Exploring the influence of metal cations on individual hydrogen bonds in Watson–Crick guanine–cytosine DNA base pair: An interacting quantum atoms analysis,Journal of Computational Chemistry

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Exploring the influence of metal cations on individual hydrogen bonds in Watson–Crick guanine–cytosine DNA base pair: An interacting quantum atoms analysis
Journal of Computational Chemistry ( IF 3.4 ) Pub Date : 2024-06-24 , DOI: 10.1002/jcc.27441
F Pakzad ₁ , K Eskandari ₁

Affiliation

This study delves into the nature of individual hydrogen bonds and the relationship between metal cations and hydrogen bonding in the Watson–Crick guanine–cytosine (GC) base pair and its alkali and alkaline earth cation-containing complexes (Mⁿ⁺–GC). The findings reveal how metal cations affect the nature and strength of individual hydrogen bonds. The study employs interacting quantum atoms (IQA) analysis to comprehensively understand three individual hydrogen bonds within the GC base pair and its cationic derivatives. These analyses unveil the nature and strength of hydrogen bonds and serve as a valuable reference for exploring the impact of cations (and other factors) on each hydrogen bond. All the H

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D interactions (H is hydrogen and D is oxygen or nitrogen) in the GC base pair are primarily electrostatic in nature, with the charge transfer component playing a substantial role. Introducing a metal cation perturbs all H

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D interatomic interactions in the system, weakening the nearest hydrogen bond to the cation (indicated by a) and reinforcing the other (b and c) interactions. Notably, the interaction a, the strongest H

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D interaction in the GC base pair, becomes the weakest in the Mⁿ⁺–GC complexes. A broader perspective on the stability of GC and Mⁿ⁺–GC complexes is provided through interacting quantum fragments (IQF) analysis. This approach considers all pairwise interactions between fragments and intra-fragment components, offering a complete view of the factors that stabilize and destabilize GC and Mⁿ⁺–GC complexes. The IQF analysis underscores the importance of electron sharing, with the dominant contribution arising from the inter-fragment exchange-correlation term, in shaping and sustaining GC and Mⁿ⁺–GC complexes. From this point of view, alkaline and alkaline earth cations have distinct effects, with alkaline cations generally weakening inter-fragment interactions and alkaline earth cations strengthening them. In addition, IQA and IQF calculations demonstrate that the hydration of cations led to small changes in the hydrogen bonding network. Finally, the IQA interatomic energies associated with the hydrogen bonds and also inter-fragment interaction energies provide robust indicators for characterizing hydrogen bonds and complex stability, showing a strong correlation with total interaction energies.

中文翻译：

探索金属阳离子对 Watson-Crick 鸟嘌呤-胞嘧啶 DNA 碱基对中单个氢键的影响：相互作用的量子原子分析

这项研究深入研究了沃森-克里克鸟嘌呤-胞嘧啶（GC）碱基对及其含碱金属和碱土金属阳离子的配合物（M ⁿ⁺ -GC）中单个氢键的性质以及金属阳离子和氢键之间的关系。研究结果揭示了金属阳离子如何影响单个氢键的性质和强度。该研究采用相互作用量子原子 (IQA) 分析来全面了解 GC 碱基对及其阳离子衍生物内的三个单独的氢键。这些分析揭示了氢键的性质和强度，并为探索阳离子（和其他因素）对每个氢键的影响提供了有价值的参考。所有的H

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GC 碱基对中的 D 相互作用（H 是氢，D 是氧或氮）本质上主要是静电作用，其中电荷转移成分发挥着重要作用。引入金属阳离子会扰乱所有 H

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D 系统中的原子间相互作用，削弱了与阳离子最近的氢键（由a表示）并增强了其他（ b和c ）相互作用。值得注意的是，相互作用a ，最强的 H

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GC 碱基对中的 D 相互作用在 M ^{n +} –GC 复合物中变得最弱。通过相互作用量子碎片 (IQF) 分析，为 GC 和 Mn ⁺ –GC 复合物的稳定性提供了更广泛的视角。该方法考虑了片段和片段内组分之间的所有成对相互作用，提供了稳定和不稳定 GC 和 M ^{n +} –GC 复合物的因素的完整视图。 IQF 分析强调了电子共享的重要性，其中片段间交换相关项产生的主要贡献在形成和维持 GC 和 M ^{n +} –GC 复合物中。从这个角度来看，碱金属阳离子和碱土金属阳离子具有不同的作用，碱性阳离子通常削弱片段间相互作用，而碱土金属阳离子则增强片段间相互作用。此外，IQA 和 IQF 计算表明，阳离子的水合导致氢键网络发生微小变化。最后，与氢键相关的 IQA 原子间能量以及片段间相互作用能为表征氢键和络合物稳定性提供了可靠的指标，显示出与总相互作用能的强相关性。

更新日期：2024-06-24

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