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Fisher S, Malaspina LA, Gozálvez Martínez C, Prescimone A, Balmohammadi Y, Grabowsky S, Šolomek T. Leveraging Halogen Interactions for a Supramolecular Nanotube. Chemistry 2024; 30:e202400295. [PMID: 38462477 DOI: 10.1002/chem.202400295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 03/07/2024] [Accepted: 03/07/2024] [Indexed: 03/12/2024]
Abstract
We demonstrate the formation of supramolecular nanotubes from molecular triangles in a single crystal by balancing the hydrogen bonds and halogen interactions between individual macrocycles. Thereby, we template the supramolecular nanotube growth by intermolecular interactions encoded directly in the macrocycles instead of those provided by the crystallization solvent. Ultimately, we show that replacing bromines for iodines in the macrocycle is necessary to achieve this supramolecular organization by enhancing the strength of the halogen interactions and concomitant reduction of the detrimental hydrogen bonds. We investigated the nature and the interplay of the individual intermolecular interactions by analysis of the experimental single crystal data and quantum chemical calculations. This work enriches the available toolbox of supramolecular interactions and will aid and abet the development of rationally-designed materials with a long-range 1D tubular organization.
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Affiliation(s)
- Sergey Fisher
- Van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, NL-1098, XH Amsterdam, The Netherlands
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, CH-3012, Bern, Switzerland
| | - Lorraine A Malaspina
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, CH-3012, Bern, Switzerland
| | | | - Alessandro Prescimone
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, CH-4056, Basel, Switzerland
| | - Yaser Balmohammadi
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, CH-3012, Bern, Switzerland
| | - Simon Grabowsky
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, CH-3012, Bern, Switzerland
| | - Tomáš Šolomek
- Van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, NL-1098, XH Amsterdam, The Netherlands
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, CH-3012, Bern, Switzerland
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2
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Nikulshin PV, Makarov AY, Koskin IP, Becker CS, Kazantsev MS, Beckmann J, Balmohammadi Y, Grabowsky S, Mebs S, Naumova OV, Protasov DY, Svit KA, Irtegova IG, Radiush EA, Bagryanskaya IY, Shundrin LA, Zibarev AV. 1,2,3,4-Tetrafluorobiphenylene: A Prototype Janus-Headed Scaffold for Ambipolar Materials. Chempluschem 2024; 89:e202300692. [PMID: 38052725 DOI: 10.1002/cplu.202300692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 12/01/2023] [Accepted: 12/05/2023] [Indexed: 12/07/2023]
Abstract
The title compound was synthesized by Ullmann cross-coupling in low yield as the first representative of [n]phenylene containing hydrocarbon and fluorocarbon rings. Stille/Suzuki-Miyaura cross-coupling reactions, as well as substitution of fluorine in suitable starting compounds, failed to give the same product. The geometric and electronic structures of the title compound were studied by X-ray diffraction, cyclic voltammetry and density functional theory calculations, together with Hirshfeld surface and reduced density gradient analyses. The crystal structure features head-to-tail π-stacking and other fluorine-related secondary bonding interactions. From the nucleus-independent chemical shifts descriptor, the four-membered ring of the title compound is antiaromatic, and the six-membered rings are aromatic. The Janus molecule is highly polarized; and the six-membered fluoro- and hydrocarbon rings are Lewis π-acidic and π-basic, respectively. The electrochemically-generated radical cation of the title compound is long-lived as characterized by electron paramagnetic resonance, whereas the radical anion is unstable in solution. The title compound reveals electrical properties of an insulator. On expanding its molecular scaffold towards partially fluorinated [n]phenylenes (n≥2), the properties presumably can be transformed into those of semiconductors. In this context, the title compound is suggested as a prototype scaffold for ambipolar materials for organic electronics and spintronics.
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Affiliation(s)
- Pavel V Nikulshin
- Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 630090, Novosibirsk, Russia
- Current address: Topchiev Institute of Petrochemical Synthesis, Russian Academy of Sciences, 119991, Moscow, Russia
| | - Alexander Yu Makarov
- Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 630090, Novosibirsk, Russia
| | - Igor P Koskin
- Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 630090, Novosibirsk, Russia
| | - Christina S Becker
- Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 630090, Novosibirsk, Russia
| | - Maxim S Kazantsev
- Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 630090, Novosibirsk, Russia
| | - Jens Beckmann
- Institute for Inorganic Chemistry and Crystallography, University of Bremen, 28359, Bremen, Germany
| | - Yaser Balmohammadi
- Department of Chemistry, Biochemistry and Pharmaceutical Science, University of Bern, 3012, Bern, Switzerland
| | - Simon Grabowsky
- Department of Chemistry, Biochemistry and Pharmaceutical Science, University of Bern, 3012, Bern, Switzerland
| | - Stefan Mebs
- Institute for Experimental Physics, Free University of Berlin, 14195, Berlin, Germany
| | - Olga V Naumova
- Rzhanov Institute of Semiconductor Physics, Siberian Branch of the Russian Academy of Sciences, 630090, Novosibirsk, Russia
| | - Dmitry Yu Protasov
- Rzhanov Institute of Semiconductor Physics, Siberian Branch of the Russian Academy of Sciences, 630090, Novosibirsk, Russia
| | - Kirill A Svit
- Rzhanov Institute of Semiconductor Physics, Siberian Branch of the Russian Academy of Sciences, 630090, Novosibirsk, Russia
| | - Irina G Irtegova
- Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 630090, Novosibirsk, Russia
| | - Ekaterina A Radiush
- Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 630090, Novosibirsk, Russia
| | - Irina Yu Bagryanskaya
- Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 630090, Novosibirsk, Russia
| | - Leonid A Shundrin
- Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 630090, Novosibirsk, Russia
| | - Andrey V Zibarev
- Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 630090, Novosibirsk, Russia
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3
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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4
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McMonagle CJ, Fuller CA, Hupf E, Malaspina LA, Grabowsky S, Chernyshov D. Lattice response to the radiation damage of molecular crystals: radiation-induced versus thermal expansivity. Acta Crystallogr B Struct Sci Cryst Eng Mater 2024; 80:13-18. [PMID: 38174727 PMCID: PMC10848411 DOI: 10.1107/s2052520623010636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 12/12/2023] [Indexed: 01/05/2024]
Abstract
The interaction of intense synchrotron radiation with molecular crystals frequently modifies the crystal structure by breaking bonds, producing fragments and, hence, inducing disorder. Here, a second-rank tensor of radiation-induced lattice strain is proposed to characterize the structural susceptibility to radiation. Quantitative estimates are derived using a linear response approximation from experimental data collected on three materials Hg(NO3)2(PPh3)2, Hg(CN)2(PPh3)2 and BiPh3 [PPh3 = triphenylphosphine, P(C6H5)3; Ph = phenyl, C6H5], and are compared with the corresponding thermal expansivities. The associated eigenvalues and eigenvectors show that the two tensors are not the same and therefore probe truly different structural responses. The tensor of radiative expansion serves as a measure of the susceptibility of crystal structures to radiation damage.
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Affiliation(s)
| | | | - Emanuel Hupf
- University of Bremen, Department 2 – Biology/Chemistry, Leobener Str. 7, 29359 Bremen, Germany
| | - Lorraine A. Malaspina
- University of Bern, Department of Chemistry, Biochemistry and Pharmaceutical Sciences, Freiestrasse 3, 3012 Bern, Switzerland
| | - Simon Grabowsky
- University of Bern, Department of Chemistry, Biochemistry and Pharmaceutical Sciences, Freiestrasse 3, 3012 Bern, Switzerland
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5
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Stroek W, Keilwerth M, Malaspina LA, Grabowsky S, Meyer K, Albrecht M. Deciphering Iron-Catalyzed C-H Amination with Organic Azides: N 2 Cleavage from a Stable Organoazide Complex. Chemistry 2024; 30:e202303410. [PMID: 37916523 DOI: 10.1002/chem.202303410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 11/01/2023] [Accepted: 11/02/2023] [Indexed: 11/03/2023]
Abstract
Catalytic C-N bond formation by direct activation of C-H bonds offers wide synthetic potential. En route to C-H amination, complexes with organic azides are critical precursors towards the reactive nitrene intermediate. Despite their relevance, α-N coordinated organoazide complexes are scarce in general, and elusive with iron, although iron complexes are by far the most active catalysts for C-H amination with organoazides. Herein, we report the synthesis of a stable iron α-N coordinated organoazide complex from [Fe(N(SiMe3 )2 )2 ] and AdN3 (Ad=1-adamantyl) and its crystallographic, IR, NMR and zero-field 57 Fe Mössbauer spectroscopic characterization. These analyses revealed that the organoazide is in fast equilibrium between the free and coordinated state (Keq =62). Photo-crystallography experiments showed gradual dissociation of N2 , which imparted an Fe-N bond shortening and correspond to structural snapshots of the formation of an iron imido/nitrene complex. Reactivity of the organoazide complex in solution showed complete loss of N2 , and subsequent formation of a C-H aminated product via nitrene insertion into a C-H bond of the N(SiMe3 )2 ligand. Monitoring this reaction by 1 H NMR spectroscopy indicates the transient formation of the imido/nitrene intermediate, which was supported by Mössbauer spectroscopy in frozen solution.
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Affiliation(s)
- Wowa Stroek
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012, Bern, Switzerland
| | - Martin Keilwerth
- Department of Chemistry and Pharmacy, Inorganic Chemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Egerlandstraße 1, 91058, Erlangen, Germany
| | - Lorraine A Malaspina
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012, Bern, Switzerland
| | - Simon Grabowsky
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012, Bern, Switzerland
| | - Karsten Meyer
- Department of Chemistry and Pharmacy, Inorganic Chemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Egerlandstraße 1, 91058, Erlangen, Germany
| | - Martin Albrecht
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012, Bern, Switzerland
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6
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Feige F, Malaspina LA, Kleemiss F, Kögel JF, Ketkov S, Hupf E, Grabowsky S, Beckmann J. An investigation into the Brønsted acidity of the perfluorinated alkoxy silanes {(F 3C) 3CO} 3SiH and {(F 6C 5) 3CO} 2Si(Cl)H. Dalton Trans 2023; 52:5918-5925. [PMID: 37067202 DOI: 10.1039/d3dt00299c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
The perfluorinated alkoxy silanes {(F3C)3CO}3SiH (1) and {(F5C6)3CO}2Si(Cl)H (2) were prepared and fully characterized. Despite the high calculated Brønsted acidities, all attempts to deprotonate 1 and 2 to give the conjugate silanide ions failed due to the exceptionally short and strong Si-H bonds. In the solid state, the Si-H units are not involved in any intermolecular interactions, but instead the crystal packing consists of exceptionally short and strong F⋯F interactions. The cohesive energies are entirely comprised of London dispersion interactions, similarly as in the crystal structures of noble gases.
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Affiliation(s)
- Felix Feige
- Institut für Anorganische Chemie und Kristallographie, Universität Bremen, Leobener Straße 7, 28359 Bremen, Germany.
| | - Lorraine A Malaspina
- 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.
- Fakultät für Chemie und Pharmazie, Universität Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany
| | - Julius F Kögel
- Institut für Anorganische Chemie und Kristallographie, Universität Bremen, Leobener Straße 7, 28359 Bremen, Germany.
| | - Sergey Ketkov
- G. A. Razuvaev Institute of Organometallic Chemistry RAS, 49 Tropinin St., 603950 Nizhny Novgorod, Russian Federation.
| | - Emanuel Hupf
- Institut für Anorganische Chemie und Kristallographie, Universität Bremen, Leobener Straße 7, 28359 Bremen, Germany.
| | - Simon Grabowsky
- Departement für Chemie, Biochemie und Pharmazie, Universität Bern, Freiestrasse 3, 3012 Bern, Switzerland.
| | - Jens Beckmann
- Institut für Anorganische Chemie und Kristallographie, Universität Bremen, Leobener Straße 7, 28359 Bremen, Germany.
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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: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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Hupf E, Kleemiss F, Borrmann T, Pal R, Krzeszczakowska JM, Woinska M, Jayatilaka D, Genoni A, Grabowsky S. The Effects of Experimentally Obtained Electron Correlation and Polarization on Electron Densities and Exchange-Correlation Potentials . J Chem Phys 2023; 158:124103. [PMID: 37003723 DOI: 10.1063/5.0138312] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023] Open
Abstract
In X-ray constrained wavefunction (XCW) fitting, external information such as electron correlation and polarization are included into a single-determinantal isolated-molecule wavefunction. In a first step, we show that the extraction of these two physical effects by XCW fitting is complete and accurate by comparing to theoretical reference calculations. In a second step, we show that fitting to data from single-crystal X-ray diffraction measurements provides the same results qualitatively and how the physical effects can be separated, although always inherently convolved in the experiment. We further demonstrate that exchange-correlation potentials are systematically affected by XCW fitting in a physically meaningful way which could be exploited for method development in quantum chemistry, subject to some remaining challenges that we also outline.
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Affiliation(s)
| | | | | | | | | | | | - Dylan Jayatilaka
- School of Chemistry and Biochemistry, University of Western Australia, Nedlands 6009. Australia, Australia
| | - Alessandro Genoni
- Laboratory of Theoretical Physics and Chemistry, Université de Lorraine - Campus du Technopôle, France
| | - Simon Grabowsky
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Switzerland
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Borys AM, Malaspina LA, Grabowsky S, Hevia E. Towards Hexagonal Planar Nickel: A Dispersion-Stabilised Tri-Lithium Nickelate. Angew Chem Int Ed Engl 2022; 61:e202209797. [PMID: 35921213 PMCID: PMC9804205 DOI: 10.1002/anie.202209797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Indexed: 01/05/2023]
Abstract
Advancing the understanding of lithum nickelate complexes, here we report a family of homoleptic organonickelate complexes obtained by reacting Ni(COD)2 and lithium aryl-acetylides in the presence of the bidentate donor TMEDA. These compounds represent rare examples of low-valent transition-metals supported solely by organolithium ligands. Whilst the solid-state structures indicate a hexagonal planar geometry around Ni0 with Ni-Li bonds, bonding analysis via QTAIM, NCI, NBO and ELI methods reveals that the Ni-Li interactions are repulsive in nature, characterising these complexes as tri-coordinated. London dispersion forces between TMEDA and the organic substituents on nickel are found to play a crucial role in the stabilisation and thus isolation of these complexes. Preliminary reactivity studies demonstrate that the homoleptic lithium nickelates undergo stoichiometric cross-coupling with PhI to give dinickel clusters containing both anionic acetylide and neutral alkyne ligands.
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Affiliation(s)
- Andryj M. Borys
- Departement für Chemie, Biochemie und PharmazieUniversität BernFreiestrasse 33012BernSwitzerland
| | - Lorraine A. Malaspina
- Departement für Chemie, Biochemie und PharmazieUniversität BernFreiestrasse 33012BernSwitzerland
| | - Simon Grabowsky
- Departement für Chemie, Biochemie und PharmazieUniversität BernFreiestrasse 33012BernSwitzerland
| | - Eva Hevia
- Departement für Chemie, Biochemie und PharmazieUniversität BernFreiestrasse 33012BernSwitzerland
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10
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McMonagle C, Grabowsky S, Malaspina L, Balmohammadi Y, Chernyshov D. Tensor of radiation expansivity – a proposed measure of structural susceptibility to radiation damage. Acta Cryst Sect A 2022. [DOI: 10.1107/s2053273322089823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2023]
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11
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Pawlędzio S, Malinska M, Kleemiss F, Grabowsky S, Woźniak K. Influence of modelling of disorder on results of Hirshfeld atom refinement of an organo-gold(I) compound. Acta Cryst Sect A 2022. [DOI: 10.1107/s2053273322091793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2023]
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12
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Bucinsky L, Grabowsky S. Theoretical considerations of radiation damage effects in mercury-containing compounds. Acta Cryst Sect A 2022. [DOI: 10.1107/s2053273322091835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2023]
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13
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Malaspina L, Grabowsky S. Quantum crystallography of titanium amides with agostic interactions. Acta Cryst Sect A 2022. [DOI: 10.1107/s2053273322094979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2023]
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14
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Duvinage D, Malaspina L, Grabowsky S, Mebs S, Beckmann J. Lewis Superacidic Divalent Bis(m‐terphenyl)element Cations [(2,6‐Mes2C6H3)2E]+ of Group 13 Revisited and Extended (E = B, Al, Ga, In, Tl)r. Eur J Inorg Chem 2022. [DOI: 10.1002/ejic.202200482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
| | | | | | - Stefan Mebs
- Universitatsbibliothek der Freien Universitat Berlin: Freie Universitat Berlin Universitatsbibliothek Physik GERMANY
| | - Jens Beckmann
- Universität Bremen Institut fuer Biologie und Chemie Leobener Str. 28359 Bremen GERMANY
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15
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Borys AM, Malaspina LA, Grabowsky S, Hevia E. Towards Hexagonal Planar Nickel: A Dispersion‐Stabilised Tri‐Lithium Nickelate. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202209797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Andryj M. Borys
- University of Bern: Universitat Bern Departement für Chemie, Biochemie und Pharmazie SWITZERLAND
| | - Lorraine A. Malaspina
- University of Bern: Universitat Bern Departement für Chemie, Biochemie und Pharmazie SWITZERLAND
| | - Simon Grabowsky
- University of Bern: Universitat Bern DDepartement für Chemie, Biochemie und Pharmazie SWITZERLAND
| | - Eva Hevia
- Universitat Bern Department of Chemistry and Biochemistry Freiestrasse 3 3012 Bern SWITZERLAND
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16
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Pawlędzio S, Malinska M, Kleemiss F, Grabowsky S, Woźniak K. Influence of modelling disorder on Hirshfeld atom refinement results of an organo-gold(I) compound. IUCrJ 2022; 9:497-507. [PMID: 35844484 PMCID: PMC9252150 DOI: 10.1107/s2052252522005309] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 05/19/2022] [Indexed: 06/15/2023]
Abstract
Details of the validation of disorder modelling with Hirshfeld atom refinement (HAR) for a previously investigated organo-gold(I) compound are presented here. The impact of refining disorder on HAR results is discussed using an analysis of the differences of dynamic structure factors. These dynamic structure factor differences are calculated from thermally smeared quantum mechanical electron densities based on wavefunctions that include or exclude electron correlation and relativistic effects. When disorder is modelled, the electron densities stem from a weighted superposition of two (or more) different conformers. Here this is shown to impact the relative importance of electron correlation and relativistic effect estimates expressed by the structure factor magnitudes. The role of disorder modelling is also compared with the effect of the treatment of hydrogen anisotropic displacement parameter (ADP) values and atomic anharmonicity of the gold atom. The analysis of ADP values of gold and disordered carbon atoms showed that the effect of disorder significantly altered carbon ADP values and did not influence those 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, Warsaw 02-089, Poland
| | - Maura Malinska
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Żwirki i Wigury 101, Warsaw 02-089, Poland
| | - Florian Kleemiss
- Faculty for Chemistry und Pharmacy, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany
| | - Simon Grabowsky
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Krzysztof Woźniak
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Żwirki i Wigury 101, Warsaw 02-089, Poland
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17
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Duvinage D, Puylaert P, Wieduwilt EK, Malaspina LA, Edwards AJ, Lork E, Mebs S, Hupf E, Grabowsky S, Beckmann J. Nickel and Palladium Complexes of a PP(O)P Pincer Ligand Based upon a peri-Substituted Acenaphthyl Scaffold and a Secondary Phosphine Oxide. Inorg Chem 2022; 61:8406-8418. [PMID: 35609007 DOI: 10.1021/acs.inorgchem.1c03266] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A PP(O)P pincer ligand based upon a peri-substituted acenaphthyl (Ace) scaffold and a secondary phosphine oxide, (5-Ph2P-Ace-6-)2P(O)H, was prepared and fully characterized including a neutron diffraction study. The reaction with [Ni(H2O)6]Cl2 and PdCl2 produced ionic metal(II) complexes [κ3-P,P',P''((5-Ph2P-Ace-6-)2P(OH))MCl]Cl, which upon addition of Et3N gave rise to zwitterionic metal(II) complexes κ3-P,P',P''((5-Ph2P-Ace-6-)2P(O))MCl (M = Ni, Pd). The reaction with Ni(COD)2 (COD = cyclooctadiene) provided the η3-cyclooctenyl Ni(II) complex κ3-P,P',P''((5-Ph2P-Ace-6-)2P(O))Ni(η3-C8H13). A detailed complementary bonding analysis of the P-H, P-O, and P-M interactions was carried out (M = Ni, Pd).
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Affiliation(s)
- Daniel Duvinage
- Institut für Anorganische Chemie und Kristallographie, Universität Bremen, Leobener Straße 3 & 7, 28359 Bremen, Germany
| | - Pim Puylaert
- Institut für Anorganische Chemie und Kristallographie, Universität Bremen, Leobener Straße 3 & 7, 28359 Bremen, Germany
| | - Erna K Wieduwilt
- Institut für Anorganische Chemie und Kristallographie, Universität Bremen, Leobener Straße 3 & 7, 28359 Bremen, Germany.,CNRS, Laboratoire de Physique et Chimie Theoriques (LPCT), Université de Lorraine, 1 Boulevard Arago, 57078 Metz, France
| | - Lorraine A Malaspina
- Institut für Anorganische Chemie und Kristallographie, Universität Bremen, Leobener Straße 3 & 7, 28359 Bremen, Germany.,Departement für Chemie, Biochemie und Pharmazie, Universität Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Alison J Edwards
- Australian Nuclear Science and Technology Organisation, Australian Centre for Neutron Scattering, New Illawarra Road, Lucas Heights, Sydney 2234, Australia
| | - Enno Lork
- Institut für Anorganische Chemie und Kristallographie, Universität Bremen, Leobener Straße 3 & 7, 28359 Bremen, Germany
| | - Stefan Mebs
- Institut für Experimentalphysik, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Emanuel Hupf
- Institut für Anorganische Chemie und Kristallographie, Universität Bremen, Leobener Straße 3 & 7, 28359 Bremen, Germany
| | - Simon Grabowsky
- Institut für Anorganische Chemie und Kristallographie, Universität Bremen, Leobener Straße 3 & 7, 28359 Bremen, Germany.,Departement für Chemie, Biochemie und Pharmazie, Universität Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Jens Beckmann
- Institut für Anorganische Chemie und Kristallographie, Universität Bremen, Leobener Straße 3 & 7, 28359 Bremen, Germany
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18
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Davidson ML, Grabowsky S, Jayatilaka D. X-ray constrained wavefunctions based on Hirshfeld atoms. II. Reproducibility of electron densities in crystals of α-oxalic acid dihydrate. Acta Crystallogr B Struct Sci Cryst Eng Mater 2022; 78:397-415. [PMID: 35695114 DOI: 10.1107/s2052520622004103] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 04/18/2022] [Indexed: 06/15/2023]
Abstract
The Hirshfeld atom-based X-ray constrained wavefunction fitting (HA-XCW) procedure is tested for its reproducibility, and the information content of the fitted wavefunction is critically assessed. Fourteen different α-oxalic acid dihydrate data sets are used for this purpose, and the first joint fitting to 12 of these data sets is reported. There are systematic features in the electron density obtained from all data sets which agree with higher level benchmark calculations, but there are also many other strong systematic features which disagree with the reference calculations, most notably those associated with the electron density near the nuclei. To enhance reproducibility, three new protocols are described and tested to address the halting problem of XCW fitting, namely: an empirical power-function method, which is useful for estimating the accuracy of the structure factor uncertainties; an asymptotic extrapolation method based on ideas from density functional theory; and a `conservative method' whereby the smallest value of the regularization parameter is chosen from a series of data sets, or subsets.
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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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19
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Grabowsky S, Spackman MA. Structure correlation and dynamics in crystals - a tribute to Hans-Beat Bürgi. Acta Crystallogr B Struct Sci Cryst Eng Mater 2022; 78:281-282. [PMID: 35695098 DOI: 10.1107/s2052520622005248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Affiliation(s)
- Simon Grabowsky
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, Bern, CH-3012 Switzerland
| | - Mark A Spackman
- School of Molecular Sciences, University of Western Australia, 35 Stirling Highway, Perth, WA 6009, Australia
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20
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Davidson ML, Grabowsky S, Jayatilaka D. X-ray constrained wavefunctions based on Hirshfeld atoms. I. Method and review. Acta Crystallogr B Struct Sci Cryst Eng Mater 2022; 78:312-332. [PMID: 35695105 DOI: 10.1107/s2052520622004097] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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21
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Somerville RJ, Borys AM, Perez-Jimenez M, Nova A, Balcells D, Malaspina LA, Grabowsky S, Carmona E, Hevia E, Campos J. Unmasking the constitution and bonding of the proposed lithium nickelate "Li 3NiPh 3(solv) 3": revealing the hidden C 6H 4 ligand. Chem Sci 2022; 13:5268-5276. [PMID: 35655554 PMCID: PMC9093164 DOI: 10.1039/d2sc01244h] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 04/08/2022] [Indexed: 11/21/2022] Open
Abstract
More than four decades ago, a complex identified as the planar homoleptic lithium nickelate “Li3NiPh3(solv)3” was reported by Taube and co-workers. This and subsequent reports involving this complex have lain dormant since; however, the absence of an X-ray diffraction structure leaves questions as to the nature of the Ni–PhLi bonding and the coordination geometry at Ni. By systematically evaluating the reactivity of Ni(COD)2 with PhLi under different conditions, we have found that this classical molecule is instead a unique octanuclear complex, [{Li3(solv)2Ph3Ni}2(μ-η2:η2-C6H4)] (5). This is supported by X-ray crystallography and solution-state NMR studies. A theoretical bonding analysis from NBO, QTAIM, and ELI perspectives reveals extreme back-bonding to the bridging C6H4 ligand resulting in dimetallabicyclobutane character, the lack of a Ni–Ni bond, and pronounced σ-bonding between the phenyl carbanions and nickel, including a weak σC–Li → sNi interaction with the C–Li bond acting as a σ-donor. Employing PhNa led to the isolation of [Na2(solv)3Ph2NiCOD]2 (7) and [Na2(solv)3Ph2(NaC8H11)Ni(COD)]2 (8), which lack the benzyne-derived ligand. These findings provide new insights into the synthesis, structure, bonding and reactivity of heterobimetallic nickelates, whose prevalence in organonickel chemistry and catalysis is likely greater than previously believed. We disclose the actual octanuclear nature of the major compound from reacting Ni(COD)2 and PhLi, assigned for more than four decades as ‘Li3NiPh3(solv)3’. We provide a thorough bonding analysis and discuss its potential implications in catalysis.![]()
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Affiliation(s)
- Rosie J Somerville
- Instituto de Investigaciones Químicas (IIQ), Departamento de Química Inorgánica, Centro de Innovación en Química Avanzada (ORFEO-CINQA), Consejo Superior de Investigaciones Científicas (CSIC), University of Sevilla Avenida Américo Vespucio 49 41092 Sevilla Spain
| | - Andryj M Borys
- Departement für Chemie, Biochemie und Pharmazie, Universität Bern Freiestrasse 3 3012 Bern Switzerland
| | - Marina Perez-Jimenez
- Instituto de Investigaciones Químicas (IIQ), Departamento de Química Inorgánica, Centro de Innovación en Química Avanzada (ORFEO-CINQA), Consejo Superior de Investigaciones Científicas (CSIC), University of Sevilla Avenida Américo Vespucio 49 41092 Sevilla Spain
| | - Ainara Nova
- Hylleraas Centre for Quantum Molecular Sciences, Centre for Materials Science and Nanotechnology, Department of Chemistry, University of Oslo P.O. Box 1033, Blindern 0315 Oslo Norway
| | - David Balcells
- Hylleraas Centre for Quantum Molecular Sciences, Centre for Materials Science and Nanotechnology, Department of Chemistry, University of Oslo P.O. Box 1033, Blindern 0315 Oslo Norway
| | - Lorraine A Malaspina
- Departement für Chemie, Biochemie und Pharmazie, Universität Bern Freiestrasse 3 3012 Bern Switzerland
| | - Simon Grabowsky
- Departement für Chemie, Biochemie und Pharmazie, Universität Bern Freiestrasse 3 3012 Bern Switzerland
| | - Ernesto Carmona
- Instituto de Investigaciones Químicas (IIQ), Departamento de Química Inorgánica, Centro de Innovación en Química Avanzada (ORFEO-CINQA), Consejo Superior de Investigaciones Científicas (CSIC), University of Sevilla Avenida Américo Vespucio 49 41092 Sevilla Spain
| | - Eva Hevia
- Departement für Chemie, Biochemie und Pharmazie, Universität Bern Freiestrasse 3 3012 Bern Switzerland
| | - Jesús Campos
- Instituto de Investigaciones Químicas (IIQ), Departamento de Química Inorgánica, Centro de Innovación en Química Avanzada (ORFEO-CINQA), Consejo Superior de Investigaciones Científicas (CSIC), University of Sevilla Avenida Américo Vespucio 49 41092 Sevilla Spain
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22
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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 Crystallogr B Struct Sci Cryst Eng Mater 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] [What about the content of this article? (0)] [Affiliation(s)] [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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23
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Appiarius Y, Gliese PJ, Segler SAW, Rusch P, Zhang J, Gates PJ, Pal R, Malaspina LA, Sugimoto K, Neudecker T, Bigall NC, Grabowsky S, Bakulin AA, Staubitz A. BN-Substitution in Dithienylpyrenes Prevents Excimer Formation in Solution and in the Solid State. J Phys Chem C Nanomater Interfaces 2022; 126:4563-4576. [PMID: 35299818 PMCID: PMC8919264 DOI: 10.1021/acs.jpcc.1c08812] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 12/20/2021] [Indexed: 06/14/2023]
Abstract
Boron-nitrogen substitutions in polycyclic aromatic hydrocarbons (PAHs) have a strong impact on the optical properties of the molecules due to a significantly more heterogeneous electron distribution. However, besides these single-molecule properties, the observed optical properties of PAHs critically depend on the degree of intermolecular interactions such as π-π-stacking, dipolar interactions, or the formation of dimers in the excited state. Pyrene is the most prominent example showing the latter as it exhibits a broadened and strongly bathochromically shifted emission band at high concentrations in solution compared to the respective monomers. In the solid state, the impact of intermolecular interactions is even higher as it determines the crystal packing crucially. In this work, a thiophene-flanked BN-pyrene (BNP) was synthesized and compared with its all-carbon analogue (CCP) in solution and in the solid state by means of crystallography, NMR spectroscopy, UV-vis spectroscopy, and photoluminescence (PL) spectroscopy. In solution, PL spectroscopy revealed the solvent-dependent presence of excimers of CCP at high concentrations. In contrast, no excimers were found in BNP. Clear differences were also observed in the single-crystal packing motifs. While CCP revealed overlapped pyrene planes with centroid distances in the range of classical π-stacking interactions, the BNP scaffolds were displaced and significantly more spatially separated.
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Affiliation(s)
- Yannik Appiarius
- Institute
for Analytical and Organic Chemistry, University
of Bremen, Leobener Straße 7, D-28359 Bremen, Germany
- MAPEX
Center for Materials and Processes, University
of Bremen, Bibliothekstraße
1, D-28359 Bremen, Germany
| | - Philipp J. Gliese
- Institute
for Analytical and Organic Chemistry, University
of Bremen, Leobener Straße 7, D-28359 Bremen, Germany
- MAPEX
Center for Materials and Processes, University
of Bremen, Bibliothekstraße
1, D-28359 Bremen, Germany
| | - Stephan A. W. Segler
- Institute
for Analytical and Organic Chemistry, University
of Bremen, Leobener Straße 7, D-28359 Bremen, Germany
- MAPEX
Center for Materials and Processes, University
of Bremen, Bibliothekstraße
1, D-28359 Bremen, Germany
| | - Pascal Rusch
- Institute
of Physical Chemistry and Electrochemistry, Leibniz University Hannover, Callinstraße 3a, D-30167 Hannover, Germany
- Cluster
of Excellence PhoenixD (Photonics, Optics, and Engineering—Innovation
Across Disciplines), Leibniz University
Hannover, D-30167 Hannover, Germany
| | - Jiangbin Zhang
- Cavendish
Laboratory, University of Cambridge, 19 J J Thomson Avenue, CB3 0HE Cambridge, U.K.
- College of
Advanced Interdisciplinary Studies, National
University of Defense Technology, 410073 Changsha, Hunan, China
| | - Paul J. Gates
- School
of Chemistry, University of Bristol, Cantock’s Close, BS8 1TS Bristol, U.K.
| | - Rumpa Pal
- Institute
of Inorganic Chemistry and Crystallography, University of Bremen, Leobener Straße 7, D-28359 Bremen, Germany
| | - Lorraine A. Malaspina
- Institute
of Inorganic Chemistry and Crystallography, University of Bremen, Leobener Straße 7, D-28359 Bremen, Germany
- Department
of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Kunihisa Sugimoto
- Japan Synchrotron
Radiation Research Institute (JASRI), 1-1-1, Kouto, Sayo-cho, Hyogo 679-5198, Japan
| | - Tim Neudecker
- MAPEX
Center for Materials and Processes, University
of Bremen, Bibliothekstraße
1, D-28359 Bremen, Germany
- Institute for Physical and Theoretical
Chemistry, University of Bremen, Leobener Straße 7, D-28359 Bremen, Germany
- Bremen Center for Computational Materials
Science, University of Bremen, Am Fallturm 1, D-28359 Bremen, Germany
| | - Nadja C. Bigall
- Institute
of Physical Chemistry and Electrochemistry, Leibniz University Hannover, Callinstraße 3a, D-30167 Hannover, Germany
- Cluster
of Excellence PhoenixD (Photonics, Optics, and Engineering—Innovation
Across Disciplines), Leibniz University
Hannover, D-30167 Hannover, Germany
| | - Simon Grabowsky
- Institute
of Inorganic Chemistry and Crystallography, University of Bremen, Leobener Straße 7, D-28359 Bremen, Germany
- Department
of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Artem A. Bakulin
- Cavendish
Laboratory, University of Cambridge, 19 J J Thomson Avenue, CB3 0HE Cambridge, U.K.
- Department of Chemistry, Imperial College
London, Imperial College Rd, SW7 2AZ London, U.K.
| | - Anne Staubitz
- Institute
for Analytical and Organic Chemistry, University
of Bremen, Leobener Straße 7, D-28359 Bremen, Germany
- MAPEX
Center for Materials and Processes, University
of Bremen, Bibliothekstraße
1, D-28359 Bremen, Germany
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24
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Abstract
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This is the first
use of a wave-function-based crystallographic
method to characterize aurophilic interactions from X-ray diffraction
data. Theoretical calculations previously suggested the importance
of electron correlation and dispersion forces, but no influence of
relativistic corrections to the Au...Au interaction energy was found.
In this study, we confirm the importance of relativistic corrections
in the characterization of aurophilic interactions in addition to
electron correlation and dispersion. Hirshfeld
atom refinement was used to characterize aurophilic
interactions from X-ray diffraction data. An intermediate closed-shell
type of aurophilic interaction with some features of covalency was
identified when both electron correlation and relativistic corrections
were applied. Relativistic correction changes the electron density
distribution more than electron correlation. Relativistic effects
strongly dominate the metal core region also in the direction of the
noncovalent interactions and all of the valence and bonding regions
with regard to the Au···Au interaction.
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Affiliation(s)
- Sylwia Pawlȩdzio
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Żwirki i Wigury 101, 02-089 Warszawa, Poland
| | - Maura Malinska
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Żwirki i Wigury 101, 02-089 Warszawa, Poland
| | - Florian Kleemiss
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland.,Faculty for Chemistry und Pharmacy, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany
| | - Simon Grabowsky
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Krzysztof Woźniak
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Żwirki i Wigury 101, 02-089 Warszawa, Poland
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25
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Chulanova E, Radiush EA, Balmohammadi Y, Beckmann J, Grabowsky S, Zibarev AV. New charge-transfer complexes of 1,2,5-chalcogenadiazoles with tetrathiafulvalenes. CrystEngComm 2022. [DOI: 10.1039/d2ce01385a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Five new charge-transfer (CT) complexes of structurally varied 1,2,5-chalcogenadiazoles (monocyclic, 6-5 bicyclic and 6-6-5 tricyclic; chalcogen = S, Se and Te) with tetrathiafulvalenes (TTF and its bis(ethylenedithio) derivative BEDT-TTF) were...
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26
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Feige F, Malaspina LA, Rychagova E, Ketkov S, Grabowsky S, Hupf E, Beckmann J. Perfluorinated Trialkoxysilanol with Dramatically Increased Brønsted Acidity. Chemistry 2021; 27:15898-15902. [PMID: 34550614 PMCID: PMC9292728 DOI: 10.1002/chem.202103177] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Indexed: 11/17/2022]
Abstract
The Brønsted acidity of the perfluorinated trialkoxysilanol {(F3C)3CO}3SiOH is more than 13 orders of magnitude higher than that of orthosilicic acid, Si(OH)4, and even more for most previously known silanols. It is easily deprotonated by simple amines and pyridines to give the conjugate silanolates [OSi{OC(CF3)3}3]−, which possess extremely short Si−O bonds, comparable to those of silanones.
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Affiliation(s)
- Felix Feige
- Institut für Anorganische Chemie und Kristallographie, Universität Bremen, Leobener Straße 7, 28359, Bremen, Germany
| | - Lorraine A Malaspina
- Departement für Chemie, Biochemie und Pharmazie, Universität Bern, Freiestrasse 3, 3012, Bern, Schweiz
| | - Elena Rychagova
- G. A. Razuvaev Institute of Organometallic Chemistry RAS, 49 Tropinin St., 603950, Nizhny Novgorod, Russian Federation
| | - Sergey Ketkov
- G. A. Razuvaev Institute of Organometallic Chemistry RAS, 49 Tropinin St., 603950, Nizhny Novgorod, Russian Federation
| | - Simon Grabowsky
- Departement für Chemie, Biochemie und Pharmazie, Universität Bern, Freiestrasse 3, 3012, Bern, Schweiz
| | - Emanuel Hupf
- Institut für Anorganische Chemie und Kristallographie, Universität Bremen, Leobener Straße 7, 28359, Bremen, Germany
| | - Jens Beckmann
- Institut für Anorganische Chemie und Kristallographie, Universität Bremen, Leobener Straße 7, 28359, Bremen, Germany
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Feige F, Malaspina LA, Rychagova E, Ketkov S, Grabowsky S, Hupf E, Beckmann J. Cover Feature: Perfluorinated Trialkoxysilanol with Dramatically Increased Brønsted Acidity (Chem. Eur. J. 64/2021). Chemistry 2021. [DOI: 10.1002/chem.202103753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Felix Feige
- Institut für Anorganische Chemie und Kristallographie Universität Bremen Leobener Straße 7 28359 Bremen Germany
| | - Lorraine A. Malaspina
- Departement für Chemie Biochemie und Pharmazie Universität Bern Freiestrasse 3 3012 Bern Schweiz
| | - Elena Rychagova
- G. A. Razuvaev Institute of Organometallic Chemistry RAS 49 Tropinin St. 603950 Nizhny Novgorod Russian Federation
| | - Sergey Ketkov
- G. A. Razuvaev Institute of Organometallic Chemistry RAS 49 Tropinin St. 603950 Nizhny Novgorod Russian Federation
| | - Simon Grabowsky
- Departement für Chemie Biochemie und Pharmazie Universität Bern Freiestrasse 3 3012 Bern Schweiz
| | - Emanuel Hupf
- Institut für Anorganische Chemie und Kristallographie Universität Bremen Leobener Straße 7 28359 Bremen Germany
| | - Jens Beckmann
- Institut für Anorganische Chemie und Kristallographie Universität Bremen Leobener Straße 7 28359 Bremen Germany
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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 Crystallogr A Found Adv 2021; 77:519-533. [PMID: 34726630 DOI: 10.1107/s2053273321009086] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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Kleemiss F, Grabowsky S, Dolomanov OV, Puschmann H, Bodensteiner M. The benefit and challenges of non-spherical refinements – NoSpherA2. Acta Crystallogr A Found Adv 2021. [DOI: 10.1107/s0108767321087936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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30
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Malaspina LA, Grabowsky S. Quantum crystallography of systems with agostic interactions. Acta Crystallogr A Found Adv 2021. [DOI: 10.1107/s0108767321093405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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31
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Pawlędzio S, Malinska M, Kleemiss F, Grabowsky S, Woźniak K. Relativistic Hirshfeld atom refinement of organo-gold(I) and organo-mercury(II) compounds. Acta Crystallogr A Found Adv 2021. [DOI: 10.1107/s0108767321096082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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32
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Grabowsky S. Synchrotron experiments revealing the similarities and differences between crystal and enzyme environmental effects on the electron densities of protease inhibitors and ibuprofen derivatives. Acta Crystallogr A Found Adv 2021. [DOI: 10.1107/s0108767321091352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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33
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Holsten S, Malaspina LA, Kleemiss F, Mebs S, Hupf E, Grabowsky S, Beckmann J. Different Reactivities of (5-Ph2P-Ace-6-)2MeSiH toward the Rhodium(I) Chlorides [(C2H4)2RhCl]2 and [(CO)2RhCl]2. Hirshfeld Atom Refinement of a Rh–H···Si Interaction. Organometallics 2021. [DOI: 10.1021/acs.organomet.0c00804] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Sebastian Holsten
- Institut für Anorganische Chemie und Kristallographie, Universität Bremen, Leobener Straße 7, 28359 Bremen, Germany
| | - Lorraine A. Malaspina
- 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
| | - Stefan Mebs
- Institut für Experimentalphysik, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Emanuel Hupf
- Institut für Anorganische Chemie und Kristallographie, Universität Bremen, Leobener Straße 7, 28359 Bremen, Germany
| | - Simon Grabowsky
- Departement für Chemie, Biochemie und Pharmazie, Universität Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Jens Beckmann
- Institut für Anorganische Chemie und Kristallographie, Universität Bremen, Leobener Straße 7, 28359 Bremen, Germany
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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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36
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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: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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Abstract
The shape of the potential energy surface (PES) of gas-phase SN2 reactions at silicon is determined by the type of nucleophile, the leaving group, and substituents which remain bonded to silicon. In this study, we present PES scans along the reaction coordinate of six symmetrical SN2 reactions: X- + SiR3X → XSiR3 + X-, where X = Cl or F and R = H, Me, or OMe. While the fluorine systems and the ClSiH3Cl system only give single-well PESs, ClSiMe3Cl and ClSi(OMe)3Cl give triple- and double-well PESs with stable pre- and post-reaction complexes. A complementary bonding analysis (energy decomposition analysis, quantum theory of atoms in molecules, and natural bond orbitals) reveals that the leaving group (X-) is stabilized by hydrogen bonding in the XSiMe3X and XSi(OMe)3X systems. It is shown that this so far neglected stabilizing contribution, along with σ-hole bonding, is responsible for the shapes of the PESs of ClSiMe3Cl and ClSi(OMe)3Cl in the gas phase.
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Affiliation(s)
- Malte Fugel
- Fachbereich 2-Biologie/ Chemie, Universität Bremen, Leobener Str. 3, 28359 Bremen, Germany
| | - Anneke Dittmer
- Fachbereich 2-Biologie/ Chemie, Universität Bremen, Leobener Str. 3, 28359 Bremen, Germany
| | - Florian Kleemiss
- Fachbereich 2-Biologie/ Chemie, Universität Bremen, Leobener Str. 3, 28359 Bremen, Germany.,Departement für Chemie, Biochemie und Pharmazie, Universität Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Simon Grabowsky
- Fachbereich 2-Biologie/ Chemie, Universität Bremen, Leobener Str. 3, 28359 Bremen, Germany.,Departement für Chemie, Biochemie und Pharmazie, Universität Bern, Freiestrasse 3, 3012 Bern, Switzerland
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Schwickert K, Andrzejewski M, Grabowsky S, Schirmeister T. Synthesis, X-ray Structure Determination, and Comprehensive Photochemical Characterization of (Trifluoromethyl)diazirine-Containing TRPML1 Ligands. J Org Chem 2021; 86:6169-6183. [PMID: 33835801 DOI: 10.1021/acs.joc.0c02993] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Potential (trifluoromethyl)diazirine-based TRPML1 ion channel ligands were designed and synthesized, and their structures were determined by single-crystal X-ray diffraction analysis. Photoactivation studies via 19F NMR spectroscopy and HPLC-MS analysis revealed distinct kinetical characteristics in selected solvents and favorable photochemical properties in an aqueous buffer. These photoactivatable TRPML activators represent useful and valuable tools for TRPML photoaffinity labeling combined with mass spectrometry.
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Affiliation(s)
- Kevin Schwickert
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 5, 55128 Mainz, Germany
| | - Michał Andrzejewski
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Simon Grabowsky
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Tanja Schirmeister
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 5, 55128 Mainz, Germany
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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: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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40
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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 Crystallogr A Found Adv 2021; 77:54-66. [PMID: 33399131 DOI: 10.1107/s2053273320014837] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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41
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Pal R, Jelsch C, Malaspina LA, Edwards AJ, Murshed MM, Grabowsky S. syn and anti polymorphs of 2,6-dimethoxy benzoic acid and its molecular and ionic cocrystals: Structural analysis and energetic perspective. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.128721] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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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: 103] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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43
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Meyer F, Hupf E, Lork E, Grabowsky S, Mebs S, Beckmann J. Bis(6‐diphenylphosphino‐acenaphth‐5‐yl)sulfoxide: A New Ligand for Late Transition Metal Complexes. Eur J Inorg Chem 2020. [DOI: 10.1002/ejic.202000610] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Fabio Meyer
- Institut für Anorganische Chemie und Kristallographie Universität Bremen Leobener Straße 3 und 7 28359 Bremen Germany
| | - Emanuel Hupf
- Institut für Anorganische Chemie und Kristallographie Universität Bremen Leobener Straße 3 und 7 28359 Bremen Germany
| | - Enno Lork
- Institut für Anorganische Chemie und Kristallographie Universität Bremen Leobener Straße 3 und 7 28359 Bremen Germany
| | - Simon Grabowsky
- Institut für Anorganische Chemie und Kristallographie Universität Bremen Leobener Straße 3 und 7 28359 Bremen Germany
- Departement für Chemie und Biochemie Universität Bern Freiestrasse 3 3012 Bern Switzerland
| | - Stefan Mebs
- Institut für Experimentalphysik Freie Universität Berlin Arnimallee 14 14195 Berlin Germany
| | - Jens Beckmann
- Institut für Anorganische Chemie und Kristallographie Universität Bremen Leobener Straße 3 und 7 28359 Bremen Germany
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44
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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45
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Damgaard-Møller E, Krause L, Lassen H, Malaspina LA, Grabowsky S, Bamberger H, McGuire J, Miras HN, Sproules S, Overgaard J. Investigating Complex Magnetic Anisotropy in a Co(II) Molecular Compound: A Charge Density and Correlated Ab Initio Electronic Structure Study. Inorg Chem 2020; 59:13190-13200. [PMID: 32869986 DOI: 10.1021/acs.inorgchem.0c01489] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Understanding magnetic anisotropy and specifically how to tailor it is crucial in the search for high-temperature single-ion magnets. Herein, we investigate the magnetic anisotropy in a six-coordinated cobalt(II) compound that has a complex geometry and distinct triaxial magnetic anisotropy from the perspective of the electronic structure, using electronic spectra, ab initio calculations, and an experimental charge density, of which the latter two provides insight into the d-orbital splitting. The analysis showed that the d-orbital splitting satisfactorily predicted the complex triaxial magnetic anisotropy exhibited by the compound. Furthermore, a novel method to directly compare the ab initio results and the d-orbital populations obtained from the experimental charge density was developed, while a topological analysis of the density provided insights into the metal-ligand bonding. This work thus further establishes the validity of using d-orbitals for predicting magnetic anisotropy in transition metal compounds while also pointing out the need for a more frequent usage of the term triaxial anisotropy in the field of single-molecule magnetism.
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Affiliation(s)
- Emil Damgaard-Møller
- Department of Chemistry, Aarhus University, Langelandsgade 140, DK-8000 Aarhus C, Denmark
| | - Lennard Krause
- Department of Chemistry, Aarhus University, Langelandsgade 140, DK-8000 Aarhus C, Denmark
| | - Helene Lassen
- Department of Chemistry, Aarhus University, Langelandsgade 140, DK-8000 Aarhus C, Denmark
| | - Lorraine A Malaspina
- Department 2-Biology/Chemistry, University of Bremen, Leobener Str. 3, 28359 Bremen, Germany
| | - Simon Grabowsky
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Heiko Bamberger
- Institut für Physikalische Chemie, Universität Stuttgart, Pfaffenwaldring 55, D-70569 Stuttgart, Germany
| | - Jake McGuire
- WestCHEM, School of Chemistry, University of Glasgow, Glasgow G12 8QQ, Glasgow, United Kingdom
| | - Haralampos N Miras
- WestCHEM, School of Chemistry, University of Glasgow, Glasgow G12 8QQ, Glasgow, United Kingdom
| | - Stephen Sproules
- WestCHEM, School of Chemistry, University of Glasgow, Glasgow G12 8QQ, Glasgow, United Kingdom
| | - Jacob Overgaard
- Department of Chemistry, Aarhus University, Langelandsgade 140, DK-8000 Aarhus C, Denmark
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46
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Sanjuan-Szklarz WF, Woińska M, Domagała S, Dominiak PM, Grabowsky S, Jayatilaka D, Gutmann M, Woźniak K. On the accuracy and precision of X-ray and neutron diffraction results as a function of resolution and the electron density model. IUCrJ 2020; 7:920-933. [PMID: 32939284 PMCID: PMC7467170 DOI: 10.1107/s2052252520010441] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 07/28/2020] [Indexed: 05/20/2023]
Abstract
X-ray diffraction is the main source of three-dimensional structural information. In total, more than 1.5 million crystal structures have been refined and deposited in structural databanks (PDB, CSD and ICSD) to date. Almost 99.7% of them were obtained by approximating atoms as spheres within the independent atom model (IAM) introduced over a century ago. In this study, X-ray datasets for single crystals of hydrated α-oxalic acid were refined using several alternative electron density models that abandon the crude spherical approximation: the multipole model (MM), the transferable aspherical atom model (TAAM) and the Hirshfeld atom refinement (HAR) model as a function of the resolution of X-ray data. The aspherical models (MM, TAAM, HAR) give far more accurate and precise single-crystal X-ray results than IAM, sometimes identical to results obtained from neutron diffraction and at low resolution. Hence, aspherical approaches open new routes for improving existing structural information collected over the last century.
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Affiliation(s)
- W. Fabiola Sanjuan-Szklarz
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Żwirki i Wigury, Warszawa, Poland
| | - Magdalena Woińska
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Żwirki i Wigury, Warszawa, Poland
| | - Sławomir Domagała
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Żwirki i Wigury, Warszawa, Poland
| | - Paulina M. Dominiak
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Żwirki i Wigury, Warszawa, Poland
| | - Simon Grabowsky
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Dylan Jayatilaka
- School of Molecular Sciences, University of Western Australia, 35 Stirling Highway, Perth WA 6009, Australia
| | - Matthias Gutmann
- Rutherford Appleton Laboratory, ISIS Facility, Chilton, Didcot, Oxfordshire OX11 OQX, United Kingdom
| | - Krzysztof Woźniak
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Żwirki i Wigury, Warszawa, Poland
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47
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Rohdenburg M, Yang Z, Su P, Bernhardt E, Yuan Q, Apra E, Grabowsky S, Laskin J, Jenne C, Wang XB, Warneke J. Properties of gaseous closo-[B 6X 6] 2- dianions (X = Cl, Br, I). Phys Chem Chem Phys 2020; 22:17713-17724. [PMID: 32728676 DOI: 10.1039/d0cp02581j] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Electronic structure, collision-induced dissociation (CID) and bond properties of closo-[B6X6]2- (X = Cl-I) are investigated in direct comparison with their closo-[B12X12]2- analogues. Photoelectron spectroscopy (PES) and theoretical investigations reveal that [B6X6]2- dianions are electronically significantly less stable than the corresponding [B12X12]2- species. Although [B6Cl6]2- is slightly electronically unstable, [B6Br6]2- and [B6I6]2- are intrinsically stable dianions. Consistent with the trend in the electron detachment energy, loss of an electron (e- loss) is observed in CID of [B6X6]2- (X = Cl, Br) but not for [B6I6]2-. Halogenide loss (X- loss) is common for [B6X6]2- (X = Br, I) and [B12X12]2- (X = Cl, Br, I). Meanwhile, X˙ loss is only observed for [B12X12]2- (X = Br, I) species. The calculated reaction enthalpies of the three competing dissociation pathways (e-, X- and X˙ loss) indicated a strong influence of kinetic factors on the observed fragmentation patterns. The repulsive Coulomb barrier (RCB) determines the transition state for the e- and X- losses. A significantly lower RCB for X- loss than for e- loss was found in both experimental and theoretical investigations and can be rationalized by the recently introduced concept of electrophilic anions. The positive reaction enthalpies for X- losses are significantly lower for [B6X6]2- than for [B12X12]2-, while enthalpies for X˙ losses are higher. These observations are consistent with a difference in bond character of the B-X bonds in [B6X6]2- and [B12X12]2-. A complementary bonding analysis using QTAIM, NPA and ELI-D based methods suggests that B-X bonds in [B12X12]2- have a stronger covalent character than in [B6X6]2-, in which X has a stronger halide character.
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Affiliation(s)
- Markus Rohdenburg
- Institut für Angewandte und Physikalische Chemie, Universität Bremen, Fachbereich 2-Biologie/Chemie, 28359 Bremen, Germany
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48
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Mayer M, Rohdenburg M, van Lessen V, Nierstenhöfer MC, Aprà E, Grabowsky S, Asmis KR, Jenne C, Warneke J. First steps towards a stable neon compound: observation and bonding analysis of [B 12(CN) 11Ne] . Chem Commun (Camb) 2020; 56:4591-4594. [PMID: 32207481 DOI: 10.1039/d0cc01423k] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Noble gas (Ng) containing molecular anions are much scarcer than Ng containing cations. No neon containing anion has been reported so far. Here, the experimental observation of the molecular anion [B12(CN)11Ne]- and a theoretical analysis of the boron-neon bond is reported.
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Affiliation(s)
- Martin Mayer
- Wilhelm-Ostwald-Institut für Physikalische und Theoretische Chemie, Universität Leipzig, 04103 Leipzig, Germany.
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49
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Schlüter D, Kleemiss F, Fugel M, Lork E, Sugimoto K, Grabowsky S, Harmer JR, Vogt M. Non-Oxido-Vanadium(IV) Metalloradical Complexes with Bidentate 1,2-Dithienylethene Ligands: Observation of Reversible Cyclization of the Ligand Scaffold in Solution. Chemistry 2020; 26:1335-1343. [PMID: 31721322 PMCID: PMC7027510 DOI: 10.1002/chem.201904103] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Indexed: 12/14/2022]
Abstract
Derivatives of 1,2‐dithienylethene (DTE) have superb photochromic properties due to an efficient reversible photocyclization reaction of their hexatriene structure and, thus, have application potential in materials for optoelectronics and (multi‐responsive) molecular switches. Transition‐metal complexes bearing switchable DTE motifs commonly incorporate their coordination site rather distant from the hexatriene system. In this work the redox active ligand 1,2‐bis(2,5‐dimethylthiophen‐3‐yl)ethane‐1,2‐dione is described, which reacts with [V(TMEDA)2Cl2] to give a rare non‐oxido vanadium(IV) species 3(M,M/P,P). This blue complex has two bidentate en‐diolato ligands which chelate the VIV center and give rise to two five‐membered metallacycles with the adjacent hexatriene DTE backbone bearing axial chirality. Upon irradiation with UVA light or prolonged heating in solution, the blue compound 3(M,M/P,P) converts into the purple atropisomer 4(para,M/para,P). Both complexes were isolated and structurally characterized by single‐crystal X‐ray diffraction analysis (using lab source and synchrotron radiation). The antiparallel configuration (M or P helicity) present in both 3(M,M/P,P) and 4(para,M/para,P) is a prerequisite for (reversible) 6π cyclization reactions. A CW EPR spectroscopic study reveals the metalloradical character for 3(M,M/P,P) and 4(para,M/para,P) and indicates dynamic reversible cyclization of the DTE backbone in complex 3(M,M/P,P) at ambient temperature in solution.
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Affiliation(s)
- Dirk Schlüter
- Institut für Anorganische Chemie und Kristallographie, Universität Bremen, Leobener Str. 3 and 7, 28359, Bremen, Germany
| | - Florian Kleemiss
- Institut für Anorganische Chemie und Kristallographie, Universität Bremen, Leobener Str. 3 and 7, 28359, Bremen, Germany.,Abteilung für Chemie und Biochemie, Universität Bern, Freiestrasse 3, 3012, Bern, Switzerland
| | - Malte Fugel
- Institut für Anorganische Chemie und Kristallographie, Universität Bremen, Leobener Str. 3 and 7, 28359, Bremen, Germany
| | - Enno Lork
- Institut für Anorganische Chemie und Kristallographie, Universität Bremen, Leobener Str. 3 and 7, 28359, Bremen, Germany
| | - Kunihisa Sugimoto
- SPring-8/JASRI, 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
| | - Simon Grabowsky
- Institut für Anorganische Chemie und Kristallographie, Universität Bremen, Leobener Str. 3 and 7, 28359, Bremen, Germany.,Abteilung für Chemie und Biochemie, Universität Bern, Freiestrasse 3, 3012, Bern, Switzerland
| | - Jeffrey R Harmer
- Center of Advanced Imaging (CAI), University of Queensland, St. Lucia, QL, Australia
| | - Matthias Vogt
- Institut für Anorganische Chemie und Kristallographie, Universität Bremen, Leobener Str. 3 and 7, 28359, Bremen, Germany
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50
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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] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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