1
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Hu D, Mao L, Wang M, Huang H, Hu R, Ma H, Yuan J, Wei Y. In Situ Visualization of Reversible Diels-Alder Reactions with Self-Reporting Aggregation-Induced Emission Luminogens. ACS APPLIED MATERIALS & INTERFACES 2022; 14:3485-3495. [PMID: 34994541 DOI: 10.1021/acsami.1c20758] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The dynamic reversible Diels-Alder (DA) reactions play essential roles in both academic and applied fields. Currently, in situ visualization and direct monitoring of the formation and cleavage of covalent bonds in DA reactions are hampered by finite compatibility and expensive precise instruments, especially limited in solid reactions. We herein report a fluorescence system capable of in situ visualization by naked eyes and monitoring DA/retro-DA reactions. With the fluorescence quenching effect, the synthesized TPEMI could work as an innovative self-indicator for both DA termination and retro-DA occurrence. The fluorescence increases during DA reactions, and the mechanism is investigated to establish qualitative and quantitative relations. Besides rapid screening of reaction conditions and monitoring of DA exchange processes, the TPEMI fluorescence system can visualize heterogeneous and solid-state reactions with the AIE character. The TPEMI platform is expected to offer novel insights into reversible DA processes and dynamic covalent chemistry.
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Affiliation(s)
- Danning Hu
- Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Liucheng Mao
- Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Mengshi Wang
- Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Hongye Huang
- Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Renjian Hu
- Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Haijun Ma
- Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Jinying Yuan
- Key Laboratory of Organic Optoelectronics & Molecular Engineering of Ministry of Education, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Yen Wei
- Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
- Department of Chemistry, Center for Nanotechnology, Institute of Biomedical Technology, Chung Yuan Christian University, Taoyuan 32023, Taiwan, China
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2
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Wagh SB, Maslivetc VA, La Clair JJ, Kornienko A. Lessons in Organic Fluorescent Probe Discovery. Chembiochem 2021; 22:3109-3139. [PMID: 34062039 PMCID: PMC8595615 DOI: 10.1002/cbic.202100171] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/22/2021] [Indexed: 02/03/2023]
Abstract
Fluorescent probes have gained profound use in biotechnology, drug discovery, medical diagnostics, molecular and cell biology. The development of methods for the translation of fluorophores into fluorescent probes continues to be a robust field for medicinal chemists and chemical biologists, alike. Access to new experimental designs has enabled molecular diversification and led to the identification of new approaches to probe discovery. This review provides a synopsis of the recent lessons in modern fluorescent probe discovery.
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Affiliation(s)
- Sachin B Wagh
- The Department of Chemistry and Biochemistry, Texas State University, San Marcos, USA
| | - Vladimir A Maslivetc
- The Department of Chemistry and Biochemistry, Texas State University, San Marcos, USA
| | - James J La Clair
- Xenobe Research Institute, P. O. Box 3052, San Diego, CA, 92163-1062, USA
| | - Alexander Kornienko
- The Department of Chemistry and Biochemistry, Texas State University, San Marcos, USA
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3
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Briou B, Améduri B, Boutevin B. Trends in the Diels-Alder reaction in polymer chemistry. Chem Soc Rev 2021; 50:11055-11097. [PMID: 34605835 DOI: 10.1039/d0cs01382j] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The Diels-Alder (DA) reaction is regarded as quite a useful strategy in organic and macromolecular syntheses. The reversibility of this reaction and the advent of self-repair technology, as well as other applications in controlled macromolecular architectures and crosslinking, have strongly boosted the research activity, which is still attracting a huge interest in both academic and industrial research. The DA reaction is a simple and scalable toolbox. Though it is well-established that furan/maleimide is the most studied diene/dienophile couple, this perspective article reports strategies using other reversible systems with deeper features on other types of diene/dienophile pairs being either petro-sourced (cyclopentadiene, anthracene) or bio-sourced (muconic and sorbic acids, myrcene and farnesene derivatives, eugenol, cardanol). This review is composed of four sections. The first one briefly recalls the background on the DA reactions involving cyclodimerizations, dienes, and dienophiles, parameters affecting the reaction, while the second part deals with the furan/maleimide reaction. The third one deals with petro-sourced and bio-sourced (or products becoming bio-sourced) reactants involved in DA reactions are also listed and discussed. Finally, the authors' opinion is given on the potential future of the crosslinking-decrosslinking reaction, especially regarding the process (e.g., key temperatures of decrosslinking) or possibly monocomponents. It presents both fundamental and applied research on the DA reaction and its applications.
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Affiliation(s)
- Benoit Briou
- Institut Charles Gerhardt, CNRS, Université de Montpellier, ENSCM, Montpellier, France.
| | - Bruno Améduri
- Institut Charles Gerhardt, CNRS, Université de Montpellier, ENSCM, Montpellier, France.
| | - Bernard Boutevin
- Institut Charles Gerhardt, CNRS, Université de Montpellier, ENSCM, Montpellier, France.
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4
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Kang HS, Satraitis A, Meares A, Bhagavathy GV, Diers JR, Niedzwiedzki DM, Kirmaier C, Ptaszek M, Bocian DF, Holten D. Conjugated-linker dependence of the photophysical properties and electronic structure of chlorin dyads. J PORPHYR PHTHALOCYA 2021. [DOI: 10.1142/s1088424621500620] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The synthesis, photophysical properties and electronic structure of seven new chlorin dyads and associated benchmark monomers are described. Each dyad contains two identical chlorins linked at the macrocycle [Formula: see text]-pyrrole 13-position. The extent of electronic communication between chlorin constituents depends on the nature of the conjugated linker. The communication is assessed by modification of prominent ground-state absorption and redox properties, rate constants and yields of excited-state decay processes, and molecular-orbital characteristics. Relative to the benchmark monomers, the chlorin dyads in toluene exhibit a substantial bathochromic shift of the long-wavelength absorption band (30 nm average), two-fold increased radiative rate constant [average (10 ns)[Formula: see text] vs. (22 ns)[Formula: see text]], reduced singlet excited-state lifetimes (average 5.0 ns vs. 8.2 ns), and increased fluorescence quantum yields (average 0.56 vs. 0.42). The excited-state lifetime and fluorescence yield for the chlorin dyad with a benzothiadiazole linker are reduced substantially in benzonitrile vs. toluene due largely to [Formula: see text]25-fold accelerated internal conversion. The results aid design strategies for molecular architectures that may find utility in solar-energy conversion and photomedicine.
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Affiliation(s)
- Hyun Suk Kang
- Department of Chemistry, Washington University, St. Louis, Missouri 63130-4889, USA
| | - Andrius Satraitis
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland 21250, USA
| | - Adam Meares
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland 21250, USA
| | - Ganga Viswanathan Bhagavathy
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland 21250, USA
| | - James R. Diers
- Department of Chemistry, University of California, Riverside, California 92521-0403, USA
| | - Dariusz M. Niedzwiedzki
- Center for Solar Energy and Energy Storage and Department of Energy, Environmental & Chemical Engineering, Washington University, St. Louis, MO 63130-4889, USA
| | - Christine Kirmaier
- Department of Chemistry, Washington University, St. Louis, Missouri 63130-4889, USA
| | - Marcin Ptaszek
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland 21250, USA
| | - David F. Bocian
- Department of Chemistry, University of California, Riverside, California 92521-0403, USA
| | - Dewey Holten
- Department of Chemistry, Washington University, St. Louis, Missouri 63130-4889, USA
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5
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Liu C, Yang W, Zhang Y, Jiang J. Quintuple-Decker Heteroleptic Phthalocyanine Heterometallic Samarium-Cadmium Complexes. Synthesis, Crystal Structure, Electrochemical Behavior, and Spectroscopic Investigation. Inorg Chem 2020; 59:17591-17599. [PMID: 33186030 DOI: 10.1021/acs.inorgchem.0c02816] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
A one-pot synthesis methodology was employed for obtaining diverse quintuple-decker phthalocyanine heterometallic lanthanide-cadmium complexes. By using the reaction of a double-decker homoleptic/heteroleptic phthalocyanine samarium compound with metal-free phthalocyanine and cadmium acetate in 1,2,4-trichlorobenzene at 200 °C, two novel quintuple-decker heteroleptic phthalocyanine heterometallic samarium-cadmium compounds, {(Pc)Sm(Pc)Cd(Pc*)Cd(Pc)Sm(Pc)} (1) and {(Pc)Sm(Pc*)Cd(Pc*)Cd(Pc*)Sm(Pc)} (2), together with one homoleptic phthalocyanine species, {(Pc*)Sm(Pc*)Cd(Pc*)Cd(Pc*)Sm(Pc*)} (3), were successfully fabricated, where H2Pc and H2Pc* represent unsubstituted phthalocyanine and 2,3,9,10,16,17,23,24-octakis(n-pentyloxy)phthalocyanine, respectively. Their quintuple-decker structures have been disclosed by various spectroscopic techniques and single-crystal X-ray diffraction. In addition, valence tautomerization of these three quintuple-decker complexes has been achieved by the addition of phenoxathiin hexachloroantimonate, giving three oxidized forms including one-, two-, and three-electron oxidation products. From 1 to 3 with the same oxidation state, the increased number of n-pentyloxy substituents of phthalocyanine ligands induces the blue shift of electronic absorption in the IR region due to the increased gap associated with the introduction of electron-donating substituents. In particular, the electronic absorption spectra of one- and two-electron oxidation products for 1 exhibit a rare band in the middle-IR region around 3000 nm, being one of the farthest electronic transitions captured by UV-vis spectroscopy. The three-electron oxidation product of 1 displays two bands at 2231 and 2740 nm, respectively. These data are well confirmed by IR spectroscopic data and theoretical calculation results.
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Affiliation(s)
- Chao Liu
- Beijing Advanced Innovation Center for Materials Genome Engineering, Beijing Key Laboratory for Science and Application of Functional Molecular and Crystalline Materials, Department of Chemistry and Chemical Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Wei Yang
- Beijing Advanced Innovation Center for Materials Genome Engineering, Beijing Key Laboratory for Science and Application of Functional Molecular and Crystalline Materials, Department of Chemistry and Chemical Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Yuexing Zhang
- Hubei Collaborative Innovation Center for Advanced Organic Chemical Materials, Ministry-of-Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules, College of Chemistry and Chemical Engineering, Hubei University, Wuhan 430062, China
| | - Jianzhuang Jiang
- Beijing Advanced Innovation Center for Materials Genome Engineering, Beijing Key Laboratory for Science and Application of Functional Molecular and Crystalline Materials, Department of Chemistry and Chemical Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China
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6
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Gemen J, Ahrens J, Shimon LJW, Klajn R. Modulating the Optical Properties of BODIPY Dyes by Noncovalent Dimerization within a Flexible Coordination Cage. J Am Chem Soc 2020; 142:17721-17729. [PMID: 33006898 PMCID: PMC7564082 DOI: 10.1021/jacs.0c08589] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Indexed: 12/25/2022]
Abstract
Aggregation of organic molecules can drastically affect their physicochemical properties. For instance, the optical properties of BODIPY dyes are inherently related to the degree of aggregation and the mutual orientation of BODIPY units within these aggregates. Whereas the noncovalent aggregation of various BODIPY dyes has been studied in diverse media, the ill-defined nature of these aggregates has made it difficult to elucidate the structure-property relationships. Here, we studied the encapsulation of three structurally simple BODIPY derivatives within the hydrophobic cavity of a water-soluble, flexible PdII6L4 coordination cage. The cavity size allowed for the selective encapsulation of two dye molecules, irrespective of the substitution pattern on the BODIPY core. Working with a model, a pentamethyl-substituted derivative, we found that the mutual orientation of two BODIPY units in the cage's cavity was remarkably similar to that in the crystalline state of the free dye, allowing us to isolate and characterize the smallest possible noncovalent H-type BODIPY aggregate, namely, an H-dimer. Interestingly, a CF3-substituted BODIPY, known for forming J-type aggregates, was also encapsulated as an H-dimer. Taking advantage of the dynamic nature of encapsulation, we developed a system in which reversible switching between H- and J-aggregates can be induced for multiple cycles simply by addition and subsequent destruction of the cage. We expect that the ability to rapidly and reversibly manipulate the optical properties of supramolecular inclusion complexes in aqueous media will open up avenues for developing detection systems that operate within biological environments.
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Affiliation(s)
- Julius Gemen
- Department
of Organic Chemistry, Weizmann Institute
of Science, Rehovot 76100, Israel
| | - Johannes Ahrens
- Department
of Organic Chemistry, Weizmann Institute
of Science, Rehovot 76100, Israel
- BASF
SE, Carl-Bosch-Straße
38, 67056 Ludwigshafen
am Rhein, Germany
| | - Linda J. W. Shimon
- Chemical
Research Support, Weizmann Institute of
Science, Rehovot 76100, Israel
| | - Rafal Klajn
- Department
of Organic Chemistry, Weizmann Institute
of Science, Rehovot 76100, Israel
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7
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Hewavitharanage P, Warshawsky R, Rosokha SV, Vaal J, Stickler K, Bachynsky D, Jairath N. Efficient energy transfer in phenyl-ethynyl-linked asymmetric BODIPY dimers. Tetrahedron 2020. [DOI: 10.1016/j.tet.2020.131515] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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8
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Liu M, Ma S, She M, Chen J, Wang Z, Liu P, Zhang S, Li J. Structural modification of BODIPY: Improve its applicability. CHINESE CHEM LETT 2019. [DOI: 10.1016/j.cclet.2019.08.028] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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9
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Bazian A, Beyramabadi SA, Davoodnia A, Bozorgmehr MR, Pordel M. A Theoretical Investigation on the Regioselectivity of the Diels–Alder Cycloaddition of 9-(Methoxymethyl) Anthracene And Citraconic Anhydride. J STRUCT CHEM+ 2019. [DOI: 10.1134/s0022476618080085] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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10
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Zhang G, Zhao N, Bobadova-Parvanova P, Wang M, Fronczek FR, Smith KM, Vicente MGH. Syntheses, Spectroscopic Properties, and Computational Study of (E,Z)-Ethenyl and Ethynyl-Linked BODIPYs. J Phys Chem A 2018; 122:6256-6265. [DOI: 10.1021/acs.jpca.8b05149] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Guanyu Zhang
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Ning Zhao
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | | | - Maodie Wang
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Frank R. Fronczek
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Kevin M. Smith
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - M. Graça H. Vicente
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
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11
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Somai Magar KB, Edison TNJI, Lee YR. Regioselective Construction of Functionalized Biarylols by Fe(OTf)3
-Catalyzed Direct Arylation of 1-Diazonaphthalen-2(1H
)-ones and Their Fluorescence Properties. European J Org Chem 2017. [DOI: 10.1002/ejoc.201701533] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
| | - T. N. J. I. Edison
- School of Chemical Engineering; Yeungnam University; 38541 Gyeongsan Republic of Korea
| | - Yong Rok Lee
- School of Chemical Engineering; Yeungnam University; 38541 Gyeongsan Republic of Korea
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12
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Rouillé G, Jäger C, Huisken F, Henning T, Czerwonka R, Theumer G, Börger C, Bauer I, Knölker HJ. Quantitative Structure-Retention Relationships for Polycyclic Aromatic Hydrocarbons and their Oligoalkynyl-Substituted Derivatives. ChemistryOpen 2017; 6:519-525. [PMID: 28794947 PMCID: PMC5542760 DOI: 10.1002/open.201700115] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2017] [Indexed: 11/08/2022] Open
Abstract
Reversed‐phase high‐performance liquid chromatography (RP‐HPLC) has been carried out for a series of unsubstituted polycyclic aromatic hydrocarbons (PAHs) and the corresponding ethynyl, 1,3‐butadiynyl, and 1,3,5‐hexatriynyl derivatives. Theoretical values of the isotropic polarizability and several polarity descriptors have been computed for each compound by using semiempirical models and density functional theory (DFT), with the aim of evaluating linear functions as quantitative structure–retention relationships (QSRRs). The polarity has been described by using either the permanent electric dipole moment, the subpolarity, or a topological electronic index. Three types of partial atomic charges have been used to calculate the subpolarity and a topological index. The choice of the theoretical model, of the polarity descriptor, and of the partial atomic charges is discussed and the resulting QSRRs are compared. Calculating the retention times from the polarizability and the topological electronic index (AM1, PM3, or DFT‐B3LYP/6–31+G(d,p)) gives the best agreement with the experimental values.
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Affiliation(s)
- Gaël Rouillé
- Laboratory Astrophysics Group of the Max Planck Institute for Astronomy at the Friedrich Schiller University Jena Institute of Solid State Physics Helmholtzweg 3 07743 Jena Germany
| | - Cornelia Jäger
- Laboratory Astrophysics Group of the Max Planck Institute for Astronomy at the Friedrich Schiller University Jena Institute of Solid State Physics Helmholtzweg 3 07743 Jena Germany
| | - Friedrich Huisken
- Laboratory Astrophysics Group of the Max Planck Institute for Astronomy at the Friedrich Schiller University Jena Institute of Solid State Physics Helmholtzweg 3 07743 Jena Germany
| | - Thomas Henning
- Max Planck Institute for Astronomy Königstuhl 17 69117 Heidelberg Germany
| | - Regina Czerwonka
- Department Chemie Technische Universität Dresden Bergstrasse 66 01069 Dresden Germany
| | - Gabriele Theumer
- Department Chemie Technische Universität Dresden Bergstrasse 66 01069 Dresden Germany
| | - Carsten Börger
- Department Chemie Technische Universität Dresden Bergstrasse 66 01069 Dresden Germany
| | - Ingmar Bauer
- Department Chemie Technische Universität Dresden Bergstrasse 66 01069 Dresden Germany
| | - Hans-Joachim Knölker
- Department Chemie Technische Universität Dresden Bergstrasse 66 01069 Dresden Germany
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13
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Squeo BM, Gregoriou VG, Avgeropoulos A, Baysec S, Allard S, Scherf U, Chochos CL. BODIPY-based polymeric dyes as emerging horizon materials for biological sensing and organic electronic applications. Prog Polym Sci 2017. [DOI: 10.1016/j.progpolymsci.2017.02.003] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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14
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Meares A, Satraitis A, Akhigbe J, Santhanam N, Swaminathan S, Ehudin M, Ptaszek M. Amphiphilic BODIPY-Hydroporphyrin Energy Transfer Arrays with Broadly Tunable Absorption and Deep Red/Near-Infrared Emission in Aqueous Micelles. J Org Chem 2017; 82:6054-6070. [PMID: 28516773 PMCID: PMC5873324 DOI: 10.1021/acs.joc.7b00357] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BODIPY-hydroporphyrin energy transfer arrays allow for development of a family of fluorophores featuring a common excitation band at 500 nm, tunable excitation band in the deep red/near-infrared window, and tunable emission. Their biomedical applications are contingent upon retaining their optical properties in an aqueous environment. Amphiphilic arrays containing PEG-substituted BODIPY and chlorins or bacteriochlorins were prepared and their optical and fluorescence properties were determined in organic solvents and aqueous surfactants. The first series of arrays contains BODIPYs with PEG substituents attached to the boron, whereas in the second series, PEG substituents are attached to the aryl at the meso positions of BODIPY. For both series of arrays, excitation of BODIPY at 500 nm results in efficient energy transfer to and bright emission of hydroporphyrin in the deep-red (640-660 nm) or near-infrared (740-760 nm) spectral windows. In aqueous solution of nonionic surfactants (Triton X-100 and Tween 20) arrays from the second series exhibit significant quenching of fluorescence, whereas properties of arrays from the first series are comparable to those observed in polar organic solvents. Reported arrays possess large effective Stokes shift (115-260 nm), multiple excitation wavelengths, and narrow, tunable deep-red/near-IR fluorescence in aqueous surfactants, and are promising candidates for a variety of biomedical-related applications.
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Affiliation(s)
- Adam Meares
- University of Maryland, Baltimore County , 1000 Hilltop Circle, Baltimore, 21250 Maryland, United States
| | - Andrius Satraitis
- University of Maryland, Baltimore County , 1000 Hilltop Circle, Baltimore, 21250 Maryland, United States
| | - Joshua Akhigbe
- University of Maryland, Baltimore County , 1000 Hilltop Circle, Baltimore, 21250 Maryland, United States
| | - Nithya Santhanam
- University of Maryland, Baltimore County , 1000 Hilltop Circle, Baltimore, 21250 Maryland, United States
| | - Subramani Swaminathan
- University of Maryland, Baltimore County , 1000 Hilltop Circle, Baltimore, 21250 Maryland, United States
| | - Melanie Ehudin
- University of Maryland, Baltimore County , 1000 Hilltop Circle, Baltimore, 21250 Maryland, United States
| | - Marcin Ptaszek
- University of Maryland, Baltimore County , 1000 Hilltop Circle, Baltimore, 21250 Maryland, United States
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15
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Synthesis, structure and luminescent properties of three organogold(I)-9-ethynyl-anthracence-diphosphine complexes. J Organomet Chem 2017. [DOI: 10.1016/j.jorganchem.2017.02.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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16
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Toyota S, Nishiuchi M, Iwata T, Yamauchi T, Iwanaga T, Hasegawa M. Synthesis, structures, and properties of 2,5-dianthrylthiophene derivatives. CAN J CHEM 2017. [DOI: 10.1139/cjc-2016-0391] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The title thiophene derivatives bearing two 9-, 1-, or 2-anthryl groups were synthesized by cyclization of the corresponding 1,3-diynes with sodium sulfide or by Suzuki–Miyaura coupling. X-ray analysis and DFT calculations revealed that the molecules adopt nonplanar conformations depending on the steric demand of the anthryl groups. The dihedral angles between the arene units are an important contributor to the photophysical properties in the electronic spectra as well as the electrochemical data.
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Affiliation(s)
- Shinji Toyota
- Department of Chemistry, School of Science, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Mai Nishiuchi
- Department of Chemistry, Faculty of Science, Okayama University of Science, 1-1 Ridaicho, Kita-ku, Okayama 700-0005, Japan
| | - Taisei Iwata
- Department of Chemistry, Faculty of Science, Okayama University of Science, 1-1 Ridaicho, Kita-ku, Okayama 700-0005, Japan
| | - Tomokazu Yamauchi
- Department of Chemistry, Faculty of Science, Okayama University of Science, 1-1 Ridaicho, Kita-ku, Okayama 700-0005, Japan
| | - Tetsuo Iwanaga
- Department of Chemistry, Faculty of Science, Okayama University of Science, 1-1 Ridaicho, Kita-ku, Okayama 700-0005, Japan
| | - Masashi Hasegawa
- Department of Chemistry, School of Science, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara 252-0373, Japan
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17
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Wieczorek A, Buckup T, Wombacher R. Rigid tetrazine fluorophore conjugates with fluorogenic properties in the inverse electron demand Diels-Alder reaction. Org Biomol Chem 2016; 12:4177-85. [PMID: 24826902 DOI: 10.1039/c4ob00245h] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
1,2,4,5-Tetrazine fluorophore derivatives with structurally rigid molecular designs were synthesized using Sonogashira and Stille cross-coupling as well as copper-catalyzed azide-alkyne cycloaddition. The synthesized bichromophoric systems exhibit low fluorescence quantum yields due to quenching by the tetrazine. The extent of fluorescence quenching observed for those systems was shown to depend on the distance between the fluorophore and the tetrazine. The decreased fluorescence is "turned on" by conversion of the tetrazine in the inverse electron demand Diels-Alder cycloaddition. Time resolved spectroscopy indicated resonance energy transfer between BODIPY and the tetrazine as the underlying quenching mechanism. The synthesized conjugates were successfully applied in protein labeling experiments.
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Affiliation(s)
- Achim Wieczorek
- Institut für Pharmazie und Molekulare Biotechnologie, Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 364, D-69120 Heidelberg, Germany.
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18
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Meng Q, Fronczek FR, Vicente MGH. Synthesis and spectroscopic properties of β,β'-dibenzo-3,5,8-triaryl-BODIPYs. NEW J CHEM 2016; 40:5740-5751. [PMID: 27708532 PMCID: PMC5047295 DOI: 10.1039/c5nj03324a] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
A series of β,β'-bicyclo-3,5-diaryl-BODIPYs were synthesized from the corresponding β,β'-bicyclo-3,5-diiodo-BODIPYs (1a,b) via Pd(0)-mediated Suzuki cross-coupling reactions in 82-92% yields. Subsequent aromatization with DDQ afforded the corresponding β,β'-dibenzo-aryl-BODIPYs, which showed red-shifted absorptions and emissions in the near-IR range. The dibenzo-appended BODIPYs showed characteristic 1H-, 13C-, 11B- and 19F-NMR shifts, and nearly planar conformations by X-ray crystallography.
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Affiliation(s)
- Qianli Meng
- Department of Chemistry, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Frank R. Fronczek
- Department of Chemistry, Louisiana State University, Baton Rouge, LA 70803, USA
| | - M. Graça H. Vicente
- Department of Chemistry, Louisiana State University, Baton Rouge, LA 70803, USA
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19
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Kumar A, Kumar S, Chatterjee T, Ravikanth M. β-Meso Covalently linked AzaBODIPY-Pd(II) Dipyrrin Conjugate. ChemistrySelect 2016. [DOI: 10.1002/slct.201500037] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Ankit Kumar
- Department of Chemistry; Indian Institute of Technology Bombay, Powai; Mumbai 400076 India
| | - Sunit Kumar
- Department of Chemistry; Indian Institute of Technology Bombay, Powai; Mumbai 400076 India
| | - Tamal Chatterjee
- Department of Chemistry; Indian Institute of Technology Bombay, Powai; Mumbai 400076 India
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20
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Swavey S, Wang M. Bimetallic ruthenium(II) bridged by a dypyrromethene chromophore: DNA binding and light driven reactions within the photodynamic therapy window. INORG CHEM COMMUN 2015. [DOI: 10.1016/j.inoche.2015.10.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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21
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Gu X, Wang H, Roose J, He Z, Zhou Y, Yan Y, Cai Y, Shi H, Zhang Y, Sung HHY, Lam JWY, Miao Q, Zhao Y, Wong KS, Williams ID, Tang BZ. A Luminescent Nitrogen-Containing Polycyclic Aromatic Hydrocarbon Synthesized by Photocyclodehydrogenation with Unprecedented Regioselectivity. Chemistry 2015; 21:17973-80. [PMID: 26490877 DOI: 10.1002/chem.201503147] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Revised: 09/19/2015] [Indexed: 11/10/2022]
Abstract
We present a nitrogen-containing polycyclic aromatic hydrocarbon (N-PAH), namely 12-methoxy-9-(4-methoxyphenyl)-5,8-diphenyl-4-(pyridin-4-yl)pyreno[1,10,9-h,i,j]isoquinoline (c-TPE-ON), which exhibits high quantum-yield emission both in solution (blue) and in the solid state (yellow). This molecule was unexpectedly obtained by a three-fold, highly regioselective photocyclodehydrogenation of a tetraphenylethylene-derived AIEgen. Based on manifold approaches involving UV/Vis, photoluminescence, and NMR spectroscopy as well as HRMS, we propose a reasonable mechanism for the formation of the disk-like N-PAH that is supported by density functional theory calculations. In contrast to most PAHs that are commonly used, our system does not suffer from entire fluorescence quenching in the solid state due to the peripheral aromatic rings preventing π-π stacking interactions, as evidenced by single-crystal X-ray analysis. Moreover, its rod-like microcrystals exhibit excellent optical waveguide properties. Hence, c-TPE-ON comprises a N-PAH with unprecedented luminescent properties and as such is a promising candidate for fabricating organic optoelectronic devices. Our design and synthetic strategy might lead to a more general approach to the preparation of solution- and solid-state luminescent PAHs.
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Affiliation(s)
- Xinggui Gu
- HKUST-Shenzhen Research Institute, No. 9 Yuexing 1st RD, South Area, Hi-tech Park, Nanshan, Shenzhen, 518057 (P.R. China).,Departments of Chemistry, Physics, and Division of Life Science, Institute of Molecular Functional Materials and Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong (P.R. China)
| | - Hong Wang
- HKUST-Shenzhen Research Institute, No. 9 Yuexing 1st RD, South Area, Hi-tech Park, Nanshan, Shenzhen, 518057 (P.R. China).,Departments of Chemistry, Physics, and Division of Life Science, Institute of Molecular Functional Materials and Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong (P.R. China)
| | - Jesse Roose
- HKUST-Shenzhen Research Institute, No. 9 Yuexing 1st RD, South Area, Hi-tech Park, Nanshan, Shenzhen, 518057 (P.R. China).,Departments of Chemistry, Physics, and Division of Life Science, Institute of Molecular Functional Materials and Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong (P.R. China)
| | - Zikai He
- HKUST-Shenzhen Research Institute, No. 9 Yuexing 1st RD, South Area, Hi-tech Park, Nanshan, Shenzhen, 518057 (P.R. China).,Departments of Chemistry, Physics, and Division of Life Science, Institute of Molecular Functional Materials and Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong (P.R. China)
| | - Yue Zhou
- Beijing National Laboratory for Molecular Sciences (BNLMS), Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190 (P.R. China)
| | - Yongli Yan
- Beijing National Laboratory for Molecular Sciences (BNLMS), Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190 (P.R. China)
| | - Yuanjing Cai
- HKUST-Shenzhen Research Institute, No. 9 Yuexing 1st RD, South Area, Hi-tech Park, Nanshan, Shenzhen, 518057 (P.R. China).,Departments of Chemistry, Physics, and Division of Life Science, Institute of Molecular Functional Materials and Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong (P.R. China)
| | - Heping Shi
- Departments of Chemistry, Physics, and Division of Life Science, Institute of Molecular Functional Materials and Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong (P.R. China)
| | - Yilin Zhang
- Departments of Chemistry, Physics, and Division of Life Science, Institute of Molecular Functional Materials and Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong (P.R. China)
| | - Herman H Y Sung
- Departments of Chemistry, Physics, and Division of Life Science, Institute of Molecular Functional Materials and Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong (P.R. China)
| | - Jacky W Y Lam
- HKUST-Shenzhen Research Institute, No. 9 Yuexing 1st RD, South Area, Hi-tech Park, Nanshan, Shenzhen, 518057 (P.R. China).,Departments of Chemistry, Physics, and Division of Life Science, Institute of Molecular Functional Materials and Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong (P.R. China)
| | - Qian Miao
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong (P.R. China)
| | - Yongsheng Zhao
- Beijing National Laboratory for Molecular Sciences (BNLMS), Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190 (P.R. China)
| | - Kam Sing Wong
- Departments of Chemistry, Physics, and Division of Life Science, Institute of Molecular Functional Materials and Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong (P.R. China)
| | - Ian D Williams
- Departments of Chemistry, Physics, and Division of Life Science, Institute of Molecular Functional Materials and Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong (P.R. China)
| | - Ben Zhong Tang
- HKUST-Shenzhen Research Institute, No. 9 Yuexing 1st RD, South Area, Hi-tech Park, Nanshan, Shenzhen, 518057 (P.R. China). .,Departments of Chemistry, Physics, and Division of Life Science, Institute of Molecular Functional Materials and Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong (P.R. China). .,Guangdong Innovative Research Team, SCUT-HKUST Joint Research Laboratory, State Key Laboratory of Luminescent Materials and Devices, South China University of Technology, Guangzhou, 51640 (P.R. China).
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22
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Maar RR, Barbon SM, Sharma N, Groom H, Luyt LG, Gilroy JB. Evaluation of Anisole-Substituted Boron Difluoride Formazanate Complexes for Fluorescence Cell Imaging. Chemistry 2015; 21:15589-99. [DOI: 10.1002/chem.201502821] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Indexed: 11/09/2022]
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23
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Ayer SK, Kimball EA, Olvera A, Djieutedjeu H, Fotie J, Poudeu PFP. (1) H and (13) C NMR assignments for a series of Diels-Alder adducts of anthracene and 9-substituted anthracenes. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2015; 53:551-555. [PMID: 26018118 DOI: 10.1002/mrc.4268] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Revised: 04/28/2015] [Accepted: 05/01/2015] [Indexed: 06/04/2023]
Affiliation(s)
- Suraj K Ayer
- Department of Chemistry and Physics, Southeastern Louisiana University, SLU 10878, Hammond, LA, 70402-0878, USA
| | - Elizabeth A Kimball
- Department of Chemistry and Physics, Southeastern Louisiana University, SLU 10878, Hammond, LA, 70402-0878, USA
| | - Alan Olvera
- Department of Materials Science and Engineering, University of Michigan at Ann Arbor, 2300 Hayward Street, Ann Arbor, MI, 48109-2136, USA
| | - Honore Djieutedjeu
- Department of Materials Science and Engineering, University of Michigan at Ann Arbor, 2300 Hayward Street, Ann Arbor, MI, 48109-2136, USA
| | - Jean Fotie
- Department of Chemistry and Physics, Southeastern Louisiana University, SLU 10878, Hammond, LA, 70402-0878, USA
| | - Pierre F P Poudeu
- Department of Materials Science and Engineering, University of Michigan at Ann Arbor, 2300 Hayward Street, Ann Arbor, MI, 48109-2136, USA
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24
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Betancourt-Mendiola L, Valois-Escamilla I, Arbeloa T, Bañuelos J, López Arbeloa I, Flores-Rizo JO, Hu R, Lager E, Gómez-Durán CFA, Belmonte-Vázquez JL, Martínez-González MR, Arroyo IJ, Osorio-Martínez CA, Alvarado-Martínez E, Urías-Benavides A, Gutiérrez-Ramos BD, Tang BZ, Peña-Cabrera E. Scope and Limitations of the Liebeskind–Srogl Cross-Coupling Reactions Involving the Biellmann BODIPY. J Org Chem 2015; 80:5771-82. [DOI: 10.1021/acs.joc.5b00731] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
| | - Ismael Valois-Escamilla
- Departamento
de Química, Universidad de Guanajuato, Col. Noria Alta S/N, Guanajuato 36050, Mexico
| | - Teresa Arbeloa
- Departamento
de Química Física, Universidad del País Vasco-EHU, Apartado 644, 48080 Bilbao, Spain
| | - Jorge Bañuelos
- Departamento
de Química Física, Universidad del País Vasco-EHU, Apartado 644, 48080 Bilbao, Spain
| | - Iñigo López Arbeloa
- Departamento
de Química Física, Universidad del País Vasco-EHU, Apartado 644, 48080 Bilbao, Spain
| | - Juan O. Flores-Rizo
- Departamento
de Química, Universidad de Guanajuato, Col. Noria Alta S/N, Guanajuato 36050, Mexico
| | - Rongrong Hu
- Department of Chemistry, The Hong Kong University of Science & Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Erik Lager
- Departamento
de Química, Universidad de Guanajuato, Col. Noria Alta S/N, Guanajuato 36050, Mexico
| | - César F. A. Gómez-Durán
- Departamento
de Química, Universidad de Guanajuato, Col. Noria Alta S/N, Guanajuato 36050, Mexico
| | - José L. Belmonte-Vázquez
- Departamento
de Química, Universidad de Guanajuato, Col. Noria Alta S/N, Guanajuato 36050, Mexico
| | | | - Ismael J. Arroyo
- Departamento
de Química, Universidad de Guanajuato, Col. Noria Alta S/N, Guanajuato 36050, Mexico
| | | | | | - Arlette Urías-Benavides
- Departamento
de Química, Universidad de Guanajuato, Col. Noria Alta S/N, Guanajuato 36050, Mexico
| | | | - Ben Zhong Tang
- Department of Chemistry, The Hong Kong University of Science & Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Eduardo Peña-Cabrera
- Departamento
de Química, Universidad de Guanajuato, Col. Noria Alta S/N, Guanajuato 36050, Mexico
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25
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Gaffarogullari EC, Greulich P, Kobitski AY, Nierth A, Nienhaus GU, Jäschke A. Unravelling RNA-substrate interactions in a ribozyme-catalysed reaction using fluorescent turn-on probes. Chemistry 2015; 21:5864-71. [PMID: 25753253 DOI: 10.1002/chem.201406512] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Indexed: 11/07/2022]
Abstract
The Diels-Alder reaction is one of the most important C-C bond-forming reactions in organic chemistry, and much effort has been devoted to controlling its enantio- and diastereoselectivity. The Diels-Alderase ribozyme (DAse) catalyses the reaction between anthracene dienes and maleimide dienophiles with multiple-turnover, stereoselectivity, and up to 1100-fold rate acceleration. Here, a new generation of anthracene-BODIPY-based fluorescent probes was developed to monitor catalysis by the DAse. The brightness of these probes increases up to 93-fold upon reaction with N-pentylmaleimide (NPM), making these useful tools for investigating the stereochemistry of the ribozyme-catalysed reaction. With these probes, we observed that the DAse catalyses the reaction with >91% de and >99% ee. The stereochemistry of the major product was determined unambiguously by rotating-frame nuclear Overhauser NMR spectroscopy (ROESY-NMR) and is in agreement with crystallographic structure information. The pronounced fluorescence change of the probes furthermore allowed a complete kinetic analysis, which revealed an ordered bi uni type reaction mechanism, with the dienophile binding first.
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Affiliation(s)
- Ece Cazibe Gaffarogullari
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, 69120 Heidelberg (Germany), Fax: (+49) 6221-54-6430
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26
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Madhu S, Kumar S, Chatterjee T, Ravikanth M. Synthesis, X-ray structure, spectral and electrochemical properties of a β-meso covalently linked BODIPY–Ru(ii) dipyrrin complex. NEW J CHEM 2014. [DOI: 10.1039/c4nj01114g] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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27
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Marfin YS, Merkushev DA, Levshanov GA, Rumyantsev EV. Fluorescent properties of 8-phenylBODIPY in ethanol - ethylene glycol mixed solutions. J Fluoresc 2014; 24:1613-9. [PMID: 25169768 DOI: 10.1007/s10895-014-1447-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2014] [Accepted: 08/20/2014] [Indexed: 11/28/2022]
Abstract
Fluorescent characteristics of two BODIPY dyes in solutions were investigated under the viscosity variations. Investigated dyes differ in the nature of 8-substituent of ligand molecule. Viscosity variation was achieved by changing of solvent composition in the binary system ethanol - ethylene glycol and solvent temperature. 8-Phenyl substituted BODIPY is found to exhibit properties of molecular rotor, i.e. its fluorescent characteristics are highly dependent on the viscosity or rigidity of the microenvironment. Increased temperature leads to a linear decrease of fluorescence parameters unlike the solvent composition variation where fluorescence change is nonlinear. The highest specific change in the fluorescence was observed in pure ethanol. Change in the nonradiative decay rate constant values with the increasing of viscosity indicates that the analyzed phenyl substituted complex is a true molecular rotor. Investigated 8-phenylBODIPY could be recommended as promising viscosity sensor in different organic media.
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Affiliation(s)
- Y S Marfin
- Department of Inorganic Chemistry, Ivanovo State University of Chemistry and Technology, Ivanovo, 153000, Russia,
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28
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P CAS, Thilagar P. Triarylborane-Appended New Triad and Tetrad: Chromogenic and Fluorogenic Anion Recognition. Inorg Chem 2014; 53:2776-86. [DOI: 10.1021/ic402898n] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Chinna Ayya Swamy P
- Department of Inorganic and
Physical Chemistry, Indian Institute of Science, Bangalore 560012, India
| | - Pakkirisamy Thilagar
- Department of Inorganic and
Physical Chemistry, Indian Institute of Science, Bangalore 560012, India
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29
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Bessette A, Hanan GS. Design, synthesis and photophysical studies of dipyrromethene-based materials: insights into their applications in organic photovoltaic devices. Chem Soc Rev 2014; 43:3342-405. [PMID: 24577078 DOI: 10.1039/c3cs60411j] [Citation(s) in RCA: 351] [Impact Index Per Article: 35.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
This review article presents the most recent developments in the use of materials based on dipyrromethene (DPM) and azadipyrromethenes (ADPM) for organic photovoltaic (OPV) applications. These chromophores and their corresponding BF2-chelated derivatives BODIPY and aza-BODIPY, respectively, are well known for fluorescence-based applications but are relatively new in the field of photovoltaic research. This review examines the variety of relevant designs, synthetic methodologies and photophysical studies related to materials that incorporate these porphyrinoid-related dyes in their architecture. The main idea is to inspire readers to explore new avenues in the design of next generation small-molecule and bulk-heterojunction solar cell (BHJSC) OPV materials based on DPM chromophores. The main concepts are briefly explained, along with the main challenges that are to be resolved in order to take full advantage of solar energy.
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Affiliation(s)
- André Bessette
- Département de Chimie, Université de Montréal, Pavillon J.-A. Bombardier, 5155 Decelles Avenue, Montréal, Québec H3T-2B1, Canada.
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30
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Kamimura A, Nokubi T, Watanabe R, Ishikawa M, Nasu K, Uno H, Sumimoto M. 4,4′-Diarylsulfanyl-2,2′,5,5′-tetraoxybiaryl Derivatives as a Water-Soluble Fluorescent Dye. J Org Chem 2014; 79:1068-83. [DOI: 10.1021/jo402522y] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Akio Kamimura
- Department
of Applied Molecular Bioscience, Graduate School of Medicine, Yamaguchi University, Ube 755-8611, Japan
| | - Tomomi Nokubi
- Department
of Applied Molecular Bioscience, Graduate School of Medicine, Yamaguchi University, Ube 755-8611, Japan
| | - Ryusuke Watanabe
- Department
of Applied Molecular Bioscience, Graduate School of Medicine, Yamaguchi University, Ube 755-8611, Japan
| | - Mari Ishikawa
- Department
of Applied Molecular Bioscience, Graduate School of Medicine, Yamaguchi University, Ube 755-8611, Japan
| | - Kotaro Nasu
- Department
of Applied Molecular Bioscience, Graduate School of Medicine, Yamaguchi University, Ube 755-8611, Japan
| | - Hidemitsu Uno
- Department
of Chemistry, Graduate School of Science and Engineering, Ehime University, Matsuyama 790-8577, Japan
| | - Michinori Sumimoto
- Department
of Applied Chemistry, Graduate School of Science and Engineering, Yamaguchi University, Ube 755-8611, Japan
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31
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Misra R, Dhokale B, Jadhav T, Mobin SM. The quenching of fluorescence as an indicator of donor-strength in meso arylethynyl BODIPYs. Dalton Trans 2014; 43:4854-61. [DOI: 10.1039/c3dt53056f] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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32
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Gotor R, Gaviña P, Ochando LE, Chulvi K, Lorente A, Martínez-Máñez R, Costero AM. BODIPY dyes functionalized with 2-(2-dimethylaminophenyl)ethanol moieties as selective OFF–ON fluorescent chemodosimeters for the nerve agent mimics DCNP and DFP. RSC Adv 2014. [DOI: 10.1039/c4ra00710g] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Hand held sensing kits for detecting nerve agents simulants.
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Affiliation(s)
- Raúl Gotor
- Centro de Reconocimiento Molecular y Desarrollo Tecnológico (IDM)
- Universidad de Valencia
- Valencia, Spain
| | - Pablo Gaviña
- Centro de Reconocimiento Molecular y Desarrollo Tecnológico (IDM)
- Universidad de Valencia
- Valencia, Spain
| | - Luis E. Ochando
- Centro de Reconocimiento Molecular y Desarrollo Tecnológico
- Unidad Mixta Universidad de Valencia – Universidad Politécnica de Valencia
- Departamento de Geología
- Facultad de Ciencias Biológicas
- Universidad de Valencia
| | - Katherine Chulvi
- Centro de Reconocimiento Molecular y Desarrollo Tecnológico (IDM)
- Universidad de Valencia
- Valencia, Spain
| | - Alejandro Lorente
- Centro de Reconocimiento Molecular y Desarrollo Tecnológico (IDM)
- Universidad de Valencia
- Valencia, Spain
| | - Ramón Martínez-Máñez
- Centro de Reconocimiento Molecular y Desarrollo Tecnológico
- Unidad Mixta Universidad Politécnica de Valencia – Universidad de Valencia Departamento de Química
- Universidad Politécnica de Valencia Camino de Vera s/n
- Valencia, Spain
| | - Ana M. Costero
- Centro de Reconocimiento Molecular y Desarrollo Tecnológico (IDM)
- Universidad de Valencia
- Valencia, Spain
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33
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Yao L, Dan F, Liu W, Cao Q, Yang C, Zou K, Xiao S. Solid-state red emission of boron–fluorine complexes with extended π-conjugated structure. J Fluor Chem 2013. [DOI: 10.1016/j.jfluchem.2013.10.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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34
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Gaffarogullari EC, Krause A, Balbo J, Herten DP, Jäschke A. Microscale thermophoresis provides insights into mechanism and thermodynamics of ribozyme catalysis. RNA Biol 2013; 10:1815-21. [PMID: 24448206 DOI: 10.4161/rna.27101] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The analysis of binding interactions between small molecules and biopolymers is important for understanding biological processes. While fluorescence correlation spectroscopy (FCS) requires fluorescence labeling on the small molecule, which often interferes with binding, in microscale thermophoresis (MST) the label can be placed on the biopolymer. Ribozymes have not been analyzed by MST so far. The Diels-Alderase ribozyme (DAse) is a true catalyst, facilitating the Diels-Alder reaction between two free small substrates, anthracene dienes, and maleimide dienophiles. Despite high efforts, the determination of the dissociation constant (KD) of maleimide dienophiles to the DAse by FCS has been unsuccessful. Here, we determined the binding interactions of the DAse to its substrates and the Diels-Alder product using MST. The results supported a positive cooperativity for substrate binding to the DAse. By varying the temperature, we furthermore studied the thermodynamics of dienophile dissociation. The entropic contribution was found to be the energetic driving force for the binding of the dienophile to the DAse.
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Affiliation(s)
- Ece Cazibe Gaffarogullari
- Institute of Pharmacy and Molecular Biotechnology; Heidelberg University; Im Neuenheimer Feld 364; Heidelberg, Germany
| | - André Krause
- Institute of Pharmacy and Molecular Biotechnology; Heidelberg University; Im Neuenheimer Feld 364; Heidelberg, Germany
| | - Jessica Balbo
- Cellnetworks Cluster and Institute for Physical Chemistry; Heidelberg University; Im Neuenheimer Feld 267; Heidelberg, Germany
| | - Dirk-Peter Herten
- Cellnetworks Cluster and Institute for Physical Chemistry; Heidelberg University; Im Neuenheimer Feld 267; Heidelberg, Germany
| | - Andres Jäschke
- Institute of Pharmacy and Molecular Biotechnology; Heidelberg University; Im Neuenheimer Feld 364; Heidelberg, Germany
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35
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Nokubi T, Nasu K, Watanabe R, Kamimura A. A New Water-soluble Fluorescent Dye Based on 2-Sulfanylhydroquinone Dimers. CHEM LETT 2013. [DOI: 10.1246/cl.130348] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Tomomi Nokubi
- Department of Applied Molecular Bioscience, Graduate School of Medicine, Yamaguchi University
| | - Kotaro Nasu
- Department of Applied Molecular Bioscience, Graduate School of Medicine, Yamaguchi University
| | - Ryusuke Watanabe
- Department of Applied Molecular Bioscience, Graduate School of Medicine, Yamaguchi University
| | - Akio Kamimura
- Department of Applied Molecular Bioscience, Graduate School of Medicine, Yamaguchi University
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36
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Kobitski AY, Schäfer S, Nierth A, Singer M, Jäschke A, Nienhaus GU. Single-molecule FRET studies of RNA folding: a Diels-Alderase ribozyme with photolabile nucleotide modifications. J Phys Chem B 2013; 117:12800-6. [PMID: 23621553 DOI: 10.1021/jp402005m] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Enzymology at the single-molecule level by using fluorescence resonance energy transfer (smFRET) offers unprecedented insight into mechanistic aspects of catalytic reactions. Implementing spatiotemporal control of the reaction by using an external trigger is highly valuable in these challenging experiments. Here, we have incorporated a light-cleavable caging moiety into specific nucleotides of the Diels-Alderase (DAse) ribozyme. In this way, the folding energy landscape was significantly perturbed, and the catalytic activity was essentially suppressed. A careful smFRET efficiency histogram analysis at various Mg(2+) ion concentrations revealed an additional intermediate state that is not observed for the unmodified DAse ribozyme. We also observed that only a fraction of DAse molecules returns to the native state upon cleavage of the caged group by UV light. These constructs are attractive model RNA systems for further real-time single-molecule observation of the coupling between conformational changes and catalytic activity.
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Affiliation(s)
- Andrei Yu Kobitski
- Institute of Applied Physics, Institute of Toxicology and Genetics and Center for Functional Nanostructures (CFN), Karlsruhe Institute of Technology (KIT) , Wolfgang-Gaede-Strasse 1, 76131 Karlsruhe, Germany
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37
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Aydin EA, Altenbach HJ. Fluorogenic Diels–Alder reactions of novel phencyclone derivatives. Tetrahedron Lett 2013. [DOI: 10.1016/j.tetlet.2013.01.095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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38
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Nepomnyashchii AB, Pistner AJ, Bard AJ, Rosenthal J. Synthesis, Photophysics, Electrochemistry and Electrogenerated Chemiluminescence of PEG-Modified BODIPY dyes in Organic and Aqueous Solutions. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2013; 117:5599-5609. [PMID: 23626863 PMCID: PMC3633524 DOI: 10.1021/jp312166w] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
A set polyethylene glycol (PEG) appended BODIPY architectures (BOPEG1 - BOPEG3) have been prepared and studied in CH2Cl2, H2O:CH3CN (1:1) and aqueous solutions. BOPEG1 and BOPEG2 both contain a short PEG chain and differ in substitution about the BODIPY framework. BOPEG3 is comprised of a fully substituted BODIPY moiety linked to a PEG polymer that is roughly 13 units in length. The photophysics and electrochemical properties of these compounds have been thoroughly characterized in CH2Cl2 and aqueous CH3CN solutions. The behavior of BOPEG1 - BOPEG3 correlates with established rules of BODIPY stability based on substitution about the BODIPY moiety. ECL for each of these compounds was also monitored. BOPEG1, which is unsubstituted at the 2- and 6-positions dimerized upon electrochemical oxidation while BOPEG2, which contains ethyl groups at the 2- and 6-positions, was much more robust and served as an excellent ECL luminophore. BOPEG3 is highly soluble in water due to the long PEG tether and demonstrated modest ECL activity in aqueous solutions using tri-n-propylamine (TPrA) as a coreactant. As such, BOPEG3 represents the first BODIPY derivative that has been shown to display ECL in water without the need for an organic cosolvent, and marks an important step in the development of BODIPY based ECL probes for various biosensing applications.
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Affiliation(s)
| | - Allen J. Pistner
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716
| | - Allen J. Bard
- Department of Chemistry and Biochemistry, The University of Texas at Austin, Austin, Texas 78712
| | - Joel Rosenthal
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716
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39
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Nepomnyashchii AB, Bard AJ. Electrochemistry and electrogenerated chemiluminescence of BODIPY dyes. Acc Chem Res 2012; 45:1844-53. [PMID: 22515199 DOI: 10.1021/ar200278b] [Citation(s) in RCA: 223] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BODIPY (boron dipyrromethene) dyes are unique materials with spectroscopic and electrochemical properties comparable to those of aromatic hydrocarbons. Electrochemical studies are useful in understanding the redox properties of these materials and finding structure-stability relations for the radical ions; along with spectroscopy, these studies help researchers design novel compounds with desired properties. This Account represents our attempt at a full description of the electrochemical and electrogenerated chemiluminescence (ECL) properties of the BODIPY dyes. When the dyes are completely substituted with alkyl or other groups, the radical ions of BODIPY dyes are highly stable. But if they include unsubstituted positions, the radical ions can undergo dimerization or other reactions. BODIPY dyes also show unusually large separations, ~1.0 V, between the first and second cyclic voltammetric (CV) waves for both oxidation and reduction half-reactions. Alkyl-substituted BODIPY dyes show good photoluminescence (PL) quantum efficiencies, and radical ion electron transfer annihilation in these molecules produces electrogenerated chemiluminescence (ECL), the intensity of which depends on the structure of the dye. The large separation between waves and the presence of strong ECL signals are both important in the design of stable ECL-based materials. The ECL spectra provide a fast method of monitoring the electrochemical formation of dimers and aggregates from the monomers. BODIPY dyes are particularly good systems for studying stepwise electron transfer in their chemically synthesized oligomers and polymers because of the small separation between the first oxidation and first reduction waves, generally about 2.0-2.4 V, and their relative ease of reduction compared with many other aromatic compounds. The larger separation between consecutive waves for oxidation compared with reduction is noticeable for all BODIPY dimers and trimers. We also observe a more difficult addition or extraction of a third electron compared with the second for the trimers, signaling the importance of electrostatic interactions. In general, BODIPY dyes combine interesting electrochemical and spectroscopic properties that suggest useful analytical applications.
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Affiliation(s)
- Alexander B. Nepomnyashchii
- Center for Electrochemistry, Chemistry and Biochemistry Department, The University of Texas at Austin, Austin, Texas, 78712
| | - Allen J. Bard
- Center for Electrochemistry, Chemistry and Biochemistry Department, The University of Texas at Austin, Austin, Texas, 78712
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40
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Wang JN, Jin JL, Geng Y, Sun SL, Xu HL, Lu YH, Su ZM. An accurate and efficient method to predict the electronic excitation energies of BODIPY fluorescent dyes. J Comput Chem 2012; 34:566-75. [DOI: 10.1002/jcc.23168] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2012] [Revised: 09/07/2012] [Accepted: 09/30/2012] [Indexed: 01/17/2023]
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41
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Bessette A, Ferreira JG, Giguère M, Bélanger F, Désilets D, Hanan GS. Azadipyrromethene Dye Derivatives in Coordination Chemistry: the Structure–Property Relationship in Homoleptic Metal(II) Complexes. Inorg Chem 2012; 51:12132-41. [DOI: 10.1021/ic300872m] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- André Bessette
- Département
de Chimie, Université de Montréal, Pavillon J.-A. Bombardier, 5155 Decelles Avenue, Montréal,
Québec H3T-2B1, Canada
- Saint-Jean Photochimie Inc., 725 Trotter Street, Saint-Jean-sur-Richelieu,
Québec J3B 8J8, Canada
| | - Janaina G. Ferreira
- Département
de Chimie, Université de Montréal, Pavillon J.-A. Bombardier, 5155 Decelles Avenue, Montréal,
Québec H3T-2B1, Canada
| | - Martin Giguère
- Saint-Jean Photochimie Inc., 725 Trotter Street, Saint-Jean-sur-Richelieu,
Québec J3B 8J8, Canada
| | - Francis Bélanger
- Saint-Jean Photochimie Inc., 725 Trotter Street, Saint-Jean-sur-Richelieu,
Québec J3B 8J8, Canada
| | - Denis Désilets
- Saint-Jean Photochimie Inc., 725 Trotter Street, Saint-Jean-sur-Richelieu,
Québec J3B 8J8, Canada
| | - Garry S. Hanan
- Département
de Chimie, Université de Montréal, Pavillon J.-A. Bombardier, 5155 Decelles Avenue, Montréal,
Québec H3T-2B1, Canada
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42
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El-Khouly ME, Amin AN, Zandler ME, Fukuzumi S, D'Souza F. Near-IR Excitation Transfer and Electron Transfer in a BF2-Chelated Dipyrromethane-Azadipyrromethane Dyad and Triad. Chemistry 2012; 18:5239-47. [DOI: 10.1002/chem.201103074] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2011] [Revised: 12/08/2011] [Indexed: 11/05/2022]
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43
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Yin Z, Tam AYY, Wong KMC, Tao CH, Li B, Poon CT, Wu L, Yam VWW. Functionalized BODIPY with various sensory units – a versatile colorimetric and luminescent probe for pH and ions. Dalton Trans 2012; 41:11340-50. [DOI: 10.1039/c2dt30446e] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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44
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Suzuki S, Kozaki M, Nozaki K, Okada K. Recent progress in controlling photophysical processes of donor–acceptor arrays involving perylene diimides and boron-dipyrromethenes. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C-PHOTOCHEMISTRY REVIEWS 2011. [DOI: 10.1016/j.jphotochemrev.2011.10.001] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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45
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Wang C, Xie F, Suthiwangcharoen N, Sun J, Wang Q. Tuning the optical properties of BODIPY dye through Cu(I) catalyzed azide-alkyne cycloaddition (CuAAC) reaction. Sci China Chem 2011. [DOI: 10.1007/s11426-011-4452-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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46
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Karslyan EE, Konovalov AI, Borissova AO, Petrovskii PV, Kudinov AR. Photodimerization of the anthracene ruthenium complexes [(C5Me4R)Ru(η6-C14H10)]+ (R=Me, CH2OMe). MENDELEEV COMMUNICATIONS 2011. [DOI: 10.1016/j.mencom.2011.11.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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47
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Ou YP, Jiang C, Wu D, Xia J, Yin J, Jin S, Yu GA, Liu SH. Synthesis, Characterization, and Properties of Anthracene-Bridged Bimetallic Ruthenium Vinyl Complexes [RuCl(CO)(PMe3)3]2(μ-CH═CH-anthracene-CH═CH). Organometallics 2011. [DOI: 10.1021/om200622q] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Ya-Ping Ou
- Key Laboratory of Pesticide and Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, People’s Republic of China
| | - Chuanyin Jiang
- Key Laboratory of Pesticide and Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, People’s Republic of China
| | - Di Wu
- Key Laboratory of Pesticide and Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, People’s Republic of China
| | - Jianlong Xia
- Key Laboratory of Pesticide and Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, People’s Republic of China
| | - Jun Yin
- Key Laboratory of Pesticide and Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, People’s Republic of China
| | - Shan Jin
- Key Laboratory of Pesticide and Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, People’s Republic of China
| | - Guang-Ao Yu
- Key Laboratory of Pesticide and Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, People’s Republic of China
| | - Sheng Hua Liu
- Key Laboratory of Pesticide and Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, People’s Republic of China
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48
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Kraut S, Bebenroth D, Nierth A, Kobitski AY, Nienhaus GU, Jäschke A. Three critical hydrogen bonds determine the catalytic activity of the Diels-Alderase ribozyme. Nucleic Acids Res 2011; 40:1318-30. [PMID: 21976731 PMCID: PMC3273808 DOI: 10.1093/nar/gkr812] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Compared to protein enzymes, our knowledge about how RNA accelerates chemical reactions is rather limited. The crystal structures of a ribozyme that catalyzes Diels-Alder reactions suggest a rich tertiary architecture responsible for catalysis. In this study, we systematically probe the relevance of crystallographically observed ground-state interactions for catalytic function using atomic mutagenesis in combination with various analytical techniques. The largest energetic contribution apparently arises from the precise shape complementarity between transition state and catalytic pocket: A single point mutant that folds correctly into the tertiary structure but lacks one H-bond that normally stabilizes the pocket is completely inactive. In the rate-limiting chemical step, the dienophile is furthermore activated by two weak H-bonds that contribute ∼7-8 kJ/mol to transition state stabilization, as indicated by the 25-fold slower reaction rates of deletion mutants. These H-bonds are also responsible for the tight binding of the Diels-Alder product by the ribozyme that causes product inhibition. For high catalytic activity, the ribozyme requires a fine-tuned balance between rigidity and flexibility that is determined by the combined action of one inter-strand H-bond and one magnesium ion. A sharp 360° turn reminiscent of the T-loop motif observed in tRNA is found to be important for catalytic function.
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Affiliation(s)
- Stefanie Kraut
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, D-69120 Heidelberg, Germany
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49
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Strauss B, Nierth A, Singer M, Jäschke A. Direct structural analysis of modified RNA by fluorescent in-line probing. Nucleic Acids Res 2011; 40:861-70. [PMID: 21917852 PMCID: PMC3258135 DOI: 10.1093/nar/gkr733] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Chemical probing is a common method for the structural characterization of RNA. Typically, RNA is radioactively end-labelled, subjected to probing conditions, and the cleavage fragment pattern is analysed by gel electrophoresis. In recent years, many chemical modifications, like fluorophores, were introduced into RNA, but methods are lacking that detect the influence of the modification on the RNA structure with single-nucleotide resolution. Here, we first demonstrate that a 5′-terminal 32P label can be replaced by a dye label for in-line probing of riboswitch RNAs. Next, we show that small, highly structured FRET-labelled Diels–Alderase ribozymes can be directly probed, using the internal or terminal FRET dyes as reporters. The probing patterns indeed reveal whether or not the attachment of the dyes influences the structure. The existence of two dye labels in typical FRET constructs is found to be beneficial, as ‘duplexing’ allows observation of the complete RNA on a single gel. Structural information can be derived from the probing gels by deconvolution of the superimposed band patterns. Finally, we use fluorescent in-line probing to experimentally validate the structural consequences of photocaging, unambiguously demonstrating the intentional destruction of selected elements of secondary or tertiary structure.
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Affiliation(s)
- Benjamin Strauss
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, D-69120 Heidelberg, Germany
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50
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Mao M, Xiao S, Yi T, Zou K. Synthesis and characterization of novel fluorescent BOPIM dyes with large Stokes shift. J Fluor Chem 2011. [DOI: 10.1016/j.jfluchem.2011.06.018] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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