1
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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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2
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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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3
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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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4
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Fugel M, Malaspina LA, Pal R, Thomas SP, Shi MW, Spackman MA, Sugimoto K, Grabowsky S. Front Cover: Revisiting a Historical Concept by Using Quantum Crystallography: Are Phosphate, Sulfate and Perchlorate Anions Hypervalent? (Chem. Eur. J. 26/2019). Chemistry 2019. [DOI: 10.1002/chem.201901181] [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)
- Malte Fugel
- Department 2-Chemistry/BiologyInstitute of Inorganic Chemistry and CrystallographyUniversity of Bremen Leobener Str. 3 and 7 28359 Bremen Germany
| | - Lorraine A. Malaspina
- Department 2-Chemistry/BiologyInstitute of Inorganic Chemistry and CrystallographyUniversity of Bremen Leobener Str. 3 and 7 28359 Bremen Germany
| | - Rumpa Pal
- Department 2-Chemistry/BiologyInstitute of Inorganic Chemistry and CrystallographyUniversity of Bremen Leobener Str. 3 and 7 28359 Bremen Germany
- Current address: Division of PhysicsFaculty of Pure and Applied SciencesUniversity of Tsukuba 1-1-1 Tennodai Tsukuba Ibaraki 305-8571 Japan
| | - Sajesh P. Thomas
- School of Molecular SciencesUniversity of Western Australia 35 Stirling Highway Perth WA 6009 Australia
- Current address: Interdisciplinary Nanoscience Center - INANO-KemiAarhus University Langelandsgade 140 8000 Aarhus C Denmark
| | - Ming W. Shi
- School of Molecular SciencesUniversity of Western Australia 35 Stirling Highway Perth WA 6009 Australia
| | - Mark A. Spackman
- School of Molecular SciencesUniversity of Western Australia 35 Stirling Highway Perth WA 6009 Australia
| | - Kunihisa Sugimoto
- SPring-8Japan Synchrotron Radiation Research Institute 1-1-1 Kouto Sayo-cho Sayo-gun, Hyogo 679-5198 Japan
| | - Simon Grabowsky
- Department 2-Chemistry/BiologyInstitute of Inorganic Chemistry and CrystallographyUniversity of Bremen Leobener Str. 3 and 7 28359 Bremen Germany
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5
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Fugel M, Malaspina LA, Pal R, Thomas SP, Shi MW, Spackman MA, Sugimoto K, Grabowsky S. Revisiting a Historical Concept by Using Quantum Crystallography: Are Phosphate, Sulfate and Perchlorate Anions Hypervalent? Chemistry 2019. [DOI: 10.1002/chem.201901182] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Malte Fugel
- Department 2-Chemistry/BiologyInstitute of Inorganic Chemistry and CrystallographyUniversity of Bremen Leobener Str. 3 and 7 28359 Bremen Germany
| | - Lorraine A. Malaspina
- Department 2-Chemistry/BiologyInstitute of Inorganic Chemistry and CrystallographyUniversity of Bremen Leobener Str. 3 and 7 28359 Bremen Germany
| | - Rumpa Pal
- Department 2-Chemistry/BiologyInstitute of Inorganic Chemistry and CrystallographyUniversity of Bremen Leobener Str. 3 and 7 28359 Bremen Germany
- Current address: Division of PhysicsFaculty of Pure and Applied SciencesUniversity of Tsukuba 1-1-1 Tennodai Tsukuba Ibaraki 305-8571 Japan
| | - Sajesh P. Thomas
- School of Molecular SciencesUniversity of Western Australia 35 Stirling Highway Perth WA 6009 Australia
- Current address: Interdisciplinary Nanoscience Center - INANO-KemiAarhus University Langelandsgade 140 8000 Aarhus C Denmark
| | - Ming W. Shi
- School of Molecular SciencesUniversity of Western Australia 35 Stirling Highway Perth WA 6009 Australia
| | - Mark A. Spackman
- School of Molecular SciencesUniversity of Western Australia 35 Stirling Highway Perth WA 6009 Australia
| | - Kunihisa Sugimoto
- SPring-8Japan Synchrotron Radiation Research Institute 1-1-1 Kouto Sayo-cho Sayo-gun, Hyogo 679-5198 Japan
| | - Simon Grabowsky
- Department 2-Chemistry/BiologyInstitute of Inorganic Chemistry and CrystallographyUniversity of Bremen Leobener Str. 3 and 7 28359 Bremen Germany
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6
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Fugel M, Malaspina LA, Pal R, Thomas SP, Shi MW, Spackman MA, Sugimoto K, Grabowsky S. Revisiting a Historical Concept by Using Quantum Crystallography: Are Phosphate, Sulfate and Perchlorate Anions Hypervalent? Chemistry 2019; 25:6523-6532. [PMID: 30759315 DOI: 10.1002/chem.201806247] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Indexed: 11/05/2022]
Abstract
There are many examples of atoms in molecules that violate Lewis' octet rule, because they have more than four electron pairs assigned to their valence. These atoms are referred to as hypervalent. However, hypervalency may be regarded as an artifact arising from Lewis' description of molecules, which is based on the assumption that electrons are localized in two-center two-electron bonds and lone pairs. In the present paper, the isoelectronic phosphate (PO4 3- ), sulfate (SO4 2- ) and perchlorate (ClO4 - ) anions were examined with respect to the concept of hypervalency. Lewis formulas containing a hypervalent central atom exist for all three anions. Based on X-ray wavefunction refinements of high-resolution X-ray diffraction data of representative crystal structures (MgNH4 PO4 ⋅6 H2 O, Li2 SO4 ⋅H2 O, and KClO4 ), complementary bonding analyses were performed. In this way, experimental information from the new field of quantum crystallography validate long-known facts, or refute long-standing misunderstandings. It is shown that the P-O and S-O bonds are highly polarized covalent bonds and, thus, the increase in the valence population following three-center four-electron bonding is not sufficient to yield hypervalent phosphorus or sulfur atoms, respectively. However, for the highly covalent Cl-O bond, most bonding indicators imply a hypervalent chlorine atom.
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Affiliation(s)
- Malte Fugel
- Department 2-Chemistry/Biology, Institute of Inorganic Chemistry and Crystallography, University of Bremen, Leobener Str. 3 and 7, 28359, Bremen, Germany
| | - Lorraine A Malaspina
- Department 2-Chemistry/Biology, Institute of Inorganic Chemistry and Crystallography, University of Bremen, Leobener Str. 3 and 7, 28359, Bremen, Germany
| | - Rumpa Pal
- Department 2-Chemistry/Biology, Institute of Inorganic Chemistry and Crystallography, University of Bremen, Leobener Str. 3 and 7, 28359, Bremen, Germany.,Current address: Division of Physics, Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8571, Japan
| | - Sajesh P Thomas
- School of Molecular Sciences, University of Western Australia, 35 Stirling Highway, Perth, WA, 6009, Australia.,Current address: Interdisciplinary Nanoscience Center - INANO-Kemi, Aarhus University, Langelandsgade 140, 8000, Aarhus C, Denmark
| | - Ming W Shi
- School of Molecular Sciences, University of Western Australia, 35 Stirling Highway, Perth, WA, 6009, Australia
| | - Mark A Spackman
- School of Molecular Sciences, University of Western Australia, 35 Stirling Highway, Perth, WA, 6009, Australia
| | - Kunihisa Sugimoto
- SPring-8, Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5198, Japan
| | - Simon Grabowsky
- Department 2-Chemistry/Biology, Institute of Inorganic Chemistry and Crystallography, University of Bremen, Leobener Str. 3 and 7, 28359, Bremen, Germany
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7
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Köhling J, Kozel V, Jovanov V, Pajkert R, Tverdomed SN, Gridenco O, Fugel M, Grabowsky S, Röschenthaler GV, Wagner V. Synthesis and Characterization of Oxazaborinin Phosphonate for Blue OLED Emitter Applications. Chemphyschem 2019; 20:665-671. [PMID: 30645049 DOI: 10.1002/cphc.201801087] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [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: 11/23/2018] [Revised: 01/03/2019] [Indexed: 11/11/2022]
Abstract
A blue-light emitting material based on a boron complex containing heteroaromatic phosphonate ligand is synthesized and characterized. The Phospho-Fries rearrangement is used in the synthesis route of the ligand as a convenient method of introducing phosphonate groups into phenols. Structural, thermal and photophysical properties of the resulting oxazaborinin phosphonate compound have been characterized. DFT geometry optimizations were studied as well as the spatial position and symmetry of the HOMO and LUMO. Good thermal stability up to 250 °C enables vacuum deposition methods next to solution processing. Combining the work function with the optical band gap from UV-Vis measurements shows that band alignment is possible with standard contact materials. Photoluminescence reveals an emission peak at 428 nm, which is suitable for a blue light-emitter.
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Affiliation(s)
- Jonas Köhling
- Department of Physics and Earth Sciences, Jacobs University gGmbH, Campus Ring 1, 28759, Bremen, Germany
| | - Volodymyr Kozel
- Department of Life Sciences and Chemistry, Jacobs University gGmbH, Campus Ring 1, 28759, Bremen, Germany
| | - Vladislav Jovanov
- Department of Physics and Earth Sciences, Jacobs University gGmbH, Campus Ring 1, 28759, Bremen, Germany
| | - Romana Pajkert
- Department of Life Sciences and Chemistry, Jacobs University gGmbH, Campus Ring 1, 28759, Bremen, Germany
| | - Sergey N Tverdomed
- Department of Life Sciences and Chemistry, Jacobs University gGmbH, Campus Ring 1, 28759, Bremen, Germany
| | - Oleg Gridenco
- Semiconductor Optics, Institute of Solid State Physics, University of Bremen, 28359, Bremen, Germany
| | - Malte Fugel
- Institute of Inorganic Chemistry and Crystallography, University of Bremen, 28359, Bremen, Germany
| | - Simon Grabowsky
- Institute of Inorganic Chemistry and Crystallography, University of Bremen, 28359, Bremen, Germany
| | - Gerd-Volker Röschenthaler
- Department of Life Sciences and Chemistry, Jacobs University gGmbH, Campus Ring 1, 28759, Bremen, Germany
| | - Veit Wagner
- Department of Physics and Earth Sciences, Jacobs University gGmbH, Campus Ring 1, 28759, Bremen, Germany
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8
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Fugel M, Ponomarenko MV, Hesse MF, Malaspina LA, Kleemiss F, Sugimoto K, Genoni A, Röschenthaler GV, Grabowsky S. Complementary bonding analysis of the N–Si interaction in pentacoordinated silicon compounds using quantum crystallography. Dalton Trans 2019; 48:16330-16339. [DOI: 10.1039/c9dt02772f] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The unique combination of quantum crystallography and complementary bonding analysis is used to investigate the bonding of pentacoordinated silicon atoms.
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Affiliation(s)
- Malte Fugel
- University of Bremen
- Department 2: Biology/Chemistry
- Institute of Inorganic Chemistry and Crystallography
- 28359 Bremen
- Germany
| | | | - Maxie F. Hesse
- University of Bremen
- Department 2: Biology/Chemistry
- Institute of Inorganic Chemistry and Crystallography
- 28359 Bremen
- Germany
| | - Lorraine A. Malaspina
- University of Bremen
- Department 2: Biology/Chemistry
- Institute of Inorganic Chemistry and Crystallography
- 28359 Bremen
- Germany
| | - Florian Kleemiss
- University of Bremen
- Department 2: Biology/Chemistry
- Institute of Inorganic Chemistry and Crystallography
- 28359 Bremen
- Germany
| | - Kunihisa Sugimoto
- JASRI/Diffraction & Scattering Division
- Hyogo 679-5198
- Japan
- Institute for Integrated Cell-Material Sciences (iCeMS)
- Kyoto University
| | | | | | - Simon Grabowsky
- University of Bremen
- Department 2: Biology/Chemistry
- Institute of Inorganic Chemistry and Crystallography
- 28359 Bremen
- Germany
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9
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Fugel M, Hesse MF, Pal R, Beckmann J, Jayatilaka D, Turner MJ, Karton A, Bultinck P, Chandler GS, Grabowsky S. Covalency and Ionicity Do Not Oppose Each Other-Relationship Between Si-O Bond Character and Basicity of Siloxanes. Chemistry 2018; 24:15275-15286. [PMID: 29999553 DOI: 10.1002/chem.201802197] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [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: 05/02/2018] [Revised: 07/11/2018] [Indexed: 11/07/2022]
Abstract
Covalency and ionicity are orthogonal rather than antipodal concepts. We demonstrate for the case of siloxane systems [R3 Si-(O-SiR2 )n -O-SiR3 ] that both covalency and ionicity of the Si-O bonds impact on the basicity of the Si-O-Si linkage. The relationship between the siloxane basicity and the Si-O bond character has been under debate since previous studies have presented conflicting explanations. It has been shown with natural bond orbital methods that increased hyperconjugative interactions of LP(O)→σ*(Si-R) type, that is, increased orbital overlap and hence covalency, are responsible for the low siloxane basicity at large Si-O-Si angles. On the other hand, increased ionicity towards larger Si-O-Si angles has been revealed with real-space bonding indicators. To resolve this ostensible contradiction, we perform a complementary bonding analysis, which combines orbital-space, real-space, and bond-index considerations. We analyze the isolated disiloxane molecule H3 SiOSiH3 with varying Si-O-Si angles, and n-membered cyclic siloxane systems Si2 H4 O(CH2 )n-3 . All methods from quite different realms show that both covalent and ionic interactions increase simultaneously towards larger Si-O-Si angles. In addition, we present highly accurate absolute hydrogen-bond interaction energies of the investigated siloxane molecules with water and silanol as donors. It is found that intermolecular hydrogen bonding is significant at small Si-O-Si angles and weakens as the Si-O-Si angle increases until no stable hydrogen-bond complexes are obtained beyond φSiOSi =168°, angles typically displayed by minerals or polymers. The maximum hydrogen-bond interaction energy, which is obtained at an angle of 105°, is 11.05 kJ mol-1 for the siloxane-water complex and 18.40 kJ mol-1 for the siloxane-silanol complex.
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Affiliation(s)
- Malte Fugel
- University of Bremen, Department 2-Chemistry/Biology, Institute of Inorganic Chemistry and Crystallography, Leobener Str. 3 and 7, 28359, Bremen, Germany
| | - Maxie F Hesse
- University of Bremen, Department 2-Chemistry/Biology, Institute of Inorganic Chemistry and Crystallography, Leobener Str. 3 and 7, 28359, Bremen, Germany
| | - Rumpa Pal
- University of Bremen, Department 2-Chemistry/Biology, Institute of Inorganic Chemistry and Crystallography, Leobener Str. 3 and 7, 28359, Bremen, Germany
| | - Jens Beckmann
- University of Bremen, Department 2-Chemistry/Biology, Institute of Inorganic Chemistry and Crystallography, Leobener Str. 3 and 7, 28359, Bremen, Germany
| | - Dylan Jayatilaka
- University of Western Australia, School of Molecular Sciences, 35 Stirling Highway, Perth, WA, 6009, Australia
| | - Michael J Turner
- University of Western Australia, School of Molecular Sciences, 35 Stirling Highway, Perth, WA, 6009, Australia
| | - Amir Karton
- University of Western Australia, School of Molecular Sciences, 35 Stirling Highway, Perth, WA, 6009, Australia
| | - Patrick Bultinck
- Ghent University, Department of Chemistry, Krijgslaan 281 (S3), 9000, Gent, Belgium
| | - Graham S Chandler
- University of Western Australia, School of Molecular Sciences, 35 Stirling Highway, Perth, WA, 6009, Australia
| | - Simon Grabowsky
- University of Bremen, Department 2-Chemistry/Biology, Institute of Inorganic Chemistry and Crystallography, Leobener Str. 3 and 7, 28359, Bremen, Germany
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10
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Grabowsky S, Fugel M, Ponomarenko MV. Complementary bonding analyses based on quantum crystallography. Acta Crystallogr A Found Adv 2018. [DOI: 10.1107/s2053273318094020] [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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11
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Fugel M, Beckmann J, Jayatilaka D, Gibbs GV, Grabowsky S. A Variety of Bond Analysis Methods, One Answer? An Investigation of the Element-Oxygen Bond of Hydroxides H n XOH. Chemistry 2018; 24:6248-6261. [PMID: 29465756 DOI: 10.1002/chem.201800453] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [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: 01/29/2018] [Indexed: 11/10/2022]
Abstract
There is a great variety of bond analysis tools that aim to extract information on the bonding situation from the molecular wavefunction. Because none of these can fully describe bonding in all of its complexity, it is necessary to regard a balanced selection of complementary analysis methods to obtain a reliable chemical conclusion. This is, however, not a feasible approach in most studies because it is a time-consuming procedure. Therefore, we provide the first comprehensive comparison of modern bonding analysis methods to reveal their informative value. The element-oxygen bond of neutral Hn XOH model compounds (X=Li, Be, B, C, N, O, F, Na, Mg, Al, Si, P, S, Cl) is investigated with a selection of different bond analysis tools, which may be assigned into three different categories: i) real space bonding indicators (quantum theory of atoms in molecules (QTAIM), the electron localizability indicator (ELI-D), and the Raub-Jansen index), ii) orbital-based descriptors (natural bond orbitals (NBO), natural resonance theory (NRT), and valence bond (VB) calculations), and iii) energy analysis methods (energy decomposition analysis (EDA) and the Q-analysis). Besides gaining a deep insight into the nature of the element-oxygen bond across the periodic table, this systematic investigation allows us to get an impression on how well these tools complement each other. Ionic, highly polarized, polarized covalent, and charge-shift bonds are discerned from each other.
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Affiliation(s)
- Malte Fugel
- University of Bremen, Department 2: Biology/Chemistry, Institute of Inorganic Chemistry and Crystallography, Leobener Str. 3 and 7, Bremen, Germany
| | - Jens Beckmann
- University of Bremen, Department 2: Biology/Chemistry, Institute of Inorganic Chemistry and Crystallography, Leobener Str. 3 and 7, Bremen, Germany
| | - Dylan Jayatilaka
- University of Western Australia, School of Molecular Sciences, 35 Stirling Highway, Perth, WA, 6009, Australia
| | - Gerald V Gibbs
- Virginia Polytechnic Institute and State University, Departments of Geoscience, Material Science and Engineering, and Mathematics, Blacksburg, Virginia, 24061, USA
| | - Simon Grabowsky
- University of Bremen, Department 2: Biology/Chemistry, Institute of Inorganic Chemistry and Crystallography, Leobener Str. 3 and 7, Bremen, Germany
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Fugel M, Kleemiss F, Malaspina LA, Pal R, Spackman PR, Jayatilaka D, Grabowsky S. Investigating the Resonance in Nitric Acid and the Nitrate Anion Based on a Modern Bonding Analysis. Aust J Chem 2018. [DOI: 10.1071/ch17583] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The nitrate anion, NO3−, is often regarded as a textbook example for the very fundamental concept of resonance. Usually, three equivalent resonance structures with one N–O double bond and two N–O single bonds are considered. Consequently, each of the three N–O bonds should have a partial double bond character. In this study, we analyse the resonance in NO3− in comparison with the related species HNO3 and FNO3 by applying a combination of the Quantum Theory of Atoms in Molecules (QTAIM), a natural bond orbital (NBO) analysis, the electron localizability indicator (ELI), and valence bond (VB) calculations. Despite the fundamental importance of nitrate salts and nitric acid for the environment, chemistry, and industry, a bonding analysis is absent from the literature so far. The classical resonance structures are clearly reflected by the bond analysis tools, but are not the only contributions to the bonding situation. The resonance in HNO3 and FNO3 is greatly perturbed by the hydrogen and fluorine atoms. In addition to theoretical calculations, experimental electron density and wave function refinements were carried out on a KNO3 crystal.
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Fugel M, Jayatilaka D, Hupf E, Overgaard J, Hathwar VR, Macchi P, Turner MJ, Howard JAK, Dolomanov OV, Puschmann H, Iversen BB, Bürgi HB, Grabowsky S. Probing the accuracy and precision of Hirshfeld atom refinement with HARt interfaced with Olex2. IUCrJ 2018; 5:32-44. [PMID: 29354269 PMCID: PMC5755575 DOI: 10.1107/s2052252517015548] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 10/25/2017] [Indexed: 05/20/2023]
Abstract
Hirshfeld atom refinement (HAR) is a novel X-ray structure refinement technique that employs aspherical atomic scattering factors obtained from stockholder partitioning of a theoretically determined tailor-made static electron density. HAR overcomes many of the known limitations of independent atom modelling (IAM), such as too short element-hydrogen distances, r(X-H), or too large atomic displacement parameters (ADPs). This study probes the accuracy and precision of anisotropic hydrogen and non-hydrogen ADPs and of r(X-H) values obtained from HAR. These quantities are compared and found to agree with those obtained from (i) accurate neutron diffraction data measured at the same temperatures as the X-ray data and (ii) multipole modelling (MM), an established alternative method for interpreting X-ray diffraction data with the help of aspherical atomic scattering factors. Results are presented for three chemically different systems: the aromatic hydro-carbon rubrene (orthorhombic 5,6,11,12-tetra-phenyl-tetracene), a co-crystal of zwitterionic betaine, imidazolium cations and picrate anions (BIPa), and the salt potassium hydrogen oxalate (KHOx). The non-hydrogen HAR-ADPs are as accurate and precise as the MM-ADPs. Both show excellent agreement with the neutron-based values and are superior to IAM-ADPs. The anisotropic hydrogen HAR-ADPs show a somewhat larger deviation from neutron-based values than the hydrogen SHADE-ADPs used in MM. Element-hydrogen bond lengths from HAR are in excellent agreement with those obtained from neutron diffraction experiments, although they are somewhat less precise. The residual density contour maps after HAR show fewer features than those after MM. Calculating the static electron density with the def2-TZVP basis set instead of the simpler def2-SVP one does not improve the refinement results significantly. All HARs were performed within the recently introduced HARt option implemented in the Olex2 program. They are easily launched inside its graphical user interface following a conventional IAM.
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Affiliation(s)
- Malte Fugel
- Department 2: Biology/Chemistry, University of Bremen, Leobener Straße NW2, 28359 Bremen, Germany
| | - Dylan Jayatilaka
- School of Chemistry and Biochemistry, University of Western Australia, 35 Stirling Highway, Perth, WA 6009, Australia
| | - Emanuel Hupf
- Department 2: Biology/Chemistry, University of Bremen, Leobener Straße NW2, 28359 Bremen, Germany
| | - Jacob Overgaard
- Center for Materials Crystallography, Department of Chemistry and iNano, Aarhus University, Langelandsgade 140, Aarhus 8000, Denmark
| | - Venkatesha R. Hathwar
- Center for Materials Crystallography, Department of Chemistry and iNano, Aarhus University, Langelandsgade 140, Aarhus 8000, Denmark
- Division of Physics, Faculty of Pure and Applied Sciences, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Piero Macchi
- Department of Chemistry and Biochemistry, University of Bern, Freiestraße 3, Bern 3012, Switzerland
| | - Michael J. Turner
- School of Chemistry and Biochemistry, University of Western Australia, 35 Stirling Highway, Perth, WA 6009, Australia
| | | | - Oleg V. Dolomanov
- Department of Chemistry, Durham University, South Road, Durham DH1 3LE, UK
| | - Horst Puschmann
- Department of Chemistry, Durham University, South Road, Durham DH1 3LE, UK
| | - Bo B. Iversen
- Center for Materials Crystallography, Department of Chemistry and iNano, Aarhus University, Langelandsgade 140, Aarhus 8000, Denmark
| | - Hans-Beat Bürgi
- Department of Chemistry and Biochemistry, University of Bern, Freiestraße 3, Bern 3012, Switzerland
- Department of Chemistry, University of Zürich, Winterthurerstraße 190, Zürich 8057, Switzerland
| | - Simon Grabowsky
- Department 2: Biology/Chemistry, University of Bremen, Leobener Straße NW2, 28359 Bremen, Germany
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Fugel M, Grabowsky S. Comparative charge-density determination of potassium perchlorate. Acta Crystallogr A Found Adv 2017. [DOI: 10.1107/s2053273317083000] [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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Hupf E, Olaru M, Raţ CI, Fugel M, Hübschle CB, Lork E, Grabowsky S, Mebs S, Beckmann J. Mapping the Trajectory of Nucleophilic Substitution at Silicon Using aperi-Substituted Acenaphthyl Scaffold. Chemistry 2017; 23:10568-10579. [DOI: 10.1002/chem.201700992] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Indexed: 11/07/2022]
Affiliation(s)
- Emanuel Hupf
- Institut für Anorganische Chemie und Kristallographie; Fachbereich 2-Biologie/Chemie; Universität Bremen; Leobener Straße NW2 28359 Bremen Germany
- Current address: Department of Chemistry; University of Alberta; Edmonton Alberta T6G 2G2 Canada
| | - Marian Olaru
- Institut für Anorganische Chemie und Kristallographie; Fachbereich 2-Biologie/Chemie; Universität Bremen; Leobener Straße NW2 28359 Bremen Germany
- Centre of Supramolecular Organic and Organometallic Chemistry; Department of Chemistry, Faculty of Chemistry and Chemical Engineering; Babes-Bolyai University; 11 Arany Janos Street 400028 Cluj-Napoca Romania
| | - Ciprian I. Raţ
- Centre of Supramolecular Organic and Organometallic Chemistry; Department of Chemistry, Faculty of Chemistry and Chemical Engineering; Babes-Bolyai University; 11 Arany Janos Street 400028 Cluj-Napoca Romania
| | - Malte Fugel
- Institut für Anorganische Chemie und Kristallographie; Fachbereich 2-Biologie/Chemie; Universität Bremen; Leobener Straße NW2 28359 Bremen Germany
| | | | - Enno Lork
- Institut für Anorganische Chemie und Kristallographie; Fachbereich 2-Biologie/Chemie; Universität Bremen; Leobener Straße NW2 28359 Bremen Germany
| | - Simon Grabowsky
- Institut für Anorganische Chemie und Kristallographie; Fachbereich 2-Biologie/Chemie; Universität Bremen; Leobener Straße NW2 28359 Bremen Germany
| | - Stefan Mebs
- Institut für Experimentalphysik; Freie Universität Berlin; Arnimallee 14 14195 Berlin Germany
| | - Jens Beckmann
- Institut für Anorganische Chemie und Kristallographie; Fachbereich 2-Biologie/Chemie; Universität Bremen; Leobener Straße NW2 28359 Bremen Germany
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Fugel M, Weiss VC. A corresponding-states analysis of the liquid-vapor equilibrium properties of common water models. J Chem Phys 2017; 146:064505. [DOI: 10.1063/1.4975778] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
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