Pulsed-Interleaved-Excitation Two-Dimensional Fluorescence Lifetime Correlation Spectroscopy.

We report on pulsed-interleaved-excitation two-dimensional fluorescence lifetime correlation spectroscopy (PIE 2D FLCS) to study biomolecular structural dynamics with high sensitivity and high time resolution using Förster resonance energy transfer (FRET). PIE 2D FLCS is an extension of 2D FLCS, which is a unique single-molecule fluorescence method that uses fluorescence lifetime information to distinguish different fluorescence species in equilibrium and resolves their interconversion dynamics with a submicrosecond time resolution. Because 2D FLCS has used only a single-color excitation so far, it was difficult to distinguish a very low-FRET (or zero-FRET) species from only donor-labeled species. We overcome this difficulty by implementing the PIE scheme (i.e., alternate excitation of the donor and acceptor dyes using two temporally interleaved excitations with different colors) to 2D FLCS, realizing two-color excitation and two-color fluorescence detection in 2D FLCS. After proof-of-principle PIE 2D FLCS analysis on the photon data synthesized with Monte Carlo simulation, we apply PIE 2D FLCS to a DNA-hairpin sample and show that this method readily distinguishes four fluorescent species, i.e., high-FRET, low-FRET, and two single-dye-labeled species. In addition, we show that PIE 2D FLCS can also quantitatively evaluate the contributions of the donor-acceptor spectral crosstalk, which often appears as artifacts in FRET studies and degrades the information obtained.

A Toxicogenic Interaction between Intracellular Amyloid-ß and Apolipoprotein-E.

Alzheimer's disease (AD) is associated with the aggregation of amyloid ß (Aß) and tau proteins. Why ApoE variants are significant genetic risk factors remains a major unsolved puzzle in understanding AD, although intracellular interactions with ApoE are suspected to play a role. Here, we show that specific changes in the fluorescence lifetime of fluorescently tagged small Aß oligomers in rat brain cells correlate with the cellular ApoE content. An inhibitor of the Aß-ApoE interaction suppresses these changes and concomitantly reduces Aß toxicity in a dose-dependent manner. Single-molecule techniques show changes both in the conformation and in the stoichiometry of the oligomers. Neural stem cells derived from hiPSCs of Alzheimer's patients also exhibit these fluorescence lifetime changes. We infer that intracellular interaction with ApoE modifies the N-terminus of the Aß oligomers, inducing changes in their stoichiometry, membrane affinity, and toxicity. These changes can be directly imaged in live cells and can potentially be used as a rapid and quantitative cellular assay for AD drug discovery.

Unified picture of vibrational relaxation of OH stretch at the air/water interface.

The elucidation of the energy dissipation process is crucial for understanding various phenomena occurring in nature. Yet, the vibrational relaxation and its timescale at the water interface, where the hydrogen-bonding network is truncated, are not well understood and are still under debate. In the present study, we focus on the OH stretch of interfacial water at the air/water interface and investigate its vibrational relaxation by femtosecond time-resolved, heterodyne-detected vibrational sum-frequency generation (TR-HD-VSFG) spectroscopy. The temporal change of the vibrationally excited hydrogen-bonded (HB) OH stretch band (ν=1→2 transition) is measured, enabling us to determine reliable vibrational relaxation (T1) time. The T1 times obtained with direct excitations of HB OH stretch are 0.2-0.4 ps, which are similar to the T1 time in bulk water and do not noticeably change with the excitation frequency. It suggests that vibrational relaxation of the interfacial HB OH proceeds predominantly with the intramolecular relaxation mechanism as in the case of bulk water. The delayed rise and following decay of the excited-state HB OH band are observed with excitation of free OH stretch, indicating conversion from excited free OH to excited HB OH (~0.9 ps) followed by relaxation to low-frequency vibrations (~0.3 ps). This study provides a complete set of the T1 time of the interfacial OH stretch and presents a unified picture of its vibrational relaxation at the air/water interface.

Ultrafast Raman observation of the perpendicular intermediate phantom state of stilbene photoisomerization.

Trans-cis photoisomerization is generally described by a model in which the reaction proceeds via a common intermediate having a perpendicular conformation around the rotating bond, irrespective of from which isomer the reaction starts. Nevertheless, such an intermediate has yet to be identified unambiguously, and it is often called the 'phantom' state. Here we present the structural identification of the common, perpendicular intermediate of stilbene photoisomerization using ultrafast Raman spectroscopy. Our results reveal ultrafast birth and decay of an identical, short-lived transient that exhibits a vibrational signature characteristic of the perpendicular state upon photoexcitation of the trans and cis forms. In combination with ab initio molecular dynamics simulations, it is shown that the photoexcited trans and cis forms are funnelled off to the ground state through the same, perpendicular intermediate.

Ultrafast vibrational control of organohalide perovskite optoelectronic devices using vibrationally promoted electronic resonance.

Vibrational control (VC) of photochemistry through the optical stimulation of structural dynamics is a nascent concept only recently demonstrated for model molecules in solution. Extending VC to state-of-the-art materials may lead to new applications and improved performance for optoelectronic devices. Metal halide perovskites are promising targets for VC due to their mechanical softness and the rich array of vibrational motions of both their inorganic and organic sublattices. Here, we demonstrate the ultrafast VC of FAPbBr3 perovskite solar cells via intramolecular vibrations of the formamidinium cation using spectroscopic techniques based on vibrationally promoted electronic resonance. The observed short (~300 fs) time window of VC highlights the fast dynamics of coupling between the cation and inorganic sublattice. First-principles modelling reveals that this coupling is mediated by hydrogen bonds that modulate both lead halide lattice and electronic states. Cation dynamics modulating this coupling may suppress non-radiative recombination in perovskites, leading to photovoltaics with reduced voltage losses.

Complex phase of the nonresonant background in sum frequency generation spectroscopy.

Sum frequency generation (SFG) spectroscopy is an interface-selective spectroscopic technique that enables us to selectively observe the vibrational or electronic resonances of molecules within a very thin interface layer. The interfacial properties probed by SFG are contained in a complex quantity called the second-order nonlinear susceptibility (χ2). It is usually believed that the imaginary part of χ2 (Im χ2) exhibits the resonant responses of the system, whereas the nonresonant responses appear solely in the real part of χ2 (Re χ2). However, it was recently theoretically pointed out that a portion of the nonresonant responses actually contributes to the observed Im χ2 spectra when the finite thickness of the interface layer is taken into account. In this study, by considering a simple air/liquid interface without any solutes as a model system, we theoretically evaluate the nonresonant contribution to experimentally accessible Im χ2 as well as to Re χ2, from which the complex phase of the nonresonant background is estimated. It is shown that the deviation of the complex phase from 0° or 180° is less than 1° even if the thickness of the interface layer is taken into account. This means that the nonresonant contribution to Im χ2 is practically negligible, and it is a very good approximation to think that the nonresonant background appears solely in Re χ2 in the case of air/liquid interfaces. This result implies that Im χ2 practically contains only the resonant responses of the system, and molecular resonances at the interface can be conveniently studied using Im χ2 spectra at such interfaces.

Effects of the Unique Chromophore-Protein Interactions on the Primary Photoreaction of Schizorhodopsin.

Schizorhodopsin (SzR) is a newly discovered microbial rhodopsin subfamily, functioning as an unusual inward-proton (H+) pump upon absorbing light. Two major protein structural differences around the chromophore have been found, resulting in unique chromophore-protein interactions that may be responsible for its unusual function. Therefore, it is important to elucidate how such a difference affects the primary photoreaction dynamics. We study the primary dynamics of SzR and its C75S mutant by femtosecond time-resolved absorption (TA) spectroscopy. The obtained TA data revealed that the photoisomerization in SzR proceeds more slowly and less efficiently than typical outward H+-pumping rhodopsins and that it further slows in the C75S mutant. We performed impulsive stimulated Raman measurements to clarify the effect of the cysteine residue on the retinal chromophore and found that interactions with Cys75 flatten the retinal chromophore of wild-type SzR. We discuss the effect of the unique chromophore-cysteine interaction on the retinal isomerization dynamics and structure of SzR.

Local pH at Nonionic and Zwitterionic Lipid/Water Interfaces Revealed by Heterodyne-Detected Electronic Sum-Frequency Generation: A Unified View to Predict Interfacial pH of Biomembranes.

For biomembranes, which are composed of neutral as well as charged lipids, the local pH at lipid/water interfaces is extremely important in their structural formation and functional activity. In our previous study of the charged lipid/water interfaces, we found that the local pH at the interface is governed by the positive or negative sign of the charge of the lipid: i.e., the local pH is dictated by the repulsive or attractive electrostatic interaction between the charged lipid headgroup and the proton. Because of the lack of net charge in the headgroup of the neutral lipid, the factor determining the local pH at neutral lipid/water interfaces is less straightforward, and therefore it is more challenging to predict the local pH. Here we apply heterodyne-detected electronic sum frequency generation (HD-ESFG) spectroscopy to nonionic and zwitterionic lipids to investigate the local pH at the neutral lipid/water interfaces. The obtained results indicate that the local pH at the nonionic lipid/water interface is higher than in bulk water by 0.8 whereas the local pH at the zwitterionic lipid/water interface is lower by 0.6, although the latter is subject to significant uncertainty. The present HD-ESFG study on neutral lipids, combined with the previous study on charged lipids, presents a unified view to consider the local pH at biomembranes based on the balance between the electrostatic interaction and the hydrophobicity provided by the lipid.

Adsorption of SARS-CoV-2 Spike (N501Y) RBD to Human Angiotensin-Converting Enzyme 2 at a Lipid/Water Interface.

The receptor binding domain (RBD) of spike proteins plays a crucial role in the process of severe acute respiratory syndrome corona virus 2 (SARS-CoV-2) attachment to the human angiotensin-converting enzyme 2 (ACE2). The N501Y mutation and later mutations introduced extra positive charges on the spike RBD and resulted in higher transmissibility, likely due to stronger binding with the highly negatively charged ACE2. Consequently, many studies have been devoted to understanding the molecular mechanism of spike protein binding with the ACE2 receptor. Most of the theoretical studies, however, have been done on isolated proteins. ACE2 is a transmembrane protein; thus, it is important to understand the interaction of spike proteins with ACE2 in a lipid matrix. In this study, the adsorption of ACE2 and spike (N501Y) RBD at a lipid/water interface was studied using the heterodyne-detected vibrational sum frequency generation (HD-VSFG) technique. The technique is a non-linear optical spectroscopy which measures vibrational spectra of molecules at an interface and provides information on their structure and orientation. It is found that ACE2 is effectively adsorbed at the positively charged 1,2-dipalmitoyl-3-trimethylammonium-propane (DPTAP) lipid monolayer via electrostatic interactions. The adsorption of ACE2 at the DPTAP monolayer causes a reorganization of interfacial water (D2O) from the D-down to the D-up orientation, indicating that the originally positively charged DPTAP interface becomes negatively charged due to ACE2 adsorption. The negatively charged interface (DPTAP/ACE2) allows further adsorption of positively charged spike RBD. HD-VSFG spectra in the amide I region show differences for spike (N501Y) RBD adsorbed at D2O, DPTAP, and DPTAP/ACE2 interfaces. A red shift observed for the spectra of spike RBD/DPTAP suggests that spike RBD oligomers are formed upon contact with DPTAP lipids.

Elucidation of the pH-Dependent Electric Double Layer Structure at the Silica/Water Interface Using Heterodyne-Detected Vibrational Sum Frequency Generation Spectroscopy.

The silica/water interface is one of the most abundant charged interfaces in natural environments, and the elucidation of the water structure at the silica/water interface is essential. In the present study, we measured the interface-selective vibrational (χ(2)) spectra in the OH stretch region of the silica/water interface in a wide pH range of pH 2.0-12.0 while changing the salt concentration by heterodyne-detected vibrational sum-frequency generation spectroscopy. With the help of singular value decomposition analysis, it is shown that the imaginary part of the χ(2) (Imχ(2)) spectra can be decomposed into the spectra of the diffuse Gouy-Chapman layer (DL) and the compact Stern layer (SL), which enables us to quantitatively analyze the spectra of DL and SL separately. The salt-concentration dependence of the DL spectra at different pH values is analyzed using the modified Gouy-Chapman theory, and the pH-dependent surface charge density and the pKa value (4.8 ± 0.2) of the silica/water interface are evaluated. Furthermore, it is found that the pH-dependent change of the SL spectra is quantitatively explained by three spectral components that represent the three characteristic water species appearing in different pH regions in SL. The quantitative understanding obtained from the analysis of each spectral component in the Imχ(2) spectra provides a clear molecular-level picture of the electric double layer at the silica/water interface.

Photoexcited Plasmon-Driven Ultrafast Dynamics of the Adsorbate Probed by Femtosecond Time-Resolved Surface-Enhanced Time-Domain Raman Spectroscopy.

Metal nanoparticles have high potential in light-harvesting applications by transferring absorbed photon energy to the adsorbates. However, photoexcited plasmon-driven ultrafast dynamics of the adsorbate on metal nanoparticles have not been clearly understood. We studied ultrafast plasmon-driven processes of trans-1,2-bis(4-pyridyl)ethylene (BPE) adsorbed on gold nanoparticle assemblies (GNAs) using time-resolved surface-enhanced impulsive stimulated Raman spectroscopy (TR-SE-ISRS). After photoexciting the localized surface plasmon resonance (LSPR) band of the GNAs, we measured femtosecond time-resolved surface-enhanced Raman spectra of the adsorbate, which exhibited transient bleach in the Raman signal and following biphasic recovery that proceeds on the time scale of a few tens of picoseconds. The TR-SE-ISRS data were analyzed with singular value decomposition, and the obtained species-associated Raman spectra indicated that photoexcitation of the LSPR band alters chemical interaction between BPE and the GNAs on an ultrafast time scale; initial steady-state BPE is recovered through a precursor state that has weaker interaction with the GNAs.

Spectroscopic mapping of the gold complex oligomers (dimer, trimer, tetramer, and pentamer) by excited-state coherent nuclear wavepacket motion in aqueous solutions.

We investigate the excited-state dynamics of the [Au(CN)2-] oligomers following photo-initiated intermolecular Au-Au bond formation by carrying out femtosecond time-resolved absorption and emission measurements at various concentrations (0.080-0.6 mol dm-3) with different photoexcitation wavelengths (290-340 nm). The temporal profiles of the time-resolved absorption signals exhibit clear oscillations arising from the Au-Au stretch coherent wavepacket motion of the excited-state oligomers, which is initiated with the photo-induced Au-Au bond formation. The frequency of the observed oscillation is changed with the change of the concentration, excitation wavelength, and wavelength of the excited-state absorption monitored, reflecting the change in the size of the oligomers detected. Fourier transforms (FTs) of the oscillations provide 2D plots of the FT amplitude against the oscillation frequency versus the detected wavelengths. Because the FT amplitude exhibits a node at the peak wavelength of the absorption of the species that gives rise to the oscillation, the 2D plots enabled us to determine the peak wavelength of the excited-state absorption of the dimer, trimer, tetramer, and pentamer. We also performed femtosecond time-resolved absorption measurements for the 0.3 mol dm-3 solution with 260 nm photoexcitation, which is the condition employed in previous time-resolved X-ray studies (e.g., K. H. Kim et al. Nature, 2015, 518 (7539), 385-389). It was found that various excited-state oligomers, including the dimer, were simultaneously generated under this condition, although the analysis of the previous time-resolved X-ray studies was made by assuming that only the excited-state trimer was generated. The obtained results show that the excited-state dynamics of the trimer claimed based on the time-resolved X-ray data is questionable and that re-analysis and re-examining of its data are necessary.

Single-photon smFRET. III. Application to pulsed illumination.

Förster resonance energy transfer (FRET) using pulsed illumination has been pivotal in leveraging lifetime information in FRET analysis. However, there remain major challenges in quantitative single-photon, single-molecule FRET (smFRET) data analysis under pulsed illumination including 1) simultaneously deducing kinetics and number of system states; 2) providing uncertainties over estimates, particularly uncertainty over the number of system states; and 3) taking into account detector noise sources such as cross talk and the instrument response function contributing to uncertainty; in addition to 4) other experimental noise sources such as background. Here, we implement the Bayesian nonparametric framework described in the first companion article that addresses all aforementioned issues in smFRET data analysis specialized for the case of pulsed illumination. Furthermore, we apply our method to both synthetic as well as experimental data acquired using Holliday junctions.

General Design Strategy to Precisely Control the Emission of Fluorophores via a Twisted Intramolecular Charge Transfer (TICT) Process.

Fluorogenic probes for bioimaging have become essential tools for life science and medicine, and the key to their development is a precise understanding of the mechanisms available for fluorescence off/on control, such as photoinduced electron transfer (PeT) and Förster resonance energy transfer (FRET). Here we establish a new molecular design strategy to rationally develop activatable fluorescent probes, which exhibit a fluorescence off/on change in response to target biomolecules, by controlling the twisted intramolecular charge transfer (TICT) process. This approach was developed on the basis of a thorough investigation of the fluorescence quenching mechanism of N-phenyl rhodamine dyes (commercially available as the QSY series) by means of time-dependent density functional theory (TD-DFT) calculations and photophysical evaluation of their derivatives. To illustrate and validate this TICT-based design strategy, we employed it to develop practical fluorogenic probes for HaloTag and SNAP-tag. We further show that the TICT-controlled fluorescence off/on mechanism is generalizable by synthesizing a Si-rhodamine-based fluorogenic probe for HaloTag, thus providing a palette of chemical dyes that spans the visible and near-infrared range.

Ultrafast vibrational dynamics of the free OD at the air/water interface: Negligible isotopic dilution effect but large isotope substitution effect.

Vibrational relaxation dynamics of the OH stretch of water at the air/water interface has been a subject of intensive research, facilitated by recent developments in ultrafast interface-selective nonlinear spectroscopy. However, a reliable determination of the vibrational relaxation dynamics in the OD stretch region at the air/D2O interface has not been yet achieved. Here, we report a study of the vibrational relaxation of the free OD carried out by time-resolved heterodyne-detected vibrational sum frequency generation spectroscopy. The results obtained with the aid of singular value decomposition analysis indicate that the vibrational relaxation (T1) time of the free OD at the air/D2O interface and air/isotopically diluted water (HOD-H2O) interfaces show no detectable isotopic dilution effect within the experimental error, as in the case of the free OH in the OH stretch region. Thus, it is concluded that the relaxation of the excited free OH/OD predominantly proceeds with their reorientation, negating a major contribution of the intramolecular energy transfer. It is also shown that the T1 time of the free OD is substantially longer than that of the free OH, further supporting the reorientation relaxation mechanism. The large difference in the T1 time between the free OD and the free OH (factor of ∼2) may indicate the nuclear quantum effect on the diffusive reorientation of the free OD/OH because this difference is significantly larger than the value expected for a classical rotational motion.

Why the Photochemical Reaction of Phenol Becomes Ultrafast at the Air-Water Interface: The Effect of Surface Hydration.

Photochemical reactions at the air-water interface can show remarkably different rates from those in bulk water. The present study elucidates the reaction mechanism of phenol characteristic at the air-water interface by the combination of molecular dynamics simulation and quantum chemical calculations of the excited states. We found that incomplete hydrogen bonding to phenol at the air-water interface affects excited states associated with the conical intersection and significantly reduces the reaction barrier, resulting in the distinctively facilitated rate in comparison with the bulk phase. The present study indicates that the reaction dynamics can be substantially different at the interfaces in general, reflecting the difference in the stabilization energy of the electronic states in markedly different solvation at the interface.

Superresolution concentration measurement realized by sub-shot-noise absorption spectroscopy.

Absorption spectroscopy is one of the most widely used spectroscopic methods. The signal-to-noise ratio in conventional absorption spectroscopy is ultimately limited by the shot noise, which arises from the statistical property of the light used for the measurement. Here we show that the noise in absorption spectra can be suppressed below the shot-noise limit when entangled photon pairs are used for the light source. By combining broadband entangled photon pairs and multichannel detection, we realize the acquisition of sub-shot-noise absorption spectra in the entire visible wavelength. Furthermore, we demonstrate the strength of sub-shot-noise absorption spectroscopy for the identification and quantification of chemical species, which are two primary aims of absorption spectroscopy. For highly diluted binary mixture solutions, sub-shot-noise absorption spectroscopy enables us to determine the concentration of each chemical species with precision beyond the limit of conventional absorption spectroscopy. That is, sub-shot-noise absorption spectroscopy achieves superresolution in concentration measurements.

DNA-Induced Reorganization of Water at Model Membrane Interfaces Investigated by Heterodyne-Detected Vibrational Sum Frequency Generation Spectroscopy.

Lipid-DNA complexes are important nonviral vectors to be used in gene therapy, which is one of the promising strategies for the cure of many diseases. Although interfacial water is expected to play a significant role in lipid-DNA complexation, a molecular-level understanding about the role of interfacial water in the DNA-lipid complexation is still sparse. In this study, the structure and orientation of water at cationic and zwitterionic lipid monolayer/water interfaces in the presence of DNA are studied by the use of interface-selective heterodyne-detected vibrational sum frequency generation (HD-VSFG) spectroscopy. It is found that the adsorption of DNA at a cationic lipid interface drastically decreases the orientation of interfacial water reflecting the neutralization of the positively charged interface, whereas the adsorption of DNA at a zwitterionic lipid interface makes interfacial water become more "H-up", indicating that the originally zwitterionic interface becomes negatively charged due to the DNA adsorption. Furthermore, interfacial water having relatively strong hydrogen bonds is observed at both the cationic and zwitterionic lipid interfaces in the presence of DNA.