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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...
¹H NMR of Conformationally Flexible Molecules: Temporal Resolution00:52

¹H NMR of Conformationally Flexible Molecules: Temporal Resolution

At room temperature, the chair conformer of cyclohexane undergoes rapid ring flipping between two equivalent chair conformers at a rate of approximately 105 times per second. These two chair conformers are in equilibrium. The rapid ring flipping results in the interconversion of the axial proton to an equatorial proton and an equatorial to the axial proton. Such interconversions are too rapid and cannot be detected on the NMR timescale. Hence, the NMR spectrometer cannot distinguish between 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...

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Modeling Ligands into Maps Derived from Electron Cryomicroscopy
09:30

Modeling Ligands into Maps Derived from Electron Cryomicroscopy

Published on: July 19, 2024

PubChem3D: Similar conformers.

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
|May 11, 2011
PubMed
Summary
This summary is machine-generated.

A new "Similar Conformers" method identifies biologically relevant small molecules by analyzing 3-D shape and functional group orientation, complementing traditional 2-D methods for enhanced drug discovery.

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Area of Science:

  • Computational chemistry
  • Cheminformatics
  • Drug discovery

Background:

  • PubChem is a vast public resource for small molecule biological activity data.
  • Information on chemical structures and biological test results is unevenly distributed.
  • Existing 2-D similarity methods may miss related compounds with similar biological functions.

Purpose of the Study:

  • Introduce a novel "Similar Conformers" neighboring relationship.
  • Identify compounds with similar 3-D shape and pharmacophore orientation.
  • Enhance biological annotation for PubChem records.

Main Methods:

  • Compared the first two diverse 3-D conformers for 26.1 million PubChem records.
  • Utilized shape Tanimoto (ST) ≥ 0.8 and color Tanimoto (CT) ≥ 0.5.
  • Developed efficient filtering to manage computational cost for large-scale 3-D similarity analysis.

Main Results:

  • Generated billions of conformer and compound neighbor pairs.
  • Identified an average of 253 "Similar Conformers" neighbors per compound.
  • Demonstrated unique compound sets and grouping of NSAIDs, complementing 2-D similarity.

Conclusions:

  • The "Similar Conformers" method finds biologically relevant molecules missed by 2-D methods.
  • Efficient filtering significantly overcomes computational challenges for large-scale 3-D similarity.
  • This 3-D approach is a valuable complement to existing 2-D methodologies in cheminformatics.