International Research Experience for Undergraduates

Colin Reese

2002 Participant


Determination of Stable Conformations within Free Base and Zinc Porphyrin Containing Polyamide Dendrimers

Dendrimers are macromolecules that emenate from a central core region to form a fluxional, highly-branched structure. They are known to act as energy funnels, and are models of light-harvesting systems, such as those involved in photosynthesis. Our initial calculations on dendrimers are molecular dynamics simulations designed to determine structural information. One question that is not well understood is the extent to which the periphery of the dendrimer penetrates to the core. This is of crucial importance in predicting whether the energy transfer occurs through space or through bonds.

The purpose of this project is to determine probable structures for three generations of Newkome-type anthraquinone terminated dendrimers (FbP-Ga-AQn and ZnP-GaA-AQn). Dreiding and MM+ force fields are used to simulate dynamics. The goal of this method is to find conformations representing accessible minima on the potential energy surfaces. The hypothesis is that electron-transfer rates estimated from the resulting structures will be consistent with the experimentally measured rates.

The electron-transfer (ET) characteristics of these dendrimers can be explained in terms of their structure. Two mechanisms are proposed for ET between the electron-donating core and the electron-acceptor groups on the periphery. The first (through-bond) mechanism involves a series of ET steps through covalently-bonded atoms linking the core to its extended anthraquinone terminal groups. The second (through-space) mechanism results from the proximity of the electron-accepting anthraquinone groups and the porphyrin core. Comparison of calculated and experimentally determined rate constants indicates that ET occurs primarily via an intramolecular, through-space mechanism. Several proposed structural families for this series of dendrimers, with distances of 5-10 Å between anthraquinone and porphyrin groups, provide compelling evidence for this mechanism.

In addition to the ability to visualize the proposed structures and dynamics, an analysis of proximity and alignment of the ET groups is presented. Preliminary data suggests that, while overall separation for all groups decreases, a striking pattern develops. Several anthraquinone groups approach the center of the molecule, stabilizing in distance in the 7-8 Å range and aligning within 10-15 degrees to form parallel stacks with the center group. Other groups move together away from the center, maintaining relatively constant separations and angles with respect to each other. These trends are visible in dynamics snapshots. We will investigate whether or not these trends continue through all three generations.