Exploring chemistry with single-molecule and -particle fluorescence microscopy

Technologies for investigating single-molecule chemical reactions

Single molecules, the smallest independently stable units in the material world, serve as the fundamental building blocks of matter. Among different branches of single-molecule sciences, single-molecule chemical reactions, by revealing the behavior and properties of individual molecules at the molecular scale, are particularly attractive because they can advance the understanding of chemical reaction mechanisms and help to address key scientific problems in broad fields such as physics, chemistry, biology and materials science. This review provides a timely, comprehensive overview of single-molecule chemical reactions based on various technical platforms such as scanning probe microscopy, single-molecule junction, single-molecule nanostructure, single-molecule fluorescence detection and crossed molecular beam. We present multidimensional analyses of single-molecule chemical reactions, offering new perspectives for research in different areas, such as photocatalysis/electrocatalysis, organic reactions, surface reactions and biological reactions. Finally, we discuss the opportunities and challenges in this thriving field of single-molecule chemical reactions.

Metal Activation Produces Different Reaction Environments for Intermediates during Oxidative Addition

Commercial zinc metal powder requires activation for consistent and reliable use as a reductant in the formation of organozinc reagents from organohalides, and for the avoidance of supplier and batch-to-batch variability. However, the impact of activation methods on the reaction environments of subsequent intermediates has been unknown. Herein, a fluorescence lifetime imaging microscopy (FLIM) method is developed to bridge this knowledge gap, by imaging and examining reaction intermediates on zinc metal that has been activated by pretreatment through different common methods (i. e., by chemical activation with TMSCl, dibromoethane, or HCl; or by mechanical activation). The group of chemical activating agents, previously thought to act similarly by removing oxide layers, are here shown to produce markedly different reaction environments experienced by subsequent oxidative-addition intermediates from organohalides - data uniquely available through FLIM's ability to detect small quantities of intermediates in situ coupled with its microenvironmental sensitivity. These different microenvironments potentially give rise to different rates of formation, subsequent solubilization, and reactivity, despite the shared "[RZnX]" molecular structure of these intermediates. This information revises models for methods development for oxidative addition to currently sluggish metals beyond zinc by establishing diverse outcomes for pretreatment activation methods that were previously considered similar.

Optical sequencing of single synthetic polymers

Microscopic sequences of synthetic polymers play crucial roles in the polymer properties, but are generally unknown and inaccessible to traditional measurements. Here we report real-time optical sequencing of single synthetic copolymer chains under living polymerization conditions. We achieve this by carrying out multi-colour imaging of polymer growth by single catalysts at single-monomer resolution using CREATS (coupled reaction approach toward super-resolution imaging). CREATS makes a reaction effectively fluorogenic, enabling single-molecule localization microscopy of chemical reactions at higher reactant concentrations. Our data demonstrate that the chain propagation kinetics of surface-grafted polymerization contains temporal fluctuations with a defined memory time (which can be attributed to neighbouring monomer interactions) and chain-length dependence (due to surface electrostatic effects). Furthermore, the microscopic sequences of individual copolymers reveal their tendency to form block copolymers, and, more importantly, quantify the size distribution of individual blocks for comparison with theoretically random copolymers. Such sequencing capability paves the way for single-chain-level structure-function correlation studies of synthetic polymers.

Getting the Most Out of Fluorogenic Probes: Challenges and Opportunities in Using Single-Molecule Fluorescence to Image Electro- and Photocatalysis

Single-molecule fluorescence microscopy enables the direct observation of individual reaction events at the surface of a catalyst. It has become a powerful tool to image in real time both intra- and interparticle heterogeneity among different nanoscale catalyst particles. Single-molecule fluorescence microscopy of heterogeneous catalysts relies on the detection of chemically activated fluorogenic probes that are converted from a nonfluorescent state into a highly fluorescent state through a reaction mediated at the catalyst surface. This review article describes challenges and opportunities in using such fluorogenic probes as proxies to develop structure-activity relationships in nanoscale electrocatalysts and photocatalysts. We compare single-molecule fluorescence microscopy to other microscopies for imaging catalysis in situ to highlight the distinct advantages and limitations of this technique. We describe correlative imaging between super-resolution activity maps obtained from multiple fluorogenic probes to understand the chemical origins behind spatial variations in activity that are frequently observed for nanoscale catalysts. Fluorogenic probes, originally developed for biological imaging, are introduced that can detect products such as carbon monoxide, nitrite, and ammonia, which are generated by electro- and photocatalysts for fuel production and environmental remediation. We conclude by describing how single-molecule imaging can provide mechanistic insights for a broader scope of catalytic systems, such as single-atom catalysts.

The nitro to amine reduction: from millions of tons to single molecule studies

Palladium nanostructures are interesting heterogeneous catalysts because of their high catalytic activity in a vast range of highly relevant reactions such as cross couplings, dehalogenations, and nitro-to-amine reductions. In the latter case, the catalyst Pd@GW (palladium on glass wool) shows exceptional performance and durability in reducing nitrobenzene to aniline under ambient conditions in aqueous solutions. To enhance our understanding, we use a combination of optical and electron microscopy, in-flow single molecule fluorescence, and bench chemistry combined with a fluorogenic system to develop an intimate understanding of Pd@GW in nitro-to-amine reductions. We fully characterize our catalyst in situ using advanced microscopy techniques, providing deep insights into its catalytic performance. We also explore Pd cluster migration on the surface of the support under flow conditions, providing insights into the mechanism of catalysis. We show that even under flow, Pd migration from anchoring sites seems to be minimal over 4 h, with the catalyst stability assisted by APTES anchoring.

Surfactant Micellar and Vesicle Microenvironments and Structures under Synthetic Organic Conditions

Fluorescence lifetime imaging microscopy (FLIM) reveals vesicle sizes, structures, microenvironments, reagent partitioning, and system evolution with two chemical reactions for widely used surfactant-water systems under conditions relevant to organic synthesis, including during steps of Negishi cross-coupling reactions. In contrast to previous investigations, the present experiments characterize surfactant systems with representative organohalide substrates at high concentrations (0.5 M) that are reflective of the preparative-scale organic reactions performed and reported in water. In the presence of representative organic substrates, 2-iodoethylbenzene and 2-bromo-6-methoxypyridine, micelles swell into emulsion droplets that are up to 20 μm in diameter, which is 3-4 orders of magnitude larger than previously measured in the absence of an organic substrate (5-200 nm). The partitioning of reagents in these systems is imaged through FLIM─demonstrated here with nonpolar, amphiphilic, organic, basic, and oxidative-addition reactive compounds, a reactive zinc metal powder, and a palladium catalyst. FLIM characterizes the chemical species and/or provides microenvironment information inside micelles and vesicles. These data show that surfactants cause surfactant-dictated microenvironments inside smaller micelles (<200 nm) but that addition of a representative organic substrate produces internal microenvironments dictated primarily by the substrate rather than by the surfactant, concurrent with swelling. Addition of a palladium catalyst causes the internal environments to differ between vesicles─information that is not available through nor predicted from prior analytical techniques. Together, these data provide immediately actionable information for revising reaction models of surfactant-water systems that underpin the development of sustainable organic chemistry in water.

Native diffusion of fluorogenic turn-on dyes accurately report interfacial chemical reaction locations

Single-molecule fluorescence microscopy with "turn-on" dyes that change fluorescent state after a reaction report on the chemistry of interfaces relevant to analytical and bioanalytical chemistry. Paramount to accurately understanding the phenomena at the ultimate detection limit of a single molecule is ensuring fluorophore properties such as diffusion do not obscure the chemical reaction of interest. Here, we develop Monte Carlo simulations of a dye that undergoes reduction to turn-on at the cathode of a corroded iron surface taking into account the diffusion of the dye molecules in a total internal reflection fluorescence (TIRF) excitation volume, location of the cathode, and chemical reactions. We find, somewhat counterintuitively, that a fast diffusion coefficient of D = 10⁸ nm²/s, corresponding to the dye in aqueous solution, accurately reports the location of single reaction sites. The dyes turn on and are present for the acquisition of a single frame allowing for localization before diffusing out of the thin TIRF excitation volume axially. Previously turned-on (i.e., activated) dyes can also randomly hit the surface surrounding the reaction site leading to a uniform increase in the background. Using concentrations that lead to high turnover rates at the reaction site can achieve signal-to-background ratios of  ~100 in our simulation. Therefore, the interplay between diffusion, turn-on reaction rate, and concentration of the dye must be strategically considered to produce accurate images of reaction locations. This work demonstrates that modeling can assist in the design of single-molecule microscopy experiments to understand interfaces related to analytical chemistry such as electrode, nanoparticle, and sensor surfaces.

Real-Time Polymer Viscosity-Catalytic Activity Relationships on the Microscale

Polymer growth induces physical changes to catalyst microenvironments. Here, these physical changes are quantified in real time and are found to influence microscale chemical catalysis and the polymerization rate. By developing a method to "peer into" optically transparent living-polymer particles, simultaneous imaging of both viscosity changes and chemical activity was achieved for the first time with high spatiotemporal resolution through a combination of fluorescence intensity microscopy and fluorescence lifetime imaging microscopy techniques. Specifically, an increase in microenvironment viscosity led to a corresponding local decrease in the catalytic molecular ruthenium ring-opening metathesis polymerization rate, plausibly by restricting diffusional access to active catalytic centers. Consistent with this diffusional-access model, these viscosity changes were found to be monomer-dependent, showing larger changes in microenvironment viscosity in cross-linked polydicyclopentadiene compared to non-crosslinked polynorbornene. The sensitivity and high spatial resolution of the imaging technique revealed significant variations in microviscosities between different particles and subparticle regions. These revealed spatial heterogeneities would not be observable through alternative ensemble analytical techniques that provide sample-averaged measurements. The observed spatial heterogeneities provide a physical mechanism for variation in catalytic chemical activity on the microscale that may accumulate and lead to nonhomogeneous polymer properties on the bulk scale.

Reactivity Differences of Rieke Zinc Arise Primarily from Salts in the Supernatant, Not in the Solids

Contrary to prevailing thought, the salt content of supernatants is found to dictate reactivity differences of different preparation methods of Rieke zinc toward oxidative addition of organohalides. This conclusion is established through combined single-particle microscopy and ensemble spectroscopy experiments, coupled with careful removal or keeping of the supernatants during Rieke zinc preparations. Fluorescence microscopy experiments with single-Rieke-zinc-particle resolution determined the microscale surface reactivity of the Rieke zinc in the absence of supernatants, thus pinpointing its inherent reactivity independent of the convoluting supernatant composition. In parallel experiments, scanning electron microscopy, energy-dispersive spectroscopy, X-ray photoelectron spectroscopy, and inductively coupled plasma-mass spectrometry characterized the zinc metal chemical composition at the bulk and single-particle levels. Proton nuclear magnetic resonance spectroscopy kinetics characterized bench-scale Rieke zinc reactivity in the presence and absence of different supernatants and exogenous salt additives. Together, these experiments show that the differences in reactivity from sodium-reduced vs lithium-reduced Rieke zinc arise from the residual salts in the supernatant rather than the differing salt compositions of the solids. This supernatant salt also determines the structure of the ultimate organozinc product, generating either the diorganozinc or monoorganozinc halide complex. That different organozinc complexes formed upon direct insertion to different preparations of Rieke zinc was not previously reported, despite Rieke zinc's widespread use. These findings impact organozinc-reagent and nanomaterial synthesis by showing that, unexpectedly, desired Rieke zinc reactivity can be achieved through simple addition of soluble salts to solutions that were used to prepare the metals─a substantially easier synthetic manipulation than solid composition and morphology control.

In Situ Imaging of Catalytic Reactions on Tungsten Oxide Nanowires Connects Surface-Ligand Redox Chemistry with Photocatalytic Activity

Semiconductor nanocrystals are promising candidates for generating chemical feedstocks through photocatalysis. Understanding the role of ligands used to prepare colloidal nanocrystals in catalysis is challenging due to the complexity and heterogeneity of nanocrystal surfaces. We use in situ single-molecule fluorescence imaging to map the spatial distribution of active regions along individual tungsten oxide nanowires before and after functionalizing them with ascorbic acid. Rather than blocking active sites, we observed a significant enhancement in activity for photocatalytic water oxidation after treatment with ascorbic acid. While the initial nanowires contain inactive regions dispersed along their length, the functionalized nanowires show high uniformity in their photocatalytic activity. Spatial colocalization of the active regions with their surface chemical properties shows that oxidation of ascorbic acid during photocatalysis generates new oxygen vacancies along the nanowire surface. We demonstrate that controlling surface-ligand redox chemistry during photocatalysis can enhance the active site concentration on nanocrystal catalysts.