Kinetics of phase transformations in a model with metastable fluid-fluid separation: A molecular dynamics study

By molecular dynamics (MD) simulations we study the crystallization process in a model system whose particles interact by a spherical pair potential with a narrow and deep attractive well adjacent to a hard repulsive core. The phase diagram of the model displays a solid-fluid equilibrium, with a metastable fluid-fluid separation. Our computations are restricted to fairly small systems (from 2592 to 10368 particles) and cover long simulation times, with constant energy trajectories extending up to 76x10(6) MD steps. By progressively reducing the system temperature below the solid-fluid line, we first observe the metastable fluid-fluid separation, occurring readily and almost reversibly upon crossing the corresponding line in the phase diagram. The nucleation of the crystal phase takes place when the system is in the two-fluid metastable region. Analysis of the temperature dependence of the nucleation time allows us to estimate directly the nucleation free energy barrier. The results are compared with the predictions of classical nucleation theory. The critical nucleus is identified, and its structure is found to be predominantly fcc. Following nucleation, the solid phase grows steadily across the system, incorporating a large number of localized and extended defects. We discuss the relaxation processes taking place both during and after the crystallization stage. The relevance of our simulation for the kinetics of protein crystallization under normal experimental conditions is discussed. (C) 2002 American Institute of Physics.

Structure and kinetics of phosphonopyruvate hydrolase from Variovorax sp. Pal2: New insight into the divergence of catalysis within the PEP mutase/isocitrate lyase superfamily .

Phosphonopyruvate (P-pyr) hydrolase (PPH), a member of the phosphoenolpyruvate (PEP) mutase/isocitrate lyase (PEPM/ICL) superfamily, hydrolyzes P-pyr and shares the highest sequence identity and functional similarity with PEPM. Recombinant PPH from Variovorax sp. Pal2 was expressed in Escherichia coli and purified to homogeneity. Analytical gel filtration indicated that the protein exists in solution predominantly as a tetramer. The PPH pH rate profile indicates maximal activity over a broad pH range.The steady-state kinetic constants determined for a rapid equilibrium ordered kinetic mechanism with Mg+2 binding first (Kd =140 ± 40 M), are kcat = 105 ± 2 s-1 and P-pyr Km = 5 ± 1 M. PEP (slow substrate kcat = 2 × 10-4 s-1), oxalate, and sulfopyruvate are competitive inhibitors with Ki values of 2.0 ± 0.1 mM, 17 ± 1 M, and 210 ± 10 M, respectively. Three PPH crystal structures have been determined, that of a ligand-free enzyme, the enzyme bound to Mg2+ and oxalate (inhibitor), and the enzyme bound to Mg2+ and P-pyr (substrate). The complex with the inhibitor was obtained by cocrystallization, whereas that with the substrate was obtained by briefly soaking crystals of the ligand-free enzyme with P-pyr prior to flash cooling. The PPH structure resembles that of the other members of the PEPM/ICL superfamily and is most similar to the functionally related enzyme, PEPM. Each monomer of the dimer of dimers exhibits an (/)8 barrel fold with the eighth helix swapped between two molecules of the dimer. Both P-pyr and oxalate are anchored to the active site by Mg2+. The loop capping the active site is disordered in all three structures, in contrast to PEPM, where the equivalent loop adopts an open or disordered conformation in the unbound state but sequesters the inhibitor from solvent in the bound state. Crystal packing may have favored the open conformation of PPH even when the enzyme was cocrystallized with the oxalate inhibitor. Structure alignment of PPH with other superfamily members revealed two pairs of invariant or conservatively replaced residues that anchor the flexible gating loop. The proposed PPH catalytic mechanism is analogous to that of PEPM but includes activation of a water nucleophile with the loop Thr118 residue.

Studies of switching kinetics in ferroelectric thin films

Experimental studies are reported concerning the importance of interfacial capacitance (including electrode screening, space-charge layers, and/or chemically discrete dead layers). on domain switching behaviour in thin films of ferroelectric lead zirconate-titanate (PZT), strontium bismuth tantalate (SBT), and barium strontium titanate (BST). Emphasis is placed upon studies at applied field values very near the coercive field E, asymmetry in fatigue for positive and negative polarity coercive fields, and in the case of BST, of the coexistence of ferroelectric and paraelectric phases Studies of dielectric loss show important correlations between tan 6 and fatigue (polarization decrease) as a function of bipolar switching cycles N. This is a priori not obvious, since the former is a linear response and the latter, a nonlinear response. Modelling of enlarged interfacial,space-charge layers in PZT films and chemically distinct dead (paraelectric) layers in BST films shows contradictory tendencies of coercive-voltage changes with the growth of passive layers.

Insight into the key aspects of the regeneration process in the NOx storage reduction (NSR) reaction probed using fast transient kinetics coupled with isotopically labelled (NO)-N-15 over Pt and Rh-containing Ba/Al2O3 catalysts

For the first time, the coupling of fast transient kinetic switching and the use of an isotopically labelled reactant (15NO) has allowed detailed analysis of the evolution of all the products and reactants involved in the regeneration of a NOx storage reduction (NSR) material. Using realistic regeneration times (ca. 1 s) for Pt, Rh and Pt/Rh-containing Ba/Al2O3 catalysts we have revealed an unexpected double peak in the evolution of nitrogen. The first peak occurred immediately on switching from lean to rich conditions, while the second peak started at the point at which the gases switched from rich to lean. The first evolution of nitrogen occurs as a result of the fast reaction between H2 and/or CO and NO on reduced Rh and/or Pt sites. The second N2 peak which occurs upon removal of the rich phase can be explained by reaction of stored ammonia with stored NOx, gas phase NOx or O2. The ammonia can be formed either by hydrolysis of isocyanates or by direct reaction of NO and H2.

The study highlights the importance of the relative rates of regeneration and storage in determining the overall performance of the catalysts. The performance of the monometallic 1.1%Rh/Ba/Al2O3 catalyst at 250 and 350 °C was found to be dependent on the rate of NOx storage, since the rate of regeneration was sufficient to remove the NOx stored in the lean phase. In contrast, for the monometallic 1.6%Pt/Ba/Al2O3 catalyst at 250 °C, the rate of regeneration was the determining factor with the result that the amount of NOx stored on the catalyst deteriorated from cycle to cycle until the amount of NOx stored in the lean phase matched the NOx reduced in the rich phase. On the basis of the ratio of exposed metal surface atoms to total Ba content, the monometallic 1.6%Pt/Ba/Al2O3 catalyst outperformed the Rh-containing catalysts at 250 and 350 °C even when CO was used as a reductant.

Electrode kinetics and mechanism of iodine reduction in the room-temperature ionic liquid [C(4)mim][NTf2]

The fast electrochemical reduction of iodine in the RTIL 1-butyl-3-methylimidazolium bis(trifluoromethyl-sulfonyl)imide, [C(4)mim][NTf2], is reported and the kinetics and mechanism of the process elucidated. Two reduction peaks were observed. The first reduction peak is assigned to the process