Lowering Energy Barriers in Surface Reactions through Concerted Reaction Mechanisms

Any technologically important chemical reaction typically involves a number of different elementary reaction steps consisting of bond‐breaking and bond‐making processes. Usually, one assumes that such complex chemical reactions occur in a step‐wise fashion where one single bond is made or broken at a time. Using first‐principles calculations based on density functional theory we show that the barriers of rate‐limiting steps for technologically relevant surface reactions are significantly reduced if concerted reaction mechanisms are taken into account.     

Role of Water in the Reaction Mechanism and endo/exo Selectivity of 1,3-Dipolar Cycloadditions Elucidated by Quantum Chemistry and Machine Learning

Asymmetric 1,3-dipolar cycloadditions of azomethine ylides with activated olefins are among the most important and versatile methods for the synthesis of enantioenriched pyrroline and pyrrolidine derivatives. Despite both theoretical and practical importance, the role of water molecules in the reactivity and endo/exo selectivity remains unclear. To explore how water accelerates the reactions and improves the endo/exo selectivity of the cycloadditions of 1,3-dipole phthalazinium-2-dicyanomethanide ( 1 ) and two dipolarophiles, an ab initio-quality neural network potential that overcomes the computational bottleneck of explicitly considering water molecules was used. It is demonstrated that not only the nature of both the dipolarophile and the 1,3-dipole, but also the solvent medium, can perturb or even alter the reaction mechanism. An extreme case was found for the reaction of 1,3-dipole 1 with methyl vinyl ketone, in which the reaction mechanism changes from a concerted to a stepwise mode on going from MeCN to H₂O as solvent, with formation of a zwitterionic intermediate that is a very shallow minimum on the energy surface. Thus, high stereocontrol can still be expected despite the stepwise nature of the mechanism. The results indicate that water can induce global polarization along the reaction coordinate and highlight the role of microsolvation effects and bulk-phase effects in reproducing the experimentally observed aqueous acceleration and enhanced endo/exo selectivity.     

Triesterase and Promiscuous Diesterase Activities of a Di‐CoII‐Containing Organophosphate Degrading Enzyme Reaction Mechanisms

The reaction mechanism for the hydrolysis of trimethyl phosphate and of the obtained phosphodiester by the di‐Co^II derivative of organophosphate degrading enzyme from Agrobacterium radiobacter P230(OpdA), have been investigated at density functional level of theory in the framework of the cluster model approach. Both mechanisms proceed by a multistep sequence and each catalytic cycle begins with the nucleophilic attack by a metal‐bound hydroxide on the phosphorus atom of the substrate, leading to the cleavage of the phosphate‐ester bond. Four exchange‐correlation functionals were used to derive the potential energy profiles in protein environments. Although the enzyme is confirmed to work better as triesterase, as revealed by the barrier heights in the rate‐limiting steps of the catalytic processes, its promiscuous ability to hydrolyze also the product of the reaction has been confirmed. The important role played by water molecules and some residues in the outer coordination sphere has been elucidated, while the binuclear Co^II center accomplishes both structural and catalytic functions. To correctly describe the electronic configuration of the d shell of the metal ions, high‐ and low‐spin arrangement jointly with the occurrence of antiferromagnetic coupling, have been herein considered.     

Mechanism of the Asymmetric Autocatalytic Soai Reaction Studied by Density Functional Theory

The mechanism of the Soai reaction has been thoroughly investigated at the M05‐2X/6‐31G(d) level of theory, by considering ten energetically distinct paths. The study indicates the fully enantioselective catalytic cycle of the homochiral dimers to be the dominant mechanism. Two other catalytic cycles are shown to both be important for correct understanding of the Soai reaction. These are the catalytic cycle of the heterochiral dimer and the non‐enantioselective catalytic cycle of the homochiral dimers. The former has been proved to be not really competitive with the principal cycle, as required for the Soai reaction to manifest chiral amplification, whereas the latter, which is only slightly competitive with the principal one, nicely explains the experimental enantioselectivity observed in the reaction of 2‐methylpyrimidine‐5‐carbaldehyde. The study has also evidenced the inadequacy of the B3LYP functional for mechanistic investigations of the Soai reaction.     

The Search for the Mechanism of the Reaction Catalyzed by Farnesyltransferase

Atomic‐level portrait : The mechanism of the reaction catalyzed by the puzzling enzyme farnesyltransferase is elucidated by using computational methods, allowing the obtainment of the first real detailed atomistic quantum‐chemical transition‐state structure (see figure) for the reaction catalyzed by this enzyme. The results obtained provide an atomic‐level framework for the design of more potent and specific inhibitors for this important enzyme.

     

Competitive Reactivity of Tautomers in the Degradation of Organophosphates by Imidazole Derivatives

The harmful impact caused by pesticides on human health and the environment necessitates the development of efficient degradation processes and control of prohibited stocks of such substances. Organophosphates (OPs) are among the most used agrochemicals in the world and their degradation can proceed through several possible pathways. Investigating the reactivity of OPs with nucleophilic species allows one to propose new and efficient catalyst scaffolds for use in detoxification. In light of the remarkable catalytic activity of imidazole (IMZ) at promoting dephosphorylation processes of OPs, the reactivity of 4(5)-hydroxymethylimidazole (HMZ) with diethyl-2,4-dinitrophenylphosphate (DEDNPP) and Paraoxon are evaluated by combining experimental and theoretical approaches. It is observed that HMZ is an efficient and regiospecific catalyst with reactivity modulated by competing tautomers. To propose an optimal IMZ-based catalyst, quantum chemical calculations were performed for monosubstituted 4(5)IMZ derivatives that might cleave DEDNPP. Both inductive effects and hydrogen bonding by the substituents are shown to influence barriers and mechanisms.     

氟代碳酸乙烯酯添加剂对钠离子电池正极的影响

使用电解液成膜添加剂是一种简单高效的提高电池循环稳定性的方法。氟代碳酸乙烯酯(FEC)的最低未被占据分子轨道(LUMO)能量较低,易被还原,通常被认为是很好的负极成膜添加剂,但因其最高占据分子轨道(HOMO)能量也较低,抗氧化性较好,故其被认为不在正极上发生作用。本工作结合电化学,形貌分析,化学成分表征,原位结构分析等方法研究了FEC添加剂在钠离子电池中的作用。我们发现适量的FEC添加剂不仅可以显著抑制电解液溶剂碳酸丙烯酯(PC)的分解,而且会在正极上形成一层富NaF的保护层,提高循环过程中正极晶格结构稳定性,从而提高电池的循环稳定性。密度泛函理论(DFT)计算表明,FEC之所以能在正极上形成保护层,可能与其容易在正极界面与钠盐阴离子ClO_4~-结合反应有关。     

Multiple Reaction Pathways Operating in the Mechanism of Vinylogous Mannich‐Type Reaction Activated by a Water Molecule

A systematic search for reaction pathways for the vinylogous Mannich‐type reaction was performed by the artificial force induced reaction method. This reaction affords δ‐amino‐γ‐butenolide in one pot by mixing 2‐trimethylsiloxyfuran, imine, and water under solvent‐free conditions. Surprisingly, the search identified as many as five working pathways. Among them, two concertedly produce anti and syn isomers of the product. Another two give an intermediate, which is a regioisomer of the main product. This intermediate can undergo a retro‐Mannich reaction to give a pair of intermediates: an imine and 2‐furanol. The remaining pathway directly generates this intermediate pair. The imine and 2‐furanol easily react with each other to afford the product. Thus, all of these stepwise pathways finally converge to give the main product. The rate‐determining step of all five (two concerted and three stepwise) pathways have a common mechanism: concerted Si? O bond formation through the nucleophilic attack of a water molecule on the silicon atom followed by proton transfer from the water molecule to the imine. Therefore, these five pathways have comparable barriers and compete with each other.     

Reaction mechanism of apocarotenoid oxygenase (ACO): a DFT study

The mechanism of the oxidative cleavage catalyzed by apocarotenoid oxygenase (ACO) was studied by using a quantum chemical (DFT: B3 LYP) method. Based on the available crystal structure, relatively large models of the unusual active-site region, in which a ferrous ion is coordinated by four histidines and no negatively charged ligand, were selected and used in the computational investigation of the reaction mechanism. The results suggest that binding of dioxygen to the ferrous ion in the active site promotes one-electron oxidation of carotenoid leading to a substrate radical cation and a Fe-bound superoxide radical. Recombination of the two radicals, which can be realized in at least two different ways, yields a reactive peroxo species that subsequently evolves into either a dioxetane or an epoxide intermediate. The former easily decays into the final aldehyde products, whereas the oxidation of the epoxide to the proper products of the reaction requires involvement of a water molecule. The calculated activation barriers favor the dioxetane mechanism, yet the mechanism involving the epoxide intermediate cannot be ruled out.     

Study of the Lithium Storage Mechanism of N-Doped Carbon-Modified Cu2S Electrodes for Lithium-Ion Batteries

Owing to their high specific capacity and abundant reserve, Cu_xS compounds are promising electrode materials for lithium-ion batteries (LIBs). Carbon compositing could stabilize the Cu_xS structure and repress capacity fading during the electrochemical cycling, but the corresponding Li⁺ storage mechanism and stabilization effect should be further clarified. In this study, nanoscale Cu₂S was synthesized by CuS co-precipitation and thermal reduction with polyelectrolytes. High-temperature synchrotron radiation diffraction was used to monitor the thermal reduction process. During the first cycle, the conversion mechanism upon lithium storage in the Cu₂S/carbon was elucidated by operando synchrotron radiation diffraction and in situ X-ray absorption spectroscopy. The N-doped carbon-composited Cu₂S (Cu₂S/C) exhibits an initial discharge capacity of 425 mAh g⁻¹ at 0.1 A g⁻¹, with a higher, long-term capacity of 523 mAh g⁻¹ at 0.1 A g⁻¹ after 200 cycles; in contrast, the bare CuS electrode exhibits 123 mAh g⁻¹ after 200 cycles. Multiple-scan cyclic voltammetry proves that extra Li⁺ storage can mainly be ascribed to the contribution of the capacitive storage.     

Hydrogen Release from Dialkylamine–Boranes Promoted by Mg and Ca Complexes: A DFT Analysis of the Reaction Mechanism

Mg and Ca β‐diketiminato silylamides [HC{(Me)CN(2,6‐iPr₂C₆H₃)}₂M(THF)_n{N(SiMe₃)₂}] (M=Mg, n=0; M=Ca, n=1) were studied as precatalysts for the dehydrogenation/dehydrocoupling of secondary amine–boranes R₂HNBH₃. By reaction with equimolar quantities of amine–boranes, the corresponding amidoborane derivatives are formed, which further react to yield dehydrogenation products such as the cyclic dimer [BH₂?NMe₂]₂. DFT was used here to explore the mechanistic alternatives proposed on the basis of the experimental findings for both Mg and Ca amidoboranes. The influence of the steric demand of amine–boranes on the course of the reaction was examined by performing calculations on the dehydrogenation of dimethylamine–borane (DMAB), pyrrolidine–borane (PB), and diisopropylamine–borane. In spite of the analogies in the catalytic activity of Mg‐ and Ca‐based complexes in the dehydrocoupling of amine–boranes, our theoretical analysis confirmed the experimentally observed lower reactivity of Ca complexes. Differences in catalytic activity of Mg‐ and Ca‐based complexes were examined and rationalized. As a consequence of the increase in ionic radius on going from Mg²⁺ to Ca²⁺, the dehydrogenation mechanism changes and formation of a key metal hydride intermediate becomes inaccessible. Dimerization is likely to occur off‐metal in solution for DMAB and PB, whereas steric hindrance of iPr₂NHBH₃ hampers formation of the cyclic dimer. The reported results are of particular interest because, although amine–borane dehydrogenation is now well established, mechanistic insight is still lacking for many systems.     

The Roles of Counterion and Water in a Stereoselective Cysteine‐Catalyzed Rauhut–Currier Reaction: A Challenge for Computational Chemistry

The stereoselective Rauhut–Currier (RC) reaction catalyzed by a cysteine derivative has been explored computationally with density functional theory (M06‐2X). Both methanethiol and a chiral cysteine derivative were studied as nucleophiles. The complete reaction pathway involves rate‐determining elimination of the thiol catalyst from the Michael addition product. The stereoselective Rauhut–Currier reaction, catalyzed by a cysteine derivative as a nucleophile, has also been studied in detail. This reaction was experimentally found to be extremely sensitive to the reaction conditions, such as the number of water equivalents and the effect of potassium counterion. The E1cB process for catalyst elimination has been explored computationally for the eight possible stereoisomers. The effect of explicit water solvation and the presence of counterion (either K⁺ or Na⁺) has been studied for the lowest energy enantiomer pair (1S, 2R, 3S)/(1R, 2S, 3R).     

Computational Insights into Different Mechanisms for Ag-, Cu-, and Pd-Catalyzed Cyclopropanation of Alkenes and Sulfonyl Hydrazones

The [2+1] cycloaddition reaction of a metal carbene with an alkene can produce important cyclopropane products for synthetic intermediates, materials, and pharmaceutical applications. However, this reaction is often accompanied by side reactions, such as coupling and self-coupling, so that the yield of the cyclopropanation product of non-silver transition-metal carbenes and hindered alkenes is generally lower than 50 %. To solve this problem, the addition of a low concentration of diazo compound (decomposition of sulfonyl hydrazones) to alkenes catalyzed by either CuOAc or PdCl₂ was studied, but side reactions could still not be avoided. Interestingly, however, the yield of cyclopropanation products for such hindered alkenes were as high as 99 % with AgOTf as a catalyst. To explain this unexpected phenomenon, reaction pathways have been computed for four different catalysts by using DFT. By combining the results of these calculations with those obtained experimentally, it can be concluded that the efficiency of the silver catalyst is due to the barrierless concerted cycloaddition step and the kinetic inhibition of side reactions by a high concentration of alkene.     

Mercury Methylation by Cobalt Corrinoids: Relativistic Effects Dictate the Reaction Mechanism

The methylation of Hg^II(SCH₃)₂ by corrinoid‐based methyl donors proceeds in a concerted manner through a single transition state by transfer of a methyl radical, in contrast to previously proposed reaction mechanisms. This reaction mechanism is a consequence of relativistic effects that lower the energies of the mercury 6p_1/2 and 6p_3/2 orbitals, making them energetically accessible for chemical bonding. In the absence of spin–orbit coupling, the predicted reaction mechanism is qualitatively different. This is the first example of relativity being decisive for the nature of an observed enzymatic reaction mechanism.     

Insights into the Cascade Reaction of CO and Heteroallenes Mediated by Dinitrogen Hafnocene Complexes: The Indirect Effect of Nitride's Nucleophilicity

A DFT mechanistic exploration of the reactivity of the dinitrogen hafnocene complex, [{(η⁵‐C₅H₂‐1,2,4‐Me₃)₂Hf}₂(μ₂‐N₂)], towards mixtures of CO/CO₂ and CO/OCNtBu is reported. The crucial role of the nitride intermediate is highlighted, as well as the importance of the bridging mode of the cyanate ligand between the two Hf metal atoms throughout the process. Interestingly, the CO₂ addition to the nitride intermediate occurs through an outer‐sphere transition state, whereas the addition of the heteroallene is governed by the steric congestion imposed by cyclopentadienyl ligands.     

Mechanistic Insights into the Rhenium‐Catalyzed Alcohol‐To‐Olefin Dehydration Reaction

Rhenium‐based complexes are powerful catalysts for the dehydration of various alcohols to the corresponding olefins. Here, we report on both experimental and theoretical (DFT) studies into the mechanism of the rhenium‐catalyzed dehydration of alcohols to olefins in general, and the methyltrioxorhenium‐catalyzed dehydration of 1‐phenylethanol to styrene in particular. The experimental and theoretical studies are in good agreement, both showing the involvement of several proton transfers, and of a carbenium ion intermediate in the catalytic cycle.     

Elucidating the Coordination Chemistry and Mechanism of Biological Nitrogen Fixation

How does the enzyme nitrogenase reduce the inert molecule N₂ to NH₃ under ambient conditions that are so different from the energy‐expensive conditions of the best industrial practices? This review focuses on recent theoretical investigations of the catalytic site, the iron–molybdenum cofactor FeMo‐co, and the way in which it is hydrogenated by protons and electrons and then binds N₂. Density functional calculations provide reaction profiles and activation energies for possible mechanistic steps. This establishes a conceptual framework and the principles for the coordination chemistry of FeMo‐co that are essential to the chemical mechanism of catalysis. The model advanced herein explains relevant experimental data.     

A Theoretical Investigation on the Strecker Reaction Catalyzed by a TiIV‐Complex Catalyst Generated from a Cinchona Alkaloid,Achiral Substituted 2,2′‐Biphenol,and Tetraisopropyl Titanate

The mechanism and the origin of selectivity of the asymmetric Strecker reaction catalyzed by a Ti^IV‐complex catalyst generated from a cinchona alkaloid, achiral substituted 2,2′‐biphenol, and tetraisopropyl titanate have been investigated by DFT and ONIOM methods. The calculations indicate that the reaction proceeds through a dual activation mechanism, in which Ti^IV acts as Lewis acid to activate the electrophile aldimine substrate, whereas the tertiary amine in cinchona alkaloid works as Lewis base to promote the activation and isomerization of HCN. The C? C bond formation step is predicted to be the selectivity‐controlling step in the reaction with an energy barrier of 9.3 kcal mol^?1. The “asymmetric activation” is achieved by the transfer of asymmetry from the chiral cinchonine ligand to the axially flexible achiral biphenol ligand through coordination interaction with the central metal Ti^IV. The large steric hindrance from the 3,3′‐position substitute of biphenol, combined with the quinoline fragment of cinchona alkaloid and the orientation of hydrogen bonding of iPrOH, play a key role in controlling the stereoselectivity, which is in good agreement with the experimental observations.