Pal Adittya, Fagerberg Rolf, Andersen Jakob Lykke, Flamm Christoph, Dittrich Peter, Merkle Daniel
Department of Mathematics and Computer Science, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark.
Department of Theoretical Chemistry, University of Vienna, Währinger Straße 17, 1090 Wien, Austria.
J Chem Inf Model. 2025 Jul 14;65(13):6772-6787. doi: 10.1021/acs.jcim.5c00265. Epub 2025 Jun 10.
Finding pathways that optimize the formation of a particular target molecule in a chemical reaction network is a key problem in many settings, including reactor systems. Chemical reaction networks are mathematically well-represented as hypergraphs, a modeling that facilitates the search for pathways by computational means. We propose to enrich an existing search method for pathways by including thermodynamic principles. In more detail, we give a mixed-integer linear programming (mixed ILP) formulation of the search problem into which we integrate chemical potentials and concentrations for individual molecules, enabling us to constrain the search to return pathways containing only thermodynamically favorable reactions. Moreover, if multiple possible pathways are found, we can rank these by objective functions based on thermodynamics. As an example of use, we apply the framework to a chemical reaction network representing the HCN-formamide chemistry. Alternative pathways to the one currently hypothesized in literature are queried and enumerated, including some that score better according to our chosen objective function.
在包括反应器系统在内的许多场景中，寻找能够优化化学反应网络中特定目标分子形成的途径是一个关键问题。化学反应网络在数学上可以很好地表示为超图，这种建模方式便于通过计算手段搜索途径。我们建议通过纳入热力学原理来丰富现有的途径搜索方法。更详细地说，我们给出了搜索问题的混合整数线性规划（mixed ILP）公式，在其中整合了单个分子的化学势和浓度，使我们能够将搜索限制为只返回包含热力学上有利反应的途径。此外，如果找到了多个可能的途径，我们可以根据基于热力学的目标函数对这些途径进行排序。作为应用示例，我们将该框架应用于一个表示HCN - 甲酰胺化学的化学反应网络。查询并列举了文献中目前假设的途径之外的替代途径，包括一些根据我们选择的目标函数得分更高的途径。
