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. The accuracy in Gibbs energy of mixing calculations is a few tenths of a kilocalorie per mole. As a final proof of principle, we use full coarse-grained sampling through DPD thermodynamics integration to calculate log POWfor 4627 compounds with an average error of 0.84 log unit. The computational speeds per calculation are a few seconds for CG RISM-HNC and a few minutes for DPD thermodynamic integration.
Leiden Institute of Chemistry, Leiden University , Einsteinweg 55, 2300 RA Leiden, The Netherlands.|Culgi BV , Galileiweg 8, 2333 BD Leiden, The Netherlands.
Johannes G E M
JG
Fraaije
Culgi BV , Galileiweg 8, 2333 BD Leiden, The Netherlands.
Jan
J
van Male
Culgi BV , Galileiweg 8, 2333 BD Leiden, The Netherlands.
Paul
P
Becherer
Culgi BV , Galileiweg 8, 2333 BD Leiden, The Netherlands.
Rubèn
R
Serral Gracià
D000465:Algorithms; D062126:Databases, Chemical; D008956:Models, Chemical; D015394:Molecular Structure; D013816:Thermodynamics