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

Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216224%3A14740%2F15%3A00081386" target="_blank" >RIV/00216224:14740/15:00081386 - isvavai.cz</a>
Alternative codes found
RIV/68081707:_____/15:00455892
Result on the web
<a href="http://pubs.acs.org/doi/10.1021/acs.jctc.5b00515" target="_blank" >http://pubs.acs.org/doi/10.1021/acs.jctc.5b00515</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1021/acs.jctc.5b00515" target="_blank" >10.1021/acs.jctc.5b00515</a>

Result language
angličtina
Original language name
Quantum Chemical Benchmark Study on 46 RNA Backbone Families Using a Dinucleotide Unit
Original language description
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 functionmethods (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.
Czech name
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Czech description
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Type
J<sub>x</sub> - Unclassified - Peer-reviewed scientific article (Jimp, Jsc and Jost)
CEP classification
CF - Physical chemistry and theoretical chemistry
OECD FORD branch
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Project
Result was created during the realization of more than one project. More information in the Projects tab.
Continuities
P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Publication year
2015
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

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