Literature DB >> 26610000

Semiempirical Quantum Chemical PM6 Method Augmented by Dispersion and H-Bonding Correction Terms Reliably Describes Various Types of Noncovalent Complexes.

Jan Řezáč1, Jindřich Fanfrlík1, Dennis Salahub1, Pavel Hobza1.   

Abstract

Because of its construction and parametrization for more than 80 elements, the semiempirical quantum chemical PM6 method is superior to other similar methods. Despite its advantages, however, the PM6 method fails for the description of noncovalent interactions, specifically the dispersion energy and H-bonding. Upon inclusion of correction terms for dispersion and H-bonding, the performance of the method was found to be dramatically improved. The former correction included two parameters in the damping function that were parametrized to reproduce the benchmark interaction energies [CCSD(T)/complete basis set (CBS) limit] of the dispersion-bonded complexes from the S22 data set. The latter correction was parametrized on an extended set of H-bonded stabilization energies determined at the MP2/cc-pVTZ level. The resulting PM6-DH method was tested on the S22 data set, for which chemical accuracy (error < 1 kcal/mol) was achieved, and also on the JSCH2005 set, for which significant improvement over the original PM6 method was also obtained. Implementation of analytical gradients allows very efficient geometry optimization, which, for all complexes, provides better agreement with the benchmark data. Excellent results were also achieved for small peptides, and here again, chemical accuracy was obtained (i.e., the error with respect to CCSD(T)/CBS results was smaller than 1 kcal/mol). The performance of the technique was finally demonstrated on extended complexes, namely, the porphine dimer and various graphene models with DNA bases and base pairs, where the PM6-DH stabilization energies agree very well with available benchmark data obtained with DFT-D, SCS-MP2, and MP2.5 methods. The PM6-DH calculations are very efficient and can be routinely applied for systems of up to 1000 atoms. For nonaromatic systems, the use of a linear scaling version of the SCF procedure based on localized orbitals speeds up the method significantly and allows one to investigate systems with several thousand atoms. The method can thus replace force fields, which face basic problems for the description of quantum effects, in many applications.

Entities:  

Year:  2009        PMID: 26610000     DOI: 10.1021/ct9000922

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


  58 in total

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4.  Photodissociative Cross-Linking of Non-covalent Peptide-Peptide Ion Complexes in the Gas Phase.

Authors:  Huong T H Nguyen; Prokopis C Andrikopoulos; Lubomír Rulíšek; Christopher J Shaffer; František Tureček
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5.  A computational study on the role of noncovalent interactions in the stability of polymer/graphene nanocomposites.

Authors:  S Güryel; M Alonso; B Hajgató; Y Dauphin; G Van Lier; P Geerlings; F De Proft
Journal:  J Mol Model       Date:  2017-02-02       Impact factor: 1.810

Review 6.  Molecular modeling of nucleic acid structure: energy and sampling.

Authors:  T E Cheatham; B R Brooks; P A Kollman
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7.  Transferable scoring function based on semiempirical quantum mechanical PM6-DH2 method: CDK2 with 15 structurally diverse inhibitors.

Authors:  Petr Dobeš; Jindřich Fanfrlík; Jan Rezáč; Michal Otyepka; Pavel Hobza
Journal:  J Comput Aided Mol Des       Date:  2011-02-01       Impact factor: 3.686

8.  Quantum mechanical pairwise decomposition analysis of protein kinase B inhibitors: validating a new tool for guiding drug design.

Authors:  Xiaohua Zhang; Alan C Gibbs; Charles H Reynolds; Martin B Peters; Lance M Westerhoff
Journal:  J Chem Inf Model       Date:  2010-04-26       Impact factor: 4.956

9.  Nucleic acid reactivity: challenges for next-generation semiempirical quantum models.

Authors:  Ming Huang; Timothy J Giese; Darrin M York
Journal:  J Comput Chem       Date:  2015-05-06       Impact factor: 3.376

10.  The accuracy of quantum chemical methods for large noncovalent complexes.

Authors:  Robert Sedlak; Tomasz Janowski; Michal Pitoňák; Jan Rezáč; Peter Pulay; Pavel Hobza
Journal:  J Chem Theory Comput       Date:  2013-08-13       Impact factor: 6.006

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