University, Leninskie Gory 1/3, Moscow 119991, and N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, ul. Kosygina 4, Moscow 119994, Russian Federation, and Department of Chemistry, Rice University, Houston, Texas 77005.
Jazyk:	angličtina
Zdroj:	Journal of chemical theory and computation [J Chem Theory Comput] 2010 Sep 14; Vol. 6 (9), pp. 2581-90.
DOI:	10.1021/ct100101y
Abstrakt:	Methodical problems of coarse-grained-type molecular dynamics, namely, rigid-body molecular dynamics (RB MD), are studied by investigating the dynamics of nanosized molecular vehicles called nanocars that move on gold and silver surfaces. Specifically, we analyzed the role of thermostats and the effects of temperature, couplings, and correlations between rigid fragments of the nanocar molecule in extensive RB MD simulations. It is found that the use of the Nosé-Poincaré thermostat does not introduce systematic errors, but the time trajectories might be required to be limited to not accumulate large numerical integration errors. Correlations in the motion of different fragments of the molecules are also analyzed. Our theoretical computations also point to the importance of temperature, interfragment interactions, and interactions with surfaces and to the nature of the surface for understanding mechanisms of motion of single-molecule transporters.
Databáze:	MEDLINE
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