Long-lived Dark States Research Articles

Probing the Fluorescence Intermittency of Bimetallic Nanoclusters using Single-Molecule Fluorescence Spectroscopy.

Single-molecule spectroscopy (SMS) is a unique and competent technique to study molecule dynamics and sense biomolecules precisely. The design of an ultrahigh-stability single fluorophore probe with excellent photostability and long-lived dark transient states for single-molecule fluorescence microscopy is challenging. Here, we found that the photostability of bimetallic AuAg28 nanoclusters is better than monometallic Ag29 nanoclusters. The photon antibunching experiments unveiled exceptional brightness and remarkable photostability with high survival times of up to 218 s with minimal blinking. AuAg28 NCs exhibited longer "on" times and shorter "off" times as compared to Ag29 NCs. The statistical analysis was performed on at least 100 molecules that showed single-step photobleaching and almost a 5-fold enhancement in intensity on Au doping in Ag29 NCs. The distinctive and tunable photophysics of metal NCs can offer huge potential in pushing single-molecule dynamic measurements to be carried out biologically.

Multi-scale molecular dynamics simulations of enhanced energy transfer in organic molecules under strong coupling

Exciton transport can be enhanced in the strong coupling regime where excitons hybridize with confined light modes to form polaritons. Because polaritons have group velocity, their propagation should be ballistic and long-ranged. However, experiments indicate that organic polaritons propagate in a diffusive manner and more slowly than their group velocity. Here, we resolve this controversy by means of molecular dynamics simulations of Rhodamine molecules in a Fabry-Pérot cavity. Our results suggest that polariton propagation is limited by the cavity lifetime and appears diffusive due to reversible population transfers between polaritonic states that propagate ballistically at their group velocity, and dark states that are stationary. Furthermore, because long-lived dark states transiently trap the excitation, propagation is observed on timescales beyond the intrinsic polariton lifetime. These insights not only help to better understand and interpret experimental observations, but also pave the way towards rational design of molecule-cavity systems for coherent exciton transport.

Benchmarking of novel green fluorescent proteins for the quantification of protein oligomerization in living cells.

Protein-protein-interactions play an important role in many cellular functions. Quantitative non-invasive techniques are applied in living cells to evaluate such interactions, thereby providing a broader understanding of complex biological processes. Fluorescence fluctuation spectroscopy describes a group of quantitative microscopy approaches for the characterization of molecular interactions at single cell resolution. Through the obtained molecular brightness, it is possible to determine the oligomeric state of proteins. This is usually achieved by fusing fluorescent proteins (FPs) to the protein of interest. Recently, the number of novel green FPs has increased, with consequent improvements to the quality of fluctuation-based measurements. The photophysical behavior of FPs is influenced by multiple factors (including photobleaching, protonation-induced "blinking" and long-lived dark states). Assessing these factors is critical for selecting the appropriate fluorescent tag for live cell imaging applications. In this work, we focus on novel green FPs that are extensively used in live cell imaging. A systematic performance comparison of several green FPs in living cells under different pH conditions using Number & Brightness (N&B) analysis and scanning fluorescence correlation spectroscopy was performed. Our results show that the new FP Gamillus exhibits higher brightness at the cost of lower photostability and fluorescence probability (pf), especially at lower pH. mGreenLantern, on the other hand, thanks to a very high pf, is best suited for multimerization quantification at neutral pH. At lower pH, mEGFP remains apparently the best choice for multimerization investigation. These guidelines provide the information needed to plan quantitative fluorescence microscopy involving these FPs, both for general imaging or for protein-protein-interactions quantification via fluorescence fluctuation-based methods.

Formation of Long-Lived Dark States during Electronic Relaxation of Pyrimidine Nucleobases Studied Using Extreme Ultraviolet Time-Resolved Photoelectron Spectroscopy.

Ultrafast electronic relaxation of nucleobases from 1ππ* states to the ground state (S0) is considered essential for the photostability of DNA. However, transient absorption spectroscopy (TAS) has indicated that some nucleobases in aqueous solutions create long-lived 1nπ*/3ππ* dark states from the 1ππ* states with a high quantum yield of 0.4-0.5. We investigated electronic relaxation in pyrimidine nucleobases in both aqueous solutions and the gas phase using extreme ultraviolet (EUV) time-resolved photoelectron spectroscopy. Femtosecond EUV probe pulses cause ionization from all electronic states involved in the relaxation process, providing a clear overview of the electronic dynamics. The 1nπ* quantum yields for aqueous cytidine and uracil (Ura) derivatives were found to be considerably lower (<0.07) than previous estimates reported by TAS. On the other hand, aqueous thymine (Thy) and thymidine exhibited a longer 1ππ* lifetime and a higher quantum yield (0.12-0.22) for the 1nπ* state. A similar trend was found for isolated Thy and Ura in the gas phase: the 1ππ* lifetimes are 39 and 17 fs and the quantum yield for 1nπ* are 1.0 and 0.45 for Thy and Ura, respectively. The result indicates that single methylation to the C5 position hinders the out-of-plane deformation that drives the system to the conical intersection region between 1ππ* and S0, providing a large impact on the photophysics/photochemistry of a pyrimidine nucleobase. The significant reduction of 1nπ* yield in aqueous solution is ascribed to the destabilization of the 1nπ* state induced by hydrogen bonding.

Optically Modulated and Optically Activated Delayed Fluorescent Proteins through Dark State Engineering.

Modulating fluorescent protein emission holds great potential for increasing readout sensitivity for applications in biological imaging and detection. Here, we identify and engineer optically modulated yellow fluorescent proteins (EYFP, originally 10C, but renamed EYFP later, and mVenus) to yield new emitters with distinct modulation profiles and unique, optically gated, delayed fluorescence. The parent YFPs are individually modulatable through secondary illumination, depopulating a long-lived dark state to dynamically increase fluorescence. A single point mutation introduced near the chromophore in each of these YFPs provides access to a second, even longer-lived modulatable dark state, while a different double mutant renders EYFP unmodulatable. The naturally occurring dark state in the parent YFPs yields strong fluorescence modulation upon long-wavelength-induced dark state depopulation, allowing selective detection at the frequency at which the long wavelength secondary laser is intensity modulated. Distinct from photoswitches, however, this near IR secondary coexcitation repumps the emissive S1 level from the long-lived triplet state, resulting in optically activated delayed fluorescence (OADF). This OADF results from secondary laser-induced, reverse intersystem crossing (RISC), producing additional nanosecond-lived, visible fluorescence that is delayed by many microseconds after the primary excitation has turned off. Mutation of the parent chromophore environment opens an additional modulation pathway that avoids the OADF-producing triplet state, resulting in a second, much longer-lived, modulatable dark state. These Optically Modulated and Optically Activated Delayed Fluorescent Proteins (OMFPs and OADFPs) are thus excellent for background- and reference-free, high sensitivity cellular imaging, but time-gated OADF offers a second modality for true background-free detection. Our combined structural and spectroscopic data not only gives additional mechanistic details for designing optically modulated fluorescent proteins but also provides the opportunity to distinguish similarly emitting OMFPs through OADF and through their unique modulation spectra.

Dark-state impact on the exciton recombination of WS2 monolayers as revealed by multi-timescale pump-probe spectroscopy

The luminescence yield of transition metal dichalcogenide monolayers frequently suffers from the formation of long-lived dark states, which include excitons with intervalley charge carriers, spin-forbidden transitions, and a large center-of-mass momentum located outside the light cone of dispersion relations. Efficient relaxation from bright exciton states to dark states suppresses the quantum yield of photon emission. In addition, the radiative recombination of excitons is heavily influenced by Auger-type exciton-exciton scattering, which yields another nonradiative relaxation channel at room temperature. Here, we show that Auger-type scattering is promoted not only between (bright) excitons but also between excitons and long-lived dark states. We studied the luminescence dynamics of monolayer WS2 capped with hexagonal BN over broad time ranges of picoseconds to milliseconds using carefully designed pump-and-probe techniques. We observed that luminescence quenching associated with Auger-type scattering occurs on 1-100 microsecond time scales, which thus correspond to the lifetimes of the relevant dark states. The broad distribution of the measured lifetimes implies the impact of various types of long-lived states on the exciton annihilation process.

Persistent dark states in anisotropic central spin models

Long-lived dark states, in which an experimentally accessible qubit is not in thermal equilibrium with a surrounding spin bath, are pervasive in solid-state systems. We explain the ubiquity of dark states in a large class of inhomogeneous central spin models using the proximity to integrable lines with exact dark eigenstates. At numerically accessible sizes, dark states persist as eigenstates at large deviations from integrability, and the qubit retains memory of its initial polarization at long times. Although the eigenstates of the system are chaotic, exhibiting exponential sensitivity to small perturbations, they do not satisfy the eigenstate thermalization hypothesis. Rather, we predict long relaxation times that increase exponentially with system size. We propose that this intermediate chaotic but non-ergodic regime characterizes mesoscopic quantum dot and diamond defect systems, as we see no numerical tendency towards conventional thermalization with a finite relaxation time.

Light Dynamics of the Retinal-Disease-Relevant G90D Bovine Rhodopsin Mutant.

The RHO gene encodes the G‐protein‐coupled receptor (GPCR) rhodopsin. Numerous mutations associated with impaired visual cycle have been reported; the G90D mutation leads to a constitutively active mutant form of rhodopsin that causes CSNB disease. We report on the structural investigation of the retinal configuration and conformation in the binding pocket in the dark and light‐activated state by solution and MAS‐NMR spectroscopy. We found two long‐lived dark states for the G90D mutant with the 11‐cis retinal bound as Schiff base in both populations. The second minor population in the dark state is attributed to a slight shift in conformation of the covalently bound 11‐cis retinal caused by the mutation‐induced distortion on the salt bridge formation in the binding pocket. Time‐resolved UV/Vis spectroscopy was used to monitor the functional dynamics of the G90D mutant rhodopsin for all relevant time scales of the photocycle. The G90D mutant retains its conformational heterogeneity during the photocycle.

Mechanistic Investigations of Green mEos4b Reveal a Dynamic Long-Lived Dark State.

Green-to-red photoconvertible fluorescent proteins (PCFPs) are key players in advanced microscopy schemes such as photoactivated localization microscopy (PALM). Whereas photoconversion and red-state blinking in PCFPs have been studied intensively, their green-state photophysical behavior has received less attention. Yet dark states in green PCFPs can become strongly populated in PALM schemes and exert an indirect but considerable influence on the quality of data recorded in the red channel. Furthermore, green-state photoswitching in PCFPs can be used directly for PALM and has been engineered to design highly efficient reversibly switchable fluorescent proteins (RSFPs) amenable to various nanoscopy schemes. Here, we demonstrate that green mEos4b efficiently switches to a long-lived dark state through cis-trans isomerization of its chromophore, as do most RSFPs. However, by combining kinetic crystallography, molecular dynamics simulations, and Raman spectroscopy, we find that the dark state in green mEos4b is much more dynamic than that seen in switched-off green IrisFP, a biphotochromic PCFP engineered from the common EosFP parent. Our data suggest that H-bonding patterns maintained by the chromophore in green PCFPs and RSFPs in both their on- and off-states collectively control photoswitching quantum yields. The reduced number of H-bonds maintained by the dynamic dark chromophore in green mEos4b thus largely accounts for the observed lower switching contrast as compared to that of IrisFP. We also compare the long-lived dark states reached from green and red mEos4b, on the basis of their X-ray structures and Raman signatures. Altogether, these data provide a unifying picture of the complex photophysics of PCFPs and RSFPs.

Mechanistic investigation of mEos4b reveals a strategy to reduce track interruptions in sptPALM.

Green-to-red photoconvertible fluorescent proteins repeatedly enter dark states, causing interrupted tracks in single-particle-tracking localization microscopy (sptPALM). We identified a long-lived dark state in photoconverted mEos4b that results from isomerization of the chromophore and efficiently absorbs cyan light. Addition of weak 488-nm light swiftly reverts this dark state to the fluorescent state. This strategy largely eliminates slow blinking and enables the recording of longer tracks in sptPALM with minimum effort.

Long-Lived Dark Exciton Emission in Mn-Doped CsPbCl3 Perovskite Nanocrystals.

The unusual temperature dependence of exciton emission decay in CsPbX3 perovskite nanocrystals (NCs) attracts considerable attention. Upon cooling, extremely short (sub-ns) lifetimes were observed and were explained by an inverted bright–dark state splitting. Here, we report temperature-dependent exciton lifetimes for CsPbCl3 NCs doped with 0–41% Mn2+. The exciton emission lifetime increases upon cooling from 300 to 75 K. Upon further cooling, a strong and fast sub-ns decay component develops. However, the decay is strongly biexponential and also a weak, slow decay component is observed with a ∼40–50 ns lifetime below 20 K. The slow component has a ∼5–10 times stronger relative intensity in Mn-doped NCs compared to that in undoped CsPbCl3 NCs. The temperature dependence of the slow component resembles that of CdSe and PbSe quantum dots with an activation energy of ∼19 meV for the dark–bright state splitting. Based on our observations, we propose an alternative explanation for the short, sub-ns exciton decay time in CsPbX3 NCs. Slow bright–dark state relaxation at cryogenic temperatures gives rise to almost exclusively bright state emission. Incorporation of Mn2+ or high magnetic fields enhances the bright–dark state relaxation and allows for the observation of the long-lived dark state emission at cryogenic temperatures.

Laser-induced fluorescence quenching of red fluorescent dyes with green excitation: Avoiding artifacts in PIE-FRET and FCCS analysis

Multicolor excitation is at the core of many fluorescence spectroscopy techniques such as PIE-FRET, ALEX-FRET, or FCCS. However, the influence of the multiple laser excitations on the dye photophysics is often overlooked. Here, we show that green laser pulses can surprisingly quench the fluorescence of common red dyes Alexa Fluor 647 and Atto 647N, even when the conditions leading to photobleaching are avoided. The physical origin of this phenomenon is discussed via a long-lived dark state and/or photorefractive effects. These observations are important to avoid measurement artifacts as both the fluorophore concentration and the fluorescence brightness are affected.

Dynamic Control of the Coupling between Dark and Bright Excitons with Vibrational Strain.

We numerically and experimentally investigate strain-induced coupling between dark and bright excitons and its dynamic control using a gallium arsenide (GaAs) micromechanical resonator. Uniaxial strain induced by the mechanical resonance efficiently detunes the exciton energies and modulates the coupling strength via the deformation potential in GaAs. This allows optical access to the long-lived dark states without using any external electromagnetic field. This field-free approach could be expanded to a wide range of solid-state materials, leading to on-chip excitonic memories and circuits based on micromechanical resonators.

Itinerant Microwave Photon Detector.

The realization of a high-efficiency microwave single photon detector is a long-standing problem in the field of microwave quantum optics. Here, we propose a quantum nondemolition, high-efficiency photon detector that can readily be implemented in present state-of-the-art circuit quantum electrodynamics. This scheme works in a continuous fashion, gaining information about the photon arrival time as well as about its presence. The key insight that allows us to circumvent the usual limitations imposed by measurement backaction is the use of long-lived dark states in a small ensemble of inhomogeneous artificial atoms to increase the interaction time between the photon and the measurement device. Using realistic system parameters, we show that large detection fidelities are possible.

A Long-Lived Triplet State Is the Entrance Gateway to Oxidative Photochemistry in Green Fluorescent Proteins.

Though ubiquitously used as selective fluorescence markers in cellular biology, fluorescent proteins (FPs) still have not disclosed all of their surprising properties. One important issue, notably for single-molecule applications, is the nature of the triplet state, suggested to be the starting point for many possible photochemical reactions leading to phenomena such as blinking or bleaching. Here, we applied transient absorption spectroscopy to characterize dark states in the prototypical enhanced green fluorescent protein (EGFP) of hydrozoan origin and, for comparison, in IrisFP, a representative phototransformable FP of anthozoan origin. We identified a long-lived (approximately 5 ms) dark state that is formed with a quantum yield of approximately 1% and has pronounced absorption throughout the visible-NIR range (peak at around 900 nm). Detection of phosphorescence emission with identical kinetics and excitation spectrum allowed unambiguous identification of this state as the first excited triplet state of the deprotonated chromophore. This triplet state was further characterized by determining its phosphorescence emission spectrum, the temperature dependence of its decay kinetics and its reactivity toward oxygen and electron acceptors and donors. It is suggested that it is this triplet state that lies at the origin of oxidative photochemistry in green FPs, leading to phenomena such as so-called "oxidative redding", "primed photoconversion", or, in a manner similar to that previously observed for organic dyes, redox induced blinking control with the reducing and oxidizing system ("ROXS").

Quantification of Single-Molecule FRET between Quantum Dots and Organic Dyes

Single-molecule Förster resonance energy transfer (FRET) is a useful technique for studying inter- and intra-molecular dynamics in biophysics. FRET efficiency is highly sensitive to distance, with half-maximal energy transfer occurring at an inter-dye distance on the order of 5 nm, which makes it possible to quantify distances changes on the molecular scale. FRET efficiency also depends on the spectral overlap and quantum yield of the donor and acceptor molecules, and therefore the choice of dye pair is critical to the success of any experiment. Most organic dyes that are used for single-molecule imaging have bleaching lifetimes in the tens of seconds at most, which limits their use to relatively fast processes. Quantum dot nanocrystals can emit for thousands of seconds without entering a long-lived dark state, which should make them good candidates for use as a FRET donor for longer single-molecule experiments, but there has been little quantitative study of the energy transfer efficiency at the single-molecule level. In this work, we use dsDNA to couple individual quantum dot donors to fluorescent dye acceptors. We then immobilize these FRET pairs on a functionalized glass coverslip and image them using total internal fluorescence (TIRF) microscopy with additional optics that allow us to image the donor and acceptor simultaneously. The length of the DNA between the pair can be varied from 11 to 32 base pairs, allowing us to observe and quantify the energy transfer efficiency over a range of distances on the nanometer scale. Our goal is to develop the use of quantum dots as donors for quantitative single-molecule FRET experiments.

Trapping a long-lived dark state in photoconvertible fluorescent protein mEos4b

Trapping a long-lived dark state in photoconvertible fluorescent protein mEos4b

Optically Activated Delayed Fluorescence.

We harness the photophysics of few-atom silver nanoclusters to create the first fluorophores capable of optically activated delayed fluorescence (OADF). In analogy with thermally activated delayed fluorescence, often resulting from oxygen- or collision-activated reverse intersystem crossing from triplet levels, this optically controllable/reactivated visible emission occurs with the same 2.2 ns fluorescence lifetime as that produced with primary excitation alone but is excited with near-infrared light from either of two distinct, long-lived photopopulated dark states. In addition to faster ground-state recovery under long-wavelength co-illumination, this "repumped" visible fluorescence occurs many microsceconds after visible excitation and only when gated by secondary near-IR excitation of ∼1-100 μs-lived dark excited states. By deciphering the Ag nanocluster photophysics, we demonstrate that OADF improves upon previous optical modulation schemes for near-complete background rejection in fluorescence detection. Likely extensible to other fluorophores with photopopulatable excited dark states, OADF holds potential for drastically improving fluorescence signal recovery from high backgrounds.

Single-Molecule Level Insight into Nanoscale Environment-Dependent Photophysics in Blends

Organic semiconductors have attracted considerable attention due to their applications in low-cost (opto)electronic devices. Many successful organic materials utilize blends of several types of molecules that contribute different functions (e.g., serving as donors and acceptors in solar cells). In blends, the local environment, which is inherently heterogeneous, strongly influences the (opto)electronic performance and photostability. We use functionalized fluorinated pentacene (F8 TCHS-Pn) molecules as single-molecule probes of the nanoscale environment in blends containing donor and acceptor molecules incorporated into a polymer (PMMA) matrix. Single F8 TCHS-Pn donor (D) molecules were imaged in PMMA in the presence of functionalized indenofluorene (TIPS-IF) or PCBM acceptor (A) molecules using wide-field fluorescence microscopy at various concentrations. Long-lived dark states attributed to a reversible formation of an endoperoxide (TCHS-EPO) were observed, and the EPO formation and reversal processes, ...

Single photon transfer controlled by excitation phase in a two-atom cavity system

We investigate the quantum interference effect of single photon transfer in a two-atom cavity system caused by the excitation phase. In the proposed system, the two identical atoms are firstly put into a timed state by an external single photon field. During the excitation, the atoms grasp different phases which depend on the spatial position of the atoms. Due to the strong resonant interaction between the atoms and optical cavity mode, the absorbed input photon can be efficiently transferred from the atoms to the cavity mode. We show that photon transfer is sensitive to the quantum interference caused by the excitation phases of atoms. The atomic positions can also determine the coupling constants between the atoms and cavity mode as well as the interatomic dipole–dipole interaction which causes additional interference effects on the quantum transfer. Based on the characteristics of the excitation phase, we find that it is a feasible scheme to generate a long-lived dark state and it could be useful for storage and manipulation of single photon fields by controlling the excitation phase.