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首页> 外文期刊>The Journal of Chemical Physics >A polarizable QM/MM approach to the molecular dynamics of amide groups solvated in water
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A polarizable QM/MM approach to the molecular dynamics of amide groups solvated in water

机译：可极化的QM / MM方法研究水中溶剂化的酰胺基的分子动力学

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The infrared (IR) spectra of polypeptides are dominated by the so-called amide bands. Because they originate from the strongly polar and polarizable amide groups (AGs) making up the backbone, their spectral positions sensitively depend on the local electric fields. Aiming at accurate computations of these IR spectra by molecular dynamics (MD) simulations, which derive atomic forces from a hybrid quantum and molecular mechanics (QM/MM) Hamiltonian, here we consider the effects of solvation in bulk liquid water on the amide bands of the AG model compound N-methyl-acetamide (NMA). As QM approach to NMA we choose grid-based density functional theory (DFT). For the surrounding MM water, we develop, largely based on computations, a polarizable molecular mechanics (PMM) model potential called GP6P, which features six Gaussian electrostatic sources (one induced dipole, five static partial charge distributions) and, therefore, avoids spurious distortions of the DFT electron density in hybrid DFT/PMM simulations. Bulk liquid GP6P is shown to have favorable properties at the thermodynamic conditions of the parameterization and beyond. Lennard-Jones (LJ) parameters of the DFT fragment NMA are optimized by comparing radial distribution functions in the surrounding GP6P liquid with reference data obtained from a "first-principles" DFT-MD simulation. Finally, IR spectra of NMA in GP6P water are calculated from extended DFT/PMM-MD trajectories, in which the NMA is treated by three different DFT functionals (BP, BLYP, B3LYP). Method-specific frequency scaling factors are derived from DFT-MD simulations of isolated NMA. The DFT/PMM-MD simulations with GP6P and with the optimized LJ parameters then excellently predict the effects of aqueous solvation and deuteration observed in the IR spectra of NMA. As a result, the methods required to accurately compute such spectra by DFT/PMM-MD also for larger peptides in aqueous solution are now at hand. (C) 2016 AIP Publishing LLC.
机译：多肽的红外（IR）光谱由所谓的酰胺带占据主导地位。由于它们源自构成主链的强极性和可极化酰胺基团（AG），因此它们的光谱位置敏感地取决于局部电场。为了通过分子动力学（MD）模拟精确计算这些IR光谱，该模拟从混合量子和分子力学（QM / MM）哈密顿量中得出原子力，在这里我们考虑了散装液态水中的溶剂化作用对酰胺谱带的影响。 AG模型化合物N-甲基-乙酰胺（NMA）。作为NMA的质量管理方法，我们选择基于网格的密度泛函理论（DFT）。对于周围的MM水，我们主要在计算的基础上开发了称为GP6P的可极化分子力学（PMM）模型电势，该电势具有六个高斯静电源（一个感应偶极子，五个静态部分电荷分布），因此避免了虚假失真。 DFT / PMM混合模拟中DFT电子密度的变化。散装液体GP6P在参数化及更高的热力学条件下显示出良好的性能。 DFT片段NMA的Lennard-Jones（LJ）参数是通过将周围GP6P液体中的径向分布函数与从“第一原理” DFT-MD模拟获得的参考数据进行比较来优化的。最后，从扩展的DFT / PMM-MD轨迹计算GP6P水中NMA的红外光谱，其中NMA通过三种不同的DFT功能（BP，BLYP，B3LYP）处理。从隔离NMA的DFT-MD模拟得出方法特定的频率缩放因子。然后使用GP6P和优化的LJ参数对DFT / PMM-MD进行仿真，可以很好地预测NMA红外光谱中观察到的水溶剂化和氘代的影响。结果，现在也需要通过DFT / PMM-MD精确计算此类光谱的水溶液中较大肽所需的方法。 （C）2016 AIP出版有限责任公司。

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