将全局优化算法与 EXAFS 搭配使用,确定溶液中镧系元素的结构特征。

IF 5.6 2区 化学 Q1 CHEMISTRY, MEDICINAL Journal of Chemical Information and Modeling Pub Date : 2024-11-22 DOI:10.1021/acs.jcim.4c01769
Thomas J Summers, Difan Zhang, Josiane A Sobrinho, Ana de Bettencourt-Dias, Roger Rousseau, Vassiliki-Alexandra Glezakou, David C Cantu
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引用次数: 0

摘要

从原子分子动力学(ab initio molecular dynamics,AIMD)模拟中对结构进行集合平均采样,可用于预测与实验光谱密切匹配的理论扩展 X 射线吸收精细结构(EXAFS)信号。然而,AIMD 模拟既耗时又耗费资源,尤其是对于溶解的镧系离子,它们通常会形成具有高配位数的多重非刚性几何结构。为了加快溶液中镧系元素结构的表征,我们采用了西北势能面搜索引擎(NWPEsSe)--一种自适应学习的全局优化算法--来高效筛选第一壳结构。作为案例研究,我们考察了两个系统:Eu(NO3)3溶于乙腈,并带有一个特吡啶配体(terpyNO2);Nd(NO3)3溶于乙腈。将 NWPEsSe 确定的结构的理论光谱与实验光谱和 AIMD 导出的 EXAFS 光谱进行了比较。NWPEsSe 算法成功地为 Eu(NO3)3(terpyNO2) 和 Nd(NO3)(acetonitrile)3 确定了适当的溶解结构,计算出的 EXAFS 信号与 Eu 配体复合物的实验光谱非常吻合,与 Nd 盐的实验光谱也非常相似;与含配体结构的吻合度更高,这归因于刚性配体带来的较低动态配位环境。全局优化算法的主要优势在于它能够对整个势能面的配位环境进行采样,并将确定结构所需的时间从通常的一个月缩短到一周之内。此外,这种方法用途广泛,可用于表征主族金属配合物。
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Pairing a Global Optimization Algorithm with EXAFS to Characterize Lanthanide Structure in Solution.

Ensemble-average sampling of structures from ab initio molecular dynamics (AIMD) simulations can be used to predict theoretical extended X-ray absorption fine structure (EXAFS) signals that closely match experimental spectra. However, AIMD simulations are time-consuming and resource-intensive, particularly for solvated lanthanide ions, which often form multiple nonrigid geometries with high coordination numbers. To accelerate the characterization of lanthanide structures in solution, we employed the Northwest Potential Energy Surface Search Engine (NWPEsSe), an adaptive-learning global optimization algorithm, to efficiently screen first-shell structures. As case studies, we examine two systems: Eu(NO3)3 dissolved in acetonitrile with a terpyridine ligand (terpyNO2), and Nd(NO3)3 dissolved in acetonitrile. The theoretical spectra for structures identified by NWPEsSe were compared to both experimental and AIMD-derived EXAFS spectra. The NWPEsSe algorithm successfully identified the proper solvation structure for both Eu(NO3)3(terpyNO2) and Nd(NO3)(acetonitrile)3, with the calculated EXAFS signals closely matching the experimental spectra for the Eu-ligand complex and showing good similarity for the Nd salt; the better agreement with the ligand-containing structure is attributed to a less dynamic coordination environment due to the rigid ligand. The key advantage of the global optimization algorithm lies in its ability to sample the coordination environment across the potential energy surface and reduce the time required to identify structures from generally a month to within a week. Additionally, this approach is versatile and can be adapted to characterize main-group metal complexes.

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来源期刊
CiteScore
9.80
自引率
10.70%
发文量
529
审稿时长
1.4 months
期刊介绍: The Journal of Chemical Information and Modeling publishes papers reporting new methodology and/or important applications in the fields of chemical informatics and molecular modeling. Specific topics include the representation and computer-based searching of chemical databases, molecular modeling, computer-aided molecular design of new materials, catalysts, or ligands, development of new computational methods or efficient algorithms for chemical software, and biopharmaceutical chemistry including analyses of biological activity and other issues related to drug discovery. Astute chemists, computer scientists, and information specialists look to this monthly’s insightful research studies, programming innovations, and software reviews to keep current with advances in this integral, multidisciplinary field. As a subscriber you’ll stay abreast of database search systems, use of graph theory in chemical problems, substructure search systems, pattern recognition and clustering, analysis of chemical and physical data, molecular modeling, graphics and natural language interfaces, bibliometric and citation analysis, and synthesis design and reactions databases.
期刊最新文献
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