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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 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,...
Newman Projections02:06

Newman Projections

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 conformers.
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...
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.

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Structural Studies of Macromolecules in Solution using Small Angle X-Ray Scattering
07:19

Structural Studies of Macromolecules in Solution using Small Angle X-Ray Scattering

Published on: November 5, 2018

Sampling conformations in high dimensions using low-dimensional distribution functions.

Sandeep Somani1, Benjamin J Killian, Michael K Gilson

  • 1Center for Advanced Research in Biotechnology, UMBI, 9600 Gudelsky Drive, Rockville, Maryland 20850, USA.

The Journal of Chemical Physics
|April 10, 2009
PubMed
Summary
This summary is machine-generated.

This study introduces a new method to approximate molecular conformational probability density functions using lower-order correlations. This approach accurately captures molecular dynamics simulations, suggesting low-order correlations are key for understanding molecular fluctuations.

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Area of Science:

  • Computational chemistry
  • Molecular modeling
  • Statistical mechanics

Background:

  • Accurately describing a molecule's conformational probability density function (pdf) is crucial for understanding its behavior.
  • High-dimensional pdfs are computationally intensive to calculate and sample.
  • Existing methods often struggle with the complexity of molecular conformations.

Purpose of the Study:

  • To develop an approximation for N-dimensional molecular conformational pdfs using lower-order marginal pdfs.
  • To create an algorithm for sampling conformations from this approximate pdf.
  • To validate the approximation against molecular dynamics (MD) simulations.

Main Methods:

  • Approximation of N-dimensional pdf using marginal pdfs of order l (l << N).
  • Construction via recursive application of the generalized Kirkwood superposition approximation.
  • Development of a sampling algorithm based on input marginal pdfs.

Main Results:

  • The sampling algorithm was tested on three small molecule systems.
  • Conformational distributions sampled at third-order (l=3) closely matched MD simulation results.
  • Third-order approximation significantly outperformed first-order (l=1) and second-order (l=2) approximations.

Conclusions:

  • Correlations among internal degrees of freedom are vital for molecular conformational fluctuations.
  • Low-order correlations are sufficient to describe the majority of molecular conformational changes in a thermal environment.
  • The developed approximation offers an efficient alternative to full MD simulations for conformational analysis.