1
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Yanai H, Terajima Y, Kleemiss F, Grabowsky S, Matsumoto T. Reversing the Bond Length Alternation Order in Conjugated Polyenes by Substituent Effects. Chemistry 2023; 29:e202203538. [PMID: 36515459 DOI: 10.1002/chem.202203538] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/14/2022] [Accepted: 12/14/2022] [Indexed: 12/15/2022]
Abstract
We have synthesised several push-pull substituted conjugated polyenes and determined their accurate C-C bond lengths and charge-density distributions by utilising quantum crystallographic techniques. In a series of alkene, dienes, and triene bearing two (trifluoromethyl)sulfonyl (triflyl) groups on the terminal carbon atom, unique reversal of the bond-length alternation (BLA) order has been observed. This is a pronounced aberration from the molecular structure predicted by the Lewis-structure-based neutral resonance structure. Such reversal of BLA order has not been observed in push-pull compounds bearing conventional electron-withdrawing groups such as carbonyl and cyano groups instead of triflyl groups. Bonding behaviour of both normal and reversed bond length alternating systems has been revealed by complementary bonding analysis using several bond descriptors based on the experimentally fitted wavefunctions.
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Affiliation(s)
- Hikaru Yanai
- School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392, Japan
| | - Yoshihiko Terajima
- School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392, Japan
| | - Florian Kleemiss
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, CH-3012, Bern, Switzerland.,Faculty of Chemistry and Pharmacy, University of Regensburg, Universitätsstr. 31, D-93053, Regensburg, Germany
| | - Simon Grabowsky
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, CH-3012, Bern, Switzerland
| | - Takashi Matsumoto
- School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392, Japan
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2
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Kleemiss F, Wieduwilt EK, Hupf E, Shi MW, Stewart SG, Jayatilaka D, Turner MJ, Sugimoto K, Nishibori E, Schirmeister T, Schmidt TC, Engels B, Grabowsky S. Similarities and Differences between Crystal and Enzyme Environmental Effects on the Electron Density of Drug Molecules. Chemistry 2021; 27:3407-3419. [PMID: 33090581 PMCID: PMC7898524 DOI: 10.1002/chem.202003978] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Indexed: 01/28/2023]
Abstract
The crystal interaction density is generally assumed to be a suitable measure of the polarization of a low-molecular weight ligand inside an enzyme, but this approximation has seldomly been tested and has never been quantified before. In this study, we compare the crystal interaction density and the interaction electrostatic potential for a model compound of loxistatin acid (E64c) with those inside cathepsin B, in solution, and in vacuum. We apply QM/MM calculations and experimental quantum crystallography to show that the crystal interaction density is indeed very similar to the enzyme interaction density. Less than 0.1 e are shifted between these two environments in total. However, this difference has non-negligible consequences for derived properties.
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Affiliation(s)
- Florian Kleemiss
- Department 2 – Biology/Chemistry, Institute of Inorganic Chemistry and CrystallographyUniversity of BremenLeobener Str. 3 and 7, 28359 BremenGermany
- Department of Chemistry and BiochemistryUniversity of BernFreiestrasse 3, 3012 BernSwitzerland
| | - Erna K. Wieduwilt
- Department 2 – Biology/Chemistry, Institute of Inorganic Chemistry and CrystallographyUniversity of BremenLeobener Str. 3 and 7, 28359 BremenGermany
- Laboratoire de Physique et Chimie Théoriques (LPCT), UMR CNRS 7019Université de Lorraine & CNRSBoulevard Arago, 57078 MetzFrance
| | - Emanuel Hupf
- Department 2 – Biology/Chemistry, Institute of Inorganic Chemistry and CrystallographyUniversity of BremenLeobener Str. 3 and 7, 28359 BremenGermany
| | - Ming W. Shi
- School of Molecular SciencesUniversity of Western Australia35 Stirling Highway, Perth WA 6009Australia
| | - Scott G. Stewart
- School of Molecular SciencesUniversity of Western Australia35 Stirling Highway, Perth WA 6009Australia
| | - Dylan Jayatilaka
- School of Molecular SciencesUniversity of Western Australia35 Stirling Highway, Perth WA 6009Australia
| | - Michael J. Turner
- School of Molecular SciencesUniversity of Western Australia35 Stirling Highway, Perth WA 6009Australia
| | - Kunihisa Sugimoto
- Japan Synchrotron Radiation Research InstituteSPring-81-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198Japan
- Institute for Integrated Cell-Materials SciencesKyoto UniversityYoshida-Ushinomiya-cho, Sakyo-ku, Kyoto 606-8501Japan
| | - Eiji Nishibori
- Division of Physics, Faculty of Pure and Applied Sciences, Tsukuba Research Center for Energy Materials ScienceUniversity of TsukubaTsukubaJapan
| | - Tanja Schirmeister
- Institute of Pharmaceutical and Biomedical SciencesJohannes-Gutenberg University MainzStaudingerweg 5, 55128 MainzGermany
| | - Thomas C. Schmidt
- Institute for Physical and Theoretical ChemistryJulius-Maximilians-University WürzburgEmil-Fischer-Str. 42, 97074 WürzburgGermany
| | - Bernd Engels
- Institute for Physical and Theoretical ChemistryJulius-Maximilians-University WürzburgEmil-Fischer-Str. 42, 97074 WürzburgGermany
| | - Simon Grabowsky
- Department 2 – Biology/Chemistry, Institute of Inorganic Chemistry and CrystallographyUniversity of BremenLeobener Str. 3 and 7, 28359 BremenGermany
- Department of Chemistry and BiochemistryUniversity of BernFreiestrasse 3, 3012 BernSwitzerland
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3
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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] [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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4
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Yanai H, Suzuki T, Kleemiss F, Fukaya H, Dobashi Y, Malaspina LA, Grabowsky S, Matsumoto T. Chemical Bonding in Polarised Push–Pull Ethylenes. Angew Chem Int Ed Engl 2019; 58:8839-8844. [DOI: 10.1002/anie.201904176] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Indexed: 01/06/2023]
Affiliation(s)
- Hikaru Yanai
- School of PharmacyTokyo University of Pharmacy and Life Sciences 1432-1 Horinouchi Hachioji Tokyo 192-0392 Japan
| | - Takumi Suzuki
- School of PharmacyTokyo University of Pharmacy and Life Sciences 1432-1 Horinouchi Hachioji Tokyo 192-0392 Japan
| | - Florian Kleemiss
- Institut für Anorganische Chemie und KristallographieFachbereich 2-Biologie/ChemieUniversität Bremen Leobener Str. 3 28359 Bremen Germany
| | - Haruhiko Fukaya
- School of PharmacyTokyo University of Pharmacy and Life Sciences 1432-1 Horinouchi Hachioji Tokyo 192-0392 Japan
| | - Yasuo Dobashi
- School of PharmacyTokyo University of Pharmacy and Life Sciences 1432-1 Horinouchi Hachioji Tokyo 192-0392 Japan
| | - Lorraine A. Malaspina
- Institut für Anorganische Chemie und KristallographieFachbereich 2-Biologie/ChemieUniversität Bremen Leobener Str. 3 28359 Bremen Germany
| | - Simon Grabowsky
- Institut für Anorganische Chemie und KristallographieFachbereich 2-Biologie/ChemieUniversität Bremen Leobener Str. 3 28359 Bremen Germany
| | - Takashi Matsumoto
- School of PharmacyTokyo University of Pharmacy and Life Sciences 1432-1 Horinouchi Hachioji Tokyo 192-0392 Japan
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5
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Yanai H, Suzuki T, Kleemiss F, Fukaya H, Dobashi Y, Malaspina LA, Grabowsky S, Matsumoto T. Chemical Bonding in Polarised Push–Pull Ethylenes. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201904176] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Hikaru Yanai
- School of PharmacyTokyo University of Pharmacy and Life Sciences 1432-1 Horinouchi Hachioji Tokyo 192-0392 Japan
| | - Takumi Suzuki
- School of PharmacyTokyo University of Pharmacy and Life Sciences 1432-1 Horinouchi Hachioji Tokyo 192-0392 Japan
| | - Florian Kleemiss
- Institut für Anorganische Chemie und KristallographieFachbereich 2-Biologie/ChemieUniversität Bremen Leobener Str. 3 28359 Bremen Germany
| | - Haruhiko Fukaya
- School of PharmacyTokyo University of Pharmacy and Life Sciences 1432-1 Horinouchi Hachioji Tokyo 192-0392 Japan
| | - Yasuo Dobashi
- School of PharmacyTokyo University of Pharmacy and Life Sciences 1432-1 Horinouchi Hachioji Tokyo 192-0392 Japan
| | - Lorraine A. Malaspina
- Institut für Anorganische Chemie und KristallographieFachbereich 2-Biologie/ChemieUniversität Bremen Leobener Str. 3 28359 Bremen Germany
| | - Simon Grabowsky
- Institut für Anorganische Chemie und KristallographieFachbereich 2-Biologie/ChemieUniversität Bremen Leobener Str. 3 28359 Bremen Germany
| | - Takashi Matsumoto
- School of PharmacyTokyo University of Pharmacy and Life Sciences 1432-1 Horinouchi Hachioji Tokyo 192-0392 Japan
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6
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Adenot A, von Wolff N, Lefèvre G, Berthet J, Thuéry P, Cantat T. Activation of SO
2
by N/Si
+
and N/B Frustrated Lewis Pairs: Experimental and Theoretical Comparison with CO
2
Activation. Chemistry 2019; 25:8118-8126. [DOI: 10.1002/chem.201901088] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Indexed: 01/07/2023]
Affiliation(s)
- Aurélien Adenot
- NIMBE, CEA, CNRS, CEA SaclayUniversité Paris-Saclay 91191 Gif-sur-Yvette France
| | - Niklas von Wolff
- NIMBE, CEA, CNRS, CEA SaclayUniversité Paris-Saclay 91191 Gif-sur-Yvette France
| | - Guillaume Lefèvre
- NIMBE, CEA, CNRS, CEA SaclayUniversité Paris-Saclay 91191 Gif-sur-Yvette France
| | - Jean‐Claude Berthet
- NIMBE, CEA, CNRS, CEA SaclayUniversité Paris-Saclay 91191 Gif-sur-Yvette France
| | - Pierre Thuéry
- NIMBE, CEA, CNRS, CEA SaclayUniversité Paris-Saclay 91191 Gif-sur-Yvette France
| | - Thibault Cantat
- NIMBE, CEA, CNRS, CEA SaclayUniversité Paris-Saclay 91191 Gif-sur-Yvette France
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7
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Fugel M, Malaspina LA, Pal R, Thomas SP, Shi MW, Spackman MA, Sugimoto K, Grabowsky S. Revisiting a Historical Concept by Using Quantum Crystallography: Are Phosphate, Sulfate and Perchlorate Anions Hypervalent? Chemistry 2019; 25:6523-6532. [PMID: 30759315 DOI: 10.1002/chem.201806247] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Indexed: 11/05/2022]
Abstract
There are many examples of atoms in molecules that violate Lewis' octet rule, because they have more than four electron pairs assigned to their valence. These atoms are referred to as hypervalent. However, hypervalency may be regarded as an artifact arising from Lewis' description of molecules, which is based on the assumption that electrons are localized in two-center two-electron bonds and lone pairs. In the present paper, the isoelectronic phosphate (PO4 3- ), sulfate (SO4 2- ) and perchlorate (ClO4 - ) anions were examined with respect to the concept of hypervalency. Lewis formulas containing a hypervalent central atom exist for all three anions. Based on X-ray wavefunction refinements of high-resolution X-ray diffraction data of representative crystal structures (MgNH4 PO4 ⋅6 H2 O, Li2 SO4 ⋅H2 O, and KClO4 ), complementary bonding analyses were performed. In this way, experimental information from the new field of quantum crystallography validate long-known facts, or refute long-standing misunderstandings. It is shown that the P-O and S-O bonds are highly polarized covalent bonds and, thus, the increase in the valence population following three-center four-electron bonding is not sufficient to yield hypervalent phosphorus or sulfur atoms, respectively. However, for the highly covalent Cl-O bond, most bonding indicators imply a hypervalent chlorine atom.
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Affiliation(s)
- Malte Fugel
- Department 2-Chemistry/Biology, Institute of Inorganic Chemistry and Crystallography, University of Bremen, Leobener Str. 3 and 7, 28359, Bremen, Germany
| | - Lorraine A Malaspina
- Department 2-Chemistry/Biology, Institute of Inorganic Chemistry and Crystallography, University of Bremen, Leobener Str. 3 and 7, 28359, Bremen, Germany
| | - Rumpa Pal
- Department 2-Chemistry/Biology, Institute of Inorganic Chemistry and Crystallography, University of Bremen, Leobener Str. 3 and 7, 28359, Bremen, Germany.,Current address: Division of Physics, Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8571, Japan
| | - Sajesh P Thomas
- School of Molecular Sciences, University of Western Australia, 35 Stirling Highway, Perth, WA, 6009, Australia.,Current address: Interdisciplinary Nanoscience Center - INANO-Kemi, Aarhus University, Langelandsgade 140, 8000, Aarhus C, Denmark
| | - Ming W Shi
- School of Molecular Sciences, University of Western Australia, 35 Stirling Highway, Perth, WA, 6009, Australia
| | - Mark A Spackman
- School of Molecular Sciences, University of Western Australia, 35 Stirling Highway, Perth, WA, 6009, Australia
| | - Kunihisa Sugimoto
- SPring-8, Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5198, Japan
| | - Simon Grabowsky
- Department 2-Chemistry/Biology, Institute of Inorganic Chemistry and Crystallography, University of Bremen, Leobener Str. 3 and 7, 28359, Bremen, Germany
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8
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Moreno Betancourt A, Schwabedissen J, Romano RM, Della Védova CO, Beckers H, Willner H, Stammler HG, Mitzel NW. Disulfuryl Dichloride ClSO 2 OSO 2 Cl: A Conformation and Polymorphism Chameleon. Chemistry 2018; 24:10409-10421. [PMID: 29709088 DOI: 10.1002/chem.201800817] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Indexed: 11/05/2022]
Abstract
Disulfuryl dichloride ClSO2 OSO2 Cl was characterized by vibrational spectroscopy in the gaseous and liquid phase as well as in the Ar-matrix. By varying the temperature, certain bands could be assigned to several conformers. Gas-phase electron diffraction revealed a dominance of the anti-conformer at ambient temperature. The same conformation was found in the solid state. Via the in situ technique for crystallization, not less than four different modifications were identified. Among these different modifications, the structural parameters of the molecules remain relatively constant, but the aggregation pattern changes. Although the molecules aggregate by chlorine⋅⋅⋅oxygen contacts in each modification, the geometrical parameters of these interaction show significant differences and were evaluated and are in part inconsistent with the halogen bonding concept.
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Affiliation(s)
- Angélica Moreno Betancourt
- CEQUINOR (UNLP-CONICET, CCT La Plata), Departamento de Química, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, CP 1900, Argentina
| | - Jan Schwabedissen
- Fakultät für Chemie, Lehrstuhl für Anorganische Chemie und Strukturchemie, Centrum für molekulare Materialien CM2, Universität Bielefeld, Universitätsstr. 25, 33615, Bielefeld, Germany
| | - Rosana M Romano
- CEQUINOR (UNLP-CONICET, CCT La Plata), Departamento de Química, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, CP 1900, Argentina
| | - Carlos O Della Védova
- CEQUINOR (UNLP-CONICET, CCT La Plata), Departamento de Química, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, CP 1900, Argentina
| | - Helmut Beckers
- Institut für Chemie und Biochemie, Anorganische Chemie, Freie Universität Berlin, Fabeckstraße 34-36, 14195, Berlin, Germany
| | - Helge Willner
- FB C-Anorganische Chemie, Bergische Universität Wuppertal, Gaußstraße 20, 42097, Wuppertal, Germany
| | - Hans-Georg Stammler
- Fakultät für Chemie, Lehrstuhl für Anorganische Chemie und Strukturchemie, Centrum für molekulare Materialien CM2, Universität Bielefeld, Universitätsstr. 25, 33615, Bielefeld, Germany
| | - Norbert W Mitzel
- Fakultät für Chemie, Lehrstuhl für Anorganische Chemie und Strukturchemie, Centrum für molekulare Materialien CM2, Universität Bielefeld, Universitätsstr. 25, 33615, Bielefeld, Germany
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9
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Genoni A, Bučinský L, Claiser N, Contreras-García J, Dittrich B, Dominiak PM, Espinosa E, Gatti C, Giannozzi P, Gillet JM, Jayatilaka D, Macchi P, Madsen AØ, Massa L, Matta CF, Merz KM, Nakashima PNH, Ott H, Ryde U, Schwarz K, Sierka M, Grabowsky S. Quantum Crystallography: Current Developments and Future Perspectives. Chemistry 2018; 24:10881-10905. [PMID: 29488652 DOI: 10.1002/chem.201705952] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 02/27/2018] [Indexed: 11/09/2022]
Abstract
Crystallography and quantum mechanics have always been tightly connected because reliable quantum mechanical models are needed to determine crystal structures. Due to this natural synergy, nowadays accurate distributions of electrons in space can be obtained from diffraction and scattering experiments. In the original definition of quantum crystallography (QCr) given by Massa, Karle and Huang, direct extraction of wavefunctions or density matrices from measured intensities of reflections or, conversely, ad hoc quantum mechanical calculations to enhance the accuracy of the crystallographic refinement are implicated. Nevertheless, many other active and emerging research areas involving quantum mechanics and scattering experiments are not covered by the original definition although they enable to observe and explain quantum phenomena as accurately and successfully as the original strategies. Therefore, we give an overview over current research that is related to a broader notion of QCr, and discuss options how QCr can evolve to become a complete and independent domain of natural sciences. The goal of this paper is to initiate discussions around QCr, but not to find a final definition of the field.
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Affiliation(s)
- Alessandro Genoni
- Université de Lorraine, CNRS, Laboratoire LPCT, 1 Boulevard Arago, F-57078, Metz, France
| | - Lukas Bučinský
- Institute of Physical Chemistry and Chemical Physics, Slovak University of Technology, FCHPT SUT, Radlinského 9, SK-812 37, Bratislava, Slovakia
| | - Nicolas Claiser
- Université de Lorraine, CNRS, Laboratoire CRM2, Boulevard des Aiguillettes, BP 70239, F-54506, Vandoeuvre-lès-Nancy, France
| | - Julia Contreras-García
- Sorbonne Universités, UPMC Université Paris 06, CNRS, Laboratoire de Chimie Théorique (LCT), 4 Place Jussieu, F-75252, Paris Cedex 05, France
| | - Birger Dittrich
- Anorganische und Strukturchemie II, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Paulina M Dominiak
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, ul. Żwirki i Wigury 101, 02-089, Warszawa, Poland
| | - Enrique Espinosa
- Université de Lorraine, CNRS, Laboratoire CRM2, Boulevard des Aiguillettes, BP 70239, F-54506, Vandoeuvre-lès-Nancy, France
| | - Carlo Gatti
- CNR-ISTM Istituto di Scienze e Tecnologie Molecolari, via Golgi 19, Milano, I-20133, Italy.,Istituto Lombardo Accademia di Scienze e Lettere, via Brera 28, 20121, Milano, Italy
| | - Paolo Giannozzi
- Department of Mathematics, Computer Science and Physics, University of Udine, Via delle Scienze 208, I-33100, Udine, Italy
| | - Jean-Michel Gillet
- Structure, Properties and Modeling of Solids Laboratory, CentraleSupelec, Paris-Saclay University, 3 rue Joliot-Curie, 91191, Gif-sur-Yvette, France
| | - Dylan Jayatilaka
- School of Molecular Sciences, University of Western Australia, 35 Stirling Highway, Perth, WA, 6009, Australia
| | - Piero Macchi
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012, Bern, Switzerland
| | - Anders Ø Madsen
- Department of Pharmacy, University of Copenhagen, Universitetsparken 2, 2100, Copenhagen, Denmark
| | - Lou Massa
- Hunter College & the Ph.D. Program of the Graduate Center, City University of New York, New York, USA
| | - Chérif F Matta
- Department of Chemistry and Physics, Mount Saint Vincent University, Halifax, Nova Scotia, B3M 2J6, Canada.,Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, B3H 4J3, Canada.,Department of Chemistry, Saint Mary's University, Halifax, Nova Scotia, B3H 3C3, Canada.,Département de Chimie, Université Laval, Québec, QC G1V 0A6, Canada
| | - Kenneth M Merz
- Department of Chemistry and Department of Biochemistry and Molecular Biology, Michigan State University, 578 South Shaw Lane, East Lansing, Michigan, 48824, USA.,Institute for Cyber Enabled Research, Michigan State University, 567 Wilson Road, Room 1440, East Lansing, Michigan, 48824, USA
| | - Philip N H Nakashima
- Department of Materials Science and Engineering, Monash University, Victoria, 3800, Australia
| | - Holger Ott
- Bruker AXS GmbH, Östliche Rheinbrückenstraße 49, 76187, Karlsruhe, Germany
| | - Ulf Ryde
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-22100, Lund, Sweden
| | - Karlheinz Schwarz
- Technische Universität Wien, Institut für Materialwissenschaften, Getreidemarkt 9, A-1060, Vienna, Austria
| | - Marek Sierka
- Otto Schott Institute of Materials Research, Friedrich Schiller University Jena, Löbdergraben 32, 07743, Jena, Germany
| | - Simon Grabowsky
- Fachbereich 2-Biologie/Chemie, Institut für Anorganische Chemie und Kristallographie, Universität Bremen, Leobener Str. 3, 28359, Bremen, Germany
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10
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Yanai H, Almendros P, Takahashi S, Lázaro-Milla C, Alcaide B, Matsumoto T. Synthesis and Characterization of Stable Phosphorus Carbabetaines. Chem Asian J 2018; 13:1956-1961. [PMID: 29771003 DOI: 10.1002/asia.201800769] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Indexed: 12/25/2022]
Abstract
Phosphorus 1,3- and 1,4-carbabetaines with 'P(+)-C-C(-)' and 'P(+)-C-C-C(-)' structures, respectively, in which the carbanion moiety was significantly stabilized by two trifluoromethylsulfonyl groups, have been synthesized and characterized. Analysis of their X-ray crystal structures revealed that any attractive interactions between the anionic and cationic moieties were negligibly weak. This result was corroborated by using natural bond orbital (NBO) and Bader's quantum theory of atoms in molecules (QTAIM) models. In contrast, performing the same analysis of a known 1,3-carbabetaine equivalent, which can be drawn as a 'P(+)-C-C=C-O(-)' resonance structure, revealed pronounced charge-transfer interactions between the anionic and cationic moieties.
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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
| | - Pedro Almendros
- Instituto de Química Orgánica General, Consejo Superior de Investigaciones Científicas (IQOG-CSIC), Juan de la Cierva 3, 28006, Madrid, Spain
| | - Saori Takahashi
- School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392, Japan
| | - Carlos Lázaro-Milla
- Grupo de Lactamas y Heterociclos Bioactivos, Departamento de Química Orgánica I, Unidad Asociada al CSIC, Facultad de Química, Universidad Complutense de Madrid, 28040, Madrid, Spain
| | - Benito Alcaide
- Grupo de Lactamas y Heterociclos Bioactivos, Departamento de Química Orgánica I, Unidad Asociada al CSIC, Facultad de Química, Universidad Complutense de Madrid, 28040, Madrid, Spain
| | - Takashi Matsumoto
- School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392, Japan
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11
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Woińska M, Jayatilaka D, Dittrich B, Flaig R, Luger P, Woźniak K, Dominiak PM, Grabowsky S. Validation of X-ray Wavefunction Refinement. Chemphyschem 2017; 18:3334-3351. [PMID: 29168318 DOI: 10.1002/cphc.201700810] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 09/22/2017] [Indexed: 11/10/2022]
Abstract
In this work, the quality of the electron density in crystals reconstructed by the multipolar model (MM) and by X-ray wavefunction refinement (XWR) is tested on a set of high-resolution X-ray diffraction data sets of four amino acids and six tripeptides. It results in the first thorough validation of XWR. Agreement statistics, figures of merit, residual- and deformation-density maps, as well as atomic displacement parameters are used to measure the quality of the reconstruction relative to the measured structure factors. Topological analysis of the reconstructed density is carried out to obtain atomic and bond-topological properties, which are subsequently compared to the values derived from benchmarking periodic DFT geometry optimizations. XWR is simultaneously in better agreement than the MM with both benchmarking theory and the measured diffraction pattern. In particular, the obvious problems with the description of polar bonds in the MM are significantly reduced by using XWR. Similarly, modeling of electron density in the vicinity of hydrogen atoms with XWR is visibly improved.
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Affiliation(s)
- Magdalena Woińska
- Biological and Chemical Research Centre, Chemistry Department, University of Warsaw, Zwirki i Wigury 101, 02-089, Warsaw, Poland
| | - Dylan Jayatilaka
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Perth, WA, 6009, Australia
| | - Birger Dittrich
- Heinrich-Heine-Universität Düsseldorf, Anorganische Chemie und Strukturchemie, Gebäude 26.42.01.21, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Ralf Flaig
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxon, OX11 0DE, UK
| | - Peter Luger
- Freie Universität Berlin, Institut für Chemie und Biochemie, Fabeckstraße 36a, 14195, Berlin, Germany
| | - Krzysztof Woźniak
- Biological and Chemical Research Centre, Chemistry Department, University of Warsaw, Zwirki i Wigury 101, 02-089, Warsaw, Poland
| | - Paulina M Dominiak
- Biological and Chemical Research Centre, Chemistry Department, University of Warsaw, Zwirki i Wigury 101, 02-089, Warsaw, Poland
| | - Simon Grabowsky
- Institut für Anorganische Chemie und Kristallographie, Fachbereich 2-Biologie/Chemie, Universität Bremen, Leobener Straße NW2, 28359, Bremen, Germany
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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] [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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Chęcińska L, Mebs S, Ośmiałowski B, Zakrzewska A, Ejsmont K, Kohout M. Tuning the Electronic Properties of the Dative N−B Bond with Associated O−B Interaction: Electron Localizability Indicator from X-Ray Wavefunction Refinement. Chemphyschem 2016; 17:2395-406. [DOI: 10.1002/cphc.201600223] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Indexed: 11/08/2022]
Affiliation(s)
- Lilianna Chęcińska
- Department of Theoretical and Structural Chemistry; Faculty of Chemistry; University of Lodz; Pomorska 163/165 90-236 Łódź Poland
| | - Stefan Mebs
- Institut für Experimentalphysik; Freie Universität Berlin; Arnimallee 14 14195 Berlin Germany
| | - Borys Ośmiałowski
- Faculty of Chemical Technology and Engineering; University of Technology and Life Sciences; Seminaryjna 3 85-326 Bydgoszcz Poland
| | - Anna Zakrzewska
- Faculty of Chemical Technology and Engineering; University of Technology and Life Sciences; Seminaryjna 3 85-326 Bydgoszcz Poland
| | - Krzysztof Ejsmont
- Faculty of Chemistry; Opole University; Oleska Street 48 45-052 Opole Poland
| | - M. Kohout
- Max Planck Institute for Chemical Physics of Solids; Nöthnitzer Str. 40 01187 Dresden Germany
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Charge Density and Chemical Bonding. STRUCTURE AND BONDING 2016. [DOI: 10.1007/430_2015_199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
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Carl E, Demeshko S, Meyer F, Stalke D. Triimidosulfonates as Acute Bite-Angle Chelates: Slow Relaxation of the Magnetization in Zero Field and Hysteresis Loop of a CoIIComplex. Chemistry 2015; 21:10109-15. [DOI: 10.1002/chem.201406083] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Indexed: 11/07/2022]
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Dittrich B, Wandtke CM, Meents A, Pröpper K, Mondal KC, Samuel PP, Amin Sk N, Singh AP, Roesky HW, Sidhu N. Aspherical-atom modeling of coordination compounds by single-crystal X-ray diffraction allows the correct metal atom to be identified. Chemphyschem 2014; 16:412-9. [PMID: 25393218 DOI: 10.1002/cphc.201402600] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Revised: 09/13/2014] [Indexed: 11/10/2022]
Abstract
Single-crystal X-ray diffraction (XRD) is often considered the gold standard in analytical chemistry, as it allows element identification as well as determination of atom connectivity and the solid-state structure of completely unknown samples. Element assignment is based on the number of electrons of an atom, so that a distinction of neighboring heavier elements in the periodic table by XRD is often difficult. A computationally efficient procedure for aspherical-atom least-squares refinement of conventional diffraction data of organometallic compounds is proposed. The iterative procedure is conceptually similar to Hirshfeld-atom refinement (Acta Crystallogr. Sect. A- 2008, 64, 383-393; IUCrJ. 2014, 1,61-79), but it relies on tabulated invariom scattering factors (Acta Crystallogr. Sect. B- 2013, 69, 91-104) and the Hansen/Coppens multipole model; disordered structures can be handled as well. Five linear-coordinate 3d metal complexes, for which the wrong element is found if standard independent-atom model scattering factors are relied upon, are studied, and it is shown that only aspherical-atom scattering factors allow a reliable assignment. The influence of anomalous dispersion in identifying the correct element is investigated and discussed.
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Affiliation(s)
- Birger Dittrich
- Institut für Anorganische und Angewandte Chemie, Universität Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg (Germany); Institut für Anorganische Chemie, Georg-August-Universität, Tammannstrasse 4, 37077 Göttingen (Germany).
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Carl E, Stalke D. Polyimido Sulfur(VI) Phosphanyl Ligand in Metal Complexation. Chemistry 2014; 20:15849-54. [DOI: 10.1002/chem.201404860] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Indexed: 11/11/2022]
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Junold K, Mück FM, Kupper C, Baus JA, Burschka C, Tacke R. Activation of Sulfur Dioxide by Bis[N,N′-diisopropylbenzamidinato(−)]silicon(II): Synthesis of Neutral Six-Coordinate Silicon(IV) Complexes with ChelatingO,O′-Sulfito orO,O′-Dithionito Ligands. Chemistry 2014; 20:12781-5. [DOI: 10.1002/chem.201404119] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Indexed: 11/07/2022]
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Beichel W, Trapp N, Hauf C, Kohler O, Eickerling G, Scherer W, Krossing I. Charge-Scaling Effect in Ionic Liquids from the Charge-Density Analysis ofN,N′-Dimethylimidazolium Methylsulfate. Angew Chem Int Ed Engl 2014; 53:3143-6. [DOI: 10.1002/anie.201308760] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Indexed: 11/12/2022]
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Beichel W, Trapp N, Hauf C, Kohler O, Eickerling G, Scherer W, Krossing I. Charge-Scaling Effect in Ionic Liquids from the Charge-Density Analysis ofN,N′-Dimethylimidazolium Methylsulfate. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201308760] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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