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

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.

Self-assembly of reversed bilayer vesicles through pnictogen bonding: water-stable supramolecular nanocontainers for organic solvents

“…[37][38][39][40][41][42] Computational study of the pnictogen bonding An oen suggested prerequisite for strong PnBs, following studies on halogen and chalcogen bonding, is the presence of large V max (maximum in the electrostatic potential energy surface calculated on a molecular surface at 0.001 au) 43,44 values associated with the electrophilic regions of the ESP surface. 40,[45][46][47][48] A typical design strategy used to achieve this is to incorporate polar primary bonds. The replacement of O with S to enhance the stability of the primary bonds is therefore expected to result in smaller V max values and weaker PnBs.…”

Modeling of Solute-Solvent Interactions Using an External Electric Field—From Tautomeric Equilibrium in Nonpolar Solvents to the Dissociation of Alkali Metal Halides

“…Noncovalent interactions allow our world to exist. Their specific interaction energies [ 1 , 2 , 3 , 4 ], their effect on the spectral [ 5 , 6 , 7 ], chemical [ 8 , 9 ], and structural [ 10 , 11 , 12 ] properties of individual molecules, those in adducts and solutions [ 13 , 14 , 15 ], have been and remain vital to the progress of chemistry. The interpretation of spectral shifts caused by changes in the properties of a particular interaction can be carried out in sufficient detail [ 16 ].…”

Interplay between Polymorphism and Isostructurality in the 2-Fur- and 2-Thenaldehyde Semi- and Thiosemicarbazones

“…5-Nitro-2-furaldehyde semicarbazone (3β) and 5-nitro-2-thiophene semicarbazone (4) were synthesized by the same procedure, only semicarbazide hydrochloride (1 mmnol) was used instead of thiosemicarbazide. Solid samples of the synthesized compounds (1)(2)(3)(4) were dissolved in a pure solvent (MeOH, EtOH, i-PrOH, MeCN, or dmf) or solvent mixture (dmf + MeOH, dmf + EtOH, dmf + i-PrOH, dmf + MeCN, or MeOH + MeCN; 1 + 1 v/v in all cases) and heated for 10 minutes and then left for crystallization under ambient conditions (in covered, but not sealed, vessels to allow for the decelerated evaporation of solvents). Further structurally different crystalline products were obtained by the slow evaporation of solvents only for 1 and 3 (i.e., 5-nitro-2-furaldehyde thiosemicarbazone dimethylformamide dimethylformamide solvate (1·dmfα, by slow evaporation from dmf solution), 5-nitro-2-furaldehyde thiosemicarbazone dimethylformamide solvate (1·dmfβ, by slow evaporation from MeOH:dmf (1:1 v/v) solvent mixture), and 5-nitro-2-furaldehyde semicarbazone (3γ, by slow evaporation from MeOH:MeCN (1:1 v/v) solvent mixture as well as from pure MeCN)).…”

“…Knowledge about non-covalent interactions increases with each passing year [1][2][3][4][5], but is still insufficient to enable the complete design and prediction of the crystal structure of organic compounds, even with the usage of computational crystal structure prediction. Application of computational methods allows for the prognostication of crystal packing on the basis of the structural formula, but these methods still lead to ambiguous results or give an incorrect build of the crystal net in some cases [6,7].…”