1
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Langmann J, Kepenci H, Eickerling G, Batke K, Jesche A, Xu M, Canfield P, Scherer W. Experimental X-ray Charge-Density Studies─A Suitable Probe for Superconductivity? A Case Study on MgB 2. J Phys Chem A 2022; 126:8494-8507. [DOI: 10.1021/acs.jpca.2c05925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Jan Langmann
- CPM, Institut für Physik, Universität Augsburg, 86159Augsburg, Germany
| | - Hasan Kepenci
- CPM, Institut für Physik, Universität Augsburg, 86159Augsburg, Germany
| | - Georg Eickerling
- CPM, Institut für Physik, Universität Augsburg, 86159Augsburg, Germany
| | - Kilian Batke
- CPM, Institut für Physik, Universität Augsburg, 86159Augsburg, Germany
| | - Anton Jesche
- Experimentalphysik VI, Zentrum für Elektronische Korrelation und Magnetismus, Institut für Physik, Universität Augsburg, Augsburg86159, Germany
| | - Mingyu Xu
- The Ames Laboratory, Iowa State University, Ames, Iowa50011, United States
- Department of Physics and Astronomy, Iowa State University, Ames, Iowa50011, United States
| | - Paul Canfield
- The Ames Laboratory, Iowa State University, Ames, Iowa50011, United States
- Department of Physics and Astronomy, Iowa State University, Ames, Iowa50011, United States
| | - Wolfgang Scherer
- CPM, Institut für Physik, Universität Augsburg, 86159Augsburg, Germany
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2
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Fischer A, Eickerling G, Scherer W. The Effects of Chemical Bonding at Subatomic Resolution: A Case Study on α-Boron. Molecules 2021; 26:molecules26144270. [PMID: 34299544 PMCID: PMC8303496 DOI: 10.3390/molecules26144270] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 07/08/2021] [Accepted: 07/09/2021] [Indexed: 11/22/2022] Open
Abstract
Similar to classical asphericity shifts, aspherical deformations of the electron density in the atomic core region can result in core asphericity shifts in refinements using a Hansen-Coppens multipolar model (HCM), especially when highly precise experimental datasets with resolutions far beyond sin(θ)/λ ≤ 1.0 Å−1 are employed. These shifts are about two orders of magnitude smaller than their counterparts caused by valence shell deformations, and their underlying deformations are mainly of dipolar character for 1st row atoms. Here, we analyze the resolution dependence of core asphericity shifts in α-boron. Based on theoretical structure factors, an appropriate Extended HCM (EHCM) is developed, which is tested against experimental high-resolution (sin(θ)/λ ≤ 1.6 Å−1) single-crystal diffraction data. Bond length deviations due to core asphericity shifts of α-boron in the order of 4–6·10−4 Å are small but significant at this resolution and can be effectively compensated by an EHCM, although the correlation of the additional model parameters with positional parameters prevented a free refinement of all core model parameters. For high quality, high resolution data, a proper treatment with an EHCM or other equivalent methods is therefore highly recommended.
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3
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Podhorský M, Bučinský L, Jayatilaka D, Grabowsky S. HgH 2 meets relativistic quantum crystallography. How to teach relativity to a non-relativistic wavefunction. ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES 2021; 77:54-66. [PMID: 33399131 DOI: 10.1107/s2053273320014837] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 11/09/2020] [Indexed: 11/10/2022]
Abstract
The capability of X-ray constrained wavefunction (XCW) fitting to introduce relativistic effects into a non-relativistic wavefunction is tested. It is quantified how much of the reference relativistic effects can be absorbed in the non-relativistic XCW calculation when fitted against relativistic structure factors of a model HgH2 molecule. Scaling of the structure-factor sets to improve the agreement statistics is found to introduce a significant systematic error into the XCW fitting of relativistic effects.
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Affiliation(s)
- Michal Podhorský
- Institute of Physical Chemistry and Chemical Physics FCHPT, Slovak University of Technology, Radlinskeho 9, Bratislava SK-812 37, Slovakia
| | - Lukáš Bučinský
- Institute of Physical Chemistry and Chemical Physics FCHPT, Slovak University of Technology, Radlinskeho 9, Bratislava SK-812 37, Slovakia
| | - Dylan Jayatilaka
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Hwy, Perth WA 6009, Australia
| | - Simon Grabowsky
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
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4
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Sadjadi S, Matta CF, Hamilton IP. Bonding and metastability for Group 12 dications. J Comput Chem 2020; 42:40-49. [PMID: 33063900 DOI: 10.1002/jcc.26431] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 09/25/2020] [Accepted: 09/28/2020] [Indexed: 11/06/2022]
Abstract
Electronic structure and bonding properties of the Group 12 dications M2 2+ (M = Zn, Cd, Hg) are investigated and electron density-derived quantities are used to characterize the metastability of these species. Of particular interest are the complementary descriptions afforded by the Laplacian of the electron density ∇2 ρ(r) and the one-electron Bohm quantum potential (Q = ∇ 2 ρ r / 2 ρ r ) along the bond path. Further, properties derived from the pair density including the localization-delocalization matrices (LDMs) and the interacting quantum atoms (IQA) energies are analyzed within the framework of the quantum theory of atoms in molecules (QTAIM). From the crossing points of the singlet (ground) and triplet (excited) potential energy curves, the barriers for dissociation (BFD) are estimated to be 25.2 kcal/mol (1.09 eV) for Zn2 2+ , 22.8 kcal/mol (0.99 eV) for Cd2 2+ , and 26.4 kcal/mol (1.14 eV) for Hg2 2+ . For comparison and benchmarking purposes, the case of N2 2+ is considered as a texbook example of metastability. At the equilibrium geometries, LDMs, which are used here as an electronic fingerprinting tool, discriminate and group together Group 12 M2 2+ from its isoelectronic Group 11 M2 . While "classical" bonding indices are inconclusive in establishing regions of metastability in the bonding, it is shown that the one-electron Bohm quantum potential is promising in this regard.
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Affiliation(s)
- SeyedAbdolreza Sadjadi
- Department of Physics, Faculty of Science, Laboratory for Space Research, The University of Hong Kong, Hong Kong SAR, China
| | - Chérif F Matta
- Department of Chemistry and Physics, Mount Saint Vincent University, Halifax, Nova Scotia, Canada.,Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Ian P Hamilton
- Department of Chemistry and Biochemistry, Wilfrid Laurier University, Waterloo, Ontario, Canada
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5
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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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6
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Gianopoulos CG, Zhurov VV, Pinkerton AA. Charge densities in actinide compounds: strategies for data reduction and model building. IUCRJ 2019; 6:895-908. [PMID: 31576222 PMCID: PMC6760433 DOI: 10.1107/s2052252519010248] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 07/17/2019] [Indexed: 05/29/2023]
Abstract
The data quality requirements for charge density studies on actinide compounds are extreme. Important steps in data collection and reduction required to obtain such data are summarized and evaluated. The steps involved in building an augmented Hansen-Coppens multipole model for an actinide pseudo-atom are provided. The number and choice of radial functions, in particular the definition of the core, valence and pseudo-valence terms are discussed. The conclusions in this paper are based on a re-examination and improvement of a previously reported study on [PPh4][UF6]. Topological analysis of the total electron density shows remarkable agreement between experiment and theory; however, there are significant differences in the Laplacian distribution close to the uranium atoms which may be due to the effective core potential employed for the theoretical calculations.
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Affiliation(s)
| | - Vladimir V. Zhurov
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, OH 43606, USA
| | - A. Alan Pinkerton
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, OH 43606, USA
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7
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Munárriz J, Calatayud M, Contreras-García J. Valence-Shell Electron-Pair Repulsion Theory Revisited: An Explanation for Core Polarization. Chemistry 2019; 25:10938-10945. [PMID: 31206860 DOI: 10.1002/chem.201902244] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Indexed: 11/10/2022]
Abstract
Valence-shell electron-pair repulsion (VSEPR) theory constitutes one of the pillars of theoretical predictive chemistry. It was proposed even before the advent of the concept of "spin", and it is still a very useful tool in chemistry. In this article we propose an extension of VSEPR theory to understand the core structure and predict core polarization in the main-group elements. We show from first principles (Electron Localization Function analysis) how the inner- and outer-core shells are organized. In particular, electrons in these regions are structured following the shape of the dual polyhedron of the valence shell (3rd period) or the equivalent polyhedron (4th and 5th periods). We interpret these results in terms of "hard" and "soft" core character. All the studied systems follow this trend, providing a framework for predicting electron distribution in the core. We also show that lone pairs behave as "standard ligands" in terms of core polarization. The predictive character of the model was tested by proposing the core polarization in different systems not included in the original set (such as XeF4 and [Fe(CN)6 ]3- ) and checking the hypothesis by means of a posteriori calculations. From the experimental point of view, the extension of VSEPR to the core region has consequences for current crystallography research. In particular, it explains the core polarization revealed by high resolution X-ray experiments.
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Affiliation(s)
- Julen Munárriz
- Departamento de Química Física, and Instituto de Biocomputación y, Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, Zaragoza, 50009, Spain.,Laboratoire de Chimie Théorique (LCT), Sorbonne Université, CNRS, Paris, 75005, France.,Current address: Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, CA, 90095, USA
| | - Mónica Calatayud
- Laboratoire de Chimie Théorique (LCT), Sorbonne Université, CNRS, Paris, 75005, France
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8
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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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9
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Tolborg K, Jørgensen MRV, Sist M, Mamakhel A, Overgaard J, Iversen BB. Low‐Barrier Hydrogen Bonds in Negative Thermal Expansion Material H
3
[Co(CN)
6
]. Chemistry 2019; 25:6814-6822. [DOI: 10.1002/chem.201900358] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Indexed: 11/08/2022]
Affiliation(s)
- Kasper Tolborg
- Center for Materials CrystallographyDepartment of Chemistry and iNANOAarhus University Langelandsgade 140 8000 Aarhus C Denmark
| | - Mads R. V. Jørgensen
- Center for Materials CrystallographyDepartment of Chemistry and iNANOAarhus University Langelandsgade 140 8000 Aarhus C Denmark
- MAXIV LaboratoryLund University Fotongatan 2 22594 Lund Sweden
| | - Mattia Sist
- Center for Materials CrystallographyDepartment of Chemistry and iNANOAarhus University Langelandsgade 140 8000 Aarhus C Denmark
| | - Aref Mamakhel
- Center for Materials CrystallographyDepartment of Chemistry and iNANOAarhus University Langelandsgade 140 8000 Aarhus C Denmark
| | - Jacob Overgaard
- 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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Anderson JSM, Rodríguez JI, Ayers PW, Trujillo-González DE, Götz AW, Autschbach J, Castillo-Alvarado FL, Yamashita K. Molecular QTAIM Topology Is Sensitive to Relativistic Corrections. Chemistry 2019; 25:2538-2544. [PMID: 30393899 DOI: 10.1002/chem.201804464] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Indexed: 11/11/2022]
Abstract
The topology of the molecular electron density of benzene dithiol gold cluster complex Au4 -S-C6 H4 -S'-Au'4 changed when relativistic corrections were made and the structure was close to a minimum of the Born-Oppenheimer energy surface. Specifically, new bond paths between hydrogen atoms on the benzene ring and gold atoms appeared, indicating that there is a favorable interaction between these atoms at the relativistic level. This is consistent with the observation that gold becomes a better electron acceptor when relativistic corrections are applied. In addition to relativistic effects, here, we establish the sensitivity of molecular topology to basis sets and convergence thresholds for geometry optimization.
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Affiliation(s)
- James S M Anderson
- Department of Chemistry & Chemical Biology, McMaster University, Hamilton, Ontario, L8S4M1, Canada.,iTHES Research Group, RIKEN, 2-1, Hirosawa, Wako-shi, Saitama, 351-0198, Japan.,Instituto de Química, Universidad Nacional Autónoma de México, Universidad 300, Ciudad Universitaria, Ciudad de México, 04510, Mexico
| | - Juan I Rodríguez
- Escuela Superior de Física y Matemáticas, Instituto Politécnico Nacional, Edificio 9, U.P. A.L.M, Col. San Pedro Zacatenco, C.P., 07738, Ciudad de México, México
| | - Paul W Ayers
- Department of Chemistry & Chemical Biology, McMaster University, Hamilton, Ontario, L8S4M1, Canada
| | - Daniel E Trujillo-González
- Escuela Superior de Física y Matemáticas, Instituto Politécnico Nacional, Edificio 9, U.P. A.L.M, Col. San Pedro Zacatenco, C.P., 07738, Ciudad de México, México
| | - Andreas W Götz
- San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive, La Jolla, 92093-0505, California, USA
| | - Jochen Autschbach
- Department of Chemistry, University at Buffalo, State University of New York, Buffalo, 14260-3000, NY, USA
| | - Fray L Castillo-Alvarado
- Escuela Superior de Física y Matemáticas, Instituto Politécnico Nacional, Edificio 9, U.P. A.L.M, Col. San Pedro Zacatenco, C.P., 07738, Ciudad de México, México
| | - Koichi Yamashita
- Department of Chemical System Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
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11
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Pal R, Mebs S, Shi MW, Jayatilaka D, Krzeszczakowska JM, Malaspina LA, Wiecko M, Luger P, Hesse M, Chen YS, Beckmann J, Grabowsky S. Linear MgCp* 2 vs Bent CaCp* 2: London Dispersion, Ligand-Induced Charge Localizations, and Pseudo-Pregostic C-H···Ca Interactions. Inorg Chem 2018; 57:4906-4920. [PMID: 29671589 DOI: 10.1021/acs.inorgchem.7b03079] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In the family of metallocenes, MgCp*2 (Cp* = pentamethylcyclopentadienyl) exhibits a regular linear sandwich structure, whereas CaCp*2 is bent in both the gas phase and solid state. Bending is typically observed for metal ions which possess a lone pair. Here, we investigate which electronic differences cause the bending in complexes lacking lone pairs at the metal atoms. The bent gas-phase geometry of CaCp*2 suggests that the bending must have an intramolecular origin. Geometry optimizations with and without dispersion effects/d-type polarization functions on MCp2 and MCp*2 gas-phase complexes (M = Ca, Mg) establish that attractive methyl···methyl London dispersion interactions play a decisive role in the bending in CaCp*2. A sufficient polarizability of the metal to produce a shallow bending potential energy curve is a prerequisite but is not the reason for the bending. Concomitant ligand-induced charge concentrations and localizations at the metal atoms are studied in further detail, for which real-space bonding and orbital-based descriptors are used. Low-temperature crystal structures of MgCp*2 and CaCp*2 were determined which facilitated the identification and characterization of intermolecular pseudo-pregostic interactions, C-H···Ca, in the CaCp*2 crystal structure.
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Affiliation(s)
- Rumpa Pal
- Universität Bremen , Institut für Anorganische Chemie und Kristallographie , Leobener Straße 3 and 7 , 28359 Bremen , Germany
| | - Stefan Mebs
- Freie Universität Berlin , Institut für Experimentalphysik , Arnimallee 14 , 14195 Berlin , Germany
| | - Ming W Shi
- The University of Western Australia, School of Molecular Sciences , 35 Stirling Highway , Perth Western Australia 6009 , Australia
| | - Dylan Jayatilaka
- The University of Western Australia, School of Molecular Sciences , 35 Stirling Highway , Perth Western Australia 6009 , Australia
| | - Joanna M Krzeszczakowska
- University of Warsaw , Biological and Chemical Research Centre, Chemistry Department , Zwirki i Wigury 101 , 02-089 Warsaw , Poland
| | - Lorraine A Malaspina
- Universität Bremen , Institut für Anorganische Chemie und Kristallographie , Leobener Straße 3 and 7 , 28359 Bremen , Germany
| | - Michal Wiecko
- Freie Universität Berlin , Institut für Chemie und Biochemie, Anorganische Chemie , Fabeckstraße 36a , 14195 Berlin , Germany
| | - Peter Luger
- Freie Universität Berlin , Institut für Chemie und Biochemie, Anorganische Chemie , Fabeckstraße 36a , 14195 Berlin , Germany
| | - Malte Hesse
- Universität Bremen , Institut für Anorganische Chemie und Kristallographie , Leobener Straße 3 and 7 , 28359 Bremen , Germany
| | - Yu-Sheng Chen
- ChemMatCARS, Center for Advanced Radiation Sources, c/o Advanced Photon Source/ANL , The University of Chicago , 9700 South Cass Avenue , Building 434D, Argonne , Illinois 60439 , United States
| | - Jens Beckmann
- Universität Bremen , Institut für Anorganische Chemie und Kristallographie , Leobener Straße 3 and 7 , 28359 Bremen , Germany
| | - Simon Grabowsky
- Universität Bremen , Institut für Anorganische Chemie und Kristallographie , Leobener Straße 3 and 7 , 28359 Bremen , Germany
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12
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Woińska M, Jayatilaka D, Dittrich B, Flaig R, Luger P, Woźniak K, Dominiak PM, Grabowsky S. Validation of X-ray Wavefunction Refinement. Chemphyschem 2017; 18:3334-3351. [PMID: 29168318 DOI: 10.1002/cphc.201700810] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 09/22/2017] [Indexed: 11/10/2022]
Abstract
In this work, the quality of the electron density in crystals reconstructed by the multipolar model (MM) and by X-ray wavefunction refinement (XWR) is tested on a set of high-resolution X-ray diffraction data sets of four amino acids and six tripeptides. It results in the first thorough validation of XWR. Agreement statistics, figures of merit, residual- and deformation-density maps, as well as atomic displacement parameters are used to measure the quality of the reconstruction relative to the measured structure factors. Topological analysis of the reconstructed density is carried out to obtain atomic and bond-topological properties, which are subsequently compared to the values derived from benchmarking periodic DFT geometry optimizations. XWR is simultaneously in better agreement than the MM with both benchmarking theory and the measured diffraction pattern. In particular, the obvious problems with the description of polar bonds in the MM are significantly reduced by using XWR. Similarly, modeling of electron density in the vicinity of hydrogen atoms with XWR is visibly improved.
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Affiliation(s)
- Magdalena Woińska
- Biological and Chemical Research Centre, Chemistry Department, University of Warsaw, Zwirki i Wigury 101, 02-089, Warsaw, Poland
| | - Dylan Jayatilaka
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Perth, WA, 6009, Australia
| | - Birger Dittrich
- Heinrich-Heine-Universität Düsseldorf, Anorganische Chemie und Strukturchemie, Gebäude 26.42.01.21, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Ralf Flaig
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxon, OX11 0DE, UK
| | - Peter Luger
- Freie Universität Berlin, Institut für Chemie und Biochemie, Fabeckstraße 36a, 14195, Berlin, Germany
| | - Krzysztof Woźniak
- Biological and Chemical Research Centre, Chemistry Department, University of Warsaw, Zwirki i Wigury 101, 02-089, Warsaw, Poland
| | - Paulina M Dominiak
- Biological and Chemical Research Centre, Chemistry Department, University of Warsaw, Zwirki i Wigury 101, 02-089, Warsaw, Poland
| | - Simon Grabowsky
- Institut für Anorganische Chemie und Kristallographie, Fachbereich 2-Biologie/Chemie, Universität Bremen, Leobener Straße NW2, 28359, Bremen, Germany
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13
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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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14
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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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15
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Kucková L, Bučinský L, Kožíšek J. Copper atom representation in charge density analysis of (5-chlorosalicylate)-(2,9-dimethylphenanthroline)-(aqua) copper complex: Experimental and theoretical study. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2017.01.058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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16
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Shi MW, Stewart SG, Sobolev AN, Dittrich B, Schirmeister T, Luger P, Hesse M, Chen Y, Spackman PR, Spackman MA, Grabowsky S. Approaching an experimental electron density model of the biologically active
trans
‐epoxysuccinyl amide group—Substituent effects vs. crystal packing. J PHYS ORG CHEM 2017. [DOI: 10.1002/poc.3683] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Ming W. Shi
- School of Chemistry and Biochemistry The University of Western Australia Perth WA Australia
| | - Scott G. Stewart
- School of Chemistry and Biochemistry The University of Western Australia Perth WA Australia
| | - Alexandre N. Sobolev
- School of Chemistry and Biochemistry The University of Western Australia Perth WA Australia
| | - Birger Dittrich
- Anorganische Chemie und Strukturchemie Heinrich‐Heine‐Universität Düsseldorf Düsseldorf Germany
| | - Tanja Schirmeister
- Institut für Pharmazie und Biochemie Johannes‐Gutenberg‐Universität Mainz Mainz Germany
| | - Peter Luger
- Institut für Chemie und Biochemie, Anorganische Chemie Freie Universität Berlin Berlin Germany
| | - Malte Hesse
- Fachbereich 2—Biologie/Chemie, Institut für Anorganische Chemie und Kristallographie Universität Bremen Bremen Germany
| | - Yu‐Sheng Chen
- ChemMatCARS The University of Chicago Argonne IL USA
| | - Peter R. Spackman
- School of Chemistry and Biochemistry The University of Western Australia Perth WA Australia
| | - Mark A. Spackman
- School of Chemistry and Biochemistry The University of Western Australia Perth WA Australia
| | - Simon Grabowsky
- School of Chemistry and Biochemistry The University of Western Australia Perth WA Australia
- Fachbereich 2—Biologie/Chemie, Institut für Anorganische Chemie und Kristallographie Universität Bremen Bremen Germany
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17
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Bučinský L, Jayatilaka D, Grabowsky S. Importance of Relativistic Effects and Electron Correlation in Structure Factors and Electron Density of Diphenyl Mercury and Triphenyl Bismuth. J Phys Chem A 2016; 120:6650-69. [PMID: 27434184 DOI: 10.1021/acs.jpca.6b05769] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This study investigates the possibility of detecting relativistic effects and electron correlation in single-crystal X-ray diffraction experiments using the examples of diphenyl mercury (HgPh2) and triphenyl bismuth (BiPh3). In detail, the importance of electron correlation (ECORR), relativistic effects (REL) [distinguishing between total, scalar and spin-orbit (SO) coupling relativistic effects] and picture change error (PCE) on the theoretical electron density, its topology and its Laplacian using infinite order two component (IOTC) wave functions is discussed. This is to develop an understanding of the order of magnitude and shape of these different effects as they manifest in the electron density. Subsequently, the same effects are considered for the theoretical structure factors. It becomes clear that SO and PCE are negligible, but ECORR and scalar REL are important in low- and medium-order reflections on absolute and relative scales-not in the high-order region. As a further step, Hirshfeld atom refinement (HAR) and subsequent X-ray constrained wavefunction (XCW) fitting have been performed for the compound HgPh2 with various relativistic and nonrelativistic wave functions against the experimental structure factors. IOTC calculations of theoretical structure factors and relativistic HAR as well as relativistic XCW fitting are presented for the first time, accounting for both scalar and spin-orbit relativistic effects.
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Affiliation(s)
- Lukáš Bučinský
- Institute of Physical Chemistry and Chemical Physics FCHPT, Slovak University of Technology , Radlinskeho 9, Bratislava SK-812 37, Slovakia
| | - Dylan Jayatilaka
- School of Chemistry and Biochemistry, The University of Western Australia , 35 Stirling Highway, Perth WA 6009, Australia
| | - Simon Grabowsky
- Fachbereich 2 - Biologie/Chemie, Universität Bremen , Leobener Straβe NW2, 28359 Bremen, Germany
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18
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Batke K, Eickerling G. Communication: Determination of relativistic effects from X-ray structure factors. J Chem Phys 2016; 144:071101. [PMID: 26896969 DOI: 10.1063/1.4942244] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
In this communication, a procedure is presented which allows for the determination of the scalar-relativistic contraction of individual electronic shells of transition metal atoms from X-ray structure factor data. The procedure is verified and benchmarked employing theoretical and experimental F(hkl) data, revealing an overall good agreement between the experimentally determined results and the theoretical reference values. From the experimental data, the relativistic contraction of the n = 2 shell of a cerium atom is, for example, determined as 0.097 pm, compared to a theoretical reference value of 0.116 pm. It is further demonstrated that the reproducibility of the results is excellent when comparing different experimental data sets. Finally, the dependency of the according results on the data resolution of the structure factor data is investigated.
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Affiliation(s)
- Kilian Batke
- Institut für Physik, Universität Augsburg, Universitätsstraße 1, D-86159 Augsburg, Germany
| | - Georg Eickerling
- Institut für Physik, Universität Augsburg, Universitätsstraße 1, D-86159 Augsburg, Germany
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19
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Ahmed M, Nassour A, Noureen S, Lecomte C, Jelsch C. Experimental and theoretical charge-density analysis of 1,4-bis(5-hexyl-2-thienyl)butane-1,4-dione: applications of a virtual-atom model. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2016; 72:75-86. [PMID: 26830798 DOI: 10.1107/s2052520615019083] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 10/09/2015] [Indexed: 06/05/2023]
Abstract
The experimental and theoretical charge densities of 1,4-bis(5-hexyl-2-thienyl)butane-1,4-dione, a precursor in the synthesis of thiophene-based semiconductors and organic solar cells, are presented. A dummy bond charges spherical atom model is applied besides the multipolar atom model. The results show that the dummy bond charges model is accurate enough to calculate electrostatic-derived properties which are comparable with those obtained by the multipolar atom model. The refinement statistics and the residual electron density values are found to be intermediate between the independent atom and the multipolar formalisms.
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Affiliation(s)
- Maqsood Ahmed
- Department of Chemistry, The Islamia University of Bahawalpur, 63100, Pakistan
| | - Ayoub Nassour
- Laboratoire de Cristallographie, Résonance Magnétique et Modélisations, CNRS UMR 7036 CRM2, Université de Lorraine, BP 70239, 54506, France
| | - Sajida Noureen
- Department of Chemistry, The Islamia University of Bahawalpur, 63100, Pakistan
| | - Claude Lecomte
- Laboratoire de Cristallographie, Résonance Magnétique et Modélisations, CNRS UMR 7036 CRM2, Université de Lorraine, BP 70239, 54506, France
| | - Christian Jelsch
- Laboratoire de Cristallographie, Résonance Magnétique et Modélisations, CNRS UMR 7036 CRM2, Université de Lorraine, BP 70239, 54506, France
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20
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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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21
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Edelmann FT. Lanthanides and actinides: Annual survey of their organometallic chemistry covering the year 2013. Coord Chem Rev 2015. [DOI: 10.1016/j.ccr.2014.09.017] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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22
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Wu LC, Chung WC, Wang CC, Lee GH, Lu SI, Wang Y. A charge density study of π-delocalization and intermolecular interactions. Phys Chem Chem Phys 2015; 17:14177-84. [DOI: 10.1039/c5cp01575h] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The location of bond critical points (red dots) and its associated bond path (black line) provide the evidence on the existence of the weak intermolecular interactions of the π–π interactions between triazole rings of atrz molecules in crystal with the close ring distance of 3.17 Å.
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Affiliation(s)
- L.-C. Wu
- Department of Chemistry
- National Taiwan University
- Taipei
- Taiwan
| | - W.-C. Chung
- Department of Chemistry
- National Taiwan University
- Taipei
- Taiwan
| | - C.-C. Wang
- Department of Chemistry
- Soochow University
- Taipei
- Taiwan
| | - G.-H. Lee
- Instrumentation Center
- National Taiwan University
- Taipei
- Taiwan
| | - S.-I. Lu
- Department of Chemistry
- Soochow University
- Taipei
- Taiwan
| | - Y. Wang
- Department of Chemistry
- National Taiwan University
- Taipei
- Taiwan
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23
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Overgaard J, Walsh JPS, Hathwar VR, Jørgensen MRV, Hoffman C, Platts JA, Piltz R, Winpenny REP. Relationships between Electron Density and Magnetic Properties in Water-Bridged Dimetal Complexes. Inorg Chem 2014; 53:11531-9. [DOI: 10.1021/ic501411w] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Jacob Overgaard
- Department of Chemistry, Center for Materials
Crystallography, Aarhus University, DK-8000 Aarhus
C, Denmark
| | - James P. S. Walsh
- School of Chemistry and Photon Science Institute, The University of Manchester, Oxford Road, Manchester M13 9PL, U.K
| | - Venkatesha R. Hathwar
- Department of Chemistry, Center for Materials
Crystallography, Aarhus University, DK-8000 Aarhus
C, Denmark
| | - Mads R. V. Jørgensen
- Department of Chemistry, Center for Materials
Crystallography, Aarhus University, DK-8000 Aarhus
C, Denmark
- Chemical and Engineering Materials Division, Oak Ridge National Laboratory, PO Box 2008 - MS 6475, Oak Ridge, Tennessee 37831, United States
| | - Christina Hoffman
- Chemical and Engineering Materials Division, Oak Ridge National Laboratory, PO Box 2008 - MS 6475, Oak Ridge, Tennessee 37831, United States
| | - Jamie A. Platts
- School of Chemistry, Cardiff University, Park Place, Cardiff, CF10
3AT, U.K
| | - Ross Piltz
- Bragg Institute, ANSTO, Locked Bag 2001, Kirrawee DC, NSW 2232, Australia
| | - Richard E. P. Winpenny
- School of Chemistry and Photon Science Institute, The University of Manchester, Oxford Road, Manchester M13 9PL, U.K
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