Revisiting the Potential Energy Surface of the Stacked Cytosine
Dimer: FNO-CCSD(T) Interaction Energies, SAPT Decompositions,
and Benchmarking

J 2019

Revisiting the Potential Energy Surface of the Stacked Cytosine Dimer: FNO-CCSD(T) Interaction Energies, SAPT Decompositions, and Benchmarking

KRUSE, H. and Jiří ŠPONER

Basic information

Original name

Revisiting the Potential Energy Surface of the Stacked Cytosine Dimer: FNO-CCSD(T) Interaction Energies, SAPT Decompositions, and Benchmarking

Authors

KRUSE, H. (203 Czech Republic) and Jiří ŠPONER (203 Czech Republic, guarantor, belonging to the institution)

Edition

Journal of Physical Chemistry A, WASHINGTON, AMER CHEMICAL SOC, 2019, 1089-5639

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10403 Physical chemistry

Country of publisher

United States of America

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 2.600

RIV identification code

RIV/00216224:14740/19:00112871

Organization unit

Central European Institute of Technology

DOI

http://dx.doi.org/10.1021/acs.jpca.9b05940

UT WoS

000492802900024

Keywords in English

CORRELATED MOLECULAR CALCULATIONS; HYBRID DENSITY FUNCTIONALS; QUANTUM-CHEMICAL METHODS; CONSISTENT BASIS-SETS; GAUSSIAN-BASIS SETS; AB-INITIO; BASE STACKING; FORCE-FIELD; NUCLEIC-ACIDS; ACCURATELY DESCRIBE

Abstract

V originále

Nucleobase stacking interactions are crucial for the stability of nucleic acids. This study investigates base stacking energies of the cytosine homodimer in different configurations, including intermolecular separation plots, detailed twist dependence, and displaced structures. Highly accurate ab initio quantum chemical single point energies using an energy function based on MP2 complete basis set extrapolation ([6 -> 7]ZaPa-NR) and a CCSD(T)/cc-pVTZ-F12 high-level correction are presented as new reference data, providing the most accurate stacking energies of nucleobase dimers currently available. Accurate SAPT2+(3)delta MP2 energy decomposition is used to obtain detailed insights into the nature of base stacking interactions at varying vertical distances and twist values. The ab initio symmetry adapted perturbation theory (SAPT) energy decomposition suggests that the base stacking originates from an intricate interplay between dispersion attraction, short-range exchange-repulsion, and Coulomb interaction. The interpretation of the SAPT data is a complex issue as key energy terms vary substantially in the region of optimal (low energy) base stacking geometries. Thus, attempts to highlight one leading stabilizing SAPT base stacking term may be misleading and the outcome strongly depends on the used geometries within the range of geometries sampled in nucleic acids upon thermal fluctuations. Modern dispersion-corrected density functional theory (among them DSD-BLYP-D3, omega B97M-V, and omega B97M-D3BJ) is benchmarked and often reaches up to spectroscopic accuracy (below 1 kJ/mol). The classical AMBER force field is benchmarked with multiple different sets of point-charges (e.g. HF, DFT, and MP2-based) and is found to produce reasonable agreement with the benchmark data.

Links

LQ1601, research and development project

Name: CEITEC 2020 (Acronym: CEITEC2020)

Investor: Ministry of Education, Youth and Sports of the CR

Citovat

KRUSE, H. and Jiří ŠPONER. Revisiting the Potential Energy Surface of the Stacked Cytosine Dimer: FNO-CCSD(T) Interaction Energies, SAPT Decompositions, and Benchmarking. Journal of Physical Chemistry A. WASHINGTON: AMER CHEMICAL SOC, 2019, vol. 123, No 42, p. 9209-9222. ISSN 1089-5639. Available from: https://dx.doi.org/10.1021/acs.jpca.9b05940.

@article{1616817,
   author = {Kruse, H. and Šponer, Jiří},
   article_location = {WASHINGTON},
   article_number = {42},
   doi = {http://dx.doi.org/10.1021/acs.jpca.9b05940},
   keywords = {CORRELATED MOLECULAR CALCULATIONS; HYBRID DENSITY FUNCTIONALS; QUANTUM-CHEMICAL METHODS; CONSISTENT BASIS-SETS; GAUSSIAN-BASIS SETS; AB-INITIO; BASE STACKING; FORCE-FIELD; NUCLEIC-ACIDS; ACCURATELY DESCRIBE},
   language = {eng},
   issn = {1089-5639},
   journal = {Journal of Physical Chemistry A},
   title = {Revisiting the Potential Energy Surface of the Stacked Cytosine Dimer: FNO-CCSD(T) Interaction Energies, SAPT Decompositions, and Benchmarking},
   url = {https://pubs.acs.org/doi/10.1021/acs.jpca.9b05940},
   volume = {123},
   year = {2019}
}

TY  - JOUR
ID  - 1616817
AU  - Kruse, H. - Šponer, Jiří
PY  - 2019
TI  - Revisiting the Potential Energy Surface of the Stacked Cytosine Dimer: FNO-CCSD(T) Interaction Energies, SAPT Decompositions, and Benchmarking
JF  - Journal of Physical Chemistry A
VL  - 123
IS  - 42
SP  - 9209-9222
EP  - 9209-9222
PB  - AMER CHEMICAL SOC
SN  - 10895639
KW  - CORRELATED MOLECULAR CALCULATIONS
KW  - HYBRID DENSITY FUNCTIONALS
KW  - QUANTUM-CHEMICAL METHODS
KW  - CONSISTENT BASIS-SETS
KW  - GAUSSIAN-BASIS SETS
KW  - AB-INITIO
KW  - BASE STACKING
KW  - FORCE-FIELD
KW  - NUCLEIC-ACIDS
KW  - ACCURATELY DESCRIBE
UR  - https://pubs.acs.org/doi/10.1021/acs.jpca.9b05940
L2  - https://pubs.acs.org/doi/10.1021/acs.jpca.9b05940
N2  - Nucleobase stacking interactions are crucial for the stability of nucleic acids. This study investigates base stacking energies of the cytosine homodimer in different configurations, including intermolecular separation plots, detailed twist dependence, and displaced structures. Highly accurate ab initio quantum chemical single point energies using an energy function based on MP2 complete basis set extrapolation ([6 -> 7]ZaPa-NR) and a CCSD(T)/cc-pVTZ-F12 high-level correction are presented as new reference data, providing the most accurate stacking energies of nucleobase dimers currently available. Accurate SAPT2+(3)delta MP2 energy decomposition is used to obtain detailed insights into the nature of base stacking interactions at varying vertical distances and twist values. The ab initio symmetry adapted perturbation theory (SAPT) energy decomposition suggests that the base stacking originates from an intricate interplay between dispersion attraction, short-range exchange-repulsion, and Coulomb interaction. The interpretation of the SAPT data is a complex issue as key energy terms vary substantially in the region of optimal (low energy) base stacking geometries. Thus, attempts to highlight one leading stabilizing SAPT base stacking term may be misleading and the outcome strongly depends on the used geometries within the range of geometries sampled in nucleic acids upon thermal fluctuations. Modern dispersion-corrected density functional theory (among them DSD-BLYP-D3, omega B97M-V, and omega B97M-D3BJ) is benchmarked and often reaches up to spectroscopic accuracy (below 1 kJ/mol). The classical AMBER force field is benchmarked with multiple different sets of point-charges (e.g. HF, DFT, and MP2-based) and is found to produce reasonable agreement with the benchmark data.
ER  -

KRUSE, H. and Jiří ŠPONER. Revisiting the Potential Energy Surface of the Stacked Cytosine Dimer: FNO-CCSD(T) Interaction Energies, SAPT Decompositions, and Benchmarking. \textit{Journal of Physical Chemistry A}. WASHINGTON: AMER CHEMICAL SOC, 2019, vol.~123, No~42, p.~9209-9222. ISSN~1089-5639. Available from: https://dx.doi.org/10.1021/acs.jpca.9b05940.

Detailed Information on Publication Record