Elucidating the Racemization Mechanism of Aliphatic and Aromatic Amino Acids by In Silico Tools

Mateo S. Andino, José R. Mora, José L. Paz, Edgar A. Márquez, Yunierkis Perez-Castillo, Guillermin Agüero-Chapin

Research output: Contribution to journalArticlepeer-review


The racemization of biomolecules in the active site can reduce the biological activity of drugs, and the mechanism involved in this process is still not fully comprehended. The present study investigates the impact of aromaticity on racemization using advanced theoretical techniques based on density functional theory. Calculations were performed at the ωb97xd/6-311++g(d,p) level of theory. A compelling explanation for the observed aromatic stabilization via resonance is put forward, involving a carbanion intermediate. The analysis, employing Hammett’s parameters, convincingly supports the presence of a negative charge within the transition state of aromatic compounds. Moreover, the combined utilization of natural bond orbital (NBO) analysis and intrinsic reaction coordinate (IRC) calculations confirms the pronounced stabilization of electron distribution within the carbanion intermediate. To enhance our understanding of the racemization process, a thorough examination of the evolution of NBO charges and Wiberg bond indices (WBIs) at all points along the IRC profile is performed. This approach offers valuable insights into the synchronicity parameters governing the racemization reactions.

Original languageEnglish
Article number11877
JournalInternational Journal of Molecular Sciences
Issue number15
StatePublished - 25 Jul 2023


  • amino acids
  • density functional theory
  • intrinsic reaction coordinates
  • natural bond orbital
  • racemization
  • Amino Acids, Aromatic
  • Hydrogen Bonding


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