Literature DB >> 15836204

Validation of the density-functional based tight-binding approximation method for the calculation of reaction energies and other data.

Thomas Krüger1, Marcus Elstner, Peter Schiffels, Thomas Frauenheim.   

Abstract

We investigated the performance of the approximative density functional method DFTB versus BLYP and G2 with respect to zero-point corrected reaction energies, vibrational frequencies, and geometry parameters for a set of 28 reactions and 22 representative molecules containing C, H, N, and O (DFTB--density-functional based tight-binding approximation). The DFTB reaction energies show a mean absolute deviation versus the G2 reference of 4.3 kcalmol only. The corresponding value for the vibrational frequencies amounts to 75 cm(-1) versus BLYP/cc-pVTZ. With very few exceptions bond lengths and angles are in excellent agreement with the results of higher-level methods.

Entities:  

Year:  2005        PMID: 15836204     DOI: 10.1063/1.1871913

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  26 in total

1.  Unraveling the distinctive features of hemorrhagic and non-hemorrhagic snake venom metalloproteinases using molecular simulations.

Authors:  Raoni Almeida de Souza; Natalia Díaz; Ronaldo Alves Pinto Nagem; Rafaela Salgado Ferreira; Dimas Suárez
Journal:  J Comput Aided Mol Des       Date:  2015-12-16       Impact factor: 3.686

2.  Free energy study of the catalytic mechanism of Trypanosoma cruzi trans-sialidase. From the Michaelis complex to the covalent intermediate.

Authors:  Gustavo Pierdominici-Sottile; Nicole A Horenstein; Adrian E Roitberg
Journal:  Biochemistry       Date:  2011-10-27       Impact factor: 3.162

Review 3.  Semiempirical Quantum Mechanical Methods for Noncovalent Interactions for Chemical and Biochemical Applications.

Authors:  Anders S Christensen; Tomáš Kubař; Qiang Cui; Marcus Elstner
Journal:  Chem Rev       Date:  2016-04-13       Impact factor: 60.622

4.  A modified QM/MM Hamiltonian with the Self-Consistent-Charge Density-Functional-Tight-Binding Theory for highly charged QM regions.

Authors:  Guanhua Hou; Xiao Zhu; Marcus Elstner; Qiang Cui
Journal:  J Chem Theory Comput       Date:  2012-11-13       Impact factor: 6.006

5.  The hydrolysis mechanism of a GH45 cellulase and its potential relation to lytic transglycosylase and expansin function.

Authors:  Vivek S Bharadwaj; Brandon C Knott; Jerry Ståhlberg; Gregg T Beckham; Michael F Crowley
Journal:  J Biol Chem       Date:  2020-02-13       Impact factor: 5.157

6.  Discerning the catalytic mechanism of Staphylococcus aureus sortase A with QM/MM free energy calculations.

Authors:  Pooja Shrestha; Jeff Wereszczynski
Journal:  J Mol Graph Model       Date:  2016-04-27       Impact factor: 2.518

7.  Dissociation of polycyclic aromatic hydrocarbons: molecular dynamics studies.

Authors:  A Simon; M Rapacioli; G Rouaut; G Trinquier; F X Gadéa
Journal:  Philos Trans A Math Phys Eng Sci       Date:  2017-04-28       Impact factor: 4.226

8.  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

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

Authors:  Michael Gaus; Qiang Cui; Marcus Elstner
Journal:  J Chem Theory Comput       Date:  2012-04-10       Impact factor: 6.006

10.  QM/MM investigation of substrate binding of subclass B3 metallo-β-lactamase SMB-1 from Serratia marcescents: insights into catalytic mechanism.

Authors:  Xia Mu; Dingguo Xu
Journal:  J Mol Model       Date:  2020-03-07       Impact factor: 1.810

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