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  • 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 Møller–Plesset 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.
  • 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 Møller–Plesset 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)
  • Povrchy potenctialní energie vybraných trimerů bází nukleových kyselin byly zkoumaány metodu molekulové dynamiky spojené s quenchingem. Nejstabilnější struktury pak byly dále reoptimizovány metodou MP2. Bylo zjištěno že narozdíl od nemethylovaných trimerů, pro které jsou preferovány planární vodíkově vázané struktury, jsou u methylovaných trimerů preferovány struktury v patrovém uspařádání páru zatímco třetí báze je na tento pár orientována téměř kolmo. (cs)
Title
  • DNA base trimers: empirical and quantum chemical ab initio calculations
  • Trimery bází nukleových kyselin – empirické a kvantově chemické výpočty - srovnání s experimentem ve vakuu (cs)
  • DNA base trimers: empirical and quantum chemical ab initio calculations (en)
skos:prefLabel
  • DNA base trimers: empirical and quantum chemical ab initio calculations
  • Trimery bází nukleových kyselin – empirické a kvantově chemické výpočty - srovnání s experimentem ve vakuu (cs)
  • DNA base trimers: empirical and quantum chemical ab initio calculations (en)
skos:notation
  • RIV/61388963:_____/07:00090298!RIV08-AV0-61388963
http://linked.open.../vavai/riv/strany
  • 2067;2077
http://linked.open...avai/riv/aktivita
http://linked.open...avai/riv/aktivity
  • P(GA203/05/0009), P(LC512), Z(AV0Z40550506)
http://linked.open...iv/cisloPeriodika
  • 7
http://linked.open...vai/riv/dodaniDat
http://linked.open...aciTvurceVysledku
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http://linked.open...iv/duvernostUdaju
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  • 417765
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  • RIV/61388963:_____/07:00090298
http://linked.open...riv/jazykVysledku
http://linked.open.../riv/klicovaSlova
  • ab initio calculations; nucleic acid bases trimer; empirical force field; Amber; potential energy surface (en)
http://linked.open.../riv/klicoveSlovo
http://linked.open...odStatuVydavatele
  • DE - Spolková republika Německo
http://linked.open...ontrolniKodProRIV
  • [67C49296EBF3]
http://linked.open...i/riv/nazevZdroje
  • Chemistry - A European Journal
http://linked.open...in/vavai/riv/obor
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http://linked.open...vavai/riv/projekt
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http://linked.open...v/svazekPeriodika
  • 13
http://linked.open...iv/tvurceVysledku
  • Hobza, Pavel
  • Kabeláč, Martin
  • Cramer, Ch. J.
  • Sherer, E. C.
http://linked.open...n/vavai/riv/zamer
issn
  • 0947-6539
number of pages
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