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Related Concept Videos

Conformity01:20

Conformity

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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.
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Conformations of Butane02:20

Conformations of Butane

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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...
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Conformations of Cycloalkanes02:29

Conformations of Cycloalkanes

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

Conformations of Ethane and Propane

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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.
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Chair Conformation of Cyclohexane02:02

Chair Conformation of Cyclohexane

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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...
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Related Experiment Video

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Evidence-based Knowledge Synthesis and Hypothesis Validation: Navigating Biomedical Knowledge Bases via Explainable AI and Agentic Systems
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Knowledge-Based Conformer Generation Using the Cambridge Structural Database.

Jason C Cole1, Oliver Korb1, Patrick McCabe1

  • 1Cambridge Crystallographic Data Centre , 12 Union Road , Cambridge CB2 1EZ , United Kingdom.

Journal of Chemical Information and Modeling
|February 10, 2018
PubMed
Summary
This summary is machine-generated.

This study introduces a novel method for generating molecular conformations using the Cambridge Structural Database. The approach creates biologically relevant structures efficiently, outperforming existing methods in accuracy and speed.

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Area of Science:

  • Computational chemistry
  • Structural biology
  • Drug discovery

Background:

  • Accurate molecular modeling requires rapid generation of plausible molecular conformations.
  • Existing methods for conformer generation face challenges in speed and biological relevance.

Purpose of the Study:

  • To develop and evaluate a novel conformer generation approach leveraging the Cambridge Structural Database.
  • To assess the biological relevance and accuracy of generated conformations compared to existing methods.

Main Methods:

  • Utilized geometric distributions derived from the Cambridge Structural Database for conformer generation.
  • Compared the performance of the new approach against previously published evaluations and methods.
  • Analyzed the accuracy in reproducing conformations found in the Cambridge Structural Database and Protein Data Bank.

Main Results:

  • The developed method successfully generated biologically relevant conformations in most analyzed cases.
  • Demonstrated significantly improved performance in reproducing known molecular conformations compared to other fast methods.
  • Identified specific cases where the method's performance was limited.

Conclusions:

  • The approach offers a fast and accurate method for generating molecular conformations.
  • Leveraging the Cambridge Structural Database enhances the biological relevance of generated structures.
  • This method shows promise for applications in molecular modeling and drug discovery.