Electrophoresis simulations using Chebyshev pseudo-spectral method on a moving mesh

We present the implementation and demonstration of the Chebyshev pseudo-spectral method coupled with an adaptive mesh method for performing fast and highly accurate electrophoresis simulations. The Chebyshev pseudo-spectral method offers higher numerical accuracy than all other finite difference methods and is applicable for simulating all electrophoresis techniques in channels with open or closed boundaries. To improve the computational efficiency, we use a novel moving mesh scheme that clusters the grid points in the regions with poor numerical resolution. We demonstrate the application of the Chebyshev pseudo-spectral method on a moving mesh for simulating nonlinear electrophoretic processes through examples of isotachophoresis (ITP), isoelectric focusing (IEF), and electromigration-dispersion in capillary zone electrophoresis (CZE) at current densities as high as 1000 A/m. We also show the efficacy of our moving mesh method over existing methods that cluster the grid points in the regions with large concentration gradients. We have integrated the adaptive Chebyshev pseudo-spectral method in the open-source SPYCE simulator and verified its implementation with other electrophoresis simulators.     

Synthesis and absolute configuration of (1S,8S)-as-hydrindacene-1,8-diol as determined by the circular dichroism exciton chirality method

2,3,6,7-Tetrahydro-as-indacene-1,8-dione 4 was prepared in 4 steps starting from 2-methyl-furan by modification of a literature procedure. Appliance of Noyori’s asymmetric transfer hydrogenation, resulted in (1S,8S)-1,2,3,6,7,8-hexahydro-as-indacene-1,8-diol 5 in high yield (81%) and excellent enantioselectivity (>99% ee) or (8S)-8-hydroxy-3,6,7,8-tetrahydro-2H-as-indacen-1-one 6 in moderate yield (58%) and equally high enantioselectivity (98.5% ee), depending on the conditions. The asymmetric reduction was expected to yield the (S)-alcohols using the (S,S)-Ts-DPEN ligand, which was confirmed by the appliance of the exciton chirality method on the corresponding bis(p-dimethylamino)benzoate 7.     

GRECP/MRD‐CI calculations on the Hg atom and HgH molecule

Multireference single‐ and double‐excitation configuration interaction (MRD‐CI) calculations of transition energies for the Hg atom and spectroscopic constants for the HgH molecule are carried out with the generalized relativistic effective core potential (GRECP) method. A new selection criterium for the reference configurations is discussed. The calculated spectroscopic constants are compared with experimental data and results of calculations of other groups. Improvement of accuracy is mainly observed for bond lengths from the GRECP/MRD‐CI calculations (without applying the T = 0 correction) with respect to the results of other groups. Analysis of the quality of the approximations employed is carried out. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002     

Reactivity ratios in conventional and nickel-mediated radical copolymerization of methyl methacrylate and functionalized methacrylate monomers

Copolymerization of an excess of methyl methacrylate (MMA) relative to 2-hydroxyethyl methacrylate (HEMA) was carried out in toluene at 80 °C according to both conventional and controlled Ni-mediated radical polymerizations. Reactivity ratios were derived from the copolymerization kinetics using the Jaacks method for MMA and integrated conversion equation for HEMA (r_MMA = 0.62 ± 0.04; r_HEMA = 2.03 ± 0.74). Poly(ethylene glycol) α-methyl ether, ω-methacrylate (PEGMA, M_n = 475 g mol⁻¹) was substituted for HEMA in the copolymerization experiments and reactivity ratios were also determined (r_MMA = 0.75 ± 0.07; r_PEGMA ∼ 1.33). Both the functionalized comonomers were consumed more rapidly than MMA indicating the preferred formation of heterogeneous bottle-brush copolymer structures with bristles constituted by the hydrophilic (macro)monomers. Reactivity ratios for nickel-mediated living radical polymerization were comparable with those obtained by conventional free radical copolymerization. Interactions between functional monomers and the catalyst (NiBr₂(PPh₃)₂) were observed by ¹H NMR spectroscopy.     

Kinetics of CO oxidation on the surface of heterophase catalysts. Modeling by the Monte Carlo method

The Monte Carlo method has been used to simulate CO oxidation on a lattice consisting of various alternating patches: M1, where s(CO)>s(O₂) and M2, where s(CO)2). The reaction is shown to proceed over all the surface at low temperature as CO_ads spillover from M1 to M2 and backwards.     

Electronic structure and conformational flexibility of 1,2-dihydropyridine, 1,2- and 1,6-dihydropyrimidines,and their ylide derivatives

Molecular and electronic structures of 1,2-dihydropyridine, 1,2- and 1,6-dihydropyrimidine, and their oxo, imino, and methylene derivatives were studied by the semiempirical quantum-chemical AM1 method. In all compounds, the heterocycle exhibits a high conformational flexibility. The transition from a planar equilibrium conformation to a distorted sofa conformation with the =C-NH-C-C(N)= torsion angle of ±20° causes an increase in the energy by less than 1.7 kcal mol^–1. All molecules have similar -electronic structures, which, apparently, determines the similarity in their conformational behavior. The bending strain and the nonaromatic character of the cyclic -system are the factors that stabilize the nonplanar conformation of the ring in unsubstituted dihydroazines and ylide derivatives, respectively.Translated fromIzvestiva Akademii Nauk. Seriya Khimicheskaya, No. 8, pp. 1934–1937, August, 1996.     

Grouped coordinate minimization using Newton's method for inexact minimization in one vector coordinate

Letf(x,y) be a function of the vector variablesx R ⁿ andy R ^m. The grouped (variable) coordinate minimization (GCM) method for minimizingf consists of alternating exact minimizations in either of the two vector variables, while holding the other fixed at the most recent value. This scheme is known to be locally,q-linearly convergent, and is most useful in certain types of statistical and pattern recognition problems where the necessary coordinate minimizers are available explicitly. In some important cases, the exact minimizer in one of the vector variables is not explicitly available, so that an iterative technique such as Newton's method must be employed. The main result proved here shows that a single iteration of Newton's method solves the coordinate minimization problem sufficiently well to preserve the overall rate of convergence of the GCM sequence.The authors are indebted to Professor R. A. Tapia for his help in improving this paper.     

Thermal decomposition of sodium nitrite and sodium nitrate pre-adsorbed on TiO2 surfaces

The thermal decomposition of sodium nitrite or nitrate pre-adsorbed upon TiO₂ surfaces has been investigated by employing several techniques as infrared spectroscopy (IR) and temperature programmed desorption in conjunction with mass spectrometry analysis (TPD-MS) to study the features observed during these thermal decompositions. Differential thermal analysis (DTA) in combination with X-ray diffraction analysis (XRD) were used to investigate the possibility of a solid state chemical reaction between the solid products originated from the thermal decomposition of the pre-adsorbed species and the TiO₂. On the basis of our results, various characteristic features of these thermal decomposition reactions will be discussed.This work was supported by JUNTA DE ANDALUCIA (financial support for research groups/1990).     

New Methods for the Synthesis of Glycosides and Oligosaccharides—Are There Alternatives to the Koenigs-Knorr Method? [New Synthetic Methods (56)]

Glycoproteins, glycolipids, and glycophospholipids (glycoconjugates) are components of membranes. The oligosaccharide residue is responsible for intercellular recognition and interaction; it acts as a receptor for proteins, hormones, and viruses and governs immune reactions. These significant activities have stimulated interest in oligosaccharides and glycoconjugates. With their help it should be possible to clarify the molecular basis of these phenomena and to derive new principles of physiological activity. Major advances in the synthesis of oligosaccharides have been made by the use of the Koenigs-Knorr method, in which glycosyl halides in the presence of heavy-metal salts are employed to transfer the glycosyl group to nucleophiles. The disadvantages of this procedure have led to an intensive search for new methods. Such methods will be discussed in this article. Emphasis is placed on glycoside and saccharide formation by 1-O-alkylation, on the trichloroacetimidate method, and on activation through the formation of glycosylsulfonium salts and glycosyl fluorides.     

Time-resolved fluorescence analysis of the mobile flavin cofactor in p -hydroxybenzoate hydroxylase

Conformational heterogeneity of the FAD cofactor in p-hydroxybenzoate hydroxylase (PHBH) was investigated with time-resolved polarized flavin fluorescence. For binary enzyme/substrate (analogue) complexes of wild-type PHBH and Tyr222 mutants, crystallographic studies have revealed two distinct flavin conformations; the ‘in’ conformation with the isoalloxazine ring located in the active site, and the ‘out’ conformation with the isoalloxazine ring disposed towards the protein surface. Fluorescence-lifetime analysis of these complexes revealed similar lifetime distributions for the ‘in’ and ‘out’ conformations. The reason for this is twofold. First, the active site of PHBH contains various potential fluorescence-quenching sites close to the flavin. Fluorescence analysis of uncomplexed PHBH Y222V and Y222A showed that Tyr222 is responsible for picosecond fluorescence quenching free enzyme. In addition, other potential quenching sites, including a tryptophan and two tyrosines involved in substrate binding, are located nearby. Since the shortest distance between these quenching sites and the isoalloxazine ring differs only little on average, these aromatic residues are likely to contribute to fluorescence quenching. Second, the effect of flavin conformation on the fluorescence lifetime distribution is blurred by binding of the aromatic substrates: saturation with aromatic substrates induces highly efficient fluorescence quenching. The flavin conformation is therefore only reflected in the small relative contributions of the longer lifetimes.