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Buczkowski A, Gorzkiewicz M, Stepniak A, Malinowska-Michalak M, Tokarz P, Urbaniak P, Ionov M, Klajnert-Maculewicz B, Palecz B. Physicochemical and in vitro cytotoxicity studies of inclusion complex between gemcitabine and cucurbit[7]uril host. Bioorg Chem 2020; 99:103843. [PMID: 32305692 DOI: 10.1016/j.bioorg.2020.103843] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 04/05/2020] [Accepted: 04/08/2020] [Indexed: 12/21/2022]
Abstract
Gemcitabine, a cytostatic drug from the pyrimidine antimetabolite group, exhibits limited storage stability and numerous side effects during therapy. One of the strategies to improve the effectiveness of therapy with such drugs is the use of supramolecular nano-containers, including dendrimers and macrocyclic compounds. The ability of gemcitabine to attach a proton in an aqueous environment necessitates the search for a carrier that is well-tolerated by an organism and capable of supramolecular binding of a ligand (drug) in a cationic form. In the current study a promising strategy was tested for using cucurbituril Q7 to bind gemcitabine cations for its efficient intracellular delivery on three selected cancer cell lines (MOLT4, THP-1 and U937). Based on physicochemical studies (equilibrium dialysis, UV and 1H NMR titrations, DOSY 1H NMR measurements, DSC calorimetry) and cytotoxicity tests on cells with a free and blocked hENT1 transporter, the conclusion was drawn about the binding and penetration of the cucurbituril-drug complex into cancer cells.
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Affiliation(s)
- Adam Buczkowski
- Unit of Biophysical Chemistry, Department of Physical Chemistry, Faculty of Chemistry, University of Lodz, 165 Pomorska St., 90-236 Lodz, Poland.
| | - Michał Gorzkiewicz
- Department of General Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, 141/143 Pomorska St., 90-236 Lodz, Poland
| | - Artur Stepniak
- Unit of Biophysical Chemistry, Department of Physical Chemistry, Faculty of Chemistry, University of Lodz, 165 Pomorska St., 90-236 Lodz, Poland
| | - Małgorzata Malinowska-Michalak
- Unit of Biophysical Chemistry, Department of Physical Chemistry, Faculty of Chemistry, University of Lodz, 165 Pomorska St., 90-236 Lodz, Poland
| | - Paweł Tokarz
- Molecular Spectroscopy Laboratory, Department of Organic Chemistry, Faculty of Chemistry, University of Lodz, Tamka 12, Lodz 91-403, Poland
| | - Paweł Urbaniak
- Department of Inorganic and Analytical Chemistry, Faculty of Chemistry, University of Lodz, 12 Tamka St., 91-403 Lodz, Poland
| | - Maksim Ionov
- Department of General Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, 141/143 Pomorska St., 90-236 Lodz, Poland
| | - Barbara Klajnert-Maculewicz
- Department of General Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, 141/143 Pomorska St., 90-236 Lodz, Poland
| | - Bartlomiej Palecz
- Unit of Biophysical Chemistry, Department of Physical Chemistry, Faculty of Chemistry, University of Lodz, 165 Pomorska St., 90-236 Lodz, Poland
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2
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Chakraborty D, Chattaraj PK. Host-guest interactions between octa acid and cations/nucleobases. J Comput Chem 2018; 39:161-175. [PMID: 29105789 DOI: 10.1002/jcc.25097] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 10/14/2017] [Accepted: 10/17/2017] [Indexed: 11/12/2022]
Abstract
The nature of host-guest interaction in between octa acid cavitand (OA) and some representative cationic guests (Li+ , Na+ , K+ , Be+2 , Mg+2 , Ca+2 , Li3 O+ , Na3 O+ , K3 O+ ) as well as heterocyclic moieties like [adenine (A), guanine (G), cytosine (C), thymine (T), uracil (U), and tetrathiafulvalene (TTF)] has been examined with the aid of density functional theory (DFT)-based computations. Thermochemical results indicate that all the guests bind with OA in a thermodynamically favorable fashion at 298.15 K temperature and one atmospheric pressure. OA exhibits high selectivity in binding the lighter cations/metal cluster cations as compared to the heavier congeners along each given series. Moreover, OA exhibits enhanced affinity as well as selectivity in binding A/G/TTF molecules as compared to C/T/U. Noncovalent interaction and energy decomposition analyses reveal that in addition to the van der Waals interaction, significant contribution from electrostatic as well as orbital interactions dictate the outcome in all the host-guest complexes. Time dependent DFT calculations have been carried out to assess the role of the guests in tuning the electronic properties as well as absorption spectrum of OA. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Debdutta Chakraborty
- Department of Chemistry and Centre for Theoretical Studies, Indian Institute of Technology, Kharagpur, West Bengal, 721302, India
| | - Pratim Kumar Chattaraj
- Department of Chemistry and Centre for Theoretical Studies, Indian Institute of Technology, Kharagpur, West Bengal, 721302, India
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3
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Choudhury R, Ramamurthy V. Understanding the complexation of aliphatic and aromatic acids guests with octa acid. J PHYS ORG CHEM 2017. [DOI: 10.1002/poc.3795] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Rajib Choudhury
- Department of Chemistry; University of Miami; Coral Gables FL USA
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4
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Rodrigues MAA, Mendes DC, Ramamurthy V, Da Silva JP. ESI-MS of Cucurbituril Complexes Under Negative Polarity. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:2508-2514. [PMID: 28756543 DOI: 10.1007/s13361-017-1758-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 07/05/2017] [Accepted: 07/05/2017] [Indexed: 06/07/2023]
Abstract
Electrospray ionization mass spectrometry (ESI-MS) is a powerful tool to study host-guest supramolecular interactions. ESI-MS can be used for detailed gas-phase reactivity studies, to clarify the structure, or simply to verify the formation of complexes. Depending on the structure of the host and of the guest, negative and/or positive ESI are used. Here we report the unexpected formation of host-guest complexes between cucurbit[n]urils (n = 7, 8, CB[n]) and amine, styryl pyridine, and styryl pyridine dimer cations, under negative ESI. Non-complexed CB[n] form double charged halide (Br-, Cl-, F-) adducts. Under negative ESI, halide ions interact with CB[n] outer surface hydrogen atoms. One to one host-guest complexes (1:1) of CB[n] with positive charged guests were also observed as single and double charged ions under negative ESI. The positive charge of guests is neutralized by ion-pairing with halide anions. Depending on the number of positive charges guests retain in the gas phase, one or two additional halide ions are required for neutralization. Complexes 1:2 of CB[8] with styryl pyridines retain two halide ions in the gas phase, one per guest. Styryl pyridine dimers form 1:1 complexes possessing a single extra halide ion and therefore a single positive charge. Negative ESI is sensitive to small structural differences between complexes, distinguishing between 1:2 complexes of styryl pyridine-CB[8] and corresponding 1:1 complexes with the dimer. Negative ESI gives simpler spectra than positive ESI and allows the determination of guest charge state of CB[n] complexes in the gas phase. Graphical Abstract ᅟ.
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Affiliation(s)
- Maria A A Rodrigues
- Meditbio, University of Algarve, Campus de Gambelas, 8005-139, Faro, Portugal
| | - Débora C Mendes
- Meditbio, University of Algarve, Campus de Gambelas, 8005-139, Faro, Portugal
| | | | - José P Da Silva
- Meditbio, University of Algarve, Campus de Gambelas, 8005-139, Faro, Portugal.
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5
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Cendejas K, Parker HE, Molina D, Choudhury R. Supramolecular self-assembly of water-soluble cavitands: investigated by molecular dynamics simulation. J INCL PHENOM MACRO 2017. [DOI: 10.1007/s10847-017-0750-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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6
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Predicting conformations and orientations of guests within a water soluble host: a molecular docking approach. J INCL PHENOM MACRO 2017. [DOI: 10.1007/s10847-017-0707-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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7
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Bansal N, Zheng Z, Cerutti DS, Merz KM. On the fly estimation of host-guest binding free energies using the movable type method: participation in the SAMPL5 blind challenge. J Comput Aided Mol Des 2016; 31:47-60. [PMID: 27699553 DOI: 10.1007/s10822-016-9980-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2016] [Accepted: 09/24/2016] [Indexed: 11/28/2022]
Abstract
We review our performance in the SAMPL5 challenge for predicting host-guest binding affinities using the movable type (MT) method. The challenge included three hosts, acyclic Cucurbit[2]uril and two octa-acids with and without methylation at the entrance to their binding cavities. Each host was associated with 6-10 guest molecules. The MT method extrapolates local energy landscapes around particular molecular states and estimates the free energy by Monte Carlo integration over these landscapes. Two blind submissions pairing MT with variants of the KECSA potential function yielded mean unsigned errors of 1.26 and 1.53 kcal/mol for the non-methylated octa-acid, 2.83 and 3.06 kcal/mol for the methylated octa-acid, and 2.77 and 3.36 kcal/mol for Cucurbit[2]uril host. While our results are in reasonable agreement with experiment, we focused on particular cases in which our estimates gave incorrect results, particularly with regard to association between the octa-acids and an adamantane derivative. Working on the hypothesis that differential solvation effects play a role in effecting computed binding affinities for the parent octa-acid and the methylated octa-acid and that the ligands bind inside the pockets (rather than on the surface) we devised a new solvent accessible surface area term to better quantify solvation energy contributions in MT based studies. To further explore this issue a, molecular dynamics potential of mean force (PMF) study indicates that, as found by our docking calculations, the stable binding mode for this ligand is inside (rather than surface bound) the octa-acid cavity whether the entrance is methylated or not. The PMF studies also obtained the correct order for the methylation-induced change in binding affinities and associated the difference, to a large extent to differential solvation effects. Overall, the SAMPL5 challenge yielded in improvements our solvation modeling and also demonstrated the need for thorough validation of input data integrity prior to any computational analysis.
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Affiliation(s)
- Nupur Bansal
- Department of Chemistry, Michigan State University, 578 South Shaw Lane, East Lansing, MI, 48824-1322, USA
| | - Zheng Zheng
- Department of Chemistry, Michigan State University, 578 South Shaw Lane, East Lansing, MI, 48824-1322, USA
| | - David S Cerutti
- Department of Chemistry, Michigan State University, 578 South Shaw Lane, East Lansing, MI, 48824-1322, USA
| | - Kenneth M Merz
- Department of Chemistry, Michigan State University, 578 South Shaw Lane, East Lansing, MI, 48824-1322, USA.
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8
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Chakraborty D, Pan S, Chattaraj PK. Encapsulation of small gas molecules and rare gas atoms inside the octa acid cavitand. Theor Chem Acc 2016. [DOI: 10.1007/s00214-016-1876-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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9
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Gao K, Yin J, Henriksen NM, Fenley AT, Gilson MK. Binding enthalpy calculations for a neutral host-guest pair yield widely divergent salt effects across water models. J Chem Theory Comput 2015; 11:4555-64. [PMID: 26574247 DOI: 10.1021/acs.jctc.5b00676] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Dissolved salts are a part of the physiological milieu and can significantly influence the kinetics and thermodynamics of various biomolecular processes, such as binding and catalysis; thus, it is important for molecular simulations to reliably describe their effects. The present study uses a simple, nonionized host-guest model system to study the sensitivity of computed binding enthalpies to the choice of water and salt models. Molecular dynamics simulations of a cucurbit[7]uril host with a neutral guest molecule show striking differences in the salt dependency of the binding enthalpy across four water models, TIP3P, SPC/E, TIP4P-Ew, and OPC, with additional sensitivity to the choice of parameters for sodium and chloride. In particular, although all of the models predict that binding will be less exothermic with increasing NaCl concentration, the strength of this effect varies by 7 kcal/mol across models. The differences appear to result primarily from differences in the number of sodium ions displaced from the host upon binding the guest rather than from differences in the enthalpy associated with this displacement, and it is the electrostatic energy that contributes most to the changes in enthalpy with increasing salt concentration. That a high sensitivity of salt affecting the choice of water model, as observed for the present host-guest system despite it being nonionized, raises issues regarding the selection and adjustment of water models for use with biological macromolecules, especially as these typically possess multiple ionized groups that can interact relatively strongly with ions in solution.
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Affiliation(s)
- Kaifu Gao
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego , 9500 Gilman Drive, La Jolla, California 92093-0736, United States
| | - Jian Yin
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego , 9500 Gilman Drive, La Jolla, California 92093-0736, United States
| | - Niel M Henriksen
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego , 9500 Gilman Drive, La Jolla, California 92093-0736, United States
| | - Andrew T Fenley
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego , 9500 Gilman Drive, La Jolla, California 92093-0736, United States
| | - Michael K Gilson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego , 9500 Gilman Drive, La Jolla, California 92093-0736, United States
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10
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Ramamurthy V, Mondal B. Supramolecular photochemistry concepts highlighted with select examples. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C-PHOTOCHEMISTRY REVIEWS 2015. [DOI: 10.1016/j.jphotochemrev.2015.04.002] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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11
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Abstract
This review focuses on molecular containers formed by assembly processes driven by the hydrophobic effect, and summarizes the progress made in the field over the last ten years. This small but growing facet of supramolecular chemistry discusses three classes of molecules used by researchers to investigate how self-assembly can be applied to form discrete, mono-dispersed, and structurally well-defined supramolecular entities. The approaches demonstrate the importance of preorganization of arrays of rigid moieties to define a specific form predisposed to bind, fold, or assemble. As the examples demonstrate, studying these systems and their properties is teaching us how to control supramolecular chemistry in water, shedding light on aspects of aqueous solutions chemistry, and illustrating novel applications that harness the unique properties of the hydrophobic effect.
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Affiliation(s)
- Jacobs H Jordan
- Department of Chemistry, Tulane University, New Orleans, LA 70118, USA.
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12
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Joseph R, Nkrumah A, Clark RJ, Masson E. Stabilization of cucurbituril/guest assemblies via long-range Coulombic and CH···O interactions. J Am Chem Soc 2014; 136:6602-7. [PMID: 24738650 DOI: 10.1021/ja4092165] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cucurbit[n]urils (CB[n], n = 6-8) interact strongly with metal-bound 4'-substituted terpyridine ligands (M = Fe(II) and Ir(III)) via CH···O hydrogen bonding, despite significant separation between the positive metallic cation and the carbonylated rim of CB[n], and the location of the latter in the second coordination sphere of the metal ion. While water has been shown to mediate interactions between cations and CB[n]s in some assemblies, mediation by organic ligands is unprecedented. The recognition process is driven by the contrasted combination of extremely favorable binding enthalpies (up to 20.2 kcal/mol) and very unfavorable entropic components (as low as -10.2 kcal/mol). Dynamic oligomers were prepared in the presence of CB[8], which acts as a "soft", noncovalent linker between metal/terpyridine complexes, and interconnects two 4'-substituents inside its cavity. Social self-sorting between CB[8] and metal/terpyridine complexes bearing 4'-(2-naphthyl) and 4'-(2,3,5,6-tetrafluorophenyl) substituents was also observed, and could afford well-organized oligomers with alternating Fe(II) and Ir(III) cations.
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Affiliation(s)
- Roymon Joseph
- Department of Chemistry and Biochemistry, Ohio University , Athens, Ohio 45701, United States
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13
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Dash C, Yousufuddin M, Cundari TR, Dias HVR. Gold-Mediated Expulsion of Dinitrogen from Organic Azides. J Am Chem Soc 2013; 135:15479-88. [DOI: 10.1021/ja406027x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Chandrakanta Dash
- Department
of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, Texas 76019, United States
| | - Muhammed Yousufuddin
- Department
of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, Texas 76019, United States
| | - Thomas R. Cundari
- Department
of Chemistry, Center for Advanced Scientific Computing and Modeling (CASCaM), University of North Texas, Denton, Texas 76203, United States
| | - H. V. Rasika Dias
- Department
of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, Texas 76019, United States
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Jayaraj N, Jagadesan P, Samanta SR, Da Silva JP, Ramamurthy V. Release of Guests from Encapsulated Masked Hydrophobic Precursors by a Phototrigger. Org Lett 2013; 15:4374-7. [DOI: 10.1021/ol4019024] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Nithyanandhan Jayaraj
- Department of Chemistry, University of Miami, Coral Gables, Florida 33124, United States, and Centro de Investigação em Química do Algarve, FCT, Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal
| | - Pradeepkumar Jagadesan
- Department of Chemistry, University of Miami, Coral Gables, Florida 33124, United States, and Centro de Investigação em Química do Algarve, FCT, Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal
| | - Shampa R. Samanta
- Department of Chemistry, University of Miami, Coral Gables, Florida 33124, United States, and Centro de Investigação em Química do Algarve, FCT, Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal
| | - José P. Da Silva
- Department of Chemistry, University of Miami, Coral Gables, Florida 33124, United States, and Centro de Investigação em Química do Algarve, FCT, Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal
| | - V. Ramamurthy
- Department of Chemistry, University of Miami, Coral Gables, Florida 33124, United States, and Centro de Investigação em Química do Algarve, FCT, Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal
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Kulasekharan R, Maddipatla MVSN, Parthasarathy A, Ramamurthy V. Role of Free Space and Conformational Control on Photoproduct Selectivity of Optically Pure α-Alkyldeoxybenzoins within a Water-Soluble Organic Capsule. J Org Chem 2013; 78:942-9. [DOI: 10.1021/jo3023928] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Revathy Kulasekharan
- Department of Chemistry, University of Miami, Coral Gables, Florida 33124, United States
| | | | - Anand Parthasarathy
- Department of Chemistry, University of Miami, Coral Gables, Florida 33124, United States
| | - V. Ramamurthy
- Department of Chemistry, University of Miami, Coral Gables, Florida 33124, United States
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