Stereoselective formation of glycosyl sulfoxides and their subsequent equilibration: ring inversion of an alpha-xylopyranosyl sulfoxide dependent on the configuration at sulfur

A series of four S-allyl D-thiopyranosides, alpha- and beta-manno and xylo, were oxidized with MCPBA at low temperature to give seven of the eight possible sulfoxides, whose configuration at sulfur was determined either directly by X-ray crystallography or by correlation with closely related structures. For the axial thioglycosides oxidation leads very predominantly to the (R)(S)-diastereomer in the xylo series and exclusively so in the manno series; the configuration at C2 is of little importance in determining the stereoselectivity of oxidation of axial thioglycopyranosides. In the equatorial series the configuration at C2 has a significant effect on the outcome of the reaction as, although both series favored the (S)(S)-sulfoxide, selectivity was significantly higher in the case of the beta-mannoside than of the beta-xyloside. The two alpha-xylo sulfoxides have different conformations of the pyranoside ring with the (R)(S)-isomer adopting the (1)C(4) chair and the (S)(S)-diastereomer the (4)C(1). Each pair of diastereomeric sulfoxides was thermally equilibrated in C(6)D(6) and in CD(3)OD. In the mannose series the kinetic isomers are also thermodynamically preferred. In the xylose series, on the other hand, the nature of the thermodynamic isomer in both the alpha- and beta-anomers is a function of solvent with a switch observed on going from C(6)D(6) to CD(3)OD. The results are rationalized in terms of the exo-anomeric effect, steric shielding provided by H3 and H5 in the axial series, the interaction of the C2-O2 and sulfoxide dipoles, and increased steric interactions on hydrogen bonding of the sulfoxides to CD(3)OD.     

Evaluation of enzymatic digestion and liquid chromatography-mass spectrometry peptide mapping of the integral membrane protein bacteriorhodopsin

A method for the complete peptide mapping of the model integral membrane protein bacteri-orhodopsin is demonstrated. Utilizing more effective enzymatic digestion, procedures with capillary liquid chromatography-electrospray ionization-mass spectrometry (LC-ESI-MS) and tandem mass spectrometry (MS/MS), all predicted tryptic digestion products were detected, as well as peptides from all previously reported post-translational modifications of bacteriorhodopsin. A significant contribution of chymotryptic-like digestion products was also observed. A characterization of the behavior of hydrophobic integral membrane peptides in a reversed-phase liquid chromatographic separation is also provided. The method reported here offers improved compatibility of the solubilizing reagents with both the chromatography and mass spectrometry, rendering it suitable for high-throughput proteomic applications.     

Chloroheptakis(dimethyl sulfoxide)­uranium(IV) trichloride

In the title complex, [UCl(C₂H₆OS)₇]Cl₃, the uranium metal center is coordinated in a distorted bicapped trigonal prism geometry by seven O atoms from di­methyl sulfoxide ligands and by a terminal chloride ligand. Charge balance is maintained by three outer‐sphere chloride ions per uranium(IV) metal center. Principle bond lengths include U—O 2.391 (2)–2.315 (2) Å, U—Cl 2.7207 (9) Å, and average S—O 1.540 (5) Å.     

Diverse redox-active molecules bearing O-, S-, or Se-terminated tethers for attachment to silicon in studies of molecular information storage

A molecular approach to information storage employs redox-active molecules tethered to an electroactive surface. Attachment of the molecules to electroactive surfaces requires control over the nature of the tether (linker and surface attachment group). We have synthesized a collection of redox-active molecules bearing different linkers and surface anchor groups in free or protected form (hydroxy, mercapto, S-acetylthio, and Se-acetylseleno) for attachment to surfaces such as silicon, germanium, and gold. The molecules exhibit a number of cationic oxidation states, including one (ferrocene), two [zinc(II)porphyrin], three [cobalt(II)porphyrin], or four (lanthanide triple-decker sandwich compound). Electrochemical studies of monolayers of a variety of the redox-active molecules attached to Si(100) electrodes indicate that molecules exhibit a regular mode of attachment (via a Si-X bond, X = O, S, or Se), relatively homogeneous surface organization, and robust reversible electrochemical behavior. The acetyl protecting group undergoes cleavage during the surface deposition process, enabling attachment to silicon via thio or seleno groups without handling free thiols or selenols.     

Physically based molecular device model in a transient circuit simulator

Two efficient, physically based models for the real-time simulation of molecular device characteristics of single molecules are developed. These models assume that through-molecule tunnelling creates a steady-state Lorentzian distribution of excess electron density on the molecule and provides for smooth transitions for the electronic degrees of freedom between the tunnelling, molecular-excitation, and charge-hopping transport regimes. They are implemented in the fREEDA™ transient circuit simulator to allow for the full integration of nanoscopic molecular devices in standard packages that simulate entire devices including CMOS circuitry. Methods are presented to estimate the parameters used in the models via either direct experimental measurement or density-functional calculations. The models require 6–8 orders of magnitude less computer time than do full a priori simulations of the properties of molecular components. Consequently, molecular components can be efficiently implemented in circuit simulators. The molecular-component models are tested by comparison with experimental results reported for 1,4-benzenedithiol.     

Comparison of dynamical heterogeneity in hard-sphere and attractive glass formers

Using molecular dynamics simulations, we have determined that the nature of dynamical heterogeneity in jammed liquids is very sensitive to short-ranged attractions. Weakly attractive systems differ little from dense hard-sphere and Lennard-Jones fluids. Particle motion is punctuated and tends to proceed in steps of roughly a single particle diameter. Both of these basic features change in the presence of appreciable short-ranged attractions. Transient periods of particle mobility and immobility cannot be discerned at intermediate attraction strength, for which structural relaxation is greatly enhanced. Strong attractions, known to dramatically inhibit relaxation, restore bimodality of particle motion. But in this regime, transiently mobile particles move in steps that are significantly more biased toward large displacements than those in the case of weak attractions. This modified feature of dynamical heterogeneity, which cannot be captured by conventional mode coupling theory, verifies recent predictions from a model of spatially correlated facilitating defects.     

Impact of prefractionation using Gradiflow on two-dimensional gel electrophoresis and protein identification by matrix assisted laser desorption/ionization-time of flight-mass spectrometry

Prefractionation of protein samples prior to two-dimensional electrophoresis (2-DE) has the potential to increase the dynamic detection range for proteomic analysis. We evaluated a membrane-based electrophoretic separation technique (Gradiflow) for its ability to fractionate an exoproteome sample from the filamentous fungus Trichoderma reesei. The sample was separated on the basis of size and charge. Buffer optimization was found to be necessary for successful size fractionation. Fractionation by charge was used to resolve the sample into four fractions that were subjected to analysis by two-dimensional electrophoresis (2-DE). Enhanced detection of low-abundance proteins with selective removal of high-abundance species was achieved. Fractionated and unfractionated samples were examined for differences in the ability to identify proteins following 2-DE using trypsin in-gel digestion followed by peptide mass fingerprinting using matrix assisted laser desorption/ionization-time of flight-mass spectrometry (MALDI-TOF-MS). Fractionated samples showed marked improvement in protein identification ability and sequence coverage. This study demonstrates the utility of the Gradiflow for fractionation, resulting in an enhancement of resolution and characterization of a moderately complex proteome.     

Selection rules for helicate ligand component self-assembly: steric, pH, charge, and solvent effects

The reaction between 1,10-phenanthroline-2,9-dicarboxaldehyde, copper(I), and certain primary amines was found to give quantitatively a dicopper double-helicate product (two of which were crystallographically characterized) by imine self-assembly around Cu(I) templates. The parameters of this reaction were investigated, and important roles were found to be played by (i) the steric bulk of the amine, (ii) the charge of the amine, (iii) the solvent used, and (iv) the pH of the solution. Water was found to allow the broadest range of structures to form, and ligand-component exchange reactions (involving the substitution of an aromatic for an aliphatic amine) were demonstrated to proceed readily in this solvent.     

Determination of alcohol polyether average molar oligomer value/distribution via supercritical fluid chromatography coupled with UV and MS detection

Supercritical fluid chromatography (SFC) was used for the analysis of ethoxylated and propoxylated surfactants. Samples were derivatized to phenylated silyl ethers with a disilazane-chlorosilane mixture. Addition of a phenyl group to the surfactant allowed UV-absorbance detection of each oligomer. Acetonitrile and methanol were evaluated as mobile phase modifiers. Better peak shape was realized with methanol-modified CO2 on an octadecyl silica bonded phase than with acetonitrile-modified CO2. Peak assignments were made via SFC coupled with electrospray ionization-mass spectrometry (ESI-MS) in the positive ion mode. A sulfonamide-embedded alkyl stationary phase was also evaluated for separation of the derivatized samples. SFC-UV and SFC-ESI-MS data were jointly used for calculation of average molar oligomer values which were then compared to values calculated from 1H NMR data of non-derivatized samples. The derivatization or separation method using the sulfonamide embedded phase required no preliminary cleanup and yielded reproducible oligomer values that were consistent with those of the manufacturer's nominal values.     

Isolation and structure of [HC[CH(SiMe(3))(SnMe(3))](2)](+): a remarkably stable sec-alkyl cation

The reaction of the tin-substituted propene Me3Sn(R)CHCH=CHR (R = SiMe3) with MCl4 in dichloromethane in the presence of Me3SnCl gives the first examples of isolable sec-alkyl carbocation salts, [HC{CH(R)SnMe3}2]+M2Cl9- (M = Zr, Hf). The compounds are thermally stable and, unlike previously isolated trialkyl carbocations, do not require superacidic media or weakly coordinating anions for stability. The crystal structure and DFT calculations suggest polarization of the Sn substituents and hyperconjugation as the reason for the unexpected stability. The stabilizing effect of tin is significantly stronger than that of Si. The carbocations are effective initiators for the polymerization of isobutene, isoprene, and alpha-methylstyrene.