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Journal articles on the topic 'Hirshfeld Atom Refinement'

Author: Grafiati

Published: 8 June 2024

Last updated: 31 July 2025

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1

Grabowsky, Simon, Magdalena Woinska, and Dylan Jayatilaka. "Hirshfeld Atom Refinement." Nihon Kessho Gakkaishi 58, Supplement (2016): s18. http://dx.doi.org/10.5940/jcrsj.58.s18.

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2

Capelli, Silvia C., Hans-Beat Bürgi, Birger Dittrich, Simon Grabowsky, and Dylan Jayatilaka. "Hirshfeld atom refinement." IUCrJ 1, no. 5 (2014): 361–79. http://dx.doi.org/10.1107/s2052252514014845.

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Hirshfeld atom refinement (HAR) is a method which determines structural parameters from single-crystal X-ray diffraction data by using an aspherical atom partitioning of tailor-madeab initioquantum mechanical molecular electron densities without any further approximation. Here the original HAR method is extended by implementing an iterative procedure of successive cycles of electron density calculations, Hirshfeld atom scattering factor calculations and structural least-squares refinements, repeated until convergence. The importance of this iterative procedure is illustratedviathe example of c

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3

Midgley, Laura, Luc J. Bourhis, Oleg V. Dolomanov, et al. "Vanishing of the atomic form factor derivatives in non-spherical structural refinement – a key approximation scrutinized in the case of Hirshfeld atom refinement." Acta Crystallographica Section A Foundations and Advances 77, no. 6 (2021): 519–33. http://dx.doi.org/10.1107/s2053273321009086.

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When calculating derivatives of structure factors, there is one particular term (the derivatives of the atomic form factors) that will always be zero in the case of tabulated spherical atomic form factors. What happens if the form factors are non-spherical? The assumption that this particular term is very close to zero is generally made in non-spherical refinements (for example, implementations of Hirshfeld atom refinement or transferable aspherical atom models), unless the form factors are refinable parameters (for example multipole modelling). To evaluate this general approximation for one s

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4

Chodkiewicz, Michał Leszek, Magdalena Woińska, and Krzysztof Woźniak. "Hirshfeld atom like refinement with alternative electron density partitions." IUCrJ 7, no. 6 (2020): 1199–215. http://dx.doi.org/10.1107/s2052252520013603.

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Hirshfeld atom refinement is one of the most successful methods for the accurate determination of structural parameters for hydrogen atoms from X-ray diffraction data. This work introduces a generalization of the method [generalized atom refinement (GAR)], consisting of the application of various methods of partitioning electron density into atomic contributions. These were tested on three organic structures using the following partitions: Hirshfeld, iterative Hirshfeld, iterative stockholder, minimal basis iterative stockholder and Becke. The effects of partition choice were also compared wit

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5

Orben, Claudia M., та Birger Dittrich. "Hydrogen ADPs with CuKα data? Invariom and Hirshfeld atom modelling of fluconazole". Acta Crystallographica Section C Structural Chemistry 70, № 6 (2014): 580–83. http://dx.doi.org/10.1107/s2053229614010195.

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For the structure of fluconazole [systematic name: 2-(2,4-difluorophenyl)-1,3-bis(1H-1,2,4-triazol-1-yl)propan-2-ol] monohydrate, C13H12F2N6O·H2O, a case study on different model refinements is reported, based on single-crystal X-ray diffraction data measured at 100 K with CuKα radiation to a resolution of sin θ/λ of 0.6 Å−1. The structure, anisotropic displacement parameters (ADPs) and figures of merit from the independent atom model are compared to `invariom' and `Hirshfeld atom' refinements. Changing from a spherical to an aspherical atom model lowers the figures of merit and improves both

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6

Malaspina, Lorraine A., Anna A. Hoser, Alison J. Edwards, et al. "Hydrogen atoms in bridging positions from quantum crystallographic refinements: influence of hydrogen atom displacement parameters on geometry and electron density." CrystEngComm 22, no. 28 (2020): 4778–89. http://dx.doi.org/10.1039/d0ce00378f.

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7

Chodkiewicz, Michał, Sylwia Pawlędzio, Magdalena Woińska, and Krzysztof Woźniak. "Fragmentation and transferability in Hirshfeld atom refinement." IUCrJ 9, no. 2 (2022): 298–315. http://dx.doi.org/10.1107/s2052252522000690.

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Hirshfeld atom refinement (HAR) is one of the most effective methods for obtaining accurate structural parameters for hydrogen atoms from X-ray diffraction data. Unfortunately, it is also relatively computationally expensive, especially for larger molecules due to wavefunction calculations. Here, a fragmentation approach has been tested as a remedy for this problem. It gives an order of magnitude improvement in computation time for larger organic systems and is a few times faster for metal–organic systems at the cost of only minor differences in the calculated structural parameters when compar

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8

Woińska, Magdalena, Dylan Jayatilaka, Mark A. Spackman, et al. "Hirshfeld atom refinement for modelling strong hydrogen bonds." Acta Crystallographica Section A Foundations and Advances 70, no. 5 (2014): 483–98. http://dx.doi.org/10.1107/s2053273314012443.

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High-resolution low-temperature synchrotron X-ray diffraction data of the salt L-phenylalaninium hydrogen maleate are used to test the new automated iterative Hirshfeld atom refinement (HAR) procedure for the modelling of strong hydrogen bonds. The HAR models used present the first examples ofZ′ > 1 treatments in the framework of wavefunction-based refinement methods. L-Phenylalaninium hydrogen maleate exhibits several hydrogen bonds in its crystal structure, of which the shortest and the most challenging to model is the O—H...O intramolecular hydrogen bond present in the hydrogen maleate a

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9

Ruth, Paul Niklas, Regine Herbst-Irmer, and Dietmar Stalke. "Hirshfeld atom refinement based on projector augmented wave densities with periodic boundary conditions." IUCrJ 9, no. 2 (2022): 286–97. http://dx.doi.org/10.1107/s2052252522001385.

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Hirshfeld atom refinement (HAR) is an X-ray diffraction refinement method that, in numerous publications, has been shown to give H-atom bond lengths in close agreement with neutron diffraction derived values. Presented here is a first evaluation of an approach using densities derived from projector augmented wave (PAW) densities with three-dimensional periodic boundary conditions for HAR. The results show an improvement over refinements that neglect the crystal environment or treat it classically, while being on a par with non-periodic approximations for treating the solid-state environment qu

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10

SATO, Hiroyasu, and Akihito YAMANO. "An Overview and Examples for Hirshfeld Atom Refinement." Nihon Kessho Gakkaishi 61, no. 2 (2019): 130–35. http://dx.doi.org/10.5940/jcrsj.61.130.

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11

Chodkiewicz, Michał, Magdalena Woińska, Sylwia Pawlędzio, Leonid Patrikeev, and Krzysztof Woźniak. "Testing various variants of Hirshfeld atom-like refinement." Acta Crystallographica Section A Foundations and Advances 77, a2 (2021): C564. http://dx.doi.org/10.1107/s0108767321091303.

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12

Lübben, Jens, Christian Volkmann, Simon Grabowsky, et al. "On the temperature dependence of H-Uisoin the riding hydrogen model." Acta Crystallographica Section A Foundations and Advances 70, no. 4 (2014): 309–16. http://dx.doi.org/10.1107/s2053273314010626.

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The temperature dependence of H-UisoinN-acetyl-L-4-hydroxyproline monohydrate is investigated. Imposing a constant temperature-independent multiplier of 1.2 or 1.5 for the riding hydrogen model is found to be inaccurate, and severely underestimates H-Uisobelow 100 K. Neutron diffraction data at temperatures of 9, 150, 200 and 250 K provide benchmark results for this study. X-ray diffraction data to high resolution, collected at temperatures of 9, 30, 50, 75, 100, 150, 200 and 250 K (synchrotron and home source), reproduce neutron results only when evaluated by aspherical-atom refinement models

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13

Dittrich, B., J. J. McKinnon, and J. E. Warren. "Improvement of anisotropic displacement parameters from invariom-model refinements for three L-hydroxylysine structures." Acta Crystallographica Section B Structural Science 64, no. 6 (2008): 750–59. http://dx.doi.org/10.1107/s0108768108032163.

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Three L-hydroxylysine structures have been determined at 100 K by single-crystal X-ray diffraction. High-resolution data using either a laboratory or synchrotron source were collected and subjected to invariom- and independent atom-model (IAM) refinements. Anisotropic displacement parameters (ADPs) obtained from invariom refinement were compared (i) with results from a full multipole and (ii) with an IAM high-order refinement. Differences were visualized with the program PEANUT and were complemented by quantitative results from a Hirshfeld test. Influences of scale factor differences, and of r

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14

Malaspina, Lorraine A., Alessandro Genoni, and Simon Grabowsky. "lamaGOET: an interface for quantum crystallography." Journal of Applied Crystallography 54, no. 3 (2021): 987–95. http://dx.doi.org/10.1107/s1600576721002545.

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In quantum crystallography, theoretical calculations and crystallographic refinements are closely intertwined. This means that the employed software must be able to perform both quantum-mechanical calculations and crystallographic least-squares refinements. So far, the program Tonto is the only one able to do that. The lamaGOET interface described herein deals with this issue since it interfaces dedicated quantum-chemical software (the widely used Gaussian package and the specialized ELMOdb program) with the refinement capabilities of Tonto. Three different flavours of quantum-crystallographic

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15

Krupp, Anna, Eva Rebecca Barth, Rana Seymen, and Carsten Strohmann. "Crystal structures, Hirshfeld atom refinements and Hirshfeld surface analyses of tris(4,5-dihydrofuran-2-yl)methylsilane and tris(4,5-dihydrofuran-2-yl)phenylsilane." Acta Crystallographica Section E Crystallographic Communications 76, no. 9 (2020): 1514–19. http://dx.doi.org/10.1107/s2056989020011470.

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The title compounds, C13H18O3Si (1) and C18H20O3Si (2), represent functionalizable dihydrofuranylsilanes, which permit substitution by a variety of nucleophiles. The crystal structures of 1 and 2 display weak intermolecular C—H...O hydrogen-bonding interactions (quantified by Hirshfeld surface analysis), leading to a two-dimensional supramolecular network for 1 and a one-dimensional supramolecular network for 2. The crystal structures of 1 and 2 were refined both on the basis of the independent atom model (IAM) and the Hirshfeld atom refinement (HAR) approach, and the results are comparatively

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16

Woińska, Magdalena, Michał L. Chodkiewicz, and Krzysztof Woźniak. "Towards accurate and precise positions of hydrogen atoms bonded to heavy metal atoms." Chemical Communications 57, no. 30 (2021): 3652–55. http://dx.doi.org/10.1039/d0cc07661a.

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Positions and anisotropic thermal motion of H-Atoms bound to heavy atoms in transition-metal hydride complexes were successfully refined using Hirshfeld Atom Refinement (HAR) against low resolution X-ray diffraction data.

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17

Woinska, Magdalena. "Hirshfeld atom refinement for polymeric structures: MOFs and COFs." Acta Crystallographica Section A Foundations and Advances 80, a1 (2024): e181-e181. https://doi.org/10.1107/s2053273324098188.

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18

Arhangelskis, Mihails, Y. Xu, M. L. Chodkiewicz, et al. "Hirshfeld atom refinement of metal–organic framework crystal structures." Acta Crystallographica Section A Foundations and Advances 80, a1 (2024): e200-e200. https://doi.org/10.1107/s2053273324097997.

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19

Malaspina, L. A., R. Sankolli, F. Kleemiss, E. Wieduwilt, A. Genoni, and S. Grabowsky. "Hydrogen atom restraints and disorder treatment in Hirshfeld atom refinement of polypeptides." Acta Crystallographica Section A Foundations and Advances 79, a2 (2023): C176. http://dx.doi.org/10.1107/s2053273323094330.

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20

Pawlędzio, Sylwia, Maura Malinska, Magdalena Woińska, et al. "Relativistic Hirshfeld atom refinement of an organo-gold(I) compound." IUCrJ 8, no. 4 (2021): 608–20. http://dx.doi.org/10.1107/s2052252521004541.

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The main goal of this study is the validation of relativistic Hirshfeld atom refinement (HAR) as implemented in Tonto for high-resolution X-ray diffraction datasets of an organo-gold(I) compound. The influence of the relativistic effects on statistical parameters, geometries and electron density properties was analyzed and compared with the influence of electron correlation and anharmonic atomic motions. Recent work in this field has indicated the importance of relativistic effects in the static electron density distribution of organo-mercury compounds. This study confirms that differences in

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21

Chodkiewicz, Michał, Leonid Patrikeev, Sylwia Pawlędzio, and Krzysztof Woźniak. "The quest for more accurate Hirshfeld atom refinement related methods." Acta Crystallographica Section A Foundations and Advances 80, a1 (2024): e186-e186. https://doi.org/10.1107/s2053273324098139.

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22

Malaspina, Lorraine A., Alessandro Genoni, Dylan Jayatilaka, et al. "The advanced treatment of hydrogen bonding in quantum crystallography." Journal of Applied Crystallography 54, no. 3 (2021): 718–29. http://dx.doi.org/10.1107/s1600576721001126.

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Although hydrogen bonding is one of the most important motifs in chemistry and biology, H-atom parameters are especially problematic to refine against X-ray diffraction data. New developments in quantum crystallography offer a remedy. This article reports how hydrogen bonds are treated in three different quantum-crystallographic methods: Hirshfeld atom refinement (HAR), HAR coupled to extremely localized molecular orbitals and X-ray wavefunction refinement. Three different compound classes that form strong intra- or intermolecular hydrogen bonds are used as test cases: hydrogen maleates, the t

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23

Jha, Kunal Kumar, Barbara Gruza, Prashant Kumar, Michal Leszek Chodkiewicz, and Paulina Maria Dominiak. "TAAM: a reliable and user friendly tool for hydrogen-atom location using routine X-ray diffraction data." Acta Crystallographica Section B Structural Science, Crystal Engineering and Materials 76, no. 3 (2020): 296–306. http://dx.doi.org/10.1107/s2052520620002917.

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Hydrogen is present in almost all of the molecules in living things. It is very reactive and forms bonds with most of the elements, terminating their valences and enhancing their chemistry. X-ray diffraction is the most common method for structure determination. It depends on scattering of X-rays from electron density, which means the single electron of hydrogen is difficult to detect. Generally, neutron diffraction data are used to determine the accurate position of hydrogen atoms. However, the requirement for good quality single crystals, costly maintenance and the limited number of neutron

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24

Chodkiewicz, Michał, Leonid Patrikeev, Sylwia Pawlędzio, and Krzysztof Woźniak. "Transferable Hirshfeld atom model for rapid evaluation of aspherical atomic form factors." IUCrJ 11, no. 2 (2024): 249–59. http://dx.doi.org/10.1107/s2052252524001507.

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Form factors based on aspherical models of atomic electron density have brought great improvement in the accuracies of hydrogen atom parameters derived from X-ray crystal structure refinement. Today, two main groups of such models are available, the banks of transferable atomic densities parametrized using the Hansen–Coppens multipole model which allows for rapid evaluation of atomic form factors and Hirshfeld atom refinement (HAR)-related methods which are usually more accurate but also slower. In this work, a model that combines the ideas utilized in the two approaches is tested. It uses ato

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25

Puschmann, Horst, and Oleg Dolomanov. "Accurate hydrogen-atom positions from standard X-ray data: Hirshfeld atom refinement and Olex2." Acta Crystallographica Section A Foundations and Advances 74, a2 (2018): e40-e40. http://dx.doi.org/10.1107/s2053273318094603.

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26

Ibrahim, Mukaila A., Kathryn E. Preuss, and René T. Boeré. "N,N,N′-Tris(trimethylsilyl)-2-pyridinecarboximidamide." Molbank 2025, no. 3 (2025): M2031. https://doi.org/10.3390/m2031.

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N,N,N′-tris(trimethylsilyl)-carboximidamides are effective reagents in synthetic chemistry in reactions with both non-metal and metal halides, because the side product is the mild and volatile ClSi(CH3)3 rather than corrosive HCl. The title compound inserts the 2-pyridylamidinate fragment into several non-metal systems, including custom chelating radical ligands. The single-crystal X-ray diffraction structure was determined and modeled by Hirshfeld atom refinement using custom aspherical atomic scattering factors. Excellent data quality led to a model with enhanced precision of all interatomic

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27

Wanat, Monika, Maura Malinska, Anna A. Hoser, and Krzysztof Woźniak. "Further Validation of Quantum Crystallography Approaches." Molecules 26, no. 12 (2021): 3730. http://dx.doi.org/10.3390/molecules26123730.

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Quantum crystallography is a fast-developing multidisciplinary area of crystallography. In this work, we analyse the influence of different charge density models (i.e., the multipole model (MM), Hirshfeld atom refinement (HAR), and the transferable aspherical atom model (TAAM)), modelling of the thermal motion of hydrogen atoms (anisotropic, isotropic, and with the aid of SHADE or NoMoRe), and the type of radiation used (Mo Kα and Cu Kα) on the final results. To achieve this aim, we performed a series of refinements against X-ray diffraction data for three model compounds and compared their fi

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28

Köhler, Christian, Jens Lübben, Lennard Krause, Christina Hoffmann, Regine Herbst-Irmer, and Dietmar Stalke. "Comparison of different strategies for modelling hydrogen atoms in charge density analyses." Acta Crystallographica Section B Structural Science, Crystal Engineering and Materials 75, no. 3 (2019): 434–41. http://dx.doi.org/10.1107/s2052520619004517.

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The quality of various approximation methods for modelling anisotropic displacement parameters (ADPs) for hydrogen atoms was investigated in a comparative study. A multipole refinement was performed against high-resolution single crystal X-ray data of 9-diphenylthiophosphoranylanthracene (SPAnH) and 9,10-bis-diphenylthiophosphoranylanthracene·toluene (SPAnPS). Hydrogen-atom parameters and structural properties derived from our collected neutron data sets were compared with those obtained from the SHADE-server, the software APD-Toolkit based on the invariom database, the results from Hirshfeld

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29

Palme, Paul R., Richard Goddard, Markus Leutzsch, Adrian Richter, Peter Imming, and Rüdiger W. Seidel. "Structural Elucidation of the Triethylammonium Betaine of Squaric Acid." Molbank 2023, no. 4 (2023): M1737. http://dx.doi.org/10.3390/m1737.

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Betaines of squaric acid have gained research interest because of their structural and spectral properties. We elucidated the crystal and molecular structure of the triethylammonium betaine of squaric acid (1) by X-ray crystallography, IR, and NMR spectroscopy augmented by Hirshfeld surface analysis and DFT calculations. The crystal structure determination using Hirshfeld atom refinement reveals that the resonance hybrid structure with partial enolate character of the two lateral squaric acid C=O groups describes 1 best. The solid-state supramolecular structure features weak intermolecular C−H

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30

Taffoureau, Baptiste, Isabelle Gillaizeau, Pascal Retailleau, and Cyril Nicolas. "2,3,5-Tri-O-benzyl-d-xylofuranose." Molbank 2022, no. 2 (2022): M1382. http://dx.doi.org/10.3390/m1382.

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The synthesis and crystallization of 2,3,5-tri-O-benzyl-d-xylofuranose permitted us to isolate the alpha anomer with a small contamination of the beta form (ca 10%), whose first crystallographic structure obtained in the P212121 space group was determined at 100 K up to a resolution of sin θmax/λ = 0.71 Å−1 and refined to an R1 value of 0.0171 with a Hirshfeld atom refinement (HAR) approach.

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Woinska, Magdalena, Simon Grabowsky, Paulina M. Dominiak, Krzysztof Wozniak, and Dylan Jayatilaka. "Hirshfeld atom refinement for determining hydrogen positions in routine X-ray experiments." Acta Crystallographica Section A Foundations and Advances 71, a1 (2015): s107. http://dx.doi.org/10.1107/s2053273315098435.

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32

Boeré, René T. "Crystal Structures of CuCl2·2H2O (Eriochalcite) and NiCl2∙6H2O (Nickelbischofite) at Low Temperature: Full Refinement of Hydrogen Atoms Using Non-Spherical Atomic Scattering Factors." Crystals 13, no. 2 (2023): 293. http://dx.doi.org/10.3390/cryst13020293.

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New structure determinations of CuCl2∙2H2O and NiCl2∙6H2O are reported from 100 K X-ray diffraction experiments using both Mo Kα and Cu Kα radiation. Combined density functional theory (ORCA) and non-spherical atomic scattering factor (NoSpherA2) computations enabled Hirshfeld atom refinements (HAR) using custom atom scattering factors based on accurately polarized atom electron densities. The water hydrogen atoms could be positionally refined resulting in distinctly longer O–H bond lengths than those reported from previous X-ray diffraction experiments, but in good agreement with legacy neutr

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33

Kirchhoff, Jan-Lukas, Lukas Brieger, and Carsten Strohmann. "Crystal structure and Hirshfeld surface analysis of (S)-N-methyl-1-phenylethan-1-aminium chloride." Acta Crystallographica Section E Crystallographic Communications 78, no. 2 (2022): 130–34. http://dx.doi.org/10.1107/s2056989021013645.

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The title compound C9H14N+·Cl−, (1), can be synthesized starting from (S)-N-methyl-1-phenylethan-1-amine (2). Compound 2 upon addition of HCl·Et2O leads to crystallization of compound 1 as colorless blocks. The configuration of compound 1 is stable as well as preserved in space group P212121. Ammonium chlorides, like the title compound, are often observed as undesirable by-products in aminosilylation of chlorosilanes. Additionally, these by-products are usually soluble in selected organic solvents, which require difficult separation steps. Therefore, detailed studies on structural features and

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34

Pal, Rumpa, Christian Jelsch, Koichi Momma та Simon Grabowsky. "π-Hole bonding in a new co-crystal hydrate of gallic acid and pyrazine: static and dynamic charge density analysis". Acta Crystallographica Section B Structural Science, Crystal Engineering and Materials 78, № 2 (2022): 231–46. http://dx.doi.org/10.1107/s2052520622001457.

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A new cocrystal hydrate of gallic acid with pyrazine (4GA, Py, 4H2O; GA4PyW4) was obtained and characterized by single crystal X-ray diffraction. In addition to structure determination, experimental charge density analysis was carried out in terms of Multipole Modelling (MP), X-ray wavefunction refinement (XWR) and maximum entropy method (MEM). As a part of XWR, the structural refinement via Hirshfeld atom refinement was carried out and resulted in O—H bond lengths close to values from neutron diffraction. A systematic comparison of molecular conformations and aromatic interactions in this new

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35

Chęcińska, Lilianna, Wolfgang Morgenroth, Carsten Paulmann, Dylan Jayatilaka, and Birger Dittrich. "A comparison of electron density from Hirshfeld-atom refinement, X-ray wavefunction refinement and multipole refinement on three urea derivatives." CrystEngComm 15, no. 11 (2013): 2084. http://dx.doi.org/10.1039/c2ce26964c.

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36

Pawlędzio, Sylwia, Maura Malinska, Florian Kleemiss, Simon Grabowsky, and Krzysztof Woźniak. "Relativistic Hirshfeld atom refinement of organo-gold(I) and organo-mercury(II) compounds." Acta Crystallographica Section A Foundations and Advances 77, a2 (2021): C71. http://dx.doi.org/10.1107/s0108767321096082.

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37

Rodić, Marko V., Milan S. Nešić, Matic Lozinšek та Niko Radulović. "Insight into α-iminoamidines: Hirshfeld atom refinement and evaluation of intermolecular interaction energies". Acta Crystallographica Section A Foundations and Advances 80, a1 (2024): e178-e178. https://doi.org/10.1107/s2053273324098218.

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38

Davidson, Max L., Simon Grabowsky, and Dylan Jayatilaka. "X-ray constrained wavefunctions based on Hirshfeld atoms. I. Method and review." Acta Crystallographica Section B Structural Science, Crystal Engineering and Materials 78, no. 3 (2022): 312–32. http://dx.doi.org/10.1107/s2052520622004097.

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The X-ray constrained wavefunction (XCW) procedure for obtaining an experimentally reconstructed wavefunction from X-ray diffraction data is reviewed. The two-center probability distribution model used to perform nuclear-position averaging in the original paper [Grimwood & Jayatilaka (2001). Acta Cryst. A57, 87–100] is carefully distinguished from the newer one-center probability distribution model. In the one-center model, Hirshfeld atoms are used, and the Hirshfeld atom based X-ray constrained wavefunction (HA-XCW) procedure is described for the first time, as well as its efficient imple

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39

Bučinský, Lukáš, Dylan Jayatilaka, and Simon Grabowsky. "Relativistic quantum crystallography of diphenyl- and dicyanomercury. Theoretical structure factors and Hirshfeld atom refinement." Acta Crystallographica Section A Foundations and Advances 75, no. 5 (2019): 705–17. http://dx.doi.org/10.1107/s2053273319008027.

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Quantum crystallographic refinement of heavy-element-containing compounds is a challenge, because many physical effects have to be accounted for adequately. Here, the impact and magnitude of relativistic effects are compared with those of electron correlation, polarization through the environment, choice of basis set and treatment of thermal motion effects on the structure factors of diphenylmercury(II) [Hg(Ph)2] and dicyanomercury(II) [Hg(CN)2]. Furthermore, the individual atomic contributions to the structure factors are explored in detail (using Mulliken population analysis and the exponent

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40

Fugel, Malte, Dylan Jayatilaka, Emanuel Hupf, et al. "Probing the accuracy and precision of Hirshfeld atom refinement with HARt interfaced with Olex2." IUCrJ 5, no. 1 (2018): 32–44. http://dx.doi.org/10.1107/s2052252517015548.

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Hirshfeld atom refinement (HAR) is a novel X-ray structure refinement technique that employs aspherical atomic scattering factors obtained from stockholder partitioning of a theoretically determined tailor-made static electron density. HAR overcomes many of the known limitations of independent atom modelling (IAM), such as too short element–hydrogen distances, r(X—H), or too large atomic displacement parameters (ADPs). This study probes the accuracy and precision of anisotropic hydrogen and non-hydrogen ADPs and of r(X—H) values obtained from HAR. These quantities are compared and found to agr

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Lee, Jung-Seop, Matthias Zeller, Shrikant Dashrath Warkad, and Satish Balasaheb Nimse. "Synthesis, Characterization, and Crystal Structure of N-(3-nitrophenyl)cinnamamide." Crystals 9, no. 11 (2019): 599. http://dx.doi.org/10.3390/cryst9110599.

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N-(3-nitrophenyl)cinnamamide 1 with formula C15H12N2O3 was synthesized, and its crystal structure was determined by single-crystal X-ray diffraction analysis. Compound 1 crystallizes in the monoclinic space group P21/n with unit cell dimensions: a = 6.7810 (5) Å, b = 23.0913 (15) Å, c = 8.2079 (5) Å, V = 1282.76 (15) Å3, Z = 4, determined at 150 K with MoKα radiation. The experimental structure refined against atomic scattering factors is compared with the structure obtained using a Hirshfeld Atom Refinement (HAR) approach and Density Functional Theory (DFT) geometry optimizations.

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42

Capelli, Silvia C., Hans-Beat Bürgi, Sax A. Mason, and Dylan Jayatilaka. "Glycyl-L-alanine: a multi-temperature neutron study." Acta Crystallographica Section C Structural Chemistry 70, no. 10 (2014): 949–52. http://dx.doi.org/10.1107/s2053229614019809.

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Neutron diffraction data have been collected at 12, 50, 150 and 295 K for the dipeptide glycyl-L-alanine, C5H10N2O3, in order to obtain accurate positional and anisotropic displacement parameters for the H atoms. The values of these parameters serve as a benchmark for assessing the equivalent parameters obtained from a so-called Hirshfeld-atom refinement of X-ray diffraction data described elsewhere [Capelliet al.(2014).IUCrJ,1, 361–379]. The flexibility of the glycyl-L-alanine molecule in the solid and the hydrogen-bonding interactions as a function of temperature are also considered.

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Wozniak, Krzysztof, Michal Chodkiewicz, Roman Gajda, Vitali B. Prakapenka, and Przemyslaw Dera. "Accurate crystal structures of ices from X-ray and ED with Hirshfeld atom refinement." Acta Crystallographica Section A Foundations and Advances 79, a1 (2023): a189. http://dx.doi.org/10.1107/s2053273323098108.

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Woźniak, K., M. Chodkiewicz, R. Gajda, V. B. Prakapenka, and P. Dera. "Accurate crystal structures of ices from X-ray and ED with Hirshfeld atom refinement." Acta Crystallographica Section A Foundations and Advances 79, a2 (2023): C568. http://dx.doi.org/10.1107/s2053273323090484.

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Faroque, Muhammad Umer, Sajida Noureen, Maqsood Ahmed, and Muhammad Nawaz Tahir. "Electrostatic properties of the pyrimethamine–2,4-dihydroxybenzoic acid cocrystal in methanol studied using transferred electron-density parameters." Acta Crystallographica Section C Structural Chemistry 74, no. 1 (2018): 100–107. http://dx.doi.org/10.1107/s2053229617017788.

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The crystal structure of the cocrystal salt form of the antimalarial drug pyrimethamine with 2,4-dihydroxybenzoic acid in methanol [systematic name: 2,4-diamino-5-(4-chlorophenyl)-6-ethylpyrimidin-1-ium 2,4-dihydroxybenzoate methanol monosolvate, C12H14ClN4 +·C7H5O4 −·CH3OH] has been studied using X-ray diffraction data collected at room temperature. The crystal structure was refined using the classical Independent Atom Model (IAM) and the Multipolar Atom Model by transferring electron-density parameters from the ELMAM2 database. The Cl atom was refined anharmonically. The results of both refi

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46

Sanjuan-Szklarz, W. Fabiola, Magdalena Woińska, Sławomir Domagała, et al. "On the accuracy and precision of X-ray and neutron diffraction results as a function of resolution and the electron density model." IUCrJ 7, no. 5 (2020): 920–33. http://dx.doi.org/10.1107/s2052252520010441.

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X-ray diffraction is the main source of three-dimensional structural information. In total, more than 1.5 million crystal structures have been refined and deposited in structural databanks (PDB, CSD and ICSD) to date. Almost 99.7% of them were obtained by approximating atoms as spheres within the independent atom model (IAM) introduced over a century ago. In this study, X-ray datasets for single crystals of hydrated α-oxalic acid were refined using several alternative electron density models that abandon the crude spherical approximation: the multipole model (MM), the transferable aspherical a

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Malinska, Maura, and Zbigniew Dauter. "Transferable aspherical atom model refinement of protein and DNA structures against ultrahigh-resolution X-ray data." Acta Crystallographica Section D Structural Biology 72, no. 6 (2016): 770–79. http://dx.doi.org/10.1107/s2059798316006355.

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In contrast to the independent-atom model (IAM), in which all atoms are assumed to be spherical and neutral, the transferable aspherical atom model (TAAM) takes into account the deformed valence charge density resulting from chemical bond formation and the presence of lone electron pairs. Both models can be used to refine small and large molecules,e.g.proteins and nucleic acids, against ultrahigh-resolution X-ray diffraction data. The University at Buffalo theoretical databank of aspherical pseudo-atoms has been used in the refinement of an oligopeptide, of Z-DNA hexamer and dodecamer duplexes

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Parsons, Simon, Trixie Wagner, Oliver Presly, Peter A. Wood, and Richard I. Cooper. "Applications of leverage analysis in structure refinement." Journal of Applied Crystallography 45, no. 3 (2012): 417–29. http://dx.doi.org/10.1107/s0021889812015191.

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Leverages measure the influence that observations (intensity data and restraints) have on the fit obtained in crystal structure refinement. Further analysis enables the influence that observations have on specific parameters to be measured. The results of leverage analyses are discussed in the context of the amino acid alanine and an incomplete high-pressure data set of the complex bis(salicylaldoximato)copper(II). Leverage analysis can reveal situations where weak data are influential and allows an assessment of the influence of restraints. Analysis of the high-pressure refinement of the copp

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Woinska, Magdalena, Monika Wanat, Przemyslaw Taciak, Tomasz Pawinski, Wladek Minor, and Krzysztof Wozniak. "Energetics of interactions in the solid state of 2-hydroxy-8-X-quinoline derivatives (X = Cl, Br, I, S-Ph): comparison of Hirshfeld atom, X-ray wavefunction and multipole refinements." IUCrJ 6, no. 5 (2019): 868–83. http://dx.doi.org/10.1107/s2052252519007358.

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In this work, two methods of high-resolution X-ray data refinement: multipole refinement (MM) and Hirshfeld atom refinement (HAR) – together with X-ray wavefunction refinement (XWR) – are applied to investigate the refinement of positions and anisotropic thermal motion of hydrogen atoms, experiment-based reconstruction of electron density, refinement of anharmonic thermal vibrations, as well as the effects of excluding the weakest reflections in the refinement. The study is based on X-ray data sets of varying quality collected for the crystals of four quinoline derivatives with Cl, Br, I atoms

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Bergmann, Justin, Max Davidson, Esko Oksanen, Ulf Ryde, and Dylan Jayatilaka. "fragHAR: towards ab initio quantum-crystallographic X-ray structure refinement for polypeptides and proteins." IUCrJ 7, no. 2 (2020): 158–65. http://dx.doi.org/10.1107/s2052252519015975.

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The first ab initio aspherical structure refinement against experimental X-ray structure factors for polypeptides and proteins using a fragmentation approach to break up the protein into residues and solvent, thereby speeding up quantum-crystallographic Hirshfeld atom refinement (HAR) calculations, is described. It it found that the geometric and atomic displacement parameters from the new fragHAR method are essentially unchanged from a HAR on the complete unfragmented system when tested on dipeptides, tripeptides and hexapeptides. The largest changes are for the parameters describing H atoms

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