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)max = 1.143 Å−1 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–3 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.
Highlights
Chemistry Department, Università degli Studi di Milano, Via Golgi 19, 20133 Milano, Italy; Istituto Nazionale di Fisica Nucleare (INFN), Laboratori Nazionali di Frascati, 00044 Frascati, Italy
It was on the basis of this test that the authors of the neutron study of 1-MUR [29] deemed anharmonic treatment unwarranted because none of the resulting small reductions in agreement factors was significant at the 99.5% confidence level
The Hamilton test was used by Stewart, Larsen, and coworkers [25] to choose the best anharmonicity model in a charge-density study of tetrafluoroterephthalonitrile, where third-order GC coefficients were applied only to the nitrogen atom because a test refinement with anharmonic motion on all five independent atoms could be rejected at the 50% level of confidence
Summary
“I think that it is very interesting that one can see the functions of Schrödinger’s wave mechanics by means of the X-ray study of crystals. From the crystallographic R value to the thermal motion and the density parameters, with a main focus on the effects on the residual density distribution and the EDD topology but without analysis of the influence of anharmonic motion modelling on integrated atomic charges, volumes, or electrostatic potential and electric moments. [30], which extended to sinθ/λ < 1.08 Å−1 , four different refinement models were tested, but none included anharmonic corrections to the ADPs. That X-ray investigation retrieved electrostatic properties from the diffraction data, the data quality was not the best, as revealed by inconsistencies in the cell parameters with respect to the values of the neutron investigation and by anomalies in the U33 ’s of all nine non-H atoms (the 1-MUR molecular plane is orthogonal to the c axis of the crystals). Grated atomic volumes and charges as calculated with PAMoC from the experimental ρ
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