Halogen bonding in metal–organic–supramolecular networks

A knowledge-based halogen bonding scoring function for predicting protein-ligand interactions

Halogen bonding, a non-covalent interaction between the halogen σ-hole and Lewis bases, could not be properly characterized by majority of current scoring functions. In this study, a knowledge-based halogen bonding scoring function, termed XBPMF, was developed by an iterative method for predicting protein-ligand interactions. Three sets of pairwise potentials were derived from two training sets of protein-ligand complexes from the Protein Data Bank. It was found that two-dimensional pairwise potentials could characterize appropriately the distance and angle profiles of halogen bonding, which is superior to one-dimensional pairwise potentials. With comparison to six widely used scoring functions, XBPMF was evaluated to have moderate power for predicting protein-ligand interactions in terms of "docking power", "ranking power" and "scoring power". Especially, it has a rather satisfactory performance for the systems with typical halogen bonds. To the best of our knowledge, XBPMF is the first halogen bonding scoring function that is not dependent on any dummy atom, and is practical for high-throughput virtual screening. Therefore, this scoring function should be useful for the study and application of halogen bonding interactions like molecular docking and lead optimization.

A redox active proton transfer and hydrogen-bonding system of tetrathiafulvalene-dicarboxylic acid and pyridine bases

Hydrogen bonds are important in supramolecular chemistry and responsible for proton transfer processes. This manuscript reports new hydrogen-bonding systems of redox-active acid-base assemblies consisting of dimethylthio-tetrathiafulvalene dicarboxylic acid (H(2)L) coupled with pyridine (py), 2,2'-bipyridine (2,2'-bpy), and 4,4'-bipyridine (4,4'-bpy). The (1)H NMR chemical shifts of the pyridines and the redox potential shifts of the tetrathiafulvalene moiety indicate that proton-transfer and strong hydrogen-bonding interactions exist between the acid and the bases in aprotic solvents. The results of cyclic voltammetry show a two-step square reaction with a redox and proton transfer coupled mechanism. The nature of the hydrogen bonds was characterized by X-ray single crystal analysis. In contrast to the mono-carboxyl-py system, in this ortho-substituted dicarboxyl-py system one proton of the H(2)L transfers completely from the carboxyl to the py group. The conjugated intramolecular and intermolecular hydrogen bonds are responsible for the proton transfer.

ETS-NOCV description of σ-hole bonding

The ETS-NOCV analysis was applied to describe the σ-hole in a systematic way in a series of halogen compounds, CF3-X (X = I, Br, Cl, F), CH3I, and C(CH3)nH3-n-I (n = 1,2,3), as well as for the example germanium-based systems. GeXH3, X = F, Cl, H. Further, the ETS-NOCV analysis was used to characterize bonding with ammonia for these systems. The results show that the dominating contribution to the deformation density, Δρ 1 , exhibits the negative-value area with a minimum, corresponding to σ-hole. The "size" (spatial extension of negative value) and "depth" (minium value) of the σ-hole varies for different X in CF3-X, and is influenced by the carbon substituents (fluorine atoms, hydrogen atoms, methyl groups). The size and depth of σ-hole decreases in the order: I, Br, Cl, F in CF3-X. In CH3-I and C(CH3)nH3-n-I, compared to CF3-I, introduction of hydrogen atoms and their subsequent replacements by methyl groups lead to the systematic decrease in the σ-hole size and depth. The ETS-NOCV σ-hole picture is consistent with the existence the positive MEP area at the extension of σ-hole generating bond. Finally, the NOCV deformation density contours as well as by the ETS orbital-interaction energy indicate that the σ-hole-based bond with ammonia contains a degree of covalent contribution. In all analyzed systems, it was found that the electrostatic energy is approximately two times larger than the orbital-interaction term, confirming the indisputable role of the electrostatic stabilization in halogen bonding and σ-hole bonding.

5-Iodo-1,2,3-triazolium-based multidentate halogen-bond donors as activating reagents

Bi- and tridentate polycationic halogen bond donors based on 5-iodo-1,2,3-triazolium groups have been synthesized by 1,3-dipolar cycloaddition reactions. These halogen-based Lewis acids have been evaluated as activators in a halide-abstraction benchmark reaction.

Communication: Competition between π···π interaction and halogen bond in solution: a combined 13C NMR and density functional theory study

Competition between π···π interaction and halogen bond in solution has been investigated by using carbon nuclear magnetic resonance spectroscopy ((13)C NMR) combined with density functional theory calculation. Both experimental and theoretical results clearly show that there are no C-Cl···π or C-Br···π halogen bonds and only the π···π interactions exist in the binary liquid mixtures of C(6)D(6) with C(6)F(5)Cl and C(6)F(5)Br, respectively. The case is totally different for the binary liquid mixtures of C(6)D(6) with C(6)F(5)I in which the C-I···π halogen bonds not the π···π interactions are present. The important role of entropy in the competition between π···π interaction and halogen bond in solution was also discussed.

Theoretical description of halogen bonding - an insight based on the natural orbitals for chemical valence combined with the extended-transition-state method (ETS-NOCV)

In the present study we have characterized the halogen bonding in selected molecules H3N-ICF3 (1-NH 3 ), (PH3)2C-ICF3 (1-CPH 3 ), C3H7Br-(IN2H2C3)2C6H4 (2-Br), H2-(IN2H2C3)2C6H4 (2-H 2 ) and Cl-(IC6F5)2C7H10N2O5 (3-Cl), containing from one halogen bond (1-NH 3 , 1-CPH 3 ) up to four connections in 3-Cl (the two Cl-HN and two Cl-I), based on recently proposed ETS-NOCV analysis. It was found based on the NOCV-deformation density components that the halogen bonding C-X (…) B (X-halogen atom, B-Lewis base), contains a large degree of covalent contribution (the charge transfer to X (…) B inter-atomic region) supported further by the electron donation from base atom B to the empty σ*(C-X) orbital. Such charge transfers can be of similar importance compared to the electrostatic stabilization. Further, the covalent part of halogen bonding is due to the presence of σ-hole at outer part of halogen atom (X). ETS-NOCV approach allowed to visualize formation of the σ-hole at iodine atom of CF3I molecule. It has also been demonstrated that strongly electrophilic halogen bond donor, [C6H4(C3H2N2I)2][OTf]2, can activate chemically inert isopropyl bromide (2-Br) moiety via formation of Br-I bonding and bind the hydrogen molecule (2-H 2 ). Finally, ETS-NOCV analysis performed for 3-Cl leads to the conclusion that, in terms of the orbital-interaction component, the strength of halogen (Cl-I) bond is roughly three times more important than the hydrogen bonding (Cl-HN).

Structural competition between halogen bonds and lone-pair···π interactions in solution

Structural competition between halogen bonds and lone-pair···π interactions in solution is studied using (13)C NMR combined with density functional theory calculations. Among the halogen bonds considered, only the iodine bonds and a few bromine bonds are strong enough to compete successfully with the lone-pair···π interactions.