Simulation and analysis of the diffusion properties of chloroform solution of carbosilane dendrimers

Abstract

Diffusion properties of macromolecules are important for theoretical studies and practical application. The hydrodynamic radius Rh, calculated from simulation data is usually used as a test of the correctness of the simulation, in other words, the radius is used to calibrate the simulation using its experimental values. However, as it was shown in this work, the traditional method of the extraction of the diffusion coefficient and hence the calculation of Rh, for dendrimers, as a rule, faces difficulties that require simulation resources several times more than, for example, a linear analogue. Here we study translation mobility of poly(butyl)carbosilane dendrimers in chloroform solution using molecular dynamics simulations. Different methods to estimate Rh for a dendrimer are discussed comparing to experimental data. Features, such as simulation time, substance characteristics, types of barostats, sizes of the involved elements, that may influence on accuracy of the result are considered and compared to existing papers. Based on problems, which occur during translational mobility studies, we offer an alternative way: to consider rotational diffusion which gives practically the same results for Rh compared to traditional method.