Noncovalent Carbon‐Bonding Interactions in Proteins

Abstract

Carbon bonds (C‐bonds) are the highly directional noncovalent interactions between carbonyl‐oxygen acceptors and sp3‐hybridized‐carbon σ‐hole donors through n→σ* electron delocalization. We have shown the ubiquitous existence of C‐bonds in proteins with the help of careful protein structure analysis and quantum calculations, and have precisely determined C‐bond energies. The importance of conventional noncovalent interactions such as hydrogen bond (H‐bonds) and halogen bond (X‐bonds) in the structure and function of biological molecules are well established, while carbon bonds C‐bonds have still to be recognized. We have shown that C‐bonds are present in proteins, contribute enthalpically to the overall hydrophobic interaction and play a significant role in the photodissociation mechanism of myoglobin and the binding of nucleobases to proteins.

Conformation control through concurrent N–H⋯S and N–H⋯OC hydrogen bonding and hyperconjugation effects

“…[10][11][12] Recently, there has been an increased awareness of the importance of contributions to secondary structure stabilization from other types of non-covalent interactions, including less conventional H-bonds such as intra-residue C5 H-bonds ( Fig. 1), [13][14][15] or C-H/O interactions, 16,17 as well as phenomena such as n / p* hyperconjugative interactions, 18 Cbonds, 19 cation-p interactions, 20,21 and others. 22 Reports of non-covalent interactions in proteins which specically implicate the side-chain heteroatom of sulfurcontaining residues are rare and do not involve H-bonds; rather, they take the form of sulfur-aromatic interactions 23,24 or chalcogen bonds.…”

Hexacoordinated Tetrel‐Bonded Complexes between TF4 (T=Si, Ge, Sn, Pb) and NCH: Competition between σ‐ and π‐Holes

“…[1][2][3][4] These noncovalent bonds, sometimes generically referred to as σ-hole interactions due to the deficiency of electron density that lies directly opposite a covalent bond in which the bridging atom is involved [5][6][7] have been extensively studied over the last few years and are consequently rather well understood. [9,10] Scores of tetrel bonds have been identified within protein structures, [11][12][13][14][15] and are implicated in the catalytic process of several enzymes. These tetrel bonds differ a bit from the others in this set of noncovalent bonds primarily in that the central atom is typically covalently bonded to four substituents, as compared to only one for a halogen bond or as many as three for a pnicogen bond.…”

“…This sort of bond can, for example, be considered a preliminary step in the very common S N 2 reaction. [9,10] Scores of tetrel bonds have been identified within protein structures, [11][12][13][14][15] and are implicated in the catalytic process of several enzymes. [16][17][18][19][20][21] There is a rapidly growing literature [22][23][24][25][26][27] that has provided a wealth of insights into the chemical and physical phenomena that underlie tetrel bonds.…”

On the capability of metal–halogen groups to participate in halogen bonds

“…The resulting area of positive electrostatic potential has gained the sobriquet of a σ-hole, which can attract an anion or any other nucleophile. The XB is not dependent solely on this electrostatic attraction, but also benefits from polarization/charge transfer and dispersion contributions 15-18 . This sort of phenomenon is not limited to halogen atoms; replacement of X by atoms from the chalcogen [19][20][21][22][23][24][25][26][27] , pnicogen [28][29][30][31][32][33][34][35][36][37][38][39] , and tetrel [40][41][42][43][44][45][46][47][48][49][50][51][52][53][54][55] families of elements can lead to very similar noncovalent bonds, which are generally named after the particular type of atom, e.g. tetrel bonds.…”