Quantum Chemical Benchmark Study on 46 RNA Backbone Families
Using a Dinucleotide Unit

J 2015

Quantum Chemical Benchmark Study on 46 RNA Backbone Families Using a Dinucleotide Unit

KRUSE, Holger, Arnošt MLÁDEK, Konstantinos GKIONIS, Andreas HANSEN, Sstefan GRIMME et. al.

Basic information

Original name

Quantum Chemical Benchmark Study on 46 RNA Backbone Families Using a Dinucleotide Unit

Authors

KRUSE, Holger (276 Germany, belonging to the institution), Arnošt MLÁDEK (203 Czech Republic), Konstantinos GKIONIS (300 Greece, belonging to the institution), Andreas HANSEN (276 Germany), Sstefan GRIMME (276 Germany) and Jiří ŠPONER (203 Czech Republic, guarantor, belonging to the institution)

Edition

Journal of Chemical Theory and Computation, Washington DC, American Chemical Society, 2015, 1549-9618

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: 5.301

RIV identification code

RIV/00216224:14740/15:00081386

Organization unit

Central European Institute of Technology

DOI

http://dx.doi.org/10.1021/acs.jctc.5b00515

UT WoS

000362921700045

Keywords in English

MOLECULAR-DYNAMICS SIMULATIONS; DENSITY-FUNCTIONAL THEORY; SUGAR-PHOSPHATE BACKBONE; ELECTRONIC-STRUCTURE CALCULATIONS; MAIN-GROUP THERMOCHEMISTRY; BASIS-SET CALCULATIONS; LONG NONCODING RNAS; NUCLEIC-ACID BASES; AMBER FORCE-FIELD; B-DNA STRUCTURE

Abstract

V originále

We have created a benchmark set of quantum chemical structure energy data denoted as UpU46, which consists of 46 uracil dinucleotides (UpU), representing all known 46 RNA backbone conformational families. Penalty-function-based restrained optimizations with COSMO TPSS-D3/def2-TZVP ensure a balance between keeping the target conformation and geometry relaxation. The backbone geometries are close to the clustering-means of their respective RNA bioinformatics family classification. High-level wave function methods (DLPNO-CCSD(T) as reference) and a wide-range of dispersion-corrected or inclusive DFT methods (DFT-D3, VV10, LC-BOP-LRD, M06-2X, M11, and more) are used to evaluate the conformational energies. The results are compared to the Amber RNA bsc0 chi(OL3) force field. Most dispersion-corrected DFT methods surpass the Amber force field significantly in accuracy and yield mean absolute deviations (MADs) for relative conformational energies of similar to 0.4-0.6 kcal/mol. Double-hybrid density functionals represent the most accurate class of density functionals. Low-cost quantum chemical methods such as PM6-D3H+, HF-3c, DFTB3-D3, as well as small basis set calculations corrected for basis set superposition errors (BSSEs) by the gCP procedure are also tested. Unfortunately, the presently available low-cost methods are struggling to describe the UpU conformational energies with satisfactory accuracy. The UpU46 benchmark is an ideal test for benchmarking and development of fast methods to describe nucleic acids, including force fields.

Links

ED1.1.00/02.0068, research and development project

Name: CEITEC - central european institute of technology

GBP305/12/G034, research and development project

Name: Centrum biologie RNA

286154, interní kód MU

Name: SYLICA - Synergies of Life and Material Sciences to Create a New Future (Acronym: SYLICA)

Investor: European Union, Capacities

Citovat

KRUSE, Holger, Arnošt MLÁDEK, Konstantinos GKIONIS, Andreas HANSEN, Sstefan GRIMME and Jiří ŠPONER. Quantum Chemical Benchmark Study on 46 RNA Backbone Families Using a Dinucleotide Unit. Journal of Chemical Theory and Computation. Washington DC: American Chemical Society, 2015, vol. 11, No 10, p. 4972-4991. ISSN 1549-9618. Available from: https://dx.doi.org/10.1021/acs.jctc.5b00515.

@article{1322783,
   author = {Kruse, Holger and Mládek, Arnošt and Gkionis, Konstantinos and Hansen, Andreas and Grimme, Sstefan and Šponer, Jiří},
   article_location = {Washington DC},
   article_number = {10},
   doi = {http://dx.doi.org/10.1021/acs.jctc.5b00515},
   keywords = {MOLECULAR-DYNAMICS SIMULATIONS; DENSITY-FUNCTIONAL THEORY; SUGAR-PHOSPHATE BACKBONE; ELECTRONIC-STRUCTURE CALCULATIONS; MAIN-GROUP THERMOCHEMISTRY; BASIS-SET CALCULATIONS; LONG NONCODING RNAS; NUCLEIC-ACID BASES; AMBER FORCE-FIELD; B-DNA STRUCTURE},
   language = {eng},
   issn = {1549-9618},
   journal = {Journal of Chemical Theory and Computation},
   title = {Quantum Chemical Benchmark Study on 46 RNA Backbone Families Using a Dinucleotide Unit},
   url = {http://pubs.acs.org/doi/10.1021/acs.jctc.5b00515},
   volume = {11},
   year = {2015}
}

TY  - JOUR
ID  - 1322783
AU  - Kruse, Holger - Mládek, Arnošt - Gkionis, Konstantinos - Hansen, Andreas - Grimme, Sstefan - Šponer, Jiří
PY  - 2015
TI  - Quantum Chemical Benchmark Study on 46 RNA Backbone Families Using a Dinucleotide Unit
JF  - Journal of Chemical Theory and Computation
VL  - 11
IS  - 10
SP  - 4972-4991
EP  - 4972-4991
PB  - American Chemical Society
SN  - 15499618
KW  - MOLECULAR-DYNAMICS SIMULATIONS
KW  - DENSITY-FUNCTIONAL THEORY
KW  - SUGAR-PHOSPHATE BACKBONE
KW  - ELECTRONIC-STRUCTURE CALCULATIONS
KW  - MAIN-GROUP THERMOCHEMISTRY
KW  - BASIS-SET CALCULATIONS
KW  - LONG NONCODING RNAS
KW  - NUCLEIC-ACID BASES
KW  - AMBER FORCE-FIELD
KW  - B-DNA STRUCTURE
UR  - http://pubs.acs.org/doi/10.1021/acs.jctc.5b00515
L2  - http://pubs.acs.org/doi/10.1021/acs.jctc.5b00515
N2  - We have created a benchmark set of quantum chemical structure energy data denoted as UpU46, which consists of 46 uracil dinucleotides (UpU), representing all known 46 RNA backbone conformational families. Penalty-function-based restrained optimizations with COSMO TPSS-D3/def2-TZVP ensure a balance between keeping the target conformation and geometry relaxation. The backbone geometries are close to the clustering-means of their respective RNA bioinformatics family classification. High-level wave function methods (DLPNO-CCSD(T) as reference) and a wide-range of dispersion-corrected or inclusive DFT methods (DFT-D3, VV10, LC-BOP-LRD, M06-2X, M11, and more) are used to evaluate the conformational energies. The results are compared to the Amber RNA bsc0 chi(OL3) force field. Most dispersion-corrected DFT methods surpass the Amber force field significantly in accuracy and yield mean absolute deviations (MADs) for relative conformational energies of similar to 0.4-0.6 kcal/mol. Double-hybrid density functionals represent the most accurate class of density functionals. Low-cost quantum chemical methods such as PM6-D3H+, HF-3c, DFTB3-D3, as well as small basis set calculations corrected for basis set superposition errors (BSSEs) by the gCP procedure are also tested. Unfortunately, the presently available low-cost methods are struggling to describe the UpU conformational energies with satisfactory accuracy. The UpU46 benchmark is an ideal test for benchmarking and development of fast methods to describe nucleic acids, including force fields.
ER  -

KRUSE, Holger, Arnošt MLÁDEK, Konstantinos GKIONIS, Andreas HANSEN, Sstefan GRIMME and Jiří ŠPONER. Quantum Chemical Benchmark Study on 46 RNA Backbone Families Using a Dinucleotide Unit. \textit{Journal of Chemical Theory and Computation}. Washington DC: American Chemical Society, 2015, vol.~11, No~10, p.~4972-4991. ISSN~1549-9618. Available from: https://dx.doi.org/10.1021/acs.jctc.5b00515.

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