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在 23K 下通过实验 X 射线衍射电荷密度测定对 1-甲基尿嘧啶的非谐热运动建模。

Anharmonic Thermal Motion Modelling in the Experimental XRD Charge Density Determination of 1-Methyluracil at T = 23 K.

机构信息

Chemistry Department, Università degli Studi di Milano, Via Golgi 19, 20133 Milano, Italy.

Department of Molecular and Cell Biology, Leicester Institute of Structural and Chemical Biology, University of Leicester, Lancaster Road, Leicester LE1 7HB, UK.

出版信息

Molecules. 2021 May 21;26(11):3075. doi: 10.3390/molecules26113075.

Abstract

The experimental electron density distribution (EDD) of 1-methyluracil (1-MUR) was obtained by single crystal X-ray diffraction (XRD) experiments at 23 K. Four different structural models fitting an extensive set of XRD data to a resolution of (sinθ/λ) = 1.143 Å are compared. Two of the models include anharmonic temperature factors, whose inclusion is supported by the Hamilton test at a 99.95% level of confidence. Positive Fourier residuals up to 0.5 eÅ in magnitude were found close to the methyl group and in the region of hydrogen bonds. Residual density analysis (RDA) and molecular dynamics simulations in the solid-state demonstrate that these residuals can be likely attributed to unresolved disorder, possibly dynamical and long-range in nature. Atomic volumes and charges, molecular moments up to hexadecapoles, as well as maps of the molecular electrostatic potential were obtained from distributed multipole analysis of the EDD. The derived electrostatic properties neither depend on the details of the multipole model, nor are significantly affected by the explicit inclusion of anharmonicity in the least-squares model. The distribution of atomic charges in 1-MUR is not affected by the crystal environment in a significant way. The quality of experimental findings is discussed in light of in-crystal and gas-phase quantum simulations.

摘要

通过在 23 K 下进行单晶 X 射线衍射 (XRD) 实验,获得了 1-甲基尿嘧啶 (1-MUR) 的实验电子密度分布 (EDD)。比较了四个不同的结构模型,这些模型拟合了广泛的 XRD 数据,分辨率为 (sinθ/λ) = 1.143 Å。其中两个模型包括非谐温度因子,其包含在置信水平为 99.95%的 Hamilton 检验中得到支持。在靠近甲基和氢键区域,发现了高达 0.5 eÅ 的正傅立叶残差。残余密度分析 (RDA) 和固态分子动力学模拟表明,这些残余可能归因于未解析的无序,可能是动力学和长程的。从 EDD 的分布式多极分析中获得了原子体积和电荷、高达十六极矩的分子矩,以及分子静电势图。得出的静电性质既不依赖于多极模型的细节,也不受最小二乘模型中明确包含非谐性的显著影响。1-MUR 中原子电荷的分布方式不会受到晶体环境的显著影响。实验结果的质量在考虑晶体和气相量子模拟的情况下进行了讨论。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7bc3/8196607/8a27b8dc5be8/molecules-26-03075-g001.jpg

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