Picosecond time-resolved photon antibunching measures nanoscale exciton motion and the true number of chromophores

Bayesian Inference of Binding Kinetics from Fluorescence Time Series

The study of binding kinetics via the analysis of fluorescence time traces is often confounded by measurement noise and photophysics. Although photoblinking can be mitigated by using labels less likely to photoswitch, photobleaching generally cannot be eliminated. Current methods for measuring binding and unbinding rates are, therefore, limited by concurrent photobleaching events. Here, we propose a method to infer binding and unbinding rates alongside photobleaching rates using fluorescence intensity traces. Our approach is a two-stage process involving analyzing individual regions of interest (ROIs) with a hidden Markov model to infer the fluorescence intensity levels of each trace. We then use the inferred intensity level state trajectory from all of the ROIs to infer kinetic rates. Our method has several advantages, including the ability to analyze noisy traces, account for the presence of photobleaching events, and provide uncertainties associated with the inferred binding kinetics. We demonstrate the effectiveness and reliability of our method through simulations and data from DNA origami binding experiments.

The Quantum Information Science Challenge for Chemistry

We discuss the goals and the need for quantum information science (QIS) in chemistry. It is important to identify concretely how QIS matters to chemistry, and we articulate some of the most pressing and interesting research questions at the interface between chemistry and QIS, that is, "chemistry-centric" research questions relevant to QIS. We propose in what ways and in what new directions the field should innovate, in particular where a chemical perspective is essential. Examples of recent research in chemistry that inspire scrutiny from a QIS perspective are provided, and we conclude with a wish list of open research problems.

Giant Purcell Broadening and Lamb Shift for DNA-Assembled Near-Infrared Quantum Emitters

Controlling the light emitted by individual molecules is instrumental to a number of advanced nanotechnologies ranging from super-resolution bioimaging and molecular sensing to quantum nanophotonics. Molecular emission can be tailored by modifying the local photonic environment, for example, by precisely placing a single molecule inside a plasmonic nanocavity with the help of DNA origami. Here, using this scalable approach, we show that commercial fluorophores may experience giant Purcell factors and Lamb shifts, reaching values on par with those recently reported in scanning tip experiments. Engineering of plasmonic modes enables cavity-mediated fluorescence far detuned from the zero-phonon-line (ZPL)─at detunings that are up to 2 orders of magnitude larger than the fluorescence line width of the bare emitter and reach into the near-infrared. Our results point toward a regime where the emission line width can become dominated by the excited-state lifetime, as required for indistinguishable photon emission, bearing relevance to the development of nanoscale, ultrafast quantum light sources and to the quest toward single-molecule cavity QED. In the future, this approach may also allow the design of efficient quantum emitters at infrared wavelengths, where standard organic sources have a reduced performance.

Exciton annihilation and diffusion length in disordered multichromophoric nanoparticles

Efficient exciton transport is the essential property of natural and synthetic light-harvesting (LH) devices. Here we investigate exciton transport properties in LH organic polymer nanoparticles (ONPs) of 40 nm diameter. The ONPs are loaded with a rhodamine B dye derivative and bulky counterion, enabling dye loadings as high as 0.3 M, while preserving fluorescence quantum yields larger than 30%. We use time-resolved fluorescence spectroscopy to monitor exciton-exciton annihilation (EEA) kinetics within the ONPs dispersed in water. We demonstrate that unlike the common practice for photoluminescence investigations of EEA, the non-uniform intensity profile of the excitation light pulse must be taken into account to analyse reliably intensity-dependent population dynamics. Alternatively, a simple confocal detection scheme is demonstrated, which enables (i) retrieving the correct value for the bimolecular EEA rate which would otherwise be underestimated by a typical factor of three, and (ii) revealing minor EEA by-products otherwise unnoticed. Considering the ONPs as homogeneous rigid solutions of weakly interacting dyes, we postulate an incoherent exciton hoping mechanism to infer a diffusion constant exceeding 0.003 cm2 s-1 and a diffusion length as large as 70 nm. This work demonstrates the success of the present ONP design strategy at engineering efficient exciton transport in disordered multichromophoric systems.

Exciton annihilation in molecular aggregates suppressed through qu antum interference

Exciton-exciton annihilation (EEA), an important loss channel in optoelectronic devices and photosynthetic complexes, has conventionally been assumed to be an incoherent, diffusion-limited process. Here we challenge this assumption by experimentally demonstrating the ability to control EEA in molecular aggregates using the quantum phase relationships of excitons. We employed time-resolved photoluminescence microscopy to independently determine exciton diffusion constants and annihilation rates in two substituted perylene diimide aggregates featuring contrasting excitonic phase envelopes. Low-temperature EEA rates were found to differ by more than two orders of magnitude for the two compounds, despite comparable diffusion constants. Simulated rates based on a microscopic theory, in excellent agreement with experiments, rationalize this EEA behaviour based on quantum interference arising from the presence or absence of spatial phase oscillations of delocalized excitons. These results offer an approach for designing molecular materials using quantum interference where low annihilation can coexist with high exciton concentrations and mobilities.

Detection of Single Charge Trapping Defects in Semiconductor Particles by Evaluating Photon Antibunching in Delayed Photoluminescence

Time-resolved analysis of photon cross-correlation function g⁽²⁾(τ) is applied to photoluminescence (PL) of individual submicrometer size MAPbI₃ perovskite crystals. Surprisingly, an antibunching effect in the long-living tail of PL is observed, while the prompt PL obeys the photon statistics typical for a classical emitter. We propose that antibunched photons from the PL decay tail originate from radiative recombination of detrapped charge carriers which were initially captured by a very limited number (down to one) of shallow defect states. The concentration of these trapping sites is estimated to be in the range 10¹³-10¹⁶ cm^-3. In principle, photon correlations can be also caused by highly nonlinear Auger recombination processes; however, in our case it requires unrealistically large Auger recombination coefficients. The potential of the time-resolved g⁽²⁾(0) for unambiguous identification of charge rerecombination processes in semiconductors considering the actual number of charge carries and defects states per particle is demonstrated.

The Pursuit of Shortwave Infrared-Emitting Nanoparticles with Bright Fluorescence through Molecular Design and Excited-State Engineering of Molecular Aggregates

Shortwave infrared (SWIR) fluorescence detection gradually becomes a pivotal real-time imaging modality, allowing one to elucidate biological complexity in deep tissues with subcellular resolution. The key challenge for the further growth of this imaging modality is the design of new brighter biocompatible fluorescent probes. This review summarizes the recent progress in the development of organic-based nanomaterials with an emphasis on new strategies that extend the fluorescence wavelength from the near-infrared to the SWIR spectral range and amplify the fluorescence brightness. We first introduce the most representative molecular design strategies to obtain near-infrared-SWIR wavelength fluorescence emission from small organic molecules. We then discuss how the formation of nanoparticles based on small organic molecules contributes to the improvement of fluorescence brightness and the shift of fluorescence to SWIR, with a special emphasis on the excited-state engineering of molecular probes in an aggregate state and spatial packing of the molecules in nanoparticles. We build our discussion based on a historical perspective on the photophysics of molecular aggregates. We extend this discussion to nanoparticles made of conjugated polymers and discuss how fluorescence characteristics could be improved by molecular design and chain conformation of the polymer molecules in nanoparticles. We conclude the article with future directions necessary to expand this imaging modality to wider bioimaging applications including single-particle deep tissue imaging. Issues related to the characterization of SWIR fluorophores, including fluorescence quantum yield unification, are also mentioned.

Interfacing DNA nanotechnology and biomimetic photonic complexes: advances and prospects in energy and biomedicine

Self-assembled photonic systems with well-organized spatial arrangement and engineered optical properties can be used as efficient energy materials and as effective biomedical agents. The lessons learned from natural light-harvesting antennas have inspired the design and synthesis of a series of biomimetic photonic complexes, including those containing strongly coupled dye aggregates with dense molecular packing and unique spectroscopic features. These photoactive components provide excellent features that could be coupled to multiple applications including light-harvesting, energy transfer, biosensing, bioimaging, and cancer therapy. Meanwhile, nanoscale DNA assemblies have been employed as programmable and addressable templates to guide the formation of DNA-directed multi-pigment complexes, which can be used to enhance the complexity and precision of artificial photonic systems and show the potential for energy and biomedical applications. This review focuses on the interface of DNA nanotechnology and biomimetic photonic systems. We summarized the recent progress in the design, synthesis, and applications of bioinspired photonic systems, highlighted the advantages of the utilization of DNA nanostructures, and discussed the challenges and opportunities they provide.

Modeling Non-additive Effects in Neighboring Chemically Identical Fluorophores

Quantitative fluorescence analysis is often used to derive chemical properties, including stoichiometries, of biomolecular complexes. One fundamental underlying assumption in the analysis of fluorescence data─whether it be the determination of protein complex stoichiometry by super-resolution, or step-counting by photobleaching, or the determination of RNA counts in diffraction-limited spots in RNA fluorescence in situ hybridization (RNA-FISH) experiments─is that fluorophores behave identically and do not interact. However, recent experiments on fluorophore-labeled DNA origami structures such as fluorocubes have shed light on the nature of the interactions between identical fluorophores as these are brought closer together, thereby raising questions on the validity of the modeling assumption that fluorophores do not interact. Here, we analyze photon arrival data under pulsed illumination from fluorocubes where distances between dyes range from 2 to 10 nm. We discuss the implications of non-additivity of brightness on quantitative fluorescence analysis.

Vibrations Responsible for Luminescence from HJ-Aggregates of Conjugated Polymers Identified by Cryogenic Spectroscopy of Single Nanoparticles

A single polymer chain can be thought of as a covalently bound J-aggregate, where the microscopic transition-dipole moments line up to emit in phase. Packing polymer chains into a bulk film can result in the opposite effect, inducing H-type coupling between chains. Cofacial transition-dipole moments oscillate out of phase, canceling each other out, so that the lowest-energy excited state turns dark. H-aggregates of conjugated polymers can, in principle, be coaxed into emitting light by mixing purely electronic and vibronic transitions. However, it is challenging to characterize this electron-phonon coupling experimentally. In a bulk film, many different conformations exist with varying degrees of intrachain J-type and interchain H-type coupling strengths, giving rise to broad and featureless aggregate absorption and emission spectra. Even if single nanoparticles consisting of only a few single chains are grown in a controlled fashion, the luminescence spectra remain broad, owing to the underlying molecular dynamics and structural heterogeneity at room temperature. At cryogenic temperatures, emission from H-type aggregates should be suppressed because, in the absence of thermal energy, internal conversion drives the aggregate to the lowest-energy dark state. At the same time, electronic and vibronic transitions narrow substantially, facilitating the attribution of spectral signatures to distinct vibrational modes. We demonstrate how to distinguish signatures of interchain H-type aggregate species from those of intramolecular J-type coupling. Whereas all dominant vibronic modes revealed in the photoluminescence (PL) and surface-enhanced resonance Raman scattering spectra of a single chromophore within a single polymer chain are identified in the J-type aggregate luminescence spectra, they are not all present at once in the H-type spectra. Universal spectral features are found for the luminescence from strongly HJ-coupled chains, clearly resolving the vibrations responsible for the nonadiabatic excited-state molecular dynamics that enable light emission. We discuss the possible combinations of vibrational modes responsible for H-type aggregate PL and demonstrate that only one, mainly the lowest energy one, of the three dominant vibrational modes contributes to the 0-1 transition, whereas combinations of all three are found in the 0-2 transition. From this analysis, we can distinguish between energy shifts due to either J-type intrachain coupling or H-type interchain interactions, offering a means to directly discriminate between structural and energetic disorder.

How Blinking Affects Photon Correlations in Multichromophoric Nanoparticles

A single chromophore can only emit a maximum of one single photon per excitation cycle. This limitation results in a phenomenon commonly referred to as photon antibunching (pAB). When multiple chromophores contribute to the fluorescence measured, the degree of pAB has been used as a metric to "count" the number of chromophores. But the fact that chromophores can switch randomly between bright and dark states also impacts pAB and can lead to incorrect chromophore numbers being determined from pAB measurements. By both simulations and experiment, we demonstrate how pAB is affected by independent and collective chromophore blinking, enabling us to formulate universal guidelines for correct interpretation of pAB measurements. We use DNA-origami nanostructures to design multichromophoric model systems that exhibit either independent or collective chromophore blinking. Two approaches are presented that can distinguish experimentally between these two blinking mechanisms. The first one utilizes the different excitation intensity dependence on the blinking mechanisms. The second approach exploits the fact that collective blinking implies energy transfer to a quenching moiety, which is a time-dependent process. In pulsed-excitation experiments, the degree of collective blinking can therefore be altered by time gating the fluorescence photon stream, enabling us to extract the energy-transfer rate to a quencher. The ability to distinguish between different blinking mechanisms is valuable in materials science, such as for multichromophoric nanoparticles like conjugated-polymer chains as well as in biophysics, for example, for quantitative analysis of protein assemblies by counting chromophores.

Nanoscale π-conjugated ladders

It is challenging to increase the rigidity of a macromolecule while maintaining solubility. Established strategies rely on templating by dendrons, or by encapsulation in macrocycles, and exploit supramolecular arrangements with limited robustness. Covalently bonded structures have entailed intramolecular coupling of units to resemble the structure of an alternating tread ladder with rungs composed of a covalent bond. We introduce a versatile concept of rigidification in which two rigid-rod polymer chains are repeatedly covalently associated along their contour by stiff molecular connectors. This approach yields almost perfect ladder structures with two well-defined π-conjugated rails and discretely spaced nanoscale rungs, easily visualized by scanning tunnelling microscopy. The enhancement of molecular rigidity is confirmed by the fluorescence depolarization dynamics and complemented by molecular-dynamics simulations. The covalent templating of the rods leads to self-rigidification that gives rise to intramolecular electronic coupling, enhancing excitonic coherence. The molecules are characterized by unprecedented excitonic mobility, giving rise to excitonic interactions on length scales exceeding 100 nm. Such interactions lead to deterministic single-photon emission from these giant rigid macromolecules, with potential implications for energy conversion in optoelectronic devices.

An update on molecular counting in fluorescence microscopy

Quantitative assessment of protein complexes, such as receptor clusters in the context of cellular signalling, has become a pressing objective in cell biology. The advancements in the field of single molecule fluorescence microscopy have led to different approaches for counting protein copy numbers in various cellular structures. This has resulted in an increasing interest in robust calibration protocols addressing photophysical properties of fluorescent labels and the effect of labelling efficiencies. Here, we want to give an update on recent methods for protein counting with a focus on novel calibration protocols. In this context, we discuss different types of calibration samples and identify some of the challenges arising in molecular counting experiments. Some recently published applications offer potential approaches to tackle these challenges.