Broadband single-molecule excitation spectroscopy

Fluctuations in the Photoluminescence Excitation Spectra of Individual Semiconductor Nanocrystals

Most single quantum emitters display non-steady emission properties. Models that explain this effect have primarily relied on photoluminescence measurements that reveal variations in intensity, wavelength, and excited-state lifetime. While photoluminescence excitation spectroscopy could provide complementary information, existing experimental methods cannot collect spectra before individual emitters change in intensity (blink) or wavelength (spectrally diffuse). Here, we present an experimental approach that circumvents such issues, allowing the collection of excitation spectra from individual emitters. Using rapid modulation of the excitation wavelength, we collect and classify excitation spectra from individual CdSe/CdS/ZnS core/shell/shell quantum dots. The spectra, along with simultaneous time-correlated single-photon counting, reveal two separate emission-reduction mechanisms caused by charging and trapping, respectively. During bright emission periods, we also observe a correlation between emission red-shifts and the increased oscillator strength of higher excited states. Quantum-mechanical modeling indicates that diffusion of charges in the vicinity of an emitter polarizes the exciton and transfers the oscillator strength to higher-energy transitions.

Single-Molecule Ultrafast Fluorescence-Detected Pump-Probe Microscopy

We introduce fluorescence-detected pump-probe microscopy by combining a wavelength-tunable ultrafast laser with a confocal scanning fluorescence microscope, enabling access to the femtosecond time scale on the micrometer spatial scale. In addition, we obtain spectral information from Fourier transformation over excitation pulse-pair time delays. We demonstrate this new approach on a model system of a terrylene bisimide (TBI) dye embedded in a PMMA matrix and acquire the linear excitation spectrum as well as time-dependent pump-probe spectra simultaneously. We then push the technique toward single TBI molecules and analyze the statistical distribution of their excitation spectra. Furthermore, we demonstrate the ultrafast transient evolution of several individual molecules, highlighting their different behavior in contrast to the ensemble due to their individual local environment. By correlating the linear and nonlinear spectra, we assess the effect of the molecular environment on the excited-state energy.

Fluorescence-Detected Pump-Probe Spectroscopy

We introduce a new approach to transient spectroscopy, fluorescence-detected pump-probe (F-PP) spectroscopy, that overcomes several limitations of traditional PP. F-PP suppresses excited-state absorption, provides background-free detection, removes artifacts resulting from pump-pulse scattering, from non-resonant solvent response, or from coherent pulse overlap, and allows unique extraction of excited-state dynamics under certain conditions. Despite incoherent detection, time resolution of F-PP is given by the duration of the laser pulses, independent of the fluorescence lifetime. We describe the working principle of F-PP and provide its theoretical description. Then we illustrate specific features of F-PP by direct comparison with PP, theoretically and experimentally. For this purpose, we investigate, with both techniques, a molecular squaraine heterodimer, core-shell CdSe/ZnS quantum dots, and fluorescent protein mCherry. F-PP is broadly applicable to chemical systems in various environments and in different spectral regimes.

Investigating Single-Molecule Fluorescence Spectral Heterogeneity of Rhodamines Using High-Throughput Single-Molecule Spectroscopy

We experimentally investigated several intramolecular coordinate and environmental changes as potential causes of single-molecule fluorescence spectral heterogeneities (smFSH). We developed a high-throughput single-molecule spectroscopy method to analyze more than 5000 single-molecule emission spectra from each of 9 commonly used fluorophores with different structural rigidities and deposited on substrates with different polarities. We observed an unexpectedly high smFSH from structurally rigid Rhodamine B compared with a structurally flexible Cyanine dye-Alexa Fluor 647. Based on experimentally measured smFSH, we ruled out the system's noise uncertainty, single-molecule spectral diffusion, and environmental polarity as the primary causes of the high smFSH. We found that the rotational flexibility of N,N-dialkylated groups contributed to the smFSH. With the high smFSH observed in structurally more rigid model fluorophores, we speculated that other intramolecular coordinate and environmental changes might also contribute to the high smFSH in Rhodamines.

Ultrafast Transient Holographic Microscopy

Nanotechnology is increasingly being applied in many emerging technologies, ranging from metamaterials to next-generation nanodrugs. A key ingredient for its success is the ability to specifically tailor ultrafast nanoscale light-matter interactions over very large areas. Unfortunately, dynamic imaging by ultrafast nanoscopy so far remains limited to very small 2D areas. This shortcoming prevents connecting single-particle observations with large-scale functionality. Here, we address this experimental challenge by combining concepts of ultrafast spectroscopy, wide-field nanoscopy, and digital holography. We introduce an ultrafast holographic transient microscope for wide-field transient nanoscale imaging with high frequency all-optical signal demodulation. We simultaneously record ultrafast transient dynamics of many individual nano-objects and demonstrate time-resolved spectroscopy of gold nanoparticles over a large volume irrespective of their x-y-z position. Our results pave the way to single-shot 3D microscopy of 2D and 3D materials on arbitrary time scales from femtosecond carrier dynamics in optoelectronic materials to millisecond dynamics in complex tissues.

Photon-level broadband spectroscopy and interferometry with two frequency combs

Dual-comb spectroscopy has emerged a powerful technique of Fourier transform spectroscopy without moving parts. Broad spectra can be acquired with a single photodetector in any spectral range where laser frequency combs are available. Because the technique is multiplex, systematic effects are minimized and a great consistency of the spectra can be achieved. We show that dual-comb spectroscopy can be implemented with photon-counting instrumentation and work at power levels one-billion-fold weaker than those usually employed. Our demonstration opens many scenarios for applications of this powerful spectroscopic technique.

Control of Vibronic Transition Rates by Resonant Single-Molecule-Nanoantenna Coupling

Plasmonic nanostructures dramatically alter the radiative and nonradiative properties of single molecules in their vicinity. This coupling-induced change in decay channels selectively enhances specific vibronic transitions, which can enable plasmonic control of molecular reactivity. Here, we report coupling-dependent spectral emission shaping of single Rhodamine 800 molecules in the vicinity of plasmonic gold nanorods. We show that the relative vibronic transition rates of the first two vibronic transitions of the spontaneous emission spectrum can be tuned in the weak coupling regime, by approximately 25-fold, on the single molecule level.

Room-Temperature Excitation-Emission Spectra of Single LH2 Complexes Show Remarkably Little Variation

Excitation spectroscopy gives direct insight into the excited state manifold, energy transfer, transient intermediates, vibrations, and so on. Unfortunately, excitation spectroscopy of single molecules under ambient conditions has remained challenging. Here we present excitation spectra alongside emission spectra of the same individual light-harvesting complex LH2 of the purple bacteria Rps. acidophila. The acquisition of both the excited and ground state spectra allows us to quantify disorder and interband correlations, which are key variables for the interpretation of observed long-lasting coherences. We have overcome the low photostability and small fluorescence quantum yield that are inherent to many biologically relevant systems by combining single-molecule Fourier transform spectroscopy, low excitation intensities, and effective data analysis. We find that LH2 complexes show little spectral variation (130-170 cm^-1), that their two absorption bands (B800-B850) are uncorrelated, and that the Stokes shift is not constant. The low amount of spectral disorder underlines the protective role of the protein scaffold, benefiting the efficient energy transport throughout the light-harvesting membrane.

Ultrafast stimulated emission microscopy of single nanocrystals

Single-molecule detection is a powerful method used to distinguish different species and follow time trajectories within the ensemble average. However, such detection capability requires efficient emitters and is prone to photobleaching, and the slow, nanosecond spontaneous emission process only reports on the lowest excited state. We demonstrate direct detection of stimulated emission from individual colloidal nanocrystals at room temperature while simultaneously recording the depleted spontaneous emission, enabling us to trace the carrier population through the entire photocycle. By capturing the femtosecond evolution of the stimulated emission signal, together with the nanosecond fluorescence, we can disentangle the ultrafast charge trajectories in the excited state and determine the populations that experience stimulated emission, spontaneous emission, and excited-state absorption processes.

Development of a Multicolor Line-Focus Microscope for Rapid Acquisitions of Excitation Spectra

To conduct rapid microscope observations with the excitation spectral measurement for photosynthetic organisms, a wavelength-dispersive line-focus microscope was developed. In the developed system, fluorescence signals at multiple positions on a sample excited with different wavelengths can be detected as a two-dimensional image on the EMCCD camera at the same time. Using the developed system, one can obtain excitation spectra at every pixel over the excitation wavelength range from 635 to 695 nm, which covers the full range of the Q_y bands of both chlorophyll-a and chlorophyll-b. Recording the reference laser spectra at the same time ensures robust measurement against the moderate spectral fluctuation in the excitation laser. Using an objective lens with a numerical aperture of 0.9, the lateral and axial resolutions of 0.56 and 1.08 μm, respectively, were achieved. The theoretically limited and experimentally estimated spectral resolutions of the excitation spectral measurement were 0.86 and 1.3 nm, respectively. The validity of the system was demonstrated by measuring fluorescent beads and single cells of a model alga, Chlamydomonas reinhardtii. Intrachloroplast inhomogeneity in the relative intensity of the chlorophyll-b band could be visualized in Chlamydomonas cells. The inhomogeneity reflects the intrachloroplast variation in the local peripheral antenna size.

High-Throughput Single-Molecule Spectroscopy Resolves the Conformational Isomers of BODIPY Chromophores

A borondipyrromethene (BODIPY) chromophore is connected to a benzoxazole, benzothiazole, or nitrobenzothiazole heterocycle through an olefinic bridge with trans configuration. Rotation about the two [C-C] bonds flanking the olefinic bridge occurs with fast kinetics in solution, leading to the equilibration of four conformational isomers for each compound. Ensemble spectroscopic measurements in solutions fail to distinguish the coexisting isomers. They reveal instead averaged absorption and emission bands with dependence of the latter on the excitation wavelength. Using high-throughput single-molecule spectroscopy, two main populations of single molecules with distinct spectral centroids are observed for each compound on glass substrates. Computational analyses suggest the two populations of molecules to be conformational isomers with antiperiplanar and periplanar arrangements of the BODIPY chromophores about its [C-C] bond to the olefinic bridge. Thus, statistical analysis of multiple single-molecule emission spectra can discriminate stereoisomers that would otherwise be impossible to distinguish by ensemble measurements alone.

Stokes shift microscopy by excitation and emission imaging

In this contribution, we present a new method, based on a tunable excitation laser source and a robust common path interferometer in the detection channel. Its purpose is to image spectral excitation and emission information on a monochrome complementary metal oxide semiconductor (CMOS) camera. This allows us to spatially obtain both excitation and emission spectra of the whole imaged area and create derived images such as red-green-blue (RGB), excitation and emission maxima, and Stokes shift images. Our presented method is a further development of hyperspectral imaging that usually is limited to recording spatially resolved emission spectra. Taking advantage of the full camera chip should speed up the acquisition versus line scan or pointwise hyperspectral imaging.

Single-molecule excitation-emission spectroscopy

Single-molecule spectroscopy (SMS) provides a detailed view of individual emitter properties and local environments without having to resort to ensemble averaging. While the last several decades have seen substantial refinement of SMS techniques, recording excitation spectra of single emitters still poses a significant challenge. Here we address this problem by demonstrating simultaneous collection of fluorescence emission and excitation spectra using a compact common-path interferometer and broadband excitation, which is implemented as an extension of a standard SMS microscope. We demonstrate the technique by simultaneously collecting room-temperature excitation and emission spectra of individual terrylene diimide molecules and donor-acceptor dyads embedded in polystyrene. We analyze the resulting spectral parameters in terms of optical lineshape theory to obtain detailed information on the interactions of the emitters with their nanoscopic environment. This analysis finally reveals that environmental fluctuations between the donor and acceptor in the dyads are not correlated.

Monitoring of Nonadiabatic Effects in Individual Chromophores by Femtosecond Double-Pump Single-Molecule Spectroscopy: A Model Study

We explore, by theoretical modeling and computer simulations, how nonadiabatic couplings of excited electronic states of a polyatomic chromophore manifest themselves in single-molecule signals on femtosecond timescales. The chromophore is modeled as a system with three electronic states (the ground state and two non-adiabatically coupled excited states) and a Condon-active vibrational mode which, in turn, is coupled to a harmonic oscillator heat bath. For this system, we simulate double-pump single-molecule signals with fluorescence detection for different system-field interaction strengths, from the weak-coupling regime to the strong-coupling regime. While the signals are determined by the coherence of the electronic density matrix in the weak-coupling regime, they are determined by the populations of the electronic density matrix in the strong-coupling regime. As a consequence, the signals in the strong coupling regime allow the monitoring of nonadiabatic electronic population dynamics and are robust with respect to temporal inhomogeneity of the optical gap, while signals in the weak-coupling regime are sensitive to fluctuations of the optical gap and do not contain information on the electronic population dynamics.

Excitation-multiplexed multicolor superresolution imaging with fm-STORM and fm-DNA-PAINT

Recent advancements in single-molecule-based superresolution microscopy have made it possible to visualize biological structures with unprecedented spatial resolution. Determining the spatial coorganization of these structures within cells under physiological and pathological conditions is an important biological goal. This goal has been stymied by the current limitations of carrying out superresolution microscopy in multiple colors. Here, we develop an approach for simultaneous multicolor superresolution imaging which relies solely on fluorophore excitation, rather than fluorescence emission properties. By modulating the intensity of the excitation lasers at different frequencies, we show that the color channel can be determined based on the fluorophore's response to the modulated excitation. We use this frequency multiplexing to reduce the image acquisition time of multicolor superresolution DNA-PAINT while maintaining all its advantages: minimal color cross-talk, minimal photobleaching, maximal signal throughput, ability to maintain the fluorophore density per imaged color, and ability to use the full camera field of view. We refer to this imaging modality as "frequency multiplexed DNA-PAINT," or fm-DNA-PAINT for short. We also show that frequency multiplexing is fully compatible with STORM superresolution imaging, which we term fm-STORM. Unlike fm-DNA-PAINT, fm-STORM is prone to color cross-talk. To overcome this caveat, we further develop a machine-learning algorithm to correct for color cross-talk with more than 95% accuracy, without the need for prior information about the imaged structure.

Life under the Microscope: Single-Molecule Fluorescence Highlights the RNA World

The emergence of single-molecule (SM) fluorescence techniques has opened up a vast new toolbox for exploring the molecular basis of life. The ability to monitor individual biomolecules in real time enables complex, dynamic folding pathways to be interrogated without the averaging effect of ensemble measurements. In parallel, modern biology has been revolutionized by our emerging understanding of the many functions of RNA. In this comprehensive review, we survey SM fluorescence approaches and discuss how the application of these tools to RNA and RNA-containing macromolecular complexes in vitro has yielded significant insights into the underlying biology. Topics covered include the three-dimensional folding landscapes of a plethora of isolated RNA molecules, their assembly and interactions in RNA-protein complexes, and the relation of these properties to their biological functions. In all of these examples, the use of SM fluorescence methods has revealed critical information beyond the reach of ensemble averages.

Nature of Large Temporal Fluctuations of Hydrogen Transfer Rates in Single Molecules

Double hydrogen transfer was monitored in single molecules of parent porphycene and its tetra- t-butyl derivative using confocal fluorescence microscopy. The molecules have been embedded in a polymer matrix. Under such conditions, a significant fraction of the population reveals a huge decrease of the tautomerization rate with respect to the value obtained from ensemble studies in solution. This effect is explained by a model that assumes that the rate is determined by the reorganization coordinate that involves slow relaxation of the polymer matrix. The model provides indirect evidence for the dominant role of tunneling. It is proposed that tautomerization in single molecules of the porphycene family can be used to probe polymer relaxation dynamics on the time scale ranging from picoseconds to minutes.

Exploring Electronic Structure and Order in Polymers via Single-Particle Microresonator Spectroscopy

PSS, a transparent electrically conductive polymer, finds widespread use in electronic devices. While empirical efforts have increased conductivity, a detailed understanding of the coupled electronic and morphological landscapes in PEDOT:PSS has lagged due to substantial structural heterogeneity on multiple length-scales. We use an optical microresonator-based absorption spectrometer to perform single-particle measurements, providing a bottom-up examination of electronic structure and morphology ranging from single PEDOT:PSS polymers to nascent films. Using single-particle spectroscopy with complementary theoretical calculations and ultrafast spectroscopy, we demonstrate that PEDOT:PSS displays bulk-like optical response even in single polymers. We find highly ordered PEDOT assemblies with long-range ordering mediated by the insulating PSS matrix and reveal a preferential surface orientation of PEDOT nanocrystallites absent in bulk films with implications for interfacial electronic communication. Our single-particle perspective provides a unique window into the microscopic structure and electronic properties of PEDOT:PSS.

Excitation-emission Fourier-transform spectroscopy based on a birefringent interferometer

The correlation of molecular excitation and emission events provides a powerful multidimensional spectroscopy tool, by relating transitions from electronic ground and excited states through two-dimensional excitation-emission maps. Here we present a compact, fast and versatile Fourier-transform spectrometer, combining absorption and excitation-emission fluorescence spectroscopy in the visible. We generate phase-locked excitation pulse pairs via an inherently stable birefringent wedge-based common-path interferometer, retaining all the advantages of Fourier-transform spectroscopy but avoiding active stabilization or auxiliary tracking beams. We employ both coherent and incoherent excitation sources on dye molecules in solution, with data acquisition times in the range of seconds and minutes, respectively.

Spacer-controlled emission of randomly oriented fluorophores enhanced with surface plasmon-polaritons

In surface plasmon-polariton enhanced fluorescence, the use of spacers is simply understood to control the distance between the fluorescence dyes and metals to avoid quenching. However, the presence of a spacer layer over the metallic surface not only manipulates the quantum yield, but also affects the surface plasmon-polariton resonance, which in turn modifies the florescence excitation rate as well as the far-field radiation pattern of the emission. This study presents a systematic investigation on the spacer-controlled emission of randomly oriented emitters in the Kretschmann configuration, with the full leverage of the coupled transfer matrix, reciprocity and plane-wave decomposition methods. It demonstrates that the introduction of a spacer between the metal film and fluorescence dyes decreases the excitation rate. Furthermore, the excitation rate decreases more for spacers with a higher refractive index due to the reduction of the effective power that goes into the resonance excitation. Combining the excitation rate with the quantum yield and photon-collection efficiency, the detected fluorescence enhancement from either the medium side or substrate side is determined and optimized for the spacer thickness and material. It was found that the highest enhancement of a randomly oriented fluorophore's emission was generally achieved in detection from the substrate side with a low refractive index spacer (e.g. Teflon and SiO₂). In addition, the substrate-side measurements were thought to benefit from highly directional radiation and a more stable enhancement compared to the medium-side measurements. Our results clearly reveal physical insights into the spacer-controlled emission and provide concrete guidance in the design and measurement of fluorescence-based sensing and imaging systems.

Rapid and robust control of single quantum dots

The combination of single particle detection and ultrafast laser pulses is an instrumental method to track dynamics at the femtosecond time scale in single molecules, quantum dots and plasmonic nanoparticles. Optimal control of the extremely short-lived coherences of these individual systems has so far remained elusive, yet its successful implementation would enable arbitrary external manipulation of otherwise inaccessible nanoscale dynamics. In ensemble measurements, such control is often achieved by resorting to a closed-loop optimization strategy, where the spectral phase of a broadband laser field is iteratively optimized. This scheme needs long measurement times and strong signals to converge to the optimal solution. This requirement is in conflict with the nature of single emitters whose signals are weak and unstable. Here we demonstrate an effective closed-loop optimization strategy capable of addressing single quantum dots at room temperature, using as feedback observable the two-photon photoluminescence induced by a phase-controlled broadband femtosecond laser. Crucial to the optimization loop is the use of a deterministic and robust-against-noise search algorithm converging to the theoretically predicted solution in a reduced amount of steps, even when operating at the few-photon level. Full optimization of the single dot luminescence is obtained within ~100 trials, with a typical integration time of 100 ms per trial. These times are faster than the typical photobleaching times in single molecules at room temperature. Our results show the suitability of the novel approach to perform closed-loop optimizations on single molecules, thus extending the available experimental toolbox to the active control of nanoscale coherences.

Ultrasensitive Label-Free Nanosensing and High-Speed Tracking of Single Proteins

Label-free detection, analysis, and rapid tracking of nanoparticles is crucial for future ultrasensitive sensing applications, ranging from understanding of biological interactions to the study of size-dependent classical-quantum transitions. Yet optical techniques to distinguish nanoparticles directly among their background remain challenging. Here we present amplified interferometric scattering microscopy (a-iSCAT) as a new all-optical method capable of detecting individual nanoparticles as small as 15 kDa proteins that is equivalent to half a GFP. By balancing scattering and reflection amplitudes the interference contrast of the nanoparticle signal is amplified 1 to 2 orders of magnitude. Beyond high sensitivity, a-iSCAT allows high-speed image acquisition exceeding several hundreds of frames-per-second. We showcase the performance of our approach by detecting single Streptavidin binding events and by tracking single Ferritin proteins at 400 frames-per-second with 12 nm localization precision over seconds. Moreover, due to its extremely simple experimental realization, this advancement finally enables a cheap and routine implementation of label-free all-optical single nanoparticle detection platforms with sensitivity operating at the single protein level.

Nonequilibrium Chemical Effects in Single-Molecule SERS Revealed by Ab Initio Molecular Dynamics Simulations

Recent developments in nanophotonics have paved the way for achieving significant advances in the realm of single-molecule chemical detection, imaging, and dynamics. In particular, surface-enhanced Raman scattering (SERS) is a powerful analytical technique that is now routinely used to identify the chemical identity of single molecules. Understanding how nanoscale physical and chemical processes affect single-molecule SERS spectra and selection rules is a challenging task and is still actively debated. Herein, we explore underappreciated chemical phenomena in ultrasensitive SERS. We observe a fluctuating excited electronic state manifold, governed by the conformational dynamics of a molecule (4,4'-dimercaptostilbene, DMS) interacting with a metallic cluster (Ag₂₀). This affects our simulated single-molecule SERS spectra; the time trajectories of a molecule interacting with its unique local environment dictates the relative intensities of the observable Raman-active vibrational states. Ab initio molecular dynamics of a model Ag₂₀-DMS system are used to illustrate both concepts in light of recent experimental results.

Dynamics of Single-Molecule Stokes Shifts: Influence of Conformation and Environment

We report on time-dependent Stokes shift measurements of single molecules. Excitation and emission spectroscopy were applied to study the temporal Stokes shift evolution of single perylene diimide molecules embedded in a polymer matrix on the time scale of seconds. The Stokes shift varied between individual molecules as well as for single molecules undergoing different conformations and geometries. From the distribution and temporal evolution of Stokes shifts, we unravel the interplay of nanoenvironment and molecular conformation. We found that Stokes shift fluctuations are related to simultaneous and unidirectional shifts of both emission and excitation spectra.