Literature DB >> 23204947

DFTB3: Extension of the self-consistent-charge density-functional tight-binding method (SCC-DFTB).

Michael Gaus, Qiang Cui, Marcus Elstner.   

Abstract

The self-consistent-charge density-functional tight-binding method (class="Chemical">spaclass="Chemical">n class="Chemical">paclass="Chemical">n>n class="Gene">SCCclass="Chemical">span>-paspan>n class="Chemical">DFTB) is an approximate quantum chemical method derived from density functional theory (DFT) based on a second-order expansion of the DFT total energy around a reference density. In the present study we combine earlier extensions and improve them consistently with, first, an improved Coulomb interaction between atomic partial charges, and second, the complete third-order expansion of the DFT total energy. These modifications lead us to the next generation of the DFTB methodology called class="Chemical">DFTB3, which substantially improves the description of charged systems containing elements C, H, N, O, and P, especially regarding class="Chemical">pan class="Chemical">hydrogen binding energies and proton affinities. As a result, DFTB3 is particularly applicable to biomolecular systems. Remaining challenges and possible solutions are also briefly discussed.

Entities:  

Year:  2012        PMID: 23204947      PMCID: PMC3509502          DOI: 10.1021/ct100684s

Source DB:  PubMed          Journal:  J Chem Theory Comput        ISSN: 1549-9618            Impact factor:   6.006


  45 in total

1.  Generalized Gradient Approximation Made Simple.

Authors: 
Journal:  Phys Rev Lett       Date:  1996-10-28       Impact factor: 9.161

2.  On the accuracy of density-functional theory exchange-correlation functionals for H bonds in small water clusters: benchmarks approaching the complete basis set limit.

Authors:  Biswajit Santra; Angelos Michaelides; Matthias Scheffler
Journal:  J Chem Phys       Date:  2007-11-14       Impact factor: 3.488

3.  Initial steps toward automating the fitting of DFTB Erep(r).

Authors:  J M Knaup; B Hourahine; Th Frauenheim
Journal:  J Phys Chem A       Date:  2007-04-12       Impact factor: 2.781

4.  Modeling carbon nanostructures with the self-consistent charge density-functional tight-binding method: vibrational spectra and electronic structure of C(28), C(60), and C(70).

Authors:  Henryk A Witek; Stephan Irle; Guishan Zheng; Wibe A de Jong; Keiji Morokuma
Journal:  J Chem Phys       Date:  2006-12-07       Impact factor: 3.488

5.  Does water relay play an important role in phosphoryl transfer reactions? Insights from theoretical study of a model reaction in water and tert-butanol.

Authors:  Yang Yang; Qiang Cui
Journal:  J Phys Chem B       Date:  2009-04-09       Impact factor: 2.991

6.  Description of phosphate hydrolysis reactions with the Self-Consistent-Charge Density-Functional-Tight-Binding (SCC-DFTB) theory. 1. Parameterization.

Authors:  Yang Yang; Haibo Yu; Darrin York; Marcus Elstner; Qiang Cui
Journal:  J Chem Theory Comput       Date:  2008       Impact factor: 6.006

7.  Long-distance proton transfer with a break in the bacteriorhodopsin active site.

Authors:  Prasad Phatak; Jan S Frähmcke; Marius Wanko; Michael Hoffmann; Paul Strodel; Jeremy C Smith; Sándor Suhai; Ana-Nicoleta Bondar; Marcus Elstner
Journal:  J Am Chem Soc       Date:  2009-05-27       Impact factor: 15.419

8.  Are current semiempirical methods better than force fields? A study from the thermodynamics perspective.

Authors:  Gustavo de M Seabra; Ross C Walker; Adrian E Roitberg
Journal:  J Phys Chem A       Date:  2009-10-29       Impact factor: 2.781

Review 9.  Proton transfer function of carbonic anhydrase: Insights from QM/MM simulations.

Authors:  Demian Riccardi; Shuo Yang; Qiang Cui
Journal:  Biochim Biophys Acta       Date:  2009-08-11

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
Journal:  Biochemistry       Date:  2009-03-24       Impact factor: 3.162

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  139 in total

1.  Copper Oxidation/Reduction in Water and Protein: Studies with DFTB3/MM and VALBOND Molecular Dynamics Simulations.

Authors:  Haiyun Jin; Puja Goyal; Akshaya Kumar Das; Michael Gaus; Markus Meuwly; Qiang Cui
Journal:  J Phys Chem B       Date:  2015-12-17       Impact factor: 2.991

2.  Simulations of allosteric motions in the zinc sensor CzrA.

Authors:  Dhruva K Chakravorty; Bing Wang; Chul Won Lee; David P Giedroc; Kenneth M Merz
Journal:  J Am Chem Soc       Date:  2011-11-14       Impact factor: 15.419

Review 3.  A hybrid approach to simulation of electron transfer in complex molecular systems.

Authors:  Tomáš Kubař; Marcus Elstner
Journal:  J R Soc Interface       Date:  2013-07-24       Impact factor: 4.118

4.  Density functional tight binding: values of semi-empirical methods in an ab initio era.

Authors:  Qiang Cui; Marcus Elstner
Journal:  Phys Chem Chem Phys       Date:  2014-07-28       Impact factor: 3.676

Review 5.  Metal Ion Modeling Using Classical Mechanics.

Authors:  Pengfei Li; Kenneth M Merz
Journal:  Chem Rev       Date:  2017-01-03       Impact factor: 60.622

6.  Lagrangian formulation with dissipation of Born-Oppenheimer molecular dynamics using the density-functional tight-binding method.

Authors:  Guishan Zheng; Anders M N Niklasson; Martin Karplus
Journal:  J Chem Phys       Date:  2011-07-28       Impact factor: 3.488

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

Authors:  Shuo Yang; Qiang Cui
Journal:  Biophys J       Date:  2011-07-06       Impact factor: 4.033

8.  Density-functional expansion methods: generalization of the auxiliary basis.

Authors:  Timothy J Giese; Darrin M York
Journal:  J Chem Phys       Date:  2011-05-21       Impact factor: 3.488

9.  Analysis of Density Functional Tight Binding with Natural Bonding Orbitals.

Authors:  Xiya Lu; Juan Duchimaza-Heredia; Qiang Cui
Journal:  J Phys Chem A       Date:  2019-08-15       Impact factor: 2.781

10.  QM/MM free energy simulations: recent progress and challenges.

Authors:  Xiya Lu; Dong Fang; Shingo Ito; Yuko Okamoto; Victor Ovchinnikov; Qiang Cui
Journal:  Mol Simul       Date:  2016-07-05       Impact factor: 2.178

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