Investigations with the finite element method on the Cyber 205

We are trying to investigate systematically the application of the finite element method (FEM) for solving the Schrödinger equation. The present paper is devoted to the calculation of vibrational transition probabilities for the collinear reactive system A + BC (i.e. H+H₂ and their isotopes). The calculations are fully two-dimensional and the results are compared with earlier FEM calculations and conventional basis set expansion methods using the the R-matrix or S-matrix propagation.We made extensive analysis of FEM on the vector-computer Cyber 205 and developed a vector code for the efficient use in two dimensions, so that in the near future applications even in three dimensions will be possible.For the hydrogen exchange reactions we investigated the following isotope combinations: (a) H + H₂, b) H + DH, D + HD and H + MuH (symmetric reaction), (c) D + HH, H + DD and Mu + DD (asymmetric reaction). We calculated the transition probabilities for up to five open vibrational channels and found excellent agreement with known exact values.     

Protease sensors for bioimaging

Optical imaging of specific molecular targets and pathways in vivo has recently become possible through continued developments in imaging equipment, reconstruction algorithms, and more importantly the availability of imaging reporter molecules. These reporter molecules encompass photoproteins expressed in vivo and exogenously administered probes detectable by fluorescence and/or bioluminescence imaging. One particularly enticing aspect of optical imaging is the ability to design activatible probes with inherent amplification. This review summarizes our experience in developing novel near-infrared fluorescent (NIRF) imaging agents that report on protease activities. These agents are designed to be biocompatible, highly activatible, and able to produce bright NIRF following protease cleavage.     

Molecular fluorescence excitation-emission matrices relevant to tissue spectroscopy

In vivo and ex vivo studies of fluorescence from endogenous and exogenous molecules in tissues and cells are common for applications such as detection or characterization of early disease. A systematic determination of the excitation-emission matrices (EEM) of known and putative endogenous fluorophores and a number of exogenous fluorescent photodynamic therapy drugs has been performed in solution. The excitation wavelength range was 250-520 nm, with fluorescence emission spectra collected in the range 260-750 nm. In addition, EEM of intact normal and adenomatous human colon tissues are presented as an example of the relationship to the EEM of constituent fluorophores and illustrating the effects of tissue chromophore absorption. As a means to make this large quantity of spectral data generally available, an interactive database has been developed. This currently includes EEM and also absorption spectra of 35 different endogenous and exogenous fluorophores and chromophores and six photosensitizing agents. It is intended to maintain and extend this database in the public domain, accessible through the Photochemistry and Photobiology website (http://www.aspjournal. com/).     

Categorical quasivarieties revisited

Quasivarieties (and varieties) which are categorical in some power not less than the power of their language have been completely characterized by S. Givant [6], [7] and independently by E. A. Palyutin [11], [12]. These classes fall into two radically different families. A class in the first family is derived from the class of permutational representations of a group. Its members are [n]-th powers of algebras whose operations are unary, for some fixed positive integern. A class in the second family consists of affine algebras. Its members are polynomially equivalent (but not usually definitionally equivalent) to modules over a ring which is isomorphic to the ring ofn-by-n matrices with entries in a division ring.The general results are faithfully represented in the family of-categorical quasivarieties of countable type. Each of them is generated by a finite algebra, and the results can be viewed as very interesting facts about finite algebras and the classes they generate. In this paper, we offer simple new characterizations of-categorical quasivarieties and varieties of countable type. Our arguments are distinguished by the absence of any sophisticated model theory. In the beginning we use some very basic model theory, but after that we find that combinatorial reasoning about finite sets and elementary algebraic arguments, combined with two classical theorems describing the structure of finite simple rings and their modules, suffice to derive the results. Theorems 3.1 and 4.12 combine to give the characterization of-categorical quasivarieties. Theorems 3.2 and 4.13 combine to give the characterization of-categorical varieties.The heart of this paper is §2. There we prove that a nontrivial algebra of least cardinality in an-categorical quasivariety (which must generate the class) is a finite tame algebra. Tameness is the principal tool used in a relatively quick and painless proof that the generating algebra must be affine or an [n]-th power of a unary algebra. The concept of a tame algebra was introduced in [9] where we proved, among other things, that finite simple algebras are tame. When we had gained some experience with this concept, it became clear to us that the arguments in this present paper should exist (and it didn't take long to find them).The author thanks the referee for a thoughtful critique of the first submitted version of this paper.Research supported by United States National Science Foundation grant MCS 8103455.Presented by W. Taylor.     

The high resolution mass spectrum of 2-acetamido-1,3,4,6-tetra-O-acetyl-2-deoxy-α-D-glucopyranose

2-Acetamido-1,3,4,6-tetra-O-acetyl-2-deoxy-α-D-glucopyranose (I), and its analogs specifically mono (trideuterioacetylated) at O-1 (III), at N-2 (II), at O-4 (IV) and at O-6 (V), have been examined by high-resolution mass spectrometry. From the elemental compositions of the fragment ions, the mass-number shifts resulting from deuterium incorporation and analysis of metastable transitions, it has been possible to specify in detail the fragmentation pathways undergone by this molecule. The principal degradations of I proceed by initial rapid decomposition of the molecular ion (whose intensity is insignificant) by three routes: (i) by loss of the C-1 acetoxyl group as a radical to give the glycosyl cation (a), (ii) by loss of the 1-acetyl group as a radical to give an acyclic ion m/e 346 (b) and (iii) by loss of a C-6 fragment and acetic acid derived from the 3-acetate group to give m/e 241 (c).     

Trends in lipase-catalyzed asymmetric access to enantiomerically pure/enriched compounds

Over the last few years, there has been a dramatic increase in the number of publications in the field of lipase-catalyzed reactions performed in common organic solvents, ionic liquids or even non-conventional solvents. A fairly large percentage of these publications have emerged from organic chemists who have recognized the potential of biocatalysis as a viable and popular technique in organic synthesis. Considerable research has shown that reactions catalyzed by enzymes are more selective and efficiently performed than many of their analogues in the organic chemistry laboratory. This review article focuses on some of the recent developments in the rapidly growing field of lipase-catalyzed asymmetric access to enantiomerically pure/enriched compounds. The literature search is dated back to the last five years and covers some comprehensive examples.     

Reactions of N-silylphosphoranimines with alcohols: synthesis and structure of cyclotriphosphazenes with nongeminal methyl and phenyl substituents

The reactions of Me(3)SiN=P(OR")RR'(R" = Ph, CH(2)CF(3); R, R' = Me, Ph) with alcohols were investigated. With nonequivalent amounts of CF(3)CH(2)OH, the reactions produced high yields of the cyclic phosphazene (Me(2)PN)(3) and both the cis and trans isomers of nongeminally substituted [(Ph)(Me)PN](3). The isomers of this new cyclic phosphazene were separated by column chromatography and characterized by NMR and IR spectroscopy, elemental analysis, and X-ray crystallography. Crystals of the cis isomer 6a have a monoclinic crystal system, while the trans isomer 6b has a triclinic crystal system with two different molecules in an asymmetric unit. The bond lengths and bond angles are very similar to those of the simpler cyclic trimers (Me(2)PN)(3) and (Ph(2)PN)(3.) A likely pathway for the formation of these compounds is discussed.     

Use of the tubulin bound paclitaxel conformation for structure-based rational drug design

A new computational docking protocol has been developed and used in combination with conformational information inferred from REDOR-NMR experiments on microtubule bound 2-(p-fluorobenzoyl)paclitaxel to delineate a unique tubulin binding structure of paclitaxel. A conformationally constrained macrocyclic taxoid bearing a linker between the C-14 and C-3'N positions has been designed and synthesized to enforce this "REDOR-taxol" conformation. The novel taxoid SB-T-2053 inhibits the growth of MCF-7 and LCC-6 human breast cancer cells (wild-type and drug resistant) on the same order of magnitude as paclitaxel. Moreover, SB-T-2053 induces in vitro tubulin polymerization at least as well as paclitaxel, which directly validates our drug design process. These results open a new avenue for drug design of next generation taxoids and other microtubule-stabilizing agents based on the refined structural information of drug-tubulin complexes, in accordance with typical enzyme-inhibitor medicinal chemistry precepts.     

Ab initio investigations of the bound rovibrational levels of NeH 2 + , NeHD+, and NeD 2 +

Summary Bound rovibrational levels have been calculated for NeH ₂ ⁺ , NeHD⁺, and NeD ₂ ⁺ using three recent fits to an accurateab initio PES. The NeH ₂ ⁺ molecule behaves essentially as a linear molecule, the predicted rotational constant is 2.57 cm^–1. The fundamental frequencies are 811, 1189, and 1748 cm^–1 for the Ne-H ₂ ⁺ stretch, the Ne-H ₂ ⁺ bend and H ₂ ⁺ stretching modes, respectively.Dedicated to the 60th birthday of Prof. W. Kutzelnigg, Bochum     

Microfluidic devices for energy conversion: planar integration and performance of a passive, fully immersed H2-O2 fuel cell

We describe the fabrication and performance of a passive, microfluidics-based H2-O2 microfluidic fuel cell using thin film Pt electrodes embedded in a poly(dimethylsiloxane) (PDMS) device. The electrode array is fully immersed in a liquid electrolyte confined inside the microchannel network, which serves also as a thin gas-permeable membrane through which the reactants are fed to the electrodes. The cell operates at room temperature with a maximum power density of around 700 microW/cm(2), while its performance, as recorded by monitoring the corresponding polarization curves and the power density plots, is affected by the pH of the electrolyte, its concentration, the surface area of the Pt electrodes, and the thickness of the PDMS membrane. The best results were obtained in basic solutions using electrochemically roughened Pt electrodes, the roughness factor, R(f), of which was around 90 relative to a smooth Pt film. In addition, the operating lifetime of the fuel cell was found to be longer for the one using higher surface area electrodes.