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Gupta A, Chakraborty S, Ghosh D, Ramakrishnan R. Data-driven modeling of S 0 → S 1 excitation energy in the BODIPY chemical space: High-throughput computation, quantum machine learning, and inverse design. J Chem Phys 2021; 155:244102. [PMID: 34972385 DOI: 10.1063/5.0076787] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Derivatives of BODIPY are popular fluorophores due to their synthetic feasibility, structural rigidity, high quantum yield, and tunable spectroscopic properties. While the characteristic absorption maximum of BODIPY is at 2.5 eV, combinations of functional groups and substitution sites can shift the peak position by ±1 eV. Time-dependent long-range corrected hybrid density functional methods can model the lowest excitation energies offering a semi-quantitative precision of ±0.3 eV. Alas, the chemical space of BODIPYs stemming from combinatorial introduction of-even a few dozen-substituents is too large for brute-force high-throughput modeling. To navigate this vast space, we select 77 412 molecules and train a kernel-based quantum machine learning model providing <2% hold-out error. Further reuse of the results presented here to navigate the entire BODIPY universe comprising over 253 giga (253 × 109) molecules is demonstrated by inverse-designing candidates with desired target excitation energies.
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Affiliation(s)
- Amit Gupta
- Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research, Hyderabad 500107, India
| | - Sabyasachi Chakraborty
- Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research, Hyderabad 500107, India
| | - Debashree Ghosh
- Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Raghunathan Ramakrishnan
- Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research, Hyderabad 500107, India
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Cu-catalyzed click conjugation of cobalamin to a BODIPY-based fluorophore: A versatile tool to explore the cellular biology of vitamin B 12. J Inorg Biochem 2020; 210:111105. [PMID: 32763615 DOI: 10.1016/j.jinorgbio.2020.111105] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Revised: 05/06/2020] [Accepted: 05/07/2020] [Indexed: 11/21/2022]
Abstract
The Cu-catalyzed click conjugation of an azide-functionalized vitamin B12 (cobalamin) and an alkyne-labeled 4,4-difluoro-4-bora-3a,4a-diaza-s-indacene (BODIPY) led to the formation of a highly stable fluorescent BODIPY-labeled vitamin B12 (λex/λem = 495/508 nm). The formation of what has been identified as an iodine adduct of the conjugate was also observed as a side-product during this reaction and could be removed using HPLC. BODIPY-labeled vitamin B12 was characterized by NMR and HR-ESI-MS. In vitro studies on wild-type human fibroblasts indicated that BODIPY-labeled vitamin B12 could internalize in a manner similar to that of untagged vitamin B12. ATP-binding cassette sub-family D member 4 (ABCD4) is a lysosomal localized transporter required to export vitamin B12 from the lysosomal lumen to the cytosol. Mutations in this transporter result in the accumulation of vitamin B12 in lysosomes. In human fibroblasts harbouring a mutation in ABCD4, BODIPY-labeled vitamin B12 accumulated in the lumen of lysosomes. Our data suggests the potential use of BODIPY-labeled vitamin B12 to investigate the intracellular behavior of the vitamin in the context of disorders related to the abnormal cellular utilization of the vitamin. Moreover, results presented here demonstrate that click chemistry could be exploited for the conjugation of vitamin B12 to various other fluorophores.
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3
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Easter QT, Blum SA. Organic and Organometallic Chemistry at the Single-Molecule, -Particle, and -Molecular-Catalyst-Turnover Level by Fluorescence Microscopy. Acc Chem Res 2019; 52:2244-2255. [PMID: 31310095 DOI: 10.1021/acs.accounts.9b00219] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Mechanistic studies have historically played a key role in the discovery and optimization of reactions in organic and organometallic chemistry. However, even apparently simple organic and organometallic transformations may have surprisingly complicated multistep mechanisms, increasing the difficulty of extracting this mechanistic information. The resulting reaction intermediates often constitute a small fraction of the total reaction mixture, for example, creating a long-term analytical challenge of detection. This challenge is particularly pronounced in cases where the positions of intermediates on the reaction energy surface mean that they do not "build up" to the quantities needed for observation by traditional ensemble analytical tools. Thus, their existence and single-step elementary reactivity cannot be studied directly. New approaches for obtaining this otherwise-missing mechanistic information are therefore needed. Single-turnover, single-molecule, single-particle, and other subensemble fluorescence microscopy techniques are ideally suited for this role because of their sensitivity and spatiotemporal resolution. Inspired by the robust development of single-molecule fluorescence microscopy tools for studying enzyme catalysis, our laboratory has developed analogous fluorescence microscopy techniques to overcome mechanistic challenges in synthetic chemistry, with sensitivity as high as the single-complex, single-turnover, and single-molecule level. These techniques free the experimenter from the previous restriction that intermediates must "build up" to quantities needed for detection by ensemble analytical tools and are suited to systems where synchronization through flash photolysis or stopped flow would be inconvenient or inaccessible. In this process, the techniques transform certain previously "unobservable" intermediates and their elementary single-step reactivities into "observable" ones through sensitive and selective spectral handles. Our program has focused on imaging reactions in small-molecule, organic, and polymer synthetic chemistry with an accent on the reactivity of molecular transition metal complexes and catalysts. Our laboratory initiated studies in this area in 2008 with the imaging of individual palladium complexes that were tagged with spectator fluorophores. To enable imaging, we started with fluorophore selection and development, overcame challenges with imaging in organic solvents, and developed strategies compatible with air-sensitive chemistry and concentrations of reagents generally used in small-molecule synthesis. These studies grew to include characterization of previously unknown organometallic intermediates in the synthesis of organozinc reagents and the direct study of their elementary-step reactivity. The ability to directly observe this behavior generated predictive power for selecting salts that accelerated organozinc reagent formation in synthesis, including salts that had not yet been reported synthetically. In 2017 we also developed the first single-turnover imaging of molecular (chemo)catalysts, which through the technique's spatiotemporal resolution revealed abruptly time-variable polymerization kinetics wherein molecular ruthenium ring-opening metathesis polymerization (ROMP) catalysts changed rates independently from other catalysts less than 1 μm away. Individual catalytic turnovers, each corresponding to one single-chain-elongation reaction arising from insertion of single ROMP or enyne monomers at individual Grubbs II molecular ruthenium catalysts, were spatiotemporally resolved as green flashes in growing polymers. In this Account, we discuss the development of this technique from idea to application, including challenges overcome and strategies created to image synthetic organic and organometallic molecular chemistry at the highest levels of detection sensitivity. We also describe challenges not yet solved and provide an outlook for this growing field at the intersection of microscopy and synthetic/molecular chemistry.
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Affiliation(s)
- Quinn T. Easter
- Department of Chemistry, University of California, Irvine, California 92697−2025, United States
| | - Suzanne A. Blum
- Department of Chemistry, University of California, Irvine, California 92697−2025, United States
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Viirlaid E, Ilisson M, Kopanchuk S, Mäeorg U, Rinken A, Rinken T. Immunoassay for rapid on-site detection of glyphosate herbicide. ENVIRONMENTAL MONITORING AND ASSESSMENT 2019; 191:507. [PMID: 31342281 DOI: 10.1007/s10661-019-7657-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 07/15/2019] [Indexed: 06/10/2023]
Abstract
Glyphosate is the most widespread herbicide and its global use is steadily increasing. Although glyphosate is considered to have low toxicity, its wide application has raised concerns about its effects on human health. The extensive use of glyphosate has risen a need of its continuous monitoring in drinking and surface waters to assure in accordance with the set standards. Within the present study, we have developed a novel assay for the on-site detection of glyphosate by combining flow-through technology with the high specificity of immunorecognition. The proposed biosensing system was based on the detection of fluorescence signal generated by the quantitative replacement of glyphosate in antigen-antibody complex with IgY-type anti-glyphosate antibodies on microbeads by synthetic 5-carboxytetramethylrhodamine (5-TAMRA) conjugated glyphosate. The working range of this assay was in low millimolar range and the time required for glyphosate detection around 0.5 h. The applicability of the immunoassay for glyphosate detection in surface water was tested and the biosensor results were validated with high-performance liquid chromatography.
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Affiliation(s)
- E Viirlaid
- Institute of Chemistry, University of Tartu, Ravila 14A, 50411, Tartu, Estonia.
| | - M Ilisson
- Institute of Chemistry, University of Tartu, Ravila 14A, 50411, Tartu, Estonia
| | - S Kopanchuk
- Institute of Chemistry, University of Tartu, Ravila 14A, 50411, Tartu, Estonia
| | - U Mäeorg
- Institute of Chemistry, University of Tartu, Ravila 14A, 50411, Tartu, Estonia
| | - A Rinken
- Institute of Chemistry, University of Tartu, Ravila 14A, 50411, Tartu, Estonia
| | - T Rinken
- Institute of Chemistry, University of Tartu, Ravila 14A, 50411, Tartu, Estonia
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Halter O, Spielmann J, Kanai Y, Plenio H. Monitoring Ligand Substitution in (Catalytically Active) Metal Complexes with Bodipy-Tagged Diimines and NHC Ligands. Organometallics 2019. [DOI: 10.1021/acs.organomet.9b00130] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Oliver Halter
- Organometallic Chemistry, TU Darmstadt, Alarich-Weiss-Str. 12, 64287 Darmstadt, Germany
| | - Jonas Spielmann
- Organometallic Chemistry, TU Darmstadt, Alarich-Weiss-Str. 12, 64287 Darmstadt, Germany
| | - Yuki Kanai
- Organometallic Chemistry, TU Darmstadt, Alarich-Weiss-Str. 12, 64287 Darmstadt, Germany
| | - Herbert Plenio
- Organometallic Chemistry, TU Darmstadt, Alarich-Weiss-Str. 12, 64287 Darmstadt, Germany
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Easter QT, Garcia A, Blum SA. Single-Polymer–Particle Growth Kinetics with Molecular Catalyst Speciation and Single-Turnover Imaging. ACS Catal 2019. [DOI: 10.1021/acscatal.9b00095] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Quinn T. Easter
- Department of Chemistry, University of California, Irvine, Irvine, California 92697−2925, United States
| | - Antonio Garcia
- Department of Chemistry, University of California, Irvine, Irvine, California 92697−2925, United States
| | - Suzanne A. Blum
- Department of Chemistry, University of California, Irvine, Irvine, California 92697−2925, United States
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Halter O, Plenio H. Fluorescent Dyes in Organometallic Chemistry: Coumarin‐Tagged NHC–Metal Complexes. Eur J Inorg Chem 2018. [DOI: 10.1002/ejic.201800395] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Oliver Halter
- Organometallic Chemistry TU Darmstadt Alarich‐Weiss‐Str.12 64287 Darmstadt Germany
| | - Herbert Plenio
- Organometallic Chemistry TU Darmstadt Alarich‐Weiss‐Str.12 64287 Darmstadt Germany
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8
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Kitagawa K, Blum SA. Structure–Reactivity Studies of Intermediates for Mechanistic Information by Subensemble Fluorescence Microscopy. ACS Catal 2017. [DOI: 10.1021/acscatal.7b00627] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kazuhiro Kitagawa
- Department of Chemistry, University of California, Irvine, California 92697−2025, United States
| | - Suzanne A. Blum
- Department of Chemistry, University of California, Irvine, California 92697−2025, United States
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Ramesh P, Karabline-Kuks J, Weiss-Shtofman M, Portnoy M. Design and Synthesis of BODIPY-Cored Near IR-emitting Lipophilic and Water-Soluble Dendritic Platforms. ChemistrySelect 2017. [DOI: 10.1002/slct.201700377] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Palakuri Ramesh
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences; Tel Aviv University; Tel Aviv 699678 Israel
| | - Jeny Karabline-Kuks
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences; Tel Aviv University; Tel Aviv 699678 Israel
| | - Mor Weiss-Shtofman
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences; Tel Aviv University; Tel Aviv 699678 Israel
| | - Moshe Portnoy
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences; Tel Aviv University; Tel Aviv 699678 Israel
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Raeisolsadati Oskouei M, Brouwer AM. Organocatalytic Fluorogenic Synthesis of Chromenes. J Fluoresc 2017; 27:1141-1147. [PMID: 28224357 PMCID: PMC5393152 DOI: 10.1007/s10895-017-2049-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 02/09/2017] [Indexed: 11/25/2022]
Abstract
Two fluorescent derivatives of 2-amino-3-carbonitrile-4H-chromene were synthesized by means of a fluorogenic Michael addition of dimedone to dicyano alkene labeled BODIPY derivatives. Different organocatalysts were used in different conditions to obtain compounds 3 and 4 in good yield (up to 65% and 85%) and moderate enantiomeric excess (51% and 41% ee, respectively). This work provides the first example of an enantioselective organocatalytic conversion combined with fluorogenesis.
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Affiliation(s)
- Mina Raeisolsadati Oskouei
- van 't Hoff Institute for Molecular Sciences, University of Amsterdam, PO Box 94157, 1090 GD, Amsterdam, The Netherlands
| | - Albert M Brouwer
- van 't Hoff Institute for Molecular Sciences, University of Amsterdam, PO Box 94157, 1090 GD, Amsterdam, The Netherlands.
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Navarro M, Wang S, Müller-Bunz H, Redmond G, Farràs P, Albrecht M. Triazolylidene Metal Complexes Tagged with a Bodipy Chromophore: Synthesis and Monitoring of Ligand Exchange Reactions. Organometallics 2017. [DOI: 10.1021/acs.organomet.6b00672] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Miquel Navarro
- Department für
Chemie und Biochemie, Universität Bern, CH−3012 Bern, Switzerland
- School of Chemistry, University College Dublin, Belfield, Dublin 4, Ireland
| | - Suxiao Wang
- School of Chemistry, University College Dublin, Belfield, Dublin 4, Ireland
| | - Helge Müller-Bunz
- School of Chemistry, University College Dublin, Belfield, Dublin 4, Ireland
| | - Gareth Redmond
- School of Chemistry, University College Dublin, Belfield, Dublin 4, Ireland
| | - Pau Farràs
- School of
Chemistry, NUI Galway, Galway, Ireland
| | - Martin Albrecht
- Department für
Chemie und Biochemie, Universität Bern, CH−3012 Bern, Switzerland
- School of Chemistry, University College Dublin, Belfield, Dublin 4, Ireland
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12
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Halter O, Plenio H. Fluorescence resonance energy transfer (FRET) for the verification of dual gold catalysis. Chem Commun (Camb) 2017; 53:12461-12464. [DOI: 10.1039/c7cc07018g] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Two gold complexes with different bodipy-tagged N-heterocyclic carbene ligands, which are a potential FRET pair, were synthesized. It was shown, that the formation of dinuclear intermediates in alkyne transformations (“dual gold catalysis”) are characterized by a FRET signal.
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Affiliation(s)
- O. Halter
- Organometallic Chemistry
- 64287 Darmstadt
- Germany
| | - H. Plenio
- Organometallic Chemistry
- 64287 Darmstadt
- Germany
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13
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Lee J, Kim KH, Lee OS, Choi TL, Lee HS, Ihee H, Sohn JH. Preference of Ruthenium-Based Metathesis Catalysts toward Z- and E-Alkenes as a Guide for Selective Reactions to Alkene Stereoisomers. J Org Chem 2016; 81:7591-6. [DOI: 10.1021/acs.joc.6b01276] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Jihong Lee
- Department
of Chemistry, Chungnam National University, Daejeon 305-764, Republic of Korea
| | - Kyung Hwan Kim
- Center
for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 305-701, Republic of Korea
| | - Ok Suk Lee
- Department
of Chemistry, Chungnam National University, Daejeon 305-764, Republic of Korea
| | - Tae-Lim Choi
- Department
of Chemistry, Seoul National University, Seoul 151-747, Republic of Korea
| | - Hee-Seung Lee
- Department
of Chemistry, KAIST, Daejeon 305-701, Republic of Korea
| | - Hyotcherl Ihee
- Center
for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 305-701, Republic of Korea
- Department
of Chemistry, KAIST, Daejeon 305-701, Republic of Korea
| | - Jeong-Hun Sohn
- Department
of Chemistry, Chungnam National University, Daejeon 305-764, Republic of Korea
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Wirtz M, Grüter A, Rebmann P, Dier T, Volmer DA, Huch V, Jung G. Two-color emissive probes for click reactions. Chem Commun (Camb) 2015; 50:12694-7. [PMID: 25200167 DOI: 10.1039/c4cc05288a] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Cu(I)-catalyzed azide-alkyne cyclization (CuAAC) is the paradigmatic click reaction of continuous interest. Especially fluorogenic and FRET probes have become indispensable tools for life sciences. Here, we present a fluorescent alkyne for monitoring CuAAC, which undergoes a bathochromic shift upon reaction. Application in single-molecule and catalysis research is foreseen.
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Affiliation(s)
- Marcel Wirtz
- Biophysical Chemistry, Saarland University, Campus Building B2.2, 66123 Saarbrücken, Germany.
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