Calculation of Diffusion Coefficients through Coarse-Grained Simulations Using the...

Area of Science:

• Computational Chemistry
• Molecular Dynamics Simulations
• Physical Chemistry

Background:

• Accurate calculation of diffusion coefficients is crucial for understanding molecular transport in various systems.
• Existing methods often rely on empirical correlations or computationally expensive all-atom simulations.
• There is a need for efficient and accurate simulation models for predicting molecular diffusion.

Purpose of the Study:

• To introduce and validate a novel coarse-grained molecular simulation model for calculating diffusion coefficients.
• To assess the model's performance on experimental diffusion data for small organic and drug-like molecules.
• To demonstrate the capability of molecular simulations to reproduce established empirical correlations.

Main Methods:

• Utilized dissipative particle dynamics (DPD) for coarse-grained molecular simulations.
• Employed an automated fragmentation and parametrization protocol, calibrated with the COSMO-RS thermodynamic model.
• Performed extensive simulations across the CULGI database (>11,000 molecules).

Main Results:

• The DPD model successfully predicts diffusion coefficients, validated against experimental data for diverse molecules.
• Simulations reproduced the empirical Wilke-Chang correlation between diffusion coefficient and molar volume.
• Established a conversion factor: 1 DPD time unit ≈ 64 ± 13 picoseconds of real time.

Conclusions:

• The developed DPD model offers a reliable and efficient approach for calculating molecular diffusion coefficients.
• This work marks the first theoretical/simulation-based demonstration of the Wilke-Chang correlation.
• The findings provide a valuable tool for computational chemistry and drug discovery research.