C-H⋯S hydrogen bonding interactions

Abstract

The short C-H⋯S contacts found in available structural data for both small molecules and larger biomolecular systems suggest that such contacts are an often overlooked yet important stabilizing interaction. Moreover, many of these short C-H⋯S contacts meet the definition of a hydrogen bonding interaction. Using available structural data from the Cambridge Structural Database (CSD), as well as selected examples from the literature in which important C-H⋯S contacts may have been overlooked, we highlight the generality of C-H⋯S hydrogen bonding as an important stabilizing interaction. To uncover and establish the generality of these interactions, we compare C-H⋯S contacts with other traditional hydrogen bond donors and acceptors as well as investigate how coordination number and metal bonding affect the preferred geometry of interactions in the solid state. This work establishes that the C-H⋯S bond meets the definition of a hydrogen bond and serves as a guide to identify C-H⋯S hydrogen bonds in diverse systems.

Fig. 1.

Bond lengths and bond angles often measured in HB systems and will be described throughout the text.

Fig. 2.

Absence and presence of C–H HB in p-toluic acid and o-toluic acid, respectively.

Fig. 3.

Crystal structures of arylethynyl bisurea receptors shown to bind (a) Cl^–, (b) HS^–, and (c) HSe^– in the solid state. All three anions interact with the aryl C–H HB donor on the central ring.

Fig. 4.

Other supramolecular hosts demonstrated to reversibly bind HS^–. Both hosts feature C–H HB donors in their design (highlighted in red) and exhibit 1:1 binding with HS^– (depicted as a yellow sphere). Crystallographic structural data for these host-guest complexes have not been reported.

Fig. 5.

a) Cone angle of hydrogen bonding. b) 3D histogram visualizing over 423,000 C–H^…S contacts identified in the CSD. c) Cone-corrected 3D histogram of all C–H^…S contacts. The white dashed line represents estimate of the sum of the van der Waal radii of H and S.

Fig. 6.

A relatively short and linear C–H^…S contact in a disulfide cyclophane may help stabilize strained torsional angles.

Fig. 7.

3D histogram of a) N–H and b) O–H hydrogen bond donors with S.

Fig. 8.

Cone-corrected 3D histograms of C–H…A contacts found in the CSD with a) N, b) O, c) F, d) P, e) S, f) Cl, g) Se, h) Br, i) Te, and j) I. White dashed line represents estimate of the sum of the van der Waal radii of H and A.

Fig. 9.

a) cis/trans Isomerization of synthetic peptoids. A C–H^…A HB helps favor the cis conformation. b) The crystal structure shows a strong C–H^…S HB in the solid state that helps favor the cis conformation in the thioamide derivative.

Fig. 10.

a) Crystal packing of the luminogen reveals C–H^…O (atom denoted in red), C–H^…N (blue) and C–H^…S (yellow) intermolecular C–H HBs.

Fig. 11.

Cone-corrected 3D histograms of S bonded to a) one non-metal atom, b) two non-metal atoms, and c) three non-metal atoms.

Fig. 12.

a) Out isomer and b) in isomer of sulfur-strapped Zn-porphyrins.

Fig. 13.

Cone-corrected 3D histograms of C–H^…S contacts with a) sp³ alkyl C–H HB donors and b) sp² aryl C–H HB donors.

Fig. 14.

Leucine and valine amino acid residues in contact with HS^– in the first discovered bacterial ion channel for HS^–. The labeled lengths correspond to C–S distances. (PDB: 3TDX)

Fig. 15.

Tryptophan and threonine amino acid residues in contact with the biotin thioether in the streptavidin-biotin complex. (PDB: 6M9B)

Fig. 16.

Bi-weighted 3D histograms of C–H^…A contacts found in the CSD with a) N, b) O, c) F, d) P, e) S, f) Cl, g) Se, h) Br, i) Te, and j) I.

Fig. 17.

C–H hydrogen bonding interactions in the primary coordination sphere of metal complexes as demonstrated by Szymczak and coworkers.

Fig. 18.

Lengths and angles referred to in this section, where the HB acceptor (A) is bound to a metal.

Fig. 19.

Cone corrected histograms of a) C–H^…S–M, and b) C–H^…Cl–M contacts in d-block metals where S or Cl are in the primary coordination sphere. The white line for each plot indicates the sum of the van der Waal radii between A and H.

Fig. 20.

Cone corrected histograms of C–H^…S–M of groups a) 7, b) 8, c) 9, d) 10, e) 11, and f) 12 of the transition metals.

Fig. 21.

X-ray structures of a) sulfide bound Hb1 isolated from L. Pectinata and b) sulfide bound Hb isolated from human Hb. The labeled lengths correspond to C–S distances.

Fig. 22.

Cone corrected histograms of C–H^…(SH)–M with d-block metals.

Fig. 23.

Graphical representation of C-H^…S-Zn hydrogen bonding interactions observed in a ^iPrTpZnSH complex.