| KRUSE, Holger, Marek HAVRILA a Jiří ŠPONER. QM Computations on Complete Nucleic Acids Building Blocks: Analysis of the Sarcin-Ricin RNA Motif Using DFT-D3, HF-3c, PM6-D3H, and MM Approaches. Journal of Chemical Theory and Computation. Washington: American Chemical Society, roč. 10, č. 6, s. 2615-2629. ISSN 1549-9618. doi:10.1021/ct500183w. 2014. |
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@article{1200002,
author = {Kruse, Holger and Havrila, Marek and Šponer, Jiří},
article_location = {Washington},
article_number = {6},
doi = {http://dx.doi.org/10.1021/ct500183w},
keywords = {DENSITY-FUNCTIONAL THEORY; MOLECULAR-DYNAMICS SIMULATIONS; QUANTUM-CHEMICAL COMPUTATIONS; BASE-PHOSPHATE INTERACTIONS; AUXILIARY BASIS-SETS; PARTICLE MESH EWALD; AMBER FORCE-FIELD; NONCOVALENT INTERACTIONS; INTERACTION ENERGIES; STRUCTURAL BIOLOGY},
language = {eng},
issn = {1549-9618},
journal = {Journal of Chemical Theory and Computation},
title = {QM Computations on Complete Nucleic Acids Building Blocks: Analysis of the Sarcin-Ricin RNA Motif Using DFT-D3, HF-3c, PM6-D3H, and MM Approaches},
url = {http://pubs.acs.org/doi/abs/10.1021/ct500183w},
volume = {10},
year = {2014}
}
TY - JOUR
ID - 1200002
AU - Kruse, Holger - Havrila, Marek - Šponer, Jiří
PY - 2014
TI - QM Computations on Complete Nucleic Acids Building Blocks: Analysis of the Sarcin-Ricin RNA Motif Using DFT-D3, HF-3c, PM6-D3H, and MM Approaches
JF - Journal of Chemical Theory and Computation
VL - 10
IS - 6
SP - 2615-2629
EP - 2615-2629
PB - American Chemical Society
SN - 15499618
KW - DENSITY-FUNCTIONAL THEORY
KW - MOLECULAR-DYNAMICS SIMULATIONS
KW - QUANTUM-CHEMICAL COMPUTATIONS
KW - BASE-PHOSPHATE INTERACTIONS
KW - AUXILIARY BASIS-SETS
KW - PARTICLE MESH EWALD
KW - AMBER FORCE-FIELD
KW - NONCOVALENT INTERACTIONS
KW - INTERACTION ENERGIES
KW - STRUCTURAL BIOLOGY
UR - http://pubs.acs.org/doi/abs/10.1021/ct500183w
L2 - http://pubs.acs.org/doi/abs/10.1021/ct500183w
N2 - A set of conformations obtained from explicit solvent molecular dynamics (MD) simulations of the Sarcin-Ricin internal loop (SRL) RNA motif is investigated using quantum mechanical (QM, TPSS-D3/def2-TZVP DFT-D3) and molecular mechanics (MM, AMBER parm99bsc0+chi(ol3) force field) methods. Solvent effects are approximated using implicit solvent methods (COSMO for DFT-D3; GB and PB for MM). Large-scale DFT-D3 optimizations of the full 11-nucleotide motif are compared to MM results and reveal a higher flexibility of DFT-D3 over the MM in the optimization procedure. Conformational energies of the SRL motif expose significant differences in the DFT-D3 and MM energy descriptions that explain difficulties in MD simulations of the SRL motif. The TPSS-D3 data are in excellent agreement with results obtained by the hybrid functionals PW6B95-D3 and M06-2X. Computationally more efficient methods such as PM6-D3H and HF-3c show promising but partly inconsistent results. It is demonstrated that large-scale DFT-D3 computations on complete nucleic acids building blocks are a viable tool to complement the picture obtained from MD simulations and can be used as benchmarks for faster computational methods. Methodological challenges of large-scale QM computations on nucleic acids such as missing solvent-solute interactions and the truncation of the studied systems are discussed.
ER -
KRUSE, Holger, Marek HAVRILA a Jiří ŠPONER. QM Computations on Complete Nucleic Acids Building Blocks: Analysis of the Sarcin-Ricin RNA Motif Using DFT-D3, HF-3c, PM6-D3H, and MM Approaches. \textit{Journal of Chemical Theory and Computation}. Washington: American Chemical Society, roč.~10, č.~6, s.~2615-2629. ISSN~1549-9618. doi:10.1021/ct500183w. 2014.
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