High–quality protein backbone reconstruction from alpha carbons using Gaussian mixture models

Coarse‐grained protein structure models offer increased efficiency in structural modeling, but these must be coupled with fast and accurate methods to revert to a full‐atom structure. Here, we present a novel algorithm to reconstruct mainchain models from C traces. This has been parameterized by fitting Gaussian mixture models (GMMs) to short backbone fragments centered on idealized peptide bonds. The method we have developed is statistically significantly more accurate than several competing methods, both in terms of RMSD values and dihedral angle differences. The method produced Ramachandran dihedral angle distributions that are closer to that observed in real proteins and better Phaser molecular replacement log‐likelihood gains. Amino acid residue sidechain reconstruction accuracy using SCWRL4 was found to be statistically significantly correlated to backbone reconstruction accuracy. Finally, the PD2 method was found to produce significantly lower energy full‐atom models using Rosetta which has implications for multiscale protein modeling using coarse‐grained models. A webserver and C++ source code is freely available for noncommercial use from: http://www.sbg.bio.ic.ac.uk/phyre2/PD2_ca2main/ . © 2013 Wiley Periodicals, Inc.     

PHI: A powerful new program for the analysis of anisotropic monomeric and exchange‐coupled polynuclear d‐ and f‐block complexes

A new program, PHI, with the ability to calculate the magnetic properties of large spin systems and complex orbitally degenerate systems, such as clusters of d‐block and f‐block ions, is presented. The program can intuitively fit experimental data from multiple sources, such as magnetic and spectroscopic data, simultaneously. PHI is extensively parallelized and can operate under the symmetric multiprocessing, single process multiple data, or GPU paradigms using a threaded, MPI or GPU model, respectively. For a given problem PHI is been shown to be almost 12 times faster than the well‐known program MAGPACK, limited only by available hardware. © 2013 Wiley Periodicals, Inc.     

The effect of terminal chain modifications on the mesomorphic properties of 4,4′-disubstituted diphenyldiacetylenes

The typical sidewalls produced in the fabrication of protrusion electrodes are proposed to create a low voltage (4.5 V_rms) and high transmittance (93%) blue-phase liquid crystal display (BP-LCD). The tilted electrodes produce a strong horizontal electrical field that reduces the operating voltage considerably. The common problem of the ‘dead zones’ is solved by reflecting the light onto the electrodes. In order to estimate the phase retardation of the reflected light, a ray tracing simulation program for anisotropic mediums has been developed. The proposed device is more competitive than vertical field switching based BP-LCD and also, has the advantages of protruded in-plane-switching structures. These facts make this technology a potential candidate for the next generation of BP-LCDs.     

The Extraction of Polycyclic Aromatic Hydrocarbons from Atmospheric Particulate Matter Samples by Accelerated Solvent Extraction (ASE)

Abstract

The Accelerated solvent extraction (ASE) of PAHs (23 2- to 6-ring species) spiked onto glass fibre filters (GFFs) was studied as a function of variable extraction solvents, pressure, temperature and extraction times. Acceptable recoveries (85% ± 15%) were obtained for certain combinations of conditions and a tentative method (1500 psi, 150°C, 70:30 hexane:acetone mixture, 7 min heat-up time, 5 min static extraction time, 60% flush volume, 2 static cycles was selected for further testing. However, this method did not prove as effective as the traditional Soxhlet method of extraction when these parameters were used to extract native PAHs from ambient atmospheric particulate matter collected on a GFF by Integrated Atmospheric Deposition Network (IADN) sampling protocols. The extraction recovery study for spiked GFFs was repeated using slightly different extraction conditions: 2000 psi, 100°C, 70:30 hexane:acetone, 5 min heat-up time, 5 min static extraction time, 150% flush volume, 3 static cycles. When this method was applied to the extraction of native PAHs from ambient atmospheric particulate matter collected on GFFs, the results showed equivalent or better recoveries to that of the Soxhlet method. The total time of extraction was 25 min requiring only 30 mL of solvent. This ASE method is presently used to quantitatively determine PAHs in IADN particle-phase samples.     

FeIII Quinolylsalicylaldimine Complexes: A Rare Mixed‐Spin‐State Complex and Abrupt Spin Crossover

A new synthesis of (8‐quinolyl)‐5‐methoxysalicylaldimine (Hqsal‐5‐OMe) is reported and its crystal structure is presented. Two Fe^III complexes, [Fe(qsal‐5‐OMe)₂]Cl ? solvent (solvent=2 MeOH ? 0.5 H₂O ( 1 ) and MeCN ? H₂O ( 2 )) have been prepared and their structural, electronic and magnetic properties studied. [Fe(qsal‐5‐OMe)₂] Cl ? 2 MeOH ? 0.5 H₂O ( 1 ) exhibits rare crystallographically independent high‐spin and low‐spin Fe^III centres at 150 K, whereas [Fe(qsal‐5‐OMe)₂]Cl ? MeCN ? H₂O ( 2 ) is low spin at 100 K. In both structures there are extensive π–π and C? H???π interactions. SQUID magnetometry of 2 reveals an unusual abrupt stepped‐spin crossover with T_1/2=245 K and 275 K for steps 1 and 2, respectively, with a slight hysteresis of 5 K in the first step and a plateau of 15 K between the steps. In contrast, 1 is found to undergo an abrupt half‐spin crossover also with a hysteresis of 10 K. The two compounds are the first Fe^III complexes of a substituted qsal ligand to exhibit abrupt spin crossover. These conclusions are supported by ⁵⁷Fe Mössbauer spectroscopy. Both complexes exhibit reversible reduction to Fe^II at ?0.18 V and irreversible oxidation of the coordinated qsal‐5‐OMe ligand at +1.10 V.     

Ion chromatograph with three-dimensional printed absorbance detector for indirect ultraviolet absorbance detection of phosphate in effluent and natural waters

An ion chromatography system employing a low-cost three-dimensional printed absorbance detector for indirect ultraviolet detection towards portable phosphate analysis of environmental and industrial waters has been developed. The optical detection cell was fabricated using stereolithography three-dimensional printing of nanocomposite material. Chromatographic analysis and detection of phosphate were carried out using a CS5A 4 × 250 mm analytical column with indirect ultraviolet detection using a 255 nm light-emitting diode. Isocratic elution using a 0.6 mM potassium phthalate eluent combined with 1.44 mM sodium bicarbonate was employed at a flow rate of 0.75 mL/min. A linear calibration range of 0.5 to 30 mg/L PO₄³⁻ applicable to environmental and wastewater analysis was achieved. For retention time and peak area repeatability, relative standard deviation values were 0.68 and 4.09%, respectively. Environmental and wastewater samples were analyzed with the optimized ion chromatography platform and the results were compared to values obtained by an accredited ion chromatograph. For the analysis of environmental samples, relative errors of <14 % were achieved. Recovery analysis was also carried out on both freshwater and wastewater samples and recovery results were within the acceptable range for water analysis using standard ion chromatography methods.     

An Investigation of Photo‐ and Pressure‐Induced Effects in a Pair of Isostructural Two‐Dimensional Spin‐Crossover Framework Materials

Two new isostructural iron(II) spin‐crossover (SCO) framework (SCOF) materials of the type [Fe(dpms)₂(NCX)₂] (dpms=4,4′‐dipyridylmethyl sulfide; X=S ( SCOF‐6(S) ), X=Se ( SCOF‐6(Se) )) have been synthesized. The 2D framework materials consist of undulating and interpenetrated rhomboid (4,4) nets. SCOF‐6(S) displays an incomplete SCO transition with only approximately 30 % conversion of high‐spin (HS) to low‐spin iron(II) sites over the temperature range 300–4 K (T_1/2=75 K). In contrast, the NCSe^? analogue, SCOF‐6(Se) , displays a complete SCO transition (T_1/2=135 K). Photomagnetic characterizations reveal quantitative light‐ induced excited spin‐state trapping (LIESST) of metastable HS iron(II) sites at 10 K. The temperature at which the photoinduced stored information is erased is 58 and 50 K for SCOF‐6(S) and SCOF‐6(Se) , respectively. Variable‐pressure magnetic measurements were performed on SCOF‐6(S) , revealing that with increasing pressure both the T_1/2 value and the extent of spin conversion are increased; with pressures exceeding 5.2 kbar a complete thermal transition is achieved. This study confirms that kinetic trapping effects are responsible for hindering a complete thermally induced spin transition in SCOF‐6(S) at ambient pressure due to an interplay between close T_1/2 and T(LIESST) values.     

Elastic π + p and π + π + scattering at LHC

We discuss the possibility of measuring leading neutron production at the LHC. These data could be used to extract from it π ⁺ p and π ⁺ π ⁺ cross sections. In this note we give some estimates for the case of elastic cross sections and discuss related problems and prospects.     

Real‐time measurement of peroxyacetyl nitrate using selected ion flow tube mass spectrometry

The on‐line detection of gaseous peroxyacetyl nitrate (PAN) using selected ion flow tube mass spectrometry (SIFT‐MS) has been investigated using a synthetic sample of PAN in air at a humidity of ～30%. Using the H₃O⁺ reagent ion, signals due to PAN at m/z 122, 77 and 95 have been identified. These correspond to protonated PAN, protonated peractetic acid and its water cluster, respectively. These products and their energetics have been probed through quantum mechanical calculations. The rate coefficient of H₃O⁺ has been estimated to be 4.5 × 10^?9 cm³ s^?1, leading to a PAN sensitivity of 138 cps/ppbv. This gives a limit of detection of 20 pptv in 10 s using the [M+H]⁺ ion of PAN at m/z 122. Copyright © 2010 John Wiley & Sons, Ltd.