title: How to understand quantum chemical computations on DNA and RNA systems? A practical guide for non-specialists.
abstract: In this review primarily written for non-experts we explain basic methodological aspects and interpretation of modern quantum chemical (QM) computations applied to nucleic acids. We introduce current reference QM computations on small model systems consisting of dozens of atoms. Then we comment on recent advance of fast and accurate dispersion-corrected density functional theory methods, which will allow computations of small but complete nucleic acids building blocks in the near future. The qualitative difference between QM and molecular mechanics (MM, force field) computations is discussed. We also explain relation of QM and molecular simulation computations to experiments.
authors.affiliation: Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolská 135, 612 65 Brno, Czech Republic; CEITEC - Central European Institute of Technology, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic. Electronic address: sponer@ncbr.muni.cz.
authors.forename: Jiří
authors.initials: J
authors.lastname: Šponer
authors.forename: Judit E
authors.initials: JE
authors.lastname: Šponer
authors.forename: Arnošt
authors.initials: A
authors.lastname: Mládek
authors.forename: Pavel
authors.initials: P
authors.lastname: Banáš
authors.forename: Petr
authors.initials: P
authors.lastname: Jurečka
authors.forename: Michal
authors.initials: M
authors.lastname: Otyepka
mesh_terms: D003198:Computer Simulation; D004247:DNA / Q000737:chemistry*; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*
chemical_list: D012313:RNA; D004247:DNA
keywords: DNA structure; Molecular mechanics; Molecular structures and energies; Quantum chemistry