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Related Concept Videos

Infrared (IR) Spectroscopy: Overview01:09

Infrared (IR) Spectroscopy: Overview

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When electromagnetic radiation passes through a material, atoms or molecules transition from a lower to a higher energy state by absorbing radiation corresponding to the energy difference between the two states. The absorption of infrared (IR) radiation causes transitions between vibrational energy levels in a molecule. Therefore, IR spectroscopy is a useful analytical tool for determining the molecular structure of molecules.
Different compounds display unique properties due to their...
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IR Spectroscopy: Molecular Vibration Overview01:24

IR Spectroscopy: Molecular Vibration Overview

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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...
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Applications of IR Spectroscopy: Overview01:11

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The non-destructive nature and ability to provide valuable chemical information make IR spectroscopy a versatile technique with broad applications in various scientific and industrial fields. IR spectroscopy is commonly used to identify and characterize organic and inorganic compounds. It provides information about the functional groups present in a molecule and the bonding between atoms. This helps in the structural elucidation of compounds during organic synthesis, pharmaceutical research,...
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IR Spectrometers01:25

IR Spectrometers

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There are two main infrared (IR) spectrophotometers: dispersive IR spectrometers and Fourier transform infrared (FTIR) spectrometers. In a dispersive IR spectrometer, a beam of infrared radiation produced by a hot wire is divided into two parallel equal-intensity beams using mirrors. One beam passes through the sample, while another is a reference beam. The beams then move through the monochromator, which separates the radiations into a continuous spectrum of different frequencies. The...
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IR Spectroscopy: Hooke's Law Approximation of Molecular Vibration01:16

IR Spectroscopy: Hooke's Law Approximation of Molecular Vibration

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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...
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Raman Spectroscopy Instrumentation: Overview01:26

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A conventional Raman spectrophotometer includes a laser source, a sample holding system, a wavelength selector, and a detector.
The monochromatic laser source, typically using visible or near-infrared radiation, generates a highly focused beam of light. This light interacts with the molecules of the sample, scattering some of the light. Liquid and gaseous samples are usually tested in ordinary glass capillaries, while solids can be analyzed as powders packed in capillaries or as potassium...
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Related Experiment Video

Updated: Sep 27, 2025

Proton Transfer and Protein Conformation Dynamics in Photosensitive Proteins by Time-resolved Step-scan Fourier-transform Infrared Spectroscopy
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AIM: A Mapping Program for Infrared Spectroscopy of Proteins.

Kim E van Adrichem1, Thomas L C Jansen1

  • 1Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands.

Journal of Chemical Theory and Computation
|April 7, 2022
PubMed
Summary

A new program, AIM, extracts protein vibrational Hamiltonians from molecular dynamics for advanced infrared spectroscopy modeling. This tool aids in studying protein structure and dynamics through detailed spectral analysis.

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Area of Science:

  • Computational Chemistry
  • Biophysics
  • Spectroscopy

Background:

  • Protein structure and dynamics are crucial for biological function.
  • Molecular dynamics (MD) simulations provide insights into protein motion.
  • Vibrational spectroscopy offers detailed information on protein conformation and dynamics.

Purpose of the Study:

  • To introduce AIM, a novel analysis program for extracting vibrational Hamiltonians from MD trajectories.
  • To enable accurate modeling of protein infrared (IR) absorption and vibrational circular dichroism (VCD) spectra.
  • To facilitate the study of protein structure and dynamics using advanced spectroscopic techniques.

Main Methods:

  • Utilizing molecular dynamics (MD) trajectories to extract the vibrational amide-I Hamiltonian.
  • Employing the AIM program for Hamiltonian construction and spectral calculations.
  • Applying the program to the Trypsin Inhibitor protein as a case study.

Main Results:

  • AIM successfully extracts vibrational Hamiltonians from MD simulations.
  • The program enables the calculation of IR absorption, VCD, and 2D IR spectra.
  • Demonstration with Trypsin Inhibitor showcases the program's utility in analyzing protein spectra.

Conclusions:

  • AIM provides a valuable tool for protein infrared spectroscopy modeling.
  • The program facilitates the investigation of protein structure and dynamics.
  • AIM is freely available, promoting accessibility for researchers in the field.