Literature DB >> 21361527

Density-functional approaches to noncovalent interactions: a comparison of dispersion corrections (DFT-D), exchange-hole dipole moment (XDM) theory, and specialized functionals.

Lori A Burns1, Alvaro Vázquez-Mayagoitia, Bobby G Sumpter, C David Sherrill.   

Abstract

A systematic study of techniques for treating noncovalent interactions within the computationally efficient density functional theory (DFT) framework is presented through comparison to benchmark-quality evaluations of binding strength compiled for molecular complexes of diverse size and nature. In particular, the efficacy of functionals deliberately crafted to encompass long-range forces, a posteriori DFT+dispersion corrections (DFT-D2 and DFT-D3), and exchange-hole dipole moment (XDM) theory is assessed against a large collection (469 energy points) of reference interaction energies at the CCSD(T) level of theory extrapolated to the estimated complete basis set limit. The established S22 [revised in J. Chem. Phys. 132, 144104 (2010)] and JSCH test sets of minimum-energy structures, as well as collections of dispersion-bound (NBC10) and hydrogen-bonded (HBC6) dissociation curves and a pairwise decomposition of a protein-ligand reaction site (HSG), comprise the chemical systems for this work. From evaluations of accuracy, consistency, and efficiency for PBE-D, BP86-D, B97-D, PBE0-D, B3LYP-D, B970-D, M05-2X, M06-2X, ωB97X-D, B2PLYP-D, XYG3, and B3LYP-XDM methodologies, it is concluded that distinct, often contrasting, groups of these elicit the best performance within the accessible double-ζ or robust triple-ζ basis set regimes and among hydrogen-bonded or dispersion-dominated complexes. For overall results, M05-2X, B97-D3, and B970-D2 yield superior values in conjunction with aug-cc-pVDZ, for a mean absolute deviation of 0.41 - 0.49 kcal/mol, and B3LYP-D3, B97-D3, ωB97X-D, and B2PLYP-D3 dominate with aug-cc-pVTZ, affording, together with XYG3/6-311+G(3df,2p), a mean absolute deviation of 0.33 - 0.38 kcal/mol.

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Year:  2011        PMID: 21361527     DOI: 10.1063/1.3545971

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


  36 in total

1.  The assessment and application of an approach to noncovalent interactions: the energy decomposition analysis (EDA) in combination with DFT of revised dispersion correction (DFT-D3) with Slater-type orbital (STO) basis set.

Authors:  Wei Gao; Huajie Feng; Xiaopeng Xuan; Liuping Chen
Journal:  J Mol Model       Date:  2012-05-29       Impact factor: 1.810

2.  Natures of benzene-water and pyrrole-water interactions in the forms of σ and π types: theoretical studies from clusters to liquid mixture.

Authors:  Wei Gao; Jiqing Jiao; Huajie Feng; Xiaopeng Xuan; Liuping Chen
Journal:  J Mol Model       Date:  2012-11-23       Impact factor: 1.810

3.  Comparison of some dispersion-corrected and traditional functionals with CCSD(T) and MP2 ab initio methods: dispersion, induction, and basis set superposition error.

Authors:  Dipankar Roy; Mateusz Marianski; Neepa T Maitra; J J Dannenberg
Journal:  J Chem Phys       Date:  2012-10-07       Impact factor: 3.488

4.  DFT and MD study of the divalent-cation-mediated interaction of ochratoxin A with DNA nucleosides.

Authors:  Jozef Motyčka; Pavel Mach; Milan Melicherčík; Jan Urban
Journal:  J Mol Model       Date:  2014-05-27       Impact factor: 1.810

5.  Hydrogen-Bond-Dependent Conformational Switching: A Computational Challenge from Experimental Thermochemistry.

Authors:  James Luccarelli; Robert S Paton
Journal:  J Org Chem       Date:  2019-01-09       Impact factor: 4.354

6.  An Efficient Method to Evaluate Intermolecular Interaction Energies in Large Systems Using Overlapping Multicenter ONIOM and the Fragment Molecular Orbital Method.

Authors:  Naoya Asada; Dmitri G Fedorov; Kazuo Kitaura; Isao Nakanishi; Kenneth M Merz
Journal:  J Phys Chem Lett       Date:  2012-08-28       Impact factor: 6.475

7.  Chloroperoxidase-catalyzed epoxidation of cis-β-methylstyrene: distal pocket flexibility tunes catalytic reactivity.

Authors:  Alexander N Morozov; David C Chatfield
Journal:  J Phys Chem B       Date:  2012-10-19       Impact factor: 2.991

8.  The BioFragment Database (BFDb): An open-data platform for computational chemistry analysis of noncovalent interactions.

Authors:  Lori A Burns; John C Faver; Zheng Zheng; Michael S Marshall; Daniel G A Smith; Kenno Vanommeslaeghe; Alexander D MacKerell; Kenneth M Merz; C David Sherrill
Journal:  J Chem Phys       Date:  2017-10-28       Impact factor: 3.488

9.  Substituent effect of the stacking interaction between carbon monoxide and benzene.

Authors:  Qiang Zhao
Journal:  J Mol Model       Date:  2018-05-25       Impact factor: 1.810

10.  DNA-protein π-interactions in nature: abundance, structure, composition and strength of contacts between aromatic amino acids and DNA nucleobases or deoxyribose sugar.

Authors:  Katie A Wilson; Jennifer L Kellie; Stacey D Wetmore
Journal:  Nucleic Acids Res       Date:  2014-04-17       Impact factor: 16.971

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