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首页> 外文期刊>Chemistry: A European journal >Oxoanion binding by guanidiniocarbonylpyrrole cations in water: A combined DFT and MD investigation
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Oxoanion binding by guanidiniocarbonylpyrrole cations in water: A combined DFT and MD investigation

机译：胍基羰基吡咯阳离子在水中与氧阴离子的结合：DFT和MD的组合研究

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摘要

Structures and properties of nonbonding interactions involving guanidinium-functionalized hosts and carboxylate substrates were investigated by a combination of ab initio and molecular dynamics approaches. The systems under study are on one hand intended to be a model of the arginine-anion bond, so often observed in proteins and nucleic acids, and on the other to provide an opportunity to investigate the influence of molecular structure on the formation of supramolecular complexes in detail. Use of DFT calculations, including extended basis sets and implicit water treatment, allowed us to determine minimum-energy structures and binding enthalpies that compared well with experimental data. Intermolecular forces were found to be mostly due to electrostatic interactions through three hydrogen bonds, one of which is bifurcate, and are sufficiently strong to induce a conformational change in the ligand consisting of a rotation of about 180 degrees around the guanidiniocarbonylpyrrole axis. Free binding energies of the complexes were evaluated through MD simulations performed in the presence of explicit water molecules by use of the molecular mechanics Poisson-Boltzmann solvent accessible surface area (MM-PBSA) and linear interaction energy (LIE) approaches. LIE energies were in quantitative agreement with experimental data. A detailed analysis of the MD simulations revealed that the complexes cannot be described in terms of a single binding structure, but that they are characterized by a significant internal mobility responsible for several low-energy metastable structures.
机译：通过从头算和分子动力学方法的结合，研究了涉及胍基官能化主体和羧酸酯底物的非键相互作用的结构和性质。所研究的系统一方面旨在作为精氨酸-阴离子键的模型，因此经常在蛋白质和核酸中观察到，另一方面为研究分子结构对超分子复合物形成的影响提供了机会详细。 DFT计算的使用，包括扩展的基础集和隐式水处理，使我们能够确定与实验数据进行比较的最小能量结构和结合焓。发现分子间力主要归因于通过三个氢键的静电相互作用，其中三个氢键之一是分叉的，并且足够强以引起配体的构象变化，该构象变化包括围绕胍基羰基吡咯轴旋转约180度。使用分子力学泊松-玻尔兹曼溶剂可及表面积（MM-PBSA）和线性相互作用能（LIE）方法，通过在明显水分子存在下进行的MD模拟，评估复合物的自由结合能。 LIE能量与实验数据定量一致。对MD模拟的详细分析表明，复合物不能用单一的结合结构来描述，但是它们的特征是明显的内部迁移率，导致了几种低能的亚稳结构。

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