Reaction Free Energy Profile Research Articles

Density functional theory study of furfural electrochemical oxidation on the Pt (1 1 1) surface

Electro-oxidation of furfural may allow for tunability of product selectivity by varying the electrode potential. We have applied density functional theory (DFT) to investigate the electrocatalytic oxidation mechanism on the Pt (1 1 1) surface. The potential-dependent reaction free energy profiles for furfural electrocatalytic oxidation to furoic acid, succinic acid, maleic acid, and maleic anhydride are reported. After comparing several possible furfural oxidation paths, we conclude that the electro-oxidation of furfural preferentially proceeds to furoic acid, with further oxidation slowed by difficult CC bond dissociation. Oxidation beyond furoic acid can proceed to succinic acid via 2(3H)-furanone as an intermediate and to maleic acid and maleic anhydride via 2(5H)-furanone as an intermediate. The rate of these processes is likely limited by the decarboxylation of furoic acid. DFT analysis of elementary step thermodynamics and kinetics suggests that the selectivity between furoic acid, succinic acid, maleic acid, or other oxidized products is tunable by varying the electrode potential. Initial experimental results show furoic acid as the most significant product (>80% selectivity) at 0.9 V-RHE on a Pt electrode, in agreement with DFT results. These results broaden our fundamental understanding into electrocatalytic oxidation of furfural, which is applicable in upgrading renewable biomass derivatives.

Exploring Free Energy Profiles of Uracil and Cytosine Reactions with Formaldehyde.

Simple polymers can be potentially formed by the co-oligomerization of pyrimidine nucleobases, uracil and cytosine, with the small molecule formaldehyde. Using density functional calculations, we have constructed a free energy map outlining the thermodynamics and kinetics for (1) the addition of formaldehyde to uracil and cytosine to form hydroxymethylated uracil (HMU) and hydroxymethylated cytosine (HMC), (2) the deamination of cytosine and HMC to uracil and HMU, respectively, and (3) the initial oligomerization of 5-HMU. For the initial formation of monomeric HMU, addition of formaldehyde to the C5 and C6 positions is thermodynamically favored over N1 and N3, but faces higher kinetic barriers, and explains why 5-HMU is the main product observed experimentally. Oligomerization of 5-HMU is thermodynamically favorable although decreasingly so at the tetramer stage. In addition, decreasing concentrations of initial monomer shifts the equilibrium disfavoring oligomer formation.

Room Temperature Methane Capture and Activation by Ni Clusters Supported on TiC(001): Effects of Metal-Carbide Interactions on the Cleavage of the C-H Bond.

Methane is an extremely stable molecule, a major component of natural gas, and also one of the most potent greenhouse gases contributing to global warming. Consequently, the capture and activation of methane is a challenging and intensively studied topic. A major research goal is to find systems that can activate methane, even at low temperatures. Here, combining ultrahigh vacuum catalytic experiments, X-ray photoemission spectra, and accurate density functional theory (DFT) based calculations, we show that small Ni clusters dispersed on the (001) surface of TiC are able to capture and dissociate methane at room temperature. Our DFT calculations reveal that two-dimensional Ni clusters are responsible for this chemical transformation, confirming that the lability of the supported clusters appears to be a critical aspect in the strong adsorption of methane. A small energy barrier of 0.18 eV is predicted for CH4 dissociation into adsorbed methyl and atomic hydrogen species. In addition, the calculated reaction free energy profile at 300 K and 1 atm of CH4 shows no effective energy barriers in the system. Comparison with other reported systems which activate methane at room temperature, including oxide and zeolite-based materials, indicates that a different chemistry takes place on our metal/carbide system. The discovery of a carbide-based surface able to activate methane at low temperatures paves the road for the design of new types of catalysts which can efficiently convert this hydrocarbon into other added-value chemicals, with implications in climate change mitigation.

Accelerated computation of free energy profile at ab initio quantum mechanical/molecular mechanical accuracy via a semi-empirical reference potential. II. Recalibrating semi-empirical parameters with force matching.

An efficient and accurate reference potential simulation protocol is proposed for producing ab initio quantum mechanical/molecular mechanical (AI-QM/MM) quality free energy profiles for chemical reactions in a solvent or macromolecular environment. This protocol involves three stages: (a) using force matching to recalibrate a semi-empirical quantum mechanical (SE-QM) Hamiltonian for the specific reaction under study; (b) employing the recalibrated SE-QM Hamiltonian (in combination with molecular mechanical force fields) as the reference potential to drive umbrella samplings along the reaction pathway; and (c) computing AI-QM/MM energy values for collected configurations from the sampling and performing weighted thermodynamic perturbation to acquire an AI-QM/MM corrected reaction free energy profile. For three model reactions (identity SN2 reaction, Menshutkin reaction, and glycine proton transfer reaction) in aqueous solution and one enzyme reaction (Claisen arrangement in chorismate mutase), our simulations using recalibrated PM3 SE-QM Hamiltonians well reproduced QM/MM free energy profiles at the B3LYP/6-31G* level of theory all within 1 kcal mol-1 with a 20 to 45 fold reduction in the computer time.

Rapid Convergence of Energy and Free Energy Profiles with Quantum Mechanical Size in Quantum Mechanical-Molecular Mechanical Simulations of Proton Transfer in DNA.

In recent years, a number of quantum mechanical-molecular mechanical (QM/MM) enzyme studies have investigated the dependence of reaction energetics on the size of the QM region using energy and free energy calculations. In this study, we revisit the question of QM region size dependence in QM/MM simulations within the context of energy and free energy calculations using a proton transfer in a DNA base pair as a test case. In the simulations, the QM region was treated with a dispersion-corrected AM1/d-PhoT Hamiltonian, which was developed to accurately describe phosphoryl and proton transfer reactions, in conjunction with an electrostatic embedding scheme using the particle-mesh Ewald summation method. With this rigorous QM/MM potential, we performed rather extensive QM/MM sampling, and found that the free energy reaction profiles converge rapidly with respect to the QM region size within ca. ±1 kcal/mol. This finding suggests that the strategy of QM/MM simulations with reasonably sized and selected QM regions, which has been employed for over four decades, is a valid approach for modeling complex biomolecular systems. We point to possible causes for the sensitivity of the energy and free energy calculations to the size of the QM region, and potential implications.

Closed-Shell Organic Compounds Might Form Dimers at the Surface of Molecular Clusters.

The role of covalently bound dimer formation is studied using high-level quantum chemical methods. Reaction free energy profiles for dimer formation between common oxygen-containing functional groups are calculated, and based on the Gibbs free energy differences between transition states and reactants, we show that none of the studied two-component gas-phase reactions are kinetically feasible at 298.15 K and 1 atm. Therefore, the catalyzing effect of water, base, or acid molecules is calculated, and sulfuric acid is identified to lower the activation free energies significantly. We find that the reactions yielding hemiacetal, peroxyhemiacetal, α-hydroxyester, and geminal diol products occur with activation free energies of less than 10 kcal/mol with sulfuric acid as a catalyst, indicating that these reactions could potentially take place on the surface of sulfuric acid clusters. Additionally, the formed dimer products bind stronger onto the pre-existing cluster than the corresponding reagent monomers do. This implies that covalent dimerization reactions stabilize the existing cluster thermodynamically and make it less likely to evaporate. However, the studied small organic compounds, which contain only one functional group, are not able to form dimer products that are stable against evaporation at atmospheric conditions. Calculations of dimer formation onto a cluster surface and the clustering ability of dimer products should be extended to large terpene oxidation products in order to estimate the real atmospheric significance.

Theoretical Investigation of the Reaction Mechanism of Photodeamination Induced by Excited-State Intramolecular Proton Transfer of Cresol Derivatives.

The novel photodeamination process of cresol derivatives 1 and 3 has been reported experimentally ( J. Org. Chem . 2015 , 80 , 10817 ). However, a full theoretical interpretation of the mechanism is still lacking. In the present study, we aim to provide insight into the factors that promote the deamination reaction through density functional theory (DFT) and time-dependent DFT methods. Calculated absorption and emission spectra are in good agreement with the experimental results. Hydrogen-bond strengthening in the excited state has been verified by analyzing relevant bond parameters and vibrational frequencies as well as frontier molecular orbitals (FMOs), implying that hydrogen-bond interaction acts as the important parameter for the excited-state intramolecular proton-transfer (ESIPT) reaction. The proton-transfer and deamination reactions have been qualitatively analyzed through Gibbs free-energy reaction profiles in different electronic states. It can be concluded that the ESIPT and photodeamination reactions occur in the excited state. To further illustrate the photodeamination mechanism, the constructed 2D potential-energy surface indicates that the photodeamination reaction is infeasible without the ESIPT reaction. This work provides the first theoretical rationale for ESIPT-induced photodeamination occurring spontaneously because of protonation of a basic nitrogen atom.

Dioxomolybdenum(VI) compounds with α-amino acid donor ligands as catalytic precursors for the selective oxyfunctionalization of olefins

A series of cis-dioxomolybdenum(VI) α-amino acid containing compounds I–V has been investigated as potential catalyst precursors for the mild and selective oxyfunctionalization of conjugated or unconjugated olefins like styrene, α-methylstyrene, cis-β-methylstyrene, cyclohexene and cyclooctene, using tert-butyl hydroperoxide (TBHP) as main oxidant. All the I–V complexes behaved as active heterogeneous and recyclable catalysts, showing good to quantitative conversion values of the substrate. In all cases, high selectivity toward the corresponding epoxide formation was detected. No substantial difference in terms of efficiency has been observed among the different catalysts I–V, thus confirming that the different nature of the amino acidic side-chain does not strictly affect the catalytic process. Insights into mechanistic details and reaction free energy profile of catalytic oxidations by means of quantum chemical calculations have been discussed.

Why does the Y326I mutant of monoamine oxidase B decompose an endogenous amphetamine at a slower rate than the wild type enzyme? Reaction step elucidated by multiscale molecular simulations.

This work investigates the Y326I point mutation effect on the kinetics of oxidative deamination of phenylethylamine (PEA) catalyzed by the monoamine oxidase B (MAO B) enzyme. PEA is a neuromodulator capable of affecting the plasticity of the brain and is responsible for the mood enhancing effect caused by physical exercise. Due to a similar functionality, PEA is often regarded as an endogenous amphetamine. The rate limiting step of the deamination was simulated at the multiscale level, employing the Empirical Valence Bond approach for the quantum treatment of the involved valence states, whereas the environment (solvated protein) was represented with a classical force field. A comparison of the reaction free energy profiles delivered by simulation of the reaction in the wild type MAO B and its Y326I mutant yields an increase in the barrier by 1.06 kcal mol-1 upon mutation, corresponding to a roughly 6-fold decrease in the reaction rate. This is in excellent agreement with the experimental kinetic studies. Inspection of simulation trajectories reveals possible sources of the point mutation effect, namely vanishing favorable electrostatic interactions between PEA and a Tyr326 side chain and an increased amount of water molecules at the active site due to the replacement of tyrosine by a less spacious isoleucine residue, thereby increasing the dielectric shielding of the catalytic environment provided by the enzyme.

SN2 Reaction Rate Enhancement by β-Cyclodextrin at the Liquid/Liquid Interface

An inverse phase transfer catalyst typically enhances the rate of biphasic reaction by bringing the water-insoluble reactant from the organic to the aqueous phase. We use the empirical valence bond (EVB) approach to obtain reaction free energy profiles for a model SN2 reaction inside the β-cyclodextrin (β-CD) cavity at the water/1-bromooctane interface and in bulk water to show that a significant rate enhancement is taking place at the liquid/liquid interface rather than in the bulk. By examining several solvent–solute structural and energetic properties, we demonstrate that the rate enhancement when the reaction takes place inside the cavity at the interface is primarily due to limited accessibility of interfacial water molecules, which results in destabilization of the reactants. Greater accessibility of water molecules when the catalyst is in the bulk stabilizes the reactants and does not lead to rate enhancement despite the significant hydrophobicity of the cavity’s interior.

A Multidimensional B-Spline Correction for Accurate Modeling Sugar Puckering in QM/MM Simulations.

The computational efficiency of approximate quantum mechanical methods allows their use for the construction of multidimensional reaction free energy profiles. It has recently been demonstrated that quantum models based on the neglect of diatomic differential overlap (NNDO) approximation have difficulty modeling deoxyribose and ribose sugar ring puckers and thus limit their predictive value in the study of RNA and DNA systems. A method has been introduced in our previous work to improve the description of the sugar puckering conformational landscape that uses a multidimensional B-spline correction map (BMAP correction) for systems involving intrinsically coupled torsion angles. This method greatly improved the adiabatic potential energy surface profiles of DNA and RNA sugar rings relative to high-level ab initio methods even for highly problematic NDDO-based models. In the present work, a BMAP correction is developed, implemented, and tested in molecular dynamics simulations using the AM1/d-PhoT semiempirical Hamiltonian for biological phosphoryl transfer reactions. Results are presented for gas-phase adiabatic potential energy surfaces of RNA transesterification model reactions and condensed-phase QM/MM free energy surfaces for nonenzymatic and RNase A-catalyzed transesterification reactions. The results show that the BMAP correction is stable, efficient, and leads to improvement in both the potential energy and free energy profiles for the reactions studied, as compared with ab initio and experimental reference data. Exploration of the effect of the size of the quantum mechanical region indicates the best agreement with experimental reaction barriers occurs when the full CpA dinucleotide substrate is treated quantum mechanically with the sugar pucker correction.

Entropy and Enzyme Catalysis.

The role played by entropy for the enormous rate enhancement achieved by enzymes has been debated for many decades. There are, for example, several confirmed cases where the activation free energy is reduced by around 10 kcal/mol due to entropic effects, corresponding to a rate enhancement of ∼107 compared to the uncatalyzed reaction. However, despite substantial efforts from both the experimental and theoretical side, no real consensus has been reached regarding the origin of such large entropic contributions to enzyme catalysis. Another remarkable instance of entropic effects is found in enzymes that are adapted by evolution to work at low temperatures, near the freezing point of water. These cold-adapted enzymes invariably show a more negative entropy and a lower enthalpy of activation than their mesophilic orthologs, which counteracts the exponential damping of reaction rates at lower temperature. The structural origin of this universal phenomenon has, however, remained elusive. The basic problem with connecting macroscopic thermodynamic quantities, such as activation entropy and enthalpy derived from Arrhenius plots, to the 3D protein structure is that the underlying detailed (microscopic) energetics is essentially inaccessible to experiment. Moreover, attempts to calculate entropy contributions by computer simulations have mostly focused only on substrate entropies, which do not provide the full picture. We have recently devised a new approach for accessing thermodynamic activation parameters of both enzyme and solution reactions from computer simulations, which turns out to be very successful. This method is analogous to the experimental Arrhenius plots and directly evaluates the temperature dependence of calculated reaction free energy profiles. Hence, by extensive molecular dynamics simulations and calculations of up to thousands of independent free energy profiles, we are able to extract activation parameters with sufficient precision for making direct comparisons to experiment. We show here that the agreement with the measured quantities, for both enzyme catalyzed and spontaneous solution reactions, is quite remarkable. Importantly, we can now address some of the most spectacular entropy effects in enzymes and clarify their detailed microscopic origin. Herein, we discuss as examples the conversion of cytidine to uridine catalyzed by cytidine deaminase and reactions taking place on the ribosome, namely, peptide bond formation and GTP hydrolysis by elongation factor Tu. It turns out that the large entropy contributions to catalysis in these cases can now be rationalized by our computational approach. Finally, we address the problem of cold adaptation of enzyme reaction rates and prove by computational experiments that the universal activation enthalpy-entropy phenomenon originates from mechanical properties of the outer protein surface.

Free energy profiles for two ubiquitous damaging agents: methylation and hydroxylation of guanine in B-DNA.

DNA methylation and hydroxylation are two ubiquitous reactions in DNA damage induction, yet insights are scarce concerning the free energy of activation within B-DNA. We resort to multiscale simulations to investigate the attack of a hydroxyl radical and of the primary diazonium onto a guanine embedded in a solvated dodecamer. Reaction free energy profiles characterize two strongly exergonic processes, yet allow unprecedented quantification of the barrier towards this damage reaction, not higher than 6 kcal mol-1 and sometimes inexistent, and of the exergonicities. In the case of the [G(C8)-OH]˙ intermediate, we challenge the functional dependence of such simulations: recently-proposed functionals, such as M06-2X and LC-BLYP, agree on a ∼4 kcal mol-1 barrier, whereas the hybrid GGA B3LYP functional predicts a barrier-less pathway. In the long term, multiscale approaches can help build up a unified panorama of DNA lesion induction. These results stress the importance of DFT/MM-MD simulations involving new functionals towards the sound modelling of biomolecule damage even in the ground state.

Thermodynamics of the Purine Nucleoside Phosphorylase Reaction Revealed by Computer Simulations

Enzymes are able to catalyze chemical reactions by reducing the activation free energy, yielding significant increases in the reaction rates. This can thermodynamically be accomplished by either reducing the activation enthalpy or increasing the activation entropy. The effect of remote mutations on the thermodynamic activation parameters of human purine nucleoside phosphorylase is examined using extensive molecular dynamics and free energy simulations. More than 2700 independent reaction free energy profiles for six different temperatures have been calculated to obtain high-precision computational Arrhenius plots. On the basis of these, the activation enthalpies and entropies were computed from linear regression of the plots with ΔG⧧ as a function of 1/T, and the obtained thermodynamic activation parameters are in very good agreement with those from experiments. The Arrhenius plots immediately show that the 6-oxopurines (INO and GUO) have identical slopes, whereas the 6-aminopurine (ADO) has a significantly different slope, indicating that the substrate specificity is related to the difference in thermodynamic activation parameters. Furthermore, the calculations show that the human PNP specificity for 6-oxopurines over 6-aminopurines originates from significant differences in electrostatic preorganization. The effect of the remote double mutation, K22E and H104R (E:R), has also been examined, as it alters human PNP toward the bovine PNP. These residues are situated on the protein surface, 28-35 Å from the active site, and the mutation alters the enthalpy-entropy balance with little effect on the catalytic rates. It is thus quite remarkable that the empirical valence bond method can reproduce the enthalpies and entropies induced by these long-range mutations.

How theory and simulation can drive fuel cell electrocatalysis

Over the last decade, theory and modeling have become essential tools to navigate the parameter space that governs activity and stability of electrocatalyst systems for polymer electrolyte fuel cells. This perspective covers essential phenomena from atomic scale to nanoscale and discusses the impact of the key parameters at play. It is centered around the development of first-principles electrochemical methods as a foremost goal in the field. The general modeling framework entails at its core a self-consistency problem that must be solved to relate the metal phase potential to descriptors of catalyst activity and stability. Density functional theory has captured a central role in this rapidly evolving field. The article puts more than usual emphasis on aspects of the multifaceted challenges in fuel cell electrocatalysis that at present lie beyond the capabilities of density functional theory; they include metal charging and solvent effects. Following the general discussion of the theoretical-computational framework, an approach for “deciphering” the oxygen reduction reaction is demonstrated; it reconciles reaction pathways and free energy profiles obtained from density functional theory simulations with kinetic modeling of surface reactions and effective kinetic parameters. Another section dwells on the importance of metal charging phenomena that are especially important for the catalytic function of nanoporous media. The penultimate section exposes the ambivalent role of Pt oxide formation in modulating catalytic properties for the oxygen reduction reaction as well as for catalyst corrosion.

Molecular Basis of Hydroperoxide Specificity in Peroxiredoxins: The Case of AhpE from Mycobacterium tuberculosis.

Peroxiredoxins (Prxs) constitute a ubiquitous family of Cys-dependent peroxidases that play essential roles in reducing hydrogen peroxide, peroxynitrite, and organic hydroperoxides in almost all organisms. Members of the Prx subfamilies show differential oxidizing substrate specificities that await explanations at a molecular level. Among them, alkyl hydroperoxide reductases E (AhpE) is a novel subfamily comprising Mycobacterium tuberculosis AhpE and AhpE-like proteins expressed in some bacteria and archaea. We previously reported that MtAhpE reacts ∼10(4) times faster with an arachidonic acid derived hydroperoxide than with hydrogen peroxide, and suggested that this surprisingly high reactivity was related to the presence of a hydrophobic groove at the dimer interface evidenced in the crystallography structure of the enzyme. In this contribution we experimentally confirmed the existence of an exposed hydrophobic patch in MtAhpE. We found that fatty acid hydroperoxide reduction by the enzyme showed positive activation entropy that importantly contributed to catalysis. Computational dynamics indicated that interactions of fatty acid-derived hydroperoxides with the enzyme properly accommodated them inside the active site and modifies enzyme's dynamics. The computed reaction free energy profile obtained via QM/MM simulations is consistent with a greater reactivity in comparison with hydrogen peroxide. This study represents new insights on the understanding of the molecular basis that determines oxidizing substrate selectivity in the peroxiredoxin family, which has not been investigated at an atomic level so far.

A Striking Case of Enantioinversion in Gold Catalysis and Its Probable Origins.

The cyclization of the hydroxy-allene 2 to the tetrahydrofuran 3 catalyzed by the gold-phosphoramidite complex 1, after ionization with an appropriate silver salt AgX, is one of the most striking cases of enantioinversion known to date. The major reason why the sense of induction can be switched from (S) to (R) solely by changing either the solvent or the temperature or the nature of the counterion X is likely found in the bias of the organogold intermediates to undergo assisted proto-deauration. Such assistance can be provided by a protic solvent, a reasonably coordinating counterion or even by a second substrate molecule itself; in this case, the reaction free energy profile gains a strong entropic component that can ultimately dictate the stereochemical course.

Mechanical Heterogeneity Favors Fragmentation of Strained Actin Filaments

We present a general model of actin filament deformation and fragmentation in response to compressive forces. The elastic free energy density along filaments is determined by their shape and mechanical properties, which were modeled in terms of bending, twisting, and twist-bend coupling elasticities. The elastic energy stored in filament deformation (i.e., strain) tilts the fragmentation-annealing reaction free-energy profile to favor fragmentation. The energy gradient introduces a local shear force that accelerates filament intersubunit bond rupture. The severing protein, cofilin, renders filaments more compliant in bending and twisting. As a result, filaments that are partially decorated with cofilin are mechanically heterogeneous (i.e., nonuniform) and display asymmetric shape deformations and energy profiles distinct from mechanically homogenous (i.e., uniform), bare actin, or saturated cofilactin filaments. The local buckling strain depends on the relative size of the compliant segment as well as the bending and twisting rigidities of flanking regions. Filaments with a single bare/cofilin-decorated boundary localize energy and force adjacent to the boundary, within the compliant cofilactin segment. Filaments with small cofilin clusters were predicted to fragment within the compliant cofilactin rather than at boundaries. Neglecting contributions from twist-bend coupling elasticity underestimates the energy density and gradients along filaments, and thus the net effects of filament strain to fragmentation. Spatial confinement causes compliant cofilactin segments and filaments to adopt higher deformation modes and store more elastic energy, thereby promoting fragmentation. The theory and simulations presented here establish a quantitative relationship between actin filament fragmentation thermodynamics and elasticity, and reveal how local discontinuities in filament mechanical properties introduced by regulatory proteins can modulate both the severing efficiency and location along filaments. The emergent behavior of mechanically heterogeneous filaments, particularly under confinement, emphasizes that severing in cells is likely to be influenced by multiple physical and chemical factors.

Exploring reaction pathways for O-GlcNAc transferase catalysis. A string method study.

The inverting O-GlcNAc glycosyltransferase (OGT) is an important post-translation enzyme, which catalyzes the transfer of N-acetylglucosamine from UDP-N-acetylglucosamine (UDP-GlcNAc) to the hydroxyl group of the Ser/Thr of cytoplasmic, nuclear, and mitochondrial proteins. In the past, three different catalytic bases were proposed for the reaction: His498, α-phosphate, and Asp554. In this study, we used hybrid quantum mechanics/molecular mechanics (QM/MM) Car-Parrinello molecular dynamics to investigate reaction paths using α-phosphate and Asp554 as the catalytic bases. The string method was used to calculate the free-energy reaction profiles of the tested mechanisms. During the investigations, an additional mechanism was observed. In this mechanism, a proton is transferred to α-phosphate via a water molecule. Our calculations show that the mechanism with α-phosphate acting as the base is favorable. This reaction has a rate-limiting free-energy barrier of 23.5 kcal/mol, whereas reactions utilizing Asp554 and water-assisted α-phosphate have barriers of 41.7 and 40.9 kcal/mol, respectively. Our simulations provide a new insight into the catalysis of OGT and may thus guide rational drug design of transition-state analogue inhibitors with potential therapeutic use.

Fundamental reaction pathway and free energy profile of proteasome inhibition by syringolin A (SylA).

In this study, molecular dynamics (MD) simulations and first-principles quantum mechanical/molecular mechanical free energy (QM/MM-FE) calculations have been performed to uncover the fundamental reaction pathway of proteasome with a representative inhibitor syringolin A (SylA). The calculated results reveal that the reaction process consists of three steps. The first step is a proton transfer process, activating Thr1-O(γ) directly by Thr1-N(z) to form a zwitterionic intermediate. The next step is a nucleophilic attack on the olefin carbon of SylA by the negatively charged Thr1-O(γ) atom. The last step is a proton transfer from Thr1-N(z) to another olefin carbon of SylA to complete the inhibition reaction process. The calculated free energy profile demonstrates that the second step should be the rate-determining step and has the highest free energy barrier of 24.6 kcal mol(-1), which is reasonably close to the activation free energy (∼22.4-23.0 kcal mol(-1)) derived from the available experimental kinetic data. In addition, our computational results indicate that no water molecule can assist the rate-determining step, since the second step is not involved in a proton transfer process. The obtained mechanistic insights should be valuable for understanding the inhibition process of proteasome by SylA and structurally related inhibitors at a molecular level, and thus provide a solid mechanistic base and valuable clues for future rational design of novel, more potent inhibitors of proteasome.