Prediction of the mechanisms of enzyme-catalysed reactions using hybrid quantum mechanical/molecular mechanical methods

The use of hybrid methods, involving both quantum mechanics and molecular mechanics, to model the mechanism of enzyme-catalysed reactions, is discussed. Two alternative approaches to treating the electrostatic interactions between the quantum mechanical and molecular mechanical regions are studied, involving either the inclusion of this term in the electronic Hamiltonian (QM/MM), or evaluating it purely classically (MO + MM). In the latter scheme, possible problems of using force fields that are standard for macromolecular modelling are identified. The use of QM/MM schemes to investigate the mechanism of the enzymes thymidine phosphorylase (ThdPase) and protein tyrosine phosphatase (PTP) is described. For both systems, transition states have been identified using a PM3 Hamiltonian. For ThdPase, concerted motion of the enzyme during the course of the reaction is suggested and, for PTP, a two-step dephosphorylation reaction is indicated, both with quite low barriers.     

A comparison of lobe and cartesian gaussian basis sets for molecular calculations

Lobe gaussian and cartesian gaussian basis sets, of approximately minimal basis Slater accuracy, have been compared for molecular calculations. The basis sets were constructed so that they only differed in the representation of the angular dependence of the p function. Calculation of total energy and several one-electron properties for a series of nine molecules shows that, for molecular calculations, the lobe and cartesian gaussian representations are equivalent.     

Evaluation of argon metastable number densities in the inductively coupled plasma by continuum source absorption spectrometry

Absolute number densities for the metastable and radiative 4s argon levels in an inductively coupled plasma have been determined for a variety of plasma conditions by the technique of continuum source absorption. As primary source, a 300 W xenon arc was used and much care was taken in screening the optical detection system from the intense background emission of the plasma. A 1.29-m focal length grating monochromator provided a variable bandwidth so that absorption measurements could be carried out, with varying degree of sensitivity, on 19 different argon lines. The number densities were derived from the corresponding curves of growth, calculated for each line. Concentrations ranging from 2.3 × 10¹⁰ to 7.4 × 10¹¹ cm⁻³ were obtained for the different levels, depending upon the presence or absence of nebulizing gas and water in the plasma. At observation heights greater than 20 mm above the coil, the number density approaches the value predicted by Boltzman equilibrium for a temperature of 6500 K. The detection sensitivity of the present apparatus is about 5 × 10⁹ cm⁻³. For seven lines, damping parameter values were also estimated and found to vary from 0.4 to 1.1.     

One‐Dimensional Arsenic Allotropes: Polymerization of Yellow Arsenic Inside Single‐Wall Carbon Nanotubes

The pnictogen nanomaterials, including phosphorene and arsenene, display remarkable electronic and chemical properties. Yet, the structural diversity of these main group elements is still poorly explored. Here we fill single‐wall carbon nanotubes with elemental arsenic from the vapor phase. Using electron microscopy, we find chains of highly reactive As₄ molecules as well as two new one‐dimensional allotropes of arsenic: a single‐stranded zig‐zag chain and a double‐stranded zig‐zag ladder. These linear structures are important intermediates between the gas‐phase clusters of arsenic and the extended sheets of arsenene. Raman spectroscopy indicates weak electronic interaction between the arsenic and the nanotubes which implies that the formation of the new allotropes is driven primarily by the geometry of the confinement. The relative stabilities of the new arsenic structures are estimated computationally. Band‐gap calculations predict that the insulating As₄ chains become semiconducting, once converted to the zig‐zag ladder, and form a fully metallic allotrope of arsenic as the zig‐zag chain.     

Matrix assisted laser desorption ionisation ion mobility separation mass spectrometry imaging of ex-vivo human skin

Matrix assisted laser desorption ionisation ion mobility separation mass spectrometry imaging (MALDI-IMS-MSI) has been employed to image the distribution of proteins in ex-vivo human skin. Using a “bottom-up” proteomics approach employing “on-tissue” digestion the distribution of abundant skin proteins; collagen, keratin, decorin and serum albumin could be mapped. Images have been recorded at 150 and 30 μm spatial resolution. Multivariate statistical analysis of the data has been employed to associate specific proteins with layers of the skin. The improved specificity given by the use of ion mobility separation in mass spectrometric imaging has been demonstrated by separation of peptide ions from phospholipids.     

An assay for the enzyme N-acetyl-beta-D-glucosaminidase (NAGase) based on electrochemical detection using screen-printed carbon electrodes (SPCEs).

An electrochemical assay for the enzyme N-acetyl-beta-D-glucosaminidase (NAGase) is described, using bare screen-printed carbon electrodes (SPCEs). The enzyme substrate, 1-naphthyl-N-acetyl-beta-D-glucosaminide, was added to the NAGase-containing sample under hydrodynamic conditions and was hydrolysed to 1-naphthol, which was monitored amperometrically at an Eapp of +650 mV versus SCE. A pH study revealed the apparent Vmax for the assay to occur at pH 4.5. corresponding to an apparent substrate Km of 0.28 mM. In order to be compatible with the analysis of biological fluids, a final operating pH of 5.4 was selected, and, using a data recording time of 100 s post-substrate addition, the assay gave a linear response (r2 = 0.988) over the range 3.1 to 108 mU ml(-1) NAGase (RSD = 15.4%). This assay has the potential to monitor NAGase levels in a number of application areas.     

A separable non-remainder of

We prove that there is a compact separable continuum that (consistently) is not a remainder of the real line.