Molecular simulations of dendritic molecules : a study of PAMAM and phenyl-acetylene dendrimers

Dendrimers are branched molecules that often have chemical properties similar to proteins and other large organic molecules. Dendrimers presently have applications as reactive surfaces for catalysis, and as hosts for drug delivery. Computer simulations of dendritic molecules are difficult due to their relatively large size and the tendency of atoms within a dendrimer to come within very close proximity to each other. The large number of steric interactions makes modeling of dendrimers difficult due to unphysically high energies that arise when a modeler attempts to construct a starting dendrimer from which to minimize its energy. Here we present Dendmol, a code that uses rigid body mechanics and a Monte Carlo method to set up the initial conditions for a dendrimer and present our findings. We found that this method is able to rapidly find conformations of dendrimers that can be readily placed into molecular mechanics, and molecular dynamics codes for further study of the dendrimer.

Name thesis:degree_name

Computer Science

Level thesis:degree_level

Thesis

Discipline thesis:degree_discipline

Department of Computer Science

Year

2010

Author dc:creator

• Fleharty, Mark

Contributors dc:contributor

• Luan, Shuang
• Evans, Deborah
• Stefanovic, Darko

• dendrimer
• optimization
• monte carlo
• dendmol

Language dc:language

English

Identifier

https://digitalrepository.unm.edu/cs_etds/56

OAI identifier oai:identifier

oai:digitalrepository.unm.edu:cs_etds-1055