The role played by oxygen plasma on Teflon: relevance to the concept of "cryptoelectrons"

Dr Williams (AIP Adv., 2012, 2, 010701) suggested that cleaning Teflon by high pressure oxygen plasma may have affected our result that Cu(2+) and Pd(2+) ions can be absorbed but not chemically reduced by a Teflon surface rubbed by PMMA (Phys. Chem. Chem. Phys., 2012, 14, 5551). In response, we show that this treatment does not affect the adsorption of Cu(2+) and Pd(2+). We reaffirm our statement that Cu(2+) and Pd(2+) ions can be adsorbed by a Teflon surface only after rubbing with the organic polymers, not before rubbing.     

On the log-product of the subtree-sizes of random trees

We determine the asymptotic behavior of the expected value and the variance of the log-product of the subtree-sizes of trees T_n belonging to simply generated families of rooted trees. © 1998 John Wiley & Sons, Inc. Random Struct. Alg., 12, 197–212, 1998     

Low-concentration series in general dimension

We discuss recent work on the development and analysis of low-concentration series. For many models, the recent breakthrough in the extremely efficient no- free-end method of series generation facilitates the derivation of 15th-order series for multiple moments in general dimension. The 15th-order series have been obtained for lattice animals, percolation, and the Edwards-Anderson Ising spin glass. In the latter cases multiple moments have been found. From complete graph tables through to 13th order, general dimension 13th-order series have been derived for the resistive susceptibility, the moments of the logarithms of the distribution of currents in resistor networks, and the average transmission coefficient in the quantum percolation problem, 11th-order series have been found for several other systems, including the crossover from animals to percolation, the full resistance distribution, nonlinear resistive susceptibility and current distribution in dilute resistor networks, diffusion on percolation clusters, the dilute Ising model, dilute antiferromagnet in a field, and random field Ising model and self-avoiding walks on percolation clusters. Series for the dilute spin-1/2 quantum Heisenberg ferromagnet are in the process of development. Analysis of these series gives estimates for critical thresholds, amplitude ratios, and critical exponents for all dimensions. Where comparisons are possible, our series results are in good agreement with both-expansion results near the upper critical dimension and with exact results (when available) in low dimensions, and are competitive with other numerical approaches in intermediate realistic dimensions.     

Activation of sepharose withN,N′-disuccinimidyl carbonate

A method is described for the activation of Sepharose withN,N′-disuccimidyl carbonate. The activated carbonate reacts smoothly with amine-containing ligands yielding stable carbamate derivatives.     

Homochiral oligopeptides generated by induced "mirror symmetry breaking" lattice-controlled polymerizations in racemic crystals of phenylalanine N-carboxyanhydride

The formation of diastereoisomeric libraries of oligopeptides through the heterogeneous polymerization of racemic crystals of phenylalanine N-carboxyanhydride (PheNCA) is reported. The diastereoisomeric compositions of the oligopeptides formed on polymerization of (R,S) crystals incorporating the deuterium-tagged S enantiomer were determined by MALDI-TOF mass spectrometry. The racemic mixtures of the oligopeptides longer than pentamers are represented primarily by diastereoisomers of homochiral sequence and with peptides containing only one heterochiral repeating unit. A mechanism comprising the following three sequential steps to account for this unusual observation is proposed: 1) formation of dimers and trimers at a partially damaged liquid/solid interface, 2) chain propagation that takes place within the bulk of the crystal through a lattice-controlled "zipper-like" mechanism between homochiral molecules arranged in a head-to-tail motif to yield crystalline antiparallel beta-sheets of alternating oligopeptide chains of homochiral sequence of opposite handedness, and 3) enantiomeric cross-inhibition that results in chain termination. Induced desymmetrization of the racemic mixtures of the formed peptides was achieved by the polymerization of the mixed quasi-racemic crystals of (R)-PheNCA, ((S)-PheNCA), and (S)-ThieNCA (3-(2-thienyl)-alanine N-carboxyanhydride) of various compositions. These experiments resulted in the formation of nonracemic libraries of oligopeptides composed of homochiral chains of (R)-Phe and copolymers of randomly distributed (S)-Phe and (S)-Thie sequences. From these findings, we propose a stochastic model for the generation of libraries of nonracemic mixtures of oligopeptides from the polymerization of host (R,S)-PheNCA with racemic mixtures of other guest NCA amino acids dissolved in limited quantities in the crystal.     

Laser excited S2 → S1 and S1 → S0 emission spectra and the S2 → Sn absorption spectrum of azulene in solution

We present the S₁ → S₀ fluorescence spectrum, between 740 and 940 nm, of azulene solutions (10^?3 M in methanol) excited with a Q-switched ruby laser. The nitrogen-laser excited S₂ → S₁ fluorescence spectrum, between 700 and 930 nm, is also reported. The transient S₁ → S_n spectrum between 500 and 650 nm was studied, using synchronous nitrogen laser and dye laser excitation. The S₅ (¹B₁(3)) state of azulene was found to be located at 45500 cm^?1 and the cross section σ₂₅ of the transient absorption S₂ → S₅ is estimated to be 3 × 10^?18 cm²/molecule.     

Phosphaalkynes as ligands in organometallic chemistry. Syntheses and 31p NMR spectra of platinum(II), palladium(II) and rhodium(I) complexes of dη5-cyclopentadienyltetracarbonyl-μ-(3,3-dimethyl-1-phosphabutyne)dimolybdenum, [Mo2(CO)4(η-c5H5)2tBuCP)]

Syntheses of the complexes trans-[PtCl₂(PR₃)Mo₂(CO)₄(η⁵-C₅H₅)₂(^tBuCP)], (PR₃=PEt₃, PPr₃, PBu₃, PPh₂Me, PPhMe₂) trans-[PdCl₂(PBu₃)Mo₂(CO)₄(η⁵-C₅H₅)₂(^tBuCP)], and trans[RhCl{(PF₂NMe)₂CO}Mo₂(CO)₄(η⁵-C₅H₅)₂(^tBuCP)] are described and their ³¹P NMR spectra presented and discussed.     

Application of machine learning to improve the results of high-throughput docking against the HIV-1 protease

We have previously reported that the application of a Laplacian-modified naive Bayesian (NB) classifier may be used to improve the ranking of known inhibitors from a random database of compounds after High-Throughput Docking (HTD). The method relies upon the frequency of substructural features among the active and inactive compounds from 2D fingerprint information of the compounds. Here we present an investigation of the role of extended connectivity fingerprints in training the NB classifier against HTD studies on the HIV-1 protease using three docking programs: Glide, FlexX, and GOLD. The results show that the performance of the NB classifier is due to the presence of a large number of features common to the set of known active compounds rather than a single structural or substructural scaffold. We demonstrate that the Laplacian-modified naive Bayesian classifier trained with data from high-throughput docking is superior at identifying active compounds from a target database in comparison to conventional two-dimensional substructure search methods alone.