Novel Simplification Approach for Large-Scale Structural Models of Coal: Three-Dimensional Molecules to Two-Dimensional Lattices. Part 1: Lattice Creation

The utility of complex structural models of coal could be expanded for enhanced structural visualization, and behavioral studies of liquefaction and pyrolysis chemistry if three-dimensional (3D) models and two-dimensional (2D) lattice manipulation could be linked: lattices can be used to describe thermolysis reactions through practical and inexpensive statistical approaches. A computational tool was created that enables a systematic simplification of complex 3D structural models of coal into corresponding 2D lattice representations via atom typing, pattern recognition, and graph theory. The simplification is performed via a Perl script that modifies the 3D model through manipulation of the text in InsightII molecular files. The tool scans the original model file and generates a 3D skeletal version consisting of nodes that are representative of unreactive coal fragments (assumed here to be aromatic entities). We use a novel coarse-graining-like approach to identify these ring structures, collapsing conjugated systems in singular nodes. Similarly connecting lines are produced, connecting nodes and capturing cross-links and the network typology. Consequently, a 2D lattice is constructed from the "coarse-grained" model to aid structural visualization. The principle of granularity is applied here, and although similar to the initial stage of molecular dynamic coarse-graining methods, we stop after the creation of the beads and do not pursue parametrization for dynamics simulations. The goal in this paper is the molecular simplification and 2D lattice construction approach to aid in viewing structural information and representation of the network structure. A 2D lattice network structure specific to a large-scale molecular representation is also expected to be helpful for numerical lattice-based simulations of coal thermal breakdown.