Activation Barrier Of Reaction Research Articles

Exploring the covalent inhibition mechanisms of inhibitors with two different warheads acting on SARS-CoV-2 Mpro by QM/MM simulations

SARS-CoV-2 Mpro had been reported to react with covalent inhibitors 14c and C7, containing a vinyl sulfanilamide and chloromethylamide as the warheads, respectively. However, the detailed reaction mechanisms and warhead effects are still unclear. In this study, the initial state of the catalytic dyad Cys145/His41 is determined as neutral during the non-covalent binding, through MM-PBSA free energy calculations. The Potential of Mean Forces (PMFs) have been computed by QM/MM MD method, obtaining the free energy changes from reactants to products. Both reactions follow asynchronous mechanism. Except the similar proton transfer (PT1), subsequently, nucleophilic addition and an additional proton transfer (PT2) for 14c, while an SN2 nucleophilic substitution for C7 are underwent, respectively. The reaction activation barrier and free energy trends both are in consistent with the experimental IC50 results. Our research enhances understanding of the inhibitory mechanism, and provides insights for designing novel and more effective inhibitors targeting SARS-CoV-2 Mpro.

Trimetallic Alloys as an Electrocatalyst for Fuel Cells: The Case of Methyl Formate on Pt3Pd3Sn2.

The shift toward renewable energy sources plays a central role in the quest for a circular economy. In this context, methyl formate (MF) has garnered attention as a compelling hydrogen carrier and alternative fuel, because of its remarkable characteristics (energy density, ease of storage and transport, and low boiling point). In this study, DFT calculations supported by online electrochemical mass spectroscopy (OE-MS) were performed to investigate the MF electro-oxidation (MFEO) on Pt3Pd3Sn2 (111). The DFT calculations provide insight into the role of Pt, Pd, and Sn atoms in MFEO. Pt and Pd together provide a preferred active site for initiating MFEO through the O-H bond scission, and Sn plays an essential role in the mitigation of CO through oxygenation or water activation. By comparing the reaction energies and activation barriers for all possible reactions in MFEO, the suggested path necessitates a minimum energy of 0.14 eV to initiate the MFEO. This value was supported by the experimental results, showing that the oxidation wave of MF starts at 0.15 V (70 °C). Density functional theory (DFT) results, supported by OE-MS, indicate that the hydrolysis of MF prior to MFEO is not preferred on Pt3Pd3Sn2 (111) surfaces, although the formation of methanol is plausible via a CH3O intermediate. Among the three small organic molecules (SOMs) studied─MF, methanol, and formic acid─MF has the lowest activation energy for the initial bond breaking that starts the whole oxidation process (0.13 eV), compared to formic acid (0.45 eV) and methanol (0.61 eV); thus, MF is the preferred fuel on Pt3Pd3Sn2 (111).

Preferred Electric Field Mechanism for Frustrated Lewis Pair Reactivity.

This study employs computational methods to investigate the mechanism of H2 activation by frustrated Lewis pair (FLP) species, including both intermolecular and intramolecular nitrothane/borane FLP systems. Previous studies have proposed two qualitative reactivity mechanism models to explain the facile cleavage of H2 by FLPs. The findings of this study support the electric field mechanism as the favorable pathway for H2 cleavage. Utilizing frontier molecular orbital theory and energy decomposition analysis, the study explores the electronic structure and nature of the reactions under an external electric field (EEF). Analysis using the activation strain model highlights the significant influence of geometrical deformation energies of FLPs on the activation barriers of H2 activation reactions. Computational results suggest that H2 activation by FLP molecules follows the electric field mechanism, indicating the potential of the FLP/EEF combination as an effective activator for inert molecules.

Nitrosation mechanisms, kinetics, and dynamics of the guanine and 9-methylguanine radical cations by nitric oxide-Radical-radical combination at different electron configurations.

As a precursor to various reactive nitrogen species formed in biological systems, nitric oxide (•NO) participates in numerous processes, including enhancing DNA radiosensitivity in ionizing radiation-based radiotherapy. Forming guanine radical cations is another common DNA lesion resulting from ionization and oxidation damage. As such, the interaction of •NO with guanine radical cations (G•+) may contribute to the radiosensitization of •NO. An intriguing aspect of this process is the participation of multiple spin configurations in the reaction, including open-shell singlet 1,OS[G•+(↑)⋯(↓)•NO], closed-shell singlet 1,CS[G(↑↓)⋯NO+], and triplet 3[G•+(↑)⋯(↑)•NO]. In this study, the reactions of •NO with both unsubstituted guanine radical cations (in the 9HG•+ conformation) and 9-methylguanine radical cations (9MG•+, a guanosine-mimicking model compound) were investigated in the absence and presence of monohydration of radical cations. Kinetic-energy dependent reaction product ions and cross sections were measured using an electrospray ionization guided-ion beam tandem mass spectrometer. The reaction mechanisms, kinetics, and dynamics were comprehended by interpreting the reaction potential energy surface using spin-projected density functional theory, coupled cluster theory, and multiconfiguration complete active space second-order perturbation theory, followed by RRKM kinetics modeling. The combined experimental and computational findings revealed closed-shell singlet 1,CS[7-NO-9MG]+ as the major, exothermic product and triplet 3[8-NO-9MG]+ as the minor, endothermic product. Singlet biradical products were not detected due to high reaction endothermicities, activation barriers, and inherent instability.

Unraveling high-temperature mechanism of NO + CO reaction on BaO-Y2O3: An in situ DRIFTS and microkinetic study

Understanding high-temperature mechanism of NO reduction by CO on heat-resistant metal oxides is crucial for exhaust aftertreatment systems. We employed the NO + CO light off experiment, in situ diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS), density functional theory (DFT), and microkinetic study to elucidate the reaction mechanism on BaO-Y2O3 nanocatalyst. The catalytic cycle consisting of “decomposition-oxidation” mode, Mars-van Krevelen (MvK) mechanism, and Langmuir-Hinshelwood (L-H) mechanism is described by in situ DRIFTS and DFT calculations. Their reaction energies and activation barriers are then employed for the microkinetic analysis, revealing that the activity rate is temperature-dependent and aligns with the experimental result. The high-temperature reaction process is primarily governed by the MvK mechanism with rate-determining steps (RDS) of CO + OL ↔ CO2 + Ov, followed by the “decomposition-oxidation” mode. Critically, local CO32- coverage on the BaO surface can facilitate NO and CO adsorption while withstanding the elementary steps such as N2O dissociation and CO oxidation by lattice oxygen. BaCO3-Y2O3 model can be used to interpret the low-temperature reaction process with the RDS of N2O2 ↔ N2O + O, but it impedes reaction kinetics at high temperatures with the rate contribution also predominantly originating from the MvK mechanism. This work provides fundamental insights into how the reaction proceed, and guide the design and optimization of catalysts that can withstand high temperature while maintaining high activity.

The origin of selectivity in the trimerization of 1,3-cyclopentadiene from an activation strain perspective.

Quantum chemical modeling (DFT-PBE0/cc-pVTZ) of the [4 + 2]-cycloaddition reaction of 1,3-cyclopentadiene (CPD) to (exo/endo)-dicyclopentadiene (DCPD) was carried out, resulting in 14 products-CPD trimers. According to calculations, exo-addition of CPD to the norbornene (NB) fragment of DCPD and trans-addition of CPD to the cyclopentene (CP) fragment of DCPD are kinetically preferred. Ring strain energies ERS were calculated for all trimers using the homodesmotic reaction approach. The least strained trimers are formed by exo-addition of CPD to the NB fragment of exo-DCPD, while the most strained ones are formed by endo-addition of CPD to the NB fragment of endo-DCPD. ERS values are in good agreement with thermodynamic stability of trimers. Analysis of activation energy using the activation strain model showed steric effects causing deformation of the DCPD molecule upon reaching the transition state to be the leading factor of the magnitude of the cycloaddition reaction activation barrier. Deformation of the DCPD molecule mostly occurs in two dihedral angles-the angle of escape of H atoms from the plane of the double bond involved in cycloaddition and the angle between the NB and CP fragments. The sum of deviations of these angles in the transition states (or products) structures is in good agreement with Gibbs activation energies of cycloaddition reactions of CPD to DCPD. Quantum chemical calculations were carried out using density functional theory in Gaussian 09 software. Hybrid exchange-correlation PBE0 functional was used with cc-pVTZ basis set.

Modeling Interfacial Proton-Coupled Electron Transfer Reactions Involving Imidazolium Proton Donors

Proton-coupled electron transfer (PCET) is an elementary reaction that plays a pivotal role in various electrochemical energy conversion and storage processes. PCET reactions involving nonaqueous proton donors are of interest for applications in energy storage such as redox flow batteries, as well as in CO2 and O2 reduction catalysis. Yet, there remains much to be understood about the molecular reactivity of these systems. In this talk, I will describe periodic density functional theory (DFT) studies of interfacial PCET reactions involving different imidazolium proton donors on Pt(111) electrode surfaces.The imidazole conjugate bases adsorb strongly to the electrode surface; however, this adsorption behavior varies with isomers that feature distinct proton positions and with different functional substituent groups. Because the adsorption of imidazole conjugate bases could affect reactivity, these models are used as a foundation to understand the intrinsic PCET kinetics of these systems. The Volmer and Heyrovsky steps of hydrogen evolution reaction are two of the most basic heterogeneous electrochemical PCET reactions and are therefore chosen as model interfacial PCET reactions in this study. Potential-dependent reaction energies and activation barriers are calculated using the charge extrapolation method, where the electrode potential is tuned by modifying proton coverage for different-sized unit cells. This approach is used to develop relationships between PCET reaction thermodynamics and kinetics through Brønsted–Evans–Polanyi (BEP) relationships for different imidazoles, where BEP slopes are analogs to charge transfer coefficients in the Butler–Volmer equation. Investigating reaction parameters influencing charge transfer kinetics at the electrode-electrolyte interface is crucial for designing efficient energy storage systems, impacting overall device performance. These studies show trends in the kinetic behavior of different functionalized imidazoles, which can aid in the design of catalytic and energy storage systems.

Insights into the mechanism, selectivity, and substituent effects in the Diels-Alder reaction of azatrienes with electron-rich dienophiles: An MEDT study

The reactivity and mechanistic intricacies of azatrienes in Diels-Alder reactions have been relatively unexplored despite their intriguing potential applications. In this study, we employ Molecular Electron Density Theory to theoretically investigate the hetero-Diels–Alder reaction involving azatrienes with ethyl vinyl ether and allenyl methyl ether. Analysis of Conceptual Density Functional Theory, energetic profiles, and the topological characteristics is conducted to elucidate the reactions. The revealed mechanism manifests as a polar one-step two-stages process under kinetic control. We establish a clear relationship of between the periselectivity, regioselectivity, and stereoselectivity on one hand and the characteristics of the reactions mechanism on the other hand. The influence of weak interactions on reaction activation barriers and bonding evolution are discussed in detail. We demonstrate that substituents enhancing the reverse electron density flux facilitate the feasibility of the reactions. The results lay ground for a meticulous control of the reaction of azatriene in similar synthetic scenarios.

DFT Simulations on the Nitrogen Reduction Reaction Activity of Transition Metal Nitride and Oxynitride

Transition metal nitride (TMN) is a promising material towards the energy related applications including catalysis and energy storage.1 The sluggish nitrogen reduction reaction (NRR) due to the high energy input to activate N2 remains a significant challenge for NRR electrocatalysts. The surface N of TMN can be a solution to this with initial N vacancy formation via hydrogenation steps and ammonia formation. In addition, with a small amount of surface oxygen present in the catalyst surface, the resulting oxynitride seems very interesting and active towards NRR.2 But the mechanism behind this is not yet understood.In this study, we first focused on the modelling of the structure of metal nitride (ZrN) and oxynitride (ZrOxNy/ZrN) surfaces. The structure of oxynitride is obtained by running molecular dynamics (MD) calculations at both room temperature and experimental deposition temperature (90°C and 750°C). NRR reaction is then studied via the Mars-Van Krevelen (MvK) mechanism with introducing surface N vacancy and subsequent N2 adsorption and N filling. With computing the reaction energy and activation barriers of key reaction steps on both ZrN and ZrOxNy/ZrN, we can find a clue on how surface N of TMN helps to activate N2 and the role of small amount of surface oxygen on activating N2. To study the origin of small amount of oxygen, reaction energies and full reaction pathway along the deposition process are computed and plotted. Finally, dopant effect will be modeled with transition metal dopants (e.g. Cu and Hf) at surface region to study any localized electronic effect on NRR.These results can be useful to design and deposit ZrN acting as effective NRR electrocatalysts.

Double-proton transfer triggering mechanism of nitromethane caused by intermolecular hydrogen bonding at low temperature

The initial triggering mechanism of nitromethane is investigated by first-principles molecular dynamics simulations and temperature-dependent Raman spectroscopy experiment. The Raman spectra at different temperature are obtained by Car-Parrinello molecular dynamics simulation to explore the activated vibration modes caused by low-temperature heat. The temperature-dependent Raman spectra experiment is constructed to compare with the theoretical data. Each possible initial reaction path caused by the activated vibration mode is analyzed to reveal the triggering mechanism of the initial chemical bond breaking for nitromethane. The results show that the intermolecular double-proton transfer is the first reaction step which is triggered by the intermolecular hydrogen bond reinforced with the active C–H stretching vibration (near 3000 cm−1), which is not reported before. The scanning energy barrier related to the increase of C–H bond lengths is about 60 kcal/mol, which is consistent with the calculated activation barrier (59.8 kcal/mol) of intermolecular proton transfer reaction. This proves the reliability of our conclusions. The results provide a new interpretation for the long-debated initial decomposition mechanism of nitromethane.

Importance of hydrogen bonding in base-catalyzed transesterification reactions with vicinal diols

The transesterification reaction kinetics of 2-(benzoyloxy)ethyl benzoate with various alcohols (ethylene glycol, 1,3-propanediol, 1-butanol, propylene glycol and 1,2-butylene glycol) using various cyclic amidine catalysts were investigated. For transesterification with excess glycol (glycolysis), the rate was nearly zero order in diester and glycol concentration, which is substantially different from classical transesterification kinetics with mono-alcohols. The measured kinetic parameters during glycolysis are consistent with a reaction path that is kinetically limited by the decomposition of the reaction intermediate formed from the alkoxide and diester. The DFT-calculated reaction energy and activation barrier for decomposition of this intermediate reveal a critical role of intramolecular hydrogen-bond stabilization made possible by the vicinal –OH of the glycol that effectively increases the concentration of the intermediate during reaction resulting in acceleration of the overall transesterification rate. These findings indicate the nature of both the alcohol solvent and the catalyst influence transesterification rate, and results suggest they are also important in the deconstruction of carbonyl-containing condensation polymers.

Mechanism of Interaction of Nitro Compounds with Olefins in Acetonitrile

The interaction of 4-fluorostyrene with 4-CN-PhNO2 in the presence of various solvents has been simulated by quantum chemistry methods. The reaction mechanism and activation barriers of its stages are proposed. The software package Gaussian03 was used for calculations. The optimal geometric parameters of the structures under study were obtained by means of the DFT/WB97XD/DGDZVP2 methods, the TDSCF/DFT/WB97XD/DGDZVP2 and TD-SCF/DFT/PBEPBE/6-311g++(3d2f,3p2d) methods were used to calculate excited singlet and triplet states, and the IEFPCM model was employed to account for the solvent effects. The transition states were calculated by the TS method using the DFT/PBEPBE/6-311g++(3d2f,3p2d) method.

Insights into Electrolyte Reactivity and Solid Electrolyte Interphase Formation at the Li Metal Anode Surface from DFT Simulations

Solid electrolyte interphase (SEI) is a critical component of lithium ion batteries, yet is poorly characterized and not well understood. We use plane wave density functional theory simulations to perform a comprehensive study of the degradation reaction mechanisms of four electrolyte solvents and additives, ethylene carbonate (EC), propylene carbonate (PC), fluoroethylene carbonate (FEC), and vinylene carbonate (VC), at the Li (001) metal anode surface. The calculations provide fundamental insights into electrolyte decomposition and spontaneous SEI formation. Utilizing automated workflows implemented in the Schrödinger Materials Science Suite, we compute the adsorption energies and calculate the reaction energies for each decomposition pathway. Furthermore, we employ nudged elastic band calculations to compute the decomposition reaction barriers and provide mechanistic insights into the onset of SEI formation. We analyze trends in decomposition reaction energies and the relationships between the reaction energies and the activation barriers for the various electrolyte molecules as a function of applied bias potential. We find that the preferred decomposition pathways are different for the solvent molecules (EC and PC) than for the additives (FEC and VC). Calculations also suggest that applied bias reduces decomposition reaction barriers thus enhancing SEI formation. Such a comprehensive dataset of reaction energies and activation barriers provides useful benchmarks for the development and validation of reactive machine learned force fields for modeling advanced battery chemistries at a larger scale.

Reactivity of the Intramolecular Vicinal Group-13/P- and B/Group-15-Based Frustrate Lewis Pairs with Sulfur Dioxide: Mechanistic Insight from DFT.

The emission of SO2 gas by industrialized societies contributes to the occurrence of acid rain in natural environments. In this study, we put forward a theoretical investigation into the capture reactions of SO2. Our analysis centers on the energy profiles of intramolecular 1,2-cyclohexylene-bridged FLP-associated molecules. We will particularly examine the reactions involving G13/P-based (with G13 denoting Group 13 element) and B/G15-based (with G15 representing Group 15 element) FLP-associated molecules. Except for Tl/P-FLP, B/N-FLP, and B/Bi-FLP, our theoretical examinations indicate that the remaining six FLP-associated molecules, namely G13'/P-FLP (G13' = B, Al, Ga, and In) and B/G15 ' -FLP (G15' = P, As, and Sb), can easily undergo SO2 capture reactions due to their energetic feasibility. Particularly, our theoretical findings suggested that 1,2-cyclohexylene-bridged Al/P-FLP, Ga/P-FLP, B/As-FLP, and B/Sb-FLP are capable of undergoing a reversible reaction and returning to the initial reactant state. Our theoretical evidence indicates that the G13-G15 bond length in the 1,2-cyclohexylene-linked G13/G15-FLP can serve as a basis for evaluating the free activation barrier associated with its reaction with SO2. Two theoretical methods, namely, the frontier molecular orbital theory and the energy decomposition analysis-natural orbitals of chemical valence approach, are utilized to investigate the electronic structure and bonding nature of the reactions under consideration. Moreover, the analyses based on the activation strain model revealed that it is the geometrical deformation energies of G13/G15-FLP, which is the key factor that greatly influences the activation barriers of such SO2 capture reactions. Further, our theoretical computations indicate that such capturing reactions of SO2 by intramolecular 1,2-cyclohexylene-linked G13/G15-based FLP-type molecules obey the Hammond postulate.

Mean field model parameterization to recover coverage-dependent kinetics

Lateral interactions between adsorbates introduce coverage dependence into adsorption energies and activation barriers of surface reactions. Lattice-based kinetic Monte Carlo (kMC) simulations can capture these interactions quantitatively but are laborious to parameterize and solve. Mean field models are more tractable, but protocols to construct and parameterize them are unclear. Here we explore the ability of a coverage-aware mean-field model to map to a lattice-kMC model of a generic two-step reaction network, including quasi-equilibrated adsorption and rate-limiting dissociation steps. We derive expressions for mean-field and coverage-dependent adsorption energies and dissociation barriers and parameterize against lattice-kMC predictions. We show that the parameterized mean-field rates correlate with ground truth lattice-kMC results across a wide range of reaction conditions and identify regions where the mean field fails. The mean field model similarly captures kMC-derived rate-order, Arrhenius and Sabatier plots at a greatly reduced computational cost. The results provide guidance for parameterizing mean-field models, benchmarked against explicit lattice-based approaches for incorporating the influence of coverage effects.

A quantum chemical perspective on the potential application of Fe-decorated C24N24 porous fullerene for catalytic ethylene epoxidation

Density functional theory calculations are used to investigate the reaction mechanisms and activation barriers of ethylene (C2H4) epoxidation by molecular oxygen (O2) using Fe-decorated C24N24 porous fullerene. Calculated adsorption energies demonstrate that the decorated Fe atom has a greater propensity to adsorb O2 molecules than C2H4. The results, on the other hand, indicate that ethylene epoxidation by O2 proceed through the Langmuir Hinshelwood (LH) mechanism. The whole ethylene epoxidation reaction is exothermic, with activation energies ranging from 0.36 to 0.68 eV, showing that this process is both thermodynamically and kinetically favorable. The side reaction, i.e., formation of acetaldehyde, is almost impossible over the proposed catalyst due to its large activation energy.

Cooperative Activation of Small Molecules by Base-Stabilized Borylenes.

Computational investigations were carried out using density functional theory (ωB97XD(toluene)/6-311+G*) on a series of base-stabilized borylenes to understand their ligand properties and potential toward the activation of enthalpically strong E-H bonds (E = H, NH2, SiH2Ph, and CH3) as well as binding with small molecules such as CO and CNMe. The calculated reaction free energies and activation barriers suggest the ability of hitherto unexplored carbene-stabilized borylenes to not only split such bonds but also bind with CO and CNMe. A detailed mechanistic study of these bond activation processes reveals the noninnocent behavior of the carbene moiety attached to the boron center, thereby leading to cooperative splitting of the bonds of interest. The binding of CO and CNMe to the base-stabilized borylenes was investigated by energy decomposition analysis (EDA) with natural orbitals for chemical valence (NOCV), which gave appreciable interaction energy (ΔEint) values, thereby indicating strong binding of CO and CNMe to these borylenes.

Heterostructured mixed metal oxide electrocatalyst for the hydrogen evolution reaction.

The hydrogen evolution reaction (HER) has attracted considerable attention lately because of the high energy density and environmental friendliness of hydrogen energy. However, lack of efficient electrocatalysts and high price hinder its wide application. Compared to a single-phase metal oxide catalyst, mixed metal oxide (MMO) electrocatalysts emerge as a potential HER catalyst, especially providing heterostructured interfaces that can efficiently overcome the activation barrier for the hydrogen evolution reaction. In this mini-review, several design strategies for the synergistic effect of the MMO catalyst on the HER are summarized. In particular, metal oxide/metal oxide and metal/metal oxide interfaces are explained with fundamental mechanistic insights. Finally, existing challenges and future perspectives for the HER are discussed.

First-principles insights into sulfur oxides (SO2 and SO3) adsorption and dissociation on layered iron sulfide (FeS) catalyst

The adsorption of sulfur oxides (SOx) represents the fundamental step towards their conversion to lower-risk sulfur-containing species. Herein, we investigate the adsorption and dissociation mechanism of sulfur dioxide (SO2) and sulfur trioxide (SO3) on layered iron sulfide (FeS) nanocatalyst (001), (011), and (111) surfaces using density functional theory methodology. Both SO2 and SO3 exhibit strong reactivity towards the (011) and (111) surfaces, with the most stable geometry for SO2 and SO3 on the (011) surface predicted to be a tridentate η23(S,O,O) and a bidentate η22(O,O) configuration, respectively, whereas on the (111) surface, they are predicted to be coordinated in a monodentate η21(S) and η21(O) geometry, respectively. Significant charge donation from the FeS surface to the SOx species is observed, which resulted in elongation of S−O bond lengths, confirmed by vibrational frequency analyses. Favourable reaction energy and activation barrier is predicted for SO2 dissociation at the (111) surface.

Ultrathin MoS2 nanosheets decorated on NiSe nanowire arrays as advanced trifunctional electrocatalyst for overall water splitting and urea electrolysis

Developing highly-efficient and low-cost electrocatalysts act as pressing impacts on the flourishing of hydrogen energy, including electrochemical water splitting is a kind of prevailing energy conversion technology. However, it is hampered by the high activation barrier of oxygen evolution reaction (OER). Herein, a hybrid electrocatalyst with trifunctional and 3D core–shell structure is designed by hydrothermal process in order to achieve outstanding OER, hydrogen evolution reaction (HER) and urea oxidation reaction (UOR) properties. NiSe@MoS2/NF catalyst is composed of the heterogeneous interface formed by NiSe nanowire arrays which supported by nickel foam and MoS2 nanosheets. The synergistic effect and strong electronic interaction between the interface display the dominant impact of OER, HER and UOR. Especially in basic electrolyte, the potential is as low as 310 mV at 100 mA cm−2, even Tafel slope is 70.8 mV dec-1, representing the predominant OER property. The HER and UOR also demonstrate enormous prospect with 210, 233 mV at 100 mA cm−2. When NiSe@MoS2/NF||NiSe@MoS2/NF catalyst as anode and cathode, only requires potential of 1.48 V at 10 mA cm−2 for overall water splitting test. The work offers a plain, high-efficiency and inexpensive method to evolve the progressive trifunctional electrocatalysts for other energy-related applications.