Noncanonical hydrogen bonding in nucleic acids. Benchmark evaluation of key base-phosphate interactions in folded RNA molecules using quantum-chemical calculations and molecular dynamics simulations.

Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61989592%3A15310%2F11%3A10224679" target="_blank" >RIV/61989592:15310/11:10224679 - isvavai.cz</a>
Alternative codes found
RIV/68081707:_____/11:00370405 RIV/00216224:14740/11:00050559
Result on the web
<a href="http://dx.doi.org/10.1021/jp204820b" target="_blank" >http://dx.doi.org/10.1021/jp204820b</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1021/jp204820b" target="_blank" >10.1021/jp204820b</a>

Result language
angličtina
Original language name
Noncanonical hydrogen bonding in nucleic acids. Benchmark evaluation of key base-phosphate interactions in folded RNA molecules using quantum-chemical calculations and molecular dynamics simulations.
Original language description
RNA molecules are stabilized by a wide range of noncanonical interactions that are not present in DNA. Among them, the recently classified basephosphate (BPh) interactions belong to the most important ones. Twelve percent of nucleotides in the ribosomalcrystal structures are involved in BPh interactions. Here we provide assessment of the energetics of BPh interactions using MP2 computations extrapolated to the complete basis set of atomic orbitals and corrected for higher-order electron correlation effects. The reference computations are compared with DFT-D and DFT-D3 approaches, the SAPT method, and the molecular mechanics force field. The computations, besides providing the basic benchmark for the BPh interactions, allow some refinements of the original classification, including identification of some potential doubly bonded BPh patterns. The reference computations are followed by analysis of some larger RNA fragments that consider the context of the BPh interactions.
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)<br>S - Specificky vyzkum na vysokych skolach

Publication year
2011
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

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