The classification of orthogonal electromagneto-fluid-dynamic flows

A theoretical analysis based on the equations of electromagneto-fluid-dynamics is undertaken in order to completely classify the flow geometries admitted by these equations. The steady two-dimensional flow of a viscous incompressible fluid of finite electrical conductivity and non-zero electric charge density is considered. The flow equations are formulated in terms of the streamfunction and magnetic flux function as independent variables. The exact analytical solution of the resulting equations is obtained when the magnetic field and the velocity field are everywhere orthogonal to each other. It is shown that the only possible flow is a uniform parallel flow.     

Simultaneous detection of 19 K‐ras mutations by free‐solution conjugate electrophoresis of ligase detection reaction products on glass microchips

We demonstrate here the power and flexibility of free‐solution conjugate electrophoresis (FSCE) as a method of separating DNA fragments by electrophoresis with no sieving polymer network. Previous work introduced the coupling of FSCE with ligase detection reaction (LDR) to detect point mutations, even at low abundance compared to the wild‐type DNA. Here, four large drag‐tags are used to achieve free‐solution electrophoretic separation of 19 LDR products ranging in size from 42 to 66 nt that correspond to mutations in the K‐ras oncogene. LDR‐FSCE enabled electrophoretic resolution of these 19 LDR‐FSCE products by CE in 13.5 min (E = 310 V/cm) and by microchip electrophoresis in 140 s (E = 350 V/cm). The power of FSCE is demonstrated in the unique characteristic of free‐solution separations where the separation resolution is constant no matter the electric field strength. By microchip electrophoresis, the electric field was increased to the maximum of the power supply (E = 700 V/cm), and the 19 LDR‐FSCE products were separated in less than 70 s with almost identical resolution to the separation at E = 350 V/cm. These results will aid the goal of screening K‐ras mutations on integrated “sample‐in/answer‐out” devices with amplification, LDR, and detection all on one platform.     

Stepwise synthesis of metal-organic frameworks: replacement of structural organic linkers

We demonstrate how a single-crystal to single-crystal transformation resulting from bridging-linker replacement is possible in extended 2D and 3D metal-organic frameworks (MOFs) by introducing pillared paddlewheel MOF structures into a solution containing dipyridyl linkers. No lateral movement of the layers was observed during this transformation, creating a templating effect from the "parent" structure to the "daughter" structure. A previously unattainable structure was obtained by a two-step synthetic method utilizing the bridging-linker replacement transformation method. Additionally, a bridging-linker insertion was observed when excess linker was used with the 2D MOF structure, inducing an overall 2D to 3D transformation.     

Self-assembled monolayer and multilayer films of the nanocluster [HxPMo12O40 subsetH4Mo72Fe30(O2CMe)15O254(H2O)68] on gold

Films of the molybdenum-iron nanocluster [H x PMo 12O 40 subsetH 4Mo 72Fe 30(O 2CMe) 15O 254(H2O) 68] (FeMoC) were generated on gold via the self-assembly technique using two divergent routes. The first route entails the self-assembly of unfunctionalized FeMoC onto a preprepared carboxyl-terminated SAM on gold. The second route involves the preparation of thiol-terminated functionalized FeMoC clusters, which are then allowed to self-assemble onto bare gold surfaces. Monolayer films of FeMoC clusters are attained via both routes, with the second route requiring shorter immersion times (2 days) than the first route (6 days). Multilayer films of FeMoC are formed via the second route for immersion times longer than 2 days. Characterization of these films using optical ellipsometry, X-ray photoelectron spectroscopy, and atomic force microscopy confirm the self-assembly of the clusters on the surfaces.     

Role of hydration in determining the structure and vibrational spectra of L-alanine and N-acetyl L-alanine N′-methylamide in aqueous solution: a combined theoretical and experimental approach

In this work we have utilized recent density functional theory Born-Oppenheimer molecular dynamics simulations to determine the first principles locations of the water molecules in the first solvation shell which are responsible for stabilizing the zwitterionic structure of L-alanine. Previous works have used chemical intuition or classical molecular dynamics simulations to position the water molecules. In addition, a complete shell of water molecules was not previously used, only the water molecules which were thought to be strongly interacting (H-bonded) with the zwitterionic species. In a previous work by Tajkhorshid et al. (J Phys Chem B 102:5899) the L-alanine zwitterion was stabilized by 4 water molecules, and a subsequent work by Frimand et al. (Chem Phys 255:165) the number was increased to 9 water molecules. Here we found that 20 water molecules are necessary to fully encapsulate the zwitterionic species when the molecule is embedded within a droplet of water, while 11 water molecules are necessary to encapsulate the polar region with the methyl group exposed to the surface, where it migrates during the MD simulation. Here we present our vibrational absorption, vibrational circular dichroism and Raman and Raman optical activity simulations, which we compare to the previous simulations and experimental results. In addition, we report new VA, VCD, Raman and ROA measurements for L-alanine in aqueous solution with the latest commercially available FTIR VA/VCD instrument (Biotools, Jupiter, FL, USA) and Raman/ROA instrument (Biotools). The signal to noise of the spectra of L-alanine measured with these new instruments is significantly better than the previously reported spectra. Finally we reinvestigate the causes for the stability of the P_π structure of the alanine dipeptide, also called N-acetyl-L-alanine N′-methylamide, in aqueous solution. Previously we utilized the B3LYP/6-31G* + Onsager continuum level of theory to investigate the stability of the NALANMA4WC Han et al. (J Phys Chem B 102:2587) Here we use the B3PW91 and B3LYP hybrid exchange correlation functionals, the aug-cc-pVDZ basis set and the PCM and CPCM (COSMO) continuum solvent models, in addition to the Onsager and no continuum solvent model. Here by the comparison of the VA, VCD, Raman and ROA spectra we can confirm the stability of the NALANMA4WC due to the strong hydrogen bonding between the four water molecules and the peptide polar groups. Hence we advocate the use of explicit water molecules and continuum solvent treatment for all future spectral simulations of amino acids, peptides and proteins in aqueous solution, as even the structure (conformer) present cannot always be found without this level of theory. Festschift in Honor of Philip J. Stephens’ 65th Birthday. During the proof stage of this article a very relevant article has been published by M. Losada and Y. Xu titled “Chirality transfer through hydrogen-bonding: Experimental and ab initio analyses of vibrational circular dichroism spectra of methyl lactate in water” in Phys Chem Chem Phys 2007, 9: 3127–3135. In that work they confirm that the effects of water are seen in the VCD spectra and hence it is fundamental to include explicit water molecules in modeling studies of the vibrational spectra of biomolecules in aqueous solution.     

A novel efficient and versatile route to the synthesis of 5-O-feruloylquinic acids

A novel synthesis of 5-O-feruloylquinic acid, a polyphenolic compound found in coffee beans, and its methyl ester derivative has been optimized. The sequence involves 6 steps and is compatible with the preparation of potential human metabolites of these compounds. The key reaction is a Knoevenagel condensation of 4-hydroxy-3-methoxy-benzaldehyde and a malonate ester of quinic acid.     

Lipid composition greatly affects the in vitro surface activity of lung surfactant protein mimics

A crucial aspect of developing a functional, biomimetic lung surfactant (LS) replacement is the selection of the synthetic lipid mixture and surfactant proteins (SPs) or suitable mimics thereof. Studies elucidating the roles of different lipids and surfactant proteins in natural LS have provided critical information necessary for the development of synthetic LS replacements that offer performance comparable to the natural material. In this study, the in vitro surface-active behaviors of peptide- and peptoid-based mimics of the lung surfactant proteins, SP-B and SP-C, were investigated using three different lipid formulations. The lipid mixtures were chosen from among those commonly used for the testing and characterization of SP mimics--(1) dipalmitoyl phosphatidylcholine:palmitoyloleoyl phosphatidylglycerol 7:3 (w/w) (PCPG), (2) dipalmitoyl phosphatidylcholine:palmitoyloleoyl phosphatidylglycerol:palmitic acid 68:22:9 (w/w) (TL), and (3) dipalmitoyl phosphatidylcholine:palmitoyloleoyl phosphatidylcholine:palmitoyloleoyl phosphatidylglycerol:palmitoyloleoyl phosphatidylethanolamine:palmitoyloleoyl phosphatidylserine:cholesterol 16:10:3:1:3:2 (w/w) (IL). The lipid mixtures and lipid/peptide or lipid/peptoid formulations were characterized in vitro using a Langmuir-Wilhelmy surface balance, fluorescent microscopic imaging of surface film morphology, and a pulsating bubble surfactometer. Results show that the three lipid formulations exhibit significantly different surface-active behaviors, both in the presence and absence of SP mimics, with desirable in vitro biomimetic behaviors being greatest for the TL formulation. Specifically, the TL formulation is able to reach low-surface tensions at physiological temperature as determined by dynamic PBS and LWSB studies, and dynamic PBS studies show this to occur with a minimal amount of compression, similar to natural LS.