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Opportunities and challenges in single-molecule and single-particle fluorescence microscopy for mechanistic studies of chemical reactions



In recent years, single-molecule and single-particle fluorescence microscopy has emerged as a tool to investigate chemical systems. After an initial lag of over a decade with respect to biophysical studies, this powerful imaging technique is now revealing mechanisms of 'classical' organic reactions, spatial distribution of chemical reactivity on surfaces and the phase of active catalysts. The recent advance into commercial imaging systems obviates the need for home-built laser systems and thus opens this technique to traditionally trained synthetic chemists. We discuss the requisite photophysical and chemical properties of fluorescent reporters and highlight the main challenges in applying single-molecule techniques to chemical questions. The goal of this Perspective is to provide a snapshot of an emerging multidisciplinary field and to encourage broader use of this young experimental approach that aids the observation of chemical reactions as depicted in many textbooks: molecule by molecule.

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Figure 1: Types of fluorophore used in chemical single-molecule studies.
Figure 2: Examples of single-molecule fluorescence microscopy studies of stochiometric chemical reactions.
Figure 3: Examples of single-molecule fluorescence microscopy studies of catalytic chemical reactions.
Figure 4: Comprehensive list of all fluorophores used to study chemical reactions on the level of single-molecules.
Figure 5: Classes of fluorophores, their photophysical behaviour in solution, and microscopy cells suited to studying chemical reactions.


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T.C. was supported by the Zernike Institute for Advanced Materials and the Centre for Synthetic Biology (University of Groningen). S.A.B. thanks the US Department of Energy, Office of Basic Energy Sciences for support (DE-FG02-08ER15994).

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Correspondence to Thorben Cordes or Suzanne A. Blum.

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The authors declare no competing financial interests.

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Cordes, T., Blum, S. Opportunities and challenges in single-molecule and single-particle fluorescence microscopy for mechanistic studies of chemical reactions. Nature Chem 5, 993–999 (2013).

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