Predicting solvatochromic shifts and colours of a solvated organic dye: The example of nile red

Taming the third order cumulant approximation to linear optical spectroscopy

The second order cumulant method offers a promising pathway to predicting optical properties in condensed phase systems. It allows for the computation of linear absorption spectra from excitation energy fluctuations sampled along molecular dynamics (MD) trajectories, fully accounting for vibronic effects, direct solute-solvent interactions, and environmental polarization effects. However, the second order cumulant approximation only guarantees accurate line shapes for energy gap fluctuations obeying Gaussian statistics. A third order correction has recently been derived but often yields unphysical spectra or divergent line shapes for moderately non-Gaussian fluctuations due to the neglect of higher order terms in the cumulant expansion. In this work, we develop a corrected cumulant approach, where the collective effect of neglected higher order contributions is approximately accounted for through a dampening factor applied to the third order cumulant term. We show that this dampening factor can be expressed as a function of the skewness and kurtosis of energy gap fluctuations and can be parameterized from a large set of randomly sampled model Hamiltonians for which exact spectral line shapes are known. This approach is shown to systematically remove unphysical contributions in the form of negative absorbances from cumulant spectra in both model Hamiltonians and condensed phase systems sampled from MD and dramatically improves over the second order cumulant method in describing systems exhibiting Duschinsky mode mixing effects. We successfully apply the approach to the coumarin-153 dye in toluene, obtaining excellent agreement with experiment.

Beyond the Condon limit: Condensed phase optical spectra from atomistic simulations

While dark transitions made bright by molecular motions determine the optoelectronic properties of many materials, simulating such non-Condon effects in condensed phase spectroscopy remains a fundamental challenge. We derive a Gaussian theory to predict and analyze condensed phase optical spectra beyond the Condon limit. Our theory introduces novel quantities that encode how nuclear motions modulate the energy gap and transition dipole of electronic transitions in the form of spectral densities. By formulating the theory through a statistical framework of thermal averages and fluctuations, we circumvent the limitations of widely used microscopically harmonic theories, allowing us to tackle systems with generally anharmonic atomistic interactions and non-Condon fluctuations of arbitrary strength. We show how to calculate these spectral densities using first-principles simulations, capturing realistic molecular interactions and incorporating finite-temperature, disorder, and dynamical effects. Our theory accurately predicts the spectra of systems known to exhibit strong non-Condon effects (phenolate in various solvents) and reveals distinct mechanisms for electronic peak splitting: timescale separation of modes that tune non-Condon effects and spectral interference from correlated energy gap and transition dipole fluctuations. We further introduce analysis tools to identify how intramolecular vibrations, solute-solvent interactions, and environmental polarization effects impact dark transitions. Moreover, we prove an upper bound on the strength of cross correlated energy gap and transition dipole fluctuations, thereby elucidating a simple condition that a system must follow for our theory to accurately predict its spectrum.

Theoretical Advances in Polariton Chemistry and Molecular Cavity Quantum Electrodynamics

When molecules are coupled to an optical cavity, new light-matter hybrid states, so-called polaritons, are formed due to quantum light-matter interactions. With the experimental demonstrations of modifying chemical reactivities by forming polaritons under strong light-matter interactions, theorists have been encouraged to develop new methods to simulate these systems and discover new strategies to tune and control reactions. This review summarizes some of these exciting theoretical advances in polariton chemistry, in methods ranging from the fundamental framework to computational techniques and applications spanning from photochemistry to vibrational strong coupling. Even though the theory of quantum light-matter interactions goes back to the midtwentieth century, the gaps in the knowledge of molecular quantum electrodynamics (QED) have only recently been filled. We review recent advances made in resolving gauge ambiguities, the correct form of different QED Hamiltonians under different gauges, and their connections to various quantum optics models. Then, we review recently developed ab initio QED approaches which can accurately describe polariton states in a realistic molecule-cavity hybrid system. We then discuss applications using these method advancements. We review advancements in polariton photochemistry where the cavity is made resonant to electronic transitions to control molecular nonadiabatic excited state dynamics and enable new photochemical reactivities. When the cavity resonance is tuned to the molecular vibrations instead, ground-state chemical reaction modifications have been demonstrated experimentally, though its mechanistic principle remains unclear. We present some recent theoretical progress in resolving this mystery. Finally, we review the recent advances in understanding the collective coupling regime between light and matter, where many molecules can collectively couple to a single cavity mode or many cavity modes. We also lay out the current challenges in theory to explain the observed experimental results. We hope that this review will serve as a useful document for anyone who wants to become familiar with the context of polariton chemistry and molecular cavity QED and thus significantly benefit the entire community.

Probing disorder in 2CzPN using core and valence states

Molecules which exhibit thermally activated delayed fluorescence (TADF) show great promise for use in efficient, environmentally-friendly OLEDs, and thus the design of new TADF emitters is an active area of research. However, when used in devices, they are typically in the form of disordered thin films, where both the external molecular environment and thermally-induced internal variations in parameters such as the torsion angle can strongly influence their electronic structure. In this work, we use density functional theory and X-ray photoelectron spectroscopy to investigate the impact of disorder on both core and valence states in the TADF emitter 2CzPN (1,2-bis(carbazol-9-yl)-4,5-dicyanobenzene). By simulating gas phase molecules displaying varying levels of disorder, we assess the relative sensitivity of the different states to factors such as varying torsion angle. The theoretical results for both core and valence states show good agreement with experiment, thereby also highlighting the advantages of our approach for interpreting experimental spectra of large aromatic molecules, which are too complex to interpret based solely on experimental data.

Improvement of theoretical UV-Vis spectra calculations by empirical solvatochromic parameters: Case study of 5-arylazo-3-cyano-1-ethyl-6-hydroxy-4-methyl-2-pyridones

In order to improve the performance of theoretical UV-Vis spectra predictions, a theoretical and experimental study of solvatochromic properties of ten azo pyridone dyes has been performed. For quantitative estimation of intermolecular solvent-solute interactions, a concept of the linear solvation energy relationships has been applied using Kamlet-Taft and Catalán models. Theoretical UV-Vis spectra for all dyes have been calculated using four TD-DFT methods in nine different solvents with the aim to define the most reliable model. Finally, new polylinear equations for more accurate theoretical prediction of UV-Vis maxima are developed using empirical Kamlet-Taft and Catalán solvent parameters as additive corrections for specific and nonspecific solvent-solute interactions.

Efficiently Computing Excitations of Complex Systems: Linear-Scaling Time-Dependent Embedded Mean-Field Theory in Implicit Solvent

Quantum embedding schemes have the potential to significantly reduce the computational cost of first-principles calculations while maintaining accuracy, particularly for calculations of electronic excitations in complex systems. In this work, I combine time-dependent embedded mean field theory (TD-EMFT) with linear-scaling density functional theory and implicit solvation models, extending previous work within the ONETEP code. This provides a way to perform multilevel calculations of electronic excitations on very large systems, where long-range environmental effects, both quantum and classical in nature, are important. I demonstrate the power of this method by performing simulations on a variety of systems, including a molecular dimer, a chromophore in solution, and a doped molecular crystal. This work paves the way for high accuracy calculations to be performed on large-scale systems that were previously beyond the reach of quantum embedding schemes.

Fabrication of Microfiber-Templated Microfluidic Chips with Microfibrous Channels for High Throughput and Continuous Production of Nanoscale Droplets

A polydimethylsiloxane (PDMS) microfluidic chip with well-interconnected microfibrous channels was fabricated by using an electrospun poly(ε-caprolactone) (PCL) microfibrous matrix and 3D-printed pattern as templates. The microfiber-templated microfluidic chip (MTMC) was used to produce nanoscale emulsions and spheres through multiple emulsification at many small micro-orifice junctions among microfibrous channels. The emulsion formation mechanisms in the MTMC were the cross-junction dripping or Y-junction splitting at the micro-orifice junctions. We demonstrated the high throughput and continuous production of water-in-oil emulsions and polyethylene glycol-diacrylate (PEG-DA) spheres with controlled size ranges from 2.84 μm to 83.6 nm and 1.03 μm to 45.7 nm, respectively. The average size of the water droplets was tuned by changing the micro-orifice diameter of the MTMC and the flow rate of the continuous phase. The MTMC theoretically produced 58 trillion PEG-DA nanospheres per hour without high shear force. In addition, we demonstrated the higher encapsulation efficiency of the PEG-DA microspheres in the MTMC than that of the microspheres fabricated by ultrasonication. The MTMC can be used as a powerful platform for the large-scale and continuous productions of emulsions and spheres.

Ultrafast transient absorption spectroelectrochemistry: femtosecond to nanosecond excited-state relaxation dynamics of the individual components of an anthraquinone redox couple

Many photoactivated processes involve a change in oxidation state during the reaction pathway and formation of highly reactive photoactivated species. Isolating these reactive species and studying their early-stage femtosecond to nanosecond (fs-ns) photodynamics can be challenging. Here we introduce a combined ultrafast transient absorption-spectroelectrochemistry (TA-SEC) approach using freestanding boron doped diamond (BDD) mesh electrodes, which also extends the time domain of conventional spectrochemical measurements. The BDD electrodes offer a wide solvent window, low background currents, and a tuneable mesh size which minimises light scattering from the electrode itself. Importantly, reactive intermediates are generated electrochemically, via oxidation/reduction of the starting stable species, enabling their dynamic interrogation using ultrafast TA-SEC, through which the early stages of the photoinduced relaxation mechanisms are elucidated. As a model system, we investigate the ultrafast spectroscopy of both anthraquinone-2-sulfonate (AQS) and its less stable counterpart, anthrahydroquinone-2-sulfonate (AH2QS). This is achieved by generating AH2QS in situ from AQS via electrochemical means, whilst simultaneously probing the associated early-stage photoinduced dynamical processes. Using this approach we unravel the relaxation mechanisms occurring in the first 2.5 ns, following absorption of ultraviolet radiation; for AQS as an extension to previous studies, and for the first time for AH2QS. AQS relaxation occurs via formation of triplet states, with some of these states interacting with the buffered solution to form a transient species within approximately 600 ps. In contrast, all AH2QS undergoes excited-state single proton transfer with the buffered solution, resulting in formation of ground state AHQS- within approximately 150 ps.

The Influence of Electronic Polarization on Nonlinear Optical Spectroscopy

The environment surrounding a chromophore can dramatically affect the energy absorption and relaxation process, as manifested in optical spectra. Simulations of nonlinear optical spectroscopy, such as two-dimensional electronic spectroscopy (2DES) and transient absorption (TA), will be influenced by the computational model of the environment. We here compare a fixed point charge molecular mechanics model and a quantum mechanical (QM) model of the environment in computed 2DES and TA spectra of Nile red in water and the chromophore of photoactive yellow protein (PYP) in water and protein environments. In addition to simulating these nonlinear optical spectra, we directly juxtapose the computed excitation energy correlation function to the dynamic Stokes shift function often used to analyze environment dynamics. Overall, we find that for the three systems studied here the mutual electronic polarization provided by the QM environment manifests in broader 2DES signals, as well as a larger reorganization energy and a larger static Stokes shift due to stronger coupling between the chromophore and the environment.

Accurate and Efficient Computation of Optical Absorption Spectra of Molecular Crystals: The Case of the Polymorphs of ROY

When calculating the optical absorption spectra of molecular crystals from first principles, the influence of the crystalline environment on the excitations is of significant importance. For such systems, however, methods to describe the excitations accurately can be computationally prohibitive due to the relatively large system sizes involved. In this work, we demonstrate a method that allows optical absorption spectra to be computed both efficiently and at high accuracy. Our approach is based on the spectral warping method successfully applied to molecules in solvent. It involves calculating the absorption spectrum of a supercell of the full molecular crystal using semi-local time-dependent density functional theory (TDDFT), before warping the spectrum using a transformation derived from smaller-scale semi-local and hybrid TDDFT calculations on isolated dimers. We demonstrate the power of this method on three polymorphs of the well-known color polymorphic compound ROY and find that it outperforms both small-scale hybrid TDDFT dimer calculations and large-scale semi-local TDDFT supercell calculations, when compared to the experiment.

Modeling Molecular Emitters in Organic Light-Emitting Diodes with the Quantum Mechanical Bespoke Force Field

Combined molecular dynamics (MD) and quantum mechanics (QM) simulation procedures have gained popularity in modeling the spectral properties of functional organic molecules. However, the potential energy surfaces used to propagate long-time scale dynamics in these simulations are typically described using general, transferable force fields designed for organic molecules in their electronic ground states. These force fields do not typically include spectroscopic data in their training, and importantly, there is no general protocol for including changes in geometry or intermolecular interactions with the environment that may occur upon electronic excitation. In this work, we show that parameters tailored for thermally activated delayed fluorescence (TADF) emitters used in organic light-emitting diodes (OLEDs), in both their ground and electronically excited states, can be readily derived from a small number of QM calculations using the QUBEKit (QUantum mechanical BEspoke toolKit) software and improve the overall accuracy of these simulations.

Vibronic and Environmental Effects in Simulations of Optical Spectroscopy

Including both environmental and vibronic effects is important for accurate simulation of optical spectra, but combining these effects remains computationally challenging. We outline two approaches that consider both the explicit atomistic environment and the vibronic transitions. Both phenomena are responsible for spectral shapes in linear spectroscopy and the electronic evolution measured in nonlinear spectroscopy. The first approach utilizes snapshots of chromophore-environment configurations for which chromophore normal modes are determined. We outline various approximations for this static approach that assumes harmonic potentials and ignores dynamic system-environment coupling. The second approach obtains excitation energies for a series of time-correlated snapshots. This dynamic approach relies on the accurate truncation of the cumulant expansion but treats the dynamics of the chromophore and the environment on equal footing. Both approaches show significant potential for making strides toward more accurate optical spectroscopy simulations of complex condensed phase systems.

Substituted 9-Diethylaminobenzo[a]phenoxazin-5-ones (Nile Red Analogues): Synthesis and Photophysical Properties

Nile Red is a benzo[a]phenoxazone dye containing a diethylamino substituent at the 9-position. In recent years, it has become a popular histological stain for cellular membranes and lipid droplets due to its unrivaled fluorescent properties in lipophilic environments. This makes it an attractive lead for chemical decoration to tweak its attributes and optimize it for more specialized microscopy techniques, e.g., fluorescence lifetime imaging or two-photon excited fluorescence microscopy, to which Nile Red has never been optimized. Herein, we present synthesis approaches to a series of monosubstituted Nile Red derivatives (9-diethylbenzo[a]phenoxazin-5-ones) starting from 1-naphthols or 1,3-naphthalenediols. The solvatochromic responsiveness of these fluorophores is reported with focus on how the substituents affect the absorption and emission spectra, luminosity, fluorescence lifetimes, and two-photon absorptivity. Several of the analogues emerge as strong candidates for reporting the polarity of their local environment. Specifically, the one- and two-photon excited fluorescence of Nile Red turns out to be very responsive to substitution, and the spectroscopic features can be finely tuned by judiciously introducing substituents of distinct electronic character at specific positions. This new toolkit of 9-diethylbenzo[a]phenoxazine-5-ones constitutes a step toward the next generation of optical molecular probes for advancing the understanding of lipid structures and cellular processes.

Reinvestigating the Photoprotection Properties of a Mycosporine Amino Acid Motif

With the growing concern regarding commercially available ultraviolet (UV) filters damaging the environment, there is an urgent need to discover new UV filters. A family of molecules called mycosporines and mycosporine-like amino acids (referred to as MAAs collectively) are synthesized by cyanobacteria, fungi and algae and act as the natural UV filters for these organisms. Mycosporines are formed of a cyclohexenone core structure while mycosporine-like amino acids are formed of a cyclohexenimine core structure. To better understand the photoprotection properties of MAAs, we implement a bottom-up approach by first studying a simple analog of an MAA, 3-aminocyclohex-2-en-1-one (ACyO). Previous experimental studies on ACyO using transient electronic absorption spectroscopy (TEAS) suggest that upon photoexcitation, ACyO becomes trapped in the minimum of an S₁ state, which persists for extended time delays (>2.5 ns). However, these studies were unable to establish the extent of electronic ground state recovery of ACyO within 2.5 ns due to experimental constraints. In the present studies, we have implemented transient vibrational absorption spectroscopy (as well as complementary TEAS) with Fourier transform infrared spectroscopy and density functional theory to establish the extent of electronic ground state recovery of ACyO within this time window. We show that by 1.8 ns, there is >75% electronic ground state recovery of ACyO, with the remaining percentage likely persisting in the electronic excited state. Long-term irradiation studies on ACyO have shown that a small percentage degrades after 2 h of irradiation, plausibly due to some of the aforementioned trapped ACyO going on to form a photoproduct. Collectively, these studies imply that a base building block of MAAs already displays characteristics of an effective UV filter.

Exploring the Photochemistry of an Ethyl Sinapate Dimer: An Attempt Toward a Better Ultraviolet Filter

The photochemistry and photostability of a potential ultraviolet (UV) radiation filter, dehydrodiethylsinapate, with a broad absorption in the UVA region, is explored utilizing a combination of femtosecond time-resolved spectroscopy and steady-state irradiation studies. The time-resolved measurements show that this UV filter candidate undergoes excited state relaxation after UV absorption on a timescale of ~10 picoseconds, suggesting efficient relaxation. However, steady-state irradiation measurements show degradation under prolonged UV exposure. From a photochemical standpoint, this highlights the importance of considering both the ultrafast and “ultraslow” timescales when designing new potential UV filters.

Nonlinear spectroscopy in the condensed phase: The role of Duschinsky rotations and third order cumulant contributions

First-principles modeling of nonlinear optical spectra in the condensed phase is highly challenging because both environment and vibronic interactions can play a large role in determining spectral shapes and excited state dynamics. Here, we compute two dimensional electronic spectroscopy (2DES) signals based on a cumulant expansion of the energy gap fluctuation operator, with specific focus on analyzing mode mixing effects introduced by the Duschinsky rotation and the role of the third order term in the cumulant expansion for both model and realistic condensed phase systems. We show that for a harmonic model system, the third order cumulant correction captures effects introduced by a mismatch in curvatures of ground and excited state potential energy surfaces, as well as effects of mode mixing. We also demonstrate that 2DES signals can be accurately reconstructed from purely classical correlation functions using quantum correction factors. We then compute nonlinear optical spectra for the Nile red and methylene blue chromophores in solution, assessing the third order cumulant contribution for realistic systems. We show that the third order cumulant correction is strongly dependent on the treatment of the solvent environment, revealing the interplay between environmental polarization and the electronic-vibrational coupling.

The ONETEP linear-scaling density functional theory program

We present an overview of the onetep program for linear-scaling density functional theory (DFT) calculations with large basis set (plane-wave) accuracy on parallel computers. The DFT energy is computed from the density matrix, which is constructed from spatially localized orbitals we call Non-orthogonal Generalized Wannier Functions (NGWFs), expressed in terms of periodic sinc (psinc) functions. During the calculation, both the density matrix and the NGWFs are optimized with localization constraints. By taking advantage of localization, onetep is able to perform calculations including thousands of atoms with computational effort, which scales linearly with the number or atoms. The code has a large and diverse range of capabilities, explored in this paper, including different boundary conditions, various exchange-correlation functionals (with and without exact exchange), finite electronic temperature methods for metallic systems, methods for strongly correlated systems, molecular dynamics, vibrational calculations, time-dependent DFT, electronic transport, core loss spectroscopy, implicit solvation, quantum mechanical (QM)/molecular mechanical and QM-in-QM embedding, density of states calculations, distributed multipole analysis, and methods for partitioning charges and interactions between fragments. Calculations with onetep provide unique insights into large and complex systems that require an accurate atomic-level description, ranging from biomolecular to chemical, to materials, and to physical problems, as we show with a small selection of illustrative examples. onetep has always aimed to be at the cutting edge of method and software developments, and it serves as a platform for developing new methods of electronic structure simulation. We therefore conclude by describing some of the challenges and directions for its future developments and applications.

One- and two-photon solvatochromism of the fluorescent dye Nile Red and its CF3, F and Br-substituted analogues

Nile Red is a valuable fluorescent dye for studying lipophilic environments. This study presents how solvent polarity and decoration with simple electron-withdrawing substituents influence its absorption, fluorescence and two-photon cross-section.

Unravelling photoprotection in microbial natural products

Mycosporine-like amino acids have long been known as a natural form of photoprotection for fungi and cyanobacteria. This review will highlight the key time-resolved experimental and theoretical techniques unravelling their photochemistry and photophysics, and directly link this to their use in commercial skin-care products, namely as sunscreen filters. Three case studies have been selected, each having aided advancement in this burgeoning field of research. We discuss these studies in the context of photoprotection and conclude by evaluating the necessary future steps towards translating the photochemistry and photophysics insight of these nature derived sunscreen filters to commercial application.

Probing of local polarity in poly(methyl methacrylate) with the charge transfer transition in Nile red

The permittivity of polymers and its spatial distribution play a crucial role in the behavior of thin films, such as those used, e.g., as sensor coatings. In an attempt to develop a conclusive approach to determine these quantities, the polarity of the model polymer poly(methyl methacrylate) (PMMA) in 600 nm thin films on a glass support was probed by the energy of the charge transfer transition in the oxazine dye Nile red (NR) at 25 °C. The absorption and fluorescence spectra of NR were observed to shift to the red with increasing solvent polarity, because of the intramolecular charge transfer character of the optical transition. New types of solvatochromic plots of emission frequency against absorption frequency and vice versa afforded the Onsager radius-free estimation of the ground and excited states dipole moment ratio. With this approach the values of these dipole moments of 11.97 D and 18.30–19.16 D, respectively, were obtained for NR. An effective local dielectric constant of 5.9–8.3 for PMMA thin films was calculated from the solvatochromic plot and the fluorescence maximum of NR observed in the PMMA films. The fluorescence band of NR in the rigid PMMA films shifted to the red by 130 cm⁻¹ with increasing excitation wavelength from 470 to 540 nm, while in a series of liquids the position of the emission maximum of NR remained constant within same range of the excitation wavelength. It is concluded that the fluorescence spectrum of NR in PMMA undergoes inhomogeneous broadening due to different surroundings of NR molecules in the ground state and slow sub-glass transition (T_g) relaxations in PMMA.

Examining solvent effects on the ultrafast dynamics of catechol

We consider the effect of a polar, hydrogen bond accepting, solvent environment on the excited state decay of catechol following excitation to its first excited singlet state (S₁). A comparison of Fourier transform infrared spectroscopy and explicit-solvent ab initio frequency prediction suggests that 5 mM catechol in acetonitrile is both nonaggregated and in its "closed" conformation, contrary to what has been previously proposed. Using ultrafast transient absorption spectroscopy, we then demonstrate the effects of aggregation on the photoexcited S₁ lifetime: at 5 mM catechol (nonaggregated) in acetonitrile, the S₁ lifetime is 713 ps. In contrast at 75 mM catechol in acetonitrile, the S₁ lifetime increases to 1700 ps. We attribute this difference to aggregation effects on the excited-state landscape. This work has shown that explicit-solvent methodology is key when calculating the vibrational frequencies of molecules in a strongly interacting solvent. Combining this with highly complementary steady-state and transient absorption spectroscopy enables us to gain key dynamical insights into how a prominent eumelanin building block behaves when in polar, hydrogen bond accepting solvents both as a monomer and as an aggregated species.

Optical spectra in the condensed phase: Capturing anharmonic and vibronic features using dynamic and static approaches

Simulating optical spectra in the condensed phase remains a challenge for theory due to the need to capture spectral signatures arising from anharmonicity and dynamical effects, such as vibronic progressions and asymmetry. As such, numerous simulation methods have been developed that invoke different approximations and vary in their ability to capture different physical regimes. Here, we use several models of chromophores in the condensed phase and ab initio molecular dynamics simulations to rigorously assess the applicability of methods to simulate optical absorption spectra. Specifically, we focus on the ensemble scheme, which can address anharmonic potential energy surfaces but relies on the applicability of extreme nuclear-electronic time scale separation; the Franck-Condon method, which includes dynamical effects but generally only at the harmonic level; and the recently introduced ensemble zero-temperature Franck-Condon approach, which straddles these limits. We also devote particular attention to the performance of methods derived from a cumulant expansion of the energy gap fluctuations and test the ability to approximate the requisite time correlation functions using classical dynamics with quantum correction factors. These results provide insights as to when these methods are applicable and able to capture the features of condensed phase spectra qualitatively and, in some cases, quantitatively across a range of regimes.

Theoretical insights into UV-Vis absorption spectra of difluoroboron β-diketonates with an extended π system: An analysis based on DFT and TD-DFT calculations

The UV-Vis absorption spectra of difluoroboron β-diketonates with aromatic substituents at the β-carbon are studied thoroughly using DFT and TD-DFT with the CAM-B3LYP functional. The complicated experimental spectra of these dyes can be correctly interpreted by considering their structural features. A closer look at the calculated data shows that the conformational flexibility of these compounds markedly influences their spectral shape. For the complexes with an extended π system, several conformers with significantly different absorption spectra are present in the equilibrium mixture in solution. Introducing a donor group alters the electronic structure of the complexes, so the charge distribution asymmetry in the molecules increases and the nature of the electronic transitions changes. Thus, both types of substituents, aromatic and donor ones, affect the spectral shape. Understanding their roles may help one to explain the absorption spectra of these and similar compounds and predict their response to analytes and other factors.

Mapping Surface Hydrophobicity of α-Synuclein Oligomers at the Nanoscale

Proteins fold into a single structural ensemble but can also misfold into many diverse structures including small aggregates and fibrils, which differ in their toxicity. The aggregate surface properties play an important role in how they interact with the plasma membrane and cellular organelles, potentially inducing cellular toxicity, however, these properties have not been measured to date due to the lack of suitable methods. Here, we used a spectrally resolved, super-resolution imaging method combined with an environmentally sensitive fluorescent dye to measure the surface hydrophobicity of individual aggregates formed by the protein α-synuclein (αS), whose aggregation is associated with Parkinson's disease. We show that the surface of soluble oligomers is more hydrophobic than fibrils and populates a diverse range of coexisting states. Overall, our data show that the conversion of oligomers to fibril-like aggregates and ultimately to fibrils results in a reduction in both hydrophobicity and the variation in hydrophobicity. This funneling characteristic of the energy landscape explains many of the observed properties of αS aggregates and may be a common feature of aggregating proteins.

Evaluation of Nile Red-Loaded Mesoporous Silica Nanoparticles for Developing Water-Soaked Fingerprints on Thermal Paper

Nile red has been an alternative reagent for detecting latent fingerprints on wetted substrates. However, the presence of methanol in nile red solution could make injury to handlers and destroy the traces on surfaces, such as texts on thermal papers. A novel small particle reagent formulation constituting of mesoporous silica nanoparticles (MSNs) based on nile red was prepared to overcome the problem. Compared with the conventional reagents Oil Red O or nile red solution, the nile red-loaded MSNs are highly selective to lipid residues of fingerprints and showed a greater ability to develop clear, sharp, and detailed fingerprints on thermal papers after these were immersed in water. In addition, it can retain texts on the thermal papers well and use only water as a solvent. These suggested that nile red-loaded MSNs are a safe, efficient, and convenient method to develop latent fingerprints on wide range of substrates of forensic importance.

Unraveling electronic absorption spectra using nuclear quantum effects: Photoactive yellow protein and green fluorescent protein chromophores in water

Many physical phenomena must be accounted for to accurately model solution-phase optical spectral line shapes, from the sampling of chromophore-solvent configurations to the electronic-vibrational transitions leading to vibronic fine structure. Here we thoroughly explore the role of nuclear quantum effects, direct and indirect solvent effects, and vibronic effects in the computation of the optical spectrum of the aqueously solvated anionic chromophores of green fluorescent protein and photoactive yellow protein. By analyzing the chromophore and solvent configurations, the distributions of vertical excitation energies, the absorption spectra computed within the ensemble approach, and the absorption spectra computed within the ensemble plus zero-temperature Franck-Condon approach, we show how solvent, nuclear quantum effects, and vibronic transitions alter the optical absorption spectra. We find that including nuclear quantum effects in the sampling of chromophore-solvent configurations using ab initio path integral molecular dynamics simulations leads to improved spectral shapes through three mechanisms. The three mechanisms that lead to line shape broadening and a better description of the high-energy tail are softening of heavy atom bonds in the chromophore that couple to the optically bright state, widening the distribution of vertical excitation energies from more diverse solvation environments, and redistributing spectral weight from the 0-0 vibronic transition to higher energy vibronic transitions when computing the Franck-Condon spectrum in a frozen solvent pocket. The absorption spectra computed using the combined ensemble plus zero-temperature Franck-Condon approach yield significant improvements in spectral shape and width compared to the spectra computed with the ensemble approach. Using the combined approach with configurations sampled from path integral molecular dynamics trajectories presents a significant step forward in accurately modeling the absorption spectra of aqueously solvated chromophores.

Combining the ensemble and Franck-Condon approaches for calculating spectral shapes of molecules in solution

The correct treatment of vibronic effects is vital for the modeling of absorption spectra of many solvated dyes. Vibronic spectra for small dyes in solution can be easily computed within the Franck-Condon approximation using an implicit solvent model. However, implicit solvent models neglect specific solute-solvent interactions on the electronic excited state. On the other hand, a straightforward way to account for solute-solvent interactions and temperature-dependent broadening is by computing vertical excitation energies obtained from an ensemble of solute-solvent conformations. Ensemble approaches usually do not account for vibronic transitions and thus often produce spectral shapes in poor agreement with experiment. We address these shortcomings by combining zero-temperature vibronic fine structure with vertical excitations computed for a room-temperature ensemble of solute-solvent configurations. In this combined approach, all temperature-dependent broadening is treated classically through the sampling of configurations and quantum mechanical vibronic contributions are included as a zero-temperature correction to each vertical transition. In our calculation of the vertical excitations, significant regions of the solvent environment are treated fully quantum mechanically to account for solute-solvent polarization and charge-transfer. For the Franck-Condon calculations, a small amount of frozen explicit solvent is considered in order to capture solvent effects on the vibronic shape function. We test the proposed method by comparing calculated and experimental absorption spectra of Nile red and the green fluorescent protein chromophore in polar and non-polar solvents. For systems with strong solute-solvent interactions, the combined approach yields significant improvements over the ensemble approach. For systems with weak to moderate solute-solvent interactions, both the high-energy vibronic tail and the width of the spectra are in excellent agreement with experiments.

On the nature of solvatochromic effect: The riboflavin absorption spectrum as a case study

We present here the calculation of the absorption spectrum of riboflavin in acetonitrile and dimethyl sulfoxide using a hybrid quantum/classical approach, namely the perturbed matrix method, based on quantum mechanical calculations and molecular dynamics simulations. The calculated spectra are compared to the absorption spectrum of riboflavin previously calculated in water and to the experimental spectra obtained in all three solvents. The experimentally observed variations in the absorption spectra upon change of the solvent environment are well reproduced by the calculated spectra. In addition, the nature of the excited states of riboflavin interacting with different solvents is investigated, showing that environment effects determine a recombination of the gas-phase electronic states and that such a recombination is strongly affected by the polarity of the solvent inducing significant changes in the absorption spectra.