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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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2
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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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Pilicer SL, Bakhshi PR, Bentley KW, Wolf C. Biomimetic Chirality Sensing with Pyridoxal-5'-phosphate. J Am Chem Soc 2017; 139:1758-1761. [PMID: 28128945 DOI: 10.1021/jacs.6b12056] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Pyridoxal-5'-phosphate (PLP) is introduced to a biomimetic indicator displacement assay for simultaneous determination of the absolute configuration, enantiomeric composition and concentration of unprotected amino acids, amino alcohols and amines. The chiroptical assay is based on fast imine metathesis with a PLP aryl imine probe to capture the target compound for circular dichroism and fluorescence sensing analysis. The substrate binding yields characteristic Cotton effects that provide information about the target compound ee and the synchronous release of the indicator results in a nonenantioselective off-on fluorescence response that is independent of the enantiomeric sample composition and readily correlated to the total analyte concentration.
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Affiliation(s)
- Samantha L Pilicer
- Department of Chemistry, Georgetown University , Washington, D.C. 20057, United States
| | - Pegah R Bakhshi
- Department of Chemistry, Georgetown University , Washington, D.C. 20057, United States
| | - Keith W Bentley
- Department of Chemistry, Georgetown University , Washington, D.C. 20057, United States
| | - Christian Wolf
- Department of Chemistry, Georgetown University , Washington, D.C. 20057, United States
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Miklós F, Fülöp F. A Simple Green Protocol for the Condensation of Anthranilic Hydrazide with Cyclohexanone andN-Benzylpiperidinone in Water. J Heterocycl Chem 2014. [DOI: 10.1002/jhet.1844] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Ferenc Miklós
- Institute of Pharmaceutical Chemistry; University of Szeged; Eötvös utca 6 H-6720 Szeged Hungary
| | - Ferenc Fülöp
- Institute of Pharmaceutical Chemistry; University of Szeged; Eötvös utca 6 H-6720 Szeged Hungary
- Stereochemistry Research Group of the Hungarian Academy of Sciences; University of Szeged; Eötvös utca 6 H-6720 Szeged Hungary
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Kwiecień A, Barys M, Ciunik Z. Stable hemiaminals with a cyano group and a triazole ring. Molecules 2014; 19:11160-77. [PMID: 25079658 PMCID: PMC6271600 DOI: 10.3390/molecules190811160] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Revised: 07/04/2014] [Accepted: 07/11/2014] [Indexed: 11/30/2022] Open
Abstract
Under neutral conditions the reactions between 4-amino-1,2,4-triazole and cyano-substituted benzaldehyde derivatives yield stable hemiaminals. Addition of small amounts of acid catalyst promotes further step of dehydration resulting in formation of Schiff bases. Four new hemiaminals and the corresponding imines have been obtained. The molecular stability of the hemiaminal intermediates results from both the 1,2,4-triazole moiety and electron withdrawing substituents on the phenyl ring, so no further stabilisation by intramolecular interaction is required. Hemiaminal molecules possess stereogenic centres on carbon and nitrogen atoms. The chirality of these centres is strongly correlated with the conformation of the molecules due to heteroatom hyperconjugation effects.
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Affiliation(s)
- Anna Kwiecień
- Faculty of Chemistry, University of Wrocław, F. Joliot-Curie 14, Wrocław 50-383, Poland.
| | - Maciej Barys
- Faculty of Chemistry, University of Wrocław, F. Joliot-Curie 14, Wrocław 50-383, Poland.
| | - Zbigniew Ciunik
- Faculty of Chemistry, University of Wrocław, F. Joliot-Curie 14, Wrocław 50-383, Poland.
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Gökcan H, Konuklar FAS. Stereoelectronic explanations for the mechanistic details of transimination and HF elimination reactions. J Mol Graph Model 2014; 51:173-83. [PMID: 24929816 DOI: 10.1016/j.jmgm.2014.05.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Revised: 05/21/2014] [Accepted: 05/22/2014] [Indexed: 11/26/2022]
Abstract
The β-fluoroamines are commonly used as substrate analogs to determine the mechanistic details of enzymatic reactions. Presence of fluorine atom gives rise to the alterations in the electronic profile and the pKa of molecules which results in mechanistic deviations. The fluorine-substituted mechanism-based substrate analogs are widely used in the inactivation of pyridoxal 5'-phosphate (PLP)-dependent enzymes. The presence of fluorine atom also alters the sequence of reactions taking place in PLP-dependent enzymes where the HF elimination reaction appears in between the transimination and inactivation reactions. Despite the amount of the works on β-fluoroamines, the effect of stereoelectronic differences on the transimination and HF elimination reactions taking place in PLP-dependent enzymes has not been investigated yet. A density functional theory study is conducted to elucidate mechanistic details of the reactions occurring in PLP-dependent enzymes. In order to understand the mechanistic insights of different isomers and the effect of the fluorine atom, 4-amino-3-fluorobutanoic acid (3-F-GABA) enantiomers are chosen to be investigated besides 4-aminobutanoic acid (GABA), which is the natural substrate for γ-aminobutyric acid aminotransferase (GABA-AT). The investigated β-fluoroamines are the experimentally proposed potential inhibitors of PLP-dependent enzyme GABA-AT.
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Affiliation(s)
- Hatice Gökcan
- Istanbul Technical University, Informatics Institute, Computational Science and Engineering Division, Ayazağa Campus, 34496 Maslak, Istanbul, Turkey
| | - F Aylin Sungur Konuklar
- Istanbul Technical University, Informatics Institute, Computational Science and Engineering Division, Ayazağa Campus, 34496 Maslak, Istanbul, Turkey.
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7
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Wang X, Canary JW. Rapid catalyst-free hydrazone ligation: protein-pyridoxal phosphoramides. Bioconjug Chem 2012. [PMID: 23185966 DOI: 10.1021/bc300430k] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Pyridoxal-5'-phosphate (PLP) represents an active form of Vitamin B(6) that shows relatively fast imine formation with hydrazines under physiological conditions without the need of a catalyst. A convenient phosphate/amine conjugation protocol was developed to covalently link PLP to proteins, affording proteins capable of hydrazone formation with bioorthogonal hydrazinyl functional groups. Thus, the lectin Concanavalin A (Con A) was labeled with PLP. Pretreatment with fluorescein hydrazide gave dye-labeled Con A that labeled cell surfaces efficiently. Alternatively, pretargeting was achieved by labeling cells with Con A-PLP, then treatment in vitro with Alexa Fluor 488 hydrazide.
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Affiliation(s)
- Xiaojian Wang
- Department of Chemistry, New York University, New York, NY 10003, USA
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8
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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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9
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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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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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11
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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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12
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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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13
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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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14
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Miklós F, Fülöp F. “Dry” and “Wet” Green Synthesis of 2,2′-Disubstituted Quinazolinones. European J Org Chem 2010. [DOI: 10.1002/ejoc.200901052] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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15
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The oxidized form of cholesterol 3β-hydroxy-5-oxo-5,6-secocholestan-6-al induces structural and thermotropic changes in phospholipid membranes. Chem Phys Lipids 2009; 161:95-102. [DOI: 10.1016/j.chemphyslip.2009.07.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2009] [Accepted: 07/26/2009] [Indexed: 11/17/2022]
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16
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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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17
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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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18
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Lee MH, Kim BR, Kim HT. Investigation of the active site at the deuterated Schiff-base complex formed between the coenzyme vitamin B6 and the primary amine. Chem Phys Lett 2007. [DOI: 10.1016/j.cplett.2007.05.107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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19
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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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Investigation of Fragmentation Patterns in Pyridoxal-primary Amine Complexes by Electrospray Ionization Mass Spectrometry. B KOREAN CHEM SOC 2006. [DOI: 10.5012/bkcs.2006.27.6.947] [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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21
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Ab initio and DFT theoretical studies of pyridoxal-5′-phosphate methylamine Schiff base isomers. J Mol Struct 2005. [DOI: 10.1016/j.molstruc.2004.11.043] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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22
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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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