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

¹³C NMR: Distortionless Enhancement by Polarization Transfer (DEPT)01:20

¹³C NMR: Distortionless Enhancement by Polarization Transfer (DEPT)

When proton-coupled carbon-13 spectra are simplified by a broadband proton decoupling technique, structural information about the coupled protons is lost. Distortionless enhancement by polarization transfer (DEPT) is a technique that provides information on the number of hydrogens attached to each carbon in a molecule. While the DEPT experiment utilizes complex pulse sequences, the pulse delay and flip angle are specifically manipulated. The resulting signals have different phases depending on...
NMR Spectroscopy Of Amines01:19

NMR Spectroscopy Of Amines

In proton NMR spectroscopy, primary amines and secondary amines showcase their N–H protons as a broad signal in the chemical shift range between δ 0.5 and 5 ppm. The exact position in this range depends on several factors, including sample concentration, hydrogen bonding, and the type of solvent used. Since amine protons undergo fast proton exchange in solution, the protons are labile and therefore do not participate in any splitting with adjacent protons. Thus, the observed peak is broad and...
IR Spectrum Peak Splitting: Symmetric vs Asymmetric Vibrations01:08

IR Spectrum Peak Splitting: Symmetric vs Asymmetric Vibrations

Identical bonds within a polyatomic group can stretch symmetrically (in-phase) or asymmetrically (out-of-phase). Similar to hydrogen bonding, these vibrations also influence the shape of the IR peak. Generally, asymmetric stretching frequencies are higher than symmetric stretching frequencies. For example, primary amines exhibit two distinct IR peaks between 3300–3500 cm−1 corresponding to the symmetric and asymmetric N-H stretching, while secondary amines exhibit a single stretching vibration...
Mass Spectrometry of Amines01:15

Mass Spectrometry of Amines

In mass spectroscopy, amines undergo fragmentation to give parent ions with odd molecule weights. This observed mass spectrum follows the nitrogen rule; a molecule with an odd number of nitrogen atoms produces a molecular ion with an odd molecular weight. Amines undergo fragmentation through α cleavage, producing nitrogen-containing cations—iminium ions—and alkyl radicals. Mass spectra of aromatic and cyclic aliphatic amines exhibit strong molecular ion peaks, but acyclic aliphatic amines show...
Molecular Shape and Polarity03:37

Molecular Shape and Polarity

Dipole Moment of a Molecule
Physical Properties of Amines01:26

Physical Properties of Amines

Amines with low molecular weight are usually gaseous at room temperature, while those with high molecular weight are liquid or solids in nature. Usually, low molecular weight amines have a rotten fish-like smell. Diamines typically have a pungent smell. For instance, cadaverine and putrescine, depicted in Figure 1, are two molecules responsible for decaying tissue.

You might also read

Related Articles

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

Sort by
Same author

Bimodal Peptide Collision Cross Section Distribution Reflects Two Stable Conformations in the Gas Phase.

Journal of proteome research·2026
Same author

Surface properties of Ga-Cu based liquid-metal alloys: impact of Cu dilution, topography, and alloy liquefaction.

RSC applied interfaces·2026
Same author

Operando Study of the Active Phase in Liquid GaPt Alloy Catalysts.

Small science·2026
Same author

Full Mass Range ΦSDM Orbitrap Mass Spectrometry for DIA Proteome Analysis.

Molecular & cellular proteomics : MCP·2024
Same author

Author Correction: Isolated Rh atoms in dehydrogenation catalysis.

Scientific reports·2023
Same author

Prioritized mass spectrometry increases the depth, sensitivity and data completeness of single-cell proteomics.

Nature methods·2023

Related Experiment Video

Updated: Jun 13, 2026

Insights into the Interactions of Amino Acids and Peptides with Inorganic Materials Using Single-Molecule Force Spectroscopy
05:44

Insights into the Interactions of Amino Acids and Peptides with Inorganic Materials Using Single-Molecule Force Spectroscopy

Published on: March 6, 2017

Spectroscopic polarizable force field for amide groups in polypeptides.

Bernhard Schropp1, Christoph Wichmann, Paul Tavan

  • 1Lehrstuhl für Biomolekulare Optik, Ludwig-Maximilians-Universität, Oettingenstrasse 67, 80538 München, Germany.

The Journal of Physical Chemistry. B
|April 24, 2010
PubMed
Summary

This study refines a polarizable molecular mechanics (PMM) force field for amide groups in polypeptides. The improved PMM force field accurately computes infrared amide bands, aiding polypeptide structure decoding.

More Related Videos

Covalent Attachment of Single Molecules for AFM-based Force Spectroscopy
10:37

Covalent Attachment of Single Molecules for AFM-based Force Spectroscopy

Published on: March 16, 2020

Force Spectroscopy of Single Protein Molecules Using an Atomic Force Microscope
06:45

Force Spectroscopy of Single Protein Molecules Using an Atomic Force Microscope

Published on: February 28, 2019

Related Experiment Videos

Last Updated: Jun 13, 2026

Insights into the Interactions of Amino Acids and Peptides with Inorganic Materials Using Single-Molecule Force Spectroscopy
05:44

Insights into the Interactions of Amino Acids and Peptides with Inorganic Materials Using Single-Molecule Force Spectroscopy

Published on: March 6, 2017

Covalent Attachment of Single Molecules for AFM-based Force Spectroscopy
10:37

Covalent Attachment of Single Molecules for AFM-based Force Spectroscopy

Published on: March 16, 2020

Force Spectroscopy of Single Protein Molecules Using an Atomic Force Microscope
06:45

Force Spectroscopy of Single Protein Molecules Using an Atomic Force Microscope

Published on: February 28, 2019

Area of Science:

  • Spectroscopy
  • Computational Chemistry
  • Biophysics

Background:

  • Infrared spectra of polypeptides are characterized by amide bands, arising from coupled vibrations of polar amide groups (AGs).
  • The high polarizability of AGs makes amide bands sensitive to external electric fields, enabling them to encode polypeptide structure.
  • Previous work introduced a polarizable molecular mechanics (PMM) force field for AGs to compute amide bands.

Purpose of the Study:

  • To extend and refine the existing PMM force field for amide groups.
  • To improve the computation of polypeptide infrared spectra by incorporating field-dependent properties of AGs.
  • To enhance the decoding of polypeptide backbone structure from amide band shapes.

Main Methods:

  • Developed an extended PMM force field using suitable internal coordinates for AGs.
  • Included the complete AG Hessian and its field dependence in the force field.
  • Calculated force field parameters using density functional theory (DFT).

Main Results:

  • The refined PMM force field demonstrates improved accuracy in describing amide bands.
  • Demonstrated the PMM force field's capability using simple examples.
  • The study provides a foundation for more accurate molecular dynamics simulations of polypeptides.

Conclusions:

  • The refined PMM force field offers a more accurate representation of amide group behavior in electric fields.
  • This advancement facilitates the decoding of polypeptide structure from their infrared spectra.
  • The improved PMM approach holds promise for future biophysical and computational chemistry studies.