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Janicki R, Starynowicz P. Analysis of charge density in nonaaquagadolinium(III) trifluoromethanesulfonate - insight into Gd III-OH 2 bonding. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2020; 76:572-580. [PMID: 32831276 DOI: 10.1107/s2052520620006903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 05/21/2020] [Indexed: 06/11/2023]
Abstract
The experimental charge-density distribution in [Gd(H2O)9](CF3SO3)3 has been analysed and compared with the theoretical density functional theory calculations. Although the Gd-OH2 bonds are mainly ionic, a covalent contribution is detectable when inspecting both the topological parameters of these bonds and the natural bond orbital results. This contribution originates from small electron transfer from the lone pairs of oxygen atoms to empty 5d and 6s spin orbitals of Gd3+.
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Affiliation(s)
- Rafał Janicki
- Wydział Chemii, Uniwersytet Wrocławski, ul. F. Joliot-Curie 14, Wrocław, 50-383, Poland
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Kalugin AE, Komarov PD, Minyaev ME, Lyssenko KA, Roitershtein DM, Nifant’ev IE. Bis[μ-bis-(2,6-diiso-propyl-phen-yl) phosphato-κ 2 O: O']bis-[(2,2'-bi-pyridine-κ 2 N, N')lithium] toluene disolvate and its catalytic activity in ring-opening polymerization of ∊-caprolactone and l-dilactide. Acta Crystallogr E Crystallogr Commun 2019; 75:848-853. [PMID: 31391980 PMCID: PMC6658944 DOI: 10.1107/s2056989019006960] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 05/14/2019] [Indexed: 12/04/2022]
Abstract
The solvated centrosymmmtric title compound, [Li2(C24H34O4P)2(C10H8N2)2]·2C7H8, was formed in the reaction between {Li[(2,6-iPr2C6H3-O)2POO](MeOH)3}(MeOH) and 2,2'-bi-pyridine (bipy) in toluene. The structure has monoclinic (P21/n) symmetry at 120 K and the asymmetric unit consists of half a complex mol-ecule and one mol-ecule of toluene solvent. The diaryl phosphate ligand demonstrates a μ-κO:κO'-bridging coordination mode and the 2,2'-bi-pyridine ligand is chelating to the Li+ cation, generating a distorted tetra-hedral LiN2O2 coordination polyhedron. The complex exhibits a unique dimeric Li2O4P2 core. One isopropyl group is disordered over two orientations in a 0.621 (4):0.379 (4) ratio. In the crystal, weak C-H⋯O and C-H⋯π inter-actions help to consolidate the packing. Catalytic systems based on the title complex and on the closely related complex {Li[(2,6-iPr2C6H3-O)2POO](MeOH)3}(MeOH) display activity in the ring-opening polymerization of ∊-caprolactone and l-dilactide.
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Affiliation(s)
- Alexey E. Kalugin
- A.V. Topchiev Institute of Petrochemical Synthesis, Russian Academy of Sciences, 29 Leninsky Prospect, 119991, Moscow, Russian Federation
- Moscow Institute of Physics and Technology, Department of Biological and Medical Physics, 9 Institutskiy Per., Dolgoprudny, Moscow Region, 141701, Russian Federation
| | - Pavel D. Komarov
- A.V. Topchiev Institute of Petrochemical Synthesis, Russian Academy of Sciences, 29 Leninsky Prospect, 119991, Moscow, Russian Federation
| | - Mikhail E. Minyaev
- A.V. Topchiev Institute of Petrochemical Synthesis, Russian Academy of Sciences, 29 Leninsky Prospect, 119991, Moscow, Russian Federation
| | - Konstantin A. Lyssenko
- G.V. Plekhanov Russian University of Economics, 36 Stremyanny Per., Moscow, 117997, Russian Federation
- Chemistry Department, M.V. Lomonosov Moscow State University, 1 Leninskie Gory Str., Building 3, Moscow 119991, Russian Federation
| | - Dmitrii M. Roitershtein
- A.V. Topchiev Institute of Petrochemical Synthesis, Russian Academy of Sciences, 29 Leninsky Prospect, 119991, Moscow, Russian Federation
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 47 Leninsky Prospect, Moscow 119991, Russian Federation
| | - Ilya E. Nifant’ev
- A.V. Topchiev Institute of Petrochemical Synthesis, Russian Academy of Sciences, 29 Leninsky Prospect, 119991, Moscow, Russian Federation
- Chemistry Department, M.V. Lomonosov Moscow State University, 1 Leninskie Gory Str., Building 3, Moscow 119991, Russian Federation
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Jarzembska KN, Řlepokura K, Kamiński R, Gutmann MJ, Dominiak PM, Woźniak K. Multi-temperature study of potassium uridine-5'-monophosphate: electron density distribution and anharmonic motion modelling. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2017; 73:550-564. [PMID: 28762967 DOI: 10.1107/s2052520617005534] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 04/12/2017] [Indexed: 06/07/2023]
Abstract
Uridine, a nucleoside formed of a uracil fragment attached to a ribose ring via a β-N1-glycosidic bond, is one of the four basic components of ribonucleic acid. Here a new anhydrous structure and experimental charge density distribution analysis of a uridine-5'-monophosphate potassium salt, K(UMPH), is reported. The studied case constitutes the very first structure of a 5'-nucleotide potassium salt according to the Cambridge Structural Database. The excellent crystal quality allowed the collection of charge density data at various temperatures, i.e. 10, 100, 200 and 300 K on one single crystal. Crystal structure and charge density data were analysed thoroughly in the context of related literature-reported examples. Detailed analysis of the charge density distribution revealed elevated anharmonic motion of part of the uracil ring moiety relatively weakly interacting with the neighbouring species. The effect was manifested by alternate positive and negative residual density patterns observed for these atoms, which `disappear' at low temperature. It also occurred that the potassium cation, quite uniformly coordinated by seven O atoms from all molecular fragments of the UMPH- anion, including the O atom from the ribofuranose ring, can be treated as spherical in the charge density model which was supported by theoretical calculations. Apart from the predominant electrostatic interactions, four relatively strong hydrogen bond types further support the stability of the crystal structure. This results in a compact and quite uniform structure (in all directions) of the studied crystal, as opposed to similar cases with layered architecture reported in the literature.
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Affiliation(s)
- Katarzyna N Jarzembska
- Department of Chemistry, University of Warsaw, Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Katarzyna Řlepokura
- Department of Chemistry, University of Wrocław, Joliot-Curie 14, 50-383 Wrocław, Poland
| | - Radosław Kamiński
- Department of Chemistry, University of Warsaw, Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Matthias J Gutmann
- ISIS Neutron and Muon Source, Science and Technology Facilities Council, Rutherford Appleton Laboratory, Harwell Campus, Didcot, Oxfordshire OX11 0QX, England
| | - Paulina M Dominiak
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Krzysztof Woźniak
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Żwirki i Wigury 101, 02-089 Warsaw, Poland
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Mermer A, Lis T, Starynowicz P. Charge density distribution and theoretical analysis of low and high energy phosphate esters. RSC Adv 2015. [DOI: 10.1039/c5ra12605c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
There is a strict relation between the energy of hydrolysis of phosphate esters and the extent of interactions between the p ester oxygen lone pair and the antibonding orbitals of the rest of the molecule. Its impact on experimental charge density distribution is analyzed.
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Affiliation(s)
- Adrian Mermer
- Wydział Chemii
- Uniwersytet Wrocławski
- 50-383 Wrocław
- Poland
| | - Tadeusz Lis
- Wydział Chemii
- Uniwersytet Wrocławski
- 50-383 Wrocław
- Poland
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