Theoretical characterizations on three oxygen-containing polyatomic anion binding of the single/double pincer-like receptors

IF 2.9 4区 化学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY
Pei Zhao, Qingqing Yao, Yue Li, Wenbo Zhang, Yanzhi Liu, Zhi-Feng Li, Kun Yuan
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引用次数: 0

Abstract

Context

In this paper, density functional theory calculations were used to systematically characterize the binding behavior of the two types of pincer-like receptors with different configurations (E-type and Z-type) to three oxygen-containing polyatomic anions (SO42−, C2O42− and NO3−). The E-type receptor (2ENH2) shows slightly preferential binding of SO42−. Independent gradient model based on Hirshfeld partition (IGMH) analysis characterized the non-covalent interaction patterns between the receptor and anion. Meanwhile, molecular electrostatic potential (ESP) analysis revealed changes in charge distribution upon anion binding. UV–Vis spectra and 1H NMR calculations provided complementary information on the electronic and structural changes induced by complexation between anion and receptor. In addition, ab initio molecular dynamics (AIMD) simulations were used to examine the structural persistence of representative host–guest complexes. Overall, the results clarify how receptor configuration, hydrogen-bonding topology, anion properties, and solvent environment collectively influence anion recognition.

Methods

All geometries were optimized at the B3LYP-D3BJ/def2-SVP level of theory without any symmetry constraints. The host–guest binding energies (ΔEbcp) were corrected for basis set superposition error (BSSE). Additional calculations using B3LYP-D3BJ/def2-TZVP with counterpoise correction were performed for selected complexes to assess the robustness of the binding energies. Wave function analyses were performed using the Multiwfn program. AIMD simulations were using the ORCA 5.0 program with the composite method of B97-3c developed by Grimme and coworkers. All other calculations were performed using the Gaussian 16 program.

Graphical abstract

单/双钳状受体三含氧多原子阴离子结合的理论表征
本文采用密度泛函理论计算,系统表征了两种不同构型的钳状受体(e型和z型)与三种含氧多原子阴离子(SO42−、C2O42−和NO3−)的结合行为。e型受体(2ENH2)对SO42−表现出轻微的优先结合。基于Hirshfeld分割(IGMH)分析的独立梯度模型表征了受体与阴离子之间的非共价相互作用模式。同时,分子静电势(ESP)分析揭示了阴离子结合后电荷分布的变化。紫外可见光谱和1H NMR计算提供了阴离子与受体络合引起的电子和结构变化的补充信息。此外,采用从头算分子动力学(AIMD)模拟来检验具有代表性的主-客体复合物的结构持久性。总的来说,结果阐明了受体结构、氢键拓扑结构、阴离子性质和溶剂环境如何共同影响阴离子识别。方法所有几何形状均在理论的b3lypp - d3bj /def2-SVP水平上进行优化,不受任何对称性约束。对主客体结合能(ΔEbcp)进行了基集叠加误差(BSSE)校正。使用B3LYP-D3BJ/def2-TZVP对所选配合物进行了附加计算,并进行了平衡校正,以评估结合能的鲁棒性。使用Multiwfn程序进行波函数分析。AIMD仿真采用ORCA 5.0程序,采用Grimme等人开发的B97-3c复合方法。所有其他计算均使用高斯16程序进行。图形抽象
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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