CH⋅⋅⋅N Hydrogen-Bonding Interaction in 7-Azaindole:CHX3(X=F, Cl) Complexes

Factors contributing to halogen bond strength and stretch or contraction of internal covalent bond

The halogen bond formed by a series of Lewis acids TF₃X (T = C, Si, Ge, Sn, Pb; X = Cl, Br, I) with NH₃ is studied by quantum chemical calculations. The interaction energy is closely mimicked by the depth of the σ-hole on the X atom as well as the full electrostatic energy. There is a first trend by which the hole is deepened if the T atom to which X is attached becomes more electron-withdrawing: C > Si > Ge > Sn > Pb. On the other hand, larger more polarizable T atoms are better able to transmit the electron-withdrawing power of the F substituents. The combination of these two opposing factors leaves PbF₃X forming the strongest XBs, followed by CF₃X, with SiF₃X engaging in the weakest bonds. The charge transfer from the NH₃ lone pair into the σ*(TX) antibonding orbital tends to elongate the covalent TX bond, and this force is largest for the heavier X and T atoms. On the other hand, the contraction of this bond deepens the σ-hole at the X atom, which would enhance both the electrostatic component and the full interaction energy. This bond-shortening effect is greatest for the lighter X atoms. The combination of these two opposing forces leaves the T-X bond contracting for X = Cl and Br, but lengthening for I.

C-HS interaction exhibits all the characteristics of conventional hydrogen bonds

This is a tale of a pair of a hydrogen bond donor and acceptor, namely the CH donor and sulphur acceptor, neither of which is a conventional hydrogen bond participant. Sulfur (S), being less electronegative (2.58) compared to its first row analogue oxygen (3.44), has not been considered as a potential HB acceptor for a long time. The C-HY (Y = HB acceptor) interaction has its own history of exhibiting omnidirectional shifts in the CH stretching frequency upon complex formation. Therefore, a systematic investigation of the C-HS interaction was the primary goal of the work presented here. Together with gas-phase vibrational spectroscopy and ab initio quantum chemical calculations, the nature and strength of the C-HS hydrogen bond (HB) have been investigated in the complexes of 1,2,4,5-tetracyanobenzene (TCNB) with various sulfur containing solvents. Despite the unconventional nature of both HB donor and HB acceptor (C-H and S, respectively), it was found that the C-HS hydrogen bond exhibits all the characteristics of the conventional hydrogen bond. The binding strength of the C-HS H-bond in these complexes was found to be comparable to that of the conventional hydrogen bonds. The unusual stabilities of these HBs have been mainly attributed to the attractive dispersion interaction.

Acid-Base Formalism Extended to Excited State for O-H···S Hydrogen Bonding Interaction

Hydrogen bond can be regarded as an interaction between a base and a proton covalently bound to another base. In this context the strength of hydrogen bond scales with the proton affinity of the acceptor base and the pKa of the donor, i.e., it follows the acid-base formalism. This has been amply demonstrated in conventional hydrogen bonds. Is this also true for the unconventional hydrogen bonds involving lesser electronegative elements such as sulfur atom? In our previous work, we had established that the strength of O-H···S hydrogen bonding (HB) interaction scales with the proton affinity (PA) of the acceptor. In this work, we have investigated the other counterpart, i.e., the H-bonding interaction between the photoacids with different pKa values with a common base such as the H2O and H2S. The 1:1 complexes of five para substituted phenols p-aminophenol, p-cresol, p-fluorophenol, p-chlorophenol, and p-cyanophenol with H2O and H2S were investigated experimentally and computationally. The investigations were also extended to the excited states. The experimental observations of the spectral shifts in the O-H stretching frequency and the S1-S0 band origins were correlated with the pKa of the donors. Ab initio calculations at the MP2 and various dispersion corrected density functional levels of theory were performed to compute the dissociation energy (D0) of the complexes. The quantum theory of atoms in molecules (QTAIM), noncovalent interaction (NCI) method, natural bonding orbital (NBO) analysis, and natural decomposition analysis (NEDA) were carried out for further characterization of HB interaction. The O-H stretching frequency red shifts and the dissociation energies were found to be lower for the O-H···S hydrogen bonded systems compared to those for the O-H···O H-bound systems. Despite being dominated by the dispersion interaction the O-H···S interaction in the H2S complexes also conformed to the acid-base formalism, i.e., the D0 and the O-H red shift scaled with the pKa of the donor, similar to that observed in the O-H···O interaction. However, the two classes of H-bonds follow different correlations. In addition we also discuss the nuances associated with the similarity and differences in the hydrogen bonding properties of the two classes in the ground electronic state as well as in the excited state.

Structure-activity study of N-((trans)-4-(2-(7-cyano-3,4-dihydroisoquinolin-2(1H)-yl)ethyl)cyclohexyl)-1H-indole-2-carboxamide (SB269652), a bitopic ligand that acts as a negative allosteric modulator of the dopamine D2 receptor

We recently demonstrated that SB269652 (1) engages one protomer of a dopamine D2 receptor (D2R) dimer in a bitopic mode to allosterically inhibit the binding of dopamine at the other protomer. Herein, we investigate structural determinants for allostery, focusing on modifications to three moieties within 1. We find that orthosteric "head" groups with small 7-substituents were important to maintain the limited negative cooperativity of analogues of 1, and replacement of the tetrahydroisoquinoline head group with other D2R "privileged structures" generated orthosteric antagonists. Additionally, replacement of the cyclohexylene linker with polymethylene chains conferred linker length dependency in allosteric pharmacology. We validated the importance of the indolic NH as a hydrogen bond donor moiety for maintaining allostery. Replacement of the indole ring with azaindole conferred a 30-fold increase in affinity while maintaining negative cooperativity. Combined, these results provide novel SAR insight for bitopic ligands that act as negative allosteric modulators of the D2R.

Evidence of blue-shifting N–H⋯N hydrogen bonding despite elongation of the N–H bond

N–H⋯N hydrogen bonding between pyrrole and N₂ results blue shift of ν_N–H accompanied by an increase in the N–H bond length.

On the properties of S⋯O and S⋯π noncovalent interactions: the analysis of geometry, interaction energy and electron density

We report computational studies on the origin and magnitude of non-covalent S⋯O and S⋯π interactions.

Thermo-reversible gelation of rod-coil and coil-rod-coil molecules based on poly(dimethyl siloxane) and perylene imides and self-sorting of the homologous pair

Organogels with perylene derivatives and phthalocyanines reported in the literature so far involve self-assembly promoted by hydrogen bonds, in addition to aromatic and van der Waals interactions. Although the self assembly of these types of molecules without a hydrogen bonding group in the structure occurs in solution or during crystallization, the gelation studies reported so far incorporated a hydrogen bonding pair of the type N-H···O=C in the structure of the molecule. We present a case of thermo-reversible gelation without a hydrogen bonding group in the structure of (1) a coil-rod-coil molecule based on perylenetetracarboxylic diimide (PTCDI) and poly(dimethyl siloxane) (PDMS) and (2) a rod-coil molecule with perylene dicarboxylic imide (PDI) and PDMS. However IR spectroscopy shows the presence of multiple types of hydrogen bonding between the solvents and the gelator molecules. In addition, publications so far on gelation of perylene diimide based molecules involve groups attached to both imide nitrogens and with or without substitution in the bay position. We discuss here the gelation with a Mono-substituted perylene imide. The PDMS segment was attached to one side of PDI (Mono-PDMS) or to both imide nitrogens of PTCDI (Di-PDMS). The Mono-PDMS is an inverse macromolecular surfactant applicable to non-aqueous systems, and the Di-PDMS is a Gemini surfactant. The PDMS segment that we attached to PTCDI here is longer than most substituents used by other authors. These molecules gel propylamine, as well as mixed solvents of hexane-water and diisopropylamine-water. Both hexane and diisopropylamine dissolve Mono-PDMS and Di-PDMS at room temperature and addition of water results in precipitation. However, heating the solution to about 70 °C, adding water (5-15 wt%) and slowly cooling the solution, lead to gelation. The Di-PDMS forms fibers which are not flat but curved as an eaves trough. The Mono-PDMS forms hollow spheres. Although the Mono-PDMS and Di-PDMS are a homologous pair, blends of these do not show molecular intercalation during gelation, but self-sort. The fibers of Di-PDMS based gels encapsulate the spheres of the Mono-PDMS based gels.