Dynamic Environments as a Tool to Preserve Desired Output in a Chemical Reaction Network

Current efforts to design functional molecular systems have overlooked the importance of coupling out-of-equilibrium behaviour with changes in the environment. Here, the authors use an oscillating reaction network and demonstrate that the application of environmental forcing, in the form of periodic changes in temperature and in the inflow of the concentration of one of the network components, removes the dependency of the periodicity of this network on temperature or flow rates and enforces a stable periodicity across a wide range of conditions. Coupling a system to a dynamic environment can thus be used as a simple tool to regulate the output of a network. In addition, the authors show that coupling can also induce an increase in behavioural complexity to include quasi-periodic oscillations.     

Spontaneous Emergence of Homochirality via Coherently Coupled Antagonistic and Reversible Reaction Cycles

Asymmetric synthesis aims at obtaining enantio‐enriched products in stereoselective reactions under a chiral influence. We demonstrate both mathematically and numerically that, even under nominally achiral conditions, fully homochiral steady states can be obtained in open reactive systems by spontaneous mirror‐symmetry breaking in the homogenous solution phase when the autocatalytic reaction network is closed in the form of coherently coupled antagonistic reversible reaction cycles which, paradoxically, allow for complete recycling of the reactant. We show that the fully reversible Frank mechanism for spontaneous mirror‐symmetry breaking is closely related to the Lotka–Volterra system, which models predator–prey relations in ecosystems. Amplification of total enantiomeric excess and the principle of microscopic reversibility are not in conflict for all conceivable reactions. A viable and widely applicable reaction protocol is introduced and discussed, and it permits the theoretical implications to be applied to practical laboratory examples. Implications for the possible origin of biological homochirality on early earth are discussed.     

On the Nonlinear Dynamic State Reconstruction Problem for Chemical/Biochemical Reaction Systems in the Presence of Model Uncertainty

A new approach to the unmeasurable state reconstruction problem for nonlinear chemical reaction systems in the presence of model uncertainty is proposed. In particular, a new robust nonlinear state estimation method is developed that explicitly uses all the available useful information associated with: (i) a dynamic model inevitably characterized by uncertainty, and (ii) a set of sensor measurements in order to accurately reconstruct other key quantities/variables that cannot be measured on-line due to physical and/or technical limitations. The problem of interest is conveniently formulated and addressed within the context of singular partial differential equations (PDE) theory, leading to a nonlinear state estimator that possesses a state-dependent gain computed through the solution of a system of first-order singular PDEs. A set of necessary and sufficient conditions is presented that ensure the existence and uniqueness of a locally analytic solution to the aforementioned system of singular PDEs, and a series solution method that can be easily implemented via a MAPLE code is developed. Under these conditions, the convergence of the estimation error or the mismatch between the actual unmeasurable states and their estimates is analyzed and characterized in the presence of model uncertainty. Finally, the performance of the proposed nonlinear etimator and its convergence properties are evaluated in an illustrative biochemical reaction system that exhibits nonlinear behavior coupled with parametric uncertainty, and the estimation objective is to accurately reconstruct the unmeasurable substrate concentration using the available cell mass concentration measurements and the model of the system under consideration.     

Formation of Azulene-Embedded Nanographene: Naphthalene to Azulene Rearrangement During the Scholl Reaction

Incorporation of a non-hexagonal ring into a nanographene framework can lead to new electronic properties. During the attempted synthesis of naphthalene-bridged double [6]helicene and heptagon-containing nanographene by the Scholl reaction, an unexpected azulene-embedded nanographene and its triflyloxylated product were obtained, as confirmed by X-ray crystallographic analysis and 2D NMR spectroscopy. A 5/7/7/5 ring-fused substructure containing two formal azulene units is formed, but only one of them shows an azulene-like electronic structure. The formation of this unique structure is explained by arenium ion mediated 1,2-phenyl migration and a naphthalene to azulene rearrangement reaction according to an in-silico study. This report represents the first experimental example of the thermodynamically unfavorable naphthalene to azulene rearrangement and may lead to new azulene-based molecular materials.     

Competing Reaction Pathways in Heterogeneously Catalyzed Hydrogenation of Allyl Cyanide: The Chemical Nature of Surface Species

We present a mechanistic study on the formation of an active ligand layer over Pd(111), turning the catalytic surface highly active and selective in partial hydrogenation of an α,β-unsaturated aldehyde acrolein. Specifically, we investigate the chemical composition of a ligand layer consisting of allyl cyanide deposited on Pd(111) and its dynamic changes under the hydrogenation conditions. On pristine surface, allyl cyanide largely retains its chemical structure and forms a layer of molecular species with the CN bond oriented nearly parallel to the underlying metal. In the presence of hydrogen, the chemical composition of allyl cyanide strongly changes. At 100 K, allyl cyanide transforms to unsaturated imine species, containing the C=C and C=N double bonds. At increasing temperatures, these species undergo two competing reaction pathways. First, the C=C bond become hydrogenated and the stable N-butylimine species are produced. In the competing pathway, the unsaturated imine reacts with hydrogen to fully hydrogenate the imine group and produce butylamine. The latter species are unstable under the hydrogenation reaction conditions and desorb from the surface, while the N-butylimine adsorbates formed in the first reaction pathway remain adsorbed and act as an active ligand layer in selective hydrogenation of acrolein.     

Formation of Azulene‐Embedded Nanographene: Naphthalene to Azulene Rearrangement During the Scholl Reaction

Incorporation of a non‐hexagonal ring into a nanographene framework can lead to new electronic properties. During the attempted synthesis of naphthalene‐bridged double [6]helicene and heptagon‐containing nanographene by the Scholl reaction, an unexpected azulene‐embedded nanographene and its triflyloxylated product were obtained, as confirmed by X‐ray crystallographic analysis and 2D NMR spectroscopy. A 5/7/7/5 ring‐fused substructure containing two formal azulene units is formed, but only one of them shows an azulene‐like electronic structure. The formation of this unique structure is explained by arenium ion mediated 1,2‐phenyl migration and a naphthalene to azulene rearrangement reaction according to an in‐silico study. This report represents the first experimental example of the thermodynamically unfavorable naphthalene to azulene rearrangement and may lead to new azulene‐based molecular materials.     

Diels-Alder reactions II: The Reaction Mechanism

The possible mechanisms of the preparatively so productive Diels-Alder reactions are discussed critically on the basis of experimental data. Although most of the facts can be explained readily by a synchronous mechanism, a number of problems remains.     

Reaction Mechanism of the Hydrogermylation/Hydrostannylation of Unactivated Alkenes with Two‐Coordinate EII Hydrides (E=Ge,Sn): A Theoretical Study

Quantum chemical calculations using density functional theory with the TPSS+D3(BJ) and M06‐2X+D3(ABC) functionals have been carried out to understand the mechanisms of catalyst‐free hydrogermylation/hydrostannylation reactions between the two‐coordinate hydrido‐tetrylenes :E(H)(L⁺) (E=Ge or Sn, L⁺=N(Ar⁺)(SiiPr₃); Ar⁺=C₆H₂{C(H)Ph₂}₂iPr‐2,6,4) and a range of unactivated terminal (C₂H₃R, R=H, Ph, or tBu) and cyclic [(CH)₂(CH₂)₂(CH₂)_n, n=1, 2, or 4] alkenes. The calculations suggest that the addition reactions of the germylenes and stannylenes to the cyclic and acyclic alkenes occur as one‐step processes through formal [2+2] addition of the E?H fragment across the C?C π bond. The reactions have moderate barriers and are weakly exergonic. The steric bulk of the tetrylene amido groups has little influence on the activation barriers and on the reaction energies of the anti‐Markovnikov pathway, but the Markovnikov addition is clearly disfavored by the size of the substituents. The addition of the tetrylenes to the cyclic alkenes is less exergonic than the addition to the terminal alkenes, which agrees with the experimentally observed reversibility of the former reactions. The hydrogermylation reactions have lower activation energies and are more exergonic than the stannylene addition. An energy decomposition analysis of the transition state for the hydrogermylation of cyclohexene shows that the reaction takes place with simultaneous formation of the Ge?C and (Ge)H?C′ bonds. The dominant orbitals of the germylene are the σ‐type lone pair MO of Ge, which serves as a donor orbital, and the vacant p(π) MO of Ge, which acts as acceptor orbital for the π* and π MOs of the olefin. Inspection of the transition states of some selected reactions suggests that the differences between the activation energies come from a delicate balance between the deformation energies of the interacting species and their interaction energies.     

表面化学反应体系中非线性问题的理论研究*

本文综述了表面化学反应体系中若干重要非线性问题的研究现状及作者所取得的研究成果, 其中包括表面催化反应体系中的非平衡动力学相变, 分形表面反应体系中的非线性动力学行为, 表面反应体系中噪声诱导的时空有序结构及其转变规律, 表面反应体系中的随机共振等。     

Energy Propagation Through a Protometabolism Leading to the Local Emergence of Singular Stationary Concentration Profiles

Living systems rely on chains of energy transfer from an energy source to maintain their metabolism. This task requires functionally identified components and organizations. However, propagation of a sustained energy flux through a cascade of reaction cycles has never been reproduced at a steady state in a simple chemical system. By using energy patterning and a diffusing hub reactant, we achieved the transfer of energy through an abiotic protometabolism. Patterned illumination was applied to a liquid solution of a reversible photoacid. It resulted in the local onset of a proton pump, which subsequently drove an extended reaction–diffusion cycle that involved pH‐sensitive reactants. Thus, light has been used for locally setting out of chemical equilibrium a reaction involving “blind” reactants. The spontaneous onset of an energy‐transfer chain notably drives the local generation of singular dissipative chemical structures; continuous matter fluxes are dynamically maintained at boundaries between spatially and chemically segregated zones, in the absence of any membrane or predetermined material structure.     

The Combined Role of Catalysis and Solvent Effects on the Biginelli Reaction: Improving Efficiency and Sustainability

The traditional Biginelli reaction is a three‐component condensation between urea, benzaldehyde and an acetoacetate ester to give a dihydropyrimidinone. An investigation into catalytic and solvent effects has returned the conclusion that the diketo–enol tautomerisation equilibrium of the dicarbonyl reactant dictates the yield of the reaction. Whereas the solvent is responsible for the tautomerisation equilibrium position, the catalyst only serves to eliminate kinetic control from the reaction. Generally, to preserve reaction efficiency and improve sustainability, bio‐derivable p‐cymene was found to be a useful solvent. The metal–enolate intermediate that results from the application of a Lewis acidic catalyst often cited as promoting the reaction appears to hinder the reaction. In this instance, a Brønsted acidic solvent can be used to return greater reactivity to the dicarbonyl reagent.     

反应和分离过程的结合

本文简要介绍了近年来反应和分离过程结合的现状和发展趋势。     

The Mechanism of the Wacker Reaction: A Tale of Two Hydroxypalladations

We present a concise review on the most pertinent investigations that illuminate the complicated and elusive mechanism for the Wacker process, homogeneous olefin oxidation by palladium(II) catalysts. For more than four decades, multitudes of creative and elegant studies detailing the nucleophilic addition and other steps of the Wacker process have appeared contradictory, while in fact modern perspective has shown an intricate and colorful picture of the “textbook” organometallic reaction. A summary and critical analysis of previous studies is of great importance to explain resolved and highlight unresolved questions about this frequently misunderstood reaction.     

Sustainable Heck–Matsuda Reaction with Catalytic Amounts of Diazonium Salts: An Experimental and Theoretical Study

The palladium‐catalyzed Heck–Matsuda reaction with a catalytic amount of an in‐situ‐generated diazonium salt proceeded under mild and sustainable conditions. The reaction proceeded at room temperature, under base‐free conditions, and only generated tBuOH, H₂O, and N₂ as by‐products. Ortho‐substituted diazonium salts were more‐efficiently coupled to methyl acrylate than their corresponding para isomers, which required the addition of anisole as an additive. In support of these experimental data, we carried out theoretical studies to gain a deeper understanding of these reaction outcomes.     

Modeling the Reaction of Carboxylic Acids and Isonitriles in a Self-Assembled Capsule

Quantum chemical calculations were used to study the reaction of carboxylic acids with isonitriles inside a resorcinarene-based self-assembled capsule. Experimentally, it has been shown that the reactions between p-tolylacetic acid and n-butyl isonitrile or isopropyl isonitrile behave differently in the presence of the capsule compared both with each other and also with their solution counterparts. Herein, the reasons for these divergent behaviors are addressed by comparing the detailed energy profiles for the reactions of the two isonitriles inside and outside the capsule. An energy decomposition analysis was conducted to quantify the different factors affecting the reactivity. The calculations reproduce the experimental findings very well. Thus, encapsulation leads to lowering of the energy barrier for the first step of the reaction, the concerted α-addition and proton transfer, which in solution is rate-determining, and this explains the rate acceleration observed in the presence of the capsule. The barrier for the final step of the reaction, the 1,3 O→N acyl transfer, is calculated to be higher with the isopropyl substituent inside the capsule compared with n-butyl. With the isopropyl substituent, the transition state and the product of this step are significantly shorter than the preceding intermediate, and this results in energetically unfavorable empty spaces inside the capsule, which cause a higher barrier. With the n-butyl substituent, on the other hand, the carbon chain can untwine and hence uphold an appropriate guest length.     

The Huisgen Reaction: Milestones of the 1,3‐Dipolar Cycloaddition

The concept of 1,3‐dipolar cycloadditions was presented by Rolf Huisgen 60 years ago. Previously unknown reactive intermediates, for example azomethine ylides, were introduced to organic chemistry and the (3+2) cycloadditions of 1,3‐dipoles to multiple‐bond systems (Huisgen reaction) developed into one of the most versatile synthetic methods in heterocyclic chemistry. In this Review, we present the history of this research area, highlight important older reports, and describe the evolution and further development of the concept. The most important mechanistic and synthetic results are discussed. Quantum‐mechanical calculations support the concerted mechanism always favored by R. Huisgen; however, in extreme cases intermediates may be involved. The impact of 1,3‐dipolar cycloadditions on the click chemistry concept of K. B. Sharpless will also be discussed.     

Insight into the Mechanism of the Michael Reaction

The mechanism for the nucleophilic addition step of the Michael reaction between methanethiol as a model Michael donor and several α‐substituted methyl acrylates (X=F, Cl, Me, H, CN, NO₂) as model Michael acceptors is described in detail. We suggest a novel way to condense electrophilic Fukui functions at specific atoms in terms of the contributions from the atomic orbitals to the LUMO or, more generally, to the orbital controlling the reaction. This procedure correctly associates activation energies to local electrophilic Fukui indices for the cases treated in this work. The calculated reaction barriers strongly depend on the nature of the substituent. As a general rule, activation energies are governed by structural changes, although electronic factors are significant for electron‐withdrawing groups. Nucleophilic addition to Michael receptors is best described as a highly nonsynchronous process, in which the geometry of the transition state comprises a nonplanar six‐membered ring. Formation of the S ??? C bond, which defines the interaction between the reactants, progresses ahead of all other primitive processes in the early stages of the transformation. In view of our results, we postulate that highly complex chemical reactions, as is the case for the nucleophilic addition step studied herein, that involve cleavage/formation of a total of six bonds, lower their activation energies by favoring nonsynchronicity, that is, for these types of systems, primitive changes should advance at different rates.     

Analyzing Reaction Rates with the Distortion/Interaction‐Activation Strain Model

The activation strain or distortion/interaction model is a tool to analyze activation barriers that determine reaction rates. For bimolecular reactions, the activation energies are the sum of the energies to distort the reactants into geometries they have in transition states plus the interaction energies between the two distorted molecules. The energy required to distort the molecules is called the activation strain or distortion energy. This energy is the principal contributor to the activation barrier. The transition state occurs when this activation strain is overcome by the stabilizing interaction energy. Following the changes in these energies along the reaction coordinate gives insights into the factors controlling reactivity. This model has been applied to reactions of all types in both organic and inorganic chemistry, including substitutions and eliminations, cycloadditions, and several types of organometallic reactions.     

The Menshutkin Reaction in the Gas Phase and in Aqueous Solution: A Valence Bond Study

The recently developed (L. Song, W. Wu, Q. Zhang, S. Shaik, J. Phys. Chem. A 2004 , 108, 6017–6024) valence bond method coupled to a polarized continuum model (VBPCM) is applied to the Menshutkin reaction, NH₃+CH₃Cl→CH₃NH₃⁺+Cl^?, in the gas phase and in aqueous solution. The computed barriers and reaction energies at the level of the breathing orbital VB method (P. C. Hiberty, J. P. Flament, E. Noizet, Chem. Phys. Lett. 1992 , 189, 259), BOVB and VBPCM//BOVB, are comparable to CCSD(T) and CCSD(T)//PCM results and to experimental values in solution. The gas‐phase reaction is endothermic and leads to an ion‐pair complex via a late transition state. By contrast, the reaction in the aqueous phase is exothermic and leads to separate solvated ions as reaction products, via an early transition state. The VB calculations provide also the reactivity parameters needed to apply the valence bond state correlation diagram method, VBSCD (S. Shaik, A. Shurki, Angew. Chem. Int. Ed. 1999 , 38, 586). It is shown that the reactivity parameters along with their semiempirical derivations provide together a satisfactory qualitative and quantitative account of the barriers.