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Fukin GK, Cherkasov AV. Experimental, experimental–theoretical and theoretical estimates of intermolecular interaction energies in η6-[(5-methyl-1,3-oxazolidin-3-yl)benzene]tricarbonylchromium(0). MENDELEEV COMMUNICATIONS 2021. [DOI: 10.1016/j.mencom.2021.03.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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2
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Denhof A, Olaru M, Lork E, Mebs S, Chęcińska L, Beckmann J. Silyl Cations Stabilized by Pincer Type Ligands with Adjustable Donor Atoms. Eur J Inorg Chem 2020. [DOI: 10.1002/ejic.202000800] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Andreas Denhof
- Institut für Anorganische Chemie und Kristallographie Universität Bremen Leobener Straße 7 28359 Bremen Germany
| | - Marian Olaru
- Institut für Anorganische Chemie und Kristallographie Universität Bremen Leobener Straße 7 28359 Bremen Germany
- Department of Chemistry Supramolecular Organic and Organometallic Chemistry Centre Babes‐Bolyai University 11 Arany Janos 400028 Cluj‐Napoca Romania
| | - Enno Lork
- Institut für Anorganische Chemie und Kristallographie Universität Bremen Leobener Straße 7 28359 Bremen Germany
| | - Stefan Mebs
- Institut für Experimentalphysik Freie Universität Berlin Arnimallee 14 14195 Berlin Germany
| | - Lilianna Chęcińska
- Institut für Anorganische Chemie und Kristallographie Universität Bremen Leobener Straße 7 28359 Bremen Germany
- Department of Theoretical and Structural Chemistry Faculty of Chemistry University of Lodz Pomorska 163/165 90‐236 Lodz Poland
| | - Jens Beckmann
- Institut für Anorganische Chemie und Kristallographie Universität Bremen Leobener Straße 7 28359 Bremen Germany
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3
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Korlyukov AA, Nelyubina YV. Quantum chemical methods in charge density studies from X-ray diffraction data. RUSSIAN CHEMICAL REVIEWS 2019. [DOI: 10.1070/rcr4866] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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4
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Zobel D, Strumpel M. Electron density: historical remarks with a focus on the Berlin school. Z KRIST-CRYST MATER 2018. [DOI: 10.1515/zkri-2018-2062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
The history of electron density (ED) research is surveyed and its historical highlights in the 20th century are summarized. The progress, reached at the beginnig of the 21st century, is described including contributions from the Berlin school. Key experimental advances concern X-ray sources and synchrotron radiation, measuring reflection data at very low temperatures (down to ~10 K), as well as the introduction of area detectors. Methodological progress was reached by new software systems for the refinement and analysis of ED data sets. This allowed to obtain quantitative ED properties, making use of Bader’s Quantum Theory of Atoms in Molecules (QTAIM). More recently methods, which combine experimental X-ray data and quantum-chemically derived wave functions, established the rapidly developing new field of “Quantum Crystallography.”
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Affiliation(s)
- Dieter Zobel
- Institute for Chemistry and Biochemistry, Inorganic Chemistry , Freie Universität Berlin, Fabeckstrasse 36a , 14195 Berlin , Germany
| | - Marianna Strumpel
- Institute for Chemistry and Biochemistry, Inorganic Chemistry , Freie Universität Berlin, Fabeckstrasse 36a , 14195 Berlin , Germany
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5
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Kovalenko AA, Nelyubina YV, Korlyukov AA, Lyssenko KA, Ananyev IV. The truth is out there: the metal-π interactions in crystal of Cr(CO)3(pcp) as revealed by the study of vibrational smearing of electron density. ACTA ACUST UNITED AC 2017. [DOI: 10.1515/zkri-2017-2085] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
The vibrational smearing of electron density was studied in the crystal of complex of Cr(CO)3 with [2.2]paracyclophane. The combination of theoretical and experimental methods, including periodic calculations and screening of DFT calculated and multipole-decomposed electron densities, was utilized to reveal the vibrational smearing of electron density and its influence on the multipole-constructed electron density. The multipole model, commonly used to treat the high-resolution X-ray diffraction data, was shown to be rather inaccurate in description of electron density and its vibrational smearing in metal-π complex where the interchange between diatomic interactions can occur. Namely, some bond critical points can be hidden while analyzing multipole-decomposed electron density with proved effects of vibrational smearing even if the deconvolution problem is overcome by using the invariom approach. On the contrary, the recently proposed “clouds of critical point variation” (CCPV) approach is demonstrated as the route to gather all reasonable bonding trends and to reconstruct static electron density pattern in metal-π complexes.
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Affiliation(s)
- Anna A. Kovalenko
- M.V. Lomonosov Moscow State University , GSP-1, Leninskie Gory Str. , 119991, Moscow , Russia
- A.N. Nesmeyanov Institute of Organoelement Compounds , Russian Academy of Sciences , Vavilova Str., 28 , 119991, Moscow , Russia
- Pirogov Russian National Research Medical University , Ostrovitianov Str., 1 , 117997, Moscow , Russia
- N.D. Zelinsky Institute of Organic Chemistry RAS , Leninsky Prospect, 47 , 119991, Moscow , Russian Federation
| | - Yulia V. Nelyubina
- M.V. Lomonosov Moscow State University , GSP-1, Leninskie Gory Str. , 119991, Moscow , Russia
- A.N. Nesmeyanov Institute of Organoelement Compounds , Russian Academy of Sciences , Vavilova Str., 28 , 119991, Moscow , Russia
- Pirogov Russian National Research Medical University , Ostrovitianov Str., 1 , 117997, Moscow , Russia
- N.D. Zelinsky Institute of Organic Chemistry RAS , Leninsky Prospect, 47 , 119991, Moscow , Russian Federation
| | - Alexander A. Korlyukov
- M.V. Lomonosov Moscow State University , GSP-1, Leninskie Gory Str. , 119991, Moscow , Russia
- A.N. Nesmeyanov Institute of Organoelement Compounds , Russian Academy of Sciences , Vavilova Str., 28 , 119991, Moscow , Russia
- Pirogov Russian National Research Medical University , Ostrovitianov Str., 1 , 117997, Moscow , Russia
- N.D. Zelinsky Institute of Organic Chemistry RAS , Leninsky Prospect, 47 , 119991, Moscow , Russian Federation
| | - Konstantin A. Lyssenko
- M.V. Lomonosov Moscow State University , GSP-1, Leninskie Gory Str. , 119991, Moscow , Russia
- A.N. Nesmeyanov Institute of Organoelement Compounds , Russian Academy of Sciences , Vavilova Str., 28 , 119991, Moscow , Russia
- Pirogov Russian National Research Medical University , Ostrovitianov Str., 1 , 117997, Moscow , Russia
- N.D. Zelinsky Institute of Organic Chemistry RAS , Leninsky Prospect, 47 , 119991, Moscow , Russian Federation
| | - Ivan V. Ananyev
- A.N. Nesmeyanov Institute of Organoelement Compounds , Russian Academy of Sciences , Vavilova Str., 28 , 119991, Moscow , Russia
- N.D. Zelinsky Institute of Organic Chemistry RAS , Leninsky Prospect, 47 , 119991, Moscow , Russian Federation
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6
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Nelyubina YV, Korlyukov AA, Lyssenko KA, Fedyanin IV. Transferable Aspherical Atom Modeling of Electron Density in Highly Symmetric Crystals: A Case Study of Alkali-Metal Nitrates. Inorg Chem 2017; 56:4689-4697. [PMID: 28375004 DOI: 10.1021/acs.inorgchem.7b00340] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A comparative electron density study (from X-ray diffraction and periodic quantum chemistry) of sodium and potassium nitrates is performed to test the performance of a transferrable aspherical atom model, which is based on the invarioms, to describe chemical bonding features of ions occurring in sites of different symmetry typical of inorganic salts and in different crystal environments. Relying on tabulated entries for the isolated ions (although tailor-made to account for different site symmetries), it takes the same time to employ as the spherical atom model routinely used in X-ray diffraction studies but provides an electron density distribution that faithfully reveals all the interionic interactions-even the weakest ones (such as between the nitrate anions or a K···N interaction found in the metastable form of KNO3) yet important for properties of inorganic materials-as if obtained from high-resolution X-ray diffraction data.
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Affiliation(s)
- Yulia V Nelyubina
- A.N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences , Vavilova Street, 28, Moscow 119991, Russia
| | - Alexander A Korlyukov
- A.N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences , Vavilova Street, 28, Moscow 119991, Russia.,Pirogov Russian National Research Medical University , Ostrovitianova Street, 1, Moscow 117997, Russia
| | - Konstantin A Lyssenko
- A.N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences , Vavilova Street, 28, Moscow 119991, Russia
| | - Ivan V Fedyanin
- A.N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences , Vavilova Street, 28, Moscow 119991, Russia
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7
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Shi MW, Stewart SG, Sobolev AN, Dittrich B, Schirmeister T, Luger P, Hesse M, Chen Y, Spackman PR, Spackman MA, Grabowsky S. Approaching an experimental electron density model of the biologically active
trans
‐epoxysuccinyl amide group—Substituent effects vs. crystal packing. J PHYS ORG CHEM 2017. [DOI: 10.1002/poc.3683] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Ming W. Shi
- School of Chemistry and Biochemistry The University of Western Australia Perth WA Australia
| | - Scott G. Stewart
- School of Chemistry and Biochemistry The University of Western Australia Perth WA Australia
| | - Alexandre N. Sobolev
- School of Chemistry and Biochemistry The University of Western Australia Perth WA Australia
| | - Birger Dittrich
- Anorganische Chemie und Strukturchemie Heinrich‐Heine‐Universität Düsseldorf Düsseldorf Germany
| | - Tanja Schirmeister
- Institut für Pharmazie und Biochemie Johannes‐Gutenberg‐Universität Mainz Mainz Germany
| | - Peter Luger
- Institut für Chemie und Biochemie, Anorganische Chemie Freie Universität Berlin Berlin Germany
| | - Malte Hesse
- Fachbereich 2—Biologie/Chemie, Institut für Anorganische Chemie und Kristallographie Universität Bremen Bremen Germany
| | - Yu‐Sheng Chen
- ChemMatCARS The University of Chicago Argonne IL USA
| | - Peter R. Spackman
- School of Chemistry and Biochemistry The University of Western Australia Perth WA Australia
| | - Mark A. Spackman
- School of Chemistry and Biochemistry The University of Western Australia Perth WA Australia
| | - Simon Grabowsky
- School of Chemistry and Biochemistry The University of Western Australia Perth WA Australia
- Fachbereich 2—Biologie/Chemie, Institut für Anorganische Chemie und Kristallographie Universität Bremen Bremen Germany
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8
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Nelyubina YV, Ananyev IV, Novikov VV, Lyssenko KA. Invariom approach to electron density studies of open-shell compounds: the case of an organic nitroxide radical. RSC Adv 2016. [DOI: 10.1039/c6ra21365k] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The study reports the successful modeling of electron density with invarioms for an open-shell compound, an organic nitroxide radical.
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Affiliation(s)
- Yu. V. Nelyubina
- A.N.Nesmeyanov Institute of Organoelement Compounds
- Russian Academy of Sciences
- Moscow
- Russia
| | - I. V. Ananyev
- A.N.Nesmeyanov Institute of Organoelement Compounds
- Russian Academy of Sciences
- Moscow
- Russia
| | - V. V. Novikov
- A.N.Nesmeyanov Institute of Organoelement Compounds
- Russian Academy of Sciences
- Moscow
- Russia
| | - K. A. Lyssenko
- A.N.Nesmeyanov Institute of Organoelement Compounds
- Russian Academy of Sciences
- Moscow
- Russia
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9
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Geyer M, Baus JA, Fjellström O, Wellner E, Gustafsson L, Tacke R. Synthesis and Pharmacological Properties of Silicon-Containing GPR81 and GPR109A Agonists. ChemMedChem 2015; 10:2063-70. [DOI: 10.1002/cmdc.201500343] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Revised: 09/28/2015] [Indexed: 12/29/2022]
Affiliation(s)
- Marcel Geyer
- Universität Würzburg; Institut für Anorganische Chemie; Am Hubland 97074 Würzburg Germany
| | - Johannes A. Baus
- Universität Würzburg; Institut für Anorganische Chemie; Am Hubland 97074 Würzburg Germany
| | - Ola Fjellström
- AstraZeneca R&D Mölndal; CVMD Innovative Medicines; Pepparedsleden 1 43183 Mölndal Sweden
| | - Eric Wellner
- AstraZeneca R&D Mölndal; CVMD Innovative Medicines; Pepparedsleden 1 43183 Mölndal Sweden
| | - Linda Gustafsson
- AstraZeneca R&D Mölndal; CVMD Innovative Medicines; Pepparedsleden 1 43183 Mölndal Sweden
| | - Reinhold Tacke
- Universität Würzburg; Institut für Anorganische Chemie; Am Hubland 97074 Würzburg Germany
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10
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Nelyubina YV, Lyssenko KA. Probing Ionic Crystals by the Invariom Approach: An Electron Density Study of Guanidinium Chloride and Carbonate. Chemistry 2015; 21:9733-41. [PMID: 26015224 DOI: 10.1002/chem.201500296] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Revised: 04/21/2015] [Indexed: 11/09/2022]
Abstract
A comparative study of two guanidinium salts, chloride and carbonate, is carried out to test the performance of the invariom approach for ionic crystals. Although treating them as formed by isolated ions with no charge transfer between them, the invariom approach provides features of interionic contacts that are amazingly similar to those obtained from conventional charge density analysis of high-resolution X-ray diffraction data, thus emerging as an easy way towards reliable description of chemical bonding peculiarities in ionic crystals.
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Affiliation(s)
- Yulia V Nelyubina
- A. N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, 119991, Vavilova Str., 28, Moscow (Russia).
| | - Konstantin A Lyssenko
- A. N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, 119991, Vavilova Str., 28, Moscow (Russia)
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11
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Geyer M, Wellner E, Jurva U, Saloman S, Armstrong D, Tacke R. Can Silicon Make an Excellent Drug Even Better? An in vitro and in vivo Head-to-Head Comparison between Loperamide and Its Silicon Analogue Sila-Loperamide. ChemMedChem 2015; 10:911-24. [DOI: 10.1002/cmdc.201500040] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Indexed: 01/22/2023]
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12
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Novaković SB, Bogdanović GA, Heering C, Makhloufi G, Francuski D, Janiak C. Charge-Density Distribution and Electrostatic Flexibility of ZIF-8 Based on High-Resolution X-ray Diffraction Data and Periodic Calculations. Inorg Chem 2015; 54:2660-70. [DOI: 10.1021/ic5028256] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sladjana B. Novaković
- Vinča Institute
of Nuclear Sciences, University of Belgrade, P.O. Box 522, 11001 Belgrade, Serbia
| | - Goran A. Bogdanović
- Vinča Institute
of Nuclear Sciences, University of Belgrade, P.O. Box 522, 11001 Belgrade, Serbia
| | - Christian Heering
- Institut für Anorganische
Chemie und Strukturchemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstrasse
1, 40225 Düsseldorf, Germany
| | - Gamall Makhloufi
- Institut für Anorganische
Chemie und Strukturchemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstrasse
1, 40225 Düsseldorf, Germany
| | - Djordje Francuski
- Institute of Molecular Genetics and Genetic
Engineering, University of Belgrade, Vojvode Stepe 444a, 11010 Belgrade, Serbia
| | - Christoph Janiak
- Institut für Anorganische
Chemie und Strukturchemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstrasse
1, 40225 Düsseldorf, Germany
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13
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Kirby IL, Pitak MB, Coles SJ, Gale PA. Systematic Experimental Charge Density: Linking Structural Modifications to Electron Density Distributions. CHEM LETT 2015. [DOI: 10.1246/cl.140929] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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14
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Nelyubina YV, Korlyukov AA, Lyssenko KA. Invariom approach as a new tool in electron density studies of ionic liquids: a model case of 1-butyl-2,3-dimethylimidazolium chloride BDMIM[Cl]. RSC Adv 2015. [DOI: 10.1039/c5ra13752g] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
In this comparative study of an ionic liquid (IL), BDMIM[Cl], the invariom approximation emerges as a useful tool in search for ‘structure–property’ relations in ILs, as entangling complex interplay of interionic interactions that operate in them.
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Affiliation(s)
- Yu. V. Nelyubina
- A.N. Nesmeyanov Institute of Organoelement Compounds
- Russian Academy of Sciences
- Moscow
- Russia
| | - A. A. Korlyukov
- A.N. Nesmeyanov Institute of Organoelement Compounds
- Russian Academy of Sciences
- Moscow
- Russia
- Pirogov Russian National Research Medical University
| | - K. A. Lyssenko
- A.N. Nesmeyanov Institute of Organoelement Compounds
- Russian Academy of Sciences
- Moscow
- Russia
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15
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Luger P, Dittrich B, Tacke R. Invariom based electron density studies on the C/Si analogues haloperidol/sila-haloperidol and venlafaxine/sila-venlafaxine. Org Biomol Chem 2015. [DOI: 10.1039/c5ob00728c] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Hirshfeld surfaces of haloperidol hydropicrate (left) and sila-haloperidol hydrochloride (right) show comparable sites of ED concentrations due to comparable intermolecular environments.
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Affiliation(s)
- Peter Luger
- Institut für Chemie und Biochemie – Anorganische Chemie
- Freie Universität Berlin
- D-14195 Berlin
- Germany
| | - Birger Dittrich
- Institut für Angewandte und Anorganische Chemie
- Universität Hamburg
- D-20146 Hamburg
- Germany
| | - Reinhold Tacke
- Institut für Anorganische Chemie
- Universität Würzburg
- D-97074 Würzburg
- Germany
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16
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Dörrich S, Gelis L, Wolf S, Sunderkötter A, Mahler C, Guschina E, Tacke R, Hatt H, Kraft P. Comparative Analysis of the Olfactory Properties of Silicon/Germanium/Tin Analogues of the Lily-of-the-Valley Odorants Lilial and Bourgeonal. Chempluschem 2014. [DOI: 10.1002/cplu.201402160] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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17
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Nelyubina YV, Korlyukov AA, Lyssenko KA. Probing systematic errors in experimental charge density by multipole and invariom modeling: a twinned crystal of 1,10-phenanthroline hydrate. MENDELEEV COMMUNICATIONS 2014. [DOI: 10.1016/j.mencom.2014.09.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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18
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Nelyubina YV, Korlyukov AA, Lyssenko KA. Probing Weak Intermolecular Interactions by Using the Invariom Approach: A Comparative Study ofs-Tetrazine. Chemistry 2014; 20:6978-84. [DOI: 10.1002/chem.201304551] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Revised: 03/12/2014] [Indexed: 11/10/2022]
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19
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Ramesh R, Reddy DS. Zinc mediated allylations of chlorosilanes promoted by ultrasound: Synthesis of novel constrained sila amino acids. Org Biomol Chem 2014; 12:4093-7. [DOI: 10.1039/c4ob00294f] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
A simple, fast and efficient method for allylation and propargylation of chlorosilanes through zinc mediation and ultrasound promotion is reported. As a direct application of the resulting bis-allylsilanes, three novel, constrained sila amino acids are prepared for the first time.
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Affiliation(s)
- Remya Ramesh
- Division of Organic Chemistry
- CSIR-National Chemical Laboratory
- Pune, India
| | - D. Srinivasa Reddy
- Division of Organic Chemistry
- CSIR-National Chemical Laboratory
- Pune, India
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