Literature DB >> 31529219

The any particle molecular orbital/molecular mechanics approach.

José M Rodas1,2, Johan F Galindo1, Adrian E Roitberg3, Andrés Reyes4.   

Abstract

A computational scheme is proposed to broaden the range of applications of multicomponent methodologies for the study of local properties of big molecular systems existing in the gas phase and in solvated environments. This scheme extends the any particle molecular orbital (APMO) approach in the quantum mechanics/molecular mechanics (QM/MM) framework. As a first assessment of the performance of the proposed approach, we estimate the proton affinities (PAs) of seventy amines in the gas phase and the proton binding energies (PBEs) in the gas phase and in an explicitly solvated environment of the sixty-one protons present in the chignolin protein. These calculations are performed with the QM/MM versions of the APMO second-order proton propagator (APMO-PP2) and the APMO extended Koopmans' theorem (APMO-KT) approaches. Calculated PAs and PBEs show significant reductions in the computational effort with a reduced loss in accuracy. These results suggest that the APMO/MM scheme might be used as a low-cost multi-component alternative for studies of local properties in big molecular systems. Graphical Abstract QMMM regions and CPU times for the APMO/MM approach.

Entities:  

Keywords:  AMBER; APMO; LOWDIN; Proton affinities; Proton binding energies; QM/MM

Year:  2019        PMID: 31529219     DOI: 10.1007/s00894-019-4153-x

Source DB:  PubMed          Journal:  J Mol Model        ISSN: 0948-5023            Impact factor:   1.810


  36 in total

1.  Development and testing of a general amber force field.

Authors:  Junmei Wang; Romain M Wolf; James W Caldwell; Peter A Kollman; David A Case
Journal:  J Comput Chem       Date:  2004-07-15       Impact factor: 3.376

2.  Elimination of translational and rotational motions in nuclear orbital plus molecular orbital theory.

Authors:  Hiromi Nakai; Minoru Hoshino; Kaito Miyamoto; Shiaki Hyodo
Journal:  J Chem Phys       Date:  2005-04-22       Impact factor: 3.488

3.  Explicit dynamical electron-proton correlation in the nuclear-electronic orbital framework.

Authors:  Chet Swalina; Michael V Pak; Arindam Chakraborty; Sharon Hammes-Schiffer
Journal:  J Phys Chem A       Date:  2006-08-24       Impact factor: 2.781

4.  The implementation of a fast and accurate QM/MM potential method in Amber.

Authors:  Ross C Walker; Michael F Crowley; David A Case
Journal:  J Comput Chem       Date:  2008-05       Impact factor: 3.376

5.  Hidden aspects of the Structural theory of chemistry: MC-QTAIM analysis reveals "alchemical" transformation from a triatomic to a diatomic structure.

Authors:  Mohammad Goli; Shant Shahbazian
Journal:  Phys Chem Chem Phys       Date:  2015-01-07       Impact factor: 3.676

6.  The divide-and-conquer second-order proton propagator method based on nuclear orbital plus molecular orbital theory for the efficient computation of proton binding energies.

Authors:  Yusuke Tsukamoto; Yasuhiro Ikabata; Jonathan Romero; Andrés Reyes; Hiromi Nakai
Journal:  Phys Chem Chem Phys       Date:  2016-10-05       Impact factor: 3.676

7.  Calculation of Positron Binding Energies and Electron-Positron Annihilation Rates for Atomic Systems with the Reduced Explicitly Correlated Hartree-Fock Method in the Nuclear-Electronic Orbital Framework.

Authors:  Kurt R Brorsen; Michael V Pak; Sharon Hammes-Schiffer
Journal:  J Phys Chem A       Date:  2017-01-05       Impact factor: 2.781

8.  Theoretical calculation of polarizability isotope effects.

Authors:  Félix Moncada; Roberto Flores-Moreno; Andrés Reyes
Journal:  J Mol Model       Date:  2017-02-22       Impact factor: 1.810

9.  Reduced explicitly correlated Hartree-Fock approach within the nuclear-electronic orbital framework: applications to positronic molecular systems.

Authors:  Andrew Sirjoosingh; Michael V Pak; Chet Swalina; Sharon Hammes-Schiffer
Journal:  J Chem Phys       Date:  2013-07-21       Impact factor: 3.488

10.  Fast and accurate prediction of proton affinities: revisiting the extended Koopmans' theorem for protons.

Authors:  Laura Pedraza-González; Jorge Charry; William Quintero; Jorge Alí-Torres; Andrés Reyes
Journal:  Phys Chem Chem Phys       Date:  2017-09-27       Impact factor: 3.676

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