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Related Concept Videos

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.
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 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...
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 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...

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Related Experiment Video

Updated: Jun 2, 2026

Applying Cheminformatics to Develop a Structure Searchable Database of Analytical Methods
05:34

Applying Cheminformatics to Develop a Structure Searchable Database of Analytical Methods

Published on: June 6, 2025

A versatile method for systematic conformational searches: application to CheY.

Robert J Petrella1

  • 1Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA. petrella@fas.harvard.edu

Journal of Computational Chemistry
|May 11, 2011
PubMed
Summary
This summary is machine-generated.

The Z Method offers unbiased molecular structure prediction by systematically exploring conformations. This novel approach achieved high accuracy for the protein CheY, outperforming other methods.

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Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

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Area of Science:

  • Computational Biology
  • Structural Bioinformatics
  • Molecular Modeling

Background:

  • Accurate molecular structure prediction is crucial for understanding protein function.
  • Existing conformational search methods face challenges in unbiased sampling.

Purpose of the Study:

  • To introduce and evaluate the Z Method, a novel systematic approach for molecular structure prediction.
  • To demonstrate the Z Method's effectiveness in sampling conformational space.

Main Methods:

  • Implementation of the Z Method within the CHARMM program (Z Module).
  • Systematic, grid-based conformational search in a 36-dimensional space for the protein CheY.
  • Hierarchical build-up procedure with polar hydrogen representation and implicit solvation (EEF1).

Main Results:

  • The Z Method predicted the CheY structure within 1.56 Å of the native structure.
  • Errors in backbone dihedral angles showed approximate cancellation.
  • The Z Method outperformed Monte Carlo and simulated annealing methods in accuracy.

Conclusions:

  • The Z Method provides a versatile platform for systematic conformational search.
  • Unbiased sampling is critical for accurate macromolecular structure prediction.
  • Systematic searches with atom-based models are valuable for protein structure prediction.