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

J 2013

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

MLÁDEK, Arnošt, Miroslav KREPL, Daniel SVOZIL, Petr CECH, Michal OTYEPKA et. al.

Základní údaje

Originální název

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

Autoři

MLÁDEK, Arnošt (203 Česká republika), Miroslav KREPL (203 Česká republika), Daniel SVOZIL (203 Česká republika), Petr CECH (203 Česká republika), Michal OTYEPKA (203 Česká republika), Pavel BANÁŠ (203 Česká republika), Marie ZGARBOVA (203 Česká republika), Petr JURECKA (203 Česká republika) a Jiří ŠPONER (203 Česká republika, garant, domácí)

Vydání

Physical Chemistry Chemical Physics, CAMBRIDGE, ROYAL SOC CHEMISTRY, 2013, 1463-9076

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10403 Physical chemistry

Stát vydavatele

Velká Británie a Severní Irsko

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 4.198

Kód RIV

RIV/00216224:14740/13:00068739

Organizační jednotka

Středoevropský technologický institut

DOI

http://dx.doi.org/10.1039/c3cp44383c

UT WoS

000317980600036

Klíčová slova anglicky

GAUSSIAN-BASIS SETS; GENERALIZED GRADIENT APPROXIMATION; CORRELATED MOLECULAR CALCULATIONS; ZETA VALENCE QUALITY; AUXILIARY BASIS-SETS; NUCLEIC-ACIDS; CONFORMATIONAL-ANALYSIS; INTERACTION ENERGIES; FORCE-FIELD; BASE-PAIRS

Štítky

ok, rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 28. 6. 2013 13:19, Olga Křížová

Anotace

V originále

The DNA sugar-phosphate backbone has a substantial influence on the DNA structural dynamics. Structural biology and bioinformatics studies revealed that the DNA backbone in experimental structures samples a wide range of distinct conformational substates, known as rotameric DNA backbone conformational families. Their correct description is essential for methods used to model nucleic acids and is known to be the Achilles heel of force field computations. 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 families of DNA backbone conformations 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 calculations are then compared with other QM methods. The BLYP and TPSS functionals supplemented with Grimme's D3(BJ) dispersion term provide the best tradeoff between computational demands and accuracy and can be recommended for preliminary conformational searches as well as calculations on large model systems. 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-zeta basis set, which is, however, computationally very demanding. 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, underlining the challenges facing force field simulations of nucleic acids. 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.

Návaznosti

ED1.1.00/02.0068, projekt VaV

Název: CEITEC - central european institute of technology

Citovat

MLÁDEK, Arnošt, Miroslav KREPL, Daniel SVOZIL, Petr CECH, Michal OTYEPKA, Pavel BANÁŠ, Marie ZGARBOVA, Petr JURECKA a Jiří ŠPONER. 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. Physical Chemistry Chemical Physics. CAMBRIDGE: ROYAL SOC CHEMISTRY, 2013, roč. 15, č. 19, s. 7295-7310. ISSN 1463-9076. Dostupné z: https://dx.doi.org/10.1039/c3cp44383c.

@article{1113607,
   author = {Mládek, Arnošt and Krepl, Miroslav and Svozil, Daniel and Cech, Petr and Otyepka, Michal and Banáš, Pavel and Zgarbova, Marie and Jurecka, Petr and Šponer, Jiří},
   article_location = {CAMBRIDGE},
   article_number = {19},
   doi = {http://dx.doi.org/10.1039/c3cp44383c},
   keywords = {GAUSSIAN-BASIS SETS; GENERALIZED GRADIENT APPROXIMATION; CORRELATED MOLECULAR CALCULATIONS; ZETA VALENCE QUALITY; AUXILIARY BASIS-SETS; NUCLEIC-ACIDS; CONFORMATIONAL-ANALYSIS; INTERACTION ENERGIES; FORCE-FIELD; BASE-PAIRS},
   language = {eng},
   issn = {1463-9076},
   journal = {Physical Chemistry Chemical Physics},
   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},
   url = {http://pubs.rsc.org/en/content/articlehtml/2013/CP/C3CP44383C},
   volume = {15},
   year = {2013}
}

TY  - JOUR
ID  - 1113607
AU  - Mládek, Arnošt - Krepl, Miroslav - Svozil, Daniel - Cech, Petr - Otyepka, Michal - Banáš, Pavel - Zgarbova, Marie - Jurecka, Petr - Šponer, Jiří
PY  - 2013
TI  - 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
JF  - Physical Chemistry Chemical Physics
VL  - 15
IS  - 19
SP  - 7295-7310
EP  - 7295-7310
PB  - ROYAL SOC CHEMISTRY
SN  - 14639076
KW  - GAUSSIAN-BASIS SETS
KW  - GENERALIZED GRADIENT APPROXIMATION
KW  - CORRELATED MOLECULAR CALCULATIONS
KW  - ZETA VALENCE QUALITY
KW  - AUXILIARY BASIS-SETS
KW  - NUCLEIC-ACIDS
KW  - CONFORMATIONAL-ANALYSIS
KW  - INTERACTION ENERGIES
KW  - FORCE-FIELD
KW  - BASE-PAIRS
UR  - http://pubs.rsc.org/en/content/articlehtml/2013/CP/C3CP44383C
L2  - http://pubs.rsc.org/en/content/articlehtml/2013/CP/C3CP44383C
N2  - The DNA sugar-phosphate backbone has a substantial influence on the DNA structural dynamics. Structural biology and bioinformatics studies revealed that the DNA backbone in experimental structures samples a wide range of distinct conformational substates, known as rotameric DNA backbone conformational families. Their correct description is essential for methods used to model nucleic acids and is known to be the Achilles heel of force field computations. 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 families of DNA backbone conformations 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 calculations are then compared with other QM methods. The BLYP and TPSS functionals supplemented with Grimme's D3(BJ) dispersion term provide the best tradeoff between computational demands and accuracy and can be recommended for preliminary conformational searches as well as calculations on large model systems. 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-zeta basis set, which is, however, computationally very demanding. 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, underlining the challenges facing force field simulations of nucleic acids. 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.
ER  -

MLÁDEK, Arnošt, Miroslav KREPL, Daniel SVOZIL, Petr CECH, Michal OTYEPKA, Pavel BANÁŠ, Marie ZGARBOVA, Petr JURECKA a Jiří ŠPONER. 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. \textit{Physical Chemistry Chemical Physics}. CAMBRIDGE: ROYAL SOC CHEMISTRY, 2013, roč.~15, č.~19, s.~7295-7310. ISSN~1463-9076. Dostupné z: https://dx.doi.org/10.1039/c3cp44383c.

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