Proton Transfer Step Research Articles

Third Metal Ion Dictates the Catalytic Activity of the Two-Metal-Ion Pre-Ribosomal RNA-Processing Machinery.

Nucleic acid processing enzymes use a two-Mg2+-ion motif to promote the formation and cleavage of phosphodiester bonds. Yet, recent evidence demonstrates the presence of spatially conserved second-shell cations surrounding the catalytic architecture of proteinaceous and RNA-dependent enzymes. The RNase mitochondrial RNA processing (MRP) complex, which cleaves the ribosomal RNA (rRNA) precursor at the A3 cleavage site to yield mature 5'-end of 5.8S rRNA, hosts in the catalytic core one atypically-located Mg2+ ion, in addition to the ions forming the canonical catalytic motif. Here, we employ biased quantum classical molecular dynamics simulations of RNase MRP to discover that the third Mg2+ ion inhibits the catalytic process. Instead, its displacement in favour of a second-shell monovalent K+ ion propels phosphodiester bond cleavage by enabling the formation of a specific hydrogen bonding network that mediates the essential proton transfer step. This study points to a direct involvement of a transient K+ ion in the catalytic cleavage of the phosphodiester bond and implicates cation trafficking as a general mechanism in nucleic acid processing enzymes and ribozymes.

(Invited) Computational Models of Proton-Coupled Electron Transfer in Energy Conversion and Storage

Proton-coupled electron transfer (PCET) is a fundamental class of chemical reactions that is central to many electrochemical energy conversion and storage processes. In this talk, I will discuss recent theoretical model development for interfacial and intermolecular PCET reactions. First, I will describe a rate constant model for the reaction between reduced anatase TiO2 surfaces and a 4-MeO-TEMPO nitroxyl radical. The rate constants are modeled using vibronically nonadiabatic PCET theory, where the transferring proton and electron are treated quantum mechanically. Hybrid functional periodic density functional theory (DFT) calculations are used to derive model parameters such as driving forces, reorganization energies, and proton vibrational wavefunctions. This modeling strategy highlights the role of inner-sphere bond reorganization and excited vibronic states on the PCET reactivity of metal oxides. Next, I will show how similar computational approaches can be used to predict whether electrochemical PCET is likely to proceed through concerted electron–proton transfer or sequential electron transfer and proton transfer steps. Using PCET reactions between redox-active quinones and functionalized imidazole bases as an example, mechanistic predictions are informed by DFT-calculated potential energy surfaces. These PCET modeling strategies have broad applicability to kinetic studies of electrochemical energy conversion and storage processes.

(Invited) Single-Atom Cu Catalysts for Electrochemical CO2 Reduction – Combining Theory, Synthesis and Electrochemical Characterization

Electrochemical CO2 reduction (CO2RR) is a leading sustainable approach for transforming atmospheric CO2 into valuable chemicals. This electrocatalytic process relies on a delicate balance of electron and proton transfer steps, resulting in the formation of diverse 1-carbon and some 2-carbon products, contingent on the surface properties. Extensive exploration of various transition metals for CO2RR has revealed that the binding strength of reaction intermediates on these metals significantly influences product selectivity. Notably, metals such as Au, Ag, Pd, Zn, Cd, Bi, Sn, and In, recognized for their activity in CO2RR, exhibit lower binding strengths for CO2 intermediates, leading to the predominant production of either HCOOH or CO as sole products. In contrast, Cu, with its moderate ability to bind CO2RR intermediates, yields multiple products during CO2RR, albeit with reduced selectivity [1]. Moreover, the overall efficiency of CO2 conversion is hampered by the simultaneous occurrence of the competing hydrogen evolution reaction (HER) at the potentials required for producing desired products. Thus, it is imperative to develop new, effective catalysts. Catalysts capable of suppressing HER while enhancing selectivity are essential for advancing the overall efficiency of CO2 conversion [2].Single-atom catalysts (SACs) are a relatively new class of materials that hold great promise due to their high specific activity and maximum atom utilization [3]. These catalysts often provide singular types of active sites, enhancing selectivity in reactions. However, the vast array of possible SACs, deployable on various supports, makes it impractical, if not possible, to use the traditional trial-and-error studies to yield high performing catalysts within reasonable timeframes. To navigate this complexity, theoretical investigations, especially DFT computations and machine learning techniques, have emerged as powerful tools. They can facilitate the identification of suitable catalyst structures and enable the precise engineering of atomic arrangement, therefore achieving targeted product formation from CO2 with enhanced conversion efficiency. Additionally, conventional synthesis methods suffer from various drawbacks, involving multiple steps, harsh conditions, and a lack of control over the metal site distribution in the carbon matrix, limiting the desired coordination structure [4, 5].Therefore, the work presented in this talk represents our combined experimental-theoretical effort. Specifically, Cu single atoms were strategically deposited onto defective carbon supports and systematically investigated for their performance as CO2RR electrocatalysts. These catalysts were inspired by DFT results showing how the product profile could be manipulated on catalyst surfaces, along with a prediction of the most likely products that would arise from the reaction.These catalysts were synthesized using a novel method denoted as switched solvent synthesis. This approach involves initially impregnating metals onto a carbon support, followed by switching the solvent from aqueous to an organic solvent with a higher dipole moment, and subsequently reducing the resulting mixture under an H2 environment. This innovative method offers notable advantages, enabling the efficient production of SACs in less time, at lower temperatures (~100-500 °C), and with high yields. In this study, Cu SACs were synthesized, and the influence of reaction parameters on the distribution of Cu metal atoms was systematically examined. The confirmation of SAC formation was achieved through various characterization techniques, including aberration-corrected STEM, XRD, and XPS.To assess the electrochemical activity and CO2 reduction abilities of the Cu SACs, electrochemical characterization techniques were employed under both He and CO2-saturated 0.1 M KHCO3 electrolytes. Furthermore, the product distribution and CO2 conversion efficiencies, including activity, stability, selectivity, and faradaic efficiency, of the Cu SACs were rigorously evaluated through electrolysis in a flow cell setup. Quantification of the results was performed using an integrated GC/MS instrument.

Roles of H-Bonding and Hydride Solvation in the Reaction of Hydrated (Di)electrons with Water to Create H2 and OH.

Even though single hydrated electrons (ehyd-'s) are stable in liquid water, two hydrated electrons can bimolecularly react with water to create H2 and hydroxide: ehyd- + ehyd- + 2H2O → H2 + 2OH-. The rate of this reaction has an unusual temperature and isotope dependence as well as no dependence on ionic strength, which suggests that cosolvation of two electrons as a single hydrated dielectron (e2,hyd2-) might be an important intermediate in the mechanism of this reaction. Here, we present an ab initio density functional theory study of this reaction to better understand the potential properties, reactivity, and experimental accessibility of hydrated dielectrons. Our simulations create hydrated dielectrons by first simulating single ehyd-'s and then injecting a second electron, providing a well-defined time zero for e2,hyd2- formation and offering insight into a potential experimental route to creating dielectrons and optically inducing the reaction. We find that e2,hyd2- immediately forms in every member of our ensemble of trajectories, allowing us to study the molecular mechanism of H2 and OH- formation. The subsequent reaction involves separate proton transfer steps with a generally well-defined hydride subintermediate. The time scales for both proton transfer steps are quite broad, with the first proton transfer step spanning times over a few ps, while the second proton transfer step varies over ∼150 fs. We find that the first proton transfer rate is dictated by whether or not the reacting water is part of an H-bond chain that allows the newly created OH- to rapidly move by Grotthuss-type proton hopping to minimize electrostatic repulsion with H-. The second proton transfer step depends significantly on the degree of solvation of H-, leading to a wide range of reactive geometries where the two waters involved can lie either across the dielectron cavity or more adjacent to each other. This also allows the two proton transfer events to take place either effectively concertedly or sequentially, explaining differing views that have been presented in the literature.

Hypervalent Chalcogen Bonds Catalysis on the Intramolecular Aza-Michael Reaction of Aminochalcone: Catalytic Performance and Chalcogen Bond Properties.

Chalcogen bond (ChB) catalysis, as a new type in the field of non-covalent bond catalysis, has become a hot research topic in the field of organocatalysis in recent years. In the present work, we investigated the catalytic performance of a series of hypervalent ChB catalysis based on the intramolecular Aza-Michael reaction of aminochalcone. The reaction includes the carbon-nitrogen bond coupling step (key step) and the proton transfer step. The catalytic performance of mono-dentate pentafluorophenyl chalcogen bond donor ChB1 was comparable to that of bis-dentate chalcogen bond donor ChB4, and stronger than that of mono-dentate chalcogen bond donors ChB2 and ChB3. The formation of the chalcogen bond between the catalyst and the carbonyl oxygen atom of the reactant, causing the charge rearrangement of the reactant and C(1) charge of the -C-Ph group to become more positive, thereby the ChB catalysis promoted the nucleophile reaction. The electron density of the chalcogen bond of the pre-complex, the most positive electrostatic potentials of the catalyst, and the NPA charge of the key atom are proportional to the Gibbs energy barrier of the C-N bond coupling process, which provides an idea to predict the catalytic activity of the ChB catalysis.

Elementary Reaction Steps That Precede or Follow a Unimolecular Reaction Step Can Obfuscate Interpretation of the Driving-Force Dependence to Its Rate Constant.

Assessing the validity of a driving-force-dependent kinetic theory for a unimolecular elementary reaction step is difficult when the observed reaction rate is strongly influenced by properties of the preceding or following elementary reaction step. A well-known example occurs for bimolecular reactions with weak orbital overlap, such as outer-sphere electron transfer, where bimolecular collisional encounters that precede a fast unimolecular electron-transfer step can limit the observed rate. A lesser-appreciated example occurs for bimolecular reactions with stronger orbital overlap, including many proton-transfer reactions, where equilibration of an endergonic unimolecular proton-transfer step results in a relatively small concentration of reaction products, thus slowing the rate of the following step such that it becomes rate limiting. Incomplete consideration of these points has led to discrepancies in interpretation of data from the literature. Our reanalysis of these data suggests that proton-transfer elementary reaction steps have a nonzero intrinsic free energy barrier, implying, in the parlance of Marcus theory, that there is non-negligible nuclear reorganization. Outcomes from our analyses are generalizable to inner-sphere electron-transfer reactions such as those involved in (photo)electrochemical fuel-forming reactions.

Structure and non-reactive dynamics of the dimeric catalytic domain of human carbonic anhydrase IX

Despite the availability of high resolution crystal structure of the catalytic domain of human carbonic anhydrase IX (denoted as HCA IX-c), its solution structure and functional dynamics are mostly unknown. In this article, we report classical molecular dynamics (MD) simulation studies on the structure and non-reactive dynamics of dimeric HCA IX-c (d-HCA IX-c, with chains A and B) in water and compare them to each chain simulated in water as a monomeric solute (mA/mB). While the average solution structures appear to be largely similar in all systems, d-HCA IX-c shows significant deviations from mA and mB in terms of non-reactive reorganization of the active site needed to initiate the rate determining proton transfer step between a zinc-bound water and one of the sidechain N-atoms of a distal histidine residue (His-64). First, 2−6 water molecules are found to form fluctuating hydrogen bonded networks that would serve as proton paths across the active site. A minimally frustrated core of each monomer in the dimeric protein is found to be associated with a significantly higher likelihood of forming complete proton transfer pathways mediated by 2 water molecules synchronously at the two active sites hosted by the monomeric chains. The relative stability and kinetics of transition between two major sidechain rotamers of His-64 are also affected by dimerization. The sidechain rotation of His-64 is found to involve at least one transition as slow as 105s−1 in chain A of d-HCA IX-c thereby rendering it slower than the actual rate determining proton transfer step. This observation indicates an important deviation from the widely accepted mechanism of catalysis by HCAs.

Redirecting surface reconstruction of CoP-Cu heterojunction to promote ammonia synthesis at industrial-level current density

The electrochemical reduction of nitrate (NO3−RR) represents a compelling approach for the treatment of wastewater, serving as both a sustainable substitute to the energy-intensive Haber-Bosch process and a viable alternative to direct electroreduction of N2. However, the process involves multiple electron and proton transfer steps and a complex reaction pathway, leading to low Faraday efficiency and selectivity. Herein, we demonstrated a directional surface reconstruction to generate CoP-Cu/Co(OH)2 heterojunction for synergistic catalysis of NO3−RR. Impressively, a high ammonia generation rate of 9.91 mmol h−1cm−2 and a Faraday efficiency of 99.2 % can be achieved at an industrial-relevant current density of 2 A cm−2. Moreover, the catalyst exhibited exceptional durability, maintaining the activity for 110 h under industrial current density. Such outstanding NO3−RR performance can be ascribed to the synergistic catalytic effect among the active sites of Cu, CoP and Co(OH)2, as well as the excellent stability of self-supported catalyst. Specifically, Cu and CoP sites synergistically promote the conversion of NO3− to NO2− and NO2− to NH3. Meanwhile, the partial reconstructed Co(OH)2 from CoP enhances water dissociation, thereby supplying active hydrogen (*H) essential for NO3−RR. When applied to a membrane electrode assembly (MEA) system, CoP-Cu/Co(OH)2 can deliver satisfactory ammonia production rate with appreciable economic benefits at industrial-level current densities, highlighting its potential for industrial applications.

A non-canonical nucleophile unlocks a new mechanistic pathway in a designed enzyme

Directed evolution of computationally designed enzymes has provided new insights into the emergence of sophisticated catalytic sites in proteins. In this regard, we have recently shown that a histidine nucleophile and a flexible arginine can work in synergy to accelerate the Morita-Baylis-Hillman (MBH) reaction with unrivalled efficiency. Here, we show that replacing the catalytic histidine with a non-canonical Nδ-methylhistidine (MeHis23) nucleophile leads to a substantially altered evolutionary outcome in which the catalytic Arg124 has been abandoned. Instead, Glu26 has emerged, which mediates a rate-limiting proton transfer step to deliver an enzyme (BHMeHis1.8) that is more than an order of magnitude more active than our earlier MBHase. Interestingly, although MeHis23 to His substitution in BHMeHis1.8 reduces activity by 4-fold, the resulting His containing variant is still a potent MBH biocatalyst. However, analysis of the BHMeHis1.8 evolutionary trajectory reveals that the MeHis nucleophile was crucial in the early stages of engineering to unlock the new mechanistic pathway. This study demonstrates how even subtle perturbations to key catalytic elements of designed enzymes can lead to vastly different evolutionary outcomes, resulting in new mechanistic solutions to complex chemical transformations.

Mechanistic Studies on Rhodium-Catalyzed Chemoselective Cycloaddition of Ene-Vinylidenecyclopropanes: Water-Assisted Proton Transfer.

Rhodium-catalyzed cycloaddition reactions are a powerful tool for the construction of polycyclic compounds. Combined experimental and DFT studies were used to investigate the temperature-controlled chemoselectivity of cationic rhodium-catalyzed intramolecular cycloaddition reactions of ene-vinylidenecyclopropanes. After a series of mechanistic studies, it was found that trace amounts of water in the reaction system play an important role in generating the product with endo double bond located on a five-membered ring and revealed that trace amounts of water in the reaction system, including the rhodium catalyst, substrate and solvent, were sufficient to promote the formation of the product with endo double bond located on a five-membered ring, and additional water could not further accelerate the reaction. DFT calculation results show that the addition of water indeed significantly lowers the energy barrier of the proton transfer step, making the formation of the product with endo double bond located on a five-membered ring more likely to occur and confirming the rationality of water-assisted proton transfer occurring in the selective access to the product with endo double bond located on a five-membered ring.

CO2 Reduction by an Iron(I) Porphyrinate System: Effect of Hydrogen Bonding on the Second Coordination Sphere.

Transforming CO2 into valuable materials is an important reaction in catalysis, especially because CO2 concentrations in the atmosphere have been growing steadily due to extensive fossil fuel usage. From an environmental perspective, reduction of CO2 to valuable materials should be catalyzed by an environmentally benign catalyst and avoid the use of heavy transition-metal ions. In this work, we present a computational study into a novel iron(I) porphyrin catalyst for CO2 reduction, namely, with a tetraphenylporphyrin ligand and analogues. In particular, we investigated iron(I) tetraphenylporphyrin with one of the meso-phenyl groups substituted with o-urea, p-urea, or o-2-amide groups. These substituents can provide hydrogen-bonding interactions in the second coordination sphere with bound ligands and assist with proton relay. Furthermore, our studies investigated bicarbonate and phenol as stabilizers and proton donors in the reaction mechanism. Potential energy landscapes for double protonation of iron(I) porphyrinate with bound CO2 are reported. The work shows that the bicarbonate bridges the urea/amide groups to the CO2 and iron center and provides a tight bonding pattern with strong hydrogen-bonding interactions that facilitates easy proton delivery and reduction of CO2. Specifically, bicarbonate provides a low-energy proton shuttle mechanism to form CO and water efficiently. Furthermore, the o-urea group locks bicarbonate and CO2 in a tight orientation and helps with ideal proton transfer, while there is more mobility and lesser stability with an o-amide group in that position instead. Our calculations show that the o-urea group leads to reduction in proton-transfer barriers, in line with experimental observation. We then applied electric-field-effect calculations to estimate the environmental effects on the two proton-transfer steps in the reaction. These calculations describe the perturbations that enhance the driving forces for the proton-transfer steps and have been used to make predictions about how the catalysts can be further engineered for more enhanced CO2 reduction processes.

Hydrogenation of CO2 to CH3OH catalyzed by a ruthenium-triphos complex: Theoretical free energy profile and microkinetic modeling

Direct hydrogenation of carbon dioxide to methanol is an important goal for sustainability. The ruthenium-triphos complex was reported to be successful in achieving this transformation. However, a reliable free energy profile able to explain the experimental kinetics has not been published yet. This work presents a detailed investigation of this transformation using the accurate ωB97M-V functional, followed by a detailed microkinetic analysis. We have found two key intermediates. The first one is [(triphos)Ru(HCOO)(THF)]+, named MS5 and formed at the beginning of the catalyzed reaction. The second, and the most stable, is [(triphos)Ru(HCOO)(CH3OH)]+, named MS22 and formed later in the reaction time. The highest barrier in the catalytic cycle (28.1 kcal mol−1) corresponds to the steps MS22 → [(triphos)Ru(H)(H2)(THF)]+ → TS4, with TS4 being the hydride transfer to the coordinated formate. Formic acid released in the catalysis can participate in the important proton transfer steps along the catalytic cycle.

A Density Functional Theory Investigation of Cleavage Mechanism of Dimethylsulphoniopropionate by Lyase DddQ

Dimethylsulfide (DMS) is released from the dimethylmercaptopropionate (DMSP) lyase decomposition reaction, which is of great significance for the global sulfur cycle. Among the various DMSP lyases, DddQ is one of the most prevalent and effective enzymes, catalyzing the conversion of DMSP into DMS. Using density functional calculations, we performed a detailed investigation of the DddQ reaction employing a concerted β-elimination mechanism via Tyr131 or Tyr120 as a general base. The reaction involves several key processes, including the deprotonation of nucleophile base, hydrogen proton transfer on Cα, and Cβ-S bond cleavage. Notably, the Hα proton transfer step is a critical step in determining the reaction rate in both mechanisms.

Using the phospha-Michael reaction for making phosphonium phenolate zwitterions.

The reactions of 2,4-di-tert-butyl-6-(diphenylphosphino)phenol and various Michael acceptors (acrylonitrile, acrylamide, methyl vinyl ketone, several acrylates, methyl vinyl sulfone) yield the respective phosphonium phenolate zwitterions at room temperature. Nine different zwitterions were synthesized and fully characterized. Zwitterions with the poor Michael acceptors methyl methacrylate and methyl crotonate formed, but could not be isolated in pure form. The solid-state structures of two phosphonium phenolate molecules were determined by single-crystal X-ray crystallography. The bonding situation in the solid state together with NMR data suggests an important contribution of an ylidic resonance structure in these molecules. The phosphonium phenolates are characterized by UV-vis absorptions peaking around 360 nm and exhibit a negative solvatochromism. An analysis of the kinetics of the zwitterion formation was performed for three Michael acceptors (acrylonitrile, methyl acrylate, and acrylamide) in two different solvents (chloroform and methanol). The results revealed the proton transfer step necessary to stabilize the initially formed carbanion as the rate-determining step. A preorganization of the carbonyl bearing Michael acceptors allowed for reasonable fast direct proton transfer from the phenol in aprotic solvents. In contrast, acrylonitrile, not capable of forming a similar preorganization, is hardly reactive in chloroform solution, while in methanol the corresponding phosphonium phenolate is formed.

Photo-induced structural dynamics of o-nitrophenol by ultrafast electron diffraction.

The photo-induced dynamics of o-nitrophenol, particularly its photolysis, has garnered significant scientific interest as a potential source of nitrous acid in the atmosphere. Although the photolysis products and preceding photo-induced electronic structure dynamics have been investigated extensively, the nuclear dynamics accompanying the non-radiative relaxation of o-nitrophenol on the ultrafast timescale, which include an intramolecular proton transfer step, have not been experimentally resolved. Herein, we present a direct observation of the ultrafast nuclear motions mediating photo-relaxation using ultrafast electron diffraction. This work spatiotemporally resolves the loss of planarity which enables access to a conical intersection between the first excited state and the ground state after the proton transfer step, on the femtosecond timescale and with sub-Angstrom resolution. Our observations, supported by ab initio multiple spawning simulations, provide new insights into the proton transfer mediated relaxation mechanism in o-nitrophenol.

Pre-equilibrium reactions involving pendent relays improve CO2 reduction mediated by molecular Cr-based electrocatalysts.

Homogeneous earth abundant transition-metal electrocatalysts capable of carbon dioxide (CO2) reduction to generate value-added chemical products are a possible strategy to minimize rising anthropogenic CO2 emissions. Previously, it was determined that Cr-centered bipyridine-based N2O2 complexes for CO2 reduction are kinetically limited by a proton-transfer step during C-OH bond cleavage. Therefore, it was hypothesized that the inclusion of pendent relay groups in the secondary coordination sphere of these molecular catalysts could increase their catalytic activity. Here, it is shown that the introduction of a pendent methoxy group favorably impacts a pre-equilibrium protonation prior to the catalytic resting state, resulting in a significant increase in catalytic activity without a loss of product selectivity for generating carbon monoxide (CO) from CO2. Interestingly, combining the pendent methoxy group with a cationic acid causes a positive shift of the catalytic reduction potential of the system, while maintaining increased activity and quantitative selectivity. This work suggests that tuning the secondary coordination sphere with respect to cationic proton sources can result in activity improvements by modifying the kinetic and thermodynamic aspects of proton transfer in the catalytic cycle.

Theoretical study of electrochemical reduction of CO2 to CO using a nickel-N4-Schiff base complex.

The electrochemical reduction (ECR) of CO2 to CO by nickel-N4-Schiff base complexes as catalysts was investigated using density functional theory (DFT). Three nickel complexes, 1-Ni, 2-Ni, and [2-Ni]Me were considered. Two CO2 reduction pathways, i.e., external and internal proton transfer, were proposed and their reaction energy profiles were computed. The external proton transfer pathway which includes three steps has no transition state. The reaction energies for all steps are exothermic and the reaction catalyzed by 1-Ni has the lowest overall reaction energy (-5.72 eV) followed by those by 2-Ni (-5.56 eV) and [2-Ni]Me (-5.54 eV). The internal proton transfer pathway is composed of four steps. The internal proton transfer step (carboxylic formation) includes a transition state. The CO2 reduction by [2-Ni]Me could not proceed via this mechanism, since [2-Ni]Me does not have an NH group in the ligand and 1-Ni has a lower activation energy (0.83 eV), which is in agreement with the experiment. The charge of the pre-adsorption nickel complex seems to be related to the activity of the catalysts. The catalyst with a less positive nickel charge is more active.

What triggers the coupling of proton transfer and electron transfer at the active site of nitrogenase?

In converting N2 to NH3 the enzyme nitrogenase utilises 8 electrons and 8 protons in the complete catalytic cycle. The source of the electrons is an Fe4S4 reductase protein (Fe-protein) which temporarily docks with the MoFe-protein that contains the catalytic active cofactor, FeMo-co, and an electron transfer cluster called the P cluster. The overall mechanism involves 8 repetitions of a cycle in which reduced Fe-protein docks with the MoFe-protein, one electron transfers to the P-cluster, and then to FeMo-co, followed by dissociation of the two proteins and re-reduction of the Fe-protein. Protons are supplied serially to FeMo-co by a Grotthuss proton translocation mechanism from the protein surface along a conserved chain of water molecules (a proton wire) that terminates near S atoms of the FeMo-co cluster [CFe7S9Mo(homocitrate)] where the multiple steps of the chemical conversions are effected. It is assumed that the chemical mechanisms use proton-coupled electron-transfer (PCET) and that H atoms (e- + H+) are involved in each of the hydrogenation steps. However there is neither evidence for, or mechanism proposed, for this coupling. Here I report calculations of cluster charge distribution upon electron addition, revealing that the added negative charge is on the S atoms of FeMo-co, which thereby become more basic, and able to trigger proton transfer from H3O+ waiting at the near end of the proton wire. This mechanism is supported by calculations of the dynamics of the proton transfer step, in which the barrier is reduced by ca. 3.5 kcal mol-1 and the product stabilised by ca. 7 kcal mol-1 upon electron addition. H tunneling is probable in this step. In nitrogenase it is electron transfer that triggers proton transfer.

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

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

Chalcogen Bond Catalysis with Telluronium Cations for Bromination Reaction: Importance of Electrostatic and Polarization Effects.

Recently, chalcogen bond catalysts with telluronium cations have garnered considerable attention in organic reactions. In this work, chalcogen bond catalysis on the bromination reaction of anisole with N-bromosuccinimide (NBS) with the telluronium cationic catalysts has been explored with density functional theory (DFT). The catalytic reaction is divided into two stages: the bromine transfer step and the proton transfer step. Based on the computational results, one can find the rate-determining step is the bromine transfer step. Moreover, the present study elucidates that a stronger chalcogen bond between catalysts and NBS will give better catalytic performance. Additionally, this work also clarified the importance of the electrostatic and polarization effects in the chalcogen bond between the oxygen atom of NBS and the Te atom of the catalyst in this bromination reaction. The electrostatic and polarization effects are significantly influenced by the electron-withdrawing ability of the substitution groups on the catalysts. Moreover, the structure-property relationship between the strength of chalcogen bond, electrostatic effect, polarization effect and catalytic performance are established for the design of more efficient chalcogen bond catalysts.