Computational study of the interaction of indole-like molecules with water and hydrogen sulfide

Abstract

The characteristics of the interaction between water and hydrogen sulfide with indole and a series of analogs obtained by substituting the NH group of indole by different heteroatoms have been studied by means of ab initio calculations. In all cases, minima were found corresponding to structures where water and hydrogen sulfide interact by means of X-H···π contacts. The interaction energies for all these π complexes are quite similar, spanning from -13.5 to -18.8 kJ/mol, and exhibiting the stability sequence NH > CH(2) ≈ PH > Se ≈ S > O, for both water and hydrogen sulfide. Though interaction energies are similar, hydrogen sulfide complexes are slightly favored over their water counterparts when interacting with the π cloud. σ-Type complexes were also considered for the systems studied, but only in the case of water complexes this kind of complexes is relevant. Only for complexes formed by water and indole, a significantly more stable σ-type complex was found with an interaction energy amounting to -23.6 kJ/mol. Oxygen and phosphorous derivatives also form σ-type complexes of similar stability as that observed for π ones. Despite the similar interaction energies exhibited by complexes with water and hydrogen sulfide, the nature of the interaction is very different. For π complexes with water the main contributions to the interaction energy are electrostatic and dispersive contributing with similar amounts, though slightly more from electrostatics. On the contrary, in hydrogen sulfide complexes dispersion is by far the main stabilizing contribution. For the σ-type complexes, the interaction is clearly dominated by the electrostatic contribution, especially in the indole-water complex.

Modeling Protein S–Aromatic Motifs Reveals Their Structural and Redox Flexibility

“…Our E CP values for the H 2 S–aromatics agree well with the literature values (kcal/mol) for 3a (−2.34, −2.64, and −2.74; CCSD­(T)/aug-cc-pVXZ levels, X = D, T, and Q), 3c (−4.49; CCSD­(T) level at the complete basis set limit), and 3f (−2.78 and −3.68; aug-cc-pVDZ basis set at the B3LYP and MP2 levels, respectively) …”

“…The energetic and structural properties of S–aromatic complexes in the gas phase have been the subject of numerous computational investigations. − ,,,,,− ,− However, these studies have been limited in scope, reporting on global minimum structures only, and many focus on H 2 S–benzene. ,,− ,− To understand the chemistry of protein S–aromatic motifs, we extend the study to MeSR interactions with benzene, indole, phenol, imidazole, and their methylated forms, the latter being better models for residue side chains. Our extensive search in the configurational space of the H 2 S and MeSR complexes with the 8 aromatics uncovers 303 stable conformers plus 44 conformers for the H 2 O–aromatics.…”

Electronic and Infrared Spectroscopy of Benzene-(H2S)n (n = 1 and 2): The Prototype of the SH-π Interaction

“…Experimental and theoretical studies on model clusters of the SH-π interaction have been extensively performed. The model clusters are, for example, naphthalene-H 2 S and indole-H 2 S. − These clusters present very similar SH−π contact motifs to those of the corresponding clusters with H 2 O, and their binding energies are almost equivalent or less than those of the clusters with H 2 O. The theoretical energy decomposition of the SH-π interaction energy indicates that dispersion plays a crucial role in stabilizing the clusters.…”

Sulfur‐Aromatic Interactions: Modeling Cysteine and Methionine Binding to Tyrosinate and Histidinium Ions to Assess Their Influence on Protein Electron Transfer

“…Changes in oxidation potential could arise from protonation/deprotonation of the interacting species and/or from changes in complex stability on oxidation of one or both interacting molecules. However, computational investigations have focused on S‐aromatic interactions involving neutral aromatic compounds ,. We found just a single report on the binding energy of a sulfur ligand to an aromatic ion, that of MeSH‐imidazolium .…”