Quantifying Error Correction through a Rule-Based Model of Strand Escape from an [ n ]-Rung Ladder
Quantifying Error Correction through a Rule-Based Model of Strand Escape from an [ n ]-Rung Ladder
复制标题
通过基于规则的 [ n ] 梯级链逃逸模型量化纠错
DOI：
10.1021/jacs.9b08958
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发表时间：
2019
影响因子：
15
通讯作者：
Moore, Jeffrey S.
中科院分区：
文献类型：
--
作者：
Cencer, Morgan M.;Greenlee, Andrew J.;Moore, Jeffrey S.
3D结构（MOFs、COFs等）的合理设计目前受到我们对分子组成如何组装的理解的限制。使用可逆相互作用（共价或非共价）的常见方法变得具有挑战性，特别是当靶由多价结构单元制成和/或在缓慢交换的条件下时，因为动力学陷阱和非平衡产物分布是可能的。组装过程的时间过程建模是困难的，因为反应网络包括许多可能的途径和中间体。在这里，我们表明，基于规则的动力学模拟有效地模拟涉及多价积木的动态反应。我们研究了“链逃逸从[n]-梯级阶梯”作为一个例子，其特征在于一个复杂的反应网络的动态过程。链逃逸问题是重要的，因为它预测了一个动态系统需要从涉及[n]-错误连接的错误中回溯的时间。我们量化的解离速率系数，链价，和种子物种的函数的纠错所需的时间。我们讨论了一个简单的概率框架，捕获的幂律依赖于链的价，和梯级开放率系数的反比关系的模拟结果。该模型还测试了一个梯级的合成效用（即，发夹）种子物种，其中，在中间时间，分叉到一个长寿的，完全形成的[n]-梯级阶梯和一对分离的链。因此，基于规则的模型提供指导的动态共价合成的规划，通过预测时间的最大产量的持久性中间体的一组特定的速率系数和化合价。
The rational design of 3D structures (MOFs, COFs, etc.) is presently limited by our understanding of how the molecular constituents assemble. The common approach of using reversible interactions (covalent or noncovalent) becomes challenging, especially when the target is made from multivalent building blocks and/or under conditions of slow exchange, as kinetic traps and nonequilibrium product distributions are possible. Modeling the time course of the assembly process is difficult because the reaction networks include many possible pathways and intermediates. Here we show that rule-based kinetic simulations efficiently model dynamic reactions involving multivalent building blocks. We studied “strand escape from an [n]-rung ladder” as an example of a dynamic process characterized by a complex reaction network. The strand escape problem is important in that it predicts the time a dynamic system needs to backtrack from errors involving [n]-misconnections. We quantify the time needed for error correction as a function of the dissociation rate coefficient, strand valency, and seed species. We discuss the simulation results in relation to a simple probabilistic framework that captures the power law dependence on the strand’s valency, and the inverse relationship to the rung-opening rate coefficient. The model also tests the synthetic utility of a one-rung (i.e., hairpin) seed species, which, at intermediate times, bifurcates to a long-lived, fully formed [n]-rung ladder and a pair of separated strands. Rule-based models thus give guidance to the planning of a dynamic covalent synthesis by predicting time to maximum yield of persistent intermediates for a particular set of rate coefficients and valency.