Geometric and electronic structure probed along the isomerisation coordinate of a photoactive yellow protein chromophore

Dynamics of Anions: From Bound to Unbound States and Everything In Between

Gas-phase anions present an ideal playground for the exploration of excited-state dynamics. They offer control in terms of the mass, extent of solvation, internal temperature, and conformation. The application of a range of ion sources has opened the field to a vast array of anionic systems whose dynamics are important in areas ranging from biology to star formation. Here, we review recent experimental developments in the field of anion photodynamics, demonstrating the detailed insight into photodynamical and electron-capture processes that can be uncovered. We consider the electronic and nuclear ultrafast dynamics of electronically bound excited states along entire reaction coordinates; electronically unbound states showing that photochemical concepts, such as chromophores and Kasha's rule, are transferable to electron-driven chemistry; and nonvalence states that straddle the interface between bound and unbound states. Finally, we consider likely developments that are sure to keep the field of anion dynamics buoyant and impactful.

Photoactive Yellow Protein Represents a Distinct, Evolutionarily Novel Family of PAS Domains

Photoactive yellow protein (PYP) is a model photoreceptor. It binds a p-coumaric acid as a chromophore, thus enabling blue light sensing. The first discovered single-domain PYP from Halorhodospira halophila has been studied thoroughly in terms of its structural dynamics and photochemical properties. However, the evolutionary origins and biological role of PYP homologs are not well understood. Here, we show that PYP is an evolutionarily novel domain family of the ubiquitous PAS (Per-Arnt-Sim) superfamily. It likely originated from the phylum Myxococcota and was then horizontally transferred to representatives of a few other bacterial phyla. We show that PYP is associated with signal transduction either by domain fusion or by genome context. Key cellular functions modulated by PYP-initiated signal transduction pathways likely involve gene expression, motility, and biofilm formation. We identified three clades of the PYP family, one of which is poorly understood and potentially has novel functional properties. The Tyr42, Glu46, and Cys69 residues that are involved in p-coumaric acid binding in the model PYP from H. halophila are well conserved in the PYP family. However, we also identified cases where substitutions in these residues might have led to neofunctionalization, such as the proposed transition from light to redox sensing. Overall, this study provides definition, a newly built hidden Markov model, and the current genomic landscape of the PYP family and sets the stage for the future exploration of its signaling mechanisms and functional diversity. IMPORTANCE Photoactive yellow protein is a model bacterial photoreceptor. For many years, it was considered a prototypical model of the ubiquitous PAS domain superfamily. Here, we show that, in fact, the PYP family is evolutionarily novel, restricted to a few bacterial phyla and distinct from other PAS domains. We also reveal the diversity of PYP-containing signal transduction proteins and their potential mechanisms.

Excited-State Barrier Controls E → Z Photoisomerization in p-Hydroxycinnamate Biochromophores

Molecules based on the deprotonated p-hydroxycinnamate moiety are widespread in nature, including serving as UV filters in the leaves of plants and as the biochromophore in photoactive yellow protein. The photophysical behavior of these chromophores is centered around a rapid E → Z photoisomerization by passage through a conical intersection seam. Here, we use photoisomerization and photodissociation action spectroscopies with deprotonated 4-hydroxybenzal acetone (pCK^-) to characterize a wavelength-dependent bifurcation between electron autodetachment (spontaneous ejection of an electron from the S₁ state because it is situated in the detachment continuum) and E → Z photoisomerization. While autodetachment occurs across the entire S₁(ππ*) band (370-480 nm), E → Z photoisomerization occurs only over a blue portion of the band (370-430 nm). No E → Z photoisomerization is observed when the ketone functional group in pCK^- is replaced with an ester or carboxylic acid. The wavelength-dependent bifurcation is consistent with potential energy surface calculations showing that a barrier separates the Franck-Condon region from the E → Z isomerizing conical intersection. The barrier height, which is substantially higher in the gas phase than in solution, depends on the functional group and governs whether E → Z photoisomerization occurs more rapidly than autodetachment.

A Hückel Model for the Excited-State Dynamics of a Protein Chromophore Developed Using Photoelectron Imaging

Chemistry can be described as the movement of nuclei within molecules and the concomitant instantaneous change in electronic structure. This idea underpins the central chemical concepts of potential energy surfaces and reaction coordinates. To experimentally capture such chemical change therefore requires methods that can probe both the nuclear and electronic structure simultaneously and on the time scale of atomic motion. In this Account, we show how time-resolved photoelectron imaging can do exactly this and how it can be used to build a detailed and intuitive understanding of the electronic structure and excited-state dynamics of chromophores. The chromophore of the photoactive yellow protein (PYP) is used as a case study. This chromophore contains a para-substituted phenolate anion, where the substituent, R, can be viewed as an acrolein derivative. It is shown that the measured photoelectron angular distribution can be directly related to the electronic structure of the para-substituted phenolate anion. By incrementally considering differing R groups, it is also shown that these photoelectron angular distributions are exquisitely sensitive to the conformational flexibility of R and that when R contains a π-system the excited states of the chromophore can be viewed as a linear combination of the π* molecular orbitals on the phenolate (π_Ph*) and the R substituent (π_R*). Such Hückel treatment shows that the S₁ state of the PYP chromophore has predominantly π_R* character and that it is essentially the same as the chromophore of the green fluorescent protein (GFP). The S₁ excited-state dynamics of the PYP chromophore probed by time-resolved photoelectron imaging clearly reveals both structural (nuclear) dynamics through the energy spectrum and electronic dynamics through the photoelectron angular distributions. Both motions can be accurately assigned using quantum chemical calculations, and these are consistent with the intuitive Hückel treatment presented. The photoactive protein chromophores considered here are examples of where a chemists' intuitive Hückel view for ground-state chemistry appears to be transferable to the prediction of photochemical excited-state reactivity. While elegant and insightful, such models have limitations, including nonadiabatic dynamics, which is present in a related PYP chromophore, where a fraction of the S₁ state population forms a nonvalence (dipole-bound) state of the anion.

Photo-isomerization of the isolated photoactive yellow protein chromophore: what comes before the primary step?

Photoactive proteins typically rely on structural changes in a small chromophore to initiate a biological response. While these changes often involve isomerization as the "primary step", preceding this is an ultrafast relaxation of the molecular framework caused by the sudden change in electronic structure upon photoexcitation. Here, we capture this motion for an isolated model chromophore of the photoactive yellow protein using time-resolved photoelectron imaging. It occurs in <150 fs and is apparent from a spectral shift of ∼70 meV and a change in photoelectron anisotropy. Electronic structure calculations enable the quantitative assignment of the geometric and electronic structure changes to a planar intermediate from which the primary step can then proceed.

A photoelectron imaging study of the deprotonated GFP chromophore anion and RNA fluorescent tags

Green fluorescent protein (GFP), together with its family of variants, is the most widely used fluorescent protein for in vivo imaging. Numerous spectroscopic studies of the isolated GFP chromophore have been aimed at understanding the electronic properties of GFP. Here, we build on earlier work [A. V. Bochenkova, C. Mooney, M. A. Parkes, J. Woodhouse, L. Zhang, R. Lewin, J. M. Ward, H. Hailes, L. H. Andersen and H. H. Fielding, Chem. Sci., 2017, 8, 3154] investigating the impact of fluorine and methoxy substituents that have been employed to tune the electronic structure of the GFP chromophore for use as fluorescent RNA tags. We present photoelectron spectra following photoexcitation over a broad range of wavelengths (364-230 nm) together with photoelectron angular distributions following photoexcitation at 364 nm, which are interpreted with the aid of quantum chemistry calculations. The results support the earlier high-level quantum chemistry calculations that predicted how fluorine and methoxy substituents tune the electronic structure and we find evidence to suggest that the methoxy substituents enhance internal conversion, most likely from the 2ππ* state which has predominantly Feshbach resonance character, to the 1ππ* state.

Modeling the Photoelectron Angular Distributions of Molecular Anions: Roles of the Basis Set, Orbital Choice, and Geometry

A study investigating the effect of the basis set, orbital choice, and geometry on the modeling of photoelectron angular distributions (PADs) of molecular anions is presented. Experimental and modeled PADs for a number of molecular anions, including both closed- and open-shell systems, are considered. Guidelines are suggested for chemists who wish to design calculations to capture the correct chemical physics of the anisotropy of photodetachment, while balancing the computational cost associated with larger molecular anions.

Mode-Specific Autodetachment Dynamics of an Excited Non-valence Quadrupole-Bound State

The autodetachment dynamics of vibrational Feshbach resonances of the quadrupole-bound state (QBS) for the first time has been investigated in real time for the first excited state of the 4-cyanophenoxide (4-CP) anion. Individual vibrational resonances of the cryogenically cooled 4-CP QBS have been unambiguously identified, and their autodetachment rates state-specifically measured using the picosecond time-resolved pump-probe technique employing the photoelectron velocity-map imaging method. The autodetachment lifetime (τ) is found to be strongly dependent on mode, giving τ values of ∼56, ∼27, and ≤2.8 ps for the 12'¹ (E_vib = 406 cm^-1), 12'² (E_vib = 806 cm^-1), and 21'¹ (E_vib = 220 cm^-1) modes, respectively. The striking mode-specific behavior of the QBS lifetime has been invoked by the physical model in which the loosely bound electron falls off by the dynamic wobbling of the three-dimensional quadrupole moment ellipsoid associated with the corresponding vibrational motion in the autodetachment process.

Gas-Phase Synthesis and Characterization of the Methyl-2,2-dicyanoacetate Anion Using Photoelectron Imaging and Dipole-Bound State Autodetachment

The methyl-2,2-dicyanoacetate anion is synthesized in an electrospray ionization source through a gas-phase reaction involving tetracyanoethylene and methanol. Photoelectron imaging is used to determine the isomeric form of the product. The photoelectron spectra and angular distributions are consistent with only a single isomer. Additionally, mode-specific vibrational autodetachment is observed. This can be correlated with the emission from a photoexcited dipole-bound state by considering the IR spectrum of the neutral molecule, adding further confirmation of the isomeric form and providing a binding energy of the dipole-bound state. Our experiments show how conventional photoelectron imaging can be used to determine detailed information about gas-phase reaction products.