Calculation of point defects in rutile TiO 2 by the screened-exchange hybrid functional

The formation energies of the oxygen vacancy and titanium interstitial in rutile TiO 2 were calculated by the screened-exchange (sX) hybrid density functional method, which gives a band gap of 3.1 eV, close to the experimental value. The oxygen vacancy gives rise to a gap state lying 0.7 eV below the conduction band edge, whose charge density is localized around the two of three Ti atoms next to the vacancy. The Ti interstitial (Ti int) generates four defect states in the gap, whose unpaired electrons lie on the interstitial and the adjacent Ti 3d orbitals. The formation energy for the neutral oxygen vacancy is 1.9 eV for the O-poor chemical potential. The neutral Ti interstitial has a lower formation energy than the O vacancy under O-poor conditions. This indicates that both the O vacancy and Ti int are relevant for oxygen deficiency in rutile TiO 2 but the O vacancy will dominate under O-rich conditions. This resolves questions about defect localization and defect predominance in the literature. © 2012 American Physical Society.

Topologically invariant reaction coordinates for simulating multistate chemical reactions.

Evaluating free energy profiles of chemical reactions in complex environments such as solvents and enzymes requires extensive sampling, which is usually performed by potential of mean force (PMF) techniques. The reliability of the sampling depends not only on the applied PMF method but also the reaction coordinate space within the dynamics is biased. In contrast to simple geometrical collective variables that depend only on the positions of the atomic coordinates of the reactants, the E(gap) reaction coordinate (the energy difference obtained by evaluating a suitable force field using reactant and product state topologies) has the unique property that it is able to take environmental effects into account leading to better convergence, a more faithful description of the transition state ensemble and therefore more accurate free energy profiles. However, E(gap) requires predefined topologies and is therefore inapplicable for multistate reactions, in which the barrier between the chemically equivalent topologies is comparable to the reaction activation barrier, because undesired "side reactions" occur. In this article, we introduce a new energy-based collective variable by generalizing the E(gap) reaction coordinate such that it becomes invariant to equivalent topologies and show that it yields more well behaved free energy profiles than simpler geometrical reaction coordinates.

Accurate screened exchange band structures for the transition metal monoxides MnO, FeO, CoO and NiO.

We report calculations of the band structures and density of states of the four transition metal monoxides MnO, FeO, CoO and NiO using the hybrid density functional sX-LDA ('screened exchange local density approximation'). Late transition metal oxides are prototypical examples of strongly correlated materials, which pose challenges for electronic structure methods. We compare our results with available experimental data and show that our calculations generally yield accurate predictions for the fundamental band gaps and valence bands, in favourable agreement with previously reported theoretical studies. For MnO, the band gaps are still underestimated, suggesting additional many-body effects that are not captured by our screened hybrid functional approach.

Tests of an adaptive QM/MM calculation on free energy profiles of chemical reactions in solution.

We present reaction free energy calculations using the adaptive buffered force mixing quantum mechanics/molecular mechanics (bf-QM/MM) method. The bf-QM/MM method combines nonadaptive electrostatic embedding QM/MM calculations with extended and reduced QM regions to calculate accurate forces on all atoms, which can be used in free energy calculation methods that require only the forces and not the energy. We calculate the free energy profiles of two reactions in aqueous solution: the nucleophilic substitution reaction of methyl chloride with a chloride anion and the deprotonation reaction of the tyrosine side chain. We validate the bf-QM/MM method against a full QM simulation, and show that it correctly reproduces both geometrical properties and free energy profiles of the QM model, while the electrostatic embedding QM/MM method using a static QM region comprising only the solute is unable to do so. The bf-QM/MM method is not explicitly dependent on the details of the QM and MM methods, so long as it is possible to compute QM forces in a small region and MM forces in the rest of the system, as in a conventional QM/MM calculation. It is simple, with only a few parameters needed to control the QM calculation sizes, and allows (but does not require) a varying and adapting QM region which is necessary for simulating solutions.

Carbon source/sink function of a subtropical, eutrophic lake determined from an overall mass balance and a gas exchange and carbon burial balance

Although studies on carbon burial in lake sediments have shown that lakes are disproportionately important carbon sinks, many studies on gaseous carbon exchange across the water-air interface have demonstrated that lakes are supersaturated with CO2 and CH4 causing a net release of CO2 and CH4 to the atmosphere. In order to more accurately estimate the net carbon source/sink function of lake ecosystems, a more comprehensive carbon budget is needed, especially for gaseous carbon exchange across the water-air interface. Using two methods, overall mass balance and gas exchange and carbon burial balance, we assessed the carbon source/sink function of Lake Donghu, a subtropical, eutrophic take, from April 2003 to March 2004. With the overall mass balance calculations, total carbon input was 14 905 t, total carbon output was 4950 1, and net carbon budget was +9955 t, suggesting that Lake Donghu was a great carbon sink. For the gas exchange and carbon burial balance, gaseous carbon (CO2 and CH4) emission across the water-air interface totaled 752 t while carbon burial in the lake sediment was 9477 t. The ratio of carbon emission into the atmosphere to carbon burial into the sediment was only 0.08. This low ratio indicates that Lake Donghu is a great carbon sink. Results showed good agreement between the two methods with both showing Lake Donghu to be a great carbon sink. This results from the high primary production of Lake Donghu, substantive allochthonous carbon inputs and intensive anthropogenic activity. Gaseous carbon emission accounted for about 15% of the total carbon output, indicating that the total output would be underestimated without including gaseous carbon exchange. (C) 2007 Elsevier Ltd. All rights reserved.

Free radical scavenging and antioxidant enzymes activation of polysaccharide extract from Nostoc sphaeroides

Nostoc sphaeroides Kuetzing has been used as a traditional medicine in China to treat a variety of ailments. This research identified the antioxidant activities of polysaccharide extract from Nostoc sphaeroides. The extract, which contains 46.2% carbohydrates, exhibited an effective scavenging capability on superoxide radical, hydroxyl radicals in non site-specific as well as site-specific assays, and also performed lipid peroxidation inhibition in a dose-dependent manner. Polysaccharide extract had no 1,1-diphenyl-2-picrylhydrazyl radical scavenging potential at all test concentrations. Activities of superoxide dismutase, catalase, and glutathione peroxidase in human embryo kidney 293 cells were increased effectively when Nostoc sphaeroides extract was applied. These results suggested that the use of N. sphaeroides in treating ailments may be based on the antioxidant capacities of polysaccharide composition.

Hydrodynamics in an expanded bed of large size ion-exchange resin, and natural product adsorption

Successful applications of expanded bed adsorption (EBA) technology have been widely reported in the literature for protein purification. Little has been reported on the recovery of natural products and active components of Chinese herbal preparations using EBA technology. In this study, the hydrodynamic behavior in an expanded bed of cation resin, 001 x 7 Styrene-DVB, was investigated. Ephedrine hydrochloride (EH) was used as a model natural product to test the dynamic binding capacity (DBC) in the expanded bed. EBA of EH directly from a feedstock containing powdered herbs has also been investigated. These particles are different from commercially available expanded bed adsorbents by virtue of their large size (20S to 1030 gm). When the adsorbent bed is expanded to approximately 1.3 to 1.5 times its settled bed height, the axial liquid-phase dispersion coefficient was found to be of the order 10(-5) m(2) s(-1), which falls into the range 1.0 x 10(-6) to 1.0 X 10(-5) m(2) s(-1) observed previously in protein purification. Because of the favorable column efficiency (low axial dispersion coefficient), the recovery yield and purification factor values of EH directly from a feedstock reached 86.5% and 18, respectively. The results suggest that EBA technology holds promise for the recovery of natural products and active components of Chinese herbal preparations.

Photodegradation of 2-naphthol in aqueous solutions in the presence of humic acid and ferric ions

In this work, the photodegradation of the carcinogenic pollutant 2-naphthol in aqueous solution containing Aldrich humic acid (HA) and ferric ions (Fe(III)) under 125 W and 250 W high pressure mercury lamp (HPML, lambda >= 365 nm) irradiation was investigated. The photooxidation efficiencies were dependent on the pH values, light intensities and Fe(III)/HA concentration in the water, with higher efficiency at pHs 3-4, and 50 mu mol l(-1) Fe(III) with 20 mg l(-1) HA under 250 W HPML. The initial rate of photooxidation increases with increasing, the initial concentration of 2-naphthol from 10 mu mol l(-1) to 100 mu mol l(-1), while do not change at 50 and 100 mu mol l(-1). However, higher removal efficiency of 2-naphthol is achieved at its lower initial concentration of 10 mu mol l(-1), and initial rate of photooxidation is 0.193 mu mol l(-1) min(-1). Dissolved oxygen (DO) plays an important role in the system containing Fe(III)-HA complexes in which Fenton and photo-Fenton reactions were enhanced in the environment. Hydroxyl radicals produced in HA solution with or without ferric ions were determined by using benzene as free radical scavenger and phenol as scavenging products proportional to hydroxyl radicals. By using UV-Vis and excited fluorescence spectrum techniques, the main photooxidation products, which have higher absorption in the region of 240-340 nm, were found, and the mechanisms for the oxidative degradation is proposed.

Analysis of steric mass-action model for protein adsorption equilibrium onto porous anion-exchange adsorbent

The ion-exchange equilibrium of bovine serum albumin (BSA) to an anion exchanger, DEAE Spherodex M, has been studied by batch adsorption experiments at pH values ranging from 5.26 to 7.6 and ionic strengths from 10 to 117.1 mmol/l. Using the unadjustable adsorption equilibrium parameters obtained from batch experiments, the applicability of the steric mass-action (SMA) model was analyzed for describing protein ion-exchange equilibrium in different buffer systems. The parametric sensitivity analysis was performed by perturbing each of the model parameters, while holding the rest constant. The simulation results showed that, at high salt concentrations or low pHs close to the isoelectric point of the protein, the precision of the model prediction decreased. Parametric sensitivity analysis showed that the characteristic charge and protein steric factor had the largest effects on ion-exchange equilibrium, while the effect of equilibrium constant was about 70%-95% smaller than those of characteristic charge and steric factor under all conditions investigated. The SMA model with the relationship between the adjusted characteristic charge and the salt concentration can well predict the protein adsorption isotherms in a wide pH range from 5.84 to 7.6. It is considered that the SMA model could be further improved by taking into account the effect of salt concentration on the intermolecular interactions of proteins. (c) 2006 Elsevier Ltd. All rights reserved.

UV-sensitive P compounds: Release mechanism, seasonal fluctuation and inhibitory effects on alkaline phosphatase activity in a shallow Chinese freshwater lake (Donghu Lake)

Filtrable phosphorus compounds in a shallow Chinese freshwater lake (Donghu Lake) were fractionated by Sephadex G-25 gel-filtration chromatography. Some portions of those compounds released soluble reactive phosphorus upon irradiation with low dose ultraviolet light. Catalase and a hydroxyl radical scavenger (mannitol) markedly prevented photosensitive phosphorus release. The observed effects may be explained by the action of oxidizing reagents such as hydroxyl radicals, produced in photochemical reactions between UV irradiation and humic substances in the water. There was a strong seasonality in UV-sensitive P (UVSP) release. Michaels constants (K-m) of total alkaline phosphatase in the lake water showed a direct positive relation to UVSP. Plot of K-m against the UVSP/phosphomonoester ratio reveals a strong relationship between the two variables. These results suggest that in some situations UVSP may be a competitive inhibitor of alkaline phosphatase activity in the lake. The competitive inhibition of fractionated UVSP on alkaline phosphatase reagent (Sigma) apparently supports this hypothesis.

Electrical control of dynamic spin splitting induced by exchange interaction as revealed by time-resolved Kerr rotation in a degenerate spin-polarized electron gas

Manipulation of the spin degree of freedom has been demonstrated in a spin-polarized electron plasma in a heterostructure by using exchange-interaction-induced dynamic spin splitting rather than the Rashba and Dresselhaus types, as revealed by time-resolved Kerr rotation. The measured spin splitting increases from 0.256 meV to 0.559 meV as the bias varies from -0.3 V to -0.6 V. Both the sign switch of the Kerr signal and the phase reversal of Larmor precessions have been observed with biases, which all fit into the framework of exchange-interaction-induced spin splitting. The electrical control of it may provide a new effective scheme for manipulating spin-selected transport in spin FET-like devices. Copyright (C) EPLA, 2008.

Anisotropic exchange splitting of excitons in (001)GaAs/Al0.3Ga0.7As superlattice studied by reflectance difference spectroscopy

Anisotropic exchange splitting (AES) is induced by the joint effects of the electron-hole exchange interaction and the symmetry reduction in quantum wells and quantum dots. A model has been developed to quantitatively obtain the electron-hole exchange energy and the hole-mixing energy of quantum wells and superlattices. In this model, the AES and the degree of polarization can both be obtained from the reflectance difference spectroscopy. Thus the electron-hole exchange energy and the hole-mixing energy can be completely separated and quantitatively deduced. By using this model, a (001)5 nm GaAs/7 nm Al0.3Ga0.7As superlattice sample subjected to [110] uniaxial strains has been investigated in detail. The n=1 heavy-hole (1H1E) exciton can be analyzed by this model. We find that the AES of quantum wells can be linearly tuned by the [110] uniaxial strains. The small uniaxial strains can only influence the hole-mixing interaction of quantum wells, but have almost no contribution to the electron-hole exchange interaction. (c) 2008 American Institute of Physics.