Pair Of Reactions Research Articles

Theoretical analysis of cooperative effects of small molecule activation by frustrated Lewis pairs

The energy profiles of the activation reaction of small molecules (H(2), Br(2) and CO(2)) with boron/phosphorus frustrated Lewis pairs (FLPs) have been calculated with dispersion corrected DFT (TPSS-D3). We have investigated the cooperative nature of the reactions by analyzing interaction energies in the ternary system and for reactant pairs. The non-additive contributions to the total interaction energy add to the driving force of the activation reaction, even at early stages of the process. We propose the isosurface representation of the many-body deformation density Δρ(mb) as a qualitative tool to visualize cooperative, non-additive effects in complex chemical systems.

ChemInform Abstract: Peculiarities and Paradoxes of Photoinduced Electron Transfer Reactions

AbstractReview: 63 refs.

An extended bioreaction database that significantly improves reconstruction and analysis of genome-scale metabolic networks

The bioreaction database established by Ma and Zeng (Bioinformatics, 2003, 19, 270-277) for in silico reconstruction of genome-scale metabolic networks has been widely used. Based on more recent information in the reference databases KEGG LIGAND and Brenda, we upgrade the bioreaction database in this work by almost doubling the number of reactions from 3565 to 6851. Over 70% of the reactions have been manually updated/revised in terms of reversibility, reactant pairs, currency metabolites and error correction. For the first time, 41 spontaneous sugar mutarotation reactions are introduced into the biochemical database. The upgrade significantly improves the reconstruction of genome scale metabolic networks. Many gaps or missing biochemical links can be recovered, as exemplified with three model organisms Homo sapiens, Aspergillus niger, and Escherichia coli. The topological parameters of the constructed networks were also largely affected, however, the overall network structure remains scale-free. Furthermore, we consider the problem of computing biologically feasible shortest paths in reconstructed metabolic networks. We show that these paths are hard to compute and present solutions to find such paths in networks of small and medium size.

Theory of reversible associative-dissociative diffusion-influenced chemical reaction. I. Geminate reaction

A many-particle, in the general case, inhomogeneous reacting system of independent pairs of reactants, where geminate reversible reaction A+B⇄C takes place, is considered in the framework of the kinetic theory approach. The kinetic equations in the thermodynamic limit are obtained, and important relations between kinetic coefficients characterizing the reaction course are established, as well as the relations between the kinetic dependencies under different initial conditions including the relations that extend the familiar literature results to the case of rather realistic model of the reacting system. Universal long-term kinetic laws of the reaction course are determined.

Peculiarities and paradoxes of photoinduced electron transfer reactions

Many chemical reactions involve the electron transfer stage. The kinetics of photoinduced electron transfer reactions is commonly considered in terms of either the transition state theory as preliminary thermally activated reorganization of the medium and reactants (necessary for degeneracy of the electronic levels of the reactants and the products) or nonradiative quantum transitions, which do not require preliminary activation and are observed in the exoergic region. A new approach to the kinetics of such reactions that has been proposed recently considers a substantial reduction of the barrier in the contact reactant pair due to strong electronic interaction and takes into account the intermediate formation of a charge transfer complex. This approach has explained many well-known important features of electron transfer reactions that are inconsistent with the first two theories.

Enantioselective and Diastereoselective Tsuji–Trost Allylic Alkylation of Lactones: An Experimental and Computational Study

The Tsuji-Trost protocol has been successfully employed for the allylic alkylation of preformed lactone enolates. It has been demonstrated that this Pd-catalyzed reaction can be carried out in an enantio- and diastereoselective manner. The use of additives, such as LiCl, was found to be crucial for reaching high levels of product selectivity. For one particular pair of reactants, density functional theory was used to investigate the mechanism of the nucleophilic addition. Among the five pathways considered, the reaction between an (allyl)Pd(BINAP) complex and a LiCl-lithium enolate adduct is predicted to be the most likely route for C-C bond formation. LiCl plays a key role as the connecting link between the noble metal and the enolate in the kinetically favored transition state. The computed diastereoselectivity ratio is in good agreement with the experimentally observed value.

Lignin oxidation mechanisms under oxygen delignification conditions. Part 3. Reaction pathways and modeling

AbstractA detailed kinetic model for the lignin oxidation chemistry is presented. It is based mainly on the mechanisms and kinetics presented in the literature. Parameters that could not be found in the literature were regressed against the experimental data obtained from oxidation experiments with softwood kraft lignin. In addition to the detailed model for the chemistry, acid-base equilibrium reactions and gas-liquid mass transfer were modeled. Most of the experimental observations could be reproduced with the developed model. The reasons behind the behavior of guaiacyl and condensed phenols are discussed. The reaction routes affecting lignin solubilization and chemical consumption are presented. Model-ing of acid-base equilibria proved to be important because acid-base pairs of reactants react differently. Carbon dioxide buffers the pH and in this way affects the chemical reactions through the pH. A similar model could also be developed for other lignin treatments; for example, waste water purification or chemicals production in new biorefinery concepts. The developed reaction scheme will be used as a part of oxygen delignification model.

Effects of electrostatic potential and shape on diffusion-controlled reaction at an elliptic site

The calculation of the diffusion-controlled reaction rate of an ionic reactant on a charged elliptic site is performed in order to examine the interaction of the site charge and shape. In the absence of site charge, the reaction rate for a fixed site area is always enhanced with decrease in circularity (ratio of minor to major axis lengths), going to infinity as the circularity vanishes to zero. In the case of attractive ion-site charge forces for any finite circularity, but a very large site charge, the shape enhancement is suppressed. For repulsive ion-site forces with a very large site charge and the same finite circularity, the shape enhancement effect on the site reaction rate is increased. Away from these large site charge limits for more typical ion-site charge pairs and site circularities the same trends are observed. The results shed light on experimental and numerical simulation phenomena observed for both repulsive and attractive reactant ion-charged site pairs.

Transient Exciplex Formation Electron Transfer Mechanism

Transient exciplex formation mechanism of excited‐state electron transfer reactions is analyzed in terms of experimental data on thermodynamics and kinetics of exciplex formation and decay. Experimental profiles of free energy, enthalpy, and entropy for transient exciplex formation and decay are considered for several electron transfer reactions in various solvents. Strong electronic coupling in contact pairs of reactants causes substantial decrease of activation energy relative to that for conventional long‐range ET mechanism, especially for endergonic reactions, and provides the possibility for medium reorganization concatenated to gradual charge shift in contrast to conventional preliminary medium and reactants reorganization. Experimental criteria for transient exciplex formation (concatenated) mechanism of excited‐state electron transfer are considered. Available experimental data show that this mechanism dominates for endergonic ET reactions and provides a natural explanation for a lot of known paradoxes of ET reactions.

Laser photolysis study of the transient products of 4-carboxybenzophenone-sensitized photolysis of chlorophenoxyacetic acid-based herbicides in aqueous micellar solutions

The kinetics of the reaction of the triplet states and radicals of 4-carboxybenzophenone (CB) in aqueous sodium dodecyl sulfate micellar solutions in the absence of additives and in the presence of 2,4-dichlorophenoxyacetic acid (DCPA) or 2-methyl-4-chlorophenoxyacetic acid (MCPA) were studied. The rate constants of 3CB quenching by DCPA and MCPA were found to be 8.5 × 105 and 1.4 × 106 s−1, respectively (as calculated for a reactant pair in the micelle). As a result of quenching, radical pairs are produced in the micelle, as well as the ketyl radicals CBH· that lost their partners because of the fast disappearance of some of the DCPA and MCPA radicals. An applied external magnetic field substantially retards the recombination of radical pairs in the micelle.

Glutamates 78 and 122 in the Active Site of Saccharopine Dehydrogenase Contribute to Reactant Binding and Modulate the Basicity of the Acid-Base Catalysts

Saccharopine dehydrogenase catalyzes the NAD-dependent oxidative deamination of saccharopine to give l-lysine and alpha-ketoglutarate. There are a number of conserved hydrophilic, ionizable residues in the active site, all of which must be important to the overall reaction. In an attempt to determine the contribution to binding and rate enhancement of each of the residues in the active site, mutations at each residue are being made, and double mutants are being made to estimate the interrelationship between residues. Here, we report the effects of mutations of active site glutamate residues, Glu(78) and Glu(122), on reactant binding and catalysis. Site-directed mutagenesis was used to generate E78Q, E122Q, E78Q/E122Q, E78A, E122A, and E78A/E122A mutant enzymes. Mutation of these residues increases the positive charge of the active site and is expected to affect the pK(a) values of the catalytic groups. Each mutant enzyme was completely characterized with respect to its kinetic and chemical mechanism. The kinetic mechanism remains the same as that of wild type enzymes for all of the mutant enzymes, with the exception of E78A, which exhibits binding of alpha-ketoglutarate to E and E.NADH. Large changes in V/K(Lys), but not V, suggest that Glu(78) and Glu(122) contribute binding energy for lysine. Shifts of more than a pH unit to higher and lower pH of the pK(a) values observed in the V/K(Lys) pH-rate profile of the mutant enzymes suggests that the presence of Glu(78) and Glu(122) modulates the basicity of the catalytic groups.

PathPred: an enzyme-catalyzed metabolic pathway prediction server

The KEGG RPAIR database is a collection of biochemical structure transformation patterns, called RDM patterns, and chemical structure alignments of substrate-product pairs (reactant pairs) in all known enzyme-catalyzed reactions taken from the Enzyme Nomenclature and the KEGG PATHWAY database. Here, we present PathPred (http://www.genome.jp/tools/pathpred/), a web-based server to predict plausible pathways of muti-step reactions starting from a query compound, based on the local RDM pattern match and the global chemical structure alignment against the reactant pair library. In this server, we focus on predicting pathways for microbial biodegradation of environmental compounds and biosynthesis of plant secondary metabolites, which correspond to characteristic RDM patterns in 947 and 1397 reactant pairs, respectively. The server provides transformed compounds and reference transformation patterns in each predicted reaction, and displays all predicted multi-step reaction pathways in a tree-shaped graph.

Naphthalene Diels−Alder in a Self-Assembled Molecular Flask

Despite its inertness toward pericyclic reactions under common conditions, naphthalenes readily undergo Diels-Alder reactions when coencapsulated with a suitable dienophile within the cavity of a self-assembled host. Localization of the reactant pair significantly reduces the entropic cost of the reaction, and preorganization within the host cavity controls both the regio- and stereoselectivity of the reaction: electronically disfavored exo adducts were obtained, and with substituted naphthalenes, the reaction takes place on the less electron-rich, unsubstituted ring. Our findings highlight the fact that judicious tuning of substrate size and shape within molecular flasks can unveil new and unusual reactivities for otherwise unreactive molecules.

Kinetics of collision-induced reactions between hard-sphere reactants

We investigate the reaction kinetics of hard-sphere reactants that undergo reaction upon collision. When the reaction probability at a given collision is unity, the Noyes rate theory provides an exact expression of the rate coefficient. For the general case with the reaction probability less than unity, Noyes assumed that successive recollision times between a tagged pair of reactants are decorrelated. We show that with this renewal assumption, the rate theory of Wilemski and Fixman yields the same rate coefficient expression as the Noyes theory. To evaluate the validity of the renewal assumption, we carry out molecular dynamics simulations. Contrary to the usual expectation, we find that the renewal assumption works better at higher particle densities. The present study shows that the rate coefficient for collision-induced hard-sphere reactions can be estimated with great accuracy by using the first recollision time distribution alone, regardless of the magnitude of the reaction probability at a given collision.

A rigorous foundation of the diffusion-influenced bimolecular reaction kinetics

We formulate a general theory of the diffusion-influenced kinetics of irreversible bimolecular reactions occurring in the low concentration limit. Starting from the classical Liouville equation for the reactants and explicit solvent molecules, a formally exact expression for the bimolecular reaction rate coefficient is derived; the structures of reactant molecules and the sink functions may be arbitrarily complicated. The present theoretical formulation shows clearly how the well-known Noyes and Wilemski-Fixman rate theories are related and can be improved in a systematic manner. The general properties of the rate coefficient such as the long-time behavior and the upper and the lower bounds are analyzed. When the reaction can occur at a range of distance, the non-Markovianity of repeated encounter events between a reactant pair becomes significant and either the Noyes theory or the Wilemski-Fixman theory fails. The present theory provides a practical method for calculating the rate expression for such reactions, which improves significantly on the Wilemski-Fixman theory.

E-zyme: predicting potential EC numbers from the chemical transformation pattern of substrate-product pairs

Motivation: The IUBMB's Enzyme Nomenclature system, commonly known as the Enzyme Commission (EC) numbers, plays key roles in classifying enzymatic reactions and in linking the enzyme genes or proteins to reactions in metabolic pathways. There are numerous reactions known to be present in various pathways but without any official EC numbers, most of which have no hope to be given ones because of the lack of the published articles on enzyme assays.Results: In this article we propose a new method to predict the potential EC numbers to given reactant pairs (substrates and products) or uncharacterized reactions, and a web-server named E-zyme as an application. This technology is based on our original biochemical transformation pattern which we call an ‘RDM pattern’, and consists of three steps: (i) graph alignment of a query reactant pair (substrates and products) for computing the query RDM pattern, (ii) multi-layered partial template matching by comparing the query RDM pattern with template patterns related with known EC numbers and (iii) weighted major voting scheme for selecting appropriate EC numbers. As the result, cross-validation experiments show that the proposed method achieves both high coverage and high prediction accuracy at a practical level, and consistently outperforms the previous method.Availability: The E-zyme system is available at http://www.genome.jp/tools/e-zyme/Contact: kanehisa@kuicr.kyoto-u.ac.jp

Metabolic Pathfinding Using RPAIR Annotation

Metabolic databases contain information about thousands of small molecules and reactions, which can be represented as networks. In the context of metabolic reconstruction, pathways can be inferred by searching optimal paths in such networks. A recurrent problem is the presence of pool metabolites (e.g., water, energy carriers, and cofactors), which are connected to hundreds of reactions, thus establishing irrelevant shortcuts between nodes of the network. One solution to this problem relies on weighted networks to penalize highly connected compounds. A more refined solution takes the chemical structure of reactants into account in order to differentiate between side and main compounds of a reaction. Thanks to an intensive annotation effort at KEGG, decompositions of reactions into reactant pairs (RPAIR) categorized by their role (main, trans, cofac, ligase, and leave) are now available. The goal of this article is to evaluate the impact of RPAIR data on pathfinding in metabolic networks. To this end, we measure the impact of different parameters concerning the construction of the metabolic network: mapping of reactions and reactant pairs onto a graph, use of selected categories of reactant pairs, weighting schemes for compounds and reactions, removal of highly connected metabolites, and reaction directionality. In total, we tested 104 combinations of parameters and identified their optimal values for pathfinding on the basis of 55 reference pathways from three organisms. The best-performing metabolic network combines the biochemical knowledge encoded by KEGG RPAIR with a weighting scheme penalizing highly connected compounds. With this network, we could recover reference pathways from Escherichia coli with an average accuracy of 93% (32 pathways), from Saccharomyces cerevisiae with an average accuracy of 66% (11 pathways), and from humans with an average accuracy of 70% (12 pathways). Our pathfinding approach is available as part of the Network Analysis Tools.

Polycondensation of alkoxysilanes in an active medium as a versatile method for the preparation of polyorganosiloxanes

Hydrolytic polycondensation of functional derivatives of silicon is an important method for preparation of polysiloxanes of different structure ranging from organocyclosiloxanes to high-molecular-weight linear, cyclolinear, or branched polymers. The most widely used version of hydrolytic polycondensation is based on the use of organochlorosilanes. More than a five decade history of the industrial use of this process resulted in a broad range of organosilicon compounds without which modern technology cannot even be imagined [1]. However, until now, it was impossible to solve two fundamental problems, namely, eliminate the use of chlorosilanes in polysiloxane preparation processes and carry out hydrolytic polycondensation under homogeneous conditions. The significance of the first issue is obvious in view of the need to decrease the environmental pressure. Currently, the use of alkoxy derivatives instead of organochlorosilanes is held up not only by the lack of industrial direct synthesis of organoalkoxysilanes but also by the difficulty to control the polymer production processes from these raw materials. The solution of the latter problem would markedly increase the process controllability, most of all, through control of the product structures. A study of the reaction of organoalkoxysilanes with an excess of anhydrous acetic acid has shown that the process can be accompanied by complete conversion of alkoxysilyl groups within polyfunctional oligomers or their mixtures with alkoxysilanes. Acetic acid was used as the active reaction medium. A fundamental difference between the active medium and common organic solvents is that the former does not merely dissolve the reactants and products but is also a coreactant. Analysis of the literature concerning this pair of reactants has shown that acetic acid either functioned as an active solvent [2‐4] (in this case, water was added to the reaction mixture for hydrolysis) or as a reactant [5] (in this case, complete conversion of alkoxysilyl groups could not be attained). The authors were the first to demonstrate that an excess of anhydrous acetic acid induces the process to follow the hydrolytic polycondensation mechanism, the required water being generated in the reaction system in amounts needed for complete conversion of the alkoxysilyl groups. The key studies were performed for the reaction of acetic acid with dimethyldimethoxysilane. For the convenience of monitoring the reaction, it was carried out in deuterated acetic acid ( CD 3 COOD ). In this case, the variation of the reactant concentrations could be monitored by recording the 1 H NMR spectra of samples taken directly from the reaction mixture without any additional treatment. The signals for different methoxygroup protons (Fig. 1) were assigned on the basis of preliminary experiments including measuring the individual spectra of the major components of the reaction mixture. The absence of acetic acid protons in the spectrum made it possible to calculate the relative concentrations of functional groups in the reactants and products from the intensities I of the proton signals of these groups in the methoxy region (3.3‐3.7 ppm). In view of the fact that the sum of integral intensities in this region ( Σ I ) remains constant during the reaction, the relative concentrations of functional groups ( c rel ) in this spectral region were calculated using the formula c rel = I / Σ I .

About the mode of incorporation of silanol-terminated polysiloxanes into butylene terephthalate- b-dimethylsiloxane copolymers

The modality of the incorporation of silanol-terminated siloxanes into copolymers with butylene terephthalate were investigated and determined. Besides siloxanes, the other participants in this well-known copolymerization, called the catalyzed two-step transesterification/polycondensation reaction, are dimethyl terephthalate and 1,4-butanediol. The employed approach to this problem was to exactly examine all the possibilities of the reactions between particular pairs of reactants, as well as of single reactants. The final results were, firstly, that reactions between siloxanes and dimethyl terephthalate did not occur and, secondly, that the only possibility for silanol-terminated siloxanes to be incorporated into the copolymers was by means of their condensation with 1,4-butanediol. This means that siloxanes are incorporated into the copolymer by ether and not by ester linkages.

Electron Transfer between Guanosine Radical and Amino Acids in Aqueous Solution. 1. Reduction of Guanosine Radical by Tyrosine

As a model of chemical DNA repair, the reductive electron transfer from the aromatic amino acid tyrosine to the radical of the purine base guanosine monophosphate (GMP) was studied by time-resolved chemically induced dynamic nuclear polarization (CIDNP). The guanosyl radicals were photochemically generated in the quenching reaction of the triplet excited dye 2,2'-dipyridyl. Depending on the pH of the aqueous solution, four different guanosyl radicals were observed. The identification of the radicals was possible because of the high sensitivity of CIDNP to distinguish them through their ability or disability of participating in the degenerate electron hopping reaction with the diamagnetic molecules of guanosine monophosphate in the ground state. The CIDNP kinetics in this three-component system containing the dye, GMP, and N-acetyl tyrosine is strongly dependent on the efficiency of the electron-transfer reaction from tyrosine to the nucleotide radical. Quantitative analysis of the CIDNP kinetics obtained at different concentrations of the amino acid, together with the comparison with the CIDNP kinetics of the two-component systems (dipyridyl/tyrosine and dipyridyl/GMP) allowed for the determination of the rate constant ke of the reductive electron-transfer reaction for five pairs of reactants, with different protonation states depending on the pH: GH++*/TyrOH (pH 1.3), G+*/TyrOH (pH 2.9), G(-H)*/TyrOH (pH 7.5), G(-H)*/TyrO- (pH 11.3), and G(-2H)-*/TyrO- (pH 13.3). The rate constant ke varies from (7.1 +/- 3.0) x 10(8) M-1 s-1 (pH 1.3, 2.9) to less than 6 x 10(6) M-1 s-1 (pH 13.3).