Paper Citing NAMD - Abstract
Bertran, Oscar; Zhang, Baozhong; Schlueter, A. Dieter; Kroeger, Martin; Aleman, Carlos
Computer Simulation of Fifth Generation Dendronized Polymers: Impact of Charge on Internal Organization
JOURNAL OF PHYSICAL CHEMISTRY B, 117:6007-6017, MAY 16 2013
The internal organization of a fifth-generation dendronized polymer (PG5) has been investigated by atomistic molecular dynamics simulations in a vacuum. This study reveals an exceptional behavior of PG5 within the homologous series of g-generation PGg polymers. Three molecular configurations, which present a heterogeneous distribution of dendrons and an amount of backfolding lower than PG4 and PG6, have been obtained for PG5. The highest stability and closest agreement with available experimental data corresponds to a helical conformation characterized by a pitch of about 30 angstrom, thickness of 105 angstrom, and average density of 0.861 g/cm(3). While small angle neutron scattering studies of PG5 in solution show a constant radial density distribution around the backbone, we here in our vacuum studies find a cylindrical volume element of sharply reduced density reminiscent of a pore. This neutral PG5 was compared with its charged deprotected analogue, dePGS in water, to see in as much the positive charges in the periphery of this macromolecule would affect its conformational behavior. During deprotection of PG5, the tert-butyloxycarbonyl protected amine groups are converted into ammonium, mimicking the experimental situation during a divergent synthesis procedure. The repulsive interactions among the positively charged ammonium groups are responsible for a huge (similar to 30%) reduction of the average density and a small (similar to 1%) increase of elongation of the helical backbone, which results in a structure with a spongy appearance. Also here, we find a reduced dendron density near the backbone which is compensated for by the pore being filled with water.
