Quantum Chemical Studies of Proton-Coupled Electron Transfer in Metalloenzymes

A transition state “trapped”? QM-cluster models of engineered threonyl-tRNA synthetase

QM-cluster models demonstrate how protein bioengineering alters the local energy landscape of p-biphenylalanine to stabilize a transition state analogue.

Electronic Origin of the Competitive Mechanisms in the Thermal Activation of Methane by the Heteronuclear Cluster Oxide [Al2 ZnO4 ]

The thermal gas-phase reactions of [Al₂ ZnO₄ ]^.+ with methane have been explored by using FT-ICR mass spectrometry complemented by high-level quantum chemical calculations. Two competitive mechanisms, that is, hydrogen-atom transfer (HAT) and proton-coupled electron transfer (PCET) are operative. Interestingly, while the HAT process is influenced by the polarity of the transition structure, both the ionic nature of the metal-oxygen bond and the structural rigidity of the cluster oxide affect the PCET pathway. As compared to the previously reported homonuclear [Al₂ O₃ ]^.+ and [ZnO]^.+ , the heteronuclear oxide [Al₂ ZnO₄ ]^.+ exhibits a much higher chemoselectivity towards methane. The electronic origins of the doping effect have been explored.

On the Electronic Origin of Remarkable Ligand Effects on the Reactivities of [NiL]+ Complexes (L=C6 H5 , C5 H4 N, CN) towards Methane

The gas-phase reactions of [NiL]⁺ (L=C₆ H₅ , C₅ H₄ N, CN) with methane have been explored by using electrospray-ionization mass spectrometry (ESI-MS) complemented by quantum chemical calculations. Though the phenyl Ni complex [Ni(C₆ H₅ )]⁺ exclusively abstracts one hydrogen atom from methane at ambient conditions, the cyano Ni complex [Ni(CN)]⁺ brings about both H-atom abstraction and ligand exchange to generate [Ni(CH₃ )]⁺ . In contrast, the complex 2-pyridinyl Ni [Ni(C₅ H₄ N)]⁺ is inert towards this substrate. The presence of the empty 4s(Ni) orbital dominates the proton-coupled electron transfer (PCET) processes for the investigated systems.

Quantum chemical study of mechanism and stereoselectivity of secondary alcohol dehydrogenase

Secondary alcohol dehydrogenase from Thermoanaerobacter brockii (TbSADH) is a Zn- and NADP-dependent enzyme that catalyses the reversible transformation of secondary alcohols into ketones. It is of potential biocatalytic interest as it can be used in the synthesis of chiral alcohols by asymmetric reduction of ketones. In this paper, density functional theory calculations are employed to elucidate the origins of the enantioselectivity of TbSADH using a large model of the active site and considering two different substrates, 2-butanol and 3-hexanol. For these two substrates the enzyme has experimentally been shown to have the opposite enantioselectivity. The energy profiles for the reactions are calculated and the stationary points along the reaction path are characterised. The calculations first confirm that the general mechanism proposed for other alcohol dehydrogenases is energetically viable. In this mechanism, a proton is first transferred from the substrate to a histidine residue at the surface, followed by a hydride transfer to the NADP cofactor. The calculated overall energy barrier is consistent with the measured rate constant. Very importantly, the calculations are able to reproduce and rationalise the enantioselectivity of the enzyme for both substrates. The detailed characterisation of the energies and geometries of the involved transition states will be valuable in the rational engineering of TbSADH to expand its utility in biocatalysis.

Reversible Bond/Cation-Coupled Electron Transfer on Phenylenediamine-Based Rhodamine B and Its Application on Electrochromism

A biomimetic system on reversible bond-coupled electron transfer (BCET) has been proposed and investigated in a switchable Rh-N molecule with redox active subunits. We discover that energy barrier of C-N bond breaking is reduced dramatically to less than 1/7 (from 40.4 to 5.5 kcal/mol), and 1/3 of the oxidation potential is simultaneously lowered (from 0.67 to 0.43 V) with the oxidation of Rh-N. The concept, cation-coupled electron transfer (CCET), is highly recommended by analyzing existing proton coupled electron transfer (PCET) and metal coupled electron transfer (MCET) along with aforementioned BCET, which have same characteristic of transferring positive charges, such as proton, metal ion, and organic cation. Molecular switch can be controlled directly by electricity through BCET process. Solid electrochromic device was fabricated with extremely high coloration efficiency (720 cm²/C), great reversibility (no degradation for 600 cycles), and quick respond time (30 ms).

Recent Trends in Quantum Chemical Modeling of Enzymatic Reactions

The quantum chemical cluster approach is a powerful method for investigating enzymatic reactions. Over the past two decades, a large number of highly diverse systems have been studied and a great wealth of mechanistic insight has been developed using this technique. This Perspective reviews the current status of the methodology. The latest technical developments are highlighted, and challenges are discussed. Some recent applications are presented to illustrate the capabilities and progress of this approach, and likely future directions are outlined.

From NAD+ to Nickel Pincer Complex: A Significant Cofactor Evolution Presented by Lactate Racemase

Lactate racemase (LarA), a new nickel enzyme discovered recently, catalyzes the racemization between d- and l-lactates with a novel nickel pincer cofactor (Ni-PTTMN) derived from nicotinic acid. In this study, by using DFT and a 200-atom active-site model, LarA is revealed to employ a modified proton-coupled hydride-transfer mechanism in which a hydride is transferred to a cofactor pyridine carbon from the substrate α-carbon along with proton transfer from the substrate hydroxy group to a histidine, and then moved back from the opposite side. Tyr294 and Lys298 provide significant acceleration effects by orientating substrates and stabilizing the negative charge developing at the substrate hydroxy oxygen. The barrier was determined to be 12.0 kcal mol^-1 , which reveals enhanced racemase activity relative to the LarA reaction using NAD⁺ -like cofactors. Compared with NAD⁺ , Ni-PTTMN has a stronger hydride-addition reactivity in moderate and high environmental polarity and may fit perfectly the moderately polar active site of LarA.

Sequential Gas-Phase Activation of Carbon Dioxide and Methane by [Re(CO)2]+: The Sequence of Events Matters!

The potential of carbonyl rhenium complexes in activating and coupling carbon dioxide and methane has been explored by using a combination of gas-phase experiments (FT-ICR mass spectrometry) and high-level quantum chemical calculations. While the complexes [Re(CO)_x]⁺ (x = 0, 1, 3) are thermally unreactive toward CO₂, [Re(CO)₂]⁺ abstracts one oxygen atom from this substrate spontaneously at ambient conditions. Based on ¹³C and ¹⁸O labeling experiments, the newly generated CO ligand is preferentially eliminated, and two mechanistic scenarios are considered to account for this unexpected finding. The oxo complex [ORe(CO)₂]⁺ reacts further with CH₄ to produce the dihydridomethylene complex [ORe(CO)(CH₂)(H)₂]⁺. However, coupling of the CO and CH₂ ligands to form CH₂═C═O does not take place. Further, the complexes [Re(CO)_x(CH₂)]⁺ (x = 1, 2), generated in the thermal reaction of [Re(CO)_x]⁺ (x = 1, 2) with CH₄, are inert toward CO₂. Mechanistic insight on the origin of this remarkable reactivity pattern has been derived from detailed quantum chemical calculations.

Effects of metal-ion replacement on pyrazinamidase activity: A quantum mechanical study

Pyrazinamidase (PZase), a metalloenzyme, is responsible for acidic modification of pyrazinamide (PZA), a drug used in tuberculosis treatment. The metal coordination site of the enzyme is able to coordinate various divalent metal cofactors. Previous experimental studies have demonstrated that metal ions, such as Co²⁺, Mn²⁺, and Zn²⁺, are able to reactivate metal-depleted PZase, while others including Cu²⁺, Fe²⁺, and Mg²⁺, cannot restore activity. In this study, we investigated binding of various metal ions to the metal coordination site (MCS) of the enzyme using quantum mechanical calculations. We calculated the metal-ligand (residue) binding energy and the atomic partial charges in the presence of various ions. The results indicated that the tendency of alkaline earth metals to bind to PZase MCS is very low and not suitable for enzyme structural and catalytic function. In contrast, Co²⁺ and Ni²⁺ ions have very high binding affinity and are favorable to the structural and functional properties of the enzyme. Furthermore, we observed that the rate at which Ni²⁺, Co²⁺ and Fe²⁺ ions in PZase MCS polarize the OH bond of coordinated water molecules is much higher than the polarization rate created by other ions. This finding suggests that the coordination of Ni²⁺, Co²⁺, or Fe²⁺ to PZase facilitates the deprotonation of coordinated water molecules to generate a nucleophile that catalyzes the enzymatic reaction.

Influence of iron doping on tetravalent nickel content in catalytic oxygen evolving films

Iron doping of nickel oxide films results in enhanced activity for promoting the oxygen evolution reaction (OER). Whereas this enhanced activity has been ascribed to a unique iron site within the nickel oxide matrix, we show here that Fe doping influences the Ni valency. The percent of Fe³⁺ doping promotes the formation of formal Ni⁴⁺, which in turn directly correlates with an enhanced activity of the catalyst in promoting OER. The role of Fe³⁺ is consistent with its behavior as a superior Lewis acid.

Critical Aspects of Heme-Peroxo-Cu Complex Structure and Nature of Proton Source Dictate Metal-O(peroxo) Breakage versus Reductive O-O Cleavage Chemistry

The 4H+/4e- reduction of O2 to water, a key fuel-cell reaction also carried out in biology by oxidase enzymes, includes the critical O-O bond reductive cleavage step. Mechanistic investigations on active-site model compounds, which are synthesized by rational design to incorporate systematic variations, can focus on and resolve answers to fundamental questions, including protonation and/or H-bonding aspects, which accompany electron transfer. Here, we describe the nature and comparative reactivity of two low-spin heme-peroxo-Cu complexes, LS-4DCHIm, [(DCHIm)F8FeIII-(O22-)-CuII(DCHIm)4]+, and LS-3DCHIm, [(DCHIm)F8FeIII-(O22-)-CuII(DCHIm)3]+ (F8 = tetrakis(2,6-difluorophenyl)-porphyrinate; DCHIm = 1,5-dicyclohexylimidazole), toward different proton (4-nitrophenol and [DMF·H+](CF3SO3-)) (DMF = dimethyl-formamide) or electron (decamethylferrocene (Fc*)) sources. Spectroscopic reactivity studies show that differences in structure and electronic properties of LS-3DCHIm and LS-4DCHIm lead to significant differences in behavior. LS-3DCHIm is resistant to reduction, is unreactive toward weakly acidic 4-NO2-phenol, and stronger acids cleave the metal-O bonds, releasing H2O2. By contrast, LS-4DCHIm forms an adduct with 4-NO2-phenol, which includes an H-bond to the peroxo O-atom distal to Fe (resonance Raman (rR) spectroscopy and DFT). With addition of Fc* (2 equiv overall required), O-O reductive cleavage occurs, giving water, Fe(III), and Cu(II) products; however, a kinetic study reveals a one-electron rate-determining process, ket = 1.6 M-1 s-1 (-90 °C). The intermediacy of a high-valent [(DCHIm)F8FeIV═O] species is thus implied, and separate experiments show that one-electron reduction-protonation of [(DCHIm)F8FeIV═O] occurs faster (ket2 = 5.0 M-1 s-1), consistent with the overall postulated mechanism. The importance of the H-bonding interaction as a prerequisite for reductive cleavage is highlighted.

Thermal Methane Activation by the Metal-Free Cluster Cation [Si2 O4 ]

The thermal reaction of methane with the metal-free cluster cation [Si₂ O₄ ]^.+ has been examined by using Fourier transform-ion cyclotron resonance (FT-ICR) mass spectrometry. In addition to generating a methyl radical via hydrogen-atom abstraction, [Si₂ O₄ ]^.+ can selectively oxidize methane to formaldehyde. The mechanisms of these rather efficient reactions have been elucidated by high-level quantum-chemical calculations.

The open-cubane oxo–oxyl coupling mechanism dominates photosynthetic oxygen evolution: a comprehensive DFT investigation on O–O bond formation in the S4state

How is O₂created in nature? Comprehensive DFT investigations determine the dominance of the open-cubane oxo–oxyl coupling mechanism over alternative possibilities.

Combined experimental/theoretical study on d-glucosamine promoted regioselective sulfenylation of indoles catalyzed by copper

A combined experimental/theoretical investigation on the d-glucosamine promoted sulfenylation of indoles at the C3 position with sodium sulfinates catalyzed by copper is presented.

Thermal Methane Activation by [Si2 O5 ].+ and [Si2 O5 H2 ].+ : Reactivity Enhancement by Hydrogenation

The thermal reactions of methane with the oxygen-rich cluster cations [Si₂ O₅ ]^⋅+ and [Si₂ O₅ H₂ ]^⋅+ have been examined using Fourier transform-ion cyclotron resonance (FT-ICR) mass spectrometry in conjunction with state-of-the-art quantum chemical calculations. In contrast to the inertness of [Si₂ O₅ ]^.+ towards methane, the hydrogenated cluster [Si₂ O₅ H₂ ]^.+ brings about hydrogen-atom transfer (HAT) from methane with an efficiency of 28 % relative to the collision rate. The mechanisms of this process have been investigated in detail and the reasons for the striking reactivity difference of the two cluster ions have been revealed.

Influence of Ligand Architecture in Tuning Reaction Bifurcation Pathways for Chlorite Oxidation by Non-Heme Iron Complexes

Reaction bifurcation processes are often encountered in the oxidation of substrates by enzymes and generally lead to a mixture of products. One particular bifurcation process that is common in biology relates to electron transfer versus oxygen atom transfer by high-valent iron(IV)-oxo complexes, which nature uses for the oxidation of metabolites and drugs. In biomimicry and bioremediation, an important reaction relates to the detoxification of ClO_x^- in water, which can lead to a mixture of products through bifurcated reactions. Herein we report the first three water-soluble non-heme iron(II) complexes that can generate chlorine dioxide from chlorite at ambient temperature and physiological pH. These complexes are highly active oxygenation oxidants and convert ClO₂^- into either ClO₂ or ClO₃¯ via high-valent iron(IV)-oxo intermediates. We characterize the short-lived iron(IV)-oxo species and establish rate constants for the bifurcation mechanism leading to ClO₂ and ClO₃^- products. We show that the ligand architecture of the metal center plays a dominant role by lowering the reduction potential of the metal center. Our experiments are supported by computational modeling, and a predictive valence bond model highlights the various factors relating to the substrate and oxidant that determine the bifurcation pathway and explains the origins of the product distributions. Our combined kinetic, spectroscopic, and computational studies reveal the key components necessary for the future development of efficient chlorite oxidation catalysts.

The Decarboxylation of α,β-Unsaturated Acid Catalyzed by Prenylated FMN-Dependent Ferulic Acid Decarboxylase and the Enzyme Inhibition

Ferulic acid decarboxylase (Fdc1) is able to catalyze the decarboxylation of α,β-unsaturated acids using a novel cofactor, prenylated flavin mononucleotide (PrFMN). Using density functional theory calculations, we here have investigated the Fdc1 reaction mechanism with the substrate of α-methylcinnamic acid. It is demonstrated that Fdc1 employs a 1,3-dipolar cycloaddition mechanism involving four concerted steps, where the Glu282 acts as a crucial proton donor to protonate the α carbon (C_α). The last step, the decomposition of a pyrrolidine species, is rate-limiting with an overall barrier of 18.9 kcal mol^-1. Furthermore, when α-hydroxycinnamic acid is used, the Glu282 is found to have another face to transport the hydroxyl proton to the C_β atom to promote the tautomerization from enol intermediate to ketone species leading to the inhibition of the Fdc1 enzyme. The PrFMN roles are also discussed in detail.

Multiscale simulations reveal key features of the proton-pumping mechanism in cytochrome c oxidase

Cytochrome c oxidase (CcO) reduces oxygen to water and uses the released free energy to pump protons across the membrane. We have used multiscale reactive molecular dynamics simulations to explicitly characterize (with free-energy profiles and calculated rates) the internal proton transport events that enable proton pumping during first steps of oxidation of the fully reduced enzyme. Our results show that proton transport from amino acid residue E286 to both the pump loading site (PLS) and to the binuclear center (BNC) are thermodynamically driven by electron transfer from heme a to the BNC, but that the former (i.e., pumping) is kinetically favored whereas the latter (i.e., transfer of the chemical proton) is rate-limiting. The calculated rates agree with experimental measurements. The backflow of the pumped proton from the PLS to E286 and from E286 to the inside of the membrane is prevented by large free-energy barriers for the backflow reactions. Proton transport from E286 to the PLS through the hydrophobic cavity and from D132 to E286 through the D-channel are found to be strongly coupled to dynamical hydration changes in the corresponding pathways and, importantly, vice versa.

Donor-Dependent Kinetics of Interfacial Proton-Coupled Electron Transfer

The effect of the proton donor on the kinetics of interfacial concerted proton-electron transfer (CPET) to polycrystalline Au was probed indirectly by studying the rate of hydrogen evolution from trialkylammonium donors with different steric profiles, but the same pKa. Detailed kinetic studies point to a mechanism for HER catalysis that involves rate-limiting CPET from the proton donor to the electrode surface, allowing this catalytic reaction to serve as a proxy for the rate of interfacial CPET. In acetonitrile electrolyte, triethylammonium (TEAH(+)) displays up to 20-fold faster CPET kinetics than diisopropylethylammonium (DIPEAH(+)) at all measured potentials. In aqueous electrolyte, this steric constraint is largely lifted, suggesting a key role for water in mediating interfacial CPET. In acetonitrile, TEAH(+) also displays a much larger transfer coefficient (β = 0.7) than DIPEAH(+) (β = 0.4), and TEAH(+) displays a potential-dependent H/D kinetic isotope effect that is not observed for DIPEAH(+). These results demonstrate that proton donor structure strongly impacts the free energy landscape for CPET to extended solid surfaces and highlight the crucial role of the proton donor in the kinetics of electrocatalytic energy conversion reactions.

Molecular simulation and modeling of complex I

Molecular modeling and molecular dynamics simulations play an important role in the functional characterization of complex I. With its large size and complicated function, linking quinone reduction to proton pumping across a membrane, complex I poses unique modeling challenges. Nonetheless, simulations have already helped in the identification of possible proton transfer pathways. Simulations have also shed light on the coupling between electron and proton transfer, thus pointing the way in the search for the mechanistic principles underlying the proton pump. In addition to reviewing what has already been achieved in complex I modeling, we aim here to identify pressing issues and to provide guidance for future research to harness the power of modeling in the functional characterization of complex I. This article is part of a Special Issue entitled Respiratory complex I, edited by Volker Zickermann and Ulrich Brandt.

Mechanism of Oxygen Reduction in Cytochrome c Oxidase and the Role of the Active Site Tyrosine

Cytochrome c oxidase, the terminal enzyme in the respiratory chain, reduces molecular oxygen to water and stores the released energy through electrogenic chemistry and proton pumping across the membrane. Apart from the heme-copper binuclear center, there is a conserved tyrosine residue in the active site (BNC). The tyrosine delivers both an electron and a proton during the O-O bond cleavage step, forming a tyrosyl radical. The catalytic cycle then occurs in four reduction steps, each taking up one proton for the chemistry (water formation) and one proton to be pumped. It is here suggested that in three of the reduction steps the chemical proton enters the center of the BNC, leaving the tyrosine unprotonated with radical character. The reproprotonation of the tyrosine occurs first in the final reduction step before binding the next oxygen molecule. It is also suggested that this reduction mechanism and the presence of the tyrosine are essential for the proton pumping. Density functional theory calculations on large cluster models of the active site show that only the intermediates with the proton in the center of the BNC and with an unprotonated tyrosyl radical have a high electron affinity of similar size as the electron donor, which is essential for the ability to take up two protons per electron and thus for the proton pumping. This type of reduction mechanism is also the only one that gives a free energy profile in accordance with experimental observations for the amount of proton pumping in the working enzyme.

Computational Examination on the Active Site Structure of a (Peroxo)diiron(III) Intermediate in the Amine Oxygenase AurF

In this work, we report the first computational investigation on the structure and properties of the (peroxo)diiron(III) intermediate of the AurF enzyme. Our calculations predict that, in the oxidized state of the AurF enzyme, the peroxo ligand is depicted in a μ-1,1-coordination mode with a protonated bridging ligand and is not in a μ-η(2):η(2) or μ-1,2 mode. Computed spectral data for the μ-1,1-coordination mode correlate well with experimental observations and unravel the potential of the energetics-spectroscopic approach adapted here.

Theoretical study of the reaction mechanism of phenolic acid decarboxylase

The cofactor-free phenolic acid decarboxylases (PADs) catalyze the non-oxidative decarboxylation of phenolic acids to their corresponding p-vinyl derivatives. Phenolic acids are toxic to some organisms, and a number of them have evolved the ability to transform these compounds, including PAD-catalyzed reactions. Since the vinyl derivative products can be used as polymer precursors and are also of interest in the food-processing industry, PADs might have potential applications as biocatalysts. We have investigated the detailed reaction mechanism of PAD from Bacillus subtilis using quantum chemical methodology. A number of different mechanistic scenarios have been considered and evaluated on the basis of their energy profiles. The calculations support a mechanism in which a quinone methide intermediate is formed by protonation of the substrate double bond, followed by C-C bond cleavage. A different substrate orientation in the active site is suggested compared to the literature proposal. This suggestion is analogous to other enzymes with p-hydroxylated aromatic compounds as substrates, such as hydroxycinnamoyl-CoA hydratase-lyase and vanillyl alcohol oxidase. Furthermore, on the basis of the calculations, a different active site residue compared to previous proposals is suggested to act as the general acid in the reaction. The mechanism put forward here is consistent with the available mutagenesis experiments and the calculated energy barrier is in agreement with measured rate constants. The detailed mechanistic understanding developed here might be extended to other members of the family of PAD-type enzymes. It could also be useful to rationalize the recently developed alternative promiscuous reactivities of these enzymes.

Proton transfer in the K-channel analog of B-type Cytochrome c oxidase from Thermus thermophilus

A key enzyme in aerobic metabolism is cytochrome c oxidase (CcO), which catalyzes the reduction of molecular oxygen to water in the mitochondrial and bacterial membranes. Substrate electrons and protons are taken up from different sides of the membrane and protons are pumped across the membrane, thereby generating an electrochemical gradient. The well-studied A-type CcO uses two different entry channels for protons: the D-channel for all pumped and two consumed protons, and the K-channel for the other two consumed protons. In contrast, the B-type CcO uses only a single proton input channel for all consumed and pumped protons. It has the same location as the A-type K-channel (and thus is named the K-channel analog) without sharing any significant sequence homology. In this study, we performed molecular-dynamics simulations and electrostatic calculations to characterize the K-channel analog in terms of its energetic requirements and functionalities. The function of Glu-15B as a proton sink at the channel entrance is demonstrated by its rotational movement out of the channel when it is deprotonated and by its high pKA value when it points inside the channel. Tyr-244 in the middle of the channel is identified as the valve that ensures unidirectional proton transfer, as it moves inside the hydrogen-bond gap of the K-channel analog only while being deprotonated. The electrostatic energy landscape was calculated for all proton-transfer steps in the K-channel analog, which functions via proton-hole transfer. Overall, the K-channel analog has a very stable geometry without large energy barriers.

Moving protons and electrons in biomimetic systems

An enormous variety of biological redox reactions are accompanied by changes in proton content at enzyme active sites, in their associated cofactors, in substrates and/or products, and between protein interfaces. Understanding this breadth of reactivity is an ongoing chemical challenge. A great many workers have developed and investigated biomimetic model complexes to build new ways of thinking about the mechanistic underpinnings of such complex biological proton-coupled electron transfer (PCET) reactions. Of particular importance are those model reactions that involve transfer of one proton (H(+)) and one electron (e(-)), which is equivalent to transfer of a hydrogen atom (H(•)). In this Current Topic, we review key concepts in PCET reactivity and describe important advances in biomimetic PCET chemistry, with a special emphasis on research that has enhanced efforts to understand biological PCET reactions.