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Statements

Subject Item
n2:RIV%2F60461373%3A22310%2F13%3A43895104%21RIV14-MSM-22310___
rdf:type
skos:Concept n9:Vysledek
rdfs:seeAlso
http://pubs.rsc.org/en/content/articlepdf/2013/cp/c3cp44383c?page=search
dcterms:description
Structural biology and bioinformatics studies revealed that DNA backbone in experimental structures samples a wide range of distinct conformational substates. In this study we report the benchmark database of MP2 calculations extrapolated to the complete basis set of atomic orbitals with aug-cc-pVTZ and aug-cc-pVQZ basis sets, MP2(T,Q), augmented by DCCSD(T)/aug-cc-pVDZ corrections. The calculations are performed in the gas phase as well as using a COSMO solvent model. This study includes a complete set of 18 established and biochemically most important DNA backbone families, and several other salient conformations that we identified in experimental structures. We utilize an electronically sufficiently complete DNA sugar?phosphate?sugar (SPS) backbone model system truncated to prevent undesired intramolecular interactions. The BLYP and TPSS functionals supplemented with Grimme?s D3(BJ) dispersion term provide the best tradeoff between computational demands and accuracy. Among the tested methods, the best agreement with the benchmark database has been obtained for the double-hybrid DSD-BLYP functional in combination with a quadruple-z basis set. The new hybrid density functionals PW6B95-D3 and MPW1B95-D3 yield outstanding results and even slightly outperform the computationally more demanding PWPB95 double-hybrid functional. B3LYP-D3 is somewhat less accurate compared to the other hybrids. Extrapolated MP2(D,T) calculations are not as accurate as the less demanding DFT-D3 methods. Preliminary force field tests using several charge sets reveal an almost order of magnitude larger deviations from the reference QM data compared to modern DFT-D3. As expected, inclusion of the solvent environment approximated by a continuum approach has a large impact on the relative stabilities of different backbone substates, and is important when comparing the QM data with structural bioinformatics and other experimental data. Structural biology and bioinformatics studies revealed that DNA backbone in experimental structures samples a wide range of distinct conformational substates. In this study we report the benchmark database of MP2 calculations extrapolated to the complete basis set of atomic orbitals with aug-cc-pVTZ and aug-cc-pVQZ basis sets, MP2(T,Q), augmented by DCCSD(T)/aug-cc-pVDZ corrections. The calculations are performed in the gas phase as well as using a COSMO solvent model. This study includes a complete set of 18 established and biochemically most important DNA backbone families, and several other salient conformations that we identified in experimental structures. We utilize an electronically sufficiently complete DNA sugar?phosphate?sugar (SPS) backbone model system truncated to prevent undesired intramolecular interactions. The BLYP and TPSS functionals supplemented with Grimme?s D3(BJ) dispersion term provide the best tradeoff between computational demands and accuracy. Among the tested methods, the best agreement with the benchmark database has been obtained for the double-hybrid DSD-BLYP functional in combination with a quadruple-z basis set. The new hybrid density functionals PW6B95-D3 and MPW1B95-D3 yield outstanding results and even slightly outperform the computationally more demanding PWPB95 double-hybrid functional. B3LYP-D3 is somewhat less accurate compared to the other hybrids. Extrapolated MP2(D,T) calculations are not as accurate as the less demanding DFT-D3 methods. Preliminary force field tests using several charge sets reveal an almost order of magnitude larger deviations from the reference QM data compared to modern DFT-D3. As expected, inclusion of the solvent environment approximated by a continuum approach has a large impact on the relative stabilities of different backbone substates, and is important when comparing the QM data with structural bioinformatics and other experimental data.
dcterms:title
Benchmark quantum-chemical calculations on a complete set of rotameric families of the DNA sugar-phosphate backbone and their comparison with modern density functional theory Benchmark quantum-chemical calculations on a complete set of rotameric families of the DNA sugar-phosphate backbone and their comparison with modern density functional theory
skos:prefLabel
Benchmark quantum-chemical calculations on a complete set of rotameric families of the DNA sugar-phosphate backbone and their comparison with modern density functional theory Benchmark quantum-chemical calculations on a complete set of rotameric families of the DNA sugar-phosphate backbone and their comparison with modern density functional theory
skos:notation
RIV/60461373:22310/13:43895104!RIV14-MSM-22310___
n9:predkladatel
n14:orjk%3A22310
n3:aktivita
n22:I n22:P n22:V n22:Z
n3:aktivity
I, P(ED1.1.00/02.0068), P(ED2.1.00/03.0058), P(EE2.3.20.0017), P(GAP208/11/1822), V, Z(AV0Z50040702)
n3:cisloPeriodika
19
n3:dodaniDat
n15:2014
n3:domaciTvurceVysledku
n17:5520991
n3:druhVysledku
n21:J
n3:duvernostUdaju
n8:S
n3:entitaPredkladatele
n19:predkladatel
n3:idSjednocenehoVysledku
63075
n3:idVysledku
RIV/60461373:22310/13:43895104
n3:jazykVysledku
n18:eng
n3:klicovaSlova
COSMO; molecular mechanics; ab initio, DFT; conformation; backbone; DNA
n3:klicoveSlovo
n7:molecular%20mechanics n7:backbone n7:conformation n7:ab%20initio n7:DNA n7:DFT n7:COSMO
n3:kodStatuVydavatele
GB - Spojené království Velké Británie a Severního Irska
n3:kontrolniKodProRIV
[269811B4BF80]
n3:nazevZdroje
Physical Chemistry Chemical Physics
n3:obor
n16:CF
n3:pocetDomacichTvurcuVysledku
1
n3:pocetTvurcuVysledku
9
n3:projekt
n4:GAP208%2F11%2F1822 n4:EE2.3.20.0017 n4:ED2.1.00%2F03.0058 n4:ED1.1.00%2F02.0068
n3:rokUplatneniVysledku
n15:2013
n3:svazekPeriodika
15
n3:tvurceVysledku
Krepl, Miroslav Šponer, Jiří Banáš, Pavel Čech, Petr Mládek, Arnošt Svozil, Daniel Otyepka, Michal Jurečka, Petr Zgarbová, Marie
n3:wos
000317980600036
n3:zamer
n6:AV0Z50040702
s:issn
1463-9076
s:numberOfPages
16
n10:doi
10.1039/C3CP44383C
n11:organizacniJednotka
22310