Literature DB >> 23050059

An Efficient Method to Evaluate Intermolecular Interaction Energies in Large Systems Using Overlapping Multicenter ONIOM and the Fragment Molecular Orbital Method.

Naoya Asada1, Dmitri G Fedorov, Kazuo Kitaura, Isao Nakanishi, Kenneth M Merz.   

Abstract

We propose an approach based on the overlapping multicenter ONIOM to evaluate intermolecular interaction energies in large systems and demonstrate its accuracy on several representative systems in the complete basis set limit at the MP2 and CCSD(T) level of theory. In the application to the intermolecular interaction energy between insulin dimer and 4'-hydroxyacetanilide at the MP2/CBS level, we use the fragment molecular orbital method for the calculation of the entire complex assigned to the lowest layer in three-layer ONIOM. The developed method is shown to be efficient and accurate in the evaluation of the protein-ligand interaction energies.

Entities:  

Year:  2012        PMID: 23050059      PMCID: PMC3462021          DOI: 10.1021/jz3010688

Source DB:  PubMed          Journal:  J Phys Chem Lett        ISSN: 1948-7185            Impact factor:   6.475


  36 in total

1.  The Protein Data Bank.

Authors:  H M Berman; J Westbrook; Z Feng; G Gilliland; T N Bhat; H Weissig; I N Shindyalov; P E Bourne
Journal:  Nucleic Acids Res       Date:  2000-01-01       Impact factor: 16.971

2.  Reference MP2/CBS and CCSD(T) quantum-chemical calculations on stacked adenine dimers. Comparison with DFT-D, MP2.5, SCS(MI)-MP2, M06-2X, CBS(SCS-D) and force field descriptions.

Authors:  Claudio A Morgado; Petr Jurecka; Daniel Svozil; Pavel Hobza; Jirí Sponer
Journal:  Phys Chem Chem Phys       Date:  2010-02-12       Impact factor: 3.676

3.  Extending the power of quantum chemistry to large systems with the fragment molecular orbital method.

Authors:  Dmitri G Fedorov; Kazuo Kitaura
Journal:  J Phys Chem A       Date:  2007-05-19       Impact factor: 2.781

4.  Further analysis and comparative study of intermolecular interactions using dimers from the S22 database.

Authors:  Laszlo Fusti Molnar; Xiao He; Bing Wang; Kenneth M Merz
Journal:  J Chem Phys       Date:  2009-08-14       Impact factor: 3.488

5.  Accurate predictions of nonpolar solvation free energies require explicit consideration of binding-site hydration.

Authors:  Samuel Genheden; Paulius Mikulskis; LiHong Hu; Jacob Kongsted; Pär Söderhjelm; Ulf Ryde
Journal:  J Am Chem Soc       Date:  2011-07-29       Impact factor: 15.419

6.  Dispersion energy evaluated by using locally projected occupied and excited molecular orbitals for molecular interaction.

Authors:  Suehiro Iwata
Journal:  J Chem Phys       Date:  2011-09-07       Impact factor: 3.488

7.  Fragmentation methods: a route to accurate calculations on large systems.

Authors:  Mark S Gordon; Dmitri G Fedorov; Spencer R Pruitt; Lyudmila V Slipchenko
Journal:  Chem Rev       Date:  2011-08-26       Impact factor: 60.622

8.  Electrostatic energy in the effective fragment potential method: theory and application to benzene dimer.

Authors:  Lyudmila V Slipchenko; Mark S Gordon
Journal:  J Comput Chem       Date:  2007-01-15       Impact factor: 3.376

9.  Formal Estimation of Errors in Computed Absolute Interaction Energies of Protein-ligand Complexes.

Authors:  John C Faver; Mark L Benson; Xiao He; Benjamin P Roberts; Bing Wang; Michael S Marshall; Matthew R Kennedy; C David Sherrill; Kenneth M Merz
Journal:  J Chem Theory Comput       Date:  2011-03-08       Impact factor: 6.006

10.  Electrostatic polarization makes a substantial contribution to the free energy of avidin-biotin binding.

Authors:  Yan Tong; Ye Mei; Yong L Li; Chang G Ji; John Z H Zhang
Journal:  J Am Chem Soc       Date:  2010-04-14       Impact factor: 15.419

View more
  4 in total

1.  Mechanistic investigation of methanol to propene conversion catalyzed by H-beta zeolite: a two-layer ONIOM study.

Authors:  Yingxin Sun; Sheng Han
Journal:  J Mol Model       Date:  2013-11-06       Impact factor: 1.810

2.  Accurate Quantum Mechanical/Molecular Mechanical Calculations of Reduction Potentials in Azurin Variants.

Authors:  Lin Shen; Xiancheng Zeng; Hao Hu; Xiangqian Hu; Weitao Yang
Journal:  J Chem Theory Comput       Date:  2018-08-10       Impact factor: 6.006

3.  A two-layer ONIOM study of thiophene cracking catalyzed by proton- and cation-exchanged FAU zeolite.

Authors:  Yingxin Sun; Xinfeng Mao; Supeng Pei
Journal:  J Mol Model       Date:  2016-02-03       Impact factor: 1.810

4.  Mapping enzymatic catalysis using the effective fragment molecular orbital method: towards all ab initio biochemistry.

Authors:  Casper Steinmann; Dmitri G Fedorov; Jan H Jensen
Journal:  PLoS One       Date:  2013-04-12       Impact factor: 3.240

  4 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.