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Ochiai Y, Hirose S, Yanase E. Understanding the Regioselectivity in the Oxidative Condensation of Catechins Using Pyrogallol-type Model Compounds. J Org Chem 2020; 85:12359-12366. [DOI: 10.1021/acs.joc.0c01612] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yuto Ochiai
- Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Sayumi Hirose
- Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Emiko Yanase
- Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
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2
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Toropova AP. Medicinal Chemistry and Computational Chemistry: Mutual Influence and Harmonization. Mini Rev Med Chem 2020; 20:1320-1321. [PMID: 32600227 DOI: 10.2174/138955752014200626163614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Alla P Toropova
- Laboratory of Environmental Chemistry and Toxicology Istituto di Ricerche Farmacologiche Mario Negri IRCCS Via Mario Negri 2, 20156 Milano, Italy
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3
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Shundrin LA, Avrorov PA, Irtegova IG, Odintsov DS, Poveshchenko AF. Electrochemical reduction of 2,4-dimethyl(diethyl)-9-oxo-10-(4-heptoxyphenyl)- 9H-thioxanthenium hexafluorophosphates and 2,4-dimethyl(diethyl)- 9H-thioxanthene-9-ones. J PHYS ORG CHEM 2018. [DOI: 10.1002/poc.3853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Leonid A. Shundrin
- N. N. Vorozhtsov Institute of Organic Chemistry; Russian Academy of Sciences; Novosibirsk Russia
- Department of Natural Sciences; Novosibirsk State University; Novosibirsk Russia
- The Scientific Institute of Clinical and Experimental Lymphology; Russian Academy of Medical Sciences; Novosibirsk Russia
| | - Pavel A. Avrorov
- N. N. Vorozhtsov Institute of Organic Chemistry; Russian Academy of Sciences; Novosibirsk Russia
- The Scientific Institute of Clinical and Experimental Lymphology; Russian Academy of Medical Sciences; Novosibirsk Russia
| | - Irina G. Irtegova
- N. N. Vorozhtsov Institute of Organic Chemistry; Russian Academy of Sciences; Novosibirsk Russia
| | - Danila S. Odintsov
- N. N. Vorozhtsov Institute of Organic Chemistry; Russian Academy of Sciences; Novosibirsk Russia
| | - Alexander F. Poveshchenko
- The Scientific Institute of Clinical and Experimental Lymphology; Russian Academy of Medical Sciences; Novosibirsk Russia
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4
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Obafemi CA, Fadare OA, Jasinski JP, Millikan SP, Obuotor EM, Iwalewa EO, Famuyiwa SO, Sanusi K, Yilmaz Y, Ceylan Ü. Microwave-assisted synthesis, structural characterization, DFT studies, antibacterial and antioxidant activity of 2-methyl-4-oxo-1,2,3,4-tetrahydroquinazoline-2-carboxylic acid. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2017.11.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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5
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Luo P, Feinberg EC, Guirado G, Farid S, Dinnocenzo JP. Accurate Oxidation Potentials of 40 Benzene and Biphenyl Derivatives with Heteroatom Substituents. J Org Chem 2014; 79:9297-304. [DOI: 10.1021/jo501761c] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Pu Luo
- Department of Chemistry, University of Rochester, Rochester, New York 14627, United States
| | - Elizabeth C. Feinberg
- Department of Chemistry, University of Rochester, Rochester, New York 14627, United States
| | - Gonzalo Guirado
- Departament de Química (Quimica-Fisica), Universitat Autònoma de Barcelona, Edifi C, 08193 Bellaterra, Barcelona, Spain
| | - Samir Farid
- Department of Chemistry, University of Rochester, Rochester, New York 14627, United States
| | - Joseph P. Dinnocenzo
- Department of Chemistry, University of Rochester, Rochester, New York 14627, United States
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6
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Marenich AV, Ho J, Coote ML, Cramer CJ, Truhlar DG. Computational electrochemistry: prediction of liquid-phase reduction potentials. Phys Chem Chem Phys 2014; 16:15068-106. [PMID: 24958074 DOI: 10.1039/c4cp01572j] [Citation(s) in RCA: 314] [Impact Index Per Article: 31.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
This article reviews recent developments and applications in the area of computational electrochemistry. Our focus is on predicting the reduction potentials of electron transfer and other electrochemical reactions and half-reactions in both aqueous and nonaqueous solutions. Topics covered include various computational protocols that combine quantum mechanical electronic structure methods (such as density functional theory) with implicit-solvent models, explicit-solvent protocols that employ Monte Carlo or molecular dynamics simulations (for example, Car-Parrinello molecular dynamics using the grand canonical ensemble formalism), and the Marcus theory of electronic charge transfer. We also review computational approaches based on empirical relationships between molecular and electronic structure and electron transfer reactivity. The scope of the implicit-solvent protocols is emphasized, and the present status of the theory and future directions are outlined.
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Affiliation(s)
- Aleksandr V Marenich
- Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, 207 Pleasant Street S.E., Minneapolis, MN 55455-0431, USA.
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7
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Vakarelska-Popovska MH, Velkov ZA. Structure of Flavones and Flavonols. Part II: Role of Position on the O-H Bond Dissociation Enthalpy. ACTA ACUST UNITED AC 2014. [DOI: 10.4236/cc.2014.21001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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8
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Vasilieva NV, Irtegova IG, Loskutov VA, Shundrin LA. Redox properties and radical anions of 2-substituted thioxanthen-9-ones and their 2-methyl S-oxide derivatives. MENDELEEV COMMUNICATIONS 2013. [DOI: 10.1016/j.mencom.2013.11.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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9
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Guerard JJ, Arey JS. Critical Evaluation of Implicit Solvent Models for Predicting Aqueous Oxidation Potentials of Neutral Organic Compounds. J Chem Theory Comput 2013; 9:5046-58. [DOI: 10.1021/ct4004433] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jennifer J. Guerard
- Environmental
Chemistry Modeling
Laboratory, Swiss Federal Institute of Technology at Lausanne (EPFL), GR
C2 544, Station 2, 1015 Lausanne, Vaud, Switzerland
- Swiss Federal Institute of Aquatic Science and Technology (Eawag) Überlandstrasse 113, 8600 Dübendorf, Zurich, Switzerland
| | - J. Samuel Arey
- Environmental
Chemistry Modeling
Laboratory, Swiss Federal Institute of Technology at Lausanne (EPFL), GR
C2 544, Station 2, 1015 Lausanne, Vaud, Switzerland
- Swiss Federal Institute of Aquatic Science and Technology (Eawag) Überlandstrasse 113, 8600 Dübendorf, Zurich, Switzerland
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Todorova T, Traykov M, Tadjer A, Velkov Z. Structure of flavones and flavonols. Part I: Role of substituents on the planarity of the system. COMPUT THEOR CHEM 2013. [DOI: 10.1016/j.comptc.2013.05.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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11
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RIAHI SIAVASH, EYNOLLAHI SOLMAZ, GANJALI MOHAMMADREZA. INTERACTION OF EMODIN WITH DNA BASES: A DENSITY FUNCTIONAL THEORY. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2011. [DOI: 10.1142/s0219633610006055] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
In this study, we present work on the physicochemical interaction between the anticancer drug molecule Emodin (ED) and DNA. Comprehending the physicochemical properties of this drug besides the mechanism by which it interacts with DNA should eventually permit the rational design of novel anticancer or antiviral drugs. The final purpose is the clarification of this novel class of drugs as potential pharmaceutical agents. The properties of the isolated intercalator ED and its stacking interactions with adenine⋯thymine (AT) and guanine⋯cytosine (GC) (nucleic acid base pairs) in face-to-face and face-to-back models were studied by means of the density functional tightbinding (DFTB) method. This method was an approximate version of the density functional theory (DFT) method and it includes London dispersion energy. The molecular modeling of the complex formed between ED and DNA indicated that this complex was capable of contributing to the formation of a constant intercalation site. The results exhibit that ED changes affect DNA structure with reference to bond lengths, bond angles, torsion angles, and charges.
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Affiliation(s)
- SIAVASH RIAHI
- Institute of Petroleum Engineering, Faculty of Engineering, University of Tehran, P. O. Box 11365-4563, Tehran, Iran
- Center of Excellence in Electrochemistry, Faculty of Chemistry, University of Tehran, P. O. Box 14155-6455, Tehran, Iran
| | - SOLMAZ EYNOLLAHI
- Center of Excellence in Electrochemistry, Faculty of Chemistry, University of Tehran, P. O. Box 14155-6455, Tehran, Iran
| | - MOHAMMAD REZA GANJALI
- Center of Excellence in Electrochemistry, Faculty of Chemistry, University of Tehran, P. O. Box 14155-6455, Tehran, Iran
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12
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Camarada MB, Jaque P, Díaz FR, del Valle MA. Oxidation potential of thiophene oligomers: Theoretical and experimental approach. ACTA ACUST UNITED AC 2011. [DOI: 10.1002/polb.22360] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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13
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Pandey R, Umapathy S. Time-Resolved Resonance Raman Spectroscopic Studies on the Triplet Excited State of Thioxanthone. J Phys Chem A 2011; 115:7566-73. [DOI: 10.1021/jp202387v] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Rishikesh Pandey
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore, India
| | - Siva Umapathy
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore, India
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14
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Winget P. Comments on the paper entitled “Theoretical and experimental report on the determination of oxidation potentials of dihydroxyanthracene and thioxanthens derivatives” by Riahi et al. [Chem. Phys. 337 (2007) 33–38]. Chem Phys 2010. [DOI: 10.1016/j.chemphys.2010.10.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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15
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Ganjali MR, Larijani B, Shams H, Riahi S, Faridbod F, Norouzi P. Using dextromethorphan potentiometric membrane sensor in analysis of dextromethorphan hydrobromide in pharmaceutical formulation and urine; Computational study. JOURNAL OF ANALYTICAL CHEMISTRY 2010. [DOI: 10.1134/s1061934810100114] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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16
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Riahi S, Eynollahi S, Ganjali MR. Computational Studies on Effects of MDMA as an Anticancer Drug on DNA. Chem Biol Drug Des 2010; 76:425-32. [DOI: 10.1111/j.1747-0285.2010.01027.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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17
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Wang HJ, Shi J, Fang M, Li Z, Guo QX. Design of new neutral organic super-electron donors: a theoretical study. J PHYS ORG CHEM 2009. [DOI: 10.1002/poc.1590] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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18
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Merkel PB, Luo P, Dinnocenzo JP, Farid S. Accurate Oxidation Potentials of Benzene and Biphenyl Derivatives via Electron-Transfer Equilibria and Transient Kinetics. J Org Chem 2009; 74:5163-73. [DOI: 10.1021/jo9011267] [Citation(s) in RCA: 119] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Paul B. Merkel
- Department of Chemistry and the Center for Photoinduced Charge Transfer, University of Rochester, Rochester, New York 14627-0216
| | - Pu Luo
- Department of Chemistry and the Center for Photoinduced Charge Transfer, University of Rochester, Rochester, New York 14627-0216
| | - Joseph P. Dinnocenzo
- Department of Chemistry and the Center for Photoinduced Charge Transfer, University of Rochester, Rochester, New York 14627-0216
| | - Samir Farid
- Department of Chemistry and the Center for Photoinduced Charge Transfer, University of Rochester, Rochester, New York 14627-0216
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A computational approach to studying monomer selectivity towards the template in an imprinted polymer. J Mol Model 2009; 15:829-36. [DOI: 10.1007/s00894-008-0437-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2008] [Accepted: 11/22/2008] [Indexed: 10/21/2022]
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20
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Riahi S, Ganjali MR, Bayandori Moghaddam A, Norouzi P. Experimental and quantum chemical study on the IR, UV and electrode potential of 6-(2,3-dihydro-1,3-dioxo-2-phenyl-1H-inden-2-yl)-2,3-dihydroxybenzaldehyde. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2008; 71:1390-1396. [PMID: 18539080 DOI: 10.1016/j.saa.2008.04.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2007] [Revised: 03/28/2008] [Accepted: 04/22/2008] [Indexed: 05/26/2023]
Abstract
Electrode potential of 6-(2,3-dihydro-1,3-dioxo-2-phenyl-1H-inden-2-yl)-2,3-dihydroxybenzaldehyde (DPDB) in methanol have been calculated theoretically. For the achievement of this task, the density functional theory (B3LYP/6-31G(d)) was employed with the inclusion of the entropic and thermochemical corrections to yield the free energies of the redox reactions. The electrode potential was also obtained experimentally by means of an electrochemical technique (cyclic voltammetry). The geometric parameters, the vibrational frequency values and the UV spectrum of DPDB and 2-(2,3-dihydro-1,3-dioxo-2-phenyl-1H-inden-2-yl)-5,6-dioxocyclohexa-1,3-dienecarbaldehyde (DPDD is the oxidized form of DPDB), were computed using the same methods. The calculated IR spectrum of DPDB, used for the assignment of the IR frequencies, was observed in the experimental FT-IR spectrum. The correlation between the theoretical and experimental DPDB vibrational frequencies was 0.996. This agreement mutually verified the accuracy of the experimental method and the validity of the applied mathematical model.
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Affiliation(s)
- Siavash Riahi
- Institute of Petroleum Engineering, Faculty of Engineering, University of Tehran, P.O. Box 11365-4563 Tehran, Iran.
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Riahi S, Reza Ganjali M, Dinarvand R, Karamdoust S, Bagherzadeh K, Norouzi P. A theoretical study on interactions between mitoxantrone as an anticancer drug and DNA: application in drug design. Chem Biol Drug Des 2008; 71:474-482. [PMID: 18384527 DOI: 10.1111/j.1747-0285.2008.00653.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This research is an effort to further understand the physicochemical interaction between the novel drug, mitoxantrone (MTX) and its biologic receptor, DNA. The ultimate goal is to design drugs that interact more with DNA. Understanding the physicochemical properties of the drug as well as the mechanism by which it interacts with DNA, it should ultimately allow the rational design of novel anti-cancer or anti-viral drugs. Molecular modelling on the complex formed between MTX and DNA presented that this complex was indeed fully capable of participating in the formation of a stable intercalation site. Furthermore, the molecular geometries of MTX and the DNA bases (adenine, guanine, cytosine and thymine) were optimized with the aid of the B3LYP/6-31G* method. The properties of the isolated intercalator and its stacking interactions with the adenine...thymine (AT) and guanine...cytosine (GC) nucleic acid base pairs were studied with the DFTB method (density functional tight-binding), an approximate version of the DFT method, that was extended to cover the London dispersion energy. The B3LYP/6-31G* stabilization energies of the intercalator...base pair complexes were found 10.06 kcal/mol and 21.64 kcal/mol for AT...MTX and GC...MTX, respectively. It was concluded that the dispersion energy and the electrostatic interaction contributed to the stability of the intercalator.DNA base pair complexes. The results concluded from the comparison of the DFTB method and the Hartree-fock method point out that these methods show close results and support each other.
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Affiliation(s)
- Siavash Riahi
- Institute of Petroleum Engineering, Faculty of Engineering, University of Tehran, Tehran, IranCenter of Excellence in Electrochemistry, Faculty of Chemistry, University of Tehran, P. O. Box 14155-6455, Tehran, IranMedical Nanotechnology Research Centre, Medical Sciences/University of Tehran, Tehran, P.O. Box 14155-6451, Iran
| | - Mohammad Reza Ganjali
- Institute of Petroleum Engineering, Faculty of Engineering, University of Tehran, Tehran, IranCenter of Excellence in Electrochemistry, Faculty of Chemistry, University of Tehran, P. O. Box 14155-6455, Tehran, IranMedical Nanotechnology Research Centre, Medical Sciences/University of Tehran, Tehran, P.O. Box 14155-6451, Iran
| | - Rassoul Dinarvand
- Institute of Petroleum Engineering, Faculty of Engineering, University of Tehran, Tehran, IranCenter of Excellence in Electrochemistry, Faculty of Chemistry, University of Tehran, P. O. Box 14155-6455, Tehran, IranMedical Nanotechnology Research Centre, Medical Sciences/University of Tehran, Tehran, P.O. Box 14155-6451, Iran
| | - Sanaz Karamdoust
- Institute of Petroleum Engineering, Faculty of Engineering, University of Tehran, Tehran, IranCenter of Excellence in Electrochemistry, Faculty of Chemistry, University of Tehran, P. O. Box 14155-6455, Tehran, IranMedical Nanotechnology Research Centre, Medical Sciences/University of Tehran, Tehran, P.O. Box 14155-6451, Iran
| | - Kowsar Bagherzadeh
- Institute of Petroleum Engineering, Faculty of Engineering, University of Tehran, Tehran, IranCenter of Excellence in Electrochemistry, Faculty of Chemistry, University of Tehran, P. O. Box 14155-6455, Tehran, IranMedical Nanotechnology Research Centre, Medical Sciences/University of Tehran, Tehran, P.O. Box 14155-6451, Iran
| | - Parviz Norouzi
- Institute of Petroleum Engineering, Faculty of Engineering, University of Tehran, Tehran, IranCenter of Excellence in Electrochemistry, Faculty of Chemistry, University of Tehran, P. O. Box 14155-6455, Tehran, IranMedical Nanotechnology Research Centre, Medical Sciences/University of Tehran, Tehran, P.O. Box 14155-6451, Iran
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