Role of Coherent Low-Frequency Motion in Excited-State Proton Transfer of Green Fluorescent Protein Studied by Time-Resolved Impulsive Stimulated Raman Spectroscopy

Coherence in Chemistry: Foundations and Frontiers

Coherence refers to correlations in waves. Because matter has a wave-particle nature, it is unsurprising that coherence has deep connections with the most contemporary issues in chemistry research (e.g., energy harvesting, femtosecond spectroscopy, molecular qubits and more). But what does the word "coherence" really mean in the context of molecules and other quantum systems? We provide a review of key concepts, definitions, and methodologies, surrounding coherence phenomena in chemistry, and we describe how the terms "coherence" and "quantum coherence" refer to many different phenomena in chemistry. Moreover, we show how these notions are related to the concept of an interference pattern. Coherence phenomena are indeed complex, and ambiguous definitions may spawn confusion. By describing the many definitions and contexts for coherence in the molecular sciences, we aim to enhance understanding and communication in this broad and active area of chemistry.

Orchestrating Nuclear Dynamics in a Permanganate Doped Crystal with Chirped Pump-Probe Spectroscopy

Pump-probe spectroscopy is a powerful tool to investigate light-induced dynamical processes in molecules and solids. Targeting vibrational excitations occurring on the time scales of nuclear motions is challenging, as pulse durations shorter than a vibrational period are needed to initiate the dynamics, and complex experimental schemes are required to isolate weak signatures arising from wavepacket motion in different electronic states. Here, we demonstrate how introducing a temporal delay between the spectral components of femtosecond beams, namely a chirp resulting in the increase of their duration, can counterintuitively boost the desired signals by 2 orders of magnitude. Measuring the time-domain vibrational response of permanganate ions embedded in a KClO4 matrix, we identify an intricate dependence of the vibrational response on pulse chirps and probed wavelength that can be exploited to unveil weak signatures of the doping ions─otherwise dominated by the nonresonant matrix─or to obtain vibrational excitations pertaining only to the excited state, suppressing ground-state contributions.

Application of density matrix Wigner transforms for ultrafast macromolecular and chemical x-ray crystallography

Time-Resolved Serial Femtosecond Crystallography (TR-SFX) conducted at X-ray Free Electron Lasers (XFELs) has become a powerful tool for capturing macromolecular structural movies of light-initiated processes. As the capabilities of XFELs advance, we anticipate that a new range of coherent control and structural Raman measurements will become achievable. Shorter optical and x-ray pulse durations and increasingly more exotic pulse regimes are becoming available at free electron lasers. Moreover, with high repetition enabled by the superconducting technology of European XFEL (EuXFEL) and Linac Coherent Light Source (LCLS-II) , it will be possible to improve the signal-to-noise ratio of the light-induced differences, allowing for the observation of vibronic motion on the sub-Angstrom level. To predict and assign this coherent motion, which is measurable with a structural technique, new theoretical approaches must be developed. In this paper, we present a theoretical density matrix approach to model the various population and coherent dynamics of a system, which considers molecular system parameters and excitation conditions. We emphasize the use of the Wigner transform of the time-dependent density matrix, which provides a phase space representation that can be directly compared to the experimental positional displacements measured in a TR-SFX experiment. Here, we extend the results from simple models to include more realistic schemes that include large relaxation terms. We explore a variety of pulse schemes using multiple model systems using realistic parameters. An open-source software package is provided to perform the density matrix simulation and Wigner transformations. The open-source software allows us to define any arbitrary level schemes as well as any arbitrary electric field in the interaction Hamiltonian.

Elementary Reactions in the Functional Triads of the Blue-Light Photoreceptor BLUF Domain

The blue light using the flavin (BLUF) domain is one of the smallest photoreceptors in nature, which consists of a unique bidirectional electron-coupled proton relay process in its photoactivation reaction cycle. This perspective summarizes our recent efforts in dissecting the photocycle into three elementary processes, including proton-coupled electron transfer (PCET), proton rocking, and proton relay. Using ultrafast spectroscopy, we have determined the temporal sequence, rates, kinetic isotope effects (KIEs), and concertedness of these elementary steps. Our findings provide important implications for illuminating the photoactivation mechanism of the BLUF domain and suggest an engineering platform to characterize intricate reactions involving proton motions that are ubiquitous in nonphotosensitive protein machines.

Quantum dynamics of excited state proton transfer in green fluorescent protein

Photoexcitation of green fluorescent protein (GFP) triggers long-range proton transfer along a "wire" of neighboring protein residues, which, in turn, activates its characteristic green fluorescence. The GFP proton wire is one of the simplest, most well-characterized models of biological proton transfer but remains challenging to simulate due to the sensitivity of its energetics to the surrounding protein conformation and the possibility of non-classical behavior associated with the movement of lightweight protons. Using a direct dynamics variational multiconfigurational Gaussian wavepacket method to provide a fully quantum description of both electrons and nuclei, we explore the mechanism of excited state proton transfer in a high-dimensional model of the GFP chromophore cluster over the first two picoseconds following excitation. During our simulation, we observe the sequential starts of two of the three proton transfers along the wire, confirming the predictions of previous studies that the overall process starts from the end of the wire furthest from the fluorescent chromophore and proceeds in a concerted but asynchronous manner. Furthermore, by comparing the full quantum dynamics to a set of classical trajectories, we provide unambiguous evidence that tunneling plays a critical role in facilitating the leading proton transfer.

Optical control of ultrafast structural dynamics in a fluorescent protein

The photoisomerization reaction of a fluorescent protein chromophore occurs on the ultrafast timescale. The structural dynamics that result from femtosecond optical excitation have contributions from vibrational and electronic processes and from reaction dynamics that involve the crossing through a conical intersection. The creation and progression of the ultrafast structural dynamics strongly depends on optical and molecular parameters. When using X-ray crystallography as a probe of ultrafast dynamics, the origin of the observed nuclear motions is not known. Now, high-resolution pump-probe X-ray crystallography reveals complex sub-ångström, ultrafast motions and hydrogen-bonding rearrangements in the active site of a fluorescent protein. However, we demonstrate that the measured motions are not part of the photoisomerization reaction but instead arise from impulsively driven coherent vibrational processes in the electronic ground state. A coherent-control experiment using a two-colour and two-pulse optical excitation strongly amplifies the X-ray crystallographic difference density, while it fully depletes the photoisomerization process. A coherent control mechanism was tested and confirmed the wave packets assignment.

Serial Femtosecond Crystallography Reveals that Photoactivation in a Fluorescent Protein Proceeds via the Hula Twist Mechanism

Chromophore cis/trans photoisomerization is a fundamental process in chemistry and in the activation of many photosensitive proteins. A major task is understanding the effect of the protein environment on the efficiency and direction of this reaction compared to what is observed in the gas and solution phases. In this study, we set out to visualize the hula twist (HT) mechanism in a fluorescent protein, which is hypothesized to be the preferred mechanism in a spatially constrained binding pocket. We use a chlorine substituent to break the twofold symmetry of the embedded phenolic group of the chromophore and unambiguously identify the HT primary photoproduct. Through serial femtosecond crystallography, we then track the photoreaction from femtoseconds to the microsecond regime. We observe signals for the photoisomerization of the chromophore as early as 300 fs, obtaining the first experimental structural evidence of the HT mechanism in a protein on its femtosecond-to-picosecond timescale. We are then able to follow how chromophore isomerization and twisting lead to secondary structure rearrangements of the protein β-barrel across the time window of our measurements.

Rapid-Scan Resonant Two-Dimensional Impulsive Stimulated Raman Spectroscopy of Excited States

Photochemical reactions occur in the electronically excited state, which is effectively represented by a multidimensional potential energy surface (PES) with a vast degree of freedom of nuclear coordinates. The elucidation of the intricate shape of the PES constitutes an important topic in the field of photochemistry and has long been studied both experimentally and theoretically. Recently, fully time-domain resonant two-dimensional Raman spectroscopy has emerged as a potentially powerful tool to provide unique information about the coupling between vibrational manifolds in the excited state. However, the wide application of this technique has been significantly hampered by the technical difficulties associated with experimental implementation and remains challenging. Herein, we demonstrate time-domain resonant two-dimensional impulsive stimulated Raman spectroscopy (2D-ISRS) of excited states using sub-10 fs pulses based on the rapid scan of the time delay, which facilitates the efficient collection of time-domain vibrational signals with high sensitivity. As a proof-of-principle experiment, we performed 2D-ISRS of 6,13-bis(triisopropylsilylethynyl)pentacene (TIPS-pentacene) in solution. Through 2D Fourier transformation of the high-quality time-time oscillatory signal, we obtained a 2D frequency-frequency correlation map of excited-state TIPS-pentacene in the broad frequency window of 0-2000 cm^-1. The data clearly resolve a number of cross peaks that signify the correlations among excited-state vibrational manifolds. The high capability of the rapid-scan-based 2D-ISRS spectrometer presented in this study enables the systematic investigation of various photochemical reaction systems, thereby further promoting the understanding and applications of this new multidimensional spectroscopy.

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.

Photophysics of the red-form Kaede chromophore

The chromophore responsible for colour switching in the optical highlighting protein Kaede has unexpectedly complicated excited state dynamics, which are measured and analysed here. This will inform the development of new imaging proteins.

Different properties of two types of red fluorescent proteins in octocoral, Scleronephthya spp. as Akane families

We report the different properties of two types of red fluorescent proteins (RFP), undescribed species, extracted from two octocorals, Scleronephthya sp. 1 (S. sp. 1) and S. sp, 2 (Alcyonacea, Nephtheidae). S. sp. 1, named Alc-Orange, emits strong green emission at 492 nm and weak red emission at 590 and 630 nm when excited at 449 and 574 nm, respectively. S. sp. 2, LS-Red, emits strong deep red at 642 nm and weak green at 480 and 510 nm when excited at 574 nm and 434 nm, respectively. LS-Red has a very large Stokes shift of about 208 nm emitting at 642 nm when excited at 434 nm. Interestingly, LS-Red shows some emissions at 480 (blue emission), 514 (green emission), 563 (orange emission), and 642 nm (deep red emission) continuously at pH 7.5, which means multicolored fluorescence protein by one excitation at 434 nm. In pH dependence of fluorescence of Alc-Orange (pH 13 to 3.5), no relation between 'green and red FPs' was observed, whereas LS-Red showed the interconversion between 'green and red forms' depending on pH (11.5 to 4.5).

A Solvent-Mediated Excited-State Intermolecular Proton Transfer Fluorescent Probe for Fe3+ Sensing and Cell Imaging

Constructing excited-state intermolecular proton transfer (ESIPT-e) fluorophores represents significant challenges due to the harsh requirement of bearing a proton donor-acceptor (D-A) system and their matching proton donating-accepting ability in the same molecule. Herein, we synthesized a new-type ESIPT-e fluorophor (2-APC) using the "four-component one-pot" reaction. By the installing of a cyano-group on pyridine scaffold, the proton donating ability of -NH2 was greatly enhanced, enabling 2-APC to undergo ESIPT-e process. Surprisingly, 2-APC exhibited dual-emissions in protic solvents ethanol and normal fluorescence in aprotic solvents, which is vastly different from that of conventional ESIPT-a dyes. The ESIPT emission can be obviously suppressed by Fe3+ due to the coordination reaction of Fe3+ with the A-D system in 2-APC. From this basis, a highly sensitive and selective method was established using 2-APC as a fluorescent probe, which offers the sensitive detection of Fe3+ ranging from 0 to 13 μM with the detection limit of 7.5 nM. The recovery study of spiked Fe3+ measured by the probe showed satisfactory results (97.2103.4%) with the reasonable RSD ranging from 3.1 to 3.8%. Moreover, 2-APC can also exhibit aggregation-induced effect in poor solvent or solid-state, eliciting strong red fluorescence. 2-APC was also applied to cell-imaging, exhibiting good cell-permeability, biocompatibility and color rendering. This multi-mode emission of 2-APC is significant departure from that of conventional extended p-conjugated systems and ESIPT dyes based on a flat and rigid molecular design. The "one-pot synthesis" strategy for the construction of ESIPT molecules pioneered a new route to achieve tricolor-emissive fluorophores.

Excited-State Energy Surfaces in Molecules Revealed by Impulsive Stimulated Raman Excitation Profiles

Photophysical and photochemical processes are ruled by the interplay between transient vibrational and electronic degrees of freedom, which are ultimately determined by the multidimensional potential energy surfaces (PESs). Differences between ground and excited PESs are encoded in the relative intensities of resonant Raman bands, but they are experimentally challenging to access, requiring measurements at multiple wavelengths under identical conditions. Herein, we perform a two-color impulsive vibrational scattering experiment to launch nuclear wavepacket motions by an impulsive pump and record their coupling with a targeted excited-state potential by resonant Raman processes with a delayed probe, generating in a single measurement background-free vibrational spectra across the entire sample absorption. Building on the interference between the multiple pathways resonant with the excited-state manifold that generate the Raman signal, we show how to experimentally tune their relative phase by varying the probe chirp, decoding nuclear displacements along different normal modes and revealing the multidimensional PESs. Our results are validated against time-dependent density functional theory.

Excited-State Proton Transfer Dynamics in LSSmOrange Studied by Time-Resolved Impulsive Stimulated Raman Spectroscopy

LSSmOrange is a fluorescent protein that exhibits a large energy gap between absorption and emission, which makes it a useful tool for multicolor bioimaging. This characteristic of LSSmOrange originates from excited-state proton transfer (ESPT): The neutral chromophore is predominantly present in the ground state while the bright fluorescence is emitted from the anionic excited state after ESPT. Interestingly, it was reported that this ESPT process follows bimodal dynamics, but its origin has not clearly been understood. We investigate ESPT of LSSmOrange using time-resolved impulsive stimulated Raman spectroscopy (TR-ISRS) that provides femtosecond time-resolved Raman spectra. The results indicate that the bimodal ESPT dynamics originates from the structural heterogeneity of the chromophore. Species-associated Raman spectra obtained by spectral analysis based on singular value decomposition (SVD) suggest that cis and trans chromophores coexist in the ground state. It is considered that these two forms are photoexcited and undergo ESPT in parallel, resulting in the bimodal dynamics of ESPT in LSSmOrange.

Tracking Ultrafast Structural Dynamics by Time-Domain Raman Spectroscopy

In traditional Raman spectroscopy, narrow-band light is irradiated on a sample, and its inelastic scattering, i.e., Raman scattering, is detected. The energy difference between the Raman scattering and the incident light corresponds to the vibrational energy of the molecule, providing the Raman spectrum that contains rich information about the molecular-level properties of the materials. On the other hand, by using ultrashort optical pulses, it is possible to induce Raman-active coherent nuclear motion of the molecule and to observe the molecular vibration in real time. Moreover, this time-domain Raman measurement can be combined with femtosecond photoexcitation, triggering chemical changes, which enables tracking ultrafast structural dynamics in a form of “time-resolved” time-domain Raman spectroscopy, also known as time-resolved impulsive stimulated Raman spectroscopy. With the advent of stable, ultrashort laser pulse sources, time-resolved impulsive stimulated Raman spectroscopy now realizes high sensitivity and a wide detection frequency window from THz to 3000 cm^–1, and has seen success in unveiling the molecular mechanisms underlying the efficient functions of complex molecular systems. In this Perspective, we overview the present status of time-domain Raman spectroscopy, particularly focusing on its application to the study of femtosecond structural dynamics. We first explain the principle and a brief history of time-domain Raman spectroscopy and then describe the apparatus and recent applications to the femtosecond dynamics of complex molecular systems, including proteins, molecular assemblies, and functional materials. We also discuss future directions for time-domain Raman spectroscopy, which has reached a status allowing a wide range of applications.

Controlling Light-Induced Proton Transfer from the GFP Chromophore

Green Fluorescent Protein (GFP) is known to undergo excited-state proton transfer (ESPT). Formation of a short H-bond favors ultrafast ESPT in GFP-like proteins, such as the GFP S65T/H148D mutant, but the detailed mechanism and its quantum nature remain to be resolved. Here we study in vacuo, light-induced proton transfer from the GFP chromophore in hydrogen-bonded complexes with two anionic proton acceptors, I^- and deprotonated trichloroacetic acid (TCA^- ). We address the role of the strong H-bond and the quantum mechanical proton-density distribution in the excited state, which determines the proton-transfer probability. Our study shows that chemical modifications to the molecular network drastically change the proton-transfer probability and it can become strongly wavelength dependent. The proton-transfer branching ratio is found to be 60 % for the TCA complex and 10 % for the iodide complex, being highly dependent on the photon energy in the latter case. Using high-level ab initio calculations, we show that light-induced proton transfer takes place in S₁ , revealing intrinsic photoacid properties of the isolated GFP chromophore in strongly bound H-bonded complexes. ESPT is found to be very sensitive to the topography of the highly anharmonic potential in S₁ , depending on the quantum-density distribution upon vibrational excitation. We also show that the S₁ potential-energy surface, and hence excited-state proton transfer, can be controlled by altering the chromophore microenvironment.

Supramolecular and suprabiomolecular photochemistry: a perspective overview

In this perspective review article, we have attempted to bring out the important current trends of research in the areas of supramolecular and suprabiomolecular photochemistry. Since the spans of the subject areas are very vast, it is impossible to cover all the aspects within the limited space of this review article. Nevertheless, efforts have been made to assimilate the basic understanding of how supramolecular interactions can significantly change the photophysical and other related physiochemical properties of chromophoric dyes and drugs, which have enormous academic and practical implications. We have discussed with reference to relevant chemical systems where supramolecularly assisted modulations in the properties of chromophoric dyes and drugs can be used or have already been used in different areas like sensing, dye/drug stabilization, drug delivery, functional materials, and aqueous dye laser systems. In supramolecular assemblies, along with their conventional photophysical properties, the acid-base properties of prototropic dyes, as well as the excited state prototautomerization and related proton transfer behavior of proton donor/acceptor dye molecules, are also largely modulated due to supramolecular interactions, which are often reflected very explicitly through changes in their absorption and fluorescence characteristics, providing us many useful insights into these chemical systems and bringing out intriguing applications of such changes in different applied areas. Another interesting research area in supramolecular photochemistry is the excitation energy transfer from the donor to acceptor moieties in self-assembled systems which have immense importance in light harvesting applications, mimicking natural photosynthetic systems. In this review article, we have discussed varieties of these aspects, highlighting their academic and applied implications. We have tried to emphasize the progress made so far and thus to bring out future research perspectives in the subject areas concerned, which are anticipated to find many useful applications in areas like sensors, catalysis, electronic devices, pharmaceuticals, drug formulations, nanomedicine, light harvesting, and smart materials.

Intermolecular Hydrogen Bonding Tunes Vibronic Coupling in Heptazine Complexes

To better understand how hydrogen bonding influences the excited-state landscapes of aza-aromatic materials, we studied hydrogen-bonded complexes of 2,5,8-tris (4-methoxyphenyl)-1,3,4,6,7,9,9b-heptaazaphenalene (TAHz), a molecular photocatalyst related to graphitic carbon nitride, with a variety of phenol derivatives (R-PhOH). By varying the electron-withdrawing character of the para-substituent on the phenol, we can modulate the strength of the hydrogen bond. Using time-resolved photoluminescence, we extract a spectral component associated with the R-PhOH-TAHz hydrogen-bonded complex. Surprisingly, we noticed a striking change in the relative amplitude of vibronic peaks in the TAHz-centered emission as a function of R-group on phenol. To gain a physical understanding of these spectral changes, we employed a displaced-oscillator model of molecular emission to fit these spectra. This fit assumes that two vibrational modes are dominantly coupled to the emissive electronic transition and extracts their frequencies and relative nuclear displacements (related to the Huang-Rhys factor). With the aid of quantum chemical calculations, we found that heptazine ring-breathing and ring-puckering modes are likely responsible for the observed vibronic progression, and both modes indicate decreasing molecular distortion in the excited state with increasing hydrogen bond strength. This finding offers new insights into intermolecular excited-state hydrogen bonding, which is a crucial step toward controlling excited-state proton-coupled electron transfer and proton transfer reactions.

Electronic State-Resolved Multimode-Coupled Vibrational Wavepackets in Oxazine 720 by Two-Dimensional Electronic Spectroscopy

The difference between the excited- and ground-state vibrational wavepackets remains to be fully explored when multiple vibrational modes are coherently excited simultaneously by femtosecond pulses. In this work, we present a series of one- and two-dimensional electronic spectroscopy for studying multimode wavepackets of oxazine 720 in solution. Fourier transform (FT) maps combined with time-frequency transform (TFT) are employed to unambiguously distinguish the origin of low-frequency vibrational wavepackets, that is, an excited-state vibrational wavepacket of 586 cm^-1 with a dephasing time of 0.7 ps and a ground-state vibrational wavepacket of 595 cm^-1 with a dephasing time of 1.3-1.7 ps. We also found the additional low-frequency vibrational wavepackets resulting from the coupling of the 595 cm^-1 mode to a series of high-frequency modes centered at 1150 cm^-1 via electronic transitions. The combined use of FT maps and TFT analysis allows us to reveal the potential vibrational coupling of wavepackets and offers the possibility of disentangling the coupling between the electronic and vibrational degrees of freedom in condensed-phase systems.

Excited-state intramolecular proton transfer in the kinetic-control regime

A new series of molecules bearing a 2,11-dihydro-1H-cyclopenta[de]indeno[1,2-b]quinoline (CPIQ) chromophore with the N-HN type of intramolecular hydrogen bond are strategically designed and synthesized, among which CPIQ-OH, CPIQ-NHAc and CPIQ-NHTs in solution exhibit a single emission band with an anomalously large Stokes shift, whereas CPIQ-NH2 and CPIQ-NHMe show apparent dual-emission property. This, in combination with time-resolved spectroscopy and the computational approach, leads us to conclude that CPIQ-OH, CPIQ-NHAc and CPIQ-NHTs undergo ultrafast, highly exergonic excited-state intramolecular proton transfer (ESIPT), while a finite rate of ESIPT is observed for CPIQ-NH2 and CPIQ-NHMe with a time constant of 117 ps and 39 ps, respectively, in acetonitrile at room-temperature. Further temperature-dependent studies deduce an appreciable ESIPT barrier for CPIQ-NH2 and CPIQ-NHMe. Different from most of the barrier associated ESIPT molecules that are commonly in the thermodynamic-control regime, i.e. found in the thermal pre-equilibrium between excited normal and proton-transfer tautomer states, CPIQ-NH2 and CPIQ-NHMe cases are in the kinetic-control regime where ESIPT is irreversible with a significant barrier. The barrier is able to be tuned by the electronic properties of the -R group in the NR-H proton donor site, resulting in ratiometric fluorescence for normal versus tautomer emission.

Accessing Excited State Molecular Vibrations by Femtosecond Stimulated Raman Spectroscopy

Excited state vibrations are crucial for determining the photophysical and photochemical properties of molecular compounds. Stimulated Raman scattering can coherently stimulate and probe molecular vibrations with optical pulses, but it is generally restricted to ground state properties. Working under resonance conditions enables cross-section enhancement and selective excitation to a targeted electronic level but is hampered by an increased signal complexity due to the presence of overlapping spectral contributions. Here, we show how detailed information about ground and excited state vibrations can be disentangled by exploiting the relative time delay between Raman and probe pulses to control the excited state population, combined with a diagrammatic formalism to dissect the pathways concurring with the signal generation. The proposed method is then exploited to elucidate the vibrational properties of the ground and excited electronic states in the paradigmatic case of cresyl violet. We anticipate that the presented approach holds the potential for selective mapping of the reaction coordinates pertaining to transient electronic stages implied in photoactive compounds.

Time-Domain Observation of Surface-Enhanced Coherent Raman Scattering with 105-106 Enhancement

Combining surface-enhanced Raman scattering (SERS) with the coherent nonlinear Raman technique is a promising route for achieving higher sensitivity and time-resolved SERS measurements, yet such attempts have just been started. Here, we report time-domain Raman measurements of trans-1,2-bis(4-pyridyl)ethylene (BPE) adsorbed on gold nanoparticle assemblies (GNAs), which were carried out with impulsive stimulated Raman spectroscopy using sub-8 fs pulses. We observe coherent nuclear wavepacket motion of BPE on GNAs with drastic enhancement through the surface plasmon resonance, which provides information on the Raman-active vibrations in the time domain. Through Fourier transform of the measured time-domain Raman data, we obtained SERS spectra of BPE on GNAs with enhancement factors as high as 10⁵-10⁶. The present study not only demonstrates applicability of time-domain nonlinear Raman techniques in SERS, i.e., surface-enhanced impulsive stimulated Raman spectroscopy (SE-ISRS), but also provides a technical basis for femtosecond time-resolved SE-ISRS experiments to track ultrafast dynamics of the adsorbates.

Mapping Structural Dynamics of Proteins with Femtosecond Stimulated Raman Spectroscopy

The structure-function relationships of biomolecules have captured the interest and imagination of the scientific community and general public since the field of structural biology emerged to enable the molecular understanding of life processes. Proteins that play numerous functional roles in cellular processes have remained in the forefront of research, inspiring new characterization techniques. In this review, we present key theoretical concepts and recent experimental strategies using femtosecond stimulated Raman spectroscopy (FSRS) to map the structural dynamics of proteins, highlighting the flexible chromophores on ultrafast timescales. In particular, wavelength-tunable FSRS exploits dynamic resonance conditions to track transient-species-dependent vibrational motions, enabling rational design to alter functions. Various ways of capturing excited-state chromophore structural snapshots in the time and/or frequency domains are discussed. Continuous development of experimental methodologies, synergistic correlation with theoretical modeling, and the expansion to other nonequilibrium, photoswitchable, and controllable protein systems will greatly advance the chemical, physical, and biological sciences.

Broadband Impulsive Stimulated Raman Scattering Based on a Chirped Detection

In impulsive stimulated Raman scattering, vibrational oscillations, coherently stimulated by a femtosecond Raman pulse, are monitored in real time and read out as intensity modulations in the transmission of a temporally delayed probe pulse. Critically, in order to retrieve broadband Raman spectra, a fine sampling of the time delays between the Raman and probe pulses is required, making conventional ISRS ineffective for probing irreversible phenomena and/or weak scatterers typically demanding long acquisition times, with signal-to-noise ratios that crucially depend on the pulse fluences and overlap stabilities. To overcome such limitations, here we introduce the chirped-based impulsive stimulated raman scattering (CISRS) technique. Specifically, we show how introducing a chirp in the probe pulse can be exploited for recording the Raman information without the need to scan over the Raman-probe pulse delay. We then experimentally demonstrate with a few examples how to use the introduced scheme to measure Raman spectra.

Probing Structure and Reaction Dynamics of Proteins Using Time-Resolved Resonance Raman Spectroscopy

The mechanistic understanding of protein functions requires insight into the structural and reaction dynamics. To elucidate these processes, a variety of experimental approaches are employed. Among them, time-resolved (TR) resonance Raman (RR) is a particularly versatile tool to probe processes of proteins harboring cofactors with electronic transitions in the visible range, such as retinal or heme proteins. TR RR spectroscopy offers the advantage of simultaneously providing molecular structure and kinetic information. The various TR RR spectroscopic methods can cover a wide dynamic range down to the femtosecond time regime and have been employed in monitoring photoinduced reaction cascades, ligand binding and dissociation, electron transfer, enzymatic reactions, and protein un- and refolding. In this account, we review the achievements of TR RR spectroscopy of nearly 50 years of research in this field, which also illustrates how the role of TR RR spectroscopy in molecular life science has changed from the beginning until now. We outline the various methodological approaches and developments and point out current limitations and potential perspectives.

Protein Dynamics Preceding Photoisomerization of the Retinal Chromophore in Bacteriorhodopsin Revealed by Deep-UV Femtosecond Stimulated Raman Spectroscopy

Bacteriorhodopsin is a prototypical photoreceptor protein that functions as a light-driven proton pump. The retinal chromophore of bacteriorhodopsin undergoes C₁₃═C₁₄ trans-to-cis isomerization upon photoexcitation, and it has been believed to be the first event that triggers the cascaded structural changes in bacteriorhodopsin. We investigated the protein dynamics of bacteriorhodopsin using deep-ultraviolet resonance femtosecond stimulated Raman spectroscopy. It was found that the stimulated Raman signals of tryptophan and tyrosine residues exhibit significant changes within 0.2 ps after photoexcitation while they do not noticeably change during the isomerization process. This result implies that the protein environment changes first, and its change is small during isomerization. The obtained femtosecond stimulated Raman data indicate that ultrafast change is induced in the protein part by the sudden creation of the large dipole of the excited-state chromophore, providing an environment that realizes efficient and selective isomerization.

Role of Hydrogen Bonding in Green Fluorescent Protein-like Chromophore Emission

The fluorescence emission from green fluorescent protein (GFP) is known to be heavily influenced by hydrogen bonding between the core fluorophore and the surrounding side chains or water molecules. Yet how to utilize this feature for modulating the fluorescence of GFP chromophore or GFP-like fluorophore still remains elusive. Here we present theoretical calculations to predict how hydrogen bonding could influence the excited states of the GFP-like fluorophores. These studies provide both a new perspective for understanding the photophysical properties of GFP as well as a solid basis for the rational design of GFP-based fluorophores.

Fifth-order time-domain Raman spectroscopy of photoactive yellow protein for visualizing vibrational coupling in its excited state

We report fifth-order time-domain Raman spectroscopy of photoactive yellow protein (PYP), with the aim to visualize vibrational coupling in its excited state. After the ultrashort actinic pump pulse prepared the vibrational coherence and population in the excited state, the evolving vibrational structure was tracked by time-resolved impulsive stimulated Raman spectroscopy using sub-7-fs pulses. The obtained fifth-order time-domain Raman data were translated to a two-dimensional (2D) frequency-frequency correlation map, which visualizes the correlation between low- and high-frequency vibrational modes of the excited state. The 2D map of PYP reveals a cross peak, indicating the coupling between the phenolic C─O stretch mode of the chromophore and the low-frequency modes (~160 cm^-1), assignable to the intermolecular motions involving the surrounding hydrogen-bonded amino acids. The unveiled coupling suggests the importance of the low-frequency vibrational motion in the primary photoreaction of PYP, highlighting the unique capability of this spectroscopic approach for studying ultrafast reaction dynamics.

Probing Dynamics in Higher-Lying Electronic States with Resonance-Enhanced Femtosecond Stimulated Raman Spectroscopy

Femtosecond stimulated Raman scattering (FSRS) measurements typically probe the structural dynamics of a molecule in the first electronically excited state, S₁. While these measurements often rely on an electronic resonance condition to increase signal strength or enhance species selectivity, the effects of the resonance condition are usually neglected. However, mode-specific enhancements of the vibrational transitions in an FSRS spectrum contain detailed information about the resonant (upper) electronic state. Analogous to ground-state resonance Raman spectroscopy, the relative intensities of the Raman bands reveal displacements of the upper potential energy surface due to changes in the bonding pattern upon S _n ← S₁ electronic excitation, and therefore provide a sensitive probe of the ultrafast dynamics in the higher-lying state, S _n. Raman gain profiles from the wavelength-dependent FSRS spectrum of the model compound 2,5-diphenylthiophene (DPT) reveal several modes with large displacement in the upper potential energy surface, including strong enhancement of a delocalized C-S-C stretching and ring deformation mode. The experimental results provide a benchmark for comparison with calculated spectra using time-dependent density functional theory (TD-DFT) and equation-of-motion coupled-cluster theory with single and double excitations (EOM-CCSD), where the calculations are based on the time-dependent formalism for resonance Raman spectroscopy. The simulated spectra are obtained from S₁-S _n transition strengths and the energy gradients of the upper (S _n) potential energy surfaces along the S₁ normal mode coordinates. The experimental results provide a stringent test of the computational approach, and indicate important limitations based on the level of theory and basis set. This work provides a foundation for making more accurate assignments of resonance-enhanced excited-state Raman spectra, as well as extracting novel information about higher-lying excited states in the transient absorption spectrum of a molecule.

Molecular Coupling between Organic Molecules and Metal

Molecular couplings at interfaces play important roles in determining the performance of nanophotonics and molecular electronics. In this Letter, using femtosecond sum frequency generation to trace free-induction decay of vibrationally excited aromatic thiol molecules immobilized on metal with and without the bridged methylene group(s), metal surface free electron-coupled and uncoupled phenyl C-H stretching vibrational modes were identified, with dephasing times of ∼0.28 and ∼0.60 ps, respectively. For thiols on Au with the bridged methylene group(s) (benzyl mercaptan and phenylethanethiol), both the coupled and uncoupled modes were observed; for thiol on Au without the bridged methylene group (thiophenol), only the coupled mode was observed. This indicates that the bridged methylene group(s) serving as a spacer can be used to adjust the molecular coupling between the phenyl vibration and surface free electrons. The experimental approach can be used to tune molecular couplings in advanced nanophotonics and molecular electronics.

UV and Resonance Raman Spectroscopic and Theoretical Studies on the Solvent-Dependent Ground and Excited-State Thione → Thiol Tautomerization of 4,6-Dimethyl-2-mercaptopyrimidine (DMMP)

The vibrational spectra of 4,6-dimethyl-2-mercaptopyrimidine (DMMP) in acetonitrile, methanol, and water were assigned by resonance Raman spectroscopy through a combination of Fourier-transform infrared spectroscopy (FT-IR), FT-Raman UV-vis spectroscopy, and density functional theoretical (DFT) calculations. The FT-Raman spectra show that the neat solid DMMP is formed as a dimer due to intermolecular hydrogen bonding. In methanol and water, however, the majority of the Raman spectra were assigned to the vibrational modes of DMMP(solvent) _n ( n = 1-4) clusters containing NH···O hydrogen bonds. The intermolecular NH···O hydrogen bond interactions, which are key constituents of the stable DMMP thione structure, revealed significant structural differences in acetonitrile, methanol, and water. In addition, UV-induced hydrogen transfer isomeric reactions between the thione and thiol forms of DMMP were detected in water and acetonitrile. DFT calculations indicate that the observed thione → thiol tautomerization should occur easily in lower excited states in acetonitrile and water.

Capturing Structural Snapshots during Photochemical Reactions with Ultrafast Raman Spectroscopy: From Materials Transformation to Biosensor Responses

Chemistry studies the composition, structure, properties, and transformation of matter. A mechanistic understanding of the pertinent processes is required to translate fundamental knowledge into practical applications. The current development of ultrafast Raman as a powerful time-resolved vibrational technique, particularly femtosecond stimulated Raman spectroscopy (FSRS), has shed light on the structure-energy-function relationships of various photosensitive systems. This Perspective reviews recent work incorporating optical innovations, including the broad-band up-converted multicolor array (BUMA) into a tunable FSRS setup, and demonstrates its resolving power to watch metal speciation and photolysis, leading to high-quality thin films, and fluorescence modulation of chimeric protein biosensors for calcium ion imaging. We discuss advantages of performing FSRS in the mixed time-frequency domain and present strategies to delineate mechanisms by tracking low-frequency modes and systematically modifying chemical structures with specific functional groups. These unique insights at the chemical-bond level have started to enable the rational design and precise control of functional molecular machines in optical, materials, energy, and life sciences.

Femtosecond Time-Resolved Raman Spectroscopy Reveals Structural Evidence for meta Effect in Stilbenols

The meta effect in substituted aromatics plays a crucial role in their excited-state photophysical properties. Meta-substituted hydroxyarenes such as naphthols, stilbenols, and chromophoric constituents of green fluorescent proteins show unusual photoacidity and enhanced fluorescence lifetime and quantum yield when compared to their para-derivatives. Variation in the excited state features of the meta-derivatives when compared to the para-derivatives in stilbenols has been attributed to the enhanced torsional barrier for interconversion between the planar and the twisted perpendicular forms. Herein, we employed femtosecond time-resolved Raman spectroscopy to provide the direct structural evidence for the enhanced torsional barrier in meta-stilbenol. The Raman band profiles of the olefinic C═C stretch related to the torsional motion are found to decay with time constants of ∼750 and ∼13 ps in meta-stilbenol and para-stilbenol respectively, unraveling the structural evidence for the observed enhanced photoacidity originating from enhanced rates of excited-state proton transfer. Further, time-resolved fluorescence measurements are performed to elucidate the relaxation pathways of the excited states of the stilbenols.

The mechanism of a green fluorescent protein proton shuttle unveiled in the time-resolved frequency domain by excited state ab initio dynamics

We simulated an excited state proton transfer in green fluorescent protein by excited state ab initio dynamics, and examined the reaction mechanism in both the time and the frequency domain through a multi resolution wavelet analysis. This original approach allowed us, for the first time, to directly compare the trends of photoactivated vibrations to femtosecond stimulated Raman spectroscopy results, and to give an unequivocal interpretation of the role played by low frequency modes in promoting the reaction. We could attribute the main driving force of the reaction to an important photoinduced softening of the ring-ring orientational motion of the chromophore, thus permitting the tightening of the hydrogen bond network and the opening of the reaction pathway. We also found that both the chromophore (in terms of its inter-ring dihedral angle and phenolic C-O and imidazolinone C-N bond distances) and its pocket (in terms of the inter-molecular oxygen's dihedral angle of the chromophore pocket) relaxations are modulated by low frequency (about 120 cm-1) modes involving the oxygen atoms of the network. This is in agreement with the femtosecond Raman spectroscopy findings in the time-frequency domain. Moreover, the rate in proximity to the Franck Condon region involves a picosecond time scale, with a significant influence from fluctuations of nearby hydrogen bonded residues such as His148. This approach opens a new scenario with ab initio simulations as routinely used tools to understand photoreactivity and the results of advanced time resolved spectroscopy techniques.

Universal route to optimal few- to single-cycle pulse generation in hollow-core fiber compressors

Gas-filled hollow-core fiber (HCF) pulse post-compressors generating few- to single-cycle pulses are a key enabling tool for attosecond science and ultrafast spectroscopy. Achieving optimum performance in this regime can be extremely challenging due to the ultra-broad bandwidth of the pulses and the need of an adequate temporal diagnostic. These difficulties have hindered the full exploitation of HCF post-compressors, namely the generation of stable and high-quality near-Fourier-transform-limited pulses. Here we show that, independently of conditions such as the type of gas or the laser system used, there is a universal route to obtain the shortest stable output pulse down to the single-cycle regime. Numerical simulations and experimental measurements performed with the dispersion-scan technique reveal that, in quite general conditions, post-compressed pulses exhibit a residual third-order dispersion intrinsic to optimum nonlinear propagation within the fiber, in agreement with measurements independently performed in several laboratories around the world. The understanding of this effect and its adequate correction, e.g. using simple transparent optical media, enables achieving high-quality post-compressed pulses with only minor changes in existing setups. These optimized sources have impact in many fields of science and technology and should enable new and exciting applications in the few- to single-cycle pulse regime.

Probing the excited state dynamics of Venus: origin of dual-emission in fluorescent proteins

We present studies on a yellow fluorescent protein variant, Venus, and investigate the photophysics behind the dual emission upon UV excitation in fluorescent proteins.

Ultrafast Dynamics in Light-Driven Molecular Rotary Motors Probed by Femtosecond Stimulated Raman Spectroscopy

Photochemical isomerization in sterically crowded chiral alkenes is the driving force for molecular rotary motors in nanoscale machines. Here the excited-state dynamics and structural evolution of the prototypical light-driven rotary motor are followed on the ultrafast time scale by femtosecond stimulated Raman spectroscopy (FSRS) and transient absorption (TA). TA reveals a sub-100-fs blue shift and decay of the Franck-Condon bright state arising from relaxation along the reactive potential energy surface. The decay is accompanied by coherently excited vibrational dynamics which survive the excited-state structural evolution. The ultrafast Franck-Condon bright state relaxes to a dark excited state, which FSRS reveals to have a rich spectrum compared to the electronic ground state, with the most intense Raman-active modes shifted to significantly lower wavenumber. This is discussed in terms of a reduced bond order of the central bridging bond and overall weakening of bonds in the dark state, which is supported by electronic structure calculations. The observed evolution in the FSRS spectrum is assigned to vibrational cooling accompanied by partitioning of the dark state between the product isomer and the original ground state. Formation of the product isomer is observed in real time by FSRS. It is formed vibrationally hot and cools over several picoseconds, completing the characterization of the light-driven half of the photocycle.