Articoli di riviste: "Hirshfeld Atom Refinement"

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Grabowsky, Simon, Magdalena Woinska e 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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Capelli, Silvia C., Hans-Beat Bürgi, Birger Dittrich, Simon Grabowsky e Dylan Jayatilaka. "Hirshfeld atom refinement". IUCrJ 1, n. 5 (29 agosto 2014): 361–79. http://dx.doi.org/10.1107/s2052252514014845.

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Abstract (sommario):

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 crystalline ammonia. The new HAR method is then applied to X-ray diffraction data of the dipeptide Gly–L-Ala measured at 12, 50, 100, 150, 220 and 295 K, using Hartree–Fock and BLYP density functional theory electron densities and three different basis sets. All positions and anisotropic displacement parameters (ADPs) are freely refined without constraints or restraints – even those for hydrogen atoms. The results are systematically compared with those from neutron diffraction experiments at the temperatures 12, 50, 150 and 295 K. Although non-hydrogen-atom ADPs differ by up to three combined standard uncertainties (csu's), all other structural parameters agree within less than 2 csu's. Using our best calculations (BLYP/cc-pVTZ, recommended for organic molecules), the accuracy of determining bond lengths involving hydrogen atoms from HAR is better than 0.009 Å for temperatures of 150 K or below; for hydrogen-atom ADPs it is better than 0.006 Å2as judged from the mean absolute X-ray minus neutron differences. These results are among the best ever obtained. Remarkably, the precision of determining bond lengths and ADPs for the hydrogen atoms from the HAR procedure is comparable with that from the neutron measurements – an outcome which is obtained with a routinely achievable resolution of the X-ray data of 0.65 Å.

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Midgley, Laura, Luc J. Bourhis, Oleg V. Dolomanov, Simon Grabowsky, Florian Kleemiss, Horst Puschmann e Norbert Peyerimhoff. "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, n. 6 (29 ottobre 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 specific method, a numerical differentiation was implemented within the NoSpherA2 framework to calculate the derivatives of the structure factors in a Hirshfeld atom refinement directly as accurately as possible, thus bypassing the approximation altogether. Comparing wR 2 factors and atomic parameters, along with their uncertainties from the approximate and numerically differentiating refinements, it turns out that the impact of this approximation on the final crystallographic model is indeed negligible.

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Chodkiewicz, Michał Leszek, Magdalena Woińska e Krzysztof Woźniak. "Hirshfeld atom like refinement with alternative electron density partitions". IUCrJ 7, n. 6 (29 ottobre 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 with those caused by other factors such as quantum chemical methodology, basis set, representation of the crystal field and a combination of these factors. The differences between the partitions were small in terms of R factor (e.g. much smaller than for refinements with different quantum chemistry methods, i.e. Hartree–Fock and coupled cluster) and therefore no single partition was clearly the best in terms of experimental data reconstruction. In the case of structural parameters the differences between the partitions are comparable to those related to the choice of other factors. We have observed the systematic effects of the partition choice on bond lengths and ADP values of polar hydrogen atoms. The bond lengths were also systematically influenced by the choice of electron density calculation methodology. This suggests that GAR-derived structural parameters could be systematically improved by selecting an optimal combination of the partition and quantum chemistry method. The results of the refinements were compared with those of neutron diffraction experiments. This allowed a selection of the most promising partition methods for further optimization of GAR settings, namely the Hirshfeld, iterative stockholder and minimal basis iterative stockholder.

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Orben, Claudia M., e Birger Dittrich. "Hydrogen ADPs with CuKα data? Invariom and Hirshfeld atom modelling of fluconazole". Acta Crystallographica Section C Structural Chemistry 70, n. 6 (17 maggio 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 the accuracy and the precision of the geometrical parameters. Differences between results from the two aspherical-atom refinements are small. However, a refinement of ADPs for H atoms is only possible with the Hirshfeld atom density model. It gives meaningful results even at a resolution of 0.6 Å−1, but requires good low-order data.

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Malaspina, Lorraine A., Anna A. Hoser, Alison J. Edwards, Magdalena Woińska, Michael J. Turner, Jason R. Price, Kunihisa Sugimoto et al. "Hydrogen atoms in bridging positions from quantum crystallographic refinements: influence of hydrogen atom displacement parameters on geometry and electron density". CrystEngComm 22, n. 28 (2020): 4778–89. http://dx.doi.org/10.1039/d0ce00378f.

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Chodkiewicz, Michał, Sylwia Pawlędzio, Magdalena Woińska e Krzysztof Woźniak. "Fragmentation and transferability in Hirshfeld atom refinement". IUCrJ 9, n. 2 (26 febbraio 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 compared with the original HAR calculations. Fragmentation was also applied to polymeric and disordered systems where it provides a natural solution to problems that arise when HAR is applied. The concept of fragmentation is closely related to the transferable aspherical atom model (TAAM) and allows insight into possible ways to improve TAAM. Hybrid approaches combining fragmentation with the transfer of atomic densities between chemically similar atoms have been tested. An efficient handling of intermolecular interactions was also introduced for calculations involving fragmentation. When applied in fragHAR (a fragmentation approach for polypeptides) as a replacement for the original approach, it allowed for more efficient calculations. All of the calculations were performed with a locally modified version of Olex2 combined with a development version of discamb2tsc and ORCA. Care was taken to efficiently use the power of multicore processors by simple implementation of load-balancing, which was found to be very important for lowering computational time.

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Woińska, Magdalena, Dylan Jayatilaka, Mark A. Spackman, Alison J. Edwards, Paulina M. Dominiak, Krzysztof Woźniak, Eiji Nishibori, Kunihisa Sugimoto e Simon Grabowsky. "Hirshfeld atom refinement for modelling strong hydrogen bonds". Acta Crystallographica Section A Foundations and Advances 70, n. 5 (30 agosto 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 anion (O...O distance is about 2.41 Å). In particular, the reconstruction of the electron density in the hydrogen maleate moiety and the determination of hydrogen-atom properties [positions, bond distances and anisotropic displacement parameters (ADPs)] are the focus of the study. For comparison to the HAR results, different spherical (independent atom model, IAM) and aspherical (free multipole model, MM; transferable aspherical atom model, TAAM) X-ray refinement techniques as well as results from a low-temperature neutron-diffraction experiment are employed. Hydrogen-atom ADPs are furthermore compared to those derived from a TLS/rigid-body (SHADE) treatment of the X-ray structures. The reference neutron-diffraction experiment reveals a truly symmetric hydrogen bond in the hydrogen maleate anion. Only with HAR is it possible to freely refine hydrogen-atom positions and ADPs from the X-ray data, which leads to the best electron-density model and the closest agreement with the structural parameters derived from the neutron-diffraction experiment,e.g.the symmetric hydrogen position can be reproduced. The multipole-based refinement techniques (MM and TAAM) yield slightly asymmetric positions, whereas the IAM yields a significantly asymmetric position.

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Ruth, Paul Niklas, Regine Herbst-Irmer e Dietmar Stalke. "Hirshfeld atom refinement based on projector augmented wave densities with periodic boundary conditions". IUCrJ 9, n. 2 (26 febbraio 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 quantum mechanically. A suite of functionals were evaluated for this purpose, showing that the SCAN and revSCAN functionals are most suited to these types of calculation.

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SATO, Hiroyasu, e Akihito YAMANO. "An Overview and Examples for Hirshfeld Atom Refinement". Nihon Kessho Gakkaishi 61, n. 2 (31 maggio 2019): 130–35. http://dx.doi.org/10.5940/jcrsj.61.130.

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Chodkiewicz, Michał, Magdalena Woińska, Sylwia Pawlędzio, Leonid Patrikeev e Krzysztof Woźniak. "Testing various variants of Hirshfeld atom-like refinement". Acta Crystallographica Section A Foundations and Advances 77, a2 (14 agosto 2021): C564. http://dx.doi.org/10.1107/s0108767321091303.

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Lübben, Jens, Christian Volkmann, Simon Grabowsky, Alison Edwards, Wolfgang Morgenroth, Francesca P. A. Fabbiani, George M. Sheldrick e Birger Dittrich. "On the temperature dependence of H-Uisoin the riding hydrogen model". Acta Crystallographica Section A Foundations and Advances 70, n. 4 (28 maggio 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, since these take into account bonding and lone-pair electron density; both invariom and Hirshfeld-atom refinement models enable a more precise determination of the magnitude of H-atom displacements than independent-atom model refinements. Experimental efforts are complemented by computing displacement parameters following the TLS+ONIOM approach. A satisfactory agreement between all approaches is found.

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Dittrich, B., J. J. McKinnon e J. E. Warren. "Improvement of anisotropic displacement parameters from invariom-model refinements for three L-hydroxylysine structures". Acta Crystallographica Section B Structural Science 64, n. 6 (8 novembre 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 refinement against F^2 versus F, have been investigated. Systematic errors were observed in the IAM, especially when only low-order data were available. Although these errors were reduced in high-order IAM refinements, they only disappeared in charge density – and likewise – invariom refinements.

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Malaspina, Lorraine A., Alessandro Genoni e Simon Grabowsky. "lamaGOET: an interface for quantum crystallography". Journal of Applied Crystallography 54, n. 3 (16 aprile 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 refinements of the dipetide glycyl-L-threonine dihydrate are presented to showcase the capabilities of lamaGOET: Hirshfeld atom refinement (HAR), HAR-ELMO, namely HAR coupled with extremely localized molecular orbitals, and X-ray constrained wavefunction fitting.

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Krupp, Anna, Eva Rebecca Barth, Rana Seymen e 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, n. 9 (28 agosto 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 discussed.

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Woińska, Magdalena, Michał L. Chodkiewicz e Krzysztof Woźniak. "Towards accurate and precise positions of hydrogen atoms bonded to heavy metal atoms". Chemical Communications 57, n. 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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Malaspina, L. A., R. Sankolli, F. Kleemiss, E. Wieduwilt, A. Genoni e S. Grabowsky. "Hydrogen atom restraints and disorder treatment in Hirshfeld atom refinement of polypeptides". Acta Crystallographica Section A Foundations and Advances 79, a2 (22 agosto 2023): C176. http://dx.doi.org/10.1107/s2053273323094330.

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Pawlędzio, Sylwia, Maura Malinska, Magdalena Woińska, Jakub Wojciechowski, Lorraine Andrade Malaspina, Florian Kleemiss, Simon Grabowsky e Krzysztof Woźniak. "Relativistic Hirshfeld atom refinement of an organo-gold(I) compound". IUCrJ 8, n. 4 (26 maggio 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 electron density due to relativistic effects are also of significant magnitude for organo-gold compounds. Relativistic effects dominate not only the core region of the gold atom, but also influence the electron density in the valence and bonding region, which has measurable consequences for the HAR refinement model parameters. To study the effects of anharmonic motion on the electron density distribution, dynamic electron density difference maps were constructed. Unlike relativistic and electron correlation effects, the effects of anharmonic nuclear motion are mostly observed in the core area of the gold atom.

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Jha, Kunal Kumar, Barbara Gruza, Prashant Kumar, Michal Leszek Chodkiewicz e 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, n. 3 (10 aprile 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 diffraction facilities means that these kind of results are rarely available. Here it is shown that the use of Transferable Aspherical Atom Model (TAAM) instead of Independent Atom Model (IAM) in routine structure refinement with X-ray data is another possible solution which largely improves the precision and accuracy of X—H bond lengths and makes them comparable to averaged neutron bond lengths. TAAM, built from a pseudoatom databank, was used to determine the X—H bond lengths on 75 data sets for organic molecule crystals. TAAM parametrizations available in the modified University of Buffalo Databank (UBDB) of pseudoatoms applied through the DiSCaMB software library were used. The averaged bond lengths determined by TAAM refinements with X-ray diffraction data of atomic resolution (d min ≤ 0.83 Å) showed very good agreement with neutron data, mostly within one single sample standard deviation, much like Hirshfeld atom refinement (HAR). Atomic displacements for both hydrogen and non-hydrogen atoms obtained from the refinements systematically differed from IAM results. Overall TAAM gave better fits to experimental data of standard resolution compared to IAM. The research was accompanied with development of software aimed at providing user-friendly tools to use aspherical atom models in refinement of organic molecules at speeds comparable to routine refinements based on spherical atom model.

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Malaspina, Lorraine A., Alessandro Genoni, Dylan Jayatilaka, Michael J. Turner, Kunihisa Sugimoto, Eiji Nishibori e Simon Grabowsky. "The advanced treatment of hydrogen bonding in quantum crystallography". Journal of Applied Crystallography 54, n. 3 (16 aprile 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 tripeptide L-alanyl-glycyl-L-alanine co-crystallized with water, and xylitol. The differences in the quantum-mechanical electron densities underlying all the used methods are analysed, as well as how these differences impact on the refinement results.

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Puschmann, Horst, e 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 (22 agosto 2018): e40-e40. http://dx.doi.org/10.1107/s2053273318094603.

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Chodkiewicz, Michał, Leonid Patrikeev, Sylwia Pawlędzio e Krzysztof Woźniak. "Transferable Hirshfeld atom model for rapid evaluation of aspherical atomic form factors". IUCrJ 11, n. 2 (1 marzo 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 atomic electron densities based on Hirshfeld partitions of electron densities, which are precalculated and stored in a databank. This model was also applied during the refinement of the structures of five small molecules. A comparison of the resulting hydrogen atom parameters with those derived from neutron diffraction data indicates that they are more accurate than those obtained with the Hansen–Coppens based databank, and only slightly less accurate than those obtained with a version of HAR that neglects the crystal environment. The advantage of using HAR becomes more noticeable when the effects of the environment are included. To speed up calculations, atomic densities were represented by multipole expansion with spherical harmonics up to l = 7, which used numerical radial functions (a different approach to that applied in the Hansen–Coppens model). Calculations of atomic form factors for the small protein crambin (at 0.73 Å resolution) took only 68 s using 12 CPU cores.

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Wanat, Monika, Maura Malinska, Anna A. Hoser e Krzysztof Woźniak. "Further Validation of Quantum Crystallography Approaches". Molecules 26, n. 12 (18 giugno 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 final structures, geometries, shapes of ADPs, and charge density distributions. Our results were also supported by theoretical calculations that enabled comparisons of the lattice energies of these structures. It appears that geometrical parameters are better described (closer to the neutron values) when HAR is used; however, bonds to H atoms more closely match neutron values after MM or TAAM refinement. Our analysis shows the superiority of the NoMoRe method in the description of H-atom ADPs. Moreover, the shapes of the ADPs of H atoms, as well as their electron density distributions, were better described with low-resolution Cu Kα data in comparison to low-resolution Mo Kα data.

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Köhler, Christian, Jens Lübben, Lennard Krause, Christina Hoffmann, Regine Herbst-Irmer e 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, n. 3 (24 maggio 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 atom refinement conducted in the OLEX2 GUI (HARt), and the results of anisotropic hydrogen refinement within XD2016. Additionally, a free refinement of H-atom positions against X-ray data was performed with fixed ADPs from various methods. The resulting C—H bond distances were compared with distances from neutron diffraction experiments and the HARt results. Surprisingly, the refinement of anisotropic hydrogen displacement parameters against the X-ray data yielded the smallest deviations from the neutron values. However, the refinement of bond-directed quadrupole parameters turned out to be vital for the quality of the resulting ADPs. In both model structures, SHADE and, to a lesser extent, APD-Toolkit showed problems in dealing with atoms bonded to carbon atoms with refined Gram-Charlier parameters for anharmonic motion. The HARt method yields the most accurate C—H bond distances compared to neutron data results. Unconstrained refinement of hydrogen atom positions using ADPs derived from all other used approximation methods showed that even with well approximated hydrogen ADPs, the resulting distances were still significantly underestimated.

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Woinska, Magdalena, Simon Grabowsky, Paulina M. Dominiak, Krzysztof Wozniak e Dylan Jayatilaka. "Hirshfeld atom refinement for determining hydrogen positions in routine X-ray experiments". Acta Crystallographica Section A Foundations and Advances 71, a1 (23 agosto 2015): s107. http://dx.doi.org/10.1107/s2053273315098435.

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Palme, Paul R., Richard Goddard, Markus Leutzsch, Adrian Richter, Peter Imming e Rüdiger W. Seidel. "Structural Elucidation of the Triethylammonium Betaine of Squaric Acid". Molbank 2023, n. 4 (16 ottobre 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···O hydrogen bonds. The number of C=O bands in the IR spectrum in the solid-state is consistent with local C2v symmetry of the squaric acid residue in 1. The 13C NMR signals of this group in solution were assigned based on 2D NMR experiments and computational prediction using the Gauge-Independent Atom Orbital (GIAO) method. The present study provides the first structural characterization of a betaine of squaric acid containing a four-coordinate nitrogen atom directly attached to the four-membered ring.

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Taffoureau, Baptiste, Isabelle Gillaizeau, Pascal Retailleau e Cyril Nicolas. "2,3,5-Tri-O-benzyl-d-xylofuranose". Molbank 2022, n. 2 (7 giugno 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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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, n. 2 (9 febbraio 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 neutron diffraction studies. Anisotropic displacement factors were employed, for the first time in these compounds by any technique. The outcomes from using the different X-ray sources with this new HAR method are compared, and the precision of the H-atom refinements evaluated where possible.

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Chęcińska, Lilianna, Wolfgang Morgenroth, Carsten Paulmann, Dylan Jayatilaka e Birger Dittrich. "A comparison of electron density from Hirshfeld-atom refinement, X-ray wavefunction refinement and multipole refinement on three urea derivatives". CrystEngComm 15, n. 11 (2013): 2084. http://dx.doi.org/10.1039/c2ce26964c.

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Kirchhoff, Jan-Lukas, Lukas Brieger e Carsten Strohmann. "Crystal structure and Hirshfeld surface analysis of (S)-N-methyl-1-phenylethan-1-aminium chloride". Acta Crystallographica Section E Crystallographic Communications 78, n. 2 (7 gennaio 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 intermolecular interactions performed by Hirshfeld atom refinement (HAR) using NoSpherA2 [Kleemiss et al. (2021). Chem. Sci. 12, 1675–1692] and Hirshfeld surface analysis were used to address structural issues on that separation problem.

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Pal, Rumpa, Christian Jelsch, Koichi Momma e 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, n. 2 (23 marzo 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 cocrystal hydrate was performed with other existing polymorphs of gallic acid. In GA4PyW4, the two symmetry-independent gallic acid molecules have a syn COOH orientation and form the common (COOH)2 dimeric synthon. The carboxyl C atom displays the characteristics of π-holes with electropositive regions above and below the molecular plane and engages in acceptor–donor interactions with oxygen atoms of acidic O—H groups and phenol groups of neighbouring gallic acid molecules. The signature of the π-hole was identified from experimental charge density analysis, both in static density maps in MP and XWR as well as dynamic density in MEM, but it cannot be pinned down to a specific atom–atom interaction. This study presents the first comparison between an XWR and a MEM experimental electron-density determination.

32

Pawlędzio, Sylwia, Maura Malinska, Florian Kleemiss, Simon Grabowsky e Krzysztof Woźniak. "Relativistic Hirshfeld atom refinement of organo-gold(I) and organo-mercury(II) compounds". Acta Crystallographica Section A Foundations and Advances 77, a2 (14 agosto 2021): C71. http://dx.doi.org/10.1107/s0108767321096082.

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33

Bučinský, Lukáš, Dylan Jayatilaka e Simon Grabowsky. "Relativistic quantum crystallography of diphenyl- and dicyanomercury. Theoretical structure factors and Hirshfeld atom refinement". Acta Crystallographica Section A Foundations and Advances 75, n. 5 (12 agosto 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 exponential decay of atomic displacement parameters) to compare the contributions of lighter atoms, especially hydrogen atoms, against mercury. Subsequently, relativistic Hirshfeld atom refinement (HAR) is validated against theoretical structure factors of Hg(Ph)2 and Hg(CN)2, starting from perturbed geometries, to test if the relativistic variant of HAR leads to multiple solutions. Generally, relativistic HAR is successful, leading to a perfect match with the reference geometries, but some limitations are pointed out.

34

Fugel, Malte, Dylan Jayatilaka, Emanuel Hupf, Jacob Overgaard, Venkatesha R. Hathwar, Piero Macchi, Michael J. Turner et al. "Probing the accuracy and precision of Hirshfeld atom refinement with HARt interfaced with Olex2". IUCrJ 5, n. 1 (1 gennaio 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 agree with those obtained from (i) accurate neutron diffraction data measured at the same temperatures as the X-ray data and (ii) multipole modelling (MM), an established alternative method for interpreting X-ray diffraction data with the help of aspherical atomic scattering factors. Results are presented for three chemically different systems: the aromatic hydrocarbon rubrene (orthorhombic 5,6,11,12-tetraphenyltetracene), a co-crystal of zwitterionic betaine, imidazolium cations and picrate anions (BIPa), and the salt potassium hydrogen oxalate (KHOx). The non-hydrogen HAR-ADPs are as accurate and precise as the MM-ADPs. Both show excellent agreement with the neutron-based values and are superior to IAM-ADPs. The anisotropic hydrogen HAR-ADPs show a somewhat larger deviation from neutron-based values than the hydrogen SHADE-ADPs used in MM. Element–hydrogen bond lengths from HAR are in excellent agreement with those obtained from neutron diffraction experiments, although they are somewhat less precise. The residual density contour maps after HAR show fewer features than those after MM. Calculating the static electron density with the def2-TZVP basis set instead of the simpler def2-SVP one does not improve the refinement results significantly. All HARs were performed within the recently introduced HARt option implemented in the Olex2 program. They are easily launched inside its graphical user interface following a conventional IAM.

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Davidson, Max L., Simon Grabowsky e 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, n. 3 (31 maggio 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 implementation. In this context, the definition of the related X-ray wavefunction refinement (XWR) method is refined. The key halting problem for the XCW method – the procedure by which one determines when overfitting has occurred – is named and work on it reviewed.

36

Lee, Jung-Seop, Matthias Zeller, Shrikant Dashrath Warkad e Satish Balasaheb Nimse. "Synthesis, Characterization, and Crystal Structure of N-(3-nitrophenyl)cinnamamide". Crystals 9, n. 11 (15 novembre 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.

37

Capelli, Silvia C., Hans-Beat Bürgi, Sax A. Mason e Dylan Jayatilaka. "Glycyl-L-alanine: a multi-temperature neutron study". Acta Crystallographica Section C Structural Chemistry 70, n. 10 (28 settembre 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 e 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 (7 luglio 2023): a189. http://dx.doi.org/10.1107/s2053273323098108.

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39

Woźniak, K., M. Chodkiewicz, R. Gajda, V. B. Prakapenka e 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 (22 agosto 2023): C568. http://dx.doi.org/10.1107/s2053273323090484.

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40

Faroque, Muhammad Umer, Sajida Noureen, Maqsood Ahmed e 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, n. 1 (1 gennaio 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 refinement methods have been compared. The intermolecular interactions have been characterized on the basis of Hirshfeld surface analysis and topological analysis using Bader's theory of Atoms in Molecules. The results show that the molecular assembly is built primarily on the basis of charge transfer between 2,4-dihydroxybenzoic acid and pyrimethamine, which results in strong intermolecular hydrogen bonds. This fact is further validated by the calculation of the electrostatic potential based on transferred electron-density parameters.

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Sanjuan-Szklarz, W. Fabiola, Magdalena Woińska, Sławomir Domagała, Paulina M. Dominiak, Simon Grabowsky, Dylan Jayatilaka, Matthias Gutmann e Krzysztof Woźniak. "On the accuracy and precision of X-ray and neutron diffraction results as a function of resolution and the electron density model". IUCrJ 7, n. 5 (25 agosto 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 atom model (TAAM) and the Hirshfeld atom refinement (HAR) model as a function of the resolution of X-ray data. The aspherical models (MM, TAAM, HAR) give far more accurate and precise single-crystal X-ray results than IAM, sometimes identical to results obtained from neutron diffraction and at low resolution. Hence, aspherical approaches open new routes for improving existing structural information collected over the last century.

42

Malinska, Maura, e 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, n. 6 (25 maggio 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, and of bovine trypsin. The application of the TAAM to these data improves the quality of the electron-density maps and the visibility of H atoms. It also lowers the conventionalRfactors and improves the atomic displacement parameters and the results of the Hirshfeld rigid-bond test. An additional advantage is that the transferred charge density allows the estimation of Coulombic interaction energy and electrostatic potential.

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Parsons, Simon, Trixie Wagner, Oliver Presly, Peter A. Wood e Richard I. Cooper. "Applications of leverage analysis in structure refinement". Journal of Applied Crystallography 45, n. 3 (16 maggio 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 copper complex shows that the influence of the highest-leverage intensity observations increases when completeness is reduced, but low leverages stay low. The influence of restraints, notably those applying the Hirshfeld rigid-bond criterion, also increases dramatically. In alanine the precision of the Flack parameter is determined by medium-resolution data with moderate intensities. The results of a leverage analysis can be incorporated into a weighting scheme designed to optimize the precision of a selected parameter. This was applied to absolute structure refinement of light-atom crystal structures. The standard uncertainty of the Flack parameter could be reduced to around 0.1 even for a hydrocarbon.

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Woinska, Magdalena, Monika Wanat, Przemyslaw Taciak, Tomasz Pawinski, Wladek Minor e 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, n. 5 (15 luglio 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 and the -S-Ph group as substituents. Energetic investigations are performed, comprising the calculation of the energy of intermolecular interactions, cohesive and geometrical relaxation energy. The results obtained for experimentally derived structures are verified against the values calculated for structures optimized using dispersion-corrected periodic density functional theory. For the high-quality data sets (the Cl and -S-Ph compounds), both MM and XWR could be successfully used to refine the atomic displacement parameters and the positions of hydrogen atoms; however, the bond lengths obtained with XWR were more precise and closer to the theoretical values. In the application to the more challenging data sets (the Br and I compounds), only XWR enabled free refinement of hydrogen atom geometrical parameters, nevertheless, the results clearly showed poor data quality. For both refinement methods, the energy values (intermolecular interactions, cohesive and relaxation) calculated for the experimental structures were in similar agreement with the values associated with the optimized structures – the most significant divergences were observed when experimental geometries were biased by poor data quality. XWR was found to be more robust in avoiding incorrect distortions of the reconstructed electron density as a result of data quality issues. Based on the problem of anharmonic thermal motion refinement, this study reveals that for the most correct interpretation of the obtained results, it is necessary to use the complete data set, including the weak reflections in order to draw conclusions.

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Bergmann, Justin, Max Davidson, Esko Oksanen, Ulf Ryde e Dylan Jayatilaka. "fragHAR: towards ab initio quantum-crystallographic X-ray structure refinement for polypeptides and proteins". IUCrJ 7, n. 2 (17 gennaio 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 involved in hydrogen-bond interactions, but it is shown that these discrepancies can be removed by including the interacting fragments as a single larger fragment in the fragmentation scheme. Significant speed-ups are observed for the larger systems. Using this approach, it is possible to perform a highly parallelized HAR in reasonable times for large systems. The method has been implemented in the TONTO software.

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Sovago, Ioana, Matthias J. Gutmann, Hans Martin Senn, Lynne H. Thomas, Chick C. Wilson e Louis J. Farrugia. "Electron density, disorder and polymorphism: high-resolution diffraction studies of the highly polymorphic neuralgic drug carbamazepine". Acta Crystallographica Section B Structural Science, Crystal Engineering and Materials 72, n. 1 (23 gennaio 2016): 39–50. http://dx.doi.org/10.1107/s2052520615019538.

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Analysis of neutron and high-resolution X-ray diffraction data on form (III) of carbamazepine at 100 K using the atoms in molecules (AIM) topological approach afforded excellent agreement between the experimental results and theoretical densities from the optimized gas-phase structure and from multipole modelling of static theoretical structure factors. The charge density analysis provides experimental confirmation of the partially localized π-bonding suggested by the conventional structural formula, but the evidence for any significant C—N π bonding is not strong. Hirshfeld atom refinement (HAR) gives H atom positional and anisotropic displacement parameters that agree very well with the neutron parameters. X-ray and neutron diffraction data on the dihydrate of carbemazepine strongly indicate a disordered orthorhombic crystal structure in the space groupCmca, rather than a monoclinic crystal structure in space groupP21/c. This disorder in the dihydrate structure has implications for both experimental and theoretical studies of polymorphism.

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Wanat, Monika, Maura Malinska, Matthias J. Gutmann, Richard I. Cooper e Krzysztof Wozniak. "HAR, TAAM and BODD refinements of model crystal structures using Cu Kα and Mo Kα X-ray diffraction data". Acta Crystallographica Section B Structural Science, Crystal Engineering and Materials 77, n. 1 (15 gennaio 2021): 41–53. http://dx.doi.org/10.1107/s2052520620014936.

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The Independent Atom Model (IAM) of electron density is used in routine X-ray data analysis. However, this model does not give a quantitative description of the electron-density distribution. A better model that allows for modelling of aspherical charge density deformations is introduced by the Hansen–Coppens variant of the multipole model of electron density. However, the application of this model requires crystals of excellent quality and high-resolution XRD data which are quite often difficult criteria to fulfil. Therefore, Mo Kα and Cu Kα data of three model compounds (tricyclic imide, xylitol and methyluracil) were refined using IAM and new methods which enabled the refinement and reconstruction of charge density based on the Cu Kα data. These methods were the Bond-Oriented Deformation Density (BODD) model, Hirshfeld Atom Refinement (HAR) and the Transferable Aspherical Atom Model (TAAM). The final results were compared to the model obtained from neutron diffraction experiments. Our results demonstrated not only that Cu Kα data may be refined using BODD, HAR and TAAM methods, but also revealed systematic errors arising from the use of Cu Kα data. These errors were a result of the limited information in the low-resolution data set that manifested as higher values for the anisotropic displacement parameters (ADPs) and smaller maxima and minima of the residual electron density for the Cu Kα data compared to the Mo Kα data. Notably, these systematic errors were much less significant than those found for the IAM. Therefore, the application of BODD, HAR and TAAM on Cu Kα data has a more significant influence on the final results of refinement than for the Mo Kα data.

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Wojtulewski, Sławomir, Jakub Wladyslaw Strawa, Michal Tomczyk, Magdalena Gawel e Krzysztof Brzezinski. "A new look at two polymorphic crystal structures of dibenzoylmethane: relationship between the crystal packing and the hydrogen atom position revealed by quantum chemistry and quantum crystallography methods". Acta Crystallographica Section B Structural Science, Crystal Engineering and Materials 76, n. 6 (1 novembre 2020): 957–66. http://dx.doi.org/10.1107/s2052520620012196.

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Chalcones, including dibenzoylmethane, are an important subgroup of natural polyphenolic compounds that exhibit a wide spectrum of pharmacological and industrial applications. Dibenzoylmethane was isolated from Hottonia palustris L. (Primulaceae). The compound was crystallized in two polymorphic forms: in monoclinic space group P21/c and orthorhombic space group Pbca. Crystal structures of the polymorphs were solved and refined against diffraction data measured at 100 and 293 K. In both crystal structures, the chalcone occurs in its keto–enol tautomeric form with the hydroxyl H atom mutually bound by two oxygen atoms rather than covalently attached to a particular oxygen atom. To explain this phenomenon in more detail, density functional theory and quantum theory of atoms in molecules based quantum chemistry calculations were applied. Additionally, high-resolution experimental data of very high quality measured for the monoclinic and orthorhombic crystals at 100 K allowed the engagement of the quantum crystallography method, based on Hirshfeld atom refinement, to determine the position of each individual H atom. It is suggested that the presence of the particular tautomeric form of dibenzoylmethane with a centred H atom position results from the π-stacking interaction between the phenyl ring and the malondialdehyde quasi-ring causes delocalization of the electron density in the latter.

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Faroque, Muhammad Umer, Sajida Noureen, Shafaat Hussain Mirza, Muhammad Nawaz Tahir e Maqsood Ahmed. "Structure and electrostatic properties of the pyrimethamine–3,5-dihydroxybenzoic acid cocrystal in water solvent studied using transferred electron-density parameters". Acta Crystallographica Section C Structural Chemistry 75, n. 1 (1 gennaio 2019): 46–53. http://dx.doi.org/10.1107/s2053229618017060.

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Pyrimethamine is an antimalarial drug. The cocrystal salt form of pyrimethamine with 3,5-dihydroxybenzoic acid in water solvent has been synthesized, namely 2,4-diamino-5-(4-chlorophenyl)-6-ethylpyrimidin-1-ium 3,5-dihydroxybenzoate hemihydrate, C12H14ClN4 +·C7H5O4 −·0.5H2O. X-ray diffraction data were collected at room temperature. Refinement of the crystal structure was carried out using the classical Independent Atom Model (IAM), while the electrostatic properties were studied by transferring electron-density parameters from an electron-density database. The Cl atom was refined anharmonically. The results of both refinement methods were compared. Topological analyses were carried out using Bader's theory of Atoms in Molecules (AIM). The three-dimensional Hirshfeld surface analysis and the two-dimensional fingerprint maps of individual molecules revealed that the crystal structures are dominated by H...O/O...H and H...H contacts. Other close contacts are also present, including weak C...H/H...C contacts. Charge transfer between the pyrimethamine and 3,5-dihydroxybenzoic acid molecules results in a molecular assembly based on strong intermolecular hydrogen bonds. This is further validated by the calculation of the electrostatic potential based on transferred electron-density parameters. The current work proves the significance of the transferability principle in studying the electron-density-derived properties of molecules in cases where high-resolution diffraction data at low temperature are not available.

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Pawlędzio, S., M. Malinska, F. Kleemiss, S. Grabowsky e K. Woźniak. "Influence of modelling of disorder on results of Hirshfeld atom refinement of an organo-gold(I) compound". Acta Crystallographica Section A Foundations and Advances 78, a2 (23 agosto 2022): a588. http://dx.doi.org/10.1107/s2053273322091793.

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