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, 2014, roč. 10, č. 6, s. 2615-2629. ISSN 1549-9618. Dostupné z: https://dx.doi.org/10.1021/ct500183w. |
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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, 2014, roč.~10, č.~6, s.~2615-2629. ISSN~1549-9618. Dostupné z: https://dx.doi.org/10.1021/ct500183w.
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