An automated method for graph-based chemical space exploration and transition state finding

Algorithms that automatically explore the chemical space have been limited to chemical systems with a low number of atoms due to expensive involved quantum calculations and the large amount of possible reaction pathways. The method described here presents a novel solution to the problem of chemical exploration by generating reaction networks with heuristics based on chemical theory. First, a second version of the reaction network is determined through molecular graph transformations acting upon functional groups of the reacting. Only transformations that break two chemical bonds and form two new ones are considered, leading to a significant performance enhancement compared to previously presented algorithm. Second, energy barriers for this reaction network are estimated through quantum chemical calculations by a growing string method, which can also identify non-octet species missed during the previous step and further define the reaction network. The proposed algorithm has been successfully applied to five different chemical reactions, in all cases identifying the most important reaction pathways.     

关于反应分子数定义的讨论

There are two different views on the definition of reaction molecularity in physical chemistry textbooks and related literatures so far. We give a deep discussion about this conception herein. Starting with the development of chemical kinetics and the definition of elementary reaction and state-state reaction, we clarify that elementary reaction and state-state reaction are the conceptions belonging to macro-and micro-systems, respectively, and reaction molecularity is also belonging to micro-conception. Based on this conclusion, we think that the more reasonable definition of reaction molecularity should be "the number of chemical particles that take part in a state-state reaction (or an elementary chemi-physical reaction) as a reactant".     

Effects of Reversible Chemical Reaction on Morphology and Domain Growth of Phase Separating Binary Mixtures with Viscosity Difference

Summary: The effects of a reversible chemical reaction on morphology and dynamics of phase separating binary mixtures with viscosity difference are studied by numerically solving modified time‐dependent Ginzburg‐Landau and Navier‐Stokes equations. Much more interesting morphologies are observed in the system due to the coupling of reversible chemical reaction and viscosity difference between two components. When the chemical reaction rate is relatively low, the impact of viscosity difference on morphologies is prominent, so that the resulting patterns are affected by both reversible chemical reaction and viscosity difference. However, increasing the chemical reaction rate weakens the impact of viscosity difference on morphologies. Similarly, increasing the chemical reaction rate also suppresses the effects of viscosity difference on domain growth dynamics, which is prominent at the early stage of phase separation when the chemical reaction rate is relatively low. For both cases with relatively low and high chemical reaction rates, the average domain size eventually attains an equilibrium value due to the competition between the mixing of reversible chemical reaction and demixing of phase separation.

Domain patterns of a critical system with ϕ_ini = 0, and Γ₁ = Γ₂ = 0.001.     

Dynamic instabilities of model electrochemical system with electrocatalytic oxidation and preceding chemical reaction

The method of impedance spectroscopy was used to study the regularities of behavior of a model electrochemical system with an electrocatalytic reaction on a planar electrode which is preceded by a homogeneous chemical reaction. It is shown that in the case of low rates of the homogeneous chemical reaction, two types of bifurcations may exist in the system at the chosen attraction constant value; namely, the Hopf bifurcation leading to spontaneous oscillations and saddle-node bifurcation resulting in bistability of the system. The Hopf bifurcation disappears from the system at medium and high rates of the homogeneous chemical reaction, while the saddle-node bifurcation is retained.     

Interacting Quantum Atoms Analysis of the Reaction Force: A Tool to Analyze Driving and Retarding Forces in Chemical Reactions

The analysis of the reaction force and its topology has provided a wide range of fruitful concepts in the theory of chemical reactivity over the years, allowing to identify chemically relevant regions along a reaction profile. The reaction force (RF), a projection of the Hellmann-Feynman forces acting on the nuclei of a molecular system onto a suitable reaction coordinate, is partitioned using the interacting quantum atoms approach (IQA). The exact IQA molecular energy decomposition is now shown to open a unique window to identify and quantify the chemical entities that drive or retard a chemical reaction. The RF/IQA coupling offers an extraordinarily detailed view of the type and number of elementary processes that take reactants into products, as tested on two sets of simple reactions.     

Theoretical study of cytosine deamination from the perspective of the reaction force analysis

A theoretical study of two different mechanisms for the spontaneous deamination of cytosine is presented. In the first mechanism, a tetrahedral intermediate results in a two-step mechanism whereas in the second one, it is the result of a concerted step. In this work a link is made between the two pathways through the study of the evolution along the reaction coordinates of chemical concepts such as chemical potential, hardness and electronic populations within the framework of the reaction force analysis. The reaction force profile suggests that the concerted mechanism is composed of two asynchronous events. The observation of the reaction force profile appears as an easy way to identify asynchronous concerted steps and as a privileged tool to study the more or less asynchronous character of chemical reactions.     

非线性化学反应在低维介质中的动力学行为

通过数值模拟对３分子自催化反应Ａ＋２Ｘ＝３Ｘ在一维和二维介质中的动力学行为进行了研究。发现在一维和二维情形下，如果施以不同的微观反应规则，该反应的渐近行为既可能偏经典化学反应动力学（平均场理论）所预言的平衡极限行为，也可能与之一致。     

Propagation of photosensitive chemical waves on the circular routes

The propagation of chemical waves in the photosensitive Belousov-Zhabotinsky (BZ) reaction was investigated using an excitable field in the shape of a circular ring or figure "8" that was drawn by computer software and then projected on a film soaked with BZ solution using a liquid-crystal projector. For a chemical wave in a circular reaction field, the shape of the chemical wave was investigated depending on the ratio of the inner and outer radii. When two chemical waves were generated on a field shaped like a figure "8" (one chemical wave in each circle) as the initial condition, the location of the collision of the waves either was constant or alternated depending on the degree of overlap of the two circular rings. These experimental results were analyzed on the basis of a geometrical discussion and theoretically reproduced on the basis of a reaction-diffusion system using a modified Oregonator model. These results suggest that the photosensitive BZ reaction may be useful for creating spatio-temporal patterns depending on the geometric arrangement of excitable fields.     

Geometric description of chemical reactions

We use the formalism of Geometrothermodynamics to describe chemical reactions in the context of equilibrium thermodynamics. Any chemical reaction in a closed system is shown to be described by a geodesic in a 2-dimensional manifold that can be interpreted as the equilibrium space of the reaction. We first show this in the particular cases of a reaction with only two species corresponding to either two ideal gases or two van der Waals gases. We then consider the case of a reaction with an arbitrary number of species. The initial equilibrium state of the geodesic is determined by the initial conditions of the reaction. The final equilibrium state, which follows from a thermodynamic analysis of the reaction, is shown to correspond to a coordinate singularity of the thermodynamic metric which describes the equilibrium manifold.     

Electroreduction of 6-amino-5-nitroso-1,3-dimethyluracil on polycrystalline platinum and nickel cathodes in acid aqueous solution

The reduction of 6-amino-5-nitroso-1,3-dimethyluracil (ANDMU) is a key step in caffeine synthesis. Electroreduction technology is a promising green chemical process. The voltammetric behavior of ANDMU at polycrystalline platinum and nickel cathodes was studied. The Nicholson theory was used to resolve the reduction process semi-quantitatively. The results show that ANDMU mainly undergoes an ECE (electron transfer, chemical reaction, electron transfer) process involving four electrons on the platinum and nickel cathodes in which the two electron-transfer steps occur at almost the same potential and the rate of the coupling chemical reaction between two electron-transfer steps is very fast. Apparent kinetic data and diffusion coefficient were determined for the platinum rotating-disk electrode.     

A graph-based toy model of chemistry

Large scale chemical reaction networks are a ubiquitous phenomenon, from the metabolism of living cells to processes in planetary atmospheres and chemical technology. At least some of these networks exhibit distinctive global features such as the "small world" behavior. The systematic study of such properties, however, suffers from substantial sampling biases in the few networks that are known in detail. A computational model for generating them is therefore required. Here we present a Toy Model that provides a consistent framework in which generic properties of extensive chemical reaction networks can be explored in detail and that at the same time preserves the "look-and-feel" of chemistry: Molecules are represented as labeled graphs, i.e., by their structural formulas; their basic properties are derived by a caricature version of the Extended Hückel MO theory that operates directly on the graphs; chemical reaction mechanisms are implemented as graph rewriting rules acting on the structural formulas; reactivities and selectivities are modeled by a variant of the Frontier Molecular Orbital Theory based on the Extended Hückel scheme. The approach is illustrated for two types of reaction networks: Diels-Alder reactions and the formose reaction implicated in prebiotic sugar synthesis.     

具有平方衰减项的平方自催化开放系统中的化学波研究

建立了开放系统中伴随平方衰减反应的双分子自催化反应理论模型,给出了系统的动力学分析,在给定初边值下解的估计及存在化学波的必要条件、化学波波速的最小值及平方衰减项对化学波的影响.随着衰减系数的增加,平方衰减项逐步成为系统反应中化学波波形的决定因素.     

Ethanol Oxidation Reaction Mechanism on Gold Nanowires from Density Functional Theory

Thin gold nanowires (NWs) are materials that could be used as support in different chemical reactions. Using density functional theory (DFT) it was shown that NWs that form linear atomic chains (LACs) are suitable for stimulating chemical reactions. To this end, the oxidation reaction of ethanol supported on the LACs of Au−NWs was investigated. Two types of LACs were used for the study, one pure and the other with an oxygen impurity. The results showed that the oxygen atom in the LAC fulfills important functions throughout the reaction pathway. Before the chemical reaction, it was observed that the LAC with impurity gains structural stability, that is, the oxygen acts as an anchor for the gold atoms in the LAC. In addition, the LAC was shown to be sensitive to disturbances in its vicinity, which modifies its nucleophilic character. During the chemical reaction, the oxidation of ethanol occurs through two different reaction paths and in two stages, both producing acetaldehyde (CH₃CHO). The different reaction pathways are a consequence of the presence of oxygen in the LAC (oxygen conditions the formation of reaction intermediates). In addition, the oxygen in the LAC also modifies the kinetic behavior in both reaction stages. It was observed that, by introducing an oxygen impurity in the LAC, the activation energy barriers decrease ∼69 % and ∼97 % in the first and second reaction stages, respectively.     

Thermolysis of polyethylene hydroperoxides in the melt, Part 12: Mechanisms and kinetics of thermolysis

The thermolysis of polyethylene hydroperoxides is attributed to the reaction of two hydroperoxide groups. This bimolecular reaction appears as a first-order reaction with the mean values of the hydroperoxide concentrations that can be used for the experimental verification of the kinetics. In low molecular mass liquids and solutions these findings would be irreconcilable. However, in polymer melts, this contradiction is more apparent than real. It is a consequence of the heterogeneous kinetics valid in polymer melts. The bimolecular reaction involves the decomposition of pairs of hydroperoxide groups that are relatively close in the elementary oxidation volumes. By diffusion these hydroperoxide groups can come close enough for reaction. From the chemical point of view the decomposition is a bimolecular reaction. However, from the kinetic point of view it is a first-order reaction of the hydroperoxide pairs. The dependency of the first-order rate on the initial hydroperoxide concentration is explained by the heterogeneous kinetics. The activation energy of the overall process can be related to the sum of the activation energies pertaining to the chemical reaction and to the diffusion process.     

Model experiments for the interfacial reaction between polymers during reactive polymer blending

Bilayer film Fourier transform infrared (FTIR) model experiments are designed to provide a well-defined interface for study which can be probed by infrared spectroscopy during the interdiffusion and reaction of two reactive polymers. This provides a model experiment to determine the kinetics and extent of reaction between functionalized polymers during reactive polymer blending. This type of experiment provides data on the reaction at a stagnant interface which is necessary for the analysis of the interface while it is simultaneously undergoing deformation. It is also useful as a screening or preliminary experiment on reactive blending systems in that the extent of reaction may be followed for different systems at different temperatures. Experiments reported here trace the reaction of a styrene–maleic anhydride copolymer with two different amine terminated polymers. Results are obtained for the interdiffusion and reaction of a styrene-maleic anhydride copolymer with two amine terminated polymers: a butadiene-acrylonitrile copolymer and Nylon 11. The kinetics from these experiments include contributions due to both interdiffusion and chemical reaction. The chemical reaction kinetics may be isolated from the diffusion kinetics by performing experiments on well-mixed systems which are prepared by casting films of the polymer mixtures from a mutual solvent. © 1994 John Wiley & Sons, Inc.     

Computer-Assisted Solution of Chemical Problems—The Historical Development and the Present State of the Art of a New Discipline of Chemistry

The topic of this article is the development and the present state of the art of computer chemistry, the computer-assisted solution of chemical problems. Initially the problems in computer chemistry were confined to structure elucidation on the basis of spectroscopic data, then programs for synthesis design based on libraries of reaction data for relatively narrow classes of target compounds were developed, and now computer programs for the solution of a great variety of chemical problems are available or are under development. Previously it was an achievement when any solution of a chemical problem could be generated by computer assistance. Today, the main task is the efficient, transparent, and non-arbitrary selection of meaningful results from the immense set of potential solutions—that also may contain innovative proposals. Chemistry has two aspects, constitutional chemistry and stereochemistry, which are interrelated, but still require different approaches. As a result, about twenty years ago, an algebraic model of the logical structure of chemistry was presented that consisted of two parts: the constitution-oriented algebra of be- and r-matrices, and the theory of the stereochemistry of the chemical identity group. New chemical definitions, concepts, and perspectives are characteristic of this logic-oriented model, as well as the direct mathematical representation of chemical processes. This model enables the implementation of formal reaction generators that can produce conceivable solutions to chemical problems—including unprecedented solutions—without detailed empirical chemical information. New formal selection procedures for computer-generated chemical information are also possible through the above model. It is expedient to combine these with interactive methods of selection. In this review, the Munich project is presented and discussed in detail. It encompasses the further development and implementation of the mathematical model of the logical structure of chemistry as well as the experimental verification of the computer-generated results. The article concludes with a review of new reactions, reagents, and reaction mechanisms that have been found with the PC-programs IGOR and RAIN.     

Simple voltammetric approach for characterization of two-step surface electrode mechanism in protein-film voltammetry

Many enzymes embedding multivalent metal ions or quinone moieties as redox-active centres undergo electrochemical transformation via two successive electron transfer steps. If electrochemical features of such redox enzymes are analyzed with “protein-film voltammetry”, one frequently meets a challenging reaction scenario where the two electron transfers take place at the same formal potential. Under such conditions, one observes voltammogram with a single oxidation-reduction pattern hiding voltammetric features of both redox reactions. By exploring some aspects of the two-step surface EECrev mechanism one can develop simple methodology under conditions of square-wave voltammetry to enable recognizing and characterizing each electron transfer step. The method relies on the voltammetric features of the second electron transfer, which is coupled to a follow-up chemical reaction. The response of the second electron transfer step shifts to more positive potentials by increasing the rate of the chemical reaction. The proposed methodology can be experimentally applied by modifying the concentration of an electrochemically inactive substrate, which affects the rate of the follow-up chemical reaction. The final voltammetric output is represented by two well-separated square-wave voltammetric peaks that can be further exploited for complete thermodynamic and kinetic analysis of the EECrev mechanism.

     

A new approximate method for the stochastic simulation of chemical systems: the representative reaction approach

We have developed two new approximate methods for stochastically simulating chemical systems. The methods are based on the idea of representing all the reactions in the chemical system by a single reaction, i.e., by the “representative reaction approach” (RRA). Discussed in the article are the concepts underlying the new methods along with flowchart with all the steps required for their implementation. It is shown that the two RRA methods {with the reaction as the representative reaction (RR)} perform creditably with regard to accuracy and computational efficiency, in comparison to the exact stochastic simulation algorithm (SSA) developed by Gillespie and are able to successfully reproduce at least the first two moments of the probability distribution of each species in the systems studied. As such, the RRA methods represent a promising new approach for stochastically simulating chemical systems. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2012     

Nucleotide-Selective Templated Self-Assembly of Nanoreactors under Dissipative Conditions

Nature adopts complex chemical networks to finely tune biochemical processes. Indeed, small biomolecules play a key role in regulating the flux of metabolic pathways. Chemistry, which was traditionally focused on reactions in simple mixtures, is dedicating increasing attention to the network reactivity of highly complex synthetic systems, able to display new kinetic phenomena. Herein, we show that the addition of monophosphate nucleosides to a mixture of amphiphiles and reagents leads to the selective templated formation of self-assembled structures, which can accelerate a reaction between two hydrophobic reactants. The correct matching between nucleotide and the amphiphile head group is fundamental for the selective formation of the assemblies and for the consequent up-regulation of the chemical reaction. Transient stability of the nanoreactors is obtained under dissipative conditions, driven by enzymatic dephosphorylation of the templating nucleotides. These results show that small molecules can play a key role in modulating network reactivity, by selectively templating self-assembled structures that are able to up-regulate chemical reaction pathways.     

Investigations on Substituent and Solvent Effects of Solvolysis Reactions. VIII. The Influence of Water and Nonaqueous Solvents on the Imidazolysis of 4-Nitrophenyl Acetate

The aminolysis reaction of 4-nitrophenyl acetate with imidazole was investigated in water, acetonitrile, propylene carbonate, and 1,4-dioxane at different temperatures. the observed rates can be evaluated with the help of a reaction mechanism consisting of two competitive reaction paths; the first is the bimolecular nucleophilic substitution of the phenol moiety by imidazole; the second path is performed via general base catalysis by a second imidazole molecule. The rate constants of the bimolecular reaction are quantitatively correlated with the four-parameter Taft–Kamlet equation for solvent effects on chemical reactions. A qualitative interpretation of the data shows that the two reaction paths are influenced to the same extent by the solvent.