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

Spin–Spin Coupling: One-Bond Coupling01:17

Spin–Spin Coupling: One-Bond Coupling

Coupling interactions are strongest between NMR-active nuclei bonded to each other, where spin information can be transmitted directly through the pair of bonding electrons. While nuclei polarize their electrons to the opposite spins, the bonding electron pair has opposite spins. Configurations with antiparallel nuclear spins are expected to be lower in energy. When coupling makes antiparallel states more favorable, J is considered to have a positive value. The one-bond coupling constant, 1J,...
Spin–Spin Coupling: Three-Bond Coupling (Vicinal Coupling)01:22

Spin–Spin Coupling: Three-Bond Coupling (Vicinal Coupling)

Vicinal or three-bond coupling is commonly observed between protons attached to adjacent carbons. Here, nuclear spin information is primarily transferred via electron spin interactions between adjacent C‑H bond orbitals. This generally favors the antiparallel arrangement of spins, so 3J values are usually positive.
The extent of coupling depends on the C‑C bond length, the two H‑C‑C angles, any electron-withdrawing substituents, and the dihedral angle between the involved orbitals. The...
The Equilibrium Binding Constant and Binding Strength02:18

The Equilibrium Binding Constant and Binding Strength

The equilibrium binding constant (Kb) quantifies the strength of a protein-ligand interaction. Kb can be calculated as follows when the reaction is at equilibrium:
The Equilibrium Binding Constant and Binding Strength02:18

The Equilibrium Binding Constant and Binding Strength

The equilibrium binding constant (Kb) quantifies the strength of a protein-ligand interaction. Kb can be calculated as follows when the reaction is at equilibrium:
¹H NMR: Long-Range Coupling01:27

¹H NMR: Long-Range Coupling

The coupling interactions of nuclei across four or more bonds are usually weak, with J values less than 1 Hz. While these are usually not observed in spectra, the presence of multiple bonds along the coupling pathway can result in observable long-range coupling.
In alkenes, spin information is communicated via σ–π overlap, as seen in allylic (four-bond) and homoallylic (five-bond) couplings. These coupling interactions are stronger when the σ bond is parallel to the alkene π orbitals.
Spin–Spin Coupling: Two-Bond Coupling (Geminal Coupling)01:20

Spin–Spin Coupling: Two-Bond Coupling (Geminal Coupling)

Two NMR-active nuclei bonded to a central atom can be involved in geminal or two-bond coupling. Geminal coupling is commonly seen between diastereotopic protons in chiral molecules and unsymmetrical alkenes, among others.
The central atom need not be NMR-active because its electrons are affected by the electron polarization of the spin-active atoms. However, spin information is transmitted less effectively than in one-bond coupling, and 2J values are usually weaker than 1J values. The energy of...

You might also read

Related Articles

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

Sort by
Same author

Quantifying the Uncertainty of Molecular Dynamics Simulations: Good-Turing Statistics Revisited.

Journal of computational chemistry·2026
Same author

Atomic density distributions in proteins: structural and functional implications.

Journal of molecular graphics & modelling·2025
Same author

The Curious Case of A31P, a Topology-Switching Mutant of the Repressor of Primer Protein: A Molecular Dynamics Study of Its Folding and Misfolding.

Journal of chemical information and modeling·2024
Same author

A proof-of-concept study of the secondary structure of influenza A, B M2 and MERS- and SARS-CoV E transmembrane peptides using folding molecular dynamics simulations in a membrane mimetic solvent.

Physical chemistry chemical physics : PCCP·2022
Same author

Folding molecular dynamics simulation of T-peptide, a HIV viral entry inhibitor: Structure, dynamics, and comparison with the experimental data.

Journal of computational chemistry·2022
Same author

Unambiguous Tracking of Protein Phosphorylation by Fast High-Resolution FOSY NMR*.

Angewandte Chemie (International ed. in English)·2021

Related Experiment Video

Updated: May 27, 2026

Molecular Spring Constant Analysis by Biomembrane Force Probe Spectroscopy
08:10

Molecular Spring Constant Analysis by Biomembrane Force Probe Spectroscopy

Published on: November 20, 2021

Using J-coupling constants for force field validation: application to hepta-alanine.

Panagiota S Georgoulia1, Nicholas M Glykos

  • 1Department of Molecular Biology and Genetics, Democritus University of Thrace, University Campus, 68100 Alexandroupolis, Greece.

The Journal of Physical Chemistry. B
|November 18, 2011
PubMed
Summary

Optimizing biomolecular force fields for protein folding simulations is crucial. Longer simulations and peptide chains revealed the AMBER99SB force field achieves statistical consistency with experimental data, improving protein folding predictions.

More Related Videos

Synthesizing Amino Acids Modified with Reactive Carbonyls in Silico to Assess Structural Effects Using Molecular Dynamics Simulations
05:57

Synthesizing Amino Acids Modified with Reactive Carbonyls in Silico to Assess Structural Effects Using Molecular Dynamics Simulations

Published on: April 26, 2024

Realistic Membrane Modeling Using Complex Lipid Mixtures in Simulation Studies
07:31

Realistic Membrane Modeling Using Complex Lipid Mixtures in Simulation Studies

Published on: September 1, 2023

Related Experiment Videos

Last Updated: May 27, 2026

Molecular Spring Constant Analysis by Biomembrane Force Probe Spectroscopy
08:10

Molecular Spring Constant Analysis by Biomembrane Force Probe Spectroscopy

Published on: November 20, 2021

Synthesizing Amino Acids Modified with Reactive Carbonyls in Silico to Assess Structural Effects Using Molecular Dynamics Simulations
05:57

Synthesizing Amino Acids Modified with Reactive Carbonyls in Silico to Assess Structural Effects Using Molecular Dynamics Simulations

Published on: April 26, 2024

Realistic Membrane Modeling Using Complex Lipid Mixtures in Simulation Studies
07:31

Realistic Membrane Modeling Using Complex Lipid Mixtures in Simulation Studies

Published on: September 1, 2023

Area of Science:

  • Computational chemistry
  • Biomolecular simulation
  • Structural biology

Background:

  • The protein folding problem is a major challenge in biomolecular simulation.
  • Accurate force fields are essential for reliable protein folding simulations.
  • Previous studies showed deviations between simulated and experimental J-couplings for short peptides.

Purpose of the Study:

  • To investigate the accuracy of biomolecular force fields in predicting peptide conformations.
  • To optimize force fields by comparing simulation data with experimental J-coupling measurements.
  • To assess the suitability of chi-squared values for evaluating force field performance.

Main Methods:

  • Simulations of a seven-residue polyalanine peptide using three different force fields.
  • Extended simulation times (2 μs) to achieve convergence.
  • Comparison of simulated J-couplings with experimental NMR-derived data.

Main Results:

  • The AMBER99SB force field achieved a chi-squared value of 0.99, indicating statistical consistency with experimental J-coupling data.
  • This represents a significant improvement over previous studies with shorter peptides.
  • Analysis revealed potential limitations in using chi-squared values as sole indicators of force field accuracy.

Conclusions:

  • Achieving statistical consistency between biomolecular simulations and experimental data is feasible with sufficient simulation length and optimized force fields.
  • The AMBER99SB force field shows promise for accurate protein folding simulations.
  • Careful consideration of error estimations is necessary when interpreting goodness-of-fit metrics like chi-squared.