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Related Concept Videos

Stability of Substituted Cyclohexanes02:30

Stability of Substituted Cyclohexanes

This lesson discusses the stability of substituted cyclohexanes with a focus on energies of various conformers and the effect of 1,3-diaxial interactions.
The two chair conformations of cyclohexanes undergo rapid interconversion at room temperature. Both forms have identical energies and stabilities, each comprising equal amounts of the equilibrium mixture. Replacing a hydrogen atom with a functional group makes the two conformations energetically non-equivalent.
For example, in...
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,...
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.
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...
Mass Spectrometry: Cycloalkane Fragmentation01:05

Mass Spectrometry: Cycloalkane Fragmentation

In mass spectrometry, cycloalkanes exhibit distinct fragmentation patterns due to the inherent stability of their molecular ions compared to linear or branched alkanes. The ring structure of cycloalkanes provides additional stability to the molecular ions, often resulting in prominent ion peaks in the mass spectrum.
For example, cyclohexane molecular ions have a mass-to-charge ratio (m/z) of 84, which tends to produce a stronger signal than linear alkanes like hexane. This stability comes from...
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...

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Unraveling Entropic Rate Acceleration Induced by Solvent Dynamics in Membrane Enzymes
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Unraveling Entropic Rate Acceleration Induced by Solvent Dynamics in Membrane Enzymes

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Cyclo-hexa-peptides at the water/cyclohexane interface: a molecular dynamics simulation.

Min Cen1, Jian Fen Fan, Dong Yan Liu

  • 1College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou, 215123, People's Republic of China.

Journal of Molecular Modeling
|September 18, 2012
PubMed
Summary

Molecular dynamic simulations reveal how cyclo-hexa-peptides (CHPs) with varied side chains behave at water-cyclohexane interfaces. Hydrophobicity influences structure, and CHP dynamics are coupled with interfacial water molecules.

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Multiscale Sampling of a Heterogeneous Water/Metal Catalyst Interface using Density Functional Theory and Force-Field Molecular Dynamics
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Multiscale Sampling of a Heterogeneous Water/Metal Catalyst Interface using Density Functional Theory and Force-Field Molecular Dynamics

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Last Updated: May 18, 2026

Unraveling Entropic Rate Acceleration Induced by Solvent Dynamics in Membrane Enzymes
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Published on: January 16, 2016

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Multiscale Sampling of a Heterogeneous Water/Metal Catalyst Interface using Density Functional Theory and Force-Field Molecular Dynamics
10:52

Multiscale Sampling of a Heterogeneous Water/Metal Catalyst Interface using Density Functional Theory and Force-Field Molecular Dynamics

Published on: April 12, 2019

Area of Science:

  • Physical Chemistry
  • Computational Chemistry
  • Biophysics

Background:

  • Cyclo-hexa-peptides (CHPs) are cyclic peptides with potential applications.
  • Understanding peptide behavior at liquid interfaces is crucial for various scientific fields.
  • The water-cyclohexane interface presents a model system for studying amphipathic molecule interactions.

Purpose of the Study:

  • To investigate the structural and dynamic behaviors of ten different CHPs at the water/cyclohexane interface using molecular dynamic (MD) simulations.
  • To elucidate the influence of hydrophilic/hydrophobic side chains on CHP conformations and interactions.
  • To determine the relationship between interaction energies and diffusion dynamics at the interface.

Main Methods:

  • Molecular dynamic (MD) simulations were employed to model ten distinct cyclo-hexa-peptides (CHPs).
  • Simulations were conducted at the water/cyclohexane interface to observe peptide behavior.
  • Radial Distribution Function (RDF) analysis was used to study hydrogen bonding and interactions.

Main Results:

  • All CHPs adopted a "horse-saddle" conformation at the interface.
  • The hydrophilicity/hydrophobicity of side chains significantly affected backbone structural deformations.
  • A direct correlation was observed between differences in interaction energies (ΔΔE) and lateral diffusion coefficients (Dxy).
  • Hydrogen bonds formed between CHP backbones and water molecules, and CHP dynamics were coupled with interfacial water.

Conclusions:

  • CHP behavior at the water/cyclohexane interface is dictated by side chain properties and influences backbone structure.
  • Interfacial interactions and dynamics are strongly coupled between CHPs and water molecules.
  • MD simulations provide valuable insights into the complex behavior of peptides at liquid-liquid interfaces.