Conformational energies of DNA sugar-phosphate backbone: Reference QM calculations and a comparison with density functional theory and molecular mechanics

0356082 - BFÚ 2011 RIV US eng J - Článek v odborném periodiku
Mládek, Arnošt - Šponer, Judit E. - Jurečka, P. - Banáš, P. - Otyepka, M. - Svozil, D. - Šponer, Jiří
Conformational energies of DNA sugar-phosphate backbone: Reference QM calculations and a comparison with density functional theory and molecular mechanics.
Journal of Chemical Theory and Computation. Roč. 6, č. 12 (2010), s. 3817-3835. ISSN 1549-9618. E-ISSN 1549-9626
Grant CEP: GA AV ČR(CZ) IAA400040802; GA ČR(CZ) GA203/09/1476; GA ČR(CZ) GAP208/10/2302
Grant ostatní: GA ČR(CZ) GD203/09/H046; GA MŠk(CZ) LC06030; GA MŠk(CZ) LC512
Program: GD; LC; LC
Výzkumný záměr: CEZ:AV0Z50040507; CEZ:AV0Z50040702
Klíčová slova: intramolecular hydrogen-bonds * main-group thermochemistry * set superposition error
Kód oboru RIV: BO - Biofyzika
Impakt faktor: 5.138, rok: 2010

The study investigates electronic structure and gas-phase energetics of the DNA sugar-phosphate backbone via advanced quantum chemical (QM) methods. The analysis has been carried out on biologically relevant backbone conformations composed of 11 canonical BI-DNA structures, 8 pathological structures with R/γ torsion angles in the g+/t region, and 3 real noncanonical γ-trans structures occurring in the loop region of guanine quadruplex DNA. The influence of backbone conformation on the intrinsic energetics was primarily studied using a model system consisting of two sugar moieties linked together via a phosphodiester bond (SPSOM model). To get the conformation of the studied system fully under control, for each calculation we have frozen majority of the dihedral angles to their target values. CCSD(T) energies extrapolated to the complete basis set were utilized as reference values.
Trvalý link: http://hdl.handle.net/11104/0194699