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Peptide Bonds

Peptide Bonds

A peptide bond covalently attaches amino acids through a dehydration reaction. One amino acid's carboxyl group and another amino acid's amino group combine, releasing a water molecule. The resulting bond is the peptide bond. The products that such linkages form are peptides. As more amino acids join this growing chain, the resulting chain is a polypeptide. Each polypeptide has a free amino group at one end. This end has the N-terminal, or the amino-terminal, and the other end has a free...

Peptide Identification Using Tandem Mass Spectrometry

Peptide Identification Using Tandem Mass Spectrometry

Tandem mass spectrometry, also known as MS/MS or MS2, is an analytical technique that employs two mass analyzers. Essentially it is a series of mass spectrometers that helps isolate a particular biomolecule and then helps study its chemical properties.
This technique helps gather information regarding the protein from which the peptide was obtained and to study the peptides’ amino acid sequence. Identifying peptides from a complex mixture is an important component of the growing field of...

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Updated: Sep 17, 2025

Formation of Ordered Biomolecular Structures by the Self-assembly of Short Peptides

Formation of Ordered Biomolecular Structures by the Self-assembly of Short Peptides

Published on: November 21, 2013

Exploring Peptide Bond Formation Using Transition State Search and Wave Packet Dynamics.

Sarah Ghazanfari^1,2,3, Yulun Han^3,4, Amara Arshad¹

¹Department of Civil, Construction, and Environmental Engineering, North Dakota State University, Fargo, North Dakota 58108, United States.

The Journal of Physical Chemistry Letters

|June 30, 2025

Summary

Amino acids interact favorably with montmorillonite clay, especially surfaces with silicon vacancies. Quantum tunneling may explain low-temperature peptide bond formation, offering insights for biotechnology and prebiotic chemistry.

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Area of Science:

Computational chemistry
Materials science
Biogeochemistry

Background:

Montmorillonite clays are crucial in geological and biological processes.
Understanding clay-amino acid interactions is key for prebiotic chemistry and biotechnology.
First-principles calculations provide atomic-level insights into surface interactions.

Purpose of the Study:

Investigate amino acid interactions with various montmorillonite clay surfaces.
Analyze the mechanism of dipeptide formation on clay surfaces.
Explore the role of quantum effects in peptide bond formation.

Main Methods:

Density Functional Theory (DFT) for electronic structure and binding energies.
Transition state searches to identify reaction pathways.
Circular dichroism spectroscopy and wave packet dynamics for chiral and quantum effects.

Main Results:

All clay surfaces showed favorable (negative) binding energies with amino acids.
The silicon vacancy surface exhibited the strongest amino acid binding.
Proton transfer is critical for peptide bond formation, with quantum tunneling potentially lowering activation energy at low temperatures.

Conclusions:

Clay-amino acid interactions are thermodynamically favorable, particularly with defect sites.
Peptide bond formation involves proton transfer and quantum tunneling.
Findings support the use of clay-based materials in biotechnology and prebiotic chemistry.