Ribonucleotide Reductases: Structure, Chemistry, and Metabolism Suggest New Therapeutic Targets.

Ribonucleotide reductases (RNRs) catalyze the de novo conversion of nucleotides to deoxynucleotides in all organisms, controlling their relative ratios and abundance. In doing so, they play an important role in fidelity of DNA replication and repair. RNRs' central role in nucleic acid metabolism has resulted in five therapeutics that inhibit human RNRs. In this review, we discuss the structural, dynamic, and mechanistic aspects of RNR activity and regulation, primarily for the human and Escherichia coli class Ia enzymes. The unusual radical-based organic chemistry of nucleotide reduction, the inorganic chemistry of the essential metallo-cofactor biosynthesis/maintenance, the transport of a radical over a long distance, and the dynamics of subunit interactions all present distinct entry points toward RNR inhibition that are relevant for drug discovery. We describe the current mechanistic understanding of small molecules that target different elements of RNR function, including downstream pathways that lead to cell cytotoxicity. We conclude by summarizing novel and emergent RNR targeting motifs for cancer and antibiotic therapeutics.

Protein engineering a PhotoRNR chimera based on a unifying evolutionary apparatus among the natural classes of ribonucleotide reductases.

Ribonucleotide reductases (RNRs) are essential enzymes that catalyze the de novo transformation of nucleoside 5'-di(tri)phosphates [ND(T)Ps, where N is A, U, C, or G] to their corresponding deoxynucleotides. Despite the diversity of factors required for function and the low sequence conservation across RNRs, a unifying apparatus consolidating RNR activity is explored. We combine aspects of the protein subunit simplicity of class II RNR with a modified version of Escherichia coli class la photoRNRs that initiate radical chemistry with light to engineer a mimic of a class II enzyme. The design of this RNR involves fusing a truncated form of the active site containing α subunit with the functionally important C-terminal tail of the radical-generating ß subunit to render a chimeric RNR. Inspired by a recent cryo-EM structure, a [Re] photooxidant is located adjacent to Y356[ß], which is an essential component of the radical transport pathway in class I RNRs. Combination of this RNR photochimera with cytidine diphosphate (CDP), adenosine triphosphate (ATP), and light resulted in the generation of Y356• along with production of deoxycytidine diphosphate (dCDP) and cytosine. The photoproducts reflect an active site chemistry consistent with both the consensus mechanism of RNR and chemistry observed when RNR is inactivated by mechanism-based inhibitors in the active site. The enzymatic activity of the RNR photochimera in the absence of any ß metallocofactor highlights the adaptability of the 10-stranded αß barrel finger loop to support deoxynucleotide formation and accommodate the design of engineered RNRs.

Riboflavin synthesis from gaseous nitrogen and carbon dioxide by a hybrid inorganic-biological system.

Microbes can provide a more sustainable and energy-efficient method of food and nutrient production compared to plant and animal sources, but energy-intensive carbon (e.g., sugars) and nitrogen (e.g., ammonia) inputs are required. Gas-fixing microorganisms that can grow on H2 from renewable water splitting and gaseous CO2 and N2 offer a renewable path to overcoming these limitations but confront challenges owing to the scarcity of genetic engineering in such organisms. Here, we demonstrate that the hydrogen-oxidizing carbon- and nitrogen-fixing microorganism Xanthobacter autotrophicus grown on a CO2/N2/H2 gas mixture can overproduce the vitamin riboflavin (vitamin B2). We identify plasmids and promoters for use in this bacterium and employ a constitutive promoter to overexpress riboflavin pathway enzymes. Riboflavin production is quantified at 15 times that of the wild-type organism. We demonstrate that riboflavin overproduction is maintained when the bacterium is grown under hybrid inorganic-biological conditions, in which H2 from water splitting, along with CO2 and N2, is fed to the bacterium, establishing the viability of the approach to sustainably produce food and nutrients.

Proton-coupled electron transfer of macrocyclic ring hydrogenation: The chlorinphlorin.

SignificanceThe chemical reduction of unsaturated bonds occurs by hydrogenation with H2 as the reductant. Conversely, in biology, the unavailability of H2 engenders the typical reduction of unsaturated bonds with electrons and protons from different cofactors, requiring olefin hydrogenation to occur by proton-coupled electron transfer (PCET). Moreover, the redox noninnocence of tetrapyrrole macrocycles furnishes unusual PCET intermediates, including the phlorin, which is an intermediate in tetrapyrrole ring reductions. Whereas the phlorin of a porphyrin is well established, the phlorin of a chlorin is enigmatic. By controlling the PCET reactivity of a chlorin, including the use of a hangman functionality to manage the proton transfer, the formation of a chlorinphlorin by PCET is realized, and the mechanism for its formation is defined.

Proton-coupled electron transfer in biology: results from synergistic studies in natural and model systems.

Proton-coupled electron transfer (PCET) underpins energy conversion in biology. PCET may occur with the unidirectional or bidirectional transfer of a proton and electron and may proceed synchronously or asynchronously. To illustrate the role of PCET in biology, this review presents complementary biological and model systems that explore PCET in electron transfer (ET) through hydrogen bonds [azurin as compared to donor-acceptor (D-A) hydrogen-bonded networks], the activation of C-H bonds [alcohol dehydrogenase and soybean lipoxygenase (SLO) as compared to Fe(III) metal complexes], and the generation and transport of amino acid radicals [photosystem II (PSII) and ribonucleotide reductase (RNR) as compared to tyrosine-modified photoactive Re(I) and Ru(II) complexes]. In providing these comparisons, the fundamental principles of PCET in biology are illustrated in a tangible way.

Continuous electrochemical water splitting from natural water sources via forward osmosis.

Electrochemical water splitting stores energy as equivalents of hydrogen and oxygen and presents a potential route to the scalable storage of renewable energy. Widespread implementation of such energy storage, however, will be facilitated by abundant and accessible sources of water. We describe herein a means of utilizing impure water sources (e.g., saltwater) for electrochemical water splitting by leveraging forward osmosis. A concentration gradient induces the flow of water from an impure water source into a more concentrated designed electrolyte. This concentration gradient may subsequently be maintained by water splitting, where rates of water influx (i.e., forward osmosis) and effective outflux (i.e., water splitting) are balanced. This approach of coupling forward osmosis to water splitting allows for the use of impure and natural sources without pretreatment and with minimal losses in energy efficiency.

Lithium superoxide encapsulated in a benzoquinone anion matrix.

Lithium peroxide is the crucial storage material in lithium-air batteries. Understanding the redox properties of this salt is paramount toward improving the performance of this class of batteries. Lithium peroxide, upon exposure to p-benzoquinone (p-C6H4O2) vapor, develops a deep blue color. This blue powder can be formally described as [Li2O2][Formula: see text] [LiO2][Formula: see text] {Li[p-C6H4O2]}0.7, though spectroscopic characterization indicates a more nuanced structural speciation. Infrared, Raman, electron paramagnetic resonance, diffuse-reflectance ultraviolet-visible and X-ray absorption spectroscopy reveal that the lithium salt of the benzoquinone radical anion forms on the surface of the lithium peroxide, indicating the occurrence of electron and lithium ion transfer in the solid state. As a result, obligate lithium superoxide is formed and encapsulated in a shell of Li[p-C6H4O2] with a core of Li2O2 Lithium superoxide has been proposed as a critical intermediate in the charge/discharge cycle of Li-air batteries, but has yet to be isolated, owing to instability. The results reported herein provide a snapshot of lithium peroxide/superoxide chemistry in the solid state with redox mediation.

Generation of Pure Oxygen from Briny Water by Binary Catalysis.

Whereas the emphasis of water splitting is typically on hydrogen generation, there is value in the oxygen produced, especially in the undersea environment and for medicinal applications in the developing world. The generation of pure and breathable oxygen from abundant and accessible sources of water, such as brine and seawater, is challenging owing to the prevalence of the competing halide oxidation reaction to produce halogen and hypohalous acids. We show here that pure O2 may be generated from briny water by using an oxygen evolution catalyst with an overlayer that fulfills the criteria of (i) possessing a point of zero charge that results in halide anion rejection and (ii) promoting the disproportionation of hypohalous acids.

Radical Transport Facilitated by a Proton Transfer Network at the Subunit Interface of Ribonucleotide Reductase.

Ribonucleotide reductases (RNRs) play an essential role in the conversion of nucleotides to deoxynucleotides in all organisms. The Escherichia coli class Ia RNR requires two homodimeric subunits, α and ß. The active form is an asymmetric αα'ßß' complex. The α subunit houses the site for nucleotide reduction initiated by a thiyl radical (C439•), and the ß subunit houses the diferric-tyrosyl radical (Y122•) that is essential for C439• formation. The reactions require a highly regulated and reversible long-range proton-coupled electron transfer pathway involving Y122•[ß] ↔ W48?[ß] ↔ Y356[ß] ↔ Y731[α] ↔ Y730[α] ↔ C439[α]. In a recent cryo-EM structure, Y356[ß] was revealed for the first time and it, along with Y731[α], spans the asymmetric α/ß interface. An E52[ß] residue, which is essential for Y356 oxidation, allows access to the interface and resides at the head of a polar region comprising R331[α], E326[α], and E326[α'] residues. Mutagenesis studies with canonical and unnatural amino acid substitutions now suggest that these ionizable residues are important in enzyme activity. To gain further insights into the roles of these residues, Y356• was photochemically generated using a photosensitizer covalently attached adjacent to Y356[ß]. Mutagenesis studies, transient absorption spectroscopy, and photochemical assays monitoring deoxynucleotide formation collectively indicate that the E52[ß], R331[α], E326[α], and E326[α'] network plays the essential role of shuttling protons associated with Y356 oxidation from the interface to bulk solvent.

Oxidation Chemistry of Bicarbonate and Peroxybicarbonate: Implications for Carbonate Management in Energy Storage.

Carbonate formation presents a major challenge to energy storage applications based on low-temperature CO2 electrolysis and recyclable metal-air batteries. While direct electrochemical oxidation of (bi)carbonate represents a straightforward route for carbonate management, knowledge of the feasibility and mechanisms of direct oxidation is presently lacking. Herein, we report the isolation and characterization of the bis(triphenylphosphine)iminium salts of bicarbonate and peroxybicarbonate, thus enabling the examination of their oxidation chemistry. Infrared spectroelectrochemistry combined with time-resolved infrared spectroscopy reveals that the photoinduced oxidation of HCO3- by an Ir(III) photoreagent results in the generation of the short-lived bicarbonate radical in less than 50 ns. The highly acidic bicarbonate radical undergoes proton transfer with HCO3- to furnish the carbonate radical anion and H2CO3, leading to the eventual release of CO2 and H2O, thus accounting for the appearance of H2O and CO2 in both electrochemical and photochemical oxidation experiments. The back reaction of the carbonate radical subsequently oxidizes the Ir(II) photoreagent, leading to carbonate. In the absence of this back reaction, dimerization of the carbonate radical provides entry into peroxybicarbonate, which we show undergoes facile oxidation to O2 and CO2. Together, the results reported identify tangible pathways for the design of catalysts for the management of carbonate in energy storage applications.

Reversible CO2 Capture and On-Demand Release by an Acidity-Matched Organic Photoswitch.

Separation of carbon dioxide (CO2) from point sources or directly from the atmosphere can contribute crucially to climate change mitigation plans in the coming decades. A fundamental practical limitation for the current strategies is the considerable energy cost required to regenerate the sorbent and release the captured CO2 for storage or utilization. A directly photochemically driven system that demonstrates efficient passive capture and on-demand CO2 release triggered by sunlight as the sole external stimulus would provide an attractive alternative. However, little is known about the thermodynamic requirements for such a process or mechanisms for modulating the stability of CO2-derived dissolved species by using photoinduced metastable states. Here, we show that an organic photoswitchable molecule of precisely tuned effective acidity can repeatedly capture and release a near-stoichiometric quantity of CO2 according to dark-light cycles. The CO2-derived species rests as a solvent-separated ion pair, and key aspects of its excited-state dynamics that regulate the photorelease efficiency are characterized by transient absorption spectroscopy. The thermodynamic and kinetic concepts established herein will serve as guiding principles for the development of viable solar-powered negative emission technologies.

Ag(III)···Ag(III) Argentophilic Interaction in a Cofacial Corrole Dyad.

Metallophilic interactions between closed-shell metal centers are exemplified by d10 ions, with Au(I) aurophilic interactions as the archetype. Such an interaction extends to d8 species, and examples involving Au(III) are prevalent. Conversely, Ag(III) argentophilic interactions are uncommon. Here, we identify argentophilic interactions in silver corroles, which are authentic Ag(III) species. The crystal structure of a monomeric silver corrole is a dimer in the solid state, and the macrocycle exhibits an atypical domed conformation. In order to evaluate whether this represents an authentic metallophilic interaction or a crystal-packing artifact, the analogous cofacial or "pacman" corrole was prepared. The conformation of the monomer was recapitulated in the silver pacman corrole, exhibiting a short 3.67 Å distance between metal centers and a significant compression of the xanthene backbone. Theoretical calculations support the presence of a rare Ag(III)···Ag(III) argentophilic interaction in the pacman complex.

Template-stabilized oxidic nickel oxygen evolution catalysts.

Earth-abundant oxygen evolution catalysts (OECs) with extended stability in acid can be constructed by embedding active sites within an acid-stable metal-oxide framework. Here, we report stable NiPbOx films that are able to perform oxygen evolution reaction (OER) catalysis for extended periods of operation (>20 h) in acidic solutions of pH 2.5; conversely, native NiOx catalyst films dissolve immediately. In situ X-ray absorption spectroscopy and ex situ X-ray photoelectron spectroscopy reveal that PbO2 is unperturbed after addition of Ni and/or Fe into the lattice, which serves as an acid-stable, conductive framework for embedded OER active centers. The ability to perform OER in acid allows the mechanism of Fe doping on Ni catalysts to be further probed. Catalyst activity with Fe doping of oxidic Ni OEC under acid conditions, as compared to neutral or basic conditions, supports the contention that role of Fe3+ in enhancing catalytic activity in Ni oxide catalysts arises from its Lewis acid properties.

Polypyrrole-Silicon Nanowire Arrays for Controlled Intracellular Cargo Delivery.

Intracellular cargo delivery is a critical and challenging step in controlling cell states. Silicon nanowire (NW) arrays have emerged as a powerful platform for accessing the intracellular space through a combination of their nanoscale dimensions and electrical properties. Here, we develop and characterize a conductive polypyrrole (PPy)-NW device for temporally controlled intracellular delivery. Fluorescent cargos, doped in electroresponsive PPy matrices at wire tips as well as entire NW arrays, are released with an applied reducing potential. Intracellular delivery into endothelial cells from PPy-Si substrates demonstrated comparable kinetics to solution-based delivery methods while requiring an order of magnitude less cargo loading. This hybrid polymer-semiconductor platform extends methods available for intracellular delivery and links electrical signaling from artificial systems with living molecular transduction.

Substrate-Mediator Duality of 1,4-Dicyanobenzene in Electrochemical C(sp2 )-C(sp3 ) Bond Formation with Alkyl Bromides.

Electrochemical approaches to form C(sp2 )-C(sp3 ) bonds have focused on coupling C(sp3 ) electrophiles that form stabilized carbon-centered radicals upon reduction or oxidation. Whereas alkyl bromides are desirable C(sp3 ) coupling partners owing to their availability and cost-effectiveness, their tendency to undergo radical-radical homocoupling makes them challenging substrates for electroreductive cross-coupling. Herein, we disclose a metal-free regioselective cross-coupling of 1,4-dicyanobenzene, a useful precursor to aromatic nitriles, and alkyl bromides. Alkyl bromide reduction is mediated directly by 1,4-dicyanobenzene radical anions, leading to negligible homocoupling and high cross-selectivity to form 1,4-alkyl cyanobenzenes. The cross-coupling scheme is compatible with oxidatively sensitive and acidic functional groups such as amines and alcohols, which have proven difficult to incorporate in alternative electrochemical approaches using carboxylic acids as C(sp3 ) precursors.

Proton-Coupled Electron Transfer: The Engine of Energy Conversion and Storage.

Proton-coupled electron transfer (PCET) underpins energy conversion in chemistry and biology. Four energy systems are described whose discoveries are based on PCET: the water splitting chemistry of the Artificial Leaf, the carbon fixation chemistry of the Bionic Leaf-C, the nitrogen fixation chemistry of the Bionic Leaf-N and the Coordination Chemistry Flow Battery (CCFB). Whereas the Artificial Leaf, Bionic Leaf-C, and Bionic Leaf-N require strong coupling between electron and proton to reduce energetic barriers to enable high energy efficiencies, the CCFB requires complete decoupling of the electron and proton so as to avoid parasitic energy-wasting reactions. The proper design of PCET in these systems facilitates their implementation in the areas of (i) centralized large scale grid storage of electricity and (ii) decentralized energy storage/conversion using only sunlight, air and any water source to produce fuel and food within a sustainable cycle for the biogenic elements of C, N and P.

Taming the Chlorine Radical: Enforcing Steric Control over Chlorine-Radical-Mediated C-H Activation.

Chlorine radicals readily activate C-H bonds, but the high reactivity of these intermediates precludes their use in regioselective C-H functionalization reactions. We demonstrate that the secondary coordination sphere of a metal complex can confine photoeliminated chlorine radicals and afford steric control over their reactivity. Specifically, a series of iron(III) chloride pyridinediimine complexes exhibit activity for photochemical C(sp3)-H chlorination and bromination with selectivity for primary and secondary C-H bonds, overriding thermodynamic preference for weaker tertiary C-H bonds. Transient absorption spectroscopy reveals that Cl· remains confined through formation of a Cl·|arene complex with aromatic groups on the pyridinediimine ligand. Furthermore, photocrystallography confirms that this selectivity arises from the generation of Cl· within the steric environment defined by the iron secondary coordination sphere.

Solvent-Induced Spin-State Change in Copper Corroles.

The electronic structure of copper corroles has been a topic of debate and revision since the advent of corrole chemistry. The ground state of these compounds is best described as an antiferromagnetically coupled Cu(II) corrole radical cation. In coordinating solvents, these molecules become paramagnetic, and this is often accompanied by a color change. The underlying chemistry of these solvent-induced properties is currently unknown. Here, we show that a coordinating solvent, such as pyridine, induces a change in the ground spin state from an antiferromagnetically coupled Cu(II) corrole radical cation to a ferromagnetically coupled triplet. Over time, the triplet reacts to produce a species with spectral signatures that are characteristic of the one-electron-reduced Cu(II) corrole. These observations account for the solvent-induced paramagnetism and the associated color changes that have been observed for copper corroles in coordinating solvents.

Syntheses and Properties of Metalated Tetradehydrocorrins.

The monoanionic tetrapyrrolic macrocycle B,C-tetradehydrocorrin (TDC) resides chemically between corroles and corrins. This chemical space remains largely unexplored due to a lack of reliable synthetic strategies. We now report the preparation and characterization of Co(II)- and Ni(II)-metalated TDC derivatives ([Co-TDC]+ and [Ni-TDC]+, respectively) with a combination of crystallographic, electrochemical, computational, and spectroscopic techniques. [Ni-TDC]+ was found to undergo primarily ligand-centered electrochemical reduction, leading to hydrogenation of the macrocycle under cathodic electrolysis in the presence of acid. Transient absorption (TA) spectroscopy reveals that [Ni-TDC]+ and the two-electron-reduced [Ni-TDC]- possess long-lived excited states, whereas the excited state of singly reduced [Ni-TDC] exhibits picosecond dynamics. The Co(I) compound [Co-TDC] is air stable, highlighting the notable property of the TDC ligand to stabilize low-valent metal centers in contradistinction to other tetrapyrroles such as corroles, which typically stabilize metals in higher oxidation states.

Radicals in Biology: Your Life Is in Their Hands.

Radicals in biology, once thought to all be bad actors, are now known to play a central role in many enzymatic reactions. Of the known radical-based enzymes, ribonucleotide reductases (RNRs) are pre-eminent as they are essential in the biology of all organisms by providing the building blocks and controlling the fidelity of DNA replication and repair. Intense examination of RNRs has led to the development of new tools and a guiding framework for the study of radicals in biology, pointing the way to future frontiers in radical enzymology.