Anharmonic Thermal Motion Modelling in the Experimental XRD Charge Density Determination of 1-Methyluracil at T = 23 K
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)<sub>max</sub> = 1.143 Å<sup>−...
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| Format: | Article |
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MDPI AG
2021-05-01
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| Series: | Molecules |
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| Online Access: | https://www.mdpi.com/1420-3049/26/11/3075 |
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| author | Riccardo Destro Pietro Roversi Mario Barzaghi Leonardo Lo Presti |
| author_facet | Riccardo Destro Pietro Roversi Mario Barzaghi Leonardo Lo Presti |
| author_sort | Riccardo Destro |
| collection | DOAJ |
| description | 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)<sub>max</sub> = 1.143 Å<sup>−1</sup> 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<sup>–3</sup> 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. |
| first_indexed | 2024-03-10T11:11:37Z |
| format | Article |
| id | doaj.art-c810344835684afd901bd77ba83013f9 |
| institution | Directory Open Access Journal |
| issn | 1420-3049 |
| language | English |
| last_indexed | 2024-03-10T11:11:37Z |
| publishDate | 2021-05-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Molecules |
| spelling | doaj.art-c810344835684afd901bd77ba83013f92023-11-21T20:44:12ZengMDPI AGMolecules1420-30492021-05-012611307510.3390/molecules26113075Anharmonic Thermal Motion Modelling in the Experimental XRD Charge Density Determination of 1-Methyluracil at T = 23 KRiccardo Destro0Pietro Roversi1Mario Barzaghi2Leonardo Lo Presti3Chemistry Department, Università degli Studi di Milano, Via Golgi 19, 20133 Milano, ItalyDepartment of Molecular and Cell Biology, Leicester Institute of Structural and Chemical Biology, University of Leicester, Lancaster Road, Leicester LE1 7HB, UKConsiglio Nazionale delle Ricerche (CNR), Piazzale Aldo Moro 7, 00185 Roma, ItalyChemistry Department, Università degli Studi di Milano, Via Golgi 19, 20133 Milano, ItalyThe 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)<sub>max</sub> = 1.143 Å<sup>−1</sup> 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<sup>–3</sup> 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.https://www.mdpi.com/1420-3049/26/11/30751-methyluracilX-ray diffractioncharge densityelectrostatic momentsquantum theory of atoms in moleculesanharmonicity |
| spellingShingle | Riccardo Destro Pietro Roversi Mario Barzaghi Leonardo Lo Presti Anharmonic Thermal Motion Modelling in the Experimental XRD Charge Density Determination of 1-Methyluracil at T = 23 K Molecules 1-methyluracil X-ray diffraction charge density electrostatic moments quantum theory of atoms in molecules anharmonicity |
| title | Anharmonic Thermal Motion Modelling in the Experimental XRD Charge Density Determination of 1-Methyluracil at T = 23 K |
| title_full | Anharmonic Thermal Motion Modelling in the Experimental XRD Charge Density Determination of 1-Methyluracil at T = 23 K |
| title_fullStr | Anharmonic Thermal Motion Modelling in the Experimental XRD Charge Density Determination of 1-Methyluracil at T = 23 K |
| title_full_unstemmed | Anharmonic Thermal Motion Modelling in the Experimental XRD Charge Density Determination of 1-Methyluracil at T = 23 K |
| title_short | Anharmonic Thermal Motion Modelling in the Experimental XRD Charge Density Determination of 1-Methyluracil at T = 23 K |
| title_sort | anharmonic thermal motion modelling in the experimental xrd charge density determination of 1 methyluracil at t 23 k |
| topic | 1-methyluracil X-ray diffraction charge density electrostatic moments quantum theory of atoms in molecules anharmonicity |
| url | https://www.mdpi.com/1420-3049/26/11/3075 |
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