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@article{1352746,
author = {Gkionis, Konstantinos and Kruse, Holger and Šponer, Jiří},
article_location = {Washington DC},
article_number = {4},
doi = {http://dx.doi.org/10.1021/acs.jctc.5b01025},
keywords = {MOLECULAR-DYNAMICS SIMULATIONS; QUANTUM-CHEMICAL COMPUTATIONS; CONTINUUM SOLVATION MODELS; DENSITY-FUNCTIONAL THEORY; SUGAR-PHOSPHATE BACKBONE; AIM TOPOLOGICAL ANALYSIS; TELOMERIC G-QUADRUPLEX; AB-INITIO CALCULATIONS},
language = {eng},
issn = {1549-9618},
journal = {Journal of Chemical Theory and Computation},
title = {Derivation of Reliable Geometries in QM Calculations of DNA Structures: Explicit Solvent QM/MM and Restrained Implicit Solvent QM Optimizations of G-Quadruplexes},
url = {http://pubs.acs.org/doi/full/10.1021/acs.jctc.5b01025},
volume = {12},
year = {2016}
}
TY - JOUR
ID - 1352746
AU - Gkionis, Konstantinos - Kruse, Holger - Šponer, Jiří
PY - 2016
TI - Derivation of Reliable Geometries in QM Calculations of DNA Structures: Explicit Solvent QM/MM and Restrained Implicit Solvent QM Optimizations of G-Quadruplexes
JF - Journal of Chemical Theory and Computation
VL - 12
IS - 4
SP - 2000-2016
EP - 2000-2016
PB - American Chemical Society
SN - 15499618
KW - MOLECULAR-DYNAMICS SIMULATIONS
KW - QUANTUM-CHEMICAL COMPUTATIONS
KW - CONTINUUM SOLVATION MODELS
KW - DENSITY-FUNCTIONAL THEORY
KW - SUGAR-PHOSPHATE BACKBONE
KW - AIM TOPOLOGICAL ANALYSIS
KW - TELOMERIC G-QUADRUPLEX
KW - AB-INITIO CALCULATIONS
UR - http://pubs.acs.org/doi/full/10.1021/acs.jctc.5b01025
L2 - http://pubs.acs.org/doi/full/10.1021/acs.jctc.5b01025
N2 - Modern dispersion-corrected DFT methods have made it possible to perform reliable QM studies on complete nucleic acid (NA) building blocks having hundreds of atoms. Such calculations, although still limited to investigations of potential energy surfaces, enhance the portfolio of computational methods applicable to NAs and offer considerably more accurate intrinsic descriptions of NAs than standard MM. However, in practice such calculations are hampered by the use of implicit solvent environments and truncation of the systems. Conventional QM optimizations are spoiled by spurious intramolecular interactions and severe structural deformations. Here we compare two approaches designed to suppress such artifacts: partially restrained continuum solvent QM and explicit solvent QM/MM optimizations. We report geometry relaxations of a set of diverse double-quartet guanine quadruplex (GQ) DNA stems. Both methods provide neat structures without major artifacts. However, each one also has distinct weaknesses. In restrained optimizations, all errors in the target geometries (i.e., low-resolution X-ray and NMR structures) are transferred to the optimized geometries. In QM/MM, the initial solvent configuration causes some heterogeneity in the geometries. Nevertheless, both approaches represent a decisive step forward compared to conventional optimizations. We refine earlier computations that revealed sizable differences in the relative energies of GQ stems computed with AMBER MM and QM. We also explore the dependence of the QM/MM results on the applied computational protocol.
ER -
GKIONIS, Konstantinos, Holger KRUSE a Jiří ŠPONER. Derivation of Reliable Geometries in QM Calculations of DNA Structures: Explicit Solvent QM/MM and Restrained Implicit Solvent QM Optimizations of G-Quadruplexes. \textit{Journal of Chemical Theory and Computation}. Washington DC: American Chemical Society, 2016, roč.~12, č.~4, s.~2000-2016. ISSN~1549-9618. Dostupné z: https://dx.doi.org/10.1021/acs.jctc.5b01025.
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