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. 2019 Sep 12;24(18):3329.
doi: 10.3390/molecules24183329.

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

Mariusz Michalczyk  1 , Wiktor Zierkiewicz  2 , Rafał Wysokiński  3 , Steve Scheiner  4
Affiliations

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

Mariusz Michalczyk et al. Molecules. .

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.

Keywords: NBO; NMR shielding; atomic charge; energy decomposition; stretching frequency.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Optimized geometries of indicated Lewis acids with N-methylacetamide (NMA). Distances in Å, angles in degrees.
Figure 2
Figure 2
Regions of density gain (purple) and loss (green) in complexes pairing NMA with (a) H2FP, (b) H2FAs, and (c) H2FSb. Contour shown is ±0.0015 au.
Figure 3
Figure 3
Relationship between MP2/aug-cc-pVDZ interaction energy and changes in frequencies of F–X stretch (green points), amide I (red), and amide II (blue). Broken lines indicate linear fits.
Figure 4
Figure 4
Relationship between MP2/aug-cc-pVDZ interaction energy and changes in NMR shielding of indicated atoms of NMA. Broken lines indicate linear fits.
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