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

Unlabelled: 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.

Coarse-Grained Models for Automated Fragmentation and Parametrization of Molecular Databases.

We calibrate coarse-grained interaction potentials suitable for screening large data sets in top-down fashion. Three new algorithms are introduced: (i) automated decomposition of molecules into coarse-grained units (fragmentation); (ii) Coarse-Grained Reference Interaction Site Model-Hypernetted Chain (CG RISM-HNC) as an intermediate proxy for dissipative particle dynamics (DPD); and (iii) a simple top-down coarse-grained interaction potential/model based on activity coefficient theories from engineering (using COSMO-RS). We find that the fragment distribution follows Zipf and Heaps scaling laws.