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¹H NMR of Conformationally Flexible Molecules: Temporal Resolution

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 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...

Conformations of Ethane and Propane

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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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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Updated: Apr 18, 2026

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

Generating conformational transitions using the euclidean distance matrix.

Xiao-Bo Li, Forbes Burkowski

IEEE Transactions on Nanobioscience

|January 22, 2015

Summary

This summary is machine-generated.

Elastic Network Interpolation (ENI) can now use distances-squared for protein dynamics. This mathematical generalization aids in studying protein conformations and their movements.

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Area of Science:

Computational Biology
Biophysics
Structural Bioinformatics

Background:

Elastic Network Interpolation (ENI) is a computational method for modeling protein dynamics.
The current ENI formulation relies on interatomic distances to generate intermediate protein conformations.

Purpose of the Study:

To generalize the Elastic Network Interpolation method to utilize interatomic distances-squared.
To explore the mathematical framework of protein dynamics on positive semidefinite (PSD) matrices.

Main Methods:

Generalization of the Elastic Network Interpolation (ENI) formulation from interatomic distances to distances-squared.
Testing the generalized ENI scheme using lattice structures to evaluate its performance and identify limitations.

Main Results:

Demonstrated the feasibility of using interatomic distances-squared within the ENI framework.
Identified and discussed limitations of the generalized ENI approach through lattice structure tests.

Conclusions:

The generalization of ENI to distances-squared offers a new mathematical perspective for studying protein dynamics.
Further research is suggested to refine the method and address observed limitations for broader applications in structural bioinformatics.