Radius measurement via super-resolution microscopy enables the development of a variable radii proximity labeling platform.

The elucidation of protein interaction networks is critical to understanding fundamental biology as well as developing new therapeutics. Proximity labeling platforms (PLPs) are state-of-the-art technologies that enable the discovery and delineation of biomolecular networks through the identification of protein-protein interactions. These platforms work via catalytic generation of reactive probes at a biological region of interest; these probes then diffuse through solution and covalently "tag" proximal biomolecules. The physical distance that the probes diffuse determines the effective labeling radius of the PLP and is a critical parameter that influences the scale and resolution of interactome mapping. As such, by expanding the degrees of labeling resolution offered by PLPs, it is possible to better capture the various size scales of interactomes. At present, however, there is little quantitative understanding of the labeling radii of different PLPs. Here, we report the development of a superresolution microscopy-based assay for the direct quantification of PLP labeling radii. Using this assay, we provide direct extracellular measurements of the labeling radii of state-of-the-art antibody-targeted PLPs, including the peroxidase-based phenoxy radical platform (269 ± 41 nm) and the high-resolution iridium-catalyzed µMap technology (54 ± 12 nm). Last, we apply these insights to the development of a molecular diffusion-based approach to tuning PLP resolution and introduce a new aryl-azide-based µMap platform with an intermediate labeling radius (80 ± 28 nm).

Molecular Photothermal Conversion Catalyst Promotes Photocontrolled Atom Transfer Radical Polymerization.

Photothermal conversion is a growing research area that promotes thermal transformations with visible light irradiation. However, few examples of dual photothermal conversion and catalysis limit the power of this phenomenon. Here, we take inspiration from nature's ability to use porphyrinic compounds for nonradiative relaxation to convert light into heat to facilitate thermal polymerization catalysis. We identify the photothermal conversion catalytic activity of a vitamin B12 derivative, heptamethyl ester cobyrinate (HME-Cob), to perform atom transfer radical polymerization (ATRP) under irradiation. Rapid polymerization are obtained under photothermal activation while maintaining good control over polymerization with the aid of a photoinitiator to enable light-induced catalyst regeneration. The catalyst exhibits exquisite temporal control in photocontrolled thermal polymerization. Ultimately, the activation of this complex is accessed across a broad range of wavelengths, including near-IR light, with excellent temporal control. This work showcases the potential of developing photothermal conversion catalysts.

A Telecom O-Band Emitter in Diamond.

Color centers in diamond are promising platforms for quantum technologies. Most color centers in diamond discovered thus far emit in the visible or near-infrared wavelength range, which are incompatible with long-distance fiber communication and unfavorable for imaging in biological tissues. Here, we report the experimental observation of a new color center that emits in the telecom O-band, which we observe in silicon-doped bulk single crystal diamonds and microdiamonds. Combining absorption and photoluminescence measurements, we identify a zero-phonon line at 1221 nm and phonon replicas separated by 42 meV. Using transient absorption spectroscopy, we measure an excited state lifetime of around 270 ps and observe a long-lived baseline that may arise from intersystem crossing to another spin manifold.

Mechanism and Dynamics of Photodecarboxylation Catalyzed by Lactate Monooxygenase.

Photoenzymes are a rare class of biocatalysts that use light to facilitate chemical reactions. Many of these catalysts utilize a flavin cofactor to absorb light, suggesting that other flavoproteins might have latent photochemical functions. Lactate monooxygenase is a flavin-dependent oxidoreductase previously reported to mediate the photodecarboxylation of carboxylates to afford alkylated flavin adducts. While this reaction holds a potential synthetic value, the mechanism and synthetic utility of this process are unknown. Here, we combine femtosecond spectroscopy, site-directed mutagenesis, and a hybrid quantum-classical computational approach to reveal the active site photochemistry and the role the active site amino acid residues play in facilitating this decarboxylation. Light-induced electron transfer from histidine to flavin was revealed, which has not been reported in other proteins. These mechanistic insights enable the development of catalytic oxidative photodecarboxylation of mandelic acid to produce benzaldehyde, a previously unknown reaction for photoenzymes. Our findings suggest that a much wider range of enzymes have the potential for photoenzymatic catalysis than has been realized to date.

Regioselective Radical Alkylation of Arenes Using Evolved Photoenzymes.

Substituted arenes are ubiquitous in molecules with medicinal functions, making their synthesis a critical consideration when designing synthetic routes. Regioselective C-H functionalization reactions are attractive for preparing alkylated arenes; however, the selectivity of existing methods is modest and primarily governed by the substrate's electronic properties. Here, we demonstrate a biocatalyst-controlled method for the regioselective alkylation of electron-rich and electron-deficient heteroarenes. Starting from an unselective "ene"-reductase (ERED) (GluER-T36A), we evolved a variant that selectively alkylates the C4 position of indole, an elusive position using prior technologies. Mechanistic studies across the evolutionary series indicate that changes to the protein active site alter the electronic character of the charge transfer (CT) complex responsible for radical formation. This resulted in a variant with a significant degree of ground-state CT in the CT complex. Mechanistic studies on a C2-selective ERED suggest that the evolution of GluER-T36A helps disfavor a competing mechanistic pathway. Additional protein engineering campaigns were carried out for a C8-selective quinoline alkylation. This study highlights the opportunity to use enzymes for regioselective radical reactions, where small molecule catalysts struggle to alter selectivity.

Ring currents modulate optoelectronic properties of aromatic chromophores at 25 T.

The properties of organic molecules can be influenced by magnetic fields, and these magnetic field effects are diverse. They range from inducing nuclear Zeeman splitting for structural determination in NMR spectroscopy to polaron Zeeman splitting organic spintronics and organic magnetoresistance. A pervasive magnetic field effect on an aromatic molecule is the aromatic ring current, which can be thought of as an induction of a circular current of π-electrons upon the application of a magnetic field perpendicular to the π-system of the molecule. While in NMR spectroscopy the effects of ring currents on the chemical shifts of nearby protons are relatively well understood, and even predictable, the consequences of these modified electronic states on the spectroscopy of molecules has remained unknown. In this work, we find that photophysical properties of model phthalocyanine compounds and their aggregates display clear magnetic field dependences up to 25 T, with the aggregates showing more drastic magnetic field sensitivities depending on the intermolecular interactions with the amplification of ring currents in stacked aggregates. These observations are consistent with ring currents measured in NMR spectroscopy and simulated in time-dependent density functional theory calculations of magnetic field-dependent phthalocyanine monomer and dimer absorption spectra. We propose that ring currents in organic semiconductors, which commonly comprise aromatic moieties, may present new opportunities for the understanding and exploitation of combined optical, electronic, and magnetic properties.

µMap-Red: Proximity Labeling by Red Light Photocatalysis.

Modern proximity labeling techniques have enabled significant advances in understanding biomolecular interactions. However, current tools primarily utilize activation modes that are incompatible with complex biological environments, limiting our ability to interrogate cell- and tissue-level microenvironments in animal models. Here, we report µMap-Red, a proximity labeling platform that uses a red-light-excited SnIV chlorin e6 catalyst to activate a phenyl azide biotin probe. We validate µMap-Red by demonstrating photonically controlled protein labeling in vitro through several layers of tissue, and we then apply our platform in cellulo to label EGFR microenvironments and validate performance with STED microscopy and quantitative proteomics. Finally, to demonstrate labeling in a complex biological sample, we deploy µMap-Red in whole mouse blood to profile erythrocyte cell-surface proteins. This work represents a significant methodological advance toward light-based proximity labeling in complex tissue environments and animal models.

Accessing non-natural reactivity by irradiating nicotinamide-dependent enzymes with light.

Enzymes are ideal for use in asymmetric catalysis by the chemical industry, because their chemical compositions can be tailored to a specific substrate and selectivity pattern while providing efficiencies and selectivities that surpass those of classical synthetic methods. However, enzymes are limited to reactions that are found in nature and, as such, facilitate fewer types of transformation than do other forms of catalysis. Thus, a longstanding challenge in the field of biologically mediated catalysis has been to develop enzymes with new catalytic functions. Here we describe a method for achieving catalytic promiscuity that uses the photoexcited state of nicotinamide co-factors (molecules that assist enzyme-mediated catalysis). Under irradiation with visible light, the nicotinamide-dependent enzyme known as ketoreductase can be transformed from a carbonyl reductase into an initiator of radical species and a chiral source of hydrogen atoms. We demonstrate this new reactivity through a highly enantioselective radical dehalogenation of lactones-a challenging transformation for small-molecule catalysts. Mechanistic experiments support the theory that a radical species acts as an intermediate in this reaction, with NADH and NADPH (the reduced forms of nicotinamide adenine nucleotide and nicotinamide adenine dinucleotide phosphate, respectively) serving as both a photoreductant and the source of hydrogen atoms. To our knowledge, this method represents the first example of photo-induced enzyme promiscuity, and highlights the potential for accessing new reactivity from existing enzymes simply by using the excited states of common biological co-factors. This represents a departure from existing light-driven biocatalytic techniques, which are typically explored in the context of co-factor regeneration.

Engineering a Non-Natural Photoenzyme for Improved Photon Efficiency.

Photoenzymes are biological catalysts that use light to convert starting materials into products. These catalysts require photon absorption for each turnover, making quantum efficiency an important optimization parameter. Flavin-dependent "ene"-reductases (EREDs) display latent photoenzymatic activity for synthetically valuable hydroalkylations; however, protein engineering has not been used to optimize this non-natural function. We describe a protein engineering platform for the high throughput optimization of photoenzymes. A single round of engineering results in improved catalytic function toward the synthesis of γ, δ, ϵ-lactams, and acyclic amides. Mechanistic studies show that key mutations can alter the enzyme's excited state dynamics, enhance its photon efficiency, and ultimately increase catalyst performance. Transient absorption spectroscopy reveals that engineered variants display dramatically decreased radical lifetimes, indicating an evolution toward a concerted mechanism.

Photoenzymatic Reductions Enabled by Direct Excitation of Flavin-Dependent "Ene"-Reductases.

Non-natural photoenzymatic reactions reported to date have depended on the excitation of electron donor-acceptor complexes formed between substrates and cofactors within protein active sites to facilitate electron transfer. While this mechanism has unlocked new reactivity, it limits the types of substrates that can be involved in this area of catalysis. Here we demonstrate that direct excitation of flavin hydroquinone within "ene"-reductase active sites enables new substrates to participate in photoenzymatic reactions. We found that by using photoexcitation these enzymes gain the ability to reduce acrylamides through a single electron transfer mechanism.

Quaternary Charge-Transfer Complex Enables Photoenzymatic Intermolecular Hydroalkylation of Olefins.

Intermolecular C-C bond-forming reactions are underdeveloped transformations in the field of biocatalysis. Here we report a photoenzymatic intermolecular hydroalkylation of olefins catalyzed by flavin-dependent 'ene'-reductases. Radical initiation occurs via photoexcitation of a rare high-order enzyme-templated charge-transfer complex that forms between an alkene, α-chloroamide, and flavin hydroquinone. This unique mechanism ensures that radical formation only occurs when both substrates are present within the protein active site. This active site can control the radical terminating hydrogen atom transfer, enabling the synthesis of enantioenriched γ-stereogenic amides. This work highlights the potential for photoenzymatic catalysis to enable new biocatalytic transformations via previously unknown electron transfer mechanisms.

Charge Localization after Ultrafast Photoexcitation of a Rigid Perylene Perylenediimide Dyad Visualized by Transient Stark Effect.

The intramolecular charge-transfer (CT) dynamics of a rigid and strongly conjugated perylenediimide-bridge-perylene dyad (PDIPe) has been investigated in dichloromethane using ultrafast transient electronic absorption spectroscopy and quantum chemical calculations. The strong electronic coupling between the dyad units gives rise to a CT band. Its photoexcitation forms a delocalized CT state with well-preserved ion bands despite the strong coupling. In the dyad, the electronic transition dipole moment of the electron donor perylene is aligned along the axis of the electric field vector with respect to the CT species. This alignment makes the donor sensitive to the Stark effect and thus charge density fluctuations in the CT state. Charge localization on the picosecond time scale manifests as a time-dependent Stark shift in the visible region. Quantum chemical calculations reveal a twist around the acetylene bridging unit to be the responsible mechanism generating a partial to an almost complete CT state. An estimate of the electric field strength in the CT state yields approximately 25 MV/cm, which increases to around 31 MV/cm during charge localization. Furthermore, the calculations illustrate the complexity of electronic structure in this strongly delocalized superchromophore and reflect the complications in the interpretation of transient absorption results when compared to steady-state approaches such as spectroelectrochemistry and model chromophore experiments such as photoinduced bimolecular charge transfer.

Photophysical characterization and time-resolved spectroscopy of a anthradithiophene dimer: exploring the role of conformation in singlet fission.

Quantitative singlet fission has been observed for a variety of acene derivatives such as tetracene and pentacene, and efforts to extend the library of singlet fission compounds is of current interest. Preliminary calculations suggest anthradithiophenes exhibit significant exothermicity between the first optically-allowed singlet state, S1, and 2 × T1 with an energy difference of >5000 cm-1. Given the fulfillment of this ingredient for singlet fission, here we investigate the singlet fission capability of a difluorinated anthradithiophene dimer (2ADT) covalently linked by a (dimethylsilyl)ethane bridge and derivatized by triisobutylsilylethynyl (TIBS) groups. Photophysical characterization of 2ADT and the single functionalized ADT monomer were carried out in toluene and acetone solution via absorption and fluorescence spectroscopy, and their photo-initiated dynamics were investigated with time-resolved fluorescence (TRF) and transient absorption (TA) spectroscopy. In accordance with computational predictions, two conformers of 2ADT were observed via fluorescence spectroscopy and were assigned to structures with the ADT cores trans or cis to one another about the covalent bridge. The two conformers exhibited markedly different excited state deactivation mechanisms, with the minor trans population being representative of the ADT monomer showing primarily radiative decay, while the dominant cis population underwent relaxation into an excimer geometry before internally converting to the ground state. The excimer formation kinetics were found to be solvent dependent, yielding time constants of ∼1.75 ns in toluene, and ∼600 ps in acetone. While the difference in rates elicits a role for the solvent in stabilizing the excimer structure, the rate is still decidedly long compared to most singlet fission rates of analogous dimers, suggesting that the excimer is neither a kinetic nor a thermodynamic trap, yet singlet fission was still not observed. The result highlights the sensitivity of the electronic coupling element between the singlet and correlated triplet pair states, to the dimer conformation in dictating singlet fission efficiency even when the energetic requirements are met.

Single-residue insertion switches the quaternary structure and exciton states of cryptophyte light-harvesting proteins.

Observation of coherent oscillations in the 2D electronic spectra (2D ES) of photosynthetic proteins has led researchers to ask whether nontrivial quantum phenomena are biologically significant. Coherent oscillations have been reported for the soluble light-harvesting phycobiliprotein (PBP) antenna isolated from cryptophyte algae. To probe the link between spectral properties and protein structure, we determined crystal structures of three PBP light-harvesting complexes isolated from different species. Each PBP is a dimer of αß subunits in which the structure of the αß monomer is conserved. However, we discovered two dramatically distinct quaternary conformations, one of which is specific to the genus Hemiselmis. Because of steric effects emerging from the insertion of a single amino acid, the two αß monomers are rotated by ∼73° to an "open" configuration in contrast to the "closed" configuration of other cryptophyte PBPs. This structural change is significant for the light-harvesting function because it disrupts the strong excitonic coupling between two central chromophores in the closed form. The 2D ES show marked cross-peak oscillations assigned to electronic and vibrational coherences in the closed-form PC645. However, such features appear to be reduced, or perhaps absent, in the open structures. Thus cryptophytes have evolved a structural switch controlled by an amino acid insertion to modulate excitonic interactions and therefore the mechanisms used for light harvesting.

Exciton delocalization drives rapid singlet fission in nanoparticles of acene derivatives.

We compare the singlet fission dynamics of five pentacene derivatives precipitated to form nanoparticles. Two nanoparticle types were distinguished by differences in their solid-state order and kinetics of triplet formation. Nanoparticles that comprise primarily weakly coupled chromophores lack the bulk structural order of the single crystal and exhibit nonexponential triplet formation kinetics (Type I), while nanoparticles that comprise primarily more strongly coupled chromophores exhibit order resembling that of the bulk crystal and triplet formation kinetics associated with the intrinsic singlet fission rates (Type II). In the highly ordered nanoparticles, singlet fission occurs most rapidly. We relate the molecular packing arrangement derived from the crystal structure of the pentacene derivatives to their singlet fission dynamics and find that slip stacking leads to rapid, subpicosecond singlet fission. We present evidence that exciton delocalization, coincident with an increased relative admixture of charge-transfer configurations in the description of the exciton wave function, facilitates rapid triplet pair formation in the case of single-step singlet fission. We extend the study to include two hexacene derivatives and find that these conclusions are generally applicable. This work highlights acene derivatives as versatile singlet fission chromophores and shows how chemical functionalization affects both solid-state order and exciton interactions and how these attributes in turn affect the rate of singlet fission.

B800-B850 coherence correlates with energy transfer rates in the LH2 complex of photosynthetic purple bacteria.

Until recently, no analytical measure of many-body delocalization in open systems had been developed, yet such a measure enables characterization of how molecular excitons delocalize in photosynthetic light-harvesting complexes, and in turn helps us understand quantum coherent aspects of electronic energy transfer. In this paper we apply these measures to a model peripheral light-harvesting complex, LH2 from Rhodopseudomonas acidophila. We find how many chromophores collectively contribute to the "delocalization length" of an excitation within LH2 and how the coherent delocalization is distributed spatially. We also investigate to what extent this delocalization length is effective, by examining the impact of bipartite and multipartite entanglement in inter-ring energy transfer in LH2.

Broadband Transient Absorption and Two-Dimensional Electronic Spectroscopy of Methylene Blue.

Broadband transient absorption and two-dimensional electronic spectroscopy (2DES) studies of methylene blue in aqueous solution are reported. By isolating the coherent oscillations of the nonlinear signal amplitude and Fourier transforming with respect to the population time, we analyzed a significant number of coherences in the frequency domain and compared them with predictions of the vibronic spectrum from density function theory (DFT) calculations. We show here that such a comparison enables reliable assignments of vibrational coherences to particular vibrational modes, with their constituent combination bands and overtones also being identified via Franck­Condon analysis aided by DFT. Evaluation of the Fourier transform (FT) spectrum of transient absorption recorded to picosecond population times, in coincidence with 2D oscillation maps that disperse the FT spectrum into the additional excitation axis, is shown to be a complementary approach toward detailed coherence determination. Using the Franck­Condon overlap integrals determined from DFT calculations, we modeled 2D oscillation maps up to two vibrational quanta in the ground and excited state (six-level model), showing agreement with experiment. This semiquantitative analysis is used to interpret the geometry change upon photoexcitation as an expansion of the central sulfur/nitrogen containing ring due to the increased antibonding character in the excited state.

Structural refinement of ladder-type perylenediimide dimers: a classical tale of conformational dynamics.

We have synthesized and thoroughly characterized two representative ladder-type acetylene-bridged perylenediimide dimers bearing long alkyl chain solubilizing groups, bis[1-ethynyl-N,N'-bis(1-hexylheptyl)-perylene-3,4:9,10-tetracarboxylic diimide] ([PDICC]2, 1) and 1,1'-ethynyl-bis[N,N'-bis(1-hexylheptyl)-perylene-3,4:9,10-tetracarboxylic diimide] ([PDI]2CC, 2). In these dimeric PDI molecules, NMR-based structural characterization became nontrivial because severe (1)H spectral broadening and greater than expected numbers of observed (13)C resonances substantially complicated the interpretation of traditional 1-D spectra. However, rational two-dimensional NMR approaches based on both homo- and heteronuclear couplings ((1)H-(1)H COSY; (1)H-(13)C HSQC), in conjunction with high-level structural DFT calculations (GIAO/B3LYP/6-31G(d,p)/PCM, chloroform), were readily applied to these structures, producing well-defined analytical characterization, and the associated methodology is described in detail. Furthermore, on the basis of dynamic NMR experiments, both 1 and 2 were found to exist in a perylene-centered conformational dynamic equilibrium (ΔG‡ = 13-17 kcal/mol), which primarily caused the observed ambiguities in conventional 1-D spectra.

Using enzymes to tame nitrogen-centred radicals for enantioselective hydroamination.

The formation of C-N bonds-of great importance to the pharmaceutical industry-can be facilitated enzymatically using nucleophilic and nitrene transfer mechanisms. However, neither natural nor engineered enzymes are known to generate and control nitrogen-centred radicals, which serve as valuable species for C-N bond formation. Here we use flavin-dependent 'ene'-reductases with an exogenous photoredox catalyst to selectively generate amidyl radicals within the protein active site. These enzymes are engineered through directed evolution to catalyse 5-exo, 6-endo, 7-endo, 8-endo, and intermolecular hydroamination reactions with high levels of enantioselectivity. Mechanistic studies suggest that radical initiation occurs via an enzyme-gated mechanism, where the protein thermodynamically activates the substrate for reduction by the photocatalyst. Molecular dynamics studies indicate that the enzymes bind substrates using non-canonical binding interactions, which may serve as a handle to further manipulate reactivity. This approach demonstrates the versatility of these enzymes for controlling the reactivity of high-energy radical intermediates and highlights the opportunity for synergistic catalyst strategies to unlock previously inaccessible enzymatic functions.