Conformational Energies of DNA Sugar Phosphate Backbone: Reference QM Calculations and a Comparison with Density Functional Theory and Molecular Mechanics

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216224%3A14310%2F10%3A00046151" target="_blank" >RIV/00216224:14310/10:00046151 - isvavai.cz</a>

Nalezeny alternativní kódy

RIV/68081707:_____/10:00356082 RIV/61989592:15310/10:10215631

Výsledek na webu

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DOI - Digital Object Identifier

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Jazyk výsledku

angličtina

Název v původním jazyce

Conformational Energies of DNA Sugar Phosphate Backbone: Reference QM Calculations and a Comparison with Density Functional Theory and Molecular Mechanics

Popis výsledku v původním jazyce

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 alpha/gamma torsion angles in the g+/t region, and 3 real noncanonical gamma-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 phosphodiester bond (SPSOM model). In order to get conformation of the studied system fully under control, for each calculation we have frozenmajority of the dihedral angles to their target values. CCSD(T) energies extrapolated to the complete basis set were utilized as reference values.

Název v anglickém jazyce

Conformational Energies of DNA Sugar Phosphate Backbone: Reference QM Calculations and a Comparison with Density Functional Theory and Molecular Mechanics

Popis výsledku anglicky

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 alpha/gamma torsion angles in the g+/t region, and 3 real noncanonical gamma-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 phosphodiester bond (SPSOM model). In order to get conformation of the studied system fully under control, for each calculation we have frozenmajority of the dihedral angles to their target values. CCSD(T) energies extrapolated to the complete basis set were utilized as reference values.

Druh

J_x - Nezařazeno - Článek v odborném periodiku (Jimp, Jsc a Jost)

CEP obor

BO - Biofyzika

OECD FORD obor

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Projekt

Výsledek vznikl pri realizaci vícero projektů. Více informací v záložce Projekty.

Návaznosti

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)<br>Z - Vyzkumny zamer (s odkazem do CEZ)

Rok uplatnění

2010

Kód důvěrnosti údajů

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Název periodika

Journal of Chemical Theory and Computation

ISSN

1549-9618

e-ISSN

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Svazek periodika

6/2010

Číslo periodika v rámci svazku

12

Stát vydavatele periodika

CZ - Česká republika

Počet stran výsledku

19

Strana od-do

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Kód UT WoS článku

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EID výsledku v databázi Scopus

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