Počet záznamů: 1  

Energies and 2 '-Hydroxyl Group Orientations of RNA Backbone Conformations. Benchmark CCSD(T)/CBS Database, Electronic Analysis, and Assessment of DFT Methods and MD Simulations

  1. 1.
    0435465 - BFÚ 2015 RIV US eng J - Článek v odborném periodiku
    Mládek, Arnošt - Banáš, P. - Jurečka, P. - Otyepka, M. - Zgarbová, M. - Šponer, Jiří
    Energies and 2 '-Hydroxyl Group Orientations of RNA Backbone Conformations. Benchmark CCSD(T)/CBS Database, Electronic Analysis, and Assessment of DFT Methods and MD Simulations.
    Journal of Chemical Theory and Computation. Roč. 10, č. 1 (2014), s. 463-480. ISSN 1549-9618. E-ISSN 1549-9626
    Grant CEP: GA ČR(CZ) GAP208/12/1878; GA MŠMT(CZ) ED1.1.00/02.0068
    Institucionální podpora: RVO:68081707
    Klíčová slova: DENSITY-FUNCTIONAL THEORY * SUGAR-PHOSPHATE BACKBONE * QUANTUM-CHEMICAL CALCULATIONS
    Kód oboru RIV: BO - Biofyzika
    Impakt faktor: 5.498, rok: 2014

    Sugar-phosphate backbone is an electronically complex molecular segment imparting RNA molecules high flexibility and architectonic heterogeneity necessary for their biological functions. The structural variability of RNA molecules is amplified by the presence of the 2'-hydroxyl group, capable of forming multitude of intra- and intermolecular interactions. Bioinformatics studies based on X-ray structure database revealed that RNA backbone samples at least 46 substates known as rotameric families. The present study provides a comprehensive analysis of RNA backbone conformational preferences and 2'-hydroxyl group orientations. First, we create a benchmark database of estimated CCSD(T)/CBS relative energies of all rotameric families and test performance of dispersion-corrected DFT-D3 methods and molecular mechanics in vacuum and in continuum solvent. The performance of the DFT-D3 methods is in general quite satisfactory. The B-LYP-D3 method provides the best trade-off between accuracy and computational demands. B3-LYP-D3 slightly outperforms the new PW6B95-D3 and MPW1B95-D3 and is the second most accurate density functional of the study.
    Trvalý link: http://hdl.handle.net/11104/0239335

     
     
Počet záznamů: 1  

  Tyto stránky využívají soubory cookies, které usnadňují jejich prohlížení. Další informace o tom jak používáme cookies.