Proton-coupled electron transfer: a unifying mechanism for biological charge transport, amino acid radical initiation and propagation, and bond making/breaking reactions of water and oxygen

The role of Tyr34 in proton coupled electron transfer and product inhibition of manganese superoxide dismutase

Human manganese superoxide dismutase (MnSOD) plays a crucial role in controlling levels of reactive oxygen species (ROS) by converting superoxide (O 2 ∙ - ) to molecular oxygen (O2) and hydrogen peroxide (H2O2) with proton-coupled electron transfers (PCETs). A key catalytic residue, Tyr34, determines the activity of human MnSOD and also becomes post-translationally inactivated by nitration in various diseases associated with mitochondrial dysfunction. Tyr34 has an unusual pKa due to its proximity to the Mn metal and undergoes cyclic deprotonation and protonation events to promote the electron transfers of MnSOD. Neutron diffraction, X-ray spectroscopy, and quantum chemistry calculations in oxidized, reduced and product inhibited enzymatic states shed light on the role of Tyr34 in MnSOD catalysis. The data identify the contributions of Tyr34 in MnSOD activity that support mitochondrial function and give a thorough characterization of how a single tyrosine modulates PCET catalysis. Product inhibition occurs by an associative displacement mechanism.

Revealing the atomic and electronic mechanism of human manganese superoxide dismutase product inhibition

Human manganese superoxide dismutase (MnSOD) is a crucial oxidoreductase that maintains the vitality of mitochondria by converting superoxide (O2●-) to molecular oxygen (O2) and hydrogen peroxide (H2O2) with proton-coupled electron transfers (PCETs). Human MnSOD has evolved to be highly product inhibited to limit the formation of H2O2, a freely diffusible oxidant and signaling molecule. The product-inhibited complex is thought to be composed of a peroxide (O22-) or hydroperoxide (HO2-) species bound to Mn ion and formed from an unknown PCET mechanism. PCET mechanisms of proteins are typically not known due to difficulties in detecting the protonation states of specific residues that coincide with the electronic state of the redox center. To shed light on the mechanism, we combine neutron diffraction and X-ray absorption spectroscopy of the product-bound, trivalent, and divalent states of the enzyme to reveal the positions of all the atoms, including hydrogen, and the electronic configuration of the metal ion. The data identifies the product-inhibited complex, and a PCET mechanism of inhibition is constructed.

Deconstructing synthetic biology across scales: a conceptual approach for training synthetic biologists

Synthetic biology allows us to reuse, repurpose, and reconfigure biological systems to address society's most pressing challenges. Developing biotechnologies in this way requires integrating concepts across disciplines, posing challenges to educating students with diverse expertise. We created a framework for synthetic biology training that deconstructs biotechnologies across scales-molecular, circuit/network, cell/cell-free systems, biological communities, and societal-giving students a holistic toolkit to integrate cross-disciplinary concepts towards responsible innovation of successful biotechnologies. We present this framework, lessons learned, and inclusive teaching materials to allow its adaption to train the next generation of synthetic biologists.

The role of Tyr34 in proton-coupled electron transfer of human manganese superoxide dismutase

Human manganese superoxide dismutase (MnSOD) plays a crucial role in controlling levels of reactive oxygen species (ROS) by converting superoxide (O2 ●-) to molecular oxygen (O2) and hydrogen peroxide (H2O2) with proton-coupled electron transfers (PCETs). The reactivity of human MnSOD is determined by the state of a key catalytic residue, Tyr34, that becomes post-translationally inactivated by nitration in various diseases associated with mitochondrial dysfunction. We previously reported that Tyr34 has an unusual pKa due to its proximity to the Mn metal and undergoes cyclic deprotonation and protonation events to promote the electron transfers of MnSOD. To shed light on the role of Tyr34 MnSOD catalysis, we performed neutron diffraction, X-ray spectroscopy, and quantum chemistry calculations of Tyr34Phe MnSOD in various enzymatic states. The data identifies the contributions of Tyr34 in MnSOD activity that support mitochondrial function and presents a thorough characterization of how a single tyrosine modulates PCET catalysis.

The role of Tyr34 in proton-coupled electron transfer of human manganese superoxide dismutase

Human manganese superoxide dismutase (MnSOD) plays a crucial role in controlling levels of reactive oxygen species (ROS) by converting superoxide (O 2 •- ) to molecular oxygen (O 2 ) and hydrogen peroxide (H 2 O 2 ) with proton-coupled electron transfers (PCETs). The reactivity of human MnSOD is determined by the state of a key catalytic residue, Tyr34, that becomes post-translationally inactivated by nitration in various diseases associated with mitochondrial dysfunction. We previously reported that Tyr34 has an unusual pK a due to its proximity to the Mn metal and undergoes cyclic deprotonation and protonation events to promote the electron transfers of MnSOD. To shed light on the role of Tyr34 MnSOD catalysis, we performed neutron diffraction, X-ray spectroscopy, and quantum chemistry calculations of Tyr34Phe MnSOD in various enzymatic states. The data identifies the contributions of Tyr34 in MnSOD activity that support mitochondrial function and presents a thorough characterization of how a single tyrosine modulates PCET catalysis.

Revealing the atomic and electronic mechanism of human manganese superoxide dismutase product inhibition

Human manganese superoxide dismutase (MnSOD) is a crucial oxidoreductase that maintains the vitality of mitochondria by converting O 2 ∙ - to O 2 and H 2 O 2 with proton-coupled electron transfers (PCETs). Since changes in mitochondrial H 2 O 2 concentrations are capable of stimulating apoptotic signaling pathways, human MnSOD has evolutionarily gained the ability to be highly inhibited by its own product, H 2 O 2 . A separate set of PCETs is thought to regulate product inhibition, though mechanisms of PCETs are typically unknown due to difficulties in detecting the protonation states of specific residues that coincide with the electronic state of the redox center. To shed light on the underlying mechanism, we combined neutron diffraction and X-ray absorption spectroscopy of the product-bound, trivalent, and divalent states to reveal the all-atom structures and electronic configuration of the metal. The data identifies the product-inhibited complex for the first time and a PCET mechanism of inhibition is constructed.

Revealing the atomic and electronic mechanism of human manganese superoxide dismutase product inhibition

Human manganese superoxide dismutase (MnSOD) is a crucial oxidoreductase that maintains the vitality of mitochondria by converting O 2 ●- to O 2 and H 2 O 2 with proton-coupled electron transfers (PCETs). Since changes in mitochondrial H 2 O 2 concentrations are capable of stimulating apoptotic signaling pathways, human MnSOD has evolutionarily gained the ability to be highly inhibited by its own product, H 2 O 2 . A separate set of PCETs is thought to regulate product inhibition, though mechanisms of PCETs are typically unknown due to difficulties in detecting the protonation states of specific residues that coincide with the electronic state of the redox center. To shed light on the underlying mechanism, we combined neutron diffraction and X-ray absorption spectroscopy of the product-bound, trivalent, and divalent states to reveal the all-atom structures and electronic configuration of the metal. The data identifies the product-inhibited complex for the first time and a PCET mechanism of inhibition is constructed.

The solvent-regulated excited state reaction mechanism of 2-(2'-hydroxyphenyl)benzothiazole aggregates

The excited state relaxation dynamics of 2-(2'-hydroxyphenyl)benzothiazole (HBT) in the gas phase and the solvents have been explored experimentally and theoretically. However, the fundamental mechanism of its emission in aggregates is still unexplored. In this article, we have presented a detail investigation of solvent-regulated excited state (ES) reactions for HBT aggregates with the aid of several experimental and theoretical research. The careful investigation of solvatochromic and electrochemical behavior elucidates that the emission around 460 nm of HBT in DMSO and DMSO-water fraction correspond to the excited state internal charge transfer (ESICT). The quantum chemical analysis further supports this observation. The concentration-dependent 1H NMR and emission studies of HBT in DMSO revealed the formation of aggregates at higher concentrations that facilitate the charge transfer. The emission pattern of HBT in the AcN-water fraction demonstrates that the sequential internal charge transfer-proton transfer (ESICT-ESIPT) occurs in HBT aggregates. The pH studies show that HBT aggregates are potential ratiometric sensors for near-physiological pH ranges. Moreover, a ground-state zwitterionic conformation of HBT is observed in the basic medium formed by ground-state internal proton transfer (GSIPT). Overall, this study provides a better understanding of solvent-regulated ES reaction mechanism in the case of HBT aggregates and other substituted HBT compound aggregates published previously.

Proton Affinity in the Chemistry of Beta-Octamolybdate: HPLC-ICP-AES, NMR and Structural Studies

The affinity of [β-Mo8O26]4- toward different proton sources has been studied in various conditions. The proposed sites for proton coordination were highlighted with single crystal X-ray diffraction (SCXRD) analysis of (Bu4N)3[β-{Ag(py-NH2)Mo8O26]}] (1) and from analysis of reported structures. Structural rearrangement of [β-Mo8O26]4- as a direct response to protonation was studied in solution with 95Mo NMR and HPLC-ICP-AES techniques. A new type of proton transfer reaction between (Bu4N)4[β-Mo8O26] and (Bu4N)4H2[V10O28] in DMSO results in both polyoxometalates transformation into [V2Mo4O19]4-, which was confirmed by the 95Mo, 51V NMR and HPLC-ICP-AES techniques. The same type of reaction with [H4SiW12O40] in DMSO leads to metal redistribution with formation of [W2Mo4O19]2-.

Hybrid bilayer membranes as platforms for biomimicry and catalysis

Hybrid bilayer membrane (HBM) platforms represent an emerging nanoscale bio-inspired interface that has broad implications in energy catalysis and smart molecular devices. An HBM contains multiple modular components that include an underlying inorganic surface with a biological layer appended on top. The inorganic interface serves as a support with robust mechanical properties that can also be decorated with functional moieties, sensing units and catalytic active sites. The biological layer contains lipids and membrane-bound entities that facilitate or alter the activity and selectivity of the embedded functional motifs. With their structural complexity and functional flexibility, HBMs have been demonstrated to enhance catalytic turnover frequency and regulate product selectivity of the O₂ and CO₂ reduction reactions, which have applications in fuel cells and electrolysers. HBMs can also steer the mechanistic pathways of proton-coupled electron transfer (PCET) reactions of quinones and metal complexes by tuning electron and proton delivery rates. Beyond energy catalysis, HBMs have been equipped with enzyme mimics and membrane-bound redox agents to recapitulate natural energy transport chains. With channels and carriers incorporated, HBM sensors can quantify transmembrane events. This Review serves to summarize the major accomplishments achieved using HBMs in the past decade.

Selenium Valence-to-Core X-ray Emission Spectroscopy and Kβ HERFD X-ray Absorption Spectroscopy as Complementary Probes of Chemical and Electronic Structure

Selenium X-ray absorption spectroscopy (XAS) has found widespread use in investigations of Se-containing materials, geochemical processes, and biologically active sites. In contrast to sulfur Kβ X-ray emission spectroscopy (XES), which has been found to contain electronic and structural information complementary to S XAS, Se Kβ XES remains comparatively underexplored. Herein, we present the first Se Valence-to-Core (VtC) XES studies of reduced Se-containing compounds and FeSe dimers. Se VtC XES is found to be sensitive to changes in covalent Se bonding interactions (Se–Se/Se–C/Se–H bonding) while being relatively insensitive to changes in Fe oxidation states as selenide bridges in FeSe dimers ([Fe₂Se₂]²⁺ vs [Fe₂Se₂]⁺). In contrast, Se Kβ HERFD XAS is demonstrated to be quite sensitive to changes in the Fe oxidation state with Se Kβ HERFD XAS demonstrating experimental resolution equivalent to Kα HERFD XAS. Additionally, computational studies reveal both Se VtC XES and XAS to be sensitive to selenium protonation in FeSe complexes.

Selenium is a trace element that plays vital roles in biological and geochemical cycles, energy storage, photovoltaics, and nanomaterials. Herein, selenium Valence-to-Core X-ray emission spectroscopy is explored as a new method of probing the chemical and electronic structure in selenium-containing compounds, demonstrating sensitivity to selenium bonding interactions. When paired with high-resolution Se X-ray absorption spectroscopy (HERFD XAS), these two methods have the potential to reveal greater insight into protonation and redox changes of Se-substituted FeS clusters.

Excited-state structural dynamics of nickel complexes probed by optical and X-ray transient absorption spectroscopies: insights and implications

Excited states of nickel complexes undergo a variety of photochemical processes, such as charge transfer, ligation/deligation, and redox reactions, relevant to solar energy conversion and photocatalysis. The efficiencies of the aforementioned processes are closely coupled to the molecular structures in the ground and excited states. The conventional optical transient absorption spectroscopy has revealed important excited-state pathways and kinetics, but information regarding the metal center, in particular transient structural and electronic properties, remains limited. These deficiencies are addressed by X-ray transient absorption (XTA) spectroscopy, a detailed probe of 3d orbital occupancy, oxidation state and coordination geometry. The examples of excited-state structural dynamics of nickel porphyrin and nickel phthalocyanine have been described from our previous studies with highlights on the unique structural information obtained by XTA spectroscopy. We close by surveying prospective applications of XTA spectroscopy to active areas of Ni-based photocatalysis based on the knowledge gained from our previous studies.

Proton in the ring: spectroscopy and dynamics of proton bonding in macrocycle cavities

The proton bond is a paradigmatic quantum molecular interaction and a major driving force of supramolecular chemistry. The ring cavities of crown ethers provide an intriguing environment, promoting competitive proton sharing with multiple coordination anchors. This study shows that protons confined in crown ether cavities form dynamic bonds that migrate to varying pairs of coordinating atoms when allowed by the flexibility of the macrocycle backbone. Prototypic native crown ethers (12-crown-4, 15-crown-5 and 18-crown-6) and aza-crown ethers (cyclen, 1-aza-18-crown-6 and hexacyclen) are investigated. For each system, Infrared action spectroscopy experiments and ab initio Molecular Dynamics computations are employed to elucidate the structural effects associated with proton diffusion and its entanglement with the conformational and vibrational dynamics of the protonated host.

Metalloprotein catalysis: structural and mechanistic insights into oxidoreductases from neutron protein crystallography

Metalloproteins catalyze a range of reactions, with enhanced chemical functionality due to their metal cofactor. The reaction mechanisms of metalloproteins have been experimentally characterized by spectroscopy, macromolecular crystallography and cryo-electron microscopy. An important caveat in structural studies of metalloproteins remains the artefacts that can be introduced by radiation damage. Photoreduction, radiolysis and ionization deriving from the electromagnetic beam used to probe the structure complicate structural and mechanistic interpretation. Neutron protein diffraction remains the only structural probe that leaves protein samples devoid of radiation damage, even when data are collected at room temperature. Additionally, neutron protein crystallography provides information on the positions of light atoms such as hydrogen and deuterium, allowing the characterization of protonation states and hydrogen-bonding networks. Neutron protein crystallography has further been used in conjunction with experimental and computational techniques to gain insight into the structures and reaction mechanisms of several transition-state metal oxidoreductases with iron, copper and manganese cofactors. Here, the contribution of neutron protein crystallography towards elucidating the reaction mechanism of metalloproteins is reviewed.

Water-Assisted Concerted Proton-Electron Transfer at Co(II)-Aquo Sites in Polyoxotungstates With Photogenerated RuIII (bpy)33+ Oxidant

The cobalt substituted polyoxotungstate [Co6 (H2 O)2 (α-B-PW9 O34 )2 (PW6 O26 )]17- (Co6) displays fast electron transfer (ET) kinetics to photogenerated RuIII (bpy)33+ , 4 to 5 orders of magnitude faster than the corresponding ET observed for cobalt oxide nanoparticles. Mechanistic evidence has been acquired indicating that: (i) the one-electron oxidation of Co6 involves Co(II) aquo or Co(II) hydroxo groups (abbreviated as Co6(II)-OH2 and Co6(II)-OH, respectively, whose speciation in aqueous solution is associated to a pKa of 7.6), and generates a Co(III)-OH moiety (Co6(III)-OH), as proven by transient absorption spectroscopy; (ii) at pH>pKa , the Co6(II)-OH→RuIII (bpy)33+ ET occurs via bimolecular kinetics, with a rate constant k close to the diffusion limit and dependent on the ionic strength of the medium, consistent with reaction between charged species; (iii) at pH Collapse

Key Words

• Co-aquo moiety
• cobalt polyoxometalate
• flash photolysis
• hydrogen bonding
• proton coupled electron transfer

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MESH Headings

• Cobalt/chemistry
• Coordination Complexes/chemical synthesis
• Coordination Complexes/chemistry
• Electrons
• Kinetics
• Light
• Organometallic Compounds/chemistry
• Organometallic Compounds/radiation effects
• Oxidants/chemistry
• Oxidants/radiation effects
• Oxidation-Reduction
• Polymers/chemical synthesis
• Polymers/chemistry
• Protons
• Ruthenium/chemistry
• Ruthenium/radiation effects
• Tungsten Compounds/chemical synthesis
• Tungsten Compounds/chemistry
• Water/chemistry

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Grants

• Fondazione Cariparo
• 10BIRD2018-UNIPD Department of Chemical Sciences at University of Padova
• 2017PBXPN4 Department of Chemical Sciences at University of Padova
• FAR 2020 University of Ferrara
• Fondazione Cariparo
• University of Ferrara

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Affiliation(s)

Francesco Rigodanza Department of Chemical SciencesUniversity of Padovavia Marzolo 135131PadovaItaly Consiglio Nazionale delle Ricerche (C.N.R.)Institute on Membrane Technology section of Padovavia Marzolo 135131PadovaItaly
Nadia Marino Department of Chemistry and Chemical TechnologiesUniversity of Calabria87036Arcavacata di Rende (CS)Italy
Alessandro Bonetto Dept. Environmental Sciences, Informatics and StatisticsUniversity Ca' Foscari Venice VegaparkVia delle Industrie 21/830175Marghera, VeniceItaly
Antonio Marcomini Dept. Environmental Sciences, Informatics and StatisticsUniversity Ca' Foscari Venice VegaparkVia delle Industrie 21/830175Marghera, VeniceItaly
Marcella Bonchio Department of Chemical SciencesUniversity of Padovavia Marzolo 135131PadovaItaly Consiglio Nazionale delle Ricerche (C.N.R.)Institute on Membrane Technology section of Padovavia Marzolo 135131PadovaItaly
Mirco Natali Department of Chemical, Pharmaceutical and Agricultural Sciences (DOCPAS)University of Ferrara, and Centro Interuniversitario per la Conversione Chimica dell'Energia Solare (SOLARCHEM) sez. di Ferraravia L. Borsari 4644121FerraraItaly
Andrea Sartorel Department of Chemical SciencesUniversity of Padovavia Marzolo 135131PadovaItaly

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Collaborators Collapse

Proton Removal Kinetics That Govern the Hydrogen Peroxide Oxidation Activity of Heterogeneous Bioinorganic Platforms

Precise regulation of proton-coupled electron-transfer (PCET) rates holds the key to simultaneously optimizing the turnover frequency and product selectivity of redox reactions that are central to the realization of renewable energy schemes in a sustainable future. In this work, a self-assembled monolayer (SAM) of a Ru complex electrografted onto a glassy carbon (GC) electrode was prepared as a heterogeneous electrocatalytic interface to facilitate the hydrogen peroxide (H₂O₂) oxidation half-cell reaction of a direct hydrogen peroxide/hydrogen peroxide fuel cell. A functional lipid membrane embedded with catalytic amounts of proton carriers was appended on top of the Ru SAM to construct a hybrid bilayer membrane (HBM) platform that can modulate the thermodynamics and kinetics of proton- and electron-transfer steps independently. The performances of the as-prepared Ru SAMs and HBMs toward H₂O₂ oxidation were investigated using electrochemical means, kinetic isotope effect (KIE) studies, and Tafel analyses. Proton carriers featuring borate, phosphate, and nitrile headgroups were found to dictate the transmembrane proton removal rate, thereby controlling the H₂O₂ oxidation activity. The first significance of this work was the expansion of HBM platforms to GC substrates to overcome the limited redox potential window on gold thiol systems, thereby enabling electrochemical investigations of anodic reactions at the SAM-lipid interface. The second highlight of this work was demonstrating for the first time that deprotonation kinetics can be taken advantage of to enhance the electrocatalytic oxidation performance of a metal complex anchored at the SAM-lipid interface of a HBM platform. When the knowledge gaps regarding how PCET steps govern redox pathways are closed, the advances achieved using our unique bioinorganic platform are envisioned to accelerate the understanding and optimization of electrocatalytic processes involving proton- and electron- transfer steps that are fundamental to the development of high-performance energy devices.

Direct detection of coupled proton and electron transfers in human manganese superoxide dismutase

Human manganese superoxide dismutase is a critical oxidoreductase found in the mitochondrial matrix. Concerted proton and electron transfers are used by the enzyme to rid the mitochondria of O2•-. The mechanisms of concerted transfer enzymes are typically unknown due to the difficulties in detecting the protonation states of specific residues and solvent molecules at particular redox states. Here, neutron diffraction of two redox-controlled manganese superoxide dismutase crystals reveal the all-atom structures of Mn3+ and Mn2+ enzyme forms. The structures deliver direct data on protonation changes between oxidation states of the metal. Observations include glutamine deprotonation, the involvement of tyrosine and histidine with altered pKas, and four unusual strong-short hydrogen bonds, including a low barrier hydrogen bond. We report a concerted proton and electron transfer mechanism for human manganese superoxide dismutase from the direct visualization of active site protons in Mn3+ and Mn2+ redox states.

Proton-Electron Transfer to the Active Site Is Essential for the Reaction Mechanism of Soluble Δ9-Desaturase

A full understanding of the catalytic action of non-heme iron (NHFe) and non-heme diiron (NHFe₂) enzymes is still beyond the grasp of contemporary computational and experimental techniques. Many of these enzymes exhibit fascinating chemo-, regio-, and stereoselectivity, in spite of employing highly reactive intermediates which are necessary for activations of most stable chemical bonds. Herein, we study in detail one intriguing representative of the NHFe₂ family of enzymes: soluble Δ⁹ desaturase (Δ⁹D), which desaturates rather than performing the thermodynamically favorable hydroxylation of substrate. Its catalytic mechanism has been explored in great detail by using QM(DFT)/MM and multireference wave function methods. Starting from the spectroscopically observed 1,2-μ-peroxo diferric P intermediate, the proton-electron uptake by P is the favored mechanism for catalytic activation, since it allows a significant reduction of the barrier of the initial (and rate-determining) H-atom abstraction from the stearoyl substrate as compared to the "proton-only activated" pathway. Also, we ruled out that a Q-like intermediate (high-valent diamond-core bis-μ-oxo-[Fe^IV]₂ unit) is involved in the reaction mechanism. Our mechanistic picture is consistent with the experimental data available for Δ⁹D and satisfies fairly stringent conditions required by Nature: the chemo-, stereo-, and regioselectivity of the desaturation of stearic acid. Finally, the mechanisms evaluated are placed into a broader context of NHFe₂ chemistry, provided by an amino acid sequence analysis through the families of the NHFe₂ enzymes. Our study thus represents an important contribution toward understanding the catalytic action of the NHFe₂ enzymes and may inspire further work in NHFe₍₂₎ biomimetic chemistry.

Fate of oxygen species from O2 activation at dimetal cofactors in an oxidase enzyme revealed by 57Fe nuclear resonance X-ray scattering and quantum chemistry

Oxygen (O₂) activation is a central challenge in chemistry and catalyzed at prototypic dimetal cofactors in biological enzymes with diverse functions. Analysis of intermediates is required to elucidate the reaction paths of reductive O₂ cleavage. An oxidase protein from the bacterium Geobacillus kaustophilus, R2lox, was used for aerobic in-vitro reconstitution with only ⁵⁷Fe(II) or Mn(II) plus ⁵⁷Fe(II) ions to yield [FeFe] or [MnFe] cofactors under various oxygen and solvent isotopic conditions including ^16/18O and H/D exchange. ⁵⁷Fe-specific X-ray scattering techniques were employed to collect nuclear forward scattering (NFS) and nuclear resonance vibrational spectroscopy (NRVS) data of the R2lox proteins. NFS revealed Fe/Mn(III)Fe(III) cofactor states and Mössbauer quadrupole splitting energies. Quantum chemical calculations of NRVS spectra assigned molecular structures, vibrational modes, and protonation patterns of the cofactors, featuring a terminal water (H₂O) bound at iron or manganese in site 1 and a metal-bridging hydroxide (μOH^-) ligand. A procedure for quantitation and correlation of experimental and computational NRVS difference signals due to isotope labeling was developed. This approach revealed that the protons of the ligands as well as the terminal water at the R2lox cofactors exchange with the bulk solvent whereas ¹⁸O from ¹⁸O₂ cleavage is incorporated in the hydroxide bridge. In R2lox, the two water molecules from four-electron O₂ reduction are released in a two-step reaction to the solvent. These results establish combined NRVS and QM/MM for tracking of iron-based oxygen activation in biological and chemical catalysts and clarify the reductive O₂ cleavage route in an enzyme.

Molecular Oxygen Binding in the Mitochondrial Electron Transfer Flavoprotein

Reactive oxygen species such as superoxide are potentially harmful byproducts of the aerobic metabolism in the inner mitochondrial membrane, and complexes I, II, III of the electron transport chain have been identified as primary sources. The mitochondrial fatty acid b-oxidation pathway may also play a yet uncharacterized role in reactive oxygen species generation, apparently at the level of the electron transfer flavoprotein:ubiquinone oxidoreductase (ETF:QO) and/or its redox partner electron-transfer flavoprotein (ETF). These enzymes comprise a key pathway through which electrons are sequentially shuttled from several dehydrogenases to the respiratory chain. The exact mechanisms of superoxide production have not been fully established, but a crucial starting point would be the binding of molecular oxygen within one of the protein complexes. The present investigation offers a comprehensive computational approach for the determination of binding modes and characteristic binding times of small molecules inside proteins, which is then used to reveal several O₂ binding sites near the flavin adenine dinucleotide cofactor of the ETF enzyme. The binding sites are further characterized to extract the necessary parameters for further studies of possible electron transfer between flavin and O₂ leading to radical pair formation and possible superoxide production.

H2 Kinetic Isotope Fractionation Superimposed by Equilibrium Isotope Fractionation During Hydrogenase Activity of D. vulgaris Strain Miyazaki

We determined ²H stable isotope fractionation at natural abundances associated with hydrogenase activity by whole cells of Desulfovibrio vulgaris strain Miyazaki F expressing a NiFe(Se) hydrogenase. Inhibition of sulfate reduction by molybdate inhibited the overall oxidation of hydrogen but still facilitated an equilibrium isotope exchange reaction with water. The theoretical equilibrium isotope exchange δ²H-values of the chemical exchange reaction were identical to the hydrogenase reaction, as confirmed using three isotopically different waters with δ²H-values of – 62, +461, and + 1533‰. Expected kinetic isotope fractionation of hydrogen oxidation by non-inhibited cells was also superimposed by an equilibrium isotope exchange. The isotope effects were solely catalyzed biotically as hydrogen isotope signatures did not change in control experiments without cells of D. vulgaris Miyazaki.

Rapid activation of basic hydrogen peroxide by borate and efficient destruction of toxic industrial chemicals (TICs) and chemical warfare agents (CWAs)

The activation process of the B(OH)₃-activated H₂O₂ solution and its performance toward toxic industrial chemicals (TICs) and chemical warfare agents (CWAs) were investigated to find an efficient way to destroy TICs and CWAs. ¹¹B NMR analysis proved that B(OH)₃ reacted rapidly with basic H₂O₂ to produce peroxoborates ([B(OH)_(4-x)(OOH)_x]^-), and the proportional contents were closely related to the pH and temperature. ¹O₂ and ·O₂^- were generated, and their production increased exponentially with pH. TICs thioanisole and paraoxon were used as simulants of CWAs to investigate the decontamination performance and nucleophilic/oxidizing reactivity of the B(OH)₃-activated H₂O₂. Batch experiments proved that peroxoborates acted as the oxidants for the primary oxidation of the sulfide at a pH range of 8-12 and that ·O₂^- was responsible for the further oxidation of sulfoxide. Paraoxon degraded through OOH^--mediated S_N2 displacement with high stereo-selectivity, and the degradation rate increased exponentially with pH. Mustard gas, soman, and VX degraded effectively into nontoxic products in the B(OH)₃-activated H₂O₂ solution. A pH of 9-11 was recommended as the suitable acidity for developing the B(OH)₃-activated H₂O₂ solution to be a candidate for nucleophilic/oxidizing decontaminant, with advantages in rapid activation and low loss rate of reactive oxygen species.

Electro- and Solar-Driven Fuel Synthesis with First Row Transition Metal Complexes

The synthesis of renewable fuels from abundant water or the greenhouse gas CO2 is a major step toward creating sustainable and scalable energy storage technologies. In the last few decades, much attention has focused on the development of nonprecious metal-based catalysts and, in more recent years, their integration in solid-state support materials and devices that operate in water. This review surveys the literature on 3d metal-based molecular catalysts and focuses on their immobilization on heterogeneous solid-state supports for electro-, photo-, and photoelectrocatalytic synthesis of fuels in aqueous media. The first sections highlight benchmark homogeneous systems using proton and CO2 reducing 3d transition metal catalysts as well as commonly employed methods for catalyst immobilization, including a discussion of supporting materials and anchoring groups. The subsequent sections elaborate on productive associations between molecular catalysts and a wide range of substrates based on carbon, quantum dots, metal oxide surfaces, and semiconductors. The molecule-material hybrid systems are organized as "dark" cathodes, colloidal photocatalysts, and photocathodes, and their figures of merit are discussed alongside system stability and catalyst integrity. The final section extends the scope of this review to prospects and challenges in targeting catalysis beyond "classical" H2 evolution and CO2 reduction to C1 products, by summarizing cases for higher-value products from N2 reduction, C x>1 products from CO2 utilization, and other reductive organic transformations.

The future of quantum biology

Biological systems are dynamical, constantly exchanging energy and matter with the environment in order to maintain the non-equilibrium state synonymous with living. Developments in observational techniques have allowed us to study biological dynamics on increasingly small scales. Such studies have revealed evidence of quantum mechanical effects, which cannot be accounted for by classical physics, in a range of biological processes. Quantum biology is the study of such processes, and here we provide an outline of the current state of the field, as well as insights into future directions.

pH-Driven Mechanistic Switching from Electron Transfer to Energy Transfer between [Ru(bpy)3]2+ and Ferrocene Derivatives

The metal-to-ligand charge transfer excited states of [Ru(bpy)3]2+ (bpy = 2,2'-bipyridine) may be deactivated via energy transfer or electron transfer with ferrocene derivatives in aqueous conditions. Stern-Volmer quenching analysis revealed that the rate constant for [Ru(bpy)3]2+ excited-state quenching depends on solution pH when a ferrocenyl-amidinium derivative (Fc-am) containing a proton-responsive functionality tethered to the ferrocene center was present. By contrast, the rate constant with which the [Ru(bpy)3]2+ excited state is quenched by an analogous ferrocene derivative (ferrocenyl-trimethylammonium, Fc-mam) that lacks a protonic group does not depend on pH. These results show that the presence (or absence) of a readily transferrable proton modulates quenching rate constants in bimolecular events involving [Ru(bpy)3]2+ and ferrocene. More surprisingly, transient absorption spectroscopy reveals that the mechanism by which the [Ru(bpy)3]2+ excited state is quenched by Fc-am appears to be modulated by solution proton availability, switching from energy transfer at low pH when Fc-am is protonated, to electron transfer at high pH when Fc-am is deprotonated. The mechanistic switching that is observed for this system cannot be aptly explained using a simple driving force dependence argument, suggesting that more subtle factors dictate the pathway by which the [Ru(bpy)3]2+ excited state is deactivated by ferrocene in aqueous solutions.

Surface enhanced resonance Raman spectroscopy of iron Hangman complexes on electrodes during electrocatalytic oxygen reduction: advantages and problems of common drycast methods

Drycast methods have been used frequently in recent decades to adsorb a range of synthetic catalysts on electrodes. The uncoordinated multilayers that are formed via this immobilization method can however have a strong impact on the electrocatalytic reaction pathway as slow electron transfer and intermolecular interactions can alter the chemistry of the catalysts on the surface. To gain insight into the structure of Fe porphyrin Hangman catalysts during electrocatalytic oxygen reduction a combination of electrochemistry and surface enhanced resonance Raman spectroscopy (SERRS) was applied. The Hangman complexes were attached to the electrodes via different methods and the influence of the immobilisation technique on oxygen chemistry was studied. In multilayer systems, new intermediates could be identified via potential dependent SERRS that were not present in solution or in monolayer systems under catalytic conditions. A comparison of Raman spectra obtained either via Soret or Q-band excitation showed that the porphyrin symmetry is strongly distorted under reducing conditions, which was interpreted by the transient formation of dimer complexes during catalysis.

Synchronized Collective Proton-Assisted Electron Transfer in Solid State by Hydrogen-Bonding Ru(II)/Ru(III) Mixed-Valence Molecular Crystals

A proton-coupled electron transfer (PCET) reaction was widely studied with isolated organic molecules and metal complexes in solution in view of the biological catalytic reaction, while studying this reaction in the crystalline or solid-state phase, which has a novel example, would give insight into the rather internal environment of proteins without solvation and a creation of new molecular materials. We tried to crystallize a hydrogen-bonded (H-bonded) coordination polymer with one-dimensional nanoporous channels, formed from redox-active Ru^III complexes, [Ru^III(Hbim)₃] (Hbim^- = 2,2'-biimidazolate monoanion). As a result, a synchronized collective PCET phenomenon was observed for the molecular nanoporous crystal by novel solid-state cyclic voltammetry (CV), which could be measured by only setting some crystals on the electrode surface. The nanoporous crystals, {[Ru^III(Hbim)₃]}_n (1), are simultaneously induced to a synchronized collective Ru^IIRu^III mixed-valence state, {Ru^IIRu^III}_n, with alternating arrays of Ru^II and Ru^III complexes by PCET in a way of the reductive state of {Ru^IIRu^II}_n. Further, a new crystal with {Ru^IIRu^III}_n, {[Ru^II(H₂bim)(Hbim)₂][Ru^III(bim) (Hbim)₂][K(MeOBz)₆]}_n (2), was also prepared, and the solid-state CV revealed the same electrochemical behavior of {Ru^IIRu^III}_n with 1. The single crystal with {Ru^IIRu^III}_n of 2 was unusually a semiconductor with 5.12 × 10^-6 S/cm conductivity at 298 K by an impedance method (8.01 × 10^-6 S/cm by a direct-current method at 277 K). Thus, an unprecedented electron-hopping conductor driven by a low-barrier proton transfer through a PCET mechanism (E_a = 0.30 eV) was realized in the H-bonding molecular crystal with {Ru^IIRu^III}_n. Such studies on a PCET reaction in the crystalline state is not only worthwhile as a model of essential biological reactions without solvation, but also proposed to a new design of molecular materials to occur an electron transfer by using an intermolecular H-bond.

Mechanism of the Primary Charge Transfer Reaction in the Cytochrome bc1 Complex

The bc₁ complex is a critical enzyme for the ATP production in photosynthesis and cellular respiration. Its biochemical function relies on the so-called Q-cycle, which is well established and operates via quinol substrates that bind inside the protein complex. Despite decades of research, the quinol-protein interaction, which initiates the Q-cycle, has not yet been completely described. Furthermore, the initial charge transfer reactions of the Q-cycle lack a physical description. The present investigation utilizes classical molecular dynamics simulations in tandem with quantum density functional theory calculations, to provide a complete and consistent quantitative description of the primary events that occur within the bc₁ complex upon quinol binding. In particular, the electron and proton transfer reactions that trigger the Q-cycle in the bc₁ complex from Rhodobacter capsulatus are studied. The coupled nature of these charge transfer reactions was revealed by obtaining the transition energy path connecting configurations of the Q_o-site prior and after the transfers. The analysis of orbitals and partial charge distribution of the different states of the Q_o-site has further supported the conclusion. Finally, key structural elements of the bc₁ complex that trigger the charge transfer reactions were established, manifesting the importance of the environment in the process, which is furthermore evidenced by free energy calculations.

Design of Heteronuclear Metalloenzymes

Heteronuclear metalloenzymes catalyze some of the most fundamentally interesting and practically useful reactions in nature. However, the presence of two or more metal ions in close proximity in these enzymes makes them more difficult to prepare and study than homonuclear metalloenzymes. To meet these challenges, heteronuclear metal centers have been designed into small and stable proteins with rigid scaffolds to understand how these heteronuclear centers are constructed and the mechanism of their function. This chapter describes methods for designing heterobinuclear metal centers in a protein scaffold by giving specific examples of a few heme-nonheme bimetallic centers engineered in myoglobin and cytochrome c peroxidase. We provide step-by-step procedures on how to choose the protein scaffold, design a heterobinuclear metal center in the protein scaffold computationally, incorporate metal ions into the protein, and characterize the resulting metalloproteins, both structurally and functionally. Finally, we discuss how an initial design can be further improved by rationally tuning its secondary coordination sphere, electron/proton transfer rates, and the substrate affinity.

Proton transfer dynamics control the mechanism of O2 reduction by a non-precious metal electrocatalyst

Many chemical and biological processes involve the transfer of both protons and electrons. The complex mechanistic details of these proton-coupled electron transfer (PCET) reactions require independent control of both electron and proton transfer. In this report, we make use of lipid-modified electrodes to modulate proton transport to a Cu-based catalyst that facilitates the O2 reduction reaction (ORR), a PCET process important in fuel cells and O2 reduction enzymes. By quantitatively controlling the kinetics of proton transport to the catalyst, we demonstrate that undesired side products such as H2O2 and O2(-) arise from a mismatch between proton and electron transfer rates. Whereas fast proton kinetics induce H2O2 formation and sluggish proton flux produces O2(-), proton transfer rates commensurate with O-O bond breaking rates ensure that only the desired H2O product forms. This fundamental insight aids in the development of a comprehensive framework for understanding the ORR and PCET processes in general.

Bio-functionalized hybrid nanocomposite membranes for direct methanol fuel cells

Featured methanol-blocking characteristics of nanocomposite membrane.

Titanium-catalyzed multicomponent couplings: efficient one-pot syntheses of nitrogen heterocycles

Nitrogen-based heterocycles are important frameworks for pharmaceuticals, natural products, organic dyes for solar cells, and many other applications. Catalysis for the formation of heterocyclic scaffolds, like many C-C and C-N bond-forming reactions, has focused on the use of rare, late transition metals like palladium and gold. Our group is interested in the use of Earth-abundant catalysts based on titanium to generate heterocycles using multicomponent coupling strategies, often in one-pot reactions. To be of maximal utility, the catalysts need to be easily prepared from inexpensive reagents, and that has been one guiding principle in the research. For this purpose, a series of easily prepared pyrrole-based ligands has been developed. Titanium imido complexes are known to catalyze the hydroamination of alkynes, and this reaction has been used to advantage in the production of α,β-unsaturated imines from 1,3-enynes and pyrroles from 1,4-diynes. Likewise, catalyst design can be used to find complexes applicable to hydrohydrazination, coupling of a hydrazine and alkyne, which is a method for the production of hydrazones. Many of the hydrazones synthesized are converted to indoles through Fischer cyclization by addition of a Lewis acid. However, more complex products are available in a single catalytic cycle through coupling of isonitriles, primary amines, and alkynes to give tautomers of 1,3-diimines, iminoamination (IA). The products of IA are useful intermediates for the one-pot synthesis of pyrazoles, pyrimidines, isoxazoles, quinolines, and 2-amino-3-cyanopyridines. The regioselectivity of the reactions is elucidated in some detail for some of these heterocycles. The 2-amino-3-cyanopyridines are synthesized through isolable intermediates, 1,2-dihydro-2-iminopyridines, which undergo Dimroth rearrangement driven by aromatization of the pyridine ring; the proposed mechanism of the reaction is discussed. The IA-based heterocyclic syntheses can be accomplished start to finish (catalyst generation to heterocyclic synthesis) in a single vessel. The catalyst can be formed in situ from commercially available Ti(NMe2)4 and the protonated form of the ligand. Then, the primary amine, alkyne, and isonitrile are added to the flask, and the IA product is synthesized. The volatiles are removed (if necessary), and the next reagent is added. A brief video showing the process for the simple heterocycle 4-phenylpyrazole from phenylacetylene, cyclohexylamine, tert-butylisonitrile, and hydrazine hydrate is included. Further development in this field will unlock new, efficient reactions for the production of carbon-carbon and carbon-nitrogen bonds. As an example of such a process recently discovered, a catalyst for the regioselective production of pyrazoles in a single step from terminal alkynes, hydrazines, and cyclohexylisonitrile is discussed. Using titanium catalysis, many heterocyclic cores can be accessed easily and efficiently. Further, the early metal chemistry described is often orthogonal to late metal-based reactions, which use substrates like aryl halides, silyl groups, boryl groups, and so forth. As a result, earth-abundant and nontoxic titanium can fulfill important roles in the synthesis of useful classes of compounds like heterocycles.