Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Chair Conformation of Cyclohexane02:02

Chair Conformation of Cyclohexane

21.4K
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...
21.4K
Conformations of Cyclohexane02:11

Conformations of Cyclohexane

17.3K
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...
17.3K
¹H NMR of Conformationally Flexible Molecules: Temporal Resolution00:52

¹H NMR of Conformationally Flexible Molecules: Temporal Resolution

1.4K
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...
1.4K
Conformations of Cycloalkanes02:29

Conformations of Cycloalkanes

16.7K
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...
16.7K
[4+2] Cycloaddition of Conjugated Dienes: Diels–Alder Reaction01:16

[4+2] Cycloaddition of Conjugated Dienes: Diels–Alder Reaction

13.7K
The Diels–Alder reaction is an example of a thermal pericyclic reaction between a conjugated diene and an alkene or alkyne, commonly referred to as a dienophile. The reaction involves a concerted movement of six π electrons, four from the diene and two from the dienophile, forming an unsaturated six-membered ring. As a result, these reactions are classified as [4+2] cycloadditions.
13.7K
Stability of Substituted Cyclohexanes02:30

Stability of Substituted Cyclohexanes

17.3K
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...
17.3K

You might also read

Related Articles

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

Sort by
Same author

Enhancing machine learning-based binder design with high-throughput screening: A comparison of mRNA and yeast display technologies.

Protein science : a publication of the Protein Society·2026
Same author

Reconstruction of septin higher-order nano-size structures in ovarian cancer cells uncover susceptibility to the septin-targeting small molecule UR214-9.

bioRxiv : the preprint server for biology·2026
Same author

A practical implementation science framework for education.

NPJ science of learning·2026
Same author

Macrocycle screening against the C-terminal region of CHD4 uncovers its role as an interaction hub in the formation of the nucleosome remodeling and deacetylase complex.

bioRxiv : the preprint server for biology·2026
Same author

Mechanistic role of APOE lipidation in Alzheimer's disease pathogenesis.

Theranostics·2026
Same author

Modular Deep Learning for Direct RNA Sequence Design via Self-Contained RNA Units.

bioRxiv : the preprint server for biology·2026

Related Experiment Video

Updated: Mar 30, 2026

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
08:49

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

Published on: June 20, 2025

1.5K

Dynamic Docking of Conformationally Constrained Macrocycles: Methods and Applications.

Scott E Allen1, Nikolay V Dokholyan1, Albert A Bowers1

  • 1Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, and ‡Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599, United States.

ACS Chemical Biology
|November 18, 2015
PubMed
Summary

Large, flexible macrocycles from natural products are promising drug scaffolds. Advanced molecular docking methods now enable better analysis and optimization of these complex molecules for medicinal chemistry applications.

More Related Videos

Interactive Molecular Model Assembly with 3D Printing
06:15

Interactive Molecular Model Assembly with 3D Printing

Published on: August 13, 2020

11.2K
Development of Inhibitors of Protein-protein Interactions through REPLACE: Application to the Design and Development Non-ATP Competitive CDK Inhibitors
10:33

Development of Inhibitors of Protein-protein Interactions through REPLACE: Application to the Design and Development Non-ATP Competitive CDK Inhibitors

Published on: October 26, 2015

11.9K

Related Experiment Videos

Last Updated: Mar 30, 2026

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
08:49

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

Published on: June 20, 2025

1.5K
Interactive Molecular Model Assembly with 3D Printing
06:15

Interactive Molecular Model Assembly with 3D Printing

Published on: August 13, 2020

11.2K
Development of Inhibitors of Protein-protein Interactions through REPLACE: Application to the Design and Development Non-ATP Competitive CDK Inhibitors
10:33

Development of Inhibitors of Protein-protein Interactions through REPLACE: Application to the Design and Development Non-ATP Competitive CDK Inhibitors

Published on: October 26, 2015

11.9K

Area of Science:

  • Medicinal Chemistry
  • Computational Biology
  • Natural Products Chemistry

Background:

  • Natural products often feature large, flexible macrocycles with extensive target contact points.
  • These macrocycles bind to protein surfaces, making them ideal for inhibiting challenging targets like protein-protein interactions.
  • Advances in biosynthetic and semisynthetic modifications allow these natural products to serve as starting points for drug discovery.

Purpose of the Study:

  • To review computational methods for docking large, flexible macrocyclic natural products.
  • To discuss how these methods facilitate medicinal chemistry campaigns.
  • To highlight advances in treating complex binding modalities of macrocycles.

Main Methods:

  • Comprehensive review of molecular docking techniques.
  • Analysis of methods for handling macrocycle flexibility and large contact areas.
  • Discussion of computational strategies for natural product-like structures.

Main Results:

  • Enhanced molecular docking methods are crucial for analyzing macrocyclic natural products.
  • These improved methods address complex binding modes and flexible scaffolds.
  • Successful application of these methods drives rational drug design.

Conclusions:

  • Macrocyclic natural products are valuable scaffolds for medicinal chemistry.
  • Modern docking approaches are essential for exploiting their therapeutic potential.
  • Continued development of computational tools will accelerate drug discovery using these compounds.