Soot and char molecular representations generated directly from HRTEM lattice fringe images using Fringe3D

Char and soot are complex carbonaceous structures that are important in traditional energy generation, reactivity, biomass combustion, pollution, climate change, and human health. HRTEM lattice fringe images have significantly improved how we "see" these complex structures. Yet our attempts to use molecular modeling to explore the structure behavior relationships are hampered by the complexity and difficulty in capturing the alignment, graphene to polyaromatic "hydrocarbon" stacks, any symmetry, and more importantly the distribution of structural features. It is the structural detail, which often controls the behavior of soots and chars that are otherwise similar in bulk properties. As a consequence, modeling efforts are often highly simplistic or highly complex with considerable expense being utilized in obtaining structures that do not capture all these structural details. Here we attempt a new approach: Fringe3D to directly generate the lattice fringe images in molecular space from HRTEM lattice fringe images. Image analysis determines the Cartesian coordinates, fringe length, orientation, and more importantly the distributions of those parameters. A Perl script populates the model space with a centroid representing the center of each fringe. From calibration files, either a known molecule or selected number of carbon atoms in the desired catenation style, molecules are constructed for each fringe around each centroid. The molecules are pitched to match fringe orientation. In this manner the: symmetry, stacking, orientation, and structural distributions are retained along with fine-structural details. The approach is demonstrated, with a bituminous coal char and a primary diesel soot particle, to produce initially simplistic atomistic representations of the aromatic carbon structure with greater ease, and far more rapidly than existing approaches.