Literature DB >> 18464990

Benchmark database on isolated small peptides containing an aromatic side chain: comparison between wave function and density functional theory methods and empirical force field.

Haydee Valdes1, Kristýna Pluhácková, Michal Pitonák, Jan Rezác, Pavel Hobza.   

Abstract

A detailed quantum chemical study on five peptides (WG, WGG, FGG, GGF and GFA) containing the residues phenylalanyl (F), glycyl (G), tryptophyl (W) and alanyl (A) -- where F and W are of aromatic character -- is presented. When investigating isolated small peptides, the dispersion interaction is the dominant attractive force in the peptide backbone-aromatic side chain intramolecular interaction. Consequently, an accurate theoretical study of these systems requires the use of a methodology covering properly the London dispersion forces. For this reason we have assessed the performance of the MP2, SCS-MP2, MP3, TPSS-D, PBE-D, M06-2X, BH&H, TPSS, B3LYP, tight-binding DFT-D methods and ff99 empirical force field compared to CCSD(T)/complete basis set (CBS) limit benchmark data. All the DFT techniques with a '-D' symbol have been augmented by empirical dispersion energy while the M06-2X functional was parameterized to cover the London dispersion energy. For the systems here studied we have concluded that the use of the ff99 force field is not recommended mainly due to problems concerning the assignment of reliable atomic charges. Tight-binding DFT-D is efficient as a screening tool providing reliable geometries. Among the DFT functionals, the M06-2X and TPSS-D show the best performance what is explained by the fact that both procedures cover the dispersion energy. The B3LYP and TPSS functionals-not covering this energy-fail systematically. Both, electronic energies and geometries obtained by means of the wave-function theory methods compare satisfactorily with the CCSD(T)/CBS benchmark data.

Entities:  

Mesh:

Substances:

Year:  2008        PMID: 18464990     DOI: 10.1039/b719294k

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


  16 in total

1.  Localized orbital corrections applied to thermochemical errors in density functional theory: The role of basis set and application to molecular reactions.

Authors:  Dahlia A Goldfeld; Arteum D Bochevarov; Richard A Friesner
Journal:  J Chem Phys       Date:  2008-12-07       Impact factor: 3.488

2.  Comprehensive conformational studies of five tripeptides and a deduced method for efficient determinations of peptide structures.

Authors:  Wenbo Yu; Zhiqing Wu; Huibin Chen; Xu Liu; Alexander D MacKerell; Zijing Lin
Journal:  J Phys Chem B       Date:  2012-02-10       Impact factor: 2.991

3.  Nature of intermediates in organo-SOMO catalysis of alpha-arylation of aldehydes.

Authors:  Joann M Um; Osvaldo Gutierrez; Franziska Schoenebeck; K N Houk; David W C MacMillan
Journal:  J Am Chem Soc       Date:  2010-05-05       Impact factor: 15.419

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.  Parameterization of a B3LYP specific correction for non-covalent interactions and basis set superposition error on a gigantic dataset of CCSD(T) quality non-covalent interaction energies.

Authors:  Severin T Schneebeli; Arteum D Bochevarov; Richard A Friesner
Journal:  J Chem Theory Comput       Date:  2011-03-08       Impact factor: 6.006

6.  Quantum mechanics study of the hydroxyethylamines-BACE-1 active site interaction energies.

Authors:  Carlos Gueto-Tettay; Juan Carlos Drosos; Ricardo Vivas-Reyes
Journal:  J Comput Aided Mol Des       Date:  2011-06-21       Impact factor: 3.686

7.  On the zwitterionic nature of gas-phase peptides and protein ions.

Authors:  Roberto Marchese; Rita Grandori; Paolo Carloni; Simone Raugei
Journal:  PLoS Comput Biol       Date:  2010-05-06       Impact factor: 4.475

Review 8.  Enzyme informatics.

Authors:  Rosanna G Alderson; Luna De Ferrari; Lazaros Mavridis; James L McDonagh; John B O Mitchell; Neetika Nath
Journal:  Curr Top Med Chem       Date:  2012       Impact factor: 3.295

9.  A DFT study on the role of long range correlation interaction and solvent effects in homochiral and heterochiral cyclic trimerization of imidazole based heterocyclic amino acids.

Authors:  N V Suresh Kumar
Journal:  J Mol Model       Date:  2016-05-25       Impact factor: 1.810

10.  Force Field Benchmark of Organic Liquids: Density, Enthalpy of Vaporization, Heat Capacities, Surface Tension, Isothermal Compressibility, Volumetric Expansion Coefficient, and Dielectric Constant.

Authors:  Carl Caleman; Paul J van Maaren; Minyan Hong; Jochen S Hub; Luciano T Costa; David van der Spoel
Journal:  J Chem Theory Comput       Date:  2011-12-07       Impact factor: 6.006

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.