Competing reaction processes on a lattice as a paradigm for catalyst deactivation

We mobilize both a generating function approach and the theory of finite Markov processes to compute the probability of irreversible absorption of a randomly diffusing species on a lattice with competing reaction centers. We consider an N-site lattice populated by a single deep trap, and N-1 partially absorbing traps (absorption probability 0<s<1). The influence of competing reaction centers on the probability of reaction at a target site (the deep trap) and the mean walk length of the random walker before localization (a measure of the reaction efficiency) are computed for different geometries. Both analytic expressions and numerical results are given for reactive processes on two-dimensional surfaces of Euler characteristic Ω=0 and Ω=2. The results obtained allow a characterization of catalyst deactivation processes on planar surfaces and on catalyst pellets where only a single catalytic site remains fully active (deep trap), the other sites being only partially active as a result of surface poisoning. The central result of our study is that the predicted dependence of the reaction efficiency on system size N and on s is in qualitative accord with previously reported experimental results, notably catalysts exhibiting selective poisoning due to surface sites that have different affinities for chemisorption of the poisoning agent (e.g., acid zeolite catalysts). Deviations from the efficiency of a catalyst with identical sites are quantified, and we find that such deviations display a significant dependence on the topological details of the surface (for fixed values of N and s we find markedly different results for, say, a planar surface and for the polyhedral surface of a catalyst pellet). Our results highlight the importance of surface topology for the efficiency of catalytic conversion processes on inhomogeneous substrates, and in particular for those aimed at industrial applications. From our exact analysis we extract results for the two limiting cases s≈1 and s≈0, corresponding respectively to weak and strong catalyst poisoning (decreasing s leads to a monotonic decrease in the efficiency of catalytic conversion). The results for the s≈0 case are relevant for the dual problem of light-energy conversion via trapping of excitations in the chlorophyll antenna network. Here, decreasing the probability of excitation trapping s at sites other than the target molecule does not result in a decrease of the efficiency as in the catalyst case, but rather in enhanced efficiency of light-energy conversion, which we characterize in terms of N and s. The one-dimensional case and its connection with a modified version of the gambler's ruin problem are discussed. Finally, generalizations of our model are described briefly.

PCDD/PCDF and dl-PCB in the ambient air of a tropical Andean city: passive and active sampling measurements near industrial and vehicular pollution sources

Concentration gradients were observed in gas and particulate phases of PCDD/F originating from industrial and vehicular sources in the densely populated tropical Andean city of Manizales, using passive and active air samplers. Preliminary results suggest greater concentrations of dl-PCB in the mostly gaseous fraction (using quarterly passive samplers) and greater concentrations of PCDD/F in the mostly particle fraction (using daily active samplers). Dioxin-like PCB predominance was associated with the semi-volatility property, which depends on ambient temperature. Slight variations of ambient temperature in Manizales during the sampling period (15°C-27°C) may have triggered higher concentrations in all passive samples. This was the first passive air sampling monitoring of PCDD/F conducted in an urban area of Colombia. Passive sampling revealed that PCDD/F in combination with dioxin-like PCB ranged from 16 WHO-TEQ2005/m(3) near industrial sources to 7 WHO-TEQ2005/m(3) in an intermediate zone-a reduction of 56% over 2.8 km. Active sampling of particulate phase PCDD/F and dl-PCB were analyzed in PM10 samples. PCDD/F combined with dl-PCB ranged from 46 WHO-TEQ2005/m(3) near vehicular sources to 8 WHO-TEQ2005/m(3) in the same intermediate zone, a reduction of 83% over 2.6 km. Toxic equivalent quantities in both PCDD/F and dl-PCB decreased toward an intermediate zone of the city. Variations in congener profiles were consistent with variations expected from nearby sources, such as a secondary metallurgy plant, areas of concentrated vehicular emissions and a municipal solid waste incinerator (MSWI). These variations in congener profile measurements of dioxins and dl-PCBs in passive and active samples can be partly explained by congener variations expected from the various sources.

Long-term sampling of dioxin-like substances from a clinker kiln stack using alternative fuels

The aim of this work is to characterize atmospheric emissions of polychlorinated dibenzo-p-dioxins (PCDDs)/polychlorinated dibenzofurans (PCDFs) and dioxin-like polychlorinated biphenyls (dl-PCBs) from a cement production plant where the existing clinker production line was completely replaced by a new state-of-the-art installation. The project started in April 2008 with the installation of a long-term sampling system in the stack of the clinker kiln that used petroleum coke as fuel; PCDD/PCDF and dl-PCB emissions were then evaluated for a two year period. To carry out the second part of the study, in 2010 the sampling system was moved to the new installation in which, apart from conventional fuel, recovered derived fuel (RDF) and WWTP sludge were used as alternative fuels. For both the old and new clinker kilns, PCDD/PCDF emission values were well below the limit established by the European Waste Incineration Directive 2000/76/CE (EWID) of 100 pg I-TEQ/Nm(3); values ranged from 0.43 to 2.02 and from 0.07 to 3.31 pg I-TEQ/Nm(3), respectively. dl-PCBs accounted for approximately 25% of the WHO-TEQ toxicity. These results prove that the installation is capable of reducing PCDD/PCDF and dl-PCB emissions when alternative fuels are integrated into the process. In the case of PCDDs/PCDFs, the major contributions to total TEQ were usually from 2,3,7,8-TCDD (owing to its relative abundance) and 2,3,4,7,8-PeCDF (due to its high I-TEF of 0.5); while for dl-PCBs, the major contribution was from PCB-126. The slight shift in the congener profile between the old and new installations was characterized and a regression model was proposed for dl-PCB emissions depending on the RDF flow rate in the clinker.

Reaction mechanism of the bicopper enzyme peptidylglycine α-hydroxylating monooxygenase

Peptidylglycine α-hydroxylating monooxygenase is a noninteracting bicopper enzyme that stereospecifically hydroxylates the terminal glycine of small peptides for its later amidation. Neuroendocrine messengers, such as oxytocin, rely on the biological activity of this enzyme. Each catalytic turnover requires one oxygen molecule, two protons from the solvent, and two electrons. Despite this enzyme having been widely studied, a consensus on the reaction mechanism has not yet been found. Experiments and theoretical studies favor a pro-S abstraction of a hydrogen atom followed by the rebinding of an OH group. However, several hydrogen-abstracting species have been postulated; because two protons are consumed during the reaction, several protonation states are available. An electron transfer between the copper atoms could play a crucial role for the catalysis as well. This leads to six possible abstracting species. In this study, we compare them on equal footing. We perform quantum mechanics/molecular mechanics calculations, considering the glycine hydrogen abstraction. Our results suggest that the most likely mechanism is a protonation of the abstracting species before the hydrogen abstraction and another protonation as well as a reduction before OH rebinding.

Lattice statistical theory of random walks on a fractal-like geometry

We have designed a two-dimensional, fractal-like lattice and explored, both numerically and analytically, the differences between random walks on this lattice and a regular, square-planar Euclidean lattice. We study the efficiency of diffusion-controlled processes for flows from external sites to a centrosymmetric reaction center and, conversely, for flows from a centrosymmetric source to boundary sites. In both cases, we find that analytic expressions derived for the mean walk length on the fractal-like lattice have an algebraic dependence on system size, whereas for regular Euclidean lattices the dependence can be transcendental. These expressions are compared with those derived in the continuum limit using classical diffusion theory. Our analysis and the numerical results quantify the extent to which one paradigmatic class of spatial inhomogeneities can compromise the efficiency of adatom diffusion on solid supports and of surface-assisted self-assembly in metal-organic materials.

Metallicity enhancement in core–shell SiO2@RuO2nanowires

SiO₂@RuO₂composite nanowires exhibit an enhanced metallic nature of the external RuO₂shell, reflected in a significantly improved electronic conductance.

Quasi-resonant neutralization of He+ ions at a germanium surface

When low-energy He ions are scattered from a Ge surface, the fraction of positive ions exhibits characteristic oscillations as a function of ion energy. These oscillations are caused by quasi-resonant neutralization (qRN), a process which is active for materials with a narrow band nearly resonant with the unperturbed He 1s-level. In this paper we measure the fraction of He+ backscattered from Ge(100). In conjunction with recently developed theoretical methods, we extract quantitative information on the efficiency of qRN. Our evaluation reveals that qRN is a highly efficient process leading to ion fractions two orders of magnitude lower than in systems for which neutralization is only due to Auger processes.

Evanescent continuous-time random walks

We study how an evanescence process affects the number of distinct sites visited by a continuous-time random walker in one dimension. We distinguish two very different cases, namely, when evanescence can only occur concurrently with a jump, and when evanescence can occur at any time. The first is characteristic of trapping processes on a lattice, whereas the second is associated with spontaneous death processes such as radioactive decay. In both of these situations we consider three different forms of the waiting time distribution between jumps, namely, exponential, long tailed, and ultraslow.

Energetics of Multi-Ion Conduction Pathways in Potassium Ion Channels

Potassium ion channels form pores in cell membranes, allowing potassium ions through while preventing the passage of sodium ions. Despite numerous high-resolution structures, it is not yet possible to relate their structure to their single molecule function other than at a qualitative level. Over the past decade, there has been a concerted effort using molecular dynamics to capture the thermodynamics and kinetics of conduction by calculating potentials of mean force (PMF). These can be used, in conjunction with the electro-diffusion theory, to predict the conductance of a specific ion channel. Here, we calculate seven independent PMFs, thereby studying the differences between two potassium ion channels, the effect of the CHARMM CMAP forcefield correction, and the sensitivity and reproducibility of the method. Thermodynamically stable ion-water configurations of the selectivity filter can be identified from all the free energy landscapes, but the heights of the kinetic barriers for potassium ions to move through the selectivity filter are, in nearly all cases, too high to predict conductances in line with experiment. This implies it is not currently feasible to predict the conductance of potassium ion channels, but other simpler channels may be more tractable.

Tailoring structural and electronic properties of RuO2 nanotubes: a many-body approach and electronic transport

The electrical conduction properties of ruthenium oxide nanocables are of high interest. These cables can be built as thin shells of RuO2 surrounding an inner solid nanowire of a dielectric insulating silica material. With this motivation we have investigated the structural, electronic and transport properties of RuO2 nanotubes using the density functional formalism, and applying many-body corrections to the electronic band structure. The structures obtained for the thinnest nanotubes are of the rutile type. The structures of nanotubes with larger diameters deviate from the rutile structure and have in common the formation of dimerized Ru-Ru rows along the axial direction. The cohesive energy shows an oscillating behavior as a function of the tube diameter. With the exception of the thinnest nanotubes, there is a correlation such that the electronic band structures of tubes with high cohesive energies show small gaps at the Fermi energy, whereas the less stable nanotubes exhibit metallic behavior, with bands crossing the Fermi surface. The electronic conductance of nanotubes of finite length connected to gold electrodes has been calculated using a Green-function formalism, and correlations have been established between the electronic band structure and the conductance at zero bias.

Detailed Examination of a Single Conduction Event in a Potassium Channel

Although extensively studied, it has proved difficult to describe in detail how potassium ion channels conduct cations and water. We present a computational study that, by using stratified umbrella sampling, examines nearly an entire conduction event of the Kv1.2/2.1 paddle chimera and thereby identifies the expected stable configurations of ions and waters in the selectivity filter of the channel. We describe in detail the motions of the ions and waters during a conduction event, focusing on how waters and ions enter the filter, the rotation of water molecules inside the filter, and how potassium ions are coordinated as they move from a water to a protein environment. Finally, we analyze the small conformational changes undergone by the protein, showing that the stable configurations are most similar to the experimental crystal structure.

Polychlorinated dibenzo-p-dioxins, dibenzofurans, biphenyls, paraffins and polybrominated diphenyl ethers in marine fish species from Ebro River Delta (Spain)

The results of a surveillance programme on the determination of polychlorinated dibenzo-p-dioxins (PCDDs), polychlorinated dibenzofurans (PCDFs), polychlorinated biphenyls (PCBs), polybrominated diphenyl ethers (PBDEs) and short chain chlorinated paraffins (SCCPs) in marine fish and shellfish species which are fished, commercialised and consumed in the Ebro River Delta area (NE, Spain) are presented. The study included the analysis of five marine fish species (sardine, gilthead sea bream, conger, eel and flounder) and three shellfish species (murex, carpet shell and mussel) collected in 2012 in five fishing harbours near to this area. WHO-TEQ concentrations for PCDD/Fs and dioxin like PCBs (dl-PCBs) ranged from 0.03 to 0.31 pg WHO-TEQ2005PCDD/Fg(-1)wetweight (ww) and from 0.02 to 3.15 pg WHO-TEQ2005PCBg(-1)ww, respectively. All levels were below the maximum concentrations established by the EU Regulation. The PCBs and PCDD/Fs accumulation pattern found in the samples analysed showed a distribution typically reported for marine samples. For marker PCBs and PBDEs, concentration levels ranging from 929 to 57494 pg g(-1)ww and from 36.2 to 827 pg g(-1)ww were obtained, respectively, meanwhile for SCCPs levels were between 3.1 and 141 ng g(-1)ww. Finally, the trends in the levels of PCDD/F and dl-PCBs found from 2006 to 2012 in fish and shellfish species were studied. A slight decrease of PCDD/F and dl-PCB concentrations was found since 2006.

Exploration and trapping of mortal random walkers

Exploration and trapping properties of random walkers that may evanesce at any time as they walk have seen very little treatment in the literature, and yet a finite lifetime is a frequent occurrence, and its effects on a number of random walk properties may be profound. For instance, whereas the average number of distinct sites visited by an immortal walker grows with time without bound, that of a mortal walker may, depending on dimensionality and rate of evanescence, remain finite or keep growing with the passage of time. This number can in turn be used to calculate other classic quantities such as the survival probability of a target surrounded by diffusing traps. If the traps are immortal, the survival probability will vanish with increasing time. However, if the traps are evanescent, the target may be spared a certain death. We analytically calculate a number of basic and broadly used quantities for evanescent random walkers.

On the organic energy gap problem

In conjugated organic molecules, the difference between the HOMO and LUMO Kohn-Sham eigenvalues is significantly smaller than the transport gap measured experimentally. We discuss here, within a local-orbital formulation of DFT, how this problem can be corrected using appropriate hybrid potentials, that add a fraction of Hartree-Fock exchange interaction in the DFT calculation. We illustrate this approach presenting calculations for two simple systems: H(2) and C(6)H(6); then, we discuss how to implement this hybrid approach in a general local-orbital calculation, adjusting the hybrid contribution to yield the correct experimental HOMO/LUMO energy gap for the molecule. We also consider the case of an organic molecule on a metal and analyze the effect of the molecule-metal interaction on the organic energy gap. In particular, we discuss how to introduce in this hybrid-potential scheme the effect of the image potential, and present results for the organic molecules PTCDA, TTF, benzene and pentacene on the metal surfaces Au(111), Ag(111) and Cu(111).

Survival probability of an immobile target in a sea of evanescent diffusive or subdiffusive traps: a fractional equation approach

We calculate the survival probability of an immobile target surrounded by a sea of uncorrelated diffusive or subdiffusive evanescent traps (i.e., traps that disappear in the course of their motion). Our calculation is based on a fractional reaction-subdiffusion equation derived from a continuous time random walk model of the system. Contrary to an earlier method valid only in one dimension (d=1), the equation is applicable in any Euclidean dimension d and elucidates the interplay between anomalous subdiffusive transport, the irreversible evanescence reaction, and the dimension in which both the traps and the target are embedded. Explicit results for the survival probability of the target are obtained for a density ρ(t) of traps which decays (i) exponentially and (ii) as a power law. In the former case, the target has a finite asymptotic survival probability in all integer dimensions, whereas in the latter case there are several regimes where the values of the decay exponent for ρ(t) and the anomalous diffusion exponent of the traps determine whether or not the target has a chance of eternal survival in one, two, and three dimensions.