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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.
Intermolecular Forces and Physical Properties02:56

Intermolecular Forces and Physical Properties

Intermolecular Forces03:13

Intermolecular Forces

Atoms and molecules interact through bonds (or forces): intramolecular and intermolecular. The forces are electrostatic as they arise from interactions (attractive or repulsive) between charged species (permanent, partial, or temporary charges) and exist with varying strengths between ions, polar, nonpolar, and neutral molecules. The different types of intermolecular forces are ion–dipole, dipole–dipole, hydrogen bonds, and dispersion; among these, dipole–dipole, hydrogen bonds, and dispersion...
Intermolecular Forces03:13

Intermolecular Forces

Atoms and molecules interact through bonds (or forces): intramolecular and intermolecular. The forces are electrostatic as they arise from interactions (attractive or repulsive) between charged species (permanent, partial, or temporary charges) and exist with varying strengths between ions, polar, nonpolar, and neutral molecules. The different types of intermolecular forces are ion–dipole, dipole–dipole, hydrogen bonds, and dispersion; among these, dipole–dipole, hydrogen bonds, and dispersion...
Intermolecular Forces in Solutions02:28

Intermolecular Forces in Solutions

The formation of a solution is an example of a spontaneous process, a process that occurs under specified conditions without energy from some external source.
When the strengths of the intermolecular forces of attraction between solute and solvent species in a solution are no different than those present in the separated components, the solution is formed with no accompanying energy change. Such a solution is called an ideal solution. A mixture of ideal gases (or gases such as helium and argon,...
Noncovalent Attractions in Biomolecules02:35

Noncovalent Attractions in Biomolecules

Noncovalent attractions are associations within and between molecules that influence the shape and structural stability of complexes. These interactions differ from covalent bonding in that they do not involve sharing of electrons.
Four types of noncovalent interactions are hydrogen bonds, van der Waals forces, ionic bonds, and hydrophobic interactions.
Hydrogen bonding results from the electrostatic attraction of a hydrogen atom covalently bonded to a strong-electronegative atom like oxygen,...

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Related Experiment Video

Updated: May 29, 2026

Thermochemical Studies of Ni(II) and Zn(II) Ternary Complexes Using Ion Mobility-Mass Spectrometry
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Thermochemical Studies of Ni(II) and Zn(II) Ternary Complexes Using Ion Mobility-Mass Spectrometry

Published on: June 8, 2022

Perturbation analyses of intermolecular interactions.

Yohei M Koyama1, Tetsuya J Kobayashi, Hiroki R Ueda

  • 1Laboratory for Synthetic Biology, Quantitative Biology Center, RIKEN, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan. ym.koyama@gmail.com

Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics
|September 21, 2011
PubMed
Summary

Environmental molecules significantly impact protein function by altering conformational fluctuations. A new distance-dependent intermolecular perturbation analysis (DIPA) method effectively identifies protein conformational states and key environmental interactions.

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Spatial Separation of Molecular Conformers and Clusters
10:37

Spatial Separation of Molecular Conformers and Clusters

Published on: January 9, 2014

Area of Science:

  • Computational Chemistry
  • Biophysics
  • Protein Dynamics

Background:

  • Protein conformational fluctuations are crucial for biological function.
  • Environmental molecules (water, ions, ligands) modulate these fluctuations.
  • Understanding complex intermolecular interactions is challenging.

Purpose of the Study:

  • To develop systematic methods for analyzing intermolecular interactions influencing protein conformational fluctuations.
  • To introduce distance-independent (IPA) and distance-dependent (DIPA) perturbation analyses.
  • To compare the efficacy of IPA and DIPA in identifying conformational states and interactions.

Main Methods:

  • Developed Intermolecular Perturbation Analysis (IPA) using principal component analysis of truncated potential energy terms.
  • Developed Distance-Dependent Intermolecular Perturbation Analysis (DIPA) using functional principal component analysis of forces and cumulative densities.
  • Applied both methods to alanine dipeptide isomerization and chignolin folding in explicit water.

Main Results:

  • DIPA clearly identified three conformational states (α, PPII, β) for alanine dipeptide, outperforming IPA.
  • DIPA showed faster eigenvalue convergence and retained crucial distance information.
  • DIPA successfully identified four states (native, misfolded, unfolded) for chignolin folding, pinpointing key water interactions.

Conclusions:

  • Distance-Dependent Intermolecular Perturbation Analysis (DIPA) is a more practical and effective method than IPA for identifying protein conformational states.
  • DIPA systematically analyzes contributions of environmental interactions to different conformational states.
  • DIPA provides a feasible approach for studying conformational dynamics and interactions in larger biomolecules.