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Andrys-Olek J, Kluza A, Tataruch M, Heider J, Korecki J, Borowski T. Bacteria at Work - Experimental and Theoretical Studies Reveal the Catalytic Mechanism of Ectoine Synthase. Chemistry 2024; 30:e202304163. [PMID: 38258332 DOI: 10.1002/chem.202304163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 01/21/2024] [Accepted: 01/22/2024] [Indexed: 01/24/2024]
Abstract
Ectoine synthase (EctC) catalyses the ultimate step of ectoine biosynthesis, a kosmotropic compound produced as compatible solute by many bacteria and some archaea or eukaryotes. EctC is an Fe2+-dependent homodimeric cytoplasmic protein. Using Mössbauer spectroscopy, molecular dynamics simulations and QM/MM calculations, we determined the most likely coordination number and geometry of the Fe2+ ion and proposed a mechanism of the EctC-catalysed reaction. Most notably, we show that apart from the three amino acids binding to the iron ion (Glu57, Tyr84 and His92), one water molecule and one hydroxide ion are required as additional ligands for the reaction to occur. They fill the first coordination sphere of the Fe2+-cofactor and act as critical proton donors and acceptors during the cyclization reaction.
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Affiliation(s)
- Justyna Andrys-Olek
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, 30-239, Kraków, Poland
| | - Anna Kluza
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, 30-239, Kraków, Poland
| | - Mateusz Tataruch
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, 30-239, Kraków, Poland
| | - Johann Heider
- Department of Biology, Philipps-Universität Marburg, 35043, Marburg, Germany
| | - Józef Korecki
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, 30-239, Kraków, Poland
| | - Tomasz Borowski
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, 30-239, Kraków, Poland
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Serafim LF, Jayasinghe-Arachchige VM, Wang L, Rathee P, Yang J, Moorkkannur N S, Prabhakar R. Distinct chemical factors in hydrolytic reactions catalyzed by metalloenzymes and metal complexes. Chem Commun (Camb) 2023. [PMID: 37366367 DOI: 10.1039/d3cc01380d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
Abstract
The selective hydrolysis of the extremely stable phosphoester, peptide and ester bonds of molecules by bio-inspired metal-based catalysts (metallohydrolases) is required in a wide range of biological, biotechnological and industrial applications. Despite the impressive advances made in the field, the ultimate goal of designing efficient enzyme mimics for these reactions is still elusive. Its realization will require a deeper understanding of the diverse chemical factors that influence the activities of both natural and synthetic catalysts. They include catalyst-substrate complexation, non-covalent interactions and the electronic nature of the metal ion, ligand environment and nucleophile. Based on our computational studies, their roles are discussed for several mono- and binuclear metallohydrolases and their synthetic analogues. Hydrolysis by natural metallohydrolases is found to be promoted by a ligand environment with low basicity, a metal bound water and a heterobinuclear metal center (in binuclear enzymes). Additionally, peptide and phosphoester hydrolysis is dominated by two competing effects, i.e. nucleophilicity and Lewis acid activation, respectively. In synthetic analogues, hydrolysis is facilitated by the inclusion of a second metal center, hydrophobic effects, a biological metal (Zn, Cu and Co) and a terminal hydroxyl nucleophile. Due to the absence of the protein environment, hydrolysis by these small molecules is exclusively influenced by nucleophile activation. The results gleaned from these studies will enhance the understanding of fundamental principles of multiple hydrolytic reactions. They will also advance the development of computational methods as a predictive tool to design more efficient catalysts for hydrolysis, Diels-Alder reaction, Michael addition, epoxide opening and aldol condensation.
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Affiliation(s)
- Leonardo F Serafim
- Department of Chemistry, University of Miami, Coral Gables, FL 33146, USA.
| | | | - Lukun Wang
- Department of Chemistry, University of Miami, Coral Gables, FL 33146, USA.
| | - Parth Rathee
- Department of Chemistry, University of Miami, Coral Gables, FL 33146, USA.
| | - Jiawen Yang
- Department of Chemistry, University of Miami, Coral Gables, FL 33146, USA.
| | | | - Rajeev Prabhakar
- Department of Chemistry, University of Miami, Coral Gables, FL 33146, USA.
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Hu Q, Jayasinghe-Arachchige VM, Prabhakar R. Degradation of a Main Plastic Pollutant Polyethylene Terephthalate by Two Distinct Proteases (Neprilysin and Cutinase-like Enzyme). J Chem Inf Model 2021; 61:764-776. [PMID: 33534993 DOI: 10.1021/acs.jcim.0c00797] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
In this DFT study, hydrolysis of polyethylene terephthalate (PET), a major cause of plastic pollution, by two distinct enzymes, neprilysin (NEP, a mononuclear metalloprotease) and cutinase-like enzyme (CLE, a serine protease), has been investigated. These enzymes utilize different mechanisms for the degradation of PET. NEP uses either the metal-bound hydroxide attack (MH) mechanism or reverse protonation (RP) mechanism, while CLE utilizes a general acid/base mechanism that includes acylation and deacylation processes. Additionally, the RP mechanism of NEP can proceed through three pathways, RP0, RP1, and RP2. The DFT calculations predict that, among all these mechanisms, the MH mechanism is the energetically most favorable one for the NEP enzyme. In comparison, CLE catalyzes this reaction with a significantly higher barrier. These results suggest that the Lewis acid and nucleophile activations provided by the Zn metal center of NEP are more effective than the hydrogen bonding interactions afforded by the catalytic Ser85-His180-Asp165 triad of CLE. They have provided intrinsic details regarding PET degradation and will pave the way for the design of efficient metal-based catalysts for this critical reaction.
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Affiliation(s)
- Qiaoyu Hu
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
| | | | - Rajeev Prabhakar
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
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Hu Q, Jayasinghe‐Arachchige VM, Sharma G, Serafim LF, Paul TJ, Prabhakar R. Mechanisms of peptide and phosphoester hydrolysis catalyzed by two promiscuous metalloenzymes (insulin degrading enzyme and glycerophosphodiesterase) and their synthetic analogues. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2020. [DOI: 10.1002/wcms.1466] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Qiaoyu Hu
- Department of Chemistry, University of Miami Coral Gables Florida
| | | | - Gaurav Sharma
- Department of Chemistry, University of Miami Coral Gables Florida
| | | | - Thomas J. Paul
- Department of Chemistry, University of Miami Coral Gables Florida
| | - Rajeev Prabhakar
- Department of Chemistry, University of Miami Coral Gables Florida
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Lai R, Tang WJ, Li H. Catalytic Mechanism of Amyloid-β Peptide Degradation by Insulin Degrading Enzyme: Insights from Quantum Mechanics and Molecular Mechanics Style Møller-Plesset Second Order Perturbation Theory Calculation. J Chem Inf Model 2018; 58:1926-1934. [PMID: 30133282 PMCID: PMC6670292 DOI: 10.1021/acs.jcim.8b00406] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Insulin degrading enzyme (IDE), a metalloprotease that degrades amyloid-β (Aβ) peptides and insulin, is associated with Alzheimer's disease and diabetes. The mechanism of IDE catalyzed degrading of Aβ peptides, which is of fundamental importance in the design of therapeutic methods for Alzheimer's disease, has not been fully understood. In this work, combined quantum mechanics and molecular mechanics (QM/MM) style Møller-Plesset second order perturbation theory (MP2) geometry optimization calculations are performed to investigate the catalytic mechanism of the Aβ40 Phe19-Phe20 peptide bond cleavage by human IDE. The analyses using QM/MM MP2 optimization suggest that a neutral water molecule is at the active site of the enzyme-substrate (ES) complex. The water molecule is in hydrogen bonding with the nearby anionic Glu111 of IDE but not directly bound to the catalytic Zn ion. This is confirmed by QM/MM DFTB3 molecular dynamics simulation. Our studies also reveal that the hydrolysis of the Aβ40 Phe19-Phe20 peptide bond by IDE consists of four key steps. The neutral water is first activated by moving toward and binding to the Zn ion. A gem-diol intermediate is then formed by the activated neutral water molecule attacking the C atom of the Phe19-Phe20 peptide bond. The next is the protonation of the N atom of Phe19-Phe20 peptide bond to form an intermediate with an elongated C-N bond. The final step is the breaking of the Phe19-Phe20 C-N bond. The final step is the rate-determining step with a calculated Gibbs free energy of activation of 17.34 kcal/mol, in good agreement with the experimental value 16.7 kcal/mol. This mechanism provides the basis for the design of biochemical methods to modulate the activity of IDE in humans.
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Affiliation(s)
- Rui Lai
- Department of Chemistry, Nebraska Center for Materials and Nanoscience, and Center for Integrated Biomolecular Communication , University of Nebraska-Lincoln , Lincoln , Nebraska 68588-0304 , United States
| | - Wei-Jen Tang
- Ben May Department for Cancer Research , The University of Chicago , Chicago , Illinois 60637 , United States
| | - Hui Li
- Department of Chemistry, Nebraska Center for Materials and Nanoscience, and Center for Integrated Biomolecular Communication , University of Nebraska-Lincoln , Lincoln , Nebraska 68588-0304 , United States
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Jayasinghe‐Arachchige VM, Hu Q, Sharma G, Paul TJ, Lundberg M, Quinonero D, Parac‐Vogt TN, Prabhakar R. Hydrolysis of chemically distinct sites of human serum albumin by polyoxometalate: A hybrid QM/MM (ONIOM) study. J Comput Chem 2018; 40:51-61. [DOI: 10.1002/jcc.25528] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Revised: 06/22/2018] [Accepted: 06/23/2018] [Indexed: 12/28/2022]
Affiliation(s)
| | - Qiaoyu Hu
- Department of Chemistry University of Miami Coral Gables Florida 33146
| | - Gaurav Sharma
- Department of Chemistry University of Miami Coral Gables Florida 33146
| | - Thomas J. Paul
- Department of Chemistry University of Miami Coral Gables Florida 33146
| | - Marcus Lundberg
- Department of Chemistry ‐ Ångström Laboratory Uppsala University 751 21, Uppsala Sweden
| | - David Quinonero
- Department of Chemistry Universitat de les Illes Balears Palma de Mallorca Spain
| | | | - Rajeev Prabhakar
- Department of Chemistry University of Miami Coral Gables Florida 33146
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Paul TJ, Barman A, Ozbil M, Bora RP, Zhang T, Sharma G, Hoffmann Z, Prabhakar R. Mechanisms of peptide hydrolysis by aspartyl and metalloproteases. Phys Chem Chem Phys 2016; 18:24790-24801. [DOI: 10.1039/c6cp02097f] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Peptide hydrolysis has been involved in a wide range of biological, biotechnological, and industrial applications.
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Affiliation(s)
- Thomas J. Paul
- Department of Chemistry
- University of Miami
- Coral Gables
- USA
| | - Arghya Barman
- Department of Chemistry
- University of Miami
- Coral Gables
- USA
| | - Mehmet Ozbil
- Department of Chemistry
- University of Miami
- Coral Gables
- USA
| | | | - Tingting Zhang
- Department of Chemistry
- University of Miami
- Coral Gables
- USA
| | - Gaurav Sharma
- Department of Chemistry
- University of Miami
- Coral Gables
- USA
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Zhang T, Ozbil M, Barman A, Paul TJ, Bora RP, Prabhakar R. Theoretical insights into the functioning of metallopeptidases and their synthetic analogues. Acc Chem Res 2015; 48:192-200. [PMID: 25607542 DOI: 10.1021/ar500301y] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
CONSPECTUS: The selective hydrolysis of a peptide or amide bond (-(O═)C-NH-) by a synthetic metallopeptidase is required in a wide range of biological, biotechnological, and industrial applications. In nature, highly specialized enzymes known as proteases and peptidases are used to accomplish this daunting task. Currently, many peptide bond cleaving enzymes and synthetic reagents have been utilized to achieve efficient peptide hydrolysis. However, they possess some serious limitations. To overcome these inadequacies, a variety of metal complexes have been developed that mimic the activities of natural enzymes (metallopeptidases). However, in comparison to metallopeptidases, the hydrolytic reactions facilitated by their existing synthetic analogues are considerably slower and occur with lower catalytic turnover. This could be due to the following reasons: (1) they lack chemical properties of amino acid residues found within enzyme active sites; (2) they contain a higher metal coordination number compared with naturally occurring enzymes; and (3) they do not have access to second coordination shell residues that provide substantial rate enhancements in enzymes. Additionally, the critical structural and mechanistic information required for the development of the next generation of synthetic metallopeptidases cannot be readily obtained through existing experimental techniques. This is because most experimental techniques cannot follow the individual chemical steps in the catalytic cycle due to the fast rate of enzymes. They are also limited by the fact that the diamagnetic d(10) Zn(II) center is silent to electronic, electron spin resonance, and (67)Zn NMR spectroscopies. Therefore, we have employed molecular dynamics (MD), quantum mechanics (QM), and hybrid quantum mechanics/molecular mechanics (QM/MM) techniques to derive this information. In particular, the role of the metal ions, ligands, and microenvironment in the functioning of mono- and binuclear metal center containing enzymes such as insulin degrading enzyme (IDE) and bovine lens leucine aminopeptidase (BILAP), respectively, and their synthetic analogues have been investigated. Our results suggested that in the functioning of IDE, the chemical nature of the peptide bond played a role in the energetics of the reaction and the peptide bond cleavage occurred in the rate-limiting step of the mechanism. In the cocatalytic mechanism used by BILAP, one metal center polarized the scissile peptide bond through the formation of a bond between the metal and the carbonyl group of the substrate, while the second metal center delivered the hydroxyl nucleophile. The Zn(N3) [Zn(His, His, His)] core of matrix metalloproteinase was better than the Zn(N2O) [Zn(His, His, Glu)] core of IDE for peptide hydrolysis. Due to the synergistic interaction between the two metal centers, the binuclear metal center containing Pd2(μ-OH)([18]aneN6)](4+) complex was found to be ∼100 times faster than the mononuclear [Pd(H2O)4](2+) complex. A successful small-molecule synthetic analogue of a mononuclear metallopeptidase must contain a metal with a strong Lewis acidity capable of reducing the pKa of its water ligand to less than 7. Ideally, the metal center should include three ligands with low basicity. The steric effects or strain exerted by the microenvironment could be used to weaken the metal-ligand interactions and increase the activity of the metallopeptidase.
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Affiliation(s)
- Tingting Zhang
- Department
of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
| | - Mehmet Ozbil
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Arghya Barman
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302-3965, United States
| | - Thomas J. Paul
- Department
of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
| | - Ram Prasad Bora
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-1062, United States
| | - Rajeev Prabhakar
- Department
of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
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da Cruz CHB, Seabra GM. QM/MM simulations of amyloid-β 42 degradation by IDE in the presence and absence of ATP. J Chem Inf Model 2015; 55:72-83. [PMID: 25539133 DOI: 10.1021/ci500544c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The ability of the insulin-degrading enzyme (IDE) to degrade amyloid-β 42 (Aβ42), a process regulated by ATP, has been studied as an alternative path in the development of drugs against Alzheimer's disease. In this study, we calculated the potential of mean force for the degradation of Aβ42 by IDE in the presence and absence of ATP by umbrella sampling with hybrid quantum mechanics and molecular mechanics (QM/MM) calculations, using the SCC-DFTB QM Hamiltonian and Amber ff99SB force field. Results indicate that the reaction occurs in two steps: The first step is characterized by the formation of the intermediate. The second step is characterized by breaking the peptide bond of the substrate, the latter being the rate-determining step. In our simulations, the activation energy barrier in the absence of ATP is 15 ± 2 kcal mol(-1), which is 7 kcal mol(-1) lower than in the presence of ATP, indicating that the presence of the nucleotide decreases the reaction rate by about 10(5) times.
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Affiliation(s)
- Carlos H B da Cruz
- Departamento de Química Fundamental, Universidade Federal de Pernambuco , Av. Jornalista Aníbal Fernandes, s/n, Cidade Universitária, Recife-PE, Brazil , 50.740-560
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10
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Elton ES, Zhang T, Prabhakar R, Arif AM, Berreau LM. Pb(II)-Promoted Amide Cleavage: Mechanistic Comparison to a Zn(II) Analogue. Inorg Chem 2013; 52:11480-92. [DOI: 10.1021/ic401782x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Eric S. Elton
- Department
of Chemistry and Biochemistry, Utah State University, 0300 Old
Main Hill, Logan, Utah 84322-0300, United States
| | - Tingting Zhang
- Department
of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, Florida 33146-0431, United States
| | - Rajeev Prabhakar
- Department
of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, Florida 33146-0431, United States
| | - Atta M. Arif
- Department
of Chemistry, University of Utah, 315 S. 1400 E., Salt Lake City, Utah 84112-0850, United States
| | - Lisa M. Berreau
- Department
of Chemistry and Biochemistry, Utah State University, 0300 Old
Main Hill, Logan, Utah 84322-0300, United States
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Grasso G, Pietropaolo A, Spoto G, Pappalardo G, Tundo GR, Ciaccio C, Coletta M, Rizzarelli E. Copper(I) and Copper(II) Inhibit Aβ Peptides Proteolysis by Insulin-Degrading Enzyme Differently: Implications for Metallostasis Alteration in Alzheimer’s Disease. Chemistry 2011; 17:2752-62. [DOI: 10.1002/chem.201002809] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2010] [Indexed: 02/02/2023]
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Bora RP, Barman A, Zhu X, Ozbil M, Prabhakar R. Which One Among Aspartyl Protease, Metallopeptidase, and Artificial Metallopeptidase is the Most Efficient Catalyst in Peptide Hydrolysis? J Phys Chem B 2010; 114:10860-75. [DOI: 10.1021/jp104294x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Ram Prasad Bora
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, Florida 33146
| | - Arghya Barman
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, Florida 33146
| | - Xiaoxia Zhu
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, Florida 33146
| | - Mehmet Ozbil
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, Florida 33146
| | - Rajeev Prabhakar
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, Florida 33146
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Bora RP, Prabhakar R. Elucidation of Interactions of Alzheimer Amyloid β Peptides (Aβ40 and Aβ42) with Insulin Degrading Enzyme: A Molecular Dynamics Study. Biochemistry 2010; 49:3947-56. [DOI: 10.1021/bi1002103] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Ram Prasad Bora
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, Florida 33146
| | - Rajeev Prabhakar
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, Florida 33146
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