Tracking Ultrafast Vibrational Cooling during Excited-State Proton Transfer Reaction with Anti-Stokes and Stokes Femtosecond Stimulated Raman Spectroscopy

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.

Mastering Femtosecond Stimulated Raman Spectroscopy: A Practical Guide

Femtosecond stimulated Raman spectroscopy (FSRS) is a powerful nonlinear spectroscopic technique that probes changes in molecular and material structure with high temporal and spectral resolution. With proper spectral interpretation, this is equivalent to mapping out reactive pathways on highly anharmonic excited-state potential energy surfaces with femtosecond to picosecond time resolution. FSRS has been used to examine structural dynamics in a wide range of samples, including photoactive proteins, photovoltaic materials, plasmonic nanostructures, polymers, and a range of others, with experiments performed in multiple groups around the world. As the FSRS technique grows in popularity and is increasingly implemented in user facilities, there is a need for a widespread understanding of the methodology and best practices. In this review, we present a practical guide to FSRS, including discussions of instrumentation, as well as data acquisition and analysis. First, we describe common methods of generating the three pulses required for FSRS: the probe, Raman pump, and actinic pump, including a discussion of the parameters to consider when selecting a beam generation method. We then outline approaches for effective and efficient FSRS data acquisition. We discuss common data analysis techniques for FSRS, as well as more advanced analyses aimed at extracting small signals on a large background. We conclude with a discussion of some of the new directions for FSRS research, including spectromicroscopy. Overall, this review provides researchers with a practical handbook for FSRS as a technique with the aim of encouraging many scientists and engineers to use it in their research.

Capturing excited-state structural snapshots of evolutionary green-to-red photochromic fluorescent proteins

Photochromic fluorescent proteins (FPs) have proved to be indispensable luminous probes for sophisticated and advanced bioimaging techniques. Among them, an interplay between photoswitching and photoconversion has only been observed in a limited subset of Kaede-like FPs that show potential for discovering the key mechanistic steps during green-to-red photoconversion. Various spectroscopic techniques including femtosecond stimulated Raman spectroscopy (FSRS), X-ray crystallography, and femtosecond transient absorption were employed on a set of five related FPs with varying photoconversion and photoswitching efficiencies. A 3-methyl-histidine chromophore derivative, incorporated through amber suppression using orthogonal aminoacyl tRNA synthetase/tRNA pairs, displays more dynamic photoswitching but greatly reduced photoconversion versus the least-evolved ancestor (LEA). Excitation-dependent measurements of the green anionic chromophore reveal that the varying photoswitching efficiencies arise from both the initial transient dynamics of the bright cis state and the final trans-like photoswitched off state, with an exocyclic bridge H-rocking motion playing an active role during the excited-state energy dissipation. This investigation establishes a close-knit feedback loop between spectroscopic characterization and protein engineering, which may be especially beneficial to develop more versatile FPs with targeted mutations and enhanced functionalities, such as photoconvertible FPs that also feature photoswitching properties.

Energy Dissipation into the Solvent during Proton Transfer Occurs via Acoustic Phonons

In photochemistry, rapid energy dissipation into the solvent is mandatory to prevent radiation damages. By optical pump THz spectroscopy, we are able to follow the details of the energy dissipation mechanism upon photoexcitation of the photoacid to the hydrogen-bonded network of water: Based on the frequency maps subsequent to photoexcitation, we propose that energy transfer takes place via propagation of an acoustic phonon. The dissipation into the solvent can be rationalized by an initial first hydration shell response followed by energy dissipation via an acoustic phonon. Surprisingly, for the first 10 ps, the propagation in the water network can be described by a wave packet with a constant group velocity, indicating a long-range correlation. After 300 ps, thermalization in the liquid jet is reached and the THz spectrum reflects a Boltzmann population, corresponding a temperature increase of ΔT = 0.5 °C.

Excited-State Dynamics in 4-[4'(Dimethylamino)styryl]pyridine, a Photobase: Role of Photoinitiated Proton-Coupled Electron Transfer

The photoinitiated proton-coupled electron transfer (PCET) process in photoacid-based adducts is predominantly governed by the evolution of the electron-proton transfer state. However, such a process is underexplored in the case of photobases as the excited states evolve through multiple competitive channels. Here, we elucidate the excited-state dynamics of a photobase, 4-[4'-(dimethylamino)styryl]pyridine (DMASP), in the presence of hexafluoroisopropanol (HFIP) that enables PCET. Transient absorption measurements show the evolution of a protonated species in the excited state with a time constant of ∼2.5 ps. Fluorescence upconversion measurements reveal the signatures of an emissive intramolecular charge transfer state and a protonated state. The role of such states is further confirmed by time-resolved measurements in the presence of trifluoroacetic acid and computational analysis. Furthermore, the proton-abstraction dynamics of DMASP is analyzed in bulk methanol and butanol solvents. The extent of proton abstraction by DMASP is found to be higher in the presence of HFIP when compared with the normal alcohols over a time period of a few picoseconds.

Investigation of Excited-State Intramolecular Proton Transfer and Structural Dynamics in Bis-Benzimidazole Derivative (BBM)

The bis-benzimidazole derivative (BBM) molecule, consisting of two 2-(2'-hydroxyphenyl) benzimidazole (HBI) halves, has been synthesized and successfully utilized as a ratiometric fluorescence sensor for the sensitive detection of Cu²⁺ based on enol-keto excited-state intramolecular proton transfer (ESIPT). In this study, we strategically implement femtosecond stimulated Raman spectroscopy and several time-resolved electronic spectroscopies, aided by quantum chemical calculations to investigate the detailed primary photodynamics of the BBM molecule. The results demonstrate that the ESIPT from BBM-enol* to BBM-keto* was observed in only one of the HBI halves with a time constant of 300 fs; after that, the rotation of the dihedral angle between the two HBI halves generated a planarized BBM-keto* isomer in 3 ps, leading to a dynamic redshift of BBM-keto* emission.

Photogrammetry of Ultrafast Excited-State Intramolecular Proton Transfer Pathways in the Fungal Pigment Draconin Red

Proton transfer processes of organic molecules are key to charge transport and photoprotection in biological systems. Among them, excited-state intramolecular proton transfer (ESIPT) reactions are characterized by quick and efficient charge transfer within a molecule, resulting in ultrafast proton motions. The ESIPT-facilitated interconversion between two tautomers (PS and PA) comprising the tree fungal pigment Draconin Red in solution was investigated using a combination of targeted femtosecond transient absorption (fs-TA) and excited-state femtosecond stimulated Raman spectroscopy (ES-FSRS) measurements. Transient intensity (population and polarizability) and frequency (structural and cooling) dynamics of -COH rocking and -C=C, -C=O stretching modes following directed stimulation of each tautomer elucidate the excitation-dependent relaxation pathways, particularly the bidirectional ESIPT progression out of the Franck-Condon region to the lower-lying excited state, of the intrinsically heterogeneous chromophore in dichloromethane solvent. A characteristic overall excited-state PS-to-PA transition on the picosecond timescale leads to a unique "W"-shaped excited-state Raman intensity pattern due to dynamic resonance enhancement with the Raman pump-probe pulse pair. The ability to utilize quantum mechanics calculations in conjunction with steady-state electronic absorption and emission spectra to induce disparate excited-state populations in an inhomogeneous mixture of similar tautomers has broad implications for the modeling of potential energy surfaces and delineation of reaction mechanisms in naturally occurring chromophores. Such fundamental insights afforded by in-depth analysis of ultrafast spectroscopic datasets are also beneficial for future development of sustainable materials and optoelectronics.

Delineating Ultrafast Structural Dynamics of a Green-Red Fluorescent Protein for Calcium Sensing

Fluorescent proteins (FPs) are indispensable tools for noninvasive bioimaging and sensing. Measuring the free cellular calcium (Ca²⁺) concentrations in vivo with genetically encodable FPs can be a relatively direct measure of neuronal activity due to the complex signaling role of these ions. REX-GECO1 is a recently developed red-green emission and excitation ratiometric FP-based biosensor that achieves a high dynamic range due to differences in the chromophore response to light excitation with and without calcium ions. Using steady-state electronic measurements (UV/Visible absorption and emission), along with time-resolved spectroscopic techniques including femtosecond transient absorption (fs-TA) and femtosecond stimulated Raman spectroscopy (FSRS), the potential energy surfaces of these unique biosensors are unveiled with vivid details. The ground-state structural characterization of the Ca²⁺-free biosensor via FSRS reveals a more spacious protein pocket that allows the chromophore to efficiently twist and reach a dark state. In contrast, the more compressed cavity within the Ca²⁺-bound biosensor results in a more heterogeneous distribution of chromophore populations that results in multi-step excited state proton transfer (ESPT) pathways on the sub-140 fs, 600 fs, and 3 ps timescales. These results enable rational design strategies to enlarge the spectral separation between the protonated/deprotonated forms and the Stokes shift leading to a larger dynamic range and potentially higher fluorescence quantum yield, which should be broadly applicable to the calcium imaging and biosensor communities.

Mapping the Complete Photocycle that Powers a Large Stokes Shift Red Fluorescent Protein

Large Stokes shift (LSS) red fluorescent proteins (RFPs) are highly desirable for bioimaging advances. The RFP mKeima, with coexisting cis- and trans-isomers, holds significance as an archetypal system for LSS emission due to excited-state proton transfer (ESPT), yet the mechanisms remain elusive. We implemented femtosecond stimulated Raman spectroscopy (FSRS) and various time-resolved electronic spectroscopies, aided by quantum calculations, to dissect the cis- and trans-mKeima photocycle from ESPT, isomerization, to ground-state proton transfer in solution. This work manifests the power of FSRS with global analysis to resolve Raman fingerprints of intermediate states. Importantly, the deprotonated trans-isomer governs LSS emission at 620 nm, while the deprotonated cis-isomer's 520 nm emission is weak due to an ultrafast cis-to-trans isomerization. Complementary spectroscopic techniques as a table-top toolset are thus essential to study photochemistry in physiological environments.

Ultrafast Spectroscopies of Nitrophenols and Nitrophenolates in Solution: From Electronic Dynamics and Vibrational Structures to Photochemical and Environmental Implications

Nitrophenols are a group of small organic molecules with significant environmental implications from the atmosphere to waterways. In this work, we investigate a series of nitrophenols and nitrophenolates, with the contrasting ortho-, meta-, and para-substituted nitro group to the phenolic hydroxy or phenolate oxygen site (2/3/4NP or NP-), implementing a suite of steady-state and time-resolved spectroscopic techniques that include UV/Visible spectroscopy, femtosecond transient absorption (fs-TA) spectroscopy with probe-dependent and global analysis, and femtosecond stimulated Raman spectroscopy (FSRS), aided by quantum calculations. The excitation-dependent (400 and 267 nm) electronic dynamics in water and methanol, for six protonated or deprotonated nitrophenol molecules (three regioisomers in each set), enable a systematic investigation of the excited-state dynamics of these functional "nanomachines" that can undergo nitro-group twisting (as a rotor), excited-state intramolecular or intermolecular proton transfer (donor-acceptor, ESIPT, or ESPT), solvation, and cooling (chromophore) events on molecular timescales. In particular, the meta-substituted compound 3NP or 3NP- exhibits the strongest charge-transfer character with FSRS signatures (e.g., C-N peak frequency), and thus, does not favor nitroaromatic twist in the excited state, while the ortho-substituted compound 2NP can undergo ESIPT in water and likely generate nitrous acid (HONO) after 267 nm excitation. The delineated mechanistic insights into the nitro-substituent-location-, protonation-, solvent-, and excitation-wavelength-dependent effects on nitrophenols, in conjunction with the ultraviolet-light-induced degradation of 2NP in water, substantiates an appealing discovery loop to characterize and engineer functional molecules for environmental applications.

To twist or not to twist: From chromophore structure to dynamics inside engineered photoconvertible and photoswitchable fluorescent proteins

Green-to-red photoconvertible fluorescent proteins (FPs) are vital biomimetic tools for powerful techniques such as super-resolution imaging. A unique Kaede-type FP named the least evolved ancestor (LEA) enables delineation of the evolutionary step to acquire photoconversion capability from the ancestral green fluorescent protein (GFP). A key residue, Ala69, was identified through several steady-state and time-resolved spectroscopic techniques that allows LEA to effectively photoswitch and enhance the green-to-red photoconversion. However, the inner workings of this functional protein have remained elusive due to practical challenges of capturing the photoexcited chromophore motions in real time. Here, we implemented femtosecond stimulated Raman spectroscopy and transient absorption on LEA-A69T, aided by relevant crystal structures and control FPs, revealing that Thr69 promotes a stronger π-π stacking interaction between the chromophore phenolate (P-)ring and His193 in FP mutants that cannot photoconvert or photoswitch. Characteristic time constants of ~60-67 ps are attributed to P-ring twist as the onset for photoswitching in LEA (major) and LEA-A69T (minor) with photoconversion capability, different from ~16/29 ps in correlation with the Gln62/His62 side-chain twist in ALL-GFP/ALL-Q62H, indicative of the light-induced conformational relaxation preferences in various local environments. A minor subpopulation of LEA-A69T capable of positive photoswitching was revealed by time-resolved electronic spectroscopies with targeted light irradiation wavelengths. The unveiled chromophore structure and dynamics inside engineered FPs in an aqueous buffer solution can be generalized to improve other green-to-red photoconvertible FPs from the bottom up for deeper biophysics with molecular biology insights and powerful bioimaging advances.

do Casal M, Pinheiro M, Toldo JM, Barbatti M. Modeling the heating and cooling of a chromophore after photoexcitation

The heating of a chromophore due to internal conversion and its cooling down due to energy dissipation to the solvent are crucial phenomena to characterize molecular photoprocesses. In this work, we simulated the ab initio nonadiabatic dynamics of cytosine, a prototypical chromophore undergoing ultrafast internal conversion, in three solvents—argon matrix, benzene, and water—spanning an extensive range of interactions. We implemented an analytical energy-transfer model to analyze these data and extract heating and cooling times. The model accounts for nonadiabatic effects, and excited- and ground-state energy transfer, and can analyze data from any dataset containing kinetic energy as a function of time. Cytosine heats up in the subpicosecond scale and cools down within 25, 4, and 1.3 ps in argon, benzene, and water, respectively. The time constants reveal that a significant fraction of the benzene and water heating occurs while cytosine is still electronically excited.

An analytical energy-transfer model is implemented to obtain a chromophore's heating and cooling times in a given solvent by using quantities available in nonadiabatic dynamics simulations.

Fluorescence Modulation by Ultrafast Chromophore Twisting Events: Developing a Powerful Toolset for Fluorescent-Protein-Based Imaging

The advancement of modern life sciences has benefited tremendously from the discovery and development of fluorescent proteins (FPs), widely expressed in live cells to track a myriad of cellular events. The chromophores of various FPs can undergo many ultrafast photophysical and/or photochemical processes in the electronic excited state and emit fluorescence with different colors. However, the chromophore becomes essentially nonfluorescent in solution environment due to its intrinsic twisting capability upon photoexcitation. To study "microscopic" torsional events and their effects on "macroscopic" fluorescence, we have developed an integrated ultrafast characterization platform involving femtosecond transient absorption (fs-TA) and wavelength-tunable femtosecond stimulated Raman spectroscopy (FSRS). A wide range of naturally occurring, circularly permuted, non-canonical amino-acid-decorated FPs and FP-based optical highlighters with photochromicity, photoconversion, and/or photoswitching capabilities have been recently investigated in great detail. Twisting conformational motions were elucidated to exist in all of these systems but to various extents. The associated different ultrafast pathways can be monitored via frequency changes of characteristic Raman bands during primary events and functional processes. The mapped electronic and structural dynamics information is crucial and has shown great potential and initial success for the rational design of proteins and other photoreceptors with novel functions and fluorescence properties.

Elucidating Inner Workings of Naturally Sourced Organic Optoelectronic Materials with Ultrafast Spectroscopy

Recent advances in sustainable optoelectronics including photovoltaics, light-emitting diodes, transistors, and semiconductors have been enabled by π-conjugated organic molecules. A fundamental understanding of light-matter interactions involving these materials can be realized by time-resolved electronic and vibrational spectroscopies. In this Minireview, the photoinduced mechanisms including charge/energy transfer, electronic (de)localization, and excited-state proton transfer are correlated with functional properties encompassing optical absorption, fluorescence quantum yield, conductivity, and photostability. Four naturally derived molecules (xylindein, dimethylxylindein, alizarin, indigo) with ultrafast spectral insights showcase efficient energy dissipation involving H-bonding networks and proton motions, which yield high photostability. Rational design principles derived from such investigations could increase the efficiency for light harvesting, triplet formation, and photosensitivity for improved and versatile optoelectronic performance.

Tracking Ultrafast Fluorescence Switch-On and Color-Tuned Dynamics in Acceptor-Donor-Acceptor Chromophore

Understanding how the conformational change of conjugated molecules with acceptor-donor-acceptor (A-D-A) architecture affects their physical and optoelectronic properties is critical for determining their ultimate performance in organic electronic devices. Here, we utilized femtosecond transient absorption, time-resolved upconversion photoluminescence spectroscopy, and tunable femtosecond-stimulated Raman spectroscopy, aided by quantum chemical calculations, to systematically investigate the excited state structural dynamics of the intramolecular charge transfer of the tetramethoxy anthracene-based fluorophore 2,3,6,7-tetramethoxy 9,10-dibenzaldehydeanthracene (AnDA) and its derivative 2,3,6,7-tetramethoxy 9,10-diphenylanthracene (TMDPAn) in chloroform. In the AnDA molecule, the tetramethoxy anthracene and benzaldehyde moieties exhibit a strong ability to donate and withdraw electrons. Upon photoexcitation, AnDA shows intriguing ultrafast fluorescence switch-on and red shift dynamics on charge transfer states, and the temporal evolution of AnDA recorded by ultrafast spectroscopy reveals a dynamic picture of two-step intramolecular charge transfer assisted by ultrafast conformational changes and solvation processes. Removing the aldehyde group from TMDPAn significantly decreases the electron pulling capacity of the phenyl unit and disables charge transfer characteristics.

An Engineered Biliverdin-Compatible Cyanobacteriochrome Enables a Unique Ultrafast Reversible Photoswitching Pathway

Cyanobacteriochromes (CBCRs) are promising optogenetic tools for their diverse absorption properties with a single compact cofactor-binding domain. We previously uncovered the ultrafast reversible photoswitching dynamics of a red/green photoreceptor AnPixJg2, which binds phycocyanobilin (PCB) that is unavailable in mammalian cells. Biliverdin (BV) is a mammalian cofactor with a similar structure to PCB but exhibits redder absorption. To improve the AnPixJg2 feasibility in mammalian applications, AnPixJg2_BV4 with only four mutations has been engineered to incorporate BV. Herein, we implemented femtosecond transient absorption (fs-TA) and ground state femtosecond stimulated Raman spectroscopy (GS-FSRS) to uncover transient electronic dynamics on molecular time scales and key structural motions responsible for the photoconversion of AnPixJg2_BV4 with PCB (Bpcb) and BV (Bbv) cofactors in comparison with the parent AnPixJg2 (Apcb). Bpcb adopts the same photoconversion scheme as Apcb, while BV4 mutations create a less bulky environment around the cofactor D ring that promotes a faster twist. The engineered Bbv employs a reversible clockwise/counterclockwise photoswitching that requires a two-step twist on ~5 and 35 picosecond (ps) time scales. The primary forward P_fr → P_o transition displays equal amplitude weights between the two processes before reaching a conical intersection. In contrast, the primary reverse P_o → P_fr transition shows a 2:1 weight ratio of the ~35 ps over 5 ps component, implying notable changes to the D-ring-twisting pathway. Moreover, we performed pre-resonance GS-FSRS and quantum calculations to identify the Bbv vibrational marker bands at ~659,797, and 1225 cm^-1. These modes reveal a stronger H-bonding network around the BV cofactor A ring with BV4 mutations, corroborating the D-ring-dominant reversible photoswitching pathway in the excited state. Implementation of BV4 mutations in other PCB-binding GAF domains like AnPixJg4, AM1_1870g3, and NpF2164g5 could promote similar efficient reversible photoswitching for more directional bioimaging and optogenetic applications, and inspire other bioengineering advances.

Tracking Ultrafast Structural Dynamics in a Dual-Emission Anti-Kasha-Active Fluorophore Using Femtosecond Stimulated Raman Spectroscopy

The anti-Kasha process provides the possibility of using high-energy excited states to develop novel applications. Our previous research (Nature communications, 2020, 11, 793) has demonstrated a dual-emission anti-Kasha-active fluorophore for bioimaging application, which exhibits near-infrared emissions from the S₁ state and visible anti-Kasha emissions from the S₂ state. Here, we applied tunable blue-side femtosecond stimulated Raman spectroscopy (FSRS) and transient absorption spectroscopy, assisted by quantum calculations, to reveal the anti-Kasha dual emission mechanism, in which the emergence of two fluorescing states is due to the retardation of internal conversion from the S₂ state to the S₁ state. It has been demonstrated that the facts of anti-Kasha high-energy emission are commonly attributed to a large energy gap between the two excited states, leading to a decrease in the internal conversion rate due to a poor Franck-Condon factor. In this study, analysis of the calculation and FSRS experimental results provide us further insight into the dual-emission anti-Kasha mechanism, where the observation of hydrogen out-of-plane Raman modes from FSRS suggested that, in addition to the energy-gap law, the initial photoinduced molecular conformational change plays a key role in influencing the rate of internal conversion.

Direct Tracking Excited-State Intramolecular Charge Redistribution of Acceptor-Donor-Acceptor Molecule by Means of Femtosecond Stimulated Raman Spectroscopy

Symmetric quadrupolar molecules generally exhibit apolar ground states and dipolar excited states in a polar environment, which is explained by the excited state evolution from initial charge delocalization over all molecules to localization on one branch of the molecules after a femtosecond pulse excitation. However, direct observation of excited-state charge redistribution (delocalization/localization) is hardly accessible. Here, the intramolecular charge delocalization/localization character of a newly synthesized acceptor-donor-acceptor molecule (ADA) has been intensively investigated by femtosecond stimulated Raman scattering (FSRS) together with femtosecond transient absorption (fs-TA) spectroscopy. By tracking the excited state Raman spectra of the specific alkynyl (-C≡C-) bonds at each branch of ADA, we found that the nature of the relaxed S₁ state is strongly governed by solvent polarity: symmetric delocalized intramolecular charge transfer (ICT) characters occurred in apolar solvent, whereas the asymmetric localized ICT characters appeared in polar solvent because of solvation. The solvation dynamics of ADA extracted from fs-TA is consistent with the time constants obtained by FSRS, but the FSRS clearly tracks the excited state intramolecular charge transfer delocalization/localization.

Discovering a rotational barrier within a charge-transfer state of a photoexcited chromophore in solution

Methylation occurs in a myriad of systems with protective and regulatory functions. 8-methoxypyrene-1,3,6-trisulfonate (MPTS), a methoxy derivative of a photoacid, serves as a model system to study effects of methylation on the excited state potential energy landscape. A suite of spectroscopic techniques including transient absorption, wavelength-tunable femtosecond stimulated Raman spectroscopy (FSRS), and fluorescence quantum yield measurements via steady-state electronic spectroscopy reveal the energy dissipation pathways of MPTS following photoexcitation. Various solvents enable a systematic characterization of the H-bonding interaction, viscosity, and dynamic solvation that influence the ensuing relaxation pathways. The formation of a charge-transfer state out of the Franck-Condon region occurs on the femtosecond-to-picosecond solvation timescale before encountering a rotational barrier. The rotational relaxation correlates with the H-bond donating strength of solvent, while the rotational time constant lengthens as solvent viscosity increases. Time-resolved excited-state FSRS, aided by quantum calculations, provides crucial structural dynamics knowledge and reveals the sulfonate groups playing a dominant role during solvation. Several prominent vibrational motions of the pyrene ring backbone help maneuver the population toward the more fluorescent state. These ultrafast correlated electronic and nuclear motions ultimately govern the fate of the photoexcited chromophore in solution. Overall, MPTS in water displays the highest probability to fluoresce, while the aprotic and more viscous dimethyl sulfoxide enhances the nonradiative pathways. These mechanistic insights may apply robustly to other photoexcited chromophores that do not undergo excited-state proton transfer or remain trapped in a broad electronic state and also provide design principles to control molecular optical responses with site-specific atomic substitution.

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.

Ultrafast excited-state proton transfer dynamics in dihalogenated non-fluorescent and fluorescent GFP chromophores

Green fluorescent protein (GFP) has enabled a myriad of bioimaging advances due to its photophysical and photochemical properties. To deepen the mechanistic understanding of such light-induced processes, novel derivatives of GFP chromophore p-HBDI were engineered by fluorination or bromination of the phenolic moiety into superphotoacids, which efficiently undergo excited-state proton transfer (ESPT) in aqueous solution within the short lifetime of the excited state, as opposed to p-HBDI where efficient ESPT is not observed. In addition, we tuned the excited-state lifetime from picoseconds to nanoseconds by conformational locking of the p-HBDI backbone, essentially transforming the nonfluorescent chromophores into highly fluorescent ones. The unlocked superphotoacids undergo a barrierless ESPT without much solvent activity, whereas the locked counterparts exhibit two distinct solvent-involved ESPT pathways. Comparative analysis of femtosecond transient absorption spectra of these unlocked and locked superphotoacids reveals that the ESPT rates adopt an "inverted" kinetic behavior as the thermodynamic driving force increases upon locking the backbone. Further experimental and theoretical investigations are expected to shed more light on the interplay between the modified electronic structure (mainly by dihalogenation) and nuclear motions (by conformational locking) of the functionalized GFP derivatives (e.g., fluorescence on and off).

Unveiling coupled electronic and vibrational motions of chromophores in condensed phases

The quest for capturing molecular movies of functional systems has motivated scientists and engineers for decades. A fundamental understanding of electronic and nuclear motions, two principal components of the molecular Schrödinger equation, has the potential to enable the de novo rational design for targeted functionalities of molecular machines. We discuss the development and application of a relatively new structural dynamics technique, femtosecond stimulated Raman spectroscopy with broadly tunable laser pulses from the UV to near-IR region, in tracking the coupled electronic and vibrational motions of organic chromophores in solution and protein environments. Such light-sensitive moieties hold broad interest and significance in gaining fundamental knowledge about the intramolecular and intermolecular Hamiltonian and developing effective strategies to control macroscopic properties. Inspired by recent experimental and theoretical advances, we focus on the in situ characterization and spectroscopy-guided tuning of photoacidity, excited state proton transfer pathways, emission color, and internal conversion via a conical intersection.

Photoinduced charge flow inside an iron porphyrazine complex

Tracking inorganic photochemistry with high resolution poses considerable challenges. Here, sub-picosecond electronic and structural motions and MLCT/d-d intersystem crossing in a cationic iron-porphyrazine are probed using ultrafast transient absorption, stimulated Raman spectroscopy, and quantum calculations. By delineating photoinduced energy relaxation, strategies for extending the lifetime of MLCT state are discussed.

Nitration of Tyrosine Channels Photoenergy through a Conical Intersection in Water

Nitration of tyrosine occurs under oxidative stress in vivo. The product, 3-nitrotyrosine (3NY), has a dramatically decreased quantum yield and can be used as a molecular ruler. In this study, femtosecond transient absorption spectroscopy and quantum calculations were implemented to elucidate the photoinduced relaxation processes of anionic 3NY in water. Upon 400 nm excitation into an excited electronic state with notable charge-transfer (CT) character, a barrierless nitro-twisting motion rapidly (<100 fs) guides the chromophore into an adjacent twisted intramolecular CT state, therein reaching a sloped S₁/S₀ conical intersection on the ∼100 fs time scale. Once in the hot ground state, excess energy is further released through vibrational cooling with biexponential time constants of ∼140 and 680 fs in water. Nitro back-twisting occurs on longer time scales (∼1.1 and 9 ps in water), returning the system to original ground state. Systematic evaluations of excited-state potential energies of anionic 3NY were performed by density functional theory (DFT) and time-dependent DFT calculations, showing that intersystem crossing (ISC) from the first singlet state (S₁) to the first or second triplet state (T₁ or T₂) is unlikely. Inclusion of an explicit water molecule in calculations leads to improved mapping of the excited-state energy ordering of the second singlet state (S₂) and T₂, further diminishing ISC probability from S₁ and favoring an ultrafast internal conversion to S₀. These results provide deep insights into the highly efficient nonradiative decay of anionic 3NY in aqueous solution, with nitro-site-specific information that can help infer the characterization and potential optogenetic control of 3NY in protein environment.

Excited state structural dynamics of 4-cyano-4′-hydroxystilbene: deciphering the signatures of proton-coupled electron transfer using ultrafast Raman loss spectroscopy

The photo-initiated proton-coupled electron transfer process in the 4-cyano-4′-hydroxystilbene–tert-butylamine adduct strongly affects the excited-state structural dynamics of CHSB.

Watching an Engineered Calcium Biosensor Glow: Altered Reaction Pathways before Emission

Biosensors have become an indispensable tool set in life sciences. Among them, fluorescent protein-based biosensors have great biocompatibility and tunable emission properties but their development is largely on trial and error. To facilitate a rational design, we implement tunable femtosecond stimulated Raman spectroscopy, aided by transient absorption and quantum calculations, to elucidate the working mechanisms of a single-site Pro377Arg mutant of an emission ratiometric Ca²⁺ biosensor based on a green fluorescent protein-calmodulin complex. Comparisons with the parent protein and the Ca²⁺-free/bound states unveil more structural inhomogeneity yet an overall faster excited-state proton-transfer (ESPT) reaction inside the Ca²⁺-bound biosensor. The correlated photoreactant and photoproduct vibrational modes in the excited state reveal more chromophore twisting and trapping in the Ca²⁺-bound state during ESPT and the largely conserved chromophore dynamics in the Ca²⁺-free state from parent protein. The uncovered structural dynamics insights throughout an ESPT reaction inside a calcium biosensor provide important design principles in maintaining a hydrophilic, less compact, and more homogeneous environment with directional H-bonding (from the chromophore to surrounding protein residues) via bioengineering methods to improve the ESPT efficiency and quantum yield while maintaining photostability.

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.

Uncovering the Hidden Excited State toward Fluorescence of an Intracellular pH Indicator

Intracellular pH (pH_i) imaging is of paramount importance for life sciences. In this work, we implement the ultrafast electronic and stimulated Raman spectroscopies to unravel the fluorescence mechanism of an excitation-ratiometric pH_i indicator in basic aqueous solution. After photoexcitation of the pH_i indicator HPTS, a hidden charge-transfer (CT) state following the locally excited (LE) state is uncovered as an essential step prior to fluorescence and this LE → CT transition is gated by ultrafast solvation dynamics. A 835 cm^-1 intermolecular vibrational mode is identified to potentially facilitate the CT-state formation on the 700 fs time scale. Dynamic correlation with the other excited-state Raman marker bands suggests that the transition between transient electronic states is aided by solvation events mostly in the molecular plane of HPTS. These vivid structural dynamics insights can enable the rational design of more efficient and bright pH_i indicators in an H-bonding environment with controllable properties.

Excited State Structural Evolution of a GFP Single-Site Mutant Tracked by Tunable Femtosecond-Stimulated Raman Spectroscopy

Tracking vibrational motions during a photochemical or photophysical process has gained momentum, due to its sensitivity to the progression of reaction and change of environment. In this work, we implemented an advanced ultrafast vibrational technique, femtosecond-stimulated Raman spectroscopy (FSRS), to monitor the excited state structural evolution of an engineered green fluorescent protein (GFP) single-site mutant S205V. This mutation alters the original excited state proton transfer (ESPT) chain. By strategically tuning the Raman pump to different wavelengths (i.e., 801, 539, and 504 nm) to achieve pre-resonance with transient excited state electronic bands, the characteristic Raman modes of the excited protonated (A*) chromophore species and intermediate deprotonated (I*) species can be selectively monitored. The inhomogeneous distribution/population of A* species go through ESPT with a similar ~300 ps time constant, confirming that bridging a water molecule to protein residue T203 in the ESPT chain is the rate-limiting step. Some A* species undergo vibrational cooling through high-frequency motions on the ~190 ps time scale. At early times, a portion of the largely protonated A* species could also undergo vibrational cooling or return to the ground state with a ~80 ps time constant. On the photoproduct side, a ~1330 cm⁻¹ delocalized motion is observed, with dispersive line shapes in both the Stokes and anti-Stokes FSRS with a pre-resonance Raman pump, which indicates strong vibronic coupling, as the mode could facilitate the I* species to reach a relatively stable state (e.g., the main fluorescent state) after conversion from A*. Our findings disentangle the contributions of various vibrational motions active during the ESPT reaction, and offer new structural dynamics insights into the fluorescence mechanisms of engineered GFPs and other analogous autofluorescent proteins.

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.

Photoinduced proton transfer inside an engineered green fluorescent protein: a stepwise-concerted-hybrid reaction

Photoactivated proton transfer (PT) wire is responsible for the glow of green fluorescent protein (GFP), which is crucial for bioimaging and biomedicine. In this work, a new GFP-S65T/S205V double mutant is developed from wild-type GFP in which the PT wire is significantly modified. We implement femtosecond transient absorption (fs-TA) and femtosecond stimulated Raman spectroscopy (FSRS) to delineate the PT process in action. The excited state proton transfer proceeds on the ∼110 ps timescale, which infers that the distance of one key link (water to T203) in the PT wire of GFP-S205V is shortened by the extra S65T mutation. The rise of an imidazolinone ring deformation mode at ∼871 cm-1 in FSRS further suggests that this PT reaction is in a concerted manner. A ∼4 ps component prior to large-scale proton dissociation through the PT wire is also retrieved, indicative of some small-scale proton motions and heavy-atom rearrangement in the vicinity of the chromophore. Our work provides deep insights into the novel hybrid PT mechanism in engineered GFP and demonstrates the power of tunable FSRS methodology in tracking ultrafast photoreactions with the desirable structural specificity in physiological environments.

Correlated Molecular Structural Motions for Photoprotection after Deep-UV Irradiation

Exposure to ultraviolet (UV) light could cause photodamage to biomolecular systems and degrade optoelectronic devices. To mitigate such detrimental effects from the bottom up, we strategically select a photosensitive molecule pyranine and implement femtosecond electronic and Raman spectroscopies to elucidate its ultrafast photoprotection mechanisms in solution. Our results show that pyranine undergoes excited-state proton transfer in water, while this process is blocked in methanol regardless of excitation wavelengths (267, 400 nm). After 267 nm irradiation, the molecule relaxes from a higher lying electronic state into a lower lying singlet state with a <300 fs time constant, followed by solvation events. Transient Raman marker bands exhibit different patterns of intensity dynamics and frequency shift that elucidate the real-time interplay among conformational motions, photochemical reaction, and vibrational cooling after excitation. More energetic photons are revealed to selectively enhance certain relaxation pathways. These mechanistic findings offer new guidelines to improve the UV tolerance and stability of the engineered functional molecules in materials and life sciences.

Difference Bands in Time-Resolved Femtosecond Stimulated Raman Spectra of Photoexcited Intermolecular Electron Transfer from Chloronaphthalene to Tetracyanoethylene

The time-resolved femtosecond stimulated Raman spectra (FSRS) of a charge transfer (CT) excited noncovalent complex tetracyanoethylene:1-chloronaphthalene (TCNE:ClN) in dichloromethane (DCM) is reported with 40 fs time resolution. In the frequency domain, five FSRS peaks are observed with frequencies of 534, 858, 1069, 1392, and 1926 cm^-1. The most intense peaks at 534 and 1392 cm^-1 correspond to fundamentals while the features at 858, 1069, and 1926 cm^-1 are attributed to a difference frequency, an overtone and a combination frequency of the fundamentals, respectively. The frequency of the 1392 cm^-1 fundamental corresponding to the central C═C stretch of TCNE^•- is red-shifted from the frequency of the steady state radical due to the close proximity and electron affinity of the countercation. The observation of a FSRS band at a difference frequency is analyzed. This analysis lends evidence for alternative nonlinear pathways of inverse Raman gain scattering (IRGS) or vertical-FSRS (VFSRS) which may contribute to the time-evolving FSRS spectrum on-resonance. Impulsive stimulated Raman measurements of the complex show coherent oscillations of the stimulated emission with frequencies of 153, 278, and 534 cm^-1. The 278 cm^-1 mode corresponds to Cl bending of the dichloromethane solvent. The center frequency of the 278 cm^-1 mode is modulated by a frequency of ∼30 cm^-1 which is attributed to the effect of librational motion of the dichloromethane solvent as it reorganizes around the nascent contact ion pair. The 153 ± 15 cm^-1 mode corresponds to an out-of-plane bending motion of TCNE. This motion modulates the intermolecular separation of the contact ion pair and thereby the overlap of the frontier orbitals which is crucial for rapid charge recombination in 5.9 ± 0.2 ps. High time-frequency resolution vibrational spectra provide unique molecular details regarding charge localization and recombination.

Unveiling Structural Motions of a Highly Fluorescent Superphotoacid by Locking and Fluorinating the GFP Chromophore in Solution

Superphotoacidity involves ultrafast proton motions implicated in numerous chemical and biological processes. We used conformational locking and strategic addition of electron-withdrawing substituents to synthesize a new GFP chromophore analogue: p-HO-3,5-diF-BDI:BF₂ (diF). It is highly fluorescent and exhibits excited-state proton transfer (ESPT) in various solvents, placing it among the strongest photoacids. Tunable femtosecond stimulated Raman spectroscopy with unique resonance conditions and transient absorption are complementarily employed to elucidate the structural basis for superphotoacidity. We reveal a multistep ESPT reaction from diF to methanol with an initial proton dissociation on the ∼600 fs time scale that forms a charge-separated state, stabilized by solvation, and followed by a diffusion-controlled proton transfer on the ∼350 ps time scale. A ∼1580 cm^-1 phenolic ring motion is uncovered to accompany ESPT before 1 ps. This study provides a vivid movie of the photoinduced proton dissociation of a superphotoacid with bright fluorescence, effectively bridging fundamental mechanistic insights to precise control of macroscopic functions.

Influence of Solvent Relaxation on Ultrafast Excited-State Proton Transfer to Solvent

A thorough understanding of the microscopic mechanism of excited-state proton transfer (ESPT) and the influence of the solvent environment on its dynamics are of great fundamental interest. We present here a detailed investigation of an ESPT to solvent (DMSO) using time-resolved broadband fluorescence and transient absorption spectroscopies. All excited-state species are resolved spectrally and kinetically using a global target analysis based on the two-step Eigen-Weller model. Reversibility of the initial short-range proton transfer producing excited contact ion pairs (CIP*) is observed unambiguously in fluorescence and must be explicitly considered to obtain the individual rate constants. Close inspection of the early dynamics suggests that the relative populations of the protonated form (ROH*) and CIP* are governed by solvent relaxation that influences the relative energies of the excited states. This constitutes a breakdown of the Eigen-Weller model, although the overall agreement between the data and the analysis using classical rate equations is excellent.

Ionic effects on the proton transfer mechanism in aqueous solutions

Proton dissociation (PD) reactions of weak acids and proton transfer (PT) processes in aqueous solutions are strongly influenced by ions.

How do the interfacial properties of zwitterionic sulfobetaine micelles differ from those of cationic alkyl quaternary ammonium micelles? An excited state proton transfer study

The interface of a zwitterionic sulfobetaine micelle is more packed and less hydrated compared to a cationic alkyl-ammonium micelle with an identical alkyl tail.