Elucidating the Racemization Mechanism of Aliphatic and Aromatic Amino Acids by In Silico Tools. 2023

Mateo S Andino, and José R Mora, and José L Paz, and Edgar A Márquez, and Yunierkis Perez-Castillo, and Guillermin Agüero-Chapin
Department of Chemical Engineering, Universidad San Francisco de Quito USFQ, Diego de Robles s/n y Av. Interoceánica, Quito 170157, Ecuador.

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.

UI MeSH Term Description Entries
D006860 Hydrogen Bonding A low-energy attractive force between hydrogen and another element. It plays a major role in determining the properties of water, proteins, and other compounds. Hydrogen Bonds,Bond, Hydrogen,Hydrogen Bond
D024322 Amino Acids, Aromatic Amino acids containing an aromatic side chain. Aromatic Amino Acids,Amino Acid, Aromatic,Aromatic Amino Acid

Related Publications

Mateo S Andino, and José R Mora, and José L Paz, and Edgar A Márquez, and Yunierkis Perez-Castillo, and Guillermin Agüero-Chapin
May 2005, The Journal of organic chemistry,
Mateo S Andino, and José R Mora, and José L Paz, and Edgar A Márquez, and Yunierkis Perez-Castillo, and Guillermin Agüero-Chapin
February 1992, European journal of biochemistry,
Mateo S Andino, and José R Mora, and José L Paz, and Edgar A Márquez, and Yunierkis Perez-Castillo, and Guillermin Agüero-Chapin
April 1993, International journal of peptide and protein research,
Mateo S Andino, and José R Mora, and José L Paz, and Edgar A Márquez, and Yunierkis Perez-Castillo, and Guillermin Agüero-Chapin
March 1971, Nature,
Mateo S Andino, and José R Mora, and José L Paz, and Edgar A Márquez, and Yunierkis Perez-Castillo, and Guillermin Agüero-Chapin
May 2012, Journal of peptide science : an official publication of the European Peptide Society,
Mateo S Andino, and José R Mora, and José L Paz, and Edgar A Márquez, and Yunierkis Perez-Castillo, and Guillermin Agüero-Chapin
May 1990, Antibiotiki i khimioterapiia = Antibiotics and chemoterapy [sic],
Mateo S Andino, and José R Mora, and José L Paz, and Edgar A Márquez, and Yunierkis Perez-Castillo, and Guillermin Agüero-Chapin
November 1970, Science (New York, N.Y.),
Mateo S Andino, and José R Mora, and José L Paz, and Edgar A Márquez, and Yunierkis Perez-Castillo, and Guillermin Agüero-Chapin
January 1971, International journal of radiation biology and related studies in physics, chemistry, and medicine,
Mateo S Andino, and José R Mora, and José L Paz, and Edgar A Márquez, and Yunierkis Perez-Castillo, and Guillermin Agüero-Chapin
September 1971, Science (New York, N.Y.),
Mateo S Andino, and José R Mora, and José L Paz, and Edgar A Márquez, and Yunierkis Perez-Castillo, and Guillermin Agüero-Chapin
February 1992, Journal of photochemistry and photobiology. B, Biology,
Copied contents to your clipboard!