Evaluation of the intramolecular basis set superposition error in the calculations of larger molecules: [n]helicenes and Phe‐Gly‐Phe tripeptide

Abstract

Correlated ab initio calculations on large systems, such as the popular MP2 (or RI-MP2) method, suffer from the intramolecular basis set superposition error (BSSE). This error is typically manifested in molecules with folded structures, characterized by intramolecular dispersion interactions. It can dramatically affect the energy differences between various conformers as well as intramolecular stabilities, and it can even impair the accuracy of the predictions of the equilibrium molecular structures. In this study, we will present two extreme cases of intramolecular BSSE, the internal stability of [n]helicene molecules and the relative energies of various conformers of phenylalanyl-glycyl-phenylalanine tripeptide (Phe-Gly-Phe), and compare the calculated data with benchmark values (experimental or high-level theoretical data). As a practical and cheap solution to the accurate treatment of the systems with large anticipated value of intramolecular BSSE, the recently developed density functional method augmented with an empirical dispersion term (DFT-D) is proposed and shown to provide very good results in both of the above described representative cases.

Infrared spectra of protonated neurotransmitters: dopamine

“…Thus, these additional calculations suggest that the higher stabilization of the g isomers observed at the MP2 level as compared to the B3LYP level are not due to effects of basis set superposition error in folded conformers. 31 Moreover, they also indicate that the dispersion forces are not severely overestimated at the MP2 level for the present system, 32 as they are similar at the DFT-D levels. Selected structural and energetic parameters for the most stable gauche and trans isomers of dopamineH + , gÀ1, g+1, and t1, are summarized in Table 2.…”

Tyrosine-glycine revisited: Resolving the discrepancy between theory and experiment

“…The relative populations of the 20 conformers at those temperatures, calculated according to a Maxwell-Boltzmann distribution ( Table 1), suggest that at least one of the folded conformers (1-6) should be found, as well as 7 and 10. Also, a clear effect of the entropic correction is to heavily disfavour extended conformers with a hydrogen bond (numbers [13][14][15][16][17][18][19][20]. When the 20 conformers were re-optimised with B97-D/6-31+G* and M06-2X/6-31+G*, they all became more folded, as quantified by a decrease in the distance between the C carb (Gly) and C1(Tyr) atoms.…”

“…They exemplify two different empirical approaches to recovering the missing dispersion in DFTthe former [14] by including an atom-pairwise dispersion correction of the form C 6 ·R −6 , the latter [15] through parameters derived from training sets containing dispersion-bound complexes. DFT in general is largely free of BSSE [16]. Gibbs free energy corrections for the newly-optimised structures were also calculated at 298.15 K and 400 K using the corresponding model chemistries.…”

Geometrical and Electronic Structure Variability of the Sugar−phosphate Backbone in Nucleic Acids

“…102,103 Though several schemes for the intramolecular BSSE compensation were proposed, 97 the most physically justified method to eliminate intramolecular (as well as intermolecular) BSSE is to perform the calculations with large basis set, 98 ideally going up to the CBS limit. 95,103 The PES for the SPM model was explored at the B3LYP/6-31+G* level with a grid spacing of 30°. At each grid point, the model was fully optimized, but for R and γ (fixed at the grid values) and δ (fixed at a fiber diffraction value of 143°), it was started from the corresponding ff99 geometry (see above).…”