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Mikra C, Mitrakas A, Ghizzani V, Katsani KR, Koffa M, Koukourakis M, Psomas G, Protti S, Fagnoni M, Fylaktakidou KC. Effect of Arylazo Sulfones on DNA: Binding, Cleavage, Photocleavage, Molecular Docking Studies and Interaction with A375 Melanoma and Non-Cancer Cells. Int J Mol Sci 2023; 24:ijms24031834. [PMID: 36768159 PMCID: PMC9915714 DOI: 10.3390/ijms24031834] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 01/04/2023] [Accepted: 01/12/2023] [Indexed: 01/19/2023] Open
Abstract
A set of arylazo sulfones, known to undergo N-S bond cleavage upon light exposure, has been synthesized, and their activity in the dark and upon irradiation towards DNA has been investigated. Their interaction with calf-thymus DNA has been examined, and the significant affinity observed (most probably due to DNA intercalation) was analyzed by means of molecular docking "in silico" calculations that pointed out polar contacts, mainly via the sulfonyl moiety. Incubation with plasmid pBluescript KS II revealed DNA cleavage that has been studied over time and concentration. UV-A irradiation considerably improved DNA damage for most of the compounds, whereas under visible light the effect was slightly lower. Moving to in vitro experiments, irradiation was found to slightly enhance the death of the cells in the majority of the compounds. Naphthylazosulfone 1 showed photo-disruptive effect under UV-A irradiation (IC50 ~13 μΜ) followed by derivatives 14 and 17 (IC50 ~100 μΜ). Those compounds were irradiated in the presence of two non-cancer cell lines and were found equally toxic only upon irradiation and not in the dark. The temporal and spatial control of light, therefore, might provide a chance for these novel scaffolds to be useful for the development of phototoxic pharmaceuticals.
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Affiliation(s)
- Chrysoula Mikra
- Laboratory of Organic Chemistry, Faculty of Chemistry, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Achilleas Mitrakas
- Laboratory of Cellular Biology and Cell Cycle, Molecular Biology and Genetics Department, Democritus University of Thrace, University Campus, Dragana, 68100 Alexandroupolis, Greece
- Department of Radiotherapy and Oncology, Democritus University of Thrace, University General Hospital of Alexandroupolis, 68100 Alexandroupolis, Greece
| | - Virginia Ghizzani
- PhotoGreen Lab, Department of Chemistry, University of Pavia, V. Le Taramelli 12, 27100 Pavia, Italy
| | - Katerina R. Katsani
- Laboratory of Biochemistry and Molecular Virology, Molecular Biology and Genetics Department, Democritus University of Thrace, Dragana, 68100 Alexandroupolis, Greece
| | - Maria Koffa
- Laboratory of Cellular Biology and Cell Cycle, Molecular Biology and Genetics Department, Democritus University of Thrace, University Campus, Dragana, 68100 Alexandroupolis, Greece
| | - Michael Koukourakis
- Department of Radiotherapy and Oncology, Democritus University of Thrace, University General Hospital of Alexandroupolis, 68100 Alexandroupolis, Greece
| | - George Psomas
- Laboratory of Inorganic Chemistry, Faculty of Chemistry, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Stefano Protti
- PhotoGreen Lab, Department of Chemistry, University of Pavia, V. Le Taramelli 12, 27100 Pavia, Italy
| | - Maurizio Fagnoni
- PhotoGreen Lab, Department of Chemistry, University of Pavia, V. Le Taramelli 12, 27100 Pavia, Italy
- Correspondence: (M.F.); (K.C.F.)
| | - Konstantina C. Fylaktakidou
- Laboratory of Organic Chemistry, Faculty of Chemistry, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
- Correspondence: (M.F.); (K.C.F.)
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Gritzapis PS, Varras PC, Andreou NP, Katsani KR, Dafnopoulos K, Psomas G, Peitsinis ZV, Koumbis AE, Fylaktakidou KC. p-Pyridinyl oxime carbamates: synthesis, DNA binding, DNA photocleaving activity and theoretical photodegradation studies. Beilstein J Org Chem 2020; 16:337-350. [PMID: 32256851 PMCID: PMC7082612 DOI: 10.3762/bjoc.16.33] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 02/19/2020] [Indexed: 12/23/2022] Open
Abstract
A number of p-pyridinyl oxime carbamate derivatives were prepared upon the reaction of the corresponding oximes with isocyanates. These novel compounds reacted photochemically in the presence of supercoiled plasmid DNA. Structure-activity relationship (SAR) studies revealed that the substituent on the imine group was not affecting the extend of the DNA damage, whereas the substituent of the carbamate group was critical, with the halogenated derivatives to be able to cause extensive single and double stranded DNA cleavages, acting as "synthetic nucleases", independently of oxygen and pH. Calf thymus-DNA affinity studies showed a good-to-excellent affinity of selected both active and non-active derivatives. Preliminary theoretical studies were performed, in an effort to explain the reasons why some derivatives cause photocleavage and some others not, which were experimentally verified using triplet state activators and quenchers. These theoretical studies seem to allow the prediction of the activity of derivatives able to pass intersystem crossing to their triplet energy state and thus create radicals able to damage DNA. With this study, it is shown that oxime carbamate derivatives have the potential to act as novel effective photobase generating DNA-photocleavers, and are proposed as new leads for "on demand" biotechnological applications in drug discovery and medicine.
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Affiliation(s)
- Panagiotis S Gritzapis
- Laboratory of Organic, Bioorganic and Natural Product Chemistry, Molecular Biology and Genetics Department, Democritus University of Thrace, University Campus, Dragana, 68100, Alexandroupolis, Greece
| | - Panayiotis C Varras
- Laboratory of Organic, Bioorganic and Natural Product Chemistry, Molecular Biology and Genetics Department, Democritus University of Thrace, University Campus, Dragana, 68100, Alexandroupolis, Greece
| | - Nikolaos-Panagiotis Andreou
- Laboratory of Organic, Bioorganic and Natural Product Chemistry, Molecular Biology and Genetics Department, Democritus University of Thrace, University Campus, Dragana, 68100, Alexandroupolis, Greece
| | - Katerina R Katsani
- Laboratory of Biochemistry and Molecular Virology, Molecular Biology and Genetics Department, Democritus University of Thrace, University Campus, Dragana, 68100, Alexandroupolis, Greece
| | - Konstantinos Dafnopoulos
- Laboratory of Organic, Bioorganic and Natural Product Chemistry, Molecular Biology and Genetics Department, Democritus University of Thrace, University Campus, Dragana, 68100, Alexandroupolis, Greece
- Laboratory of Inorganic Chemistry, Chemistry Department, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - George Psomas
- Laboratory of Inorganic Chemistry, Chemistry Department, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Zisis V Peitsinis
- Laboratory of Organic Chemistry, Chemistry Department, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Alexandros E Koumbis
- Laboratory of Organic Chemistry, Chemistry Department, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Konstantina C Fylaktakidou
- Laboratory of Organic, Bioorganic and Natural Product Chemistry, Molecular Biology and Genetics Department, Democritus University of Thrace, University Campus, Dragana, 68100, Alexandroupolis, Greece
- Laboratory of Organic Chemistry, Chemistry Department, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
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Palmajumder E, Dash SR, Mitra J, Mukherjea KK. A Multifunctional Biomimicking Oxidovanadium(V) Complex: Synthesis, DFT Calculations, Bromo‐peroxidation and DNA Nuclease Activities. ChemistrySelect 2018. [DOI: 10.1002/slct.201800817] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | - Soumya Ranjan Dash
- CSIR - Central Salt & Marine Chemicals Research InstituteGijubhaiBadheka Marg Bhavnagar - 364002, Gujarat India
| | - Joyee Mitra
- CSIR - Central Salt & Marine Chemicals Research InstituteGijubhaiBadheka Marg Bhavnagar - 364002, Gujarat India
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Dhanju S, Blazejewski BW, Crich D. Synthesis of Trialkylhydroxylamines by Stepwise Reduction of O-Acyl N,N-Disubstituted Hydroxylamines: Substituent Effects on the Reduction of O-(1-Acyloxyalkyl)hydroxylamines and on the Conformational Dynamics of N-Alkoxypiperidines. J Org Chem 2017; 82:5345-5353. [DOI: 10.1021/acs.joc.7b00717] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sandeep Dhanju
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | | | - David Crich
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
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Saha U, Palmajumder E, Mukherjea KK. Synthesis, structure, DNA binding studies and nuclease activities of two luminescent neodymium complexes. J COORD CHEM 2016. [DOI: 10.1080/00958972.2016.1218483] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Urmila Saha
- Department of Chemistry, Jadavpur University, Kolkata, India
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Pyridine and p-Nitrophenyl Oxime Esters with Possible Photochemotherapeutic Activity: Synthesis, DNA Photocleavage and DNA Binding Studies. Molecules 2016; 21:molecules21070864. [PMID: 27376258 PMCID: PMC6272938 DOI: 10.3390/molecules21070864] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Revised: 06/22/2016] [Accepted: 06/28/2016] [Indexed: 12/20/2022] Open
Abstract
Compared to standard treatments for various diseases, photochemotherapy and photo-dynamic therapy are less invasive approaches, in which DNA photocleavers represent promising tools for novel “on demand” chemotherapeutics. A series of p-nitrobenzoyl and p-pyridoyl ester conjugated aldoximes, amidoximes and ethanone oximes were subjected to UV irradiation at 312 nm with supercoiled circular plasmid DNA. The compounds which possessed appropriate properties were additionally subjected to UVA irradiation at 365 nm. The ability of most of the compounds to photocleave DNA was high at 312 nm, whereas higher concentrations were required at 365 nm as a result of their lower UV absorption. The affinity of selected compounds to calf-thymus (CT) DNA was studied by UV spectroscopy, viscosity experiments and competitive studies with ethidium bromide (EB) revealing that all compounds interacted with CT DNA. The fluorescence emission spectra of the pre-treated EB-DNA exhibited a moderate to significant quenching in the presence of the compounds indicating the binding of the compounds to CT DNA via intercalation as concluded also by DNA-viscosity experiments. For the oxime esters the DNA photocleavage and affinity studies aimed to clarify the role of the oxime nature (aldoxime, ketoxime, amidoxime) and the role of the pyridine and p-nitrophenyl moieties both as oxime substituents and ester conjugates.
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Li Z, Qiao J, Jia Z, Meng S. Synthesis of the Pyridine Hydrazones as Metal-free Artificial Nucleases. CHEM LETT 2015. [DOI: 10.1246/cl.150428] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Zhifen Li
- School of Chemical and Environmental Engineering, Datong University
| | - Jun Qiao
- School of Chemical and Environmental Engineering, Datong University
| | - Zhifang Jia
- School of Chemical and Environmental Engineering, Datong University
| | - Shuangming Meng
- School of Chemical and Environmental Engineering, Datong University
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8
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Karamtzioti P, Papastergiou A, Stefanakis JG, Koumbis AE, Anastasiou I, Koffa M, Fylaktakidou KC. O-Benzoyl pyridine aldoxime and amidoxime derivatives: novel efficient DNA photo-cleavage agents. MEDCHEMCOMM 2015. [DOI: 10.1039/c4md00548a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Pyridine oxime esters are effective DNA photocleavers, causing single-/double-stranded DNA cleavage at concentrations as low as 1 μM.
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Affiliation(s)
- Paraskevi Karamtzioti
- Laboratory of Organic
- Bioorganic and Natural Product Chemistry
- Molecular Biology and Genetics Department
- Democritus University of Thrace
- University Campus
| | - Asterios Papastergiou
- Laboratory of Organic
- Bioorganic and Natural Product Chemistry
- Molecular Biology and Genetics Department
- Democritus University of Thrace
- University Campus
| | - John G. Stefanakis
- Laboratory of Organic Chemistry
- Chemistry Department
- Aristotle University of Thessaloniki
- Thessaloniki
- Greece
| | - Alexandros E. Koumbis
- Laboratory of Organic Chemistry
- Chemistry Department
- Aristotle University of Thessaloniki
- Thessaloniki
- Greece
| | - Ioanna Anastasiou
- Laboratory of Organic
- Bioorganic and Natural Product Chemistry
- Molecular Biology and Genetics Department
- Democritus University of Thrace
- University Campus
| | - Maria Koffa
- Laboratory of Organic
- Bioorganic and Natural Product Chemistry
- Molecular Biology and Genetics Department
- Democritus University of Thrace
- University Campus
| | - Konstantina C. Fylaktakidou
- Laboratory of Organic
- Bioorganic and Natural Product Chemistry
- Molecular Biology and Genetics Department
- Democritus University of Thrace
- University Campus
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Hwu JR, Tsay SC, Hong SC, Hsu MH, Liu CF, Chou SSP. Relationship Between Structure of Conjugated Oxime Esters and Their Ability to Cleave DNA. Bioconjug Chem 2013; 24:1778-83. [DOI: 10.1021/bc400060h] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Jih Ru Hwu
- Department
of Chemistry, National Tsing Hua University, No. 101, Section 2, Kuang-Fu Road, Hsinchu 30013, Taiwan
- Department
of Chemistry, National Central University, Jhongli 32001, Taiwan
| | - Shwu-Chen Tsay
- Department
of Chemistry, National Central University, Jhongli 32001, Taiwan
- Department
of Chemistry, Fu Jen Catholic University, Taipei 24205, Taiwan
| | - Shih Chin Hong
- Department
of Chemistry, National Tsing Hua University, No. 101, Section 2, Kuang-Fu Road, Hsinchu 30013, Taiwan
| | - Ming-Hua Hsu
- Department
of Chemistry, National Tsing Hua University, No. 101, Section 2, Kuang-Fu Road, Hsinchu 30013, Taiwan
| | - Chih-Fen Liu
- Department
of Chemistry, Fu Jen Catholic University, Taipei 24205, Taiwan
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Synthesis of Aryl-1,2,4,5-tetrazinane-3-thiones, in vitro DNA binding studies, nuclease activity and its antimicrobial activity. J Mol Struct 2012. [DOI: 10.1016/j.molstruc.2012.03.049] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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11
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Li ZF, Chen HL, Zhang LJ, Lu ZL. Synthesis of [12]aneN3-dipeptide conjugates as metal-free DNA nucleases. Bioorg Med Chem Lett 2012; 22:2303-7. [PMID: 22364814 DOI: 10.1016/j.bmcl.2012.01.075] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2011] [Revised: 01/16/2012] [Accepted: 01/20/2012] [Indexed: 11/28/2022]
Abstract
In this Letter, a series of macrocyclic polyamine [12]aneN(3)-dipeptide conjugates as a new type of metal-free nucleases were synthesized and fully characterized with (1)H NMR, (13)C NMR, IR, and HR-MS. Results indicate that these conjugates can bind to calf thymus DNA mainly through electrostatic interaction and can cleave the plasmid DNA at 200 μM (pH 7.2, 37°C), with an acceleration of 10(6)-fold via hydrolytic pathway.
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Affiliation(s)
- Zhi-Fen Li
- College of Chemistry, Beijing Normal University, Beijing, China
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12
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Orth ES, Medeiros M, Bortolotto T, Terenzi H, Kirby AJ, Nome F. Dephosphorylation Reactions with Deferoxamine, A Potential Chemical Nuclease. J Org Chem 2011; 76:10345-8. [DOI: 10.1021/jo202074y] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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13
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Ullrich S, Nazir Z, Büsing A, Scheffer U, Wirth D, Bats JW, Dürner G, Göbel MW. Cleavage of phosphodiesters and of DNA by a bis(guanidinium)naphthol acting as a metal-free anion receptor. Chembiochem 2011; 12:1223-9. [PMID: 21500334 DOI: 10.1002/cbic.201100022] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2011] [Indexed: 11/07/2022]
Abstract
Phosphoric acid diesters form anions at neutral pH. As a result of charge repulsion they are notoriously resistant to hydrolysis. Nucleophilic attack, however, can be promoted by different types of electrophilic catalysts that bind to the anions and reduce their negative charge density. Although in most cases phosphodiester-cleaving enzymes and synthetic catalysts rely on Lewis acidic metal ions, some exploit the guanidinium residues of arginine as metal-free electrophiles. Here we report that a combination of two guanidines and a hydroxy group yields highly reactive receptor molecules that can attack a broad range of phosphodiester substrates by nucleophilic displacement at phosphorus in a single-turnover mode. Some stable O-phosphates were isolated and characterized further by NMR spectroscopy. The bis(guanidinium)naphthols also cleave plasmid DNA, presumably by a transphosphorylation mechanism.
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Affiliation(s)
- Stefan Ullrich
- Institut für Organische Chemie und Chemische Biologie, Johann Wolfgang Goethe-Universität Frankfurt, Frankfurt am Main, Germany
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Synthesis and crystal structure of and DFT calculations on bisglycinato-bis(p-hydroxymethylpyridine)nickel(II). JOURNAL OF THE SERBIAN CHEMICAL SOCIETY 2010. [DOI: 10.2298/jsc091028101z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
A new Ni(II) complex of bisglycinato-bis(phydroxylmethylpyridine) was synthesized and characterized by elemental analysis, IR, UV-Vis spectroscopy and X-ray single crystal diffraction analysis. The thermal stability of the title complex was also determined. The complex adopts a distorted octahedral geometry and possesses inversion symmetry with the Ni(II) ion as the center of inversion. Density function theory (DFT) calculations of the structure, electronic absorption spectra, electron structure and natural population analysis (NPA) at the B3LYP/LANL2DZ level of theory were performed. The predicted geometric parameters and electronic spectra were compared with the experimental values and they supported each other. The NPA results indicate that the electronic transitions were mainly derived from the contribution of an intra-ligand (IL) transition, a ligand-to-metal charge transfer (LMCT) transition and a d-d transition. The electron structure calculations suggest that the central Ni(II) ion uses its 4s and 3d orbitals to form covalent bonds with coordinated N and O atoms. The calculated bond orders are also consistent with the thermal decomposition results. Based on vibrational analysis, the thermodynamic properties of the title complex were predicted and the correlative equations between these thermodynamic properties and temperature are also reported.
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15
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Li J, Zhang J, Lu QS, Yue Y, Huang Y, Zhang DW, Lin HH, Chen SY, Yu XQ. Hydrolytic cleavage of DNA by urea-bridged macrocyclic polyamines. Eur J Med Chem 2009; 44:5090-3. [DOI: 10.1016/j.ejmech.2009.06.030] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2009] [Revised: 06/22/2009] [Accepted: 06/29/2009] [Indexed: 10/20/2022]
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16
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Silva M, Mello RS, Farrukh MA, Venturini J, Bunton CA, Milagre HMS, Eberlin MN, Fiedler HD, Nome F. The Mechanism of Dephosphorylation of Bis(2,4-dinitrophenyl) Phosphate in Mixed Micelles of Cationic Surfactants and Lauryl Hydroxamic Acid. J Org Chem 2009; 74:8254-60. [DOI: 10.1021/jo9017638] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Marcelo Silva
- Departamento de Química, Universidade Federal de Santa Catarina, 88040-900 Florianópolis, SC, Brazil
| | - Renata S. Mello
- Departamento de Química, Universidade Federal de Santa Catarina, 88040-900 Florianópolis, SC, Brazil
| | - M. Akhyar Farrukh
- Departamento de Química, Universidade Federal de Santa Catarina, 88040-900 Florianópolis, SC, Brazil
| | - Janio Venturini
- Departamento de Química, Universidade Federal de Santa Catarina, 88040-900 Florianópolis, SC, Brazil
| | - Clifford A. Bunton
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106
| | - Humberto M. S. Milagre
- ThoMSon Mass Spectrometry Laboratory, Institute of Chemistry, University of Campinas, UNICAMP, 13083-970 Campinas, SP, Brazil
| | - Marcos N. Eberlin
- ThoMSon Mass Spectrometry Laboratory, Institute of Chemistry, University of Campinas, UNICAMP, 13083-970 Campinas, SP, Brazil
| | - Haidi D. Fiedler
- Departamento de Química, Universidade Federal de Santa Catarina, 88040-900 Florianópolis, SC, Brazil
| | - Faruk Nome
- Departamento de Química, Universidade Federal de Santa Catarina, 88040-900 Florianópolis, SC, Brazil
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