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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...
¹H NMR of Conformationally Flexible Molecules: Variable-Temperature NMR01:15

¹H NMR of Conformationally Flexible Molecules: Variable-Temperature NMR

The axial and equatorial protons in cyclohexane can be distinguished by performing a variable-temperature NMR experiment. In this process, except for one proton, the remaining eleven protons are replaced by deuterium. The deuterium substitution avoids the possible peak splitting caused by the spin-spin coupling between the adjacent protons. The remaining proton flips between the axial and equatorial positions.
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...
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 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,...
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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Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
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An ant algorithm for the conformational analysis of flexible molecules.

Frits Daeyaert1, Marc De Jonge, Luc Koymans

  • 1Molmo Services BVBA, Campus Blairon 424, 2300 Turnhout, Belgium. frits@molmo.be

Journal of Computational Chemistry
|January 24, 2007
PubMed
Summary

This study adapts the ant system algorithm for continuous conformational analysis. The enhanced algorithm efficiently optimizes molecular structures in complex search spaces.

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Area of Science:

  • Computational Chemistry
  • Bioinformatics
  • Algorithm Development

Background:

  • The ant system algorithm is effective for discrete optimization problems.
  • Continuous search spaces, like conformational analysis, present unique challenges.
  • Adapting discrete algorithms to continuous domains requires careful parameterization.

Purpose of the Study:

  • To adapt the ant system algorithm for continuous conformational analysis.
  • To evaluate the algorithm's performance on various molecular structures.
  • To establish a novel computational tool for molecular modeling.

Main Methods:

  • Parameter tuning of the ant system algorithm using undecane and imatinib.
  • Application of the adapted algorithm to conformational analysis of drug molecules, vitamin A, and alanine tetrapeptide.
  • Validation of the algorithm's optimization capabilities in continuous spaces.

Main Results:

  • Successful adaptation of the ant system for continuous conformational analysis.
  • Demonstrated efficacy across diverse molecules, including drug candidates.
  • Identified optimal molecular conformations through the algorithm's application.

Conclusions:

  • The adapted ant system provides a robust method for continuous conformational analysis.
  • This approach offers a valuable tool for computational chemistry and drug discovery.
  • Further research can explore extensions to more complex molecular systems.