. . . . "13" . "ab initio calculations; nucleic acid bases trimer; empirical force field; Amber; potential energy surface"@en . . "0947-6539" . . . "DE - Spolkov\u00E1 republika N\u011Bmecko" . "2067;2077" . "DNA base trimers: empirical and quantum chemical ab initio calculations"@en . . . "7" . "P(GA203/05/0009), P(LC512), Z(AV0Z40550506)" . "Povrchy potenctialn\u00ED energie vybran\u00FDch trimer\u016F b\u00E1z\u00ED nukleov\u00FDch kyselin byly zkouma\u00E1ny metodu molekulov\u00E9 dynamiky spojen\u00E9 s quenchingem. Nejstabiln\u011Bj\u0161\u00ED struktury pak byly d\u00E1le reoptimizov\u00E1ny metodou MP2. Bylo zji\u0161t\u011Bno \u017Ee narozd\u00EDl od nemethylovan\u00FDch trimer\u016F, pro kter\u00E9 jsou preferov\u00E1ny plan\u00E1rn\u00ED vod\u00EDkov\u011B v\u00E1zan\u00E9 struktury, jsou u methylovan\u00FDch trimer\u016F preferov\u00E1ny struktury v patrov\u00E9m uspa\u0159\u00E1d\u00E1n\u00ED p\u00E1ru zat\u00EDmco t\u0159et\u00ED b\u00E1ze je na tento p\u00E1r orientov\u00E1na t\u00E9m\u011B\u0159 kolmo."@cs . "DNA base trimers: empirical and quantum chemical ab initio calculations" . "DNA base trimers: empirical and quantum chemical ab initio calculations"@en . "Chemistry - A European Journal" . . "Sherer, E. C." . "417765" . . "2"^^ . "11"^^ . "4"^^ . "Trimery b\u00E1z\u00ED nukleov\u00FDch kyselin \u2013 empirick\u00E9 a kvantov\u011B chemick\u00E9 v\u00FDpo\u010Dty - srovn\u00E1n\u00ED s experimentem ve vakuu"@cs . . "A complete scan of the potential energy surfaces for selected DNA base trimers has been performed by a molecular dynamics/quenching technique using the force field of Cornell et al. implemented in the AMBER7 program. The resulting most stable/populated structures were then reoptimized at a correlated ab initio level employing Resolution of the Identity M\u00F8ller\u2013Plesset second-order perturbation theory (RI-MP2). We found that stacked structures of two bases with the third base in a T-shape arrangement are the global minima in all of the methylated systems: they are more stable than the cyclic planar structures by about 10 kcalmol-1. The different behavior of non-methylated and methylated trimers is discussed."@en . "RIV/61388963:_____/07:00090298" . . . "RIV/61388963:_____/07:00090298!RIV08-AV0-61388963" . "Trimery b\u00E1z\u00ED nukleov\u00FDch kyselin \u2013 empirick\u00E9 a kvantov\u011B chemick\u00E9 v\u00FDpo\u010Dty - srovn\u00E1n\u00ED s experimentem ve vakuu"@cs . . . . . "[67C49296EBF3]" . "Hobza, Pavel" . "DNA base trimers: empirical and quantum chemical ab initio calculations" . . . "Kabel\u00E1\u010D, Martin" . "A complete scan of the potential energy surfaces for selected DNA base trimers has been performed by a molecular dynamics/quenching technique using the force field of Cornell et al. implemented in the AMBER7 program. The resulting most stable/populated structures were then reoptimized at a correlated ab initio level employing Resolution of the Identity M\u00F8ller\u2013Plesset second-order perturbation theory (RI-MP2). We found that stacked structures of two bases with the third base in a T-shape arrangement are the global minima in all of the methylated systems: they are more stable than the cyclic planar structures by about 10 kcalmol-1. The different behavior of non-methylated and methylated trimers is discussed." . "Cramer, Ch. J." . .