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 (<pan class="Chemical">span class="Gene">SCCclass="Chemical">pan>-<class="Chemical">sppan>an 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 <class="Chemical">span class="Chemical">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 DFTB3, which substantially improves the description of charged systems containing elements C, H, N, O, and P, especially regarding 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

View more
  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

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.