Radical initiation in the class I ribonucleotide reductase: long-range proton-coupled electron transfer?

Iridium Polypyridyl Carboxylates as Excited-State PCET Catalysts for the Functionalization of Unactivated C-H Bonds

The design of catalysts capable of functionalizing unactivated C(sp3)-H bonds remains a significant goal in synthetic organic chemistry. Herein, we present a novel set of iridium polypyridyl complexes bearing pendent Brønsted basic carboxylates that become potent hydrogen atom abstraction catalysts upon visible light irradiation. Thermochemical and spectroscopic characterization reveal that these excited-state complexes exhibit bond dissociation free energies (BDFEs) of up to 105 kcal mol-1 with long excited-state lifetimes. We demonstrate that these complexes can catalyze C-H alkylation reactions in which the Ir carboxylate mediates both C-H abstraction and formation steps. Mechanistic, spectroscopic, and computational studies are consistent with C-H abstraction proceeding through an excited-state proton-coupled electron transfer (PCET) step. The modular nature of these Ir polypyridyl complexes establishes a foundation for designing tunable and efficient C-H functionalization catalysts based on covalent tethering of excited-state oxidants and bases.

Bio-inspired oxidation catalysis based on proton-coupled electron transfer: Toward efficient and selective oxidation of methane to methanol

In this paper, a trail of my research is described starting from oxidation of alkanes by FeIII-TPA (TPA = tris(2-pyridylmethyl)amine) complexes with alkyl hydroperoxides to Ru-pyridylamine complexes which can be converted to RuIV-oxo complexes in different spin states (S = 1 or 0) through proton-coupled electron-transfer oxidation of the corresponding RuII-aqua complexes, clarifying that those spin states do not affect the reactivity in water. The introduction of strongly donating N-heterocyclic carbene (NHC) moiety allows us to create a RuIII-oxyl complex showing different reactivity from that of RuIV-oxo complexes. Manipulation of second coordination spheres (SCSs) of Ru-TPA complexes is also described, visualizing unique functionality. The introduction of hydrophobic SCS to a FeII-NHC complex enables to catalyze selective oxidation of methane to form methanol in high selectivity in aqueous media based on the "catch-and-release" strategy, which can also allow us to achieve highly selective two-electron oxidation of aromatic compounds.

Redirecting electron flows in glutamate oxidases by selective anchoring of osmium complexes

l-Glutamate is the most abundant and essential excitatory neurotransmitter in the nervous system. However, its direct electrochemical detection is challenging due to its inherently non-electroactive nature. In this study, we redesigned l-glutamate oxidase (GlutOx) by covalently attaching osmium polypyridyl complexes as electron mediators at selected sites. Most engineered enzymes retained their native catalytic activity, while exhibiting significantly altered catalytic currents during l-glutamate oxidation, depending on the proximity, orientation, and microenvironments of the osmium complexes relative to the FAD cofactors. Notably, two mutants significantly enhanced catalytic currents, revealing selectively and efficiently rerouted electron transfer pathways from the enzyme active site to Os complexes. These findings provide an effective strategy for designing redox-active enzymes for electrochemical biosensors.

Explaining Kinetic Isotope Effects in Proton-Coupled Electron Transfer Reactions

ConspectusProton-coupled electron transfer (PCET) is essential for a wide range of chemical and biological processes. Understanding the mechanism of PCET reactions is important for controlling and tuning these processes. The kinetic isotope effect (KIE), defined as the ratio of the rate constants for hydrogen and deuterium transfer, is used to probe PCET mechanisms experimentally but is often challenging to interpret. Herein, a theoretical framework is described for interpreting KIEs of concerted PCET reactions. The first step is to classify the reaction in terms of vibronic and electron-proton nonadiabaticities, which reflect the relative time scales of the electrons, protons, and environment. The second step is to select the appropriate rate constant expression based on this classification. The third step is to compute the input quantities with computational methods.Vibronically adiabatic PCET reactions occur on the electronic and vibrational ground state and can be described within the transition state theory framework. The nuclear-electronic orbital (NEO) method, which treats specified protons quantum mechanically on the same level as the electrons, can be used to generate the electron-proton vibronic free energy surface for hydrogen and deuterium and to compute the corresponding free energy barriers. Such reactions typically exhibit moderate KIEs that arise from zero-point energy and shallow tunneling effects.Vibronically nonadiabatic PCET reactions involve excited electron-proton vibronic states and can be described with a golden rule formalism corresponding to nonadiabatic transitions between pairs of reactant and product vibronic states. Such reactions can exhibit KIEs ranging from unity, or even slightly less than unity, to more than 500. These KIEs can be explained in terms of multiple, competing reaction pathways corresponding to electron and proton tunneling between different pairs of vibronic states. The tunneling probability is determined by the vibronic coupling, which can be computed using a general expression but often is proportional to the overlap between the reactant and product proton vibrational wave functions. In this regime, the KIE is influenced by the vibronic couplings, the proton donor-acceptor equilibrium distance and motion, and contributions from excited vibronic states.Three illustrative examples of vibronically nonadiabatic PCET are discussed. The unusually large KIEs in soybean lipoxygenase of ∼80 for the wild-type enzyme and ∼700 for a double mutant are explained in terms of a large equilibrium proton donor-acceptor distance and nonoptimal orientation, leading to a small overlap between vibrational wave functions and therefore a large difference in hydrogen and deuterium tunneling probabilities. The KIEs for benzimidazole-phenol molecules ranging from unity to moderate are explained in terms of the dominance of different pairs of vibronic states with different vibrational wave function overlaps. The potential-dependent KIE observed for proton discharge from triethylammonium acid to a gold surface in acetonitrile is explained in terms of different pairs of vibronic states contributing for hydrogen and deuterium, with the reaction channels exhibiting different dependencies on the applied potential. These examples show that the KIE can vary widely, depending on which pairs of vibronic states dominate and their corresponding vibronic couplings. This work has broad implications for the interpretation of experimentally measured KIEs of PCET reactions.

Structural Elucidation of the Reduced Mn(III)/Fe(III) Intermediate of the Radical-Initiating Metallocofactor in Chlamydia trachomatis Ribonucleotide Reductase

Ribonucleotide reductases (RNRs) are the sole de novo source of deoxyribonucleotides for DNA synthesis and repair across all organisms and carry out their reaction via a radical mechanism. RNR from Chlamydia trachomatis generates its turnover-initiating cysteinyl radical by long-range reduction of a Mn(IV)/Fe(III) cofactor, producing a Mn(III)/Fe(III) intermediate. Herein, we characterize the protonation states of the inorganic ligands in this reduced state using advanced pulse electron paramagnetic resonance (EPR) spectroscopy and 2H-isotope labeling. A strongly coupled deuteron is observed by hyperfine sublevel correlation (HYSCORE) spectroscopy experiments and indicates the presence of a bridging hydroxo ligand. Isotope-dependent EPR line broadening analysis and the magnitude of the estimated Mn-Fe exchange coupling constant together suggest a μ-oxo/μ-hydroxo core. Two distinct signals detected in electron-nuclear double resonance (ENDOR) spectra are attributable to less strongly coupled hydrons of a terminal water ligand to Mn(III). Together, these experiments imply that the reduced cofactor has a mixed μ-oxo/μ-hydroxo core with a terminal water ligand on Mn(III). This structural assignment sheds light generally on the reactivity of Mn/Fe heterobimetallic sites and, more specifically, on the proton-coupling in the electron transfer that initiates ribonucleotide reduction in this subclass of RNRs.

Hydrogen Tunneling and Conformational Motions in Nonadiabatic Proton-Coupled Electron Transfer between Interfacial Tyrosines in Ribonucleotide Reductase

Ribonucleotide reductase (RNR) is essential for DNA synthesis and repair in all living organisms. The mechanism of E. coli RNR requires long-range radical transport through a proton-coupled electron transfer (PCET) pathway spanning two different protein subunits. Herein, the direct PCET reaction between the interfacial tyrosine residues, Y356 and Y731, is investigated with a vibronically nonadiabatic theory that treats the transferring proton and all electrons quantum mechanically. The input quantities to the PCET rate constant expression are computed with a combination of density functional theory and molecular dynamics simulations. The calculations highlight the importance of hydrogen tunneling in this PCET reaction. Compression of the distance between the proton donor and acceptor oxygen atoms of the interfacial tyrosine residues is essential to facilitate hydrogen tunneling by increasing the overlap between the reactant and product proton vibrational wave functions. This compression occurs by thermal conformational fluctuations of these interfacial tyrosine residues. N733 and R411 are identified as key residues that can hydrogen bond to Y731 and Y356, respectively, and thereby compete with the hydrogen-bonding interaction between Y731 and Y356 required for direct PCET. Understanding the roles of hydrogen tunneling and conformational motions in this interfacial PCET reaction, as well as identifying other residues that may impact the kinetics, is important for targeted protein engineering efforts to modulate RNR activity.

Recent Insights into the Reaction Mechanisms of Non-Heme Diiron Enzymes Containing Oxoiron(IV) Complexes

Oxoiron(IV) complexes are key intermediates in the catalytic reactions of some non-heme diiron enzymes. These enzymes, across various subfamilies, activate dioxygen to generate high-valent diiron-oxo species, which, in turn, drive the activation of substrates and mediate a variety of challenging oxidative transformations. In this review, we summarize the structures, formation mechanisms, and functions of high-valent diiron-oxo intermediates in eight representative diiron enzymes (sMMO, RNR, ToMO, MIOX, PhnZ, SCD1, AlkB, and SznF) spanning five subfamilies. We also categorize and analyze the structural and mechanistic differences among these enzymes.

The Influence of pH on Long-Range Electron Transfer and Proton-Coupled Electron Transfer in Ruthenium-Modified Azurin

Long-range electron transfer (ET) is an essential component of all biological systems. Reactions of metalloproteins are important in this context. Recent work on protein "charge ladders" has revealed how the redox state of embedded metal ions can influence the ionization of amino acid residues at protein surface sites. Inspired by these observations, we carried out a variable pH investigation of intramolecular ET reactions in a ruthenium-modified protein system built on azurin from Pseudomonas aeruginosa. We also generate a Pourbaix diagram that describes the variable pH redox behavior of a Ru model complex, Ru(2,2'-bipyridyl)2(imidazole)2(PF6)2. The intramolecular ET rate constants for the oxidation of azurin-Cu+ by flash-quench-generated Ru3+ oxidants do not follow the predictions of the semi-classical ET rate expression with fixed values of reorganization energy (λ) and electronic coupling (HDA). Based on the pH dependence of the Ru3+/2+ redox couple, we propose a model where pure ET is operative at acidic pH values (≤ 7) and the mechanism changes to proton-coupled electron transfer at pH ≥ 7.5. The implications of this mechanistic proposal are discussed in the context of biological redox reactions and with respect to other examples of intramolecular ET reactions in the literature.

A Structural and Functional Mimic of P680. Angew Chem Int Ed Engl 2025;64:e202415688. [PMID: 39440919 DOI: 10.1002/anie.202415688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0]

One or multiple chlorophyll a molecules are employed in the reaction center of photosystem II's main electron donor (defined as P680). We have a poor understanding of how the reaction center facilitates water oxidation in photosystem II and the roles that mono- and/or multimeric chlorophyll groups play when P680 oxidizes a neighboring tyrosine in order to drive water oxidation at the oxygen evolving complex. We have prepared a dimeric MgII-porphyrin complex [Mg2(BTPP)] (1, H4-BTPP=1,2-bis-(10,15,20-triphenylporphyrin-5-yl)-benzene) as a structural and functional mimic of the dimeric core of P680. 1 was oxidized by one-electron to the corresponding π-cation radical complex 2. The radical cation was characterized by UV/Vis-NIR, FT-IR, and EPR spectroscopic techniques. 2 was shown to be reactive towards phenols to give the corresponding phenoxyl radicals, mimicking the reactivity of the P680 cation radical which oxidizes tyrosine to tyrosyl radical. Critically, the dimeric π-cation radical showed markedly higher rates of proton coupled electron transfer oxidation (PCET) of phenols when compared to its monomeric counterpart [Mg(TPP)] (TPP=5,10,15,20-tetraphenylporphyrin). Our findings demonstrate that MgII-porphyrin complexes are reliable mimics of photosynthetic PCET processes and suggest that photosynthetic reaction centers with multiple π-conjugated complexes likely lower the barrier to PCET oxidation by π-cation radical species.

Synthesis of Non-canonical Tryptophan Variants via Rh-catalyzed C-H Functionalization of Anilines

Tryptophan and its non-canonical variants play critical roles in pharmaceutical molecules and various enzymes. Facile access to this privileged class of amino acids from readily available building blocks remains a long-standing challenge. Here, we report a regioselective synthesis of non-canonical tryptophans bearing C4-C7 substituents via Rh-catalyzed annulation between structurally diverse tert-butyloxycarbonyl (Boc)-protected anilines and alkynyl chlorides readily prepared from amino acid building blocks. This transformation harnesses Boc-directed C-H metalation and demetalation to afford a wide range of C2-unsubstituted indole products in a redox-neutral fashion. This umpolung approach compared to the classic Larock indole synthesis offers a novel mechanism for heteroarene annulation and will be useful for the synthesis of natural products and drug molecules containing non-canonical tryptophan residues in a highly regioselective manner.

Nuclear Quantum Effects in Quantum Mechanical/Molecular Mechanical Free Energy Simulations of Ribonucleotide Reductase

The enzyme ribonucleotide reductase plays a critical role in DNA synthesis and repair. Its mechanism requires long-range radical transfer through a series of proton-coupled electron transfer (PCET) steps. Nuclear quantum effects such as zero-point energy, proton delocalization, and hydrogen tunneling are known to be important in PCET. We present a strategy for efficiently incorporating nuclear quantum effects into multidimensional free energy surfaces and real-time dynamical simulations for condensed-phase systems such as enzymes. This strategy is based on the nuclear-electronic orbital (NEO) method, which treats specified protons quantum mechanically on the same level as the electrons. NEO density functional theory (NEO-DFT) is combined with the quantum mechanical/molecular mechanical finite temperature string method with umbrella sampling via a simple reweighting procedure. Application of this strategy to PCET between two tyrosines, Y731 and Y730, in ribonucleotide reductase illustrates that nuclear quantum effects could either raise or lower the free energy barrier, leading to a range of possible kinetic isotope effects. Real-time time-dependent DFT (RT-NEO-TDDFT) simulations highlight nuclear-electronic quantum dynamics. These approaches enable the incorporation of nuclear quantum effects into a wide range of chemically and biologically important processes.

2.6-Å resolution cryo-EM structure of a class Ia ribonucleotide reductase trapped with mechanism-based inhibitor N3CDP

Ribonucleotide reductases (RNRs) reduce ribonucleotides to deoxyribonucleotides using radical-based chemistry. For class Ia RNRs, the radical species is stored in a separate subunit (β2) from the subunit housing the active site (α2), requiring the formation of a short-lived α2β2 complex and long-range radical transfer (RT). RT occurs via proton-coupled electron transfer (PCET) over a long distance (~32-Å) and involves the formation and decay of multiple amino acid radical species. Here, we use cryogenic electron microscopy and a mechanism-based inhibitor 2'-azido-2'-deoxycytidine-5'-diphosphate (N3CDP) to trap a wild-type α2β2 complex of Escherichia coli class Ia RNR. We find that one α subunit has turned over and that the other is trapped, bound to β in a midturnover state. Instead of N3CDP in the active site, forward RT has resulted in N2 loss, migration of the third nitrogen from the ribose C2' to C3' positions, and attachment of this nitrogen to the sulfur of cysteine-225. In this study, an inhibitor has been visualized as an adduct to an RNR. Additionally, this structure reveals the positions of PCET residues following forward RT, complementing the previous structure that depicted a preturnover PCET pathway and suggesting how PCET is gated at the α-β interface. This N3CDP-trapped structure is also of sufficient resolution (2.6 Å) to visualize water molecules, allowing us to evaluate the proposal that water molecules are proton acceptors and donors as part of the PCET process.

Expanding the Genetic Code of Bioelectrocatalysis and Biomaterials

Genetic code expansion is a promising genetic engineering technology that incorporates noncanonical amino acids into proteins alongside the natural set of 20 amino acids. This enables the precise encoding of non-natural chemical groups in proteins. This review focuses on the applications of genetic code expansion in bioelectrocatalysis and biomaterials. In bioelectrocatalysis, this technique enhances the efficiency and selectivity of bioelectrocatalysts for use in sensors, biofuel cells, and enzymatic electrodes. In biomaterials, incorporating non-natural chemical groups into protein-based polymers facilitates the modification, fine-tuning, or the engineering of new biomaterial properties. The review provides an overview of relevant technologies, discusses applications, and highlights achievements, challenges, and prospects in these fields.

2.6-Å resolution cryo-EM structure of a class Ia ribonucleotide reductase trapped with mechanism-based inhibitor N3CDP

Ribonucleotide reductases (RNRs) reduce ribonucleotides to deoxyribonucleotides using radical-based chemistry. For class Ia RNRs, the radical species is stored in a separate subunit (β2) from the subunit housing the active site (α2), requiring the formation of a short-lived α2β2 complex and long-range radical transfer (RT). RT occurs via proton-coupled electron transfer (PCET) over a long distance (~32-Å) and involves the formation and decay of multiple amino acid radical species. Here, we use cryogenic-electron microscopy and a mechanism-based inhibitor 2'-azido-2'-deoxycytidine-5'-diphosphate (N3CDP) to trap a wild-type α2β2 complex of E. coli class Ia RNR. We find that one α subunit has turned over and that the other is trapped, bound to β in a mid-turnover state. Instead of N3CDP in the active site, forward RT has resulted in N2 loss, migration of the third nitrogen from the ribose C2' to C3' positions, and attachment of this nitrogen to the sulfur of cysteine-225. To the best of our knowledge, this is the first time an inhibitor has been visualized as an adduct to an RNR. Additionally, this structure reveals the positions of PCET residues following forward RT, complementing the previous structure that depicted a pre-turnover PCET pathway and suggesting how PCET is gated at the α-β interface. This N3CDP-trapped structure is also of sufficient resolution (2.6 Å) to visualize water molecules, allowing us to evaluate the proposal that water molecules are proton acceptors and donors as part of the PCET process.

Nonadiabatic Hydrogen Tunneling Dynamics for Multiple Proton Transfer Processes with Generalized Nuclear-Electronic Orbital Multistate Density Functional Theory

Proton transfer and hydrogen tunneling play key roles in many processes of chemical and biological importance. The generalized nuclear-electronic orbital multistate density functional theory (NEO-MSDFT) method was developed in order to capture hydrogen tunneling effects in systems involving the transfer and tunneling of one or more protons. The generalized NEO-MSDFT method treats the transferring protons quantum mechanically on the same level as the electrons and obtains the delocalized vibronic states associated with hydrogen tunneling by mixing localized NEO-DFT states in a nonorthogonal configuration interaction scheme. Herein, we present the derivation and implementation of analytical gradients for the generalized NEO-MSDFT vibronic state energies and the nonadiabatic coupling vectors between these vibronic states. We use this methodology to perform adiabatic and nonadiabatic dynamics simulations of the double proton transfer reactions in the formic acid dimer and the heterodimer of formamidine and formic acid. The generalized NEO-MSDFT method is shown to capture the strongly coupled synchronous or asynchronous tunneling of the two protons in these processes. Inclusion of vibronically nonadiabatic effects is found to significantly impact the double proton transfer dynamics. This work lays the foundation for a variety of nonadiabatic dynamics simulations of multiple proton transfer systems, such as proton relays and hydrogen-bonding networks.

Effect of monodentate heterocycle co-ligands on the μ-1,2-peroxo-diiron(III) mediated aldehyde deformylation reactions

Peroxo-diiron(III) species are present in the active sites of many metalloenzymes that carry out challenging organic transformations. The reactivity of these species is influenced by various factors, such as the structure and topology of the supporting ligands, the identity of the axial and equatorial co-ligands, and the oxidation states of the metal ion(s). In this study, we aim to diversify the importance of equatorial ligands in controlling the reactivity of peroxo-diiron(III) species. As a model compound, we chose the previously published and fully characterized [(PBI)2(CH3CN)FeIII(μ-O2)FeIII(CH3CN)(PBI)2]4+ complex, where the steric effect of the four PBI ligands is minimal, so the labile CH3CN molecules easily can be replaced by different monodentate co-ligands (substituted pyridines and N-donor heterocyclic compounds). Thus, their effect on the electronic and spectral properties of peroxo-divas(III) intermediates could be easily investigated. The relationship between structure and reactivity was also investigated in the stoichiometric deformylation of PPA mediated by peroxo-diiron(III) complexes. It was found that the deformylation rates are influenced by the Lewis acidity and redox properties of the metal centers, and showed a linear correlation with the FeIII/FeII redox potentials (in the range of 197 to 415 mV).

Preparation and characterization of MnIIMnIII complexes with relevance to class Ib ribonucleotide reductases

The Mn2 complex [MnII2(TPDP)(O2CPh)2](BPh4) (1, TPDP = 1,3-bis(bis(pyridin-2-ylmethyl)amino)propan-2-ol, Ph =phenyl) was prepared and subsequently characterized via single-crystal X-ray diffraction, X-ray absorption, electronic absorption, and infrared spectroscopies, and mass spectrometry. 1 was prepared in order to explore its properties as a structural and functional mimic of class Ib ribonucleotide reductases (RNRs). 1 reacted with superoxide anion (O2•-) to generate a peroxido-MnIIMnIII complex, 2. The electronic absorption and electron paramagnetic resonance (EPR) spectra of 2 were similar to previously published peroxido-MnIIMnIII species. Furthermore, X-ray near edge absorption structure (XANES) studies indicated the conversion of a MnII2 core in 1 to a MnIIMnIII state in 2. Treatment of 2 with para-toluenesulfonic acid (p-TsOH) resulted in the conversion to a new MnIIMnIII species, 3, rather than causing O-O bond scission, as previously encountered. 3 was characterized using electronic absorption, EPR, and X-ray absorption spectroscopies. Unlike other reported peroxido-MnIIMnIII species, 3 was capable of oxidative O-H activation, mirroring the generation of tyrosyl radical in class Ib RNRs, however without accessing the MnIIIMnIV state.

The thioredoxin system determines CHK1 inhibitor sensitivity via redox-mediated regulation of ribonucleotide reductase activity

Checkpoint kinase 1 (CHK1) is critical for cell survival under replication stress (RS). CHK1 inhibitors (CHK1i's) in combination with chemotherapy have shown promising results in preclinical studies but have displayed minimal efficacy with substantial toxicity in clinical trials. To explore combinatorial strategies that can overcome these limitations, we perform an unbiased high-throughput screen in a non-small cell lung cancer (NSCLC) cell line and identify thioredoxin1 (Trx1), a major component of the mammalian antioxidant-system, as a determinant of CHK1i sensitivity. We establish a role for redox recycling of RRM1, the larger subunit of ribonucleotide reductase (RNR), and a depletion of the deoxynucleotide pool in this Trx1-mediated CHK1i sensitivity. Further, the TrxR inhibitor auranofin, an approved anti-rheumatoid arthritis drug, shows a synergistic interaction with CHK1i via interruption of the deoxynucleotide pool. Together, we show a pharmacological combination to treat NSCLC that relies on a redox regulatory link between the Trx system and mammalian RNR activity.

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 β subunit to render a chimeric RNR. Inspired by a recent cryo-EM structure, a [Re] photooxidant is located adjacent to Y356[β], 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 β metallocofactor highlights the adaptability of the 10-stranded αβ barrel finger loop to support deoxynucleotide formation and accommodate the design of engineered RNRs.

Photocatalysis Meets Confinement: An Emerging Opportunity for Photoinduced Organic Transformations

The self-assembled metal-organic cages (MOCs) have been evolved as a paradigm of enzyme-mimic catalysts since they are able to synergize multifunctionalities inherent in metal and organic components and constitute microenvironments characteristic of enzymatic spatial confinement and versatile host-guest interactions, thus facilitating unconventional organic transformations via unique driving-forces such as weak noncovalent binding and electron/energy transfer. Recently, MOC-based photoreactors emerged as a burgeoning platform of supramolecular photocatalysis, displaying anomalous reactivities and selectivities distinct from bulk solution. This perspective recaps two decades journey of the photoinduced radical reactions by using photoactive metal-organic cages (PMOCs) as artificial reactors, outlining how the cage-confined photocatalysis was evolved from stoichiometric photoreactions to photocatalytic turnover, from high-energy UV-irradiation to sustainable visible-light photoactivation, and from simple radical reactions to multi-level chemo- and stereoselectivities. We will focus on PMOCs that merge structural and functional biomimicry into a single-cage to behave as multi-role photoreactors, emphasizing their potentials in tackling current challenges in organic transformations through single-electron transfer (SET) or energy transfer (EnT) pathways in a simple, green while feasible manner.

Accessing a synthetic FeIIIMnIV core to model biological heterobimetallic active sites

Metalloproteins with dinuclear cores are known to bind and activate dioxygen, with a subclass of these proteins having active sites containing FeMn cofactors and activities ranging from long-range proton-coupled electron transfer (PCET) to post-translational peptide modification. While mechanistic studies propose that these metallocofactors access FeIIIMnIV intermediates, there is a dearth of related synthetic analogs. Herein, the first well-characterized synthetic FeIII-(μ-O)-MnIV complex is reported; this complex shows similar spectroscopic features as the catalytically competent FeIIIMnIV intermediate X found in Class Ic ribonucleotide reductase and demonstrates PCET function towards phenolic substrates. This complex is prepared from the oxidation of the isolable FeIII-(μ-O)-MnIII species, whose stepwise assembly is facilitated by a tripodal ligand containing phosphinic amido groups. Structural and spectroscopic studies found proton movement involving the FeIIIMnIII core, whereby the initial bridging hydroxido ligand is converted to an oxido ligand with concomitant protonation of one phosphinic amido group. This series of FeMn complexes allowed us to address factors that may dictate the preference of an active site for a heterobimetallic cofactor over one that is homobimetallic: comparisons of the redox properties of our FeMn complexes with those of the di-Fe analogs suggested that the relative thermodynamic ease of accessing an FeIIIMnIV core can play an important role in determining the metal ion composition when the key catalytic steps do not require an overly potent oxidant. Moreover, these complexes allowed us to demonstrate the effect of the hyperfine interaction from non-Fe nuclei on 57Fe Mössbauer spectra which is relevant to MnFe intermediates in proteins.

Probing Nonadiabaticity of Proton-Coupled Electron Transfer in Ribonucleotide Reductase

The enzyme ribonucleotide reductase, which is essential for DNA synthesis, initiates the conversion of ribonucleotides to deoxyribonucleotides via radical transfer over a 32 Å pathway composed of proton-coupled electron transfer (PCET) reactions. Previously, the first three PCET reactions in the α subunit were investigated with hybrid quantum mechanical/molecular mechanical (QM/MM) free energy simulations. Herein, the fourth PCET reaction in this subunit between C439 and guanosine diphosphate (GDP) is simulated and found to be slightly exoergic with a relatively high free energy barrier. To further elucidate the mechanisms of all four PCET reactions, we analyzed the vibronic and electron-proton nonadiabaticities. This analysis suggests that interfacial PCET between Y356 and Y731 is vibronically and electronically nonadiabatic, whereas PCET between Y731 and Y730 and between C439 and GDP is fully adiabatic and PCET between Y730 and C439 is in the intermediate regime. These insights provide guidance for selecting suitable rate constant expressions for these PCET reactions.

Class Ib Ribonucleotide Reductases: Activation of a Peroxido-MnIIMnIII to Generate a Reactive Oxo-MnIIIMnIV Oxidant

In the postulated catalytic cycle of class Ib Mn2 ribonucleotide reductases (RNRs), a MnII2 core is suggested to react with superoxide (O2·-) to generate peroxido-MnIIMnIII and oxo-MnIIIMnIV entities prior to proton-coupled electron transfer (PCET) oxidation of tyrosine. There is limited experimental support for this mechanism. We demonstrate that [MnII2(BPMP)(OAc)2](ClO4) (1, HBPMP = 2,6-bis[(bis(2 pyridylmethyl)amino)methyl]-4-methylphenol) was converted to peroxido-MnIIMnIII (2) in the presence of superoxide anion that converted to (μ-O)(μ-OH)MnIIIMnIV (3) via the addition of an H+-donor (p-TsOH) or (μ-O)2MnIIIMnIV (4) upon warming to room temperature. The physical properties of 3 and 4 were probed using UV-vis, EPR, X-ray absorption, and IR spectroscopies and mass spectrometry. Compounds 3 and 4 were capable of phenol oxidation to yield a phenoxyl radical via a concerted PCET oxidation, supporting the proposed mechanism of tyrosyl radical cofactor generation in RNRs. The synthetic models demonstrate that the postulated O2/Mn2/tyrosine activation mechanism in class Ib Mn2 RNRs is plausible and provides spectral insights into intermediates currently elusive in the native enzyme.

Ultrafast Vibrational Wave Packet Dynamics of the Aqueous Guanine Radical Anion Induced by Photodetachment

Studying the ultrafast dynamics of ionized aqueous biomolecules is important for gaining an understanding of the interaction of ionizing radiation with biological matter. Guanine plays an essential role in biological systems as one of the four nucleobases that form the building blocks of deoxyribonucleic acid (DNA). Guanine radicals can induce oxidative damage to DNA, particularly due to the lower ionization potential of guanine compared to the other nucleobases, sugars, and phosphate groups that are constituents of DNA. This study utilizes femtosecond optical pump-probe spectroscopy to observe the ultrafast vibrational wave packet dynamics of the guanine radical anion launched by photodetachment of the aqueous guanine dianion. The vibrational wave packet motion is resolved into 11 vibrational modes along which structural reorganization occurs upon photodetachment. These vibrational modes are assigned with the aid of density functional theory (DFT) calculations. Our work sheds light on the ultrafast vibrational dynamics following the ionization of nucleobases in an aqueous medium.

The stability of oxygen-centered radicals and its response to hydrogen bonding interactions

The stability of various alkoxy/aryloxy/peroxy radicals, as well as TEMPO and triplet dioxygen (3 O2 ) has been explored at a variety of theoretical levels. Good correlations between RSEtheor and RSEexp are found for hybrid DFT methods, for compound schemes such as G3B3-D3, and also for DLPNO-CCSD(T) calculations. The effects of hydrogen bonding interactions on the stability of oxygen-centered radicals have been probed by addition of a single solvating water molecule. While this water molecule always acts as a H-bond donor to the oxygen-centered radical itself, it can act as a H-bond donor or acceptor to the respective closed-shell parent.

Coligands Controlled Reactivities of Ruthenium(II) Precursors: Antiferromagnetically Coupled Ruthenium(III)-Phenoxyl versus Ruthenium(II)-Phenoxyl Forms

The study disclosed that the reactivities of [RuII (PPh3)3Cl2] and [RuII(PPh3)3(CO)(H)Cl] precursors toward a trimethoxyarylimino-phenol derivative are sensibly different. The former promotes methoxy demethylation reaction affording a [Phenolato-RuIII-Phenolato] unit, while the latter containing π-acidic CO and hydride as coligands leads to C-H activation reaction, generating a [Phenolato-RuII-Aryl] unit. Notably, the oxidized analogues of these two forms produce antiferromagnetically coupled [RuIII-phenoxyl] and paramagnetic [RuII-phenoxyl] forms, which exhibit diverse reactivities. Surprisingly, the magnetically coupled [RuIII-phenoxyl] form obtained from [Phenolato-RuIII-Phenolato] motif leads to coligand, PPh3 oxidation and undergoes dimerization, making a Ru-Ru bond (2.599(2) Å), while the [RuII-phenoxyl] form obtained from [Phenolato-RuII-Aryl] motif leads to C-C coupling and H abstraction reactions. The coupling reaction affords a 4,4'-dibenzosemiquinonate anion radical complex, but the H-abstraction of the phenoxyl form gives a [RuII-Phenol] complex. For comparison, [RuII(IQR 0)] and [RuII(ISQR·-)] complexes were also isolated, where IQR 0 and ISQR·- are p-R-o-iminobenzoquinone and p-R-o-iminobenzosemiquinonate anion radicals. However, they fail to promote any bond-formation reaction. The molecular and electronic structures of the ruthenium (II/III) complexes were confirmed by single-crystal X-ray crystallography, EPR spectroscopy, and DFT calculations.

Modeling the Weak pH Dependence of Proton-Coupled Electron Transfer for Tryptophan Derivatives

The oxidation of tryptophan (Trp) is an important step in many biological processes and often occurs by sequential or concerted proton-coupled electron transfer (PCET). The apparent rate constants for the photochemical oxidation of two Trp derivatives in water have been shown to be pH-independent at low pH and to exhibit weak pH dependence at higher pH. Herein, these systems are investigated with a general, multi-channel model that includes sequential and concerted mechanisms as well as various proton donors and acceptors. This model can reproduce the kinetic data for both Trp derivatives with physically meaningful parameters and suggests that the weak pH dependence may arise from the competition between OH- and H2O as proton acceptors in concerted PCET. Deprotonation of an ammonium group for one of the systems leads to a more complex pH dependence at higher pH. This work demonstrates the importance of considering multiple competing channels for the analysis of the pH dependence of apparent PCET rate constants.

Theoretical Insights into the Generation Mechanism of the Tyr122 Radical Catalyzed by Intermediate X in Class Ia Ribonucleotide Reductase

Ribonucleotide reductase (RNR) catalyzes the reduction of ribonucleotides to deoxyribonucleotides in all organisms. There is an ∼35 Å long-range electron-hole transfer pathway during the catalytic process of class Ia RNR, which can be described as Tyr122β ↔ [Trp48β]? ↔ Tyr356β ↔ Tyr731α ↔ Tyr730α ↔ Cys439α. The formation of the Y122• radical initiates this long-range radical transfer process. However, the generation mechanism of Y122• is not yet clear due to confusion over the intermediate X structures. Based on the two reported X structures, we examined the possible mechanisms of Y122• generation by density functional theory (DFT) calculations. Our examinations revealed that the generation of the Y122• radical from the two different core structures of X was via a similar two-step reaction, with the first step of proton transfer for the formation of the proton receptor of Y122 and the second step of a proton-coupled long-range electron transfer reaction with the proton transfer from the Y122 hydroxyl group to the terminal hydroxide ligand of Fe1III and simultaneously electron transfer from the side chain of Y122 to Fe2IV. These findings provide an insight into the formation mechanism of Y122• catalyzed by the double-iron center of the β subunit of class Ia RNR.

Jellyfish-type Dinuclear Hafnium Azido Complexes: Synthesis and Reactivity

Di- and multinuclear hafnium complexes bridged by ligands have been rarely reported. In this article, a novel 3,5-disubstituted pyrazolate-bridged ligand LH5 with two [N2 N]2- -type chelating side arms was designed and synthesized, which supported a series of dinuclear hafnium complexes. Dinuclear hafnium azides [LHf2 (μ-1,1-N3 )2 (N3 )2 ][Na(THF)4 ] 3 and [LHf2 (μ-1,1-N3 )2 (N3 )2 ][Na(2,2,2-Kryptofix)] 4 were further synthesized and structurally characterized, featuring two sets of terminal and bridging azido ligands like jellyfishes. The reactivity of 3 under reduction conditions was conducted, leading to a formation of a tetranuclear hafnium imido complex [L1 Hf2 (μ1 -NH)(N3 ){μ2 -K}]2 5. DFT calculations revealed that the mixed imido azide 5 was generated via an intramolecular C-H insertion from a putative dinuclear HfIV -nitridyl intermediate.

Structure of a ribonucleotide reductase R2 protein radical

Aerobic ribonucleotide reductases (RNRs) initiate synthesis of DNA building blocks by generating a free radical within the R2 subunit; the radical is subsequently shuttled to the catalytic R1 subunit through proton-coupled electron transfer (PCET). We present a high-resolution room temperature structure of the class Ie R2 protein radical captured by x-ray free electron laser serial femtosecond crystallography. The structure reveals conformational reorganization to shield the radical and connect it to the translocation path, with structural changes propagating to the surface where the protein interacts with the catalytic R1 subunit. Restructuring of the hydrogen bond network, including a notably short O-O interaction of 2.41 angstroms, likely tunes and gates the radical during PCET. These structural results help explain radical handling and mobilization in RNR and have general implications for radical transfer in proteins.

Interrogating bioinspired ESIPT/PCET-based Ir(iii)-complexes as organelle-targeted phototherapeutics: a redox-catalysis under hypoxia to evoke synergistic ferroptosis/apoptosis

Installing proton-coupled electron transfer (PCET) in Ir-complexes is indeed a newly explored phenomenon, offering high quantum efficiency and tunable photophysics; however, the prospects for its application in various fields, including interrogating biological systems, are quite open and exciting. Herein, we developed various organelle-targeted Ir(iii)-complexes by leveraging the photoinduced PCET process to see the opportunities in phototherapeutic application and investigate the underlying mechanisms of action (MOAs). We diversified the ligands' nature and also incorporated a H-bonded benzimidazole-phenol (BIP) moiety with π-conjugated ancillary ligands in Ir(iii) to study the excited-state intramolecular proton transfer (ESIPT) process for tuning dual emission bands and to tempt excited-state PCET. These visible or two-photon-NIR light activatable Ir-catalysts generate reactive hydroxyl radicals (˙OH) and simultaneously oxidize electron donating biomolecules (1,4-dihydronicotinamide adenine dinucleotide or glutathione) to disrupt redox homeostasis, downregulate the GPX4 enzyme, and amplify oxidative stress and lipid peroxide (LPO) accumulation. Our homogeneous photocatalytic platform efficiently triggers organelle dysfunction mediated by a Fenton-like pathway with spatiotemporal control upon illumination to evoke ferroptosis poised with the synergistic action of apoptosis in a hypoxic environment leading to cell death. Ir2 is the most efficient photochemotherapy agent among others, which provided profound cytophototoxicity to 4T1 and MCF-7 cancerous cells and inhibited solid hypoxic tumor growth in vitro and in vivo.

Electron Tunneling in Biology: When Does it Matter?

Electrons can tunnel between cofactor molecules positioned along biological electron transport chains up to a distance of ≃ 20 Å on the millisecond time scale of enzymatic turnover. This tunneling range determines the design of biological energy chains facilitating the cross-membrane transport of electrons. Tunneling distance and cofactors' redox potentials become the main physical parameters affecting the rate of electron transport. In addition, universal charge-transport properties are assigned to all proteins, making protein identity, flexibility, and dynamics insignificant. This paradigm is challenged by dynamical models of electron transfer, showing that the electron hopping rate is constant within the crossover distance R* ≃ 12 Å, followed with an exponential falloff at longer distances. If this hypothesis is fully confirmed, natural and man-made energy chains for electron transport should be best designed by placing redox cofactors near the crossover distance R*. Protein flexibility and dynamics affect the magnitude of the maximum hopping rate within the crossover distance. Changes in protein flexibility between forward and backward transitions contribute to vectorial charge transport. For biological energy chains, charge transport through proteins is not defined by universal parameters, and protein identity matters.

Tyrosine residues initiated photopolymerization in living organisms

Towards intracellular engineering of living organisms, the development of new biocompatible polymerization system applicable for an intrinsically non-natural macromolecules synthesis for modulating living organism function/behavior is a key step. Herein, we find that the tyrosine residues in the cofactor-free proteins can be employed to mediate controlled radical polymerization under 405 nm light. A proton-coupled electron transfer (PCET) mechanism between the excited-state TyrOH* residue in proteins and the monomer or the chain transfer agent is confirmed. By using Tyr-containing proteins, a wide range of well-defined polymers are successfully generated. Especially, the developed photopolymerization system shows good biocompatibility, which can achieve in-situ extracellular polymerization from the surface of yeast cells for agglutination/anti-agglutination functional manipulation or intracellular polymerization inside yeast cells, respectively. Besides providing a universal aqueous photopolymerization system, this study should contribute a new way to generate various non-natural polymers in vitro or in vivo to engineer living organism functions and behaviours.

Exploring Proton-Coupled Electron Transfer at Multiple Scales

The coupling of electron and proton transfer is critical for chemical and biological processes spanning a wide range of length and time scales and often occurring in complex environments. Thus, diverse modeling strategies, including analytical theories, quantum chemistry, molecular dynamics, and kinetic modeling, are essential for a comprehensive understanding of such proton-coupled electron transfer reactions. Each of these computational methods provides one piece of the puzzle, and all these pieces must be viewed together to produce the full picture.

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 β. The active form is an asymmetric αα'ββ' complex. The α subunit houses the site for nucleotide reduction initiated by a thiyl radical (C439•), and the β 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•[β] ↔ W48?[β] ↔ Y356[β] ↔ Y731[α] ↔ Y730[α] ↔ C439[α]. In a recent cryo-EM structure, Y356[β] was revealed for the first time and it, along with Y731[α], spans the asymmetric α/β interface. An E52[β] 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[β]. Mutagenesis studies, transient absorption spectroscopy, and photochemical assays monitoring deoxynucleotide formation collectively indicate that the E52[β], 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.

Capturing a bis-Fe(IV) State in Methylosinus trichosporium OB3b MbnH

The diheme bacterial cytochrome c peroxidase (bCcP)/MauG superfamily is a diverse set of enzymes that remains largely uncharacterized. One recently discovered member, MbnH, converts a tryptophan residue in its substrate protein, MbnP, to kynurenine. Here we show that upon reaction with H₂O₂, MbnH forms a bis-Fe(IV) intermediate, a state previously detected in just two other enzymes, MauG and BthA. Using absorption, Mössbauer, and electron paramagnetic resonance (EPR) spectroscopies coupled with kinetic analysis, we characterized the bis-Fe(IV) state of MbnH and determined that this intermediate decays back to the diferric state in the absence of MbnP substrate. In the absence of MbnP substrate, MbnH can also detoxify H₂O₂ to prevent oxidative self damage, unlike MauG, which has long been viewed as the prototype for bis-Fe(IV) forming enzymes. MbnH performs a different reaction from MauG, while the role of BthA remains unclear. All three enzymes can form a bis-Fe(IV) intermediate but within distinct kinetic regimes. The study of MbnH significantly expands our knowledge of enzymes that form this species. Computational and structural analyses indicate that electron transfer between the two heme groups in MbnH and between MbnH and the target tryptophan in MbnP likely occurs via a hole-hopping mechanism involving intervening tryptophan residues. These findings set the stage for discovery of additional functional and mechanistic diversity within the bCcP/MauG superfamily.

Spectroscopic Properties of a Biologically Relevant [Fe2 (μ-O)2 ] Diamond Core Motif with a Short Iron-Iron Distance

Diiron cofactors in enzymes perform diverse challenging transformations. The structures of high valent intermediates (Q in methane monooxygenase and X in ribonucleotide reductase) are debated since Fe-Fe distances of 2.5-3.4 Å were attributed to "open" or "closed" cores with bridging or terminal oxido groups. We report the crystallographic and spectroscopic characterization of a Fe^III ₂ (μ-O)₂ complex (2) with tetrahedral (4C) centres and short Fe-Fe distance (2.52 Å), persisting in organic solutions. 2 shows a large Fe K-pre-edge intensity, which is caused by the pronounced asymmetry at the T_D Fe^III centres due to the short Fe-μ-O bonds. A ≈2.5 Å Fe-Fe distance is unlikely for six-coordinate sites in Q or X, but for a Fe₂ (μ-O)₂ core containing four-coordinate (or by possible extension five-coordinate) iron centres there may be enough flexibility to accommodate a particularly short Fe-Fe separation with intense pre-edge transition. This finding may broaden the scope of models considered for the structure of high-valent diiron intermediates formed upon O₂ activation in biology.

Direct Proton-Coupled Electron Transfer between Interfacial Tyrosines in Ribonucleotide Reductase

Ribonucleotide reductase (RNR) regulates DNA synthesis and repair in all organisms. The mechanism of Escherichia coli RNR requires radical transfer over a proton-coupled electron transfer (PCET) pathway spanning ∼32 Å across two protein subunits. A key step along this pathway is the interfacial PCET reaction between Y356 in the β subunit and Y731 in the α subunit. Herein, this PCET reaction between two tyrosines across an aqueous interface is explored with classical molecular dynamics and quantum mechanical/molecular mechanical (QM/MM) free energy simulations. The simulations suggest that the water-mediated mechanism involving double proton transfer through an intervening water molecule is thermodynamically and kinetically unfavorable. The direct PCET mechanism between Y356 and Y731 becomes feasible when Y731 is flipped toward the interface and is predicted to be approximately isoergic with a relatively low free energy barrier. This direct mechanism is facilitated by the hydrogen bonding of water to both Y356 and Y731. These simulations provide fundamental insights into radical transfer across aqueous interfaces.

Chances and challenges of long-distance electron transfer for cellular redox reactions

Biological redox reactions often use a set-up in which final redox partners are localized in different compartments and electron transfer (ET) among them is mediated by redox-active molecules. In enzymes, these ET processes occur over nm distances, whereas multi-protein filaments bridge μm ranges. Electrons are transported over cm ranges in cable bacteria, which are formed by thousands of cells. In this review, we describe molecular mechanisms that explain how respiration in a compartmentalized set-up ensures redox homeostasis. We highlight mechanistic studies on ET through metal-free peptides and proteins demonstrating that long-distance ET is possible because amino acids Tyr, Trp, Phe, and Met can act as relay stations. This cuts one long ET into several short reaction steps. The chances and challenges of long-distance ET for cellular redox reactions are then discussed.

Theory of Protein Charge Transfer: Electron Transfer between Tryptophan Residue and Active Site of Azurin

One reaction step in the conductivity relay of azurin, electron transfer between the Cu-based active site and the tryptophan residue, is studied theoretically and by classical molecular dynamics simulations. Oxidation of tryptophan results in electrowetting of this residue. This structural change makes the free energy surfaces of electron transfer nonparabolic as described by the Q-model of electron transfer. We analyze the medium dynamical effect on protein electron transfer produced by coupled Stokes-shift dynamics and the dynamics of the donor-acceptor distance modulating electron tunneling. The equilibrium donor-acceptor distance falls in the plateau region of the rate constant, where it is determined by the protein-water dynamics, and the probability of electron tunneling does not affect the rate. The crossover distance found here puts most intraprotein electron-transfer reactions under the umbrella of dynamical control. The crossover between the medium-controlled and tunneling-controlled kinetics is combined with the effect of the protein-water medium on the activation barrier to formulate principles of tunability of protein-based charge-transfer chains. The main principle in optimizing the activation barrier is the departure from the Gaussian-Gibbsian statistics of fluctuations promoting activated transitions. This is achieved either by incomplete (nonergodic) sampling, breaking the link between the Stokes-shift and variance reorganization energies, or through wetting-induced structural changes of the enzyme's active site.

Nonadiabatic Dynamics of Hydrogen Tunneling with Nuclear-Electronic Orbital Multistate Density Functional Theory

Proton transfer reactions play a critical role in many chemical and biological processes. The development of computationally efficient approaches to describe the quantum dynamics of proton transfer, which often involves hydrogen tunneling, is challenging. Herein, the nuclear-electronic orbital multistate density functional theory (NEO-MSDFT) method is combined with both Ehrenfest and surface hopping nonadiabatic dynamics methods to describe hydrogen tunneling. The NEO-MSDFT method treats the transferring hydrogen nucleus quantum mechanically on the same level as the electrons and incorporates both static and dynamical correlation by mixing localized NEO-DFT solutions with a nonorthogonal configuration interaction scheme. The other nuclei are propagated on the NEO-MSDFT vibronic surfaces during the Ehrenfest or surface hopping dynamics. These methods are applied to proton transfer in malonaldehyde as a prototypical hydrogen tunneling system. The inclusion of vibronically nonadiabatic effects is found to significantly impact the proton transfer time and tunneling dynamics. This approach is applicable to a wide range of other proton transfer reactions.

Spectroscopic Characterization of a Diferric Mycobacterial Hemerythrin-Like Protein with Unprecedented Reactivity toward Nitric Oxide

Hemerythrin-like proteins (HLPs) are broadly distributed across taxonomic groups and appear to play highly diverse functional roles in prokaryotes. Mycobacterial HLPs contribute to the survival of these pathogenic bacteria in mammalian macrophages, but their modes of action remain unclear. A recent crystallographic characterization of Mycobacterium kansasii HLP (Mka-HLP) revealed the unexpected presence of a tyrosine sidechain (Tyr54) near the coordination sphere of one of the two iron centers. Here, we show that Tyr54 is a true ligand to the Fe2(III) ion which, in conjunction with the presence of a μ-oxo group bridging the two iron(III), brings unique reactivity toward nitric oxide (NO). Monitoring the titration of Mka-HLP with NO by Fourier-transform infrared and electron paramagnetic resonance spectroscopies shows that both diferric and diferrous forms of Mka-HLP accumulate an uncoupled high-spin and low-spin {FeNO}⁷ pair. We assign the reactivity of the diferric protein to an initial radical reaction between NO and the μ-oxo bridge to form nitrite and a mixed-valent diiron center that can react further with NO. Amperometric measurements of NO consumption by Mka-HLP confirm that this reactivity can proceed at low micromolar concentrations of NO, before additional NO consumption, supporting a NO scavenging role for mycobacterial HLPs.

A theoretical insight into excited-state decay and proton transfer of p-nitrophenylphenol in the gas phase and methanol solution

The excited-state decay (ESD) and proton transfer (EPT) of p-nitrophenylphenol (NO₂-Bp-OH), especially in the triplet states, were not characterized with high-level theoretical methods to date. Herein, the MS-CASPT2//CASSCF and QM(MS-CASPT2//CASSCF)/MM methods were employed to gain an atomic-level understanding of the ESD and EPT of NO₂-Bp-OH in the gas phase and its hydrogen-bonded complex in methanol. Our calculation results revealed that the S₁ and S₂ states of NO₂-Bp-OH are of ¹ππ* and ¹nπ* characters at the Franck-Condon (FC) point, which correspond to the ICT-EPT and intramolecular charge-transfer (ICT) states in spectroscopic experiments. The former state has a charge-transfer property that could facilitate the EPT reaction, while the latter one might be unfavorable for EPT. The vertical excitation energies of these states are almost degenerate at the FC region and the electronic configurations of ¹ππ* and ¹nπ* will exchange from the S₁ FC region to the S₁ minimum, which means that the ¹nπ* state will participate in ESD once NO₂-Bp-OH departs from the S₁ FC region. Besides, we found that three triplets lie below the first bright state and will play very important roles in intersystem crossing processes. In terms of several pivotal surface crossings and relevant linearly interpolated internal coordinate (LIIC) paths, three feasible but competing ESD channels that could effectively lead the system to the ground state or the lowest triplet state were put forward. Once arrived at the T₁ state, the system has enough time and internal energy to undergo the EPT reaction. The methanol solvent has a certain effect on the relative energies and spin-orbit couplings, but does not qualitatively change the ESD processes of NO₂-Bp-OH. By contrast, the solvent effects will remarkably stabilize the proton-transferred product by the hydrogen bond networks and assist to form the triplet anion. Our present work would pave the road to properly understand the mechanistic photochemistry of similar hydroxyaromatic compounds.

Proton-coupled energy transfer in molecular triads

We experimentally discovered and theoretically analyzed a photochemical mechanism, which we term proton-coupled energy transfer (PCEnT). A series of anthracene-phenol-pyridine triads formed a local excited anthracene state after light excitation at a wavelength of ~400 nanometers (nm), which led to fluorescence around 550 nm from the phenol-pyridine unit. Direct excitation of phenol-pyridine would have required ~330-nm light, but the coupled proton transfer within the phenol-pyridine unit lowered its excited-state energy so that it could accept excitation energy from anthracene. Singlet-singlet energy transfer thus occurred despite the lack of spectral overlap between the anthracene fluorescence and the phenol-pyridine absorption. Moreover, theoretical calculations indicated negligible charge transfer between the anthracene and phenol-pyridine units. We construe PCEnT as an elementary reaction of possible relevance to biological systems and future photonic devices.

Kinetic model for reversible radical transfer in ribonucleotide reductase

The enzyme ribonucleotide reductase (RNR), which catalyzes the reduction of ribonucleotides to deoxynucleotides, is vital for DNA synthesis, replication, and repair in all living organisms. Its mechanism requires long-range radical translocation over ∼32 Å through two protein subunits and the intervening aqueous interface. Herein, a kinetic model is designed to describe reversible radical transfer in Escherichia coli RNR. This model is based on experimentally studied photoRNR systems that allow the photochemical injection of a radical at a specific tyrosine residue, Y356, using a photosensitizer. The radical then transfers across the interface to another tyrosine residue, Y731, and continues until it reaches a cysteine residue, C439, which is primed for catalysis. This kinetic model includes radical injection, an off-pathway sink, radical transfer between pairs of residues along the pathway, and the conformational flipping motion of Y731 at the interface. Most of the input rate constants for this kinetic model are obtained from previous experimental measurements and quantum mechanical/molecular mechanical free-energy simulations. Ranges for the rate constants corresponding to radical transfer across the interface are determined by fitting to the experimentally measured Y356 radical decay times in photoRNR systems. This kinetic model illuminates the time evolution of radical transport along the tyrosine and cysteine residues following radical injection. Further analysis identifies the individual rate constants that may be tuned to alter the timescale and probability of the injected radical reaching C439. The insights gained from this kinetic model are relevant to biochemical understanding and protein-engineering efforts with potential pharmacological implications.

Inhibitors of the Cancer Target Ribonucleotide Reductase, Past and Present

Ribonucleotide reductase (RR) is an essential multi-subunit enzyme found in all living organisms; it catalyzes the rate-limiting step in dNTP synthesis, namely, the conversion of ribonucleoside diphosphates to deoxyribonucleoside diphosphates. As expression levels of human RR (hRR) are high during cell replication, hRR has long been considered an attractive drug target for a range of proliferative diseases, including cancer. While there are many excellent reviews regarding the structure, function, and clinical importance of hRR, recent years have seen an increase in novel approaches to inhibiting hRR that merit an updated discussion of the existing inhibitors and strategies to target this enzyme. In this review, we discuss the mechanisms and clinical applications of classic nucleoside analog inhibitors of hRRM1 (large catalytic subunit), including gemcitabine and clofarabine, as well as inhibitors of the hRRM2 (free radical housing small subunit), including triapine and hydroxyurea. Additionally, we discuss novel approaches to targeting RR and the discovery of new classes of hRR inhibitors.

19F Electron-Nuclear Double Resonance Reveals Interaction between Redox-Active Tyrosines across the α/β Interface of E. coli Ribonucleotide Reductase

Ribonucleotide reductases (RNRs) catalyze the reduction of ribonucleotides to deoxyribonucleotides, thereby playing a key role in DNA replication and repair. Escherichia coli class Ia RNR is an α₂β₂ enzyme complex that uses a reversible multistep radical transfer (RT) over 32 Å across its two subunits, α and β, to initiate, using its metallo-cofactor in β₂, nucleotide reduction in α₂. Each step is proposed to involve a distinct proton-coupled electron-transfer (PCET) process. An unresolved step is the RT involving Y₃₅₆(β) and Y₇₃₁(α) across the α/β interface. Using 2,3,5-F₃Y₁₂₂-β₂ with 3,5-F₂Y₇₃₁-α₂, GDP (substrate) and TTP (allosteric effector), a Y₃₅₆^• intermediate was trapped and its identity was verified by 263 GHz electron paramagnetic resonance (EPR) and 34 GHz pulse electron–electron double resonance spectroscopies. 94 GHz ¹⁹F electron-nuclear double resonance spectroscopy allowed measuring the interspin distances between Y₃₅₆^• and the ¹⁹F nuclei of 3,5-F₂Y₇₃₁ in this RNR mutant. Similar experiments with the double mutant E₅₂Q/F₃Y₁₂₂-β₂ were carried out for comparison to the recently published cryo-EM structure of a holo RNR complex. For both mutant combinations, the distance measurements reveal two conformations of 3,5-F₂Y₇₃₁. Remarkably, one conformation is consistent with 3,5-F₂Y₇₃₁ within the H-bond distance to Y₃₅₆^•, whereas the second one is consistent with the conformation observed in the cryo-EM structure. The observations unexpectedly suggest the possibility of a colinear PCET, in which electron and proton are transferred from the same donor to the same acceptor between Y₃₅₆ and Y₇₃₁. The results highlight the important role of state-of-the-art EPR spectroscopy to decipher this mechanism.

Concerted Electron-Nuclear Motion in Proton-Coupled Electron Transfer-Driven Grotthuss-Type Proton Translocation

Photoinduced proton-coupled electron transfer and long-range two-proton transport via a Grotthuss-type mechanism are investigated in a biomimetic construct. The ultrafast, nonequilibrium dynamics are assessed via two-dimensional electronic vibrational spectroscopy, in concert with electrochemical and computational techniques. A low-frequency mode is identified experimentally and found to promote double proton and electron transfer, supported by recent theoretical simulations of a similar but abbreviated (non-photoactive) system. Excitation frequency peak evolution and center line slope dynamics show direct evidence of strongly coupled nuclear and electronic degrees of freedom, from which we can conclude that the double proton and electron transfer processes are concerted (up to an uncertainty of 24 fs). The nonequilibrium pathway from the photoexcited Franck-Condon region to the E2PT state is characterized by an ∼110 fs time scale. This study and the tools presented herein constitute a new window into hot charge transfer processes involving an electron and multiple protons.

Insights into the Thermodynamics and Kinetics of Amino-Acid Radicals in Proteins

Some oxidoreductase enzymes use redox-active tyrosine, tryptophan, cysteine, and/or glycine residues as one-electron, high-potential redox (radical) cofactors. Amino-acid radical cofactors typically perform one of four tasks-they work in concert with a metallocofactor to carry out a multielectron redox process, serve as storage sites for oxidizing equivalents, activate the substrate molecules, or move oxidizing equivalents over long distances. It is challenging to experimentally resolve the thermodynamic and kinetic redox properties of a single-amino-acid residue. The inherently reactive and highly oxidizing properties of amino-acid radicals increase the experimental barriers further still. This review describes a family of stable and well-structured model proteins that was made specifically to study tyrosine and tryptophan oxidation-reduction. The so-called α₃X model protein system was combined with very-high-potential protein film voltammetry, transient absorption spectroscopy, and theoretical methods to gain a comprehensive description of the thermodynamic and kinetic properties of protein tyrosine and tryptophan radicals.