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Related Concept Videos

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...
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.
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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...
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Conserved Binding Sites

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.
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Next-generation Sequencing03:00

Next-generation Sequencing

The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
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Conformations of Cycloalkanes02:29

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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 was based on the...

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Freely available conformer generation methods: how good are they?

Jean-Paul Ebejer1, Garrett M Morris, Charlotte M Deane

  • 1Oxford Protein Informatics Group, Department of Statistics, University of Oxford, 1 South Parks Road, Oxford OX1 3TG, UK.

Journal of Chemical Information and Modeling
|April 10, 2012
PubMed
Summary

We evaluated free conformer generation software for drug discovery. RDKit and Confab accurately reproduced experimental structures, with RDKit offering a viable, cost-effective alternative after postprocessing optimization.

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Area of Science:

  • Computational chemistry
  • Cheminformatics
  • Drug discovery

Background:

  • Conformer generation is crucial for computational drug discovery.
  • Software quality impacts virtual screening outcomes.
  • Evaluating free tools against commercial options is needed.

Purpose of the Study:

  • Assess accuracy in reproducing experimental structures.
  • Evaluate the diversity of generated conformers.
  • Benchmark computational time for different tools.

Main Methods:

  • Tested Balloon, Confab, Frog2, RDKit, and MOE.
  • Used 708 drug-like molecules with known X-ray structures.
  • Analyzed conformer accuracy (rmsd), diversity, and speed.

Main Results:

  • RDKit and Confab showed superior accuracy in generating low-rmsd conformers.
  • Confab excelled with molecules having many rotatable bonds (≥10).
  • RDKit was the second fastest tool, enhanced by a postprocessing algorithm for diversity.

Conclusions:

  • RDKit, with postprocessing, is a strong free alternative to commercial conformer generation software.
  • Both RDKit and Confab offer high accuracy for structure reproduction.
  • The study provides benchmarks for selecting appropriate cheminformatics tools.