利用图论中的规则组合推断化学反应模式
Inferring Chemical Reaction Patterns Using Rule Composition in Graph Grammars
摘要：
将分子建模为无向图，将化学反应建模为图的重写操作，是一种自然而方便的化学建模方法。图形语法规则最自然地用于模拟基本反应，如分子的合并、分裂和异构化。特别是在分析较大的体系时，将几个后续反应归纳为一个单一的复合化学反应通常是方便的。我们使用一个通用的方法组成的图形语法规则来定义一个化学上有用的规则组合物。我们迭代地将这些规则组合应用于初等变换，以自动推断复杂的变换模式。这对于理解复杂催化循环的净效应（如福尔莫斯反应）是有用的。自动推断的图形语法规则是通用代表，其也涵盖了福尔摩糖循环的总体反应模式，即可以与结合的乙醇醛反应成第二乙醇醛的两个羰基。规则组合也可以用来研究聚合反应以及更复杂的迭代反应方案。例如，萜烯和聚酮化合物形成两种天然存在的具有最大药学意义的化合物，其可以被理解为分别由五碳（异戊二烯）和二碳单元组成的“广义聚合物”。
英文摘要：
Modeling molecules as undirected graphs and chemical reactions as graph rewriting operations is a natural and convenient approach tom odeling chemistry. Graph grammar rules are most naturally employed to model elementary reactions like merging, splitting, and isomerisation of molecules. It is often convenient, in particular in the analysis of larger systems, to summarize several subsequent reactions into a single composite chemical reaction. We use a generic approach for composing graph grammar rules to define a chemically useful rule compositions. We iteratively apply these rule compositions to elementary transformations in order to automatically infer complex transformation patterns. This is useful for instance to understand the net effect of complex catalytic cycles such as the Formose reaction. The automatically inferred graph grammar rule is a generic representative that also covers the overall reaction pattern of the Formose cycle, namely two carbonyl groups that can react with a bound glycolaldehyde to a second glycolaldehyde. Rule composition also can be used to study polymerization reactions as well as more complicated iterative reaction schemes. Terpenes and the polyketides, for instance, form two naturally occurring classes of compounds of utmost pharmaceutical interest that can be understood as "generalized polymers" consisting of five-carbon (isoprene) and two-carbon units, respectively.
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