Intermediate Reaction Rates Research Articles

Contribution from biogenic organic compounds to particle growth during the 2010 BEACHON-ROCS campaign in a Colorado temperate needleleaf forest

Abstract. New particle formation (NPF) is an important atmospheric phenomenon. During an NPF event, particles first form by nucleation and then grow further in size. The growth step is crucial because it controls the number of particles that can become cloud condensation nuclei. Among various physical and chemical processes contributing to particle growth, condensation by organic vapors has been suggested as important. In order to better understand the influence of biogenic emissions on particle growth, we carried out modeling studies of NPF events during the BEACHON-ROCS (Bio–hydro–atmosphere interactions of Energy, Aerosol, Carbon, H2O, Organics & Nitrogen – Rocky Mountain Organic Carbon Study) campaign at Manitou Experimental Forest Observatory in Colorado, USA. The site is representative of the semi-arid western USA. With the latest Criegee intermediate reaction rates implemented in the chemistry scheme, the model underestimates sulfuric acid concentration by 50 %, suggesting either missing sources of atmospheric sulfuric acid or an overestimated sink term. The results emphasize the contribution from biogenic volatile organic compound emissions to particle growth by demonstrating the effects of the oxidation products of monoterpenes and 2-Methyl-3-buten-2-ol (MBO). Monoterpene oxidation products are shown to influence the nighttime particle loadings significantly, while their concentrations are insufficient to grow the particles during the day. The growth of ultrafine particles in the daytime appears to be closely related to the OH oxidation products of MBO.

Theory of Transient Permeation Through Reactive Barrier Films II. Two Layer Reactive-passive Structures with Dynamic Interface

The theory of transient permeation through homogeneous and structures incorporating non–catalytic solute scavenger is developed in Part II. It is based on the authors' earlier analytical solutions for the steady state model of permeation through passive films and reactive films with immobile catalytic scavenger dispersed within the layer. For consumable scavengers, the steady-unsteady solution matching method is introduced to describe scavenger consumption dynamics as a moving interface between reactive and passive layers of the film. The scavenger exhaustion time equation is derived in the approximation of fast reaction but it is shown to be also valid for intermediate reaction rates. The transient transmission rate dependence on time, boundary conditions, reactivity and reactive capacity of the scavenger, and layer sequence is derived. The terminology, notation, and section numbering continue from Part I of this series [1].

In Vitro and in Vivo Dimerization of Human Endonuclease III Stimulates Its Activity

Human endonuclease III (hNTH1), a DNA glycosylase with associated abasic lyase activity, repairs various mutagenic and toxic-oxidized DNA lesions, including thymine glycol. We demonstrate for the first time that the full-length hNTH1 positively cooperates in product formation as a function of enzyme concentration. The protein concentrations that caused cooperativity in turnover also exhibited dimerization, independent of DNA binding. Earlier we had found that the hNTH1 consists of two domains: a well conserved catalytic domain, and an inhibitory N-terminal tail. The N-terminal truncated proteins neither undergo dimerization, nor do they show cooperativity in turnover, indicating that the homodimerization of hNTH1 is specific and requires the N-terminal tail. Further kinetic analysis at transition states reveals that this homodimerization stimulates an 11-fold increase in the rate of release of the final product, an AP-site with a 3'-nick, and that it does not affect other intermediate reaction rates, including those of DNA N-glycosylase or AP lyase activities that are modulated by previously reported interacting proteins, YB-1, APE1, and XPG. Thus, the site of modulating action of the dimer on the hNTH1 reaction steps is unique. Moreover, the high intranuclear (2.3 microM) and cytosolic (0.65 microM) concentrations of hNTH1 determined here support the possibility of in vivo dimerization; indeed, in vivo protein cross-linking showed the presence of the dimer in the nucleus of HeLa cells. Therefore, it is likely that the dimerization of hNTH1 involving the N-terminal tail masks the inhibitory effect of this tail and plays a critical role in its catalytic turnover in the cell.

Unraveling the Schneeberg garnet puzzle: a numerical model of multiple nucleation and coalescence

A quantitative kinetic model for the growth of the different garnet porphyroblast microstructures (type 1 and type 2) of the Western Schneeberg Complex (WSC) is presented. These porphyroblasts formed by a multiple nucleation and coalescence mechanism. Our numerical simulation shows that at constant diffusion rates: (1) low interface reaction rates result in a fully amalgamated porphyroblast (type 2); (2) intermediate reaction rates result in a porphyroblast, where coalescence of grains closer to the margin prevented amalgamation of those in the centre (similar to type 1 porphyroblasts); and (3) high interface reaction rates result in a porphyroblast microstructure with an atoll form. All three microstructures are characterised by distinctive cluster size distributions. A 2-D cluster size distribution analysis of type 1 porphyroblasts of WSC shows that these did not form because of intermediate interface reaction rates, but because the diffusion rate of nutrients was too low to keep pace with the interface reaction rate.

Effect of chemical kinetics on feasible splits for reactive distillation

AbstractFeasible direct and indirect sharp splits for multicomponent single‐feed continuous reactive distillation are predicted with a model, in which each column section is represented by a series of cocurrent isobaric flashes. In the limits of no reaction and equilibrium chemical reaction, the model reduces to conventional models for distillation lines, and each column section can be represented by the same equations. At intermediate reaction rates, however, the models for the column sections differ, and new results for fixed points and feasible products are obtained. A bifurcation study shows the limits of feasibility, including the influence of flow rate, catalyst level and holdup. Unlike distillation without reaction, limited ranges of feasibility in all of these variables are found. The method has been applied to five examples, one of which is described in detail. Feasibility predictions are validated by column simulations.

Feasible products for kinetically controlled reactive distillation of ternary mixtures

AbstractA method to determine feasible product compositions from a single‐feed reactive distillation column for finite rates of reaction is presented. Tracking of pinch points to estimate the limit at minimum reflux is combined with performance modeling for the limit at the minimum number of stages. Using two examples it is shown how the product composition regions deform from the known limit of no reaction through intermediate rates of reaction and finally collapse onto the chemical equilibrium curve at extremely fast reaction rates. However, compositions can be achieved at intermediate reaction rates that do not lie between the limits for slow (no reaction) and fast (chemical equilibrium) reactions.

Role of Enzyme–substrate Flexibility in Catalytic Activity: an Evolutionary Perspective

Site-directed mutagenesis has proved an effective experimental technique to investigate catalytic mechanisms and to determine relations between enzyme structure and function. This article invokes an analytical model based on evolution by mutation and natural selection—Nature's analogue of site-directed mutagenesis—to derive a set of general rules relating enzyme structure and activity. The catalysts are described in terms of the structural parameters, rigidity and flexibility, and the functional variables, reaction rate and substrate specificity. The evolutionary model predicts the following structure–activity relations: (a) rigid enzyme–flexible substrate: large variation in reaction rates, broad substrate specificity; (b) rigid enzyme–rigid substrate: diffusion controlled rates, absolute specificity; (c) flexible enzyme–rigid substrate: intermediate reaction rates, group specificity; (d) flexible enzyme–flexible substrate: slow rates, absolute specificity.Spectroscopic methods and X-ray crystallography now yield important characteristics of enzyme–substrate complexes such as molecular flexibility. The evolutionary analysis we have exploited provides general principles for inferring catalytic activity from structural studies of enzyme–substrate complexes.

Evolutionary dynamics of enzymes.

This paper codifies and rationalizes the large diversity in reaction rates and substrate specificity of enzymes in terms of a model which postulates that the kinetic properties of present-day enzymes are the consequence of the evolutionary force of mutation and selection acting on a class of primordial enzymes with poor catalytic activity and broad substrate specificity. Enzymes are classified in terms of their thermodynamic parameters, activation enthalpy delta H* and activation entropy delta S*, in their kinetically significant transition states as follows: type 1, delta H* > 0, delta S* < 0; type 2, delta H* < or = 0, delta S* < or = 0; type 3, delta H* > 0, delta S* > 0. We study the evolutionary dynamics of these three classes of enzymes subject to mutation, which acts at the level of the gene which codes for the enzyme and selection, which acts on the organism that contains the enzyme. Our model predicts the following evolutionary trends in the reaction rate and binding specificity for the three classes of molecules. In type 1 enzymes, evolution results in random, non-directional changes in the reaction rate and binding specificity. In type 2 and 3 enzymes, evolution results in a unidirectional increase in both the reaction rate and binding specificity. We exploit these results in order to codify the diversity in functional properties of present-day enzymes. Type 1 molecules will be described by intermediate reaction rates and broad substrate specificity. Type 2 enzymes will be characterized by diffusion-controlled rates and absolute substrate specificity. The type 3 catalysts can be further subdivided in terms of their activation enthalpy into two classes: type 3a (delta H* small) and type 3b (delta H* large). We show that type 3a will be represented by the same functional properties that identify type 2, namely, diffusion-controlled rates and absolute substrate specificity, whereas type 3b will be characterized by non-diffusion-controlled rates and absolute substrate specificity. We infer from this depiction of the three classes of enzymes, a general relation between the two functional properties, reaction rate and substrate specificity, namely, enzymes with diffusion-controlled rates have absolute substrate specificity. By appealing to energetic considerations, we furthermore show that enzymes with diffusion-controlled rates (types 2 and 3a) form a small subset of the class of all enzymes. This codification of present-day enzymes derived from an evolutionary model, essentially relates the structural properties of enzymes, as described by their thermodynamic parameters, to their functional properties, as represented by the reaction rate and substrate specificity.

COMPETING DRYING AND REACTION MECHANISMS IN THE FORMATION OF SOL-TO-GEL FILMS, FIBERS, AND SPHERES

ABSTRACT Drying of films, fibers, and spheres undergoing sol-to-gel transformation is greatly affected by the strong dependence of the diffusion coefficients on composition, molecular weight, and temperature. This dependence is probed by solving the equations of mass and heat transfer by diffusion or conduction and associated convection, along with chemical reaction. A one-dimensional analysis is used that encompasses the planar, cylindrical, and spherical configurations. The solutions are obtained by Galerkin's method with finite element basis functions and entail large-scale computation. Skinning and solidification phenomena in silica sol-to-gel systems are greatly affected not only by falling diffusion coefficients, but also by the competition between drying and reaction. The kinetics of silica reactions are modeled with the statistical scheme of Kay and Assink (1988). Gelation is predicted by the recursive technique of Bailey et al. (1990). Results show that at intermediate reaction rates, high molecu...

Chromatography of reversibly reacting mixtures: mutarotation effects in sugar separations

A mathematical model is developed to describe the chromatographic behavior of a reversibly reacting mixture of two linearly adsorbed components. When the distribution coefficient between the fluid and the solid phases is different for the two components, the elution profiles are broadened to an extent that depends upon the rate of reaction. For low reaction rates, the two components behave independently and two separate peaks are obtained when an equilibrium mixture is injected. At intermediate reaction rates, the elution profiles are stretched between the characteristic elution times of the two components. Finally, at high reaction rates, the two components propagate through the column as an equilibrium mixture and two superimposed symmetrical peaks are obtained. The mathematical development is used in the analysis of experimental results for the chromatographic separation of glucose—fructose mixtures at diferent temperatures. Each component peak is broadened and distorted by the simultaneous occurrence of mutarotation, which results in the formation of differently sorbed tautomers for each sugar. The model developed allows a determination of equilibrium and rate constants for each tautomer and a successful prediction of the chromatographic behavior.

Retrospective Clinical Study of Hypersensitivity Reactions to Aztreonam and Six Other β-Lactam Antibiotics in Cystic Fibrosis Patients Receiving Multiple Treatment Courses

A total of 2,793 courses of treatment with seven beta-lactam antibiotics were administered to 121 cystic fibrosis patients chronically infected with Pseudomonas aeruginosa, and the patients were evaluated with respect to clinical hypersensitivity reactions. Seventy-five patients (62%) experienced 125 reactions, for an overall frequency (based on the number of courses) of 4.5%. Immediate reactions occurred in 34 patients (28.1%) during 53 courses (1.9%). The highest rate of reactions involved piperacillin (50.9% of patients), and the lowest rate involved imipenem and aztreonam (4.0% and 6.5% of patients, respectively); intermediate reaction rates were noted for carbenicillin (23.6% of patients), azlocillin (20.8%), cefsulodin (17.1%), and ceftazidime (13.0%). Cross-reactivity did not appear to be a major problem. Reactions to aztreonam seemed to be restricted to a small group of patients with a high propensity for beta-lactam hypersensitivity.

Thiol distribution and mercaptalbumin reactivity in the blood plasma of different vertebrates.

SummaryBlood plasma of man, rabbit, mouse, rat and guinea‐pig contains 3 groups of thiol compounds. Non‐protein thiols are present to the extent of approximately 52%. The albumin fraction contains 75% thiols as determined with di‐(5‐carboxy‐4‐nitrophenyl) disulphide and about 10% higher values are obtained when determinel with 4,4′‐dipyridyldisulphide. Approximately 20% of the plasma thiols are present in proteins other than albumin.The reaction of the plasma thiols with the disulphides is mainly due to mercaptalbumin, and the reactivity of plasma thiols and the isolated albumins with di‐(5‐carboxy‐4‐nitrophenyl) disulphide and 4,4′‐dipyridyldisulphide varies according to species and pH. Human and guinea‐pig mercaptalbumin react slowly with di‐(5‐carboxy‐4‐nitrophenyl) disulphide at pH 6·5 whereas a fast reaction takes place with rat's mercaptalbumin. Intermediate reaction rates are seen with rabbit and mouse plasma.Species differences are also noted in the unmasking of thiol groups of plasma and isolated albumins by urea, guanidine hydrochloride and lauryl sulphate.Certain positions of the thiol groups in the mercaptalbumin structures are suggested and genetic considerations and evolutionary aspects of mercaptalbumin coding are discussed.

Slowly Reacting Gas Mixture in a Heat Conductivity Cell

A hypothetical gas mixture composed of A2, B2, and AB which reacts bimolecularly, 2AB ⇌ A2 + B2, is placed in a thermal conductivity cell. The heat flux as well as the chemical and thermal profiles are calculated numerically for fast, slow, and intermediate reaction rates. Since the chemical composition is not in equilibrium with the local temperature, considerable calculational difficulties are encountered. An approximation scheme is given for estimating the behavior of such systems. It is found that for fast reactions, local equilibrium applies. If the rate of the chemical reactions is slow compared to the rate of diffusion (an exact criterion is given), the chemical composition within the cell becomes homogeneous throughout the cell. This composition is determined by the set of equations ∫ T CT HλRi dT=0,where λ is the coefficient of heat conductivity and ℛi is the net rate of production of molecules of the ith species. Conversely, from a knowledge of the steady-state chemical composition we may determine the chemical reaction rates. Calculations are made for a mixture of H2, I2, and HI. This system should be easy to study experimentally since the I2 concentration can be determined from optical absorption and the HI concentration can be determined from infrared absorption.