Macromol. Biosci. 1/2013

Front Cover: Highly aligned 3D silk scaffolds using directional freezing in a custom designed chamber was demonstrated. The method is versatile and holds potential to produce complex, multicomponent aligned structures for various tissue engineering and biomedical applications, needing immediate cell alignment to mimic native tissue hierarchy and function. Further details can be found in the article by B. B. Mandal, E. S. Gil, B. Panilaitis, and D. L. Kaplan* on page 48 .

     

Neuronal metabolomics by ion mobility mass spectrometry: cocaine effects on glucose and selected biogenic amine metabolites in the frontal cortex, striatum, and thalamus of the rat

We report results of studies of global and targeted neuronal metabolomes by ambient pressure ion mobility mass spectrometry. The rat frontal cortex, striatum, and thalamus were sampled from control nontreated rats and those treated with acute cocaine or pargyline. Quantitative evaluations were made by standard additions or isotopic dilution. The mass detection limit was ～100 pmol varying with the analyte. Targeted metabolites of dopamine, serotonin, and glucose followed the rank order of distribution expected between the anatomical areas. Data was evaluated by principal component analysis on 764 common metabolites (identified by m/z and reduced mobility). Differences between anatomical areas and treatment groups were observed for 53 % of these metabolites using principal component analysis. Global and targeted metabolic differences were observed between the three anatomical areas with contralateral differences between some areas. Following drug treatments, global and targeted metabolomes were found to shift relative to controls and still maintained anatomical differences. Pargyline reduced 3,4-dihydroxyphenylacetic acid below detection limits, and 5-HIAA varied between anatomical regions. Notable findings were: (1) global metabolomes were different between anatomical areas and were altered by acute cocaine providing a broad but targeted window of discovery for metabolic changes produced by drugs of abuse; (2) quantitative analysis was demonstrated using isotope dilution and standard addition; (3) cocaine changed glucose and biogenic amine metabolism in the anatomical areas tested; and (4) the largest effect of cocaine was on the glycolysis metabolome in the thalamus confirming inferences from previous positron emission tomography studies using 2-deoxyglucose.

A polarizable empirical force field for molecular dynamics simulation of liquid hydrocarbons

Electronic polarizability is usually treated implicitly in molecular simulations, which may lead to imprecise or even erroneous molecular behavior in spatially electronically inhomogeneous regions of systems such as proteins, membranes, interfaces between compounds, or mixtures of solvents. The majority of available molecular force fields and molecular dynamics simulation software packages does not account explicitly for electronic polarization. Even the simplest charge‐on‐spring (COS) models have only been developed for few types of molecules. In this work, we report a polarizable COS model for cyclohexane, as this molecule is a widely used solvent, and for linear alkanes, which are also used as solvents, and are the precursors of lipids, amino acid side chains, carbohydrates, or nucleic acid backbones. The model is an extension of a nonpolarizable united‐atom model for alkanes that had been calibrated against experimental values of the density, the heat of vaporization and the Gibbs free energy of hydration for each alkane. The latter quantity was used to calibrate the parameters governing the interaction of the polarizable alkanes with water. Subsequently, the model was tested for other structural, thermodynamic, dielectric, and dynamic properties such as trans/gauche ratios, excess free energy, static dielectric permittivity, and self‐diffusion. A good agreement with the experimental data for a large set of properties for each considered system was obtained, resulting in a transferable set of polarizable force‐field parameters for CH₂, CH₃, and CH₄ moieties. © 2014 Wiley Periodicals, Inc.     

Grid control over high currents in a cesium discharge with a cathode spot

We report on the results of investigation of a plasma switch with complete grid control in a discharge with a cathode spot on the liquid-metal cesium cathode without grid diaphragming. The retention of the working area of the grid relative to the anode area leads to an order-of-magnitude increase in the switching anode current (up to 20 A/cm² over the anode area) and a substantial (up to 100 V and higher) increase in the switching voltages. The use of the cathode jet makes it possible to reduce the working pressures of cesium vapor (down to 10^–3 Torr). We discuss the results of analysis of peculiarities of grid discharge quenching in such a switch, which make it possible to determine possible reasons for limitation of the working parameters of the switch and the ways of their further increase.     

High-Field Asymmetric-Waveform Ion Mobility Spectrometry and Electron Detachment Dissociation of Isobaric Mixtures of Glycosaminoglycans

High-field asymmetric waveform ion mobility spectrometry (FAIMS) is shown to be capable of resolving isomeric and isobaric glycosaminoglycan negative ions and to have great utility for the analysis of this class of molecules when combined with Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) and tandem mass spectrometry. Electron detachment dissociation (EDD) and other ion activation methods for tandem mass spectrometry can be used to determine the sites of labile sulfate modifications and for assigning the stereochemistry of hexuronic acid residues of glycosaminoglycans (GAGs). However, mixtures with overlapping mass-to-charge values present a challenge, as their precursor species cannot be resolved by a mass analyzer prior to ion activation. FAIMS is shown to resolve two types of mass-to-charge overlaps. A mixture of chondroitin sulfate A (CSA) oligomers with 4–10 saccharides units produces ions of a single mass-to-charge by electrospray ionization, as the charge state increases in direct proportion to the degree of polymerization for these sulfated carbohydrates. FAIMS is shown to resolve the overlapping charge. A more challenging type of mass-to-charge overlap occurs for mixtures of diastereomers. FAIMS is shown to separate two sets of epimeric GAG tetramers. For the epimer pairs, the complexity of the separation is reduced when the reducing end is alkylated, suggesting that anomers are also resolved by FAIMS. The resolved components were activated by EDD and the fragment ions were analyzed by FTICR-MS. The resulting tandem mass spectra were able to distinguish the two epimers from each other.

Determination of organophosphate pesticides at a carbon nanotube/organophosphorus hydrolase electrochemical biosensor

An amperometric biosensor for oganophosphorus (OP) pesticides based on a carbon nanotube (CNT)-modified transducer and an organophosphorus hydrolase (OPH) biocatalyst is described. A bilayer approach with the OPH layer atop of the CNT film was used for preparing the CNT/OPH biosensor. The CNT layer leads to a greatly improved anodic detection of the enzymatically generated p-nitrophenol product, including higher sensitivity and stability. The sensor performance was optimized with respect to the surface modification and operating conditions. Under the optimal conditions the biosensor was used to measure as low as 0.15 μM paraoxon and 0.8 μM methyl parathion with sensitivities of 25 and 6 nA/μM, respectively.     

Electrical Conductivity in TCNQ Salts of Bis(4-dimethylaminophenylimino) sulfur and its Structural Analogues

Four compounds, N,N,N',N'-tetramethyl-p-phenylene diamine, N,N,N',N'-tetramethyl-benzidine, 4,4'-bis(dimethylamino)azobenzene and bis(4-dimethylaminophenylimino)sulfur (BAPIS) were examined electrochemically and spectroscopically. Each was shown to be a fairly good donor forming in its first oxidation state a radical-cation. The latter two materials surprisingly exhibited only single one-electron oxidations. Conformational flexibility about the -NSN- unit was studied by NMR spectroscopy and ab initio molecular orbital theory. The experimental ΔG* for a cis-trans to trans-cis interconversion in BAPIS was found to be 11.9 kcal/mole.

The four donors all form 1:1 adducts with TCNQ. The compaction resistances of the complexes have been measured as a function of temperature. Of the four, (BAPIS)(TCNQ) appears to be a one-dimensional material. The other three complexes behave as typical mixed stack organic semiconductors.