title: Structure, energetics, vibrational frequencies and charge transfer of base pairs, nucleoside pairs, nucleotide pairs and B-DNA pairs of trinucleotides: ab initio HF/MINI-1 and empirical force field study.
abstract: Geometries, interaction energies and vibrational frequencies of base pairs, nucleoside pairs and nucleotide pairs were studied by ab initio Hartree-Fock (HF) method using MINI-1 basis set and empirical Cornell et al. force field (AMBER 4.1). A good agreement was found between HF/MINI-1 and AMBER results. In addition, both methods provide reasonable agreement with available high-level ab initio data. Finally, AMBER potential was used to determine the structure, energetics and vibrational frequencies of B-DNA pairs of trinucleotides. Stabilization energies of clusters are lowered when passing from base pairs to nucleoside pairs, nucleotide pairs and to pairs of trinucleotides. The lowest vibrations of base pairs and nucleoside pairs correspond to intermolecular motions of bases, specifically to buckle and propeller motions. In the case of pairs of larger subunits the lowest vibrations are of intramolecular nature (rotation around glycosidic bond, sugar and phosphate vibration). The spectra of these clusters became more complicated and quasi-degenerate. Intermolecular charge transfer between bases in H-bonded and stacked pairs is negligible, while a significant intramolecular charge transfer was observed.
authors.affiliation: J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Prague.
authors.forename: M
authors.initials: M
authors.lastname: Kabelác
authors.forename: M
authors.initials: M
authors.lastname: Kratochvíl
authors.forename: J
authors.initials: J
authors.lastname: Sponer
authors.forename: P
authors.initials: P
authors.lastname: Hobza
mesh_terms: D020029:Base Pairing; D002241:Carbohydrates / Q000737:chemistry; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry*; D006860:Hydrogen Bonding; D007700:Kinetics; D008958:Models, Molecular; D010710:Phosphates / Q000737:chemistry; D012984:Software
chemical_list: D002241:Carbohydrates; D010710:Phosphates; D004247:DNA