Self-assembly of phenylalanine-based molecules.

Using molecular dynamics, we study the self-assembly of phenylalanine with charged end-groups at various temperatures and concentrations. As in the case of diphenylalanine, we observe the formation of nanotubes; however, phenylalanine aggregates in layers of four, not six, molecules. The observed aggregates are consistent with recent experimental measurements of fibrils obtained from mice with phenylketonuria.

Novel computational study on π-stacking to understand mechanistic interactions of Tryptanthrin analogues with DNA.

Based on recently published initial experimental results on the intercalation of a class of broad spectrum antiparasitic compounds, we present a purely theoretical approach for determining if these compounds may preferentially intercalate with guanosine/cytosine (GC)-rich or adenosine/thymidine (TA)-rich regions of DNA. The predictive model presented herein is based upon utilization of density functional theory (DFT) to determine a priori how the best intercalator may energetically and sterically interact with each of the nucleoside base pairs. A potential new method using electrostatic potential maps (EPMs) to visually select the best poses is introduced and compared to the existing brute-force center of mass (COM) approach.