Quantum Chemical Studies of Proton-Coupled Electron Transfer in Metalloenzymes

Density functional theory (DFT) studies in HDAC-based chemotherapeutics: Current findings, case studies and future perspectives

Density Functional Theory (DFT) is a quantum chemical computational method used to predict and analyze the electronic properties of atoms, molecules, and solids based on the density of electrons rather than wavefunctions. It provides insights into the structure, bonding, and behavior of different molecules, including those involved in the development of chemotherapeutic agents, such as histone deacetylase inhibitors (HDACis). HDACs are a wide group of metalloenzymes that facilitate the removal of acetyl groups from acetyl-lysine residues situated in the N-terminal tail of histones. Abnormal HDAC recruitment has been linked to several human diseases, especially cancer. Therefore, it has been recognized as a prospective target for accelerating the development of anticancer therapies. Researchers have studied HDACs and its inhibitors extensively using a combination of experimental methods and diverse in-silico approaches such as machine learning and quantitative structure-activity relationship (QSAR) methods, molecular docking, molecular dynamics, pharmacophore mapping, and more. In this context, DFT studies can make significant contribution by shedding light on the molecular properties, interactions, reaction pathways, transition states, reactivity and mechanisms involved in the development of HDACis. This review attempted to elucidate the scope in which DFT methodologies may be used to enhance our comprehension of the molecular aspects of HDAC inhibitors, aiding in the rational design and optimization of these compounds for therapeutic applications in cancer and other ailments. The insights gained can guide experimental efforts toward developing more potent and selective HDAC inhibitors.

Catalytic divergencies in the mechanism of L-arginine hydroxylating nonheme iron enzymes

Many enzymes in nature utilize a free arginine (L-Arg) amino acid to initiate the biosynthesis of natural products. Examples include nitric oxide synthases, which generate NO from L-Arg for blood pressure control, and various arginine hydroxylases involved in antibiotic biosynthesis. Among the groups of arginine hydroxylases, several enzymes utilize a nonheme iron(II) active site and let L-Arg react with dioxygen and α-ketoglutarate to perform either C3-hydroxylation, C4-hydroxylation, C5-hydroxylation, or C4-C5-desaturation. How these seemingly similar enzymes can react with high specificity and selectivity to form different products remains unknown. Over the past few years, our groups have investigated the mechanisms of L-Arg-activating nonheme iron dioxygenases, including the viomycin biosynthesis enzyme VioC, the naphthyridinomycin biosynthesis enzyme NapI, and the streptothricin biosynthesis enzyme OrfP, using computational approaches and applied molecular dynamics, quantum mechanics on cluster models, and quantum mechanics/molecular mechanics (QM/MM) approaches. These studies not only highlight the differences in substrate and oxidant binding and positioning but also emphasize on electronic and electrostatic differences in the substrate-binding pockets of the enzymes. In particular, due to charge differences in the active site structures, there are changes in the local electric field and electric dipole moment orientations that either strengthen or weaken specific substrate C-H bonds. The local field effects, therefore, influence and guide reaction selectivity and specificity and give the enzymes their unique reactivity patterns. Computational work using either QM/MM or density functional theory (DFT) on cluster models can provide valuable insights into catalytic reaction mechanisms and produce accurate and reliable data that can be used to engineer proteins and synthetic catalysts to perform novel reaction pathways.

Reconciling Imbalanced and Nonadiabatic Reactivity in Transition Metal-Oxo-Mediated Concerted Proton Electron Transfer (CPET)

Recently, there have been several experimental demonstrations of how the rates of concerted proton electron transfer (CPET) are affected by stepwise thermodynamic parameters of only proton (ΔG°PT) or electron (ΔG°ET) transfer. Semiclassical structure-activity relationships have been invoked to rationalize these linear free energy relationships, but it is not clear how they would manifest in a nonadiabatic reaction. Using density functional theory calculations, we demonstrate how a decrease in ΔG°PT can lead to transition state imbalance in a nonadiabatic framework. We then use these calculations to anchor a theoretical model that reproduces experimental trends with ΔG°PT and ΔG°ET. Our results reconcile predictions from semiclassical transition state theory with models that treat proton transfer quantum mechanically in CPET reactivity, make new predictions about the importance of basicity for uphill CPET reactions, and suggest similar treatments may be possible for other nonadiabatic reactions.

Methane Activation by [AlFeO3 ]+ : the Hidden Spin Selectivity

The performance of heteronuclear cluster [AlFeO3 ]+ in activating methane has been explored by a combination of high-level quantum chemical calculations with gas-phase experiments. At room temperature, [AlFeO3 ]+ is a mixture of 7 [AlFeO3 ]+ and 5 [AlFeO3 ]+ , in which two states lead to different reactivity and chemoselectivity for methane activation. While hydrogen extracted from methane is the only product channel for the 7 [AlFeO3 ]+ /CH4 couple, 5 [AlFeO3 ]+ is able to convert this substrate to formaldehyde. In addition, the introduction of an external electric field may regulate the reactivity and product selectivity. The interesting doping effect of Fe and the associated electronic origins are discussed, which may guide one on the design of Fe-involved catalyst for methane conversion.

Size Effects in Gas-phase C-H Activation

The gas-phase clusters reaction permits addressing fundamental aspects of the challenges related to C-H activation. The size effect plays a key role in the activation processes as it may substantially affect both the reactivity and selectivity. In this paper, we reviewed the size effect related to the hydrocarbon oxidation by early transition metal oxides and main group metal oxides, methane activation mediated by late transition metals. Based on mass-spectrometry experiments in conjunction with quantum chemical calculations, mechanistic discussions were reviewed to present how and why the size greatly regulates the reactivity and product distribution.

Reaction mechanism of the PuDddK dimethylsulfoniopropionate lyase and cofactor effects of various transition metal ions

The microbial cleavage of dimethylsulfoniopropionate (DMSP) produces volatile dimethyl sulfide (DMS) via the lyase pathway, playing a crucial role in the global sulfur cycle. Herein, the DMSP decomposition catalyzed by PuDddK (a DMSP lyase) devised with various transition metal ion cofactors are investigated using density functional calculations. The PuDddK reaction has been demonstrated to employ a concerted β-elimination mechanism, where the substrate α-proton abstraction by the deprotonated Tyr64 occurs simultaneously with the C_β-S bond cleavage and C_α = C_β double bond formation. The PuDddK enzymes with diverse divalent metal ions (Ni²⁺, Mn²⁺, Fe²⁺, Co²⁺, Zn²⁺, and Cu²⁺) incorporated prefer DMSP as a monodentate ligand. The cases of Ni²⁺, Mn²⁺, Fe²⁺, Co²⁺, and Zn²⁺ with the same 3His-1Glu ligands have close reaction energy barriers, indicating that the lyase activity may be hardly affected by the divalent transition metal type with the same ligand type and number. The coordination loss of one histidine in Cu²⁺, forming a 2His-1Glu architecture, leads to a lower activity, revealing that the 3His-1Glu ligand set used by DddK appears to be a scaffold capable of more efficiently catalyzing the DMSP decomposition. Further analysis reveals that the inactivation of Fe³⁺-dependent PuDddK is derived from an electron transfer from the Tyr64 phenolate to Fe³⁺, with the implication that the PuDddK activity may be primarily affected by the redox effects induced by a strongly oxidizing transition metal ion (like Fe³⁺).

Modulation of proton-coupled electron transfer reactions in lysine-containing alpha-helixes: alpha-helixes promoting long-range electron transfer

The proton-coupled electron transfer (PCET) reaction plays an important role in promoting many biological and chemical reactions. Usually, the rate of the PCET reaction increases with an increase in the electron transfer distance because long-range electron transfer requires more free energy barriers. Our density functional theory calculations here reveal that the mechanism of PCET occurring in lysine-containing alpha(α)-helixes changes with an increasing number of residues in the α-helical structure and the different conformations because of the modulation of the excess electron distribution by the α-helical structures. The rate constants of the corresponding PCET reactions are independent of or substantially shallower dependent on the electron transfer distances along α-helixes. This counter-intuitive behavior can be attributed to the fact that the formation of larger macro-cylindrical dipole moments in longer helixes can promote electron transfer along the α-helix with a low energy barrier. These findings may be useful to gain insights into long-range electron transfer in proteins and design α-helix-based electronics via the regulation of short-range proton transfer.

Proton-electron-coupled functionalities of conductivity, magnetism, and optical properties in molecular crystals

Proton-electron-coupled reactions, specifically proton-coupled electron transfer (PCET), in biological and chemical processes have been extensively investigated for use in a wide variety of applications, including energy conversion and storage. However, the exploration of the functionalities of the conductivity, magnetism, and dielectrics by proton-electron coupling in molecular materials is challenging. Dynamic and static proton-electron-coupled functionalities are to be expected. This feature article highlights the recent progress in the development of functionalities of dynamic proton-electron coupling in molecular materials. Herein, single-unit conductivity by self-doping, quantum spin liquid state coupled with quantum fluctuation of protons, switching of conductivity and magnetism triggered by the disorder-order transition of deuterons, and their external responses under pressure and in the presence of an electric field are introduced. In addition, as for the functionalities of proton-d/π-electron coupling in metal dithiolene complexes, magnetic switching with multiple PCET and vapochromism induced by electron transfer through hydrogen-bond (H-bond) formation is introduced experimentally and theoretically. We also outlined the basic and applied issues and potential challenges for development of proton-electron-coupled molecular materials, functionalities, and devices.

Free Energies of Proton-Coupled Electron Transfer Reagents and Their Applications

We present an update and revision to our 2010 review on the topic of proton-coupled electron transfer (PCET) reagent thermochemistry. Over the past decade, the data and thermochemical formalisms presented in that review have been of value to multiple fields. Concurrently, there have been advances in the thermochemical cycles and experimental methods used to measure these values. This Review (i) summarizes those advancements, (ii) corrects systematic errors in our prior review that shifted many of the absolute values in the tabulated data, (iii) provides updated tables of thermochemical values, and (iv) discusses new conclusions and opportunities from the assembled data and associated techniques. We advocate for updated thermochemical cycles that provide greater clarity and reduce experimental barriers to the calculation and measurement of Gibbs free energies for the conversion of X to XH_n in PCET reactions. In particular, we demonstrate the utility and generality of reporting potentials of hydrogenation, E°(V vs H₂), in almost any solvent and how these values are connected to more widely reported bond dissociation free energies (BDFEs). The tabulated data demonstrate that E°(V vs H₂) and BDFEs are generally insensitive to the nature of the solvent and, in some cases, even to the phase (gas versus solution). This Review also presents introductions to several emerging fields in PCET thermochemistry to give readers windows into the diversity of research being performed. Some of the next frontiers in this rapidly growing field are coordination-induced bond weakening, PCET in novel solvent environments, and reactions at material interfaces.

Methane Activation by the Heteronuclear Cluster [TiAlO4]+: Direct Hydrogen Abstraction by a Nonradical Oxygen

The gas-phase reactions of [TiAlO₄]⁺ with methane have been explored by using FT-ICR mass spectrometry complemented by quantum chemical calculations. Interestingly, the [TiAlO₄]⁺ ions can activate two methane molecules continuously. Moreover, in contrast to the previous reports on gas-phase methane activation by metal oxide clusters, in which hydrogen-atom transfer and/or proton-coupled electron transfer prevail, a hydride transfer process dominates the [TiAlO₄]⁺/CH₄ system. The associated electronic origins have been discussed, and such a terminal metal-oxo active center as addressed in the [TiAlO₄]⁺ cluster has proven to be promising in the construction of efficient catalysts concerning methane conversion.

On the origin of reactivity variation upon sequential ligation: the [Re(Cl)x]+/CH4 (x = 1-3) couples

The potential of [ReCl_x]⁺ (x = 1-3) in activating methane has been explored by using a combination of gas-phase experiments and high-level quantum calculations. When the number of Cl ligands increases, the reactivity towards methane activation varies accordingly. While [ReCl_x]⁺ (x = 1-2) are able to dehydrogenate methane by a three-state reactivity scenario, [ReCl₃]⁺ shows inertness towards methane at ambient conditions. Furthermore, the product ion [ClRe(H)CH]⁺ of the [ReCl]⁺/CH₄ couple could continue to activate methane and liberate molecular dihydrogen but another product ion [Cl₂ReCH₂]⁺ is unreactive with methane. Obviously, the nature and the number of ligands make a difference to the reactivity towards methane activation. The associated reaction mechanism and the electron origins for the rather different reactivities are discussed in detail. Finally and more importantly, instructive information concerning the rational design of Re-catalysts for methane conversion is obtained.

Direct Aerobic Generation of a Ferric Hydroperoxo Intermediate Via a Preorganized Secondary Coordination Sphere

Enzymes exert control over the reactivity of metal centers with precise tuning of the secondary coordination sphere of active sites. One particularly elegant illustration of this principle is in the controlled delivery of proton and electron equivalents in order to activate abundant but kinetically inert oxidants such as O2 for oxidative chemistry. Chemists have drawn inspiration from biology in designing molecular systems where the secondary coordination sphere can shuttle protons or electrons to substrates. However, a biomimetic activation of O2 requires the transfer of both protons and electrons, and molecular systems where ancillary ligands are designed to provide both of these equivalents are comparatively rare. Here, we report the use of a dihydrazonopyrrole (DHP) ligand complexed to Fe to perform exactly such a biomimetic activation of O2. In the presence of O2, this complex directly generates a high spin Fe(III)-hydroperoxo intermediate which features a DHP• ligand radical via ligand-based transfer of an H atom. This system displays oxidative reactivity and ultimately releases hydrogen peroxide, providing insight on how secondary coordination sphere interactions influence the evolution of oxidizing intermediates in Fe-mediated aerobic oxidations.

On the origins of the mechanistic variants in the thermal reactions of Sx+ (x = 1-3) with benzene

The S-π interaction between sulfur atom(s) and aromatic ring prevails in chemical and biochemical processes. The thermal gas-phase reactions of the S_n⁺ (n = 1-3) ions with benzene have been explored by using Quadrupole-Ion Trap (Q-IT) mass spectrometry complemented by quantum chemical calculations. Charge transfer was found to be the only reaction channel for S₂⁺/C₆H₆, while both charge transfer and bond activation are available for the S⁺/C₆H₆ and S₃⁺/C₆H₆ couples. Upon interrogating the associated electronic origins, multiple factors were found to matter for these processes. In contrast to the σ-type two-center three-electron (2c-3e) S-π hemibond as reported previously, unusual S-π hemibonds were addressed for the S_n⁺/C₆H₆ couples, i.e. the 2c-3e π(S061Eπ) and the three-center three-electron (3c-3e) σ(S₂061Eπ) hemibonds. Such S-π interaction was found to be responsible for the charge transfer processes in S⁺/C₆H₆ and S₂⁺/C₆H₆, but uninvolved in any transformation for S₃⁺/C₆H₆.

Activation of O2 and NO in heme-copper oxidases - mechanistic insights from computational modelling

Heme-copper oxidases are transmembrane enzymes involved in aerobic and anaerobic respiration. The largest subgroup contains the cytochrome c oxidases (CcO), which reduce molecular oxygen to water. A significant part of the free energy released in this exergonic process is conserved as an electrochemical gradient across the membrane, via two processes, electrogenic chemistry and proton pumping. A deviant subgroup is the cytochrome c dependent NO reductases (cNOR), which reduce nitric oxide to nitrous oxide and water. This is also an exergonic reaction, but in this case none of the released free energy is conserved. Computational studies applying hybrid density functional theory to cluster models of the bimetallic active sites in the heme-copper oxidases are reviewed. To obtain a reliable description of the reaction mechanisms, energy profiles of the entire catalytic cycles, including the reduction steps have to be constructed. This requires a careful combination of computational results with certain experimental data. Computational studies have elucidated mechanistic details of the chemical parts of the reactions, involving cleavage and formation of covalent bonds, which have not been obtainable from pure experimental investigations. Important insights regarding the mechanisms of energy conservation have also been gained. The computational studies show that the reduction potentials of the active site cofactors in the CcOs are large enough to afford electrogenic chemistry and proton pumping, i.e. efficient energy conservation. These results solve a conflict between different types of experimental data. A mechanism for the proton pumping, involving a specific and crucial role for the active site tyrosine, conserved in all CcOs, is suggested. For the cNORs, the calculations show that the low reduction potentials of the active site cofactors are optimized for fast elimination of the toxic NO molecules. At the same time, the low reduction potentials lead to endergonic reduction steps with high barriers. To prevent even higher barriers, which would lead to a too slow reaction, when the electrochemical gradient across the membrane is present, the chemistry must occur in a non-electrogenic manner. This explains why there is no energy conservation in cNOR.

Remote Water-Mediated Proton Transfer Triggers Inter-Cu Electron Transfer: Nitrite Reduction Activation in Copper-Containing Nitrite Reductase

The copper-containing nitrite reductase (CuNiR) catalyzes the biological conversion of nitrite to nitric oxide; key long-range electron/proton transfers are involved in the catalysis. However, the details of the electron-/proton-transfer mechanism are still unknown. In particular, the driving force of the electron transfer from the type-1 copper (T1Cu) site to the type-2 copper (T2Cu) site is ambiguous. Here, we explored the two possible proton-transfer channels, the high-pH proton channel and the primary proton channel, by using two-layered ONIOM calculations. Our calculation results reveal that the driving force for electron transfer from T1Cu to T2Cu comes from a remote water-mediated triple-proton-coupled electron-transfer mechanism. In the high-pH proton channel, the water-mediated triple-proton transfer occurs from Glu113 to an intermediate water molecule, whereas in the primary channel, the transfer is from Lys128 to His260. Subsequently, the two channels employ another two or three distinct proton-transfer steps to deliver the proton to the nitrite substrate at the T2Cu site. These findings explain the detailed proton-/electron-transfer mechanisms of copper-containing nitrite reductase and could extend our understanding of the diverse proton-coupled electron-transfer mechanisms in complicated proteins.

Consecutive methane activation mediated by single metal boride cluster anions NbB4. Phys Chem Chem Phys 2021;23:12592-12599. [PMID: 34047332 DOI: 10.1039/d1cp01418h]

Cleavage of all C-H bonds in two methane molecules by gas-phase cluster ions at room temperature is a challenging task. Herein, mass spectrometry and quantum chemical calculations have been used to identify one single metal boride cluster anions NbB4- that can activate eight C-H bonds in two methane molecules and release one H2 molecule each time under thermal collision conditions. In these consecutive reactions, the loaded Nb atoms and the support B4 units play different roles but act synergistically to activate CH4, which is responsible for the interesting reactivity of NbB4-. Moreover, there are some mechanistic differences in these two reactions, including the mechanisms for the first C-H bond activation steps, dihydrogen desorption sites, and major electron donors. This study shows that non-noble metal boride species are reactive enough to facilitate thermal C-H bond cleavages, and boron-based materials may be one kind of potential support material facilitating surface hydrogen transport.

On the limit of proton-coupled electronic doping in a Ti(iv)-containing MOF

Ti^IV-containing metal–organic frameworks are known to accumulate electrons in their conduction bands, accompanied by protons, when irradiated in the presence of alcohols. The archetypal system, MIL-125, was recently shown to reach a limit of 2e⁻ per Ti₈ octomeric node. However, the origin of this limit and the broader applicability of this unique chemistry relies not only on the presence of Ti^IV, but also access to inorganic inner-sphere Lewis basic anions in the MOF nodes. Here, we study the loading of protons and electrons in MIL-125, and assess the thermodynamic limit of doping these materials. We find that the limit is determined by the reduction potential of protons: in high charging regimes the MOF exceeds the H⁺/H₂ potential. Generally, we offer the design principle that inorganic anions in MOF nodes can host adatomic protons, which may stabilize meta-stable low valent transition metals. This approach highlights the unique chemistry afforded by MOFs built from inorganic clusters, and provides one avenue to developing novel catalytic scaffolds for hydrogen evolution and transfer hydrogenation.

Photo-promoted doping of MIL-125 is limited by the potential of MOF-bound protons exceeding the hydrogen evolution reaction.

Theoretical study of aromatic hydroxylation of the [Cu2(H-XYL)O2]2+ complex mediated by a side-on peroxo dicopper core and Cu-ligand effects

In this work, the aromatic hydroxylation mechanism of the [Cu₂(H-XYL)O₂]²⁺ complex mediated by a peroxo dicopper core and Cu-ligand effects are investigated by using hybrid density functional theory (DFT) and the broken symmetry B3LYP method. Based on the calculated free-energy profiles, we proposed two available mechanisms. The first reaction steps of both mechanisms involve concerted O-O bond cleavage and C-O bond formation and the second step involves the Wagner-Meerwein rearrangement of the substrate by a [1,2] H shift (H_A shift from C_A to C_C) or (H_A shift from C_A to O_A) across the phenyl ring to form stable dienone intermediates, and this is followed by the protonation of bridging oxygen atoms to produce the final hydroxylated dicopper(ii) product. The H_A shift from C_A to C_C mechanism is the energetically most favorable, in which the first reaction step is the rate-limiting reaction, with a calculated free-energy barrier of 19.0 kcal mol^-1 and a deuterium kinetic isotope effect of 1.0, in agreement with experimental observations. The calculation also shows that the reaction started from the P-type species of [Cu₂(H-XYL)O₂]²⁺ which is capable of mediating the direct hydroxylation of aromatic substrates without the intermediacy of an O-type species. Finally, we designed some new complexes with different Cu-ligands and found the complex that computationally possesses a higher activity in mediating the hydroxylation of the ligand based aromatic substrate; here, Cu loses a pyridyl ligand donor by dissociation, compared to the [Cu₂(H-XYL)O₂]²⁺ complex.

Catalytic Hydrolysis Mechanism of Cocaine by Human Carboxylesterase 1: An Orthoester Intermediate Slows Down the Reaction

Human carboxylesterase 1 (hCES1) is a major carboxylesterase in the human body and plays important roles in the metabolism of a wide variety of substances, including lipids and drugs, and therefore is attracting more and more attention from areas including lipid metabolism, pharmacokinetics, drug–drug interactions, and prodrug activation. In this work, we studied the catalytic hydrolysis mechanism of hCES1 by the quantum mechanics computation method, using cocaine as a model substrate. Our results support the four-step theory of the esterase catalytic hydrolysis mechanism, in which both the acylation stage and the deacylation stage include two transition states and a tetrahedral intermediate. The roles and cooperation of the catalytic triad, S221, H468, and E354, were also analyzed in this study. Moreover, orthoester intermediates were found in hCES1-catalyzed cocaine hydrolysis reaction, which significantly elevate the free energy barrier and slow down the reaction. Based on this finding, we propose that hCES1 substrates with β-aminocarboxylester structure might form orthoester intermediates in hCES1-catalyzed hydrolysis, and therefore prolong their in vivo half-life. Thus, this study helps to clarify the catalytic mechanism of hCES1 and elucidates important details of its catalytic process, and furthermore, provides important insights into the metabolism of hCES1 substrates and drug designing.

Mechanism and Inhibitor Exploration with Binuclear Mg Ketol-Acid Reductoisomerase: Targeting the Biosynthetic Pathway of Branched-Chain Amino Acids

Binuclear Mg ketol-acid reductoisomerase (KARI), which converts (S)-2-acetolactate into (R)-2,3-dihydroxyisovalerate, is responsible for the second step of the biosynthesis of branched-chain amino acids in plants and microorganisms and thus serves as a key inhibition target potentially without effects on mammals. Here, through the use of density functional calculations and a chemical model, the KARI-catalyzed reaction has been demonstrated to include the initial deprotonation of the substrate C2 hydroxy group, bridged by the two Mg ions, alkyl migration from the C2-alkoxide carbon atom to the C3-carbonyl carbon atom, and hydride transfer from a nicotinamide adenine dinucleotide phosphate [NAD(P)H] cofactor to C2. A dead-end mechanism with a hydride transferred to the C3 carbonyl group has been ruled out. The nucleophilicity (migratory aptitude) of the migrating carbon atom and the provision of additional negative charge to the di-Mg coordination sphere have significant effects on the steps of alkyl migration and hydride transfer, respectively. Other important mechanistic characteristics are also revealed. Inspired by the mechanism, an inhibitor (2-carboxylate-lactic acid) was designed and predicted by barrier analysis to be effective in inactivating KARI, hence probably enriching the antifungal and antibacterial library. Two types of slow substrate analogues (2-trihalomethyl acetolactic acids and 2-glutaryl lactic acid) were also found.

Long-range proton-coupled electron transfer in biological energy conversion: towards mechanistic understanding of respiratory complex I

Biological energy conversion is driven by efficient enzymes that capture, store and transfer protons and electrons across large distances. Recent advances in structural biology have provided atomic-scale blueprints of these types of remarkable molecular machinery, which together with biochemical, biophysical and computational experiments allow us to derive detailed energy transduction mechanisms for the first time. Here, I present one of the most intricate and least understood types of biological energy conversion machinery, the respiratory complex I, and how its redox-driven proton-pump catalyses charge transfer across approximately 300 Å distances. After discussing the functional elements of complex I, a putative mechanistic model for its action-at-a-distance effect is presented, and functional parallels are drawn to other redox- and light-driven ion pumps.

Theoretical Studies of Nickel-Dependent Enzymes

The advancements of quantum chemical methods and computer power allow detailed mechanistic investigations of metalloenzymes. In particular, both quantum chemical cluster and combined QM/MM approaches have been used, which have been proven to successfully complement experimental studies. This review starts with a brief introduction of nickel-dependent enzymes and then summarizes theoretical studies on the reaction mechanisms of these enzymes, including NiFe hydrogenase, methyl-coenzyme M reductase, nickel CO dehydrogenase, acetyl CoA synthase, acireductone dioxygenase, quercetin 2,4-dioxygenase, urease, lactate racemase, and superoxide dismutase.

Palladium(II) Ion Mediated Disulfide/Thiolate Interconversion: Predicting the Disulfide Group State from First Principles

Different reactivity of homologous disulfides toward Pd²⁺ was previously reported: stepwise complexation to Pd²⁺ for l-cystine and cystamine ligands, while for dl-homocystine and 3,3'-dithiodipropionic acid, disulfide's disproportionation toward thiolate and sulfinic acid complexes is observed. The disulfide/thiolate interconversion of four different disulfide ligands in the presence of nonredox metal cation Pd²⁺ in aqueous solution has been computationally investigated. We see this different reactivity in different capacities of considered homologous disulfides to stabilize forming S,S'-binuclear complexes, which are believed to be key intermediates toward interconversion products. We thus devise a theoretical model that rationalizes experimentally observed phenomenon of disulfides different reactivity toward nonredox transition metal cation Pd²⁺.

Thermal Activation of CH4 and H2 as Mediated by the Ruthenium Oxide Cluster Ions [RuOx ]+ (x=1-3): On the Influence of Oxidation States

Thermal gas-phase reactions of the ruthenium-oxide clusters [RuO_x ]⁺ (x=1-3) with methane and dihydrogen have been explored by using FT-ICR mass spectrometry complemented by high-level quantum chemical calculations. For methane activation, as compared to the previously studied [RuO]⁺ /CH₄ couple, the higher oxidized Ru systems give rise to completely different product distributions. [RuO₂ ]⁺ brings about the generations of [Ru,O,C,H₂ ]⁺ /H₂ O, [Ru,O,C]⁺ /H₂ /H₂ O, and [Ru,O,H₂ ]⁺ /CH₂ O, whereas [RuO₃ ]⁺ exhibits a higher selectivity and efficiency in producing formaldehyde and syngas (CO+H₂ ). Regarding the reactions with H₂ , as compared to CH₄ , both [RuO]⁺ and [RuO₂ ]⁺ react similarly inefficiently with oxygen-atom transfer being the main reaction channel; in contrast, [RuO₃ ]⁺ is inert toward dihydrogen. Theoretical analysis reveals that the reduction of the metal center drives the overall oxidation of methane, whereas the back-bonding orbital interactions between the cluster ions and dihydrogen control the H-H bond activation. Furthermore, the reactivity patterns of [RuO_x ]⁺ (x=1-3) with CH₄ and H₂ have been compared with the previously reported results of Group 8 analogues [OsO_x ]⁺ /CH₄ /H₂ (x=1-3) and the [FeO]⁺ /H₂ system. The electronic origins for their distinctly different reaction behaviors have been addressed.

How does Mo-dependent perchlorate reductase work in the decomposition of oxyanions?

The mechanisms of Mo-dependent perchlorate reductase (PcrAB)-catalyzed decomposition of perchlorate, bromate, iodate, and nitrate were revealed by density functional calculations.

Synthetic Fe/Cu Complexes: Toward Understanding Heme-Copper Oxidase Structure and Function

Heme-copper oxidases (HCOs) are terminal enzymes on the mitochondrial or bacterial respiratory electron transport chain, which utilize a unique heterobinuclear active site to catalyze the 4H+/4e- reduction of dioxygen to water. This process involves a proton-coupled electron transfer (PCET) from a tyrosine (phenolic) residue and additional redox events coupled to transmembrane proton pumping and ATP synthesis. Given that HCOs are large, complex, membrane-bound enzymes, bioinspired synthetic model chemistry is a promising approach to better understand heme-Cu-mediated dioxygen reduction, including the details of proton and electron movements. This review encompasses important aspects of heme-O2 and copper-O2 (bio)chemistries as they relate to the design and interpretation of small molecule model systems and provides perspectives from fundamental coordination chemistry, which can be applied to the understanding of HCO activity. We focus on recent advancements from studies of heme-Cu models, evaluating experimental and computational results, which highlight important fundamental structure-function relationships. Finally, we provide an outlook for future potential contributions from synthetic inorganic chemistry and discuss their implications with relevance to biological O2-reduction.

Selective C-O Coupling Hidden in the Thermal Reaction of [Al2 CuO5 ]+ with Methane

The thermal gas-phase reaction of [Al₂ CuO₅ ]⁺ with methane has been explored by using FT-ICR mass spectrometry complemented by high-level quantum chemical calculations. The generation of atomic [Cu]⁺ from the [Al₂ CuO₅ ]⁺ /CH₄ couple corresponds to the only reaction channel. Labeling experiments and computational studies strongly suggest that methane activation is indeed involved in the production of [Cu]⁺ , and generation of CH₂ O prevails. Mechanistic aspects and the associated doping effects are discussed.

Coupled-perturbed DFTB-QM/MM metadynamics: Application to proton-coupled electron transfer

We present a new concept of free energy calculations of chemical reactions by means of extended sampling molecular dynamics simulations. Biasing potentials are applied on partial atomic charges, which may be combined with atomic coordinates either in a single collective variable or in multi-dimensional biasing simulations. The necessary additional gradients are obtained by solving coupled-perturbed equations within the approximative density-functional tight-binding method. The new computational scheme was implemented in a combination of Gromacs and Plumed. As a prospective application, proton-coupled electron transfer in a model molecular system is studied. Two collective variables are introduced naturally, one for the proton transfer and the other for the electron transfer. The results are in qualitative agreement with the extended free simulations performed for reference. Free energy minima as well as the mechanism of the process are identified correctly, while the topology of the transition region and the height of the energy barrier are only reproduced qualitatively. The application also illustrates possible difficulties with the new methodology. These may be inefficient sampling of spatial coordinates when atomic charges are biased exclusively and a decreased stability of the simulations. Still, the new approach represents a viable alternative for free energy calculations of a certain class of chemical reactions, for instance a proton-coupled electron transfer in proteins.

A Theoretical Study of the Benzoylformate Decarboxylase Reaction Mechanism

Density functional theory calculations are used to investigate the detailed reaction mechanism of benzoylformate decarboxylase, a thiamin diphosphate (ThDP)-dependent enzyme that catalyzes the nonoxidative decarboxylation of benzoylformate yielding benzaldehyde and carbon dioxide. A large model of the active site is constructed on the basis of the X-ray structure, and it is used to characterize the involved intermediates and transition states and evaluate their energies. There is generally good agreement between the calculations and available experimental data. The roles of the various active site residues are discussed and the results are compared to mutagenesis experiments. Importantly, the calculations identify off-cycle intermediate species of the ThDP cofactor that can have implications on the kinetics of the reaction.

Investigation of the proton relay system operative in human cystosolic aminopeptidase P

Aminopeptidase P, a metalloprotease, targets Xaa-Proline peptides for cleavage [1-4]. There are two forms of human AMPP, a membrane-bound form (hmAMPP) and a soluble cytosolic form (hcAMPP)[5]. Similar to the angiotensin-I-converting enzyme, AMPP plays an important role in the catabolism of inflammatory and vasoactive peptides, known as kinins. The plasma kinin, bradykinin, was used as the substrate to conduct enzymatic activity analyses and to determine the Michaelis constant (Km) of 174 μM and the catalytic rate constant (kcat) of 10.8 s-1 for hcAMPP. Significant differences were observed in the activities of Y527F and R535A hcAMPP mutants, which displayed a 6-fold and 13.5-fold for decrease in turnover rate, respectively. Guanidine hydrochloride restored the activity of R535A hcAMPP, increasing the kcat/Km 20-fold, yet it had no impact on the activities of the wild-type or Y527F mutant hcAMPPs. Activity restoration by guanidine derivatives followed the order guanidine hydrochloride >> methyl-guanidine > amino-guanidine > N-ethyl-guanidine. Overall, the results indicate the participation of R535 in the hydrogen bond network that forms a proton relay system. The quaternary structure of hcAMPP was determined by using analytical ultracentrifugation (AUC). The results show that alanine replacement of Arg535 destabilizes the hcAMPP dimer and that guanidine hydrochloride restores the native monomer-dimer equilibrium. It is proposed that Arg535 plays an important role in hcAMMP catalysis and in stabilization of the catalytically active dimeric state.

Mechanism and Structure of γ-Resorcylate Decarboxylase

γ-Resorcylate decarboxylase (γ-RSD) has evolved to catalyze the reversible decarboxylation of 2,6-dihydroxybenzoate to resorcinol in a nonoxidative fashion. This enzyme is of significant interest because of its potential for the production of γ-resorcylate and other benzoic acid derivatives under environmentally sustainable conditions. Kinetic constants for the decarboxylation of 2,6-dihydroxybenzoate catalyzed by γ-RSD from Polaromonas sp. JS666 are reported, and the enzyme is shown to be active with 2,3-dihydroxybenzoate, 2,4,6-trihydroxybenzoate, and 2,6-dihydroxy-4-methylbenzoate. The three-dimensional structure of γ-RSD with the inhibitor 2-nitroresorcinol (2-NR) bound in the active site is reported. 2-NR is directly ligated to a Mn²⁺ bound in the active site, and the nitro substituent of the inhibitor is tilted significantly from the plane of the phenyl ring. The inhibitor exhibits a binding mode different from that of the substrate bound in the previously determined structure of γ-RSD from Rhizobium sp. MTP-10005. On the basis of the crystal structure of the enzyme from Polaromonas sp. JS666, complementary density functional calculations were performed to investigate the reaction mechanism. In the proposed reaction mechanism, γ-RSD binds 2,6-dihydroxybenzoate by direct coordination of the active site manganese ion to the carboxylate anion of the substrate and one of the adjacent phenolic oxygens. The enzyme subsequently catalyzes the transfer of a proton to C1 of γ-resorcylate prior to the actual decarboxylation step. The reaction mechanism proposed previously, based on the structure of γ-RSD from Rhizobium sp. MTP-10005, is shown to be associated with high energies and thus less likely to be correct.

A Major Structural Change of the Homocitrate Ligand of Probable Importance for the Nitrogenase Mechanism

Mo-containing nitrogenase is the main enzyme that is able to take N₂ from the air and form ammonia. The active-site cofactor of the enzyme, termed FeMoco, is unique in nature. It has seven Fe and one Mo atoms connected by S bridges, with a C atom in the center of the cofactor. Another unusual feature is that it has a large homocitrate ligand known to be of importance for catalysis. In the present computational study, the role of the homocitrate ligand is investigated. It is found that a large structural change, which makes Mo^III five-coordinated, is energetically favorable in the more reduced states. This is of probable importance for the nitrogenase mechanism.

On the photocatalytic cycle of water splitting with small manganese oxides and the roles of water clusters as direct sources of oxygen molecules

A study on the photocatalytic cycle of water splitting and coupled proton electron-wavepacket transfer (CPEWT) as key processes of the mechanism.