A systematic study on RNA NMR chemical shift calculation based on the automated fragmentation QM/MM approach

Xinsheng Jin, Tong Zhu, John Zhang, Xiao He

Research output: Contribution to journalArticle

Abstract

1H, 13C and 15N NMR chemical shift calculations on RNAs were performed using the automated fragmentation quantum mechanics/molecular mechanics (AF-QM/MM) approach. Systematic investigation was carried out to examine the influence of density functionals, force fields, ensemble average and explicit solvent molecules on NMR chemical shift calculations. By comparing the performance of a series of density functionals, the results demonstrate that the mPW1PW91 functional is one of the best functionals for predicting RNA 1H and 13C chemical shifts. This study also shows that the performance of the force fields in describing H-bond strength can be validated by AF-QM/MM calculated imino proton chemical shifts. The polarized nucleic acid-specific charge (PNC) model significantly improves the accuracy of imino hydrogen and nitrogen NMR chemical shift prediction as compared to the FF10 force field, which underscores that the electrostatic polarization effect is critical to stabilizing the hydrogen bonds between base pairs in RNAs. Furthermore, the accuracy of the chemical shift of amino proton can be improved by adding explicit water molecules.

Original languageEnglish (US)
Pages (from-to)108590-108602
Number of pages13
JournalRSC Advances
Volume6
Issue number110
DOIs
StatePublished - 2016

Fingerprint

Chemical shift
RNA
Nuclear magnetic resonance
Molecular mechanics
Quantum theory
Protons
Molecules
Nucleic acids
Nucleic Acids
Hydrogen
Electrostatics
Hydrogen bonds
Nitrogen
Polarization
Water

ASJC Scopus subject areas

  • Chemistry(all)
  • Chemical Engineering(all)

Cite this

A systematic study on RNA NMR chemical shift calculation based on the automated fragmentation QM/MM approach. / Jin, Xinsheng; Zhu, Tong; Zhang, John; He, Xiao.

In: RSC Advances, Vol. 6, No. 110, 2016, p. 108590-108602.

Research output: Contribution to journalArticle

Jin, Xinsheng ; Zhu, Tong ; Zhang, John ; He, Xiao. / A systematic study on RNA NMR chemical shift calculation based on the automated fragmentation QM/MM approach. In: RSC Advances. 2016 ; Vol. 6, No. 110. pp. 108590-108602.
@article{3425e5c02a5e4e2494373d247002615a,
title = "A systematic study on RNA NMR chemical shift calculation based on the automated fragmentation QM/MM approach",
abstract = "1H, 13C and 15N NMR chemical shift calculations on RNAs were performed using the automated fragmentation quantum mechanics/molecular mechanics (AF-QM/MM) approach. Systematic investigation was carried out to examine the influence of density functionals, force fields, ensemble average and explicit solvent molecules on NMR chemical shift calculations. By comparing the performance of a series of density functionals, the results demonstrate that the mPW1PW91 functional is one of the best functionals for predicting RNA 1H and 13C chemical shifts. This study also shows that the performance of the force fields in describing H-bond strength can be validated by AF-QM/MM calculated imino proton chemical shifts. The polarized nucleic acid-specific charge (PNC) model significantly improves the accuracy of imino hydrogen and nitrogen NMR chemical shift prediction as compared to the FF10 force field, which underscores that the electrostatic polarization effect is critical to stabilizing the hydrogen bonds between base pairs in RNAs. Furthermore, the accuracy of the chemical shift of amino proton can be improved by adding explicit water molecules.",
author = "Xinsheng Jin and Tong Zhu and John Zhang and Xiao He",
year = "2016",
doi = "10.1039/c6ra22518g",
language = "English (US)",
volume = "6",
pages = "108590--108602",
journal = "RSC Advances",
issn = "2046-2069",
publisher = "Royal Society of Chemistry",
number = "110",

}

TY - JOUR

T1 - A systematic study on RNA NMR chemical shift calculation based on the automated fragmentation QM/MM approach

AU - Jin, Xinsheng

AU - Zhu, Tong

AU - Zhang, John

AU - He, Xiao

PY - 2016

Y1 - 2016

N2 - 1H, 13C and 15N NMR chemical shift calculations on RNAs were performed using the automated fragmentation quantum mechanics/molecular mechanics (AF-QM/MM) approach. Systematic investigation was carried out to examine the influence of density functionals, force fields, ensemble average and explicit solvent molecules on NMR chemical shift calculations. By comparing the performance of a series of density functionals, the results demonstrate that the mPW1PW91 functional is one of the best functionals for predicting RNA 1H and 13C chemical shifts. This study also shows that the performance of the force fields in describing H-bond strength can be validated by AF-QM/MM calculated imino proton chemical shifts. The polarized nucleic acid-specific charge (PNC) model significantly improves the accuracy of imino hydrogen and nitrogen NMR chemical shift prediction as compared to the FF10 force field, which underscores that the electrostatic polarization effect is critical to stabilizing the hydrogen bonds between base pairs in RNAs. Furthermore, the accuracy of the chemical shift of amino proton can be improved by adding explicit water molecules.

AB - 1H, 13C and 15N NMR chemical shift calculations on RNAs were performed using the automated fragmentation quantum mechanics/molecular mechanics (AF-QM/MM) approach. Systematic investigation was carried out to examine the influence of density functionals, force fields, ensemble average and explicit solvent molecules on NMR chemical shift calculations. By comparing the performance of a series of density functionals, the results demonstrate that the mPW1PW91 functional is one of the best functionals for predicting RNA 1H and 13C chemical shifts. This study also shows that the performance of the force fields in describing H-bond strength can be validated by AF-QM/MM calculated imino proton chemical shifts. The polarized nucleic acid-specific charge (PNC) model significantly improves the accuracy of imino hydrogen and nitrogen NMR chemical shift prediction as compared to the FF10 force field, which underscores that the electrostatic polarization effect is critical to stabilizing the hydrogen bonds between base pairs in RNAs. Furthermore, the accuracy of the chemical shift of amino proton can be improved by adding explicit water molecules.

UR - http://www.scopus.com/inward/record.url?scp=84997132541&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84997132541&partnerID=8YFLogxK

U2 - 10.1039/c6ra22518g

DO - 10.1039/c6ra22518g

M3 - Article

AN - SCOPUS:84997132541

VL - 6

SP - 108590

EP - 108602

JO - RSC Advances

JF - RSC Advances

SN - 2046-2069

IS - 110

ER -