Alanine racemase free energy profiles from global analyses of progress curves

Free energy profiles for alanine racemase from Bacillus stearothermophilus have been determined at pH 6.9 and 8.9 from global analysis of racemization progress curves. This required a careful statistical design due to the problems in finding the global minimum in mean square for a system with eight adjustable parameters (i.e., the eight rate constants that describe the stepwise chemical mechanism). The free energy profiles obtained through these procedures are supported by independent experimental evidence: (1). steady-state kinetic constants, (2). solvent viscosity dependence, (3). spectral analysis of reaction intermediates, (4). equilibrium overshoots for progress curves measured in D(2)O, and (5). the magnitudes of calculated intrinsic kinetic isotope effects. The free energy profiles for the enzyme are compared to those of the uncatalyzed and the PLP catalyzed reactions. At pH 6.9, PLP lowers the free energy of activation for deprotonation by 8.4 kcal/mol, while the inclusion of apoenzyme along with PLP additionally lowers it by 11 kcal/mol.     

Structural characterization of a pentacene monolayer on an amorphous SiO2 substrate with grazing incidence x-ray diffraction

Grazing incidence X-ray diffraction reveals that a pentacene monolayer, grown on an amorphous SiO2 substrate that is commonly used as a dielectric layer in organic thin film transistors (OTFTs), is crystalline. A preliminary energy-minimized model of the monolayer, based on the GIXD data, reveals that the pentacene molecules adopt a herringbone arrangement with their long axes tilted slightly from the substrate normal. Although this arrangement resembles the general packing features of the (001) layer in single crystals of bulk pentacene, the monolayer lattice parameters and crystal structure differ from those of the bulk. Because carrier transport in pentacene OTFTs is presumed to occur in the semiconductor layers near the dielectric interface, the discovery of a crystalline monolayer structure on amorphous SiO2 has important implications for transport in OTFTs.     

Pore morphologies in disordered nanoporous thin films

Materials with nanometer size heterogeneities are commonplace in the chemical and biological sciences (e.g, polymer blends, microemulsions, gels) and often exhibit complex morphologies. Although this morphology has a dramatic effect on the materials' properties, it is often difficult to accurately characterize. We describe a method, using small-angle X-ray scattering data, of generating representative three-dimensional morphologies of isotropic two-phase materials where the morphology is disordered, and we apply this to thin films containing nanometer sized pores with a range of porosities (4-44%). These representations provide a visualization of the pore morphology, give the pore size scale and extent of interconnection, and permit the determination of the transitions from closed pore to interconnected pores to bicontinuous morphology.     

Photon channelling in foams

Experiments by Gittings, Bandyopadhyay and Durian (Europhys. Lett. 65, 414 (2004)) demonstrate that light possesses a higher probability to propagate in the liquid phase of a foam due to total reflection. The authors term this observation photon channelling which we investigate in this article theoretically. We first derive a central relation in the work of Gitting et al. without any free parameters. It links the photon's path-length fraction f in the liquid phase to the liquid fraction ɛ. We then construct two-dimensional Voronoi foams, replace the cell edges by channels to represent the liquid films and simulate photon paths according to the laws of ray optics using transmission and reflection coefficients from Fresnel's formulas. In an exact honeycomb foam, the photons show superdiffusive behavior. It becomes diffusive as soon as disorder is introduced into the foams. The dependence of the diffusion constant on channel width and refractive index is explained by a one-dimensional random-walk model. It contains a photon channelling state that is crucial for the understanding of the numerical results. At the end, we shortly comment on the observation that photon channelling only occurs in a finite range of ɛ.     

Biliverdin reduction by cyanobacterial phycocyanobilin:ferredoxin oxidoreductase (PcyA) proceeds via linear tetrapyrrole radical intermediates

Cyanobacterial phycocyanobilin:ferredoxin oxidoreductase (PcyA) catalyzes the four electron reduction of biliverdin IXalpha (BV) to phycocyanobilin, a key step in the biosynthesis of the linear tetrapyrrole (bilin) prosthetic groups of cyanobacterial phytochromes and the light-harvesting phycobiliproteins. Using an anaerobic assay protocol, optically detected bilin-protein intermediates, produced during the PcyA catalytic cycle, were shown to correlate well with the appearance and decay of an isotropic g approximately 2 EPR signal measured at low temperature. Absorption spectral simulations of biliverdin XIIIalpha reduction support a mechanism involving direct electron transfers from ferredoxin to protonated bilin:PcyA complexes.     

The phase behavior of a polymer‐fullerene bulk heterojunction system that contains bimolecular crystals

Polymer:fullerene blends have been widely studied as an inexpensive alternative to traditional silicon solar cells. Some polymer:fullerene blends, such as blends of poly(2,5‐bis(3‐tetradecylthiophen‐2‐yl)thieno[3,2‐b]thiophene (pBTTT) with phenyl‐c71‐butyric acid methyl ester (PC₇₁BM), form bimolecular crystals due to fullerene intercalation between the polymer side chains. Here we present the determination of the eutectic pBTTT:PC₇₁BM phase diagram using differential scanning calorimetry (DSC) and two‐dimensional grazing incidence X‐ray scattering (2D GIXS) with in‐situ thermal annealing. The phase diagram explains why the most efficient pBTTT:PC₇₁BM solar cells have 75–80 wt % PC₇₁BM since these blends lie in the center of the only room‐temperature phase region containing both electron‐conducting (PC₇₁BM) and hole‐conducting (bimolecular crystal) phases. We show that intercalation can be suppressed in 50:50 pBTTT:PC₇₁BM blends by using rapid thermal annealing to heat the blends above the eutectic temperature, which forces PC₇₁BM out of the bimolecular crystal, followed by quick cooling to kinetically trap the pure PC₇₁BM phase. © 2011 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys, 2011     

Light-enhanced catalysis by pyridoxal phosphate-dependent aspartate aminotransferase

The mechanisms of pyridoxal 5'-phosphate (PLP)-dependent enzymes require substrates to form covalent "external aldimine" intermediates, which absorb light strongly between 410 and 430 nm. Aspartate aminotransferase (AAT) is a prototypical PLP-dependent enzyme that catalyzes the reversible interconversion of aspartate and α-ketoglutarate with oxalacetate and glutamate. From kinetic isotope effects studies, it is known that deprotonation of the aspartate external aldimine C(α)-H bond to give a carbanionic quinonoid intermediate is partially rate limiting in the thermal AAT reaction. We show that excitation of the 430-nm external aldimine absorption band increases the steady-state catalytic activity of AAT, which is attributed to the photoenhancement of C(α)-H deprotonation on the basis of studies with Schiff bases in solution. Blue light (250 mW) illumination gives an observed 2.3-fold rate enhancement for WT AAT activity, a 530-fold enhancement for the inactive K258A mutant, and a 58600-fold enhancement for the PLP-Asp Schiff base in water. These different levels of enhancement correlate with the intrinsic reactivities of the C(α)-H bond in the different environments, with the less reactive Schiff bases exhibiting greater enhancement. Time-resolved spectroscopy, ranging from femtoseconds to minutes, was used to investigate the nature of the photoactivation of C(α)-H bond cleavage in PLP-amino acid Schiff bases both in water and bound to AAT. Unlike the thermal pathway, the photoactivation pathway involves a triplet state with a C(α)-H pK(a) that is estimated to be between 11 and 19 units lower than the ground state for the PLP-Val Schiff base in water.     

Influence of surfactant structure on reverse micelle size and charge for nonpolar electrophoretic inks

Electrophoretic inks, which are suspensions of colorant particles that are controllably concentrated and dispersed by applied electric fields, are the leading commercial technology for high-quality reflective displays. Extending the state of the art for high-fidelity color in these displays requires improved understanding and control of the colloidal systems. In these inks, reverse micelles in nonpolar media play key roles in media and particle charging. Here we investigate the effect of surfactant structure on reverse micelle size and charging properties by synthesizing different surfactants with variations in polyamine polar head groups. Small-angle X-ray scattering (SAXS) and dynamic light scattering (DLS) were used to determine the micelle core plus shell size and micelle hydrodynamic radius, respectively. The results from SAXS agreed with DLS and showed that increasing polyamines in the surfactant head increased the micelle size. The hydrodynamic radius was also calculated on the basis of transient current measurements and agreed well with the DLS results. The transient current technique further determined that increasing polyamines increased the charge stabilization capability of the micelles and that an analogous commercial surfactant OLOA 11000 made for a lower concentration of charge-generating ions in solution. Formulating magenta inks with the various surfactants showed that the absence of amine in the surfactant head was detrimental to particle stabilization and device performance.