Visualization: A cognition amplifier

Computational codes produce huge quantities of numbers, but what scientists seek is insight. That is, they want to know what these numbers reveal about the phenomena under study. Visualization, transforming data into graphical structures, can enhance research effectiveness by leveraging human visual perceptual capabilities. Evolved over millions of years for survival, these capabilities enable us to see structures and perceive correlations and regularities around us. When properly visualized, we can apply these same perception capabilities, with little rational effort, to our data. In this tutorial, after analyzing a short definition of visualization, its major concepts will be seen in action using a popular chemistry visualization tool. The tutorial closes discussing paths for continued exploration of the future potential of these visualization techniques and tools. © 2013 Wiley Periodicals, Inc.     

Visualization and Experimental Analysis of Fluid Behavior in Grooved Heat Pipes

High-performance grooved heat pipe modelling requires improved knowledge of flow behavior inside grooves. Even if this flow is usually laminar, a free surface governed by capillarity leads to many difficulties when calculating the mean friction factor of grooves. In the present study, an experimental bench has been developed in order to visualize the liquid–vapor interface channels of four different axially grooved heat pipes. Subsequent experimentation, which is associated with image processing programs, allows for measurement of liquid height and meniscus radius evolution in a groove along the heat pipe axis. As regards laminar flow inside the grooves typically used in heat pipes, the mean friction factor has been measured.     

ZINC(II), CADMIUM(II), MERCURY(II) AND LEAD(II) SEMIQUINONE-TYPE COMPLEXES OF A NEW SCHIFF-BASE LIGAND: ANTIBACTERIAL STUDIES

Abstract

A new Schiff-base ligand LH₂, has been prepared by reaction of 2,9-diformv 1-1,10-phenan-throline with 2,3-diamino-l,4-naphthoquinone. The formation and characterization of complexes of Zn(II), Cd(II), Hg(II) and Pb(II) with the semi-oxidized ligand LH is described. The M(LH)X₂ (X = CI, Br and AcO) radical species are paramagnetic and the observed EPR signals in the solid state at room temperature, with g values close to the electron free g value are proof of the semiquinonic character of the ligand. The antibacterial activity of the ligand and the metal complexes prepared were tested against four bacteria strains and compared with the activity of penicillin.     

Polyhydroxylated macrolide isolated from the endophytic fungus Pestalotiopsis mangiferae

A new polyhydroxylated macrolide, named mangiferaelactone (1) was isolated from a solid culture of the endophytic fungus Pestalotiopsis manguiferae, together with ten known compounds [(6S,1′S)-LL-P880α; (6S,1′S,2′R)-LL-P880β; (1′S,2′R)-LL-880γ; (1′R)-dehydropestalotin; (−)-5-carboxylmellein; (−)-5-methylmellein; (−)-5-hydroxylmethylmellein; arabenoic acid; 5,6-dihydro-4-methoxy-2H-pyran-2-one; and the (−)-2-hexylidene-3-methylsuccinic acid]. P. manguiferae was isolated from Hyptis dilatata, a small shrub common in the central region of Panama. The structure of compound 1 was elucidated by a combination of spectroscopic methods (IR, MS, optical rotation, 1D and 2D NMR spectroscopy). The absolute configuration of 1 was established as 4R,7R,8R,9S by application of vibrational circular dichroism (VCD). Compound 1 showed a minimum inhibitory concentration (MIC) of 1.6863 mg/mL against Listeria monocytogenes, and 0.5529 mg/mL against Bacillus cereus. No activity was observed for compound 1 against Plasmodium falciparum or Trypanosoma cruzi; likewise, no cytotoxic activity was observed against A2058 and H522-T1 cells.     

Synthesis and DFT Defined trans (O5O6) Molecular Structure of Cs[Fe(1,3- pddadp )] · 2H2O. Strain Analysis and Spectral Assignment of the Complex

Summary. An iron(III) complex with the hexadentate ligand 1,3-propanediamine-N,N′-diacetate-N,N′-di-3-propionate (1,3-pddadp) was prepared, chromatographically isolated as its isomer trans(O₅O₆)-Cs[Fe(1,3-pddadp)] · 2H₂O, and characterized. The trans(O₅O₆) configuration of the iron(III) compound was found to dominate and this geometry was established by means of IR spectroscopy and Density Functional Theory (DFT). Structural data correlating the octahedral geometry of the [Fe(1,3-pddadp)]⁻ unit and an extensive strain analysis are discussed in relation to the information obtained for similar complexes. Antibacterial activities of the free ligand and its corresponding iron(III) complex towards common Gram-negative and Gram-positive bacteria are reported as well.     

Determination of peptidoglycan-associated protein in Escherichia coli NCIB 8545 by capillary zone electrophoresis

An efficient reliable and sensitive capillary zone electrophoresis assay for the six major bacterial peptidoglycan-associated proteins of Escherichia coli NCIB 8545 is described. The method provides the facility to determine quantitatively the effect of antibacterials on bacterial peptidoglycan-associated protein synthesis and thus to further elucidate the mechanism of antibacterial action of such drugs as the antifolates which recently have been shown to adversely affect peptidoglycan synthesis.     

基于着色模型实时构造的海洋流场动态流线可视化方法研究

为了实现海洋流场流向、流速等特征信息的直观高效可视化表达,提出了一种基于着色模型实时构造的海洋流场动态流线可视化方法。设计了一种可适应三维纹理的流线属性信息存储结构,构建面向动态流线的着色模型并进行流线实时构造,实现复杂海洋流场的动态可视化表达。实验结果表明,相较于静态流线可视化方法和基于动态图元的流线可视化方法,该方法显著提高了流场海量数据集的可读性以及流场可视化的渲染效率与表达效果,更直观、流畅地反映了流场的时空特征和复杂动态过程。     

Gabedit—A graphical user interface for computational chemistry softwares

Gabedit is a freeware graphical user interface, offering preprocessing and postprocessing adapted (to date) to nine computational chemistry software packages. It includes tools for editing, displaying, analyzing, converting, and animating molecular systems. A conformational search tool is implemented using a molecular mechanics or a semiempirical potential. Input files can be generated for the computational chemistry software supported by Gabedit. Some molecular properties of interest are processed directly from the output of the computational chemistry programs; others are calculated by Gabedit before display. Molecular orbitals, electron density, electrostatic potential, nuclear magnetic resonance shielding density, and any other volumetric data properties can be displayed. It can display electronic circular dichroism, UV–visible, infrared, and Raman‐computed spectra after a convolution. Gabedit can generate a Povray file for geometry, surfaces, contours, and color‐coded planes. Output can be exported to a selection of popular image and vector graphics file formats; the program can also generate a series of pictures for animation. Quantum mechanical electrostatic potentials can be calculated using the partial charges on atoms, or by solving the Poisson equation using the multigrid method. The atoms in molecule charges can also be calculated. Gabedit is platform independent. The code is distributed under free open source X11 style license and is available at http://gabedit.sourceforge.net/ . © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

Multi-biofunctional complexes combining antiseptic copper(II) with antibiotic sulfonamide ligands: Structural, redox and antibacterial study

Copper(II) and nickel(II) complexes of sulfadimethoxine, sulfadiazine, sulfamerazine and sulfamethazine were synthesized with a good yield according to an original procedure. These complexes were first characterized by single-crystal X-ray diffraction and electrochemistry. Structural inspections showed that the antibacterial entity of ligands remains non-coordinated to metal ions in the complex high-lighting the fact that in each cluster, antiseptic activity of the metal has been associated to the antibiotic activity of the ligand. In order to confirm this possibility, antibacterial activities of the complexes were studied on several bacteria. The antibacterial activity of the complex is as important as the ligands one with the addition of antiseptic activity via the incorporation of copper ions.     

Preparation of active antibacterial LDPE surface through multistep physicochemical approach: I. Allylamine grafting, attachment of antibacterial agent and antibacterial activity assessment

Low-density polyethylene (LDPE) samples were treated in air plasma discharge, coated by polyallyamine brush thought copolymeric grafting surface-from reaction and deposited four common antibacterial agents (benzalkonium chloride, bronopol, chlorhexidine and triclosan) to gain material with active antibacterial properties. Surface characteristics were evaluated by static contact angle measurement with surface energy evaluation ATR-FTIR, X-ray Photoelectron Spectroscopy (XPS) and SEM analysis. Inhibition zone on agar was used as in vitro test of antibacterial properties on two representative gram positive Staphylococcus aureus (S. aureus) and gram negative Escherichia coli (E. coli) strains. It was confirmed, that after grafting of polyallyamine, more antibacterial agent is immobilized on the surface. The highest increase of antibacterial activity was observed by the sample containing triclosan. Samples covered by bronopol did not show significant antibacterial activity.