Transition State Research Articles

Nonlinear composition dependence of hydrogen bond lifetime in water-DMSO binary mixtures: The role of hydrophobic interaction.

The lifetime of a hydrogen bond between water and dimethyl sulfoxide (DMSO) is found to be considerably longer than that between two water molecules in neat water. This is counter-intuitive because the charge on the oxygen in DMSO is considerably less than that in water. Additionally, the strength of the water-dimethyl sulfoxide (w-D) hydrogen bond is found to be strongly composition dependent; the lifetime of the hydrogen bond is ten times larger at 30% than at very low concentrations. Using computer simulations, we perform microscopic structural and dynamic analysis to find that these anomalies arise at least partly from an "action-at-a-distance" effect where the attraction between the hydrophobic methyl groups results in the self-aggregation of DMSO molecules that "cages" both the rotational and linear motions of the molecules involved. This is reflected in the observed strong correlation of the lifetime with the local coordination number of the associated methyl groups. The elongated w-D h-bond lifetime causes a slowdown of collective dynamics and affects the lifetime of the w-w h-bond. This nonlinear feedback mechanism explains the strong composition dependence of viscosity and is anticipated to play a dominant role in many self-assemblies. Furthermore, the w-D hydrogen bond breaking mechanism changes from low to high DMSO concentration, a phenomenon not anticipated a priori. We introduce a new order parameter-based free energy surface of the bond breaking pathway. A two-dimensional transition state rate theory calculation is performed for the lifetime of the w-D h-bond that is found to be semi-quantitatively accurate.

Sequential nucleophilic aromatic substitutions on cyanuric chloride: synthesis of BODIPY derivatives and mechanistic insights.

Herein we report a study on the sequential substitution of different nucleophiles on cyanuric chloride to obtain potential candidates for metal sensors (5a-c). The set of nucleophiles on the 1,3,5-triazine ring includes a phenolic BODIPY, an aminoalkyl pyridine and aminoalkyl phosphoramidates, each one designed to play a specific role in the final fluoroionophore. Three new triazine triads were synthesized in similar yields: 5a (45%), 5b (43%) and 5c (52%) after a methodical sequential combination of the nucleophiles via thermodependent nucleophilic aromatic substitution of the three chlorine atoms of cyanuric chloride. To ratify the synthetic results we simulated the reaction mechanisms for the different nucleophiles, aiming to address the distinctive orthogonality and temperature control inherent in this process, identifying and providing a sound rationale for any preferential sequence of nucleophiles inserted into the triazine core. According to our experimental and computational analysis (thermo- and kinetic preferences), we have identified the following preferential order for the sequential substitution: p-hydroxybenzaldehyde > 2-(pyridin-2-yl)ethanamine > aminoalkyl phosphoramidate, indicating that all steps follow a single-step process (concerted) in two stages, where nucleophilic addition precedes leaving group dissociation. The Meisenheimer σ-complex was identified as a transition state structure, with insufficient stability to exist as an intermediate. We observed a consistent and progressive increase in barrier height: 2-8 kcal mol-1 for the first step, 9-15 kcal mol-1 for the second step, and >15 kcal mol-1 for the third substitution. These findings align with the experimental observation of thermodependency in the sequential substitution.

Physicochemical Mechanics Instead of Transition State Theory.

This article initially reminds the basics of transition state theory (TST) and gives a textbook example illustrating the often-forgotten problems with TST-based description of reversible reactions. Then, we briefly describe a suggested by us approach called physicochemical mechanics. It was initially developed to describe both the rates and equilibria of chemical mass transport. Here, we show that the same classical mechanics-based approach is working for the kinetics of elementary mono-, bimolecular, and electrochemical reactions. Traditional assumptions regarding pseudoequilibrium for transition state formation are not necessary anymore. A simple interpretation of compensation and tunneling effects is given. The inversion zone for rate constants of strongly exothermic redox reactions is also explained.

Molecular Models of Atomically Dispersed Uranium at MoS2 Surfaces Reveal Cooperative Mechanism of Water Reduction.

Single atoms of uranium supported on molybdenum sulfide surfaces (U@MoS2) have been recently demonstrated to facilitate the hydrogen evolution reaction (HER) through electrocatalysis. Theoretical calculations have predicted uranium hydroxide moieties bound to edge-sulfur atoms of MoS2 as a proposed transition state involved in the HER process. However, the isolation of relevant intermediates involved in this process remains a challenge, rendering mechanistic hypotheses unverified. The present work describes the isolation and characterization of a uranium-hydroxide intermediate on molybdenum sulfide surfaces using [(Cp*3Mo3S4)UCp*], a molecular model of a reduced uranium center supported at MoS2. Mechanistic investigations highlight the metalloligand cooperativity with uranium involved in the water activation pathway. The corresponding uranium-oxo analogue, [(Cp*3Mo3S4)Cp*U(═O)], was also accessed from the hydroxide cluster via hydrogen atom transfer and from [(Cp*3Mo3S4)UCp*] through an alternative direct oxygen atom transfer. These results provide an atomistic perspective on the reactivity of low-valent uranium at molybdenum sulfide surfaces toward water, modeling key intermediates associated with the HER of U@MoS2 catalysts.

Axially Chiral N‐Oxide Catalysts for the Allylation and Crotylation of Aromatic Aldehydes: Exploiting Nonlinear Effects

A new family of IAN‐type amine N‐oxides is presented as catalysts for the allylation and crotylation of aromatic aldehydes with allyltrichlorosilanes. The catalyst design anticipates the formation of dimers, which translates into a remarkably positive nonlinear effect in the allylation reaction. This nonlinear effect enables utilization of the catalyst in its subenantiopure form. As enantiopure catalysts are not required under this regime, the synthesis of these N‐oxides is straightforward through asymmetric synthesis, avoiding lenghty synthesis from the chiral pool or resolution of diastereoisomers. Studies of the corresponding crotylation with Z‐ and E‐crotylsilanes suggest that the reaction proceeds through a chair‐like transition state

α’‐Selective Selenium‐catalyzed Allylic C‐H Amination of Enol Derivatives

A transition metal‐free Se‐catalyzed C‐H amination protocol for α’‐amination of enol derivatives has been developed. This reaction can be used to functionalize a wide variety of oxygen‐ and halogen‐substituted alkenes spanning a vast range of nucleophilicities, giving α’‐aminated enol derivatives with high regioselectivity. Amination of E/Z mixtures of alkenes proceeds stereoconvergently to give the (Z)‐enol derivatives exclusively. Mechanistic studies revealed that the relative reactivity and α’‐regioselectivity of these transformations is determined by substantial resonance donation to the heteroatom‐bound carbon in the transition state. These products participate in traditional reactions of enol derivatives, allowing for efficient functionalization of both α‐ and α’‐positions from a single enol derivative with high diastereocontrol.

α'-Selective Selenium-catalyzed Allylic C-H Amination of Enol Derivatives.

A transition metal-free Se-catalyzed C-H amination protocol for α'-amination of enol derivatives has been developed. This reaction can be used to functionalize a wide variety of oxygen- and halogen-substituted alkenes spanning a vast range of nucleophilicities, giving α'-aminated enol derivatives with high regioselectivity. Amination of E/Z mixtures of alkenes proceeds stereoconvergently to give the (Z)-enol derivatives exclusively. Mechanistic studies revealed that the relative reactivity and α'-regioselectivity of these transformations is determined by substantial resonance donation to the heteroatom-bound carbon in the transition state. These products participate in traditional reactions of enol derivatives, allowing for efficient functionalization of both α- and α'-positions from a single enol derivative with high diastereocontrol.

Ab Initio Chemical Kinetics for Oxidation of CH3OH by N2O4: Elucidation of the Mechanism for Major Product Formation and Its Relevancy to Tropospheric Chemistry.

Next to CH4, CH3OH is the most abundant C1 organics in the troposphere. The redox reaction of CH3OH with N2O4 had been shown experimentally to produce CH3ONO, instead of CH3ONO2. The mechanism for the reaction remains unknown to date. We have investigated the reaction by ab initio MO calculations at the UCCSD(T)/6-311+G(3df,2p)//UB3LYP/6-311+G(3df,2p) level. The result indicates that the reaction takes place primarily by the isomerization of N2O4 to ONONO2 through a very loose transition state within the N2O4-CH3OH collision complex with a 14.3 kcal/mol barrier, followed by the rapid attack of ONONO2 at CH3OH producing CH3ONO and HNO3. The predicted mechanism for the redox reaction compares closely with the hydrolysis of N2O4. The computed rate constant, k1 = 1.43 × 10-8 T1.96 exp (-9092/T) (200-2000 K) cm3molecule-1s-1, for the formation of CH3ONO and HNO3 agrees reasonably with available low-temperature kinetic data and is found to be similar to that of the isoelectronic N2O4 + CH3NH2 reaction. We have also estimated the kinetics for the termolecular reaction, 2 NO2 + CH3OH, and compared it with the direct bimolecular process; the latter was found to be 4.4 × 105 times faster under the troposphere condition. On the basis of the known pollution levels of NO2, N2O4, and CH3OH, both processes were estimated to be of negligible importance to tropospheric chemistry, however.

Study on dynamic behavior of atomic diffusion at interface between TiAlN coating and WC matrix

Abstract The molecular dynamics method was used to simulate the dynamic behavior change of atomic diffusion at interface between TiAlN coating and WC matrix in the carbide tool with TiAlN coating. It was determined that the one-way diffusion of C atom to TiAlN coating resulted in serious lattice distortion on the surface. Meanwhile, the whole diffusion process was accompanied by the continuous increase of stress, resulting in gradual deformation of the material. The interface bonding performance also decreases. Then, the surface energy and atomic layer convergence are calculated by the first-principles method. The TiAlN crystal surface is stable at 8 atomic layers, and the WC crystal surface is stable at 6 atomic layers, and then a stable microinterface model can be built. The relaxation processing for the established model was performed to determine the diffusion path of C atom. Then, the energy barrier, adhesion work, interface energy and fracture toughness of different transition state structures in the diffusion path of C atom are calculated, and it is determined that with the deepening of the diffusion of C atom in the coating, the binding ability of the interface of the coating base and the performance of the coating tool are more and more serious damage. Finally, the cutting experiment of TiAlN coated tool is designed. According to the surface topography of TiALN coated tool in different periods, the simulation and theoretical analysis mentioned above are verified, which provides a theoretical basis for the subsequent research on improving the performance of coated tool.

Experimentally Delineating the Catalytic Effect of a Single Water Molecule in the Photochemical Rearrangement of the Phenylperoxy Radical to the Oxepin-2(5H)-one-5-yl Radical.

Catalysis plays a pivotal role in both chemistry and biology, primarily attributed to its ability to stabilize transition states and lower activation free energies, thereby accelerating reaction rates. While computational studies have contributed valuable mechanistic insights, there remains a scarcity of experimental investigations into transition states. In this work, we embark on an experimental exploration of the catalytic energy lowering associated with transition states in the photorearrangement of the phenylperoxy radical-water complex to the oxepin-2(5H)-one-5-yl radical. Employing matrix isolation spectroscopy, density functional theory, and post-HF computations, we scrutinize the (photo)catalytic impact of a single water molecule on the rearrangement. Our computations indicate that the barrier heights for the water-assisted unimolecular isomerization steps are approximately 2-3 kcal mol-1 lower compared to the uncatalyzed steps. This decrease directly coincides with the energy difference in the required wavelength during the transformation (Δλ = λ546nm - λ579nm ≡ 52.4-49.4 = 3.0 kcal mol-1), allowing us to elucidate the differential transition state energy in the photochemical rearrangement of the phenylperoxy radical catalyzed by a single water molecule. Our work highlights the important role of water catalysis and has, among others, implications for understanding the mechanism of organic reactions under atmospheric conditions.

How Droplets Can Accelerate Reactions─Coacervate Protocells as Catalytic Microcompartments.

ConspectusCoacervates are droplets formed by liquid-liquid phase separation (LLPS) and are often used as model protocells-primitive cell-like compartments that could have aided the emergence of life. Their continued presence as membraneless organelles in modern cells gives further credit to their relevance. The local physicochemical environment inside coacervates is distinctly different from the surrounding dilute solution and offers an interesting microenvironment for prebiotic reactions. Coacervates can selectively take up reactants and enhance their effective concentration, stabilize products, destabilize reactants and lower transition states, and can therefore play a similar role as micellar catalysts in providing rate enhancement and selectivity in reaction outcome. Rate enhancement and selectivity must have been essential for the origins of life by enabling chemical reactions to occur at appreciable rates and overcoming competition from hydrolysis.In this Accounts, we dissect the mechanisms by which coacervate protocells can accelerate reactions and provide selectivity. These mechanisms can similarly be exploited by membraneless organelles to control cellular processes. First, coacervates can affect the local concentration of reactants and accelerate reactions by copartitioning of reactants or exclusion of a product or inhibitor. Second, the local environment inside the coacervate can change the energy landscape for reactions taking place inside the droplets. The coacervate is more apolar than the surrounding solution and often rich in charged moieties, which can affect the stability of reactants, transition states and products. The crowded nature of the droplets can favor complexation of large molecules such as ribozymes. Their locally different proton and water activity can facilitate reactions involving a (de)protonation step, condensation reactions and reactions that are sensitive to hydrolysis. Not only the coacervate core, but also the surface can accelerate reactions and provides an interesting site for chemical reactions with gradients in pH, water activity and charge. The coacervate is often rich in catalytic amino acids and can localize catalysts like divalent metal ions, leading to further rate enhancement inside the droplets. Lastly, these coacervate properties can favor certain reaction pathways, and thereby give selectivity over the reaction outcome.These mechanisms are further illustrated with a case study on ribozyme reactions inside coacervates, for which there is a fine balance between concentration and reactivity that can be tuned by the coacervate composition. Furthermore, coacervates can both catalyze ribozyme reactions and provide product selectivity, demonstrating that coacervates could have functioned as enzyme-like catalytic microcompartments at the origins of life.

Accurate NMR Shieldings with σ-Functionals.

In recent years, density-functional methods relying on a new type of fifth-rung correlation functionals called σ-functionals have been introduced. σ-Functionals are technically closely related to the random phase approximation and require the same computational effort but yield distinctively higher accuracies for reaction and transition state energies of main group chemistry and even outperform double-hybrid functionals for these energies. In this work, we systematically investigate how accurate σ-functionals can describe nuclear magnetic resonance (NMR) shieldings. It turns out that σ-functionals yield very accurate NMR shieldings, even though in their optimization, exclusively, energies are employed as reference data and response properties such as NMR shieldings are not involved at all. This shows that σ-functionals combine universal applicability with accuracy. Indeed, the NMR shieldings from a σ-functional using input orbitals and eigenvalues from Kohn-Sham calculations with the exchange-correlation functional of Perdew, Burke and Ernzerhof (PBE) turned out to be the most accurate ones among the NMR shieldings calculated with various density-functional methods including methods using double-hybrid functionals. That σ-functionals can be used for calculating both reliable energies and response properties like NMR shieldings characterizes them as all-purpose functionals, which is appealing from an application point of view.

Rationally Designed L12-Pt2RhFe Intermetallic Catalyst with High CO-Tolerance for Alkaline Methanol Electrooxidation.

It is a grand challenge to deep understanding of and precise control over functional sites for the rational design of highly efficient catalysts for methanol electrooxidation. Here, an L12-Pt2RhFe intermetallic catalyst with integrated functional components is demonstrated, which exhibits exceptional CO tolerance. The Pt2RhFe/C achieves a superior mass activity of 6.43 A mgPt -1, which is 2.23-fold and 3.53-fold higher than those of PtRu/C and Pt/C. Impressively, the Pt2RhFe/C exhibits a significant enhancement in durability owing to its high CO-tolerance and stability. Density functional theory calculations reveal that high performance of Pt2RhFe intermetallic catalyst arises from the synergistic effect: the strong OH binding energy (OHBE) at Fe sites induce stably adsorbed OH species and thus facilitate the dehydrogenation step of methanol via rapid hydrogen transfer, while moderate OHBE at Rh sites promote the formation of the transition state (Pt-CO···OH-Rh) with a low activation barrier for CO removal. This work provides new insights into the role of OH binding strength in the removal of CO species, which is beneficial for the rational design of highly efficient catalysts.

Synthesis and Ring‐Closing Reactions of Aminocyclohexane Derivatives Bearing Unsaturated Side Chains at C2: Stereocontrolled Approaches to cis‐ and trans‐Fused Perhydro‐indoles and ‐Quinolines

AbstractTwo epimeric pairs of N‐Ts‐protected cyclohexylamines that incorporate an unsaturated side‐chain at the C2 position have been prepared. Contrary to expectations, none of these underwent clean, photochemically‐induced intramolecular hydroamination reactions to give the corresponding perhydro‐indole or ‐quinolines. However, they did participate in efficient olefin cross metathesis (OCM) reactions with methyl crotonate. Three of the four acrylates so‐formed engaged in base‐promoted and completely diastereoselective, intramolecular aza‐Michael addition (cyclization) reactions to give the isomeric and C2‐substituted perhydro‐indoles or ‐quinolines with the structures of these being confirmed by single‐crystal X‐ray analyses. DFT calculations generated results consistent with the observed diastereoselectivities and the proposed transition states. Manipulation of the ester groups associated with the cyclization products allowed for their conversion, inter alia, into the corresponding n‐propyl residues and thus providing novel analogues of neurotoxic alkaloids such as pumiliotoxin C.

Novel Insights into the Catalytic Mechanism of Collagenolysis by Zn(II)-Dependent Matrix Metalloproteinase-1.

Collagen hydrolysis, catalyzed by Zn(II)-dependent matrix metalloproteinases (MMPs), is a critical physiological process. Despite previous computational investigations into the catalytic mechanisms of MMP-mediated collagenolysis, a significant knowledge gap in understanding remains regarding the influence of conformational sampling and entropic contributions at physiological temperature on enzymatic collagenolysis. In our comprehensive multilevel computational study, employing quantum mechanics/molecular mechanics (QM/MM) metadynamics (MetD) simulations, we aimed to bridge this gap and provide valuable insights into the catalytic mechanism of MMP-1. Specifically, we compared the full enzyme-substrate complex in solution, clusters in solution, and gas-phase to elucidate insights into MMP-1-catalyzed collagenolysis. Our findings reveal significant differences in the catalytic mechanism when considering thermal effects and the dynamic evolution of the system, contrasting with conventional static potential energy surface QM/MM reaction path studies. Notably, we observed a significant stabilization of the critical tetrahedral intermediate, attributed to contributions from conformational flexibility and entropy. Moreover, we found that protonation of the scissile bond nitrogen occurs via proton transfer from a Zn(II)-coordinated hydroxide rather than from a solvent water molecule. Following C-N bond cleavage, the C-terminus remains coordinated to the catalytic Zn(II), while the N-terminus forms a hydrogen bond with a solvent water molecule. Subsequently, the release of the C-terminus is facilitated by the coordination of a water molecule. Our study underscores the pivotal role of protein conformational dynamics at physiological temperature in stabilizing the transition state of the rate-limiting step and key intermediates, compared to the corresponding reaction in solution. These fundamental insights into the mechanism of collagen degradation provide valuable guidance for the development of MMP-1-specific inhibitors.

Chain-Length Dependence of Peptide-Lipid Bilayer Interaction Strength and Binding Kinetics: A Combined Theoretical and Experimental Approach.

Physical interactions between polypeptide chains and lipid membranes underlie critical cellular processes. Yet, despite fundamental importance, key mechanistic aspects of these interactions remain elusive. Bulk experiments have revealed a linear relationship between free energy and peptide chain length in a model system, but does this linearity extend to the interaction strength and to the kinetics of lipid binding? To address these questions, we utilized a combination of coarse-grained molecular dynamics (CG MD) simulations, analytical modeling, and atomic force microscopy (AFM)-based single molecule force spectroscopy. Following previous bulk experiments, we focused on interactions between short hydrophobic peptides (WLn, n = 1, ..., 5) with 1-palmitoyl-2-oleoyl-glycero-3-phosphocholine (POPC) bilayers, a simple system that probes peptide primary structure effects. Potentials of mean force extracted from CG MD recapitulated the linearity of free energy with the chain length. Simulation results were quantitatively connected to bulk biochemical experiments via a single scaling factor of order unity, corroborating the methodology. Additionally, CG MD revealed an increase in the distance to the transition state, a result that weakens the dependence of the dissociation force on the peptide chain length. AFM experiments elucidated rupture force distributions and, through modeling, intrinsic dissociation rates. Taken together, the analysis indicates a rupture force plateau in the WLn-POPC system, suggesting that the final rupture event involves the last 2 or 3 residues. In contrast, the linear dependence on chain length was preserved in the intrinsic dissociation rate. This study advances the understanding of peptide-lipid interactions and provides potentially useful insights for the design of peptides with tailored membrane-interacting properties.

Acid-base synergistic effect towards catalytic transfer hydrogenation reactions

Catalytic transfer hydrogenation (CTH) of aldehydes/ketones by using alcohols as hydrogen donors is an attractive and environmentally friendly hydrogenation technology, which has evoked widespread attention in synthesis of fine chemicals from biomass resources. In this work, a Co-Al mixed metal oxide catalyst (Co1Al2-MMO-200) was obtained through structural topological transformation process of layered double hydroxides, which was used in the CTH reaction of furfural with isopropanol. Notably, the reaction rate achieves 0.023 mol g−1 h−1, which is preponderate to acid-base catalysts earlier reported. The joint research based on CO2-TPD, NH3-TPD and poisoning experiment substantiates that the synergy effect of acid-base sites plays an essential role in this catalytic system. Isotopic labelling MS, in-situ FT-IR and DFT studies further verify that the CTH reaction of furfural occurs via the Meerwein-Ponndorf-Verley (MPV) route, in which the basic site promotes the deprotonation of isopropanol whilst the acid site facilitates the formation of a six-membered ring transition state. This work demonstrates an acid-base synergetic catalysis for the CTH reaction by revealing the structure-property correlation and exploring reaction route, which is instructive for designing high-performance heterogenous catalysts.

Steric Effect and Intrinsic Electrophilicity and Nucleophilicity from a Conceptual Density Functional Theory and Information-Theoretic Approach as Quantitative Probes of Chemical Reactions.

Appreciating reactivity in terms of physicochemical effects for chemical processesis one of the most important undertakings in chemistry. While transition state (TS) theory provides the framework enabling the reliable calculation of the barrier height for a given elementary step, analytical tools are necessary to gain insight into key factors governing the different processes during chemical reactions. In this contribution, we partition the potential energy surface of an elementary step along the intrinsic coordinate into three segments, the so-called Pre-TS, TS, and Post-TS regions, and then determine the most important factors dictating each segment. This analysis is based on the use of both reactivity descriptors from conceptual density functional theory and concepts from the information-theoretic approach in density functional theory. We found that in both Pre-TS and Post-TS regions, steric effects are the dominant factors, whereas in the TS region, it is the intrinsic electrophilic and nucleophilic propensity of the transition state structure that governs the reactivity. The wide applicability of our approach is shown by a validation for a total of 37 organic and inorganic reactions. This work thus, in our view, provides a novel perspective on how chemical reactivity can be quantified at different stages of chemical reactions.

Mechanism, thermochemistry, and kinetics of formation of PhC(O)H and HOPhC(O)H during unimolecular decomposition of P-PhC(O2•)HPhOH.

Bisphenols are one of the main components of bio-oil, produced during the pyrolysis of lignin-containing biomass. Synthetic bisphenols are used in polycarbonate plastics, epoxy resins, and thermal papers. Their mechanism of oxidation is important for the determination of the fire safety of these materials and the possibility of using them as additives in fuels for the decrease and description of ignition delays, as well as for the determination of their health risk assessment in medicine. One representative of bisphenols is p-benzylphenol (p-PhCH2PhOH), which is formed during the fast pyrolysis of lignine-containing biomass. Its thermochemistry of oxidation has been partially studied previously. It is shown that the reaction of chain oxidation of p-PhCH2PhOH is thermochemically favorable at low temperatures. However, these studies consider only two pathways of this reaction: (1) the chain oxidation of RH by RO2• and (2) the tautomerization of R'HO2• to R'O2H with following production of R'O• and OH radicals. At the same time, the reactions of intramolecular rearrangement of RO2•, produced PhC(O)H and •PhOH or HOPhC(O)H and •Ph, are not reported but can be an important part of its oxidation mechanism. The five DFT (M06-2X (i = 1), B3LYP (i = 2), wB97XD (i = 3), M08HX (i = 4), MN15 (i = 5)) approaches with 6-311 + + G(d,p) basis set are used for the determination of standard enthalpies of atomization (ΔraH°(Xi)) of considered compounds (molecules, radicals, and transition states). These values of ΔraH°(Xi) are corrected using the empirical linear calibration dependencies, reported previously. The different calibration dependencies are used for the hydrocarbons (including the aromatics and simple oxygenated derivatives) and for the peroxides. The corrected values of ΔraH°(Xi, CORR) are used according to Hess's law for the determination of ΔfH°(Xi, CORR). The most consistent values of ΔfH°(X, MEAN) are derived from the coordination of the values of ΔfH°(Xi,CORR) using the intersection of their values of standard deviations (3SDi). These values of ΔfH°(X, MEAN), as well as the B3LYP values of S°(X), which are accounting the frequencies correction and internal rotations, as well as their temperature dependencies, are used for the determination of thermochemistry of considered reactions and of the calculation, within transition state theory (TST), of the values of high pressure limits of the rate constant. The values of H°(Xi), S°(Xi), and G°(Xi) are calculated using the Gaussian 16w program. The considered mechanism is prepared using ISIS/Draw package. The temperature dependencies of thermochemical properties and the values of rate constants are determined using the ChemRate program (v.1.5). The optimized structures are visualized using the Chemcraft package.

Structural and mechanistic analysis of Ca2+-dependent regulation of transglutaminase 2 activity using a Ca2+-bound intermediate state

Mammalian transglutaminases, a family of Ca2+-dependent proteins, are implicated in a variety of diseases. For example, celiac disease (CeD) is an autoimmune disorder whose pathogenesis requires transglutaminase 2 (TG2) to deamidate select glutamine residues in diet-derived gluten peptides. Deamidation involves the formation of transient γ-glutamyl thioester intermediates. Recent studies have revealed that in addition to the deamidated gluten peptides themselves, their corresponding thioester intermediates are also pathogenically relevant. A mechanistic understanding of this relevance is hindered by the absence of any structure of Ca2+-bound TG2. We report the X-ray crystallographic structure of human TG2 bound to an inhibitory gluten peptidomimetic and two Ca2+ ions in sites previously designated as S1 and S3. Together with additional structure-guided experiments, this structure provides a mechanistic explanation for how S1 regulates formation of an inhibitory disulfide bond in TG2, while also establishing that S3 is essential for γ-glutamyl thioester formation. Furthermore, our crystallographic findings and associated analyses have revealed that i) two interacting residues, H305 and E363, play a critical role in resolving the thioester intermediate into an isopeptide bond (transamidation) but not in thioester hydrolysis (deamidation); and ii) residues N333 and K176 stabilize preferred TG2 substrates and inhibitors via hydrogen bonding to nonreactive backbone atoms. Overall, the intermediate-state conformer of TG2 reported here represents a superior model to previously characterized conformers for both transition states of the TG2-catalyzed reaction.