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Hydrogen Bonds

Hydrogen Bonds

Hydrogen BondsHydrogen bonds are weak attractions between atoms that have formed other chemical bonds. One of these atoms is electronegative, like oxygen, and has a partial negative charge. The other is a hydrogen atom that has bonded with another electronegative atom and has a partial positive charge.Hydrogen Bonds Control the World!Because hydrogen has very weak electronegativity when it binds with a strongly electronegative atom, such as oxygen or nitrogen, electrons in the bond are...

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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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Related Experiment Video

Updated: Jul 14, 2026

Analyzing Protein Dynamics Using Hydrogen Exchange Mass Spectrometry

Analyzing Protein Dynamics Using Hydrogen Exchange Mass Spectrometry

Published on: November 29, 2013

Graph-set analysis of hydrogen-bond patterns: some mathematical concepts.

Grell¹, Bernstein, Tinhofer

¹Institute of Freshwater Ecology and Inland Fisheries, Department of Ecohydrology, Rudower Chaussee 6a, D-12489 Berlin, Germany.

Acta Crystallographica. Section B, Structural Science

|August 6, 2000

Summary

This study introduces new mathematical tools, including constructor graphs and arrowed T-labeling, to analyze hydrogen bonding patterns. These methods enable consistent and automatic identification of intermolecular interaction patterns in crystal structures.

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Area of Science:

Crystallography
Chemical Physics
Computational Chemistry

Background:

Graph sets are utilized for analyzing patterns in intermolecular interactions.
Existing methods require enhancement to incorporate directional properties of hydrogen bonds.
Mathematical formalisms are needed for consistent and automated pattern definition.

Purpose of the Study:

To develop and demonstrate mathematical concepts and tools for applying graph sets to hydrogen bonding and intermolecular interactions.
To establish a foundation for theoretical and software development in pattern analysis.
To enable the straightforward, consistent, and automatic definition of interaction patterns.

Main Methods:

Review of basic definitions and uses of graph sets.
Inclusion of directional properties of hydrogen bonds.
Development of constructor graphs and covalent distance matrices.
Introduction of arrowed T-labeling for moieties on crystallographic special positions.

Main Results:

Defined and demonstrated mathematical concepts and tools for graph set application.
Developed constructor graphs and covalent distance matrices for qualitative descriptor generation.
Created arrowed T-labeling to address special crystallographic positions.
Applied the developed concepts to polymorphic iminodiacetic acid and trans-tetraamminedinitrocobalt(III) acetate structures.

Conclusions:

The developed mathematical tools provide a robust framework for analyzing hydrogen bonding and intermolecular interactions.
These methods facilitate consistent and automated pattern definition in crystal structures.
The concepts are integrated into Cambridge Structural Database software for practical application.