Effect of repeat unit flexibility on dendrimer conformation as studied by atomistic molecular dynamics simulations

The effect of repeat unit structure on the shape and internal organization of various dendrimers was probed using atomistic molecular dynamics simulations. In this technique, care was taken to ensure complete structural equilibration by implementing a high temperature dynamics/simulated annealing protocol prior to evaluation of the molecular structure and dynamics. Both flexible and stiff repeat units that have been employed previously in the synthesis of dendrimers were considered. Flexible-unit dendrimers were found to be globular but not completely spherical. In contrast, stiff-unit dendrimers had a more eccentric, disk-like shape. For all dendrimers, the different generations within each molecule were found to be radially distributed throughout its interior. This appearance could be attributed to back-folding of some of the repeat units in the flexible case and to a branching angle effect in the stiff case. This distribution, however, did not preclude a molecular surface composed of a substantial portion of the topologically terminal groups. (C) 1999 Elsevier Science Ltd. All rights reserved.