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

ABSTRACT: 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.

SUBMITTER: Fraaije JGEM 

PROVIDER: S-EPMC5997386 | biostudies-literature | 2018 Feb

REPOSITORIES: biostudies-literature