Automated simultaneous assignment of bond orders and formal charges

Abstract Bond orders and formal charges are fundamental chemical descriptors. In cheminformatic applications it is necessary to be able to assign these properties to a given molecular structure automatically, given minimal input information. Here we describe a method for determining the bond order and formal charge assignments from only the atom types and connectivity. Our method utilises a graph theoretical description of electron positions. Each electron position assignment is scored according to lookup tables of atomic and bond dissociation energies derived from quantum chemical calculations. We tested three different optimisation methods—local optimisation, an A* pathfinding method, and an FPT optimisation method utilising tree decompositions—for finding the best electron position assignment, from which the bond orders and formal charges are extracted. We show that our method can assign bond orders and formal charges at a high degree of accuracy across a wide range of molecules from two different databases, and that the FPT algorithm provides the best combination of speed and accuracy