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Rowland C, Healy EF. Topological Analysis of the Electron Density of Molecules with Bridging Hydrogens To Tackle the Chemical Structure Monolith. Eur J Inorg Chem 2022. [DOI: 10.1002/ejic.202200538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
| | - Eamonn F. Healy
- Department of Chemistry St. Edward's University Austin TX 78704 USA
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2
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Milašinović V, Molčanov K, Krawczuk A, Bogdanov NE, Zakharov BA, Boldyreva EV, Jelsch C, Kojić-Prodić B. Charge density studies of multicentre two-electron bonding of an anion radical at non-ambient temperature and pressure. IUCRJ 2021; 8:644-654. [PMID: 34258012 PMCID: PMC8256703 DOI: 10.1107/s2052252521005273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 05/18/2021] [Indexed: 06/13/2023]
Abstract
The variation of charge density of two-electron multicentre bonding (pancake bonding) between semi-quinone radicals with pressure and temperature was studied on a salt of 5,6-di-chloro-2,3-di-cyano-semi-quinone radical anion (DDQ) with 4-cyano-N-methyl-pyridinium cation (4-CN) using the Transferable Aspheric Atom Model (TAAM) refinement. The pancake-bonded radical dimers are stacked by non-bonding π-interactions. With rising pressure, the covalent character of interactions between radicals increases, and above 2.55 GPa, the electron density indicates multicentric covalent interactions throughout the stack. The experimental charge densities were verified and corroborated by periodic DFT computations. The TAAM approach has been tested and validated for atomic resolution data measured at ambient pressure; this work shows this approach can also be applied to diffraction data obtained at pressures up to several gigapascals.
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Affiliation(s)
- Valentina Milašinović
- Department of Physical Chemistry, Rudjer Bošković Institute, Bijenička 54, Zagreb 10000, Croatia
| | - Krešimir Molčanov
- Department of Physical Chemistry, Rudjer Bošković Institute, Bijenička 54, Zagreb 10000, Croatia
| | - Anna Krawczuk
- Institute of Inorganic Chemistry, University of Göttingen, Tammannstrasse 4, Göttingen 37077, Germany
- Faculty of Chemistry, Jagiellonian University in Krakow, Gronostajowa 2, Krakow 30-387, Poland
| | - Nikita E. Bogdanov
- Boreskov Institute of Catalysis, SB RAS, Lavrentiev Avenue 5, Novosibirsk 630090, Russian Federation
- Novosibirsk State University, Pirogova Street 2, Novosibirsk 630090 Russian Federation
| | - Boris A. Zakharov
- Boreskov Institute of Catalysis, SB RAS, Lavrentiev Avenue 5, Novosibirsk 630090, Russian Federation
- Novosibirsk State University, Pirogova Street 2, Novosibirsk 630090 Russian Federation
| | - Elena V. Boldyreva
- Boreskov Institute of Catalysis, SB RAS, Lavrentiev Avenue 5, Novosibirsk 630090, Russian Federation
- Novosibirsk State University, Pirogova Street 2, Novosibirsk 630090 Russian Federation
| | - Christian Jelsch
- CRM2, CNRS, UMR 7036, Université de Lorraine, BP 70239 Nancy, France
| | - Biserka Kojić-Prodić
- Department of Physical Chemistry, Rudjer Bošković Institute, Bijenička 54, Zagreb 10000, Croatia
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3
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Multiresolution non-covalent interaction analysis for ligand–protein promolecular electron density distributions. Theor Chem Acc 2021. [DOI: 10.1007/s00214-020-02705-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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4
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Falvello LR. What is a crystal to the new chemical crystallographer, after that first, automated structure analysis? CRYSTALLOGR REV 2020. [DOI: 10.1080/0889311x.2020.1760856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Larry R. Falvello
- Department of Inorganic Chemistry and Aragón Materials Science Institute, University of Zaragoza - CSIC Zaragoza, Spain
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5
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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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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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Bučinský L, Jayatilaka D, Grabowsky S. Relativistic quantum crystallography of diphenyl- and dicyanomercury. Theoretical structure factors and Hirshfeld atom refinement. ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES 2019; 75:705-717. [PMID: 31475915 DOI: 10.1107/s2053273319008027] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 06/04/2019] [Indexed: 11/10/2022]
Abstract
Quantum crystallographic refinement of heavy-element-containing compounds is a challenge, because many physical effects have to be accounted for adequately. Here, the impact and magnitude of relativistic effects are compared with those of electron correlation, polarization through the environment, choice of basis set and treatment of thermal motion effects on the structure factors of diphenylmercury(II) [Hg(Ph)2] and dicyanomercury(II) [Hg(CN)2]. Furthermore, the individual atomic contributions to the structure factors are explored in detail (using Mulliken population analysis and the exponential decay of atomic displacement parameters) to compare the contributions of lighter atoms, especially hydrogen atoms, against mercury. Subsequently, relativistic Hirshfeld atom refinement (HAR) is validated against theoretical structure factors of Hg(Ph)2 and Hg(CN)2, starting from perturbed geometries, to test if the relativistic variant of HAR leads to multiple solutions. Generally, relativistic HAR is successful, leading to a perfect match with the reference geometries, but some limitations are pointed out.
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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
- Institute of Inorganic Chemistry and Crystallography, Department 2 - Biology/Chemistry, University of Bremen, Leobener Strasse 3, 28359 Bremen, Germany
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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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Ruiz J, Sol D, García L, Mateo MA, Vivanco M, Van der Maelen JF. Generation and Tunable Cyclization of Formamidinate Ligands in Carbonyl Complexes of Mn(I): An Experimental and Theoretical Study. Organometallics 2019. [DOI: 10.1021/acs.organomet.8b00898] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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10
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Abstract
Quantum crystallography (QCr) is a branch of crystallography aimed at obtaining the complete quantum mechanics of a crystal given its X-ray scattering data. The fundamental value of obtaining an electron density matrix that is N-representable is that it ensures consistency with an underlying properly antisymmetrized wavefunction, a requirement of quantum mechanical validity. However, X-ray crystallography has progressed in an impressive way for decades based only upon the electron density obtained from the X-ray scattering data without the imposition of the mathematical structure of quantum mechanics. Therefore, one may perhaps ask regarding N-representability “why bother?” It is the purpose of this article to answer such a question by succinctly describing the advantage that is opened by QCr.
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Affiliation(s)
- Lou Massa
- Hunter College & the PhD Program of the Graduate Center, City University of New York, NY, USA
| | - Chérif F. Matta
- Department of Chemistry and Physics, Mount Saint Vincent University, Halifax, NS B3M 2J6, Canada
- Department of Chemistry, Dalhousie University, Halifax, NS B3H 4J3, Canada
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11
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Ivanova B, Spiteller M. On the nature of the coordination bonding of metal–organics for ions with the d 10 electronic configuration – Experimental and theoretical analyses. Polyhedron 2017. [DOI: 10.1016/j.poly.2017.08.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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12
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Gatti C, Macetti G, Lo Presti L. Insights on spin delocalization and spin polarization mechanisms in crystals of azido copper(II) dinuclear complexes through the electron spin density Source Function. ACTA CRYSTALLOGRAPHICA SECTION B-STRUCTURAL SCIENCE CRYSTAL ENGINEERING AND MATERIALS 2017; 73:565-583. [DOI: 10.1107/s2052520617008083] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 05/31/2017] [Indexed: 11/11/2022]
Abstract
The Source Function (SF) tool was applied to the analysis of thetheoreticalspin density in azido CuIIdinuclear complexes, where the azido group, acting as a coupler between the CuIIcations, is linked to the metal centres either in an end-on or in an end–end fashion. Results for only the former structural arrangement are reported in the present paper. The SF highlights to which extent the magnetic centres contribute to determine the local spin delocalization and polarization at any point in the dimetallic complex and whether an atom or group of atoms of the ligands act in favour or against a given local spin delocalization/polarization. Ball-and-stick atomic SF percentage representations allow for a visualization of the magnetic pathways and of the specific role played by each atom along these paths, at given reference points. Decomposition of SF contributions in terms of a magnetic and of a relaxation component provides further insight. Reconstruction of partial spin densities by means of the Source Function has for the first time been introduced. At variance with the standard SF percentage representations, such reconstructions offer a simultaneous view of the sources originating from specific subsets of contributing atoms, in a selected molecular plane or in the whole space, and are therefore particularly informative. The SF tool is also used to evaluate the accuracy of the analysed spin densities. It is found that those obtained at the unrestricted B3LYP DFT level, relative to those computed at the CASSCF(6,6) level, greatly overestimate spin delocalization to the ligands, but comparatively underestimate magnetic connection (spin transmission) among atoms, along the magnetic pathways. As a consequence of its excessive spin delocalization, the UB3LYP method also overestimates spin polarization mechanisms between the paramagnetic centres and the ligands. Spin delocalization measures derived from the refinement of Polarized Neutron Diffraction data seem in general superior to those obtained through the DFT UB3LYP approach and closer to the far more accurate CASSCF results. It is also shown that a visual agreement on the spin-resolved electron densities ραand ρβderived from different approaches does not warrant a corresponding agreement between their associated spin densities.
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Grabowsky S, Genoni A, Bürgi HB. Quantum crystallography. Chem Sci 2017; 8:4159-4176. [PMID: 28878872 PMCID: PMC5576428 DOI: 10.1039/c6sc05504d] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 03/03/2017] [Indexed: 12/12/2022] Open
Abstract
Approximate wavefunctions can be improved by constraining them to reproduce observations derived from diffraction and scattering experiments. Conversely, charge density models, incorporating electron-density distributions, atomic positions and atomic motion, can be improved by supplementing diffraction experiments with quantum chemically calculated, tailor-made electron densities (form factors). In both cases quantum chemistry and diffraction/scattering experiments are combined into a single, integrated tool. The development of quantum crystallographic research is reviewed. Some results obtained by quantum crystallography illustrate the potential and limitations of this field.
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Affiliation(s)
- Simon Grabowsky
- Universität Bremen , Fachbereich 2 - Biologie/Chemie , Institut für Anorganische Chemie und Kristallographie , Leobener Str. NW2 , 28359 Bremen , Germany .
| | - Alessandro Genoni
- CNRS , Laboratoire SRSMC , UMR 7565 , Vandoeuvre-lès-Nancy , F-54506 , France
- Université de Lorraine , Laboratoire SRSMC , UMR 7565 , Vandoeuvre-lès-Nancy , F-54506 , France .
| | - Hans-Beat Bürgi
- Universität Bern , Departement für Chemie und Biochemie , Freiestr. 3 , CH-3012 Bern , Switzerland .
- Universität Zürich , Institut für Chemie , Winterthurerstrasse 190 , CH-8057 Zürich , Switzerland
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15
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Gianopoulos CG, Zhurov VV, Minasian SG, Batista ER, Jelsch C, Pinkerton AA. Bonding in Uranium(V) Hexafluoride Based on the Experimental Electron Density Distribution Measured at 20 K. Inorg Chem 2017; 56:1775-1778. [PMID: 28165229 DOI: 10.1021/acs.inorgchem.6b02971] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The electron density distribution of [PPh4][UF6] was obtained from high-resolution X-ray diffraction data measured at 20 K. The electron density was modeled with an augmented Hansen-Coppens multipolar formalism. Topological analysis reveals that the U-F bond is of incipient covalent nature. Theoretical calculations add further support to the bonding description gleaned from the experimental model. The impact of the uranium anomalous dispersion terms on the refinement is also discussed.
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Affiliation(s)
- Christopher G Gianopoulos
- Department of Chemistry, School of Green Chemistry and Engineering, The University of Toledo , Toledo, Ohio 43606, United States
| | - Vladimir V Zhurov
- Department of Chemistry, School of Green Chemistry and Engineering, The University of Toledo , Toledo, Ohio 43606, United States
| | - Stefan G Minasian
- Lawrence Berkeley National Laboratory (LBNL) , Berkeley, California 94720, United States
| | - Enrique R Batista
- Theoretical Division, Los Alamos National Laboratory , Los Alamos, New Mexico 87545, United States
| | - Christian Jelsch
- CRM2, CNRS, Institute Jean Barriol, Université de Lorraine , Vandoeuvre les Nancy Cedex 54000, France
| | - A Alan Pinkerton
- Department of Chemistry, School of Green Chemistry and Engineering, The University of Toledo , Toledo, Ohio 43606, United States
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16
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Guo H, Morales-Bayuelo A, Xu T, Momen R, Wang L, Yang P, Kirk SR, Jenkins S. Distinguishing and quantifying the torquoselectivity in competitive ring-opening reactions using the stress tensor and QTAIM. J Comput Chem 2016; 37:2722-2733. [DOI: 10.1002/jcc.24499] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2016] [Revised: 09/04/2016] [Accepted: 09/07/2016] [Indexed: 01/16/2023]
Affiliation(s)
- Huan Guo
- Science Faculty, Chemistry Program, Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research and Key Laboratory of Resource Fine-Processing and Advanced Materials of Hunan Province of MOE, College of Chemistry and Chemical Engineering; Hunan Normal University; Changsha Hunan 410081 China
| | - Alejandro Morales-Bayuelo
- Science Faculty, Chemistry Program; Grupo de Química Cuántica y Teórica de la Universidad de Cartagena, Facultad de Ciencias, Programa de Química, Cartagena de Indias; Colombia
| | - Tianlv Xu
- Science Faculty, Chemistry Program, Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research and Key Laboratory of Resource Fine-Processing and Advanced Materials of Hunan Province of MOE, College of Chemistry and Chemical Engineering; Hunan Normal University; Changsha Hunan 410081 China
| | - Roya Momen
- Science Faculty, Chemistry Program, Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research and Key Laboratory of Resource Fine-Processing and Advanced Materials of Hunan Province of MOE, College of Chemistry and Chemical Engineering; Hunan Normal University; Changsha Hunan 410081 China
| | - Lingling Wang
- Science Faculty, Chemistry Program, Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research and Key Laboratory of Resource Fine-Processing and Advanced Materials of Hunan Province of MOE, College of Chemistry and Chemical Engineering; Hunan Normal University; Changsha Hunan 410081 China
| | - Ping Yang
- Science Faculty, Chemistry Program, Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research and Key Laboratory of Resource Fine-Processing and Advanced Materials of Hunan Province of MOE, College of Chemistry and Chemical Engineering; Hunan Normal University; Changsha Hunan 410081 China
| | - Steven R. Kirk
- Science Faculty, Chemistry Program, Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research and Key Laboratory of Resource Fine-Processing and Advanced Materials of Hunan Province of MOE, College of Chemistry and Chemical Engineering; Hunan Normal University; Changsha Hunan 410081 China
| | - Samantha Jenkins
- Science Faculty, Chemistry Program, Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research and Key Laboratory of Resource Fine-Processing and Advanced Materials of Hunan Province of MOE, College of Chemistry and Chemical Engineering; Hunan Normal University; Changsha Hunan 410081 China
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Wellington JP, Kerridge A, Kaltsoyannis N. Should environmental effects be included when performing QTAIM calculations on actinide systems? A comparison of QTAIM metrics for Cs2UO2Cl4, U(Se2PPh2)4 and Np(Se2PPh2)4 in gas phase, COSMO and PEECM. Polyhedron 2016. [DOI: 10.1016/j.poly.2016.02.048] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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18
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Catlow CRA. Challenges in the structural science of materials. IUCRJ 2016; 3:226-227. [PMID: 27437107 PMCID: PMC4937775 DOI: 10.1107/s2052252516010022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Articles published recently in IUCrJ continue to exemplify the developments and challenges in the structural science of materials.
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Affiliation(s)
- C. Richard A. Catlow
- Department of Chemistry, University College London, 20 Gordon St., London WC1H OAJ, UK
- School of Chemistry, Cardiff University, Cardiff CF10 3AT, UK
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Ananyev IV, Lyssenko KA. A chemist's point of view: the noncylindrical symmetry of electron density means nothing but still means something. MENDELEEV COMMUNICATIONS 2016. [DOI: 10.1016/j.mencom.2016.07.024] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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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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