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

Van der Waals Interactions01:24

Van der Waals Interactions

Atoms and molecules interact with each other through intermolecular forces. These electrostatic forces arise from attractive or repulsive interactions between particles with permanent, partial, or temporary charges. The intermolecular forces between neutral atoms and molecules are ion–dipole, dipole–dipole, and dispersion forces, collectively known as van der Waals forces.Polar molecules have a partial positive charge on one end and a partial negative charge on the other end of the molecule,...
Atomic Absorption Spectroscopy: Interference01:25

Atomic Absorption Spectroscopy: Interference

Interference leads to systematic error in atomic absorption (AA) measurements by enhancing or diminishing the analytical signal or the background. These interferences can be grouped into three main categories: spectral interference, chemical interference, and physical interference.
Spectral interference occurs when signals from other elements or molecules overlap with the analyte signal, falsely elevating or masking the analyte's absorbance. This interference can be corrected using Zeeman,...
NMR Spectrometers: Resolution and Error Correction01:14

NMR Spectrometers: Resolution and Error Correction

When magnetic nuclei in a sample achieve resonance and undergo relaxation, the signal detected in NMR is an approximately exponential free induction decay. Fourier transform of an exponential decay yields a Lorentzian peak in the frequency domain. Lorentzian peaks in an NMR spectrum are defined by their amplitude, full width at half maximum, and position, where the peak width is governed by the spin-spin relaxation time alone. In real experiments, however, the applied magnetic field is rendered...
¹H NMR: Interpreting Distorted and Overlapping Signals01:02

¹H NMR: Interpreting Distorted and Overlapping Signals

Spin systems where the difference in chemical shifts of the coupled nuclei is greater than ten times J are called first-order spin systems. These nuclei are weakly coupled, and their chemical shifts and coupling constant can generally be estimated from the well-separated signals in the spectrum.
As Δν decreases and the signals move closer, the doublets appear increasingly distorted. The intensities of the inner lines increase at the cost of those of the outer lines as the signals are slanted or...
Distribution and Dispersion00:54

Distribution and Dispersion

Ecology is the study of how organisms interact with their environment and with one another. An important aspect of ecology is understanding where species are found and how individuals are distributed within those areas. The geographic range of a species refers to the total area where its members are located, while dispersion describes the pattern of spacing of individuals within that range.Geographic Range and Dispersion PatternsWithin a species’ geographic range, individuals may be distributed...

You might also read

Related Articles

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

Sort by
Same author

Linking biochemical and cellular efficacy of MERS coronavirus main protease inhibitors.

ACS pharmacology & translational science·2026
Same author

Bridging between Structure-Based and Data-Driven Affinity Prediction.

Journal of chemical information and modeling·2026
Same author

Context-dependent peptide recognition shapes tyrosine kinase substrate specificity beyond consensus motifs.

bioRxiv : the preprint server for biology·2026
Same author

Mapping the avoid-ome: a systematic open-science approach to predictive ADMET.

Nature communications·2026
Same author

Large-Scale Collaborative Assessment of Binding Free Energy Calculations for Drug Discovery Using OpenFE.

Journal of chemical information and modeling·2026
Same author

A Hidden Binding Pocket in the β- ketoacyl-ACP Synthase FabB.

bioRxiv : the preprint server for biology·2026

Related Experiment Video

Updated: Jul 10, 2026

Computation of Atmospheric Concentrations of Molecular Clusters from ab initio Thermochemistry
12:11

Computation of Atmospheric Concentrations of Molecular Clusters from ab initio Thermochemistry

Published on: April 8, 2020

Accurate and efficient corrections for missing dispersion interactions in molecular simulations.

Michael R Shirts1, David L Mobley, John D Chodera

  • 1Department of Chemistry, Columbia University, New York, New York 10027, USA. michael.shirts@columbia.edu

The Journal of Physical Chemistry. B
|October 24, 2007
PubMed
Summary

Neglecting molecular dispersion interactions in simulations introduces significant errors in macromolecular systems. New methods ensure accurate binding free energy calculations, even with shorter simulation cutoffs, improving efficiency.

More Related Videos

Excitonic Hamiltonians for Calculating Optical Absorption Spectra and Optoelectronic Properties of Molecular Aggregates and Solids
08:04

Excitonic Hamiltonians for Calculating Optical Absorption Spectra and Optoelectronic Properties of Molecular Aggregates and Solids

Published on: May 27, 2020

15N CPMG Relaxation Dispersion for the Investigation of Protein Conformational Dynamics on the µs-ms Timescale
08:09

15N CPMG Relaxation Dispersion for the Investigation of Protein Conformational Dynamics on the µs-ms Timescale

Published on: April 19, 2021

Related Experiment Videos

Last Updated: Jul 10, 2026

Computation of Atmospheric Concentrations of Molecular Clusters from ab initio Thermochemistry
12:11

Computation of Atmospheric Concentrations of Molecular Clusters from ab initio Thermochemistry

Published on: April 8, 2020

Excitonic Hamiltonians for Calculating Optical Absorption Spectra and Optoelectronic Properties of Molecular Aggregates and Solids
08:04

Excitonic Hamiltonians for Calculating Optical Absorption Spectra and Optoelectronic Properties of Molecular Aggregates and Solids

Published on: May 27, 2020

15N CPMG Relaxation Dispersion for the Investigation of Protein Conformational Dynamics on the µs-ms Timescale
08:09

15N CPMG Relaxation Dispersion for the Investigation of Protein Conformational Dynamics on the µs-ms Timescale

Published on: April 19, 2021

Area of Science:

  • Computational chemistry
  • Molecular dynamics simulations
  • Biophysics

Background:

  • Dispersion interactions are crucial in molecular simulations but often neglected beyond a cutoff radius (approx. 1 nm).
  • Existing analytical corrections for dispersion energy are typically designed for isotropic systems and may not accurately represent complex systems like macromolecules.
  • This neglect or improper correction can lead to statistically significant errors in calculated properties, particularly for macromolecular systems.

Purpose of the Study:

  • To investigate the impact of dispersion interaction cutoffs on simulation accuracy in systems containing macromolecules.
  • To review and identify limitations of current methods for addressing cutoff-dependent dispersion energy behavior.
  • To introduce novel, computationally efficient formalisms for accurate binding free energy calculations in macromolecular systems.

Main Methods:

  • Analysis of molecular dynamics simulation data for systems with varying dispersion interaction cutoff radii.
  • Evaluation of existing analytical correction methods for dispersion energy in the context of macromolecular simulations.
  • Development and validation of two new formalisms to eliminate cutoff-dependent errors in binding free energy calculations.

Main Results:

  • The choice of dispersion interaction cutoff significantly impacts computed properties, including ligand-protein binding free energies (errors of 1-2 kcal/mol).
  • Current methods for handling dispersion energy cutoffs fail in specific scenarios, particularly with macromolecules.
  • The newly developed formalisms provide consistent results across different cutoffs and can be applied post-simulation.

Conclusions:

  • Standard simulation practices neglecting dispersion interactions beyond a cutoff introduce substantial errors in macromolecular systems.
  • The proposed formalisms effectively correct for cutoff-dependent dispersion energy errors, enhancing the reliability of binding free energy calculations.
  • These methods allow for potentially shorter simulation cutoffs, increasing computational efficiency without sacrificing accuracy.