PhotochemCAD 3: Diverse Modules for Photophysical Calculations with Multiple Spectral Databases

Water-dispersable photoreactors based on core-shell mesoporous silica particles

Robust solid-core silica particles with submicrometer size and anthracene-containing mesoporous shell were obtained and studied as model water-dispersable photoreactors. An anthracene derivative containing a triethoxysilyl group was synthesized and co-condensed with tetraethoxysilane in various ratios to form a photoactive mesoporous shell with a thickness up to approximately 80 nm on previously prepared solid silica particles. Mesopores of as-synthesized particles, without a commonly applied removal of the micellar templates, offered a confined space for solubilization of hydrophobic molecules. Efficient excitation energy transfer from anthracene chromophores to both hydrophobic (perylene) and hydrophilic (fluoresceine) encapsulated acceptors was observed in an aqueous dispersion of the particles. Photosensitized oxidation of encapsulated perylene was shown to proceed efficiently in such systems serving as water-dispersable photoreactors. Importantly, the designed core-shell systems were found to be stable for a long time (at least 24 months) and robust enough, thanks to the presence of solid cores, to be handled by centrifugation in aqueous dispersions. All these features make them promising candidates for reusable systems for the photosensitized degradation of water pollutants, especially hydrophobic pollutants.

An ultraviolet-driven rescue pathway for oxidative stress to eye lens protein human gamma-D crystallin

Human gamma-D crystallin (HGD) is a major constituent of the eye lens. Aggregation of HGD contributes to cataract formation, the leading cause of blindness worldwide. It is unique in its longevity, maintaining its folded and soluble state for 50-60 years. One outstanding question is the structural basis of this longevity despite oxidative aging and environmental stressors including ultraviolet radiation (UV). Here we present crystallographic structures evidencing a UV-induced crystallin redox switch mechanism. The room-temperature serial synchrotron crystallographic (SSX) structure of freshly prepared crystallin mutant (R36S) shows no post-translational modifications. After aging for nine months in the absence of light, a thiol-adduct (dithiothreitol) modifying surface cysteines is observed by low-dose SSX. This is shown to be UV-labile in an acutely light-exposed structure. This suggests a mechanism by which a major source of crystallin damage, UV, may also act as a rescuing factor in a finely balanced redox system.

Fluorescent proteins generate a genetic color polymorphism and counteract oxidative stress in intertidal sea anemones

Fluorescent proteins (FPs) are ubiquitous tools in research, yet their endogenous functions in nature are poorly understood. In this work, we describe a combination of functions for FPs in a clade of intertidal sea anemones whose FPs control a genetic color polymorphism together with the ability to combat oxidative stress. Focusing on the underlying genetics of a fluorescent green "Neon" color morph, we show that allelic differences in a single FP gene generate its strong and vibrant color, by increasing both molecular brightness and FP gene expression level. Natural variation in FP sequences also produces differences in antioxidant capacity. We demonstrate that these FPs are strong antioxidants that can protect live cells against oxidative stress. Finally, based on structural modeling of the responsible amino acids, we propose a model for FP antioxidant function that is driven by molecular surface charge. Together, our findings shed light on the multifaceted functions that can co-occur within a single FP and provide a framework for studying the evolution of fluorescence as it balances spectral and physiological functions in nature.

Chalcone-based Turn-Off Chemosensor for Selective and Susceptible Detection of Fe2+ Ions: Spectroscopic and DFT Investigations

Herein, in this report we are introducing newly synthesized chalcone derivative, "(E)-1-phenyl-3-(4-((5-(((Z)-thiophen-2-ylmethylene)amino)-1,3,4-thiadiazol-2-yl)thio)phenyl)prop-2-en-1-one" (5), as a chemosensor to detect Fe2+ metal ions in HEPES buffer solution of pH 7.5. Spectroscopic techniques were used to confirm the synthesized sensor. To determine the chemical reactivity and molecular stability of the probe, a frontier molecular orbitals investigation was carried out. A molecular electrostatic potential map was investigated to know the binding site of 5 for metal ion coordination. The theoretical absorption and fluorescence emission properties were estimated and correlated with the experimental observations. The sensor showed excellent selectivity for Fe2+ compared to all other studied metal ions. The fluorescence binding studies were carried out by adding different amounts of Fe2+ ions for a fixed concentration of probe 5. The inclusion of Fe2+ ions resulted in a decrease in fluorescence intensity with a bathochromic shift of emission wavelength of 5 due to the 5-Fe2+ complexation. The binding affinity value for the probe was found to be 576.2 M-1 with the help of the Stern-Volmer plot. The Job's plot and mass spectra supported the 2:1 (5: Fe2+) stoichiometry of complex formation. The detection limit and limit of quantification of 5 for Fe2+ were calculated to be 4.79 × 10-5 M and 14.54 × 10-5 M. Further, in addition to this, the photophysical parameters such as fluorescence lifetime of 5 and 5-Fe2+ complex measured to be 0.1439 and 0.1574 ns. The quantum yield of 5 and 5-Fe2+ was found to be 0.0398 and 0.0376. All these experimental findings revealed that probe 5 has excellent selectivity and sensitivity for Fe2+ ions.

Geometry-Independent Ultrafast Energy Transfer in Bioinspired Arrays Containing Electronically Coupled BODIPY Dimers as Energy Donors

In photosynthetic light-harvesting complexes, strong interaction between chromophores enables efficient absorption of solar radiation and has been suggested to enable ultrafast energy funneling to the reaction center. To examine whether similar effects can be realized in synthetic systems, and to determine the mechanisms of energy transfer, we synthesized and characterized a series of bioinspired arrays containing strongly-coupled BODIPY dimers as energy donors and chlorin derivatives as energy acceptors. The BODIPY dimers feature broad absorption in the range of 500-600 nm, complementing the chlorin absorption to provide absorption across the entire visible spectrum. Ultrafast (~10 ps) energy transfer was observed from photoexcited BODIPY dyads to chlorin subunits. Surprisingly, the energy-transfer rate is nearly independent of the position where the BODIPY dimer is attached to the chlorin and of the type of connecting linker. In addition, the energy-transfer rate from BODIPY dimers to chlorin is slower than the corresponding rate in arrays containing BODIPY monomers. The lower rate, corresponding to less efficient through-bond transfer, is most likely due to weaker electronic coupling between the ground state of the chlorin acceptor and the delocalized electronic state of the BODIPY dimer, compared to the localized state of a BODIPY monomer.

Tolyporphins-Exotic Tetrapyrrole Pigments in a Cyanobacterium-A Review

Tolyporphins were discovered some 30 years ago as part of a global search for antineoplastic compounds from cyanobacteria. To date, the culture HT-58-2, comprised of a cyanobacterium-microbial consortium, is the sole known producer of tolyporphins. Eighteen tolyporphins are now known-each is a free base tetrapyrrole macrocycle with a dioxobacteriochlorin (14), oxochlorin (3), or porphyrin (1) chromophore. Each compound displays two, three, or four open β-pyrrole positions and two, one, or zero appended C-glycoside (or -OH or -OAc) groups, respectively; the appended groups form part of a geminal disubstitution motif flanking the oxo moiety in the pyrroline ring. The distinct structures and repertoire of tolyporphins stand alone in the large pigments-of-life family. Efforts to understand the cyanobacterial origin, biosynthetic pathways, structural diversity, physiological roles, and potential pharmacological properties of tolyporphins have attracted a broad spectrum of researchers from diverse scientific areas. The identification of putative biosynthetic gene clusters in the HT-58-2 cyanobacterial genome and accompanying studies suggest a new biosynthetic paradigm in the tetrapyrrole arena. The present review provides a comprehensive treatment of the rich science concerning tolyporphins.

Design Rules for Obtaining Narrow Luminescence from Semiconductors Made in Solution

Solution-processed semiconductors are in demand for present and next-generation optoelectronic technologies ranging from displays to quantum light sources because of their scalability and ease of integration into devices with diverse form factors. One of the central requirements for semiconductors used in these applications is a narrow photoluminescence (PL) line width. Narrow emission line widths are needed to ensure both color and single-photon purity, raising the question of what design rules are needed to obtain narrow emission from semiconductors made in solution. In this review, we first examine the requirements for colloidal emitters for a variety of applications including light-emitting diodes, photodetectors, lasers, and quantum information science. Next, we will delve into the sources of spectral broadening, including "homogeneous" broadening from dynamical broadening mechanisms in single-particle spectra, heterogeneous broadening from static structural differences in ensemble spectra, and spectral diffusion. Then, we compare the current state of the art in terms of emission line width for a variety of colloidal materials including II-VI quantum dots (QDs) and nanoplatelets, III-V QDs, alloyed QDs, metal-halide perovskites including nanocrystals and 2D structures, doped nanocrystals, and, finally, as a point of comparison, organic molecules. We end with some conclusions and connections, including an outline of promising paths forward.

Spectroscopic Insights of an Emissive Complex between 4'-N,N-Diethylaminoflavonol in Octa-Acid Deep-Cavity Cavitand and Rhodamine 6G

Excited-state chemistry relies on the communication between molecules, making it a crucial aspect of the field. One important question that arises is whether intermolecular communication and its rate can be modified when a molecule is confined. To explore the interaction in such systems, we investigated the ground and excited states of 4'-N,N-diethylaminoflavonol (DEA3HF) in an octa acid-based (OA) confined medium and in ethanolic solution, both in the presence of Rhodamine 6G (R6G). Despite the observed spectral overlap between the flavonol emission and the R6G absorption, as well as the fluorescence quenching of the flavonol in the presence of R6G, the almost constant fluorescence lifetime at different amounts of R6G discards the presence of FRET in the studied systems. Steady-state and time-resolved fluorescence indicate the formation of an emissive complex between the proton transfer dye encapsulated within water-soluble supramolecular host octa acid (DEA3HF@(OA)₂) and R6G. A similar result was observed between DEA3HF:R6G in ethanolic solution. The respective Stern-Volmer plots corroborate with these observations, suggesting a static quenching mechanism for both systems.

Phyllobilins - Bioactive Natural Products Derived from Chlorophyll - Plant Origins, Structures, Absorption Spectra, and Biomedical Properties

Phyllobilins are open-chain products of the biological degradation of chlorophyll a in higher plants. Recent studies reveal that phyllobilins exert anti-oxidative and anti-inflammatory properties, as well as activities against cancer cells, that contribute to the human health benefits of numerous plants. In general, phyllobilins have been overlooked in phytochemical analyses, and - more importantly - in the analyses of medicinal plant extracts. Nevertheless, over the past three decades, > 70 phyllobilins have been identified upon examination of more than 30 plant species. Eight distinct chromophoric classes of phyllobilins are known: phyllolumibilins (PluBs), phylloleucobilins (PleBs), phylloxanthobilins (PxBs), and phylloroseobilins (PrBs)-each in type-I or type-II groups. Here, we present a database of absorption and fluorescence spectra that has been compiled of 73 phyllobilins to facilitate identification in phytochemical analyses. The spectra are provided in digital form and can be viewed and downloaded at www.photochemcad.com. The present review describes the plant origin, molecular structure, and absorption and fluorescence features of the 73 phyllobilins, along with an overview of key medicinal properties. The review should provide an enabling tool for the community for the straightforward identification of phyllobilins in plant extracts, and the foundation for deeper understanding of these ubiquitous but underexamined plant-derived micronutrients for human health.

Digital Database of Absorption Spectra of Diverse Flavonoids Enables Structural Comparisons and Quantitative Evaluations

Flavonoids play diverse roles in plants, comprise a non-negligible fraction of net primary photosynthetic production, and impart beneficial effects in human health from a plant-based diet. Absorption spectroscopy is an essential tool for quantitation of flavonoids isolated from complex plant extracts. The absorption spectra of flavonoids typically consist of two major bands, band I (300-380 nm) and band II (240-295 nm), where the former engenders a yellow color; in some flavonoids the absorption tails to 400-450 nm. The absorption spectra of 177 flavonoids and analogues of natural or synthetic origin have been assembled, including molar absorption coefficients (109 from the literature, 68 measured here). The spectral data are in digital form and can be viewed and accessed at http://www.photochemcad.com. The database enables comparison of the absorption spectral features of 12 distinct types of flavonoids including flavan-3-ols (e.g., catechin, epigallocatechin), flavanones (e.g., hesperidin, naringin), 3-hydroxyflavanones (e.g., taxifolin, silybin), isoflavones (e.g., daidzein, genistein), flavones (e.g., diosmin, luteolin), and flavonols (e.g., fisetin, myricetin). The structural features that give rise to shifts in wavelength and intensity are delineated. The availability of digital absorption spectra for diverse flavonoids facilitates analysis and quantitation of these valuable plant secondary metabolites. Four examples are provided of calculations─multicomponent analysis, solar ultraviolet photoprotection, sun protection factor (SPF), and Förster resonance energy transfer (FRET)─for which the spectra and accompanying molar absorption coefficients are sine qua non.

Electronic Energy Migration in Microtubules

The repeating arrangement of tubulin dimers confers great mechanical strength to microtubules, which are used as scaffolds for intracellular macromolecular transport in cells and exploited in biohybrid devices. The crystalline order in a microtubule, with lattice constants short enough to allow energy transfer between amino acid chromophores, is similar to synthetic structures designed for light harvesting. After photoexcitation, can these amino acid chromophores transfer excitation energy along the microtubule like a natural or artificial light-harvesting system? Here, we use tryptophan autofluorescence lifetimes to probe energy hopping between aromatic residues in tubulin and microtubules. By studying how the quencher concentration alters tryptophan autofluorescence lifetimes, we demonstrate that electronic energy can diffuse over 6.6 nm in microtubules. We discover that while diffusion lengths are influenced by tubulin polymerization state (free tubulin versus tubulin in the microtubule lattice), they are not significantly altered by the average number of protofilaments (13 versus 14). We also demonstrate that the presence of the anesthetics etomidate and isoflurane reduce exciton diffusion. Energy transport as explained by conventional Förster theory (accommodating for interactions between tryptophan and tyrosine residues) does not sufficiently explain our observations. Our studies indicate that microtubules are, unexpectedly, effective light harvesters.

Machine Learning Models for Predicting Molecular UV-Vis Spectra with Quantum Mechanical Properties

Accurate understanding of ultraviolet-visible (UV-vis) spectra is critical for the high-throughput synthesis of compounds for drug discovery. Experimentally determining UV-vis spectra can become expensive when dealing with a large quantity of novel compounds. This provides us an opportunity to drive computational advances in molecular property predictions using quantum mechanics and machine learning methods. In this work, we use both quantum mechanically (QM) predicted and experimentally measured UV-vis spectra as input to devise four different machine learning architectures, UVvis-SchNet, UVvis-DTNN, UVvis-Transformer, and UVvis-MPNN, and assess the performance of each method. We find that the UVvis-MPNN model outperforms the other models when using optimized 3D coordinates and QM predicted spectra as input features. This model has the highest performance for predicting UV-vis spectra with a training RMSE of 0.06 and validation RMSE of 0.08. Most importantly, our model can be used for the challenging task of predicting differences in the UV-vis spectral signatures of regioisomers.

Dyads with tunable near-infrared donor-acceptor excited-state energy gaps: molecular design and Förster analysis for ultrafast energy transfer

Bacteriochlorophylls, nature's near-infrared absorbers, play an essential role in energy transfer in photosynthetic antennas and reaction centers. To probe energy-transfer processes akin to those in photosynthetic systems, nine synthetic bacteriochlorin-bacteriochlorin dyads have been prepared wherein the constituent pigments are joined at the meso-positions by a phenylethyne linker. The phenylethyne linker is an unsymmetric auxochrome, which differentially shifts the excited-state energies of the phenyl- or ethynyl-attached bacteriochlorin constituents in the dyad. Molecular designs utilized known effects of macrocycle substituents to engineer bacteriochlorins with S₀ → S₁ (Q_y) transitions spanning 725-788 nm. The design-predicted donor-acceptor excited-state energy gaps in the dyads agree well with those obtained from time dependent density functional theory calculations and with the measured range of 197-1089 cm^-1. Similar trends with donor-acceptor excited-state energy gaps are found for (1) the measured ultrafast energy-transfer rates of (0.3-1.7 ps)^-1, (2) the spectral overlap integral (J) in Förster energy-transfer theory, and (3) donor-acceptor electronic mixing manifested in the natural transition orbitals for the S₀ → S₁ transition. Subtle outcomes include the near orthogonal orientation of the π-planes of the bacteriochlorin macrocycles, and the substituent-induced shift in transition-dipole moment from the typical coincidence with the NH-NH axis; the two features together afforded the Förster orientation term κ² ranging from 0.55-1.53 across the nine dyads, a value supportive of efficient excited-state energy transfer. The molecular design and collective insights on the dyads are valuable for studies relevant to artificial photosynthesis and other processes requiring ultrafast energy transfer.

In vivo detection of bile duct pre-cancer with endoscopic light scattering spectroscopy

Bile duct cancer is the second most common primary liver cancer, with most diagnoses occurring in the advanced stages. This leads to a poor survival rate, which means a technique capable of reliably detecting pre-cancer in the bile duct is urgently required. Unfortunately, radiological imaging lacks adequate accuracy for distinguishing dysplastic and benign biliary ducts, while endoscopic techniques, which can directly assess the bile duct lining, often suffer from insufficient sampling. Here, we report an endoscopic optical light scattering technique for clinical evaluation of the malignant potential of the bile duct. This technique employs an ultraminiature spatial gating fiber optic probe compatible with cholangioscopes and endoscopic retrograde cholangiopancreatography (ERCP) catheters. The probe allowed us to investigate the internal cellular composition of the bile duct epithelium with light scattering spectroscopy (LSS) and phenotypic properties of the underlying connective tissue with diffuse reflectance spectroscopy (DRS). In a pilot in vivo double-blind prospective study involving 29 patients undergoing routine ERCP procedures, the technique detected malignant transformation with 97% accuracy, showing that biliary duct pre-cancer can be reliably identified in vivo non-invasively.

Wearable Photomedicine for Neonatal Jaundice Treatment Using Blue Organic Light-Emitting Diodes (OLEDs): Toward Textile-Based Wearable Phototherapeutics

Neonatal jaundice is a very common disease in newborns and can lead to brain damage or death in severe cases. Phototherapy with light-emitting diode (LED) arrays is widely used as the easiest and fastest way to relieve jaundice in newborns, but it has distinct disadvantages such as loss of water in the patient, damage to the retina, and separation from parents. In this paper, a novel light source-based phototherapy for neonatal jaundice is proposed using a textile-based wearable organic light-emitting diode (OLED) platform that can move flexibly and conform to the curvature of the human body. The soft and flexible textile-based blue OLED platform is designed to have a peak wavelength of 470 nm, suitable for jaundice treatment, and shows performance (>20 µW cm^-2 nm^{- 1} ) suitable for intensive jaundice treatment even at low voltage (<4.0 V). The textile-based OLEDs fabricated in this study exhibit an operating reliability of over 100 h and low-temperature operation (<35 °C). The results of an in vitro jaundice treatment test using a large-area blue OLED confirm that the bilirubin level decreases to 12 mg dL^-1 with 3 h of OLED irradiation.

Real-Time Fluorescence Imaging of the Abscisic Acid Receptor Allows Nondestructive Visualization of Plant Stress

Environmental stress greatly decreases crop yield. The application of noninvasive techniques is one of the most practical and feasible ways of monitoring the health condition of plants under stress. However, it remains largely unsolved. A chemical fluorescent probe can be applied as a typical nondestructive method, but it has not been applied in living plants for stress detection to date. The abscisic acid (ABA) receptor plays a central role in conferring tolerance to environmental stresses and is an excellent target for developing fluorescent probes. Herein, we developed a fluorescence molecular imaging technology to monitor live plant stress by visualizing the protein expression level of the ABA receptor PYR1. A computer-aided designed indicator dye, flubactin, exhibited an 8-fold enhancement in fluorescence intensity upon interaction with PYR1. In vitro and in vivo experiments showed that flubactin is suitable to be used to detect salt stress in plants in real time. Moreover, the low toxicity of flubactin promotes its application in the future. Our work opens a new era for the nondestructive visualization of plant stress in vivo.

On the Importance of Well-Defined Thermal Correlation Functions in Simulating Vibronic Spectra

Two difficulties associated with the computations of thermal vibrational correlation functions are discussed. The first one is the lack of a well-behaved expression that is valid at both high-temperature and T → 0 K limits. Specifically, if the partition function and the propagator are considered separately, then thermal vibrational correlation functions may have an indeterminate form 0/0 in the limit T → 0 K. This difficulty is resolved when the partition function and the propagator are jointly considered in the harmonic approximation, which allows a problematic term that emanates from the zero-point energy to be canceled out, thereby producing a thermal correlation function with a determinate form in the T → 0 K limit. The second difficulty is related to the multivaluedness of the vibrational correlation function. We show numerically that an improper selection of branch leads to discontinuities in the computed correlation function and incorrect vibronic spectra. We propose a phase tracking procedure that ensures continuity of both real and imaginary parts of the correlation function to recover the correct spectra. We support our findings by simulating the UV-vis absorption spectra of pentacene at 4 K and benzene at 298 K. Both are found to be in good agreement with their experimental counterparts.

Data-Driven and Multiscale Modeling of DNA-Templated Dye Aggregates

Dye aggregates are of interest for excitonic applications, including biomedical imaging, organic photovoltaics, and quantum information systems. Dyes with large transition dipole moments (μ) are necessary to optimize coupling within dye aggregates. Extinction coefficients (ε) can be used to determine the μ of dyes, and so dyes with a large ε (>150,000 M−1cm−1) should be engineered or identified. However, dye properties leading to a large ε are not fully understood, and low-throughput methods of dye screening, such as experimental measurements or density functional theory (DFT) calculations, can be time-consuming. In order to screen large datasets of molecules for desirable properties (i.e., large ε and μ), a computational workflow was established using machine learning (ML), DFT, time-dependent (TD-) DFT, and molecular dynamics (MD). ML models were developed through training and validation on a dataset of 8802 dyes using structural features. A Classifier was developed with an accuracy of 97% and a Regressor was constructed with an R2 of above 0.9, comparing between experiment and ML prediction. Using the Regressor, the ε values of over 18,000 dyes were predicted. The top 100 dyes were further screened using DFT and TD-DFT to identify 15 dyes with a μ relative to a reference dye, pentamethine indocyanine dye Cy5. Two benchmark MD simulations were performed on Cy5 and Cy5.5 dimers, and it was found that MD could accurately capture experimental results. The results of this study exhibit that our computational workflow for identifying dyes with a large μ for excitonic applications is effective and can be used as a tool to develop new dyes for excitonic applications.

PyFREC 2.0: Software for excitation energy transfer modeling

Excitation energy transfer is a ubiquitous process of fundamental importance for understanding natural phenomena, such as photosynthesis, as well as advancing technologies ranging from photovoltaics to development of photosensitizers and fluorescent probes used to explore molecular interactions inside living cells. The current version of PyFREC 2.0 is an advancement of the previously reported software (D. Kosenkov, J. Comput. Chem. 2016, 37, 1847-1854). The current update is primarily focused on providing a computational tool based on Förster theory for bridging a gap between theoretically calculated molecular properties (e.g., electronic couplings, orientation factors, etc.) and experimentally measured emission and absorption spectra of molecules. The software is aimed to facilitate deeper understanding of photochemical mechanisms of fluorescence resonance energy transfer (FRET) in donor-acceptor pairs. Specific updates of the software include implementations of overlap integrals between donor emission and acceptor absorption spectra of FRET pairs, estimation of Strickler-Berg fluorescence lifetimes, calculation of Förster radii, energy transfer efficiency, and radiation zones that, in particular, determine applicability of the Förster theory.

Sensitization of Nd3+ Luminescence by Simultaneous Two-Photon Excitation through a Coordinating Polymethinic Antenna

We have designed and synthesized two new cyaninic Nd³⁺ complexes where the lanthanide emission can be induced from simultaneous two-photon absorption followed by energy migration. These complexes correspond to a molecular design that uses an antenna ligand formed by the functionalization of a heptamethine dye with 5-ol-phenanthroline or 4-phenyl-terpyridine derivatives. These complexes employ the important nonlinear optical properties of symmetric polymethines to sensitize the lanthanide ion. We verified that simultaneous biphotonic excitation indirectly induces the ⁴F_3/2 → ⁴I_11/2 Nd³⁺ emission using femtosecond laser pulses tuned below the first electronic transition of the antenna. The simultaneous two-photon excitation events initially form the nonlinear-active second excited singlet of the polymethine antenna, which rapidly evolves into its first excited singlet. This state in turn induces the formation of the emissive Nd³⁺ states through energy transfer. The role of the first excited singlet of the antenna as the donor state in this process was verified through time resolution of the antenna's fluorescence. These measurements also provided the rates for antenna-lanthanide energy transfer, which indicate that the phenanthroline-type ligand is approximately five times more efficient for energy transfer than the phenyl-terpyridine derivative due to their relative donor-acceptor distances. The simultaneous two-photon excitation of this polymethine antenna allows for high spatial localization of the Nd³⁺excitation events.

Q-Band relaxation in chlorophyll: new insights from multireference quantum dynamics

The ultrafast relaxation within the Q-bands of chlorophyll plays a crucial role in photosynthetic light-harvesting. We investigate this process via nuclear and electronic quantum dynamics on multireference potential energy surfaces.

Introducing the Tellurophene-Appended BODIPY: PDT Agent with Mass Cytometry Tracking Capabilities

The synthesis and characterization of the first BODIPY appended to the five-membered heterocylic tellurophene [Te] moiety is reported. By incorporating tellurophene at the meso position, the tellurophene-appended boron-dipyrromethene dye (BODIPY) acts as a multimodal agent, becoming a potent photosensitizer with a mass cytometry tag. To synthesize the compound, we developed a method to enable late-stage Suzuki-Miyaura coupling by preparing and isolating tellurophene-2-BPin in a one-step procedure from the parent tellurophene. Coupling to a meso-substituted BODIPY functionalized with a pendant aryl bromide provides the desired tellurophene-appended BODIPY. This compound demonstrated a singlet oxygen quantum yield of 0.26 ± 0.01 and produced a light dose-dependent cytotoxicity with nanomolar IC50 values against 2D cultured HeLa cells and high efficacy against 3D cultured HeLa tumor spheroids, proving to be a strong photosensitizer. The presence of the tellurophene moiety could be detected using mass cytometry, thus showcasing the ability of a tellurophene-appended BODIPY as a novel photodynamic-therapy-mass-cytometry theranostic agent.

UV-adVISor: Attention-Based Recurrent Neural Networks to Predict UV-Vis Spectra

Ultraviolet-visible (UV-Vis) absorption spectra are routinely collected as part of high-performance liquid chromatography (HPLC) analysis systems and can be used to identify chemical reaction products by comparison to the reference spectra. Here, we present UV-adVISor as a new computational tool for predicting the UV-Vis spectra from a molecule's structure alone. UV-Vis prediction was approached as a sequence-to-sequence problem. We utilized Long-Short Term Memory and attention-based neural networks with Extended Connectivity Fingerprint Diameter 6 or molecule SMILES to generate predictive models for the UV spectra. We have produced two spectrum datasets (dataset I, N = 949, and dataset II, N = 2222) using different compound collections and spectrum acquisition methods to train, validate, and test our models. We evaluated the prediction accuracy of the complete spectra by the correspondence of wavelengths of absorbance maxima and with a series of statistical measures (the best test set median model parameters are in parentheses for model II), including RMSE (0.064), R² (0.71), and dynamic time warping (DTW, 0.194) of the entire spectrum curve. Scrambling molecule structures with the experimental spectra during training resulted in a degraded R², confirming the utility of the approaches for prediction. UV-adVISor is able to provide fast and accurate predictions for libraries of compounds.

Dithiane Based Boronic Acid as a Carbohydrate Sensor in an Aqueous Solution at pH 7.5: Theoretical and Experimental Approach

Carbohydrate sensing in an aqueous solution remains a very challenging area of interest. Using the idea of covalent reversible interaction between boronic acids and the diol groups in carbohydrates enable us to design a carbohydrate sensor 1-thianthrenylboronic acid (1T), which has high selectivity towards fructose. To elucidate the sensing and binding properties of 1T with sugars, we have incorporated theoretical (DFT and TD-DFT) and spectroscopic techniques. For an optimized geometry, the complete vibrational assignments were done with FT-IR and FT-Raman spectra. Physiochemical parameters were obtained by implementing frontier molecular orbital (FMO) analysis. Further, excited state properties were determined by performing TD-DFT calculations in solvent and these properties were in good agreement with the experiment. The steady state fluorescence measurements with varying concentration of sugars, revealed that the fluorescence intensity of boronic acid is enhanced by studied sugars due to the structural modification. We also noticed remarkable changes in fluorescence lifetimes and quantum yield after adding sugars. The article also reports influence of pH on boronic acid's fluorescence intensity with and without sugars. The fluorescence of boronic acid increases with the increase in pH. These changes are due to acid-base equilibrium of boronic acid and led us to estimate the pKa value of 7.6. All the theoretical and experimental evidences suggested that 1T can be used as a possible fluorescent sensor for fructose. In addition, 1T showed very good affinity for Cu²⁺ ion with K_a = 150 × 10² M^-1, which suggests that 1T can also be used as a chemosensor for Cu²⁺ ions.

Light Technology for Efficient and Effective Photodynamic Therapy: A Critical Review

Photodynamic therapy (PDT) is a cancer treatment with strong potential over well-established standard therapies in certain cases. Non-ionising radiation, localisation, possible repeated treatments, and stimulation of immunological response are some of the main beneficial features of PDT. Despite the great potential, its application remains challenging. Limited light penetration depth, non-ideal photosensitisers, complex dosimetry, and complicated implementations in the clinic are some limiting factors hindering the extended use of PDT. To surpass actual technological paradigms, radically new sources, light-based devices, advanced photosensitisers, measurement devices, and innovative application strategies are under extensive investigation. The main aim of this review is to highlight the advantages/pitfalls, technical challenges and opportunities of PDT, with a focus on technologies for light activation of photosensitisers, such as light sources, delivery devices, and systems. In this vein, a broad overview of the current status of superficial, interstitial, and deep PDT modalities-and a critical review of light sources and their effects on the PDT process-are presented. Insight into the technical advancements and remaining challenges of optical sources and light devices is provided from a physical and bioengineering perspective.

Design, Synthesis, and Utility of Defined Molecular Scaffolds

A growing theme in chemistry is the joining of multiple organic molecular building blocks to create functional molecules. Diverse derivatizable structures—here termed “scaffolds” comprised of “hubs”—provide the foundation for systematic covalent organization of a rich variety of building blocks. This review encompasses 30 tri- or tetra-armed molecular hubs (e.g., triazine, lysine, arenes, dyes) that are used directly or in combination to give linear, cyclic, or branched scaffolds. Each scaffold is categorized by graph theory into one of 31 trees to express the molecular connectivity and overall architecture. Rational chemistry with exacting numbers of derivatizable sites is emphasized. The incorporation of water-solubilization motifs, robust or self-immolative linkers, enzymatically cleavable groups and functional appendages affords immense (and often late-stage) diversification of the scaffolds. Altogether, 107 target molecules are reviewed along with 19 syntheses to illustrate the distinctive chemistries for creating and derivatizing scaffolds. The review covers the history of the field up through 2020, briefly touching on statistically derivatized carriers employed in immunology as counterpoints to the rationally assembled and derivatized scaffolds here, although most citations are from the past two decades. The scaffolds are used widely in fields ranging from pure chemistry to artificial photosynthesis and biomedical sciences.

Weakly conjugated bacteriochlorin-bacteriochlorin dyad: Synthesis and photophysical properties

Dyads containing two near-infrared absorbing and emitting bacteriochlorins with distinct spectral properties have been prepared and characterized by absorption, emission, and transient-absorption spectroscopies. The dyads exhibit ultrafast ([Formula: see text]3 ps) energy transfer from the bacteriochlorin with the higher-energy S1 state to the bacteriochlorin emitting at the longer wavelength. The dyads exhibit strong fluorescence and relatively long excited state lifetimes ([Formula: see text]4 ns) in both non-polar and polar solvents, which indicates negligible photoinduced electron transfer between the two bacteriochlorins in the dyads. These dyads are thus attractive for the development of light-harvesting arrays and fluorophores for in vivo bioimaging.

Conformational Changes of Whey and Pea Proteins upon Emulsification Approached by Front-Surface Fluorescence

Proteins are widely used to stabilize emulsions, and plant proteins have raised increasing interest for this purpose. The interfacial and emulsifying properties of proteins depend largely on their molecular properties. We used fluorescence spectroscopy to characterize the conformation of food proteins from different biological origins (dairy or pea) and transformation processes (commercial or lab-made isolates) in solution and at the oil-water interface. The fourth derivative of fluorescence spectra provided insights in the local environment of tryptophan (Trp) residues and thus in the protein structure. In emulsions, whey proteins adsorbed with their Trp-rich region at the oil-water interface. Proteins in the commercial pea isolate were present as soluble aggregates, and no changes in the local environment of the Trp residues were detected upon emulsification, suggesting that these structures adsorb without conformational changes. The lab-purified pea proteins were less aggregated and a Trp-free region of the vicilin adsorbed at the oil-water interface.

Enhancing Single-Molecule Fluorescence Spectroscopy with Simple and Robust Hybrid Nanoapertures

Plasmonic nanoapertures have found exciting applications in optical sensing, spectroscopy, imaging, and nanomanipulation. The subdiffraction optical field localization, reduced detection volume (~attoliters), and background-free operation make them particularly attractive for single-particle and single-molecule studies. However, in contrast to the high field enhancements by traditional "nanoantenna"-based structures, small field enhancement in conventional nanoapertures results in weak light-matter interactions and thus small enhancement of spectroscopic signals (such as fluorescence and Raman signals) of the analytes interacting with the nanoapertures. In this work, we propose a hybrid nanoaperture design termed "gold-nanoislands-embedded nanoaperture" (AuNIs-e-NA), which provides multiple electromagnetic "hotspots" within the nanoaperture to achieve field enhancements of up to 4000. The AuNIs-e-NA was able to improve the fluorescence signals by more than 2 orders of magnitude with respect to a conventional nanoaperture. With simple design and easy fabrication, along with strong signal enhancements and operability over variable light wavelengths and polarizations, the AuNIs-e-NA will serve as a robust platform for surface-enhanced optical sensing, imaging, and spectroscopy.

Molecular excited states through a machine learning lens

Theoretical simulations of electronic excitations and associated processes in molecules are indispensable for fundamental research and technological innovations. However, such simulations are notoriously challenging to perform with quantum mechanical methods. Advances in machine learning open many new avenues for assisting molecular excited-state simulations. In this Review, we track such progress, assess the current state of the art and highlight the critical issues to solve in the future. We overview a broad range of machine learning applications in excited-state research, which include the prediction of molecular properties, improvements of quantum mechanical methods for the calculations of excited-state properties and the search for new materials. Machine learning approaches can help us understand hidden factors that influence photo-processes, leading to a better control of such processes and new rules for the design of materials for optoelectronic applications.

A new dynamic masking technique for time resolved PIV analysis

Abstract

Time resolved PIV encompassing moving and/or deformable objects interfering with the light source requires the employment of dynamic masking (DM). A few DM techniques have been recently developed, mainly in microfluidics and multiphase flows fields. Most of them require ad-hoc design of the experimental setup, and may spoil the accuracy of the resulting PIV analysis. A new DM technique is here presented which envisages, along with a dedicated masking algorithm, the employment of fluorescent coating to allow for accurate tracking of the object. We show results from measurements obtained through a validated PIV setup demonstrating the need to include a DM step even for objects featuring limited displacements. We compare the proposed algorithm with both a no-masking and a static masking solution. In the framework of developing low cost, flexible and accurate PIV setups, the proposed algorithm is made available through a freeware application able to generate masks to be used by an existing, freeware PIV analysis package.

Graphic abstract

A Skin Cancer Prophylaxis Study in Hairless Mice Using Methylene Blue, Riboflavin, and Methyl Aminolevulinate as Photosensitizing Agents in Photodynamic Therapy

The high incidence of sunlight-induced human skin cancers reveals a need for more effective photosensitizing agents. In this study, we compared the efficacy of prophylactic photodynamic therapy (PDT) when methylene blue (MB), riboflavin (RF), or methyl aminolevulinate (MAL) were used as photosensitizers. All mice in four groups of female C3.Cg/TifBomTac hairless immunocompetent mice (N = 100) were irradiated with three standard erythema doses of solar-simulated ultraviolet radiation (UVR) thrice weekly. Three groups received 2 × 2 prophylactic PDT treatments (days 45 + 52 and 90 + 97). The PDT treatments consisted of topical administration of 16% MAL, 20% MB, or 20% RF, and subsequent illumination that matched the photosensitizers’ absorption spectra. Control mice received no PDT. We recorded when the first, second, and third skin tumors developed. The pattern of tumor development after MB-PDT or RF-PDT was similar to that observed in irradiated control mice (p > 0.05). However, the median times until the first, second, and third skin tumors developed in mice given MAL-PDT were significantly delayed, compared with control mice (256, 265, and 272 vs. 215, 222, and 230 days, respectively; p < 0.001). Only MAL-PDT was an effective prophylactic treatment against UVR-induced skin tumors in hairless mice.

Two-photon induced isomerization through a cyaninic molecular antenna in azo compounds

We present a new design for non-linear optically responsive molecules based on a modular scheme where a polymethinic antenna section with important two-photon absorption properties is bonded to an isomerizable actuator section composed of a stilbenyl-azopyrrole unit. Upon two photon excitation, energy migration from the antenna-localized second singlet excited state to the stilbenyl-azopyrrole section allows for efficient indirect excitation and phototransformation of this actuator.

The TDDFT Excitation Energies of the BODIPYs; The DFT and TDDFT Challenge Continues

The derivatives of 4,4-difluoro-4-bora-3a,4a-diaza-s-indacene (BODIPY) are pivotal ingredients for a large number of functional, stimuli-responsive materials and therapeutic molecules based on their photophysical properties, and there is a urgent need to understand and predict their optical traits prior to investing a large amount of resources in preparing them. Density functional theory (DFT) and time-dependent DFT (TDDFT) computations were performed to calculate the excitation energies of the lowest-energy singlet excited state of a large series of common BODIPY derivatives employing various functional aiming at the best possible combination providing the least deviations from the experimental values. Using the common "fudge" correction, a series of combinations was investigated, and a methodology is proposed offering equal or better performances than what is reported in the literature.

Increasing antibiotic activity by rapid bioorthogonal conjugation of drug to resistant bacteria using an upconverted light-activated photocatalyst

Antibiotic vancomycin (Van) is often used as the drug of last resort to treat methicillin resistant Staphylococcus aureus. Due to the emergence of Van-resistant microbes, it is necessary to continuously design strategies to increase the efficacy of Van against resistant cells. In this study, an efficient method of bio-conjugating Van to bacteria is proposed using near-infrared (NIR)-light activation. A Nd³⁺-sensitized upconversion nanocrystal (UCNC) decorated with toluidine blue O (TB) on its surface undergoes upconverted energy transfer from the UCNC to TB when excited by 808 nm light. The photoexcited TB then catalyses the conversion of the dihydrotetrazine (dHTz) moiety in a Van-dHTz conjugate system to tetrazine which undergoes an efficient inverse electron demand Diels-Alder reaction with prior attached norbornene molecules on bacterial cell walls. The enhanced affinity of Van to bacteria by covalent bonding improves the activity of the drug against drug-resistant Enterococci, and the MIC is reduced by 6- to 7-fold as compared to neat Van. We demonstrate that the mode of action is due to increased inhibition of peptidoglycan cell wall biosynthesis. The findings in this study demonstrate that on-demand NIR-light activated bioorthogonal conjugation of Van to microbes is a viable alternative treatment in combating drug-resistant bacteria.

Tolyporphins A–R, unusual tetrapyrrole macrocycles in a cyanobacterium from Micronesia, assessed quantitatively from the culture HT-58-2

Tolyporphins A–R are the newest additions to the family of native tetrapyrroles. LC-MS-dMRM and absorption spectroscopy have been employed for analysis of mixtures containing the 18 distinctive natural products.

Absorption and Fluorescence Spectral Database of Chlorophylls and Analogues

Absorption spectra and fluorescence spectra are essential for use across the photosciences, yet such spectra along with the all-important values for molar absorption coefficient (ε) and fluorescence quantum yield (Φ_f ) often are found with great difficulty. Here, a literature survey concerning the vital class of chlorophyll compounds has led to identification of spectra for 150 members. Spectra in print form have been digitized (with baseline corrections) and assembled into a database along with literature references, solvent identity and values for ε and Φ_f (where available). The database encompasses photosynthetic tetrapyrroles wherein the chromophore is a porphyrin (e.g. chlorophyll c₁ , protochlorophyll a), chlorin (e.g. chlorophyll a, bacteriochlorophyll c) or bacteriochlorin (e.g. bacteriochlorophyll a). Altogether, the database contains 305 absorption spectra (from 19 porphyrins, 109 chlorins and 22 bacteriochlorins) and 72 fluorescence spectra (from 10 porphyrins, 30 chlorins and 4 bacteriochlorins). The spectral database should facilitate comparisons and quantitative calculations. All spectra are available in print form in the Supporting Information. The entire database in digital form is available with the PhotochemCAD program for free downloading and further use at http://www.photochemcad.com.

Single-step approach to sensitized luminescence through bulk-embedded organics in crystalline fluorides

Luminescent materials enable warm white LEDs, molecular tagging, enhanced optoelectronics and can improve energy harvesting. With the recent development of multi-step processes like down- and upconversion and the difficulty in sensitizing these, it is clear that optimizing all properties simultaneously is not possible within a single material class. In this work, we have utilized the layer-by-layer approach of atomic layer deposition to combine broad absorption from an aromatic molecule with the high emission yields of crystalline multi-layer lanthanide fluorides in a single-step nanocomposite process. This approach results in complete energy transfer from the organic molecule while providing inorganic fluoride-like lanthanide luminescence. Sm³⁺ is easily quenched by organic sensitizers, but in our case we obtain strong fluoride-like Sm³⁺ emission sensitized by strong UV absorption of terephthalic acid. This design allows combinations of otherwise incompatible species, both with respect to normally incompatible synthesis requirements and in controlling energy transfer and quenching routes.

Theoretical lateral and axial sensitivity limits and choices of molecular reporters for Cherenkov-excited luminescence in tissue during x-ray beam scanning

PURPOSE

Unlike fluorescence imaging utilizing an external excitation source, Cherenkov emissions and Cherenkov-excited luminescence occur within a medium when irradiated with high-energy x-rays. Methods to improve the understanding of the lateral spread and axial depth distribution of these emissions are needed as an initial step to improve the overall system resolution.

METHODS

Monte Carlo simulations were developed to investigate the lateral spread of thin sheets of high-energy sources and compared to experimental measurements of similar sources in water. Additional simulations of a multilayer skin model were used to investigate the limits of detection using both 6- and 18-MV x-ray sources with fluorescence excitation for inclusion depths up to 1 cm.

RESULTS

Simulations comparing the lateral spread of high-energy sources show approximately 100  ×   higher optical yield from electrons than photons, although electrons showed a larger penumbra in both the simulations and experimental measurements. Cherenkov excitation has a roughly inverse wavelength squared dependence in intensity but is largely redshifted in excitation through any distance of tissue. The calculated emission spectra in tissue were convolved with a database of luminescent compounds to produce a computational ranking of potential Cherenkov-excited luminescence molecular contrast agents.

CONCLUSIONS

Models of thin x-ray and electron sources were compared with experimental measurements, showing similar trends in energy and source type. Surface detection of Cherenkov-excited luminescence appears to be limited by the mean free path of the luminescence emission, where for the given simulation only 2% of the inclusion emissions reached the surface from a depth of 7 mm in a multilayer tissue model.

Solvent-dependent energy and charge transfer dynamics in hydroporphyrin-BODIPY arrays

Arrays of hydroporphyrins with boron complexes of dipyrromethene (BODIPY) are a promising platform for biomedical imaging or solar energy conversion, but their photophysical properties have been relatively unexplored. In this paper, we use time-resolved fluorescence, femtosecond transient absorption spectroscopy, and density-functional-theory calculations to elucidate solvent-dependent energy and electron-transfer processes in a series of chlorin- and bacteriochlorin-BODIPY arrays. Excitation of the BODIPY moiety results in ultrafast energy transfer to the hydroporphyrin moiety, regardless of the solvent. In toluene, energy is most likely transferred via the through-space Förster mechanism from the S₁ state of BODIPY to the S₂ state of hydroporphyrin. In DMF, substantially faster energy transfer is observed, which implies a contribution of the through-bond Dexter mechanism. In toluene, excited hydroporphyrin components show bright fluorescence, with quantum yield and fluorescence lifetime comparable to those of the benchmark monomer, whereas in DMF, moderate to significant reduction of both quantum yield and fluorescence lifetime are observed. We attribute this quenching to photoinduced charge transfer from hydroporphyrin to BODIPY. No direct spectral signature of the charge-separated state is observed, which suggests that either (1) the charge-separated state decays very quickly to the ground state or (2) virtual charge-separated states, close in energy to S₁ of hydroporphyrin, promote ultrafast internal conversion.

Rational design of small molecule fluorescent probes for biological applications

Fluorescent small molecules are powerful tools for visualizing biological events, embodying an essential facet of chemical biology. Since the discovery of the first organic fluorophore, quinine, in 1845, both synthetic and theoretical efforts have endeavored to "modulate" fluorescent compounds. An advantage of synthetic dyes is the ability to employ modern organic chemistry strategies to tailor chemical structures and thereby rationally tune photophysical properties and functionality of the fluorophore. This review explores general factors affecting fluorophore excitation and emission spectra, molar absorption, Stokes shift, and quantum efficiency; and provides guidelines for chemist to create novel probes. Structure-property relationships concerning the substituents are discussed in detail with examples for several dye families. We also present a survey of functional probes based on PeT, FRET, and environmental or photo-sensitivity, focusing on representative recent work in each category. We believe that a full understanding of dyes with diverse chemical moieties enables the rational design of probes for the precise interrogation of biochemical and biological phenomena.