On the Effect of the Various Assumptions and Approximations used in Molecular Simulations on the Properties of Bio-Molecular Systems: Overview and Perspective on Issues

Computer simulations of molecular systems enable structure-energy-function relationships of molecular processes to be described at the sub-atomic, atomic, supra-atomic or supra-molecular level and plays an increasingly important role in chemistry, biology and physics. To interpret the results of such simulations appropriately, the degree of uncertainty and potential errors affecting the calculated properties must be considered. Uncertainty and errors arise from (1) assumptions underlying the molecular model, force field and simulation algorithms, (2) approximations implicit in the interatomic interaction function (force field), or when integrating the equations of motion, (3) the chosen values of the parameters that determine the accuracy of the approximations used, and (4) the nature of the system and the property of interest. In this overview, advantages and shortcomings of assumptions and approximations commonly used when simulating bio-molecular systems are considered. What the developers of bio-molecular force fields and simulation software can do to facilitate and broaden research involving bio-molecular simulations is also discussed.     

Olefin oxygenation by the hydroperoxide adduct of a nonheme manganese(IV) complex: epoxidations by a metallo-peracid produces gentle selective oxidations

The reactive intermediates and mechanisms of oxygenation of olefins by manganese complexes were investigated by treating olefins with newly synthesized [MnIV(Me2EBC)(OH)2](PF6)2 in the presence and absence of peroxide and by studying its catalytic epoxidation reaction in normal aqueous solution and, individually, with isotopically labeled H218O, 18O2, and H218O2. The manganese oxo species is not the reactive intermediate for the oxygen transfer process mediated by this manganese complex. A novel manganese(IV) peroxide intermediate, MnIV(Me2EBC)(O)(OOH)+, was captured by mass spectrometry and is proposed as the intermediate that oxygenates olefins in this catalytic system.     

Optical properties of erbium-doped fluorochlorozirconate glasses

We report the optical properties of a fluorochlorozirconate (FCZ) glass with the composition 53% ZrF₄, 20% NaF, 3.5% AlF₃, 3% LaF₃, 0.5% InF₃, (20 ? x)% BaCl₂, x% BaF₂ with x varying from 0% to 2%, and doped with various amounts of trivalent erbium by the addition of ErCl₃. Annealing of the as-prepared glass in inert (N₂) or reducing (5%H₂ + 95%Ar) atmospheres at temperatures that ensure the conversion of the glass into a glass-ceramic by the nucleation of BaCl₂ nanocrystals, does not significantly change any of Er³⁺ related absorption and photoluminescence (PL) characteristics. We have carried out a Judd–Ofelt analysis of the absorption spectra and obtained Ω₂ = (1.92 ± 0.3) × 10^? 20 cm², Ω₄ = (0.88 ± 0.16) × 10^? 20 cm² and Ω₆ = (0.59 ± 0.08) × 10^? 20 cm², and also the radiative lifetimes of the ⁴I_13/2→⁴I_15/2, ⁴I_11/2→⁴I_15/2 and ⁴S_3/2→⁴I_15/2 bands. The radiative lifetime from the Judd–Ofelt analysis for the ⁴I_13/2→⁴I_15/2 band is in good agreement with the experimentally measured PL decay time. The examination of the optical properties of powdered samples with different average particle size does not show any photon trapping effects. We have determined the spectral absorption and emission cross-sections and then estimated the possible spectral optical gain for varying degrees of relative populations of the ⁴I_13/2 and ⁴I_15/2 manifolds.     

Identification of inorganic ions in post‐blast explosive residues using portable CE instrumentation and capacitively coupled contactless conductivity detection

Novel CE methods have been developed on portable instrumentation adapted to accommodate a capacitively coupled contactless conductivity detector for the separation and sensitive detection of inorganic anions and cations in post‐blast explosive residues from homemade inorganic explosive devices. The methods presented combine sensitivity and speed of analysis for the wide range of inorganic ions used in this study. Separate methods were employed for the separation of anions and cations. The anion separation method utilised a low conductivity 70 mM Tris/70 mM CHES aqueous electrolyte (pH 8.6) with a 90 cm capillary coated with hexadimethrine bromide to reverse the EOF. Fifteen anions could be baseline separated in 7 min with detection limits in the range 27–240 μg/L. A selection of ten anions deemed most important in this application could be separated in 45 s on a shorter capillary (30.6 cm) using the same electrolyte. The cation separation method was performed on a 73 cm length of fused‐silica capillary using an electrolyte system composed of 10 mM histidine and 50 mM acetic acid, at pH 4.2. The addition of the complexants, 1 mM hydroxyisobutyric acid and 0.7 mM 18‐crown‐6 ether, enhanced selectivity and allowed the separation of eleven inorganic cations in under 7 min with detection limits in the range 31–240 μg/L. The developed methods were successfully field tested on post‐blast residues obtained from the controlled detonation of homemade explosive devices. Results were verified using ion chromatographic analyses of the same samples.     

Quantification of appetite suppressing steroid glycosides from Hoodia gordonii in dried plant material, purified extracts and food products using HPLC-UV and HPLC-MS methods

High-performance liquid chromatography (HPLC)-UV and HPLC-Mass Spectrometry (MS) methods were developed for the quantitative analysis of the family of Hoodia gordonii steroid glycosides with appetite suppressing properties in dried plant material, in purified and enriched extracts and in various prototype food-products fortified with H. gordonii extracts. For solid materials, e.g. dried plants or for non-fatty foods, extraction of the steroid glycosides is performed using methanol. For products where the steroid glycosides are present in an oil matrix, direct injection of the oil after dilution in tetrahydrofuran is applied. The HPLC separation is performed on an octyl-modified reversed-phase column in the gradient mode with UV detection at lambda = 220 nm. Quantification is performed against an external calibration line prepared using either one of the pure steroid glycosides or geranyl-tiglate. Short- and long-term repeatabilities of the methods are better than 3 and 6%, respectively. Recoveries are better than 85%, even in the analysis of the least abundant steroid glycosides in a complex yoghurt drink. Linearity is better than 3-4 orders of magnitude and the detection limits are below approximately 2 microg g(-1) for the individual steroid glycosides in dried plant material and food products. HPLC-MS is used to confirm that the steroid glycosides contain the characteristic steroid core, the carbohydrate chain and the tigloyl group.