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Mitoraj MP, Sagan F, Babashkina MG, Isaev AY, Chichigina YM, Safin DA. N
-Thiophosphorylthioureas RNHC(S)NHP(S)(Oi
Pr)2
as an Excellent Platform for Studying the Synergy between Hydrogen-Hydrogen Bonding and Other Families of Non-Covalent Interactions. European J Org Chem 2018. [DOI: 10.1002/ejoc.201801041] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Mariusz P. Mitoraj
- Department of Theoretical Chemistry; Faculty of Chemistry; Jagiellonian University; Gronostajowa 2 30-387 Cracow Poland
| | - Filip Sagan
- Department of Theoretical Chemistry; Faculty of Chemistry; Jagiellonian University; Gronostajowa 2 30-387 Cracow Poland
| | - Maria G. Babashkina
- Institute of Condensed Matter and Nanosciences; Université catholique de Louvain; Place L. Pasteur 1 1348 Louvain-la-Neuve Belgium
| | - Alexey Y. Isaev
- Institute of Chemistry; University of Tyumen; Perekopskaya Str. 15a 625003 Tyumen Russian Federation
| | - Yana M. Chichigina
- Institute of Chemistry; University of Tyumen; Perekopskaya Str. 15a 625003 Tyumen Russian Federation
| | - Damir A. Safin
- Institute of Condensed Matter and Nanosciences; Université catholique de Louvain; Place L. Pasteur 1 1348 Louvain-la-Neuve Belgium
- Institute of Chemistry; University of Tyumen; Perekopskaya Str. 15a 625003 Tyumen Russian Federation
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Mebs S, Kalläne SI, Braun T. Hapticity of asymmetric rhodium-allyl compounds in the light of real-space bonding indicators. Z KRIST-CRYST MATER 2018. [DOI: 10.1515/zkri-2017-2141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
AbstractRhodium boryl complexes are valuable catalysts for hydro- or diboration reactions of alkenes, but can also react with ketones (R2C=O) and imines (R2C=NR′) giving rise to insertion products having formally Rh–R2C–O/NR′–B linkages. The resulting molecular structures, however, may show complex metal–ligand and ligand–ligand interaction patterns with often unclear metal–ligand connectivities (hapticities, ηn). In order to assign the correct hapticity in a set of asymmetric rhodium-allyl compounds with molecular structures indicating η1−5bonding, a comprehensive DFT study was conducted. The study comprises determination of a variety of real-space bonding indicators derived from computed electron and pair densities according to the AIM, ELI-D, NCI, and DORI topological and surface approaches, which uncover the metal–ligand connectivties and suggest an asymmetric ligand–metal donation/metal–ligand back-donation framework according to the Dewar–Chatt–Duncanson model.
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Affiliation(s)
- Stefan Mebs
- Institut für Experimentelle Physik , Freie Universität Berlin , Arnimalle 14 , D-14195 Berlin , Germany , Tel.: +493083856084
| | - Sabrina Imke Kalläne
- Institut für Chemie , Humboldt-Universität zu Berlin , Brook-Taylor-Str. 2 , D-12489 Berlin , Germany
| | - Thomas Braun
- Institut für Chemie , Humboldt-Universität zu Berlin , Brook-Taylor-Str. 2 , D-12489 Berlin , Germany
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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: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [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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Complex modes of bonding: NCI/ELI-D vs. DORI surface analyses of hapticities and hydrogen–hydrogen contacts in zincocene related compounds. Chem Phys Lett 2016. [DOI: 10.1016/j.cplett.2016.03.046] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Mebs S, Braun B, Kositzki R, Limberg C, Haumann M. Abrupt versus Gradual Spin-Crossover in Fe(II)(phen)2(NCS)2 and Fe(III)(dedtc)3 Compared by X-ray Absorption and Emission Spectroscopy and Quantum-Chemical Calculations. Inorg Chem 2015; 54:11606-24. [PMID: 26624918 DOI: 10.1021/acs.inorgchem.5b01822] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Molecular spin-crossover (SCO) compounds are attractive for information storage and photovoltaic technologies. We compared two prototypic SCO compounds with Fe(II)N6 (1, [Fe(phen)2(NCS)2], with phen = 1,10-phenanthroline) or Fe(III)S6 (2, [Fe(dedtc)3], with dedtc = N,N'-diethyldithiocarbamate) centers, which show abrupt (1) or gradual (2) thermally induced SCO, using K-edge X-ray absorption and Kβ emission spectroscopy (XAS/XES) in a 8-315 K temperature range, single-crystal X-ray diffraction (XRD), and density functional theory (DFT). Core-to-valence and valence-to-core electronic transitions in the XAS/XES spectra and bond lengths change from XRD provided benchmark data, verifying the adequacy of the TPSSh/TZVP DFT approach for the description of low-spin (LS) and high-spin (HS) species. Determination of the spin densities, charge distributions, bonding descriptors, and valence-level configurations, as well as similar experimental and calculated enthalpy changes (ΔH), suggested that the varying metal-ligand bonding properties and deviating electronic structures converge to similar enthalpic contributions to the free-energy change (ΔG) and thus presumably are not decisive for the differing SCO behavior of 1 and 2. Rather, SCO seems to be governed by vibrational contributions to the entropy changes (ΔS) in both complexes. Intra- and intermolecular interactions in crystals of 1 and 2 were identified by atoms-in-molecules analysis. Thermal excitation of individual dedtc ligand vibrations accompanies the gradual SCO in 2. In contrast, extensive inter- and intramolecular phen/NCS vibrational mode coupling may be an important factor in the cooperative SCO behavior of 1.
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Affiliation(s)
- Stefan Mebs
- Institut für Experimentalphysik, Freie Universität Berlin , 14195 Berlin, Germany
| | - Beatrice Braun
- Institut für Chemie, Humboldt-Universität zu Berlin , 12489 Berlin, Germany
| | - Ramona Kositzki
- Institut für Experimentalphysik, Freie Universität Berlin , 14195 Berlin, Germany
| | - Christian Limberg
- Institut für Chemie, Humboldt-Universität zu Berlin , 12489 Berlin, Germany
| | - Michael Haumann
- Institut für Experimentalphysik, Freie Universität Berlin , 14195 Berlin, Germany
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Safin DA, Babashkina MG, Robeyns K, Mitoraj MP, Kubisiak P, Garcia Y. Influence of the Homopolar Dihydrogen Bonding CH⋅⋅⋅HC on Coordination Geometry: Experimental and Theoretical Studies. Chemistry 2015; 21:16679-87. [DOI: 10.1002/chem.201501499] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Indexed: 11/07/2022]
Affiliation(s)
- Damir A. Safin
- Institute of Condensed Matter and Nanosciences, Molecules, Solids and Reactivity (IMCN/MOST), Université catholique de Louvain, Place L. Pasteur 1, 1348 Louvain‐la‐Neuve (Belgium)
| | - Maria G. Babashkina
- Institute of Condensed Matter and Nanosciences, Molecules, Solids and Reactivity (IMCN/MOST), Université catholique de Louvain, Place L. Pasteur 1, 1348 Louvain‐la‐Neuve (Belgium)
| | - Koen Robeyns
- Institute of Condensed Matter and Nanosciences, Molecules, Solids and Reactivity (IMCN/MOST), Université catholique de Louvain, Place L. Pasteur 1, 1348 Louvain‐la‐Neuve (Belgium)
| | - Mariusz P. Mitoraj
- Department of Theoretical Chemistry, Faculty of Chemistry, Jagiellonian University, R. Ingardena 3, 30‐060 Krakow (Poland)
| | - Piotr Kubisiak
- Department of Theoretical Chemistry, Faculty of Chemistry, Jagiellonian University, R. Ingardena 3, 30‐060 Krakow (Poland)
| | - Yann Garcia
- Institute of Condensed Matter and Nanosciences, Molecules, Solids and Reactivity (IMCN/MOST), Université catholique de Louvain, Place L. Pasteur 1, 1348 Louvain‐la‐Neuve (Belgium)
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Mebs S, Chilleck MA, Meindl K, Hübschle CB. Fundamental relation between molecular geometry and real-space topology. Combined AIM, ELI-D, and ASF analysis of hapticities and intramolecular hydrogen-hydrogen bonds in zincocene-related compounds. J Phys Chem A 2014; 118:4351-62. [PMID: 24856733 DOI: 10.1021/jp503667g] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Despite numerous advanced and widely distributed bonding theories such as MO, VB, NBO, AIM, and ELF/ELI-D, complex modes of bonding such as M-Cp*((R)) interactions (hapticities) in asymmetrical metallocenes or weak intramolecular interactions (e.g., hydrogen-hydrogen (H···H) bonds) still remain a challenge for these theories in terms of defining whether or not an atom-atom interaction line (a "chemical bond") should be drawn. In this work the intramolecular Zn-C(Cp*(R)) (R = Me, -(CH2)2NMe2, and -(CH2)3NMe2) and H···H connectivity of a systematic set of 12 zincocene-related compounds is analyzed in terms of AIM and ELI-D topology combined with the recently introduced aspherical stockholder fragment (ASF) surfaces. This computational analysis unravels a distinct dependency of the AIM and ELI-D topology against the molecular geometry for both types of interactions, which confirms and extends earlier findings on smaller sets of compounds. According to these results the complete real-space topology including strong, medium, and weak interactions of very large compounds such as proteins may be reliably predicted by sole inspection of accurately determined molecular geometries, which would on the one hand afford new applications (e.g., accurate estimation of numbers, types, and strengths of intra- and intermolecular interactions) and on the other hand have deep implications on the significance of the method.
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Affiliation(s)
- Stefan Mebs
- Department of Experimental Physics, Freie Universität Berlin , Arnimallee 14, D-14195 Berlin, Germany
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