New global minimum conformers for the Pt\(_{19}\) and Pt\(_{20}\) clusters: low symmetric species featuring different active sites

IF 2.1 4区 化学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY Journal of Molecular Modeling Pub Date : 2024-08-17 DOI:10.1007/s00894-024-06099-5
José Manuel Guevara-Vela, Miguel Gallegos, Tomás Rocha-Rinza, Álvaro Muñoz-Castro, Peter L. Rodríguez Kessler, Ángel Martín Pendás
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Abstract

Context

The study of platinum (Pt) clusters and nanoparticles is essential due to their extensive range of potential technological applications, particularly in catalysis. The electronic properties that yield optimal catalytic performance at the nanoscale are significantly influenced by the size and structure of Pt clusters. This research aimed to identify the lowest-energy conformers for Pt\(_{18}\), Pt\(_{19}\), and Pt\(_{20}\) species using Density Functional Theory (DFT). We discovered new low-symmetry conformers for Pt\(_{19}\) and Pt\(_{20}\), which are 3.0 and 1.0 kcal/mol more stable, respectively, than previously reported structures. Our study highlights the importance of using density functional approximations that incorporate moderate levels of exact Hartree-Fock exchange, alongside basis sets of at least quadruple-zeta quality. The resulting structures are asymmetric with varying active sites, as evidenced by sigma hole analysis on the electrostatic potential surface. This suggests a potential correlation between electronic structure and catalytic properties, warranting further investigation.

Methods

An equivariant graph neural network interatomic potential (NequIP) within the Atomic Simulation Environment suite (ASE) was used to provide initial geometries of the aggregates under study. DFT calculations were performed with the ORCA 5 package, using functional approximations that included Generalized Gradient Approximation (PBE), meta-GGA (TPSS, M06-L), hybrid (PBE0, PBEh), meta-GGA hybrid (TPSSh), and range-separated hybrid (\(\omega \)B97x) functionals. Def2-TZVP and Def2-QZVP as well as members of the cc-pwCVXZ-PP family to check basis set convergence were used. QTAIM calculations were performed using the AIMAll suite. Structures were visualized with the AVOGADRO code.

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铂 19 簇和铂 20 簇的新全局最小构象:具有不同活性位点的低对称物种。
背景:铂(Pt)团簇和纳米粒子具有广泛的潜在技术应用,尤其是在催化方面,因此对它们的研究至关重要。在纳米尺度上产生最佳催化性能的电子特性在很大程度上受到铂簇大小和结构的影响。这项研究旨在利用密度泛函理论(DFT)确定铂 18、铂 19 和铂 20 物种的最低能量构象。我们发现了 Pt 19 和 Pt 20 新的低对称性构象,与之前报道的结构相比,它们分别稳定了 3.0 和 1.0 kcal/mol。我们的研究强调了使用密度泛函近似的重要性,这种近似结合了中等水平的精确哈特里-福克交换以及至少四重zeta质量的基集。静电位面上的σ孔分析表明,由此产生的结构是不对称的,活性位点各不相同。这表明电子结构与催化特性之间存在潜在关联,值得进一步研究:方法:使用原子模拟环境套件(ASE)中的等变图神经网络原子间势(NequIP)来提供所研究聚合体的初始几何图形。DFT 计算使用 ORCA 5 软件包进行,使用的函数近似包括广义梯度近似(PBE)、元-GGA(TPSS、M06-L)、混合(PBE0、PBEh)、元-GGA 混合(TPSSh)和范围分离混合(ω B97x)函数。使用了 Def2-TZVP 和 Def2-QZVP 以及 cc-pwCVXZ-PP 系列成员来检查基集收敛性。QTAIM 计算使用 AIMAll 套件进行。使用 AVOGADRO 代码对结构进行了可视化处理。
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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