Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Conformity01:20

Conformity

47.9K
Conformity is the change in a person’s behavior to go along with the group, even if that person does not agree with the group.
47.9K
Conformations of Butane02:20

Conformations of Butane

17.8K
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...
17.8K
Conformations of Cycloalkanes02:29

Conformations of Cycloalkanes

14.2K
Adolf von Baeyer attempted to explain the instabilities of small and large cycloalkane rings using the concept of angle strain — the strain caused by the deviation of bond angles from the ideal 109.5° tetrahedral value for sp3  hybridized carbons. However, while cyclopropane and cyclobutane are strained, as expected from their highly compressed bond angles, cyclopentane is more strained than predicted, and cyclohexane is virtually strain-free. Hence, Baeyer’s theory that...
14.2K
Conformations of Cyclohexane02:11

Conformations of Cyclohexane

15.3K
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...
15.3K
Conformations of Ethane and Propane02:18

Conformations of Ethane and Propane

16.9K
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...
16.9K
Chair Conformation of Cyclohexane02:02

Chair Conformation of Cyclohexane

18.2K
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...
18.2K

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Narrowing the gap between machine learning scoring functions and free energy perturbation using augmented data.

Communications chemistry·2025
Same author

Sort & Slice: a simple and superior alternative to hash-based folding for extended-connectivity fingerprints.

Journal of cheminformatics·2024
Same author

cclib 2.0: An updated architecture for interoperable computational chemistry.

The Journal of chemical physics·2024
Same author

QupKake: Integrating Machine Learning and Quantum Chemistry for Micro-p<i>K</i><sub>a</sub> Predictions.

Journal of chemical theory and computation·2024
Same author

It is theoretically possible to avoid misfolding into non-covalent lasso entanglements using small molecule drugs.

PLoS computational biology·2024
Same author

PoseBusters: AI-based docking methods fail to generate physically valid poses or generalise to novel sequences.

Chemical science·2024
Same journal

Multimodal feature fusion for molecular property classification.

Journal of cheminformatics·2026
Same journal

P2MAT: A machine learning (ML) driven software for Property Prediction of MATerial.

Journal of cheminformatics·2026
Same journal

Computational design of low-volatility lubricants for space using interpretable machine learning.

Journal of cheminformatics·2026
Same journal

OpenStats: how to combine statistics and research data management (RDM) to leverage efficient scientific data analysis by guided statistics.

Journal of cheminformatics·2026
Same journal

Unified heterogeneity-aware benchmark of drug synergy prediction: a cross-study analysis of traditional machine learning and graph deep learning models.

Journal of cheminformatics·2026
Same journal

Count your bits: fingerprint benchmarking to assess broad chemical space representation.

Journal of cheminformatics·2026
See all related articles

Related Experiment Video

Updated: Jan 24, 2026

Spatial Separation of Molecular Conformers and Clusters
10:37

Spatial Separation of Molecular Conformers and Clusters

Published on: January 9, 2014

11.7K

Bayesian optimization for conformer generation.

Lucian Chan1, Geoffrey R Hutchison2, Garrett M Morris1

  • 1Department of Statistics, University of Oxford, 24-29 St Giles', Oxford, OX1 3LB, UK.

Journal of Cheminformatics
|May 23, 2019
PubMed
Summary
This summary is machine-generated.

A new Bayesian optimization algorithm (BOA) efficiently finds the lowest energy molecular conformations. BOA requires fewer evaluations than traditional methods, often discovering superior low-energy conformers for complex molecules.

Keywords:
Bayesian optimizationConformational spaceConformer generationGaussian processesMolecular energeticsRotatable bondTorsion angle

More Related Videos

A Novel Bayesian Change-point Algorithm for Genome-wide Analysis of Diverse ChIPseq Data Types
12:39

A Novel Bayesian Change-point Algorithm for Genome-wide Analysis of Diverse ChIPseq Data Types

Published on: December 10, 2012

11.7K
High-Pressure NMR Experiments for Detecting Protein Low-Lying Conformational States
04:37

High-Pressure NMR Experiments for Detecting Protein Low-Lying Conformational States

Published on: June 29, 2021

3.1K

Related Experiment Videos

Last Updated: Jan 24, 2026

Spatial Separation of Molecular Conformers and Clusters
10:37

Spatial Separation of Molecular Conformers and Clusters

Published on: January 9, 2014

11.7K
A Novel Bayesian Change-point Algorithm for Genome-wide Analysis of Diverse ChIPseq Data Types
12:39

A Novel Bayesian Change-point Algorithm for Genome-wide Analysis of Diverse ChIPseq Data Types

Published on: December 10, 2012

11.7K
High-Pressure NMR Experiments for Detecting Protein Low-Lying Conformational States
04:37

High-Pressure NMR Experiments for Detecting Protein Low-Lying Conformational States

Published on: June 29, 2021

3.1K

Area of Science:

  • Computational Chemistry
  • Molecular Modeling
  • Cheminformatics

Background:

  • Conformer generation is crucial for molecular modeling and cheminformatics.
  • Existing methods often prioritize diversity over energetic accuracy.
  • Finding the lowest energy conformation remains a significant challenge.

Purpose of the Study:

  • Introduce a novel stochastic search method, the Bayesian optimization algorithm (BOA).
  • Evaluate BOA's performance in identifying low-energy molecular conformations.
  • Compare BOA against uniform random search and systematic search (Confab).

Main Methods:

  • Developed and implemented the Bayesian optimization algorithm (BOA).
  • Utilized Confab for systematic conformer search.
  • Employed energetic difference, root-mean-square deviation, and torsion fingerprint deviation for performance quantification.

Main Results:

  • BOA significantly reduces the number of evaluations needed to find low-energy minima compared to random and systematic searches.
  • For molecules with >= 4 rotatable bonds, BOA requires substantially fewer energy evaluations than Confab's median.
  • BOA successfully identifies lower-energy conformations than Confab in 20-40% of cases for complex molecules.

Conclusions:

  • The Bayesian optimization algorithm (BOA) offers a more efficient approach to conformer generation.
  • BOA demonstrates superior performance in finding energetically favorable molecular conformations.
  • This method holds promise for advancing computational chemistry and molecular modeling applications.