Calculation of Diffusion Coefficients through Coarse-Grained Simulations Using the Automated-Fragmentation-Parametrization Method and the Recovery of Wilke-Chang Statistical Correlation

We introduce a model for the calculation of diffusion coefficients using dissipative particle dynamics coarse-grained molecular simulations. We validate the model on experimental diffusion data of small organics and drug-like molecules in water. The new model relies on our automated-fragmentation-parametrization protocol for cutting molecules into fragments, which are calibrated using the COSMO-RS thermodynamic model (J. Chem. Inf. Model. 2016, 56 (12), 2361-2377, DOI: 10.1021/acs.jcim.6b00003). By simulations over the entire CULGI database of more than 11000 molecules, we recover the decades-old empirical Wilke-Chang correlation between diffusion coefficient and molar volume. We believe this is the first demonstration of the correlation by simulation or theory. From a comparison of simulated and experimental diffusion coefficients, we find that one full time unit of coarse-grained simulation equals 64 +/- 13 ps real time.