论文标题

是什么使反应网络“化学”?

What makes a reaction network "chemical"?

论文作者

Müller, Stefan, Flamm, Christoph, Stadler, Peter F.

论文摘要

反应网络(RNS)包括一组$ x $的物种和一个$ \ mathscr {r} $ y'$ y'$的$ y \ y'$,每个$ y'$,每个转换一个多组的$ y \ y \ subseteq x $中的产品$ y'\ y'\ y'\ subseteq x $ of产品。 RN等同于定向超图。但是,并非所有RN都一定会接受化学解释。取而代之的是,它们可能与物理学的基本原理相矛盾,例如能量和质量或化学反应的可逆性。在文献中广泛讨论了这些必要条件对化学计量矩阵$ \ mathbf {s} \ in \ Mathbb {r}^{x \ times \ Mathscr {r}} $的后果。在这里,我们为$ \ mathbf {s} $提供了足够的条件,以保证分别按平衡的总和公式和结构公式来解释RN。 化学上合理的RN既不允许使用无限制能源生产的反应的“徒劳循环”,也不允许质量的“徒劳循环”。据说这样的RN在热力学上是合理的和保守的。对于有限的RN,这两个条件都可以等效地表示为$ \ Mathbf {s} $的属性。第一个条件对于可逆网络是空置的,但它不包括不可逆转的徒劳周期,并且在更严格的意义上 - 甚至包含不可逆反应的徒劳循环。第二条件等于存在严格的阳性反应不变。此外,这足以实现总和公式,遵守“原子”的保护。特别是,可以选择这些实现,以使任何两个物种都具有独特的总和公式,除非$ \ mathbf {s} $意味着它们是“强制性异构体”。就结构公式而言,每种化合物都是标记的多编码,本质上是刘易斯公式,反应仅包含键的重排,因此保留了总债券顺序。

Reaction networks (RNs) comprise a set $X$ of species and a set $\mathscr{R}$ of reactions $Y\to Y'$, each converting a multiset of educts $Y\subseteq X$ into a multiset $Y'\subseteq X$ of products. RNs are equivalent to directed hypergraphs. However, not all RNs necessarily admit a chemical interpretation. Instead, they might contradict fundamental principles of physics such as the conservation of energy and mass or the reversibility of chemical reactions. The consequences of these necessary conditions for the stoichiometric matrix $\mathbf{S} \in \mathbb{R}^{X\times\mathscr{R}}$ have been discussed extensively in the literature. Here, we provide sufficient conditions for $\mathbf{S}$ that guarantee the interpretation of RNs in terms of balanced sum formulas and structural formulas, respectively. Chemically plausible RNs allow neither a perpetuum mobile, i.e., a "futile cycle" of reactions with non-vanishing energy production, nor the creation or annihilation of mass. Such RNs are said to be thermodynamically sound and conservative. For finite RNs, both conditions can be expressed equivalently as properties of $\mathbf{S}$. The first condition is vacuous for reversible networks, but it excludes irreversible futile cycles and - in a stricter sense - futile cycles that even contain an irreversible reaction. The second condition is equivalent to the existence of a strictly positive reaction invariant. Furthermore, it is sufficient for the existence of a realization in terms of sum formulas, obeying conservation of "atoms". In particular, these realizations can be chosen such that any two species have distinct sum formulas, unless $\mathbf{S}$ implies that they are "obligatory isomers". In terms of structural formulas, every compound is a labeled multigraph, in essence a Lewis formula, and reactions comprise only a rearrangement of bonds such that the total bond order is preserved.

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