Dataset Construction to Explore Chemical Space with 3D Geometry and Deep Learning

Abstract

Dataset is the basis of deep learning model development, and the success of deep learning models heavily relies on the quality and size of the dataset. In this work, we present a new data preparation protocol and build a large fragment-based dataset Frag20, which consists of optimized 3D geometries and calculated molecular properties from Merck Molecular Force Field (MMFF) and DFT at B3LYP/6-31G* level of theory for more than half a million molecules composed of H, B, C, O, N, F, P, S, Cl, Br with no larger than 20 heavy atoms. Based on the new dataset, we develop robust molecular energy prediction models using a simplified PhysNet architecture for both DFT-optimized and MMFF-optimized geometries, which achieve better than or close to chemical accuracy (1 kcal/mol) on multiple test sets, including CSD20 and Plati20 based on experimental crystal structures.