Paper Citing NAMD - Abstract
Rodriguez-Ropero, Francisco; Canales, Manel; Zanuy, David; Zhang, Afang; Schlueter, Dieter; Aleman, Carlos
Helical Dendronized Polymers with Chiral Second-Generation Dendrons: Atomistic View and Driving Forces for Structure Formation
JOURNAL OF PHYSICAL CHEMISTRY B, 113:14868-14876, NOV 12 2009
The secondary structures of protected (neutral) and deprotected (charged) second generation dendronized polymethylmethacrylates carrying chiral 4-aminoproline-based dendrons were investigated using atomistic molecular dynamics simulations. Trajectories involving a total of similar to 280 ns on molecular systems containing up to 101 909 explicit particles allowed the correlation of the structural parameters, rigidity, and thermal stability with the microscopic interactions that govern these systems. In both the neutral and the charged systems a right-handed helix is found. This screw-sense is enforced by the packing of the dendrons and allows for a very similar arrangement of the poly methyl meth acryl ate backbones, independently of their tacticity. The properties of the secondary structures are mainly defined by the interdendron interactions, whereby the remarkable thermal stability and the rigid rod-like behavior found for the protected polymer is due to the interdendron network of hydrogen bonds. For the deprotected congener instead, where also a helical secondary structure is found, a specific arrangement of the dendritic side chains minimize the repulsive interactions between the positive charges of neighboring repeat units. In addition, the impact of the conformational changes produced when the protected system transforms into the deprotected one by the addition of acid has been evaluated.
