Nitration of Tyrosine Channels Photoenergy through a Conical Intersection in Water

Electronic dynamics through conical intersections via non-Markovian stochastic Schrödinger equation with complex modes

Conical intersections (CIs) play a crucial role in photochemical reactions, offering an efficient channel for ultrafast non-adiabatic relaxation of excited states. This significantly influences the reaction pathways and the resulting products. In this work, we utilize the non-Markovian stochastic Schrödinger equation with complex modes method to explore the dynamics of electronic transitions through conical intersections (CIs) in pyrazine. The linear vibronic coupling model serves as the foundational framework, incorporating both intra-state and inter-state electron-vibrational interactions. The dynamics of the excited electronic transitions are analyzed across varying strengths of system-bath coupling and different bath relaxation times. The accuracy of this method is demonstrated by comparing its predictions with those from the hierarchical equations of motion method.

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.

Selective detection of nitrotyrosine using dual-fluorescent carbon dots

The post-translational modification of amino acid plays a critical role in normal and diseased biological states. Specifically, nitrotyrosine (nTyr) has been linked to diseases, including neurodegeneration, among others. Hence, alternative methods are required for detection and differentiation of nTyr from other structurally similar analogues, such as Tyrosine (Tyr) or phosphotyrosine (pTyr). Herein, the selective detection of nTyr, over other congeners, was achieved by using dual-fluorescent carbon dots (CDs) in buffered solution, artificial saliva, bovine serum albumin and diluted equine serum. The nTyr induced fluorescence quenching of the blue and red emissions of CDs, in the 20-105 μM linear range, and with the limit of detection (LOD) at 34 μM, which was well below the physiological concentration required for detection. The sensor was functional at biological pH values, with optimal quenching efficiency at basic pH. The sensor was highly selective for nTyr even in the presence of common biological interferences (metal cations, organic anions, amino acids, nucleosides and other biologicals). The mechanism of quenching (a combination of static and dynamic) was ascribed to the nonradiative energy transfer, due to electronic overlap between nTyr absorbance and CDs fluorescence emission, and electron transfer from excited CDs state to nTyr as an electron acceptor. The dual-fluorescent CDs represent viable sensors for key biological modifications, and their selectivity and sensitivity may be further improved through tailored chemical synthesis of CDs, such as tunable surface chemistry to promote selective recognition of analyte of interest.

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.

A Novel Dialkylamino GFP Chromophore as an Environment-Polarity Sensor Reveals the Role of Twisted Intramolecular Charge Transfer

We discovered a novel fluorophore by incorporating a dimethylamino group (–NMe2) into the conformationally locked green fluorescent protein (GFP) scaffold. It exhibited a marked solvent-polarity-dependent fluorogenic behavior and can potentially find broad applications as an environment-polarity sensor in vitro and in vivo. The ultrafast femtosecond transient absorption (fs-TA) spectroscopy in combination with quantum calculations revealed the presence of a twisted intramolecular charge transfer (TICT) state, which is formed by rotation of the –NMe2 group in the electronic excited state. In contrast to the bright fluorescent state (FS), the TICT state is dark and effectively quenches fluorescence upon formation. We employed a newly developed multivariable analysis approach to the FS lifetime in various solvents and showed that the FS → TICT reaction barrier is mainly modulated by H-bonding capability instead of viscosity of the solvent, accounting for the observed polarity dependence. These deep mechanistic insights are further corroborated by the dramatic loss of fluorogenicity for two similar GFP-derived chromophores in which the rotation of the –NMe2 group is inhibited by structural locking.

Shedding light on ultrafast ring-twisting pathways of halogenated GFP chromophores from the excited to ground state

Since green fluorescent protein (GFP) has revolutionized molecular and cellular biology for about three decades, there has been a keen interest in understanding, designing, and controlling the fluorescence properties of GFP chromophore (i.e., HBDI) derivatives from the protein matrix to solution. Amongst these cross-disciplinary efforts, the elucidation of excited-state dynamics of HBDI derivatives holds the key to correlating the light-induced processes and fluorescence quantum yield (FQY). Herein, we implement steady-state electronic spectroscopy, femtosecond transient absorption (fs-TA), femtosecond stimulated Raman spectroscopy (FSRS), and quantum calculations to study a series of mono- and dihalogenated HBDI derivatives (X = F, Cl, Br, 2F, 2Cl, and 2Br) in basic aqueous solution, gaining new insights into the photophysical reaction coordinates. In the excited state, the halogenated "floppy" chromophores exhibit an anti-heavy atom effect, reflected by strong correlations between FQY vs. Franck-Condon energy (EFC) or Stokes shift, and knrvs. EFC, as well as a swift bifurcation into the I-ring (major) and P-ring (minor) twisting motions. In the ground state, both ring-twisting motions become more susceptible to sterics and exhibit spectral signatures from the halogen-dependent hot ground-state absorption band decay in TA data. We envision this type of systematic analysis of the halogenated HBDI derivatives to provide guiding principles for the site-specific modification of GFP chromophores, and expand design space for brighter and potentially photoswitchable organic chemical probes in aqueous solution with discernible spectral signatures throughout the photocycle.

Transient electronic and vibrational signatures during reversible photoswitching of a cyanobacteriochrome photoreceptor

Cyanobacteriochromes (CBCRs) are an emerging class of photoreceptors that are distant relatives of the phytochromes family. Unlike phytochromes, CBCRs have gained popularity in optogenetics due to their highly diverse spectral properties spanning the UV to near-IR region and only needing a single compact binding domain. AnPixJg2 is a CBCR that can reversibly photoswitch between its red-absorbing (^15ZP_r) and green-absorbing (^15EP_g) forms of the phycocyanobilin (PCB) cofactor. To reveal primary events of photoconversion, we implemented femtosecond transient absorption spectroscopy with a homemade LED box and a miniature peristaltic pump flow cell to track transient electronic responses of the photoexcited AnPixJg2 on molecular time scales. The 525 nm laser-induced P_g-to-P_r reverse conversion exhibits a ~3 ps excited-state lifetime before reaching the conical intersection (CI) and undergoing further relaxation on the 30 ps time scale to generate a long-lived Lumi-G ground state intermediate en route to P_r. The 650 nm laser-induced P_r-to-P_g forward conversion is less efficient than reverse conversion, showing a longer-lived excited state which requires two steps with ~13 and 217 ps time constants to enter the CI region. Furthermore, using a tunable ps Raman pump with broadband Raman probe on both the Stokes and anti-Stokes sides, we collected the pre-resonance ground-state femtosecond stimulated Raman spectroscopy (GS-FSRS) data with mode assignments aided by quantum calculations. Key vibrational marker bands at ~850, 1050, 1615, and 1649 cm^-1 of the P_r conformer exhibit a notable blueshift to those of the P_g conformer inside AnPixJg2, reflecting the PCB chromophore terminal D (major) and A (minor) ring twist along the primary photoswitching reaction coordinate. This integrated ultrafast spectroscopy and computational platform has the potential to elucidate photochemistry and photophysics of more CBCRs and photoactive proteins in general, providing the highly desirable mechanistic insights to facilitate the rational design of functional molecular sensors and devices.

Ultrafast Dynamics and Photoresponse of a Fungi-Derived Pigment Xylindein from Solution to Thin Films

Organic semiconductor materials have recently gained momentum due to their non-toxicity, low cost, and sustainability. Xylindein is a remarkably photostable pigment secreted by fungi that grow on decaying wood, and its relatively strong electronic performance is enabled by π-π stacking and hydrogen-bonding network that promote charge transport. Herein, femtosecond transient absorption spectroscopy with a near-IR probe was used to unveil a rapid excited-state intramolecular proton transfer reaction. Conformational motions potentially lead to a conical intersection that quenches fluorescence in the monomeric state. In concentrated solutions, nascent aggregates exhibit a faster excited state lifetime due to excimer formation, confirmed by the excimer→charge-transfer excited-state absorption band of the xylindein thin film, thus limiting its optoelectronic performance. Therefore, extending the xylindein sidechains with branched alkyl groups may hinder the excimer formation and improve optoelectronic properties of naturally derived materials.

Switching between Ultrafast Pathways Enables a Green-Red Emission Ratiometric Fluorescent-Protein-Based Ca2+ Biosensor

Ratiometric indicators with long emission wavelengths are highly preferred in modern bioimaging and life sciences. Herein, we elucidated the working mechanism of a standalone red fluorescent protein (FP)-based Ca2+ biosensor, REX-GECO1, using a series of spectroscopic and computational methods. Upon 480 nm photoexcitation, the Ca2+-free biosensor chromophore becomes trapped in an excited dark state. Binding with Ca2+ switches the route to ultrafast excited-state proton transfer through a short hydrogen bond to an adjacent Glu80 residue, which is key for the biosensor's functionality. Inspired by the 2D-fluorescence map, REX-GECO1 for Ca2+ imaging in the ionomycin-treated human HeLa cells was achieved for the first time with a red/green emission ratio change (ΔR/R0) of ~300%, outperforming many FRET- and single FP-based indicators. These spectroscopy-driven discoveries enable targeted design for the next-generation biosensors with larger dynamic range and longer emission wavelengths.

Deciphering the unusual fluorescence in weakly coupled bis-nitro-pyrrolo[3,2-b]pyrroles

Electron-deficient π-conjugated functional dyes lie at the heart of organic optoelectronics. Adding nitro groups to aromatic compounds usually quenches their fluorescence via inter-system crossing (ISC) or internal conversion (IC). While strong electronic coupling of the nitro groups with the dyes ensures the benefits from these electron-withdrawing substituents, it also leads to fluorescence quenching. Here, we demonstrate how such electronic coupling affects the photophysics of acceptor-donor-acceptor fluorescent dyes, with nitrophenyl acceptors and a pyrrolo[3,2-b]pyrrole donor. The position of the nitro groups and the donor-acceptor distance strongly affect the fluorescence properties of the bis-nitrotetraphenylpyrrolopyrroles. Concurrently, increasing solvent polarity quenches the emission that recovers upon solidifying the media. Intramolecular charge transfer (CT) and molecular dynamics, therefore, govern the fluorescence of these nitro-aromatics. While balanced donor-acceptor coupling ensures fast radiative deactivation and slow ISC essential for large fluorescence quantum yields, vibronic borrowing accounts for medium dependent IC via back CT. These mechanistic paradigms set important design principles for molecular photonics and electronics.

Dissecting Optical Response and Molecular Structure of Fluorescent Proteins With Non-canonical Chromophores

Tracking the structural dynamics of fluorescent protein chromophores holds the key to unlocking the fluorescence mechanisms in real time and enabling rational design principles of these powerful and versatile bioimaging probes. By combining recent chemical biology and ultrafast spectroscopy advances, we prepared the superfolder green fluorescent protein (sfGFP) and its non-canonical amino acid (ncAA) derivatives with a single chlorine, bromine, and nitro substituent at the ortho site to the phenolate oxygen of the embedded chromophore, and characterized them using an integrated toolset of femtosecond transient absorption and tunable femtosecond stimulated Raman spectroscopy (FSRS), aided by quantum calculations of the vibrational normal modes. A dominant vibrational cooling time constant of ~4 and 11 ps is revealed in Cl-GFP and Br-GFP, respectively, facilitating a ~30 and 12% increase of the fluorescent quantum yield vs. the parent sfGFP. Similar time constants were also retrieved from the transient absorption spectra, substantiating the correlated electronic and vibrational motions on the intrinsic molecular timescales. Key carbon-halogen stretching motions coupled with phenolate ring motions of the deprotonated chromophores at ca. 908 and 890 cm-1 in Cl-GFP and Br-GFP exhibit enhanced activities in the electronic excited state and blue-shift during a distinct vibrational cooling process on the ps timescale. The retrieved structural dynamics change due to targeted site-specific halogenation of the chromophore thus provides an effective means to design new GFP derivatives and enrich the bioimaging probe toolset for life and medical sciences.

Novel Solid-State Emissive Polymers and Polymeric Blends from a T-Shaped Benzodifuran Scaffold: A Comparative Study

Two novel polyimines were synthesized from a benzodifuran based diamino monomer and two dialdehydes bearing bulky groups and a flexible spacer. The polymers display tuned luminescence performance according to the presence of half-salen groups. The effect of the intramolecular bond on the emission properties were examined. Two model compounds, replicating the same emissive Schiff base cores, were synthetized. From the models, dye-doped blends in the fluorophore/matrix ratio, resembling the polymers, were produced. Amorphous thin films of the covalent polymers and the polymeric blends were obtained by spin-coating technique. The Photoluminescent (PL) response of the different macromolecular systems were qualitatively and quantitatively examined and compared.

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.

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).

Dual Illumination Enhances Transformation of an Engineered Green-to-Red Photoconvertible Fluorescent Protein

The molecular mechanisms for the photoconversion of fluorescent proteins remain elusive owing to the challenges of monitoring chromophore structural dynamics during the light-induced processes. We implemented time-resolved electronic and stimulated Raman spectroscopies to reveal two hidden species of an engineered ancestral GFP-like protein LEA, involving semi-trapped protonated and trapped deprotonated chromophores en route to photoconversion in pH 7.9 buffer. A new dual-illumination approach was examined, using 400 and 505 nm light simultaneously to achieve faster conversion and higher color contrast. Substitution of UV irradiation with visible light benefits bioimaging, while the spectral benchmark of a trapped chromophore with characteristic ring twisting and bridge-H bending motions enables rational design of functional proteins. With the improved H-bonding network and structural motions, the photoexcited chromophore could increase the photoswitching-aided photoconversion while reducing trapped species.

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.