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Herbst-Irmer R. In data we trust: X-ray diffraction experiments for charge density investigations. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2023; 79:344-345. [PMID: 37721942 PMCID: PMC10552599 DOI: 10.1107/s205252062300776x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/20/2023]
Abstract
A short commentary is given on the paper by Vosegaard et al. [Acta Cryst. (2023), 79, 380-391], which compares charge density models derived from four datasets measured on conventional diffractometers with the results of a high-quality dataset from SPring-8.
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Affiliation(s)
- Regine Herbst-Irmer
- Institut für Anorganische Chemie, Georg-August-Universität Göttingen, Tammannstraße 4, Göttingen, Lower Saxony 37077, Germany
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2
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Vosegaard ES, Ahlburg JV, Krause L, Iversen BB. Comparative study of conventional and synchrotron X-ray electron densities on molecular crystals. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2023; 79:380-391. [PMID: 37669152 PMCID: PMC10552600 DOI: 10.1107/s2052520623006625] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 07/30/2023] [Indexed: 09/07/2023]
Abstract
Five different electron density datasets obtained from conventional and synchrotron single crystal X-ray diffraction experiments are compared. The general aim of the study is to investigate the quality of data for electron density analysis from current state-of-the-art conventional sources, and to see how the data perform in comparison with high-quality synchrotron data. A molecular crystal of melamine was selected as the test compound due to its ability to form excellent single crystals, the light atom content, and an advantageous suitability factor of 3.6 for electron density modeling. These features make melamine an optimal system for conventional X-ray diffractometers since the inherent advantages of synchrotron sources such as short wavelength and high intensity are less critical in this case. Data were obtained at 100 K from new in-house diffractometers Rigaku Synergy-S (Mo and Ag source, HyPix100 detector) and Stoe Stadivari (Mo source, EIGER2 1M CdTe detector), and an older Oxford Diffraction Supernova (Mo source, Atlas CCD detector). The synchrotron data were obtained at 25 K from BL02B1 beamline at SPring-8 in Japan (λ = 0.2480 Å, Pilatus3 X 1M CdTe detector). The five datasets were compared on general quality parameters such as resolution, ⟨I/σ⟩, redundancy and R factors, as well as the more model specific fractal dimension plot and residual density maps. Comparison of the extracted electron densities reveals that all datasets can provide reliable multipole models, which overall convey similar chemical information. However, the new laboratory X-ray diffractometers with advanced pixel detector technology clearly measure data with significantly less noise and much higher reliability giving densities of higher quality, compared to the older instrument. The synchrotron data have higher resolution and lower measurement temperature, and they allow for finer details to be modeled (e.g. hydrogen κ parameters).
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Affiliation(s)
- Emilie S. Vosegaard
- Center for Integrated Materials Research, Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus C, DK-8000, Denmark
| | - Jakob V. Ahlburg
- Center for Integrated Materials Research, Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus C, DK-8000, Denmark
| | - Lennard Krause
- Center for Integrated Materials Research, Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus C, DK-8000, Denmark
| | - Bo B. Iversen
- Center for Integrated Materials Research, Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus C, DK-8000, Denmark
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3
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Ishchenko AA, Pak AM, Nelyubina YV. Electron Density Distribution in the Crystal of the Biocompatible Metal–Organic Framework. RUSS J COORD CHEM+ 2022. [DOI: 10.1134/s107032842201002x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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4
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Cao J, Yang Z, Xiong W, Zhou Y, Wu Y, Jia M, Zhou C, Xu Z. Ultrafine metal species confined in metal–organic frameworks: Fabrication, characterization and photocatalytic applications. Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2021.213924] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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5
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Svane B, Tolborg K, Kato K, Iversen BB. Multipole electron densities and structural parameters from synchrotron powder X-ray diffraction data obtained with a MYTHEN detector system (OHGI). ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES 2021; 77:85-95. [PMID: 33646194 DOI: 10.1107/s2053273320016605] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Accepted: 12/22/2020] [Indexed: 11/11/2022]
Abstract
Powder X-ray diffraction has some inherent advantages over traditional single-crystal X-ray diffraction in accurately determining electron densities and structural parameters due to the lower requirements for sample crystallinity, simpler corrections and measurement simultaneity. For some simple inorganic materials, it has been shown that these advantages can compensate for disadvantages such as peak overlap and error-prone background subtraction. Although it is challenging to extend powder X-ray diffraction-based electron-density studies to organic materials with significant peak overlap, previous results using a dedicated vacuum diffractometer with a large image-plate camera (AVID) demonstrated that it can be done. However, the vacuum setup with the off-line detector system was found to prohibit a widespread use. Fast microstrip detectors, which have been employed at a number of powder diffraction beamlines, have the potential to facilitate electron-density studies. Nevertheless, no electron-density studies even for materials with slight peak overlap have been performed with microstrip detectors. One of the most critical problems has been a difference in sensitivity between microstrip channels, which substantially defines the dynamic range of a detector. Recently, a robust approach to this problem has been developed and applied to a total scattering measurement system (OHGI) with 15 MYTHEN microstrip modules. In the present study, synchrotron powder X-ray diffraction data obtained with OHGI are evaulated in terms of multipole electron densities and structural parameters (atomic positions and displacement parameters). These results show that, even without a dedicated setup and perfect samples, electron-density modelling can be carried out on high-quality powder X-ray diffraction data. However, it was also found that the required prior information about the sample prohibits widespread use of the method. With the presently obtainable data quality, electron densities of molecular crystals in general are not reliably obtained from powder data, but it is an excellent, possibly superior, alternative to single-crystal measurements for small-unit-cell inorganic solids. If aspherical atomic scattering factors can be obtained from other means (multipole databases, theoretical calculations), then atomic positions (including for hydrogen) and anisotropic atomic displacement parameters (non-hydrogen atoms) of excellent accuracy can be refined from synchrotron powder X-ray diffraction data on organic crystals.
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Affiliation(s)
- Bjarke Svane
- Department of Chemistry, Aarhus University, Aarhus, DK-8000, Denmark
| | - Kasper Tolborg
- Department of Chemistry, Aarhus University, Aarhus, DK-8000, Denmark
| | - Kenichi Kato
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
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6
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Münch A, Knauer L, Ott H, Sindlinger C, Herbst-Irmer R, Strohmann C, Stalke D. Insight into the Bonding and Aggregation of Alkyllithiums by Experimental Charge Density Studies and Energy Decomposition Analyses. J Am Chem Soc 2020; 142:15897-15906. [PMID: 32811141 DOI: 10.1021/jacs.0c06035] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this Article, the organolithiums [((-)-sparteine)LitBu] (1), [(ABCO)LitBu]2 (2), and [(ABCO)2(LiiPr)4] (3) are investigated by means of experimental and theoretical charge density determination to elucidate the nature of the Li-C and Li-N bonds. Furthermore, the valence shell charge concentrations (VSCCs) in the nonbonding region of the deprotonated Cα-atom will provide some insight on the localization of the carbanionic lone pair. Analysis of the electron density (ρ(rBCP)), Laplacian (∇2ρ(rBCP)), and the energy decomposition (EDA) confirmed that the Li-C/N bond exhibits astonishingly similar characteristics, to reveal an increasingly polar contact with decreasing aggregate size. This explains former observations on the incorporation of halide salts in organolithium reagents. Furthermore, it could be shown that the bonding properties of the iPr group are similar to those of the tBu substituent. The accuracy of fit to all previously determined properties in organolithiums is remarkable.
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Affiliation(s)
- Annika Münch
- Institut für Anorganische Chemie, Georg-August-Universität Göttingen, Tammannstraβe 4, Göttingen 37077, Germany
| | - Lena Knauer
- Institut für Anorganische Chemie, Technische Universität Dortmund, Otto-Hahn-Straβe 6, Dortmund 44227, Germany
| | - Holger Ott
- Bruker AXS GmbH, Östliche Rheinbrückenstraβe 49, Karlsruhe 76187, Germany
| | - Christian Sindlinger
- Institut für Anorganische Chemie, Georg-August-Universität Göttingen, Tammannstraβe 4, Göttingen 37077, Germany
| | - Regine Herbst-Irmer
- Institut für Anorganische Chemie, Georg-August-Universität Göttingen, Tammannstraβe 4, Göttingen 37077, Germany
| | - Carsten Strohmann
- Institut für Anorganische Chemie, Technische Universität Dortmund, Otto-Hahn-Straβe 6, Dortmund 44227, Germany
| | - Dietmar Stalke
- Institut für Anorganische Chemie, Georg-August-Universität Göttingen, Tammannstraβe 4, Göttingen 37077, Germany
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7
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Krause L, Tolborg K, Grønbech TBE, Sugimoto K, Iversen BB, Overgaard J. Accurate high-resolution single-crystal diffraction data from a Pilatus3 X CdTe detector. J Appl Crystallogr 2020; 53:635-649. [PMID: 32684879 PMCID: PMC7312157 DOI: 10.1107/s1600576720003775] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 03/14/2020] [Indexed: 11/10/2022] Open
Abstract
Hybrid photon-counting detectors are widely established at third-generation synchrotron facilities and the specifications of the Pilatus3 X CdTe were quickly recognized as highly promising in charge-density investigations. This is mainly attributable to the detection efficiency in the high-energy X-ray regime, in combination with a dynamic range and noise level that should overcome the perpetual problem of detecting strong and weak data simultaneously. These benefits, however, come at the expense of a persistent problem for high diffracted beam flux, which is particularly problematic in single-crystal diffraction of materials with strong scattering power and sharp diffraction peaks. Here, an in-depth examination of data collected on an inorganic material, FeSb2, and an organic semiconductor, rubrene, revealed systematic differences in strong intensities for different incoming beam fluxes, and the implemented detector intensity corrections were found to be inadequate. Only significant beam attenuation for the collection of strong reflections was able to circumvent this systematic error. All data were collected on a bending-magnet beamline at a third-generation synchrotron radiation facility, so undulator and wiggler beamlines and fourth-generation synchrotrons will be even more prone to this error. On the other hand, the low background now allows for an accurate measurement of very weak intensities, and it is shown that it is possible to extract structure factors of exceptional quality using standard crystallographic software for data processing (SAINT-Plus, SADABS and SORTAV), although special attention has to be paid to the estimation of the background. This study resulted in electron-density models of substantially higher accuracy and precision compared with a previous investigation, thus for the first time fulfilling the promise of photon-counting detectors for very accurate structure factor measurements.
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Affiliation(s)
- Lennard Krause
- Center for Materials Crystallography, Department of Chemistry, Aarhus University, Langelandsgade 140, Aarhus 8000, Denmark
| | - Kasper Tolborg
- Center for Materials Crystallography, Department of Chemistry, Aarhus University, Langelandsgade 140, Aarhus 8000, Denmark
| | - Thomas Bjørn Egede Grønbech
- Center for Materials Crystallography, Department of Chemistry, Aarhus University, Langelandsgade 140, Aarhus 8000, Denmark
| | - Kunihisa Sugimoto
- SPring-8, JASRI, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Bo Brummerstedt Iversen
- Center for Materials Crystallography, Department of Chemistry, Aarhus University, Langelandsgade 140, Aarhus 8000, Denmark
| | - Jacob Overgaard
- Center for Materials Crystallography, Department of Chemistry, Aarhus University, Langelandsgade 140, Aarhus 8000, Denmark
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8
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Two octahedral σ-borane metal (MnI and RuII) complexes containing a tripod κ3N,H,H-ligand: Synthesis, structural characterization, and theoretical topological study of the charge density. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2019.127217] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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9
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Tolborg K, Iversen BB. Electron Density Studies in Materials Research. Chemistry 2019; 25:15010-15029. [DOI: 10.1002/chem.201903087] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Revised: 08/13/2019] [Indexed: 11/07/2022]
Affiliation(s)
- Kasper Tolborg
- Center for Materials CrystallographyDepartment of Chemistry and iNANOAarhus University Langelandsgade 140 8000 Aarhus C Denmark
| | - Bo B. Iversen
- Center for Materials CrystallographyDepartment of Chemistry and iNANOAarhus University Langelandsgade 140 8000 Aarhus C Denmark
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10
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Korlyukov AA, Nelyubina YV. Quantum chemical methods in charge density studies from X-ray diffraction data. RUSSIAN CHEMICAL REVIEWS 2019. [DOI: 10.1070/rcr4866] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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11
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Svane B, Tolborg K, Jørgensen LR, Roelsgaard M, Jørgensen MRV, Brummerstedt Iversen B. Multipole electron densities and atomic displacement parameters in urea from accurate powder X-ray diffraction. ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES 2019; 75:600-609. [PMID: 31264644 DOI: 10.1107/s205327331900799x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 06/04/2019] [Indexed: 11/10/2022]
Abstract
Electron density determination based on structure factors obtained through powder X-ray diffraction has so far been limited to high-symmetry inorganic solids. This limit is challenged by determining high-quality structure factors for crystalline urea using a bespoke vacuum diffractometer with imaging plates. This allows the collection of data of sufficient quality to model the electron density of a molecular system using the multipole method. The structure factors, refined parameters as well as chemical bonding features are compared with results from the high-quality synchrotron single-crystal study by Birkedal et al. [Acta Cryst. (2004), A60, 371-381] demonstrating that powder X-ray diffraction potentially provides a viable alternative for electron density determination in simple molecular crystals where high-quality single crystals are not available.
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Affiliation(s)
- Bjarke Svane
- Center for Materials Crystallography, Department of Chemistry and iNANO, Aarhus University, Aarhus, DK-8000, Denmark
| | - Kasper Tolborg
- Center for Materials Crystallography, Department of Chemistry and iNANO, Aarhus University, Aarhus, DK-8000, Denmark
| | - Lasse Rabøl Jørgensen
- Center for Materials Crystallography, Department of Chemistry and iNANO, Aarhus University, Aarhus, DK-8000, Denmark
| | - Martin Roelsgaard
- Center for Materials Crystallography, Department of Chemistry and iNANO, Aarhus University, Aarhus, DK-8000, Denmark
| | - Mads Ry Vogel Jørgensen
- Center for Materials Crystallography, Department of Chemistry and iNANO, Aarhus University, Aarhus, DK-8000, Denmark
| | - Bo Brummerstedt Iversen
- Center for Materials Crystallography, Department of Chemistry and iNANO, Aarhus University, Aarhus, DK-8000, Denmark
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12
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Genoni A, Bučinský L, Claiser N, Contreras-García J, Dittrich B, Dominiak PM, Espinosa E, Gatti C, Giannozzi P, Gillet JM, Jayatilaka D, Macchi P, Madsen AØ, Massa L, Matta CF, Merz KM, Nakashima PNH, Ott H, Ryde U, Schwarz K, Sierka M, Grabowsky S. Quantum Crystallography: Current Developments and Future Perspectives. Chemistry 2018; 24:10881-10905. [PMID: 29488652 DOI: 10.1002/chem.201705952] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 02/27/2018] [Indexed: 11/09/2022]
Abstract
Crystallography and quantum mechanics have always been tightly connected because reliable quantum mechanical models are needed to determine crystal structures. Due to this natural synergy, nowadays accurate distributions of electrons in space can be obtained from diffraction and scattering experiments. In the original definition of quantum crystallography (QCr) given by Massa, Karle and Huang, direct extraction of wavefunctions or density matrices from measured intensities of reflections or, conversely, ad hoc quantum mechanical calculations to enhance the accuracy of the crystallographic refinement are implicated. Nevertheless, many other active and emerging research areas involving quantum mechanics and scattering experiments are not covered by the original definition although they enable to observe and explain quantum phenomena as accurately and successfully as the original strategies. Therefore, we give an overview over current research that is related to a broader notion of QCr, and discuss options how QCr can evolve to become a complete and independent domain of natural sciences. The goal of this paper is to initiate discussions around QCr, but not to find a final definition of the field.
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Affiliation(s)
- Alessandro Genoni
- Université de Lorraine, CNRS, Laboratoire LPCT, 1 Boulevard Arago, F-57078, Metz, France
| | - Lukas Bučinský
- Institute of Physical Chemistry and Chemical Physics, Slovak University of Technology, FCHPT SUT, Radlinského 9, SK-812 37, Bratislava, Slovakia
| | - Nicolas Claiser
- Université de Lorraine, CNRS, Laboratoire CRM2, Boulevard des Aiguillettes, BP 70239, F-54506, Vandoeuvre-lès-Nancy, France
| | - Julia Contreras-García
- Sorbonne Universités, UPMC Université Paris 06, CNRS, Laboratoire de Chimie Théorique (LCT), 4 Place Jussieu, F-75252, Paris Cedex 05, France
| | - Birger Dittrich
- Anorganische und Strukturchemie II, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Paulina M Dominiak
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, ul. Żwirki i Wigury 101, 02-089, Warszawa, Poland
| | - Enrique Espinosa
- Université de Lorraine, CNRS, Laboratoire CRM2, Boulevard des Aiguillettes, BP 70239, F-54506, Vandoeuvre-lès-Nancy, France
| | - Carlo Gatti
- CNR-ISTM Istituto di Scienze e Tecnologie Molecolari, via Golgi 19, Milano, I-20133, Italy.,Istituto Lombardo Accademia di Scienze e Lettere, via Brera 28, 20121, Milano, Italy
| | - Paolo Giannozzi
- Department of Mathematics, Computer Science and Physics, University of Udine, Via delle Scienze 208, I-33100, Udine, Italy
| | - Jean-Michel Gillet
- Structure, Properties and Modeling of Solids Laboratory, CentraleSupelec, Paris-Saclay University, 3 rue Joliot-Curie, 91191, Gif-sur-Yvette, France
| | - Dylan Jayatilaka
- School of Molecular Sciences, University of Western Australia, 35 Stirling Highway, Perth, WA, 6009, Australia
| | - Piero Macchi
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012, Bern, Switzerland
| | - Anders Ø Madsen
- Department of Pharmacy, University of Copenhagen, Universitetsparken 2, 2100, Copenhagen, Denmark
| | - Lou Massa
- Hunter College & the Ph.D. Program of the Graduate Center, City University of New York, New York, USA
| | - Chérif F Matta
- Department of Chemistry and Physics, Mount Saint Vincent University, Halifax, Nova Scotia, B3M 2J6, Canada.,Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, B3H 4J3, Canada.,Department of Chemistry, Saint Mary's University, Halifax, Nova Scotia, B3H 3C3, Canada.,Département de Chimie, Université Laval, Québec, QC G1V 0A6, Canada
| | - Kenneth M Merz
- Department of Chemistry and Department of Biochemistry and Molecular Biology, Michigan State University, 578 South Shaw Lane, East Lansing, Michigan, 48824, USA.,Institute for Cyber Enabled Research, Michigan State University, 567 Wilson Road, Room 1440, East Lansing, Michigan, 48824, USA
| | - Philip N H Nakashima
- Department of Materials Science and Engineering, Monash University, Victoria, 3800, Australia
| | - Holger Ott
- Bruker AXS GmbH, Östliche Rheinbrückenstraße 49, 76187, Karlsruhe, Germany
| | - Ulf Ryde
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-22100, Lund, Sweden
| | - Karlheinz Schwarz
- Technische Universität Wien, Institut für Materialwissenschaften, Getreidemarkt 9, A-1060, Vienna, Austria
| | - Marek Sierka
- Otto Schott Institute of Materials Research, Friedrich Schiller University Jena, Löbdergraben 32, 07743, Jena, Germany
| | - Simon Grabowsky
- Fachbereich 2-Biologie/Chemie, Institut für Anorganische Chemie und Kristallographie, Universität Bremen, Leobener Str. 3, 28359, Bremen, Germany
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13
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Craven M, Nygaard MH, Zadrozny JM, Long JR, Overgaard J. Determination of d-Orbital Populations in a Cobalt(II) Single-Molecule Magnet Using Single-Crystal X-ray Diffraction. Inorg Chem 2018; 57:6913-6920. [PMID: 29862809 DOI: 10.1021/acs.inorgchem.8b00513] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The tetrahedral cobalt(II) compound (Ph4P)2[Co(SPh)4] was the first mononuclear transition-metal complex shown to exhibit slow relaxation of the magnetization in zero external magnetic field. Because the relative populations of the d orbitals play a vital role in dictating the magnitude of the magnetic anisotropy, the magnetic behavior of this complex is directly related to its electronic structure, yet the exact role of the soft, thiophenolate ligands in influencing the d-electron configuration has previously only been investigated via theoretical methods. To provide detailed experimental insight into the effect of this ligand field, the electron density distribution in this compound was determined from low-temperature, single-crystal X-ray diffraction data and subsequent multipole modeling. Topological analysis of the electron density indicates significant covalent contributions to the cobalt-sulfur bonds. The derived d-orbital populations further reveal a fully occupied d z2 orbital, minor d xz orbital population, and nearly equal population of the d xy, d x2- y2, and d yz orbitals. Notably, we find that an electrostatic interaction between Co(II) and one hydrogen atom from a thiophenolate group in the xz plane increases the energy of the d x2- y2 orbital, leading to the nearly equal population with d xy and strong magnetic anisotropy.
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Affiliation(s)
- Matthew Craven
- Department of Chemistry , Aarhus University , Langelandsgade 140 , DK-8000 Aarhus C , Denmark
| | - Mathilde H Nygaard
- Department of Chemistry , Aarhus University , Langelandsgade 140 , DK-8000 Aarhus C , Denmark
| | | | - Jeffrey R Long
- Materials Sciences Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States
| | - Jacob Overgaard
- Department of Chemistry , Aarhus University , Langelandsgade 140 , DK-8000 Aarhus C , Denmark
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14
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Kasai H, Tolborg K, Sist M, Zhang J, Hathwar VR, Filsø MØ, Cenedese S, Sugimoto K, Overgaard J, Nishibori E, Iversen BB. X-ray electron density investigation of chemical bonding in van der Waals materials. NATURE MATERIALS 2018; 17:249-252. [PMID: 29434305 DOI: 10.1038/s41563-017-0012-2] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 12/12/2017] [Indexed: 06/08/2023]
Abstract
Van der Waals (vdW) solids have attracted great attention ever since the discovery of graphene, with the essential feature being the weak chemical bonding across the vdW gap. The nature of these weak interactions is decisive for many extraordinary properties, but it is a strong challenge for current theory to accurately model long-range electron correlations. Here we use synchrotron X-ray diffraction data to precisely determine the electron density in the archetypal vdW solid, TiS2, and compare the results with density functional theory calculations. Quantitative agreement is observed for the chemical bonding description in the covalent TiS2 slabs, but significant differences are identified for the interactions across the gap, with experiment revealing more electron deformation than theory. The present data provide an experimental benchmark for testing theoretical models of weak chemical bonding.
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Affiliation(s)
- Hidetaka Kasai
- Faculty of Pure and Applied Sciences, Tsukuba Research Center for Energy Materials Science (TREMS), University of Tsukuba, Tsukuba, Japan
- Center for Materials Crystallography (CMC), Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Denmark
| | - Kasper Tolborg
- Center for Materials Crystallography (CMC), Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Denmark
| | - Mattia Sist
- Center for Materials Crystallography (CMC), Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Denmark
| | - Jiawei Zhang
- Center for Materials Crystallography (CMC), Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Denmark
| | - Venkatesha R Hathwar
- Faculty of Pure and Applied Sciences, Tsukuba Research Center for Energy Materials Science (TREMS), University of Tsukuba, Tsukuba, Japan
| | - Mette Ø Filsø
- Center for Materials Crystallography (CMC), Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Denmark
| | - Simone Cenedese
- Center for Materials Crystallography (CMC), Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Denmark
| | - Kunihisa Sugimoto
- Japan Synchrotron Radiation Research Institute (JASRI), Sayo-gun, Japan
| | - Jacob Overgaard
- Center for Materials Crystallography (CMC), Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Denmark
| | - Eiji Nishibori
- Faculty of Pure and Applied Sciences, Tsukuba Research Center for Energy Materials Science (TREMS), University of Tsukuba, Tsukuba, Japan
| | - Bo B Iversen
- Center for Materials Crystallography (CMC), Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Denmark.
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15
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16
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Tolborg K, Jørgensen MRV, Christensen S, Kasai H, Becker J, Walter P, Dippel AC, Als-Nielsen J, Iversen BB. Accurate charge densities from powder X-ray diffraction - a new version of the Aarhus vacuum imaging-plate diffractometer. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2017; 73:521-530. [PMID: 28762964 DOI: 10.1107/s2052520617006357] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 04/27/2017] [Indexed: 06/07/2023]
Abstract
In recent years powder X-ray diffraction has proven to be a valuable alternative to single-crystal X-ray diffraction for determining electron-density distributions in high-symmetry inorganic materials, including subtle deformation in the core electron density. This was made possible by performing diffraction measurements in vacuum using high-energy X-rays at a synchrotron-radiation facility. Here we present a new version of our custom-built in-vacuum powder diffractometer with the sample-to-detector distance increased by a factor of four. In practice this is found to give a reduction in instrumental peak broadening by approximately a factor of three and a large improvement in signal-to-background ratio compared to the previous instrument. Structure factors of silicon at room temperature are extracted using a combined multipole-Rietveld procedure and compared with ab initio calculations and the results from the previous diffractometer. Despite some remaining issues regarding peak asymmetry, the new diffractometer yields structure factors of comparable accuracy to the previous diffractometer at low angles and improved accuracy at high angles. The high quality of the structure factors is further assessed by modelling of core electron deformation with results in good agreement with previous investigations.
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Affiliation(s)
- Kasper Tolborg
- Center for Materials Crystallography, Department of Chemistry and iNANO, Aarhus University, Langelandsgade 140, DK-8000 Aarhus C, Denmark
| | - Mads R V Jørgensen
- Center for Materials Crystallography, Department of Chemistry and iNANO, Aarhus University, Langelandsgade 140, DK-8000 Aarhus C, Denmark
| | - Sebastian Christensen
- Center for Materials Crystallography, Department of Chemistry and iNANO, Aarhus University, Langelandsgade 140, DK-8000 Aarhus C, Denmark
| | - Hidetaka Kasai
- Center for Materials Crystallography, Department of Chemistry and iNANO, Aarhus University, Langelandsgade 140, DK-8000 Aarhus C, Denmark
| | - Jacob Becker
- Center for Materials Crystallography, Department of Chemistry and iNANO, Aarhus University, Langelandsgade 140, DK-8000 Aarhus C, Denmark
| | - Peter Walter
- PETRA III, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, D-22607 Hamburg, Germany
| | - Ann Christin Dippel
- PETRA III, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, D-22607 Hamburg, Germany
| | - Jens Als-Nielsen
- Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
| | - Bo B Iversen
- Center for Materials Crystallography, Department of Chemistry and iNANO, Aarhus University, Langelandsgade 140, DK-8000 Aarhus C, Denmark
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17
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Herbst-Irmer R, Stalke D. Experimental charge-density studies: data reduction and model quality: the more the better? ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2017; 73:531-543. [PMID: 28762965 DOI: 10.1107/s2052520617007016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 05/10/2017] [Indexed: 06/07/2023]
Abstract
In this review, recent developments concerning data and model quality in experimental charge-density investigations from a personal view-point are described. Data quality is not only achieved by the high resolution, high I/σ(I) values, low merging R values and high multiplicity. The quality of the innermost reflections especially is crucial for mapping the density distribution of the outermost valence electrons and can be monitored by (I/σ)asymptotic. New detector technologies seem to be promising improvements. Empirical corrections to correct for low-energy contamination of mirror-focused X-ray data and for resolution- and temperature-dependent errors caused by factors such as thermal diffuse scattering are described. Shashlik-like residual density patterns can indicate the need for an anharmonic description of the thermal motion of individual atoms. The physical reliability of the derived model must be thoroughly analysed. The derived probability density functions for the mean-squared atomic vibrational displacements especially should have only small negative values. The treatment of H atoms has been improved by methods to estimate anisotropic thermal motion. For very high resolution data, the polarization of the core density cannot be neglected. Several tools to detect systematic errors are described. A validation tool is presented that easily detects when the refinement of additional parameters yields a real improvement in the model or simply overfits the given data. In all investigated structures, it is proved that the multipole parameters of atoms with a comparable chemical environment should be constrained to be identical. The use of restraints could be a promising alternative.
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Affiliation(s)
- Regine Herbst-Irmer
- Institut für Anorganische Chemie, Georg-August Universität, Tammannstr. 4, 37077 Göttingen, Germany
| | - Dietmar Stalke
- Institut für Anorganische Chemie, Georg-August Universität, Tammannstr. 4, 37077 Göttingen, Germany
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18
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Destro R, Ruffo R, Roversi P, Soave R, Loconte L, Lo Presti L. Anharmonic motions versus dynamic disorder at the Mg ion from the charge densities in pyrope (Mg 3Al 2Si 3O 12) crystals at 30 K: six of one, half a dozen of the other. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2017; 73:722-736. [PMID: 28762982 PMCID: PMC6181205 DOI: 10.1107/s2052520617006102] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 04/22/2017] [Indexed: 06/07/2023]
Abstract
The possible occurrence of static/dynamic disorder at the Mg site in pyrope (Mg3Al2Si3O12), with or without anharmonic contribution to the thermal vibrations even at low temperatures, has been largely debated but conclusions were contrasting. Here a report is given on the experimental charge density distribution, ρEXP, of synthetic pyrope at T = 30 K, built through a Stewart multipolar expansion up to l = 5 and based on a very precise and accurate set of in-home measured single-crystal X-ray diffraction amplitudes with a maximum resolution of 0.44 Å. Local and integral topological properties of ρEXP are in substantial agreement with those of ρTHEO, the corresponding DFT-grade quantum charge density of an ideal pyrope crystal, and those derived from synchrotron investigations of chemical bonding in olivines. Relevant thermal atomic displacements, probably anharmonic in nature, clearly affect the whole structure down to 30 K. No significant (> 2.5σ) residual Fourier peaks are detectable from the ρEXP distribution around Mg, after least-squares refinement of a multipole model with anharmonic thermal motion at the Mg site. Experimental findings were confirmed by a full analysis of normal vibration modes of the DFT-optimized structure of the perfect pyrope crystal. Mg undergoes wide displacements from its equilibrium position even at very low temperatures, as it is allocated in a ∼ 4.5 Å large dodecahedral cavity and involved in several soft phonon modes. Implications on the interplay among static/dynamic disorder of Mg and lattice vibrational degrees of freedom are discussed.
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Affiliation(s)
- Riccardo Destro
- Department of Chemistry, Università degli Studi di Milano, Via Golgi 19, 20133 Milano, Italy
| | - Riccardo Ruffo
- Department of Materials Science, Università degli Studi di Milano-Bicocca, Via Cozzi 55, 20125 Milano, Italy
| | - Pietro Roversi
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, England
| | - Raffaella Soave
- Istituto di Scienze e Tecnologie Molecolari, Italian CNR, Via Golgi 19, 20133 Milano, Italy
| | - Laura Loconte
- Department of Chemistry, Università degli Studi di Milano, Via Golgi 19, 20133 Milano, Italy
| | - Leonardo Lo Presti
- Department of Chemistry, Università degli Studi di Milano, Via Golgi 19, 20133 Milano, Italy
- Centre for Materials Crystallography, Århus University, Langelandsgade 140, 8000 Århus, Denmark
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19
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Detection of Ambient Oxidation of Ultrasmall Supported Platinum Nanoparticles with Benchtop Powder X-Ray Diffraction. Catal Letters 2017. [DOI: 10.1007/s10562-017-2060-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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21
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Helliwell JR. Concerning the measurement of charge density X-ray diffraction data at synchrotron sources: challenges and opportunities. CRYSTALLOGR REV 2017. [DOI: 10.1080/0889311x.2017.1295038] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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22
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A topological analysis of the bonding in [M2(CO)10] and [M3(μ-H)3(CO)12] complexes (M = Mn, Tc, Re). Theor Chem Acc 2016. [DOI: 10.1007/s00214-016-1821-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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23
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Wahlberg N, Bindzus N, Christensen S, Becker J, Dippel AC, Jørgensen MRV, Iversen BB. Low-temperature powder X-ray diffraction measurements in vacuum: analysis of the thermal displacement of copper. J Appl Crystallogr 2016. [DOI: 10.1107/s1600576715022621] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
A serious limitation of the all-in-vacuum diffractometer reported by Straasø, Dippel, Becker & Als-Nielsen [J. Synchrotron Rad.(2014),21, 119–126] has so far been the inability to cool samples to near-cryogenic temperatures during measurement. The problem is solved by placing the sample in a jet of helium gas cooled by liquid nitrogen. The resulting temperature change is quantified by determining the change in unit-cell parameter and atomic displacement parameter of copper. The cooling proved successful, with a resulting temperature of ∼95 (3) K. The measured powder X-ray diffraction data are of superb quality and high resolution [up to sinθ/λ = 2.2 Å−1], permitting an extensive modelling of the thermal displacement. The anharmonic displacement of copper was modelled by a Gram–Charlier expansion of the temperature factor. As expected, the corresponding probability distribution function shows an increased probability away from neighbouring atoms and a decreased probability towards them.
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Wahlberg N, Bindzus N, Bjerg L, Becker J, Dippel AC, Iversen BB. Synchrotron powder diffraction of silicon: high-quality structure factors and electron density. ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES 2016; 72:28-35. [PMID: 26697864 DOI: 10.1107/s2053273315018318] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 09/30/2015] [Indexed: 11/10/2022]
Abstract
Crystalline silicon is an ideal compound to test the current state of experimental structure factors and corresponding electron densities. High-quality structure factors have been measured on crystalline silicon with synchrotron powder X-ray diffraction. They are in excellent agreement with benchmark Pendellösung data having comparable accuracy and precision, but acquired in far less time and to a much higher resolution (sin θ/λ < 1.7 Å(-1)). The extended data range permits an experimental modelling of not only the valence electron density but also the core deformation in silicon, establishing an increase of the core density upon bond formation in crystalline silicon. Furthermore, a physically sound procedure for evaluating the standard deviation of powder-derived structure factors has been applied. Sampling statistics inherently account for contributions from photon counts as well as the limited number of diffracting particles, where especially the latter are particularly difficult to handle.
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Affiliation(s)
- Nanna Wahlberg
- Department of Chemistry, Aarhus University, Langelandsgade 140, Aarhus 8000, Denmark
| | - Niels Bindzus
- Department of Chemistry, Aarhus University, Langelandsgade 140, Aarhus 8000, Denmark
| | - Lasse Bjerg
- Department of Chemistry, Aarhus University, Langelandsgade 140, Aarhus 8000, Denmark
| | - Jacob Becker
- Department of Chemistry, Aarhus University, Langelandsgade 140, Aarhus 8000, Denmark
| | - Ann Christin Dippel
- Department of Chemistry, Aarhus University, Langelandsgade 140, Aarhus 8000, Denmark
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25
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Macchi P, Gillet JM, Taulelle F, Campo J, Claiser N, Lecomte C. Modelling the experimental electron density: only the synergy of various approaches can tackle the new challenges. IUCRJ 2015; 2:441-51. [PMID: 26175903 PMCID: PMC4491316 DOI: 10.1107/s2052252515007538] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 04/16/2015] [Indexed: 06/01/2023]
Abstract
Electron density is a fundamental quantity that enables understanding of the chemical bonding in a molecule or in a solid and the chemical/physical property of a material. Because electrons have a charge and a spin, two kinds of electron densities are available. Moreover, because electron distribution can be described in momentum or in position space, charge and spin density have two definitions and they can be observed through Bragg (for the position space) or Compton (for the momentum space) diffraction experiments, using X-rays (charge density) or polarized neutrons (spin density). In recent years, we have witnessed many advances in this field, stimulated by the increased power of experimental techniques. However, an accurate modelling is still necessary to determine the desired functions from the acquired data. The improved accuracy of measurements and the possibility to combine information from different experimental techniques require even more flexibility of the models. In this short review, we analyse some of the most important topics that have emerged in the recent literature, especially the most thought-provoking at the recent IUCr general meeting in Montreal.
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Affiliation(s)
- Piero Macchi
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Jean-Michel Gillet
- Laboratoire Structures Propriétés et Modélisation des Solides, UMR 8580, Université Paris Saclay CentraleSupélec, CNRS, Grande Voie des Vignes, 92295 Chatenay-Malabry, France
| | - Francis Taulelle
- Institut Lavoisier de Versailles, Université de Versailles Saint Quentin en Yvelines, 45 Avenue des Etats-Unis, Versailles, 78035, France
| | - Javier Campo
- Materials Science Institute of Aragón, CSIC-University of Zaragoza, Zaragoza, 50009, Spain
| | - Nicolas Claiser
- Cristallographie, Résonance Magnetique et Modélisations, CRM2, UMR 7036, Institut Jean Barriol, Université de Lorraine, Vandoeuvre-les-Nancy, BP239, F54506, France
| | - Claude Lecomte
- Cristallographie, Résonance Magnetique et Modélisations, CRM2, UMR 7036, Institut Jean Barriol, Université de Lorraine, Vandoeuvre-les-Nancy, BP239, F54506, France
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26
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Wolf H, Jørgensen MRV, Chen YS, Herbst-Irmer R, Stalke D. Charge density investigations on [2,2]-paracyclophane – in data we trust. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2015; 71:10-19. [PMID: 25643711 DOI: 10.1107/s2052520614026080] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 11/27/2014] [Indexed: 06/04/2023]
Abstract
Four datasets on [2,2]-paracyclophane were collected in-house and at the Advanced Photon Source at two different temperatures for charge density investigation. Global data quality indicators such as high resolution, high I/σ(I) values, low merging R values and high multiplicity were matched for all four datasets. The structural parameters did not show significant differences, but the synchrotron data depicted deficiencies in the topological analysis. In retrospect these deficiencies could be assigned to the low quality of the innermost data, which could have been identified by e.g. merging R values for only these reflections. In the multipole refinement these deficiencies could be monitored using DRK-plot and residual density analysis. In this particular example the differences in the topological parameters were relatively small but significant.
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Affiliation(s)
- Hilke Wolf
- Institut für Anorganische Chemie, Georg-August-Universität, Tammannstraße 4, 37077 Göttingen, Germany
| | - Mads R V Jørgensen
- Center for Materials Crystallography, Department of Chemistry and iNANO, Aarhus University, Langelandsgade 140, Aarhus C, DK-8000, Denmark
| | - Yu-Sheng Chen
- ChemMatCARS, Advanced Photon Source, University of Chicago, 9700 S. Cass. Avenue, Argonne, IL 60539, USA
| | - Regine Herbst-Irmer
- Institut für Anorganische Chemie, Georg-August-Universität, Tammannstraße 4, 37077 Göttingen, Germany
| | - Dietmar Stalke
- Institut für Anorganische Chemie, Georg-August-Universität, Tammannstraße 4, 37077 Göttingen, Germany
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27
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Stalke D. A hybrid pixel detector at an in-house device generating stunning charge density quality data. ACTA CRYSTALLOGRAPHICA SECTION B-STRUCTURAL SCIENCE CRYSTAL ENGINEERING AND MATERIALS 2014; 70:781-2. [DOI: 10.1107/s2052520614021349] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Accepted: 09/25/2014] [Indexed: 11/10/2022]
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28
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Larsen S. Crystallography and large research infrastructures, a perfect marriage. IUCRJ 2014; 1:261-262. [PMID: 25295166 PMCID: PMC4174867 DOI: 10.1107/s2052252514019460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 08/28/2014] [Indexed: 06/03/2023]
Abstract
The role of large-scale neutron and synchrotron facilities in the development of crystallographic research is discussed.
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Affiliation(s)
- Sine Larsen
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, Copenhagen, DK-2100, Denmark
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