Conformational energies of DNA sugar-phosphate backbone: Reference QM calculations and a comparison with density functional theory and molecular mechanics

Šponer, Judit E.; Jurečka, P.; Banáš, P.; Otyepka, M.; Svozil, D.; Šponer, Jiří; Mládek, Arnošt

doi:https://dx.doi.org/10.1021/ct1004593

Počet záznamů: 1

Conformational energies of DNA sugar-phosphate backbone: Reference QM calculations and a comparison with density functional theory and molecular mechanics

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SYSNO ASEP	0356082
Druh ASEP	J - Článek v odborném periodiku
Zařazení RIV	J - Článek v odborném periodiku
Poddruh J	Článek ve WOS
Název	Conformational energies of DNA sugar-phosphate backbone: Reference QM calculations and a comparison with density functional theory and molecular mechanics
Tvůrce(i)	Mládek, Arnošt (BFU-R) Šponer, Judit E. (BFU-R)_{RID, ORCID} Jurečka, P. (CZ) Banáš, P. (CZ) Otyepka, M. (CZ) Svozil, D. (CZ) Šponer, Jiří (BFU-R)_{RID, ORCID}
Celkový počet autorů	7
Zdroj.dok.	Journal of Chemical Theory and Computation . - : American Chemical Society - ISSN 1549-9618 Roč. 6, č. 12 (2010), s. 3817-3835
Poč.str.	19 s.
Jazyk dok.	eng - angličtina
Země vyd.	US - Spojené státy americké
Klíč. slova	intramolecular hydrogen-bonds ; main-group thermochemistry ; set superposition error
Vědní obor RIV	BO - Biofyzika
CEP	IAA400040802 GA AV ČR - Akademie věd
	GA203/09/1476 GA ČR - Grantová agentura ČR
	GAP208/10/2302 GA ČR - Grantová agentura ČR
CEZ	AV0Z50040507 - BFU-R (2005-2011)
	AV0Z50040702 - BFU-R (2007-2013)
UT WOS	000285217000018
DOI	10.1021/ct1004593
Anotace	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 R/γ torsion angles in the g+/t region, and 3 real noncanonical γ-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 a phosphodiester bond (SPSOM model). To get the conformation of the studied system fully under control, for each calculation we have frozen majority of the dihedral angles to their target values. CCSD(T) energies extrapolated to the complete basis set were utilized as reference values.
Pracoviště	Biofyzikální ústav
Kontakt	Jana Poláková, polakova@ibp.cz, Tel.: 541 517 244
Rok sběru	2011

Počet záznamů: 1