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| 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. (en)
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| 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 (en)
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| 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 (en)
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| skos:notation
| - RIV/60461373:22310/13:43895104!RIV14-MSM-22310___
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| http://linked.open...avai/predkladatel
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| http://linked.open...avai/riv/aktivita
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| http://linked.open...avai/riv/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)
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| http://linked.open...iv/cisloPeriodika
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| http://linked.open...vai/riv/dodaniDat
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| http://linked.open...aciTvurceVysledku
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| http://linked.open.../riv/druhVysledku
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| http://linked.open...iv/duvernostUdaju
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| http://linked.open...titaPredkladatele
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| http://linked.open...dnocenehoVysledku
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| http://linked.open...ai/riv/idVysledku
| - RIV/60461373:22310/13:43895104
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| http://linked.open...riv/jazykVysledku
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| http://linked.open.../riv/klicovaSlova
| - COSMO; molecular mechanics; ab initio, DFT; conformation; backbone; DNA (en)
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| http://linked.open.../riv/klicoveSlovo
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| http://linked.open...odStatuVydavatele
| - GB - Spojené království Velké Británie a Severního Irska
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| http://linked.open...ontrolniKodProRIV
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| http://linked.open...i/riv/nazevZdroje
| - Physical Chemistry Chemical Physics
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| http://linked.open...in/vavai/riv/obor
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| http://linked.open...ichTvurcuVysledku
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| http://linked.open...cetTvurcuVysledku
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| http://linked.open...vavai/riv/projekt
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| http://linked.open...UplatneniVysledku
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| http://linked.open...v/svazekPeriodika
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| http://linked.open...iv/tvurceVysledku
| - Otyepka, Michal
- Čech, Petr
- Šponer, Jiří
- Svozil, Daniel
- Mládek, Arnošt
- Banáš, Pavel
- Jurečka, Petr
- Zgarbová, Marie
- Krepl, Miroslav
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| http://linked.open...ain/vavai/riv/wos
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| http://linked.open...n/vavai/riv/zamer
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| issn
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| number of pages
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| http://bibframe.org/vocab/doi
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| http://localhost/t...ganizacniJednotka
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