Literature DB >> 25208095

Accuracy of dispersion interactions in semiempirical and molecular mechanics models: the benzene dimer case.

Karol Strutyński1, José A N F Gomes, Manuel Melle-Franco.   

Abstract

The benzene dimer is arguably the simplest molecular analogue of graphitic materials. We present the systematic study of minima and transition states of the benzene dimer with semiempirical and molecular mechanics (MM) methods. Full minimizations on all conformations were performed and the results, geometries, and binding energies were compared with CCSD(T) and DFT-D results. MM yields the best results with three force fields MM3, OPLS, and AMOEBA, which reproduced nine out of the ten stationary points of the benzene dimer. We obtained new parameters for MM3 and OPLS that successfully reproduce all structures of the benzene dimer and showed improved accuracy over DFT-D in most dimer geometries. Semiempirical models were, unexpectedly, less accurate than MM methods. The most accurate semiempirical method for the benzene dimer is PM6-DH2. DFT-D was the only Hamiltonian that reproduced the variations of energy with geometry from CCSD(T) calculations accurately and is the method of choice for energies of periodic and molecular calculations of graphitic systems. In contrast, MM represents an accurate alternative to calculate geometries.

Entities:  

Year:  2014        PMID: 25208095     DOI: 10.1021/jp506860t

Source DB:  PubMed          Journal:  J Phys Chem A        ISSN: 1089-5639            Impact factor:   2.781


  5 in total

Review 1.  Enhanced semiempirical QM methods for biomolecular interactions.

Authors:  Nusret Duygu Yilmazer; Martin Korth
Journal:  Comput Struct Biotechnol J       Date:  2015-02-28       Impact factor: 7.271

2.  Self-assembled functionalized graphene nanoribbons from carbon nanotubes.

Authors:  Eunice Cunha; Maria Fernanda Proença; Florinda Costa; António J Fernandes; Marta A C Ferro; Paulo E Lopes; Mariam González-Debs; Manuel Melle-Franco; Francis Leonard Deepak; Maria C Paiva
Journal:  ChemistryOpen       Date:  2015-03-09       Impact factor: 2.911

3.  Elucidating the intercalation of methylated 1,10-phenanthroline with DNA: the important weight of the CH/H interactions and the selectivity of CH/π and CH/n interactions.

Authors:  Ángel Sánchez-González; Adrià Gil
Journal:  RSC Adv       Date:  2021-01-05       Impact factor: 3.361

4.  Influence of conventional hydrogen bonds in the intercalation of phenanthroline derivatives with DNA: The important role of the sugar and phosphate backbone.

Authors:  Ángel Sánchez-González; Pierre Grenut; Adrià Gil
Journal:  J Comput Chem       Date:  2022-03-17       Impact factor: 3.672

5.  Water Dispersible Few-Layer Graphene Stabilized by a Novel Pyrene Derivative at Micromolar Concentration.

Authors:  Eunice Cunha; Maria Fernanda Proença; Maria Goreti Pereira; Maria José Fernandes; Robert J Young; Karol Strutyński; Manuel Melle-Franco; Mariam Gonzalez-Debs; Paulo E Lopes; Maria da Conceição Paiva
Journal:  Nanomaterials (Basel)       Date:  2018-08-30       Impact factor: 5.076

  5 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.