Plasma-enhanced chemical vapor deposition of organic particle thin films

Five organic precursors, 2,5-dimethyl-2,4-hexadiene, 2,5-norbornadiene, α-terpinine, limonene, and styrene have been studied as precursors for plasma deposition of low-k films. The films have been produced under particle-forming conditions in the plasma. Accordingly, films have a granular structure with grain sizes in the range 40–400 nm, as determined by AFM. Annealing at 400 °C preserves the granular structure of the films while the grain size decreases. Of the five precursors examined, 2,5-dimethyl-2,4-hexadiene and 2,5-norbornadiene produce films with the lowest dielectric constant, with a value of 3.3. While the dielectric constant varies with deposition conditions (pressure, flow rate, concentration of precursor), we find that the grain size of the films correlates most closely with the dielectric constant and conclude that the lowest value of the dielectric constant are obtained under conditions that promote the formation of particles larger than about 200 nm.     

Chitosan derivatives as biosorbents for basic dyes

The scope of this study was to prepare and evaluate chitosan derivatives as biosorbents for basic dyes. This was achieved by grafting poly (acrylic acid) and poly (acrylamide) through persulfate induced free radical initiated polymerization processes and covalent cross-linking of the prepared materials. Remacryl Red TGL was used as the cationic dye. Equilibrium sorption experiments were carried out at different pH and initial dye concentration values. The experimental equilibrium data for each adsorbent-dye system were successfully fitted to the Langmuir, Freundlich and pH-dependent Langmuir-Freundlich sorption isotherms. Thermodynamic parameters of the adsorption process such as DeltaG degrees, DeltaH degrees, and DeltaS degrees were calculated. The negative values of free energy reflected the spontaneous nature of adsorption. The typical dependence of dye uptake on temperature and the kinetics of adsorption indicated the process to be chemisorption. The grafting modifications greatly enhanced the adsorption performance of the biosorbents, especially in the case of powdered cross-linked chitosan grafted with acrylic acid, which exhibited a maximum adsorption capacity equal to 1.068 mmol/g. Kinetic studies also revealed a significant improvement of sorption rates by the modifications. Diffusion coefficients of the dye molecule were determined to be of the order 10(-13) - 10(-12) m2/s. Furthermore, desorption experiments affirmed the regenerative capability of the loaded material.     

Distance and exposure dependent effective dielectric function

In an effort to develop a dielectric screening function for molecular dynamics simulations of biomolecules in implicit solvent, effective dielectric constants (D(eff)) for a large number of atom pairs in a typical globular protein are calculated by continuum electrostatics. Plots of D(eff) versus the intercharge distance are in general sigmoidal with the characteristics of the curve depending on the distance of the two charges from the dielectric boundary and, secondarily, on the extent to which the area surrounding each charge is occupied by solvent (the "exposure"). The D(eff) values were fitted to an empirical, analytical function of these parameters that reproduces the data reasonably well, although considerable scatter exists in the range of D(eff) from 30 to 80. In the system used for parameterization, the mean square deviation of electrostatic interaction energies with this function is 0.48 kcal/mol, compared to 1.45 for an analytical Generalized Born model and 1.52 for the linear distance-dependent dielectric model. When tested in other proteins of varying size and compactness, the present function is superior to both of the above models, except for a fully unfolded polypeptide chain, where the Generalized Born model is superior.     

Modeling peptide binding to anionic membrane pores

Peptide‐induced pore formation in membranes can be dissected into two steps: pore formation and peptide binding to the pore. A computational method is proposed to study the second step in anionic membranes. The electrostatic potential is obtained from numerical solutions to the Poisson–Boltzmann equation and is then used in conjunction with IMM1 (implicit membrane model 1). A double charge layer model is used to incorporate the effects of the membrane dipole potential. Inhomogeneity of the charge density in the pore, characterized by explicit membrane simulations of toroidal pores, is included in the model. This approach was applied to two extensively studied peptides, magainin and melittin. In agreement with previous work, binding to toroidal pores is more favorable than binding to the flat membrane. The dependence of binding energy on anionic content exhibits different patterns for the two peptides, in correlation with the different lipid selectivity that has been observed experimentally. © 2013 Wiley Periodicals, Inc.     

Thermodynamic contributions of the ordered water molecule in HIV-1 protease

Binding between biomolecules is usually accompanied by the formation of direct interactions with displacement of water from the binding sites. In some cases, however, the interactions are mediated by ordered water molecules, whose effect on binding affinity and the other thermodynamic functions is unclear. In this work, we compute the contribution of one such water molecule, the strongly bound water molecule at the binding site of HIV-1 protease, to the thermodynamic properties using statistical mechanical formulas for the energy and entropy. The requisite correlation functions are obtained by molecular dynamics simulations. We find that the entropic penalty of ordering is large but is outweighed by the favorable water-protein interactions. We also find a large negative contribution from this water molecule to the heat capacity. This approach could be useful in rational drug design by estimating which bound water molecules would be most favorable to displace.