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

Logo poskytovatele
Logo poskytovatele
Logo poskytovatele

Varování

Publikace nespadá pod Filozofickou fakultu, ale pod Středoevropský technologický institut. Oficiální stránka publikace je na webu muni.cz.
Autoři

KRUSE Holger HAVRILA Marek ŠPONER Jiří

Rok publikování 2014
Druh Článek v odborném periodiku
Časopis / Zdroj Journal of Chemical Theory and Computation
Fakulta / Pracoviště MU

Středoevropský technologický institut

Citace
www http://pubs.acs.org/doi/abs/10.1021/ct500183w
Doi http://dx.doi.org/10.1021/ct500183w
Obor Fyzikální chemie a teoretická chemie
Klíčová slova 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
Popis 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.
Související projekty:

Používáte starou verzi internetového prohlížeče. Doporučujeme aktualizovat Váš prohlížeč na nejnovější verzi.