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.
authors.affiliation: School of Chemistry and Molecular Engineering, East China Normal University , Shanghai 200062, China.
authors.forename: Xinsheng
authors.initials: X
authors.lastname: Jin
authors.affiliation: School of Chemistry and Molecular Engineering, East China Normal University , Shanghai 200062, China.|NYU-ECNU Center for Computational Chemistry at NYU Shanghai , Shanghai 200062, China.|Department of Chemistry, New York University , New York, New York 10003, United States.
authors.forename: John Z H
authors.initials: JZ
authors.lastname: Zhang
authors.affiliation: School of Chemistry and Molecular Engineering, East China Normal University , Shanghai 200062, China.|NYU-ECNU Center for Computational Chemistry at NYU Shanghai , Shanghai 200062, China.
authors.forename: Xiao
authors.identifier: http://orcid.org/0000-0002-4199-8175
authors.initials: X
authors.lastname: He
mesh_terms: D056004:Molecular Dynamics Simulation; D011789:Quantum Theory; D012313:RNA / Q000737:chemistry*; D055672:Static Electricity
chemical_list: D012313:RNA