Constructing one-dimensional supramolecular polymer structures using particle swarm optimization technique

IF 1.6 4区化学 Q4 CHEMISTRY, PHYSICAL Theoretical Chemistry Accounts Pub Date : 2024-03-05 DOI:10.1007/s00214-024-03095-z

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Abstract

In the realm of studying supramolecular polymers using computer simulations, the task of generating appropriate initial structures poses a significant challenge, primarily owing to the extensive range of potential configurations. In this study, we introduce StackGen, an open-source framework designed to efficiently create energy-optimized one-dimensional supramolecular polymer structures with minimal computational overhead. This tool utilizes the particle swarm optimization (PSO) algorithm in conjunction with a semiempirical quantum mechanical approach to identify low-energy supramolecular stack configurations from a diverse set of possibilities. These configurations result from the translational and rotational adjustments of adjacent molecules around monomers along various axes. The tool also considers various structural factors, including the presence of functional side groups and the extent of intermolecular \(\pi\) – \(\pi\) stacking interactions. Extensive testing across different molecules demonstrates StackGen’s ability to produce low-energy structures with negligible computational costs. Additionally, the tool incorporates features for optimizing PSO hyperparameters in real-time, thus improving convergence. The tool provides a convenient means of generating structures suitable for both molecular simulations and quantum mechanical calculations.

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利用粒子群优化技术构建一维超分子聚合物结构

摘要在利用计算机模拟研究超分子聚合物的领域，生成适当初始结构的任务是一项重大挑战，这主要是由于潜在构型的范围很广。在本研究中，我们介绍了 StackGen，这是一个开源框架，旨在以最小的计算开销高效地创建能量优化的一维超分子聚合物结构。该工具利用粒子群优化（PSO）算法，结合半经验量子力学方法，从各种可能性中识别出低能耗的超分子堆栈构型。这些构型来自单体周围相邻分子沿不同轴线的平移和旋转调整。该工具还考虑了各种结构因素，包括功能侧基的存在以及分子间堆叠相互作用的程度。对不同分子的广泛测试表明，StackGen 能够以可忽略不计的计算成本生成低能结构。此外，该工具还具有实时优化 PSO 超参数的功能，从而提高了收敛性。该工具为生成适用于分子模拟和量子力学计算的结构提供了便捷的方法。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Theoretical Chemistry Accounts 化学-物理化学

CiteScore

3.40

自引率

0.00%

发文量

审稿时长

3.8 months

期刊介绍： TCA publishes papers in all fields of theoretical chemistry, computational chemistry, and modeling. Fundamental studies as well as applications are included in the scope. In many cases, theorists and computational chemists have special concerns which reach either across the vertical borders of the special disciplines in chemistry or else across the horizontal borders of structure, spectra, synthesis, and dynamics. TCA is especially interested in papers that impact upon multiple chemical disciplines.