Application of Enzymes in Regioselective and Stereoselective Organic Reactions

Nowadays, biocatalysts have received much more attention in chemistry regarding their potential to enable high efficiency, high yield, and eco-friendly processes for a myriad of applications. Nature’s vast repository of catalysts has inspired synthetic chemists. Furthermore, the revolutionary technologies in bioengineering have provided the fast discovery and evolution of enzymes that empower chemical synthesis. This article attempts to deliver a comprehensive overview of the last two decades of investigation into enzymatic reactions and highlights the effective performance progress of bio-enzymes exploited in organic synthesis. Based on the types of enzymatic reactions and enzyme commission (E.C.) numbers, the enzymes discussed in the article are classified into oxidoreductases, transferases, hydrolases, and lyases. These applications should provide us with some insight into enzyme design strategies and molecular mechanisms

Shape: automatic conformation prediction of carbohydrates using a genetic algorithm

<p>Abstract</p> <p>Background</p> <p>Detailed experimental three dimensional structures of carbohydrates are often difficult to acquire. Molecular modelling and computational conformation prediction are therefore commonly used tools for three dimensional structure studies. Modelling procedures generally require significant training and computing resources, which is often impractical for most experimental chemists and biologists. <monospace>Shape</monospace> has been developed to improve the availability of modelling in this field.</p> <p>Results</p> <p>The <monospace>Shape</monospace> software package has been developed for simplicity of use and conformation prediction performance. A trivial user interface coupled to an efficient genetic algorithm conformation search makes it a powerful tool for automated modelling. Carbohydrates up to a few hundred atoms in size can be investigated on common computer hardware. It has been shown to perform well for the prediction of over four hundred bioactive oligosaccharides, as well as compare favourably with previously published studies on carbohydrate conformation prediction.</p> <p>Conclusion</p> <p>The <monospace>Shape</monospace> fully automated conformation prediction can be used by scientists who lack significant modelling training, and performs well on computing hardware such as laptops and desktops. It can also be deployed on computer clusters for increased capacity. The prediction accuracy under the default settings is good, as it agrees well with experimental data and previously published conformation prediction studies. This software is available both as open source and under commercial licenses.</p

Accretion, Outflows, and Winds of Magnetized Stars

Many types of stars have strong magnetic fields that can dynamically influence the flow of circumstellar matter. In stars with accretion disks, the stellar magnetic field can truncate the inner disk and determine the paths that matter can take to flow onto the star. These paths are different in stars with different magnetospheres and periods of rotation. External field lines of the magnetosphere may inflate and produce favorable conditions for outflows from the disk-magnetosphere boundary. Outflows can be particularly strong in the propeller regime, wherein a star rotates more rapidly than the inner disk. Outflows may also form at the disk-magnetosphere boundary of slowly rotating stars, if the magnetosphere is compressed by the accreting matter. In isolated, strongly magnetized stars, the magnetic field can influence formation and/or propagation of stellar wind outflows. Winds from low-mass, solar-type stars may be either thermally or magnetically driven, while winds from massive, luminous O and B type stars are radiatively driven. In all of these cases, the magnetic field influences matter flow from the stars and determines many observational properties. In this chapter we review recent studies of accretion, outflows, and winds of magnetized stars with a focus on three main topics: (1) accretion onto magnetized stars; (2) outflows from the disk-magnetosphere boundary; and (3) winds from isolated massive magnetized stars. We show results obtained from global magnetohydrodynamic simulations and, in a number of cases compare global simulations with observations.Comment: 60 pages, 44 figure

Biopolymer-based structuring of liquid oil into soft solids and oleogels using water-continuous emulsions as templates

Physical trapping of a hydrophobic liquid oil in a matrix of water-soluble biopolymers was achieved using a facile two-step process by first formulating a surfactant-free oil-in-water emulsion stabilized by biopolymers (a protein and a polysaccharide) followed by complete removal of the water phase (by either high- or low-temperature drying of the emulsion) resulting in structured solid systems containing a high concentration of liquid oil (above 97 wt %). The microstructure of these systems was revealed by confocal and cryo-scanning electron microscopy, and the effect of biopolymer concentrations on the consistency of emulsions as well as the dried product was evaluated using a combination of small-amplitude oscillatory shear rheometry and large deformation fracture studies. The oleogel prepared by shearing the dried product showed a high gel strength as well as a certain degree of thixotropic recovery even at high temperatures. Moreover, the reversibility of the process was demonstrated by shearing the dried product in the presence of water to obtain reconstituted emulsions with rheological properties comparable to those of the fresh emulsion

Atomic Scale Modelling of Two-Dimensional Molecular Self-Assembly on a Passivated Si Surface

International audienceThe self-assembly of two-dimensional (2D) molecular structures on a solid surface relies on the subtle balance between non covalent intermolecular and molecule-surface forces. The energetics of 2D molecular lattices forming different patterns on a passivated semiconductor surface are here investigated by a combination of atomistic simulation methods. Density-functional theory provides structure and charges of the molecules, while metadynamics with empirical forces provides a best guess for the lowest-energy adsorption sites of single molecules and dimers. Subsequently, molecular dynamics simulations of extended molecular assemblies with empirical forces yield the most favorable lattice structures at finite temperature and pressure.The theoretical results are in good agreement with scanning tunneling microscopy observations of self-assembled molecular monolayers on a B-doped Si(111) surface, thus allowing to rationalize the competition of long-range dispersion forces between the molecules and the surface. Such a result demonstrates the interest of this predictive approach for further progress in supramolecular chemistry on semiconductor surface

Identification of mungbean lines with tolerance or resistance to yellow mosaic in fields in India where different begomovirus species and different Bemisia tabaci cryptic species predominate

Mungbean (Vigna radiata (L.) Wilczek) is an important pulse crop in India. A major constraint for improved productivity is the yield loss caused by mungbean yellow mosaic disease (MYMD). This disease is caused by several begomoviruses which are transmitted by the whitefly Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae). The objective of this study was to identify the predominant begomoviruses infecting mungbean and the major cryptic species of B. tabaci associated with this crop in India. The indigenous B. tabaci cryptic species Asia II 1 was found dominant in Northern India, whereas Asia II 8 was found predominant in Southern India. Repeated samplings over consecutive years indicate a stable situation with, Mungbean yellow mosaic virus strains genetically most similar to a strain from urdbean (MYMV-Urdbean) predominant in North India, strains most similar to MYMV-Vigna predominant in South India, and Mungbean yellow mosaic India virus (MYMIV) strains predominant in Eastern India. In field studies, mungbean line NM 94 showed a high level of tolerance to the disease in the Eastern state of Odisha where MYMIV was predominant and in the Southern state of Andhra Pradesh where MYMV-Vigna was predominant, but only a moderate level of tolerance in the Southern state of Tamil Nadu. However, in Northern parts of India where there was high inoculum pressure of MYMV-Urdbean during the Kharif season, NM 94 developed severe yellow mosaic symptoms. The identification of high level of tolerance in mungbean lines such as ML 1628 and of resistance in black gram and rice bean provides hope for tackling the disease through resistance breeding

Bioinformatics and molecular modeling in glycobiology

The field of glycobiology is concerned with the study of the structure, properties, and biological functions of the family of biomolecules called carbohydrates. Bioinformatics for glycobiology is a particularly challenging field, because carbohydrates exhibit a high structural diversity and their chains are often branched. Significant improvements in experimental analytical methods over recent years have led to a tremendous increase in the amount of carbohydrate structure data generated. Consequently, the availability of databases and tools to store, retrieve and analyze these data in an efficient way is of fundamental importance to progress in glycobiology. In this review, the various graphical representations and sequence formats of carbohydrates are introduced, and an overview of newly developed databases, the latest developments in sequence alignment and data mining, and tools to support experimental glycan analysis are presented. Finally, the field of structural glycoinformatics and molecular modeling of carbohydrates, glycoproteins, and protein–carbohydrate interaction are reviewed