Literature DB >> 24850383

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

Qiang Cui1, Marcus Elstner.   

Abstract

Semi-empirical (SE) methods are derived from Hartree-Fock (HF) or Density Functional Theory (DFT) by neglect and approximation of electronic integrals. Thereby, parameters are introduced which have to be determined from reference calculations and/or by fitting to available experimental data. This leads to computational methods that are about 2-3 orders of magnitude faster than the standard HF/DFT methods using medium sized basis sets while being about 3 orders of magnitude slower than empirical force field methods (Molecular Mechanics: MM). Therefore, SE methods are most appropriate for a specific range of applications. These include the study of systems that contain a large number of atoms and therefore being too large for ab initio or DFT methods and also problems where dynamic or entropic effects are particularly important. In the latter case, the errors made by considering a very limited number of molecular structures or neglecting entropic contributions can be much larger than the accuracy lost due to the use of SE methods. Another area where SE methods are attractive concerns the analysis of systems for which reliable MM models are not readily available. Therefore, even in an era when rapid progress is being made in ab initio methods, there is considerable interest in further developing SE methods. We illustrate this point by focusing on the discussion of recent development and application of the Density Functional Tight Binding method.

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Year:  2014        PMID: 24850383      PMCID: PMC4836871          DOI: 10.1039/c4cp00908h

Source DB:  PubMed          Journal:  Phys Chem Chem Phys        ISSN: 1463-9076            Impact factor:   3.676


  93 in total

1.  Toward accurate theoretical thermochemistry of first row transition metal complexes.

Authors:  Wanyi Jiang; Nathan J DeYonker; John J Determan; Angela K Wilson
Journal:  J Phys Chem A       Date:  2011-12-14       Impact factor: 2.781

2.  Polarization effects stabilize bacteriorhodopsin's chromophore binding pocket: a molecular dynamics study.

Authors:  G Babitzki; R Denschlag; P Tavan
Journal:  J Phys Chem B       Date:  2009-07-30       Impact factor: 2.991

3.  Paradynamics: an effective and reliable model for ab initio QM/MM free-energy calculations and related tasks.

Authors:  Nikolay V Plotnikov; Shina C L Kamerlin; Arieh Warshel
Journal:  J Phys Chem B       Date:  2011-05-27       Impact factor: 2.991

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.  Improved electronic properties from third-order SCC-DFTB with cost efficient post-SCF extensions.

Authors:  Steve Kaminski; Michael Gaus; Marcus Elstner
Journal:  J Phys Chem A       Date:  2012-11-20       Impact factor: 2.781

6.  Receptor-specific scoring functions derived from quantum chemical models improve affinity estimates for in-silico drug discovery.

Authors:  Bernhard Fischer; Kaori Fukuzawa; Wolfgang Wenzel
Journal:  Proteins       Date:  2008-03

7.  Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone φ, ψ and side-chain χ(1) and χ(2) dihedral angles.

Authors:  Robert B Best; Xiao Zhu; Jihyun Shim; Pedro E M Lopes; Jeetain Mittal; Michael Feig; Alexander D Mackerell
Journal:  J Chem Theory Comput       Date:  2012-07-18       Impact factor: 6.006

8.  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

9.  Density functional tight binding.

Authors:  Marcus Elstner; Gotthard Seifert
Journal:  Philos Trans A Math Phys Eng Sci       Date:  2014-02-10       Impact factor: 4.226

Review 10.  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
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  34 in total

1.  Benchmarking density functional tight binding models for barrier heights and reaction energetics of organic molecules.

Authors:  Maja Gruden; Ljubica Andjeklović; Akkarapattiakal Kuriappan Jissy; Stepan Stepanović; Matija Zlatar; Qiang Cui; Marcus Elstner
Journal:  J Comput Chem       Date:  2017-07-24       Impact factor: 3.376

2.  Perspective: Quantum mechanical methods in biochemistry and biophysics.

Authors:  Qiang Cui
Journal:  J Chem Phys       Date:  2016-10-14       Impact factor: 3.488

3.  Exploring the applicability of density functional tight binding to transition metal ions. Parameterization for nickel with the spin-polarized DFTB3 model.

Authors:  Milena Vujović; Mioy Huynh; Sebastian Steiner; Pablo Garcia-Fernandez; Marcus Elstner; Qiang Cui; Maja Gruden
Journal:  J Comput Chem       Date:  2018-10-09       Impact factor: 3.376

Review 4.  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

5.  Improvement of d-d interactions in density functional tight binding for transition metal ions with a ligand field model: assessment of a DFTB3+U model on nickel coordination compounds.

Authors:  Stepan Stepanovic; Rui Lai; Marcus Elstner; Maja Gruden; Pablo Garcia-Fernandez; Qiang Cui
Journal:  Phys Chem Chem Phys       Date:  2020-12-07       Impact factor: 3.676

6.  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

7.  Extended Hückel Semi-Empirical Approach as an Efficient Method for Structural Defects Analysis in 4H-SiC.

Authors:  Janusz Wozny; Andrii Kovalchuk; Jacek Podgorski; Zbigniew Lisik
Journal:  Materials (Basel)       Date:  2021-03-06       Impact factor: 3.623

8.  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

9.  QM/MM Analysis of Transition States and Transition State Analogues in Metalloenzymes.

Authors:  D Roston; Q Cui
Journal:  Methods Enzymol       Date:  2016-07-01       Impact factor: 1.600

10.  Improving intermolecular interactions in DFTB3 using extended polarization from chemical-potential equalization.

Authors:  Anders S Christensen; Marcus Elstner; Qiang Cui
Journal:  J Chem Phys       Date:  2015-08-28       Impact factor: 3.488

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