Polyelectrolyte coatings prevent interferences from charged nanoparticles in SPME speciation analysis

In this work we present a new approach for protection of the fiber in solid phase microextraction (SPME) from interfering charged particles present in the sample medium. It involves coating of commercial poly(dimethylsiloxane) extraction phase with polyelectrolyte layer composed of poly(diallyldimethylammonium chloride), and poly(sodium 4-styrenesulfonate). The modified fiber provides reproducible, convenient and fast extraction capabilities toward the model analyte, triclosan (TCS). A negatively charged polyelectrolyte coating prevents sorbing oxidic nanoparticles from both partitioning into the PDMS phase and aggregation at its surface. The results for the TCS/nanoparticle sample show that the polyelectrolyte layer-modified solid phase extracts just the free form of the organic compound and enables dynamic speciation analysis of the nanoparticulate target analyte complex.     

Determining equilibrium constants for dimerization reactions from molecular dynamics simulations

With today's available computer power, free energy calculations from equilibrium molecular dynamics simulations "via counting" become feasible for an increasing number of reactions. An example is the dimerization reaction of transmembrane alpha-helices. If an extended simulation of the two helices covers sufficiently many dimerization and dissociation events, their binding free energy is readily derived from the fraction of time during which the two helices are observed in dimeric form. Exactly how the correct value for the free energy is to be calculated, however, is unclear, and indeed several different and contradictory approaches have been used. In particular, results obtained via Boltzmann statistics differ from those determined via the law of mass action. Here, we develop a theory that resolves this discrepancy. We show that for simulation systems containing two molecules, the dimerization free energy is given by a formula of the form ΔG ∝ ln(P(1) /P(0) ). Our theory is also applicable to high concentrations that typically have to be used in molecular dynamics simulations to keep the simulation system small, where the textbook dilute approximations fail. It also covers simulations with an arbitrary number of monomers and dimers and provides rigorous error estimates. Comparison with test simulations of a simple Lennard Jones system with various particle numbers as well as with reference free energy values obtained from radial distribution functions show full agreement for both binding free energies and dimerization statistics.     

Voltage-induced swelling and deswelling of weak polybase brushes

We have investigated a novel method of remotely switching the conformation of a weak polybase brush using an applied voltage. Surface-grafted polyelectrolyte brushes exhibit rich responsive behavior and show great promise as "smart surfaces", but existing switching methods involve physically or chemically changing the solution in contact with the brush. In this study, high grafting density poly(2-(dimethylamino)ethyl methacrylate) (PDMAEMA) brushes were grown from silicon surfaces using atom transfer radical polymerization. Optical ellipsometry and neutron reflectivity were used to measure changes in the profiles of the brushes in response to DC voltages applied between the brush substrate and a parallel electrode some distance away in the surrounding liquid (water or D(2)O). Positive voltages were shown to cause swelling, while negative voltages in some cases caused deswelling. Neutron reflectometry experiments were carried out on the INTER reflectometer (ISIS, Rutherford Appleton Laboratory, UK) allowing time-resolved measurements of polymer brush structure. The PDMAEMA brushes were shown to have a polymer volume fraction profile described by a Gaussian-terminated parabola both in the equilibrium and in the partially swollen states. At very high positive voltages (in this study, positive bias means positive voltage to the brush-bearing substrate), the brush chains were shown to be stretched to an extent comparable to their contour length, before being physically removed from the interface. Voltage-induced swelling was shown to exhibit a wider range of brush swelling states in comparison to pH switching, with the additional advantages that the stimulus is remotely controlled and may be fully automated.     

Preparation and characterization of 5,10,15,20‐tetraphenylporphyrin Langmuir films for gas chemsensor applications

In this work is reported the preparation and characterization of 5,10,15,20‐tetraphenylporphyrin (H₂TPP) films at the water‐air interfaces. The surface pressure‐area isotherms (π‐A) and UV‐Vis spectroscopy were used to investigate the effect of the spreading methods and parameters on the porphyrin monolayer formation. Also, Langmuir‐Blodgett (LB) and Langmuir‐Schaefer (LS) films were deposited onto glass substrates in order to study the conformation changes in porphyrin molecular packing. Quartz crystal microbalance (QCM) was utilized as the active solid substrate for the development of the NO₂ gas sensor based on the H₂TPP molecular films. The results of π‐A curves have clearly shown the significant contribution of the preparation methods and processing parameters on the conformation of porphyrin molecular films. The UV‐Vis spectroscopy results using polarized absorption dichroism have indicated different molecular packing for porphyrin films deposited by LB and LS methods, with relative tilted angles of 50° ± 5° and 35° ± 5°, respectively. Moreover, the QCM response has given strong evidence that H₂TPP porphyrin molecular films have performed as NO₂ chemsensor. Copyright © 2011 John Wiley & Sons, Ltd.     

DNA‐Based Peroxidation Catalyst—What Is the Exact Role of Topology on Catalysis and Is There a Special Binding Site for Catalysis?

In the last decade, there has been growing interests in studies aimed at delineating the strategies used by various nucleic acid enzymes to facilitate catalysis. Insights gained from such studies would enable the design of better DNA/RNA catalysts for various applications such as biosensing. DNA and RNA catalysts have been shown to be able to catalyze myriads of reactions, including peroxidation reactions, which are catalyzed by G-quadruplexes. In this report, we provide data that clarifies how G-quadruplex peroxidases achieve catalysis. Firstly, we show that by covalently linking a hemin cofactor to DNAzymes, anti-parallel G-quadruplexes, which have been previously shown to be catalytically inefficient, can be "resurrected" to become good peroxidation catalysts. We also reveal that the relative rates of peroxidation by DNAzyme peroxidases depend on the nature of the organic reductant, arguing for a special binding site in the peroxidase-mimicking DNAzymes for catalysis.     

Thiazole orange-induced c-di-GMP quadruplex formation facilitates a simple fluorescent detection of this ubiquitous biofilm regulating molecule

Recently, there has been an explosion of research activities in the cyclic dinucleotides field. Cyclic dinucleotides, such as c-di-GMP and c-di-AMP, have been shown to regulate bacterial virulence and biofilm formation. c-di-GMP can exist in different aggregate forms, and it has been demonstrated that the polymorphism of c-di-GMP is influenced by the nature of cation that is present in solution. In previous work, polymorphism of c-di-GMP could only be demonstrated at hundreds of micromolar concentrations of the dinucleotide, and it has been a matter of debate if polymorphism of c-di-GMP exists under in vivo conditions. In this Article, we demonstrate that c-di-GMP can form G-quadruplexes at low micromolar concentrations when aromatic molecules such as thiazole orange template the quadruplex formation. We then use this property of aromatic molecule-induced G-quadruplex formation of c-di-GMP to design a thiazole orange-based fluorescent detection of this important signaling molecule. We determine, using this thiazole orange assay on a crude bacterial cell lysate, that WspR D70E (a constitutively activated diguanylate cyclase) is functional in vivo when overexpressed in E. Coli . The intracellular concentration of c-di-GMP in an E. Coli cell that is overexpressed with WspR D70E is very high and can reach 2.92 mM.     

Surface-enhanced Raman scattering and DFT investigation of Eriochrome Black T metal chelating compound

The surface-enhanced Raman scattering (SERS) spectra of Eriochrome Black T (EBT) and its Cu(II), Fe(III), Mn(II) and Pb(II) complexes were recorded using a hydroxylamine reduced silver colloid. Molecular geometry optimization, molecular electrostatic potential (MEP) distribution and vibrational frequencies calculation were performed at B3LYP/6-31G(d) level of theory for the EBT molecule and its Cu(EBT), Fe(EBT) and Mn(EBT) metal complexes. Differentiation between EBT complexes of Cu(II), Fe(III), Mn(II) and Pb(II) is shown by the SERS spectral features of each complex.     

Complete assignment of the vibrational modes of C60 by inelastic neutron scattering spectroscopy and periodic-DFT

In this paper we exploit the complementarity of inelastic neutron scattering (INS), infrared and Raman spectroscopies with ab initio calculations to generate an updated assignment of the vibrational modes of C(60). We have carried out periodic-DFT calculations of the high temperature face centred cubic phase modelled as the standard structure and also of the low temperature simple cubic phase, the latter for the first time. Our assignment differs from all previous work, however, it is the only one that is able to successfully reproduce the INS spectrum in terms of both transition energies and intensities. In addition to the INS spectrum we are also able to quantitatively simulate the major features of the infrared and Raman spectra in the high temperature phase and the infrared spectrum in the low temperature phase.