Literature DB >> 21526802

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

Puja Goyal1, Marcus Elstner, Qiang Cui.   

Abstract

The self-consistent charge density functional tight-binding (SCC-DFTB) method has been actively employed to study proton-transfer processes in biological systems. Recent studies in the literature employing SCC-DFTB reported that the method favors the Zundel form of the hydrated proton over the Eigen form, both in gas-phase water clusters and in bulk water, in disagreement with both higher-level calculations and experimental data. In this work, we explore the performance of SCC-DFTB for protonated gas-phase water clusters and bulk water (the latter both with and without an excess proton) with a modified O-H repulsive potential reported in our earlier work and with on-site third-order expansion of the DFT energy. Our results show that, with the proper set of published parameters, SCC-DFTB does correctly favor the Eigen form of the hydrated proton as compared to the Zundel form, both in gas-phase clusters and in the bulk; the amphiphilic character of the hydrated proton discussed in the literature has also been observed. The analyses do, however, bring forth remaining limitations in terms of the solvation structure around the hydrated proton as well as the structure of bulk water, which can guide future improvements of the method.

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Year:  2011        PMID: 21526802      PMCID: PMC3101025          DOI: 10.1021/jp202259c

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


  47 in total

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4.  pKa calculations in solution and proteins with QM/MM free energy perturbation simulations: a quantitative test of QM/MM protocols.

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Journal:  J Phys Chem B       Date:  2005-09-22       Impact factor: 2.991

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Journal:  J Phys Chem B       Date:  2009-04-09       Impact factor: 2.991

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10.  Microscopic pKa analysis of Glu286 in cytochrome c oxidase (Rhodobacter sphaeroides): toward a calibrated molecular model.

Authors:  Nilanjan Ghosh; Xavier Prat-Resina; M R Gunner; Qiang Cui
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  15 in total

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Journal:  Phys Chem Chem Phys       Date:  2014-07-28       Impact factor: 3.676

3.  Glu-286 rotation and water wire reorientation are unlikely the gating elements for proton pumping in cytochrome C oxidase.

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Journal:  Biophys J       Date:  2011-07-06       Impact factor: 4.033

4.  A delocalized proton-binding site within a membrane protein.

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Review 5.  Semiempirical Quantum Mechanical Methods for Noncovalent Interactions for Chemical and Biochemical Applications.

Authors:  Anders S Christensen; Tomáš Kubař; Qiang Cui; Marcus Elstner
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Authors:  Santhanamoorthi Nachimuthu; Jiali Gao; Donald G Truhlar
Journal:  Chem Phys       Date:  2012-03-06       Impact factor: 2.348

7.  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

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.  Parametrization of an Orbital-Based Linear-Scaling Quantum Force Field for Noncovalent Interactions.

Authors:  Timothy J Giese; Haoyuan Chen; Ming Huang; Darrin M York
Journal:  J Chem Theory Comput       Date:  2014-02-11       Impact factor: 6.006

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