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Related Concept Videos

Hydrogen Bonds00:26

Hydrogen Bonds

Hydrogen 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 unequally shared.
Hydrogen Bonds01:04

Hydrogen Bonds

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...
Molecular Orbital Theory II03:51

Molecular Orbital Theory II

Molecular Orbital Energy Diagrams
Hybridization of Atomic Orbitals II03:35

Hybridization of Atomic Orbitals II

sp3d and sp3d 2 Hybridization
Hybridization of Atomic Orbitals I03:24

Hybridization of Atomic Orbitals I

The mathematical expression known as the wave function, ψ, contains information about each orbital and the wavelike properties of electrons in an isolated atom. When atoms are bound together in a molecule, the wave functions combine to produce new mathematical descriptions that have different shapes. This process of combining the wave functions for atomic orbitals is called hybridization and is mathematically accomplished by the linear combination of atomic orbitals. The new orbitals that...
Molecular Geometry and Dipole Moments02:36

Molecular Geometry and Dipole Moments

The VSEPR theory can be used to determine the electron pair geometries and molecular structures as follows:

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Related Experiment Video

Updated: May 29, 2026

Multiscale Sampling of a Heterogeneous Water/Metal Catalyst Interface using Density Functional Theory and Force-Field Molecular Dynamics
10:52

Multiscale Sampling of a Heterogeneous Water/Metal Catalyst Interface using Density Functional Theory and Force-Field Molecular Dynamics

Published on: April 12, 2019

HBonanza: a computer algorithm for molecular-dynamics-trajectory hydrogen-bond analysis.

Jacob D Durrant1, J Andrew McCammon

  • 1Department of Chemistry & Biochemistry, University of California San Diego, La Jolla, CA 92093-0365, United States. jdurrant@ucsd.edu

Journal of Molecular Graphics & Modelling
|September 2, 2011
PubMed
Summary
This summary is machine-generated.

The total number of hydrogen bonds does not predict drug effectiveness. Hydrogen bonds may primarily ensure specificity and proper ligand positioning within a receptor, not binding affinity.

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Last Updated: May 29, 2026

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Area of Science:

  • Computational chemistry
  • Structural biology
  • Drug discovery

Background:

  • Hydrogen bonds are crucial in molecular interactions.
  • Their role in ligand-receptor binding affinity is debated.
  • Previous studies suggest limited contribution to binding energy.

Purpose of the Study:

  • To analyze the correlation between hydrogen bonds and ligand potency.
  • To investigate the primary role of hydrogen bonds in ligand-receptor interactions.
  • To introduce a new computational tool for hydrogen bond analysis.

Main Methods:

  • Analysis of 2673 ligand-receptor complexes.
  • Statistical assessment of hydrogen bond number and ligand potency.
  • Development and application of the HBonanza software.

Main Results:

  • The total number of hydrogen bonds is a poor predictor of ligand potency.
  • No statistically significant correlation was found between hydrogen bond formation and potency.
  • Hydrogen bonds may be more important for specificity and positioning.

Conclusions:

  • Hydrogen bond count is not a reliable indicator of drug efficacy.
  • Hydrogen bonds likely play a key role in molecular recognition and orientation.
  • The HBonanza tool facilitates detailed hydrogen bond network analysis and visualization.