Quantum-Mechanical Molecular Dynamics of Charge Transfer

Victor M. Anisimov, Claudio N. Cavasotto

Research output: Chapter in Book/Report/Conference proceedingChapter

Abstract

Computational studies of biological macromolecules are challenging due to large size of biomolecules, their conformational flexibility, and the need in explicit water solvation in order to simulate conditions close to experiment. Under these circumstances studying molecular systems via quantum-mechanical calculations becomes exceedingly difficult. Natural is the attempt to reduce the complex quantum-mechanical picture to a more tractable one by accommodating classical-mechanical principles. However, the simplified models may overlook important physics details of atomic interactions. To avoid such potential pitfalls higher level of theory methods should be available to conduct validation studies. Using semiempirical linear scaling quantum-mechanical LocalSCF method we performed molecular dynamics simulation of ubiquitin in explicit water. The simulation revealed various deviations from the classical mechanics picture. The average charge on amino acids varied depending on their environment. We observed charge transfer channels transmitting electric charge between amino acids in sync with protein motion. We also noticed that the excess charge transferred from protein to water creates a charge cloud around the protein. The observed global dynamic effects of charge transfer represent a new previously unaccounted degree of freedom of biomolecules which requires QM treatment in order to obtain more accurate dynamics of biomolecules at atomic resolution.

Original languageEnglish (US)
Title of host publicationChallenges and Advances in Computational Chemistry and Physics
PublisherSpringer
Pages247-266
Number of pages20
DOIs
StatePublished - 2010

Publication series

NameChallenges and Advances in Computational Chemistry and Physics
Volume12
ISSN (Print)2542-4491
ISSN (Electronic)2542-4483

Keywords

  • Charge transfer
  • Linear scaling
  • LocalSCF
  • NDDO method
  • PM5 Hamiltonian
  • QM MD
  • Spherical boundary potential
  • Ubiquitin
  • VFL approximation
  • Water droplet

ASJC Scopus subject areas

  • Computer Science Applications
  • Chemistry (miscellaneous)
  • Physics and Astronomy (miscellaneous)

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