Theoretical Studies of IR and NMR Spectral Changes Induced by Sigma-Hole Hydrogen, Halogen, Chalcogen, Pnicogen, and Tetrel Bonds in a Model Protein Environment.

Michalczyk Michalczyk,Wysokiński Wysokiński,Zierkiewicz Zierkiewicz,Scheiner Scheiner

doi:10.3390/molecules24183329

Abstract

Various types of σ-hole bond complexes were formed with FX, HFY, H2FZ, and H3FT (X = Cl, Br, I; Y = S, Se, Te; Z = P, As, Sb; T = Si, Ge, Sn) as Lewis acid. In order to examine their interactions with a protein, N-methylacetamide (NMA), a model of the peptide linkage was used as the base. These noncovalent bonds were compared by computational means with H-bonds formed by NMA with XH molecules (X = F, Cl, Br, I). In all cases, the A–F bond, which lies opposite the base and is responsible for the σ-hole on the A atom (A refers to the bridging atom), elongates and its stretching frequency undergoes a shift to the red with a band intensification, much as what occurs for the X–H bond in a H-bond (HB). Unlike the NMR shielding decrease seen in the bridging proton of a H-bond, the shielding of the bridging A atom is increased. The spectroscopic changes within NMA are similar for H-bonds and the other noncovalent bonds. The C=O bond of the amide is lengthened and its stretching frequency red-shifted and intensified. The amide II band shifts to higher frequency and undergoes a small band weakening. The NMR shielding of the O atom directly involved in the bond rises, whereas the C and N atoms both undergo a shielding decrease. The frequency shifts of the amide I and II bands of the base as well as the shielding changes of the three pertinent NMA atoms correlate well with the strength of the noncovalent bond.

Highlights

Our understanding of the H-bond (HB) represents a cornerstone of what has been learned over the years about solvation phenomena and the structure and function of biological systems [1–4].The energetic and geometric aspects of the HB have raised our recognition of the requirements of a stable protein and the mechanism of countless enzymes
As examples [3,8,9], the red shift of the A–H stretching frequency is thought to correlate with the strength of the AH···B HB, and there is a similar type of relationship for the downfield shift of the Nuclear magnetic resonance (NMR) peak of the bridging proton
It may be noted that the relative orientations are as would be expected for each of the types of bonds under consideration here, commensurate with the positions of the σ-holes on each type of Lewis acid, and with the O atom of NMA serving as the electron donor atom

Summary

Introduction

Our understanding of the H-bond (HB) represents a cornerstone of what has been learned over the years about solvation phenomena and the structure and function of biological systems [1–4].The energetic and geometric aspects of the HB have raised our recognition of the requirements of a stable protein and the mechanism of countless enzymes. The shifts in certain IR bands or NMR peaks are frequently interpreted as a quantitative measure of the strength of each such bond [5–7]. Recent years have witnessed a growing recognition of a set of newly rediscovered noncovalent bonds. Rather than utilizing a proton as a bridge between a pair of molecules, these related interactions incorporate a more electronegative atom from the right side of the periodic table. This bridging atom may have an overall partial negative charge, a detailed examination of its surrounding

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