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Conformations of Cyclohexane02:11

Conformations of Cyclohexane

12.2K
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...
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Conformations of Cycloalkanes02:29

Conformations of Cycloalkanes

12.2K
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...
12.2K
Conformations of Ethane and Propane02:18

Conformations of Ethane and Propane

13.9K
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...
13.9K
Conformations of Butane02:20

Conformations of Butane

14.3K
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...
14.3K
¹H NMR of Conformationally Flexible Molecules: Temporal Resolution00:52

¹H NMR of Conformationally Flexible Molecules: Temporal Resolution

992
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...
992
¹H NMR of Conformationally Flexible Molecules: Variable-Temperature NMR01:15

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

1.4K
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.
1.4K

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Spatial Separation of Molecular Conformers and Clusters
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Exploring Conformer Search Workflows Using OpenBabel, Hierarchical Clustering, and Quantum Chemical Optimizations: A

Anna Elmanova1,2,3, Martin Presselt1,3

  • 1Leibniz Institute of Photonic Technology (IPHT), Albert-Einstein-Str. 9, 07745 Jena, Germany.

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Summary

This study benchmarks OpenBabel conformer generation, developing a tree-wise search strategy. The workflow combines hierarchical clustering and density functional theory (DFT) refinement for reliable identification of energetically relevant molecular conformers.

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Area of Science:

  • Computational Chemistry
  • Molecular Modeling

Background:

  • Accurate prediction of molecular properties requires identifying all energetically relevant conformers.
  • Assessing the completeness of conformer ensembles is a significant challenge in computational chemistry.
  • The open-source toolkit OpenBabel offers various conformer generation algorithms with adjustable parameters impacting search outcomes.

Purpose of the Study:

  • To systematically investigate the influence of OpenBabel methods and parameters on conformer search results.
  • To develop and validate a reliable workflow for identifying energetically relevant conformers.
  • To establish a practical framework for selecting OpenBabel parameters and optimizing conformer identification strategies.

Main Methods:

  • Conformer generation using OpenBabel for reference molecules, including Oligothiophenes and the nonfullerene acceptor Y6.
  • Hierarchical clustering of generated conformers based on geometric similarity (RMSD and normalized RMSD).
  • Density functional theory (DFT) optimization of representative conformers and iterative re-initiation of searches from DFT-relaxed structures.

Main Results:

  • A tree-wise, iterative conformer search strategy was established by combining RMSD-based genetic searches with hierarchical clustering.
  • The workflow demonstrated effective identification of previously overlooked, energetically relevant conformers.
  • A thorough benchmark and workflow analysis of the tree-wise genetic conformer search was performed on a set of small molecules.

Conclusions:

  • The developed workflow provides a practical, benchmark-based framework for selecting OpenBabel parameters.
  • The study offers reliable strategies for conformer identification through hierarchical clustering and DFT-based refinement.
  • This approach enhances the accuracy of quantum chemical predictions for molecular and material properties.