Simm Gregor N, Reiher Markus
Laboratory of Physical Chemistry, ETH Zürich , Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland.
J Chem Theory Comput. 2017 Dec 12;13(12):6108-6119. doi: 10.1021/acs.jctc.7b00945. Epub 2017 Nov 8.
The construction of a reaction network containing all relevant intermediates and elementary reactions is necessary for the accurate description of chemical processes. In the case of a complex chemical reaction (involving, for instance, many reactants or highly reactive species), the size of such a network may grow rapidly. Here, we present a computational protocol that constructs such reaction networks in a fully automated fashion steered in an intuitive, graph-based fashion through a single graphical user interface. Starting from a set of initial reagents new intermediates are explored through intra- and intermolecular reactions of already explored intermediates or new reactants presented to the network. This is done by assembling reactive complexes based on heuristic rules derived from conceptual electronic-structure theory and exploring the corresponding approximate reaction path. A subsequent path refinement leads to a minimum-energy path which connects the new intermediate to the existing ones to form a connected reaction network. Tree traversal algorithms are then employed to detect reaction channels and catalytic cycles. We apply our protocol to the formose reaction to study different pathways of sugar formation and to rationalize its autocatalytic nature.
为了准确描述化学过程，构建一个包含所有相关中间体和基元反应的反应网络是必要的。对于复杂化学反应（例如，涉及许多反应物或高活性物种的反应），这样一个网络的规模可能会迅速增长。在此，我们提出一种计算协议，该协议以完全自动化的方式构建此类反应网络，并通过一个直观的基于图形的单一图形用户界面进行引导。从一组初始试剂开始，通过已探索中间体或呈现给网络的新反应物的分子内和分子间反应来探索新的中间体。这是通过基于从概念电子结构理论导出的启发式规则组装反应复合物并探索相应的近似反应路径来完成的。随后的路径细化会产生一条将新中间体与现有中间体连接起来以形成连通反应网络的最小能量路径。然后采用树遍历算法来检测反应通道和催化循环。我们将我们的协议应用于蚁醛反应，以研究糖形成的不同途径并阐明其自催化性质。
