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.

Kód výsledku v 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>

Nalezeny alternativní kódy

RIV/68081707:_____/11:00370405 RIV/00216224:14740/11:00050559

Výsledek na webu

<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>

Jazyk výsledku

angličtina

Název v původním jazyce

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.

Popis výsledku v původním jazyce

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.

Název v anglickém jazyce

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.

Popis výsledku anglicky

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.

Druh

J_x - Nezařazeno - Článek v odborném periodiku (Jimp, Jsc a Jost)

CEP obor

CF - Fyzikální chemie a teoretická chemie

OECD FORD obor

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Projekt

Výsledek vznikl pri realizaci vícero projektů. Více informací v záložce Projekty.

Návaznosti

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)<br>S - Specificky vyzkum na vysokych skolach

Rok uplatnění

2011

Kód důvěrnosti údajů

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Název periodika

Journal of Physical Chemistry A

ISSN

1089-5639

e-ISSN

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Svazek periodika

115

Číslo periodika v rámci svazku

41

Stát vydavatele periodika

US - Spojené státy americké

Počet stran výsledku

16

Strana od-do

11277-11292

Kód UT WoS článku

000295700600019

EID výsledku v databázi Scopus

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