Hydrodynamic radius of dendrimers in solvents

The diffusion properties and hydrodynamic radius, R_h, of macromolecules are important for theoretical studies and practical application. Moreover, comparison of R_h values obtained from simulation and experimental data is used to check the correctness of simulation results. Here, we study the translation mobility of poly(butylcarbosilane) dendrimers in chloroform solution using molecular dynamics simulations and consider simulation details that may influence the accuracy of the result. Different methods to estimate R_h for a dendrimer are discussed with comparison to our experimental data. It was shown that the traditional MD simulation method for extraction of the diffusion coefficient (and calculation of R_h) of dendrimers as a rule faces difficulties and requires simulation resources several times greater than, for example, the same for a linear analogue. In the majority of MD simulation papers, the diffusion coefficient and/or R_h are calculated incorrectly. Also, we establish that correction of R_h according to the simulation box or estimation of R_h by using the gyration radius does not give values close to experimental data. To avoid the mentioned problems, we found an alternative way: to consider rotational diffusion, which gives an R_h similar to that from experiment and is practically independent of the size of the simulation box and other simulation parameters.