title: Potential energy surfaces of an adenine-thymine base pair and its methylated analogue in the presence of one and two water molecules: molecular mechanics and correlated ab initio study.
abstract: Potential energy surfaces of monohydrated and dihydrated adenine-thymine and 9-methyladenine-1-methylthymine base pairs were examined by the molecular dynamics/quenching technique using the Cornell et al. force field (J. Am. Chem. Soc. 1995, 117, 5179). Long runs of molecular dynamics/quenching calculations allowed us to evaluate the free energy surface. The most stable and populated structures found were fully reoptimized at the correlated ab initio level employing the resolution of identity Møller-Plesset method. A systematic study of the base pairs' microhydration using both the empirical and the high-level correlated ab initio approaches is presented for the first time. We show that the occurrence of water molecules and their gradually increasing number as well as the methylation of the bases favor stacked structures over the planar hydrogen-bonded ones. These results based on the correlated ab initio calculations are in the excellent agreement with data obtained from our previous empirical potential molecular dynamics study (Kabelác et al. Chem.-Eur. J. 2001, 7, 2067).
authors.affiliation: Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, and Center for Biomolecules and Complex Molecular Systems, 166 10 Prague 6, Czech Republic.
authors.forename: Martin
authors.initials: M
authors.lastname: Kabelác
authors.forename: Lucie
authors.initials: L
authors.lastname: Zendlová
authors.forename: David
authors.initials: D
authors.lastname: Reha
authors.forename: Pavel
authors.initials: P
authors.lastname: Hobza
mesh_terms: D000225:Adenine / Q000031:analogs & derivatives / Q000737:chemistry*; D020029:Base Pairing; D003198:Computer Simulation; D008745:Methylation; D008958:Models, Molecular; D015394:Molecular Structure; D013941:Thymine / Q000031:analogs & derivatives / Q000737:chemistry*; D014867:Water / Q000737:chemistry*
chemical_list: D014867:Water; D000225:Adenine; D013941:Thymine