OptDesign: extending optimizable k-dissimilarity selection to combinatorial library design

Optimizable k-dissimilarity (OptiSim) selection entails drawing a series of subsamples of size k from a population and choosing the "best" candidate from each such subsample for inclusion in the selection set. By varying the size of the subsample, one can control the balance between representativeness and diversity in the selection set obtained. In the original formulation, a uniform random sampling from among valid candidates was used to draw the subsamples from a single target population. Here we describe in detail two key modifications that serve to extend the OptiSim methodology to vector selection for interdependent variables, specifically as applied to the design of combinatorial sublibraries. The first modification involves pivoting between variables: subsamples are drawn from each reagent pool in turn, with the viability of each candidate being evaluated in isolation as well as in terms of the products it will produce from complementary reagents already selected. The filters applied may be static or dynamic in nature, with molecular weight and hydrophobicity being examples of the former and structural diversity with respect to reagents already selected being an example of the latter. The second key modification is adding the ability to bias the selection of candidate reagents for inclusion in the subsamples. Taken together, these modifications support the efficient generation of multiblock and other sparse matrix designs that are both representative and diverse, and for which "backfilling" of designs edited to remove undesirable reagents or products is straightforward. The method is intrinsically fast and efficient, since enumeration of the full combinatorial is not required- only those candidates actually considered for inclusion need be evaluated. Moreover, because the subsample selection step is separate from the diversity-based selection of the "best" candidate, incorporating such bias in favor of a competing criterion such as low price provides a "natural," nonparametric mechanism for generating designs that are likely to be "good" in a double-objective, Pareto sense.     

Modulation of the pK(a) of metal-bound water via oxidation of thiolato sulfur in model complexes of Co(III) containing nitrile hydratase: insight into possible effect of cysteine oxidation in Co-nitrile hydratase

The Co(III) complexes of N,N'-bis(2-mercaptophenyl)pyridine-2,6-dicarboxamide (PyPSH(4)), a designed pentadentate ligand with built-in carboxamide and thiolate groups, have been synthesized and studied to gain insight into the role of Cys-S oxidation in Co-containing nitrile hydratase (Co-NHase). Reaction of [Co(NH(3))(5)Cl]Cl(2) with PyPS(4)(-) in DMF affords the thiolato-bridged dimeric Co(III) complex (Et(4)N)(2)[Co(2)(PyPS)(2)] (1). Although the bridged structure is quite robust, reaction of (Et(4)N)(CN) with 1 in acetonitrile affords the monomeric species (Et(4)N)(2)[Co(PyPS)(CN)] (2). Oxidation of 2 with H(2)O(2) in acetonitrile gives rise to a mixture which, upon chromatographic purification, yields K(2)[Co(PyPSO(2)(OSO(2))(CN] (3), a species containing asymmetrically oxidized thiolates. The Co(III) metal center in 3 is coordinated to a S-bound sulfinate and an O-bound sulfonate (OSO(2)) group. Upon oxidation with H(2)O(2), 1 affords an asymmetrically oxidized dimer (Et(4)N)(2)[Co(2)(PyPS(SO(2)))(2)] (4) in which only the terminal thiolates are oxidized to form S-bound sulfinate groups while the bridging thiolates remain unchanged. The thiolato-bridge in 4 is also cleaved upon reaction with (Et(4)N)(CN) in acetonitrile, and one obtains (Et(4)N)(2)[Co(PyPS(SO(2)))(CN)] (5), a species that contains both coordinated thiolate and S-bound sulfinate around Co(III). The structures of 1-4 have been determined. The spectroscopic properties and reactivity of all the complexes have been studied to understand the behavior of the Co(III) site in Co-NHase. Unlike typical Co(III) complexes with bound CN(-) ligands, the Co(III) centers in 2 and 5 are labile and rapidly lose CN(-) in aqueous solutions. Since 3 does not show this lability, it appears that at least one thiolato sulfur donor is required in the first coordination sphere for the Co(III) center in such species to exhibit lability. Both 2 and 5 are converted to the aqua complexes [Co(PyPS)(H(2)O)](-) and [Co(PyPS(SO(2))(H(2)O)](-) in aqueous solutions. The pK(a) values of the bound water in these two species, determined by spectrophotometry, are 8.3 +/- 0.03 and 7.2 +/- 0.06, respectively. Oxidation of the thiolato sulfur (to sulfinate) therefore increases the acidity of the bound water. Since 2 and 5 promote hydrolysis of acetonitrile at pH values above their corresponding pK(a) values, it is also evident that a metal-bound hydroxide is a key player in the mechanism of hydrolysis by these model complexes of Co-NHase. The required presence of a Cys-sulfinic residue and one water molecule at the Co(III) site of Co-NHase as well as the optimal pH of the enzyme near 7 suggests that (i) modulation of the pK(a) of the bound water molecule at the active site of the enzyme could be one role of the oxidized Cys-S residue(s) and (ii) a cobalt-bound hydroxide could be responsible for the hydrolysis of nitriles by Co-NHase.     

Diffusion anomaly as a function of molecular length of linear molecules: levitation effect

Previous work on monatomic spherical sorbates has shown the existence of an anomalous peak in self-diffusivity (D) when plotted as a function of size of the diffusant. Molecular dynamics studies on linear molecules of different lengths l in zeolite NaY at 140 and 200 K are reported. It is seen that there is a peak in D as a function of l, suggesting that the levitation effect exists for linear molecules, the simplest member of polyatomics. This is confirmed by the lowering of the activation energy for the molecule whose length l exhibits highest D. Related quantities of interest such as the guest-host interaction energy and preexponential factor are discussed.     

Direct continuous supercritical fluid extraction as a novel method of wine analysis. Comparison with conventional indirect extraction and implications for wine variety identification

Direct supercritical fluid extraction (SFE) of wines with carbon dioxide was compared to SFE of the sorbent used for solid-phase extraction of the same wine samples (SPE-SFE). Compared to SPE-SFE, the direct SFE results in amore specific and representative gas chromatographic fingerprint of the wine sample. The multivariate statistical processing of the direct SFE-GC data provides a clear-cut and sharp discrimination among the individual wine varieties while the discrimination based on the SPE-SFE-GC data is relatively poor. This finding reflects the adverse effects of additional analyte-sorbent interactions and sorption/desorption steps involved in SPE-SFE.     

Bound states and dipole polarizability of hydrogen molecular ion H2 in weakly coupled hot plasmas

The effects of hot-dense plasmas on the bound states and the dipole polarizability of the ground state of Coulomb three-body molecular ion H⁺₂ have been investigated using highly correlated basis functions and by considering the Debye shielding approach of plasma modeling. The ground S state and the first excited P state energies along with the dipole polarizability for different shielding parameters are reported.     

Development and validation of a HPLC method for quantification of rivastigmine in rat urine and identification of a novel metabolite in urine by LC‐MS/MS

A sensitive, specific and accurate HPLC method for the quantification of rivastigmine (RSM) in rat urine was developed and validated. The method involves the simple liquid–liquid extraction of RSM and pyridostigmine as an internal standard (IS) from rat urine with tertiary methyl butyl ether. The chromatographic separation of RSM and IS was achieved with 20 mm ammonium acetate buffer (pH 6.5) and acetonitrile (65:35, v/v) delivered at flow‐rate of 1 mL/min on a Kromasil KR‐100. The method was in linear range from 50 to 5000 ng/mL. The validation was done as per FDA guidelines and the results met the acceptance criteria. The method was successfully applied for the quantification of RSM in rat urine. Besides method validation, we have identified two metabolites of RSM in urine. Both the metabolites were characterized by HPLC‐PDA and LC‐MS/MS and it was found that one metabolite is novel. Copyright © 2010 John Wiley & Sons, Ltd.     

Conservation of a prey-predator fishery with predator self limitation based on continuous fishing effort

The paper deals with the problem of selective harvesting in a prey-predator model with predator self limitation. Criteria for local stability and global stability for both the exploited and unexploited system are derived. The effort has been considered as a dynamic variable and taxation as a control instrument to protect the fish populations from over exploitation. Finally, the optimal taxation policy is discussed with the help of control theory.     

Aging effect of diethanolamine derived precursor sol on TiO<Subscript>2</Subscript> films deposited at different annealing temperatures

A diethanolamine stabilized precursor sol has been utilized for studying the effect of sol aging and annealing temperature on key properties of TiO₂ films. X-ray diffraction investigations have shown increased crystallite size in the films as a function of both sol aging and the thermal treatment. Fourier transform infrared studies have elucidated that cleavage of the bond involving diethanolamine and the alkoxide in the films requires high temperature annealing treatment upon the use of aged sol for the deposition of the films. Multiple step chronoamperometry has shown the ion storage capacity of the films increases as a function of sol aging, with the highest extent of Li ion insertion being obtained for films produced from as-prepared and aged sols and subsequently annealed at, 300 and 350 °C, respectively. Films with excellent optical quality were obtained. Ellipsometry revealed that the refractive indices of the films vary from 1.67 to 2.02. The highest thickness obtained in these films was nearly 900 nm. The bandgaps of the films for both direct and indirect transitions decreased as a function of precursor sol’s aging. In addition, although the indirect bandgap values have shown a decrease with increasing annealing temperature, the direct bandgap values reveal a slight increase as a function of annealing temperature.