Pair Of Reactions Research Articles

Systematic Analysis of Enzyme-Catalyzed Reaction Patterns and Prediction of Microbial Biodegradation Pathways

The roles of chemical compounds in biological systems are now systematically analyzed by high-throughput experimental technologies. To automate the processing and interpretation of large-scale data it is necessary to develop bioinformatics methods to extract information from the chemical structures of these small molecules by considering the interactions and reactions involving proteins and other biological macromolecules. Here we focus on metabolic compounds and present a knowledge-based approach for understanding reactivity and metabolic fate in enzyme-catalyzed reactions in a given organism or group. We first constructed the KEGG RPAIR database containing chemical structure alignments and structure transformation patterns, called RDM patterns, for 7091 reactant pairs (substrate-product pairs) in 5734 known enzyme-catalyzed reactions. A total of 2205 RDM patterns were then categorized based on the KEGG PATHWAY database. The majority of RDM patterns were uniquely or preferentially found in specific classes of pathways, although some RDM patterns, such as those involving phosphorylation, were ubiquitous. The xenobiotics biodegradation pathways contained the most distinct RDM patterns, and we developed a scheme for predicting bacterial biodegradation pathways given chemical structures of, for example, environmental compounds.

Aromatic Nucleophilic Substitution (S NAr) Reactions of 1,2- and 1,4-Halonitrobenzenes and 1,4-Dinitrobenzene with Carbanions in the Gas Phase

In the gas-phase reactions of halonitro- and dinitrophenide anions with X (X = F, Cl, Br, NO(2)) and NO(2) groups in ortho or para position to each other with selected C-H acids: CH(3)CN, CH(3)COCH(3), and CH(3)NO(2), products of the S(N)Ar-type reaction are formed. Nitrophenide anions are generated by decarboxylation of the respective nitrobenzenecarboxylate anions in ESI ion source and the S(N)Ar reaction takes place either in the medium-pressure zone of the ion source or in the collision chamber of the triple quadrupole mass spectrometer. In the case of F, Cl, and NO(2) derivatives, the main ionic product is the respective [NO(2)-Ph-CHR](-) anion (R = CN, COCH(3), NO(2)). In the case of Br derivatives, the main ionic product is Br(-) ion because it has lower proton affinity than the [NO(2)-Ph-CHR](-) anion (for R = CN, COCH(3)). For some halonitrophenide anion C-H acid pairs of reactants, the S(N)Ar reaction is competed by the formation of halophenolate anions. This reaction can be rationalized by the single electron-transfer mechanism or by homolytic C-H bond cleavage in the proton-bound complex, both resulting in the formation of the halonitrobenzene radical anion, which in turn undergoes -NO(2) to -ONO rearrangement followed by the NO(.) elimination.

Subdiffusion-assisted reaction kinetics in disordered media

We present a theory for describing the reaction process occurring in disordered media withenergetically disordered trapping sites and spatial constraints. The theory is based on ageneralized fractional reaction–diffusion equation, which describes the time evolution of themean distribution of a particle performing a continuous time random walk on a fractalnetwork. The motion of a particle is subdiffusive because of the spatial constraints and/orthe random detrapping times described by a waiting time distribution given byψ(t)∼t−(1+α) with 0<α<1. Assuming that the reaction occurs at a separation of contact, the reactionand transport processes are decoupled and the kinetic information for thereaction is expressed in terms of the reaction-free Green’s function obtainedwith the reflecting boundary condition at the separation of contact. Thesurvival probability of a reactant pair is shown to decay asymptotically asτ−α|ds/2−1|,where ds is the fracton dimension of the fractal network under consideration. We also check thevalidity of the analytical results by comparison with Monte Carlo simulation results.

Photoionization affected by chemical anisotropy

The kinetic constants of rhodamine 3B quenching by N,N-dimethyl aniline were extracted from the very beginning of the quenching kinetics, recently studied in a few solvents of different viscosities. They were well fitted with the conventional kinetic constant definition, provided the radial distribution function of simple liquids was ascribed to the reactant pair distribution and the contact electron transfer rate was different in all the cases. This difference was attributed to the chemical anisotropy averaging by the rotation of reactants, which is the faster in solvents of lower viscosity. With the proper choice of a space dependent encounter diffusion, the whole quenching kinetics was well fitted with an encounter theory, using the Marcus [J. Chem. Phys. 24, 966 (1956); 43, 679 (1965)] transfer rate instead of the contact Collins-Kimball [J. Colloid. Sci. 4, 425 (1949)] approximation. Not only the beginning and middle part of the quenching were equally well fitted, but the long time (Markovian) rate constant was also found to be the same as previously obtained. Moreover, the concentration dependencies of the fluorescence quantum yield and the Stern-Volmer constant were specified and await their experimental verification.

The Behavior of Exciplex Decay Processes and Interplay of Radiationless Transition and Preliminary Reorganization Mechanisms of Electron Transfer in Loose and Tight Pairs of Reactants

Exciplex emission spectra and rate constants of their decay via internal conversion and intersystem crossing are studied and discussed in terms of conventional radiationless transition approach. Exciplexes of 9-cyanophenanthrene with 1,2,3-trimethoxybenzene and 1,3,5-trimethoxybenzene were studied in heptane, toluene, butyl acetate, dichloromethane, butyronitrile, and acetonitrile. A better description of spectra and rate constants is obtained using 0-0 transition energy and Gauss broadening of vibrational bands rather than the free energy of electron transfer and reorganization energy. The coincidence of parameters describing exciplex emission spectra and dependence of exciplex decay rate constants on energy gap gives the evidence of radiationless quantum transition mechanism rather than thermally activated medium reorganization mechanism of charge recombination in exciplexes and excited charge transfer complexes (contact radical ion pairs) as well as in solvent separated radical ion pairs. Radiationless quantum transition mechanism is shown to provide an appropriate description also for the main features of exergonic excited-state charge separation reactions if fast mutual transformations of loose and tight pairs of reactants are considered. In particular, very fast electron transfer (ET) in tight pairs of reactants with strong electronic coupling of locally excited and charge transfer states can prevent the observation of an inverted region in bimolecular excited-state charge separation even for highly exergonic reactions.

Oxidation of sulfonamides, macrolides, and carbadox with free chlorine and monochloramine

The oxidation of 10 antibiotics-carbadox, erythromycin-H 2O, roxithromycin, sulfadimethoxine, sulfamerazine, sulfamethazine, sulfamethizole, sulfamethoxazole, sulfathiozole, and tylosin during chlorination and monochloramination in laboratory and surface waters was investigated to identify kinetics and treatment effectiveness. A kinetic model that incorporates pH-based speciation of both oxidant species and sulfonamide antibiotics was developed and validated. Specific rate constants for the individual ionic species were developed for the dominant reactant pairs. Liquid chromatography/mass spectrometry, preceded by solid phase extraction, was used to analyze antibiotics in kinetic experiments. With experimental conditions of 25 °C and reaction times of up to 2 h, an initial concentration of 1 mg/L of free chlorine removed an average of 88 percent of the antibiotics over a pH range of 6.1–9.1. Monochloramine was less effective at typical drinking water dosage concentrations of 3 mg/L, with average removals of 35, 10, and 0 percent at a pH of 6.1, 7.6, and 9.1, respectively.

Structure-Based Classification of Chemical Reactions without Assignment of Reaction Centers

The automatic classification of chemical reactions is of high importance for the analysis of reaction databases, reaction retrieval, reaction prediction, or synthesis planning. In this work, the classification of photochemical reactions was investigated with no explicit assignment of the reacting centers. Classifications were explored with Random Forests or Kohonen neural networks in three different situations, using different levels of information: (a) pairs of reactants were classified according to the type of reaction they produce, (b) products were classified according to the type of reaction from which they can be synthesized, and (c) reactions were classified from the difference between the descriptors of the product and the descriptors of the reactants. In all cases molecular maps of atom-level properties (MOLMAPs) were used as descriptors. They are generated by a self-organizing map and encode physicochemical properties of the bonds available in a molecule. Correct classification could be achieved for approximately 90% of the 78 reactions in an independent test set.

Kinetic Isotope Effect in the Photoreduction of o-Benzoquinones in the Presence of N,N-Dimethylaniline

The kinetics of photoinduced reduction of a series of 3,5- and 3,6-di-tert-butylbenzoquinones-1,2 was studied in the presence of N,N-dimethylaniline, its deuterated analog, and a series of para-substituted N, N-dimethylanilines. On passing from the endothermic to the exothermic range of the free energy of electron transfer ΔG e , the effective rate constants k H and k D and the quantum yields ϕH and ϕD of the reaction varied nonmonotonically with a maximum at ΔG e of approximately +0.1 eV. For the reactant pairs relevant to the ascending (left-hand) branch of the plot k H = f(ΔG e ), the H/D isotope effect takes place, varying from two to five in magnitude. For the reactant pairs at the maximum and in the descending (right-hand) branch of the plot k H = f(ΔG e ), there is no isotope effect or its value is insignificant.

Exit Routes from the Transition State: Angular Momentum Constraints on the Formation of Products

We have analyzed experimental data from a number of exothermic processes in which molecules in well-defined initial states are deactivated by inelastic, dissociative, or reactive collisions. Further, we analyze deactivation processes that do not occur in molecules despite their containing high levels of excitation. Significant common elements are found among these forms of deactivation. The initial step consists of transition to a product state involving minimum rotation state change (Delta j) consistent with energy conservation. Frequently, this process is near-energy-resonant. More critically, it may frequently require substantial angular momentum (AM) change. Analysis of experimental data indicates that constraints act upon on the formation of products in processes that involve release of excess energy. These constraints are associated with the magnitude of AM that must be generated for the initial transition to occur and this AM "load" increases with the amount of energy to be released. In general, the probability of generating rotational AM falls rapidly as Delta j increases, and this effectively limits the size of energy gap that may be bridged by a given reactant pair and at some point the constraint is sufficient to constitute a barrier that prevents the process from taking place. The choice of reactant species strongly affects the probability of each process that increases (i) when molecules efficiently interconvert momentum and (ii) when many product states are available in the critical near-resonant region. These factors increase the proportion of initial trajectories that possess the energy and momentum necessary to open a "product" channel. Evidence is presented showing that AM load-reduction strategies lead to marked enhancement of rates of collision-induced processes, suggesting that reduction of constraints in the exit channels from the transition state may constitute a previously unrecognized form of catalysis.

Electro-osmotically controllable multi-flow microreactor

An adjustable diffusion-based microfluidic reactor is presented here, which is based on electro-osmotic guiding of reagent samples. The device consists of a laminar flow chamber with two separate reagent inlets. The position and the width of the two sample streams in the flow chamber can be controlled individually by changing the flow ratio of three parallel guiding buffer streams. Since electro-osmotic flow (EOF) is used for pumping, no external pumps or other moving parts are needed. The region where the diffusive profiles of the two sample streams overlap is used for the reactions. This overlapping region can be manipulated in a predictable way by adjusting the voltages required to generate the respective electro-osmotic flow. Reaction dynamics inside the microreactor is illustrated with a reactant pair of a fluorescent calcium tracer and a calcium chloride solution. An analytical model, which is an analogue of electrical circuits to EOF, was developed and embedded into the LabView control software, allowing real-time control of the microreactor. This paper describes the simulation, fabrication and experimental characterisation of the device.

Aliphatic Thiocarbonyl Ylides and Thiobenzophenone: Experimental Study of Regiochemistry and Methylene Transfer in Cycloadditions

Abstract1,3‐Dipolar cycloadditions of aliphatic or alicyclic thiocarbonyl ylides 3A‐D – sterically hindered at least at one terminus – with thiobenzophenone produce both regioisomeric 1,3‐dithiolanes 4 and 5. According to quantum‐chemical calculations (preceding paper), a concerted cycloaddition furnishing 2,4‐substituted dithiolanes 4 competes with the formation of an intermediate C,C‐biradical 9 which cyclizes to the more crowded 4,5‐substituted dithiolanes 5. When steric hindrance of 3 increases, the cycloaddition is superseded by ‘methylene transfer’, i.e., the transfer of the less hindered terminus of 3E‐J to the S‐atom of thiobenzophenone. The thiobenzophenone S‐alkylide 11, thus formed, rapidly reacts with a second molecule ofthiobenzophenone to generate the 4,4,5,5‐tetraphenyl‐1,3‐dithiolane 12 via the highly stabilized C,C‐biradical 10. Methylene transfer occurs when the cyclization of the mixed C,C‐biradical 9 requires a higher activation barrier than its dissociation to aliphatic thioketone + 11; the threshold is surprisingly well reproduced by calculations. The structural assignment of sixteen 1,3‐dithiolanes is based on their formation from corresponding reactant pairs as well as on 1H and 13C chemical shifts. X‐ray diffraction analyses of three spiro‐1,3‐dithiolanes reveal the van der Waals strain in non‐bonded interactions, folding angles, shearing forces, and bond lengths. Comparison of the mass spectra of many 1,3‐dithiolanes allows the reconstruction of major fragmentation pathways. (© Wiley‐VCH Verlag GmbH &amp; Co. KGaA, 69451 Weinheim, Germany, 2005)

Computational Assignment of the EC Numbers for Genomic-Scale Analysis of Enzymatic Reactions

The EC (Enzyme Commission) numbers represent a hierarchical classification of enzymatic reactions, but they are also commonly utilized as identifiers of enzymes or enzyme genes in the analysis of complete genomes. This duality of the EC numbers makes it possible to link the genomic repertoire of enzyme genes to the chemical repertoire of metabolic pathways, the process called metabolic reconstruction. Unfortunately, there are numerous reactions known to be present in various pathways, but they will never get EC numbers because the EC number assignment requires published articles on full characterization of enzymes. Here we report a computerized method to automatically assign the EC numbers up to the sub-subclasses, i.e., without the fourth serial number for substrate specificity, given pairs of substrates and products. The method is based on a new classification scheme of enzymatic reactions, named the RC (reaction classification) number. Each reaction in the current dataset of the EC numbers is first decomposed into reactant pairs. Each pair is then structurally aligned to identify the reaction center, the matched region, and the difference region. The RC number represents the conversion patterns of atom types in these three regions. We examined the correspondence between computationally assigned RC numbers and manually assigned EC numbers by the jackknife cross-validation test and found that the EC sub-subclasses could be assigned with the accuracy of about 90%. Furthermore, we examined the correlation with genomic information as represented by the KEGG ortholog clusters (OC) and confirmed that the RC numbers are correlated not only with elementary reaction mechanisms but also with protein families.

ATR-SEIRAS––an approach to probe the reactivity of Pd-modified quasi-single crystal gold film electrodes

Quasi-single crystalline gold films of 20 nm thickness and preferential (1 1 1) orientation on Si hemispheres were modified by controlled potentiostatic deposition of Pd (sub-ML, ML, multi-L) from sulphate and/or chloride-containing electrolyte. The electrochemical properties of these model electrodes were characterised for hydrogen and (hydrogen-) sulphate adsorption as well as for surface oxide formation by cyclic voltammetry. Conditions were developed to fabricate defined and stable Pd monolayers. In situ ATR-SEIRAS (Attenuated Total Reflection Surface Enhanced Infrared Reflection Absorption Spectroscopy) experiments were carried out to describe the electrochemical double layer of Pd modified gold film electrodes in contact with aqueous 0.1 M H 2SO 4 with focus on interfacial water and anion adsorption. Based on an analysis of the non-resonant IR background signal the potential of zero charge is estimated to 0.10–0.20 V (vs. RHE). CO was found to be weakly physisorbed in atop sites on Au(1 1 1-20 nm)/0.1 M H 2SO 4 only in CO saturated electrolyte. CO, deposited on a quasi-single crystal gold film modified with 1 ML Pd, is chemisorbed with preferential occupation of bridge sites and atop positions at step edges. Saturated CO adlayers, as obtained by deposition at 0.10 V, contain isolated water species and are covered by a second layer of hydrogen bonded water. Potentiodynamic SEIRAS experiments of CO electro-oxidation on Pd-modified gold film electrodes demonstrate clearly the existence of a “pre-oxidation” region. They also provide spectroscopic evidence that isolated water and weakly hydrogen bonded water are consumed during the reaction and that atop CO on defect sites is a preferential reactant. The simultaneous in situ monitoring of the potential- and time-dependent evolution of characteristic vibrational modes in the OH- and CO-stretching regions are in agreement with the Gilman (“reactant pair”) mechanism of CO oxidation.

Stereoselective addition of alpha-sulfinyl carbanions to N-p-tolylsulfinylketimines: synthesis of optically pure 1,2,2'-trialkyl-2-aminoethanols.

The reactions of lithium carbanions derived from both enantiomers of methyl (1) and ethyl p-tolyl sulfoxide (2) with (S)-N-arylsulfinylketimines 3 and 4 took place in a highly stereoselective manner and good isolated yields. The configuration of the carbon bonded to nitrogen relies exclusively on the N-sulfinylimine configuration. When ethyl p-tolyl sulfoxide (2) is use as nucleophile, two chiral centers are created simultaneously, where the configuration of the carbon bonded to the sulfur is mainly controlled by 2. The asymmetric induction increases with the temperature, being total at room temperature in the case of the matched pair of reactants. A non-oxidative Pummerer reaction on the obtained aminosulfoxides allows a straightforward synthesis of optically pure 1,2-ethanolamines with one or two chiral centers, including amino alcohols with a bulky quaternary carbon bonded to the amine group.

Transition state dynamics of N2O4 2NO2 in liquid state.

Transition state dynamics of dissociation and association reactions N2O4 <==> 2NO2 in liquid state are studied by classical molecular dynamics simulations of reactive liquid NO(2) at 298 K. An OSPP+LJ potential between NO(2) molecules proposed in paper I [J. Chem. Phys. 115, 10852 (2001)], which takes into account the orientational sensitivity of the chemical bond, has been used in the simulation. The trajectory and energy evolution of various reactions are studied in the OSPP+LJ liquid, which reproduces both the observed liquid phase equilibrium constant and Raman band shape of the dissociation mode. It is found that a NO(2) pair in reactive liquid NO(2) is bound when E(T)<0 and dissociates when E(T)>0, and the dissociation of a reactant pair occurs when the transition state (TS) surface of E(T)=0 is crossed from negative to positive, where E(T) is the sum of the potential and kinetic energies of intermolecular motion of the pair. Two types of dissociation are found depending on the source of energy for dissociation; the first type D is the dissociation via collisional activation of the reactive mode by solvent molecules, and the second type T is the dissociation via bond transfer from a dimer to a monomer NO(2) through the TS of NO(2) trimer. It is concluded that the type T dissociation is found to be much more probable than the type D dissociation because of easy energy conservation. The reactant experiences the TS of NO(2) trimer for a long time (1-10 ps) in NO(2) mediated bond transfer reactions, and crossing and recrossing trajectories and dynamics in the TS neighborhood are studied.

Interactions between an Alkylamine-Terminated Perfluoropolyether and the Amorphous Hydrogenated Carbon Surface

The bonding of molecularly thin (10 A) dipropylamine-terminated ZDPA 4000 and the hydroxyl-terminated Zdol 4000 lubricant films to amorphous hydrogenated carbon (CHx) are compared from 20 to 150 °C. The kinetic results demonstrate that the rate at which both ZDPA 4000 and Zdol 4000 bond to CHx is nonclassical with a time-dependent rate coefficient that is best described by the general form: k(t) ∝ kBt-h. For ZDPA, the bonding rate coefficient is observed to scale as t-0.25 while for Zdol the bonding rate coefficient is observed to scale as t-1. The t-0.25 bonding rate is shown to be consistent with diffusion-limited kinetics that originate from a high density of ZDPA−CHx reactant pairs that leads to a segregation of reactant pairs, while the t-1 bonding rate results when bonding occurs from a more liquidlike (no segregation) Zdol film structure. Surface energy measurements are indicative of initial intermolecular interactions between the dipropylamine end groups and the CHx surface despite a low bonded f...

CO+NO surface reaction model by Monte Carlo simulation

A CO+ NO→ CO 2+ 1 2 N 2 surface reaction model is studied by means of Monte Carlo simulations. The surface is represented by triangular and square lattices and the diffusion of N and lateral interaction between reactant nearest-neighbor adatoms is considered. The influence of diffusion of N to generate a steady reactive window (SRW) on square lattice is analyzed. On a triangular lattice SRW exists even in the absence of diffusion of N. We consider repulsive and attractive lateral interaction between reactant pairs, and their effects in reactive zone are studied. With repulsive interaction and without diffusion, SRW vanished, but on a square lattice the diffusion of N helps to generate it, even increasing its width as diffusion grows. On a triangular lattice this effect is not produced. For attractive lateral interaction a SRW is formed in all cases and its width is not modified by diffusion of N at the range studied.

Short-time kinetics of an irreversible bimolecular solution reaction: Asymptotic prediction by a non-Markovian Smoluchowski approach

The effect of the nondiffusional short-time liquid dynamics on the kinetics of an irreversible bimolecular solution reaction (A+B→products) is investigated using a non-Markovian Smoluchowski approach. It is shown that due to the convolution-type basic equation in this concept, asymptotic rate coefficient predictions can be deduced from exact results of the Smoluchowski–Collins–Kimball theory. For the case that only the inertial effect plays a significant part in the nondiffusional reactant pair dynamics, an asymptotic short-time expansion of the rate coefficient was derived in this way. It explicitly indicates as a new reaction-kinetic result how the rate coefficient in the short-time region depends on the AB potential of mean force. Specified for the conditions of contact reactions in a simple hard-sphere fluid, the kinetic predictions of the new concept are compared with the results of other approaches.

Prediction of Rate Constants for Reactions of the Hydroxyl Radical in Water at High Temperatures and Pressures

There is a need for accurate data on the rate constants of many reactions involved in the radiolysis of water at high temperature and pressure, to model aqueous chemistry in the heat transport systems of water-cooled nuclear reactors. Given the absence of direct experimental data, it is usual to extrapolate rate constants from lower temperature measurements. However, recent studies of muonium kinetics show that rate constants go through a maximum and fall with temperature under near critical and supercritical conditions. This behavior can be explained by the cage effect, in particular the number of collisions between a pair of reactants over the duration of their encounter. The model developed for reactions of muonium is equally valid for fast reactions in the radiolysis of water. It is used here to estimate the rate constants of near diffusion-controlled reactions of hydroxyl radicals in sub- and supercritical water. The results show significant differences from literature values commonly used to model aqueous radiation chemistry in nuclear reactors. In view of this, it is recommended that the predictions of earlier models be reconsidered.

Irreversible Tensile Stress Development in PECVD Silicon Nitride Films

ABSTRACTThe thermo-mechanical behavior of plasma-enhanced chemical vapor deposited (PECVD) silicon nitride films are investigated during thermal cycling and annealing. It is well known that PECVD films have a large amount of incorporated hydrogen that evolves on heating. This reduction in hydrogen is shown to be directly responsible, via constrained volume decrease, for irreversible increases in tensile stress. It is demonstrated that no stress equilibrium is attained during very long time anneals. The thermal cycling behavior of PECVD films can be modeled by chemical reaction theory, with the irreversible development of film stress a mechanical consequence. The model assumes first-order reaction kinetics of Si-H and N-H bonds, which react to form molecular hydrogen and reformed network bonds. The activation energy of reaction is not single-valued, indicative of the strong influence that the local bonding environment has on bond energies. If the incorporated hydrogen reactant pairs are assumed to be normally distributed with activation energy, irreversible stress development is well modeled, and the mean activation energy ranges from 2.44 to 2.93 eV for 150 to 300 °C deposited films.