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Andino MS, Mora JR, Paz JL, Márquez EA, Perez-Castillo Y, Agüero-Chapin G. Elucidating the Racemization Mechanism of Aliphatic and Aromatic Amino Acids by In Silico Tools. Int J Mol Sci 2023; 24:11877. [PMID: 37569252 PMCID: PMC10418343 DOI: 10.3390/ijms241511877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 07/19/2023] [Accepted: 07/21/2023] [Indexed: 08/13/2023] Open
Abstract
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.
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Affiliation(s)
- Mateo S. Andino
- Department of Chemical Engineering, Universidad San Francisco de Quito USFQ, Diego de Robles s/n y Av. Interoceánica, Quito 170157, Ecuador;
| | - José R. Mora
- Department of Chemical Engineering, Universidad San Francisco de Quito USFQ, Diego de Robles s/n y Av. Interoceánica, Quito 170157, Ecuador;
| | - José L. Paz
- Departamento Académico de Química Inorgánica, Facultad de Química e Ingeniería Química, Universidad Nacional Mayor de San Marcos, Lima 15081, Peru;
| | - Edgar A. Márquez
- Grupo de Investigaciones en Química y Biología, Departamento de Química y Biología, Facultad de Ciencias Exactas, Universidad del Norte, Carrera 51B, Km 5, Vía Puerto Colombia, Barranquilla 081007, Colombia
| | - Yunierkis Perez-Castillo
- Bio-Chemoinformatics Research Group and Escuela de Ciencias Físicas y Matemáticas, Universidad de Las Américas, Quito 170504, Ecuador;
| | - Guillermin Agüero-Chapin
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208 Porto, Portugal;
- Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
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Yan L, Li Z, Zhong X, Du J, Xiong Y, Peng S, Li H. Preferential Enrichment of Enantiomer from Amino Acid Schiff Bases by Coordination Interaction and Crystallization. MATERIALS (BASEL, SWITZERLAND) 2023; 16:530. [PMID: 36676268 PMCID: PMC9861923 DOI: 10.3390/ma16020530] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/29/2022] [Accepted: 01/01/2023] [Indexed: 06/17/2023]
Abstract
In this paper, preferential enrichment (PE) is described for three pairs of novel amino acid Schiff base Cu(II)/Cu(I) complexes. Single crystal X-ray diffraction indicated that 1-S/R are one-dimensional coordination polymers (CPs) with helical structures, and 2-S/R and 3-S/R are one-dimensional CPs with auxiliary ligands. By tuning the pH, the solvent and second ligands, the 1-S/R, 3-S/R underwent polymorphic transitions, resulting in enantioselective liberation of excess enantiomers into solution, until the deposited crystals were slightly enriched with the opposite enantiomer, thereby successfully exhibiting PE. However, under the effects of Cu(II), the solvent and low pH, 2-S/R did not exhibit PE and resulted in enrichment of racemic compounds, which was attributed to amino acid Schiff base chiral complex mechanisms of PE. The three pairs of Cu complex structures were characterized by UV-vis, MS and X-ray photoelectron spectroscopy (XPS). All chiral properties were studied by circular dichroism (CD) in the solid and liquid.
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Affiliation(s)
- Li Yan
- Key Laboratory of Cluster Science of Ministry of Education, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 102488, China
- Analysis & Testing Center, Liangxiang Campus, Beijing Institute of Technology, Liangxiang East Road, Beijing 102488, China
| | - Zhongkui Li
- Key Laboratory of Cluster Science of Ministry of Education, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 102488, China
| | - Xue Zhong
- Key Laboratory of Cluster Science of Ministry of Education, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 102488, China
| | - Jianxin Du
- Analysis & Testing Center, Liangxiang Campus, Beijing Institute of Technology, Liangxiang East Road, Beijing 102488, China
| | - Yan Xiong
- Analysis & Testing Center, Liangxiang Campus, Beijing Institute of Technology, Liangxiang East Road, Beijing 102488, China
| | - Shaochun Peng
- Analysis & Testing Center, Liangxiang Campus, Beijing Institute of Technology, Liangxiang East Road, Beijing 102488, China
| | - Hui Li
- Key Laboratory of Cluster Science of Ministry of Education, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 102488, China
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Lara-Cerón JA, Jiménez-Pérez VM, Molina-Paredes AA, Sánchez M, Dias HVR, Ramírez-Montes PI, Muñoz-Flores BM. Preferential intermolecular interactions in a racemic mixture of amino acid Schiff base, conformational structures in solid state, and DFT studies. NEW J CHEM 2021. [DOI: 10.1039/d0nj04720a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In this work, we report the green synthesis of a Shiff base [N-(2-hydroxy-1-naphthylidene)-l-phenylalanine (1)] derived from an α-amino acid through an ultrasound-assisted synthesis method with excellent chemical yield in a short period of time.
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Affiliation(s)
- Jesús A. Lara-Cerón
- Universidad Autónoma de Nuevo León
- Facultad de Ciencias Químicas
- Ciudad Universitaria
- Nuevo León
- Mexico
| | - Víctor M. Jiménez-Pérez
- Universidad Autónoma de Nuevo León
- Facultad de Ciencias Químicas
- Ciudad Universitaria
- Nuevo León
- Mexico
| | - Areli A. Molina-Paredes
- Universidad Autónoma de Nuevo León
- Facultad de Ciencias Químicas
- Ciudad Universitaria
- Nuevo León
- Mexico
| | - Mario Sánchez
- Centro de Investigación en Materiales Avanzados
- S.C., Alianza Norte 202
- PIIT
- Carretera Monterrey-Aeropuerto Km. 10
- Apodaca
| | - H. V. Rasika Dias
- Department of Chemistry and Biochemistry
- The University of Texas at Arlington
- Arlington
- USA
| | - Pedro I. Ramírez-Montes
- Universidad Nacional Autónoma de México
- Facultad de Estudios Superiores Cuautitlán
- Departamento de Matemáticas
- 54714 Cuautitlán Izcalli
- Mexico
| | - Blanca M. Muñoz-Flores
- Universidad Autónoma de Nuevo León
- Facultad de Ciencias Químicas
- Ciudad Universitaria
- Nuevo León
- Mexico
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Guricová M, Pižl M, Smékal Z, Nádherný L, Čejka J, Eigner V, Hoskovcová I. Template synthesis and structure of Co(II), Ni(II), and Cu(II) complexes with pyridoxilydenetaurinate Schiff base ligand. Inorganica Chim Acta 2018. [DOI: 10.1016/j.ica.2018.03.031] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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Ogawa R, Sunatsuki Y, Suzuki T. Schiff Base Ligands Derived from l
-Histidine Methyl Ester: Characterization, Racemization, and Dimerization of Their Transition-Metal Complexes. Eur J Inorg Chem 2018. [DOI: 10.1002/ejic.201800137] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Rina Ogawa
- Department of Chemistry; Graduate School of Natural Science and Technology; Okayama University; 700-8530 Okayama Japan
| | - Yukinari Sunatsuki
- Department of Chemistry; Graduate School of Natural Science and Technology; Okayama University; 700-8530 Okayama Japan
| | - Takayoshi Suzuki
- Department of Chemistry; Graduate School of Natural Science and Technology; Okayama University; 700-8530 Okayama Japan
- Research Institute for Interdisciplinary Science; Okayama University; 700-8530 Okayama Japan
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