A systematic study of carboxylic acids in negative ion mode electrospray ionisation mass spectrometry providing a structural model for ion suppression

We report a systematic investigation of the effects and structural requirements for ion suppression in negative ion mode electrospray ionisation mass spectrometry of a series of carboxylic acids and present a structural model rationalising ion suppression effects.     

Conducting polymer diffraction gratings on gold surfaces created by microcontact printing and electropolymerization at submicron length scales

Conducting polymer diffraction gratings on Au substrates have been created using microcontact printing of C18-alkanethiols, followed by electropolymerization of either poly(aniline) (PANI) or poly(3,4-ethylenedioxythiophene) (PEDOT). Soft-polymer replicas of simple diffraction grating masters (1200 lines/mm) were used to define the alkanethiol template for polymer growth. Growth of PANI and PEDOT diffraction gratings was followed in real time, through in situ tapping-mode atomic force microscopy, and by monitoring diffraction efficiency (DE) as a function of grating depth. DE increased as grating depth increased, up to a limiting efficiency (13-26%, with white light illumination), defined by the combined optical properties of the grating and the Au substrate, and ultimately limited by the loss of resolution due to coalescence of the polymer films. Grating efficiency is strongly dependent upon the grating depth and the refractive index contrast between the grating material and the surrounding solutions. Both PEDOT and PANI gratings show refractive index changes as a function of applied potential, consistent with changes in refractive index brought about by the doping/dedoping of the conducting polymer. The DE of PANI gratings are strongly dependent on the pH of the superstrate solution; the maximum sensitivity (DeltaDE/DeltapH) is achieved with PANI gratings held at +0.4 V versus Ag/AgCl, where the redox chemistry is dominated by the acid-base equilibrium between the protonated (emeraldine salt) and deprotonated (emeraldine base) forms of PANI. Simulations of DE were conducted for various combinations of conducting polymer refractive index and grating depth, to compute sensitivity parameters, which are maximized when the grating depth is ca. 50% of its maximum obtainable depth.     

An X-ray scattering study of hydrogenated nanocrystalline silicon with varying crystalline fraction

Using X-ray diffraction (XRD) and small angle X-ray scattering (SAXS), we probed the nanostructural features of several PECVD grown nc-Si:H thin films with varying crystalline volume fraction. XRD results of a mixed phase film, 70% a-Si:H and 30% c-Si:H, show these crystallites have a preferred [220] orientation in the growth direction. Another film with approximately 90% c-Si also shows elongated grains, but with a preferred [111] orientation. The SAXS results also show an increase in scattering intensity when compared to the mixed phase material. In the mixed phase material, models show that the electron density fluctuations between the amorphous and crystalline phases are not enough to explain the measured SAXS scattering. Hydrogen clustered at the crystallite boundaries and in void regions of the a-Si phase must be included as well.     

New RNA labeling methods offer dramatic sensitivity enhancements in 2H NMR relaxation spectra

A new labeling strategy is presented that greatly facilitates the measurement of 2H spin relaxation rates in RNA molecules as a probe of pico- to nanosecond time scale dynamics. In this labeling scheme the sugar positions are uniformly 13C-labeled, with position 2' protonated and all other sites on the sugar deuterated. Pulse sequences are presented for measurement of 2H R1 and R2 relaxation rates at positions 1', 3', and 4' with sensitivity gains that are on the order of 5-fold relative to previous methods that employed random fractional deuteration. The improved sensitivity is transformative and facilitates the study of motion in moderately sized RNA molecules with good sensitivity. The utility of the approach is demonstrated with an application to HIV-2 TAR, where the site-specific measures of molecular dynamics at sugar positions obtained here complement previous studies of dynamics at aromatic sites in the molecule.     

Optimization of HNO production from N,O-bis-acylated hydroxylamine derivatives

A wide range of N,O-bis-acylated hydroxylamine derivatives with chloro or arenesulfonyl leaving groups, and a related set of N-hydroxy-N-acylsulfonamides, have been synthesized and evaluated for nitroxyl (HNO) production. Mechanistic studies have revealed that the observed aqueous chemistry is more complicated than originally anticipated, and have been used to develop a new series of efficient HNO precursors (4u-4x, 7c-7d) with tunable half-lives.     

Computational prediction of metabolism: sites, products, SAR, P450 enzyme dynamics, and mechanisms

Metabolism of xenobiotics remains a central challenge for the discovery and development of drugs, cosmetics, nutritional supplements, and agrochemicals. Metabolic transformations are frequently related to the incidence of toxic effects that may result from the emergence of reactive species, the systemic accumulation of metabolites, or by induction of metabolic pathways. Experimental investigation of the metabolism of small organic molecules is particularly resource demanding; hence, computational methods are of considerable interest to complement experimental approaches. This review provides a broad overview of structure- and ligand-based computational methods for the prediction of xenobiotic metabolism. Current computational approaches to address xenobiotic metabolism are discussed from three major perspectives: (i) prediction of sites of metabolism (SOMs), (ii) elucidation of potential metabolites and their chemical structures, and (iii) prediction of direct and indirect effects of xenobiotics on metabolizing enzymes, where the focus is on the cytochrome P450 (CYP) superfamily of enzymes, the cardinal xenobiotics metabolizing enzymes. For each of these domains, a variety of approaches and their applications are systematically reviewed, including expert systems, data mining approaches, quantitative structure-activity relationships (QSARs), and machine learning-based methods, pharmacophore-based algorithms, shape-focused techniques, molecular interaction fields (MIFs), reactivity-focused techniques, protein-ligand docking, molecular dynamics (MD) simulations, and combinations of methods. Predictive metabolism is a developing area, and there is still enormous potential for improvement. However, it is clear that the combination of rapidly increasing amounts of available ligand- and structure-related experimental data (in particular, quantitative data) with novel and diverse simulation and modeling approaches is accelerating the development of effective tools for prediction of in vivo metabolism, which is reflected by the diverse and comprehensive data sources and methods for metabolism prediction reviewed here. This review attempts to survey the range and scope of computational methods applied to metabolism prediction and also to compare and contrast their applicability and performance.     

Efficient N-terminal labeling of proteins by use of sortase

"Sorting out" N-terminal labeling: The reversibility of transpeptidase reactions makes protein N-terminal labeling challenging. Depsipeptide substrates for sortase A release alcohol by-products, which are poor nucleophiles for the reverse reaction, during ligation. Proteins with an unhindered N-terminal glycine residue can be labeled efficiently with only a minimal excess of the labeling reagent.     

Bayesian policy support for adaptive strategies using computer models for complex physical systems

In this paper, we discuss combining expert knowledge and computer simulators in order to provide decision support for policy makers managing complex physical systems. We allow future states of the complex system to be viewed after initial policy is made, and for those states to influence revision of policy. The potential for future observations and intervention impacts heavily on optimal policy for today and this is handled within our approach. We show how deriving policy dependent system uncertainty using computer models leads to an intractable backwards induction problem for the resulting decision tree. We introduce an algorithm for emulating an upper bound on our expected loss surface for all possible policies and discuss how this might be used in policy support. To illustrate our methodology, we look at choosing an optimal CO₂ abatement strategy, combining an intermediate complexity climate model and an economic utility model with climate data.     

WADM and radiation MHD simulations of compact multi-planar and cylindrical wire arrays at 1 MA currents

The radiative performance of Z-pinches created by the imploding wire array loads is defined by the ablation and implosion dynamics of these loads. Both these processes can be effectively modeled by the Wire Ablation Dynamics Model (WADM), which extends the formalism exploited earlier for the cylindrical wire arrays to the loads of arbitrary geometries. The WADM calculates the ablation rates for each array wire and provides the important dynamic parameters, such as the specific mass and velocity of the imploding plasma, which can be used to estimate the shapes of the x-ray pre-pulse and, partially, the main x-ray burst. The applications of the WADM also extend to combined material wire array loads. The ablation and implosion dynamics of novel Prism Planar Wire Array (PPWA) and combined material (Mo/Al/Mo) Triple Planar Wire Array (TPWA) loads are discussed in detail. The combined WADM and radiation MHD simulation is applied to model the radiative performance of the precursor plasma column, created by the imploding stainless steel compact cylindrical wire array. As the radiation effects intensify with the mass accumulation at the array center, the simulation reveals the transformation of quasi-uniform precursor column into a heterogeneous plasma structure with strong density and temperature gradients. We find that radiative performance of the precursor plasma is greatly affected by the load geometry as well as by the wire material.