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Chair Conformation of Cyclohexane02:02

Chair Conformation of Cyclohexane

14.9K
The chair conformation is the most stable form of cyclohexane due to the absence of angle and torsional strain. The absence of angle strain is a result of cyclohexane’s bond angle being very close to the ideal tetrahedral bond angle of 109.5° in its chair conformer. Similarly, the torsional strain is also absent owing to the perfectly staggered arrangement of bonds.
The hydrogen atoms linked to carbons are arranged in two different axial and equatorial orientations to achieve this...
14.9K
Conformations of Ethane and Propane02:18

Conformations of Ethane and Propane

14.3K
In an organic molecule, free rotation about the carbon-carbon single bond results in energetically different conformers of the molecule. Due to this rotation, called the internal rotation, ethane has two major conformations — staggered and eclipsed.
Staggered conformation is a low energy and more stable conformation with the C-H bonds on the front carbon placed at 60°dihedral angles relative to the C-H bonds on the back carbon, leading to a reduced torsional strain. In staggered...
14.3K
Conformations of Cyclohexane02:11

Conformations of Cyclohexane

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Cyclohexane does not exist in a planar form due to the high angle and torsional strain it would experience in the planar structure. Instead, it adopts non-planar chair and boat conformations.
The chair form is the most stable and derives its name from its resemblance to the “easy chair.” In the chair conformation, two carbon atoms are arranged out-of-plane — one above and one below, minimizing the torsional strain. In the chair form, the bond angle is very close to the ideal...
12.8K
Conserved Binding Sites01:49

Conserved Binding Sites

4.3K
Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...
4.3K
Conformations of Butane02:20

Conformations of Butane

14.6K
Unlike ethane and propane that have only two major conformations, butane has more than two conformers. The staggered form of butane in which the bulky methyl groups on the two carbons are placed on opposite sides, that is, at a dihedral angle of 180°, is the lowest energy, most stable form — called the anti conformer. This conformation is stabilized due to the absence of steric repulsion between the largely spaced out methyl groups. The other two staggered conformations are...
14.6K
Predicting Molecular Geometry02:27

Predicting Molecular Geometry

35.6K
VSEPR Theory for Determination of Electron Pair Geometries
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Related Experiment Video

Updated: Sep 1, 2025

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
10:58

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

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An optimization algorithm for conformer generation based on the bond contribution ranking.

Ziheng Zhang1, Kai Zhang2, Zhihui Liu3

  • 1School of Laboratory Medicine, Chongqing Medical University, Chongqing, China.

Computational Biology and Chemistry
|August 13, 2022
PubMed
Summary
This summary is machine-generated.

This study introduces an optimized conformer generation algorithm, ABCR, for computational drug discovery. It efficiently finds optimal small molecule conformers, improving protein-ligand docking and conformational searching.

Keywords:
Bond contribution rankConformer generationSystematic samplingTorsion angle

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Area of Science:

  • Computational chemistry
  • Molecular modeling
  • Drug discovery

Background:

  • Conformer generation is crucial for computational drug discovery.
  • Existing methods struggle with the combinatorial explosion of conformers and incomplete conformational space sampling.
  • Rotatable bonds are often treated uniformly, leading to inefficiencies.

Purpose of the Study:

  • To present an optimized conformer generation algorithm, the Algorithm based on Bond Contribution Ranking (ABCR).
  • To enable the efficient identification of optimal small molecule conformers based on specified scoring functions.
  • To enhance molecular conformational searching and protein-ligand docking performance.

Main Methods:

  • Developed the Algorithm based on Bond Contribution Ranking (ABCR).
  • Focused on optimizing conformer generation by ranking bond contributions.
  • Applied the algorithm to improve conformational searching and protein-ligand docking.

Main Results:

  • ABCR achieves optimal conformer identification with fewer generated conformers and iterations.
  • Demonstrated improved molecular conformational searching and protein-ligand docking performance compared to existing methods.
  • Maintained or expanded the coverage of the conformational space during global sampling.

Conclusions:

  • The ABCR algorithm offers an efficient and effective solution for small molecule conformer generation.
  • This method addresses limitations of existing approaches, particularly the combinatorial explosion and incomplete sampling.
  • ABCR shows promise for advancing computational drug discovery and molecular modeling techniques.