The oxygen reduction reaction on [NiFe] hydrogenases.

Oxygen tolerance capacity is critical for hydrogen oxidation/evolution catalysts. In nature, [NiFe] hydrogenases show excellent O2-tolerance and can rapidly reactivate the active site. This work aims to understand the reduction of O2 on the active site of [NiFe] hydrogenases. From the density functional theory (DFT) calculations, the free energy diagram for the oxygen reduction reaction (ORR) has been derived and the rate-determining step is found to be the Ni-B to Ni-SIb' step. Our calculation explains the slow reactivation for the Ni-A state compared to the Ni-B state, which is due to the particularly stable structure of the Ni-A state.

pH-Sensitive fluorophores from locked GFP chromophores by a non-alternant analogue of the photochemical meta effect.

We report the synthesis and characterization of a pH-sensitive fluorescence switch based on a conformationally-locked green fluorescent protein (GFP) chromophore. The chromophore differs from difluoroboryl-locked parent by the addition of a titratable alcohol group on the imidazolinone ring. The chromophore is fluorescent at pH ≤ 5, but becomes non-fluorescent at higher pH, where the substituent is ionized. We use a quantum chemical model to show that the mechanism of the fluorescence turn-off is electronically analogous to photochemical meta effects in aryl-containing systems.

Color in Bridge-Substituted Cyanines.

Theories of color in cyanine dyes have evolved around the idea of a "resonance" of structures with distinct bonding and charge localization. Understanding the emergence of resonance models from the underlying many-electron problem remains a central issue for these systems. Here, the issue is addressed using a maximum-entropy approach to valence-bond representations of state-averaged complete-active space self-consistent field models. The approach allows calculation of energies and couplings of high-energy valence-bond structures that mediate superexchange couplings and chemical bonding. A series of valence-bond Hamiltonians for a series of bridge-substituted derivatives of Michler's hydrol blue (a monomethine cyanine) is presented. The Hamiltonians are approximated with a simple linear model parametrized by the Brown-Okamoto σp+ parameter of the bridge substituent. A quantitative lower bound on σp+, beyond which a resonant cyanine-like ground state will not exist, is presented. The large effective coupling in two-state resonance models emerges from superexchange associated with either covalent bonding or charge-carrier delocalization, with the former contribution significantly the stronger. The results provide ab initio justification for empirical diabatic-state models of methine optical response. They are of general interest for understanding the optoelectronic response in cyanines.

Canonical-ensemble state-averaged complete active space self-consistent field (SA-CASSCF) strategy for problems with more diabatic than adiabatic states: charge-bond resonance in monomethine cyanines.

This paper reviews basic results from a theory of the a priori classical probabilities (weights) in state-averaged complete active space self-consistent field (SA-CASSCF) models. It addresses how the classical probabilities limit the invariance of the self-consistency condition to transformations of the complete active space configuration interaction (CAS-CI) problem. Such transformations are of interest for choosing representations of the SA-CASSCF solution that are diabatic with respect to some interaction. I achieve the known result that a SA-CASSCF can be self-consistently transformed only within degenerate subspaces of the CAS-CI ensemble density matrix. For uniformly distributed ("microcanonical") SA-CASSCF ensembles, self-consistency is invariant to any unitary CAS-CI transformation that acts locally on the ensemble support. Most SA-CASSCF applications in current literature are microcanonical. A problem with microcanonical SA-CASSCF models for problems with "more diabatic than adiabatic" states is described. The problem is that not all diabatic energies and couplings are self-consistently resolvable. A canonical-ensemble SA-CASSCF strategy is proposed to solve the problem. For canonical-ensemble SA-CASSCF, the equilibrated ensemble is a Boltzmann density matrix parametrized by its own CAS-CI Hamiltonian and a Lagrange multiplier acting as an inverse "temperature," unrelated to the physical temperature. Like the convergence criterion for microcanonical-ensemble SA-CASSCF, the equilibration condition for canonical-ensemble SA-CASSCF is invariant to transformations that act locally on the ensemble CAS-CI density matrix. The advantage of a canonical-ensemble description is that more adiabatic states can be included in the support of the ensemble without running into convergence problems. The constraint on the dimensionality of the problem is relieved by the introduction of an energy constraint. The method is illustrated with a complete active space valence-bond (CASVB) analysis of the charge/bond resonance electronic structure of a monomethine cyanine: Michler's hydrol blue. The diabatic CASVB representation is shown to vary weakly for "temperatures" corresponding to visible photon energies. Canonical-ensemble SA-CASSCF enables the resolution of energies and couplings for all covalent and ionic CASVB structures contributing to the SA-CASSCF ensemble. The CASVB solution describes resonance of charge- and bond-localized electronic structures interacting via bridge resonance superexchange. The resonance couplings can be separated into channels associated with either covalent charge delocalization or chemical bonding interactions, with the latter significantly stronger than the former.

Valence-bond non-equilibrium solvation model for a twisting monomethine cyanine.

We propose and analyze a two-state valence-bond model of non-equilibrium solvation effects on the excited-state twisting reaction of monomethine cyanines. Suppression of this reaction is thought responsible for environment-dependent fluorescence yield enhancement in these dyes. Fluorescence is quenched because twisting is accompanied via the formation of dark twisted intramolecular charge-transfer (TICT) states. For monomethine cyanines, where the ground state is a superposition of structures with different bond and charge localizations, there are two possible twisting pathways with different charge localizations in the excited state. For parameters corresponding to symmetric monomethines, the model predicts two low-energy twisting channels on the excited-state surface, which leads to a manifold of TICT states. For typical monomethines, twisting on the excited state surface will occur with a small barrier or no barrier. Changes in the solvation configuration can differentially stabilize TICT states in channels corresponding to different bonds, and that the position of a conical intersection between adiabatic states moves in response to solvation to stabilize either one channel or the other. There is a conical intersection seam that grows along the bottom of the excited-state potential with increasing solvent polarity. For monomethine cyanines with modest-sized terminal groups in moderately polar solution, the bottom of the excited-state potential surface is completely spanned by a conical intersection seam.

Direct observation of photodissociation products from phenylperoxyl radicals isolated in the gas phase.

Gas phase peroxyl radicals are central to our chemical understanding of combustion and atmospheric processes and are typically characterized by strong absorption in the UV (λ(max) ≈ 240 nm). The analogous maximum absorption feature for arylperoxyl radicals is predicted to shift to the visible but has not previously been characterized nor have any photoproducts arising from this transition been identified. Here we describe the controlled synthesis and isolation in vacuo of an array of charge-substituted phenylperoxyl radicals at room temperature, including the 4-(N,N,N-trimethylammonium)methyl phenylperoxyl radical cation (4-Me3N([+])CH2-C6H4OO(•)), using linear ion-trap mass spectrometry. Photodissociation mass spectra obtained at wavelengths ranging from 310 to 500 nm reveal two major photoproduct channels corresponding to homolysis of aryl-OO and arylO-O bonds resulting in loss of O2 and O, respectively. Combining the photodissociation yields across this spectral window produces a broad (FWHM ≈ 60 nm) but clearly resolved feature centered at λ(max) = 403 nm (3.08 eV). The influence of the charge-tag identity and its proximity to the radical site are investigated and demonstrate no effect on the identity of the two dominant photoproduct channels. Electronic structure calculations have located the vertical B ← X transition of these substituted phenylperoxyl radicals within the experimental uncertainty and further predict the analogous transition for unsubstituted phenylperoxyl radical (C6H5OO(•)) to be 457 nm (2.71 eV), nearly 45 nm shorter than previous estimates and in good agreement with recent computational values.

Why Bindschedler's Green is redder than Michler's Hydrol Blue.

We offer a new physical interpretation of the color shift between diarylmethane dyes and their azomethine analogues. We use an isolobal analogy between state-averaged complete active space self-consistent field solutions for corresponding methines and azomethines to show that the shift contains a significant contribution from configuration interaction between a methine-like ππ* excitation and an nπ* excitation out of the azomethine lone pair. The latter does not exist in the corresponding methine systems. This picture is qualitatively inconsistent with traditional models of the shift based on molecular orbital perturbation theory of independent π-electron Hamiltonians. A key prediction is the existence of a dipole-allowed band in the blue/near-UV spectra of the azomethines, which has polarization parallel to the lowest energy band. This forces a revision of past assumptions about the nature of the low-energy spectra of the azomethines. A band at the predicted energies has been observed in solution-state spectra.

Four-electron, three-orbital model for the low-energy electronic structure of cationic diarylmethanes: notes on a "Pauling Point".

We examine a four-electron, three-orbital complete active space self-consistent field (SA-CASSCF) and multistate multireference perturbation theory (MS-MRPT2) model of the electronic structure associated with the two lowest-lying electronic excitations of a series of cationic diarylmethanes related to Michler's Hydrol Blue. These dyes are of interest because of the sensitivity of their excited-state dynamics to environmental influence in biological and other condensed phases. We show that the model corresponds to an easily understandable physical approximation where the dye electronic structure is mapped onto the π-electron system of an allyl anion. We show that reported trends in solution-state absorbance bands and transition dipole moments associated with the first two electronic excitations can be described within reasonable accuracy by the model. We also show, for Michler's Hydrol Blue, that the four-electron, three-orbital model provides a more balanced description of the electronic difference densities associated with electronic excitation calculated with the full π-electron space than can be achieved with active space models intermediate between these limits. The valence excitation energies predicted by the model are not sensitive to the underlying basis set, so that considerable computational savings may be possible by using split-valence basis sets with a limited number of polarization functions. We conclude that the model meets the criteria for a "Pauling Point": a point where the cancellation of large errors leads to physically balanced model, and where further elaboration degrades, rather than improves, the quality of description. We advocate that this Pauling Point be exploited in condensed-phase dynamical models where the computational overhead associated with the electronic structure must kept to a minimum (for example, nonadiabatic dynamics simulations coupled to QM/MM environmental models).

A two-state model of twisted intramolecular charge-transfer in monomethine dyes.

A two-state model Hamiltonian is proposed, which can describe the coupling of twisting displacements to charge-transfer behavior in the ground and excited states of a general monomethine dye molecule. This coupling may be relevant to the molecular mechanism of environment-dependent fluorescence yield enhancement. The model is parameterized against quantum chemical calculations on different protonation states of the green fluorescent protein chromophore, which are chosen to sample different regimes of detuning from the cyanine (resonant) limit. The model provides a simple yet realistic description of the charge transfer character along two possible excited state twisting channels associated with the methine bridge. It describes qualitatively different behavior in three regions that can be classified by their relationship to the resonant (cyanine) limit. The regimes differ by the presence or absence of twist-dependent polarization reversal and the occurrence of conical intersections. We find that selective biasing of one twisting channel over another by an applied diabatic biasing potential can only be achieved in a finite range of parameters near the cyanine limit.

A three-state effective Hamiltonian for symmetric cationic diarylmethanes.

We analyze the low-energy electronic structure of a series of symmetric cationic diarylmethanes, which are bridge-substituted derivatives of Michler's Hydrol Blue. We use a four-electron, three-orbital complete active space self-consistent field and multi-state multi-reference perturbation theory model to calculate a three-state diabatic effective Hamiltonian for each dye in the series. We exploit an isolobal analogy between the active spaces of the self-consistent field solutions for each dye to represent the electronic structure in a set of analogous diabatic states. The diabatic states can be identified with the bonding structures in classical resonance-theoretic models of cyanine dyes. We identify diabatic states with opposing charge and bond-order localization, analogous to the classical resonance structures, and a third state with charge on the bridge. While the left- and right-charged structures are similar for all dyes, the structure of the bridge-charged diabatic state, and the Hamiltonian matrix elements connected to it, change significantly across the series. The change is correlated with an inversion of the sign of the charge carrier on the bridge, which changes from an electron pair to a hole as the series is traversed.

Bond alternation, polarizability, and resonance detuning in methine dyes.

We derive structure-property relationships for methine ("Brooker") dyes relating the color of the dye and its symmetric parents to its bond alternation in the ground state and also to the dipole properties associated with its low-lying charge-resonance (or charge-transfer) transition. We calibrate and test these relationships on an array of different protonation states of the green fluorescent protein chromophore motif (an asymmetric halochromic methine dye) and its symmetric parent dyes. The relationships rely on the assumption that the diabatic states that define the Platt model for methine dye color [J. R. Platt, J. Chem. Phys. 25, 80 (1956)] can also be distinguished by their single-double bond alternation and by their charge localization character. These assumptions are independent of the primary constraint that defines the diabatic states in the Platt model--specifically, the Brooker deviation rule for methine dyes [L. G. S. Brooker, Rev. Mod. Phys. 14, 275 (1942)]. Taking these assumptions, we show that the Platt model offers an alternate route to known structure-property relationships between the bond length alternation and the quadratic nonlinear polarizability ß. We show also that the Platt model can be parameterized without the need for synthesis of the symmetric parents of a given dye, using the dipole data obtained through spectroscopic measurements. This suggests that the Platt model parameters may be used as independent variables in free-energy relationships for chromophores whose symmetric parents cannot be synthesized or chromophores strongly bound to biomolecular environments. The latter category includes several recently characterized biomolecular probe constructs. We illustrate these concepts by an analysis of previously reported electroabsorption and second-harmonic generation experiments on green fluorescent proteins.

Protonic gating of excited-state twisting and charge localization in GFP chromophores: a mechanistic hypothesis for reversible photoswitching.

Reversible photoswitching fluorescent proteins can be photoswitched between fluorescent and nonfluorescent states by different irradiation regimes. Accumulating spectroscopic and crystallographic evidence suggest a correlated change in protonation state and methine bridge isomerism of the chromophore. The anion can decay by photoisomerization of either of the methine bonds, but only one channel can act as a switch. Using ab initio multiple spawning dynamics simulations, we show that protonation is sufficient to change the photoisomerization channel in the chromophore. We propose that this behavior can underlie a switch given certain other conditions. We also propose a basis for coupling between excited-state basicity changes and selection of the photoisomerization channel based on the polarity of twisted charge-transfer states for neutral and anionic forms of the chromophore.

Quantum chemical characterization of low-lying excited states of an aryl peroxycarbonate: mechanistic implications for photodissociation.

Recent experiments have revealed the existence of an excited state dissociative mechanism for certain peroxycarbonates, with the demonstration that the lifetime of the excited state matches the picosecond time scale for appearance of nascent carbon dioxide product. The data infer that the photoreaction proceeds via an effectively concerted three-body dissociation within the lifetime of the singlet excited state. Many other arylperoxides decay sequentially via [(aryloxy)carbonyl]oxy radical intermediates on nanosecond-microsecond time scales. Uncertainty as to the lifetime of the excited state relates to the character and the relative energetic ordering of states of the parent molecule, since the spectra and photochemistry imply that low-lying states may exist on each of the aryl, carbonate, and peroxide chemical functionalities. We employ many-body electronic structure calculations to determine the energies and characters of the low-lying valence states of a minimal aryl peroxycarbonate model germane to the above-mentioned experiments, methyl phenyl peroxycarbonate (MPC). Our results indicate that the lowest-lying state is an intrinsically nondissociative aryl pipi* excited state. We identify additional low-lying states that are expected to be dissociative in nature and propose that the time scales observed for the dissociation reaction may correspond to the time scale for transfer of excited state population to these states.

Influence of ion structure on thermal runaway behaviour of aprotic and protic ionic liquids.

Accelerated rate calorimetric studies have been employed to study the exothermic and thermal runaway behaviour of some aprotic and protic ionic liquids based on several families of ions including the bis(flurorsulfonyl)imide anion ([FSI]-); it was found that the protic salts are safer than aprotic salts of the [FSI]- anion.

A diabatic three-state representation of photoisomerization in the green fluorescent protein chromophore.

We give a quantum chemical description of the photoisomerization reaction of green fluorescent protein (GFP) chromophores using a representation over three diabatic states. Photoisomerization leads to nonradiative decay, and competes with fluorescence in these systems. In the protein, this pathway is suppressed, leading to fluorescence. Understanding the electronic states relevant to photoisomerization is a prerequisite to understanding how the protein suppresses it, and preserves the emitting state of the chromophore. We present a solution to the state-averaged complete active space problem, which is spanned at convergence by three fragment-localized orbitals. We generate the diabatic-state representation by block diagonalization transformation of the Hamiltonian calculated for the anionic chromophore model HBDI with multireference, multistate perturbation theory. The diabatic states are charge localized and admit a natural valence-bond interpretation. At planar geometries, the diabatic picture of the optical excitation reduces to the canonical two-state charge-transfer resonance of the anion. Extension to a three-state model is necessary to describe decay via two possible pathways associated with photoisomerization of the (methine) bridge. Parametric Hamiltonians based on the three-state ansatz can be fit directly to data generated using the underlying active space. We provide an illustrative example of such a parametric Hamiltonian.

Conical intersections, charge localization, and photoisomerization pathway selection in a minimal model of a degenerate monomethine dye.

We propose a minimal model Hamiltonian for the electronic structure of a monomethine dye, in order to describe the photoisomerization of such dyes. The model describes interactions between three diabatic electronic states, each of which can be associated with a valence bond structure. Monomethine dyes are characterized by a charge-transfer resonance; the indeterminacy of the single-double bonding structure dictated by the resonance is reflected in a duality of photoisomerization pathways corresponding to the different methine bonds. The possible multiplicity of decay channels complicates mechanistic models of the effect of the environment on fluorescent quantum yields, as well as coherent control strategies. We examine the extent and topology of intersection seams between the electronic states of the dye and how they relate to charge localization and selection between different decay pathways. We find that intersections between the S(1) and S(0) surfaces only occur for large twist angles. In contrast, S(2)/S(1) intersections can occur near the Franck-Condon region. When the molecule has left-right symmetry, all intersections are associated with con- or disrotations and never with single bond twists. For asymmetric molecules (i.e., where the bridge couples more strongly to one end) the S(2) and S(1) surfaces bias torsion about different bonds. Charge localization and torsion pathway biasing are correlated. We relate our observations with several recent experimental and theoretical results, which have been obtained for dyes with similar structure.

Bond selection in the photoisomerization reaction of anionic green fluorescent protein and kindling fluorescent protein chromophore models.

The chromophores of the most widely known fluorescent proteins (FPs) are derivatives of a core p-hydroxybenzylidene-imidazolinon-5-one (HBI) motif, which usually occurs as a phenolate anion. Double bond photoisomerization of the exocyclic bridge of HBI is widely held to be an important internal conversion mechanism for FP chromophores. Herein we describe the ground and excited-state electronic structures and potential energy surfaces of two model chromophores: 4- p-hydroxybenzylidiene-1,2-dimethyl-imidazolin-5-one anion (HBDI), representing green FPs (GFPs), and 2-acetyl-4-hydroxybenylidene-1-methyl-imidazolin-5-one anion (AHBMI), representing kindling FPs (KFPs). These chromophores differ by a single substitution, but we observe qualitative differences in the potential energy surfaces which indicate inversion of bond selection in the photoisomerization reaction. Bond selection is also modulated by whether the reaction proceeds from a Z or an E conformation. These configurations correspond to fluorescent and nonfluorescent states of structurally characterized FPs, including some which can be reversibly switched by specific illumination regimes. We explain the difference in bond selectivity via substituent stabilization effects on a common set of charge-localized chemical structures. Different combinations of these structures give rise to both optically active (planar) and twisted intramolecular charge-transfer (TICT) states of the molecules. We offer a prediction of the gas-phase absorption of AHBMI, which has not yet been measured. We offer a hypothesis to explain the unusual fluorescence of AHBMI in DMF solution, as well as an experimental proposal to test our hypothesis.

A structural basis for the pH-dependent increase in fluorescence efficiency of chromoproteins.

Within the fluorescent protein and chromoprotein family, the phenomenon of photoswitching is both intriguing and biotechnologically useful. Illumination of particular chromoproteins with intense light results in dramatic increases in fluorescence efficiency (termed kindling) and involves cis-trans isomerization of the chromophore. Here we report that chromophore isomerization can also be driven via alteration in pH. Specifically, we demonstrate that a number of naturally occurring chromoproteins, and their engineered variants, undergo a dramatic 20-100-fold increase in fluorescence efficiency at alkaline pH (>pH9.0). We have determined to 1.8 A resolution the structure of one such chromoprotein, Rtms5(H146S), in its highly far-red fluorescent form (Phi(F), 0.11 at pH 10.7) and compared it to the structure of the non-fluorescent form (Phi(F), 0.002 at pH 8.0). At high pH, the cyclic tri-peptide chromophore was observed to be mobile and distributed between a trans non-coplanar and a cis coplanar conformation, whereas at the lower pH, only a trans non-coplanar chromophore was observed. Calculation of pK(a) values suggested that titration of the side-chain of the conserved Glu215 close to the chromophore is involved in promoting the cis-coplanar conformation. Collectively, our data establish that isomerization to form a coplanar chromophore is a basis of the increased fluorescence efficiency at high pH. The phenomenon of pH-induced fluorescence gain has similarities with photoswitching, thereby providing a model to study the mechanism of kindling.

Effect of dimerization on vibrational spectra of eumelanin precursors.

We have synthesized a compound ideally suited to the study of structure-function relationships in eumelanin synthesis. N-methyl-5-hydroxy-6-methoxy-indole (MHMI) has key functional groups strategically placed on the indole framework to hinder binding in the 2, 5, 6 and 7 positions. Thus, the dimer bound exclusively in the 4-4' positions was isolated and characterized. In order to study the difference in vibrational structure between the MHMI monomer and dimer, Raman spectra were acquired of both compounds, as well as indole, indole-2-carboxylic acid and 5,6-dihydroxyindole-2-carboxylic acid (DHICA). Peaks were assigned to particular vibrational modes using B3LYP density functional theory calculations, and experimental and theoretical spectra displayed good agreement. Addition of functional groups to either benzene or pyrrole rings in the indole framework impacted vibrational spectra attributed to vibrations in either ring, and in some cases, peaks appearing unchanged between two compounds corresponded to different contributing vibrations. Dimerization resulted in an expected increase in the number of vibrational modes, but not a significant increase in the number of apparent peaks, as several modes frequently contributed to an individual observed peak. Comparison of spectral features of the monomer and dimer provides insight into eumelanin photochemistry, but final conclusions depend on the planarity of oligomeric structure in vivo.

Resveratrol's Hidden Hand: A Route to the Optical Detection of Biomolecular Binding.

Resveratrol is a stilbenoid phytoalexin with promising myriad health benefits predominantly contributed by the trans ( E) diastereomeric form. A recent study has implicated the cis ( Z) diastereomer in human health. This stereoisomer binds with high affinity to human tyrosyl-tRNA synthetase, initiating a downstream cascade that promotes the expression of genes associated with the cellular stress response. We discovered that the nonplanar structure of the cis-resveratrol conformer possesses certain chiral signals in its simulated vibrational circular dichroism (VCD) and Raman optical activity (ROA) spectra. These features may be used for the optical detection of the binding event and in understanding the more diversified biological roles of trans-resveratrol over cis-resveratrol. We use a density functional theory model, which is validated against the known results for the E diastereomer. The Z diastereomer is significantly nonplanar and can exist in two helical atropisomeric forms. These forms exchange rapidly in solution, but only one is observed to bind with the synthetase. This suggests that the binding may generate an enantiomeric excess, leading to detectable changes in the vibrational optical activity spectra. We identify candidate features at 998, 1649, and 1677 cm-1 in the ROA and at 1642 and 3834 cm-1 in the VCD spectra of Z-resveratrol that may be useful for this purpose.