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Related Concept Videos

¹H NMR of Conformationally Flexible Molecules: Temporal Resolution00:52

¹H NMR of Conformationally Flexible Molecules: Temporal Resolution

1.2K
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...
1.2K
¹H NMR of Conformationally Flexible Molecules: Variable-Temperature NMR01:15

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

1.6K
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.
1.6K
Conformations of Ethane and Propane02:18

Conformations of Ethane and Propane

16.6K
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...
16.6K
Conformations of Cyclohexane02:11

Conformations of Cyclohexane

14.9K
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...
14.9K
Conformations of Cycloalkanes02:29

Conformations of Cycloalkanes

13.9K
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...
13.9K
Chair Conformation of Cyclohexane02:02

Chair Conformation of Cyclohexane

17.7K
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...
17.7K

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Related Experiment Video

Updated: Dec 28, 2025

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
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Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis

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A Combined Systematic-Stochastic Algorithm for the Conformational Search in Flexible Acyclic Molecules.

David Ferro-Costas1, Antonio Fernández-Ramos1

  • 1Center for Research in Biological Chemistry and Molecular Materials (CIQUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain.

Frontiers in Chemistry
|February 13, 2020
PubMed
Summary

This study introduces a novel algorithm combining systematic and stochastic searches for conformational analysis. It efficiently identifies molecular conformers by intelligently exploring torsional spaces, crucial for accurate chemical calculations.

Keywords:
conformational searchgeometrical optimizationhindered rotorsstochastic methodstorsional anharmonicity

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Area of Science:

  • Computational Chemistry
  • Molecular Modeling
  • Physical Chemistry

Background:

  • Conformational analysis is vital for understanding molecular properties.
  • Efficiently exploring the vast conformational space of molecules remains a challenge.
  • Accurate calculation of partition functions requires comprehensive conformer identification.

Purpose of the Study:

  • To develop and present a novel algorithm for efficient and comprehensive molecular conformational analysis.
  • To improve the identification of stable molecular conformers.
  • To facilitate accurate calculations of multi-structural partition functions.

Main Methods:

  • A hybrid approach combining systematic torsion variation with stochastic (Monte Carlo) search.
  • Initial optimization using preconditioned torsional angles at a low electronic structure level.
  • Subsequent stochastic search generating random geometries outside optimized minima regions, followed by high-level optimization.

Main Results:

  • The algorithm successfully generates initial sets of conformers and identifies new ones during the stochastic search.
  • Storage of torsional angles prevents redundant exploration of the conformational space.
  • Demonstrated application in calculating partition functions for alcohols and L-serine.

Conclusions:

  • The proposed algorithm offers an effective strategy for comprehensive conformational searching.
  • It enhances the accuracy of computational chemistry by improving conformer identification.
  • The method is applicable to various molecules, including alcohols and amino acids.