Monovalent cation binding to model systems and the macrocyclic depsipeptide, emodepside

IF 3.4 3区 化学 Q2 CHEMISTRY, MULTIDISCIPLINARY
Govindan Subramanian, Kanika Manchanda, Yirong Mo, Rohit Y. Sathe, Prasad V. Bharatam
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Abstract

This study focuses on the systematic exploration of the emodepside conformations bound to monovalent K+ ion using quantum mechanical density functional theory (DFT) calculations at the M06-2X/6-31+G(d,p) level of theory. Nine conformers of emodepside and their complexes with K+ ion were characterized as stationary points on the potential energy surface. The conformational isomers were examined for their 3D structures, bonding, energetics, and interactions with the cation. A cavitand-like structure (CC) is identified to be the energetically most stable arrangement. To arrive at a better understanding of the K+ ion binding, calculations were initially performed on complexes formed by the K+ and Na+ ions with model ligands (methyl ester and N,N-dimethyl acetamide). Both the natural bond orbital (NBO) method and the block-localized wavefunction (BLW) energy decomposition approach was employed to assess the bonding and energetic contributions stabilizing the ion-bound model complexes. Finally, the solvent effect was evaluated through complete geometry optimizations and energy minimizations for the model ion-ligand complexes and the emodepside-K+ bound complexes using an implicit solvent model mimicking water and DMSO.

Abstract Image

单价阳离子与模型系统和大环解肽(emodepside)的结合。
本研究采用量子力学密度泛函理论(DFT),在 M06-2X/6-31+G(d,p) 理论水平上对与一价 K+ 离子结合的依莫地平构象进行了系统探索。根据势能面上的静止点,确定了依莫地平及其与 K+ 离子的复合物的九种构象。对这些构象异构体的三维结构、成键、能量以及与阳离子的相互作用进行了研究。结果表明,空穴样结构(CC)是能量上最稳定的排列。为了更好地理解 K+ 离子的结合,最初对 K+ 和 Na+ 离子与模型配体(甲酯和 N,N-二甲基乙酰胺)形成的复合物进行了计算。计算采用了自然键轨道(NBO)方法和块定位波函数(BLW)能量分解方法,以评估稳定离子结合模型复合物的成键和能量贡献。最后,利用模拟水和 DMSO 的隐式溶剂模型,通过对离子配体模型复合物和 emodepside-K+ 结合复合物进行完整的几何优化和能量最小化,评估了溶剂效应。
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来源期刊
CiteScore
6.60
自引率
3.30%
发文量
247
审稿时长
1.7 months
期刊介绍: This distinguished journal publishes articles concerned with all aspects of computational chemistry: analytical, biological, inorganic, organic, physical, and materials. The Journal of Computational Chemistry presents original research, contemporary developments in theory and methodology, and state-of-the-art applications. Computational areas that are featured in the journal include ab initio and semiempirical quantum mechanics, density functional theory, molecular mechanics, molecular dynamics, statistical mechanics, cheminformatics, biomolecular structure prediction, molecular design, and bioinformatics.
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