Monomer-dimer Reaction Research Articles

Correlated noise induced non-equilibrium phase transition in surface catalytic reaction model

In recent years, with the development of chemical study of complex systems, such as surface catalytic system, etc. the research of nonlinear dynamics problem of complex system has received much attention. These systems have high-degree complexity, and they are inevitably affected by intrinsic and extrinsic fluctuations (noise) and time delay. The combination of noise and time delay is ubiquitous in nature, and often changes fundamentally dynamical behavior of the system, and thus making the system produce more richer and complex dynamical behaviors. At present, in the theoretical studies of the nonlinear dynamic properties, the macroeconomic deterministic or stochastic dynamic equation is adopted most, and the time delay factor, especially the influences of combination of noise and time delay on complex system are rarely taken into account. Thus, the study of the character, mechanism and application has important realistic significance and scientific value. In this paper, we first introduce the Dimer-Monomer reaction model (DM model), where various dimer adsorption mechanisms in catalyst surface, namely, the local and random adsorption surface catalytic reaction models are considered. Then we use the stochastic delayed theory involved in this paper and its extension, including the analytical approximation and numerical simulation of complex systems under the action of noise and time delay. In this paper, we consider the effects of noise and time-delayed feedback in the surface catalytic reaction model, and construct a delayed monomer-dimer surface reaction model including correlated noise. According to the Langevin equation, applying small delay approximation, we obtain the delayed Fokker-Planck equation for calculating characteristic parameters of the non-equilibrium phase transition behavior (the extreme of the steady state probability distribution), analyzing the effect mechanism of noise and its correlation with the non-equilibrium phase transition. The MD model exhibits the first- and second-order phase transition, namely, the reactive window between first- and second-order phase transition. The MD models for various dimer adsorption mechanisms (namely, local and random adsorption models) are discussed. The results are indicated as follows. (1) The external noise and correlation between two noise signals cause the reactive window width to contract. (2) The influence of the internal noise on the behavior of non-equilibrium dynamical phase transition depends on the noise correlation, i.e., when the two noise signals are negatively correlated, the internal noise causes the reactive window width to expand. However when the two noise signals are positively correlated, the internal noise causes the reactive window width to contract. (3) The noise-caused changes of reaction window have important scientific significance in the first- and second-order phase transition of the MD surface reaction model.

Colloidal Lock-and-Key Dimerization Reactions of Hard Annular Sector Particles Controlled by Osmotic Pressure.

Colloidal annular sectors are a broad class of shapes that offer the interesting possibility of dimerization when osmotically compressed to high densities while undergoing Brownian motion in two dimensions (2D). Here, we lithographically create and form a stable aqueous dispersion of many microscale prismatic 270° annular sectors, and we explore their near-equilibrium behavior in a tilted 2D gravitational column. Near the top of the column where the 2D gravitational osmotic pressure Π(2D) is low, we observe a gas-like phase composed almost entirely of monomers. However, below the surface and deeper into the column where Π(2D) is higher, we observe a reaction zone where monomers and dimers coexist, followed by an arrested region containing a very high percentage of interpenetrating, lock-and-key dimers that are a racemic mixture of positive and negative chiralities. We determine particle area fractions of monomers and dimers as a function of depth and use these to obtain the system's 2D osmotic equation of state. In the reaction zone, where dimers transiently form and break up, we also use these to calculate the equilibrium constant K associated with the monomer-dimer reaction, which increases exponentially with Π(2D). This dependence can be attributed the reduction in number of accessible microstates for dimers as they become more tightly compressed.

Linear rate-equilibrium relations arising from ion channel-bilayer energetic coupling

Linear rate-equilibrium (RE) relations, also known as linear free energy relations, are widely observed in chemical reactions, including protein folding, enzymatic catalysis, and channel gating. Despite the widespread occurrence of linear RE relations, the principles underlying the linear relation between changes in activation and equilibrium energy in macromolecular reactions remain enigmatic. When examining amphiphile regulation of gramicidin channel gating in lipid bilayers, we noted that the gating process could be described by a linear RE relation with a simple geometric interpretation. This description is possible because the gating process provides a well-understood reaction, in which structural changes in a bilayer-embedded model protein can be studied at the single-molecule level. It is thus possible to obtain quantitative information about the energetics of the reaction transition state and its position on a spatial coordinate. It turns out that the linear RE relation for the gramicidin monomer-dimer reaction can be understood, and the quantitative relation between changes in activation energy and equilibrium energy can be interpreted, by considering the effects of amphiphiles on the changes in bilayer elastic energy associated with channel gating. We are not aware that a similar simple mechanistic explanation of a linear RE relation has been provided for a chemical reaction in a macromolecule. RE relations generally should be useful for examining how amphiphile-induced changes in bilayer properties modulate membrane protein folding and function, and for distinguishing between direct (e.g., due to binding) and indirect (bilayer-mediated) effects.

A Monte Carlo Simulation of a Monomer Dimer CO-O2 Catalytic Reaction on the Surface and Subsurface of a Face-centered Cubic Lattice

The presence of oxygen in the subsurface in monomer-dimer reactions (CO-O2 and NO-CO) is observed experimentally. The effect of subsurface oxygen on a CO-O2 catalytic reaction on a face-centered cubic (FCC) lattice is studied using Monte Carlo simulation. The effect of adding subsurface neighbours on the phase diagram is also extensively explored. It is observed that the subsurface oxygen totally eliminates the typical second order phase transition. It is also shown that the introduction of the diffusion of O atoms and the subsurface of the FCC lattice shifts the single transition point towards the stoichiometric ratio.

Effect of experimentally observed hot atom adsorption mechanism on the phase diagram of monomer-dimer catalytic reaction on Pt(111): a Monte-Carlo simulation study

The effect of experimentally observed hot atom mechanism on the phase diagram using Pt (111) surface of the monomer-dimer reaction has been studied. While using this mechanism, whenever O2 molecule hits the randomly vacant selected site, it breaks up into atomic form and then executes ballistic flight. The path of the two oxygen atoms is taken exactly opposite to each other i.e. anti-parallel and range of the atoms is taken equal i.e. they may fly upto 1 and 1.73 atomic spacing from the site of impact . Two cases have been studied on the basis of the range of hot atoms. The steady reactive window is observed and the continuous transition disappears. As soon as the CO partial pressure departs from zero the production of CO2 is observed, which clearly verifies the experimental observation.

Macrocyclic Lanthanide Complexes as Artificial Nucleases and Ribonucleases: Effects of pH, Metal Ionic Radii, Number of Coordinated Water Molecules, Charge, and Concentrations of the Metal Complexes

We have been interested in the design, synthesis, and characterization of artificial nucleases and ribonucleases by employing macrocyclic lanthanide complexes because their high thermodynamic stability, low kinetic lability, high coordination number, and charge density (Lewis acidity) allow more design flexibility and stability. In this paper, we report the study of the use of the europium(III) complex, EuDO2A+ (DO2A is 1,7-dicarboxymethyl-1,4,7,10-tetraazacyclododecane) and other lanthanide complexes (i.e., LaDO2A+, YbDO2A+, EuK21DA+, EuEDDA+, and EuHEDTA where K21DA is 1,7-diaza-4,10,13-trioxacyclopentadecane-N,N'-diacetic acid, EDDA is ethylenediamine-N,N'-diacetic acid, and HEDTA is N-hydroxyethyl-ethylenediamine-N,N',N'-triacetic acid), as potential catalysts for the hydrolysis of the phosphodiester bond of BNPP (sodium bis(4-nitrophenyl)-phosphate). For the pH range 7.0-11.0 studied, EuDO2A+ promotes BNPP hydrolysis with the quickest rates among LaDO2A+, EuDO2A+, and YbDO2A+. This indicates that charge density is not the only factor affecting the reaction rates. Among the four complexes, EuDO2A+, EuK21DA+, EuEDDA+, and EuHEDTA, with their respective number of inner-sphere coordinated water molecules three, two, five, and three, EuEDDA+, with the greatest number of inner-sphere coordinated water molecules and a positive charge, promotes BNPP hydrolysis more efficiently at pH below 8.4, and the observed rate trend is EuEDDA+ > EuDO2A+ > EuK21DA+ > EuHEDTA. At pH > 8.4, the EuEDDA+ solution becomes misty and precipitates form. At pH 11.0, the hydrolysis rate of BNPP in the presence of EuDO2A+ is 100 times faster than that of EuHEDTA, presumably because the positively charged EuDO2A+ is more favorable for binding with the negatively charged phosphodiester compounds. The logarithmic hydrolysis constants (pKh) were determined, and are reported in the parentheses, by fitting the kinetic k(obs) data vs pH for EuDO2A+ (8.4), LaDO2A+ (8.4), YbDO2A+ (9.4), EuK21DA+ (7.8), EuEDDA+ (9.0), and EuHEDTA (10.1). The preliminary rate constant-[EuDO2A+] data at pH 9.35 were fitted to a monomer-dimer reaction model, and the dimer rate constant is 400 times greater than that of the monomer. The fact that YbDO2A+ catalyzes BNPP less effectively than EuDO2A+ is tentatively explained by the formation of an inactive dimer, [Yb(DO2A)(OH)]2, with no coordination unsaturation for BNPP substrate binding.

Monomer-dimer reaction model with nearest-neighbor interactions at finite temperatures.

We studied a monomer-dimer catalytic surface reaction model of the type 1 / 2A(2)+BA-->A2B, where interactions between nearest-neighbor species and the temperature of the catalyst are considered. Through Monte Carlo simulations we determined the phase diagram of the model in the plane temperature versus partial pressure of the BA molecules in its gaseous phase. We found that the transition between the A-poisoned state and the active one is always continuous and the associated critical exponents are in the same universality class of the directed percolation (DP). On the other hand, the transition from the active state to the BA-poisoned one changes from continuous to first order for a given temperature value. The critical exponents of the continuous branch belong also to the DP universality class. For a small range of values of the partial pressure of BA and very low temperatures, we observe the formation of an inactive sublattice structure inside the active phase.

Nonequilibrium kinetic phase transition of a monomer-dimer reaction model with sequential dimer adsorption in two dimensions.

We study a monomer-dimer reaction model in two dimensions in which the adsorption process of a dimer on the surface sites is separated into two steps (i.e., B2+*-->B2 *, and B2 * +*-->2B*, where * is an empty site), as first introduced by Evans and co-workers. It is clear that the dissociation of a dimer is dependent on the complicated configuration of the adsorbate. We show that the continuous transition from the reactive state to the O-passivated state and the discontinuous transition to the CO-passivated state both shift toward higher values of the fraction p of the monomer in gas phase but the reaction window decreases compared to the Ziff-Gulari-Barshad model. For the model studied here, the critical exponents of the continuous phase transition still exhibit a directed percolation character as expected.

The effect of Na concentration on the kinetic phase transitions of a monomer-dimer reaction system on Na-promoted surface

A simple lattice-gas model for the reaction of CO and NO on an Na-modified surface of a square lattice is studied. The crucial property of the model is Na-induced dissociation of NO, which triggers the catalytic reaction. Some interesting features are added to the phase diagram when the range of Na-induced NO dissociation is studied in the nearest and the next-nearest neighbourhood. The moment CO partial pressure (yCO) departs from zero, the continuous production of CO2 and N2 starts. This production remains continuous until a point where the catalytic activity stops and the surface is poisoned with a combination of CO, N and O. The value of poisoning point depends upon the value of Na concentration on the surface.

Monomer-dimer reaction model with asymmetric adsorption of monomer and dimer on the catalyst surface.

The irreversible kinetics of the Ziff-Gulari-Barshad model in the presence of inhomogeneity on a catalyst surface is investigated by means of Monte Carlo simulation. We assume that only part of catalyst surface sites are active for surface catalytic reaction and randomly distributed on the catalyst surface. The adsorption of a O2 molecule is permitted if one site of a nearest-neighbor vacant pair is active. CO can adsorb on all vacant sites, but the adsorption probability is p(p<1) if the site is not active. In our modified model, the O-passivated phase disappears and the continuous phase transition between the O passivated and the reactive state is eliminated. We also find that the transition between the CO passivated and the reactive state is continuous if the concentration of the active sites is small, and it becomes discontinuous with increasing concentrations of active sites. Furthermore, it is shown that a hysteresis loop exists whether the CO-passivated transition is continuous or discontinuous. Our simulation results are in good agreement with many relevant experimental results and may provide an alternative explanation for the experimental observations.

Effect of the coordination of the superficial site in the monomer–dimer reaction on a disordered substrate

Using Monte Carlo simulation experiments, a study is made of the effect of the superficial coordination number in a square lattice of sites for the monomer–dimer surface reaction (Ziff, Gulari and Barshad model) in the case of disordered substrates showing geometric heterogeneity of the sites, such as the percolation clusters. An analysis is made of the change in character of the phase transitions and in the size of the reactive window in the phase diagram, and the results were also compared with mean field theoretical calculations for disordered systems.

Kinetic phase transitions in a contaminated monomer-dimer reaction model

The irreversible kinetics of a monomer-dimer reaction on a catalyst surface [the Ziff-Gulari-Barshad (ZGB) model] in the presence of a contaminant species is studied by means of Monte Carlo simulation. The only processes allowed to the contaminant are adsorption and desorption; it is otherwise inert. The reaction window, delimited by a second order irreversible phase transition at low monomer concentration (lower bound transition) and by a first order one at high monomer concentration (upper bound transition) in the ZGB model is found to shrink with increasing contaminant concentration in a way that depends on its adsorption-desorption kinetics. Through epidemic analysis, it is also found that the upper bound transition changes from first to second order and that the lower bound transition can also be affected depending on the contaminant adsorption-desorption kinetics. The results may provide alternative explanations for experimental observations.

Catalytic reactions over modified surfaces: a Monte Carlo study

This paper deals with a simple model of bidirectional dimer–monomer reaction over a modified catalyst surface, studied by means of the Monte Carlo simulation method. It is assumed that certain active sites of a catalyst surface are blocked by modifier (or poison) atoms and thus unable to catalyze the reactions. The influence of the modifier species concentration and the topography of their distribution on the reaction yield and selectivity is also discussed. Four types of the modifier spatial distributions are used: random, dendritic, compact and also highly ordered patterns corresponding to the stripes of inactive sites. The assumed model predicts that the reaction occurring between the same partners leads to different products depending on the state of the reacting molecules, which is directly related to the state of the adsorbing sites in the vicinity of the reacting particles. It is demonstrated that the surface concentration of the different types of sites and the topography of their distribution over the surface are both important factors, which influence the behavior of systems considered here. In particular, it has been found that the reaction direction, the reaction window location and its width depend strongly on the surface morphology. The most surprising finding is that some topographies of the modifier species related to the stripes of inactive sites can generate an unusual double reaction window.

MONTE CARLO STUDY OF SURFACE REACTIONS: BIDIRECTIONAL MONOMER-DIMER REACTION ON MODIFIED SURFACES

The Monte Carlo simulation method is used to study monomer-dimer bidirectional reactions on modified surfaces. The assumed model predicts that reaction leads to different products depending on the state of reacting molecules, which depends on the state of adjacent adsorbing sites. The model assumes that the catalyst surface is precovered by a certain amount of modifier, which partially deactivates the surface and changes the state of the adsorbed reactant species. It is demonstrated that the surface concentration of the modifier atoms and the topography of their distribution over the surface are both important factors which influence the behavior of systems considered in this paper. In particular, it has been found that the reaction direction, the reaction window location and its width depend strongly on the surface morphology. The results are in a good qualitative agreement with the experimentally observed changes in the direction of the methanol oxidation on the sulfur-modified Fe(100) catalyst.

Kinetics of the competitive response of receptors immobilised to ion-channels which have been incorporated into a tethered bilayer.

A competitive ion channel switch (ICS) biosensor has been modelled yielding ligand mediated monomer-dimer reaction kinetics of gramicidin (gA) ion-channels within a tethered bilayer lipid membrane. Through employing gramicidin A, functionalized with the water-soluble hapten digoxigenin, it is possible to cross-link gramicidin to antibody fragments tethered at the membrane/aqueous interface. The change in ionic conductivity of the channel dimers may then be used to measure the binding kinetics of hapten-protein interactions at the membrane surface. The approach involves measuring the time dependence of the increase in impedance following the addition of a biotinylated antibody fragment (b-Fab'), which cross-links the functionalized gramicidin monomers in the outer layer of the lipid bilayer to tethered membrane spanning lipid. The subsequent addition of the small molecule digoxin, (M(r) 781 Da), competes with and reverses this interaction. The model provides a quantitative description of the response to both the cross-linking following the addition of the b-Fab' and the competitive displacement of the hapten by a water-soluble small analyte. Good agreement is obtained with independent measures of the cross-linking reaction rates of the gramicidin monomer-dimer and the b-Fab: hapten complex. The rate and amplitude of the competitive response is dependent on concentration and provides a fast and sensitive detection technique. Estimates are made of the concentration of gramicidin monomers in both the inner and outer monolayer leaflets of the membrane. This is used in the calculation of the gramicidin monomer/dimer equilibrium constant, K2D3. Other considerations include the membrane impedance limit set by the membrane leakage which is also a function of the concentration of the gA monomer concentration, and the two-dimensional kinetic association constant k2D2, of the hapten: b-Fab' complex. The gA dimer concentration is dependent on both the concentration of gA-dig and of the tethered streptavidin: b-Fab' complexes. The model shows that the 2D dissociation constant k2D3(-1), must be at least 10 times faster than the 3D dissociation constant k3D2(-1) for digoxin to completely reverse the cross-linked hapten-receptor interaction at the membrane interface.

On the influence of reactant’s induced surface transformations in the behavior of a heterogeneously catalyzed dimer–monomer reaction model

A surface reaction model for the catalyzed reaction A+(12)B2→AB is studied by means of Monte Carlo simulations. Motivated by experiments on the catalytic oxidation of CO on certain Pt surfaces; i.e., A≡CO, B2≡O2, and AB≡CO2; it is assumed that the catalyst surface undergoes reactant’s induced reversible phase transitions (RIRPT’s) between two different structures, i.e., a stable (reconstructed) phase in the low (high) A-coverage regime. Also the sticking coefficient of B2-species depends on the surface structure, being negligible in the stable phase. Two cases are studied in detail depending on whether the RIRPT’s involve the whole surface and are due to the average coverage of the sample or, on the other hand, they are restricted to small patches of the surface and are driven by the local coverage. For the case of global RIRPT’s, the reactive regime of the system exhibits self-sustained oscillatory behavior. However, considering local RIRPT’s oscillations are observed in finite samples but it is shown that they will vanish in the thermodynamic limit.

Critical behavior of a one-dimensional monomer-dimer reaction model with lateral interactions

A monomer-dimer reaction lattice model with lateral repulsion among the same species is studied using a mean-field analysis and Monte Carlo simulations. For weak repulsions, the model exhibits a first-order irreversible phase transition between two absorbing states saturated by each different species. Increasing the repulsion, a reactive stationary state appears in addition to the saturated states. The irreversible phase transitions from the reactive phase to any of the saturated states are continuous and belong to the directed percolation universality class. However, a different critical behavior is found at the point where the directed percolation phase boundaries meet. The values of the critical exponents calculated at the bicritical point are in good agreement with the exponents corresponding to the parity-conserving universality class. Since the adsorption-reaction processes does not lead to a non-trivial local parity-conserving dynamics, this result confirms that the twofold symmetry between absorbing states plays a relevant role in determining the universality class. The value of the exponent $\delta_2$, which characterizes the fluctuations of an interface at the bicritical point, supports the Bassler-Brown's conjecture which states that this is a new exponent in the parity-conserving universality class.

Chemical diffusivity and wave propagation in surface reactions: Lattice-gas model mimicking CO-oxidation with high CO-mobility

We analyze the spatiotemporal behavior in a lattice-gas model for the monomer-dimer reaction on surfaces. This model, which mimics catalytic CO-oxidation, includes a mobile monomer adspecies (representing CO), an immobile dissociatively adsorbed dimer species (representing O), and a finite reaction rate (for CO2 production). We characterize in detail the propagation of the chemical wave or reaction front produced when the stable reactive steady-state of the model displaces the metastable CO-poisoned state. In the regime of high CO-mobility, such propagation can be described directly within a “hydrodynamic” reaction-diffusion equation formalism. However, we show that the chemical diffusivity of CO is dependent on the O coverage, reflecting the percolative nature of CO-transport through a background of immobile O. We also emphasize that gradients in the coverage of immobile O induce a diffusive flux in the highly mobile CO. These features significantly influence wave propagation and reaction front structure. In addition, our analysis accounts for the feature that in this hydrodynamic regime, correlations persist in the distribution of adsorbed immobile O, and that these influence the reaction kinetics, the steady states, and the percolation and diffusion properties. To this end, we utilize a “hybrid” approach which incorporates a mean-field reaction-diffusion treatment of adsorbed CO, coupled with a lattice-gas treatment of adsorbed O [Tammaro et al., J. Chem. Phys. 103, 10277 (1995)].

On kinetic phase transition of the dimer-monomer reaction model

A detailed mean field theory (MFT) based on pair approximation (PA) is constructed to illustrate the kinetic phase transition behavior of the dimer-monomer surface reaction model A+1/2B 2→AB and its variants which take into account diffusion and desorption of both adsorbed species, Eley-Rideal reaction step, finite reaction probability and “endon mechanism” for B 2 adsorption. We find that the PA-MFT can reproduce well the phase diagrams and yield quite good predictions of the effects of diffusion, desorption etc., which indicates that PA-MFT may be suitable for the description of the steady state behavior of this model.

Development of techniques for monitoring gas-phase sodium species formed during coal combustion and gasification

The development of techniques suitable for on-line analysis of gas-phase molecular sodium species, resulting from the combustion and gasification of low-rank coals is described. In particular two techniques have been demonstrated, these are: (a) laser-induced photofragment fluorescence and (b) microwave spectroscopy. The photofragment technique can be applied in situ and yields excellent detection limits (<0.1 ppb of NaCl and 1 ppb NaOH) with good discrimination between the two major gas-phase species — NaCl and NaOH. Limitations of this technique include absorption of the ultraviolet (UV) photolysis excitation by other chemical species and particulates. Microwave spectroscopy shows promise in determining the sodium species distribution in the gas-phase. A purpose built analytical instrument (known as MILLIJET HT) is being developed for application in high-temperature environments. Early results indicate detection limits of <100 ppb NaCl. Lack of sensitivity for NaOH is being attributed to the formation of NaOH dimers and larger clusters. Detailed calculations of the dimer structure and the dimer-monomer reaction have been undertaken in order to maximise the performance of the instrument.