PXLink: A simulation program of polymer crosslinking to study of polyamide membrane
PXLink: A simulation program of polymer crosslinking to study of polyamide membrane
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DOI：
10.1016/j.cpc.2023.108840
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发表时间：
2023-07
期刊：
影响因子：
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通讯作者：
Chijian Zhang;Guangle Bu;Md Symon Jahan Sajib;Lida Meng;Shiying Xu;Size Zheng;Lin Zhang;Tao Wei
中科院分区：
文献类型：
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作者：
Chijian Zhang;Guangle Bu;Md Symon Jahan Sajib;Lida Meng;Shiying Xu;Size Zheng;Lin Zhang;Tao Wei
交联型网络聚合物在工程、生物医学和环境等领域有着重要的应用。建立交联型聚合物网络是研究聚合物膜结构和功能的重要的第一步。在这项研究中，我们开发了一个名为PXLink的Python脚本，并与GROMACS软件集成，模拟了广泛应用于海水淡化和水处理的交联芳香族聚酰胺(PA)膜。利用GROMACS中实现的能量最小化和分子动力学模拟，PXLink可以在相邻的羧基和胺基团之间建立化学键，并在交联过程中松弛体系。通过对水的扩散率和溶剂化膜的结构性质的基准研究，包括孔径分布、膜密度和芳香环的堆积(密度分布和有序性)，我们的协议的准确性已经被成功地验证。此外，干膜和湿膜的比较表明，膜表面的膨胀导致了亚纳米孔的扩张和局部结构的有序化。溶胀后，膜的主要区域半径为0.2 nm的气孔数量减少，而0.22-0.38 nm范围内的气孔增多。局域结构的有序性也增加了，这从距离为0.7-0.8 nm的芳环对的有序性参数的增加可见一斑。我们开发的脚本将是设计和发现交联聚合物的宝贵工具。程序摘要程序标题：PXLinkCPC库链接到程序files:https://doi.org/10.17632/yjw2ghfzmh.1Developer‘s存储库link:https://github.com/zchinet30/PXLinkLicensing条款：GNU通用公共许可证3编程语言：Python问题的性质：形成交联的聚合物网络对于理论研究和众多实际应用是必不可少的。然而，由于其复杂的性质，涉及到大系统内物理过程和化学反应的复杂相互作用，用传统的分子动力学模拟方法模拟聚合物的交联过程是一项挑战。解决方法：为了解决这一局限性，我们开发了一个基于PXLink的脚本，它与GROMACS的分子动力学软件集成，用于模拟聚合物的交联过程。
Crosslinked network polymers have numerous important applications in engineering, biomedicine, and the environment. Establishing a crosslinked polymer network is an essential initial step toward studying the structure and function of polymer membranes. In this study, we developed a Python script named PXLink that integrates with GROMACS software to simulate the crosslinked aromatic polyamide (PA) membrane, which is widely used in desalination and water treatment. PXLink can create chemical bonds between the neighboring carboxyl and amine groups and relax the system during the crosslinking, utilizing energy minimization and molecular dynamics simulations implemented in GROMACS. The accuracy of our protocol has been successfully validated through a benchmark study of water diffusivity and the structural properties of a solvated membrane, including pore size distribution, membrane density, and the stacking of aromatic benzene rings (density profile and ordering). Moreover, the comparison between the dry and wet polymer membranes reveals that the swelling of the membrane surface leads to the expansion of subnanopores and the increased ordering of local structures. After the swelling of the membrane, the number of pores with a radius around the main region of 0.2 nm decreases, while more pores in the range of 0.22–0.38 nm are observed. There is also an increase in the orderliness of local structures, as evidenced by the increasing order parameter of aromatic ring pairs with a distance ranging from 0.7 to 0.8 nm. Our developed script will be a valuable tool for designing and discovering crosslinked polymers.Program summaryProgram Title:PXLinkCPC Library link to program files:https://doi.org/10.17632/yjw2ghfzmh.1Developer's repository link:https://github.com/zchinet30/PXLinkLicensing provisions:GNU General Public License 3Programming language:PythonNature of problem:The formation of a crosslinked polymer network is essential for theoretical studies and numerous practical applications. However, simulating the polymer crosslinking process using conventional molecular dynamic simulations presents challenges due to its intricate nature, which involves a complex interplay of physical processes and chemical reactions within a large-scale system.Solution method:To address this limitation, we developed PXLink, a python-based script, which integrates with the molecular dynamics software of GROMACS for the simulation of polymer crosslinking.