Three dimensional model of severe acute respiratory syndrome coronavirus helicase ATPase catalytic domain and molecular design of severe acute respiratory syndrome coronavirus helicase inhibitors

The modeling of the severe acute respiratory syndrome coronavirus helicase ATPase catalytic domain was performed using the protein structure prediction Meta Server and the 3D Jury method for model selection, which resulted in the identification of 1JPR, 1UAA and 1W36 PDB structures as suitable templates for creating a full atom 3D model. This model was further utilized to design small molecules that are expected to block an ATPase catalytic pocket thus inhibit the enzymatic activity. Binding sites for various functional groups were identified in a series of molecular dynamics calculation. Their positions in the catalytic pocket were used as constraints in the Cambridge structural database search for molecules having the pharmacophores that interacted most strongly with the enzyme in a desired position. The subsequent MD simulations followed by calculations of binding energies of the designed molecules were compared to ATP identifying the most successful candidates, for likely inhibitors—molecules possessing two phosphonic acid moieties at distal ends of the molecule.     

Porphyrin system containing [2.2]paracyclophane units

Meso-tetrakis([2.2]paracyclophanyl)porphyrin was obtained from [2.2]paracyclophanecarbaldehyde and pyrrole. Replacement of phenyl groups in meso-tetraphenylporphyrin by paracyclophanyl substituents remarkably influences the electronic structure of the molecule, causing bathochromic shifts of all uv-vis absorption bands, and changing the ring current of the porphyrin core. The shifts in the electron spectrum are substantially greater than those observed for other porphyrin derivatives characterized by their extended π-electron systems, such as meso-tetrakis(2-phenylethenyl)porphyrin and meso-tetrakisbiphenylporphyrin.     

Subradial functions and compact embeddings

We investigate the compactness of embeddings of certain subsets of Nikol’skii-Besov spaces (defined on ? ^d ), consisting of essentially subradial functions, into Lebesgue spaces. Particular decay properties of radial functions are our main tool here.     

Low-energy elementary surface excitations of symmetric films of liquid4He atT=0 K

It is known that low-energy elementary excitations of symmetric films of liquid⁴He atT=0 K are characterized by a momentum q parallel to the surface and may be described by bound states. We have evaluated wave functions and energies of these states for both best short-ranged and optimal long-ranged correlations. Quantities of physical interest may be expressed in terms of these eigenstates and, in particular, for very small momenta (q<0.2 Å^–1) they are mainly determined by the contribution due to the lowest-lying one. We propose analytic expressions for the lowest-lying excitations and fluctuations in the long-wavelength limit. It is proved that in this limiting case, the excitation energy _LW(q) and the averaged static structure functionS _LW(q) should go linearly to zero asq0, whereas the averaged direct correlationX _LW ^Dg (q) should diverge at the origin as 1/q. It is shown that numerical solutions exhibit the expected long-wavelength behavior provided that optimal correlations are used. All these results are displayed in a series of figures and are discussed in detail.     

Evaluation by means of magneto-acoustic emission and Barkhausen effect of time and space distribution of magnetic flux density in ferromagnetic plate magnetized by a C-core

Experimental results are shown of magneto-acoustic emission (MAE) and Barkhausen effect (BE) for two ferritic steel plates of different dimensions. The paper presents preliminary results of modelling the MAE, based on the finite element method (FEM), taking into account the key role of the eddy currents. Explanations are suggested as to the effects of MAE peak maximum growth, shift, as well as the characteristic BE profiles at the bottom of the large plates.     

Determination of the optimum conditions for the synthesis of praseodymium(III) chloride

In the present work, we have synthesized praseodymium(III) chloride, PrCl₃, from the praseodymium oxide, Pr₆O₁₁, by dry method in the presence of ammonium chloride, NH₄Cl. This study includes the establishment of an assembly synthesis under inert gas. The thermal decomposing process of pure NH₄Cl was investigated by TG–DTG. The results showed that NH₄Cl begins to lose weight at 188 °C, large loss of weight ending at 302 °C when NH₄Cl is heated at the rate of 10 °C/min under N₂ atmosphere. For chlorination, NH₄Cl participates directly in the reaction, and HCl decomposed from NH₄Cl also contributes to the chlorination reaction. The influence of various synthesis parameters (temperature, contact time and chemical composition) on the reaction yield was studied, and the optimum conditions for synthesis were, thus, determined and discussed.     

Reaction of Lewisite-1 with Alcohols,Diols, and Thiols in Water—A Simple Method of Derivatization of Thiodiglycol

Reaction of 2-chlorovinyldichloroarsine (Lewisite-1) with alcohols, thiols, diols, and hydroxy thiols in water at 40°C has been examined. The expected derivatization products, dialkyl 2-chlorovinylarsonites or corresponding arsonodithiolites, were obtained with alcohols and thiols, whereas reactions with bifunctional diols and hydroxythiols produced analogous cyclic esters. All derivatives may be easily detected using gas chromatography. This reaction was found useful to easily transform bis(2-hydroxyethyl) sulfide (thiodiglycol), a sulfur mustard decomposition product, to a stable eight-membered cyclic arsonite derivative. After extraction with dichloromethane, the derivative may be easily and selectively detected using GC/MS at a 100 ppb level thiodiglycol content in water matrices, eliminating tedious evaporation of water and then silylation. This method may be applied to analyze Chemical Weapons Convention related environmental water samples.     

Genome-wide single-nucleotide polymorphism arrays demonstrate high fidelity of multiple displacement-based whole-genome amplification

Whole-genome DNA amplification by multiple displacement (MD-WGA) is a promising tool to obtain sufficient DNA amounts from samples of limited quantity. Using Affymetrix' GeneChip Human Mapping 10K Arrays, we investigated the accuracy and allele amplification bias in DNA samples subjected to MD-WGA. We observed an excellent concordance (99.95%) between single-nucleotide polymorphisms (SNPs) called both in the nonamplified and the corresponding amplified DNA. This concordance was only 0.01% lower than the intra-assay reproducibility of the genotyping technique used. However, MD-WGA failed to amplify an estimated 7% of polymorphic loci. Due to the algorithm used to call genotypes, this was detected only for heterozygous loci. We achieved a 4.3-fold reduction of noncalled SNPs by combining the results from two independent MD-WGA reactions. This indicated that inter-reaction variations rather than specific chromosomal loci reduced the efficiency of MD-WGA. Consistently, we detected no regions of reduced amplification, with the exception of several SNPs located near chromosomal ends. Altogether, despite a substantial loss of polymorphic sites, MD-WGA appears to be the current method of choice to amplify genomic DNA for array-based SNP analyses. The number of nonamplified loci can be substantially reduced by amplifying each DNA sample in duplicate.