Fluorescent proteins: shine on, you crazy diamond.

In this Perspective we discuss recent trends in the development and applications of fluorescent proteins. We start by providing a historical and structural perspective of their spectroscopic and structural aspects and describe how these properties have made fluorescent proteins essential as 'smart labels' for biosensing and advanced fluorescence imaging. We show that the strong link between the spectroscopic properties and protein structure and properties is a necessary element in these developments and that this dependence makes the proteins excellent model systems for a variety of fields. We pay particular attention to emerging or future research opportunities and unsolved questions.

Three-dimensional visualization of defects formed during the synthesis of metal-organic frameworks: a fluorescence microscopy study.

Imperfections in the spotlight: fluorescence microscopy was used to detect defects in metal-organic frameworks formed during synthesis. In contrast to currently available techniques, confocal fluorescence microscopy offers the advantage of three-dimensional imaging at the single-crystal level combined with the sensitivity required to study the start of defect formation.

Spatially resolved observation of crystal-face-dependent catalysis by single turnover counting.

Catalytic processes on surfaces have long been studied by probing model reactions on single-crystal metal surfaces under high vacuum conditions. Yet the vast majority of industrial heterogeneous catalysis occurs at ambient or elevated pressures using complex materials with crystal faces, edges and defects differing in their catalytic activity. Clearly, if new or improved catalysts are to be rationally designed, we require quantitative correlations between surface features and catalytic activity--ideally obtained under realistic reaction conditions. Transmission electron microscopy and scanning tunnelling microscopy have allowed in situ characterization of catalyst surfaces with atomic resolution, but are limited by the need for low-pressure conditions and conductive surfaces, respectively. Sum frequency generation spectroscopy can identify vibrations of adsorbed reactants and products in both gaseous and condensed phases, but so far lacks sensitivity down to the single molecule level. Here we adapt real-time monitoring of the chemical transformation of individual organic molecules by fluorescence microscopy to monitor reactions catalysed by crystals of a layered double hydroxide immersed in reagent solution. By using a wide field microscope, we are able to map the spatial distribution of catalytic activity over the entire crystal by counting single turnover events. We find that ester hydrolysis proceeds on the lateral {1010} crystal faces, while transesterification occurs on the entire outer crystal surface. Because the method operates at ambient temperature and pressure and in a condensed phase, it can be applied to the growing number of liquid-phase industrial organic transformations to localize catalytic activity on and in inorganic solids. An exciting opportunity is the use of probe molecules with different size and functionality, which should provide insight into shape-selective or structure-sensitive catalysis and thus help with the rational design of new or more productive heterogeneous catalysts.

Energy transfer pathways in a rylene-based Triad.

Herein, a study on the excitation energy migration is reported for a newly synthesized Triad with a well-defined architecture consisting of a central terrylenediimide decorated with four perylenediimide and sixteen naphthalenemonoimide chromophores. Steady-state femto- and picosecond time-resolved spectroscopy were employed to unveil the excited states dynamics in solution. Compared with the results obtained from the corresponding model compounds, the Triad is an efficient light collector over the entire visible spectral range and the fluorescence occurs mostly from the core with a quantum yield as high as 60%. The results suggest that selective excitation of the naphthalenemonoimide chromophores results in an efficient energy transfer that occurs in a cascade fashion (through the perylenediimide chromophores) towards the terrylenediimide core with time constants of <200 fs and 3.7 ps. Naphthalenemonoimide chromophores can also transfer their excitation energy to the terrylenediimide core directly via two parallel pathways with time constants of 1.5 and 8.4 ps, respectively. Additionally, single-molecule confocal microscopy experiments revealed strong emission from the terrylenediimide unit upon excitation of the naphthalenemonoimide chromophores. As time evolved, stepwise photobleaching of the multichromophoric Triad single molecules embedded in a PMMA polymer film was observed, resulting in a 96 percent probability of observing perylenediimide emission before final photobleaching under ambient conditions, substantiating the cascade energy transfer pathway. Under nitrogen atmosphere however, no perylenediimide emission could be observed for single Triad molecules embedded in a PMMA polymer film, likely as a result of the prolonged photostability of the terrylenediimide core in absence of oxygen.

Characterization of fluorescence in heat-treated silver-exchanged zeolites.

Thermal treatment of Ag(+)-exchanged zeolites yields discrete highly photostable luminescent clusters without formation of metallic nanoparticles. Different types of emitters with characteristic luminescence colors are observed, depending on the nature of the cocation, the amount of exchanged silver, and the host topology. The dominant emission bands in LTA samples are situated around 550 and 690 nm for the samples with, respectively, low and high silver content, while in FAU-type materials only a broad band around 550 nm is observed, regardless of the degree of exchange. Analysis of the fluorescent properties in combination with ESR spectroscopy suggests that a Ag(6)(+) cluster with doublet electronic ground state is associated with the appearance of the 690-nm emitter, having a decay of a few hundred microseconds. Tentatively, the nanosecond-decaying 550-nm emitter is assigned to the Ag(3)(+) cluster. This new class of photostable luminescent particles with tunable emission colors offers interesting perspectives for various applications such as biocompatible labels for intracellular imaging.

Linking phospholipase mobility to activity by single-molecule wide-field microscopy.

Many of the biological processes taking place in cells are mediated by enzymatic reactions occurring in the cell membrane. Understanding interfacial enzymatic catalysis is therefore crucial to the understanding of cellular function. Unfortunately, a full picture of the overall mechanism of interfacial enzymatic catalysis, and particularly the important diffusion processes therein, remains unresolved. Herein we demonstrate that single-molecule wide-field fluorescence microscopy can yield important new information on these processes. We image phospholipase enzymes acting upon bilayers of their natural phospholipid substrate, tracking the diffusion of thousands of individual enzymes while simultaneously visualising local structural changes to the substrate layer. We study several enzyme types with different affinities and catalytic activities towards the substrate. Analysis of the trajectories of each enzyme type allows us successfully to correlate the mobility of phospholipase with its catalytic activity at the substrate. The methods introduced herein represent a promising new approach to the study of interfacial/heterogeneous catalysis systems.

Molecular clusters in two-dimensional surface-confined nanoporous molecular networks: structure, rigidity, and dynamics.

The self-assembly of a series of hexadehydrotribenzo[12]annulene (DBA) derivatives has been investigated by scanning tunneling microscopy (STM) at the liquid/solid interface in the absence and presence of nanographene guests. In the absence of appropriate guest molecules, DBA derivatives with short alkoxy chains form two-dimensional (2D) porous honeycomb type patterns, whereas those with long alkoxy chains form predominantly dense-packed linear type patterns. Added nanographene molecules adsorb in the pores of the existing 2D porous honeycomb type patterns or, more interestingly, they even convert the guest-free dense-packed linear-type patterns into guest-containing 2D porous honeycomb type patterns. For the DBA derivative with the longest alkoxy chains (OC20H41), the pore size, which depends on the length of the alkoxy chains, reaches 5.4 nm. Up to a maximum of six nanographene molecules can be hosted in the same cavity for the DBA derivative with the OC20H41 chains. The host matrix changes its structure in order to accommodate the adsorption of the guest clusters. This flexibility arises from the weak intermolecular interactions between interdigitating alkoxy chains holding the honeycomb structure together. Diverse dynamic processes have been observed at the level of the host matrix and the coadsorbed guest molecules.

Site-selective guest inclusion in molecular networks of butadiyne-bridged pyridino and benzeno square macrocycles on a surface.

We present here the formation of a modular 2D molecular network composed of two different types of square-shaped butadiyne-bridged macrocycles, having intrinsic molecular voids, aligned alternately at the solid-liquid interface. Site-selective inclusion of a guest cation took place at every other molecular void in the molecular network with two different recognition sites.

Guiding the self-assembly of a second-generation polyphenylene dendrimer into well-defined patterns.

A second-generation polyphenylene dendrimer 1 is shown to self-assemble into nanofibers. To guide the formation of the dendrimer fibers into well-defined patterns, 1H,1H,2H,2H-perfluorodecyltrichlorosilane is grafted in the gas phase onto a silicon substrate. De-wetting of the solution on the nanopatterned surface results in the formation of a nanostructured template, into which fiber growth subsequently occurs under the constraints set by the de-wetted morphology.

Giant molecular spoked wheels in giant voids: two-dimensional molecular self-assembly goes big.

We present here the formation of giant pores in surface-confined molecular networks of a triangular-shaped dehydrobenzo-[12]annulene derivative: the diameter of the pores reaches over 7 nm and the giant pores are used as templates to accommodate a giant molecular spoked wheel, which allows us to observe rotational and adsorption-desorption dynamics of single guest molecules.

Origin of simultaneous donor-acceptor emission in single molecules of peryleneimide-terrylenediimide labeled polyphenylene dendrimers.

Förster type resonance energy transfer (FRET) in donor-acceptor peryleneimide-terrylenediimide dendrimers has been examined at the single molecule level. Very efficient energy transfer between the donor and the acceptor prevent the detection of donor emission before photobleaching of the acceptor. Indeed, in solution, on exciting the donor, only acceptor emission is detected. However, at the single molecule level, an important fraction of the investigated individual molecules (about 10-15%) show simultaneous emission from both donor and acceptor chromophores. The effect becomes apparent mostly after photobleaching of the majority of donors. Single molecule photon flux correlation measurements in combination with computer simulations and a variety of excitation conditions were used to determine the contribution of an exciton blockade to this two-color emission. Two-color defocused wide-field imaging showed that the two-color emission goes hand in hand with an unfavorable orientation between one of the donors and the acceptor chromophore.

Molecule-molecule versus molecule-substrate interactions in the assembly of oligothiophenes at surfaces.

In this paper we present a joint experimental and theoretical approach for the study of the assembly of end-substituted oligothiophenes at surfaces with different polarities (i.e., mica vs graphite). Scanning probe microscopy studies of (sub)monolayer deposits show various types of structures (one-dimensional fibrils, two-dimensional regular layers, and monolayers), depending on the nature of the end groups and the substrate. Using molecular modeling with an atomistic approach, we focus on the interplay between the molecule-molecule (and segment-segment) interactions and the molecule-substrate interactions and their influence on the observed morphologies and the stacking geometry. Such information is relevant for controlling the structural order in thin layers of thiophene oligomers for use in field-effect transistor applications, for example, by modifying the nature of dielectric material over which those compounds are deposited.

Do enzymes sleep and work?

Single-enzyme studies suggest that dynamic disorder is a general characteristic of enzyme catalysis.

2D self-assembly of oligo(p-phenylene vinylene) derivatives: from dimers to chiral rosettes.

Enantiomerically pure oligo(p-phenylene vinylene) diaminotriazine derivatives and a short structurally related achiral diaminotriazine derivative, all having a rigid backbone in common, are studied to self-assemble at the solution-graphite interface by scanning tunneling microscopy. As a function of the length of the backbone, different two-dimensional motifs are formed (dimers and rosettes) that are rationalized in terms of the balance between different intermolecular interactions, in this case, intermolecular hydrogen bonding and the packing requirements of the alkyl chains on a graphite surface. In addition, the effect of molecular chirality on monolayer chirality is investigated, revealing molecular size-dependent expressions of the monolayer chirality.

Self-assembly at the liquid/solid interface: STM reveals.

The liquid/solid interface provides an ideal environment to investigate self-assembly phenomena, and scanning tunneling microscopy (STM) is the preferred methodology to probe the structure and the properties of physisorbed monolayers on the nanoscale. Physisorbed monolayers are of relevance in areas such as lubrication, patterning of surfaces on the nanoscale, and thin film based organic electronic devices, to name a few. It's important to gain insight in the factors which control the ordering of molecules at the liquid/solid interface in view of the targeted properties. STM provides detailed insight into the importance of molecule-substrate (epitaxy) and molecule-molecule interactions (hydrogen bonding, metal complexation, and fluorophobic/fluorophilic interactions) to direct the ordering of both achiral and chiral molecules on the atomically flat surface. By controlling the location and orientation of functional groups, chemical reactions can be induced at the liquid/solid interface, via external stimuli, such as light, or by controlled manipulation with the STM tip. The electronic properties of the self-assembled physisorbed molecules can be probed by taking advantage of the operation principle of STM, revealing spatially resolved intramolecular differences within these physisorbed molecules.

Charge transfer enhanced annihilation leading to deterministic single photon emission in rigid perylene end-capped polyphenylenes.

Two new peryleneimide end-capped polyphenylenes are shown to be deterministic single photon sources in PMMA films due to efficient annihilation between charge transfer states.

Emission from Zeolite-Occluded Manganese-Diimine Complexes.

Manganese complexes of 2,2'-bipyridine (bpy) and 1,10-phenantroline (phen) have been synthesised in the supercages of cubic NaX and NaY and in the hypercages of the hexagonal NaEMT faujasites. The coordination and redox chemistry were studied with ESCA, CA, FT-IR, FT-Raman, diffuse reflectance and emission techniques. FT-IR/FT-Raman shows cis coordination for all complexes and a high Mn-N stretching frequency in the phen complexes as a result of steric constraints imposed by the ligand. [Mn(bpy)2 ]2+ in the different zeolites shows metal-to-ligand charge transfer (MLCT; at 495 nm); for [Mn(phen)2 ]2+ -NaY the MLCt is broadened owing to complex distortion. On MLCT excitation [Mn(bpy)2 ]2+ complexes show an ipsochromic shift in the emission and an increase in quantum yield with increasing steric restrictions imposed by the zeolite. The ipsochromic shift of the emission band of [Mn(phen)2 ]2+ in NaY results from the combined effect of the ligand field (this suggests emission from a CT state) and of coordinative distortion. The key factor influencing the emission properties is found to be the overall matrix-induced complex distortion. Cation stabilisation of the ligand anion affects emission indirectly. The decay times for [Mn-(bpy)2 ]2+ -NaY are in the millisecond range (7.5-11.5 ms). A proposed model for excitation and emission properties of zeolite-occluded MnII complexes involves excitation of a quartet CT state, intersystem crossing and subsequent emission. The enhanced stability of the coordination sphere in the zeolite allows complexes to luminesce from a CT state, which is not detected in solution. The zeolite behaves as a supramolecular cryptating agent, protecting complexes from photodissociation.

Submolecular visualisation of palladium acetate complexation with a bipyridine derivative at a graphite surface.

In situ complexation of palladium acetate by a monolayer of a bipyridine derivative at a graphite/liquid interface has been observed using scanning tunneling microscopy.

Synthesis, separation, and isomer-dependent packing in two dimensions--detected by scanning tunnelling microscopy--of a TTF derivative.

The synthesis, isolation and STM imaging on graphite of the cis and trans isomers of a TTF reveal isomer-dependent packing, and constitutes a way to study the non-covalent interactions at play in these systems.