Linear scaling computation of the Fock matrix. VII. Parallel computation of the Coulomb matrix

We present parallelization of a quantum-chemical tree-code for linear scaling computation of the Coulomb matrix. Equal time partition is used to load balance computation of the Coulomb matrix. Equal time partition is a measurement based algorithm for domain decomposition that exploits small variation of the density between self-consistent-field cycles to achieve load balance. Efficiency of the equal time partition is illustrated by several tests involving both finite and periodic systems. It is found that equal time partition is able to deliver 91%-98% efficiency with 128 processors in the most time consuming part of the Coulomb matrix calculation. The current parallel quantum chemical tree code is able to deliver 63%-81% overall efficiency on 128 processors with fine grained parallelism (less than two heavy atoms per processor).     

Determination of sulphonated azo dyes in food by ion-pair liquid chromatography with photodiode array and electrospray mass spectrometry detection

An ion-pair liquid chromatography method with on-line photodiode-array and electrospray mass spectrometry detection was developed to determine 10 commonly used sulphonated azo dyes (Tartrazine, Amaranth, New Coccine, Sunset Yellow FCF, Allura Red AC, Ponceau R, Ponceau 3R, Orange I, Orange II and Metanil Yellow) in food. A reversed phase C(18) column with gradient elution was utilized to separate these compounds. Triethylamine was added in the mobile phase as an ion-pair reagent for chromatographic separation. Photodiode-array detection was employed for quantitative determination and electrospray mass spectrometry was used for identification. Good linearity (0.05-10 ppm, r(2)=0.999) and detection limit (<0.01 ppm) were determined with 5 mul injection. In addition, precision and accuracy associated with this newly developed method will be presented. A liquid extraction method was also developed to extract these dyes from different foodstuffs. The application of this method was demonstrated by analyzing sulphonated azo dyes in soft drinks, fruit jam, and salted vegetables.     

Competing energy scales in high‐temperature superconductors: Ultrafast pump–probe studies

We present a review of photoexcited quasiparticle dynamics of cuprate and pnictide high‐temperature superconductors in regimes (temperature, doping) where different phases such as superconductivity, spin‐density‐wave (SDW) and pseudogap phases coexist or compete with one another. We start with the overdoped cuprate superconductor Y_1–xCa_x Ba₂Cu₃O_7–δ, where the superconducting gap and pseudogap coexist in the superconducting state. In another cuprate Tl₂Ba₂Ca₂Cu₃O_y, we ob‐ serve a competition between SDW and superconducting orders deep in the superconducting state. Finally, in the underdoped iron pnictide superconductor (Ba,K)Fe₂As₂, SDW order forms at 85 K, followed by superconductivity at 28 K. We also find the emergence of a normal‐state order that suppresses SDW at a temperature T * ～ 60 K and argue that this normal‐state order is a precursor to superconductivity. (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Computational Study of the One‐ and Two‐Dimensional Infrared Spectra of a Proton‐Transfer Mode in a Hydrogen‐Bonded Complex Dissolved in a Polar Nanocluster

The signatures of nanosolvation on the one‐ and two‐dimensional (1D and 2D) IR spectra of a proton‐transfer mode in a hydrogen‐bonded complex dissolved in polar solvent molecule nanoclusters of varying size are elucidated by using mixed quantum–classical molecular dynamics simulations. For this particular system, increasing the number of solvent molecules successively from N=7 to N=9 initiates the transition of the system from a cluster state to a bulk‐like state. Both the 1D and 2D IR spectra reflect this transition through pronounced changes in their peak intensities and numbers, but the time‐resolved 2D IR spectra also manifest spectral features that uniquely identify the onset of the cluster‐to‐bulk transition. In particular, it is observed that in the 1D IR spectra, the relative intensities of the peaks change such that the number of peaks decreases from three to two as the size of the cluster increases from N=7 to N=9. In the 2D IR spectra, off‐diagonal peaks are observed in the N=7 and N=8 cases at zero waiting time, but not in the N=9 case. It is known that there are no off‐diagonal peaks in the 2D IR spectrum of the bulk version of this system at zero waiting time, so the disappearance of these peaks is a unique signature of the onset of bulk‐like behavior. Through an examination of the trajectories of various properties of the complex and solvent, it is possible to relate the emergence of these off‐diagonal peaks to an interplay between the vibrations of the complex and the solvent polarization dynamics.     

Colorimetric and bare-eye determination of fluoride using gold nanoparticle agglomeration probes

We report on a sensitive detection scheme for fluoride that is based on a quinone-methide-type of rearrangement reaction to trigger a color change among cloaked gold nanoparticle agglomeration probes. Fluoride ions remove silyl moieties from phenol groups on the surface of the probes, and this causes a quinone-methide-type of rearrangement reaction to occur. This is accompanied by the release of a dithiol in a spontaneous and irreversible reaction at room temperature in aqueous medium. The released dithiol causes aggregation of the AuNPs which leads to a color change from pink-red to violet-blue that can easily be seen with bare eyes.. The generation of color by this cascade reactions is only caused by fluoride and not interfered by any other anions. The assay platform developed here offers a sensitive colorimetric assay for fluoride. The lower limit of detection is 120 μM, and the dynamic concentration range is from 120 μM to 1.5 mM.

Synthesis and thermotropic studies of a novel series of nematogenic liquid crystals 2-(6-alkoxynaphthalen-2-yl)-5-cyanopyridines

A novel series of highly birefringent liquid crystalline compounds, 2-(6-alkoxynaphthalen-2-yl)-5-cyanopyridines (nO-NpPyCN, n?=?2–8) that have potential as commercially useful, were synthesised using a short two-step reaction with overall yields between 55% and 85%. Spectral analyses were in accordance with the expected structures. Their thermotropic behaviours were investigated by polarising optical microscopy and differential scanning calorimetry. It was found that the desymmetrised core results in a nematic phase with a broad mesophase range.     

Structural and Dynamic Basis of Human Cytochrome P450 7B1: A Survey of Substrate Selectivity and Major Active Site Access Channels

Cytochrome P450 (CYP) 7B1 is a steroid cytochrome P450 7α‐hydroxylase that has been linked directly with bile salt synthesis and hereditary spastic paraplegia type 5 (SPG5). The enzyme provides the primary metabolic route for neurosteroids dehydroepiandrosterone (DHEA), cholesterol derivatives 25‐hydroxycholesterol (25‐HOChol), and other steroids such as 5α‐androstane‐3β,17β‐diol (anediol), and 5α‐androstene‐3β,17β‐diol (enediol). A series of investigations including homology modeling, molecular dynamics (MD), and automatic docking, combined with the results of previous experimental site‐directed mutagenesis studies and access channels analysis, have identified the structural features relevant to the substrate selectivity of CYP7B1. The results clearly identify the dominant access channels and critical residues responsible for ligand binding. Both binding free energy analysis and total interaction energy analysis are consistent with the experimental conclusion that 25‐HOChol is the best substrate. According to 20 ns MD simulations, the Phe cluster residues that lie above the active site, particularly Phe489, are proposed to merge the active site with the adjacent channel to the surface and accommodate substrate binding in a reasonable orientation. The investigation of CYP7B1–substrate binding modes provides detailed insights into the poorly understood structural features of human CYP7B1 at the atomic level, and will be valuable information for drug development and protein engineering.     

A one-pot tandem synthesis of various 1,2-disubstituted benzimidazoles

A facile method to synthesize various 1,2-disubstituted benzimidazoles is developed. It is suggested that formation of a Meisenheimer adduct between the substrate, amine, and solvent aids the N-arylation process. The generality of the protocol is demonstrated by the efficient reactions involving numerous substituents ranging from electron-withdrawing groups to electron-donating groups.