Mechanisms of transcription control by distal enhancers from high-resolution single-gene imaging.

How distal enhancers physically control promoters over large genomic distances, to enable cell-type specific gene expression, remains obscure. Using single-gene super-resolution imaging and acute targeted perturbations, we define physical parameters of enhancer-promoter communication and elucidate processes that underlie target gene activation. Productive enhancer-promoter encounters happen at 3D distances δ200 nm - a spatial scale corresponding to unexpected enhancer-associated clusters of general transcription factor (GTF) components of the Pol II machinery. Distal activation is achieved by increasing transcriptional bursting frequency, a process facilitated by embedding a promoter into such GTF clusters and by accelerating an underlying multi-step cascade comprising early phases in the Pol II transcription cycle. These findings help clarify molecular/biochemical signals involved in long-range activation and their means of transmission from enhancer to promoter.

Beneficial Intrinsic Hole Trapping and Its Amplitude Variation in a Highly Photoluminescent Toxic-Metal-Free Quantum Dot.

Intrinsic hole trapping as well as hole detrapping have not been observed for any quantum dot (QD) or perovskite nanocrystal (PNC) system. Moreover, amplitude variation of intrinsic hole trapping (or detrapping) has not been reported at all for any QD or PNC system. However, for a CuInS2-based core/alloy-shell (CAS) QD system, (a) both intrinsic hole trapping and detrapping have been observed and (b) very significant amplitude variations of hole trapping (∼16 to ∼42%) and hole detrapping (∼44 to 23%) have been observed. Unlike detrimental electron trapping, hole trapping has been shown to be beneficial, having a direct correlation toward increasing PLQY to 96%. Simultaneous electron and hole trapping has been shown to be quite beneficial for the CuInS2-based CAS QD system leading to the longest ON time (∼130 s) for which a nontoxic metal-based QD remains only in the ON-state without blinking.

Excitation-Energy-Dependent Photoluminescence Quantum Yield is Inherent to Optically Robust Core/Alloy-Shell Quantum Dots in a Vast Energy Landscape.

The importance of alloy-shelling in optically robust Core/Alloy-Shell (CAS) QDs has been described from structural and energetic aspects. Unlike fluorescent dyes, both Core/Shell (CS) and CAS QDs exhibit excitation-energy-dependent photoluminescence quantum yield (PLQY). For both CdSe and InP CAS QDs (with metal- and nonmetal-based alloy-shelling, respectively), with increasing excitation energy, (a) the ultrafast rise-time or relaxation-time to the band-edge increases and (b) the magnitude of the normalized bleach signal decreases. Ultrasensitive single-particle spectroscopic investigation results showed that with decreasing excitation energy, (a) the fraction of ON events increases, (b) the ratio of exciton-detrapping rate/trapping rate increases, and (c) the extent of beneficial hole trapping increases. A relative decrease in PLQY with increasing excitation energy is much less pronounced in CAS QDs than in CS QDs. Unless trap states are removed completely especially in the higher-energy landscape, PLQY will remain inherently dependent on excitation energy for QDs in the vast energy landscape. When reporting the PLQY of QDs, the magnitude of the excitation energy must be mentioned.

Ultrafast dynamics and ultrasensitive single particle spectroscopy of optically robust core/alloy shell semiconductor quantum dots.

A "one-pot one-step" synthesis method of Core/Alloy Shell (CAS) quantum dots (QDs) offers the scope of large scale synthesis in a less time consuming, more economical, highly reproducible and high-throughput manner in comparison to "multi-pot multi-step" synthesis for Core/Shell (CS) QDs. Rapid initial nucleation, and smooth & uniform shell growth lead to the formation of a compositionally-gradient alloyed hetero-structure with very significantly reduced interfacial trap density in CAS QDs. Thus, interfacial strain gets reduced in a much smoother manner leading to enhanced confinement for the photo-generated charge carriers in CAS QDs. Convincing proof of alloy-shelling for a CAS QD has been provided from HRTEM images at the single particle level. The band gap could be tuned as a function of composition, temperature, reactivity difference of precursors, etc. and a high PLQY and improved photochemical stability could be achieved for a small sized CAS QD. From the ultrafast exciton dynamics in CdSe and InP CAS QDs, it has been shown that (a) the hot exciton thermalization/relaxation happens in <500 fs, (b) hot electron trapping dynamics occurs within a ∼1 ps time scale, (c) band edge exciton trapping occurs within a 10-25 ps timescale and (d) for CdSe CAS QDs the hot hole gets trapped in about 35 ps. From fast PL decay dynamics, it has been shown that the amplitude of the intermediate time constant can be correlated with the PLQY. A model has been provided to understand these ultrafast to fast exciton dynamical processes. At the ultrasensitive single particle level, unlike CS QDs, CdSe CAS QDs have been shown to exhibit (a) constancy of PLmax (i.e. no bluing) and (b) constancy of PL intensity (i.e. no bleaching) of the single CAS QDs for continuous irradiation for one hour under an air atmosphere. Thus, CAS QDs hold the promise of being a superior optical probe in comparison to CS QDs both at the ensemble and at the single particle level, leading to enhanced flexibility of the CAS QDs towards designing and developing next generation application devices.

Hydrophobicity-Dependent Heterogeneous Nanoaggregates and Fluorescence Dynamics in Room-Temperature Ionic Liquids.

The hydrophobicity of room-temperature ionic liquids (RTILs) has been shown to have a very significant effect on the optical and structural properties of and in RTILs. The average excited state lifetime of neat RTILs has been shown to be increasing with increasing hydrophobicity of the RTILs. By employing pico-nanosecond-based fluorescence anisotropy decay, the volume of the nanoaggregates in neat RTILs have been calculated. The volume of these nanoaggregates have been shown to be decreasing with increase in hydrophobicity of the RTILs. Thus, hydrophobicity has been shown to have an important role, i.e., hydrophobicity can be used as a handle to tune the properties of RTILs as designer solvents. Moreover, the excited-state lifetime of red-emitting fluorophores, i.e., whose fluorescence emission is not perturbed by the inherent emission of RTILs, has been shown to increase with the increasing hydrophobicity of the RTILs. Highly hydrophobic RTILs have been shown to exhibit positive deviation and highly hydrophilic RTIL has been shown to exhibit negative deviation from the linear correlation between average solvation time (τs) versus viscosity/temperature (η/T).

Near-Ergodic CsPbBr3 Perovskite Nanocrystal with Minimal Statistical Aging.

Optical robustness, uniformity, ergodicity, statistical aging, etc. dictate the applicability of nanocrystals. Based on a series of multimodal statistical analyses such as the Kolmogorov-Smirnov test, Lévy statistics, etc., we demonstrate that for CsPbBr3 perovskite nanocrystals (PNCs): (a) the extent of heterogeneity in the quality and associated physical processes is minimal; (b) the optical robustness is very high, and (c) indeed, a single PNC can depict optical behavior of its ensemble. In addition, toward prospective applications, an optically robust CsPbBr3 PNC exhibits (i) near-ergodicity and (ii) minimal statistical aging, which are extremely vital and complementary to its high defect tolerance.

Unravelling halide-dependent charge carrier dynamics in CsPb(Br/Cl)3 perovskite nanocrystals.

With an increasing bromide content in CsPb(Br/Cl)3 perovskite nanocrystals (PNCs), the steady state photoluminescence quantum yield value increases from 28% to 50% to 76%. Ultrafast transient absorption analyses reveal that the normalized band edge population increases more than two-fold on excitation at the band edge with increasing bromide content, and the hot exciton trapping time increases from 450 fs to 520 fs to 700 fs with increasing bromide content. Ultrasensitive single particle spectroscopic analyses reveal that the peak of the ON fraction distribution increases from 0.65 to 0.75 to 0.85 with increasing bromide content. More specifically, the percentage of PNCs with the ON fraction >75% increases four fold from 24% to 50% to 98% with increasing bromide content. Moreover, the ratio of the detrapping rate and trapping rate increases more than 25 fold with an increase in bromide content, signifying the excitons remaining in the trap state for a smaller time with increasing bromide content. In order to standardize the measurement and analyses, all these three PNCs have the same size and shape, and all the excitations have been made at the same energy above the band edge for all three PNCs and for both ultrafast transient absorption and ultrasensitive single particle measurements.

Near-Unity Photoluminescence Quantum Yield and Highly Suppressed Blinking in a Toxic-Metal-Free Quantum Dot.

There is no literature report of simultaneously achieving near-unity PLQY (ensemble level) and highly suppressed blinking (ultrasensitive single-particle spectroscopy (SPS) level) in a toxic-metal-free QD. In this Letter we report accomplishing near-unity PLQY (96%) and highly suppressed blinking (>80% ON fraction) in a toxic-metal-free CuInS2/ZnSeS Core/Alloy-Shell (CAS) QD. In addition, (i) gigantic enhancement of PLQY (from 15% (Core) to 96% (CAS QD)), (ii) ultrahigh stability over 1 year without significant reduction of PLQY at the ensemble level, (iii) high magnitude (nearly 3 times) of electron detrapping/trapping rate, and (iv) very long ON duration (∼2 min) without blinking at the SPS level enable this ultrasmall (∼3.3 nm) CAS QD to be quite suitable for single-particle tracking/bioimaging. A model explaining all these excellent optical properties has been provided. This ultrabright CAS QD has been successfully utilized toward fabrication of low-cost microcontroller-based stable and bright yellow and white QD-LEDs.

Extent of Shallow/Deep Trap States beyond the Conduction Band Minimum in Defect-Tolerant CsPbBr3 Perovskite Quantum Dot: Control over the Degree of Charge Carrier Recombination.

Perovskite quantum dots (PQDs) are known to be defect-tolerant, possessing a clean band gap with optically inactive benign defect states. However, we show that there exist significant deep trap states beyond the conduction band minimum, although the extent of shallow trap states is observed to be minimal. The extent of deep trap states beyond the conduction band minimum seems to be significant in PQDs; however, the extent is less than that of even optically robust CdSe- and InP-based core/alloy-shell QDs. In-depth analyses based on ultrafast transient absorption and ultrasensitive single-particle spectroscopic investigations decode the underlying degree of charge carrier recombination in CsPbBr3 PQDs, which is quite important for energy applications.

Suppressed Blinking under Normal Air Atmosphere in Toxic-Metal-Free, Small Sized, InP-Based Core/Alloy-Shell/Shell Quantum Dots.

Suppressed blinking has been reported in large (diameter ∼14.1 nm) core/shell InP quantum dots (QDs) under reduced air environment. We report here suppressed blinking with approximately four times smaller (diameter ∼3.6 nm) core/alloy-shell/shell InP QDs under ambient air atmosphere. The ⟨ON fraction⟩ has been obtained to be 0.65. Approximately 26% of the single QDs exhibit ON fraction >80%. The smaller ON exponent (1.19) magnitude in comparison to the OFF exponent (1.45) indicates longer ON events are interrupted by smaller OFF events. ON event truncation time is ∼1.5 times that of the OFF event, signifying the detrapping rate is much higher than the trapping rate. Interestingly, the detrapping rate/trapping rate (single-particle level property) could be directly correlated to the photoluminescence quantum yield (ensemble level property). An additional exponential term required to fit the probability density distribution of the ON event duration could be correlated with hole trapping, leading to extended ON times (>60 s).

Reply to the 'Comment on ""Where does the fluorescing moiety reside in a carbon dot?"- Investigations based on fluorescence anisotropy decay and resonance energy transfer dynamics"' by H. C. Joshi, Phys. Chem. Chem. Phys., 2019, 21, DOI: 10.1039/c9cp00136k.

The claim that the analysis regarding resonance energy transfer should have been made using different equations than those that we have used is negated based on the following points: (1) we are well aware of the equations the author has provided in his comment. The equation (eqn (3) mentioned below) that the author has written is undoubtedly too simple to describe the complex system delineated in our original paper. This particular equation is perhaps OK for simple dye (donor and acceptor) systems; however, such a simple equation is never enough for nanoparticle/quantum dot systems. (2) Another equation suggested by the author in his comment (eqn (2)) contains a parameter called donor concentration in excited state. We have categorically described in page 6-7 of our original paper why it is difficult to measure the donor concentration accurately even in the ground state. When the donor concentration can't be known accurately it can't be used in the suggested equation. (3) Donor-acceptor distance calculated by eqn (3)/Table 1 provided by the author deviates more than 100% from the distance that is physically feasible. Such kinds of problems are well documented in the literature. (4) One of the papers cited by the author in his comment and many other published papers clearly mention that in the case when all donor molecules/particles do not take part in the resonance energy transfer process or the stoichiometry of a donor-acceptor complex is not known or deviates strongly from 1 : 1, especially in quantum dots or any other nanomaterial system, it is not possible to extract accurate dynamical information related to RET from donor decay. Instead risetime of acceptor yields much more accurate information. Such situations do arise in our system as well.

Instantaneous, room-temperature, open-air atmosphere, solution-phase synthesis of perovskite quantum dots through halide exchange employing non-metal based inexpensive HCl/HI: ensemble and single particle spectroscopy.

Herein, the instantaneous synthesis of highly crystalline, uniform-sized (ca. 11.3 ± 0.1 nm), blue-to-green to yellow to red-emitting all-inorganic perovskite quantum dots (CsPbBr3 and mixed halide PQDs) was achieved at room temperature under an open-air atmosphere (no glove box) through halide exchange in the solution phase employing easily available, inexpensive non-metal-based halide sources such as HCl and HI. No complicated pre-treatment of the halide source was required. Moreover, these PQDs were stable for a few weeks under an open-air atmosphere. The PL emission spectra are quite narrow, and the PLQYs are quite high (80% for even Br/I mixed PQDs). At the single particle level, the 〈ON fraction〉 has been noted to vary from 75% to 85% for different PQDs, the m ON values are close to 1.0, and the m OFF values are >1.5. The latter indicates that long ON durations are more probable. The increase in the ON event truncation time (from 2.7 to 4.0 s) and the concomitant decrease in the OFF event truncation time (from 6.6 to 4.3 s) could be correlated with the increase in the PLQY (from 0.55 to 0.75). In addition, an interesting memory effect could be observed in both the ON and the OFF event durations.

Nearly suppressed photoluminescence blinking of small-sized, blue-green-orange-red emitting single CdSe-based core/gradient alloy shell/shell quantum dots: correlation between truncation time and photoluminescence quantum yield.

CdSe-based core/gradient alloy shell/shell semiconductor quantum dots (CGASS QDs) have been shown to be optically quite superior compared to core-shell QDs. However, very little is known about CGASS QDs at the single particle level. Photoluminescence blinking dynamics of four differently emitting (blue (λem = 510), green (λem = 532), orange (λem = 591), and red (λem = 619)) single CGASS QDs having average sizes <∼7 nm have been probed in our home-built total internal reflection fluorescence (TIRF) microscope. All four samples possess an average ON-fraction of 0.70-0.85, which hints towards nearly suppressed PL blinking in these gradiently alloyed systems. Suppression of blinking has been so far achieved with QDs having sizes greater than 10 nm and mostly emitting in the red region (λem > 600 nm). In this manuscript, we report nearly suppressed PL blinking behaviour of CGASS QDs with average sizes <∼7 nm and emitting in the entire range of the visible spectrum, i.e. from blue to green to orange to red. The probability density distribution of both ON- and OFF-event durations for all of these CGASS QDs could be fitted well with a modified inverse truncated power law with an additional exponential model equation. It has been found that unlike most of the literature reports, the power law exponent for OFF-event durations is greater than the power law exponent for ON-event durations for all four samples. This suggests that relatively large ON-event durations are interrupted by comparatively small OFF-event durations. This in turn is indicative of a suppressed non-radiative Auger recombination process for these CGASS systems. However, in these four different samples the ON-event truncation time varies inversely with the OFF-event truncation time, which hints that both the ON- and OFF-event truncation processes are dictated by some common factor. We have employed 2D joint probability distribution analysis to probe the correlation between the event durations and found that residual memory exists in both the ON- and OFF-event durations. Positively correlated successive ON-ON and OFF-OFF event durations and negatively correlated (anti-correlated) ON-OFF event durations perhaps suggest the involvement of more than one type of trapping process within the blinking framework. The timescale corresponding to the additional exponential term has been assigned to hole trapping for ON-event duration statistics. Similarly, for OFF-event duration statistics, this component suggests hole detrapping. We found that the average duration of the exponential process for the ON-event durations is an order of magnitude higher than that of the OFF-event durations. This indicates that the holes are trapped for a significantly long time. When electron trapping is followed by such a hole trapping, long ON-event durations result. We have observed long ON-event durations, as high as 50 s. The competing charge tunnelling model has been used to account for the observed blinking behaviour in these CGASS QDs. Quite interestingly, the PLQY of all of these differently emitting QDs (an ensemble level property) could be correlated with the truncation time (a property at the single particle level). A respective concomitant increase-decrease of ON-OFF event truncation times with increasing PLQY is also indicative of a varying degree of suppression of the Auger recombination processes in these four different CGASS QDs.

"Where does the fluorescing moiety reside in a carbon dot?" - Investigations based on fluorescence anisotropy decay and resonance energy transfer dynamics.

It has been shown recently that aggregated dyes are responsible for very high fluorescence in a carbon dot (CD). However, what is the location of the fluorescing moiety in CD? Is it inside the CD or attached to the CD's surface? In order to answer these intriguing questions regarding the location of the fluorescing moiety in a CD, we performed rotational anisotropy decay dynamics and resonance energy transfer (RET) dynamics. Rotational correlation time of ∼120 picoseconds nullifies the fact that the whole CD is fluorescing. Instead, we can say that the fluorescing moiety is either embedded inside the CD or attached to the surface of the CD or linked to the CD through covalent bonds. From the fluorescence anisotropy decay dynamics in solvents of different viscosities, we could show that the fluorescing moiety is not attached to the surface of the CD or for that matter, the fluorescing moiety is not in a rigid environment inside the CD. RET dynamical analysis has shown that the time for RET (from CD to acceptor Rh123) is about 5.4 ns and the RET dynamics are independent of the acceptor concentration. Using RET dynamics, we could prove that the fluorescing moiety is not outside the CD; rather, it is inside the CD, but not in a rigid environment. The geometric distance between the fluorescing moiety of the CD and the acceptor (Rh123) has been obtained to be 4.55 nm. Using Förster formulation, the distance between the fluorescing moiety inside the CD and the acceptor Rh123 has been calculated to be 4.24 nm. Thus, we could not only reveal the exact location of the fluorescing moiety in a CD, but we could also demonstrate that unlike for many other nanomaterials, Förster formulation could explain the experimental observables regarding RET involving CD reasonably well.

What type of nanoscopic environment does a cationic fluorophore experience in room temperature ionic liquids?

In the presence of a cationic fluorophore (rhodamine 6G) whose absorption has a significant spectral overlap with the emission of a room temperature ionic liquid (RTIL), the emission of the latter gets quenched, and the quenching has been shown to be dynamic in nature. It has been shown that resonance energy transfer (RET) indeed happens between the RTIL (donor) and rhodamine 6G (cationic acceptor), and RET is the reason for the quenching of the RTIL emission. The spectral and temporal aspects of the RET (between neat RTILs as the donors and rhodamine 6G as the acceptor) were closely studied by steady-state and picosecond time-resolved fluorescence spectroscopy. The influence of the alkyl chain length of the cation, size of the anion, excitation wavelength and concentration of the acceptor on the RET dynamics were also investigated. The energy transfer time (obtained from the rise time of the acceptor) was noted to vary from 2.5 ns to 4.1 ns. By employing the Förster formulation, the donor-acceptor distance was obtained, and its magnitude was found to vary between 31.8 and 37.1 Å. The magnitude of the donor-acceptor distance was shown to be independent of the alkyl chain length of the cation but dependent on the size of the anion of the RTIL. Moreover, the donor-acceptor distance was observed to be independent of the excitation wavelength or concentration of the acceptor. It was shown that the Förster formulation can possibly account for the mechanism and hence can explain the experimental observables in the RET phenomenon. Following the detailed experiments and rigorous analysis, a model has been put forward, which can successfully explain the nanoscopic environment that a cationic fluorophore experiences in an RTIL. Moreover, the nanoscopic environment experienced by the cationic probe has been noted to be different from that experienced by a neutral fluorophore.