Computational Investigation of the Effect of Backbone Chiral Inversions on Polypeptide Structure.

Studying a set of helix-folding polyalanine peptides with systematically inserted chiral inversions in explicit water, we investigate quantitatively the effect of chiral perturbations on the structural ensembles of the peptides, thereby assessing the extent to which the backbone structure is able to fold in the presence of systematic heterochiral perturbations. Starting from the homochiral l-Ala20 peptide, we invert the backbone chiralities of Ala residues one by one along a specific perturbation pathway, until reaching the homochiral d-Ala20 peptide. Analysis of the helical contents of the simulated structural ensembles of the peptides shows that even a single inversion in the middle of the peptide completely breaks the helical structure in its vicinity and drastically reduces the helical content of the peptide. Further inversions in the middle of the peptide monotonically decrease the original helical content, that is, the right-handed helical content for l-Ala, and increase the helical content of the opposite chirality. Further analysis of the peptide ensembles using several size- and shape-related order parameters also indicate the drastic global changes in the peptide structure due to the local effects caused by the chiral inversions, such as formation of a reverse turn. However, the degree of the structural changes introduced by opposite chirality substitutions depends on the position of the inversion.

Lattice model for silica polymerization: Monte Carlo simulations of the transition between gel and nanoparticle phases.

We present Monte Carlo simulations of a lattice model describing silica polymerization with an emphasis on the transition between gel states and nanoparticle states as the pH and silica concentration are varied. The pH in the system is controlled by the addition of a structure-directing agent (SDA) of the type SDA(+)(OH(-)). The silica units are represented by corner-sharing tetrahedra on a body-centered cubic lattice and the SDA(+) species by single sites with near-neighbor repulsions. We focus on two systems: one with a low silica concentration with composition comparable to that of the clear solution silicalite-1 zeolite synthesis and a high silica concentration system that leads to gel states. In the dilute system, clusters have a core-shell structure, with the core predominantly comprised of silica with some SDA(+) cations, surrounded by a shell of only SDA(+) cations. Moreover, the average cluster size gradually decreases from 2 to 1.6 nm with increasing pH. The concentrated system forms a gel that remains stable to increasing pH up to about 9.2. At pH values in the range of 9.2-10, the gel transforms to nanoparticles of size around 1.0 nm, surprisingly smaller than those in the dilute system. We also study the evolution of the Q(n) distribution (a measure of the silica network structure) for both systems and obtain good agreement with (29)Si NMR data available for the concentrated system.