Sequential Reaction Model Research Articles

Analysis of the isoprene chemistry observed during the New England Air Quality Study (NEAQS) 2002 intensive experiment

Isoprene and its first and second generation photochemical products, methyl vinyl ketone (MVK), methacrolein (MACR), and peroxymethacrylic nitric anhydride (MPAN), were measured off the coast of New England during the 2002 New England Air Quality Study (NEAQS) on board the NOAA Research Vessel Ronald H. Brown. The results of these measurements were analyzed using a simple sequential reaction model that has been used previously to examine regional oxidant chemistry. The highest isoprene impact was observed in air masses that had passed over an area of high isoprene emission WSW of Boston. The relative concentrations of isoprene and its first generation products show that the photochemistry is consistently “older” than the isoprene photochemistry observed at continental sites. The sequential reaction model was also applied to the aldehyde‐PANs (Peroxycarboxylic nitric anhydride) system, and the resulting PPN (peroxypropionic nitric anhydride)/propanal and PAN (peroxyacetic nitric anhydride)/acetaldehyde relationships were consistent with additional sources of PAN in this environment, e.g., isoprene photochemistry. This isoprene source was estimated to result in approximately 1.6 to 4 times more PAN in this environment relative to that produced from anthropogenic VOCs (volatile organic compounds) alone.

Reductive Dechlorination of Chlorinated Biphenyls by Palladized Zero-Valent Metals

Laboratory-scale reductive dechlorination studies using bimetals were conducted to detoxify chlorinated biphenyls, which are known as one of the most recalcitrant organic compounds. Palladized iron and palladized zinc readily dechlorinated mono- and di-chlorinated biphenyls while plain metals were not active. Biphenyl and less chlorinated biphenyls were detected as the major products and calculated mass balance was around 100%, indicating that predominant degradation reaction was dechlorination. For Pd/Fe, degradation rates of mono-chlorobiphenyls were higher than those of di-chlorobiphenyls. Pd/Zn showed higher reactivity than Pd/Fe for the degradation of chlorobiphenyls. Degradation rates of three mono-chlorobiphenyls were in order of 4-CBP > 3-CBP > 2-CBP and this order was matched with the selectivity and dechlorination rate of dichlorobiphenyls. Based on the detected daughter products, it was considered that degradation reaction of dichlorobiphenyls was mainly governed by stepwise dechlorination. However, sequential reaction model fittings indicated that concerted dechlorination was also partly involved in the dichlorobiphenyl degradation. This study demonstrated that catalytically modified ZVM could be successfully applied for the detoxification of chlorinated aromatic compounds including PCBs.

GC×GC measurements of C<sub>7</sub>-C<sub>11</sub> aromatic and n-alkane hydrocarbons on Crete, in air from Eastern Europe during the MINOS campaign

Abstract. During the Mediterranean Intensive Oxidant Study (MINOS) campaign in August 2001 gas-phase organic compounds were measured using comprehensive two-dimensional gas chromatography (GCxGC) at the Finokalia ground station, Crete. In this paper, C7-C11 aromatic and n-alkane measurements are presented and interpreted. The mean mixing ratios of the hydrocarbons varied from 1±1 pptv (i-propylbenzene) to 43±36 pptv (toluene). The observed mixing ratios showed strong day-to-day variations and generally higher levels during the first half of the campaign. Mean diel profiles showed maxima at local midnight and late morning, and minima in the early morning and evening. Results from analysis using a simplified box model suggest that both the chemical sink (i.e. reaction with OH) and the variability of source strengths were the causes of the observed variations in hydrocarbon mixing ratios. The logarithms of hydrocarbon concentrations were negatively correlated with the OH concentrations integral over a day prior to the hydrocarbon measurements. Slopes of the regression lines derived from these correlations for different compounds are compared with literature rate constants for their reactions with OH. The slopes for most compounds agree reasonably well with the literature rate constants. A sequential reaction model has been applied to the interpretation of the relationship between ethylbenzene and two of its potential products, i.e. acetophenone and benzeneacetaldehyde. The model can explain the good correlation observed between [acetophenone]/[ethylbenzene] and [benzeneacetaldehyde]/[ethylbenzene]. The model results and field measurements suggest that the reactivity of benzeneacetaldehyde may lie between those of acetophenone and ethylbenzene and that the ratio between yields of acetophenone and benzeneacetaldehyde may be up to 28:1. Photochemical ages of trace gases sampled at Finokalia during the campaign are estimated using the sequential reaction model and related data. They lie in the range of about 0.5-2.5 days.

Application of a sequential reaction model to PANs and aldehyde measurements in two urban areas

Measurements of the peroxycarboxylic nitric anhydrides (PANs = peroxyacetic nitric anhydride, PAN, peroxypropionic anhydride, PPN, and peroxymethacrylic nitric anhydride, MPAN) and aldehydes (acetaldehyde, propanal, and methacrolein) were made at Nashville, TN. in 1999 and Houston, TX. in 2000. The data were interpreted with a sequential reaction model that included reaction of aldehydes with hydroxyl radical and formation or loss of PANs mediated by peroxyacyl radicals {RC(O)OO}. The comparison of the measured ratios with those predicted by the model showed a disagreement for PAN/acetaldehyde and PPN/propanal in Nashville, but agreement in Houston. The Nashville data set also showed a disagreement in the case of PAN/acetaldehyde and MPAN/methacrolein, but agreement for PPN/propanal and MPAN/methacrolein. These features were consistent with the relative importance of isoprene to PAN formation at each site. The ratios were found to be highly correlated with ozone mixing ratios at each site.

Stopped-Flow Kinetics Investigation of the Imidazole-Catalyzed Peroxyoxalate Chemiluminescence Reaction

The stopped-flow technique was used to study the temperature-dependent kinetics of the imidazole-catalyzed peroxyoxalate reaction in order to further elucidate the reaction mechanism. Pseudo-first-order rate constants were obtained from the chemiluminescence intensity vs time profiles for the sequential reaction model X → Y → Z over a wide range of initial concentrations of each of the following reagents: bis(2,4,6-trichlorophenyl) oxalate (TCPO), imidazole (ImH), and hydrogen peroxide. These measurements were complemented by UV absorbance measurements of the kinetics of the step X → Y. For both reaction conditions pseudo-first-order in TCPO ([ImH], [H2O2] ≫ [TCPO]) and pseudo-first-order in H2O2 ([ImH]≫[TCPO]≫[H2O2]), the first step of the reaction is nucleophilic substitution by two imidazole molecules to form 1,1‘-oxalyldiimidazole (ODI). Under conditions of excess TCPO in the concentration range 0.075−0.25 mM, the Y → Z reaction probed the subsequent reaction of ODI with H2O2 to form the imidazoyl pe...

Kinetic evaluation of the effects of bioavailability of organic ligands on biodegradation in the presence of common sesquioxide grain coatings

AbstractRadionuclides and metals can be mobilized by chelating agents typically present in low‐level radioactive liquid wastes that are disposed of in shallow land trenches; persistence of the organic chelating agent in the subsurface environment is a critical control on solubilization and transport of the complexed nuclide. Low‐molecular‐weight organic compounds are susceptible to uptake by bacteria, yet the biodegradation rates of nuclide‐ligand complexes in a mixture of solids (soil minerals) and liquids (ground water) are poorly known. We investigated the rate of citrate uptake in the presence of cobalt by a mixed bacterial community under experimental conditions designed to explore the impacts of citrate concentration, temperature, and chemistry of mineral surfaces. Dilute solutions with a typical sandy‐aquifer groundwater composition and equimolar amounts of cobalt and citrate ranging from 4 to 320 μM were combined with four different sand treatments: uncoated quartz sand, Fe‐coated quartz sand, Mn‐coated quartz sand, and no sand. Mineralization (net 14CO2 produced) and assimilation (14C retained on a 0.2‐μm filter) were quantified. Initial rates of citrate mineralization and of assimilation were independent of temperature in the presence of Fe‐ and Mn‐coated sands but were lower at lower temperatures (15°C versus 25°C) for the no‐sand and the uncoated sand, but the fraction of total carbon taken up (respiration plus assimilation) that the cells assimilated was greater at 15°C than at 25°C. In the presence of Fe‐coated sand, the mixed culture assimilated a greater fraction of carbon at both temperatures. The van Slyke equation, based on a model of sequential irreversible reactions, was fit to the results of the heterotrophic uptake experiments. The estimated value of the van Slyke constant indicated that mass‐transfer constraints limited the overall rate of citrate uptake, and that biokinetic limitations became more important at the lower temperature for the no‐sand and uncoated sand treatments. The sorption of citrate to the sand surface did not limit the rate of uptake. Further, complexation with cobalt did not alter the rate of citrate degradation or the rate of bacterial growth. The results suggest that transmembrane citrate transport limited the rate of uptake. The benefit that the bacteria derived from being associated with the solid sand surface was not directly related to the extent of citrate sorption, but might have resulted from a local elevation in the concentration of nutrients (e.g., P or N) available to the adsorbed bacteria, which may have allowed a more efficient processing of carbon into biomass. Sesquioxide coatings enhance the sorptive properties of the mineral grains, and in these experiments, the bacteria derived benefit from being associated with the solid sand surface.

Depth distribution of SiD and SiD2complexes in silicon bombarded by 10 keV D+2ion

A secondary ion mass spectrometry (SIMS) and a neutral molecule mass spectrometry (NMMS) study of deuterium trapping in a single crystalline silicon as a result of ion irradiation at fluences 10 16 -10 18 cm -2 are presented. An attempt has been made to observe the formation and evolution of defect profiles containing one or two deuterium atoms (SiD- and SiD 2 -complexes). The proposed model of radiation-induced sequential reactions describes satisfactorily the accumulation of SiD- and SiD 2 -complexes and the reemission of D 2 -molecules.

Model for deuteron retention and reemission in graphites in a wide range of temperatures and energies

Abstract The experimental data available on hydrogen isotope trapping and release in graphite irradiated with deuterium ions under various conditions (energies 0.05–20 keV, temperatures 300–1300 K) are discussed. A new model of radiation-induced sequential reactions for hydrogen trapping and molecules reemission is proposed. The principal difference of our model from earlier models derives from the proposal that hydrogen retention occurs in two systems of traps (CD and CD2 complexes) that are formed locally and consequently in the irradiated area, and the molecular reemission takes place as a result of interaction between incoming ions and the already filled CD and CD2 traps. In our model the temperature dependence of retention and reemission is based on the assumption of the increase, at different rates, of reaction volumes with the irradiation temperature rising. Numerical simulations of hydrogen isotopes retention and reemission through the model equations agree well enough with the accumulated existing experimental data. The model could be used for the analysis of hydrogen isotopes behavior in graphite plasma-facing components.

Sequence Dependence of the Free Energy of B-Z Junction Formation in Deoxyoligonucleotides

The NaCl-induced transition from the right-handed B form to a hybrid form containing both left and right-handed DNA, joined by a B-Z junction, was investigated. Transition curves were constructed from circular dichroism spectra collected as a function of NaCl concentration for a series of 16 bp deoxyoligonucleotides. The sequence of the series (one strand of the duplex) was: 5′ CGCGCGCGAMNGACTG, where C indicates m 5dc, and -MN- was varied to include the possible Py: Py stacks: -CC-, -CT-, -TC- and -TT-, Transition curves for the conversion of all deoxyoligonucleotides were found to be biphasic. Singular value decomposition was used to analyze the experimental circular dichroism spectra obtained as a function of NaCl, and showed that the transition was not a simple two-state process, but rather required at least three species to account for the experimental data. A sequential three-state model, B⇌1⇌BZ, was derived and applied to analyze experimental transition curves. Non-linear least-squares analysis was used to evaluate the salt-dependent equilibrium constants for each step in the sequential reaction model. The results indicate that the free energy change for B-Z junction formation (ΔG j) depends on the dinucleotide sequence near the junction. At a Na activity of 5, ΔG j, values ranging from +1·2 to +1·7 kcal mol -1 were determined, depending on the sequence near the junction. ΔG j was found to be strongly dependent on salt concentration, with its magnitude decreasing with increasing Na activity. In addition to studies on linear duplex molecules, the B to BZ transition was also investigated in "dumbbell" forms of selected sequences. In these molecules, the ends were covalently linked by a single-stranded T 4 segment. These studies show that junction formation is energetically more costly in dumbbells than in their linear counterparts. A striking correlation was found between ΔG j and two independent conformational properties of the dinucleotide steps that were introduced into the linear duplex molecules. These are the free energy of unstacking and the estimated free energy change for the conversion of the dinucleotide from the B to the A conformation. The more stable against unstacking, or the more resistant to the B to A conversion, the sequence near the junction site is, the more costly is B-Z junction formation. These correlations reveal that the DNA sequence near the junction apparently must be pliable in order to accommodate the unusual structure of the junction. Thus, junction formation must directly affect, if only in subtle ways, the conformation of the neighboring right-handed region.

Conversion of methylcyclopentane and acyclic hexanes over supported platinum catalysts: II. Partial pressure and temperature effects on the formation of methylcyclopentane from the three acyclic hexanes

The sequential reaction model proposed in Part I ( J. Cutal. 112, 290 (1988)) of this series for the isomerization of acyclic hexanes via five-ring intermediates is supported by studies of the partial pressure and reaction temperature effects on methylcyclopentane (MCP) formation from n-hexane ( nC 6), 2-methylpentane (2MP), and 3-methylpentane (3MP). MCP concentration is found to increase linearly with increasing p hexane/P H2 ratio as predicted by the model. Enhanced MCP formation with increasing hexane partial pressure and with decreasing hydrogen partial pressure results from an increase in the surface concentration of the five-ring intermediates. Enhanced surface coverage by five-ring intermediates is accompanied by a decrease in hydrogenolysis presumably by reducing the surface coverage of the 3C intermediates. The sequential reaction model for the acyclic hexanes also predicts a linear relationship between ln[MCP] and 1 T with the slope of the line giving the activation energy difference between ring closure and ring opening reactions. Experimental results are in excellent agreement with this prediction. Activation energy differences between ring closure and ring opening reactions indicate that the five-ring closure between two primary carbon atoms (2MP and 3MP) has a somewhat higher activation energy than five-ring closure between a primary and a secondary carbon atom ( nC 6). Differences between five-ring closures of 2MP and 3MP and nC 6 are also evidenced by changes in reaction rates with decreasing hydrogen partial pressure and increasing reaction temperature. The relative nC 6 concentration from either MCP ring opening or 2MP and 3MP isomerization decreases with time on stream and with decreasing hydrogen partial pressure. These observations, together with results of MCP ring opening over Pt/TiO 2 catalysts, suggest that a carbonaceous layer deposited on the Pt surface during reaction sterically hinders the formation of MCP-like five-ring intermediates having tertiary-secondary CC bonds bound to the Pt surface.

Conversion of methylcyclopentane and acyclic hexanes over supported platinum catalysts: I. Isomerization kinetics and hydrogenolysis selectivities

In studies of the conversion of methylcyclopentane (MCP), n-hexane ( nC 6), 2-methylpentane (2MP), and 3-methylpentane (3MP) over a Pt/SiO 2 catalyst with an average Pt particle size less than 20 Å, it is found that MCP formation from acyclic hexanes is independent of residence time. Since a cyclic mechanism via a five-membered ring intermediate is the predominant hexane isomerization route, this observation suggests that isomerization is best approximated by a sequential reaction, ( nC 6, 2MP, or 3MP) → k 1 MCP → k 2 ( nC 6, 2MP, and 3MP), in which the quasi-steady-state approximation, d[ MCP] dt = 0 , is applicable. The quasi-steady-state approximation requires that k 2 ⪢ k 1 viz., the five-ring closure of hexane to MCP is rate-controlling. k 1 is established to be rate-controlling by experiments with mixed hexane and MCP feeds. Also, the formation of MCP from the acyclic hexanes is found to be independent of time on stream while the generation of isomerized products decreases by 30–40% with time. Based on a hydrodynamic analog of a sequential reaction, this observation indicates that k 1 and k 2 deactivate at the same rate thereby maintaining k 1 k 2 constant with time on stream. This argument implies that the ring closure of hexane to MCP and the ring opening of MCP occur on the same site and is consistent with microscopic reversibility which requires a common intermediate. Kinetic parameters calculated from the sequential reaction model using the quasi-steady-state approximation show that five-ring closure between two primary carbon atoms (2MP and 3MP) is about three times faster than that between a primary and a secondary carbon atom ( nC 6). For ring opening of five-ring intermediates, the reaction order in MCP concentration is higher with acyclic hexane feeds than with MCP feed due to a lower surface hydrocarbon coverage with the former feedstocks. During isomerization of the acyclic hexanes, hydrogenolysis to smaller molecules is a competing reaction pathway. For 2MP and 3MP, the rupture of the CC bond in β-position to the tertiary carbon atom is preferred and with the β bond in 3MP being more reactive than that in 2MP. In the case of nC 6, the center CC bond ruptures three times faster than the other CC bonds. These observations are in good agreement with literature data.

Nonequilibrium emission of fast light particles in heavy-ion collisions

A sequential three-body reaction model is shown to explain the factorization of cross-section employed in describing the observed angular correlations between highly energetic light particles and outgoing heavy reaction products in heavy-ion collisions. In particular, the characteristic forward-peaked component exhibited in the angular correlations is explained in terms of emission of fast light particles from a «l-window» and it is shown that different angular correlations are expected if positive and negative quantal deflection angles are involved.

Two-substrate reaction model for the heparin-catalyzed bovine antithrombin/protease reaction.

The kinetics of the heparin-dependent antithrombin/protease reaction were consistent with an ordered sequential two-substrate reaction model under all circumstances tested. In this model, heparin is the catalyst; while antithrombin is the first substrate and the protease is the second substrate. The first step in this reaction, the heparin-antithrombin interaction, has a KD of 25 nM but a diffusionally determined Km of about 150 nM regardless of protease substrate. The second step of the reaction, protease interaction with the heparin-antithrombin complex, was fast with a rate constant of 6.8 X 10(6) M-1.s-1 for Factor Xa and greater than 8 X 10(7) M-1.ls-1 for thrombin. Differences between thrombin and Factor Xa at low (nanomolar) concentrations of heparin were evident in this rate constant and the relative affinities for the heparin-antithrombin complex (Km for Factor Xa = 100 nM; Km for thrombin less than or equal to 2 nM). In agreement with this difference in Km, regardless of protease substrate, active site-blocked thrombin was a potent inhibitor of the antithrombin reaction; while active site-blocked Factor Xa was an ineffective inhibitor. At high heparin concentrations (micromolar), the kinetic parameters for Factor Xa were unchanged but the Km for thrombin increased dramatically to 100 nM. Other kinetic parameters were also estimated. Overall, the two-substrate reaction model provides a versatile approach for studying heparin function.

Ca 2+-dependent regulation of calmodulin binding and adenylate cyclase activation in bovine cerebellar membranes

The binding parameters of 125I-labeled calmodulin to bovine cerebellar membranes have been determined and correlted with the activation of adenylate cyclase by calmodulin. In the presence of saturating levels of free Ca 2+, calmodulin binds to a finite number of specific membrane sites with a dissociation constant ( K d) of 1.2 nM. Furthermore, Scatchard analysis reveals a second population of binding sites with a 100-fold lower affinity for calmodulin. The Ca 2+-dependence of calmodulin binding and of adenylate cyclase activation varies with the amount of calmodulin present, as can be infered from the model of sequential equilibrium reactions which describes the activation of calmodulin-dependent enzymes. On the basis of this model, a quantitative analysis of the effect of free Ca 2+ and of free calmodulin concentration on both binding and activation of adenylate cyclase was carried out. This analysis shows that both processes take place only when calmodulin is complexed with at least three Ca 2+ atoms. The concentration of the active calmodulin ·Ca 2+ species required for half-maximal activation of adenylate cyclase is very similar to the K d of the high affinity binding sites on brain membranes. A Hill coefficient of approx. 1 was found for both processes indicating an absence of cooperativity. Phenothiazines and thioxanthenes antipsychotic agents inhibit calmodulin binding to membranes and calmodulin-dependent activation of adenylate cyclase with a similar order of potency. These results suggest that the Ca 2+-dependent binding of calmodulin to specific high affinity sites on brain membranes regulates the activation of adenylate cyclase by calmodulin.

Theoretical analysis of the oxidation of amylose by periodate ion as an example of cooperative effects in polymer kinetics.

Abstract It is shown that oxidation of amylose by periodate ions can be described by a stochastic model of random sequential polymer reactions with nearest-neighbour cooperative effects. The reaction is completely described by a second order rate constant k, and two reactivity coefficients a and c which measure the degree of inhibition. Simple and rapid methods for the determination of k, a and c for a wide class of polymer reactions with nearest-neighbour cooperative effects are given.

A steady state model of sequential irreversible enzyme reactions

One of the questions which arises in the study of certain inborn errors of metabolism as well as in the field of enzyme kinetics is: what are the quantitative relationships between parameters of enzyme activity and substrate pool sizes in a metabolic pathway? A steady state model has been devised to answer this question for a homogeneous system of non-branched sequential irreversible enzyme reactions which follow Michaelis-Menten kinetics. The concentration of a substrate in such a pathway, [Si], is a function of 5 variables: (a) the KM of the enzyme which forms the substrate (KM (i−1)), (b) the KM of the enzyme which utilizes the substrate (KM i), (c) the Vmax of the enzyme which forms the substrate (Vm (i−1)), (d) the Vmax of the enzyme which utilizes the substrate (Vm i) and (e) the immediate precursor concentration [S(i−1)] where [Si] = KM i Vm (i−1) [S(i−1)]/[S(i−1)] (Vmi -Vm (i−1)) + KM (i−1)) Vmi The model introduces and defines the concept of and conditions for “amplification.” An input in the form of a steady state concentration of precursor [S(i−1)] may be “amplified” as an output in the form of an increased steady state concentration of product [Si]. The model also defines the values of the above 5 parameters which do not allow attainment of a steady state for the type of pathway considered.