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

. 2009 Jul 14 ; 5 (7) : 1749-60. [epub] 20090526

Status PubMed-not-MEDLINE Jazyk angličtina Země Spojené státy americké Médium print-electronic

Typ dokumentu časopisecké články

Perzistentní odkaz   https://www.medvik.cz/link/pmid26610000

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.

Citace poskytuje Crossref.org

Nejnovějších 20 citací...

Zobrazit více v
Medvik | PubMed

PM6-ML: The Synergy of Semiempirical Quantum Chemistry and Machine Learning Transformed into a Practical Computational Method

. 2025 Jan 28 ; 21 (2) : 678-690. [epub] 20250103

Tackling a Curious Case: Generation of Charge-Tagged Guanosine Radicals by Gas-Phase Electron Transfer and Their Characterization by UV-vis Photodissociation Action Spectroscopy and Theory

. 2021 Mar 03 ; 32 (3) : 772-785. [epub] 20210210

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

. 2018 Aug ; 29 (8) : 1706-1720. [epub] 20180507

Efficient Covalent Bond Formation in Gas-Phase Peptide-Peptide Ion Complexes with the Photoleucine Stapler

. 2016 Apr ; 27 (4) : 633-45. [epub] 20160127

Substrate Specificity, Inhibitor Selectivity and Structure-Function Relationships of Aldo-Keto Reductase 1B15: A Novel Human Retinaldehyde Reductase

. 2015 ; 10 (7) : e0134506. [epub] 20150729

Structural and functional studies of phosphoenolpyruvate carboxykinase from Mycobacterium tuberculosis

. 2015 ; 10 (3) : e0120682. [epub] 20150323

Human insulin analogues modified at the B26 site reveal a hormone conformation that is undetected in the receptor complex

. 2014 Oct ; 70 (Pt 10) : 2765-74. [epub] 20140927

The accuracy of quantum chemical methods for large noncovalent complexes

. 2013 Aug 13 ; 9 (8) : 3364-3374.

Structural basis for inhibition of cathepsin B drug target from the human blood fluke, Schistosoma mansoni

. 2011 Oct 14 ; 286 (41) : 35770-35781. [epub] 20110810

Transferable scoring function based on semiempirical quantum mechanical PM6-DH2 method: CDK2 with 15 structurally diverse inhibitors

. 2011 Mar ; 25 (3) : 223-35. [epub] 20110201

Najít záznam

Citační ukazatele

Nahrávání dat ...

    Možnosti archivace