Literature DB >> 20426461

The self-consistent charge density functional tight binding method applied to liquid water and the hydrated excess proton: benchmark simulations.

C Mark Maupin1, Bálint Aradi, Gregory A Voth.   

Abstract

The self-consistent charge density functional tight binding (SCC-DFTB) method is a relatively new approximate electronic structure method that is increasingly used to study biologically relevant systems in aqueous environments. There have been several gas phase cluster calculations that indicate, in some instances, an ability to predict geometries, energies, and vibrational frequencies in reasonable agreement with high level ab initio calculations. However, to date, there has been little validation of the method for bulk water properties, and no validation for the properties of the hydrated excess proton in water. Presented here is a detailed SCC-DFTB analysis of the latter two systems. This work focuses on the ability of the original SCC-DFTB method, and a modified version that includes a hydrogen bonding damping function (HBD-SCC-DFTB), to describe the structural, energetic, and dynamical nature of these aqueous systems. The SCC-DFTB and HBD-SCC-DFTB results are compared to experimental data and Car-Parrinello molecular dynamics (CPMD) simulations using the HCTH/120 gradient-corrected exchange-correlation energy functional. All simulations for these systems contained 128 water molecules, plus one additional proton in the case of the excess proton system, and were carried out in a periodic simulation box with Ewald long-range electrostatics. The liquid water structure for the original SCC-DFTB is shown to poorly reproduce bulk water properties, while the HBD-SCC-DFTB somewhat more closely represents bulk water due to an improved ability to describe hydrogen bonding energies. Both SCC-DFTB methods are found to underestimate the water dimer interaction energy, resulting in a low heat of vaporization and a significantly elevated water oxygen diffusion coefficient as compared to experiment. The addition of an excess hydrated proton to the bulk water resulted in the Zundel cation (H(5)O(2)(+)) stabilized species being the stable form of the charge defect, which diffuses at a rate similar to the underlying water diffusion. These SCC-DFTB results differ significantly from other existing computational descriptions of the hydrated excess proton in water, as well as from the available experimental data.

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Year:  2010        PMID: 20426461     DOI: 10.1021/jp1010555

Source DB:  PubMed          Journal:  J Phys Chem B        ISSN: 1520-5207            Impact factor:   2.991


  14 in total

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5.  Insights into the mechanism of proton transport in cytochrome c oxidase.

Authors:  Takefumi Yamashita; Gregory A Voth
Journal:  J Am Chem Soc       Date:  2012-01-06       Impact factor: 15.419

6.  Metadynamics combined with auxiliary density functional and density functional tight-binding methods: alanine dipeptide as a case study.

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Journal:  J Mol Model       Date:  2017-02-15       Impact factor: 1.810

7.  Application of the SCC-DFTB method to neutral and protonated water clusters and bulk water.

Authors:  Puja Goyal; Marcus Elstner; Qiang Cui
Journal:  J Phys Chem B       Date:  2011-04-28       Impact factor: 2.991

8.  Using Machine Learning to Greatly Accelerate Path Integral Ab Initio Molecular Dynamics.

Authors:  Chenghan Li; Gregory A Voth
Journal:  J Chem Theory Comput       Date:  2022-01-04       Impact factor: 6.006

9.  Benchmark Study of the SCC-DFTB Approach for a Biomolecular Proton Channel.

Authors:  Ruibin Liang; Jessica M J Swanson; Gregory A Voth
Journal:  J Chem Theory Comput       Date:  2014-01-14       Impact factor: 6.006

10.  Microscopic basis for kinetic gating in Cytochrome c oxidase: insights from QM/MM analysis.

Authors:  Puja Goyal; Shuo Yang; Qiang Cui
Journal:  Chem Sci       Date:  2015-01       Impact factor: 9.825

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