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

IR Spectroscopy: Hooke's Law Approximation of Molecular Vibration01:16

IR Spectroscopy: Hooke's Law Approximation of Molecular Vibration

3.7K
A covalently bonded heteronuclear diatomic molecule can be modeled as two vibrating masses connected by a spring. The vibrational frequency of the bond can be expressed using an equation derived from Hooke's law, which describes how the force applied to stretch or compress a spring is proportional to the displacement of the spring. In this case, the atoms behave like masses, and the bond acts like a spring.
According to Hooke's law, the vibrational frequency is directly proportional to...
3.7K
IR Absorption Frequency: Delocalization01:04

IR Absorption Frequency: Delocalization

1.8K
Electron delocalization refers to the distribution of electrons across multiple atoms within a molecule rather than being confined to a single atom or bond. This phenomenon is common in systems with conjugated bonds—structures where alternating single and double bonds allow π-electrons to move freely across the network. The movement of electrons stabilizes the molecule and can affect various chemical properties, including vibrational frequencies observed in IR spectroscopy.
In IR...
1.8K
Modes of Standing Waves - I01:03

Modes of Standing Waves - I

4.3K
A close look at earthquakes provides evidence for the conditions appropriate for resonance, standing waves, and constructive and destructive interference. A building may vibrate for several seconds with a driving frequency matching the building's natural frequency of vibration; this produces a resonance that results in one building collapsing while the neighboring buildings do not. Often, buildings of a certain height are devastated, while other taller buildings remain intact. This...
4.3K
Valence Bond Theory and Hybridized Orbitals02:38

Valence Bond Theory and Hybridized Orbitals

33.0K
According to valence bond theory, a covalent bond results when: (1) an orbital on one atom overlaps an orbital on a second atom, and (2) the single electrons in each orbital combine to form an electron pair. The strength of a covalent bond depends on the extent of overlap of the orbitals involved. Maximum overlap is possible when the orbitals overlap on a direct line between the two nuclei.
A σ bond (single bond in a Lewis structure) is a covalent bond in which the electron density is...
33.0K
Resonance and Hybrid Structures02:16

Resonance and Hybrid Structures

29.0K
According to the theory of resonance, if two or more Lewis structures with the same arrangement of atoms can be written for a molecule, ion, or radical, the actual distribution of electrons is an average of that shown by the various Lewis structures.
Resonance Structures and Resonance Hybrids
The Lewis structure of a nitrite anion (NO2−) may actually be drawn in two different ways, distinguished by the locations of the N–O and N=O bonds.
29.0K
IR Spectroscopy: Molecular Vibration Overview01:24

IR Spectroscopy: Molecular Vibration Overview

6.2K
When Infrared (IR) radiation passes through a covalently bonded molecule, the bonds transition from lower to higher vibrational levels. The fundamental vibrational motions that result in infrared absorption can be classified as stretching or bending vibrations.
Stretching vibrations are vibrational motions that occur along the bond line, changing the bond length or distance between two bonded atoms. They are further distinguished as symmetric or asymmetric. In symmetric stretching, the...
6.2K

You might also read

Related Articles

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

Sort by
Same author

PyMolGen: Database-Driven Molecular Generation of Drug-Like Compounds.

Journal of chemical information and modeling·2026
Same author

Coulomb explosion imaging identifies a K-CsI complex formed at the surface of helium nanodroplets.

The Journal of chemical physics·2026
Same author

The primary near-UV photochemistry of aqueous pyruvic acid.

Physical chemistry chemical physics : PCCP·2026
Same author

Query Matters: How Selection Strategies Influence Active Learning in Drug Discovery.

Journal of chemical information and modeling·2026
Same author

The primary deep-UV photochemistry of aqueous fumarate and maleate.

Physical chemistry chemical physics : PCCP·2026
Same author

A Multiomic Liquid Biopsy for the Earlier Detection of Colorectal Cancer.

Cancer prevention research (Philadelphia, Pa.)·2025

Related Experiment Video

Updated: Mar 29, 2026

Analyzing Melts and Fluids from Ab Initio Molecular Dynamics Simulations with the UMD Package
06:37

Analyzing Melts and Fluids from Ab Initio Molecular Dynamics Simulations with the UMD Package

Published on: September 17, 2021

5.2K

Harmonic Vibrational Analysis in Delocalized Internal Coordinates.

Frank Jensen1, David S Palmer1

  • 1Department of Chemistry, University of Aarhus, DK-8000 Aarhus, Denmark.

Journal of Chemical Theory and Computation
|November 26, 2015
PubMed
Summary
This summary is machine-generated.

Principal component analysis helps select internal coordinates for accurate vibrational normal mode calculations. This method is particularly useful for describing low-frequency protein deformation modes.

More Related Videos

Author Spotlight: Unveiling the Potential of VSFG Microscopy in Studying Mesoscopically Heterogeneous Self-Assembled Structures
08:49

Author Spotlight: Unveiling the Potential of VSFG Microscopy in Studying Mesoscopically Heterogeneous Self-Assembled Structures

Published on: December 1, 2023

2.2K
An Analog Macroscopic Technique for Studying Molecular Hydrodynamic Processes in Dense Gases and Liquids
11:03

An Analog Macroscopic Technique for Studying Molecular Hydrodynamic Processes in Dense Gases and Liquids

Published on: December 4, 2017

9.1K

Related Experiment Videos

Last Updated: Mar 29, 2026

Analyzing Melts and Fluids from Ab Initio Molecular Dynamics Simulations with the UMD Package
06:37

Analyzing Melts and Fluids from Ab Initio Molecular Dynamics Simulations with the UMD Package

Published on: September 17, 2021

5.2K
Author Spotlight: Unveiling the Potential of VSFG Microscopy in Studying Mesoscopically Heterogeneous Self-Assembled Structures
08:49

Author Spotlight: Unveiling the Potential of VSFG Microscopy in Studying Mesoscopically Heterogeneous Self-Assembled Structures

Published on: December 1, 2023

2.2K
An Analog Macroscopic Technique for Studying Molecular Hydrodynamic Processes in Dense Gases and Liquids
11:03

An Analog Macroscopic Technique for Studying Molecular Hydrodynamic Processes in Dense Gases and Liquids

Published on: December 4, 2017

9.1K

Area of Science:

  • Computational chemistry
  • Molecular dynamics
  • Biophysics

Background:

  • Calculating vibrational normal modes is crucial for understanding molecular dynamics.
  • Traditional methods often struggle with redundant internal coordinates, leading to inaccuracies.
  • Describing global deformation modes in large molecules like proteins remains challenging.

Purpose of the Study:

  • To introduce a novel method for selecting nonredundant internal coordinates.
  • To demonstrate the utility of principal component analysis in this selection process.
  • To improve the description of vibrational normal modes, especially low-frequency modes in proteins.

Main Methods:

  • Applying principal component analysis (PCA) to a large set of internal coordinates.
  • Extracting a nonredundant set of delocalized internal coordinates using PCA.
  • Utilizing the selected coordinates for harmonic vibrational normal mode calculations.

Main Results:

  • PCA effectively identifies a nonredundant set of internal coordinates.
  • The choice of coordinates significantly influences the description of vibrational normal modes.
  • Long-range internal coordinates proved particularly effective for modeling low-frequency protein deformation modes.

Conclusions:

  • Principal component analysis offers a flexible approach to defining internal coordinates for vibrational analysis.
  • This method enhances the accuracy and interpretability of vibrational normal modes.
  • The findings have significant implications for studying protein dynamics and conformational changes.