Adaptive local grid refinement algorithms for finite-element collocation

An adaptive grid refinement procedure allows accurate solutions to advection-dominated, time-dependent flows using finite-element collocation. The technique relies on a data structure that is readily amenable to parallel computing. The paper discusses computational aspects of the method.     

Methodology for the preparation of C1-monoalkylated 1,2-dihydro[C70)] derivatives: formation of the "other" regioisomer

Deprotonation of 1,2-C(70)H(2) with TBAOH, followed by alkylation with methyl bromoacetate, results in formation of a C1-monoalkylated 1,2-dihydro-C(70) derivative. The position of the alkyl group (C1) was established by NMR spectroscopy and comparison with literature spectra of C2-monoalkylated analogs. Presumably, C1-alkylation is the major process due to selective deprotonation of 1,2-C(70)H(2) at C1. Substitution of benzyl bromide for methyl bromoacetate results in rapid dialkylation, unless the amount of base is carefully controlled, in which case C1-monobenzylation is the major process. This methodology for alkylation at C1 is complimentary to methods for the C2-monoalkylation of C(70) with Zn and methyl bromoacetate.     

Design,synthesis, and evaluation of 6-carboxyalkyl and 6-phosphonoxyalkyl derivatives of 7-oxo-8-ribitylaminolumazines as inhibitors of riboflavin synthase and lumazine synthase

A series of 6-carboxyalkyl and 6-phosphonoxyalkyl derivatives of 7-oxo-8-D-ribityllumazine were synthesized as inhibitors of both Escherichia coli riboflavin synthase and Bacillus subtilis lumazine synthase. The compounds were designed to bind to both the ribitylpurine binding site and the phosphate binding site of lumazine synthase. In the carboxyalkyl series, maximum activity against both enzymes was observed with the 3'-carboxypropyl compound 22. Lengthening or shortening the chain linking the carboxyl group to the lumazine by one carbon resulted in decreased activity. In the phosphonoxyalkyl series, the 3'-phosphonoxypropyl compound 33 was more potent than the 4'-phosphonoxybutyl derivative 39 against lumazine synthase, but it was less potent against riboflavin synthase. Molecular modeling suggested that the terminal carboxyl group of 6-(3'-carboxypropyl)-7-oxo-8-D-ribityllumazine (22) may bind to the side chains of Arg127 and Lys135 of the enzyme. A hypothetical molecular model was also constructed for the binding of 6-(2'-carboxyethyl)-7-oxolumazine (15) in the active site of E. coli riboflavin synthase, which demonstrated that the active site could readily accommodate two molecules of the inhibitor.     

Synthesis of spiro-fused (C5)-isoxazolino-(C4)-pyrazolones (1-oxa-2,7,8-triazaspiro[4,4]-2,8-dien-6-ones) via 1,3-dipolar cycloaddition and cycloelimination

An efficient and selective method for the synthesis of spiro-fused (C5)-isoxazolino-(C4)-pyrazolones (C) is reported. The process consists of utilizing the Baylis-Hillman reaction-or a quicker, stepwise MAC procedure-to give I followed by 1,3-dipolar cycloaddition and Swern oxidation to give beta-ketoesters H, which were condensed with hydrazine derivatives to provide hydrazones that underwent cycloelimination. These novel spiro-fused (C5)-isoxazolino-(C4)-pyrazolones were confirmed by spectroscopic analysis as well as single-crystal X-ray of 5. We also concluded that all condensations/cycloeliminations, except with hydrazine itself, were more effective with catalysts or higher reaction temperatures. For example, TiCl(4) was an efficient catalyst for hydrazone formation and cycloelimination with methylhydrazine, while phenyl-, benzyl-, and (4-methoxyphenyl)hydrazine reacted effectively without catalyst in refluxing xylene.     

Energetics of the Preyssler anion's molecular orbitals: quantifying the effect of the encapsulated-cation's charge

The ground state electronic properties of metal-exchanged Preyssler heteropolyoxoanions [M(n+)P(5)W(30)O(110)](n-15), in which the encapsulated M(n+) ions are the spherical, diamagnetic ions Na(+), Ca(2+), Sr(2+), Y(3+), La(3+) and Th(4+), are studied using a combination of electrochemical, optical, and NMR experiments. We have designed experiments that focus on the influence of the charge (n) of the encapsulated cations, which themselves have no redox response, and its effect upon the W-O framework MOs. As n increases, the cluster anions accept electrons into their LUMOs with increasing ease, and their lowest-energy LMCT bands reveal a corresponding blue shift, which is indicative of an increase of the LUMO-HOMO energy splitting with increasing n. (183)W NMR spectra are used to identify the atomic origin of the LUMO states, which are shown to be composed primarily of orbitals from the ring of 5 W atoms near M(n+). The cation charge correlates directly and linearly with the half-wave potentials of the first redox couples, the LMCT band energies, and the W chemical shifts. We have combined this suite of experimental results to construct an energy level diagram of the frontier MOs for the Preyssler cluster anions. In so doing, we provide a fundamental perspective that is not otherwise available on the cation's role with specific regard to the electronic behavior of the W-O orbitals. These results are expected to provide benchmarking information as theorists begin to study these large POM systems.     

Synthesis of the ladybug alkaloids (±)-propyleine and (±)-isopropyleine. Modification of the published structure of propyleine

The total syntheses of the ladybug alkaloids (±)-propyleine and (±)-isopropyleine are described. Evidence that the alkaloid propyleine is actually a rapidly interconverting mixture of propyleine and a previously unknown isomer isopropyleine is presented.     

A novel anthracenyl tagged protecting group for "phase-switching" applications in parallel synthesis

A new "phase-switching" protecting group 1 that facilitates the parallel synthesis of carboxylic acids, esters, and carboxamides is described. Its use permits chemistries to be performed in solution, which may be conveniently monitored with conventional analytical techniques, followed by subsequent immobilization onto a solid-phase support to aid compound purification. Carboxylic acids, esters, and carboxamides are then cleaved from the solid support following activation of the "safety-catch" and treatment with the desired nucleophile.     

Effects of deformability, uneven surface charge distributions, and multipole moments on biocolloid electrophoretic migration

Liposomes have been widely used as cellular and bioparticle mimics due to their lipid bilayer structure and relative ease of production and manipulation. Such biocolloids are frequently characterized by capillary electrophoresis (CE), which promises a wealth of information about such properties as surface charge, composition, and rigidity. The applicability of this information is somewhat limited, however, since it is interpreted with colloidal theories that do not account for the unique properties of biocolloids. In this work, the effects of deformability, mobile surface charges, intrinsic polarizability, and uneven surface charge distributions are incorporated into colloidal theories in order to better model the electrophoretic behaviors of liposomes.     

Engineering cytochrome P-450s

Cytochrome P-450 isozymes represent a critical component of nature’s spectrum of detoxification catalysts that could be exploited for bioremediation. The ethanol-inducible human cytochrome P-450 2E1 serves as a model eukaryotic P-450 that complements the bacterial P-450 cam in dehalogenation and detoxification of environmental pollutants. We explored the construction of novel chimeric P-450s using cytochrome P-450 camC and 2E1 genes. For construction of chimera 1 (478 amino acids, 55.14 kDa), 145 amino acids from the N-terminus of P-450 2E1 protein (493 amino acids, 56.84 kDa) were replaced with 130 amino acids from the N-terminus of P-450 camC protein (415 amino acids, 46.66 kDa). In chimera 2 (525 amino acids, 60.24 kDa) the strategy involves replacement of 28 amino acids in the C-terminus of chimera 1 with 75 amino acids from the C-terminus of P-450 camC gene. Homology models of both the chimeric proteins were developed using SWISS-MODEL based on the known crystal structure of cytochrome P-450 camC, BM-3, 1DT6A, and 2C17A. The models indicated that the proposed heme-binding site was intact, which is inevitable for catalytic activity of cytochrome P-450s. The expression of chimera 1 and 2 genes in Escherichia coli DH5α was evident from light-pink cell pellets, protein band in sodium dodecyl sulfate polyacrylamide gel electrophoresis, and diagnostic carbon monoxide-difference spectra. Our studies show that strategies can be developed to exploit the natural diversity of the P-450 superfamily to generate chimeric biocatalysts that would provide new templates amenable to directed evolution.