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Related Concept Videos

Conformations of Cyclohexane02:11

Conformations of Cyclohexane

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 tetrahedral value,...
Conformations of Cycloalkanes02:29

Conformations of Cycloalkanes

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 was based on the...
Conformations of Butane02:20

Conformations of Butane

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 degenerate and have...
Conformations of Ethane and Propane02:18

Conformations of Ethane and Propane

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 ethane, the...
Chair Conformation of Cyclohexane02:02

Chair Conformation of Cyclohexane

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 staggered...
Molecular Models02:00

Molecular Models

Physical models representing molecular architectures of chemical compounds play essential roles in understanding chemistry. The use of molecular models makes it easier to visualize the structures and shapes of atoms and molecules.

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Curation of Computational Chemical Libraries Demonstrated with Alpha-Amino Acids
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Published on: April 13, 2022

PubChem3D: Conformer generation.

Evan E Bolton1, Sunghwan Kim, Stephen H Bryant

  • 1National Center for Biotechnology Information National Library of Medicine National Institutes of Health Department of Health and Human Services 8600 Rockville Pike, Bethesda, MD 20894, USA. bolton@ncbi.nlm.nih.gov.

Journal of Cheminformatics
|January 29, 2011
PubMed
Summary
This summary is machine-generated.

This study optimized 3D conformer generation parameters for PubChem3D, developing a predictive equation for accuracy. These findings improve the reliability of theoretical 3D chemical structure models for biological activity prediction.

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Area of Science:

  • Computational Chemistry
  • Cheminformatics
  • Structural Biology

Background:

  • PubChem provides tools for analyzing small molecule biological activities, including structure similarity searches.
  • PubChem3D enhances similarity searching by incorporating 3D conformer data alongside 2D chemical structure graphs.
  • Accurate theoretical 3D conformer models are crucial for relating chemical structures to experimental biological activity.

Purpose of the Study:

  • To investigate the impact of key conformer generation parameters on the accuracy of theoretical 3D models.
  • To determine optimal settings for generating conformer models and sampling within PubChem3D.
  • To ensure theoretical conformer models can reliably reproduce experimentally determined bioactive conformations.

Main Methods:

  • Systematic testing of conformer generation parameters using the OMEGA software package.
  • Generation of theoretical 3D conformer models for 25,972 experimentally determined small-molecule ligands.
  • Development of a regression equation to predict Root Mean Square Deviation (RMSD) accuracy based on molecular size and flexibility.

Main Results:

  • Increased fragment sampling rate did not improve model accuracy.
  • Larger energy windows generally increased accuracy, with optimal convergence at 10-15 kcal/mol.
  • Excluding Coulomb terms and using MMFF94s improved accuracy at lower energy windows.
  • Accuracy showed a linear correlation with molecular size (non-hydrogen atom count) and flexibility (effective rotor count).

Conclusions:

  • Optimal parameters for OMEGA conformer generation were identified.
  • A predictive equation was developed to guide RMSD sampling for accurate bioactive conformation reproduction.
  • These optimized parameters and sampling values are implemented in the PubChem3D project for generating theoretical conformer models.