3D chemical model for geological macromolecules

Abstract

This study defines a chemical representation of the kerogen macromolecule based on data from physicochemical analyses. The model should permit: creation of various schematic drawings representing an average macromolecule; future integration of new analytical results (for instance on structures of biomarkers or biopolymers); and determination of the distribution of chemical bonds. The models developed in this study can be represented in a 3D space, using classical chemical symbols, in the form of cyclic groups linked to each other by aliphatic chains. One cyclic group is a connected set of aromatic, naphthenoaromatic or naphthenic rings. These cyclic groups are constructed using basic elements such as atoms and bonds defined by their length and direction. Modeling of kerogen is done in three successive steps. A library is first created to define atoms, bonds and cyclic groups. Secondly, starting from a set of equations describing the analytical results, cyclic and aliphatic groups are chosen in the appropriate stoechiometric amount to match the analytical data. Finally the construction is done: cyclic groups are placed randomly in a 3D space, connections are made by aliphatic chains, and functional groups are added. The molecular modeling software Xmol TM can be operated on APOLLO stations. It allows the creation of libraries, the calculation of chemical bonds corresponding to the analyses and the construction of macromolecules. An example is given for a type III kerogen at the beginning of diagenesis.