The Ad-MD method to calculate NMR shift including effects due to conformational dynamics: The 31P NMR shift in DNA

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61388963%3A_____%2F22%3A00547591" target="_blank" >RIV/61388963:_____/22:00547591 - isvavai.cz</a>

Nalezeny alternativní kódy

RIV/00216208:11320/21:10434628 RIV/68407700:21230/22:00354102

Výsledek na webu

<a href="https://doi.org/10.1002/jcc.26778" target="_blank" >https://doi.org/10.1002/jcc.26778</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1002/jcc.26778" target="_blank" >10.1002/jcc.26778</a>

Jazyk výsledku

angličtina

Název v původním jazyce

The Ad-MD method to calculate NMR shift including effects due to conformational dynamics: The 31P NMR shift in DNA

Popis výsledku v původním jazyce

A method for averaging of NMR parameters by molecular dynamics (MD) has been derived from the method of statistical averaging in MD snapshots, benchmarked and applied to structurally dynamic interpretation of the 31P NMR shift (δ31P) in DNA phosphates. The method employs adiabatic dependence of an NMR parameter on selected geometric parameter(s) that is weighted by MD-calculated probability distribution(s) for the geometric parameter(s) (Ad-MD method). The usage of Ad-MD for polymers is computationally convenient when one pre-calculated structural dependence of an NMR parameter is employed for all chemically equivalent units differing only in dynamic behavior. The Ad-MD method is benchmarked against the statistical averaging method for δ31P in the model phosphates featuring distinctively different structures and dynamic behavior. The applicability of Ad-MD is illustrated by calculating 31P NMR spectra in the Dickerson-Drew DNA dodecamer. δ31P was calculated with the B3LYP/IGLO-III/PCM(water) and the probability distributions for the torsion angles adjacent to the phosphorus atoms in the DNA phosphates were calculated using the OL15 force field.

Název v anglickém jazyce

The Ad-MD method to calculate NMR shift including effects due to conformational dynamics: The 31P NMR shift in DNA

Popis výsledku anglicky

A method for averaging of NMR parameters by molecular dynamics (MD) has been derived from the method of statistical averaging in MD snapshots, benchmarked and applied to structurally dynamic interpretation of the 31P NMR shift (δ31P) in DNA phosphates. The method employs adiabatic dependence of an NMR parameter on selected geometric parameter(s) that is weighted by MD-calculated probability distribution(s) for the geometric parameter(s) (Ad-MD method). The usage of Ad-MD for polymers is computationally convenient when one pre-calculated structural dependence of an NMR parameter is employed for all chemically equivalent units differing only in dynamic behavior. The Ad-MD method is benchmarked against the statistical averaging method for δ31P in the model phosphates featuring distinctively different structures and dynamic behavior. The applicability of Ad-MD is illustrated by calculating 31P NMR spectra in the Dickerson-Drew DNA dodecamer. δ31P was calculated with the B3LYP/IGLO-III/PCM(water) and the probability distributions for the torsion angles adjacent to the phosphorus atoms in the DNA phosphates were calculated using the OL15 force field.

Druh

J_imp - Článek v periodiku v databázi Web of Science

CEP obor

—

OECD FORD obor

10610 - Biophysics

Projekt

<a href="/cs/project/GA19-13436S" target="_blank" >GA19-13436S: Nový vhled do struktury a dynamiky páteře nukleových kyselin užitím pokročilých DFT-MD výpočtů a 31P NMR spektroskopie</a><br>

Návaznosti

I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Rok uplatnění

2022

Kód důvěrnosti údajů

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

Název periodika

Journal of Computational Chemistry

ISSN

0192-8651

e-ISSN

1096-987X

Svazek periodika

43

Číslo periodika v rámci svazku

2

Stát vydavatele periodika

US - Spojené státy americké

Počet stran výsledku

12

Strana od-do

132-143

Kód UT WoS článku

000713981100001

EID výsledku v databázi Scopus

2-s2.0-85118502615