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Meurer F, Kleemiss F, Riesinger C, Balázs G, Vuković V, Shenderovich IG, Jelsch C, Bodensteiner M. Probing the Isolobal Relation between Cp'''NiP 3 and White Phosphorus by Experimental Charge Density Analysis. Chemistry 2024; 30:e202303762. [PMID: 38277228 DOI: 10.1002/chem.202303762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 12/20/2023] [Accepted: 01/26/2024] [Indexed: 01/28/2024]
Abstract
An in-depth analysis of the description of bonding within Cp'''Ni-cyclo-P3 (Cp'''=1,2,4-tri-tert-butylcyclopentadienyl, [Ni]P3) employing X-ray diffraction based multipolar modeling, density functional theory (DFT) as well as an "experimental wavefunction" obtained from X-ray restrained wavefunction (XRW) fitting is presented. The results are compared to DFT calculations on white phosphorus - an isolobal analogue to [Ni]P3. A complementary bonding analysis shows insights into the reactivity of [Ni]P3. The isolobal principle is reflected in every aspect of our analysis and the employed methods seamlessly predict the differences in reactivity of [Ni]P3 and P4. Crystallographic modeling, solid-state NMR, and DFT calculations describe the dynamic behavior of the cyclo-P3 unit in the title molecule.
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Affiliation(s)
- Florian Meurer
- Faculty for Chemistry and Pharmacy, University of Regensburg, Universitätsstraße 31, 93053, Regensburg, Germany
| | - Florian Kleemiss
- Faculty for Chemistry and Pharmacy, University of Regensburg, Universitätsstraße 31, 93053, Regensburg, Germany
- Institute for Inorganic Chemistry, RWTH Aachen, Landoltweg 1a, 52074, Aachen, Germany
| | - Christoph Riesinger
- Faculty for Chemistry and Pharmacy, University of Regensburg, Universitätsstraße 31, 93053, Regensburg, Germany
| | - Gábor Balázs
- Faculty for Chemistry and Pharmacy, University of Regensburg, Universitätsstraße 31, 93053, Regensburg, Germany
| | - Vedran Vuković
- Faculty for Chemistry and Pharmacy, University of Regensburg, Universitätsstraße 31, 93053, Regensburg, Germany
- Cristallographie, Résonance Magnétique et Modélisations CNRS, UMR 7036, Institut Jean Barriol, CNRS, Université de Lorraine BP 70239, F54506, Vandoeuvre-lès-Nancy CEDEX, France
| | - Ilya G Shenderovich
- Faculty for Chemistry and Pharmacy, University of Regensburg, Universitätsstraße 31, 93053, Regensburg, Germany
| | - Christian Jelsch
- Cristallographie, Résonance Magnétique et Modélisations CNRS, UMR 7036, Institut Jean Barriol, CNRS, Université de Lorraine BP 70239, F54506, Vandoeuvre-lès-Nancy CEDEX, France
| | - Michael Bodensteiner
- Faculty for Chemistry and Pharmacy, University of Regensburg, Universitätsstraße 31, 93053, Regensburg, Germany
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2
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Singh A, Avinash K, Malaspina LA, Banoo M, Alhameedi K, Jayatilaka D, Grabowsky S, Thomas SP. Dynamic Covalent Bonds in the Ebselen Class of Antioxidants Probed by X-ray Quantum Crystallography. Chemistry 2024; 30:e202303384. [PMID: 38126954 DOI: 10.1002/chem.202303384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 12/19/2023] [Accepted: 12/20/2023] [Indexed: 12/23/2023]
Abstract
Dynamic bonds are essential structural ingredients of dynamic covalent chemistry that involve reversible cleavage and formation of bonds. Herein, we explore the electronic characteristics of Se-N bonds in the organo-selenium antioxidant ebselen and its derivatives for their propensity to function as dynamic covalent bonds by employing high-resolution X-ray quantum crystallography and complementary computational studies. An analysis of the experimentally reconstructed X-ray wavefunctions reveals the salient electronic features of the Se-N bonds with very low electron density localized at the bonding region and a positive Laplacian value at the bond critical point. Bond orders and percentage covalency and ionicity estimated from the X-ray wavefunctions, along with localized orbital locator (LOL) and electron localization function (ELF) analyses show that the Se-N bond is unique in its closed shell-like features, despite being a covalent bond. Time-dependent DFT calculations simulate the cleavage of Se-N bonds in ebselen in the excited state, further substantiating their nature as dynamic bonds.
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Affiliation(s)
- Ashi Singh
- Department of Chemistry, Indian Institute of Technology Delhi, New Delhi, 110016, India
| | - Kiran Avinash
- Department of Chemistry, Indian Institute of Technology Delhi, New Delhi, 110016, India
| | - Lorraine A Malaspina
- University of Bern, Department of Chemistry, Biochemistry and Pharmaceutical Sciences, Freiestrasse 3, 3012, Bern, Switzerland
| | - Masoumeh Banoo
- Department of Chemistry, Indian Institute of Technology Delhi, New Delhi, 110016, India
| | - Khidhir Alhameedi
- School of Molecular Sciences, University of Western Australia, Perth, WA, 6009, Australia
- Faculty of Education for Pure Sciences -, University of Kerbala, Karbala, Iraq
| | - Dylan Jayatilaka
- School of Molecular Sciences, University of Western Australia, Perth, WA, 6009, Australia
| | - Simon Grabowsky
- University of Bern, Department of Chemistry, Biochemistry and Pharmaceutical Sciences, Freiestrasse 3, 3012, Bern, Switzerland
| | - Sajesh P Thomas
- Department of Chemistry, Indian Institute of Technology Delhi, New Delhi, 110016, India
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3
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Yanai H. Development of Stable Carbanionic Substituents. CHEM REC 2023; 23:e202300076. [PMID: 37058109 DOI: 10.1002/tcr.202300076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/29/2023] [Indexed: 04/15/2023]
Abstract
During the past decade, carbon (C-H) acids depicted as 'Tf2 CHR' (Tf=CF3 SO2 ) have attracted considerable attention as a new class of superacidic molecules, which show stronger acidity than sulfuric acid molecules. In recent years, the author has developed a synthetic methodology for such strong acids and has opened the door to chemistry of highly stabilised carbanions [Tf2 CR]- , which are the conjugate bases of the carbon acids. These carbanion-containing salts are stable and easy-to-handle species. Our efforts have revealed that the ionic but lipophilic characters of this type of carbanion can be used as a unique 'substituent' for increasing both the water solubility and the lipophilicity of organic compounds. This Personal Account provides an overview of our [Tf2 CR]- chemistry, including its synthesis, structure, reactivity, and applications.
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Affiliation(s)
- Hikaru Yanai
- School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392, Japan
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4
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Genoni A. Elucidating the nature of chemical bonds in a coordination compound through quantum crystallographic techniques. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2023; 79:253-254. [PMID: 37561073 DOI: 10.1107/s2052520623006364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 07/21/2023] [Indexed: 08/11/2023]
Abstract
Investigations simultaneously involving multiple techniques of quantum crystallography could be very useful to prove the consistency of obtained results or to highlight different facets of the same scientific phenomenon or problem. Pinto et al. [Acta Cryst. (2023), B79, 282-296] exploit three different quantum crystallographic techniques (Hansen & Coppens multipole model refinement, QTAIM analysis of the electron density, and Hirshfeld atom refinement) to characterize the nature of chemical bonds and of intra/intermolecular interactions in an organometallic compound.
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Affiliation(s)
- Alessandro Genoni
- Université de Lorraine and CNRS, Laboratoire de Physique et Chimie Théoriques, 1 Boulevard Arago, Metz, F-57070, France
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5
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Yanai H, Terajima Y, Kleemiss F, Grabowsky S, Matsumoto T. Reversing the Bond Length Alternation Order in Conjugated Polyenes by Substituent Effects. Chemistry 2023; 29:e202203538. [PMID: 36515459 DOI: 10.1002/chem.202203538] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/14/2022] [Accepted: 12/14/2022] [Indexed: 12/15/2022]
Abstract
We have synthesised several push-pull substituted conjugated polyenes and determined their accurate C-C bond lengths and charge-density distributions by utilising quantum crystallographic techniques. In a series of alkene, dienes, and triene bearing two (trifluoromethyl)sulfonyl (triflyl) groups on the terminal carbon atom, unique reversal of the bond-length alternation (BLA) order has been observed. This is a pronounced aberration from the molecular structure predicted by the Lewis-structure-based neutral resonance structure. Such reversal of BLA order has not been observed in push-pull compounds bearing conventional electron-withdrawing groups such as carbonyl and cyano groups instead of triflyl groups. Bonding behaviour of both normal and reversed bond length alternating systems has been revealed by complementary bonding analysis using several bond descriptors based on the experimentally fitted wavefunctions.
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Affiliation(s)
- Hikaru Yanai
- School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392, Japan
| | - Yoshihiko Terajima
- School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392, Japan
| | - Florian Kleemiss
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, CH-3012, Bern, Switzerland.,Faculty of Chemistry and Pharmacy, University of Regensburg, Universitätsstr. 31, D-93053, Regensburg, Germany
| | - Simon Grabowsky
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, CH-3012, Bern, Switzerland
| | - Takashi Matsumoto
- School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392, Japan
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Macetti G, Genoni A. Introduction of a weighting scheme for the X-ray restrained wavefunction approach: advantages and drawbacks. Acta Crystallogr A Found Adv 2023; 79:25-40. [PMID: 36601761 DOI: 10.1107/s2053273322010221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 10/23/2022] [Indexed: 11/22/2022] Open
Abstract
In a quite recent study [Genoni et al. (2017). IUCrJ, 4, 136-146], it was observed that the X-ray restrained wavefunction (XRW) approach allows a more efficient and larger capture of electron correlation effects on the electron density if high-angle reflections are not considered in the calculations. This is due to the occurrence of two concomitant effects when one uses theoretical X-ray diffraction data corresponding to a single-molecule electron density in a large unit cell: (i) the high-angle reflections are generally much more numerous than the low- and medium-angle ones, and (ii) they are already very well described at unrestrained level. Nevertheless, since high-angle data also contain important information that should not be disregarded, it is not advisable to neglect them completely. For this reason, based on the results of the previous investigation, this work introduces a weighting scheme for XRW calculations to up-weight the contribution of low- and medium-angle reflections, and, at the same time, to reasonably down-weight the importance of the high-angle data. The proposed strategy was tested through XRW computations with both theoretical and experimental structure-factor amplitudes. The tests have shown that the new weighting scheme works optimally if it is applied with theoretically generated X-ray diffraction data, while it is not advantageous when traditional experimental X-ray diffraction data (even of very high resolution) are employed. This also led to the conclusion that the use of a specific external parameter λJ for each resolution range might not be a suitable strategy to adopt in XRW calculations exploiting experimental X-ray data as restraints.
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Affiliation(s)
- Giovanni Macetti
- Université de Lorraine and CNRS, Laboratoire de Physique et Chimie Théoriques, 1 Boulevard Arago, Metz, F-57078, France
| | - Alessandro Genoni
- Université de Lorraine and CNRS, Laboratoire de Physique et Chimie Théoriques, 1 Boulevard Arago, Metz, F-57078, France
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7
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Electron density is not spherical: the many applications of the transferable aspherical atom model. Comput Struct Biotechnol J 2022; 20:6237-6243. [DOI: 10.1016/j.csbj.2022.10.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 10/12/2022] [Accepted: 10/13/2022] [Indexed: 11/20/2022] Open
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Bürgi HB, Genoni A. Remarks on X-ray constrained/restrained wavefunction fitting. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2022; 78:298-304. [PMID: 35695103 DOI: 10.1107/s2052520622004164] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Accepted: 04/19/2022] [Indexed: 06/15/2023]
Abstract
X-ray constrained/restrained wavefunctions (XCWs/XRWs) result from a combination of theory and experiment and are therefore affected by experimental errors and model uncertainties. The present XCW/XRW procedure does not take this into account, thus limiting the meaning and significance of the obtained wavefunctions.
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Affiliation(s)
- Hans Beat Bürgi
- Department of Chemistry, Biochemistry and Pharmacy, University of Berne, Freiestr. 12, Bern, CH-3012, Switzerland
| | - Alessandro Genoni
- Université de Lorraine and CNRS, Laboratoire de Physique et Chimie Théoriques, 1 Boulevard Arago, Metz, 57050, France
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9
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Davidson ML, Grabowsky S, Jayatilaka D. X-ray constrained wavefunctions based on Hirshfeld atoms. I. Method and review. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2022; 78:312-332. [PMID: 35695105 DOI: 10.1107/s2052520622004097] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 04/18/2022] [Indexed: 06/15/2023]
Abstract
The X-ray constrained wavefunction (XCW) procedure for obtaining an experimentally reconstructed wavefunction from X-ray diffraction data is reviewed. The two-center probability distribution model used to perform nuclear-position averaging in the original paper [Grimwood & Jayatilaka (2001). Acta Cryst. A57, 87-100] is carefully distinguished from the newer one-center probability distribution model. In the one-center model, Hirshfeld atoms are used, and the Hirshfeld atom based X-ray constrained wavefunction (HA-XCW) procedure is described for the first time, as well as its efficient implementation. In this context, the definition of the related X-ray wavefunction refinement (XWR) method is refined. The key halting problem for the XCW method - the procedure by which one determines when overfitting has occurred - is named and work on it reviewed.
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Affiliation(s)
- Max L Davidson
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley 6009, Western Australia, Australia
| | - Simon Grabowsky
- Departement für Chemie, Biochemie und Pharmazie, Universität Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Dylan Jayatilaka
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley 6009, Western Australia, Australia
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10
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Pal R, Jelsch C, Momma K, Grabowsky S. π-Hole bonding in a new co-crystal hydrate of gallic acid and pyrazine: static and dynamic charge density analysis. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2022; 78:231-246. [PMID: 35411861 PMCID: PMC9004022 DOI: 10.1107/s2052520622001457] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Accepted: 02/07/2022] [Indexed: 06/14/2023]
Abstract
A new cocrystal hydrate of gallic acid with pyrazine (4GA, Py, 4H2O; GA4PyW4) was obtained and characterized by single crystal X-ray diffraction. In addition to structure determination, experimental charge density analysis was carried out in terms of Multipole Modelling (MP), X-ray wavefunction refinement (XWR) and maximum entropy method (MEM). As a part of XWR, the structural refinement via Hirshfeld atom refinement was carried out and resulted in O-H bond lengths close to values from neutron diffraction. A systematic comparison of molecular conformations and aromatic interactions in this new cocrystal hydrate was performed with other existing polymorphs of gallic acid. In GA4PyW4, the two symmetry-independent gallic acid molecules have a syn COOH orientation and form the common (COOH)2 dimeric synthon. The carboxyl C atom displays the characteristics of π-holes with electropositive regions above and below the molecular plane and engages in acceptor-donor interactions with oxygen atoms of acidic O-H groups and phenol groups of neighbouring gallic acid molecules. The signature of the π-hole was identified from experimental charge density analysis, both in static density maps in MP and XWR as well as dynamic density in MEM, but it cannot be pinned down to a specific atom-atom interaction. This study presents the first comparison between an XWR and a MEM experimental electron-density determination.
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Affiliation(s)
- Rumpa Pal
- Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8571, Japan
- Institute of Inorganic Chemistry and Crystallography, Department 2 – Biology/Chemistry, University of Bremen, Leobener Str. 3, 28359 Bremen, Germany
| | | | - Koichi Momma
- National Museum of Nature and Science, 4-1-1 Amakubo, Tsukuba, Ibaraki, Japan
| | - Simon Grabowsky
- Institute of Inorganic Chemistry and Crystallography, Department 2 – Biology/Chemistry, University of Bremen, Leobener Str. 3, 28359 Bremen, Germany
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
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11
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Yanai H. Chemistry of Carbanions Stabilised by (Trifluoromethyl) sulfonyl Group: Synthesis, Structure and Applications. J SYN ORG CHEM JPN 2022. [DOI: 10.5059/yukigoseikyokaishi.80.186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Hikaru Yanai
- School of Pharmacy, Tokyo University of Pharmacy and Life Sciences
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12
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Landeros-Rivera B, Gallegos M, Munarriz J, Laplaza R, Contreras García J. New venues in electron density analysis. Phys Chem Chem Phys 2022; 24:21538-21548. [DOI: 10.1039/d2cp01517j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We provide a comprehensive overview of the chemical information within the electron density: how to extract information, but also how to obtain and how to assess the quality of the...
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13
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Wenger JS, Wang X, Johnstone TC. H-Atom Assignment and Sb-O Bonding of [Mes 3SbOH][O 3SPh] Confirmed by Neutron Diffraction, Multipole Modeling, and Hirshfeld Atom Refinement. Inorg Chem 2021; 60:16048-16052. [PMID: 34661394 DOI: 10.1021/acs.inorgchem.1c02229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Neutron wavelength-resolved Laue diffraction experiments permit accurate refinement of the H-atom positions and anisotropic displacement parameters of [Mes3SbOH][O3SPh]. A multipole-based charge density refinement and a topological analysis of the refined electron density were also performed. Hirshfeld atom refinement (HAR) recovers the neutron-determined H-atom parameters, and the quantum-mechanical electron density used in HAR recovers the electron density topology from the refined multipole model. These results confirm that [Mes3SbOH][O3SPh] does indeed feature a hydroxystibonium cation with a nominal Sb-O single bond and not a stibine oxide with an Sb=O/Sb+-O- bond.
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Affiliation(s)
- John S Wenger
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California 95064, United States
| | - Xiaoping Wang
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Timothy C Johnstone
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California 95064, United States
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14
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Midgley L, Bourhis LJ, Dolomanov OV, Grabowsky S, Kleemiss F, Puschmann H, Peyerimhoff N. Vanishing of the atomic form factor derivatives in non-spherical structural refinement - a key approximation scrutinized in the case of Hirshfeld atom refinement. ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES 2021; 77:519-533. [PMID: 34726630 DOI: 10.1107/s2053273321009086] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 09/02/2021] [Indexed: 11/10/2022]
Abstract
When calculating derivatives of structure factors, there is one particular term (the derivatives of the atomic form factors) that will always be zero in the case of tabulated spherical atomic form factors. What happens if the form factors are non-spherical? The assumption that this particular term is very close to zero is generally made in non-spherical refinements (for example, implementations of Hirshfeld atom refinement or transferable aspherical atom models), unless the form factors are refinable parameters (for example multipole modelling). To evaluate this general approximation for one specific method, a numerical differentiation was implemented within the NoSpherA2 framework to calculate the derivatives of the structure factors in a Hirshfeld atom refinement directly as accurately as possible, thus bypassing the approximation altogether. Comparing wR2 factors and atomic parameters, along with their uncertainties from the approximate and numerically differentiating refinements, it turns out that the impact of this approximation on the final crystallographic model is indeed negligible.
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Affiliation(s)
- Laura Midgley
- Department of Mathematical Sciences, Durham University, Upper Mountjoy Campus, Stockton Road, Durham, DH1 3LE, United Kingdom
| | - Luc J Bourhis
- Bruker, 4 Allée Lorentz, Champs-sur-Marne, 77447 Marne-la-Vallée cedex 2, France
| | - Oleg V Dolomanov
- OlexSys Ltd, Department of Chemistry, Durham University, South Road, Durham, DH1 3LE, United Kingdom
| | - Simon Grabowsky
- Departement für Chemie, Biochemie und Pharmazie, Universität Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Florian Kleemiss
- Departement für Chemie, Biochemie und Pharmazie, Universität Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Horst Puschmann
- OlexSys Ltd, Department of Chemistry, Durham University, South Road, Durham, DH1 3LE, United Kingdom
| | - Norbert Peyerimhoff
- Department of Mathematical Sciences, Durham University, Upper Mountjoy Campus, Stockton Road, Durham, DH1 3LE, United Kingdom
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15
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Pawlędzio S, Malinska M, Woińska M, Wojciechowski J, Andrade Malaspina L, Kleemiss F, Grabowsky S, Woźniak K. Relativistic Hirshfeld atom refinement of an organo-gold(I) compound. IUCRJ 2021; 8:608-620. [PMID: 34258009 PMCID: PMC8256711 DOI: 10.1107/s2052252521004541] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 04/28/2021] [Indexed: 06/13/2023]
Abstract
The main goal of this study is the validation of relativistic Hirshfeld atom refinement (HAR) as implemented in Tonto for high-resolution X-ray diffraction datasets of an organo-gold(I) compound. The influence of the relativistic effects on statistical parameters, geometries and electron density properties was analyzed and compared with the influence of electron correlation and anharmonic atomic motions. Recent work in this field has indicated the importance of relativistic effects in the static electron density distribution of organo-mercury compounds. This study confirms that differences in electron density due to relativistic effects are also of significant magnitude for organo-gold compounds. Relativistic effects dominate not only the core region of the gold atom, but also influence the electron density in the valence and bonding region, which has measurable consequences for the HAR refinement model parameters. To study the effects of anharmonic motion on the electron density distribution, dynamic electron density difference maps were constructed. Unlike relativistic and electron correlation effects, the effects of anharmonic nuclear motion are mostly observed in the core area of the gold atom.
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Affiliation(s)
- Sylwia Pawlędzio
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Żwirki i Wigury 101, Warszawa 02-089, Poland
| | - Maura Malinska
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Żwirki i Wigury 101, Warszawa 02-089, Poland
| | - Magdalena Woińska
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Żwirki i Wigury 101, Warszawa 02-089, Poland
| | | | - Lorraine Andrade Malaspina
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, Bern 3012, Switzerland
| | - Florian Kleemiss
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, Bern 3012, Switzerland
| | - Simon Grabowsky
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, Bern 3012, Switzerland
| | - Krzysztof Woźniak
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Żwirki i Wigury 101, Warszawa 02-089, Poland
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16
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Wanat M, Malinska M, Hoser AA, Woźniak K. Further Validation of Quantum Crystallography Approaches. Molecules 2021; 26:molecules26123730. [PMID: 34207308 PMCID: PMC8233966 DOI: 10.3390/molecules26123730] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 06/14/2021] [Accepted: 06/14/2021] [Indexed: 11/16/2022] Open
Abstract
Quantum crystallography is a fast-developing multidisciplinary area of crystallography. In this work, we analyse the influence of different charge density models (i.e., the multipole model (MM), Hirshfeld atom refinement (HAR), and the transferable aspherical atom model (TAAM)), modelling of the thermal motion of hydrogen atoms (anisotropic, isotropic, and with the aid of SHADE or NoMoRe), and the type of radiation used (Mo Kα and Cu Kα) on the final results. To achieve this aim, we performed a series of refinements against X-ray diffraction data for three model compounds and compared their final structures, geometries, shapes of ADPs, and charge density distributions. Our results were also supported by theoretical calculations that enabled comparisons of the lattice energies of these structures. It appears that geometrical parameters are better described (closer to the neutron values) when HAR is used; however, bonds to H atoms more closely match neutron values after MM or TAAM refinement. Our analysis shows the superiority of the NoMoRe method in the description of H-atom ADPs. Moreover, the shapes of the ADPs of H atoms, as well as their electron density distributions, were better described with low-resolution Cu Kα data in comparison to low-resolution Mo Kα data.
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Affiliation(s)
- Monika Wanat
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, 101 Żwirki i Wigury, 02-089 Warszawa, Poland; (M.W.); (M.M.); (A.A.H.)
- College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences (MISMaP), University of Warsaw, 2C Stefana Banacha, 02-097 Warszawa, Poland
| | - Maura Malinska
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, 101 Żwirki i Wigury, 02-089 Warszawa, Poland; (M.W.); (M.M.); (A.A.H.)
| | - Anna A. Hoser
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, 101 Żwirki i Wigury, 02-089 Warszawa, Poland; (M.W.); (M.M.); (A.A.H.)
| | - Krzysztof Woźniak
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, 101 Żwirki i Wigury, 02-089 Warszawa, Poland; (M.W.); (M.M.); (A.A.H.)
- Correspondence:
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17
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Malaspina LA, Genoni A, Grabowsky S. lamaGOET: an interface for quantum crystallography. J Appl Crystallogr 2021; 54:987-995. [PMID: 34188618 PMCID: PMC8202027 DOI: 10.1107/s1600576721002545] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 03/08/2021] [Indexed: 11/24/2022] Open
Abstract
In quantum crystallography, theoretical calculations and crystallographic refinements are closely intertwined. This means that the employed software must be able to perform both quantum-mechanical calculations and crystallographic least-squares refinements. So far, the program Tonto is the only one able to do that. The lamaGOET interface described herein deals with this issue since it interfaces dedicated quantum-chemical software (the widely used Gaussian package and the specialized ELMOdb program) with the refinement capabilities of Tonto. Three different flavours of quantum-crystallographic refinements of the dipetide glycyl-l-threonine dihydrate are presented to showcase the capabilities of lamaGOET: Hirshfeld atom refinement (HAR), HAR-ELMO, namely HAR coupled with extremely localized molecular orbitals, and X-ray constrained wavefunction fitting.
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Affiliation(s)
- Lorraine A. Malaspina
- Universität Bern, Departement für Chemie, Biochemie und Pharmazie, Freiestrasse 3, 3012 Bern, Switzerland
- Universität Bremen, Fachbereich 2 – Biologie/Chemie, Institut für Anorganische Chemie und Kristallographie, Leobener Strasse 3, 28359 Bremen, Germany
| | - Alessandro Genoni
- Université de Lorraine and CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT), UMR CNRS 7019, 1 Boulevard Arago, 57078 Metz, France
| | - Simon Grabowsky
- Universität Bern, Departement für Chemie, Biochemie und Pharmazie, Freiestrasse 3, 3012 Bern, Switzerland
- Universität Bremen, Fachbereich 2 – Biologie/Chemie, Institut für Anorganische Chemie und Kristallographie, Leobener Strasse 3, 28359 Bremen, Germany
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18
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Malaspina LA, Genoni A, Jayatilaka D, Turner MJ, Sugimoto K, Nishibori E, Grabowsky S. The advanced treatment of hydrogen bonding in quantum crystallography. J Appl Crystallogr 2021; 54:718-729. [PMID: 34188611 PMCID: PMC8202034 DOI: 10.1107/s1600576721001126] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 01/31/2021] [Indexed: 11/16/2022] Open
Abstract
Although hydrogen bonding is one of the most important motifs in chemistry and biology, H-atom parameters are especially problematic to refine against X-ray diffraction data. New developments in quantum crystallography offer a remedy. This article reports how hydrogen bonds are treated in three different quantum-crystallographic methods: Hirshfeld atom refinement (HAR), HAR coupled to extremely localized molecular orbitals and X-ray wavefunction refinement. Three different compound classes that form strong intra- or intermolecular hydrogen bonds are used as test cases: hydrogen maleates, the tripeptide l-alanyl-glycyl-l-alanine co-crystallized with water, and xylitol. The differences in the quantum-mechanical electron densities underlying all the used methods are analysed, as well as how these differences impact on the refinement results.
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Affiliation(s)
- Lorraine A. Malaspina
- Universität Bern, Departement für Chemie, Biochemie und Pharmazie, Freiestrasse 3, 3012 Bern, Switzerland
- Universität Bremen, Fachbereich 2 – Biologie/Chemie, Institut für Anorganische Chemie und Kristallographie, Leobener Strasse 3, 28359 Bremen, Germany
| | - Alessandro Genoni
- Université de Lorraine and CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT), UMR CNRS 7019, 1 Boulevard Arago, 57078 Metz, France
| | - Dylan Jayatilaka
- The University of Western Australia, School of Molecular Sciences, 35 Stirling Highway, Perth, WA 6009, Australia
| | - Michael J. Turner
- The University of Western Australia, School of Molecular Sciences, 35 Stirling Highway, Perth, WA 6009, Australia
| | - Kunihisa Sugimoto
- Japan Synchrotron Radiation Research Institute/Diffraction and Scattering Division, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
- Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Yoshida-Ushinomiya-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Eiji Nishibori
- Department of Physics, Faculty of Pure and Applied Sciences, Tsukuba Research Center for Energy Materials Science (TREMS), University of Tsukuba, Tsukuba, Japan
| | - Simon Grabowsky
- Universität Bern, Departement für Chemie, Biochemie und Pharmazie, Freiestrasse 3, 3012 Bern, Switzerland
- Universität Bremen, Fachbereich 2 – Biologie/Chemie, Institut für Anorganische Chemie und Kristallographie, Leobener Strasse 3, 28359 Bremen, Germany
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19
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Peng D, Nakashima PNH. Measuring Density Functional Parameters from Electron Diffraction Patterns. PHYSICAL REVIEW LETTERS 2021; 126:176402. [PMID: 33988394 DOI: 10.1103/physrevlett.126.176402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Revised: 01/13/2021] [Accepted: 03/15/2021] [Indexed: 06/12/2023]
Abstract
We integrate density functional theory (DFT) into quantitative convergent-beam electron diffraction (QCBED) to create a synergy between experiment and theory called QCBED-DFT. This synergy resides entirely in the electron density which, in real materials, gives rise to the experimental CBED patterns used by QCBED-DFT to refine DFT model parameters. We use it to measure the Hubbard energy U for two strongly correlated electron systems, NiO and CeB_{6} (U=7.4±0.6 eV for d orbitals in NiO and U=3.0±0.6 eV for f orbitals in CeB_{6}), and the boron position parameter x for CeB_{6} (x=0.1992±0.0003). In verifying our measurements, we demonstrate an accuracy test for any modeled electron density.
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Affiliation(s)
- Ding Peng
- Department of Materials Science and Engineering, Monash University, Victoria 3800, Australia
| | - Philip N H Nakashima
- Department of Materials Science and Engineering, Monash University, Victoria 3800, Australia
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20
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Kleemiss F, Wieduwilt EK, Hupf E, Shi MW, Stewart SG, Jayatilaka D, Turner MJ, Sugimoto K, Nishibori E, Schirmeister T, Schmidt TC, Engels B, Grabowsky S. Similarities and Differences between Crystal and Enzyme Environmental Effects on the Electron Density of Drug Molecules. Chemistry 2021; 27:3407-3419. [PMID: 33090581 PMCID: PMC7898524 DOI: 10.1002/chem.202003978] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Indexed: 01/28/2023]
Abstract
The crystal interaction density is generally assumed to be a suitable measure of the polarization of a low-molecular weight ligand inside an enzyme, but this approximation has seldomly been tested and has never been quantified before. In this study, we compare the crystal interaction density and the interaction electrostatic potential for a model compound of loxistatin acid (E64c) with those inside cathepsin B, in solution, and in vacuum. We apply QM/MM calculations and experimental quantum crystallography to show that the crystal interaction density is indeed very similar to the enzyme interaction density. Less than 0.1 e are shifted between these two environments in total. However, this difference has non-negligible consequences for derived properties.
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Affiliation(s)
- Florian Kleemiss
- Department 2 – Biology/Chemistry, Institute of Inorganic Chemistry and CrystallographyUniversity of BremenLeobener Str. 3 and 7, 28359 BremenGermany
- Department of Chemistry and BiochemistryUniversity of BernFreiestrasse 3, 3012 BernSwitzerland
| | - Erna K. Wieduwilt
- Department 2 – Biology/Chemistry, Institute of Inorganic Chemistry and CrystallographyUniversity of BremenLeobener Str. 3 and 7, 28359 BremenGermany
- Laboratoire de Physique et Chimie Théoriques (LPCT), UMR CNRS 7019Université de Lorraine & CNRSBoulevard Arago, 57078 MetzFrance
| | - Emanuel Hupf
- Department 2 – Biology/Chemistry, Institute of Inorganic Chemistry and CrystallographyUniversity of BremenLeobener Str. 3 and 7, 28359 BremenGermany
| | - Ming W. Shi
- School of Molecular SciencesUniversity of Western Australia35 Stirling Highway, Perth WA 6009Australia
| | - Scott G. Stewart
- School of Molecular SciencesUniversity of Western Australia35 Stirling Highway, Perth WA 6009Australia
| | - Dylan Jayatilaka
- School of Molecular SciencesUniversity of Western Australia35 Stirling Highway, Perth WA 6009Australia
| | - Michael J. Turner
- School of Molecular SciencesUniversity of Western Australia35 Stirling Highway, Perth WA 6009Australia
| | - Kunihisa Sugimoto
- Japan Synchrotron Radiation Research InstituteSPring-81-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198Japan
- Institute for Integrated Cell-Materials SciencesKyoto UniversityYoshida-Ushinomiya-cho, Sakyo-ku, Kyoto 606-8501Japan
| | - Eiji Nishibori
- Division of Physics, Faculty of Pure and Applied Sciences, Tsukuba Research Center for Energy Materials ScienceUniversity of TsukubaTsukubaJapan
| | - Tanja Schirmeister
- Institute of Pharmaceutical and Biomedical SciencesJohannes-Gutenberg University MainzStaudingerweg 5, 55128 MainzGermany
| | - Thomas C. Schmidt
- Institute for Physical and Theoretical ChemistryJulius-Maximilians-University WürzburgEmil-Fischer-Str. 42, 97074 WürzburgGermany
| | - Bernd Engels
- Institute for Physical and Theoretical ChemistryJulius-Maximilians-University WürzburgEmil-Fischer-Str. 42, 97074 WürzburgGermany
| | - Simon Grabowsky
- Department 2 – Biology/Chemistry, Institute of Inorganic Chemistry and CrystallographyUniversity of BremenLeobener Str. 3 and 7, 28359 BremenGermany
- Department of Chemistry and BiochemistryUniversity of BernFreiestrasse 3, 3012 BernSwitzerland
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21
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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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22
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Affiliation(s)
- Piero Macchi
- Department, Chemistry, Materials and Chemical Engineering, Politecnico di Milano, Milano, Italy
- Center for Nano Science and Technology CNST@polimi, Italian Institute of Technology, Milano, Italy
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23
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Kleemiss F, Dolomanov OV, Bodensteiner M, Peyerimhoff N, Midgley L, Bourhis LJ, Genoni A, Malaspina LA, Jayatilaka D, Spencer JL, White F, Grundkötter-Stock B, Steinhauer S, Lentz D, Puschmann H, Grabowsky S. Accurate crystal structures and chemical properties from NoSpherA2. Chem Sci 2020; 12:1675-1692. [PMID: 34163928 PMCID: PMC8179328 DOI: 10.1039/d0sc05526c] [Citation(s) in RCA: 114] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The relationship between the structure and the properties of a drug or material is a key concept of chemistry. Knowledge of the three-dimensional structure is considered to be of such importance that almost every report of a new chemical compound is accompanied by an X-ray crystal structure – at least since the 1970s when diffraction equipment became widely available. Crystallographic software of that time was restricted to very limited computing power, and therefore drastic simplifications had to be made. It is these simplifications that make the determination of the correct structure, especially when it comes to hydrogen atoms, virtually impossible. We have devised a robust and fast system where modern chemical structure models replace the old assumptions, leading to correct structures from the model refinement against standard in-house diffraction data using no more than widely available software and desktop computing power. We call this system NoSpherA2 (Non-Spherical Atoms in Olex2). We explain the theoretical background of this technique and demonstrate the far-reaching effects that the improved structure quality that is now routinely available can have on the interpretation of chemical problems exemplified by five selected examples. NoSpherA2 brings quantum crystallography to routine structure determination and to the analysis of chemical properties for any class of materials.![]()
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Affiliation(s)
- Florian Kleemiss
- Universität Bern, Departement für Chemie und Biochemie Freiestrasse 3 3012 Bern Switzerland
| | | | - Michael Bodensteiner
- Universität Regensburg, Fakultät für Chemie und Pharmazie, Universitätsstr. 31 93053 Regensburg Germany
| | - Norbert Peyerimhoff
- Durham University, Department of Mathematical Sciences South Road Durham DH1 3LE UK
| | - Laura Midgley
- Durham University, Department of Mathematical Sciences South Road Durham DH1 3LE UK
| | - Luc J Bourhis
- Bruker France 4 Allée Lorentz, Champs-sur-Marne 77447 Marne-la-Vallée cedex 2 France
| | - Alessandro Genoni
- Université de Lorraine & CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT), UMR CNRS 7019 1 Boulevard Arago 57078 Metz France
| | - Lorraine A Malaspina
- Universität Bern, Departement für Chemie und Biochemie Freiestrasse 3 3012 Bern Switzerland
| | - Dylan Jayatilaka
- University of Western Australia, School of Molecular Sciences 35 Stirling Highway WA 6009 Perth Australia
| | - John L Spencer
- Victoria University of Wellington, School of Chemical and Physical Sciences Wellington 6012 New Zealand
| | - Fraser White
- Rigaku Europe SE Hugenottenallee 167 63263 Neu-Isenburg Germany
| | - Bernhard Grundkötter-Stock
- Freie Universität Berlin, Institut für Chemie und Biochemie Anorganische Chemie, Fabeckstr. 34/36 14195 Berlin Germany
| | - Simon Steinhauer
- Freie Universität Berlin, Institut für Chemie und Biochemie Anorganische Chemie, Fabeckstr. 34/36 14195 Berlin Germany
| | - Dieter Lentz
- Freie Universität Berlin, Institut für Chemie und Biochemie Anorganische Chemie, Fabeckstr. 34/36 14195 Berlin Germany
| | | | - Simon Grabowsky
- Universität Bern, Departement für Chemie und Biochemie Freiestrasse 3 3012 Bern Switzerland
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24
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Chodkiewicz ML, Woińska M, Woźniak K. Hirshfeld atom like refinement with alternative electron density partitions. IUCRJ 2020; 7:1199-1215. [PMID: 33209330 PMCID: PMC7642787 DOI: 10.1107/s2052252520013603] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 10/12/2020] [Indexed: 05/03/2023]
Abstract
Hirshfeld atom refinement is one of the most successful methods for the accurate determination of structural parameters for hydrogen atoms from X-ray diffraction data. This work introduces a generalization of the method [generalized atom refinement (GAR)], consisting of the application of various methods of partitioning electron density into atomic contributions. These were tested on three organic structures using the following partitions: Hirshfeld, iterative Hirshfeld, iterative stockholder, minimal basis iterative stockholder and Becke. The effects of partition choice were also compared with those caused by other factors such as quantum chemical methodology, basis set, representation of the crystal field and a combination of these factors. The differences between the partitions were small in terms of R factor (e.g. much smaller than for refinements with different quantum chemistry methods, i.e. Hartree-Fock and coupled cluster) and therefore no single partition was clearly the best in terms of experimental data reconstruction. In the case of structural parameters the differences between the partitions are comparable to those related to the choice of other factors. We have observed the systematic effects of the partition choice on bond lengths and ADP values of polar hydrogen atoms. The bond lengths were also systematically influenced by the choice of electron density calculation methodology. This suggests that GAR-derived structural parameters could be systematically improved by selecting an optimal combination of the partition and quantum chemistry method. The results of the refinements were compared with those of neutron diffraction experiments. This allowed a selection of the most promising partition methods for further optimization of GAR settings, namely the Hirshfeld, iterative stockholder and minimal basis iterative stockholder.
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Affiliation(s)
- Michał Leszek Chodkiewicz
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Żwirki i Wigury 101, Warszawa, 02-089 Warszawa, Poland
| | - Magdalena Woińska
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Żwirki i Wigury 101, Warszawa, 02-089 Warszawa, Poland
| | - Krzysztof Woźniak
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Żwirki i Wigury 101, Warszawa, 02-089 Warszawa, Poland
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25
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Kleemiss F, Justies A, Duvinage D, Watermann P, Ehrke E, Sugimoto K, Fugel M, Malaspina LA, Dittmer A, Kleemiss T, Puylaert P, King NR, Staubitz A, Tzschentke TM, Dringen R, Grabowsky S, Beckmann J. Sila-Ibuprofen. J Med Chem 2020; 63:12614-12622. [PMID: 32931274 DOI: 10.1021/acs.jmedchem.0c00813] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The synthesis, characterization, biological activity, and toxicology of sila-ibuprofen, a silicon derivative of the most common nonsteroidal anti-inflammatory drug, is reported. The key improvements compared with ibuprofen are a four times higher solubility in physiological media and a lower melting enthalpy, which are attributed to the carbon-silicon switch. The improved solubility is of interest for postsurgical intravenous administration. A potential for pain relief is rationalized via inhibition experiments of cyclooxygenases I and II (COX-I and COX-II) as well as via a set of newly developed methods that combine molecular dynamics, quantum chemistry, and quantum crystallography. The binding affinity of sila-ibuprofen to COX-I and COX-II is quantified in terms of London dispersion and electrostatic interactions in the active receptor site. This study not only shows the potential of sila-ibuprofen for medicinal application but also improves our understanding of the mechanism of action of the inhibition process.
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Affiliation(s)
- Florian Kleemiss
- University of Bremen, Institute for Inorganic Chemistry and Crystallography, Leobener Str. 3 and 7, 28359 Bremen, Germany.,University of Bern, Department of Chemistry and Biochemistry, Freiestrasse 3, 3012 Bern, Switzerland
| | - Aileen Justies
- Free University of Berlin, Institute of Chemistry and Biochemistry, Fabeckstr. 34-36, 14195 Berlin, Germany
| | - Daniel Duvinage
- University of Bremen, Institute for Inorganic Chemistry and Crystallography, Leobener Str. 3 and 7, 28359 Bremen, Germany
| | - Patrick Watermann
- University of Bremen, Center for Biomolecular Interactions Bremen and Center for Environmental Research and Sustainable Technology, Leobener Str. 5, 28359 Bremen, Germany
| | - Eric Ehrke
- University of Bremen, Center for Biomolecular Interactions Bremen and Center for Environmental Research and Sustainable Technology, Leobener Str. 5, 28359 Bremen, Germany
| | - Kunihisa Sugimoto
- Japan Synchrotron Radiation Research Institute (JASRI), Diffraction & Scattering Division, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan.,Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Yoshida-Ushinomiya-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Malte Fugel
- University of Bremen, Institute for Inorganic Chemistry and Crystallography, Leobener Str. 3 and 7, 28359 Bremen, Germany
| | - Lorraine A Malaspina
- University of Bremen, Institute for Inorganic Chemistry and Crystallography, Leobener Str. 3 and 7, 28359 Bremen, Germany.,University of Bern, Department of Chemistry and Biochemistry, Freiestrasse 3, 3012 Bern, Switzerland
| | - Anneke Dittmer
- University of Bremen, Institute for Inorganic Chemistry and Crystallography, Leobener Str. 3 and 7, 28359 Bremen, Germany
| | - Torsten Kleemiss
- University of Bremen, Institute for Inorganic Chemistry and Crystallography, Leobener Str. 3 and 7, 28359 Bremen, Germany
| | - Pim Puylaert
- University of Bremen, Institute for Inorganic Chemistry and Crystallography, Leobener Str. 3 and 7, 28359 Bremen, Germany
| | - Nelly R King
- Free University of Berlin, Institute of Chemistry and Biochemistry, Fabeckstr. 34-36, 14195 Berlin, Germany
| | - Anne Staubitz
- University of Bremen, Institute for Analytical and Organic Chemistry, Leobener Str. 7, 28359 Bremen, Germany
| | | | - Ralf Dringen
- University of Bremen, Center for Biomolecular Interactions Bremen and Center for Environmental Research and Sustainable Technology, Leobener Str. 5, 28359 Bremen, Germany
| | - Simon Grabowsky
- University of Bremen, Institute for Inorganic Chemistry and Crystallography, Leobener Str. 3 and 7, 28359 Bremen, Germany.,University of Bern, Department of Chemistry and Biochemistry, Freiestrasse 3, 3012 Bern, Switzerland
| | - Jens Beckmann
- University of Bremen, Institute for Inorganic Chemistry and Crystallography, Leobener Str. 3 and 7, 28359 Bremen, Germany.,Free University of Berlin, Institute of Chemistry and Biochemistry, Fabeckstr. 34-36, 14195 Berlin, Germany
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26
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Van der Maelen JF, Ceroni M, Ruiz J. The X-ray constrained wavefunction of the [Mn(CO) 4{(C 6H 5) 2P-S-C(Br 2)-P(C 6H 5) 2}]Br complex: a theoretical and experimental study of dihalogen bonds and other noncovalent interactions. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2020; 76:802-814. [PMID: 33017314 DOI: 10.1107/s2052520620009889] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 07/19/2020] [Indexed: 06/11/2023]
Abstract
The synthesis and X-ray structure determination of the [Mn(CO)4{(C6H5)2P-S-C(Br2)-P(C6H5)2}]Br complex (1) are described. The C-Br...Br dihalogen bond present in 1 has been characterized by means of topological studies of the electron density. Both the quantum theory of atoms in molecules and the electron localization function approaches have been applied to several theoretically calculated wavefunctions as well as to an X-ray constrained wavefunction. In addition, a number of theoretical techniques, such as the source function, the reduced density gradient method and the interacting quantum atoms approach, among others, have been used to analyse the dihalogen bond as well as several intramolecular interactions of the type C-H...Br-C which have also been detected in 1. The results show clearly that while bonding in the latter interactions are dominated by electrostatic components, the former has a high degree of covalency.
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Affiliation(s)
- Juan F Van der Maelen
- Dept. Química Física y Analítica, Universidad de Oviedo, Avda. Julián Clavería 8, Oviedo, Asturias E-33006, Spain
| | - Mario Ceroni
- Facultad de Química e Ingeniería Química, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Javier Ruiz
- Dept. Química Orgánica e Inorgánica, Universidad de Oviedo, Avda. Julián Clavería 8, Oviedo, Asturias E-33006, Spain
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27
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Abstract
In this review article, we report on the recent progresses in the field of quantum crystallography that has witnessed a massive increase of production coupled with a broadening of the scope in the last decade. It is shown that the early thoughts about extracting quantum mechanical information from crystallographic experiments are becoming reality, although a century after prediction. While in the past the focus was mainly on electron density and related quantities, the attention is now shifting toward determination of wavefunction from experiments, which enables an exhaustive determination of the quantum mechanical functions and properties of a system. Nonetheless, methods based on electron density modelling have evolved and are nowadays able to reconstruct tiny polarizations of core electrons, coupling charge and spin models, or determining the quantum behaviour at extreme conditions. Far from being routine, these experimental and computational results should be regarded with special attention by scientists for the wealth of information on a system that they actually contain.
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28
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Post-Hartree-Fock methods for Hirshfeld atom refinement: are they necessary? Investigation of a strongly hydrogen-bonded molecular crystal. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.127934] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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29
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Gruza B, Chodkiewicz ML, Krzeszczakowska J, Dominiak PM. Refinement of organic crystal structures with multipolar electron scattering factors. Acta Crystallogr A Found Adv 2020; 76:92-109. [PMID: 31908353 PMCID: PMC8127334 DOI: 10.1107/s2053273319015304] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 11/13/2019] [Indexed: 12/14/2022] Open
Abstract
A revolution in resolution is occurring now in electron microscopy arising from the development of methods for imaging single particles at cryogenic temperatures and obtaining electron diffraction data from nanocrystals of small organic molecules or macromolecules. Near-atomic or even atomic resolution of molecular structures can be achieved. The basis of these methods is the scattering of an electron beam due to the electrostatic potential of the sample. To analyse these high-quality experimental data, it is necessary to use appropriate atomic scattering factors. The independent atom model (IAM) is commonly used although various more advanced models, already known from X-ray diffraction, can also be applied to enhance the analysis. In this study a comparison is presented of IAM and TAAM (transferable aspherical atom model), the latter with the parameters of the Hansen-Coppens multipole model transferred from the University at Buffalo Databank (UBDB). By this method, TAAM takes into account the fact that atoms in molecules are partially charged and are not spherical. Structure refinements were performed on a carbamazepine crystal using electron structure-factor amplitudes determined experimentally [Jones et al. (2018). ACS Cent. Sci. 4, 1587-1592] or modelled with theoretical quantum-mechanical methods. The results show the possibilities and limitations of the TAAM method when applied to electron diffraction. Among others, the method clearly improves model fitting statistics, when compared with IAM, and allows for reliable refinement of atomic thermal parameters. The improvements are more pronounced with poorer-resolution diffraction data.
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Affiliation(s)
- Barbara Gruza
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, ul. Żwirki i Wigury 101, Warsaw, 02-089, Poland
| | - Michał Leszek Chodkiewicz
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, ul. Żwirki i Wigury 101, Warsaw, 02-089, Poland
| | - Joanna Krzeszczakowska
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, ul. Żwirki i Wigury 101, Warsaw, 02-089, Poland
| | - Paulina Maria Dominiak
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, ul. Żwirki i Wigury 101, Warsaw, 02-089, Poland
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Grabowsky S, Genoni A, Thomas SP, Jayatilaka D. The Advent of Quantum Crystallography: Form and Structure Factors from Quantum Mechanics for Advanced Structure Refinement and Wavefunction Fitting. 21ST CENTURY CHALLENGES IN CHEMICAL CRYSTALLOGRAPHY II 2020. [DOI: 10.1007/430_2020_62] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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31
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Woinska M, Wanat M, Taciak P, Pawinski T, Minor W, Wozniak K. Energetics of interactions in the solid state of 2-hydroxy-8- X-quinoline derivatives ( X = Cl, Br, I, S-Ph): comparison of Hirshfeld atom, X-ray wavefunction and multipole refinements. IUCRJ 2019; 6:868-883. [PMID: 31576220 PMCID: PMC6760436 DOI: 10.1107/s2052252519007358] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 05/20/2019] [Indexed: 05/20/2023]
Abstract
In this work, two methods of high-resolution X-ray data refinement: multipole refinement (MM) and Hirshfeld atom refinement (HAR) - together with X-ray wavefunction refinement (XWR) - are applied to investigate the refinement of positions and anisotropic thermal motion of hydrogen atoms, experiment-based reconstruction of electron density, refinement of anharmonic thermal vibrations, as well as the effects of excluding the weakest reflections in the refinement. The study is based on X-ray data sets of varying quality collected for the crystals of four quinoline derivatives with Cl, Br, I atoms and the -S-Ph group as substituents. Energetic investigations are performed, comprising the calculation of the energy of intermolecular interactions, cohesive and geometrical relaxation energy. The results obtained for experimentally derived structures are verified against the values calculated for structures optimized using dispersion-corrected periodic density functional theory. For the high-quality data sets (the Cl and -S-Ph compounds), both MM and XWR could be successfully used to refine the atomic displacement parameters and the positions of hydrogen atoms; however, the bond lengths obtained with XWR were more precise and closer to the theoretical values. In the application to the more challenging data sets (the Br and I compounds), only XWR enabled free refinement of hydrogen atom geometrical parameters, nevertheless, the results clearly showed poor data quality. For both refinement methods, the energy values (intermolecular interactions, cohesive and relaxation) calculated for the experimental structures were in similar agreement with the values associated with the optimized structures - the most significant divergences were observed when experimental geometries were biased by poor data quality. XWR was found to be more robust in avoiding incorrect distortions of the reconstructed electron density as a result of data quality issues. Based on the problem of anharmonic thermal motion refinement, this study reveals that for the most correct interpretation of the obtained results, it is necessary to use the complete data set, including the weak reflections in order to draw conclusions.
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Affiliation(s)
- Magdalena Woinska
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Zwirki i Wigury 101, Warszawa 02-089, Poland
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
| | - Monika Wanat
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Zwirki i Wigury 101, Warszawa 02-089, Poland
- College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences (MISMaP), University of Warsaw, Stefana Banacha 2C, Warszawa 02-097, Poland
| | - Przemyslaw Taciak
- Department of Drug Chemistry, Faculty of Pharmacy, Medicinal University of Warsaw, Stefana Banacha 1, Warszawa 02-091, Poland
- Department of Pharmacodynamics, Centre of Preclinical Research and Technology, Faculty of Pharmacy, Medical University of Warsaw, Stefana Banacha 1, Warszawa 02-091, Poland
| | - Tomasz Pawinski
- Department of Drug Chemistry, Faculty of Pharmacy, Medicinal University of Warsaw, Stefana Banacha 1, Warszawa 02-091, Poland
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
- Department of Chemistry, University of Warsaw, Pasteura 1, Warszawa 02-093, Poland
| | - Krzysztof Wozniak
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Zwirki i Wigury 101, Warszawa 02-089, Poland
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32
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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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33
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Cachau RE, Zhu J, Nicklaus MC. The upcoming subatomic resolution revolution. Curr Opin Struct Biol 2019; 58:53-58. [PMID: 31233975 DOI: 10.1016/j.sbi.2019.05.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 05/12/2019] [Accepted: 05/13/2019] [Indexed: 10/26/2022]
Abstract
Subatomic resolution macromolecular crystallography has been revealing the most fascinating details of macromolecular structures for many years. This most extreme form of macromolecular crystallography is going through rapid changes. A new generation of superbrilliant X-ray sources and detectors is facilitating the rapid acquisition of high-quality datasets. Equally important, a new breed of methods and highly integrated advanced computational tools for structure refinement and analysis is poised to change the way we use subatomic resolution data and reposition high-resolution macromolecular crystallography in medicinal chemistry studies. Subatomic resolution macromolecular crystallography may soon be a routine source of detailed molecular information besides precise geometries, including binding energies and other chemical descriptors, opening new possibilities of application.
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Affiliation(s)
- Raul E Cachau
- Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Leidos Biomedical Inc., Frederick, MD 21702, USA.
| | - Jianghai Zhu
- Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Leidos Biomedical Inc., Frederick, MD 21702, USA
| | - Marc C Nicklaus
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD 21702, USA
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Yanai H, Suzuki T, Kleemiss F, Fukaya H, Dobashi Y, Malaspina LA, Grabowsky S, Matsumoto T. Chemical Bonding in Polarised Push–Pull Ethylenes. Angew Chem Int Ed Engl 2019; 58:8839-8844. [DOI: 10.1002/anie.201904176] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Indexed: 01/06/2023]
Affiliation(s)
- Hikaru Yanai
- School of PharmacyTokyo University of Pharmacy and Life Sciences 1432-1 Horinouchi Hachioji Tokyo 192-0392 Japan
| | - Takumi Suzuki
- School of PharmacyTokyo University of Pharmacy and Life Sciences 1432-1 Horinouchi Hachioji Tokyo 192-0392 Japan
| | - Florian Kleemiss
- Institut für Anorganische Chemie und KristallographieFachbereich 2-Biologie/ChemieUniversität Bremen Leobener Str. 3 28359 Bremen Germany
| | - Haruhiko Fukaya
- School of PharmacyTokyo University of Pharmacy and Life Sciences 1432-1 Horinouchi Hachioji Tokyo 192-0392 Japan
| | - Yasuo Dobashi
- School of PharmacyTokyo University of Pharmacy and Life Sciences 1432-1 Horinouchi Hachioji Tokyo 192-0392 Japan
| | - Lorraine A. Malaspina
- Institut für Anorganische Chemie und KristallographieFachbereich 2-Biologie/ChemieUniversität Bremen Leobener Str. 3 28359 Bremen Germany
| | - Simon Grabowsky
- Institut für Anorganische Chemie und KristallographieFachbereich 2-Biologie/ChemieUniversität Bremen Leobener Str. 3 28359 Bremen Germany
| | - Takashi Matsumoto
- School of PharmacyTokyo University of Pharmacy and Life Sciences 1432-1 Horinouchi Hachioji Tokyo 192-0392 Japan
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35
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Yanai H, Suzuki T, Kleemiss F, Fukaya H, Dobashi Y, Malaspina LA, Grabowsky S, Matsumoto T. Chemical Bonding in Polarised Push–Pull Ethylenes. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201904176] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Hikaru Yanai
- School of PharmacyTokyo University of Pharmacy and Life Sciences 1432-1 Horinouchi Hachioji Tokyo 192-0392 Japan
| | - Takumi Suzuki
- School of PharmacyTokyo University of Pharmacy and Life Sciences 1432-1 Horinouchi Hachioji Tokyo 192-0392 Japan
| | - Florian Kleemiss
- Institut für Anorganische Chemie und KristallographieFachbereich 2-Biologie/ChemieUniversität Bremen Leobener Str. 3 28359 Bremen Germany
| | - Haruhiko Fukaya
- School of PharmacyTokyo University of Pharmacy and Life Sciences 1432-1 Horinouchi Hachioji Tokyo 192-0392 Japan
| | - Yasuo Dobashi
- School of PharmacyTokyo University of Pharmacy and Life Sciences 1432-1 Horinouchi Hachioji Tokyo 192-0392 Japan
| | - Lorraine A. Malaspina
- Institut für Anorganische Chemie und KristallographieFachbereich 2-Biologie/ChemieUniversität Bremen Leobener Str. 3 28359 Bremen Germany
| | - Simon Grabowsky
- Institut für Anorganische Chemie und KristallographieFachbereich 2-Biologie/ChemieUniversität Bremen Leobener Str. 3 28359 Bremen Germany
| | - Takashi Matsumoto
- School of PharmacyTokyo University of Pharmacy and Life Sciences 1432-1 Horinouchi Hachioji Tokyo 192-0392 Japan
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Fugel M, Malaspina LA, Pal R, Thomas SP, Shi MW, Spackman MA, Sugimoto K, Grabowsky S. Revisiting a Historical Concept by Using Quantum Crystallography: Are Phosphate, Sulfate and Perchlorate Anions Hypervalent? Chemistry 2019; 25:6523-6532. [PMID: 30759315 DOI: 10.1002/chem.201806247] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Indexed: 11/05/2022]
Abstract
There are many examples of atoms in molecules that violate Lewis' octet rule, because they have more than four electron pairs assigned to their valence. These atoms are referred to as hypervalent. However, hypervalency may be regarded as an artifact arising from Lewis' description of molecules, which is based on the assumption that electrons are localized in two-center two-electron bonds and lone pairs. In the present paper, the isoelectronic phosphate (PO4 3- ), sulfate (SO4 2- ) and perchlorate (ClO4 - ) anions were examined with respect to the concept of hypervalency. Lewis formulas containing a hypervalent central atom exist for all three anions. Based on X-ray wavefunction refinements of high-resolution X-ray diffraction data of representative crystal structures (MgNH4 PO4 ⋅6 H2 O, Li2 SO4 ⋅H2 O, and KClO4 ), complementary bonding analyses were performed. In this way, experimental information from the new field of quantum crystallography validate long-known facts, or refute long-standing misunderstandings. It is shown that the P-O and S-O bonds are highly polarized covalent bonds and, thus, the increase in the valence population following three-center four-electron bonding is not sufficient to yield hypervalent phosphorus or sulfur atoms, respectively. However, for the highly covalent Cl-O bond, most bonding indicators imply a hypervalent chlorine atom.
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Affiliation(s)
- Malte Fugel
- Department 2-Chemistry/Biology, Institute of Inorganic Chemistry and Crystallography, University of Bremen, Leobener Str. 3 and 7, 28359, Bremen, Germany
| | - Lorraine A Malaspina
- Department 2-Chemistry/Biology, Institute of Inorganic Chemistry and Crystallography, University of Bremen, Leobener Str. 3 and 7, 28359, Bremen, Germany
| | - Rumpa Pal
- Department 2-Chemistry/Biology, Institute of Inorganic Chemistry and Crystallography, University of Bremen, Leobener Str. 3 and 7, 28359, Bremen, Germany.,Current address: Division of Physics, Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8571, Japan
| | - Sajesh P Thomas
- School of Molecular Sciences, University of Western Australia, 35 Stirling Highway, Perth, WA, 6009, Australia.,Current address: Interdisciplinary Nanoscience Center - INANO-Kemi, Aarhus University, Langelandsgade 140, 8000, Aarhus C, Denmark
| | - Ming W Shi
- School of Molecular Sciences, University of Western Australia, 35 Stirling Highway, Perth, WA, 6009, Australia
| | - Mark A Spackman
- School of Molecular Sciences, University of Western Australia, 35 Stirling Highway, Perth, WA, 6009, Australia
| | - Kunihisa Sugimoto
- SPring-8, Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5198, Japan
| | - Simon Grabowsky
- Department 2-Chemistry/Biology, Institute of Inorganic Chemistry and Crystallography, University of Bremen, Leobener Str. 3 and 7, 28359, Bremen, Germany
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Fugel M, Ponomarenko MV, Hesse MF, Malaspina LA, Kleemiss F, Sugimoto K, Genoni A, Röschenthaler GV, Grabowsky S. Complementary bonding analysis of the N–Si interaction in pentacoordinated silicon compounds using quantum crystallography. Dalton Trans 2019; 48:16330-16339. [DOI: 10.1039/c9dt02772f] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The unique combination of quantum crystallography and complementary bonding analysis is used to investigate the bonding of pentacoordinated silicon atoms.
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Affiliation(s)
- Malte Fugel
- University of Bremen
- Department 2: Biology/Chemistry
- Institute of Inorganic Chemistry and Crystallography
- 28359 Bremen
- Germany
| | | | - Maxie F. Hesse
- University of Bremen
- Department 2: Biology/Chemistry
- Institute of Inorganic Chemistry and Crystallography
- 28359 Bremen
- Germany
| | - Lorraine A. Malaspina
- University of Bremen
- Department 2: Biology/Chemistry
- Institute of Inorganic Chemistry and Crystallography
- 28359 Bremen
- Germany
| | - Florian Kleemiss
- University of Bremen
- Department 2: Biology/Chemistry
- Institute of Inorganic Chemistry and Crystallography
- 28359 Bremen
- Germany
| | - Kunihisa Sugimoto
- JASRI/Diffraction & Scattering Division
- Hyogo 679-5198
- Japan
- Institute for Integrated Cell-Material Sciences (iCeMS)
- Kyoto University
| | | | | | - Simon Grabowsky
- University of Bremen
- Department 2: Biology/Chemistry
- Institute of Inorganic Chemistry and Crystallography
- 28359 Bremen
- Germany
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38
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Zobel D, Strumpel M. Electron density: historical remarks with a focus on the Berlin school. Z KRIST-CRYST MATER 2018. [DOI: 10.1515/zkri-2018-2062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
The history of electron density (ED) research is surveyed and its historical highlights in the 20th century are summarized. The progress, reached at the beginnig of the 21st century, is described including contributions from the Berlin school. Key experimental advances concern X-ray sources and synchrotron radiation, measuring reflection data at very low temperatures (down to ~10 K), as well as the introduction of area detectors. Methodological progress was reached by new software systems for the refinement and analysis of ED data sets. This allowed to obtain quantitative ED properties, making use of Bader’s Quantum Theory of Atoms in Molecules (QTAIM). More recently methods, which combine experimental X-ray data and quantum-chemically derived wave functions, established the rapidly developing new field of “Quantum Crystallography.”
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Affiliation(s)
- Dieter Zobel
- Institute for Chemistry and Biochemistry, Inorganic Chemistry , Freie Universität Berlin, Fabeckstrasse 36a , 14195 Berlin , Germany
| | - Marianna Strumpel
- Institute for Chemistry and Biochemistry, Inorganic Chemistry , Freie Universität Berlin, Fabeckstrasse 36a , 14195 Berlin , Germany
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Jarzembska KN, Kamiński R, Durka K, Woźniak K. Ground-State Charge-Density Distribution in a Crystal of the Luminescent ortho-Phenylenediboronic Acid Complex with 8-Hydroxyquinoline. J Phys Chem A 2018; 122:4508-4520. [PMID: 29672046 DOI: 10.1021/acs.jpca.8b00832] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
This contribution is devoted to the first electron density studies of a luminescent oxyquinolinato boron complex in the solid state. ortho-Phenylenediboronic acid mixed with 8-hydroxyquinoline in dioxane forms high-quality single crystals via slow solvent evaporation, which allows successful high resolution data collection (sin θ/λ = 1.2 Å-1) and charge density distribution modeling. Particular attention has been paid to the boron-oxygen fragment connecting the two parts of the complex, and to the solvent species exhibiting anharmonic thermal motion. The experiment and theory compared rather well in terms of atomic charges and volumes, except for the boron centers. Boron atoms, as expected, constitute the most electron-deficient species in the complex molecule, whereas the neighboring oxygen and carbon atoms are the most significantly negatively charged ones. This part of the molecule appears to be very much involved in the charge transfer occurring between the acid fragment and oxyquinoline moiety leading to the observed fluorescence, as supported by the time-dependent density functional theory (TDDFT) results and the generated transition density maps. TDDFT calculations indicated that p-type atomic orbitals contributing to the HOMO-1, HOMO, and LUMO play the major role in the lowest energy transitions, and enabled further comparison with the charge density features, which is discussed in details. Furthermore, the results confirmed the known fact the Q ligand character is most important for the spectroscopic properties of this class of complexes.
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Affiliation(s)
- Katarzyna N Jarzembska
- Department of Chemistry , University of Warsaw , Żwirki i Wigury 101 , 02-089 Warsaw , Poland
| | - Radosław Kamiński
- Department of Chemistry , University of Warsaw , Żwirki i Wigury 101 , 02-089 Warsaw , Poland
| | - Krzysztof Durka
- Department of Chemistry , Warsaw University of Technology , Noakowskiego 3 , 00-664 Warsaw , Poland
| | - Krzysztof Woźniak
- Biological and Chemical Research Centre, Department of Chemistry , University of Warsaw , Żwirki i Wigury 101 , 02-089 Warsaw , Poland
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Fugel M, Kleemiss F, Malaspina LA, Pal R, Spackman PR, Jayatilaka D, Grabowsky S. Investigating the Resonance in Nitric Acid and the Nitrate Anion Based on a Modern Bonding Analysis. Aust J Chem 2018. [DOI: 10.1071/ch17583] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The nitrate anion, NO3−, is often regarded as a textbook example for the very fundamental concept of resonance. Usually, three equivalent resonance structures with one N–O double bond and two N–O single bonds are considered. Consequently, each of the three N–O bonds should have a partial double bond character. In this study, we analyse the resonance in NO3− in comparison with the related species HNO3 and FNO3 by applying a combination of the Quantum Theory of Atoms in Molecules (QTAIM), a natural bond orbital (NBO) analysis, the electron localizability indicator (ELI), and valence bond (VB) calculations. Despite the fundamental importance of nitrate salts and nitric acid for the environment, chemistry, and industry, a bonding analysis is absent from the literature so far. The classical resonance structures are clearly reflected by the bond analysis tools, but are not the only contributions to the bonding situation. The resonance in HNO3 and FNO3 is greatly perturbed by the hydrogen and fluorine atoms. In addition to theoretical calculations, experimental electron density and wave function refinements were carried out on a KNO3 crystal.
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