Quantum and classical study of surface characterization by three-dimensional helium atom scattering

Exact time-dependent wavepacket calculations of helium atom scattering from model symmetric, chiral, and hexagonal surfaces are presented and compared with their classical counterparts. Analysis of the momentum distribution of the scattered wavepacket provides a convenient method to obtain the resulting energy and angle resolved scattering distributions. The classical distributions are characterized by standard rainbow scattering from corrugated surfaces. It is shown that the classical results are closely related to their quantum counterparts and capture the qualitative features appearing therein. Both the quantum and classical distributions are capable of distinguishing between the structures of the three surfaces.     

Comparison of impurities in charcoal sorbents found by neutron activation analysis

Neutron activation of gas samples in a reactor often requires a medium to retain sufficient amounts of the gas for analysis. Charcoal is commonly used to adsorb gas and hold it for activation; however, the amount of activated sodium in the charcoal after irradiation swamps most signals of interest. Neutron activation analysis was performed on several commonly available charcoal samples in an effort to determine the activation background. The results for several elements, including the dominant sodium element, are reported. It was found that ECN charcoal had the lowest elemental background, containing sodium at 2.65 ± 0.05 ppm, as well as trace levels of copper and tungsten.     

Rhodium-catalyzed enantioselective diboration of simple alkenes

Enantioselective catalytic reactions that operate directly on inexpensive unactivated alkenes are extraordinarily useful for the preparation of chiral organic building blocks and new materials. While a number of such processes have been developed, our ability to meet the intensifying demand for inexpensive stereochemically complex materials will require a significant expansion of practical catalytic asymmetric reaction methodology. In this regard, the rhodium-catalyzed enantioselective diboration reaction has been developed in order to address a number of extant problems in catalytic alkene transformation simultaneously. This process provides an enantiomerically enriched reactive dimetalated intermediate which can be converted to a variety of difunctional reaction products.     

ToF-SIMS imaging and depth profiling of HeLa cells treated with bromodeoxyuridine

Time of flight secondary ion mass spectrometry 2D images and molecular depth profiles of human HeLa cells treated with bromodeoxyuridine (BrdU) were acquired in the dual beam mode (Bi(3) (+) analysis beam, C(60) (+) etching beam). Several preparation protocols were investigated and were compared to a simple wash-and-dry method. The feasibility of using C(60) to clean the samples prior to imaging with Bi was also investigated quantitatively by calibrating full depth profiles of the cells using atomic force microscopy. BrdU was used as a marker for the cell nucleus, facilitating identification and localization of sub-cellular features during depth profiling. Results show that C(60) can be used to remove the surface contamination and to access different layers within the cells for 2D imaging. For a 1 nA, 10 keV C(60) (+) beam incident at 45° and rastered over a 500 × 500 μm(2) area, ~1 nm of biological material was sputtered every second. Our results show that HeLa cells were completely removed after etching with 1.3×10(15) C(60) (+) ions per cm(2), giving an average etching rate of 3.9 nm for every 10(13) C(60) per cm(2) at 10 keV and 45° incidence.     

The enantioselective synthesis of alpha-amino acid derivatives via organoboranes

Optically active (S)-alpha-amino acids are prepared in 54-95% ee (12 cases) by reaction of the Schiff base acetate of glycine tert-butyl ester with B-alkyl-9-BBN derivatives in the presence of the Cinchona alkaloid, cinchonidine, and base. The enantiomeric (R)-alpha-amino acids are available in 59-92% ee (3 cases) by using cinchonine as the chiral control element.     

Catalytic asymmetric carbohydroxylation of alkenes by a tandem diboration/Suzuki cross-coupling/oxidation reaction

[reaction: see text] Chiral nonsymmetric 1,2-diboron adducts are generated by catalytic enantioselective diboration. Oxidation of these adducts provides 1,2-diols in good yield. Alternatively, 1,2-diboron compounds may be reacted, in situ, with aryl halides wherein the less hindered C-B bond participates in cross-coupling. The remaining C-B bond is then oxidized in the reaction workup thereby allowing for net asymmetric carbohydroxylation of alkenes in a tandem one-pot diboration/Suzuki coupling/oxidation sequence.     

Correlation between host-guest binding and host amplification in simulated dynamic combinatorial libraries

We present a versatile computer model of diverse dynamic combinatorial libraries, and examine how molecular recognition between library members and a template can be used to amplify the best binders. The correlation between host-guest binding and amplification was examined for a set of 50 libraries with >300 components each over a wide range of template and building block concentrations. Depending on these concentrations correlations vary from poor (when using a large excess of template) to good (for very dilute libraries and/or substoichiometric template concentrations), highlighting the need to choose the experimental conditions for dynamic combinatorial libraries thoughtfully.     

Modeling of solvent flow effects in enzyme catalysis under physiological conditions

A stochastic model for the dynamics of enzymatic catalysis in explicit, effective solvents under physiological conditions is presented. Analytically-computed first passage time densities of a diffusing particle in a spherical shell with absorbing boundaries are combined with densities obtained from explicit simulation to obtain the overall probability density for the total reaction cycle time of the enzymatic system. The method is used to investigate the catalytic transfer of a phosphoryl group in a phosphoglycerate kinase-ADP-bis phosphoglycerate system, one of the steps of glycolysis. The direct simulation of the enzyme-substrate binding and reaction is carried out using an elastic network model for the protein, and the solvent motions are described by multiparticle collision dynamics which incorporates hydrodynamic flow effects. Systems where solvent-enzyme coupling occurs through explicit intermolecular interactions, as well as systems where this coupling is taken into account by including the protein and substrate in the multiparticle collision step, are investigated and compared with simulations where hydrodynamic coupling is absent. It is demonstrated that the flow of solvent particles around the enzyme facilitates the large-scale hinge motion of the enzyme with bound substrates, and has a significant impact on the shape of the probability densities and average time scales of substrate binding for substrates near the enzyme, the closure of the enzyme after binding, and the overall time of completion of the cycle.     

Dynamic combinatorial libraries for the recognition of heavy metal ions

We present the use of hydrazone dynamic combinatorial libraries (DCLs) to identify macrocyclic receptors that are selective for alkaline earth metal ions over alkali metal ions. In particular, the toxic heavy metal ions Sr(2+) and Ba(2+) induce characteristic changes in the DCLs. Four macrocycles were isolated and characterised by LCMS, HRMS, NMR and X-ray crystallography; binding studies by UV-Vis spectroscopy confirm the selectivity observed in the DCLs.     

Synthesis, characterization, and glutathionylation of cobalamin model complexes [Co(N4PyCO2Me)Cl]Cl2 and [Co(Bn-CDPy3)Cl]Cl2

Synthetic Co(III) complexes containing N5 donor sets undergo glutathionylation to generate biomimetic species of glutathionylcobalamin (GSCbl), an important form of cobalamin (Cbl) found in nature. For this study, a new Co(III) complex was synthesized derived from the polypyridyl pentadentate N5 ligand N4PyCO(2)Me (1). The compound [Co(N4PyCO(2)Me)Cl]Cl(2) (3) was characterized by X-ray crystallography, UV-vis, IR, (1)H NMR, and (13)C NMR spectroscopies and mass spectrometry (HRMS). Reaction of 3 with glutathione (GSH) in H(2)O generates the biomimetic species [Co(N4PyCO(2)Me)(SG)](2+) (5), which was generated in situ and characterized by UV-vis and (1)H NMR spectroscopies and HRMS. (1)H NMR and UV-vis spectroscopic data are consistent with ligation of the cysteine thiolate of GSH to the Co(III) center of 5, as occurs in GSCbl. Kinetic analysis indicated that the substitution of chloride by GS(-) occurs by a second-order process [k(1) = (10.1 ± 0.7) × 10(-2) M(-1) s(-1)]. The observed equilibrium constant for formation of 5 (K(obs) = 870 ± 50 M(-1)) is about 3 orders of magnitude smaller than for GSCbl. Reaction of the Co(III) complex [Co(Bn-CDPy3)Cl]Cl(2) (4) with GSH generates glutathionylated species [Co(Bn-CDPy3)(GS)](2+) (6), analogous to 5. Glutathionylation of 4 occurs at a similar rate [k(2) = (8.4 ± 0.5) × 10(-2) M(-1) s(-1)], and the observed equilibrium constant (K(obs) = 740 ± 47 M(-1)) is slightly smaller than for 5. Glutathionylation showed a significant pH dependence, where rates increased with pH. Taken together, these results suggest that glutathionylation is a general reaction for Co(III) complexes related to Cbl.