First and Second Reductions in an Aprotic Solvent: Comparing Computational and Experimental One-Electron Reduction Potentials for 345 Quinones.

Using reference reduction potentials of quinones recently measured relative to the saturated calomel electrode (SCE) in N,N-dimethylformamide (DMF), we benchmark absolute one-electron reduction potentials computed for 345 Q/Q•- and 265 Q•-/Q2- half-reactions using adiabatic electron affinities computed with density functional theory and solvation energies computed with four continuum solvation models: IEF-PCM, C-PCM, COSMO, and SM12. Regression analyses indicate a strong linear correlation between experimental and absolute computed Q/Q•- reduction potentials with Pearson's correlation coefficient (r) between 0.95 and 0.96 and the mean absolute error (MAE) relative to the linear fit between 83.29 and 89.51 mV for different solvation methods when the slope of the regression is constrained to 1. The same analysis for Q•-/Q2- gave a linear regression with r between 0.74 and 0.90 and MAE between 95.87 and 144.53 mV, respectively. The y-intercept values obtained from the linear regressions are in good agreement with the range of absolute reduction potentials reported in the literature for the SCE but reveal several sources of systematic error. The y-intercepts from Q•-/Q2- calculations are lower than those from Q/Q•- by around 320-410 mV for IEF-PCM, C-PCM, and SM12 compared to 210 mV for COSMO. Systematic errors also arise between molecules having different ring sizes (benzoquinones, naphthoquinones, and anthraquinones) and different substituents (titratable vs nontitratable). SCF convergence issues were found to be a source of random error that was slightly reduced by directly optimizing the solute structure in the continuum solvent reaction field. While SM12 MAEs were lower than those of the other solvation models for Q/Q•-, SM12 had larger MAEs for Q•-/Q2- pointing to a larger error when describing multiply charged anions in DMF. Altogether, the results highlight the advantages of, and further need for, testing computational methods using a large experimental data set that is not skewed (e.g., having more titratable than nontitratable substituents on different parent groups or vice versa) to help further distinguish between sources of random and systematic errors in the calculations.

Twisted and Disconnected Chains: Flexible Linear Tetracuprous Arrays and a Decanuclear CuI Cluster as Blue- and Green/Yellow-Light Emitters.

Defined arrays of transition metal ions embedded in tailored polydentate ligand scaffolds allow for a systematic design of their physical properties. Such molecular strings of closed-shell transition metal centers are particularly interesting for Group 11 metal ions in the oxidation state +1 if they undergo metallophilic d10···d10 contact interactions since these clusters are oftentimes efficient photoluminescence (PL) emitters. Copper is particularly attractive as a sustainable earth-abundant coinage metal source and because of the ability of several CuI complexes to serve as powerful thermally activated delayed fluorescence (TADF) emitters in molecular/organic light-emitting devices (OLEDs). Our combined synthetic, crystallographic, photophysical, and computational study describes a straight tetracuprous array possessing a centrally disconnected CuI2···CuI2 chain and a continuous helically bent CuI4 complex. This molecular helix undergoes a facile rearrangement in diethyl ether solution, yielding an unprecedented nanosized CuI10 cluster (2.9 × 2.0 nm) upon crystallization. All three clusters show either bright blue phosphorescence, TADF, or green/yellow multiband phosphorescence with quantum yields between 6.5 and 67%, which is persistent under hydrostatic pressure up to 30 kbar. Temperature-dependent PL investigations in combination with time-dependent density-functional theory (TD-DFT) calculations and void space analyses of the crystal packings complement a comprehensive correlation between the molecular structures and photoluminescence properties.

Solvent-Dependent Emissions Properties of a Model Aurone Enable Use in Biological Applications.

Fluorophores are powerful visualization tools and the development of novel small organic fluorophores are in great demand. Small organic fluorophores have been derived from the aurone skeleton, 2-benzylidenebenzofuran-3(2H)-one. In this study, we have utilized a model aurone derivative with a methoxy group at the 3' position and a hydroxyl group at the 4' position, termed vanillin aurone, to develop a foundational understanding of structural factors impacting aurone fluorescence properties. The fluorescent behaviors of the model aurone were characterized in solvent environments differing in relative polarity and dielectric constant. These data suggested that hydrogen bonding or electrostatic interactions between excited state aurone and solvent directly impact emissions properties such as peak emission wavelength, emission intensity, and Stokes shift. Time-dependent Density Functional Theory (TD-DFT) model calculations suggest that quenched aurone emissions observed in water are a consequence of stabilization of a twisted excited state conformation that disrupts conjugation. In contrast, the calculations indicate that low polarity solvents such as toluene or acetone stabilize a brightly fluorescent planar state. Based on this, additional experiments were performed to demonstrate use as a turn-on probe in an aqueous environment in response to conditions leading to planar excited state stabilization. Vanillin aurone was observed to bind to a model ATP binding protein, YME1L, leading to enhanced emissions intensities with a dissociation equilibrium constant equal to ~ 30 µM. Separately, the aurone was observed to be cell permeable with significant toxicity at doses exceeding 6.25 µM. Taken together, these results suggest that aurones may be broadly useful as turn-on probes in aqueous environments that promote either a change in relative solvent polarity or through direct stabilization of a planar excited state through macromolecular binding.

How Aqueous Solvation Impacts the Frequencies and Intensities of Infrared Absorption Bands in Flavin: The Quest for a Suitable Solvent Model.

FTIR spectroscopy accompanied by quantum chemical simulations can reveal important information about molecular structure and intermolecular interactions in the condensed phase. Simulations typically account for the solvent either through cluster quantum mechanical (QM) models, polarizable continuum models (PCM), or hybrid quantum mechanical/molecular mechanical (QM/MM) models. Recently, we studied the effect of aqueous solvent interactions on the vibrational frequencies of lumiflavin, a minimal flavin model, using cluster QM and PCM models. Those models successfully reproduced the relative frequencies of four prominent stretching modes of flavin's isoalloxazine ring in the diagnostic 1450-1750 cm-1 range but poorly reproduced the relative band intensities. Here, we extend our studies on this system and account for solvation through a series of increasingly sophisticated models. Only by combining elements of QM clusters, QM/MM, and PCM approaches do we obtain an improved agreement with the experiment. The study sheds light more generally on factors that can impact the computed frequencies and intensities of IR bands in solution.

Synthesis and Evaluation of Cereblon-Recruiting HaloPROTACs.

Target validation is key to the development of protein degrading molecules such as proteolysis-targeting chimeras (PROTACs) to identify cellular proteins amenable for induced degradation by the ubiquitin-proteasome system (UPS). Previously the HaloPROTAC system was developed to screen targets of PROTACs by linking the chlorohexyl group with the ligands of E3 ubiquitin ligases VHL and cIAP1 to recruit target proteins fused to the HaloTag for E3-catalyzed ubiquitination. Reported here are HaloPROTACs that engage the cereblon (CRBN) E3 to ubiquitinate and degrade HaloTagged proteins. A focused library of CRBN-pairing HaloPROTACs was synthesized and screened to identify efficient degraders of EGFP-HaloTag fusion with higher activities than VHL-engaging HaloPROTACs at sub-micromolar concentrations of the compound. The CRBN-engaging HaloPROTACs broadens the scope of the E3 ubiquitin ligases that can be utilized to screen suitable targets for induced protein degradation in the cell.

Alternative Strategy for Spectral Tuning of Flavin-Binding Fluorescent Proteins.

iLOV is an engineered flavin-binding fluorescent protein (FbFP) with applications for in vivo cellular imaging. To expand the range of applications of FbFPs for multicolor imaging and FRET-based biosensing, it is desirable to understand how to modify their absorption and emission wavelengths (i.e., through spectral tuning). There is particular interest in developing FbFPs that absorb and emit light at longer wavelengths, which has proven challenging thus far. Existing spectral tuning strategies that do not involve chemical modification of the flavin cofactor have focused on placing positively charged amino acids near flavin's C4a and N5 atoms. Guided by previously reported electrostatic spectral tunning maps (ESTMs) of the flavin cofactor and by quantum mechanical/molecular mechanical (QM/MM) calculations reported in this work, we suggest an alternative strategy: placing a negatively charged amino acid near flavin's N1 atom. We predict that a single-point mutant, iLOV-Q430E, has a slightly red-shifted absorption and fluorescence maximum wavelength relative to iLOV. To validate our theoretical prediction, we experimentally expressed and purified iLOV-Q430E and measured its spectral properties. We found that the Q430E mutation results in a slight change in absorption and a 4-8 nm red shift in the fluorescence relative to iLOV, in good agreement with the computational predictions. Molecular dynamics simulations showed that the carboxylate side chain of the glutamate in iLOV-Q430E points away from the flavin cofactor, which leads to a future expectation that further red shifting may be achieved by bringing the side chain closer to the cofactor.

Solvatochromic and Aggregation-Induced Emission Active Nitrophenyl-Substituted Pyrrolidinone-Fused-1,2-Azaborine with a Pre-Twisted Molecular Geometry.

Boron-nitrogen-containing heterocycles with extended conjugated π-systems such as polycyclic aromatic 1,2-azaborines, hold the fascination of organic chemists due to their unique optoelectronic properties. However, the majority of polycyclic aromatic 1,2-azaborines aggregate at high concentrations or in the solid-state, resulting in aggregation-caused quenching (ACQ) of emission. This practical limitation poses significant challenges for polycyclic aromatic 1,2-azaborines' use in many applications. Additionally, only a few solvatochromic polycyclic aromatic 1,2-azaborines have been reported and they all display minimal solvatochromism. Therefore, the scope of available polycyclic 1,2-azaborines needs to be expanded to include those displaying fluorescence at high concentration and in the solid-state as well as those that exhibit significant changes in emission intensity in various solvents due to different polarities. To address the ACQ issue, we evaluate the effect of a pre-twisted molecular geometry on the optoelectronic properties of polycyclic aromatic 1,2-azaborines. Specifically, three phenyl-substituted pyrrolidinone-fused 1,2-azaborines (PFAs) with similar structures and functionalized with diverse electronic moieties (-H, -NO2, -CN, referred to as PFA 1, 2, and 3, respectively) were experimentally and computationally studied. Interestingly, PFA 2 displays two distinct emission properties: 1) solvatochromism, in which its emission and quantum yields are tunable with respect to solvent polarity, and 2) fluorescence that can be completely "turned off" and "turned on" via aggregation-induced emission (AIE). This report provides the first example of a polycyclic aromatic 1,2-azaborine that displays both AIE and solvatochromism properties in a single BN-substituted backbone. According to time-dependent density function theory (TD-DFT) calculations, the fluorescence properties of PFA 2 can be explained by the presence of a low-lying n-π* charge transfer state inaccessible to PFA 1 or PFA 3. These findings will help in the design of future polycyclic aromatic 1,2-azaborines that are solvatochromic and AIE-active as well as in understanding how molecular geometry affects these compounds' optoelectronic properties.

Dipole effects in the photoelectron angular distributions of the sulfur monoxide anion.

Photoelectron angular distributions (PADs) in SO- photodetachment using linearly polarized 355 nm (3.49 eV), 532 nm (2.33 eV), and 611 nm (2.03 eV) light were investigated via photoelectron imaging spectroscopy. The measurements at 532 and 611 nm access the X3Σ- and a1Δ electronic states of SO, whereas the measurements at 355 nm also access the b1Σ+ state. In aggregate, the photoelectron anisotropy parameter values follow the general trend with respect to electron kinetic energy (eKE) expected for π*-orbital photodetachment. The trend is similar to O2-, but the minimum of the SO- curve is shifted to smaller eKE. This shift is mainly attributed to the exit-channel interactions of the departing electron with the dipole moment of the neutral SO core, rather than the differing shapes of the SO- and O2- molecular orbitals. Of the several ab initio models considered, two approaches yield good agreement with the experiment: one representing the departing electron as a superposition of eigenfunctions of a point dipole-field Hamiltonian, and another describing the outgoing electron in terms of Coulomb waves originating from two separated charge centers, with a partial positive charge on the sulfur and an equal negative charge on the oxygen. These fundamentally related approaches support the conclusion that electron-dipole interactions in the exit channel of SO- photodetachment play an important role in shaping the PADs. While a similar conclusion was previously reached for photodetachment from σ orbitals of CN- (Hart, Lyle, Spellberg, Krylov, Mabbs, J. Phys. Chem. Lett., 2021, 12, 10086-10092), the present work includes the first extension of the dipole-field model to detachment from π* orbitals.

Photochemically triggered cheletropic formation of cyclopropenone (c-C3H2O) from carbon monoxide and electronically excited acetylene.

For more than half a century, pericyclic reactions have played an important role in advancing our fundamental understanding of cycloadditions, sigmatropic shifts, group transfer reactions, and electrocyclization reactions. However, the fundamental mechanisms of photochemically activated cheletropic reactions have remained contentious. Here we report on the simplest cheletropic reaction: the [2+1] addition of ground state 18O-carbon monoxide (C18O, X1Σ+) to D2-acetylene (C2D2) photochemically excited to the first excited triplet (T1), second excited triplet (T2), and first excited singlet state (S1) at 5 K, leading to the formation of D2-18O-cyclopropenone (c-C3D218O). Supported by quantum-chemical calculations, our investigation provides persuasive testimony on stepwise cheletropic reaction pathways to cyclopropenone via excited state dynamics involving the T2 (non-adiabatic) and S1 state (adiabatic) of acetylene at 5 K, while the T1 state energetically favors an intermediate structure that directly dissociates after relaxing to the ground state. The agreement between experiments in low temperature ices and the excited state calculations signifies how photolysis experiments coupled with theoretical calculations can untangle polyatomic reactions with relevance to fundamental physical organic chemistry at the molecular level, thus affording a versatile strategy to unravel exotic non-equilibrium chemistries in cyclic, aromatic organics. Distinct from traditional radical-radical pathways leading to organic molecules on ice-coated interstellar nanoparticles (interstellar grains) in cold molecular clouds and star-forming regions, the photolytic formation of cyclopropenone as presented changes the perception of how we explain the formation of complex organics in the interstellar medium eventually leading to the molecular precursors of biorelevant molecules.

Quantum-classical simulations of rhodopsin reveal excited-state population splitting and its effects on quantum efficiency.

The activation of rhodopsin, the light-sensitive G-protein-coupled receptor responsible for dim-light vision in vertebrates, is driven by an ultrafast excited-state double-bond isomerization with a quantum efficiency of almost 70%. The origin of such light sensitivity is not understood and a key question is whether in-phase nuclear motion controls the quantum efficiency value. In this study we used hundreds of quantum-classical trajectories to show that, 15 fs after light absorption, a degeneracy between the reactive excited state and a neighbouring state causes the splitting of the rhodopsin population into subpopulations. These subpopulations propagate with different velocities and lead to distinct contributions to the quantum efficiency. We also show here that such splitting is modulated by protein electrostatics, thus linking amino acid sequence variations to quantum efficiency modulation. Finally, we discuss how such a linkage that in principle could be exploited to achieve higher quantum efficiencies would simultaneously increase the receptor thermal noise leading to a trade-off that may have played a role in rhodopsin evolution.

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 fexp 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 fexp values. The corresponding computed oscillator strengths (fcomp) 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 fcomp and fexp. Although fcomp and fexp are well correlated (linear regression R2 = 0.921), fcomp in most cases overestimated fexp (regression slope = 1.34). The agreement between absolute fcomp and fexp 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.

Free Energy Computation for an Isomerizing Chromophore in a Molecular Cavity via the Average Solvent Electrostatic Configuration Model: Applications in Rhodopsin and Rhodopsin-Mimicking Systems.

We present a novel technique for computing the free energy differences between two chromophore "isomers" hosted in a molecular environment (a generalized solvent). Such an environment may range from a relatively rigid protein cavity to a flexible solvent environment. The technique is characterized by the application of the previously reported "average electrostatic solvent configuration" method, and it is based on the idea of using the free energy perturbation theory along with a chromophore annihilation procedure in thermodynamic cycle calculations. The method is benchmarked by computing the ground-state room-temperature relative stabilities between (i) the cis and trans isomers of prototypal animal and microbial rhodopsins and (ii) the analogue isomers of a rhodopsin-like light-driven molecular switch in methanol. Furthermore, we show that the same technology can be used to estimate the activation free energy for the thermal isomerization of systems i-ii by replacing one isomer with a transition state. The results show that the computed relative stability and isomerization barrier magnitudes for the selected systems are in line with the available experimental observation in spite of their widely diverse complexity.

Ionic Atmosphere Effect on the Absorption Spectrum of a Flavoprotein: A Reminder to Consider Solution Ions.

This study utilizes the FMN-dependent NADH:quinone oxidoreductase from Pseudomonas aeruginosa PAO1 to investigate the effect of introducing an active site negative charge on the flavin absorption spectrum both in the absence and presence of a long-range electrostatic potential coming from solution ions. There were no observed changes in the flavin UV-visible spectrum when an active site tyrosine (Y277) becomes deprotonated in vitro. These results could only be reproduced computationally using average solvent electrostatic configuration (ASEC) QM/MM simulations that include both positive and negative solution ions. The same calculations performed with minimal ions to neutralize the total protein charge predicted that deprotonating Y277 would significantly alter the flavin absorption spectrum. Analyzing the distribution of solution ions indicated that the ions reorganize around the protein surface upon Y277 deprotonation to cancel the effect of the tyrosinate on the flavin absorption spectrum. Additional biochemical experiments were performed to test this hypothesis.

Tuning Protein Dynamics to Sense Rapid Endoplasmic-Reticulum Calcium Dynamics.

Multi-scale calcium (Ca2+ ) dynamics, exhibiting wide-ranging temporal kinetics, constitutes a ubiquitous mode of signal transduction. We report a novel endoplasmic-reticulum (ER)-targeted Ca2+ indicator, R-CatchER, which showed superior kinetics in vitro (koff ≥2×103  s-1 , kon ≥7×106  M-1 s-1 ) and in multiple cell types. R-CatchER captured spatiotemporal ER Ca2+ dynamics in neurons and hotspots at dendritic branchpoints, enabled the first report of ER Ca2+ oscillations mediated by calcium sensing receptors (CaSRs), and revealed ER Ca2+ -based functional cooperativity of CaSR. We elucidate the mechanism of R-CatchER and propose a principle to rationally design genetically encoded Ca2+ indicators with a single Ca2+ -binding site and fast kinetics by tuning rapid fluorescent-protein dynamics and the electrostatic potential around the chromophore. The design principle is supported by the development of G-CatchER2, an upgrade of our previous (G-)CatchER with improved dynamic range. Our work may facilitate protein design, visualizing Ca2+ dynamics, and drug discovery.

The effect of hydrogen-bonding on flavin's infrared absorption spectrum.

Cluster and continuum solvation computational models are employed to model the effect of hydrogen bonding interactions on the vibrational modes of lumiflavin. Calculated spectra were compared to experimental Fourier-transform infrared (FTIR) spectra in the diagnostic 1450-1800 cm-1 range, where intense νC=C, νC=N, [Formula: see text] , and [Formula: see text] stretching modes of flavin's isoalloxazine ring are found. Local mode analysis is used to describe the strength of hydrogen-bonding in cluster models. The computations indicate that νC=C and νC=N mode frequencies are relatively insensitive to intermolecular interactions while the [Formula: see text] and [Formula: see text] modes are sensitive to direct (and also indirect for [Formula: see text] ) hydrogen-bonding interactions. Although flavin is neutral, basis sets without the diffuse functions provide incorrect relative frequencies and intensities. The 6-31+G* basis set is found to be adequate for this system, and there is limited benefit to considering larger basis sets. Calculated vibrational mode frequencies agree with experimentally determined frequencies in solution when cluster models with multiple water molecules are used. Accurate simulation of relative FTIR band intensities, on the other hand, requires a continuum (or possibly quantum mechanical/molecular mechanical) model that accounts for long-range electrostatic effects. Finally, an experimental peak at ca. 1624 cm-1 that is typically assigned to the [Formula: see text] vibrational stretching mode has a complicated shape that suggests multiple underlying contributions. Our calculations show that this band has contributions from both the C6-C7 and C2 = O stretching vibrations.

A Single-Point Mutation in d-Arginine Dehydrogenase Unlocks a Transient Conformational State Resulting in Altered Cofactor Reactivity.

Proteins are inherently dynamic, and proper enzyme function relies on conformational flexibility. In this study, we demonstrated how an active site residue changes an enzyme's reactivity by modulating fluctuations between conformational states. Replacement of tyrosine 249 (Y249) with phenylalanine in the active site of the flavin-dependent d-arginine dehydrogenase yielded an enzyme with both an active yellow FAD (Y249F-y) and an inactive chemically modified green FAD, identified as 6-OH-FAD (Y249F-g) through various spectroscopic techniques. Structural investigation of Y249F-g and Y249F-y variants by comparison to the wild-type enzyme showed no differences in the overall protein structure and fold. A closer observation of the active site of the Y249F-y enzyme revealed an alternative conformation for some active site residues and the flavin cofactor. Molecular dynamics simulations probed the alternate conformations observed in the Y249F-y enzyme structure and showed that the enzyme variant with FAD samples a metastable conformational state, not available to the wild-type enzyme. Hybrid quantum/molecular mechanical calculations identified differences in flavin electronics between the wild type and the alternate conformation of the Y249F-y enzyme. The computational studies further indicated that the alternate conformation in the Y249F-y enzyme is responsible for the higher spin density at the C6 atom of flavin, which is consistent with the formation of 6-OH-FAD in the variant enzyme. The observations in this study are consistent with an alternate conformational space that results in fine-tuning the microenvironment around a versatile cofactor playing a critical role in enzyme function.

QM/MM Investigation of the Spectroscopic Properties of the Fluorophore of Bacterial Luciferase.

We employ replica-exchange molecular dynamics (REMD) and a hybrid ab initio multiconfigurational quantum mechanics/molecular mechanics (QM/MM) approach to model the absorption and fluorescence properties of bacterial luciferin-luciferase. Specifically, we employ complete active space perturbation theory (CASPT2) and study the effect of active space, basis set, and IPEA shift on the computed energies. We discuss the effect of the protein environment on the fluorophore's excited-state potential energy surface and the role that the protein plays in enhancing the fluorescence quantum yield in bacterial bioluminescence.

Probing the Electronic Structure of Bulk Water at the Molecular Length Scale with Angle-Resolved Photoelectron Spectroscopy.

We report a combined experimental and theoretical study of bulk water photoionization. Angular distributions of photoelectrons produced by ionizing the valence bands of neat water using X-ray radiation (250-750 eV) show a limited (∼20%) decrease in the ß anisotropy parameter compared to the gas phase, indicating that the electronic structure of the individual water molecules can be probed. We show that, in the high-energy regime, photoionization of bulk can be described using an incoherent superposition of individual molecules, in contrast to a low-energy regime where photoionization probes delocalized entangled states of molecular aggregates. The two regimes-low versus high energy-are limiting cases where the de Broglie wavelength of the photoelectron is larger or smaller than the intermolecular distance between water molecules, respectively. The comparison of measured and computed anisotropies reveals that the reduction in ß at high kinetic energies is mostly due to scattering rather than rehybridization due to solvation.

Excited-State Vibronic Dynamics of Bacteriorhodopsin from Two-Dimensional Electronic Photon Echo Spectroscopy and Multiconfigurational Quantum Chemistry.

Owing to the ultrafast time scale of the photoinduced reaction and high degree of spectral overlap among the reactant, product, and excited electronic states in bacteriorhodopsin (bR), it has been a challenge for traditional spectroscopies to resolve the interplay between vibrational dynamics and electronic processes occurring in the retinal chromophore of bR. Here, we employ ultrafast two-dimensional electronic photon echo spectroscopy to follow the early excited-state dynamics of bR preceding the isomerization. We detect an early periodic photoinduced absorptive signal that, employing a hybrid multiconfigurational quantum/molecular mechanical model of bR, we attribute to periodic mixing of the first and second electronic excited states (S1 and S2, respectively). This recurrent interaction between S1 and S2, induced by a bond length alternation of the retinal chromohore, supports the hypothesis that the ultrafast photoisomerization in bR is initiated by a process involving coupled nuclear and electronic motion on three different electronic states.

Electronic spectra of flavin in different redox and protonation states: a computational perspective on the effect of the electrostatic environment.

Flavins are versatile molecules due to their ability to exist in multiple redox and protonation states. At physiological conditions, they are usually encountered either as oxidized quinones, neutral semiquinones, anionic semiquinones, neutral hydroquinones, or anionic hydroquinones. We compute the electronic near-UV/vis spectra for flavin in each of these five states. Specifically, we compute vertical, adiabatic, and vibronic excitations for all excited states that have wavelengths longer than 300 nm. We employ the calculations to assign the peaks in the corresponding experimental UV/vis spectra from literature. We also compare the effect of polar and non-polar solvents on the spectra using a polarizable continuum model. Finally, we construct "electrostatic spectral tuning maps" for prominent peaks in each of the five states. These maps qualitatively describe how the flavin electronic spectra will be shifted by an anisotropic electrostatic environment such as a protein. Understanding how flavin's UV/vis absorption spectrum is modulated by its environment can aid in experiments employing flavin as a probe of internal electrostatics of a protein and in engineering new color variants of flavoproteins.