Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands.
J Chem Theory Comput. 2023 Jul 11;19(13):4040-4046. doi: 10.1021/acs.jctc.2c01186. Epub 2023 Jun 16.
Chemical reactions are ubiquitous in both materials and the biophysical sciences. While coarse-grained (CG) molecular dynamics simulations are often needed to study the spatiotemporal scales present in these fields, chemical reactivity has not been explored thoroughly in CG models. In this work, a new approach to model chemical reactivity is presented for the widely used Martini CG Martini model. Employing tabulated potentials with a single extra particle for the angle dependence, the model provides a generic framework for capturing bonded topology changes using nonbonded interactions. As a first example application, the reactive model is used to study the macrocycle formation of benzene-1,3-dithiol molecules through the formation of disulfide bonds. We show that starting from monomers, macrocycles with sizes in agreement with experimental results are obtained using reactive Martini. Overall, our reactive Martini framework is general and can be easily extended to other systems. All of the required scripts and tutorials to explain its use are provided online.
化学反应在材料科学和生物物理科学中无处不在。虽然在研究这些领域中存在的时空尺度时，通常需要使用粗粒化（CG）分子动力学模拟，但 CG 模型中尚未深入探索化学反应性。在这项工作中，为广泛使用的 Martini CG Martini 模型提出了一种新的模拟化学反应性的方法。该模型采用带有单个额外粒子的表格势来表示角度依赖性，为使用非键相互作用捕捉键合拓扑变化提供了通用框架。作为第一个示例应用，通过形成二硫键，使用反应性 Martini 研究了苯-1,3-二硫醇分子的大环形成。我们表明，从单体开始，使用反应性 Martini 可以得到与实验结果一致的大环尺寸。总体而言，我们的反应性 Martini 框架是通用的，可以轻松扩展到其他系统。所有解释其使用的所需脚本和教程都在线提供。
