The Ad-MD method to calculate NMR shift including effects due to conformational dynamics: The 31P NMR shift in DNA
The result's identifiers
Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216208%3A11320%2F21%3A10434628" target="_blank" >RIV/00216208:11320/21:10434628 - isvavai.cz</a>
Alternative codes found
RIV/61388963:_____/22:00547591 RIV/68407700:21230/22:00354102
Result on the web
<a href="https://verso.is.cuni.cz/pub/verso.fpl?fname=obd_publikace_handle&handle=gJyRKKDm-5" target="_blank" >https://verso.is.cuni.cz/pub/verso.fpl?fname=obd_publikace_handle&handle=gJyRKKDm-5</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1002/jcc.26778" target="_blank" >10.1002/jcc.26778</a>
Alternative languages
Result language
angličtina
Original language name
The Ad-MD method to calculate NMR shift including effects due to conformational dynamics: The 31P NMR shift in DNA
Original language description
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.
Czech name
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Czech description
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Classification
Type
J<sub>imp</sub> - Article in a specialist periodical, which is included in the Web of Science database
CEP classification
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OECD FORD branch
10403 - Physical chemistry
Result continuities
Project
<a href="/en/project/GA19-13436S" target="_blank" >GA19-13436S: Novel Insight into the Structure and Dynamics of Nucleic Acid Backbone by Means of Advanced DFT-MD Calculations and 31P NMR Spectroscopy</a><br>
Continuities
I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace
Others
Publication year
2021
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů
Data specific for result type
Name of the periodical
Journal of Computational Chemistry
ISSN
0192-8651
e-ISSN
—
Volume of the periodical
43
Issue of the periodical within the volume
2
Country of publishing house
US - UNITED STATES
Number of pages
12
Pages from-to
132-143
UT code for WoS article
000713981100001
EID of the result in the Scopus database
2-s2.0-85118502615