Water at biomolecular binding interfaces

Water molecules are often found at the binding interface of biomolecular complexes mediating the interaction between polar groups via hydrogen bonds, or simply filling space providing van der Waals interactions. Recent studies have demonstrated the importance of taking such water molecules into account in docking and binding affinity prediction. Here, we review the recent experimental and theoretical work aimed at quantifying the influence of interfacial water on the thermodynamic properties of binding. We highlight especially our recent results obtained by inhomogeneous fluid solvation theory in several systems and the prediction of the thermodynamic consequences of displacement of the bound water molecule by ligand modification. Finally, we discuss possible directions for further progress in this field.     

Using singlet oxygen to synthesise a [6,6,5]-bis-spiroketal in one-pot from a simple 2,5-disubstituted furan

Singlet oxygen (1O2) proves to be a powerful tool in mediating the one-pot synthesis of a salinomycin-type [6,6,5]-bis-spiroketal unit starting from a suitably substituted furan nucleus.     

Characterization of the core-shell nanoparticles formed as soluble hydrogen-bonding interpolymer complexes at low pH

The formation of soluble hydrogen-bonding interpolymer complexes between poly(acrylic acid) (PAA) and poly(acrylic acid-co-2-acrylamido-2-methyl-1-propane sulfonic acid)-graft-poly(N,N-dimethylacrylamide) (P(AA-co-AMPSA)-g-PDMAM) at pH=2.0 was studied. A viscometric study showed that in semidilute solution a physical gel is formed due to the interconnection of the anionic P(AA-co-AMPSA) backbone of the graft copolymer, in a transient network, by means of the complexes formed between the PDMAM side chains of the graft copolymer and PAA. Dynamic and static light scattering measurements, in conjunction with small-angle neutron scattering measurements, suggest the formation of core-shell colloidal nanoparticles in dilute solution, comprised by an insoluble PAA/PDMAM core surrounded by an anionic P(AA-co-AMPSA) corona. Even if larger clusters are formed in semidilute solution, the size of the insoluble core remains practically stable. Atomic force microscopy performed under ambient conditions reveal that the particles collapse and flatten upon deposition on a substrate, with dimensions close to the ones of the dry hydrophobic core.     

Investigation of the incorporation of electrolyte anions in porous anodic Al2O3 films by employing a suitable probe catalytic reaction

A new method has been developed capable of describing the incorporation of electrolyte anions along the pore wall surface and across both the barrier layer and the pore wall oxide after the establishment of the steady state of growth of porous anodic Al₂O₃ where other methods cannot be applied to obtain reliable results. The knowledge of the nature/composition of anodic oxides as regards the incorporation of species like electrolyte anions is of specific importance for both the understanding of the electrochemical mechanism of oxide production and growth and the scientific and technological applications of porous anodic Al₂O₃ films. The method consists of the selection and use of a suitable catalytic probe reaction on porous anodic oxides at thicknesses varying from a value near zero up to the maximum limiting thickness and the treatment of the experimental reaction rate results by a properly developed mathematical formalism. This method was employed in anodic Al₂O₃ films prepared in H₂SO₄ anodizing electrolyte at a constant bath temperature and different current densities using as a probe reaction the decomposition of HCOOH on these oxides, which is almost exclusively a dehydration reaction, at relatively high reaction temperatures, 350 °C and 390 °C, where the effect of other species except SO₄ ²⁻ incorporated in the oxide on the reaction rate is eliminated. It has been shown that the fraction of the intercrystallite surfaces occupied by SO₄ ²⁻ follows a parabola-like distribution. It has a significant value at the pore base surface, depending on the current density, then it passes through a maximum along the pore wall surface and across both the barrier layer and the pore walls near the pore bases at positions depending on the current density and then becomes almost zero at the mouths of the pores of the oxide with the maximum limiting thickness and at both the Al₂O₃/Al interface and cell boundaries. The maximum value of the surface coverage is almost independent of the current density and is always near 1, showing an almost complete saturation of intercrystalline surfaces at these positions. The above distribution of surface coverage predicts a qualitatively similar distribution of the SO₄ ²⁻ bulk concentration across both the barrier layer and pore wall oxide around the pore bases. The method may be improved and developed further either for a more detailed investigation of the above films or to investigate films prepared in other pore-forming electrolytes. Received: 30 July 1998 / Accepted: 30 September 1998     

Development of Analytical Strategies for the Determination of Olive Fruit Bioactive Compounds Using UPLC-HRMS and HPLC-DAD. Chemical Characterization of Kolovi Lesvos Variety as a Case Study

In this study, an overall survey regarding the determination of several bioactive compounds in olive fruit is presented. Two methodologies were developed, one UPLC-Q-TOF-MS method for the determination of olive fruit phenolic compounds and one HPLC-DAD methodology targeting the determination of pigments (chlorophylls and carotenoids), tocopherols (α-, β, -γ, δ-) and squalene. Target and suspect screening workflows were developed for the thorough fingerprinting of the phenolic fraction of olives. Both methods were validated, presenting excellent performance characteristics, and can be used as reliable tools for the monitoring of bioactive compounds in olive fruit samples. The developed methodologies were utilized to chemical characterize the fruits of the Kolovi olive variety, originating from the island of Lesvos, North Aegean Region, Greece. Twenty-five phenolic compounds were identified and quantified in Kolovi olives with verbascoside, hydroxytyrosol, oleacein and oleomissional found in significantly high concentrations. Moreover, 12 new bioactive compounds were identified in the samples using an in-house suspect database. The results of pigments analysis suggested that Kolovi variety should be characterized as low pigmentation, while the tocopherol and squalene content was relatively high compared to other olive varieties. The characterization of Kolovi olive bioactive content highlighted the high nutritional and possible economic value of the Kolovi olive fruit.     

Confined viscoplastic flows with heterogeneous wall slip

The steady, pressure-driven flow of a Herschel-Bulkley fluid in a microchannel is considered, assuming that different power-law slip equations apply at the two walls due to slip heterogeneities, allowing the velocity profile to be asymmetric. Three different flow regimes are observed as the pressure gradient is increased. Below a first critical pressure gradient G ₁, the fluid moves unyielded with a uniform velocity, and thus, the two slip velocities are equal. In an intermediate regime between G ₁ and a second critical pressure gradient G ₂, the fluid yields in a zone near the weak-slip wall and flows with uniform velocity near the stronger-slip wall. Beyond this regime, the fluid yields near both walls and the velocity are uniform only in the central unyielded core. It is demonstrated that the central unyielded region tends towards the midplane only if the power-law exponent is less than unity; otherwise, this region rends towards the weak-slip wall and asymmetry is enhanced. The extension of the different flow regimes depends on the channel gap; in particular, the intermediate asymmetric flow regime dominates when the gap becomes smaller than a characteristic length which incorporates the wall slip coefficients and the fluid properties. The theoretical results compare well with available experimental data on soft glassy suspensions. These results open new routes in manipulating the flow of viscoplastic materials in applications where the flow behavior depends not only on the bulk rheology of the material but also on the wall properties.     

Exact X-wave solutions of the hyperbolic nonlinear Schrödinger equation with a supporting potential

We find exact solutions of the two- and three-dimensional nonlinear Schrödinger equation with a supporting potential. We focus in the case where the diffraction operator is of the hyperbolic type and both the potential and the solution have the form of an X-wave. Following similar arguments, several additional families of exact solutions can also can be found irrespectively of the type of the diffraction operator (hyperbolic or elliptic) or the dimensionality of the problem. In particular we present two such examples: The one-dimensional nonlinear Schrödinger equation with a stationary and a “breathing” potential and the two-dimensional nonlinear Schrödinger with a Bessel potential.     

Metal-dielectric-metal plasmonic waveguide devices for manipulating light at the nanoscale Invited Paper

We review some of the recent advances in the development of subwavelength plasmonic devices for ma- nipulating light at the nanoscale, drawing examples from our own work in metal-dielectric-metal (MDM) plasmonic waveguide devices. We introduce bends, splitters, and mode converters for MDM waveguides with no additional loss. We also demonstrate that optical gain provides a mechanism for on/off switch- ing in MDM plasmonie waveguides. Highly efficient compact couplers between dielectric waveguides and MDM waveguides are also introduced.     

Modeling the vapor–liquid equilibria of polymer–solvent mixtures: Systems with complex hydrogen bonding behavior

The vapor–liquid equilibria of binary polymer–solvent systems was modeled using the Non-Random Hydrogen Bonding (NRHB) model. Mixtures of poly(ethylene glycol), poly(propylene glycol), poly(vinyl alcohol) and poly(vinyl acetate) with various solvents were investigated, while emphasis was put on hydrogen bonding systems, in which functional groups of the polymer chain can self-associate or cross-associate with the solvent molecules. Effort has been made to explicitly account for all hydrogen bonding interactions. The results reveal that the NRHB model offers a flexible approach to account for various self- or cross-associating interactions. In most cases model's predictions (using no binary interaction parameter k_ij = 0) and model's correlations (using one temperature independent binary interaction parameter, k_ij ≠ 0) are in satisfactory agreement with the experimental data, despite the complexity of the examined systems.