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

Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61989592%3A15310%2F21%3A73610420" target="_blank" >RIV/61989592:15310/21:73610420 - isvavai.cz</a>
Result on the web
<a href="https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.26778" target="_blank" >https://onlinelibrary.wiley.com/doi/epdf/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>

Result language
angličtina
Original language name
The Ad-MD method to calculate NMR shift including effects due to conformational dynamics: The P-31 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 P-31 NMR shift (delta(31P)) 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 delta(31P) in the model phosphates featuring distinctively different structures and dynamic behavior. The applicability of Ad-MD is illustrated by calculating P-31 NMR spectra in the Dickerson-Drew DNA dodecamer. delta(31P) 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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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

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
P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Publication year
2021
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

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