In silico mutagenesis and docking study of Ralstonia solanacearum RSL lectin: performance of docking software to predict saccharide binding

In this study, in silico mutagenesis and docking in Ralstonia solanacearum lectin (RSL) were carried out, and the ability of several docking software programs to calculate binding affinity was evaluated. In silico mutation of six amino acid residues (Agr17, Glu28, Gly39, Ala40, Trp76, and Trp81) was done, and a total of 114 in silico mutants of RSL were docked with Me-α-L-fucoside. Our results show that polar residues Arg17 and Glu28, as well as nonpolar amino acids Trp76 and Trp81, are crucial for binding. Gly39 may also influence ligand binding because any mutations at this position lead to a change in the binding pocket shape. The Ala40 residue was found to be the most interesting residue for mutagenesis and can affect the selectivity and/or affinity. In general, the docking software used performs better for high affinity binders and fails to place the binding affinities in the correct order.     

Deuterium-labelled N-acyl-L-homoserine lactones (AHLs)--inter-kingdom signalling molecules--synthesis, structural studies, and interactions with model lipid membranes

N-Acyl-l-homoserine lactones (AHLs) are synthesized by Gram-negative bacteria. These quorum-sensing molecules play an important role in the context of bacterial infection and biofilm formation. They also allow communication between microorganisms and eukaryotic cells (inter-kingdom signalling). However, very little is known about the entire mechanism of those interactions. Precise structural studies are required to analyse the different AHL isomers as only one form is biologically most active. Theoretical studies combined with experimental infrared and Raman spectroscopic data are therefore undertaken to characterise the obtained compounds. To mimic interactions between AHL and cell membranes, we studied the insertion of AHL in supported lipid bilayers, using vibrational sum-frequency-generation spectroscopy. Deuterium-labelled AHLs were thus synthesized. Starting from readily available deuterated fatty acids, a two-step procedure towards deuterated N-acyl-l-homoserine lactones with varying chain lengths is described. This included the acylation of Meldrum’s acid followed by amidation. Additionally, the detailed analytical evaluation of the products is presented herein.     

Experimentally measured permanent dipoles induced by hydrogen bonding. The Stark spectrum of indole-NH3

Hydrogen bond pairs involving the chromophore indole have been extensively studied in the gas phase. Here, we report high resolution electronic spectroscopy experiments on the indole-NH(3) hydrogen bond pair in the absence and presence of an electric field. The S(1)-S(0) origin band of this complex recorded in zero field at high resolution reveals two overlapping spectra; a consequence of NH(3) hindered internal rotation. The barrier to internal rotation is predicted by theory to be less than 20 cm(-1) in the ground state, therefore requiring a non-rigid rotor Hamiltonian to interpret the spectra. Conducting the experiment in the presence of an applied electric field further perturbs the already congested spectrum of the complex, but makes possible the measurement of the permanent electric dipole moments in its S(0) and S(1) states. These values reveal significant changes in electron distribution that arise from hydrogen bonding effects.     

Resonance Raman studies of excited state structural displacements of conjugated polymers in donor/acceptor charge transfer complexes

Resonance Raman spectra of poly(2-methoxy-5-(3'-7'-dimethyloctyloxy)-1,4-phenylenevinylene) (MDMO-PPV) and small molecule acceptor blend charge transfer (CT) complexes reveal long and detailed progressions of overtone and combination bands. These features are sensitive to the specific MDMO-PPV/acceptor interactions and enable quantitative calculations of vibrational mode specific displacements of the polymer CT complex.     

Lithium-ion batteries based on vertically-aligned carbon nanotube electrodes and ionic liquid electrolytes

In conjunction with environmentally benign ionic liquid electrolytes, vertically-aligned carbon nanotubes (VA-CNTs) sheathed with and without a coaxial layer of vanadium oxide (V(2)O(5)) were used as both cathode and anode, respectively, to develop high-performance and high-safety lithium-ion batteries. The VA-CNT anode and V(2)O(5)-VA-CNT cathode showed a high capacity (600 mAh g(-1) and 368 mAh g(-1), respectively) with a high rate capability. This led to potential to achieve a high energy density (297 Wh kg(-1)) and power density (12 kW kg(-1)) for the prototype batteries to significantly outperform the current state-of-the-art Li-ion batteries.     

Probing platinum degradation in polymer electrolyte membrane fuel cells by synchrotron X-ray microscopy

Synchrotron-based scanning transmission X-ray spectromicroscopy (STXM) was used to characterize the local chemical environment at and around the platinum particles in the membrane (PTIM) which form in operationally tested (end-of-life, EOL) catalyst coated membranes (CCMs) of polymer electrolyte membrane fuel cells (PEM-FC). The band of metallic Pt particles in operationally tested CCM membranes was imaged using transmission electron microscopy (TEM). The cathode catalyst layer in the beginning-of-life (BOL) CCMs was fabricated using commercially available catalysts created from Pt precursors with and without nitrogen containing ligands. The surface composition of these catalyst powders was measured by X-ray Photoelectron Spectroscopy (XPS). The local chemical environment of the PTIM in EOL CCMs was found to be directly related to the Pt precursor used in CCM fabrication. STXM chemical mapping at the N 1s edge revealed a characteristic spectrum at and around the dendritic Pt particles in CCMs fabricated with nitrogen containing Pt-precursors. This N 1s spectrum was identical to that of the cathode and different from the membrane. For CCM samples fabricated without nitrogen containing Pt-precursors the N 1s spectrum at the Pt particles was indistinguishable from that of the adjacent membrane. We interpret these observations to indicate that nitrogenous ligands in the nitrogen containing precursors, or decomposition product(s) from that source, are transported together with the dissolved Pt from the cathode into the membrane as a result of the catalyst degradation process. This places constraints on possible mechanisms for the PTIM band formation process.     

Hydrate-phobic surfaces: fundamental studies in clathrate hydrate adhesion reduction

Clathrate hydrate formation and subsequent plugging of deep-sea oil and gas pipelines represent a significant bottleneck for deep-sea oil and gas operations. Current methods for hydrate mitigation are expensive and energy intensive, comprising chemical, thermal, or flow management techniques. In this paper, we present an alternate approach of using functionalized coatings to reduce hydrate adhesion to surfaces, ideally to a low enough level that hydrodynamic shear stresses can detach deposits and prevent plug formation. Systematic and quantitative studies of hydrate adhesion on smooth substrates with varying solid surface energies reveal a linear trend between hydrate adhesion strength and the practical work of adhesion (γ(total)[1 + cos?θ(rec)]) of a suitable probe liquid, that is, one with similar surface energy properties to those of the hydrate. A reduction in hydrate adhesion strength by more than a factor of four when compared to bare steel is achieved on surfaces characterized by low Lewis acid, Lewis base, and van der Waals contributions to surface free energy such that the practical work of adhesion is minimized. These fundamental studies provide a framework for the development of hydrate-phobic surfaces, and could lead to passive enhancement of flow assurance and prevention of blockages in deep-sea oil and gas operations.     

Experimental validation of plugging during drop formation in a T-junction

At low capillary number, drop formation in a T-junction is dominated by interfacial effects: as the dispersed fluid flows into the drop maker nozzle, it blocks the path of the continuous fluid; this leads to a pressure rise in the continuous fluid that, in turn, squeezes on the dispersed fluid, inducing pinch-off of a drop. While the resulting drop volume predicted by this "squeezing" mechanism has been validated for a range of systems, as of yet, the pressure rise responsible for the actual pinch-off has not been observed experimentally. This is due to the challenge of measuring the pressures in a T-junction with the requisite speed, accuracy, and localization. Here, we present an empirical study of the pressures in a T-junction during drop formation. Using Laplace sensors, pressure probes we have developed, we confirm the central ideas of the squeezing mechanism; however, we also uncover other findings, including that the pressure of the dispersed fluid is not constant but rather oscillates in anti-phase with that of the continuous fluid. In addition, even at the highest capillary number for which monodisperse drops can be formed, pressure oscillations persist, indicating that drop formation in confined geometries does not transition to an entirely shear-driven mechanism, but to a mechanism combining squeezing and shearing.