Simulation of the UV/Visible Absorption Spectra of Fluorescent Protein Chromophore Models

Simulating Vibronic Spectra by Direct Application of Doktorov Formulas on a Superconducting Quantum Simulator

In this work, a direct quantum implementation of the Doktorov formulas for calculating the vibronic spectrum of molecules under the harmonic approximation is presented. It is applied to the three-atom molecules H2O, SO2, ClO2, HS2, and ZnOH. The method solves the classically hard problem of estimating the Franck-Condon (FC) factors by using the Duschinsky matrices as the only input via the Doktorov quantum circuit. This has the advantage of avoiding basis changes, artificial squeezing parameters, and symmetry dependencies. In other words, it is a general method for three-atom molecules that can easily be generalized to bigger molecules. The results are compared with other quantum algorithms and classical anharmonic algorithms. Furthermore, the circuit requirements are studied in order to estimate its applicability on real superconducting quantum hardware.

Bridge improvement work: maximising non-linear optical performance in polyoxometalate derivatives

New phenyl and stilbene-bridged polyoxometalate (POM) charge-transfer chromophores with diphenylamino donor groups produce, respectively, the highest intrinsic and absolute quadratic hyperpolarisabilities measured for such species. The β0,zzz obtained for the phenyl bridge - at 180 × 10-30 esu - is remarkable for a short conjugated system while changing to the stilbene (260 × 10-30 esu) produces a substantial increase in non-linearity for a minimal red-shift in the absorption profile. Together with TD-DFT calculations, the results show that maximising conjugation in the π-bridge is vital to high performance in such "POMophores".

Unraveling the mystery of solvation-dependent fluorescence of fluorescein dianion using computational study

Fluorescein, one of the brightest fluorescent dye molecules, is a widely used fluorophore for various applications from biomedicine to industry. The dianionic form of fluorescein is responsible for its high fluorescence quantum yield. Interestingly, the molecule was found to be nonfluorescent in the gas phase. This characteristic is attributed to the photodetachment process, which out-competes the fluorescence emission in the gas phase. In this work, we show that the calculated vertical and adiabatic detachment energies of fluorescein dianion in the gas and solvent phases account for the drastic differences observed in their fluorescence characteristics. The functional dependence of these detachment energies on the dianion's microsolvation was systematically investigated. The performance of different solvent models was also assessed. The higher thermodynamic stability of fluorescein dianion over the monoanion doublet in the solvent phase plays a crucial role in quenching photodetachment and activating the radiative channel with a high fluorescence quantum yield.

Excited-state dynamics and fluorescence lifetime of cryogenically cooled green fluorescent protein chromophore anions

Time-resolved action spectroscopy together with a fs-pump probe scheme is used in an electrostatic ion-storage ring to address lifetimes of specific vibrational levels in electronically excited states. Here we specifically consider the excited-state lifetime of cryogenically cooled green fluorescent protein (GFP) chromophore anions which is systematically measured across the S0-S1 spectral region (450-482 nm). A long lifetime of 5.2 ± 0.3 ns is measured at the S0-S1 band origin. When exciting higher vibrational levels in S1, the lifetime changes dramatically. It decreases by more than two orders of magnitude in a narrow energy region ∼250 cm-1 (31 meV) above the 0-0 transition. This is attributed to the opening of internal conversion over an excited-state energy barrier. The applied experimental technique provides a new way to uncover even small energy barriers, which are crucial for excited-state dynamics.

First hyperpolarizability of the di-8-ANEPPS and DR1 nonlinear optical chromophores in solution. An experimental and multi-scale theoretical chemistry study

The solvent effects on the linear and second-order nonlinear optical properties of an aminonaphtylethenylpyridinium (ANEP) dye are investigated by combining experimental and theoretical chemistry methods. On the one hand, deep near infrared (NIR) hyper-Rayleigh scattering (HRS) measurements (1840-1950 nm) are performed on solutions of di-8-ANEPPS in deuterated chloroform, dimethylformamide, and dimethylsulfoxide to determine their first hyperpolarizablity (βHRS). For the first time, these HRS experiments are carried out in the picosecond regime in the deep NIR with very moderate (≤3 mW) average input power, providing a good signal-to-noise ratio and avoiding solvent thermal effects. Moreover, the frequency dispersion of βHRS is investigated for Disperse Red 1 (DR1), a dye commonly used as HRS external reference. On the other hand, these are compared with computational chemistry results obtained by using a sequential molecular dynamics (MD) then quantum mechanics (QM) approach. The MD method allows accounting for the dynamical nature of the molecular structures. Then, the QM part is based on TDDFT/M06-2X/6-311+G* calculations using solvation models ranging from continuum to discrete ones. Measurements report a decrease of the βHRS of di-8-ANEPPS in more polar solvents and these effects are reproduced by the different solvation models. For di-8-ANEPPS and DR1, comparisons show that the use of a hybrid solvation model, combining the description of the solvent molecules around the probe by point charges with a continuum model, already achieves quasi quantitative agreement with experiment. These results are further improved by using a polarizable embedding that includes the atomic polarizabilities in the solvent description.

Chemosensing Properties of Coumarin Derivatives: Promising Agents with Diverse Pharmacological Properties, Docking and DFT Investigation

In this work, a three-component reaction of 3-acetyl-4-hydroxycoumarine, malononitrile, or cyanoacetate in the presence of ammonium acetate was used to form coumarin derivatives. The chemical structures of new compounds were identified by ¹H, ¹³C NMR and an elemental analysis. These compounds were examined in vitro for their antimicrobial activity against a panel of bacterial strains. In addition, these compounds were investigated for antioxidant activities by superoxideradical, DPPH (2,2-Diphenyl-1-picrylhydrazyl), and hydroxyl radical scavenging assays, in which most of them displayed significant antioxidant activities. Furthermore, these compounds were evaluated for anti-inflammatory activity by indirect hemolytic and lipoxygenase inhibition assays and revealed good activity. In addition, screening of the selected compounds 2–4 against colon carcinoma cell lines (HCT-116) and hepatocellular carcinoma cell lines (HepG-2) showed that that 2-amino-4-hydroxy-6-(4-hydroxy-2-oxo-2H-chromen-3-yl)nicotinonitrile 4 exhibited good cytotoxic activity against standard Vinblastine, while the other compounds exhibited moderate cytotoxic activity. Docking simulation showed that2-amino-4-hydroxy-6-(4-hydroxy-2-oxo-2H-chromen-3-yl)nicotinonitrile 4 is an effective inhibitor of the tumor protein HCT-116. A large fluorescence enhancement in a highly acidic medium was observed, and large fluorescence quenching by the addition of traces of Cu²⁺ and Ni²⁺ was also remarked.

TDDFT Investigation of the Raman and Resonant Raman Spectra of Fluorescent Protein Chromophore Models

The off-resonance and resonant Raman spectra have been simulated for models of fluorescent protein chromophores, those of the green fluorescent protein (GFP, called FP1) and of DsRed (called FP2), which presents a longer π-conjugated path, with the aim of providing a systematic investigation of structural but also computational aspects. These were performed at the (time-dependent) density functional theory [(TD)DFT] level. The off-resonance intensities have been calculated from the derivatives of the frequency-dependent polarizability with respect to the normal coordinates while the resonant ones have been evaluated using Huang-Rhys factors determined from the gradients of the excitation energies with respect to the normal coordinates. When applied with the M05 meta-GGA exchange-correlation functional, this simple computational scheme can reproduce most of the experimental Raman signatures of FP1 in its protonated and deprotonated forms, the differences of vibrational signatures of the cis (Z) and trans (E) isomers, as well as their changes as a function of the excitation wavelength. On the other hand, testing the predictions made for FP2 would require new experimental work. It was also observed that simulations with methods that inadequately predict the resonant Raman spectra could nevertheless produce a UV-vis absorption spectrum that is quite similar to the one obtained with better methods, once realistic peak broadening has been applied.

OS100: A Benchmark Set of 100 Digitized UV-Visible Spectra and Derived Experimental Oscillator Strengths

Excited-state quantum chemical calculations usually report excitation energies and oscillator strengths, f, for each electronic transition. On the other hand, UV-visible spectrophotometric experiments measure energy-dependent molar extinction/attenuation coefficients, ε(v), that give absorption band line shapes when plotted. ε(v) and f are related, but this relation is complicated by broadening and solvation effects. We fitted and integrated 100 experimental UV-visible spectra to obtain 164 f_exp values for absorption bands appearing in these spectra. The 100 UV-visible spectra belong to solvated organic molecules ranging in size from 6-34 atoms. We estimated uncertainties in the fitting to indicate confidence level in the reported f_exp values. The corresponding computed oscillator strengths (f_comp) were obtained with time-dependent density functional theory and a polarizable continuum solvent model. By expressing experimental and computed absorption strengths using a common quantity, we directly compared f_comp and f_exp. Although f_comp and f_exp are well correlated (linear regression R² = 0.921), f_comp in most cases overestimated f_exp (regression slope = 1.34). The agreement between absolute f_comp and f_exp values was substantially improved by accounting for a solvent refractive index factor, as suggested in some derivations in the literature. The 100 digitized UV-visible spectra are included as plain text files in the Supporting Information to aid in benchmarking computational or machine learning methods that aim to simulate realistic UV-visible absorption spectra.

Electronic spectroscopy of differential mobility-selected prototropic isomers of protonated para-aminobenzoic acid

para-Aminobenzoic acid (PABA) was electrosprayed from mixtures of protic and aprotic solvents, leading to formation of two prototropic isomers in the gas phase whose relative populations depended on the composition of the electrospray solvent. The two ion populations were separated in the gas phase using differential mobility spectrometry (DMS) within a nitrogen-only environment at atmospheric pressure. Under high-field conditions, the two prototropic isomers eluted with baseline signal separation with the N-protonated isomer having a more negative CV shift than the O-protonated isomer, in accord with previous DMS studies. The conditions most favorable for formation and separation of each tautomer were used to trap each prototropic isomer in a quadrupole ion trap for photodissociation action spectroscopy experiments. Spectral interrogation of each prototropic isomer in the UV region (3-6 eV) showed good agreement with previously recorded spectra, although a previously reported band (4.8-5.4 eV) was less intense for the O-protonated isomer in our measured spectrum. Without DMS selection, the measured spectra contained features corresponding to both protonated isomers even when solvent conditions were optimised for formation of a single isomer. Interconversion between protonated isomers within the ion trap was observed when protic ESI solvents were employed, leading to spectral cross contamination even with mobility selection. CCSD vertical excitation energies and vertical gradient (VG) Franck-Condon simulations are presented and reproduce the measured spectral features with near-quantitative agreement, providing supporting evidence for spectral assignments.

Density Functional Theory Study of Substitution Effects on the Second-Order Nonlinear Optical Properties of Lindquist-Type Organo-Imido Polyoxometalates

Density functional theory and time-dependent density functional theory have been enacted to investigate the effects of donor and acceptor on the first hyperpolarizability of Lindquist-type organo-imido polyoxometalates (POMs). These calculations employ a range-separated hybrid exchange-correlation functional (ωB97X-D), account for solvent effects using the implicit polarizable continuum model, and analyze the first hyperpolarizabilities by using the two-state approximation. They highlight the beneficial role of strong donors as well as of π-conjugated spacers (CH=CH rather than C≡C) on the first hyperpolarizabilities. Analysis based on the unit sphere representation confirms the one-dimensional push-pull π-conjugated character of the POMs substituted by donor groups and the corresponding value of the depolarization ratios close to 5. Furthermore, the use of the two-state approximation is demonstrated to be suitable for explaining the origin of the variations of the first hyperpolarizabilities as a function of the characteristics of a unique low-energy charge-transfer excited state and to attribute most of the first hyperpolarizability changes to the difference of dipole moment between the ground and that charge-transfer excited state.

One pot solvothermal synthesis of novel fluorescent phloem-mobile phenylpyrazole amide pesticides fused olefin moieties to enhance insecticidal bioactivities and photodegradation properties

In order to find a novel type of fluorescent phloem-mobile insecticides, a facile one-pot solvothermal strategy via fipronil addition-elimination substitution reaction with the corresponding acyl chloride derivatives has been employed to construct series of phenylpyrazole amide derivatives (PAs) fused olefin moieties in high yields. The investigation for insecticidal bioactivities of PAs against 3rd instar larvae of Plutella xylostella exhibited better activities than that of fipronil, which can be elucidated by enhanced phloem mobility and calcium ions' coordination with amide N-C=O, CC double bonds and chloride ions, extended conjugate moieties and decreasing steric hindrance of the stereoscopic structure. The introduction of amide units conferred phloem mobility to PAs, which was evaluated by the hydrophobic parameters determined with reversed-phase HPLC through the chromatographic capacity factor. By introducing conjugate moieties and organic chromophore into phenylpyrazole parent structure to increase their conjugation degree and light absorption abilities, PAs exhibited good photodegradation properties. The relationships between extended conjugate moieties of parent structure, electronegativity of substituted groups and photodegradation properties have been discussed. The olefin units connected to PAs caused electronic absorption and fluorescent wavelengths bathochromic shifted. Under simulated solar irradiation, PAs can be reconverted into fipronil parent fragments by photodegradation, thereby enhancing their insecticidal activity. The fluorescent quantum yields of PAs were almost 4 times that of fipronil, which also laid a foundation for the natural degradation and fluorescence detection of insecticide residues.

Ab Initio Prediction of Fluorescence Lifetimes Involving Solvent Environments by Means of COSMO and Vibrational Broadening

The fluorescence lifetime is a key property of fluorophores that can be utilized for microenvironment probing, analyte sensing, and multiplexing as well as barcoding applications. For the rational design of lifetime probes and barcodes, theoretical methods have been developed to enable the ab initio prediction of this parameter, which depends strongly on interactions with solvent molecules and other chemical species in the emitteŕs immediate environment. In this work, we investigate how a conductor-like screening model (COSMO) can account for variations in fluorescence lifetimes that are caused by such fluorophore-solvent interactions. Therefore, we calculate vibrationally broadened fluorescence spectra using the nuclear ensemble method to obtain distorted molecular geometries to sample the electronic transitions with time-dependent density functional theory (TDDFT). The influence of the solvent on fluorescence lifetimes is accounted for with COSMO. For example, for 4-hydroxythiazole fluorophore containing different heteroatoms and acidic and basic moieties in aprotic and protic solvents of varying polarity, this approach was compared to experimentally determined lifetimes in the same solvents. Our results demonstrate a good correlation between theoretically predicted and experimentally measured fluorescence lifetimes except for the polar solvents ethanol and acetonitrile that can specifically interact with the heteroatoms and the carboxylic acid of the thiazole derivative.

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.