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McFarlane NR, Gui J, Oláh J, Harvey JN. Gaseous inhibition of the transsulfuration pathway by cystathionine β-synthase. Phys Chem Chem Phys 2024. [PMID: 38832404 DOI: 10.1039/d4cp01321b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2024]
Abstract
The transsulfuration pathway plays a key role in mammals for maintaining the balance between cysteine and homocysteine, whose concentrations are critical in several biochemical processes. Human cystathionine β-synthase is a heme-containing, pyridoxal 5'-phosphate (PLP)-dependent enzyme found in this pathway. The heme group does not participate directly in catalysis, but has a regulatory function, whereby CO or NO binding inhibits the PLP-dependent reactions. In this study, we explore the detailed structural changes responsible for inhibition using quantum chemical calculations to validate the experimentally observed bonding patterns associated with heme CO and NO binding and molecular dynamics simulations to explore the medium-range structural changes triggered by gas binding and propagating to the PLP active site, which is more than 20 Å distant from the heme group. Our results support a previously proposed mechanical signaling model, whereby the cysteine decoordination associated with gas ligand binding leads to breaking of a hydrogen bond with an arginine residue on a neighbouring helix. In turn, this leads to a shift in position of the helix, and hence also of the PLP cofactor, ultimately disrupting a key hydrogen bond that stabilizes the PLP in its catalytically active form.
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Affiliation(s)
- Neil R McFarlane
- Department of Chemistry, KU Leuven, Celestijnenlaan 200f-box 2404, B-3001 Leuven, Belgium.
| | - Jiangli Gui
- Department of Chemistry, KU Leuven, Celestijnenlaan 200f-box 2404, B-3001 Leuven, Belgium.
| | - Julianna Oláh
- Department of Inorganic and Analytical Chemistry Budapest University of Technology and Economics H-1111 Budapest, Műegyeten rakpart 3, Hungary.
| | - Jeremy N Harvey
- Department of Chemistry, KU Leuven, Celestijnenlaan 200f-box 2404, B-3001 Leuven, Belgium.
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2
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Wu HHL, McDonnell T, Chinnadurai R. Physiological Associations between Vitamin B Deficiency and Diabetic Kidney Disease. Biomedicines 2023; 11:biomedicines11041153. [PMID: 37189771 DOI: 10.3390/biomedicines11041153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 03/24/2023] [Accepted: 04/10/2023] [Indexed: 05/17/2023] Open
Abstract
The number of people living with chronic kidney disease (CKD) is growing as our global population continues to expand. With aging, diabetes, and cardiovascular disease being major harbingers of kidney disease, the number of people diagnosed with diabetic kidney disease (DKD) has grown concurrently. Poor clinical outcomes in DKD could be influenced by an array of factors-inadequate glycemic control, obesity, metabolic acidosis, anemia, cellular senescence, infection and inflammation, cognitive impairment, reduced physical exercise threshold, and, importantly, malnutrition contributing to protein-energy wasting, sarcopenia, and frailty. Amongst the various causes of malnutrition in DKD, the metabolic mechanisms of vitamin B (B1 (Thiamine), B2 (Riboflavin), B3 (Niacin/Nicotinamide), B5 (Pantothenic Acid), B6 (Pyridoxine), B8 (Biotin), B9 (Folate), and B12 (Cobalamin)) deficiency and its clinical impact has garnered greater scientific interest over the past decade. There remains extensive debate on the biochemical intricacies of vitamin B metabolic pathways and how their deficiencies may affect the development of CKD, diabetes, and subsequently DKD, and vice-versa. Our article provides a review of updated evidence on the biochemical and physiological properties of the vitamin B sub-forms in normal states, and how vitamin B deficiency and defects in their metabolic pathways may influence CKD/DKD pathophysiology, and in reverse how CKD/DKD progression may affect vitamin B metabolism. We hope our article increases awareness of vitamin B deficiency in DKD and the complex physiological associations that exist between vitamin B deficiency, diabetes, and CKD. Further research efforts are needed going forward to address the knowledge gaps on this topic.
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Affiliation(s)
- Henry H L Wu
- Renal Research Laboratory, Kolling Institute of Medical Research, Royal North Shore Hospital, The University of Sydney, Sydney, NSW 2065, Australia
| | - Thomas McDonnell
- Department of Renal Medicine, Northern Care Alliance NHS Foundation Trust, Salford M6 8HD, UK
| | - Rajkumar Chinnadurai
- Department of Renal Medicine, Northern Care Alliance NHS Foundation Trust, Salford M6 8HD, UK
- Faculty of Biology, Medicine & Health, The University of Manchester, Manchester M1 7HR, UK
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3
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Gamov G, Kiselev A, Zavalishin M, Yarullin D. Formation and hydrolysis of pyridoxal-5’-phosphate hydrazones and Schiff bases: Prediction of equilibrium and rate constants. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
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4
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Yamabe S, Tsuchida N, Yamazaki S. A DFT study of the active role of the phosphate group of an internal aldimine in a transamination reaction. Org Biomol Chem 2022; 20:5334-5341. [PMID: 35748359 DOI: 10.1039/d2ob00913g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A transamination reaction from an internal aldimine ([PLP]) and (S)-alanine to pyridoxamine phosphate (PMP) and pyruvic acid was investigated by DFT calculations. As [PLP], a model where the lysine (-Lys) part was approximated by -CH[-NH-C(O)-CH3]-C(O)-NH-CH3 was adopted. (H2O)4 was also included to trace reaction paths involving proton transfers. 13 elementary processes were obtained. For (the external aldimine → quinoid), (quinoid → ketimine) and (ketimine → carbinol amine) processes, the water dimer was found to connect a phosphate-group oxygen with the moving proton. The connection promoted the Grotthuss-type proton transfer in transition states. It was revealed that the phosphate group is not a mere substituent but has the central role in the transfer.
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Affiliation(s)
- Shinichi Yamabe
- Department of Chemistry, Nara University of Education, Takabatake-cho, Nara 630-8528, Japan.
| | - Noriko Tsuchida
- Department of Liberal Arts, Faculty of Medicine, Saitama Medical University, 38 Morohongo, Moroyama-machi, Iruma-gun, Saitama 350-0495, Japan
| | - Shoko Yamazaki
- Department of Chemistry, Nara University of Education, Takabatake-cho, Nara 630-8528, Japan.
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Li Z, Zhang L, Pu M, Lei M. Mechanistic Understanding of Base‐Catalyzed Aldimine/Ketoamine Condensations: An Old Story and A New Model. ASIAN J ORG CHEM 2021. [DOI: 10.1002/ajoc.202000700] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Zhe‐wei Li
- State Key Laboratory of Chemical Resource Engineering Institute of Computational Chemistry College of Chemistry Beijing University of Chemical Technology Beijing 100029 P. R. China
| | - Lin Zhang
- State Key Laboratory of Chemical Resource Engineering Institute of Computational Chemistry College of Chemistry Beijing University of Chemical Technology Beijing 100029 P. R. China
| | - Min Pu
- State Key Laboratory of Chemical Resource Engineering Institute of Computational Chemistry College of Chemistry Beijing University of Chemical Technology Beijing 100029 P. R. China
| | - Ming Lei
- State Key Laboratory of Chemical Resource Engineering Institute of Computational Chemistry College of Chemistry Beijing University of Chemical Technology Beijing 100029 P. R. China
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6
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Thuy PT, Son NT. The conversion of L-lysine into L-β-lysine: the role of 5'-deoxyadenosyl radical and water-a DFT study. J Mol Model 2021; 27:6. [PMID: 33389163 DOI: 10.1007/s00894-020-04639-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 12/09/2020] [Indexed: 10/22/2022]
Abstract
In the current study, we deal with the crucial role of 5'-deoxyadenosyl radical and water in the mechanism of the conversion of L-lysine into L-β-lysine. The DFT (density functional theory)-B3LYP method coupled with 6-31G(d) basis set has been performed to investigate the optimized structures of transition states (TSs) and intermediates (IMs) of two processes in water: (i) the attack of 5'-deoxyadenosyl radical to complex PLP-L-lysine and (ii) hydrolysis to liberate L-β-lysine. Meanwhile, M062X/6-311++g(3df,2p) level of theory is applied to compute the relative Gibbs energy ΔG. Procedure (i) has undergone various steps but includes two main structural aziridinyl rings TS2 (ΔG = 4.1 kcal/mol) and TS3 (ΔG = 2.3 kcal/mol). In stage (ii), hydroxy group of water would help to break the bond between β-NH2 group of L-lysine and PLP better than that of Tyr389.
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Affiliation(s)
- Phan Thi Thuy
- School of Natural Sciences Education, Vinh University, Vinh, Vietnam
| | - Ninh The Son
- Institute of Chemistry, VAST, 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam.
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Nasrabadi M, Morsali A, Beyramabadi SA. An applied quantum-chemical model for genipin-crosslinked chitosan (GCS) nanocarrier. Int J Biol Macromol 2020; 165:1229-1240. [PMID: 33038394 DOI: 10.1016/j.ijbiomac.2020.10.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Revised: 09/23/2020] [Accepted: 10/01/2020] [Indexed: 12/17/2022]
Abstract
The genipin-crosslinked chitosan (GCS) nanocarrier has received a lot of attention due to its unique biological and chemical properties as an effective drug delivery system. GCS was modeled by considering two chitosan (CS) polymer sequences with six monomer units that are crosslinked by genipin. To investigate the characteristics of this model, we considered it as a nanocarrier of the anti-cancer drug cladribine (2CdA). Seven configurations of GCS and 2CdA (GCS/2CdA1-7) were optimized at M06-2X/6-31G(d,p) in aqueous solution. The average binding energy above 100 kJ mol-1 indicates a high drug loading amount. The high adsorption of the drug on GCS is due to the hydrogen bonds that were investigated by AIM analysis. Hydrogen bonds also allow the drug to be released more slowly. These results were confirmed by experimental evidence and the comparison of this model with the simple model of one polymer chain. Also, the mechanism of GCS formation was investigated by calculating the activation parameters, which indicates that solvent (H2O) molecules are explicitly involved in the formation of GCS.
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Affiliation(s)
- Marjan Nasrabadi
- Department of Chemistry, Mashhad Branch, Islamic Azad University, Mashhad, Iran; Research Center for Animal Development Applied Biology, Mashhad Branch, Islamic Azad University, Mashhad 917568, Iran
| | - Ali Morsali
- Department of Chemistry, Mashhad Branch, Islamic Azad University, Mashhad, Iran; Research Center for Animal Development Applied Biology, Mashhad Branch, Islamic Azad University, Mashhad 917568, Iran.
| | - S Ali Beyramabadi
- Department of Chemistry, Mashhad Branch, Islamic Azad University, Mashhad, Iran; Research Center for Animal Development Applied Biology, Mashhad Branch, Islamic Azad University, Mashhad 917568, Iran
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8
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Yang Y, Zhang Y, Yang J, Xue Y. Computational Insight into the Mechanism of Mannich Reaction between Glycinate and Aryl
N
‐Diphenylphosphinyl Imine Catalyzed by N‐Quaternized Pyridoxal. ChemistrySelect 2020. [DOI: 10.1002/slct.202001606] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Yongsheng Yang
- College of Chemistry, Key Lab of Green Chemistry and Technology in Ministry of EducationSichuan University Chengdu 610064 People's Republic of China
| | - Yan Zhang
- College of Chemistry, Key Lab of Green Chemistry and Technology in Ministry of EducationSichuan University Chengdu 610064 People's Republic of China
| | - Junxia Yang
- College of Chemistry, Key Lab of Green Chemistry and Technology in Ministry of EducationSichuan University Chengdu 610064 People's Republic of China
| | - Ying Xue
- College of Chemistry, Key Lab of Green Chemistry and Technology in Ministry of EducationSichuan University Chengdu 610064 People's Republic of China
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9
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Quantum chemical studies of chitosan nanoparticles as effective drug delivery systems for 5-fluorouracil anticancer drug. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.112495] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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10
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Structural insights into the mechanism of internal aldimine formation and catalytic loop dynamics in an archaeal Group II decarboxylase. J Struct Biol 2019; 208:137-151. [PMID: 31445086 DOI: 10.1016/j.jsb.2019.08.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 08/15/2019] [Accepted: 08/20/2019] [Indexed: 01/01/2023]
Abstract
Formation of the internal aldimine (LLP) is the first regulatory step that activates pyridoxal 5'-phosphate (PLP) dependent enzymes. The process involves a nucleophilic attack on PLP by an active site Lys residue, followed by proton transfers resulting in a carbinolamine (CBA) intermediate that undergoes dehydration to form the aldimine. Despite a general understanding of the pathway, the structural basis of the mechanistic roles of specific residues in each of these steps is unclear. Here we determined the crystal structure of the LLP form (holo-form) of a Group II PLP-dependent decarboxylase from Methanocaldococcus jannaschii (MjDC) at 1.7 Å resolution. By comparing the crystal structure of MjDC in the LLP form with that of the pyridoxal-P (non-covalently bound aldehyde) form, we demonstrate structural evidence for a water-mediated mechanism of LLP formation. A conserved extended hydrogen-bonding network around PLP coupled to the pyridinyl nitrogen influences activation and catalysis by affecting the electronic configuration of PLP. Furthermore, the two cofactor bound forms revealed open and closed conformations of the catalytic loop (CL) in the absence of a ligand, supporting a hypothesis for a regulatory link between LLP formation and CL dynamics. The evidence suggests that activation of Group II decarboxylases involves a complex interplay of interactions between the electronic states of PLP, the active site micro-environment and CL dynamics.
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11
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Seo MS, Jang S, Jung H, Kim H. Hydrogen-Bonding-Assisted Ketimine Formation of Benzophenone Derivatives. J Org Chem 2018; 83:14300-14306. [DOI: 10.1021/acs.joc.8b01908] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Min-Seob Seo
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Sumin Jang
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Hoimin Jung
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Hyunwoo Kim
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
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12
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Reactions of aldehyde with collagen: a DFT study. Struct Chem 2018. [DOI: 10.1007/s11224-018-1131-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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13
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Kassem MA, Hazazi OA, Ohsaka T, Awad MI. Electroanalysis of Pyridoxine at Copper Nanoparticles Modified Polycrystalline Gold Electrode. ELECTROANAL 2015. [DOI: 10.1002/elan.201500209] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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14
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Ding YQ, Cui YZ, Li TD. New views on the reaction of primary amine and aldehyde from DFT study. J Phys Chem A 2015; 119:4252-60. [PMID: 25859816 DOI: 10.1021/acs.jpca.5b02186] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
A general theoretical investigation on the reaction of primary amine with aldehyde was carried out by density functional theory. The calculation systems involve three kinds of primary amines (methylamine, vinylamine, and phenylamine) and three kinds of aldehydes (formaldehyde, acetaldehyde, and acrylaldehyde). The steric and electronic inductive effects on the reaction mechanism were studied. Results reveal that the nucleophilic attack of primary amine on aldehyde under neutral conditions leads to carbinolamines, rather than Schiff bases. The nucleophilic attack on the protonated aldehyde produces the protonated Schiff base. The steric hindrance of the aldehyde slows down the nucleophilic attack but allows enough time to abstract a H; consequently, the formation of the protonated Schiff base is preferred. During the carbinolamine protonation, the H(+) preferably locates on the amine nitrogen and then is abstracted by the hydroxyl oxygen over an energy barrier, leaving protonated Schiff base after timely water liberation. The formation of a prereaction potential energy well obviously softens the steric and electronic inductive effects on the active barrier for different reactants.
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Affiliation(s)
- Yun-qiao Ding
- Shandong Provincial Key Laboratory of Fine Chemicals, School of Chemistry and Pharmaceutical Engineering, Qilu University of Technology, 250353, Jinan, Shandong China
| | - Yue-zhi Cui
- Shandong Provincial Key Laboratory of Fine Chemicals, School of Chemistry and Pharmaceutical Engineering, Qilu University of Technology, 250353, Jinan, Shandong China
| | - Tian-duo Li
- Shandong Provincial Key Laboratory of Fine Chemicals, School of Chemistry and Pharmaceutical Engineering, Qilu University of Technology, 250353, Jinan, Shandong China
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15
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Solís-Calero C, Ortega-Castro J, Frau J, Muñoz F. Nonenzymatic Reactions above Phospholipid Surfaces of Biological Membranes: Reactivity of Phospholipids and Their Oxidation Derivatives. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2015; 2015:319505. [PMID: 25977746 PMCID: PMC4419266 DOI: 10.1155/2015/319505] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Revised: 03/24/2015] [Accepted: 03/25/2015] [Indexed: 01/03/2023]
Abstract
Phospholipids play multiple and essential roles in cells, as components of biological membranes. Although phospholipid bilayers provide the supporting matrix and surface for many enzymatic reactions, their inherent reactivity and possible catalytic role have not been highlighted. As other biomolecules, phospholipids are frequent targets of nonenzymatic modifications by reactive substances including oxidants and glycating agents which conduct to the formation of advanced lipoxidation end products (ALEs) and advanced glycation end products (AGEs). There are some theoretical studies about the mechanisms of reactions related to these processes on phosphatidylethanolamine surfaces, which hypothesize that cell membrane phospholipids surface environment could enhance some reactions through a catalyst effect. On the other hand, the phospholipid bilayers are susceptible to oxidative damage by oxidant agents as reactive oxygen species (ROS). Molecular dynamics simulations performed on phospholipid bilayers models, which include modified phospholipids by these reactions and subsequent reactions that conduct to formation of ALEs and AGEs, have revealed changes in the molecular interactions and biophysical properties of these bilayers as consequence of these reactions. Then, more studies are desirable which could correlate the biophysics of modified phospholipids with metabolism in processes such as aging and diseases such as diabetes, atherosclerosis, and Alzheimer's disease.
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Affiliation(s)
- Christian Solís-Calero
- Institut d'Investigació en Ciències de la Salut (IUNICS), Departament de Química, Universitat de les Illes Balears, 07122 Palma de Mallorca, Spain
- Instituto de Investigación Sanitaria de Palma, 07010 Palma, Spain
| | - Joaquín Ortega-Castro
- Institut d'Investigació en Ciències de la Salut (IUNICS), Departament de Química, Universitat de les Illes Balears, 07122 Palma de Mallorca, Spain
- Instituto de Investigación Sanitaria de Palma, 07010 Palma, Spain
| | - Juan Frau
- Institut d'Investigació en Ciències de la Salut (IUNICS), Departament de Química, Universitat de les Illes Balears, 07122 Palma de Mallorca, Spain
- Instituto de Investigación Sanitaria de Palma, 07010 Palma, Spain
| | - Francisco Muñoz
- Institut d'Investigació en Ciències de la Salut (IUNICS), Departament de Química, Universitat de les Illes Balears, 07122 Palma de Mallorca, Spain
- Instituto de Investigación Sanitaria de Palma, 07010 Palma, Spain
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16
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Solís-Calero C, Ortega-Castro J, Frau J, Muñoz F. Scavenger mechanism of methylglyoxal by metformin. A DFT study. Theor Chem Acc 2015. [DOI: 10.1007/s00214-015-1649-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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17
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Solís-Calero C, Ortega-Castro J, Hernández-Laguna A, Frau J, Muñoz F. A DFT study of the carboxymethyl-phosphatidylethanolamine formation from glyoxal and phosphatidylethanolamine surface. Comparison with the formation of N(ε)-(carboxymethyl)lysine from glyoxal and l-lysine. Phys Chem Chem Phys 2015; 17:8210-22. [DOI: 10.1039/c4cp05360e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Mechanisms of the generation of CML and CM-PE from the reactions between glyoxal and l-lysine, and glyoxal and phosphatidylethanolamine (PE) were studied using the DFT method.
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Affiliation(s)
- C. Solís-Calero
- Institut d’Investigació en Ciències de la Salut (IUNICS)
- Departament de Química
- Universitat de les Illes Balears
- E-07122 Palma de Mallorca
- Spain
| | - J. Ortega-Castro
- Institut d’Investigació en Ciències de la Salut (IUNICS)
- Departament de Química
- Universitat de les Illes Balears
- E-07122 Palma de Mallorca
- Spain
| | | | - J. Frau
- Institut d’Investigació en Ciències de la Salut (IUNICS)
- Departament de Química
- Universitat de les Illes Balears
- E-07122 Palma de Mallorca
- Spain
| | - F. Muñoz
- Institut d’Investigació en Ciències de la Salut (IUNICS)
- Departament de Química
- Universitat de les Illes Balears
- E-07122 Palma de Mallorca
- Spain
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18
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Solís-Calero C, Ortega-Castro J, Hernández-Laguna A, Muñoz F. DFT study of the mechanism of the reaction of aminoguanidine with methylglyoxal. J Mol Model 2014; 20:2202. [PMID: 24705776 DOI: 10.1007/s00894-014-2202-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Accepted: 03/04/2014] [Indexed: 11/28/2022]
Abstract
We have studied the mechanism of the reaction between aminoguanidine (AG) and methylglyoxal (MG) by carrying out Dmol3/DFT calculations, obtaining intermediates, transition-state structures, and free-energy profiles for all of the elementary steps of the reaction. Designed models included explicit water solvent, which forms hydrogen-bond networks around the reactants and intermediate molecules, facilitating intramolecular proton transfer in some steps of the reaction mechanism. The reaction take place in four steps, namely: (1) formation of a guanylhydrazone-acetylcarbinol adduct by condensation of AG and MG; (2) dehydration of the adduct; (3) formation of an 1,2,4-triazine derivative by ring closure; and (4) dehydration with the formation of 5-methyl 3-amino-1,2,4-triazine as the final product. From a microkinetic point of view, the first dehydration step was found to be the rate-determining step for the reaction, with the reaction having an apparent activation energy of 12.65 kcal mol⁻¹. Additionally, some analogous structures of intermediates and transition states for the reaction between AG and 2,3-dicarbonyl-phosphatidylethanolamine, a possible intermediate in Amadori-glycated phosphatidylethanolamine (Amadori-PE) autooxidation, were obtained to evaluate the reaction above a phosphatidylethanolamine (PE) surface. Our results are in agreement with experimental results obtaining by other authors, showing that AG is efficient at trapping dicarbonyl compounds such as methylglyoxal, and by extension these compounds joined to biomolecules such as PE in environments such as surfaces and their aqueous surroundings.
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Affiliation(s)
- Christian Solís-Calero
- Departament de Química, Institut d'Investigació en Ciències de la Salut (IUNICS), Universitat de les Illes Balears, E-07122, Palma de Mallorca, Spain
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19
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Srivastava M, Rani P, Singh NP, Yadav RA. Experimental and theoretical studies of vibrational spectrum and molecular structure and related properties of pyridoxine (vitamin B6). SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2013; 120:274-286. [PMID: 24184922 DOI: 10.1016/j.saa.2013.09.133] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2012] [Revised: 09/12/2013] [Accepted: 09/29/2013] [Indexed: 06/02/2023]
Abstract
Vibrational spectrum of pyridoxine has been investigated using experimental IR and Raman spectroscopic and density functional theory (DFT) methods. Vibrational assignments of the observed IR and Raman bands have been proposed in light of the results obtained from computations. In order to assign the observed IR and Raman frequencies the potential energy distributions (PEDs) have also been computed. Optimized geometrical parameters suggest that if the OH groups of the two methyl groups are replaced by H atoms the resulting molecule has Cs point group symmetry. To investigate molecular stability and bond strength we have used natural bond orbital analysis (NBO). Charge transfer occurs in the molecule have been shown by the calculated highest occupied molecular orbital-lowest unoccupied molecular orbital (HOMO-LUMO) energies. The mapping of electron density iso-surface with electrostatic potential (ESP), has been carried out to get the information about the size, shape, charge density distribution and site of chemical reactivity of the molecule.
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Affiliation(s)
- Mayuri Srivastava
- Department of Physics, UP (PG) Autonomous College, Varanasi 221002, India
| | - P Rani
- Lasers and Spectroscopy Laboratory, Department of Physics, Banaras Hindu University, Varanasi 221005, India
| | - N P Singh
- Department of Physics, UP (PG) Autonomous College, Varanasi 221002, India
| | - R A Yadav
- Lasers and Spectroscopy Laboratory, Department of Physics, Banaras Hindu University, Varanasi 221005, India.
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20
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Ren X, Yuan Y, Ju Y, Wang H. DFT Study of the Addition–Cyclization–Isomerization Reaction between Propargyl Cyanamides and Thiol or Alcohol: the Role of Catalyst. Chem Heterocycl Compd (N Y) 2013. [DOI: 10.1007/s10593-013-1243-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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21
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Zhang T, Zhou W, Jin W, Jin Q, Chen H. Direct detection of aromatic amines and observation of intermediates of Schiff-base reactions by reactive desorption electrospray ionization mass spectrometry. Microchem J 2013. [DOI: 10.1016/j.microc.2012.10.021] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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22
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C–H Activation in Pyridoxal-5′-phosphate and Pyridoxamine-5′-phosphate Schiff Bases: Effect of Metal Chelation. A Computational Study. J Phys Chem B 2013; 117:2339-47. [DOI: 10.1021/jp311861p] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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23
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Huang H, Nandhakumar R, Choi M, Su Z, Kim KM. Enantioselective Liquid–Liquid Extractions of Underivatized General Amino Acids with a Chiral Ketone Extractant. J Am Chem Soc 2013; 135:2653-8. [DOI: 10.1021/ja3105945] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Haofei Huang
- Bio-Chiral Lab, Department of Chemistry & Nano Science, Ewha Womans University, Seoul 120-750, Korea
- College of Chemical Engineering, Shandong University of Technology, Zibo 255049, P.
R. China
| | - Raju Nandhakumar
- Department of
Chemistry, Karunya University, Coimbatore-641
114, TamilNadu,
India
| | - Misun Choi
- Bio-Chiral Lab, Department of Chemistry & Nano Science, Ewha Womans University, Seoul 120-750, Korea
| | - Zhishan Su
- Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu 610064, P. R. China
| | - Kwan Mook Kim
- Bio-Chiral Lab, Department of Chemistry & Nano Science, Ewha Womans University, Seoul 120-750, Korea
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24
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25
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Yildirim A, Konuklar FAS, Catak S, Van Speybroeck V, Waroquier M, Dogan I, Aviyente V. Solvent-catalyzed ring-chain-ring tautomerization in axially chiral compounds. Chemistry 2012; 18:12725-32. [PMID: 22976311 DOI: 10.1002/chem.201200363] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2012] [Revised: 06/11/2012] [Indexed: 11/05/2022]
Abstract
The mechanism of ring-chain-ring tautomerization and the prominent effect of the solvent environment have been computationally investigated in an effort to explain the enantiomeric interconversion observed in 2-oxazolidinone derivatives, heterocyclic analogues of biphenyl atropisomers, which were isolated as single stable enantiomers and have the potential to be used as axially chiral catalysts. This study has shed light on the identity of the intermediate species involved in the ring-chain-ring tautomerization process as well as the catalytic effect of polar protic solvents. These mechanistic details will prove very useful in predicting and understanding ring-chain tautomeric equilibria in similar heterocyclic systems and will further enable experimentalists to devise appropriate experimental conditions in which axially chiral catalysts remain stable as single enantiomers.
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Affiliation(s)
- Asli Yildirim
- Department of Chemistry, Boğaziçi University, Bebek, Istanbul, Turkey
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26
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Casasnovas R, Adrover M, Ortega-Castro J, Frau J, Donoso J, Muñoz F. C–H Activation in Pyridoxal-5′-phosphate Schiff Bases: The Role of the Imine Nitrogen. A Combined Experimental and Computational Study. J Phys Chem B 2012; 116:10665-75. [DOI: 10.1021/jp303678n] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Rodrigo Casasnovas
- Institut
d’Investigació en Ciènces de la Salut (IUNICS),
Departament de Química, Universitat de les Illes Balears, E-07122 Palma de Mallorca, Spain
| | - Miquel Adrover
- Institut
d’Investigació en Ciènces de la Salut (IUNICS),
Departament de Química, Universitat de les Illes Balears, E-07122 Palma de Mallorca, Spain
| | - Joaquin Ortega-Castro
- Institut
d’Investigació en Ciènces de la Salut (IUNICS),
Departament de Química, Universitat de les Illes Balears, E-07122 Palma de Mallorca, Spain
| | - Juan Frau
- Institut
d’Investigació en Ciènces de la Salut (IUNICS),
Departament de Química, Universitat de les Illes Balears, E-07122 Palma de Mallorca, Spain
| | - Josefa Donoso
- Institut
d’Investigació en Ciènces de la Salut (IUNICS),
Departament de Química, Universitat de les Illes Balears, E-07122 Palma de Mallorca, Spain
| | - Francisco Muñoz
- Institut
d’Investigació en Ciènces de la Salut (IUNICS),
Departament de Química, Universitat de les Illes Balears, E-07122 Palma de Mallorca, Spain
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27
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A comparative DFT study of the Schiff base formation from acetaldehyde and butylamine, glycine and phosphatidylethanolamine. Theor Chem Acc 2012. [DOI: 10.1007/s00214-012-1263-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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28
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Sunoj RB, Anand M. Microsolvated transition state models for improved insight into chemical properties and reaction mechanisms. Phys Chem Chem Phys 2012; 14:12715-36. [PMID: 22893252 DOI: 10.1039/c2cp41719g] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Over the years, several methods have been developed to effectively represent the chemical behavior of solutes in solvents. The environmental effects arising due to solvation can generally be achieved either through inclusion of discrete solvent molecules or by inscribing into a cavity in a homogeneous and continuum dielectric medium. In both these approaches of computational origin, the perturbations on the solute induced by the surrounding solvent are at the focus of the problem. While the rigor and method of inclusion of solvent effects vary, such solvation models have found widespread applications, as evident from modern chemical literature. A hybrid method, commonly referred to as cluster-continuum model (CCM), brings together the key advantages of discrete and continuum models. In this perspective, we intend to highlight the latent potential of CCM toward obtaining accurate estimates on a number of properties as well as reactions of contemporary significance. The objective has generally been achieved by choosing illustrative examples from the literature, besides expending efforts to bring out the complementary advantages of CCM as compared to continuum or discrete solvation models. The majority of examples emanate from the prevalent applications of CCM to organic reactions, although a handful of interesting organometallic reactions have also been discussed. In addition, increasingly accurate computations of properties like pK(a) and solvation of ions obtained using the CCM protocol are also presented.
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Affiliation(s)
- Raghavan B Sunoj
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
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29
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Gökcan H, Konuklar FAS. Theoretical study on HF elimination and aromatization mechanisms: a case of pyridoxal 5' phosphate-dependent enzyme. J Org Chem 2012; 77:5533-43. [PMID: 22646918 DOI: 10.1021/jo3005815] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Pyridoxal 5-phosphate (PLP), the phosphorylated and the oxidized form of vitamin B6 is an organic cofactor. PLP forms a Schiff base with the ϵ-amino group of a lysine residue of PLP-dependent enzymes. γ-Aminobutyric acid (GABA) aminotransferase is a PLP-dependent enzyme that degrades GABA to succinic semialdehyde, while reduction of GABA concentration in the brain causes convolution besides several neurological diseases. The fluorine-containing substrate analogues for the inactivation of the GABA-AT are synthesized extensively in cases where the inactivation mechanisms involve HF elimination. Although two proposed mechanisms are present for the HF elimination, the details of the base-induced HF elimination are not well identified. In this density functional theory (DFT) study, fluorine-containing substrate analogue, 5-amino-2-fluorocyclohex-3-enecarboxylic acid, is particularly chosen in order to explain the details of the HF elimination reactions. On the other hand, the experimental studies revealed that aromatization competes with Michael addition mechanism in the presence of 5-amino-2-fluorocyclohex-3-enecarboxylic acid. The results allowed us to draw a conclusion for the nature of HF elimination, besides the elucidation of the mechanism preference for the inactivation mechanism. Furthermore, the solvent phase calculations carried out in this study ensure that the proton transfer steps should be assisted either by a water molecule or a base for lower activation energy barriers.
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Affiliation(s)
- Hatice Gökcan
- Informatics Institute, Computational Science and Engineering Programme, Istanbul Technical University, Ayazağa Campus 34469, Maslak, Istanbul, Turkey
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30
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Vilanova B, Gallardo JM, Caldés C, Adrover M, Ortega-Castro J, Muñoz F, Donoso J. Formation of Schiff Bases of O-Phosphorylethanolamine and O-Phospho-d,l-serine with Pyridoxal 5′-Phosphate. Experimental and Theoretical Studies. J Phys Chem A 2012; 116:1897-905. [DOI: 10.1021/jp2116033] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Bartolomé Vilanova
- Institut
Universitari d’Investigació
en Ciències de la Salut (IUNICS), Departament de
Química, Universitat de les Illes Balears, Ctra Valldemosa km 7.5, E-07122 Palma de Mallorca,
Spain
| | - Jessica M. Gallardo
- Institut
Universitari d’Investigació
en Ciències de la Salut (IUNICS), Departament de
Química, Universitat de les Illes Balears, Ctra Valldemosa km 7.5, E-07122 Palma de Mallorca,
Spain
| | - Catalina Caldés
- Institut
Universitari d’Investigació
en Ciències de la Salut (IUNICS), Departament de
Química, Universitat de les Illes Balears, Ctra Valldemosa km 7.5, E-07122 Palma de Mallorca,
Spain
| | - Miquel Adrover
- Institut
Universitari d’Investigació
en Ciències de la Salut (IUNICS), Departament de
Química, Universitat de les Illes Balears, Ctra Valldemosa km 7.5, E-07122 Palma de Mallorca,
Spain
| | - Joaquín Ortega-Castro
- Institut
Universitari d’Investigació
en Ciències de la Salut (IUNICS), Departament de
Química, Universitat de les Illes Balears, Ctra Valldemosa km 7.5, E-07122 Palma de Mallorca,
Spain
| | - Francisco Muñoz
- Institut
Universitari d’Investigació
en Ciències de la Salut (IUNICS), Departament de
Química, Universitat de les Illes Balears, Ctra Valldemosa km 7.5, E-07122 Palma de Mallorca,
Spain
| | - Josefa Donoso
- Institut
Universitari d’Investigació
en Ciències de la Salut (IUNICS), Departament de
Química, Universitat de les Illes Balears, Ctra Valldemosa km 7.5, E-07122 Palma de Mallorca,
Spain
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31
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Guan YG, Wang SL, Yu SJ, Yu SM, Zhao ZG. Changes in the initial stages of a glucose-proline Maillard reaction model system influences dairy product quality during thermal processing. J Dairy Sci 2012; 95:590-601. [DOI: 10.3168/jds.2011-4860] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2011] [Accepted: 10/08/2011] [Indexed: 11/19/2022]
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32
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Oliveira EF, Cerqueira NMFSA, Fernandes PA, Ramos MJ. Mechanism of Formation of the Internal Aldimine in Pyridoxal 5′-Phosphate-Dependent Enzymes. J Am Chem Soc 2011; 133:15496-505. [DOI: 10.1021/ja204229m] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Eduardo F. Oliveira
- REQUIMTE, Faculdade de Ciências, Universidade do Porto, Rua Campo Alegre 687, 4169-007 Porto, Portugal
| | | | - Pedro A. Fernandes
- REQUIMTE, Faculdade de Ciências, Universidade do Porto, Rua Campo Alegre 687, 4169-007 Porto, Portugal
| | - Maria J. Ramos
- REQUIMTE, Faculdade de Ciências, Universidade do Porto, Rua Campo Alegre 687, 4169-007 Porto, Portugal
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33
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Studies on molecular structure and tautomerism of a vitamin B6 analog with density functional theory. J Mol Model 2011; 18:1993-2001. [PMID: 21877155 DOI: 10.1007/s00894-011-1214-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2011] [Accepted: 08/07/2011] [Indexed: 10/17/2022]
Abstract
This work presents a computational study on the molecular structure and tautomeric equilibria of a novel Schiff base L derived from pyridoxal (PL) and o-phenylenediamine by using the density functional method B3LYP with basis sets 6-31 G(d,p), 6-31++G(d,p), 6-311 G(d,p) and 6-311++G(d,p). The optimized geometrical parameters obtained by B3LYP/6-31 G(d,p) method showed the best agreement with the experimental values. Tautomeric stability study of L inferred that the enolimine form is more stable than its ketoenamine form in both gas phase and solution. However, protonation of the pyridoxal nitrogen atom (LH) have accelerated the formation of ketoenamine form, and therefore, both ketoenamine and enolimine forms could be present in acidic media.
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34
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Caldés C, Vilanova B, Adrover M, Muñoz F, Donoso J. Understanding non-enzymatic aminophospholipid glycation and its inhibition. Polar head features affect the kinetics of Schiff base formation. Bioorg Med Chem 2011; 19:4536-43. [DOI: 10.1016/j.bmc.2011.06.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2011] [Revised: 06/01/2011] [Accepted: 06/08/2011] [Indexed: 02/02/2023]
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35
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Guan YG, Zhu SM, Yu SJ, Xu XB, Shi WH. SO32- effects the 5-hydroxymethyl-2-furaldehyde content in ammonium sulphite-glucose solutions. Int J Food Sci Technol 2011. [DOI: 10.1111/j.1365-2621.2011.02574.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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36
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Durak AT, Gökcan H, Konuklar FAS. Theoretical studies on the inactivation mechanism of γ-aminobutyric acid aminotransferase. Org Biomol Chem 2011; 9:5162-71. [DOI: 10.1039/c1ob05146f] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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37
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Solís-Calero C, Ortega-Castro J, Muñoz F. Reactivity of a phospholipid monolayer model under periodic boundary conditions: a density functional theory study of the Schiff base formation between phosphatidylethanolamine and acetaldehyde. J Phys Chem B 2010; 114:15879-85. [PMID: 21077587 DOI: 10.1021/jp1088367] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A mechanism for the formation of the Schiff base between an acetaldehyde and an amine-phospholipid monolayer model based on Dmol3/density functional theory calculations under periodic boundary conditions was constructed. This is the first time such a system has been modeled to examine its chemical reactivity at this computation level. Each unit cell contains two phospholipid molecules, one acetaldehyde molecule, and nine water molecules. One of the amine-phospholipid molecules in the cell possesses a neutral amino group that is used to model the nucleophilic attack on the carboxyl group of acetaldehyde, whereas the other has a charged amino group acting as a proton donor. The nine water molecules form a hydrogen bond network along the polar heads of the phospholipids that facilitates very fast proton conduction at the interface. Using periodic boundary conditions afforded proton transfer between different cells. The reaction takes place in two steps, namely, (1) formation of a carbinolamine and (2) its dehydration to the Schiff base. The carbinolamine is the primary reaction intermediate, and dehydration is the rate-determining step of the process, consistent with available experimental evidence for similar reactions. On the basis of the results, the cell membrane surface environment may boost phospholipid glycation via a neighboring catalyst effect.
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Affiliation(s)
- Christian Solís-Calero
- Institut d'Investigació en Ciències de la Salut (IUNICS), Departament de Química, Universitat de les Illes Balears, E-07122 Palma de Mallorca, Spain
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38
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Ortega-Castro J, Adrover M, Frau J, Salvà A, Donoso J, Muñoz F. DFT Studies on Schiff Base Formation of Vitamin B6 Analogues. Reaction between a Pyridoxamine-Analogue and Carbonyl Compounds. J Phys Chem A 2010; 114:4634-40. [DOI: 10.1021/jp909156m] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- J. Ortega-Castro
- Institut Universitari d’Investigació en Ciències de la Salut (IUNICS), Departament de Química, Universitat de les Illes Balears, Cra. Valldemossa km 7.5, E-07122 Palma de Mallorca, Spain
| | - M. Adrover
- Institut Universitari d’Investigació en Ciències de la Salut (IUNICS), Departament de Química, Universitat de les Illes Balears, Cra. Valldemossa km 7.5, E-07122 Palma de Mallorca, Spain
| | - J. Frau
- Institut Universitari d’Investigació en Ciències de la Salut (IUNICS), Departament de Química, Universitat de les Illes Balears, Cra. Valldemossa km 7.5, E-07122 Palma de Mallorca, Spain
| | - A. Salvà
- Institut Universitari d’Investigació en Ciències de la Salut (IUNICS), Departament de Química, Universitat de les Illes Balears, Cra. Valldemossa km 7.5, E-07122 Palma de Mallorca, Spain
| | - J. Donoso
- Institut Universitari d’Investigació en Ciències de la Salut (IUNICS), Departament de Química, Universitat de les Illes Balears, Cra. Valldemossa km 7.5, E-07122 Palma de Mallorca, Spain
| | - F. Muñoz
- Institut Universitari d’Investigació en Ciències de la Salut (IUNICS), Departament de Química, Universitat de les Illes Balears, Cra. Valldemossa km 7.5, E-07122 Palma de Mallorca, Spain
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39
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Flores-Morales P, Gutiérrez-Oliva S, Silva E, Toro-Labbé A. The reaction electronic flux: A new descriptor of the electronic activity taking place during a chemical reaction. Application to the characterization of the mechanism of the Schiff’s base formation in the Maillard reaction. ACTA ACUST UNITED AC 2010. [DOI: 10.1016/j.theochem.2009.11.013] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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40
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Theoretical study of the scavenging mechanism to 1,4-dicarbonyls by pyridoxamine: The water-assisted reaction. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.theochem.2009.06.043] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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41
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Flores-Morales P, Gutiérrez-Oliva S, Silva E, Toro-Labbé A. Insights into the Maillard reaction. The mechanism of Schiff's base formation from the reaction force perspective. Mol Phys 2009. [DOI: 10.1080/00268970902980060] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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42
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Casasnovas R, Salvà A, Frau J, Donoso J, Muñoz F. Theoretical study on the distribution of atomic charges in the Schiff bases of 3-hydroxypyridine-4-aldehyde and alanine. The effect of the protonation state of the pyridine and imine nitrogen atoms. Chem Phys 2009. [DOI: 10.1016/j.chemphys.2008.12.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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43
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Liao RZ, Ding WJ, Yu JG, Fang WH, Liu RZ. Theoretical studies on pyridoxal 5′-phosphate-dependent transamination of α-amino acids. J Comput Chem 2008; 29:1919-29. [DOI: 10.1002/jcc.20958] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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44
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Mothana B, Boyd RJ. A density functional theory study of the mechanism of the Paal–Knorr pyrrole synthesis. ACTA ACUST UNITED AC 2007. [DOI: 10.1016/j.theochem.2006.11.034] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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45
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Liao RZ, Ding WJ, Yu JG, Fang WH, Liu RZ. Water-Assisted Transamination of Glycine and Formaldehyde. J Phys Chem A 2007; 111:3184-90. [PMID: 17394297 DOI: 10.1021/jp070130v] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A computational study on the transamination reaction of molecular complexes that consist of NH2CH2COOH + CH2O + nH2O, where n = 0, 1, 2, is presented. This work has allowed the description of the geometries of all the intermediates and transition states of the reactions, which can be described by five steps: carbinolamine formation, dehydration, 1,3 proton transfer, hydrolysis, and carbinolamine elimination. Among the five steps of the reaction, hydrolysis and elimination occur with the existence of general acid catalysis related to the carboxylic group. The water molecules can be involved in the reaction by performing as a proton-transfer carrier and a stabilizing zwitterion. It can be predicted from our calculations that in the transamination between alpha-amino acids and alpha-keto acids, the carbinolamine is formed with small barrier or even barrierless while the dehydration occurs easily at room temperature. However, without heating the 1,3 proton transfer could not occur as the barrier is 26.7 kcal/mol relative to the reactant complex when including two water molecules. Our results are in good agreement with experimental conclusions.
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Affiliation(s)
- Rong-Zhen Liao
- College of Chemistry, Beijing Normal University, Beijing 100875, People's Republic of China
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46
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Sanz D, Perona A, Claramunt RM, Elguero J. Synthesis and spectroscopic properties of Schiff bases derived from 3-hydroxy-4-pyridinecarboxaldehyde. Tetrahedron 2005. [DOI: 10.1016/j.tet.2004.10.036] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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47
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Salvà A, Donoso J, Frau J, Muñoz F. Density Functional Theory Studies on Transimination of Vitamin B6 Analogues through Geminal Diamine Formation. J Phys Chem A 2004. [DOI: 10.1021/jp047258m] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Antoni Salvà
- Institut Universitari d'Investigació en Ciències de la Salut (IUNICS), and Departament de Química, Universitat de les Illes Balears, 07122 Palma de Mallorca, Spain
| | - Josefa Donoso
- Institut Universitari d'Investigació en Ciències de la Salut (IUNICS), and Departament de Química, Universitat de les Illes Balears, 07122 Palma de Mallorca, Spain
| | - Juan Frau
- Institut Universitari d'Investigació en Ciències de la Salut (IUNICS), and Departament de Química, Universitat de les Illes Balears, 07122 Palma de Mallorca, Spain
| | - Francisco Muñoz
- Institut Universitari d'Investigació en Ciències de la Salut (IUNICS), and Departament de Química, Universitat de les Illes Balears, 07122 Palma de Mallorca, Spain
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