Automatic determination of reaction mappings and reaction center information. 2. Validation on a biochemical reaction database

The correct identification of the reacting bonds and atoms is a prerequisite for the analysis of the reaction mechanism. We have recently developed a method based on the Imaginary Transition State Energy Minimization approach for automatically determining the reaction center information and the atom-atom mapping numbers. We test here the accuracy of this ITSE approach by comparing the predictions of the method against more than 1500 manually annotated reactions from BioPath, a comprehensive database of biochemical reactions. The results show high agreement between manually annotated mappings and computational predictions (98.4%), with significant discrepancies in only 24 cases out of 1542 (1.6%). This result validates both the computational prediction and the database, at the same time, as the results of the former agree with expert knowledge and the latter appears largely self-consistent, and consistent with a simple principle. In 10 of the discrepant cases, simple chemical arguments or independent literature studies support the predicted reaction center. In five reaction instances the differences in the automatically and manually annotated mappings are described in detail. Finally, in approximately 200 cases the algorithm finds alternate reaction centers, which need to be studied on a case by case basis, as the exact choice of the alternative may depend on the enzyme catalyzing the reaction.     

Sites of reaction of pilocarpine

Analysis of the sites of reaction of a biologically important compound, pilocarpine, a molecule with imidazole and butyrolactone rings connected by a methylene bridge, has been accomplished in a quadrupole ion trap with the aim of characterizing its structure/reactivity relationships. Ion-molecule reactions of pilocarpine with chemical ionizing agents, dimethyl ether (DME), 2-methoxyethanol, and trimethyl borate (TMB), along with collision-activated dissociation elucidated the reaction sites of pilocarpine and made possible the comparison of structural features that affect sites of reaction. Based on MS/MS experiments, methylation occurs on the imidazole ring upon reactions with CH3OCH2+ or (CH3OCH2CH2OH)H+ ions but methylation occurs on the lactone ring for reactions with (CH3O)2B+ ions. Bracketing experiments with two model compounds, alpha-methyl-gamma-butyrolactone and N-methyl imidazole, show the imidazole ring to have a greater gas-phase basicity and methyl cation affinity than the lactone ring. The contrast of methylation by TMB ions on the lactone ring is explained by initial addition of the dimethoxyborinium ion, (CH3O)2B+, on the imidazole ring with subsequent collisional activation promoting an intramolecular transfer of a methyl group to the lactone ring with concurrent loss of CH3OBO. Semiempirical molecular orbital calculations are undertaken to further address the favored reaction sites.     

The influence of dissociation reaction on ammonium nitrate thermal decomposition reaction

In order to investigate the influence of dissociation reaction on thermal decomposition of ammonium nitrate (AN), biochar was selected as an adsorbent to interfere with the dissociation of AN. The TG-DSC results showed that the notable exothermic reaction of AN with the presence of 2% or 7% biochar took place. The decomposition temperature of AN decreased with increasing amount of biochar. The notable knee point was found in the TG curves. The activation energy of AN with biochar in the initial stage was higher than that of AN itself. Remote sensing Fourier transform infrared experiments found biochar induced AN decomposition at about 190 °C, which was also confirmed by the TG-MS results. After dissociation reaction, HNO₃ (g) and NH₃ (g) were adsorbed and crystalline of AN was formed on the surface of biochar. With the increasing temperature, NH₃ escaped from the surface of biochar, while HNO₃ (g) was stayed in biochar. HNO₃ (g) catalyzed the thermal decomposition of AN and also reacted with biochar. The results indicated that dissociation reaction of AN played an important role during AN thermal decomposition process. When dissociation reaction was changed, the thermal decomposition reaction of AN would also change, catalysis or inhibition AN thermal decomposition. It is a useful reference to guide the AN additives selection and to understand the mechanism for the AN decomposition accident.

     

Diffusion-controlled reaction of polymers

An analysis is made of diffusion-controlled ring closure reaction of a polymer chain based on the general theory of Wilemski and Fixman. It is shown that the reaction rate is strongly affected by the short time behavior of the segmental motion, and consequently the harmonic spring model and the Rouse model yield quite different results. This explains the characteristic feature of the numerical results of Wilemski and Fixman. A simple intuitive interpretation is made for this difference.     

The reaction of pyridazinones with nucleophiles. An unusual reaction with cyanide

Studies on the synthesis of pyridazinone analogues of pyridone cardiotonics are reported. The synthetic scheme involves the reaction of pyridazinones and chloropyridazinones with nucleophiles. Addition occurred twice with cyanide as the nucleophile, thus providing a novel dicyanopyridazinone.     

Microwave-assisted Cannizzaro reaction—Optimisation of reaction conditions

The microwave-assisted Cannizzaro reaction was studied in order to develop fully reproducible synthetic protocols for transformation of aldehydes to carboxylic acid and alcohols. Optimised were the following process parameters: power, temperature, and time. Aromatic, heteroaromatic and aliphatic aldehydes were used in the studies. It was found that furfural, thiophene-2-carbaldehyde, pyridinecarboxaldehyde and aromatic aldehydes react under mild conditions, while 1-methyl-pyrrole-2-carboxaldehyde derivatives and aliphatic aldehydes require more drastic reaction conditions and a longer exposure time to microwave radiation.     

Capillary reaction gas chromatography

Summary Thermal decomposition of C₆ hydrocarbons (hexane, cyclohexane, 2-methylpentane, 2,2-dimethylbutane and trans-2-hexene) on a nickel catalyst and on alumina was studied by reaction gas chromatography. The products were analyzed on two capillary columns containing squalane and Citroflex and were identified on the basis of their retention indices. The degree of conversion of the initial substances and the relative contents of the products were determined. On the basis of the results obtained, the probable course of the catalytic decomposition is discussed.     

Cyanide reaction with ninhydrin: elucidation of reaction and interference mechanisms.

A new sensitive spectrophotometric method has recently been developed for the trace determination of cyanide with ninhydrin. Cyanide ion was supposed to act as a specific base catalyst. Nevertheless, this paper demonstrates that the reported assay is based on a novel reaction of cyanide with 2,2-dihydroxy-1,3-indanedione, which affords purple or blue colored salts of 2-cyano-1,2,3-trihydroxy-2H indene. Hydrindantin is merely an intermediary of the reaction. The formation of a stable and isolable ninhydrin-cyanide compound has been confirmed by its preparation in crystalline form. Also, it is thoroughly characterized by elemental as well as MS, IR, UV/VIS and 1H NMR analyses. The Ruhemann's sequence of reactions of cyanide with ninhydrin has been reconsidered and an adequate mechanism of the reaction is proposed. As a consequence, the interference of oxidizers as well as copper, silver and mercury ions with the cyanide determination has been elucidated.     

Thiourea-catalyzed Morita-Baylis-Hillman reaction

Here, we describe our studies on the thiourea-catalyzed Morita-Baylis-Hillman (MBH) reaction. Chemoselective activation of carbonyl compounds via hydrogen bonding to thiourea as a catalyst is the key to drastic rate acceleration of this reaction. The application of chiral bis-thiourea-type organocatalysts, which can form a chiral double hydrogen-bonding network, is effective for enantioselective MBH reaction. A cooperative system of bis-thiourea compounds, synthesized from 1,2-diaminocyclohexane, and a Lewis base effectively promotes the MBH reaction at lower temperature, affording the MBH adducts in 33-95% yield with 44-90% ee. A plausible transition state model of the enantioselective MBH reaction is presented.     

The reaction path intrinsic reaction coordinate method and the Hamilton-Jacobi theory

The definition and location of an intrinsic reaction coordinate path is of crucial importance in many areas of theoretical chemistry. Differential equations used to define the path hitherto are complemented in this study with a variational principle of Fermat type, as Fukui [Int. J. Quantum Chem., Quantum Chem. Symp. 15, 633 (1981)] reported in a more general form some time ago. This definition is more suitable for problems where initial and final points are given. The variational definition can naturally be recast into a Hamilton-Jacobi equation. The character of the variational solution is studied via the Weierstrass necessary and sufficient conditions. The characterization of the local minima character of the intrinsic reaction coordinate is proved. Such result leads to a numerical algorithm to find intrinsic reaction coordinate paths based on the successive minimizations of the Weierstrass E-function evaluated on a guess curve connecting the initial and final points of the desired path.     

Collective reaction behavior of an oscillating system coupled with an excitable reaction

The collective reaction behavior of limit cycles coupled to a nonoscillatory forcing is investigated experimentally and computationally. The coupled chemical system is constructed by adding 1,4-cyclohexanedione (CHD), a species which is capable of forming an oscillator with acidic bromate, into the cerium-catalyzed Belousov-Zhabotinsky reaction. Two levels of coupling exist in the system: (1) through autocatalytic reactions with bromine dioxide radicals and (2) via reactions with oxidized metal catalysts. Experiments illustrate that there is an optimum [1,4-CHD]/[cerium] ratio for inducing complex oscillations, whereas in the 1,4-CHD and malonic acid concentration phase plane two resonant ratios are observed for the onset of complex behavior. In addition, bromate, the oxidant for both suboscillators, also exhibits subtle influences on the complexity of the collective reaction behavior. The experimental observations are qualitatively reproduced with the Field-Koros-Noyes mechanism, modified to account for the coupling reactions with the 1,4-CHD-bromate system.     

Titanium-catalyzed Reformatsky-type reaction

A catalytic titanium mediated Reformatsky reaction is presented. The technique employs cyclopentadienyltitaniumdichloride(IV) (10 mol%) in conjunction with Mn (2 equiv.), as the stoichiometric reductant, and (CF₃CO)₂O (1.5 equiv.), as the scavenger, and it is based on the formation of titanocene(III) chloride as a mild and homogeneous single-electron reductant. The reaction gives moderate yields of the desired Reformatsky adduct, and it works well with aromatic and aliphatic aldehydes.     

Mechanistic investigations of the Mukaiyama aldol reaction as a two part enantioselective reaction

Herein, we report a mechanistic investigation of an enantioselective tandem Mukaiyama aldol reaction, consisting of a carbon-carbon bond-forming reaction and a silylation protection step in which the enantioselectivity results exclusively from the silylation step. The reaction is carried out in the presence of a Lewis base paired with a chiral quarternary ammonium salt. Mechanistic studies indicate that the enantioselectivity of the silylation step is a kinetic resolution of the aldolate intermediate. The effects of sterics and electronics on the aldehyde starting material are also presented.     

Recent advances on deoximation: From stoichiometric reaction to catalytic reaction

Recent advances on the deoximation reactions are reviewed in this review. It was shown that catalytic deoximation with molecular oxygen as the mild oxidant should be the developing trend of the reaction.     

Automated derivation of reaction rules for the EROS 6.0 system for reaction prediction

The purpose of the EROS 6.0 system is to predict the products of chemical reactions and to model reaction mechanisms. This is accomplished by elementary reaction steps that are selected through the rules that constitute the knowledge base of the EROS 6.0 system. These rules are derived by methods of machine learning. The learning process is based on reaction in data bases. An overview of the EROS 6.0 system is given and the structure of the knowledge as well as the generation of reaction rules are described.     

Kinetics of the Fischer-tropsch reaction

Long carbon chains: Self-assembly of monomeric carbon intermediates into long-chain hydrocarbons on catalytically reactive surface was studied when full reversibility of the chain growth is included in the kinetic model. Using Br?nsted-Evans-Polanyi relations, the maximum chain growth as a function of the surface reactivity is predicted.     

Kinetic analysis of photopolymerization reaction of lauryl acrylate with a photoinduced chemical reaction calorimeter

Calorimetric studies on kinetics of photopolymerization reactions made previously have been limited by the structures of the calorimeters. This report suggests a thermal-leak type of calorimeter for carrying out kinetic analysis of the photopolymerization reaction. The method was applied to the photopolymerization system consisting of lauryl acrylate and benzoin methyl ether. The results obtained illustrate the utility of this apparatus.     

Surface aligned reaction

This paper reflects on three decades during which the study of surface aligned reaction (SAR) has advanced. The objective in SAR, which in considerable part still lies ahead, is the simultaneous control of atomic and molecular "collision energies, collision angles, and impact parameter." Following a discussion of the benefits of such an approach we review the progress made, and, as a stimulus to experiment, present new calculations of SAR dynamics for bimolecular reaction at a metal surface. It seems reasonable to suppose that we are now entering a decade in which a combination of scanning tunneling microscopy and femtosecond laser spectroscopy will bring the full realisation of SAR.