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A hydrogen bond is formed when a weakly positive hydrogen atom already bonded to one electronegative atom (for example, the oxygen in the water molecule) is attracted to another electronegative atom from another polar molecule, such as water (H2O), hydrogen fluoride (HF), or ammonia (NH3). The huge electronegativity difference between the H atom (2.1) and the atom to which it is bonded (4.0 for an F atom, 3.5 for an O atom, or 3.0 for an N atom), combined with the very small size of an H atom...

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Updated: May 17, 2026

From Molecules to Materials: Engineering New Ionic Liquid Crystals Through Halogen Bonding

From Molecules to Materials: Engineering New Ionic Liquid Crystals Through Halogen Bonding

Published on: March 24, 2018

Halogen bonding inside a molecular container.

Hamdy S El-Sheshtawy¹, Bassem S Bassil, Khaleel I Assaf

¹School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, D 28759 Bremen, Germany.

Journal of the American Chemical Society

|November 10, 2012

Summary

This summary is machine-generated.

Cucurbit[6]uril macrocycles bind dihalogens via two unique halogen bonds. One involves water, the other a perpendicular interaction with carbonyl π-systems, offering insights into protein-ligand interactions.

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Area of Science:

Supramolecular Chemistry
Chemical Crystallography
Computational Chemistry

Background:

Cucurbit[6]uril is a synthetic macrocycle known for forming host-guest complexes.
Halogen bonding is a non-covalent interaction crucial in molecular recognition and crystal engineering.
Understanding halogen bonding in diverse chemical environments is essential for designing new materials and drugs.

Purpose of the Study:

To investigate the host-guest inclusion complexes formed between cucurbit[6]uril and molecular dibromine (Br2) and diiodine (I2).
To elucidate the nature and geometry of halogen-bonding interactions involved in stabilizing these complexes.
To compare these interactions with those observed in biological systems and explore their underlying electronic factors.

Main Methods:

X-ray crystallography was used to determine the precise structures of the inclusion complexes.
Statistical analysis of existing small-molecule crystal structures was performed.
Quantum-chemical calculations (MP2/aug-cc-pVDZ-PP) were conducted using urea as a model system.

Main Results:

Cucurbit[6]uril forms inclusion complexes with Br2 and I2, with dihalogens adopting a tilted axial geometry.
Two distinct halogen bonds stabilize the dihalogens: a conventional O···X bond with water and a perpendicular O···X bond with the carbonyl π-system.
Perpendicular halogen bonds remain attractive even with nonlinear distortions (ca. 140° O···X-X angle), similar to protein-ligand interactions.

Conclusions:

The study confirms the formation of genuine perpendicular halogen bonds between dihalogens and the π-system of carbonyl groups in cucurbit[6]uril.
These perpendicular interactions are competitive with conventional halogen bonds, particularly with electron-donating substituents on the carbonyl group.
The findings provide valuable insights into halogen bonding in both synthetic and biological contexts, particularly relevant for halogenated ligands in proteins.