Role of Electronegativity in Environmentally Persistent Free Radicals (EPFRs) Formation on ZnO.

Environmentally persistent free radicals (EPFRs), a group of emerging pollutants, have significantly longer lifetimes than typical free radicals. EPFRs form by the adsorption of organic precursors on a transition metal oxide (TMO) surface involving electron charge transfer between the organic and TMO. In this paper, dihalogenated benzenes were incorporated to study the role of electronegativity in the electron transfer process to obtain a fundamental knowledge of EPFR formation mechanism on ZnO. Upon chemisorption on ZnO nanoparticles at 250 °C, electron paramagnetic resonance (EPR) confirms the formation of oxygen adjacent carbon-centered organic free radicals with concentrations between 1016 and 1017 spins/g. The radical concentrations show a trend of 1,2-dibromobenzene (DBB) > 1,2-dichlorobenzene (DCB) > 1,2-difluorobenzene (DFB) illustrating the role of electronegativity on the amount of radical formation. X-ray absorption spectroscopy (XAS) confirms the reduction of the Zn2+ metal center, contrasting previous experimental evidence of an oxidative mechanism for ZnO single crystal EPFR formation. The extent of Zn reduction for the different organics (DBB > DCB > DFB) also correlates to their polarity. DFT calculations provide theoretical evidence of ZnO surface reduction and exhibit a similar trend of degree of reduction for different organics, further building on the experimental findings. The lifetimes of the EPFRs formed confirm a noteworthy persistency.

Formation of Environmentally Persistent Free Radicals (EPFRs) on the Phenol-Dosed α-Fe2O3(0001) Surface.

Environmentally persistent free radicals (EPFRs) are a class of toxic air pollutants that are found to form by the chemisorption of substituted aromatic molecules on the surface of metal oxides. In this study, we employ X-ray photoelectron spectroscopy (XPS) and ultraviolet photoelectron spectroscopy (UPS) to perform a temperature-dependent study of phenol adsorption on α-Fe2O3(0001) to probe the radical formation mechanism by monitoring changes in the electronic structure of both the adsorbed phenol and metal oxide substrate. Upon dosing at room temperature, new phenol-derived electronic states have been clearly observed in the UPS spectrum at saturation coverage. However, upon dosing at high temperature (>200 °C), both photoemission techniques have shown distinctive features that strongly suggest electron transfer from adsorbed phenol to Fe2O3 surface atoms and consequent formation of a surface radical. Consistent with the experiment, DFT calculations show that phenoxyl adsorption on the iron oxide surface at RT leads to a minor charge transfer to the adsorbed molecule. The experimental findings at high temperatures agree well with the EPFRs' proposed formation mechanism and can guide future experimental and computational studies.

Formation of environmentally persistent free radicals (EPFRs) on ZnO at room temperature: Implications for the fundamental model of EPFR generation.

Environmentally persistent free radicals (EPFRs) have significant environmental and public health impacts. In this study, we demonstrate that EPFRs formed on ZnO nanoparticles provide two significant surprises. First, EPR spectroscopy shows that phenoxy radicals form readily on ZnO nanoparticles at room temperature, yielding EPR signals similar to those previously measured after 250°C exposures. Vibrational spectroscopy supports the conclusion that phenoxy-derived species chemisorb to ZnO nanoparticles under both exposure temperatures. Second, DFT calculations indicate that electrons are transferred from ZnO to the adsorbed organic (oxidizing the Zn), the opposite direction proposed by previous descriptions of EPFR formation on metal oxides.

Sign Learning Kink-based (SiLK) Quantum Monte Carlo for molecular systems.

The Sign Learning Kink (SiLK) based Quantum Monte Carlo (QMC) method is used to calculate the ab initio ground state energies for multiple geometries of the H2O, N2, and F2 molecules. The method is based on Feynman's path integral formulation of quantum mechanics and has two stages. The first stage is called the learning stage and reduces the well-known QMC minus sign problem by optimizing the linear combinations of Slater determinants which are used in the second stage, a conventional QMC simulation. The method is tested using different vector spaces and compared to the results of other quantum chemical methods and to exact diagonalization. Our findings demonstrate that the SiLK method is accurate and reduces or eliminates the minus sign problem.

Environmentally persistent free radicals (EPFRs). 3. Free versus bound hydroxyl radicals in EPFR aqueous solutions.

Additional experimental evidence is presented for in vitro generation of hydroxyl radicals because of redox cycling of environmentally persistent free radicals (EPFRs) produced after adsorption of 2-monochlorophenol at 230 °C (2-MCP-230) on copper oxide supported by silica, 5% Cu(II)O/silica (3.9% Cu). A chemical spin trapping agent, 5,5-dimethyl-1-pyrroline-N-oxide (DMPO), in conjunction with electron paramagnetic resonance (EPR) spectroscopy was employed. Experiments in spiked O(17) water have shown that ∼15% of hydroxyl radicals formed as a result of redox cycling. This amount of hydroxyl radicals arises from an exogenous Fenton reaction and may stay either partially trapped on the surface of particulate matter (physisorbed or chemisorbed) or transferred into solution as free OH. Computational work confirms the highly stable nature of the DMPO-OH adduct, as an intermediate produced by interaction of DMPO with physisorbed/chemisorbed OH (at the interface of solid catalyst/solution). All reaction pathways have been supported by ab initio calculations.

Density functional calculation of the structure and electronic properties of Cu(n)O(n) (n = 1-8) clusters.

Ab initio simulations and calculations were used to study the structures and stabilities of copper oxide clusters, Cu(n)O(n) (n = 1-8). The lowest energy structures of neutral and charged copper oxide clusters were determined using primarily the B3LYP/LANL2DZ model chemistry. For n ≥ 4, the clusters are nonplanar. Selected electronic properties including atomization energies, ionization energies, electron affinities, and Bader charges were calculated and examined as a function of n.

Ab initio study of the formation and degradation reactions of chlorinated phenols.

The formation, stability, and reactivity of chlorinated phenoxyl radicials was studied using ab initio methods. All 19 congeners from mono- to penta-chlorinated species were considered. The radical species are formed in combustion reactions via unimolecular scission of the phenoxyl-hydrogen bond or hydrogen atom abstraction by hydrogen atom or hydroxyl radical. The resulting radicals are stable with respect to unimolecular decomposition and reaction with molecular oxygen is relatively slow. Activation energies are similar to those of the phenoxyl radical for both the decomposition pathway and the reaction with molecular oxygen at the more reactive para-position. Calculations were performed with the model chemistries B3LYP/6-31G(d,p), BHandHLYP/6-31G(d,p), BHandHLYP/aug-cc-pVDZ and QCISD(T)/6-31G(d,p)//BHandHLYP/6-31G(d,p) (for selected reactions.) The results suggest the radicals are sufficiently stable and unreactive to be moderately persistent in the atmosphere, especially when associated with some types of particulate matter. An additivity analysis is made to decompose the relative energetics of the congeners into contributions from hydrogen bonding, resonance stabilization, and repulsive interactions. The results of this analysis correlate well with the results of the calculations.

Constructing explicit magnetic analogies for the dynamics of glass forming liquids.

By defining a spatially varying replica overlap parameter for a supercooled liquid referenced to an ensemble of fiducial liquid state configurations, we explicitly construct a constrained replica free energy functional that maps directly onto an Ising Hamiltonian with both random fields and random interactions whose statistics depend on the liquid structure. Renormalization group results for random magnets when combined with these statistics for the Lennard-Jones glass suggest that discontinuous replica symmetry breaking would occur if a liquid with short range interactions could be equilibrated at a sufficiently low temperature where its mean field configurational entropy would vanish, even though the system strictly retains a finite configurational entropy.

Intermolecular forces and the glass transition.

Random first-order transition theory is used to determine the role of attractive and repulsive interactions in the dynamics of supercooled liquids. Self-consistent phonon theory, an approximate mean field treatment consistent with random first-order transition theory, is used to treat individual glassy configurations, whereas the liquid phase is treated using common liquid-state approximations. Free energies are calculated using liquid-state perturbation theory. The transition temperature, T*A, the temperature where the onset of activated behavior is predicted by mean field theory; the lower crossover temperature, T*C, where barrierless motions actually occur through fractal or stringy motions (corresponding to the phenomenological mode coupling transition temperature); and T*K, the Kauzmann temperature (corresponding to an extrapolated entropy crisis), are calculated in addition to T*g, the glass transition temperature that corresponds to laboratory cooling rates. Relationships between these quantities agree well with existing experimental and simulation data on van der Waals liquids. Both the isobaric and isochoric behavior in the supercooled regime are studied, providing results for DeltaCV and DeltaCp that can be used to calculate the fragility as a function of density and pressure, respectively. The predicted variations in the alpha-relaxation time with temperature and density conform to the empirical density-temperature scaling relations found by Casalini and Roland. We thereby demonstrate the microscopic origin of their observations. Finally, the relationship first suggested by Sastry between the spinodal temperature and the Kauzmann temperatures, as a function of density, is examined. The present microscopic calculations support the existence of an intersection of these two temperatures at sufficiently low temperatures.

Structural characterization of Al10O6iBu16(mu-H)2, a high aluminum content cluster: further studies of methylaluminoxane (MAO) and related aluminum complexes.

The first structurally characterized isobutyl-containing aluminoxane compound is presented. The Al10O6iBu16(mu-H)2 (I) cluster is produced from neat octakis-isobutyltetraluminoxane (Al4O2iBu8) at 80 degrees C in 6-8 h followed by slow crystallization. The crystal is triclinic (space group P1) with the molecule lying on an inversion center. This aluminoxane contains both nearly linear, 154(2) degrees, aluminum-bridging hydrides and three-coordinate aluminum sites. Solid-state 27Al magic-angle spinning (MAS) NMR experiments were done at 19.6 and 40 T (833 MHz and 1.703 GHz, 1H) and at 30-35 kHz spinning speeds, leading to the determination of the Cq and eta values for the two four-coordinate Al sites and a lower limit of Cq for the three-coordinate Al site. Geometry-optimized restricted Hartree-Fock calculations at the double-zeta level of an idealized structure (methyl substituted, D2h geometry) yielded Cq and eta in close agreement with experiment; Cq agrees within 3 MHz.

Formation and stabilization of persistent free radicals.

We demonstrate that stable and relatively unreactive "environmentally persistent free radicals (PFRs)" can be readily formed in the post-flame and cool-zone regions of combustion systems and other thermal processes. These resonance-stabilized radicals, including semiquinones, phenoxyls, and cyclopentadienyls, can be formed by the thermal decomposition of molecular precursors including catechols, hydroquinones and phenols. Association with the surfaces of fine particles imparts additional stabilization to these radicals such that they can persist almost indefinitely in the environment. A mechanism of chemisorption and electron transfer from the molecular adsorbate to a redox-active transition metal or other receptor is shown through experiment, and supported by molecular orbital calculations, to result in PFR formation. Both oxygen-centered and carbon-centered PFRs are possible that can significantly affect their environmental and biological reactivity.

Methyaluminoxane (MAO) polymerization mechanism and kinetic model from ab initio molecular dynamics and electronic structure calculations.

MAO is the co-catalyst in metallocene catalytic systems, which are widely used in single-site olefin polymerization due to their high stereoselectivity. To date, the structures of the catalytically active compound or compounds in MAO have eluded researchers. Although many structural models have been proposed, none are generally accepted. In this study, aspects of the formation mechanism of MAO are addressed. Molecular dynamics simulations at the MP2 level of theory were carried out for presumed elementary steps in MAO formation via hydrolysis of trimethylaluminum (TMA). Methane production was observed, in agreement with experiment, as well as intermediate species that are consistent with the known structural features of MAO and similar to isolated and structurally characterized aluminoxanes. A (CH3)3Al-OH2 species, which we denote as TMA-OH2, containing a stable Al-O single bond emerged as the building block molecule. From this species, a hexameric cage was formed and activation barriers for the various reactions were calculated. Three distinct channels were identified for growth beyond the hexameric cage. It was concluded that MAO formation is a step polymerization through a bifunctional monomer, with [(CH3)Al-O] as the structural unit and a kinetic model was proposed. The structures that emerged were in agreement with the crystallographic evidence for aluminoxanes and support the experimental data regarding the MAO chemical composition.

Divergence, recombination and retention of functionality during protein evolution.

We have only a vague idea of precisely how protein sequences evolve in the context of protein structure and function. This is primarily because structural and functional contexts are not easily predictable from the primary sequence, and evaluating patterns of evolution at individual residue positions is also difficult. As a result of increasing biodiversity in genomics studies, progress is being made in detecting context-dependent variation in substitution processes, but it remains unclear exactly what context-dependent patterns we should be looking for. To address this, we have been simulating protein evolution in the context of structure and function using lattice models of proteins and ligands (or substrates). These simulations include thermodynamic features of protein stability and population dynamics. We refer to this approach as 'ab initio evolution' to emphasise the fact that the equilibrium details of fitness distributions arise from the physical principles of the system and not from any preconceived notions or arbitrary mathematical distributions. Here, we present results on the retention of functionality in homologous recombinants following population divergence. A central result is that protein structure characteristics can strongly influence recombinant functionality. Exceptional structures with many sequence options evolve quickly and tend to retain functionality--even in highly diverged recombinants. By contrast, the more common structures with fewer sequence options evolve more slowly, but the fitness of recombinants drops off rapidly as homologous proteins diverge. These results have implications for understanding viral evolution, speciation and directed evolutionary experiments. Our analysis of the divergence process can also guide improved methods for accurately approximating folding probabilities in more complex but realistic systems.

Simulation of electronic and geometric degrees of freedom using a kink-based path integral formulation: application to molecular systems.

A kink-based path integral method, previously applied to atomic systems, is modified and used to study molecular systems. The method allows the simultaneous evolution of atomic and electronic degrees of freedom. The results for CH4, NH3, and H2O demonstrate this method to be accurate for both geometries and energies. A comparison with density functional theory (DFT) and second-order Moller-Plesset (MP2) level calculations show the path integral approach to produce energies in close agreement with MP2 energies and geometries in close agreement with both DFT and MP2 results.

High-field 19.6T 27Al solid-state MAS NMR of in vitro aluminated brain tissue.

The combination of (27)Al high-field solid-state NMR (19.6T) with rapid spinning speeds (17.8 kHz) is used to acquire (27)Al NMR spectra of total RNA human brain temporal lobe tissues exposed to 0.10 mM Al(3+) (as AlCl(3)) and of human retinal pigment epithelial cells (ARPE-19), grown in 0.10 mM AlCl(3). The spectra of these model systems show multiple Al(3+) binding sites, good signal/noise ratios and apparent chemical shift dispersions. A single broad peak (-3 to 11 ppm) is seen for the aluminated ARPE-19 cells, consistent with reported solution-state NMR chemical shifts of Al-transferrin. The aluminated brain tissue has a considerably different (27)Al MAS NMR spectrum. In addition to the transferrin-type resonance, additional peaks are seen. Tentative assignments include: -9 to -3 ppm, octahedral AlO(6) (phosphate and water); 9 ppm, condensed AlO(6) units (Al-O-Al bridges); 24 ppm, tetrahedral AlO(3)N and/or octahedral Al-carbonate; and 35 ppm, more N-substituted aluminum and /or tetrahedral AlO(4). Thus, brain tissue is susceptible to a broad range of coordination by aluminum. Furthermore, the moderate (27)Al C(Q) values (all less than 10 MHz) suggest future NMR studies may be performed at 9.4T and a spin rate of 20 kHz.

Tools and strategies for processing diffusion-ordered 2D NMR spectroscopy (DOSY) of a broad, featureless resonance: an application to methylaluminoxane (MAO).

UNLABELLED: DOSY has been extremely successful in many studies of molecular weight distributions, especially when the components are separable along the chemical shift axis. However, an unresolved NMR resonance yields the familiar problem of overlapping exponential decays. In a study of methylaluminoxane (MAO), a set of data processing and simulation tools were developed: read Bruker data files (Matlab); preliminary non-linear least-squares fit with f-test (Matlab); movie generation of the fits (Matlab); conversion of diffusion coefficients to molecular masses through molecular volumes (Gaussian-98); and simulation of DOSY data sets for various molecular mass distributions (Mathematica). These tools are presented here and briefly compared with other DOSY analysis methods. ELECTRONIC SUPPLEMENTARY MATERIAL: Supplementary material is available in the online version of this article at http://dx.doi.org/10.1007/s00216-003-2457-1. The following Matlab and Mathematica files are made available: Plot_Raw_DOSY.m, Fit_Two_Component.m (which calls One_Gaussian_LEASTSQ.m, Two_Gaussian_LEASTSQ.m, and pFTest.m), and DOSY_theory.nb. Note: Matlab v5.2 optimization toolbox, as supplied, lacked a confidence interval subroutine; upon our request, confint.m was provided to the authors by Mathworks, Inc. Newer versions of Matlab have a similar program already included in the optimization.

Microscopic theory of network glasses.

A theory of the glass transition of network liquids is developed using self-consistent phonon and liquid state approaches. The dynamical transition and entropy crisis characteristic of random first-order transitions are mapped as a function of the degree of bonding and density. Using a scaling relation for a soft-core model to crudely translate the densities into temperatures, theory predicts that the ratio of the dynamical transition temperature to the laboratory transition temperature rises as the degree of bonding increases, while the Kauzmann temperature falls explaining why highly coordinated liquids are "strong" while van der Waals liquids without coordination are "fragile."