An investigation of enhanced secondary ion emission under Au n + (n=1–7) bombardment

We investigate the mechanism of the nonlinear secondary ion yield enhancement using Au(n)+ (n = 1, 2, 3, 5, 7) primary ions bombarding thin films of Irganox 1010, DL-phenylalanine and polystyrene on Si, Al, and Ag substrates. The largest differences in secondary ion yields are found using Au+, Au2+, and Au3+ primary ion beams. A smaller increase in secondary ion yield is observed using Au5+ and Au7+ primary ions. The yield enhancement is found to be larger on Si than on Al, while the ion yield is smaller using an Au+ beam on Si than on Al. Using Au(n)+ ion structures obtained from Density Functional Theory, we demonstrate that the secondary yield enhancement is not simply due to an increase in energy per area deposited into the surface (energy deposition density). Instead, based on simple mechanical arguments and molecular dynamics results from Medvedeva et al, we suggest a mechanism for nonlinear secondary ion yield enhancement wherein the action of multiple concerted Au impacts leads to efficient energy transfer to substrate atoms in the near surface region and an increase in the number of secondary ions ejected from the surface. Such concerted impacts involve one, two, or three Au atoms, which explains well the large nonlinear yield enhancements observed going from Au+ to Au2+ to Au3+ primary ions. This model is also able to explain the observed substrate effect. For an Au+ ion passing through the more open Si surface, it contacts fewer substrate atoms than in the more dense Al surface. Less energy is deposited in the Si surface region by the Au+ primary ion and the secondary ion yield will be lower for adsorbates on Si than on Al. In the case of Au(n)+ the greater density of Al leads to earlier break-up of the primary ion and a consequent reduction in energy transfer to the near-surface region when compared with Si. This results in higher secondary ion yields and yield enhancements on silicon than aluminum substrates.     

Cofactor-dependent enzyme catalysis in functionalized ionic solvents

Functionalized, hydrogen-bonding ionic liquids have been successfully evaluated as media for the performance of cofactor-dependent enzyme catalysed oxidations; the effects of incorporating hydroxyl groups into both the cation and anion have been studied and the dependence of activity upon water content has been evaluated.     

Enzymic determination of cerebrospinal fluid lipid fractions

Colorimetric peroxidase-coupled procedures for the determination of several cerebrospinal fluid (CSF) lipid classes are described. These methods were modified to increase the effectiveness of each cerebrospinal fluid lipid assay by using the sample as the primary diluent for a highly concentrated reagent in an inverse concentration technique. Direct enzymic assays for the determination of CSF cholesterol (free and total), choline phospholipids, and triglycerides were adapted from existing assays to require less than 0.5 ml of sample per assay. This made determinations of the several lipid analytes possible even when samples were from pediatric specimens. In a study model, 51 pediatric CSF samples were analyzed for these lipid constituents. Mean values and standard deviations were determined. Within and between-run studies were performed by sampling from a pool of cerebrospinal fluid specimens. Within-run coefficients of variation for the several proposed procedures were less than 3% while the between-run findings for all of the procedures were less than 5%.     

OptiDock: virtual HTS of combinatorial libraries by efficient sampling of binding modes in product space

Products from combinatorial libraries generally share a common core structure that can be exploited to improve the efficiency of virtual high-throughput screening (vHTS). In general, it is more efficient to find a method that scales with the total number of reagents (Sigma growth) rather with the number of products (Pi growth). The OptiDock methodology described herein entails selecting a diverse but representative subset of compounds that span the structural space encompassed by the full library. These compounds are docked individually using the FlexX program (Rarey, M.; Kramer, B.; Lengauer, T.; Klebe, G. J. Mol. Biol. 1995, 251, 470-489) to define distinct docking modes in terms of reference placements for combinatorial core atoms. Thereafter, substituents in R-cores (consisting of the core structure substituted at a single variation site) are docked, keeping the core atoms fixed at the coordinates dictated by each reference placement. Interaction energies are calculated for each docked R-core with respect to the target protein, and energies for whole compounds are calculated by finding the reference core placement for which the sum of corresponding R-core energies is most negative. The use of diverse whole compounds to define binding modes is a key advantage of the protocol over other combinatorial docking programs. As a result, OptiDock returns better-scoring conformers than does serially applied FlexX. OptiDock is also better able to find a viable docked pose for each library member than are other combinatorial approaches.     

Renner-Teller vibronic analysis for a tetra-atomic molecule. I. The effective Hamiltonian and matrix elements

The effective vibronic Hamiltonian for a linear tetra-atomic molecule in a Pi state has been investigated. In addition to the usual vibrational and Renner-Teller coupling terms, the bending mode anharmonicity, spin-orbit coupling, and Fermi resonance interactions have been added to the model. Terms in the Hamiltonian up to the fourth order are given explicitly for molecules of C(infinityupsilon) symmetry and simplifications for symmetric D(infinityh) molecules are discussed. The matrix elements for the HCCS free radical have been obtained and are used to analyze the observed ground-state levels of HCCS and DCCS in a companion paper. The Sears resonance vibronic interaction that couples levels with the selection rules DeltaK=+/-1, DeltaSigma=-/+1, and DeltaP=0 has also been studied and the matrix elements derived. The determinable combinations of signs for the major parameters in the model are discussed.     

The chemistry of 2'' ,3''-seconucleosides II. Reactions and biological properties of 2'',3''-secopyrimidine ribonucleosides

Reaction of 2',3'-secouridine with acetone gave the 3',5'-$\text{O}$-isopropylidene derivative (1) which upon treatment with mesylchloride gave the 2'-$\text{O}$-mesyl compound (2). Replacement of the mesyl group of 2 with halide could be effected by reaction with a metal halide in DMF. The 3',5'-$\text{O}$-isopropylidene group was removed simultaneously to give a 2'-halogeno-2'-deoxy-2',3'-secouridine. 2',3'-Dichloro-2',3'-dideoxy-2',3'-secouridine upon treatment with base gave 6($\text{R}$)-chloromethyl-2($\text{R}$)-(uracil-1-yl)-1,4-dioxane in addition to O²,2'-anhydro-3'-chloro-3'-deoxy-2',3'-secouridine, as previously reported. 2',3'-Dichloro-2',3'-dideoxy-5'-0-trityl-2',3'-secouridine was converted to 2',3'-dichloro-2',3'-dideoxy-2',3'-secocytidine (16) $\text{via}$ a triazole derivative. Compound 16 was unstable and appeared to form O²,2'-anhydro-3'-chloro-3'-deoxy-2,3'-secocytidine upon standing at room temperature. 5-Vinyl- and 5-($\text{E}$) (2-bromovinyl) uridine dialdehydes have been made, as well as a number of other 5-substituted 2',3'-secouridine derivatives. None of the compounds obtained showed significant activity against a number of virus strains or tumor cell lines, except for 5-($\text{E}$)(2-bromovinyl) uridine dialdehyde, which was inhibitory to the growth of human lymphoblast (Raji, Namalva) cells at a concentration of 28 μ/ml.     

Ring-opening of unsymmetrical 1,2-dioxines using cobalt(II) salen complexes

The regioselectivity of the metal-catalyzed ring opening of unsymmetrical 1,2-dioxines to cis-gamma-hydroxyenones was investigated using two different Co(II) salen complexes. Regioselectivity was determined by direct examination of the enone ratios and by derivitization with a stabilized phosphorus ylide. The steric influence of the substituents on the 1,2-dioxine was the primary influence on regioselectivity. Temperature played little role; however, solvent and selection of Co(II) complex could be used to mildly influence the outcome of the rearrangement for selected substrates. The origins of the selectivity for the reaction are discussed.     

Lipophilicity in PK design: methyl, ethyl, futile

Lipophilicity, often expressed as distribution coefficients (log D) in octanol/water, is an important physicochemical parameter influencing processes such as oral absorption, brain uptake and various pharmacokinetic (PK) properties. Increasing log D values increases oral absorption, plasma protein binding and volume of distribution. However, more lipophilic compounds also become more vulnerable to P450 metabolism, leading to higher clearance. Molecular size and hydrogen bonding capacity are two other properties often considered as important for membrane permeation and pharmacokinetics. Interrelationships among these physicochemical properties are discussed. Increasing size (molecular weight) often gives higher potency, but inevitably also leads to either higher lipophilicity, and hence poorer dissolution/solubility, or to more hydrogen bonding capacity, which limits oral absorption. Differences in optimal properties between gastrointestinal absorption and uptake into the brain are addressed. Special attention is given to the desired lipophilicity of CNS drugs. In examples using -blockers, Ca channel antagonists and peptidic renin inhibitors we will demonstrate how potency and pharmacokinetic properties need to be balanced.     

Purification by HPLC and the UV/Vis absorption spectra of the nitrogen-containing incar-fullerenes iNC60, and iNC70

We report the purification of the nitrogen-containing incar-fullerenes iNC(60) and iNC(70), and their characterisation by UV-Vis absorption spectroscopy.     

An improved synthesis of cyclopropanes from stabilized phosphonates and 1,2-dioxines

Addition of stabilized Horner-Wadsworth-Emmons (HWE) phosphonates to substituted 1,2-dioxines leads to diastereomerically pure di- and trisubstituted cyclopropanes in high yields and represents a viable alternative to ylides in the cyclopropanation reaction involving 1,2-dioxines. While yields are comparable, reaction times with these stabilized phosphonates were accelerated and the diastereoselectivity for this cyclopropanation reaction was significantly greater than for the previously reported examples employing ylides.