Rare fluctuations of native proteins sampled by equilibrium hydrogen exchange

We present a method for determining the ensembles of native protein structures that result from the large fluctuations of low probability revealed by hydrogen-exchange experiments. The measured protection factors are used to bias Monte Carlo simulations to sample the structures of the exchange competent species. The approach is illustrated by its application to the case of alpha-lactalbumin.     

"Oscillating" metallocene catalysts: what stops the oscillation?

The 150 MHz (13)C NMR microstructural analysis of polypropylene samples produced with two representative "oscillating" metallocene catalysts of largely different steric hindrance, namely [(2-(3,5-di-tert-butyl-4-methoxyphenyl)indenyl)(2)ZrP](+) and [(2-phenylindenyl)(2)ZrP](+) (P = polymeryl), and the implications on the origin of the stereocontrol are presented and discussed in detail. The original mechanistic proposal of an "oscillation" between a rac-like (isotactic-selective) and a meso-like (nonstereoselective) conformation cannot explain the observed polymer configuration. The isotactic-stereoblock nature of the polymers obtained with the former catalyst proves unambiguously that the active cation "oscillates" between the two enantiomorphous rac-like conformations at an average frequency that, even at high propene concentration, is only slightly lower than that of monomer insertion. The less-hindered [(2-phenylindenyl)(2)ZrP](+) gives instead a largely stereoirregular polypropylene, which is the logical consequence of a faster ligand rotation; however, depending on the use conditions (in particular, on the nature of the cocatalyst and the polarity of the solvent), the polymerization products may also contain appreciable amounts of a fairly isotactic fraction. The peculiar microstructure of this fraction, with isotactic blocks of the same relative configuration spanned by very short atactic ones, rules out the possibility that the latter are due to an active species in meso-like conformation and points rather to a conformationally "locked" rac-like species with restricted ring mobility. The hypothesis of a stereorigidity induced by the proximity to a counteranion, which would play the role of the interannular bridge in the rac-bis(indenyl) ansa-metallocenes, was tested by computer modeling on a [rac-(2-phenylindenyl)(2)ZrMe(C(3)H(6))][B(C(6)F(5))(4)] ion couple and found viable.     

The nature and transport mechanism of hydrated hydroxide ions in aqueous solution

Compared to other ions, protons (H(+)) and hydroxide ions (OH(-)) exhibit anomalously high mobilities in aqueous solutions. On a qualitative level, this behaviour has long been explained by 'structural diffusion' the continuous interconversion between hydration complexes driven by fluctuations in the solvation shell of the hydrated ions. Detailed investigations have led to a clear understanding of the proton transport mechanism at the molecular level. In contrast, hydroxide ion mobility in basic solutions has received far less attention, even though bases and base catalysis play important roles in many organic and biochemical reactions and in the chemical industry. The reason for this may be attributed to the century-old notion that a hydrated OH(-) can be regarded as a water molecule missing a proton, and that the transport mechanism of such a 'proton hole' can be inferred from that of an excess proton by simply reversing hydrogen bond polarities. However, recent studies have identified OH(-) hydration complexes that bear little structural similarity to proton hydration complexes. Here we report the solution structures and transport mechanisms of hydrated hydroxide, which we obtained from first-principles computer simulations that explicitly treat quantum and thermal fluctuations of all nuclei. We find that the transport mechanism, which differs significantly from the proton hole picture, involves an interplay between the previously identified hydration complexes and is strongly influenced by nuclear quantum effects.     

Microwave-assisted acylation of 7-amino-5-aryl-6-cyanopyrido[2,3-d]pyrimidines

A microwave-assisted method is described for monoacylating 7-amino-5-aryl-6-cyanopyrido[2,3-d]pyrimidines using excess acid chlorides in pyridine. A diacylated intermediate is effectively deacylated to the product amide by a macroporous-Tris resin. A small library of 17 amides was prepared to validate the method. The integration of commercial microwave technology into the ArQule chemistry platform is also discussed.     

Sol-Gel Nanosized Semiconducting Titania-Based Powders for Thick-Film Gas Sensors

Pure, 5 at%, and 10 at% Ta- or Nb-doped TiO₂ nanosized powders were prepared by the sol-gel method. The powders heated to 400°C have the crystalline anatase structure. While the pure TiO₂ powder heated to 850°C has the rutile structure, the addition of Ta and Nb inhibited the anatase-to-rutile phase transformation at this temperature. Ta was soluble in the titania lattice up to the concentration of 10 at%, while the solubility of Nb was 5 at%. Thick films were fabricated with these powders by screen printing technology and then fired at 650°C and 850°C for 1 h. SEM observations showed that the anatase-to-rutile phase transformation induces a grain growth of about one order of magnitude for pure TiO₂. The addition of Ta and Nb is effective to keep the TiO₂ grain size at the nanometric level even at 850°C. Conductance measurements showed that a good gas response is observed only for the nanostructured titania-based films. The CO response of these materials is only slightly affected by humidity.     

Patient-specific finite element analysis of popliteal stenting

Nitinol self-expanding stents are used for the endovascular management of peripheral artery diseases of the popliteal artery, which is located behind the knee joint. Unfortunately, the complex kinematics of the artery during the leg flexion leads to severe loading conditions, favouring the mechanical failure of the stent, calling for a specific biomechanical analysis. For this reason, in the present study we reconstruct by medical image analysis the patient-specific popliteal kinematics during leg flexion, which is subsequently exploited to compute the mechanical response of a stent model, virtually implanted in the artery by structural finite element analysis (FEA). The medical image analysis indicates a non-uniform configuration change of the artery during the leg flexion, leading to an increase of the vessel curvature above the knee. The computed mechanical response of the stent reflects the non-uniform configuration change of the artery as after the flexion the average stress is higher in the part of the stent located above the knee. Although the proposed analysis is limited to a case-study, it shows the capability of patient-specific FEA simulations to compute the mechanical response of a stent model subjected to the complex and severe loading conditions of the popliteal artery during leg flexion.     

Stochastic PAC models for vacancy motions with trapping and detrapping

In order to explain PAC data for tetragonal zirconia at temperatures between 900 and 1300oC, we have developed a four-state stochastic model. The model simulates vacancies which trap and detrap at a PAC probe nucleus. While trapped, the vacancies hop around the probe in equivalent sites. The four states in this Winkler–Gerdau stochastic theory are three trapped states with equivalent electric field gradients (EFGs) of different orientations and a detrapped state with a weaker EFG whose axis of symmetry is oriented along the diagonal between the three trapped EFGs. There are three hopping rates in this model: w, the rate a trapped vacancy hops around the probe, w_D, the detrapping rate, and w_t, the trapping rate. We report results of calculations for values of these hopping rates implied by our tetragonal zirconia data, and we report heuristic fitting functions which summarize the computer results and can be used to fit data efficiently for a wide range of parameters. This revised version was published online in August 2006 with corrections to the Cover Date.     

Layouts for mobility management in wireless ATM networks

In this paper, we present a new model that combines quality of service and mobility aspects in wireless ATM networks. Namely, besides the hop count and load parameters of the basic ATM layouts, we introduce a new notion of distance that estimates the time needed to reconstruct the virtual channel of a wireless user when he moves through the network. Quality of service guarantee dictates that the rerouting phase must be imperceptible, that is, the maximum distance between two virtual channels must be maintained as low as possible. Therefore, a natural combinatorial problem arises in which suitable trade-offs must be determined between the different performance measures. We first show that establishing the existence of a layout with maximum hop count h, load l and distance d is NP-complete, even in the very restricted case h=2, l=1 and d=1. We then provide optimal layout constructions for basic interconnection networks, such as chains and rings.