Full QM Calculation of RNA Energy Using Electrostatically Embedded Generalized Molecular Fractionation with Conjugate Caps Method

Xinsheng Jin, John Zhang, Xiao He

Research output: Contribution to journalArticle

Abstract

In this study, the electrostatically embedded generalized molecular fractionation with conjugate caps (concaps) method (EE-GMFCC) was employed for efficient linear-scaling quantum mechanical (QM) calculation of total energies of RNAs. In the EE-GMFCC approach, the total energy of RNA is calculated by taking a proper combination of the QM energy of each nucleotide-centric fragment with large caps or small caps (termed EE-GMFCC-LC and EE-GMFCC-SC, respectively) deducted by the energies of concaps. The two-body QM interaction energy between non-neighboring ribonucleotides which are spatially in close contact are also taken into account for the energy calculation. Numerical studies were carried out to calculate the total energies of a number of RNAs using the EE-GMFCC-LC and EE-GMFCC-SC methods at levels of the Hartree-Fock (HF) method, density functional theory (DFT), and second-order many-body perturbation theory (MP2), respectively. The results show that the efficiency of the EE-GMFCC-SC method is about 3 times faster than the EE-GMFCC-LC method with minimal accuracy sacrifice. The EE-GMFCC-SC method is also applied for relative energy calculations of 20 different conformers of two RNA systems using HF and DFT, respectively. Both single-point and relative energy calculations demonstrate that the EE-GMFCC method has deviations from the full system results of only a few kcal/mol.

Original languageEnglish (US)
Pages (from-to)2503-2514
Number of pages12
JournalJournal of Physical Chemistry A
Volume121
Issue number12
DOIs
StatePublished - Mar 30 2017

Fingerprint

Fractionation
caps
fractionation
RNA
Density functional theory
Ribonucleotides
energy
Nucleotides
density functional theory
nucleotides
perturbation theory
fragments
deviation
scaling

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry

Cite this

Full QM Calculation of RNA Energy Using Electrostatically Embedded Generalized Molecular Fractionation with Conjugate Caps Method. / Jin, Xinsheng; Zhang, John; He, Xiao.

In: Journal of Physical Chemistry A, Vol. 121, No. 12, 30.03.2017, p. 2503-2514.

Research output: Contribution to journalArticle

@article{eb6455280f2e40879a7e4324b8d23d70,
title = "Full QM Calculation of RNA Energy Using Electrostatically Embedded Generalized Molecular Fractionation with Conjugate Caps Method",
abstract = "In this study, the electrostatically embedded generalized molecular fractionation with conjugate caps (concaps) method (EE-GMFCC) was employed for efficient linear-scaling quantum mechanical (QM) calculation of total energies of RNAs. In the EE-GMFCC approach, the total energy of RNA is calculated by taking a proper combination of the QM energy of each nucleotide-centric fragment with large caps or small caps (termed EE-GMFCC-LC and EE-GMFCC-SC, respectively) deducted by the energies of concaps. The two-body QM interaction energy between non-neighboring ribonucleotides which are spatially in close contact are also taken into account for the energy calculation. Numerical studies were carried out to calculate the total energies of a number of RNAs using the EE-GMFCC-LC and EE-GMFCC-SC methods at levels of the Hartree-Fock (HF) method, density functional theory (DFT), and second-order many-body perturbation theory (MP2), respectively. The results show that the efficiency of the EE-GMFCC-SC method is about 3 times faster than the EE-GMFCC-LC method with minimal accuracy sacrifice. The EE-GMFCC-SC method is also applied for relative energy calculations of 20 different conformers of two RNA systems using HF and DFT, respectively. Both single-point and relative energy calculations demonstrate that the EE-GMFCC method has deviations from the full system results of only a few kcal/mol.",
author = "Xinsheng Jin and John Zhang and Xiao He",
year = "2017",
month = "3",
day = "30",
doi = "10.1021/acs.jpca.7b00859",
language = "English (US)",
volume = "121",
pages = "2503--2514",
journal = "Journal of Physical Chemistry A",
issn = "1089-5639",
publisher = "American Chemical Society",
number = "12",

}

TY - JOUR

T1 - Full QM Calculation of RNA Energy Using Electrostatically Embedded Generalized Molecular Fractionation with Conjugate Caps Method

AU - Jin, Xinsheng

AU - Zhang, John

AU - He, Xiao

PY - 2017/3/30

Y1 - 2017/3/30

N2 - In this study, the electrostatically embedded generalized molecular fractionation with conjugate caps (concaps) method (EE-GMFCC) was employed for efficient linear-scaling quantum mechanical (QM) calculation of total energies of RNAs. In the EE-GMFCC approach, the total energy of RNA is calculated by taking a proper combination of the QM energy of each nucleotide-centric fragment with large caps or small caps (termed EE-GMFCC-LC and EE-GMFCC-SC, respectively) deducted by the energies of concaps. The two-body QM interaction energy between non-neighboring ribonucleotides which are spatially in close contact are also taken into account for the energy calculation. Numerical studies were carried out to calculate the total energies of a number of RNAs using the EE-GMFCC-LC and EE-GMFCC-SC methods at levels of the Hartree-Fock (HF) method, density functional theory (DFT), and second-order many-body perturbation theory (MP2), respectively. The results show that the efficiency of the EE-GMFCC-SC method is about 3 times faster than the EE-GMFCC-LC method with minimal accuracy sacrifice. The EE-GMFCC-SC method is also applied for relative energy calculations of 20 different conformers of two RNA systems using HF and DFT, respectively. Both single-point and relative energy calculations demonstrate that the EE-GMFCC method has deviations from the full system results of only a few kcal/mol.

AB - In this study, the electrostatically embedded generalized molecular fractionation with conjugate caps (concaps) method (EE-GMFCC) was employed for efficient linear-scaling quantum mechanical (QM) calculation of total energies of RNAs. In the EE-GMFCC approach, the total energy of RNA is calculated by taking a proper combination of the QM energy of each nucleotide-centric fragment with large caps or small caps (termed EE-GMFCC-LC and EE-GMFCC-SC, respectively) deducted by the energies of concaps. The two-body QM interaction energy between non-neighboring ribonucleotides which are spatially in close contact are also taken into account for the energy calculation. Numerical studies were carried out to calculate the total energies of a number of RNAs using the EE-GMFCC-LC and EE-GMFCC-SC methods at levels of the Hartree-Fock (HF) method, density functional theory (DFT), and second-order many-body perturbation theory (MP2), respectively. The results show that the efficiency of the EE-GMFCC-SC method is about 3 times faster than the EE-GMFCC-LC method with minimal accuracy sacrifice. The EE-GMFCC-SC method is also applied for relative energy calculations of 20 different conformers of two RNA systems using HF and DFT, respectively. Both single-point and relative energy calculations demonstrate that the EE-GMFCC method has deviations from the full system results of only a few kcal/mol.

UR - http://www.scopus.com/inward/record.url?scp=85019138444&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85019138444&partnerID=8YFLogxK

U2 - 10.1021/acs.jpca.7b00859

DO - 10.1021/acs.jpca.7b00859

M3 - Article

VL - 121

SP - 2503

EP - 2514

JO - Journal of Physical Chemistry A

JF - Journal of Physical Chemistry A

SN - 1089-5639

IS - 12

ER -