Collisions, caging, thermodynamics, and jamming in the barrier hopping theory of glassy hard sphere fluids

An ultralocal limit of the microscopic single particle barrier hopping theory of glassy dynamics is proposed which allows explicit analytic expressions for the characteristic length scales, energy scales, and nonequilibrium free energy to be derived. All properties are shown to be controlled by a single coupling constant determined by the fluid density and contact value of the radial distribution function. This parameter quantifies an effective mean square force exerted on a tagged particle due to collisions with its surroundings. The analysis suggests a conceptual basis for previous surprising findings of multiple inter-relationships between characteristics of the transient localized state, the early stages of cage escape, non-Gaussian or dynamic heterogeneity effects, and the barrier hopping process that defines the alpha relaxation event. The underlying physical picture is also relevant to fluids of nonspherical molecules and sticky colloidal suspensions. The possibility of a unified view of liquid dynamics is suggested spanning the range from dense gases to the zero mobility jammed state.     

Perfluorophenyl–Phenyl Interactions in the Crystallization and Topochemical Polymerization of Triacetylene Monomers

A series of symmetrically and unsymmetrically substituted octa‐2,4,6‐triyne‐1,8‐diol derivatives with benzoyl, 4‐dodecyloxybenzoyl, as well as perfluorobenzoyl substituents were prepared and investigated with respect to their crystal structures and topochemical polymerizability. Single‐crystal structures for several of these triacetylene monomers have been obtained and proved that the perfluorophenyl–phenyl interactions played a decisive role in the molecular packing. As a consequence of the geometric requirements imposed by the perfluorophenyl–phenyl interactions, packing parameters appropriate for a topochemical triacetylene polymerization in the sense of either a 1,6‐ or a 1,4‐polyaddition along different crystallographic axes were observed in two cases, and UV irradiation led to successful polymerization. Raman as well as solid‐state ¹³C NMR spectra of the obtained polymers revealed that the polymerization had predominantly proceeded in the form of a 1,4‐polyaddition.     

The Implications of (2S,4S)‐Hydroxyproline 4‐O‐Glycosylation for Prolyl Amide Isomerization

The conformations of peptides and proteins are often influenced by glycans O‐linked to serine (Ser) or threonine (Thr). (2S,4R)‐4‐Hydroxyproline (Hyp), together with L ‐proline (Pro), are interesting targets for O‐glycosylation because they have a unique influence on peptide and protein conformation. In previous work we found that glycosylation of Hyp does not affect the N‐terminal amide trans/cis ratios (K_trans/cis) or the rates of amide isomerization in model amides. The stereoisomer of Hyp—(2S,4S)‐4‐hydroxyproline (hyp)—is rarely found in nature, and has a different influence both on the conformation of the pyrrolidine ring and on K_trans/cis. Glycans attached to hyp would be expected to be projected from the opposite face of the prolyl side chain relative to Hyp; the impact this would have on K_trans/cis was unknown. Measurements of ³J coupling constants indicate that the glycan has little impact on the C^γ‐endo conformation produced by hyp. As a result, it was found that the D ‐galactose residue extending from a C^γ‐endo pucker affects both K_trans/cis and the rate of isomerization, which is not found to occur when it is projected from a C^γ‐exo pucker; this reflects the different environments delineated by the proline side chain. The enthalpic contributions to the stabilization of the trans amide isomer may be due to disruption of intramolecular interactions present in hyp; the change in enthalpy is balanced by a decrease in entropy incurred upon glycosylation. Because the different stereoisomers—Hyp and hyp—project the O‐linked carbohydrates in opposite spatial orientations, these glycosylated amino acids may be useful for understanding of how the projection of a glycan from the peptide or protein backbone exerts its influence.     

Coupling of the Reynolds Fluid-Film Equation with the 2D Navier-Stokes Equations

The pressure field in thin fluid films can quite precisely be calculated by Reynolds fluid-film equation. In some problems, it may be useful to couple thin fluid-films with general 2D or 3D fluid flows. In the current work, we analyze the fluid flow, pressure and temperature field in a hydrodynamic journal bearing with a rectangular oil groove. Pressure and temperature in the fluid gap are calculated by means of the Reynolds equation and the 2D energy equation. Cavitation effects are taken into account by incorporating a 2-phase cavitation approach. In order to calculate the velocity and pressure field in the oil groove, the 2D Navier-Stokes equations are used; the temperature distribution in the oil groove is computed by means of the 2D energy equation. Appropriate coupling conditions for velocity, pressure and temperature are formulated in order to couple the flow in the fluid gap with the flow in the oil groove. Thermal expansion of journal shaft and bearing housing are also taken into account, since the bearing clearance changes with increasing temperature. (© 2011 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim)     

The "azido gauche effect"-implications for the conformation of azidoprolines

The "azido gauche effect" was examined both experimentally and theoretically and was found to determine the conformation of, for example, (4R)- and (4S)-azidoproline (Azp) derivatives. For (4R)Azp derivatives, the azido gauche effect induces a preferred C(4)-exo conformation of the pyrrolidine ring, which leads to stabilization of the s-trans amide conformer of, e.g., Ac-(4R)Azp-OCH(3) (5R) via an n-->pi interaction between the nonbonding electrons of the oxygen of the acetyl group and the carbonyl group of the ester. For (4S)Azp derivatives, the azido gauche effect results in a C(4)-endo conformation of the pyrrolidine ring that does not allow for this stabilizing n-->pi interaction of the s-trans conformer. Consequently, a significantly higher s-trans:s-cis amide conformer ratio is observed for (4R)Azp compared to (4S)Azp derivatives (e.g., 6.1:1 versus 2.6:1 in D(2)O for Ac-(4R)Azp-OCH(3) (5R) compared to Ac-(4S)Azp-OCH(3) (5S)). These conformational preferences are reflected in the higher tendency of (4S)Azp-containing peptides to form cyclic peptides with all-cis amide bonds compared to (4R)Azp derivatives. Ab initio calculations demonstrate that the strength of the azido gauche effect is comparable to that of the well-known "fluorine gauche effect". For azidoethane derivatives N(3)-CH(2)CH(2)-X (X = N(3), NHCOH, NHAc, or N(CH(3))Ac), the ab initio calculations revealed energy differences of 5-13 kJ mol(-)(1) between the anti and gauche conformations in favor of the gauche conformer. Calculations were also performed for the (4R)Azp and (4S)Azp derivatives 5R and 5S, supporting the experimentally observed data.     

Activated hopping and dynamical fluctuation effects in hard sphere suspensions and fluids

Single particle Brownian dynamics simulation methods are employed to establish the full trajectory level predictions of our nonlinear stochastic Langevin equation theory of activated hopping dynamics in glassy hard sphere suspensions and fluids. The consequences of thermal noise driven mobility fluctuations associated with the barrier hopping process are determined for various ensemble-averaged properties and their distributions. The predicted mean square displacements show classic signatures of transient trapping and anomalous diffusion on intermediate time and length scales. A crossover to a stronger volume fraction dependence of the apparent nondiffusive exponent occurs when the entropic barrier is of order the thermal energy. The volume fraction dependences of various mean relaxation times and rates can be fitted by empirical critical power laws with parameters consistent with ideal mode-coupling theory. However, the results of our divergence-free theory are largely a consequence of activated dynamics. The experimentally measurable alpha relaxation time is found to be very similar to the theoretically defined mean reaction time for escape from the barrier-dominated regime. Various measures of decoupling have been studied. For fluid states with small or nonexistent barriers, relaxation times obey a simple log-normal distribution, while for high volume fractions the relaxation time distributions become Poissonian. The product of the self-diffusion constant and mean alpha relaxation time increases roughly as a logarithmic function of the alpha relaxation time. The cage scale incoherent dynamic structure factor exhibits nonexponential decay with a modest degree of stretching. A nearly universal collapse of the different volume fraction results occurs if time is scaled by the mean alpha relaxation time. Hence, time-volume fraction superposition holds quite well, despite the presence of stretching and volume fraction dependent decoupling associated with the stochastic barrier hopping process. The relevance of other origins of dynamic heterogeneity (e.g., mesoscopic domains), and comparison of our results with experiments, simulations, and alternative theories, is discussed.     

Dislocations and dislocation reduction in space grown GaSb

The behaviour of dislocations in GaSb crystals grown in space both from a stoichiometric melt (floating zone method, FZ) and a Bi solution (floating solution zone, FSZ) respectively, is studied. Predominantly straight 60° dislocations with Burgers vectors of the type b = a/2 <110> in (111) glide planes are identified. In the 20 mm long FZ single crystal the linear growing out of the dislocations is observed which reduces the dislocation density in the centre of the crystal to values below 300 cm^–2. The Bi incorporation in the FSZ crystal results in a misfit between seed and grown crystal and in a network of misfit dislocations at the interface. Thermocapillary convection during growth as well as the surface tension may be the reasons for the presence of curved dislocations and the higher dislocation density within a 1 – 2 mm border region at the edges of both of the crystals. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)