Rigid-body dynamics in the isothermal-isobaric ensemble: a test on the accuracy and computational efficiency

We have developed a time-reversible rigid-body (rRB) molecular dynamics algorithm in the isothermal-isobaric (NPT) ensemble. The algorithm is an extension of rigid-body dynamics [Matubayasi and Nakahara, J Chem Phys 1999, 110, 3291] to the NPT ensemble on the basis of non-Hamiltonian statistical mechanics [Martyna, G. J. et al., J Chem Phys 1994, 101, 4177]. A series of MD simulations of water as well as fully hydrated lipid bilayer systems have been undertaken to investigate the accuracy and efficiency of the algorithm. The rRB algorithm was shown to be superior to the state-of-the-art constraint-dynamics algorithm SHAKE/RATTLE/ROLL, with respect to computational efficiency. However, it was revealed that both algorithms produced accurate trajectories of molecules in the NPT as well as NVT ensembles, as long as a reasonably short time step was used. A couple of multiple time-step (MTS) integration schemes were also examined. The advantage of the rRB algorithm for computational efficiency increased when the MD simulation was carried out using MTS on parallel processing computer systems; total computer time for MTS-MD of a lipid bilayer using 64 processors was reduced by about 40% using rRB instead of SHAKE/RATTLE/ROLL.     

Boomerang‐Type Substitution Reaction: Reactivity of Fullerene Epoxides and a Halofullerenol

The C_s‐symmetric fullerene chlorohydrin C₆₀(Cl)(OH)(OOtBu)₄ reacts with 4‐dimethylaminopyridine (DMAP) and 1,4‐diazabicyclo[2.2.2]octane (DABCO) to yield two isomers with the formula C₆₀(O)(OOtBu)₄ in good yields. These isomers differ with respect to the location of the epoxy functionality. The one from DMAP is C_s symmetric, whereas that from DABCO is C₁ symmetric with the epoxy group on the central pentagon. Two different mechanisms are proposed to explain the chemoselectivity of these reactions. The reaction with DMAP involves single‐electron transfer as the key step; DMAP acts as the electron donor. A combination of an oxygen‐atom shift and S_N2′′ processes (boomerang substitution) are responsible for the formation of isomer with DACBO. Various related reactions support the proposed mechanisms. The structures of new fullerene derivatives were determined by spectroscopy, single‐crystal X‐ray analysis, and chemical correlation experiments.     

Cyclic Voltammograms of Ferrocene on Multi‐Walled Carbon Nanotubes (MWCNTs)‐Modified Edge Plane Pyrolytic Graphite (EPPG) Electrode in Room Temperature Ionic Liquids (RTILs) of 1‐Ethyl‐3‐Methylimidazolium Tetrafluoroborate (EMIBF4)

In this work, the electrochemical behavior of ferrocene (Fc) was investigated by cyclic voltammetry (CV) in room temperature ionic liquids (RTILs) of 1‐ethyl‐3‐methylimidazolium tetrafluoroborate (EMIBF₄) on glass carbon (GC), edge plane pyrolytic graphite (EPPG) and multi‐walled carbon nanotube (MWCNTs)‐modified EPPG electrodes, respectively. The results demonstrated that on GC electrode, pairs of well‐defined reversible peaks were observed, while for the electrode of EPPG, the peak potential separation (ΔE_p) is obviously larger than the theoretical value of 59 mV, hinting that the electrode of EPPG is distinguished from the commonly used electrode, consistent with the previous proposition that EPPG has many “defects”. To obtain an improved electrochemical response, multi‐walled carbon nanotubes (MWCNTs) were modified on the electrode of EPPG; the increased peak current and promoted peak potential separation not only proved the existence of “defects” in MWCNTs, but also supported that “creating active points” on an electrode is the main contribution of MWCNTs. Initiating the electrochemical research of Fc on the MWCNTs‐modified EPPG electrode in RTILs and verifying the presence of “defects” on both EPPG and MWCNTs using cyclic voltammograms (CVs) of Fc obtained in RTILs of EMIBF₄, is the main contribution of this preliminary work.     

Permselective and Preconcentration Properties of a Surfactant‐Intercalated Clay Modified Electrode

This work is focused on the voltammetric examination of the ion exchange properties of a smectite type clay, before and after its modification by the replacement of its native interlamellar cations (Na⁺, K⁺, Ca²⁺) by hexadecyltrimethylammonium cations (HDTMA⁺). The raw clay and its organically modified form were first characterized by X‐ray diffraction (XRD) and N₂ adsorption–desorption isotherms (BET method) that confirmed the modification via an intercalation process. These materials were subsequently coated onto glassy carbon surfaces, and the resulting modified electrodes were evaluated for the uptake of [Ru(NH₃)₆]³⁺ and [Fe(CN)₆]^3? ions used as redox probes. Some experimental parameters affecting the incorporation of the probes within the film, including the ionic strength, the surfactant loading and the solution pH are thoroughly examined, in order to highlight the mechanism of the process. The possibility of using the surfactant‐intercalated clay modified electrode as an electrochemical sensor for [Fe(CN)₆]^3? is also evaluated.     

Microscale sample deposition onto hydrophobic target plates for trace level detection of neuropeptides in brain tissue by MALDI-MS

A sample preparation method that combines a modified target plate with a nanoscale reversed-phase column (nanocolumn) was developed for detection of neuropeptides by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). A gold-coated MALDI plate was modified with an octadecanethiol (ODT) self-assembled monolayer to create a hydrophobic surface that could concentrate peptide samples into a approximately 200-500-microm diameter spot. The spot sizes generated were comparable to those obtained for a substrate patterned with 200-microm hydrophilic spots on a hydrophobic substrate. The sample spots on the ODT-coated plate were 100-fold smaller than those formed on an unmodified gold plate with a 1-microl sample and generated 10 to 50 times higher mass sensitivity for peptide standards by MALDI-TOF MS. When the sample was deposited on an ODT-modified plate from a nanocolumn, the detection limit for peptides was as low as 20 pM for 5-microl samples corresponding to 80 amol deposited. This technique was used to analyze extracts of microwave-fixed tissue from rat brain striatum. Ninety-eight putative peptides were detected including several that had masses matching neuropeptides expected in this brain region such as substance P, rimorphin, and neurotensin. Twenty-three peptides had masses that matched peaks detected by capillary liquid chromatography with electrospray ionization MS.     

Aza-Morita-Baylis-Hillman reactions of N-(benzylidene)polyfluoroanilines with methyl acrylate and acrylonitrile

Aza-Morita-Baylis-Hillman reactions of N-(benzylidene)polyfluoroanilines 1 with methyl acrylate or acrylonitrile were studied. It was found that Lewis base, solvent and reaction temperature can significantly affect the reaction. Using 3-hydroxyquinuclidine (3-HQD) as a Lewis base in the reactions of 1 with methyl acrylate in DMF, the normal aza-Morita-Baylis-Hillman adducts 3 were formed in moderate to excellent yields. For the reactions of 1 with acrylonitrile, 1,4-diazabicyclo[2.2.2]octane (DABCO) is the best Lewis base giving the corresponding aza-Morita-Baylis-Hillman adducts 4 as the sole product in good to moderate yield. However, upon treatment of 1 with acrolein 2c, the corresponding reaction did not occur even in the presence of a variety of catalysts.     

Profiling and comprehensive expression analysis of ABC transporter solute-binding proteins of Bacillus subtilis membrane based on a proteomic approach

We analyzed ABC transporter solute-binding proteins (SBPs) of the Bacillus subtilis membrane using a proteomic approach. We prepared a washed cell membrane fraction that was insoluble in 134 mM nondetergent sulfobetaine and then extracted proteins using mixtures of detergents in a stepwise manner. The membrane proteins were resolved by three two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) or two one-dimensional (1-D) PAGE procedures, electroblotted, and digested in the presence of 5% or 80% acetonitrile. Thereafter, matrix-assisted laser desorption/ionization-time of flight-mass spectrometry (MALDI-TOF MS) identified 637 proteins corresponding to 15.9% of the total cellular proteins. We predicted that among these, 256 were membrane proteins, 101 were lipoproteins or secretory proteins and 280 were soluble proteins containing peripheral proteins that function in both the cytoplasm and the cell membrane such as SecA and FtsY. Among the 637 proteins, we identified 30 SBPs among 38 importers predicted by a bioinformatic search of the genome. We confirmed expression of the genes for the 30 SBPs using DNA microarray analysis. We compared the 2-D gel separation profiles of submembrane fractions solubilized by 1% n-dodecyl-beta-D-maltoside from cells cultured on Luria Bertani (LB), S7, and S7 medium without glutamate as well as DNA microarray data on LB and S7. The results suggested that YcdH, YtmK and YurO are binding proteins for Mn(++), glutamate and glucose, respectively, and that YqiX and YxeM are binding proteins for amino acids (tryptophan in S7 medium).     

Large‐scale extrusion processing and characterization of hybrid nylon‐6/SiO2 nanocomposites

Solution impregnations, pulltrusion and film stacking are widely used methods to prepare thermoplastic composite materials. Extruders are used to melt the polymer and to incorporate fibers into the polymer in order to modify physical properties. In this article, the compounding of colloidal silica nanoparticles filled polyamide‐6 (PA‐6) is achieved using a twin‐screw extruder, which has a significant market share due to its low cost and easy maintenance. The experiments were performed at 250 rpm and the bulk throughput was 6 kg h^?1 with a pump pressure of 30 bars. The composites were characterized with nuclear magnetic resonance (NMR), wide angle X‐ray diffraction (WAXD), differential scanning calorimetry (DSC) and transmission electron microscopy (TEM). As determined by WAXD, the PA‐6 showed higher amounts of γ‐phase when compared to other synthesis methods such as in situ polymerization. TEM pictures showed that the silica particles aggregated nevertheless, upon addition of 14% (w/w) silica the E‐modulus increased from 2.7 to 3.9 GPa indicating that an effective mechanical coupling with the polymer was achieved. The behavior, illustrated with dynamic mechanical analysis (DMA) curves, indicated that in general when a filled system is compared to unfilled material, the values of the moduli (E′ and E″) increased and tan δ decreased. Determination of molecular mass distribution of the samples by means of size exclusion chromatography (SEC) coupled to a refractive index (RI), viscosity (DV) and light scattering (LS) detector revealed that the addition of silica did not decrease the average molecular weight of the polymer matrix, which is of importance for composite applications. Copyright © 2004 John Wiley & Sons, Ltd.     

Preparation and proton conductivity of poly(N‐methylbenzimidazole) doped with acid

To increase the solubility and film forming ability of polybenzimidazole (PBI), poly(N‐methylbenzimidazole) (PNMBI) with different degrees of methylation was synthesized. Chemical structure, degree of substitution, and solubility of PNMBI was studied. PNMBI is easier to be doped with acid than PBI. The basicity of PNMBI was improved with the introduction of methyl groups on the imidazole moiety. Effects of methylation degree, H₃PO₄ content and temperature on proton conductivity of PNMBI doped H₃PO₄ was studied. Proton conductivity of H₃PO₄ doped PNMBI‐1.2 membranes increases with increasing doping level. Temperature dependence of proton conductivity of H₃PO₄ doped PNMBI‐1.2 membranes follows the Arrhenius law. With an increase in the degree of substitution, proton conductivity of H₃PO₄ doped PNMBI decreases dramatically. The proton transport mechanism was also discussed. The proton conductivity of PNMBI/H₃PO₄ is mainly contributed by proton hopping or Grotthuss mechanism. Copyright © 2004 John Wiley & Sons, Ltd.     

In Situ Study of the Surface Oxidation of FeCr Alloys Using Grazing Incidence X‐ray Absorption Spectroscopy (GIXAS)

The surface oxidation of FeCr alloys with 18, 28, and 43 mass‐% Cr was investigated in situ using grazing‐incidence X‐ray absorption spectroscopy (GIXAS) at the chromium and iron K‐edges. Oxidation in air was monitored in situ in the temperature range from 290 K to 680 K. The standard GIXAS data analysis is extended for the treatment of a single layer model in order to estimate the chromium concentrations of the oxide layer and of the near‐interface substrate as well as the oxide layer thickness. XANES analysis shows transitions from b.c.c. Fe to corundum type Fe₂O₃ and from b.c.c. Cr to corundum type Cr₂O₃. The initial oxide layers are 1.1‐1.4 nm thick and contain 60‐90 mass‐% chromium, while the near‐interface substrate is depleted in Cr. During heating, iron oxide growth dominates up to 560‐600 K. Then the chromium oxide layer loses its passivation effect and Cr oxidation sets in.