Synthesis, structure, and spectroscopy of phenylacetylenylene rods incorporating meso-substituted dipyrrin ligands

The synthesis, structure, and spectroscopic characterization of a series of phenylacetylenylene rodlike molecules containing dipyrromethene (dipyrrin) ligands are described. The combination of the phenylacetylenylene groups with the porphyrinogenic dipyrrin moieties results in a rich absorption spectroscopy for these compounds, although the fluorescence of the phenylacetylenylene moiety is quenched by presence of the dipyrrin chelator. The Cu(2+) and Fe(3+) complexes of these ligands have been prepared and three of these compounds have been structurally characterized by using single-crystal X-ray diffraction. Unlike other octahedral metal-dipyrrin complexes described to date, one of the iron complexes demonstrates ideal threefold symmetry in the solid-state. The elongated structure and high symmetry of these complexes suggests the use of these meso-substituted phenylacetylenylene ligands as an interesting class of extended, branched molecules for the construction of supramolecular architectures.     

Artificial neural networks for quantification in unresolved capillary electrophoresis peaks

The application of the combination of experimental design (ED) and artificial neural networks (ANNs) for the quantification of overlapped peaks in capillary zone electrophoresis is described. When the total separation cannot be achieved by separation techniques, the use of ED-ANN can be a suitable approach. The unstability of EOF causes peak shift that has to be corrected in order to apply ED-ANN methods. In this work, normalization procedure of electropherograms with consequent application of ANNs for quantification purpose was developed. Both, spectra and electropherograms can be used as multivariate data. In general, both kinds of data were found to be suitable for unresolved peaks quantification by ED-ANN approach.     

Ligand-protein docking using a quantum stochastic tunneling optimization method

A novel hybrid optimization method called quantum stochastic tunneling has been recently introduced. Here, we report its implementation within a new docking program called EasyDock and a validation with the CCDC/Astex data set of ligand-protein complexes using the PLP score to represent the ligand-protein potential energy surface and ScreenScore to score the ligand-protein binding energies. When taking the top energy-ranked ligand binding mode pose, we were able to predict the correct crystallographic ligand binding mode in up to 75% of the cases. By using this novel optimization method run times for typical docking simulations are significantly shortened.     

A genetic algorithm for structure-based de novo design

Genetic algorithms have properties which make them attractive in de novo drug design. Like other de novo design programs, genetic algorithms require a method to reduce the enormous search space of possible compounds. Most often this is done using information from known ligands. We have developed the ADAPT program, a genetic algorithm which uses molecular interactions evaluated with docking calculations as a fitness function to reduce the search space. ADAPT does not require information about known ligands. The program takes an initial set of compounds and iteratively builds new compounds based on the fitness scores of the previous set of compounds. We describe the particulars of the ADAPT algorithm and its application to three well-studied target systems. We also show that the strategies of enhanced local sampling and re-introducing diversity to the compound population during the design cycle provide better results than conventional genetic algorithm protocols.     

Improved preparative electrochromatography column design

Improved chromatography column fittings were developed for the efficient and reliable application of an electric field to a preparative chromatography column (a process termed electrochromatography). The improved fittings contained electrodes in close proximity to the column packing media and allowed uniform electric fields to be applied. Membranes in the fittings prevented mixing of the electrode and the column eluent buffers. The membranes prevented gases and electrolytic products generated in the electrode chamber from entering the column eluent buffer. An electrode buffer solution was pumped through the electrode chamber to a large external container. The circulation of buffer through the electrode chamber removed the gases and electrolytic products and ensured a uniform electric field by helping to maintain a constant buffer composition. The membranes prevented macromolecules being separated on the column from coming in contact with the electrodes.     

Modern Synthetic Methods for Fluorine‐Substituted Target Molecules

Fluorine has come to be recognized as a key element in materials science: in heat‐transfer agents, liquid crystals, dyes, surfactants, plastics, elastomers, membranes, and other materials. Furthermore, many fluorine‐containing biologically active agents are finding applications as pharmaceuticals and agrochemicals. Progress in synthetic fluorine chemistry has been critical to the development of these fields and has led to the invention of many novel fluorinated molecules as future drugs and materials. As a result of the electronic effects of fluorine substituents, fluorinated substrates and reagents often exhibit unusual and unique chemical properties, which often make them incompatible with established synthetic methods. Thus, the problem of how to control the unusual properties of compounds with fluorine substituents deserves much attention, so as to promote the design of facile, efficient, and environmentally benign methods for the synthesis of valuable organofluorine targets.     

Flow injection system for hydrolysable tannin determination

A flow injection system was proposed to evaluate the transient product of a colorimetric reaction between hydrolysable tannin and potassium iodate (KIO₃) solution. The system optimization was accomplished by using statistical methods based on experimental design. Flow rate of KIO₃ solution, sample volume, carrier flow rate, and reaction coil were the selected factors for evaluation. On screening step, complete factorial 2⁴ was used and two levels for each selected factor were studied. For the optimization phase, a centered face composite design 2² + star was employed to evaluate sample volume and flow rate of KIO₃ solution, which were the factors identified in the screening phase as having more influence on the absorbance signal. After optimization, the proposed system was compared with batch determination. Some characteristics, such as analytical frequency, reagent consumption and chemical residues generation presented better results by the use of the proposed system if compared with batch method. The system presented good repeatability with standard deviation lower than 3%, for n = 10, linearity (R² = 0.9974) for tannic acid standard, analytical frequency of 15 injections h^− 1 and limit of quantification of 24 mg L^− 1 of tannic acid. Good results were obtained when the proposed system was applied to hydrolysable tannin determination in Stryphnodendron barbatimão, Eucalyptus citriodora and Phyllanthus niruri, samples of plants commonly used in popular medicine.     

NMR spectroscopy techniques for screening and identifying ligand binding to protein receptors

Binding events of ligands to receptors are the key for an understanding of biological processes. Gaining insight into protein-protein and protein-ligand interactions in solution has recently become possible on an atomic level by new NMR spectroscopic techniques. These experiments identify binding events either by looking at the resonance signals of the ligand or the protein. Ideally, both techniques together deliver a complete picture of ligand binding to a receptor. The approaches discussed in this review allow screening of compound libraries as well as a detailed identification of the groups involved in the binding events. Also, characterization of the binding strength and kinetics is possible, competitive binding as well as allosteric effects can be identified, and it has even been possible to identify ligand binding to intact viruses and membrane-bound proteins.     

Synthesis and Characterization of Fluoro- and Chloro- bimetallic Alkoxides as Precursors for Luminescent Metal Oxide Materials via Sol-Gel Technique

Heterobimetallic alkoxides are broadly recognized as versatile precursors for luminescence materials, and efforts are being made to develop novel routes by applying the concept of geometrical molecular design, for their synthesis and to design a single source precursor suited to photoluminescent materials. Novel and new series of bimetallic alkoxides has been prepared by metathesis route. They exhibit a lower sensitivity towards hydrolysis and so they are easier to handle as compared to other alkoxides. All the compounds were characterized by elemental analysis, FT-IR and multinuclear NMR spectroscopies. FT-IR revealed that the molecular structure of these metal alkoxides was retained to a large extent in 4 ： 1 halogenated alcohol-benzene solution. The heteronuclear NMR spectroscopy provided useful information about chemical shifts for better understanding the likely structure based on interactions with their coordinate metals. The mass spectra show similar types of fragmentation pattern. SEM-EDS analyses showed consistency with the formulation. XRD patterns show an enhanced homogeneity at high temperature. TGA measurements show that thermal decomposition occured in steps that depended entirely on the chemical compositions and the synthesis routes. SEM observation reveals that the morphology and particle size strongly depend on synthesis routes for their precursors.     

血红素蛋白的分子设计新趋向

综述了近年来有关血红素蛋白分子设计所出现的新趋向， 包括氨基酸选择突变与血红素修饰相结合，非天然辅基的引入，非天然氨基酸的引入，辅基与蛋白肽链的共价结合，以及全新血红素蛋白的设计与构建5个方面。这些新发展趋向对研究金属蛋白的结构-功能关系提供了重要的信息，同时也为这些理性设计的新颖金属蛋白分子拓宽了其在生物化学、生物工程和药学上的应用。