Molecular Modeling of Dendrimers


Materials and Process Simulation Center (MSC) has been in the forefront of molecular modeling, characterization of dendrimers. In the course of this work several dendrimers were and are being studied using molecular builders, visualisation and analysis tools along with the Molecular Mechanics and Molecular Dynamics simulations. Below, you'll find pictures and movies of the dendrimers studied at the MSC. The contibutors to the project (past and current) are W. A. Goddard, D. Tomalia, Adel Naylor, Tahir Cagin, Derek Bins and Paul Miklis.

  1. Simulation of Dendrimer Box
  2. Images and Movies of Dendritic Molecules
  3. Collaborations
  4. Links to Dendrimer Research Reseources

Molecular Dynamics of Meijer Dendrimer Box

Recently, the encapsulation of bengal rose molecules in the Meijer Dendrimer Box (DBox) has been studied [P. Miklis, T. Cagin and W.A. Goddard, JACS, 1997, 119, pp7458-7462]. Molecular dynamics simulations were performed for the Dendrimer Box and the fifth generation poly(propyleneimine) dendrimer (PPI-5) with both four and six bengal rose molecules.

Following links represents the time evolution of the center of mass of six bengal rose molecules in dendrimer box and PPI-5.

Dendrimers: Images and Movies

50 ps simulation	       PAMAM		    25 picosecond
(2.2 MB MPEG Color)	   7-generations	  (0.6 MB MPEG BW)

Ph-O dendrimer		    Dendrimer Box	    Ph-O dendrimer         
CPK-rendering		    Generation 5	 Solvent accesible surface

The movies are created from a POLYGRAF trajectory ran by T. Cagin. In the simulation NEIMO Molecular Dynamics method (ref. A. Jain, V. Nagarajan and W.A. Goddard) is used. This method enables the most efficient sampling of the conformational changes for such systems by eliminating the high frequency modes arising from the bond stretch and the angle bending terms. Hence, using large integration time steps ranging from 10 fs to 100 fs yield longer time simulations at least a 10 to 100 times lower compute cost.


Molecular and Process Simulation Center researchers collaborate with various research groups in this field. The research interests of these groups are extremely broad ranging from dendrimer synthesis, to polymer science and materials science to molecular recognition and catalysis to device design and fabrication.

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