A graph-based toy model of chemistry
A graph-based toy model of chemistry
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DOI：
10.1021/ci0200570
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发表时间：
2003-07-01
期刊：
影响因子：
--
通讯作者：
Stadler, PF
中科院分区：
文献类型：
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作者：
Benkö, G;Flamm, C;Stadler, PF
大规模化学反应网络是一种普遍存在的现象，从活细胞的新陈代谢到行星大气中的过程和化学技术。这些网络中至少有一些表现出独特的全球特征，例如“小世界”行为。然而，对这些特性的系统研究在少数详细了解的网络中存在很大的抽样偏差。因此需要一个生成它们的计算模型。在这里，我们提出了一个玩具模型，它提供了一个一致的框架，在该框架中可以详细探索广泛化学反应网络的通用属性，同时保留化学的“外观和感觉”：分子以标记图表示，即通过其结构式表示；它们的基本属性是由直接在图上运行的扩展休克尔 MO 理论的漫画版本导出的；化学反应机制被实现为作用于结构式的图形重写规则；反应性和选择性通过基于扩展休克尔方案的前沿分子轨道理论的变体进行建模。该方法针对两种类型的反应网络进行了说明：狄尔斯-阿尔德反应和益生元糖合成中涉及的甲糖反应。
Large scale chemical reaction networks are a ubiquitous phenomenon, from the metabolism of living cells to processes in planetary atmospheres and chemical technology. At least some of these networks exhibit distinctive global features such as the "small world" behavior. The systematic study of such properties, however, suffers from substantial sampling biases in the few networks that are known in detail. A computational model for generating them is therefore required. Here we present a Toy Model that provides a consistent framework in which generic properties of extensive chemical reaction networks can be explored in detail and that at the same time preserves the "look-and-feel" of chemistry: Molecules are represented as labeled graphs, i.e., by their structural formulas; their basic properties are derived by a caricature version of the Extended Huckel MO theory that operates directly on the graphs; chemical reaction mechanisms are implemented as graph rewriting rules acting on the structural formulas; reactivities and selectivities are modeled by a variant of the Frontier Molecular Orbital Theory based on the Extended Huckel scheme. The approach is illustrated for two types of reaction networks: Diels-Alder reactions and the formose reaction implicated in prebiotic sugar synthesis.