Investigations of Stacked DNA Base-Pair Steps: Highly Accurate Stacking Interaction Energies, Energy Decomposition, and Many-Body Stacking Effects

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61989592%3A15310%2F19%3A73597467" target="_blank" >RIV/61989592:15310/19:73597467 - isvavai.cz</a>

Alternative codes found

RIV/68081707:_____/19:00501549

Result on the web

<a href="https://pubs.acs.org/doi/10.1021/acs.jctc.8b00643" target="_blank" >https://pubs.acs.org/doi/10.1021/acs.jctc.8b00643</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1021/acs.jctc.8b00643" target="_blank" >10.1021/acs.jctc.8b00643</a>

Result language

angličtina

Original language name

Investigations of Stacked DNA Base-Pair Steps: Highly Accurate Stacking Interaction Energies, Energy Decomposition, and Many-Body Stacking Effects

Original language description

The stacking energies of 10 unique B-DNA base-pair steps were calculated with highly accurate quantum chemistry and used as reference values in a thorough benchmark of (dispersion-corrected) DFT, wave function methods, tight-binding methods, and different force fields, including charge variants thereof. The reference values were computed using a focal-point energy function based on extrapolated explicitly correlated MP2-F12 and conventional CCSD(T) data at the triple-zeta level. A collection of 29 different density functionals, sometimes with multiple dispersion corrections (D3(BJ), D3M(BJ), and VV10) were evaluated, including recent functionals like B97M-V, omega B97M-V, and SCAN-D3(BJ), which perform excellently. The double-hybrid DSD-BLYP-NL was found to be the best DFT method. Common wave function methods (MP2, SCS-MP2, and MP2.5) and the SNS-MP2 protocol were tested as well, where only the latter and DLPNO-CCSD(T)/CBS were competitive with DFT. The tight-binding methods DFTB3-D3 and GFN-xTB revealed a comparatively low accuracy. The AMBER force field outperformed CHARMM and GROMOS but still showed systematic gas-phase overbinding, which could be traced back to the electrostatic term, as revealed by comparison of different sets of point charges. High-order SAPT, e.g., SAPT2 + 3 delta(MP2), was not only benchmarked but also used to study the nature of the stacking interactions to high accuracy. The delta(MP2) term turned out to be crucially important to reach high accuracy. Finally, we investigated four-body stacking effects with DLPNO-CCSD(T) and DFT, which were found to be significant and strongest for the CpC base-pair step where they reached almost 30% of the total stacking energy.

Czech name

—

Czech description

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Type

J_imp - Article in a specialist periodical, which is included in the Web of Science database

CEP classification

—

OECD FORD branch

10403 - Physical chemistry

Project

<a href="/en/project/LO1305" target="_blank" >LO1305: Development of the center of advanced technologies and materials</a><br>

Continuities

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Publication year

2019

Confidentiality

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

Name of the periodical

Journal of Chemical Theory and Computation

ISSN

1549-9618

e-ISSN

—

Volume of the periodical

15

Issue of the periodical within the volume

1

Country of publishing house

US - UNITED STATES

Number of pages

21

Pages from-to

95-115

UT code for WoS article

000455558200012

EID of the result in the Scopus database

2-s2.0-85059676699