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Related Concept Videos

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.
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...
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Different notations are used to represent the three-dimensional structure of molecules on two-dimensional surfaces. One of the most commonly used representations is the dash-wedge formula. The dashed wedges, solid wedges, and the plane lines indicate the groups situated behind the plane, coming out of the plane, and in the plane, respectively.
The organic molecules rotate across the single bonds leading to numerous temporary three-dimensional structures of varying energy known as...
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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...
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Molecular Models02:00

Molecular Models

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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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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.
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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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Related Experiment Video

Updated: Mar 23, 2026

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
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Three-Dimensional Chemical Structure Search Using the Conformational Code for Organic Molecules (CCOM) Program.

Hiroshi Izumi1, Laurence A Nafie2,3, Rina K Dukor3

  • 1National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan.

Chirality
|April 5, 2016
PubMed
Summary
This summary is machine-generated.

The Conformational Code for Organic Molecules (CCOM) program converts 3D molecular data to 1D, aiding 3D fragment searching. Modified CCOM rules improve accuracy, revealing conformational changes in mevastatin

Keywords:
3D fragment searchPybelPythonSDF formatSMARTSSMILESmevastatinnomenclaturepravastatinvibrational circular dichroism

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Area of Science:

  • Computational Chemistry
  • Molecular Modeling
  • Organic Chemistry

Background:

  • 3D structural fragment searching of organic molecules is difficult due to geometry variations and conformational flexibility.
  • Existing methods struggle with discrepancies between experimental and theoretical molecular structures.

Purpose of the Study:

  • To develop a robust method for 3D conformational data conversion and fragment searching.
  • To introduce modifications to the Conformational Code for Organic Molecules (CCOM) program for enhanced 3D fragment searching.

Main Methods:

  • Developed the Conformational Code for Organic Molecules (CCOM) program to convert 3D conformational data into 1D data.
  • Introduced two key deviations from IUPAC Rule E-5.6 within the CCOM program for 3D fragment searching.
  • Applied the modified CCOM program with SMiles ARbitrary Target Specification (SMARTS) to search mevastatin's 3D conformational fragment (mb_3a6c4c).

Main Results:

  • The CCOM program successfully converts complex 3D conformational data into a simplified 1D format.
  • Modified CCOM rules enhance the accuracy of 3D fragment searching by refining dihedral angle determination.
  • Analysis of mevastatin's mb_3a6c4c fragment suggests conformational changes may drive protein dissociation.

Conclusions:

  • The CCOM program provides an unambiguous method for representing and searching 3D molecular conformations.
  • The introduced CCOM rule modifications improve the reliability of 3D fragment searching.
  • Conformational flexibility of molecular fragments plays a crucial role in drug-target interactions, as exemplified by mevastatin.