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.

Základní údaje

Originální název

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

Autoři

KRUSE, Holger (276 Německo, domácí); Arnošt MLÁDEK (203 Česká republika); Konstantinos GKIONIS (300 Řecko, domácí); Andreas HANSEN (276 Německo); Sstefan GRIMME (276 Německo) a Jiří ŠPONER (203 Česká republika, garant, domácí)

Vydání

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

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10403 Physical chemistry

Stát vydavatele

Spojené státy

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 5.301

Kód RIV

RIV/00216224:14740/15:00081386

Organizační jednotka

Středoevropský technologický institut

DOI

https://doi.org/10.1021/acs.jctc.5b00515

UT WoS

000362921700045

EID Scopus

2-s2.0-84944239723

Klíčová slova anglicky

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

Štítky

rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 5. 4. 2016 12:38, Mgr. Eva Špillingová

Anotace

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.

Návaznosti

ED1.1.00/02.0068, projekt VaV

Název: CEITEC - central european institute of technology

GBP305/12/G034, projekt VaV

Název: Centrum biologie RNA

286154, interní kód MU

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

Investor: Evropská unie, SYLICA - Synergies of Life and Material Sciences to Create a New Future, Kapacity

Citovat

KRUSE, Holger; Arnošt MLÁDEK; Konstantinos GKIONIS; Andreas HANSEN; Sstefan GRIMME a 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, roč. 11, č. 10, s. 4972-4991. ISSN 1549-9618. Dostupné z: https://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 = {https://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 a 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, roč.~11, č.~10, s.~4972-4991. ISSN~1549-9618. Dostupné z: https://doi.org/10.1021/acs.jctc.5b00515.

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