GMUPC: a new package for global-minimum search of large uranyl peroxide clusters with machine learning potentials and DFT calculations

IF 2.9 4区 化学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY
Yu Cheng, Xin-Yu Dai, Shu-Wen Zhang, Yang-Yang Zhang
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引用次数: 0

Abstract

Context

This study presents the development of the GMUPC package, which integrates machine learning potentials (MLPs) to efficiently and accurately identify the possible structures of fullerene-like uranyl peroxide Un clusters spanning a broad size range from U20 to U10260. The computational workflow incorporates symmetric structure generation from Wyckoff positions, isomer perturbation, duplicate structure removal, and four distinct global optimization algorithms, including the particle swarm optimization (PSO), genetic algorithm (GA), standard basin-hopping (BH), and improved basin-hopping (IBH), to systematically explore the potential energy surfaces of large uranyl peroxide systems. We note that the symmetry-seeded structural generation within GMUPC prioritizes high-symmetry cage topologies for computational efficiency; highly distorted, low-symmetry metastable isomers with significant steric strain are less frequently sampled compared to carbon fullerene search algorithms, representing a defined limitation of the present computational framework. Structural explorations uncover non-classical fullerene-like U22 clusters with unique topological structure and a series of giant icosahedral fullerene-like U60n2 (n = 1~12) clusters adhering to the isolated pentagon rule (IPR), with consistent retention of 12 pentagonal faces across all cluster sizes. Geometry analyses establish scalable evolutionary trends in cluster radius, surface area, and volume as functions of uranium atomic count, while energy analyses reveal a monotonic decrease in total energy per uranium atom with increasing cluster size. The GMUPC package enables unprecedented exploration of uranyl peroxide cluster chemistry across size scales previously inaccessible via conventional computational methods, providing atomic-level insights into structure-energy relationships and possible self-assembly principles that bridge fundamental cluster science and nuclear materials chemistry.

Methods

In the present study, the geometrical structures of fullerene-like uranyl peroxide Un (n = 20~10,260) clusters were systematically explored to identify their possible thermodynamically stable geometries. Global-minimum structural searches of Un (n = 20~60) clusters with even number of uranium atoms were independently performed using two advanced computational approaches: the recently developed GMUPC code interfaced with the multi-atomic cluster expansion (MACE) machine learning potential. For high-accuracy structural refinement, all low-energy isomers derived from preliminary searches were further re-optimized using density functional theory (DFT). The searched low-lying isomers of U22 clusters were re-optimized at the DFT Perdew-Burke-Ernzerhof (PBE) functional by using the CP2K (v2024.3) package.

GMUPC:一个新的包全局最小搜索与机器学习潜力和DFT计算的大铀酰过氧化物簇。
背景:本研究介绍了GMUPC包的开发,该包集成了机器学习电位(mlp),以有效和准确地识别从U20到U10260的广泛尺寸范围内的类富勒烯过氧化物铀酰Un簇的可能结构。计算流程结合了Wyckoff位置对称结构生成、异构体扰动、重复结构去除和四种不同的全局优化算法,包括粒子群优化(PSO)、遗传算法(GA)、标准跳盆(BH)和改进跳盆(IBH),以系统地探索大型过氧化物铀酰体系的势能面。我们注意到,GMUPC中的对称种子结构生成优先考虑高对称笼型拓扑,以提高计算效率;与碳富勒烯搜索算法相比,具有显著空间应变的高度扭曲、低对称亚稳态异构体的采样频率较低,这代表了当前计算框架的一个明确限制。结构探索揭示了具有独特拓扑结构的非经典类富勒烯U22簇和一系列遵循孤立五边形规则(IPR)的巨大二十面体类富勒烯U60n2 (n = 1~12)簇,在所有簇大小中都保持12个五边形面。几何分析建立了团簇半径、表面积和体积随铀原子数的可扩展演化趋势,而能量分析显示,随着团簇大小的增加,每个铀原子的总能量呈单调下降趋势。GMUPC包能够前所未有地探索过氧化物铀酰团簇化学,跨越以前无法通过传统计算方法实现的尺寸尺度,提供原子水平的结构-能量关系和可能的自组装原理,为基础团簇科学和核材料化学提供桥梁。方法:系统地研究了类富勒烯过氧化铀酰Un (n = 20~10,260)簇的几何结构,以确定其可能的热力学稳定几何结构。使用两种先进的计算方法独立执行具有偶数铀原子的Un (n = 20~60)团簇的全局最小结构搜索:最近开发的GMUPC代码与多原子团簇扩展(MACE)机器学习潜力接口。为了进行高精度的结构优化,所有从初步搜索得到的低能异构体都使用密度泛函理论(DFT)进一步重新优化。利用CP2K (v2024.3)包在DFT Perdew-Burke-Ernzerhof (PBE)泛函上对搜索到的U22簇低洼异构体进行重新优化。
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
Journal of Molecular Modeling
Journal of Molecular Modeling 化学-化学综合
CiteScore
3.50
自引率
4.50%
发文量
362
审稿时长
2.9 months
期刊介绍: The Journal of Molecular Modeling focuses on "hardcore" modeling, publishing high-quality research and reports. Founded in 1995 as a purely electronic journal, it has adapted its format to include a full-color print edition, and adjusted its aims and scope fit the fast-changing field of molecular modeling, with a particular focus on three-dimensional modeling. Today, the journal covers all aspects of molecular modeling including life science modeling; materials modeling; new methods; and computational chemistry. Topics include computer-aided molecular design; rational drug design, de novo ligand design, receptor modeling and docking; cheminformatics, data analysis, visualization and mining; computational medicinal chemistry; homology modeling; simulation of peptides, DNA and other biopolymers; quantitative structure-activity relationships (QSAR) and ADME-modeling; modeling of biological reaction mechanisms; and combined experimental and computational studies in which calculations play a major role.
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