Does alpha-fluorination affect the structural trans-influence and kinetic trans-effect of an alkyl ligand? Molecular structures of Pd(TMEDA)(CH(3))(R(F)) and a kinetic study of the trans to cis isomerization of Pt(TMEDA)(CH(3))(2)I(R(F)) [R(F) = CF(2)CF(3), CFHCF(3), CH(2)CF(3)

Reaction of Pd(TMEDA)(CH(3))(2) [TMEDA = tetramethylethylenediamine] with fluoroalkyl iodides R(F)I affords a series of square planar Pd(II) complexes Pd(TMEDA)(CH(3))(R(F)) [R(F) = CF(2)CF(3) (9), CFHCF(3) (10), CH(2)CF(3) (11)], presumably by oxidative addition followed by reductive elimination of CH(3)I. The solid-state structures of each compound have been determined by single crystal X-ray diffraction studies, allowing the effect of increasing alpha-fluorination on the structural trans-influence of alkyl ligands to be examined. In these compounds there is no significant difference observed in the trans-influence of the three fluorinated alkyl ligands toward the trans-N atom, although a significant cis-influence on the neighboring methyl ligand is apparent. Oxidative addition of the same series of fluoroalkyl ligands to the corresponding Pt(TMEDA)(CH(3))(2) affords octahedral Pt(IV) complexes trans-Pt(TMEDA)(CH(3))(2)(R(F))I [R(F) = CF(2)CF(3) (12), CFHCF(3) (13), CH(2)CF(3) (14)] as the kinetic products. In each case, subsequent isomerization to the corresponding all cis-isomers is observed; in the case of 13, the stereocenter at the alpha-carbon results in two diastereomeric cis-isomers, which are formed at different rates. The molecular structures of 13 and its more stable all cis-isomer 16b have been crystallographically determined. Kinetic studies of the trans-cis isomerization reactions show the mechanism to involve a polar transition state, presumably involving iodide dissociation, followed by rearrangement of the cation, and iodide recombination. High dielectric solvents increase the rate, but solvent coordinating ability has no effect. Dissolved salts (LiI, LiOTf) show normal accelerative salt effects, with no inhibition in the case of added iodide, consistent with the formation of an intimate ion pair intermediate. The kinetic parameters show that the trans-effects of fluoroalkyl ligands in these compounds follow the order expected from the relative sigma-donor properties of the ligands, with CF(2)CF(3) < CFHCF(3) < CH(2)CF(3).     

Diiodine complex of diferrocenyl(phenyl)phosphine sulfide: the structural and electrochemical behaviour of Fc2(Ph)PS · I2

The title compound, Fc₂(Ph)PS · I₂, has been prepared and characterised in both the solid state and solution. Single crystal X-ray crystallography reveals that the adduct adopts a molecular charge-transfer structure in the solid state. Mössbauer spectroscopy confirms the presence of low spin Fe²⁺ but also indicates the presence of ca. 24% of an Fe³⁺ species. The electrochemistry of Fc₂(Ph)PS · I₂, Fc₂(Ph)PS and Fc₂(Ph)P has been studied using a combination of cyclic voltammetry and differential pulse voltammetry. The data for Fc₂(Ph)PS · I₂ show two redox processes, consistent with the sequential oxidation of the ferrocenyl groups to ferrocenium species.     

Rotational and hyperfine parameters of NH2(X2B1) from LMR spectra

Seventeen rotational transitions up to N=7 of the NH₂ radical in its ground vibronic state have been measured by far infrared laser magnetic resonance spectroscopy. Analysis of the Zeeman patterns and hyperfine structure yields precise rotational, spin-rotational and distortion parameters, and isotropic and anisotropic hyperfine interaction parameters for both ¹⁴N and ¹H nuclei.     

Level decay and orientational kinetics of the rhodamine B monomer and dimer

The population kinetics and the rotational diffusion of the rhodamine B monomer and dimer were measured by using picosecond pulses from a mode-locked Nd : YAG laser to induce and time resolve the concentration-dependent transient absorption saturation of various aqueous solutions of this organic dye.     

Determination of lactate or oxalate using injected lactate oxidase and peroxidase by capillary electrophoresis with UV detection

Two reactions, catalyzed by lactate oxidase (LO) and peroxidase, are initiated by a single injection of the enzymes and the substrate 2,2'-azino-bis(3-ethylene-thiazoline-6-sulfonic acid) (ABTS) into the capillary previously filled with the sample (lactate or lactate-oxalate mixture) and the run buffer containing NADH. The oxidized ABTS product upon reaction with NADH is converted to NAD(+) which is separated and detected in less than 2 min at 266 nm with a sample throughput of 7 min (including wash steps between samples). Simplex trade mark software is used to optimize the enzyme concentrations and reaction temperature. Consumption of the more expensive LO enzyme is only 1.4 x 10(-3) U per assay assuming 27 nL per injection. Linearity is established within the range from 0.0025 to 1 mM with R(2) of 0.9982. Recoveries of lactate from five spiked serum samples averaged 101%. Application of this method for the determination of oxalate as an inhibitor of LO is demonstrated.     

A practical synthesis of (+/-)-alpha-isosparteine from a tetraoxobispidine core

[reaction: see text] The title alkaloid was synthesized in racemic form from 3,7-diallyl-2,4,6,8-tetraoxo-3,7-diazabicyclo[3.3.1]nonane (7) by a regioselective diallylation reaction followed by double ring-closing olefin metathesis and exhaustive reduction. Tetraoxobispidine 7 was itself prepared in three simple operations from dimethyl malonate. The entire sequence to alpha-isosparteine was conducted on a multigram scale and proceeded without recourse to chromatography.     

Recovery of intact proteins from silver stained gels

Silver stained proteins of a wide molecular weight (MW) range (20-116 kDa) were successfully recovered by both electroblot and electroelution. The recovery was demonstrated for nanogram loads of proteins separated by SDS-PAGE and visualized by silver staining methods compatible and incompatible with mass spectrometry (MS). It was shown that the alcohol/acid and glutaraldehyde fixation steps present in a number of staining procedures did not prevent recovery of intact proteins from gels. It was found that the recovery of intact proteins from silver stained gels was substantially increased upon pre-equilibration in a buffer containing the reducing agent, dithiothreitol (DTT). The effect of destaining on the recovery of silver stained proteins was also investigated. Comparable recovery of intact proteins within a wide MW range from silver stained gels with and without destaining step was demonstrated. Recovery of model proteins from gels visualized using silver staining method compatible with MS showed 52 to 76% yield of that from the unstained gel, depending upon method of the transfer. Comparison of the recovery of intact proteins from gels visualized using other staining procedures was also made. The above findings have implications as to the supposed irreversible nature of protein "fixation" inside polyacrylamide matrix, and confirm lack of binding of proteins in the gel to metal silver deposited on its surface. This method has the potential to be suitable for direct characterization of proteins by matrix-assisted laser desorption ionization-mass spectrometry (MALDI-MS) without additional purification steps.     

The solution photochemistry of αβ-unsaturated sulphones

1-Phenyl-2-(benzenesulphonyl)-ethylene and 1-phenyl-2-(benzenesulphonyl)-prop-1-ene have been shown to undergo $\text{Z}$,$\text{E}$-photoisomerisation, whereas 2-benzenesulphonylindene readily forms [_π2 + _π2] photoadducts with 2,3-dimethylbut-2-ene, cyclopentene, and cyclohexene.     

GlyNet: a multi-task neural network for predicting protein–glycan interactions

Advances in diagnostics, therapeutics, vaccines, transfusion, and organ transplantation build on a fundamental understanding of glycan–protein interactions. To aid this, we developed GlyNet, a model that accurately predicts interactions (relative binding strengths) between mammalian glycans and 352 glycan-binding proteins, many at multiple concentrations. For each glycan input, our model produces 1257 outputs, each representing the relative interaction strength between the input glycan and a particular protein sample. GlyNet learns these continuous values using relative fluorescence units (RFUs) measured on 599 glycans in the Consortium for Functional Glycomics glycan arrays and extrapolates these to RFUs from additional, untested glycans. GlyNet''s output of continuous values provides more detailed results than the standard binary classification models. After incorporating a simple threshold to transform such continuous outputs the resulting GlyNet classifier outperforms those standard classifiers. GlyNet is the first multi-output regression model for predicting protein–glycan interactions and serves as an important benchmark, facilitating development of quantitative computational glycobiology.

GlyNet, a neural net model of glycan-protein binding strengths. Given a glycan it outputs binding to each of several protein samples. Reproducing glycan array data, it extrapolates the binding of untested glycans against the protein samples.