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

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.

Advances in molecular quantum chemistry contained in the Q-Chem 4 program package

“…Complete basis set estimates (CBS) for MP2 were taken from references for the divalent sulphur, SW49 [155][156][157], ACONF [158], CYCONF [159], and SCONF [160] databases. MP2/CBS results for the S22 [82,83], S66 [84,85], L7 [161], and P76 [162] databases were obtained from the Benchmark Energy and Geometry DataBase (BEGDB) [163]. MP2/CBS results for the A24 databases [164] were generated for this work.…”

Quantum Chemical Benchmark Energy and Geometry Database for Molecular Clusters and Complex Molecular Systems (www.begdb.com): A Users Manual and Examples

“…We have also covered the phenomena of halogen bonding 3 . Aside from noncovalent complexes, we have studied conformers of small peptides [4][5][6] at the same level of theory. This list is not final; we are working on more systematic high-level studies.…”

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

“…1, as compared to other widely used functionals͒, we also investigate the performance of the M05-2X functional of Zhao et al, 9 both in its native form and incorporating LOCs. We have selected M05-2X for investigation because it has displayed interesting abilities to achieve reasonable results for properties that other DFT methods have great difficulty with ͑e.g., dispersion interactions͒, [10][11][12] while at the same time preserving respectable results for the traditional atomization energy benchmarks ͑the M06-2X functional 13 has similar advantages 11,12,[14][15][16] ͒ and is the most recent version of this family of functionals; its limited analysis is also carried out in this work͒. Furthermore, M05-2X has previously been benchmarked on only a subset of the G3 molecules; evaluation of results for the complete G3 set provides a fuller picture of its performance.…”