Solid-state calculations for iterative refinement in quantum crystallography using the multipole model
A quantum crystallographic refinement methodology has been developed using theoretical multipole parameters generated directly from solid-state calculations using the CRYSTAL17 program. This refinement method is comparable to other transferable form factor approaches, such as the Invariom model, but...
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International Union of Crystallography
2025-05-01
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| Online Access: | https://journals.iucr.org/paper?S2052252525002040 |
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| author | Michael Patzer Christian W. Lehmann |
| author_facet | Michael Patzer Christian W. Lehmann |
| author_sort | Michael Patzer |
| collection | DOAJ |
| description | A quantum crystallographic refinement methodology has been developed using theoretical multipole parameters generated directly from solid-state calculations using the CRYSTAL17 program. This refinement method is comparable to other transferable form factor approaches, such as the Invariom model, but in contrast to the Hirshfeld atom refinement, it uses theoretical multipole parameters to describe the electron density from a solid-state calculation performed with CRYSTAL17 in an iterative refinement procedure. For this purpose, a Python3 code named ReCrystal has been developed. To start ReCrystal, a CIF, a Gaussian basis set, a DFT functional and the number of CPUs must be defined. The Pack–Monkhorst and Gilat shrinking factors, which define a lattice in the first Brillouin zone, must also be specified. After k-point sampling, CRYSTAL17 calculates structure factors directly from the static electron density. Multipole parameters are generated from these structure factors using the XD program and are fixed during least-squares refinement. The refinement of the xylitol molecular crystal has shown that the hydrogen atom positions can be determined with reasonable agreement to those obtained in the neutron diffraction experiment. This indicates that the periodic boundary condition in ReCrystal is an improvement over gas phase refinement with HAR. The multipole parameters obtained from ReCrystal can be used for further charge density studies especially if weak interactions are the focus. In this work, we demonstrate the performance of ReCrystal on molecular crystals of the small molecules D/L-serine and xylitol with weak hydrogen-bonding motifs using multipole refinement. The advantage of this approach is that multipole parameters can be obtained from high-resolution calculated diffraction data, no database is required, and errors due to the model and errors resulting from the experiment are clearly separated. |
| format | Article |
| id | doaj-art-90abf331a56445c282c25de1fada3087 |
| institution | Kabale University |
| issn | 2052-2525 |
| language | English |
| publishDate | 2025-05-01 |
| publisher | International Union of Crystallography |
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| series | IUCrJ |
| spelling | doaj-art-90abf331a56445c282c25de1fada30872025-08-20T03:48:31ZengInternational Union of CrystallographyIUCrJ2052-25252025-05-0112332233310.1107/S2052252525002040fc5082Solid-state calculations for iterative refinement in quantum crystallography using the multipole modelMichael Patzer0Christian W. Lehmann1Chemische Kristallographie und Elektronenmikroskopie, Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, Mülheim an der Ruhr, 45470 North Rhine-Westphalia, GermanyChemische Kristallographie und Elektronenmikroskopie, Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, Mülheim an der Ruhr, 45470 North Rhine-Westphalia, GermanyA quantum crystallographic refinement methodology has been developed using theoretical multipole parameters generated directly from solid-state calculations using the CRYSTAL17 program. This refinement method is comparable to other transferable form factor approaches, such as the Invariom model, but in contrast to the Hirshfeld atom refinement, it uses theoretical multipole parameters to describe the electron density from a solid-state calculation performed with CRYSTAL17 in an iterative refinement procedure. For this purpose, a Python3 code named ReCrystal has been developed. To start ReCrystal, a CIF, a Gaussian basis set, a DFT functional and the number of CPUs must be defined. The Pack–Monkhorst and Gilat shrinking factors, which define a lattice in the first Brillouin zone, must also be specified. After k-point sampling, CRYSTAL17 calculates structure factors directly from the static electron density. Multipole parameters are generated from these structure factors using the XD program and are fixed during least-squares refinement. The refinement of the xylitol molecular crystal has shown that the hydrogen atom positions can be determined with reasonable agreement to those obtained in the neutron diffraction experiment. This indicates that the periodic boundary condition in ReCrystal is an improvement over gas phase refinement with HAR. The multipole parameters obtained from ReCrystal can be used for further charge density studies especially if weak interactions are the focus. In this work, we demonstrate the performance of ReCrystal on molecular crystals of the small molecules D/L-serine and xylitol with weak hydrogen-bonding motifs using multipole refinement. The advantage of this approach is that multipole parameters can be obtained from high-resolution calculated diffraction data, no database is required, and errors due to the model and errors resulting from the experiment are clearly separated.https://journals.iucr.org/paper?S2052252525002040quantum crystallographymultipole modelrecrystalcrystal17solid-state calculationstransferable atom form factorscharge density analysis |
| spellingShingle | Michael Patzer Christian W. Lehmann Solid-state calculations for iterative refinement in quantum crystallography using the multipole model IUCrJ quantum crystallography multipole model recrystal crystal17 solid-state calculations transferable atom form factors charge density analysis |
| title | Solid-state calculations for iterative refinement in quantum crystallography using the multipole model |
| title_full | Solid-state calculations for iterative refinement in quantum crystallography using the multipole model |
| title_fullStr | Solid-state calculations for iterative refinement in quantum crystallography using the multipole model |
| title_full_unstemmed | Solid-state calculations for iterative refinement in quantum crystallography using the multipole model |
| title_short | Solid-state calculations for iterative refinement in quantum crystallography using the multipole model |
| title_sort | solid state calculations for iterative refinement in quantum crystallography using the multipole model |
| topic | quantum crystallography multipole model recrystal crystal17 solid-state calculations transferable atom form factors charge density analysis |
| url | https://journals.iucr.org/paper?S2052252525002040 |
| work_keys_str_mv | AT michaelpatzer solidstatecalculationsforiterativerefinementinquantumcrystallographyusingthemultipolemodel AT christianwlehmann solidstatecalculationsforiterativerefinementinquantumcrystallographyusingthemultipolemodel |