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@article{1312045,
author = {Gresh, Nohad and Šponerová, Judit and Devereux, Mike and Gkionis, Konstantinos and Courcy de, Benoit and Piquemal, JeanandPhilip and Šponer, Jiří},
article_location = {WASHINGTON},
article_number = {30},
doi = {http://dx.doi.org/10.1021/acs.jpcb.5b01695},
keywords = {DENSITY-FUNCTIONAL THEORY; DISTRIBUTED MULTIPOLE ANALYSIS; PERTURBATION-THEORY APPROACH; BASIS-SET CONVERGENCE; KOHN-SHAM ORBITALS; NUCLEIC-ACID BASES; AMBER FORCE-FIELD; DYNAMICS SIMULATIONS; CHEMICAL COMPUTATIONS; CHARGE-DISTRIBUTION},
language = {eng},
issn = {1520-6106},
journal = {Journal of Physical Chemistry B},
title = {Stacked and H-Bonded Cytosine Dimers. Analysis of the Intermolecular Interaction Energies by Parallel Quantum Chemistry and Polarizable Molecular Mechanics.},
url = {http://pubs.acs.org/doi/pdf/10.1021/acs.jpcb.5b01695},
volume = {119},
year = {2015}
}
TY - JOUR
ID - 1312045
AU - Gresh, Nohad - Šponerová, Judit - Devereux, Mike - Gkionis, Konstantinos - Courcy de, Benoit - Piquemal, Jean-Philip - Šponer, Jiří
PY - 2015
TI - Stacked and H-Bonded Cytosine Dimers. Analysis of the Intermolecular Interaction Energies by Parallel Quantum Chemistry and Polarizable Molecular Mechanics.
JF - Journal of Physical Chemistry B
VL - 119
IS - 30
SP - 9477-9495
EP - 9477-9495
PB - AMER CHEMICAL SOC
SN - 15206106
KW - DENSITY-FUNCTIONAL THEORY
KW - DISTRIBUTED MULTIPOLE ANALYSIS
KW - PERTURBATION-THEORY APPROACH
KW - BASIS-SET CONVERGENCE
KW - KOHN-SHAM ORBITALS
KW - NUCLEIC-ACID BASES
KW - AMBER FORCE-FIELD
KW - DYNAMICS SIMULATIONS
KW - CHEMICAL COMPUTATIONS
KW - CHARGE-DISTRIBUTION
UR - http://pubs.acs.org/doi/pdf/10.1021/acs.jpcb.5b01695
L2 - http://pubs.acs.org/doi/pdf/10.1021/acs.jpcb.5b01695
N2 - Until now, atomistic simulations of DNA and RNA and their complexes have been executed using well calibrated but conceptually simple pair-additive empirical potentials (force fields). Although such simulations Provided Many valuable results, it is well established that simple force fields also introduce errors into the description, underlying the need for development of alternative anisotropic, polarizable molecular mechanics (APMM) potentials. One of the most abundant forces in all kinds of nucleic acids topologies is base stacking. Intra- and interstrand stacking is assumed to be the most essential factor affecting local conformational variations of B-DNA. However, stacking also contributes to formation of all kinds of noncanonical nucleic acids structures, such as quadruplexes or folded RNAs. The present study focuses on 14 stacked cytosine (Cyt) dimers and the doubly H-bonded dimer. We evaluate the extent to which an APMM procedure, SIBFA, could account quantitatively for the results of high-level quantum chemistry (QC) on the total interaction energies, and the individual energy contributions and their nonisotropic behaviors. Good agreements are found at both uncorrelated HF and correlated DFT and CCSD(T) levels. Resorting in SIBFA to distributed QC multipoles and to an explicit representation of the lone pairs is essential to respectively account for the anisotropies of the Coulomb and of the exchange-repulsion QC contributions.
ER -
GRESH, Nohad, Judit ŠPONEROVÁ, Mike DEVEREUX, Konstantinos GKIONIS, Benoit COURCY DE, Jean-Philip PIQUEMAL a Jiří ŠPONER. Stacked and H-Bonded Cytosine Dimers. Analysis of the Intermolecular Interaction Energies by Parallel Quantum Chemistry and Polarizable Molecular Mechanics. \textit{Journal of Physical Chemistry B}. WASHINGTON: AMER CHEMICAL SOC, 2015, roč.~119, č.~30, s.~9477-9495. ISSN~1520-6106. Dostupné z: https://dx.doi.org/10.1021/acs.jpcb.5b01695.
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