The Development of Computational Methods to Study the Chemical Structural Evolution of Organic Macromolecules with Diagenesis

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9614352 Cody Organic Reactions that modify the chemical structure of biomacromolecules are controlled, in part by the long range topology of the macromolecule. Understanding the role of macromolecular structure on monomer scale reactivity has important implications regarding our ability to assess the probability for preservation of ancient biomacromolecules (e.g. kerogen as a function of T, P, and fluid composition. The work defined in this proposal sets out to develop a methodology for computational organic geochemistry. A step-wise approach is outlined that starts with a statistical mechanical model of macromolecular topology (the Rotational Isomeric State Model). The rotational isomeric states are characterized through semi-empirical quantum mechanical calculations of the inter-segmental rotational energy surface. These calculations lead to the generation of a large scale, "coarse-grained" macromolecular model that includes the effects of over 10000, monomers. Construction of the macromolecular model is constrained by the RIS calculations; from the initial configuration, using a structure building algorithm, to the final equilibrium state obtained via Monte-Carlo methods. Two macromolecular systems are selected as initial problems. These are the diagenesis of lignin, a principle biomacromolecular component of the xylem tissue of wood, and the diagenesis of sporopollenin, a particularly resistant biopolymeric component of plant spores and seeds. The developed computational methods will be applied to assess the energetic penalties (or gains) of various proposed diagenetic reaction pathways in the two systems based on consideration of the total energy of the macromolecular system. The methodology obtained from the work outlined in this proposal will be exportable to a wide range of problems in organic geochemistry.