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@article{1373983,
author = {Szabla, Rafal and Havrila, Marek and Kruse, Holger and Šponer, Jiří},
article_location = {WASHINGTON},
article_number = {41},
doi = {http://dx.doi.org/10.1021/acs.jpcb.6b07551},
keywords = {MOLECULAR-DYNAMICS SIMULATIONS; QUANTUM-CHEMICAL COMPUTATIONS; AUXILIARY BASIS-SETS; PARTICLE MESH EWALD; DIRECT-COSMO-RS; B-DNA STRUCTURE; PHOSPHATE BACKBONE; EXPLICIT-SOLVENT; NUCLEIC-ACIDS; FREE-ENERGIES},
language = {eng},
issn = {1520-6106},
journal = {Journal of Physical Chemistry B},
title = {Comparative Assessment of Different RNA Tetranucleotides from the DFT-D3 and Force Field Perspective},
url = {http://pubs.acs.org/doi/abs/10.1021/acs.jpcb.6b07551},
volume = {120},
year = {2016}
}
TY - JOUR
ID - 1373983
AU - Szabla, Rafal - Havrila, Marek - Kruse, Holger - Šponer, Jiří
PY - 2016
TI - Comparative Assessment of Different RNA Tetranucleotides from the DFT-D3 and Force Field Perspective
JF - Journal of Physical Chemistry B
VL - 120
IS - 41
SP - 10635-10648
EP - 10635-10648
PB - AMER CHEMICAL SOC
SN - 15206106
KW - MOLECULAR-DYNAMICS SIMULATIONS
KW - QUANTUM-CHEMICAL COMPUTATIONS
KW - AUXILIARY BASIS-SETS
KW - PARTICLE MESH EWALD
KW - DIRECT-COSMO-RS
KW - B-DNA STRUCTURE
KW - PHOSPHATE BACKBONE
KW - EXPLICIT-SOLVENT
KW - NUCLEIC-ACIDS
KW - FREE-ENERGIES
UR - http://pubs.acs.org/doi/abs/10.1021/acs.jpcb.6b07551
L2 - http://pubs.acs.org/doi/abs/10.1021/acs.jpcb.6b07551
N2 - Classical force field (FF) molecular dynamics (MD) simulations of RNA tetranucleotides have substantial problems in reproducing conformer populations indicated by NMR experiments. To provide more information about the possible sources of errors, we performed quantum mechanical (QM, TPSS-D3/def2-TZVP) and molecular mechanics (MM, AMBER parm99bsc0+X-OL3) calculations of different r(CCCC), r(GACC), and r(UUUU) conformers obtained from explicit solvent MD simulations. Solvent effects in the static QM and MM calculations were mimicked using implicit solvent models (COSMO and Poisson-Boltzmann, respectively). The comparison of QM and MM geometries and energies revealed that the two methodologies provide qualitatively consistent results in most of the cases. Even though we found some differences, these were insufficient to indicate any systematic corrections of the RNA FF terms that could improve the performance of classical MD in simulating tetranucleotides. On the basis of these findings, we inferred that the overpopulation of intercalated conformers in the MD simulations of RNA tetramers, which were not observed experimentally, might be predominantly caused by imbalanced water-solvent and water-water interactions. Apart from the large-scale QM calculations performed to assess the performance of the AMBER FF, a representative spectrum of faster QM methods was tested.
ER -
SZABLA, Rafal, Marek HAVRILA, Holger KRUSE a Jiří ŠPONER. Comparative Assessment of Different RNA Tetranucleotides from the DFT-D3 and Force Field Perspective. \textit{Journal of Physical Chemistry B}. WASHINGTON: AMER CHEMICAL SOC, 2016, roč.~120, č.~41, s.~10635-10648. ISSN~1520-6106. Dostupné z: https://dx.doi.org/10.1021/acs.jpcb.6b07551.
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