2026-10-13T17:10:00Z https://api.figshare.com/v2/oai

oai:figshare.com:article/33777998 2026-09-15T08:14:27Z category_1 category_4 category_915 category_873 category_39 category_734 category_133 category_135 portal_63 item_type_3 month_year_09_2026

A Coarse-Grained Model for Small Organic Molecules with Optimized Lennard-Jones Parameters Renjie Zhu (8161122) Tong Zhu (8079) Ruibo Wu (1374138) Fei Xia (256985) Biophysics Biochemistry Physical Sciences not elsewhere classified Chemical Sciences not elsewhere classified Ecology Biological Sciences not elsewhere classified Plant Biology Computational Biology transfer free energies small organic molecules providing clear directions optimization strategy proposed hydration free energies gaff2 force field complex chemical molecules atom force field parameters optimized via nonoptimized water model developing cg small oljcg model vaporization enthalpies two datasets systematically evaluated systematic route results demonstrate primary sources nonbonded interactions molecule databases molecular models future refinement enabling data electrostatic interactions driven research constructing databases Developing accurate coarse-grained (CG) molecular models is crucial for constructing databases of complex chemical molecules and enabling data-driven research. Here we present the OLJCG model for small organic molecules, with Lennard-Jones (LJ) parameters optimized via the Lennard-Jones Static Potential Matching method based on the GAFF2 force field. The OLJCG model is systematically evaluated on two datasets (DS58 and DS29) for densities, vaporization enthalpies, nonaqueous solvation free energies, hydration free energies, and transfer free energies. The results demonstrate that the optimized LJ parameters effectively preserve the description of nonbonded interactions from the all-atom force field. The primary sources of error are identified as the neglect of electrostatic interactions and the use of a nonoptimized water model, providing clear directions for future refinement. The optimization strategy proposed here provides a systematic route for developing CG small-molecule databases. 2026-09-15T00:00:00Z Dataset Dataset 10.1021/acs.jpcb.6c05069.s001 https://figshare.com/articles/dataset/A_Coarse-Grained_Model_for_Small_Organic_Molecules_with_Optimized_Lennard-Jones_Parameters/33777998 CC BY-NC 4.0