Exploring Peptide Bond Formation Using Transition State Search and Wave Packet Dynamics
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2025-06-30
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American Chemical Society (ACS)
Abstract
This first-principles study investigates the interactions between amino acids and various types of montmorillonite clay surfaces, including a pristine surface, a surface with an oxygen vacancy, a surface with a silicon vacancy, and a Fe doped surface. Our results show that all clay surfaces exhibit negative binding energies, indicating that the interaction between clay and amino acids is thermodynamically favorable. Among them, the surface with a Si vacancy displays the most negative binding energy, corresponding to the strongest interaction. We also examine the reactions between two alanine molecules to form a dipeptide molecule through the elimination of a water molecule in the absence of clay surfaces. The transition state search suggests that a proton transfer plays a critical role in the peptide bond formation, based on structural and energetic features observed along the reaction path. Circular dichroism spectra computed for reactants, intermediates, and products show distinct chiral signatures. Wave packet dynamics calculations indicate that
quantum tunneling might be the mechanism underlying the reduced activation energy at low tem peratures. These findings offer insight into the physicochemical processes at clay-amino acid in terfaces and support the design of clay-based materials with applications in biotechnology and prebiotic chemistry.
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This document is the unedited Author’s version of a Submitted Work Published as Ghazanfari, Sarah, Yulun Han, Amara Arshad, Wenjie Xia, Svetlana Kilina, and Dmitri Kilin. "Exploring Peptide Bond Formation Using Transition State Search and Wave Packet Dynamics." The Journal of Physical Chemistry Letters 16 (2025): 6968-6974. doi: https://doi.org/10.1021/acs.jpclett.5c01096.
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© 2025 American Chemical Society.