Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Molecular Models

Molecular Models

Physical models representing molecular architectures of chemical compounds play essential roles in understanding chemistry. The use of molecular models makes it easier to visualize the structures and shapes of atoms and molecules.

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...

Newman Projections

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...

Conformations of Cyclohexane

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...

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

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 Cyclohexane

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...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

Metabolic and functional pathways of gut microbiota in patients with gastric cancer.

Scientific reports·2026

Same author

<sup>1</sup>H-NMR-Based Metabolomic Profiling and Phylogenetic Analysis of Dendrobium Species Identify Lineage-Correlated Metabolites in the Main Clades.

Chemical & pharmaceutical bulletin·2026

Same author

Empagliflozin reduces liver fibrosis by restoring catechol-O-methyltransferase activity associated with magnesium levels.

Scientific reports·2025

Same author

Impact of the lipase inhibitor orlistat on the human gut microbiota.

Obesity research & clinical practice·2023

Same author

Structural and Computational Analyses of the Unique Interactions of Opicapone in the Binding Pocket of Catechol <i>O</i>-Methyltransferase: A Crystallographic Study and Fragment Molecular Orbital Analyses.

Journal of chemical information and modeling·2023

Same author

Countercurrent chromatography as a frontier tool to discover new mechanical roles in liquid-liquid phase separation of cellular biomolecules.

Biomedical chromatography : BMC·2022

Search research articles

Related Experiment Video

Updated: Aug 4, 2025

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

[Molecular Design Based on Conformational Analyses].

Hiroshi Iijima¹

¹School of Pharmacy, Nihon University.

Yakugaku Zasshi : Journal of the Pharmaceutical Society of Japan

|April 2, 2023

Summary

This summary is machine-generated.

Computational conformation analysis offers valuable insights for medicinal chemists, moving beyond "black box" software. This article shares practical experiences applying simple computational methods in real-world research.

Keywords:

conformational analysis distance mapping molecular design structure–activity relationship

More Related Videos

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Published on: July 8, 2025

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

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

Published on: July 16, 2017

Related Experiment Videos

Last Updated: Aug 4, 2025

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Published on: July 8, 2025

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

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

Published on: July 16, 2017

Area of Science:

Computational chemistry
Medicinal chemistry

Context:

Sophisticated computational chemistry software requires fundamental knowledge in thermodynamics, statistics, and physical chemistry.
Risk of computational tools being used as "black boxes" due to increasing complexity.

Purpose:

Introduce the capabilities of simple computational conformation analysis.
Share practical experiences of applying computational methods in wet research.

Summary:

Demonstrates the utility of basic computational conformation analysis.
Highlights the integration of computational approaches with experimental (wet) research.

Impact:

Empowers medicinal chemists to better utilize computational tools.
Bridges the gap between theoretical computation and practical laboratory application.