Mécanique moléculaire

Résumé

vignette|Physique à l'échelle moléculaire La mécanique moléculaire correspond à l'utilisation de la mécanique newtonienne pour modéliser la structure des systèmes moléculaires. L'approche de la mécanique moléculaire est souvent appliquée pour améliorer des structures moléculaires ou des simulations utilisant soit la dynamique moléculaire, soit la méthode de Monte-Carlo. Typiquement, la mécanique moléculaire considère l'ensemble des interactions entre une collection d'atomes sphériques reliés entre eux par des ressorts fictifs qui représentent les liaisons chimiques. La représentation de tels interactions interatomiques engendre des forces internes et sont généralement décrites par de simples fonctions mathématiques qui peuvent dépendre soit de la distance entre paires atomiques ou de leurs angles. Parfois, la loi de Hooke peut-être employée pour représenter très simplement les interactions de liaison. Les interactions entre atomes peuvent être traités soit en les assimilant à des sphè

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https://fr.wikipedia.org/wiki/M%C3%A9canique_mol%C3%A9culaire

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What Singles Out the G[8-5]C Intrastrand DNA Cross-Link? Mechanistic and Structural Insights from Quantum Mechanics/Molecular Mechanics Simulations

Chandan Patel

Naturally occurring intrastrand oxidative crosslink lesions have proven to be a potent source of endogenous DNA damage. Among the variety of lesions that can be formed and have been identified, G[8-5]C damage (in which the C8 atom of a guanine is covalently bonded to the CS atom of a nearby cytosine belonging to the same strand) occurs with a low incidence yet takes on special importance because of its high mutagenicity. Hybrid Car-Parrinello molecular dynamics simulations, rooted in density functional theory and coupled to molecular mechanics, have been performed to shed light on the cyclization process. The activation free energy of the reacting subsystem embedded in a solvated dodecamer is estimated to be similar to 12.4 kcal/mol, which is similar to 3 kcal/mol higher than the value for the prototypical G[8-5m]T lesion inferred employing the same theoretical framework [Garrec, 3., Patel, C., Rothlisberger, U., and Dumont, E. (2012) J. Am. Chem. Soc. 134, 2111-2119]. This study also situates the G[8-5m]mC lesion at an intermediate activation free energy (similar to 10.5 kcal/mol). The order of reactivity in DNA (T-center dot > mC(center dot) > C-center dot) is reversed compared to that in the reacting subsystems in the gas phase (C-center dot > mC(center dot) > T-center dot), stressing the crucial role of the solvated B-helix environment. The results of our simulations also characterize a more severe distortion for G[8-5]C than for methylene-bridged intrastrand cross-links.

Amer Chemical Soc2013

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DNA damages induced by oxidative intrastrand cross-links have been the subject of intense research during the past decade. Yet, the currently available experimental protocols used to isolate such lesions only allow to get structural information about linked dinucleotides. The detailed structure of the damaged DNA macromolecule has remained elusive. In this study we generated in silico the most frequent oxidative intrastrand cross-link adduct, G[8,S-Me]T, embedded in a solvated DNA dodecamer by means of quantum mechanics/molecular mechanics (QM/MM) Car-Parrinello simulations. The free energy of activation required to bring the reactant close together and to form the C-C covalent-bond is estimated to be similar to 40 kcal/mol. We observe that the G[8,5-Me]T tandem lesion is accommodated with almost no perturbation of the Watson-Crick hydrogen-bond network and induces bend and unwinding angles of similar to 20 degrees and 8 degrees, respectively. This rather small structural distortion of the DNA macromolecule compared to other well characterized intrastrand cross-links, such as cyclobutane pyrimidines dimers or cisplatin-DNA complex adduct, is a probable rationale for the known lack of efficient repair of oxidative damages.

2012

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Ultrafast dynamics induced by the interaction of molecules with electromagnetic fields: Several quantum, semiclassical, and classical approaches

Sergey Antipov, Swarnendu Bhattacharyya, Ursula Röthlisberger, Jiri Vanicek

Several strategies for simulating the ultrafast dynamics of molecules induced by interactions with electromagnetic fields are presented. After a brief overview of the theory of molecule-field interaction, we present several representative examples of quantum, semiclassical, and classical approaches to describe the ultrafast molecular dynamics, including the multiconfiguration time-dependent Hartree method, Bohmian dynamics, local control theory, semiclassical thawed Gaussian approximation, phase averaging, dephasing representation, molecular mechanics with proton transfer, and multipolar force fields. In addition to the general overview, some focus is given to the description of nuclear quantum effects and to the direct dynamics, in which the ab initio energies and forces acting on the nuclei are evaluated on the fly. Several practical applications, performed within the framework of the Swiss National Center of Competence in Research “Molecular Ultrafast Science and Technology,” are presented: These include Bohmian dynamics description of the collision of H with H2, local control theory applied to the photoinduced ultrafast intramolecular proton transfer, semiclassical evaluation of vibrationally resolved electronic absorption, emission, photoelectron, and time-resolved stimulated emission spectra, infrared spectroscopy of H-bonding systems, and multipolar force fields applications in the condensed phase.

2017

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