Paper Citing NAMD - Abstract
Chang, Theresa; Pieterse, Koen; Broeren, Maarten A. C.; Kooijman, Huub; Spek, Anthony L.; Hilbers, Peter A. I.; Meijer, E. W.
Structural elucidation of dendritic host-guest complexes by X-ray crystallography and molecular dynamics Simulations
CHEMISTRY-A EUROPEAN JOURNAL, 13:7883-7889, 2007
The multiple monovalent binding of adamantyl-urea poly(propyleneimine) dendrimers with carboxylic acid-urea guests was investigated using molecular dynamics simulations and Xray crystallography to better understand the structure and behavior of the dynamic multivalent complex in solution. The results from the two methods are consistent and suggest a preferred molecular picture of this complicated aggregate of multiple components. The guest molecules can bind to the dendrimet in a variety of ways although most involve hydrogen-bonding interactions between urea groups of the dendrimer with urea and/or carboxylic acid groups of the guest. In addition, acid-base interactions between the carboxylic acid of the guest and the tertiary amine in the interior of the dendritic host are present. Our proposed structure gives important information about the predominant dynamic interactions between the host and guest and illustrates how they fit together and interact with each other.
