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

小行星9614352 改变生物大分子化学结构的有机反应部分受大分子的长程拓扑结构控制。 了解大分子结构对单体规模反应性的作用对于我们评估古生物大分子（例如，油母岩作为T，P和流体组成的函数）保存的可能性的能力具有重要意义。 本提案中所界定的工作旨在为计算有机地球化学制定一种方法。 一个逐步的方法概述，开始与大分子拓扑结构的统计力学模型（旋转异构态模型）。 通过对链段间转动能面的半经验量子力学计算，表征了转动异构态。 这些计算导致产生一个大规模的，“粗粒度”的大分子模型，其中包括超过10000，单体的影响。 大分子模型的构建受RIS计算的约束;从使用结构构建算法的初始构型到通过蒙特-卡罗方法获得的最终平衡态。 选择两个大分子体系作为初始问题。 这些是木质素的成岩作用，木质部组织的主要生物大分子组分，以及孢粉素的成岩作用，植物孢子和种子的特别抗性生物聚合物组分。 所开发的计算方法将被应用到评估的能量惩罚（或增益）的各种建议的成岩反应途径在两个系统的基础上考虑的大分子系统的总能量。 从本建议中概述的工作中获得的方法将可用于有机地球化学中的广泛问题。

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.