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Rubab SL, Raza AR, Nisar B, Ashfaq M, Altaf Y, Hussain R, Sajjad N, Akram MS, Tahir MN, Shaheen MA, Rehman MFU, Ali HM. Synthesis, Crystal Structure, DFT Calculations, Hirshfeld Surface Analysis and In Silico Drug-Target Profiling of ( R)-2-(2-(1,3-Dioxoisoindolin-2-yl)propanamido)benzoic Acid Methyl Ester. Molecules 2023; 28:molecules28114375. [PMID: 37298851 DOI: 10.3390/molecules28114375] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 03/22/2023] [Accepted: 03/27/2023] [Indexed: 06/12/2023] Open
Abstract
The work here reflects synthesis, DFT studies, Hirshfeld charge analysis and crystal data exploration of pharmacologically important (R)-2-(2-(1,3-dioxoisoindolin-2-yl)propanamido)benzoic acid methyl ester (5) to understand its properties for further chemical transformations. The methyl anthranilate (2) was produced by the esterification of anthranilic acid in an acidic medium. The phthaloyl-protected alanine (4) was rendered by the fusion of alanine with phthalic anhydride at 150 °C, followed by coupling with (2) furnished isoindole (5). The characterization of products was performed using IR, UV-Vis, NMR and MS. Single-crystal XRD also verified the structure of (5) in which N-H⋯O bonding stabilizes the molecular configuration of (5), resulting in the formation of S(6) hydrogen-bonded loop. The molecules of isoindole (5) are connected in the form of dimers, and the π⋯π stacking interaction between aromatic rings further stabilizes the crystal packing. DFT studies suggest that HOMO is over the substituted aromatic ring, the LUMO is present mainly over the indole side, and nucleophilic and electrophilic corners point out the reactivity of the product (5). In vitro and in silico analysis of (5) shows its potential as an antibacterial agent targeting DNA gyrase and Dihydroorotase from E. coli and tyrosyl-tRNA synthetase and DNA gyrase from Staphylococcus aureus.
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Affiliation(s)
- Syeda Laila Rubab
- Department of Chemistry, Division of Science and Technology, University of Education, Lahore 54770, Pakistan
| | - Abdul Rauf Raza
- Institute of Chemistry, Ibn e Sena Block, University of Sargodha, Sargodha 40100, Pakistan
| | - Bushra Nisar
- Department of Chemistry, The University of Lahore, Sargodha Campus, Sargodha 40100, Pakistan
| | - Muhammad Ashfaq
- Department of Physics, University of Sargodha, Sargodha 40100, Pakistan
| | - Yasir Altaf
- Department of Chemistry, Division of Science and Technology, University of Education, Lahore 54770, Pakistan
- School of Chemical and Physical Sciences, Victoria University of Wellington, Wellington 6140, New Zealand
| | - Riaz Hussain
- Department of Chemistry, Division of Science and Technology, University of Education, Lahore 54770, Pakistan
| | - Noreen Sajjad
- Department of Chemistry, The University of Lahore, Lahore 54770, Pakistan
| | | | | | | | | | - Hayssam M Ali
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
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Sheng K, Wang Z, Li L, Gao ZY, Tung CH, Sun D. Solvent-Mediated Separation and Reversible Transformation of 1D Supramolecular Polymorphs Built from [W 10O 32] 4- Templated 48-Nuclei Silver(I) Cluster. J Am Chem Soc 2023; 145:10595-10603. [PMID: 37139688 DOI: 10.1021/jacs.3c00321] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Although the C-H···O interaction is an essential component in determining the molecular packing in solids and the properties in supramolecular chemistry, it presents a significant challenge when trying to use it in the crystal engineering of complex metallosupramolecules, even though it is a relatively weak supramolecular force. The first pair of high-nuclearity silver-cluster-based one-dimensional (1D) polymorphs built from supramolecular synthon [W10O32@Ag48(CyS)24(NO3)16]·4NO3 (Cy = cyclohexyl) bridged by four grouped inorganic NO3- ligands is initially synthesized as a mixed phase and further individually crystallized as a pure phase by virtue of tuning intermolecular C-H···O interaction through altering the composition ratio of ternary solvent system. Increasing highly polar and hydrogen-bonding methanol strengthens the solvation effect reflected by the change of coordination orientation of surface NO3- ligands, which dominates the packing of the 1D chains in the crystal lattice, resulting in the crystallization of polymorphs from tetragonal to monoclinic. The two crystalline forms can also be reversibly transformed to each other in an appropriate solvent system. Correspondingly, the two polymorphs display distinct temperature-dependent photoluminescence behaviors, which are ascribed to the variation of noncovalent interchain C-H···O interactions along with the temperature. More importantly, benefiting from the suppression of fluorescence, both polymorphs offer excellent photothermal conversion properties which were further applied to remote-controlled laser ignition. These findings may open more avenues for the application of solvent-mediated intermolecular interaction in controlling the molecule arrangement as well as the optical properties.
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Affiliation(s)
- Kai Sheng
- School of Aeronautics, Shandong Jiaotong University, Ji'nan 250037, P. R. China
| | - Zhi Wang
- School of Chemistry and Chemical Engineering, State Key Laboratory of Crystal Materials, Shandong University, Ji'nan 250100, P. R. China
| | - Li Li
- School of Chemistry and Chemical Engineering, State Key Laboratory of Crystal Materials, Shandong University, Ji'nan 250100, P. R. China
| | - Zhi-Yong Gao
- School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang 453007, P. R. China
| | - Chen-Ho Tung
- School of Chemistry and Chemical Engineering, State Key Laboratory of Crystal Materials, Shandong University, Ji'nan 250100, P. R. China
| | - Di Sun
- School of Chemistry and Chemical Engineering, State Key Laboratory of Crystal Materials, Shandong University, Ji'nan 250100, P. R. China
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Voronin AP, Surov AO, Churakov AV, Vener MV. Supramolecular Organization in Salts of Riluzole with Dihydroxybenzoic Acids—The Key Role of the Mutual Arrangement of OH Groups. Pharmaceutics 2023; 15:pharmaceutics15030878. [PMID: 36986739 PMCID: PMC10051219 DOI: 10.3390/pharmaceutics15030878] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 03/05/2023] [Accepted: 03/07/2023] [Indexed: 03/11/2023] Open
Abstract
Intermolecular interactions, in particular hydrogen bonds, play a key role in crystal engineering. The ability to form hydrogen bonds of various types and strengths causes competition between supramolecular synthons in pharmaceutical multicomponent crystals. In this work, we investigate the influence of positional isomerism on the packing arrangements and the network of hydrogen bonds in multicomponent crystals of the drug riluzole with hydroxyl derivatives of salicylic acid. The supramolecular organization of the riluzole salt containing 2,6-dihydroxybenzoic acid differs from that of the solid forms with 2,4- and 2,5-dihydroxybenzoic acids. Because the second OH group is not at position 6 in the latter crystals, intermolecular charge-assisted hydrogen bonds are formed. According to periodic DFT calculations, the enthalpy of these H-bonds exceeds 30 kJ·mol−1. The positional isomerism appears to have little effect on the enthalpy of the primary supramolecular synthon (65–70 kJ·mol−1), but it does result in the formation of a two-dimensional network of hydrogen bonds and an increase in the overall lattice energy. According to the results of the present study, 2,6-dihydroxybenzoic acid can be treated as a promising counterion for the design of pharmaceutical multicomponent crystals.
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Affiliation(s)
| | - Artem O. Surov
- G.A. Krestov Institute of Solution Chemistry RAS, 153045 Ivanovo, Russia
| | - Andrei V. Churakov
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Leninskii prosp. 31, 119991 Moscow, Russia
| | - Mikhail V. Vener
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Leninskii prosp. 31, 119991 Moscow, Russia
- Correspondence:
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Kusumoto S, Atoini Y, Masuda S, Kim JY, Hayami S, Kim Y, Harrowfield J, Thuéry P. Zwitterionic and Anionic Polycarboxylates as Coligands in Uranyl Ion Complexes, and Their Influence on Periodicity and Topology. Inorg Chem 2022; 61:15182-15203. [PMID: 36083206 DOI: 10.1021/acs.inorgchem.2c02426] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The three zwitterionic di- and tricarboxylate ligands 1,1'-[(2,3,5,6-tetramethylbenzene-1,4-diyl)bis(methylene)]bis(pyridin-1-ium-4-carboxylate) (pL1), 1,1'-[(2,3,5,6-tetramethylbenzene-1,4-diyl)bis(methylene)]bis(pyridin-1-ium-3-carboxylate) (mL1), and 1,1',1″-[(2,4,6-trimethylbenzene-1,3,5-triyl)tris(methylene)]tris(pyridin-1-ium-4-carboxylate) (L2) have been used as ligands to synthesize a series of 15 uranyl ion complexes involving various anionic coligands, in most cases polycarboxylates. [(UO2)2(pL1)2(cbtc)(H2O)2]·10H2O (1, cbtc4- = cis,trans,cis-1,2,3,4-cyclobutanetetracarboxylate) is a discrete, dinuclear ring-shaped complex with a central cbtc4- pillar. While [UO2(pL1)(NO3)2] (2), [UO2(pL1)(OAc)2] (3), and [UO2(pL1)(HCOO)2] (4) are simple chains, [(UO2)2(mL1)(1,3-pda)2] (5, 1,3-pda2- = 1,3-phenylenediacetate) is a daisy chain and [UO2(pL1)(pdda)]3·10H2O (6, pdda2- = 1,2-phenylenedioxydiacetate) is a double-stranded, ribbon-like chain. Both [UO2(pL1)(pht)]·5H2O (7, pht2- = phthalate) and [(UO2)3(mL1)(pht)2(OH)2] (8) crystallize as diperiodic networks with the sql topology, the latter involving hydroxo-bridged trinuclear nodes. [(UO2)2(pL1)(c/t-1,3-chdc)2] (9, c/t-1,3-chdc2- = cis/trans-1,3-cyclohexanedicarboxylate) and [UO2(pL1)(t-1,4-chdc)]·1.5H2O (10, t-1,4-chdc2- = trans-1,4-cyclohexanedicarboxylate) are also diperiodic, with the V2O5 and sql topologies, respectively. Both [(UO2)2(mL1)(c/t-1,4-chdc)2] (11) and [(UO2)2(pL1)(1,2-pda)2] (12, 1,2-pda2- = 1,2-phenylenediacetate) crystallize as diperiodic networks with hcb topology, and they display threefold parallel interpenetration. [HL2][(UO2)3(L2)(adc)3]Br (13, adc2- = 1,3-adamantanedicarboxylate) contains a very corrugated hcb network with two different kinds of cells, and the uncoordinated HL2+ molecule associates with the coordinated L2 to form a capsule containing the bromide anion. [(UO2)2(pL1)(kpim)2] (14, kpim2- = 4-ketopimelate) is a three-periodic framework with pL1 molecules pillaring fes diperiodic subunits, whereas [(UO2)2(L2)2(t-1,4-chdc)](NO3)1.7Br0.3·6H2O (15), the only cationic complex in the series, is a triperiodic framework with dmc topology and t-1,4-chdc2- anions pillaring fes diperiodic subunits. Solid-state emission spectra and photoluminescence quantum yields are reported for all complexes.
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Affiliation(s)
- Sotaro Kusumoto
- Department of Material & Life Chemistry, Kanagawa University, 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama 221-8686, Japan
| | - Youssef Atoini
- Technical University of Munich Campus Straubing, Schulgasse 22, 94315 Straubing, Germany
| | - Shunya Masuda
- Department of Material & Life Chemistry, Kanagawa University, 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama 221-8686, Japan
| | - Jee Young Kim
- Department of Food and Nutrition, Kosin University, 194 Wachiro, Yongdo-Gu, Busan 49104, South Korea
| | - Shinya Hayami
- Department of Chemistry, Graduate School of Science and Technology, Institute of Industrial Nanomaterials (IINa), Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto 860-8555, Japan
| | - Yang Kim
- Department of Chemistry, Graduate School of Science and Technology, Institute of Industrial Nanomaterials (IINa), Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto 860-8555, Japan
| | - Jack Harrowfield
- ISIS, Université de Strasbourg, 8 allée Gaspard Monge, 67083 Strasbourg, France
| | - Pierre Thuéry
- Université Paris-Saclay, CEA, CNRS, NIMBE, 91191 Gif-sur-Yvette, France
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5
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Miller DK, Chernyshov IY, Torubaev YV, Rosokha SV. From weak to strong interactions: structural and electron topology analysis of the continuum from the supramolecular chalcogen bonding to covalent bonds. Phys Chem Chem Phys 2022; 24:8251-8259. [PMID: 35320823 DOI: 10.1039/d1cp05441d] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The relationship between covalent and supramolecular bonding, and the criteria of the assignments of different interactions were explored via the review of selenium and tellurium containing structures in the Cambridge Structural Database and their computational analysis using Quantum Theory of Atoms in Molecules (QTAIM). This combined study revealed continuums of the interatomic Se⋯Br and Te⋯I distances, dCh⋯X, in the series of associations from the sums of the van der Waals radii of these atoms (rCh + rX) to their covalent bond lengths. The electron densities, ρ(r), at Bond Critical Points (BCPs) along the chalcogen bond paths increased gradually from about 0.01 a.u. common for the non-covalent interactions to about 0.1 a.u. typical for the covalent bonds. The log ρ(r) values fell on the same linear trend line when plotted against normalized interatomic distances, RXY = dCh⋯X/(rCh + rX). The transition from the positive to negative values of the energy densities, H(r), at the BCPs (related to a changeover of essentially non-covalent into partially covalent interactions) were observed at RXY ≈ 0.80. Synchronous changes of bonding characteristics with RXY (similar to that found earlier in the halogen-bonded systems) designated normalized interatomic separation as a critical factor determining the nature of these bondings. The uninterrupted continuums of Te⋯I and Se⋯Br bond lengths and BCPs' characteristics signified an intrinsic link between limiting types of bonding involving chalcogen atoms and between covalent and supramolecular bonding in general.
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Affiliation(s)
- Daniel K Miller
- Chemistry Department, Ball State University, Muncie, IN, 47306, USA.
| | - Ivan Yu Chernyshov
- TheoMat group, ChemBio Cluster, ITMO University, Lomonosova 9, St. Petersburg, 191002, Russia
| | - Yury V Torubaev
- N.S. Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, GSP-1, L eninsky prospect, 31, Moscow, 119991, Russia
| | - Sergiy V Rosokha
- Chemistry Department, Ball State University, Muncie, IN, 47306, USA.
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Zaib S, Ibrar A, Ramay M, Zahra S, Hökelek T, Simpson J, McAdam CJ, Awwad NS, Ibrahium HA, Frontera A, Khan I. Centroid⋯centroid and hydrogen bond interactions as robust supramolecular units for crystal engineering: X-ray crystallographic, computational and urease inhibitory investigations of 1,2,4-triazolo[3,4-a]phthalazines. CrystEngComm 2022. [DOI: 10.1039/d2ce00351a] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The antiparallel π-stacked dimer of compound 6 (left) presenting a large dimerization energy (ΔE5 = −11.2 kcal mol−1) and confirming its relevance in the solid state of compound 6. 3D binding mode of 6 (right) docked in the catalytic domain of urease.
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Affiliation(s)
- Sumera Zaib
- Department of Biochemistry, Faculty of Life Sciences, University of Central Punjab, Lahore 54590, Pakistan
| | - Aliya Ibrar
- Department of Chemistry, Faculty of Life Science, The University of Haripur, KPK 22620, Pakistan
| | - Marriyam Ramay
- Department of Biochemistry, Faculty of Life Sciences, University of Central Punjab, Lahore 54590, Pakistan
| | - Shabab Zahra
- Department of Biochemistry, Faculty of Life Sciences, University of Central Punjab, Lahore 54590, Pakistan
| | - Tuncer Hökelek
- Department of Physics, Hacettepe University, Beytepe-Ankara, 06800, Turkey
| | - Jim Simpson
- Department of Chemistry, University of Otago, P.O. Box 56, Dunedin, 9054, New Zealand
| | | | - Nasser S. Awwad
- Chemistry Department, Faculty of Science, King Khalid University, P.O. Box 9004, Abha 61413, Saudi Arabia
| | - Hala A. Ibrahium
- Biology Department, Faculty of Science, King Khalid University, P.O. Box 9004, Abha 61413, Saudi Arabia
- Department of Semi Pilot Plant, Nuclear Materials Authority, P.O. Box 530, El Maadi, Egypt
| | - Antonio Frontera
- Department de Química, Universitat de les Illes Balears, Crta de Valldemossa km 7.5, 07122 Palma de Mallorca Baleares, Spain
| | - Imtiaz Khan
- Department of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
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Tosstorff A, Cole JC, Bartelt R, Kuhn B. Augmenting Structure-Based Design with Experimental Protein-Ligand Interaction Data: Molecular Recognition, Interactive Visualization, and Rescoring. ChemMedChem 2021; 16:3428-3438. [PMID: 34342128 DOI: 10.1002/cmdc.202100387] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Indexed: 11/10/2022]
Abstract
The previously introduced ratio of frequencies (RF ) framework provides statistically sound information on the relative interaction preferences of atoms in crystal structures. By applying the methodology to protein-ligand complexes, we can investigate the significance of interactions that are employed in structure-based drug design. Here, we revisit three aspects of molecular recognition in the light of the RF framework, namely stacking interactions of heteroaromatic rings with protein amide groups, interactions of acidified C-H groups, and interaction differences between syn and anti lone pairs of carboxylate groups. In addition, we introduce a highly interactive visualization tool that facilitates design idea generation in structure-enabled drug discovery projects. Finally, we show that applying the RF analysis as a simple rescoring tool after docking improves enrichment factors for the DUD-E diverse targets subset supporting the relevance of our approach.
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Affiliation(s)
- Andreas Tosstorff
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070, Basel, Switzerland
| | - Jason C Cole
- Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge, CB2 1EZ, UK
| | - Richard Bartelt
- Chemical Computing Group, Kaiser-Wilhelm-Ring 11, 50672, Cologne, Germany
| | - Bernd Kuhn
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070, Basel, Switzerland
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8
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Bortoluzzi M, Di Vera A, Pietrobon L, Castro J. Seven- and eight-coordinate lanthanide(III) amidophosphate complexes: synthesis, characterization and photoluminescence. J COORD CHEM 2021. [DOI: 10.1080/00958972.2021.1916001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Marco Bortoluzzi
- Dipartimento di Scienze Molecolari e Nanosistemi, Università Ca’ Foscari Venezia, Mestre (Ve), Italy
- Consorzio Interuniversitario Reattività Chimica e Catalisi (CIRCC), Bari, Italy
| | - Andrea Di Vera
- Dipartimento di Scienze Molecolari e Nanosistemi, Università Ca’ Foscari Venezia, Mestre (Ve), Italy
| | - Luca Pietrobon
- Dipartimento di Scienze Molecolari e Nanosistemi, Università Ca’ Foscari Venezia, Mestre (Ve), Italy
| | - Jesús Castro
- Departamento de Química Inorgánica, Facultade de Química, Edificio de Ciencias Experimentais, Universidade de Vigo, Vigo, Galicia, Spain
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9
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Ferraro V, Castro J, Agostinis L, Bortoluzzi M. Luminescent heteroleptic copper(I) complexes with polydentate benzotriazolyl-based ligands. TRANSIT METAL CHEM 2021. [DOI: 10.1007/s11243-021-00458-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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10
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Tosstorff A, Cole JC, Taylor R, Harris SF, Kuhn B. Identification of Noncompetitive Protein–Ligand Interactions for Structural Optimization. J Chem Inf Model 2020; 60:6595-6611. [DOI: 10.1021/acs.jcim.0c00858] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Andreas Tosstorff
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
- Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, U.K
| | - Jason C. Cole
- Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, U.K
| | - Robin Taylor
- Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, U.K
| | - Seth F. Harris
- Structural Biology, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Bernd Kuhn
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
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11
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Polymorph of trans-dichlorotetrakis(pyridine-N)ruthenium(II) influenced by a dihydrazone: crystal structure, spectral, Hirshfeld surfaces, antimicrobial, toxicity and in silico docking studies. J CHEM SCI 2020. [DOI: 10.1007/s12039-020-01829-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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12
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Mahmoudi G, Zangrando E, Frontera A, Gurbanov AV, Safin DA. New metal chelate constructed from Ni(NCS)2 and 1,2-diphenyl-1,2-bis((phenyl(pyridin-2-yl)methylene)hydrazono)ethane. Inorganica Chim Acta 2020. [DOI: 10.1016/j.ica.2020.119707] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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13
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Chernyshov IY, Ananyev IV, Pidko EA. Revisiting van der Waals Radii: From Comprehensive Structural Analysis to Knowledge-Based Classification of Interatomic Contacts. Chemphyschem 2020; 21:370-376. [PMID: 31912957 PMCID: PMC7079509 DOI: 10.1002/cphc.201901083] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 01/06/2020] [Indexed: 11/25/2022]
Abstract
Weak noncovalent interactions are responsible for structure and properties of almost all supramolecular systems, such as nucleic acids, enzymes, and pharmaceutical crystals. However, the analysis of their significance and structural role is not straightforward and commonly requires model studies. Herein, we describe an efficient and universal approach for the analysis of noncovalent interactions and determination of van der Waals radii using the line-of-sight (LoS) concept. The LoS allows to unambiguously identify and classify the "direct" interatomic contacts in complex molecular systems. This approach not only provides an improved theoretical base to molecular "sizes" but also enables the quantitative analysis of specificity, anisotropy, and steric effects of intermolecular interactions.
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Affiliation(s)
- Ivan Yu. Chernyshov
- TheoMAT Group, ChemBio clusterITMO UniversityLomonosova 9St. Petersburg191002Russia
| | - Ivan V. Ananyev
- Faculty of ChemistryNational Research University Higher School of EconomicsMoscow101000Russia
| | - Evgeny A. Pidko
- TheoMAT Group, ChemBio clusterITMO UniversityLomonosova 9St. Petersburg191002Russia
- Inorganic Systems Engineering GroupDelft University of TechnologyVan der Maasweg 92629 HZDelft (TheNetherlands
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14
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Staub R, Steinmann SN. Parameter-free coordination numbers for solutions and interfaces. J Chem Phys 2020; 152:024124. [PMID: 31941337 DOI: 10.1063/1.5135696] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Coordination numbers are among the central quantities to describe the local environment of atoms and are thus used in various applications such as structure analysis, fingerprints, and parameters. Yet, there is no consensus regarding a practical algorithm, and many proposed methods are designed for specific systems. In this work, we propose a scale-free and parameter-free algorithm for nearest neighbor identification. This algorithm extends the powerful Solid-Angle based Nearest-Neighbor (SANN) framework to explicitly include local anisotropy. As such, our Anisotropically corrected SANN (ASANN) algorithm provides with a fast, robust, and adaptive method for computing coordination numbers. The ASANN algorithm is applied to flat and corrugated metallic surfaces to demonstrate that the expected coordination numbers are retrieved without the need for any system-specific adjustments. The same applies to the description of the coordination numbers of metal atoms in AuCu nanoparticles, and we show that ASANN based coordination numbers are well adapted for automatically counting neighbors and the establishment of cluster expansions. Analysis of classical molecular dynamics simulations of an electrified graphite electrode reveals a strong link between the coordination number of Cs+ ions and their position within the double layer, a relation that is absent for Na+, which keeps its first solvation shell even close to the electrode.
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Affiliation(s)
- Ruben Staub
- Univ. Lyon, Ecole Normale Supérieure de Lyon, CNRS Université Lyon 1, Laboratoire de Chimie UMR 5182, 46 Allée d'Italie, F-69364 Lyon, France
| | - Stephan N Steinmann
- Univ. Lyon, Ecole Normale Supérieure de Lyon, CNRS Université Lyon 1, Laboratoire de Chimie UMR 5182, 46 Allée d'Italie, F-69364 Lyon, France
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15
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Bortoluzzi M, Castro J, Gobbo A, Ferraro V, Pietrobon L. Light harvesting indolyl-substituted phosphoramide ligand for the enhancement of Mn(ii) luminescence. Dalton Trans 2020; 49:7525-7534. [DOI: 10.1039/d0dt01659d] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Excitation of the coordinated ligands in tetrahedral complexes having the general formula [MnX2L2] (X = Cl, Br, I; L = N,N′,N′-tetramethyl-P-indol-1-ylphosphonic diamide) causes bright green luminescence from the Mn(ii) centre.
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Affiliation(s)
- Marco Bortoluzzi
- Dipartimento di Scienze Molecolari e Nanosistemi
- Università Ca’ Foscari Venezia
- 30170 Mestre (VE)
- Italy
- Consorzio Interuniversitario Reattività Chimica e Catalisi (CIRCC)
| | - Jesús Castro
- Departamento de Química Inorgánica
- Universidade de Vigo
- Facultade de Química
- Edificio de Ciencias Experimentais
- 36310 Vigo
| | - Alberto Gobbo
- Dipartimento di Chimica e Chimica Industriale
- Università di Pisa
- 56124 Pisa
- Italy
| | - Valentina Ferraro
- Dipartimento di Scienze Molecolari e Nanosistemi
- Università Ca’ Foscari Venezia
- 30170 Mestre (VE)
- Italy
| | - Luca Pietrobon
- Dipartimento di Scienze Molecolari e Nanosistemi
- Università Ca’ Foscari Venezia
- 30170 Mestre (VE)
- Italy
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16
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Bortoluzzi M, Castro J, Gobbo A, Ferraro V, Pietrobon L, Antoniutti S. Tetrahedral photoluminescent manganese(ii) halide complexes with 1,3-dimethyl-2-phenyl-1,3-diazaphospholidine-2-oxide as a ligand. NEW J CHEM 2020. [DOI: 10.1039/c9nj05083c] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Photoluminescent Mn(ii) tetrahedral complexes characterized by intense emission in the green region were isolated from the reaction of MnX2 (X = Cl, Br, I) and the ligand 1,3-dimethyl-2-phenyl-1,3-diazaphospholidine-2-oxide.
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Affiliation(s)
- Marco Bortoluzzi
- Dipartimento di Scienze Molecolari e Nanosistemi
- Università Ca' Foscari Venezia
- I-30170 Mestre (VE)
- Italy
- Consorzio Interuniversitario Reattività Chimica e Catalisi (CIRCC)
| | - Jesús Castro
- Departamento de Química Inorgánica
- Universidade de Vigo
- Facultade de Química
- Edificio de Ciencias Experimentais
- 36310 Vigo
| | - Alberto Gobbo
- Dipartimento di Scienze Molecolari e Nanosistemi
- Università Ca' Foscari Venezia
- I-30170 Mestre (VE)
- Italy
| | - Valentina Ferraro
- Dipartimento di Scienze Molecolari e Nanosistemi
- Università Ca' Foscari Venezia
- I-30170 Mestre (VE)
- Italy
- Consorzio Interuniversitario Reattività Chimica e Catalisi (CIRCC)
| | - Luca Pietrobon
- Dipartimento di Scienze Molecolari e Nanosistemi
- Università Ca' Foscari Venezia
- I-30170 Mestre (VE)
- Italy
| | - Stefano Antoniutti
- Dipartimento di Scienze Molecolari e Nanosistemi
- Università Ca' Foscari Venezia
- I-30170 Mestre (VE)
- Italy
- Consorzio Interuniversitario Reattività Chimica e Catalisi (CIRCC)
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17
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Taylor R. Identifying intermolecular atom⋯atom interactions that are not just bonding but also competitive. CrystEngComm 2020. [DOI: 10.1039/d0ce00270d] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This highlight criticises the QTAIM method and discusses algorithms for identifying intermolecular interactions that are both bonding and competitive.
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Affiliation(s)
- Robin Taylor
- Cambridge Crystallographic Data Centre
- Cambridge CB2 1EZ
- UK
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18
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Saha A, Veluthaparambath RVP, Saha BK. Directionality of P⋯O pnicogen bonding in light of geometry corrected statistical analysis. NEW J CHEM 2020. [DOI: 10.1039/d0nj01683g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Cone corrected statistical analysis suggests that the X–P⋯O angle prefers linearity which is more prominent in the case of X3P⋯O compared to X4P⋯O pnicogen bonds. This preference also increases with an increase in the electronegativity of X.
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Affiliation(s)
- Arijit Saha
- Department of Chemistry
- Pondicherry University
- Pondicherry
- India
| | | | - Binoy K. Saha
- Department of Chemistry
- Pondicherry University
- Pondicherry
- India
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19
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Kuhn B, Gilberg E, Taylor R, Cole J, Korb O. How Significant Are Unusual Protein-Ligand Interactions? Insights from Database Mining. J Med Chem 2019; 62:10441-10455. [PMID: 31730345 DOI: 10.1021/acs.jmedchem.9b01545] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
We present a new approach to derive interaction propensities of protein-ligand atom pairs from mining of the Protein Data Bank. To ensure solid statistics, we use a line-of-sight contact filter and normalize the observed frequency of hits by a statistical null model based on exposed surface areas of atom types in the protein-ligand binding site. This allows us to investigate which intermolecular interactions and geometries are found more often than expected by chance in protein-ligand complexes. We focus our study on some of the unusual interactions that were postulated to be favorable, including σ-hole bonding of halogen and sulfur atoms, weak hydrogen bonding with fluorine as acceptor, and different types of dipolar interactions. Our results confirm some and challenge other common assumptions on these interactions and highlight other contact types that are yet underexplored in structure-based drug design.
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Affiliation(s)
- Bernd Kuhn
- Roche Pharma Research and Early Development, Roche Innovation Center Basel , F. Hoffmann-La Roche Ltd. , Grenzacherstrasse 124 , CH-4070 Basel , Switzerland
| | - Erik Gilberg
- Roche Pharma Research and Early Development, Roche Innovation Center Basel , F. Hoffmann-La Roche Ltd. , Grenzacherstrasse 124 , CH-4070 Basel , Switzerland
| | - Robin Taylor
- Cambridge Crystallographic Data Centre , 12 Union Road , Cambridge CB2 1EZ , U.K
| | - Jason Cole
- Cambridge Crystallographic Data Centre , 12 Union Road , Cambridge CB2 1EZ , U.K
| | - Oliver Korb
- Roche Pharma Research and Early Development, Roche Innovation Center Basel , F. Hoffmann-La Roche Ltd. , Grenzacherstrasse 124 , CH-4070 Basel , Switzerland
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20
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Intermolecular Interactions in Functional Crystalline Materials: From Data to Knowledge. CRYSTALS 2019. [DOI: 10.3390/cryst9090478] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Intermolecular interactions of organic, inorganic, and organometallic compounds are the key to many composition–structure and structure–property networks. In this review, some of these relations and the tools developed by the Cambridge Crystallographic Data Center (CCDC) to analyze them and design solid forms with desired properties are described. The potential of studies supported by the Cambridge Structural Database (CSD)-Materials tools for investigation of dynamic processes in crystals, for analysis of biologically active, high energy, optical, (electro)conductive, and other functional crystalline materials, and for the prediction of novel solid forms (polymorphs, co-crystals, solvates) are discussed. Besides, some unusual applications, the potential for further development and limitations of the CCDC software are reported.
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21
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Taylor R, Wood PA. A Million Crystal Structures: The Whole Is Greater than the Sum of Its Parts. Chem Rev 2019; 119:9427-9477. [PMID: 31244003 DOI: 10.1021/acs.chemrev.9b00155] [Citation(s) in RCA: 134] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The founding in 1965 of what is now called the Cambridge Structural Database (CSD) has reaped dividends in numerous and diverse areas of chemical research. Each of the million or so crystal structures in the database was solved for its own particular reason, but collected together, the structures can be reused to address a multitude of new problems. In this Review, which is focused mainly on the last 10 years, we chronicle the contribution of the CSD to research into molecular geometries, molecular interactions, and molecular assemblies and demonstrate its value in the design of biologically active molecules and the solid forms in which they are delivered. Its potential in other commercially relevant areas is described, including gas storage and delivery, thin films, and (opto)electronics. The CSD also aids the solution of new crystal structures. Because no scientific instrument is without shortcomings, the limitations of CSD research are assessed. We emphasize the importance of maintaining database quality: notwithstanding the arrival of big data and machine learning, it remains perilous to ignore the principle of garbage in, garbage out. Finally, we explain why the CSD must evolve with the world around it to ensure it remains fit for purpose in the years ahead.
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Affiliation(s)
- Robin Taylor
- Cambridge Crystallographic Data Centre , 12 Union Road , Cambridge CB2 1EZ , United Kingdom
| | - Peter A Wood
- Cambridge Crystallographic Data Centre , 12 Union Road , Cambridge CB2 1EZ , United Kingdom
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22
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Giordano N, Afanasjevs S, Beavers CM, Hobday CL, Kamenev KV, O'Bannon EF, Ruiz-Fuertes J, Teat SJ, Valiente R, Parsons S. The Effect of Pressure on Halogen Bonding in 4-Iodobenzonitrile. Molecules 2019; 24:molecules24102018. [PMID: 31137795 PMCID: PMC6572472 DOI: 10.3390/molecules24102018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 05/20/2019] [Accepted: 05/22/2019] [Indexed: 11/16/2022] Open
Abstract
The crystal structure of 4-iodobenzonitrile, which is monoclinic (space group I2/a) under ambient conditions, contains chains of molecules linked through C≡N···I halogen-bonds. The chains interact through CH···I, CH···N and π-stacking contacts. The crystal structure remains in the same phase up to 5.0 GPa, the b axis compressing by 3.3%, and the a and c axes by 12.3 and 10.9 %. Since the chains are exactly aligned with the crystallographic b axis these data characterise the compressibility of the I···N interaction relative to the inter-chain interactions, and indicate that the halogen bond is the most robust intermolecular interaction in the structure, shortening from 3.168(4) at ambient pressure to 2.840(1) Å at 5.0 GPa. The π∙∙∙π contacts are most sensitive to pressure, and in one case the perpendicular stacking distance shortens from 3.6420(8) to 3.139(4) Å. Packing energy calculations (PIXEL) indicate that the π∙∙∙π interactions have been distorted into a destabilising region of their potentials at 5.0 GPa. The structure undergoes a transition to a triclinic ( P 1 ¯ ) phase at 5.5 GPa. Over the course of the transition, the initially colourless and transparent crystal darkens on account of formation of microscopic cracks. The resistance drops by 10% and the optical transmittance drops by almost two orders of magnitude. The I···N bond increases in length to 2.928(10) Å and become less linear [<C-I∙∙∙N = 166.2(5)°]; the energy stabilises by 2.5 kJ mol-1 and the mixed C-I/I..N stretching frequency observed by Raman spectroscopy increases from 249 to 252 cm-1. The driving force of the transition is shown to be relief of strain built-up in the π∙∙∙π interactions rather than minimisation of the molar volume. The triclinic phase persists up to 8.1 GPa.
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Affiliation(s)
- Nico Giordano
- Centre for Science at Extreme Conditions and EaStCHEM School of Chemistry, The University of Edinburgh, King's Buildings, West Mains Road, Edinburgh, Scotland EH9 3FD, UK.
- Advanced Light Source, 1 Cyclotron Road, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
| | - Sergejs Afanasjevs
- Centre for Science at Extreme Conditions and School of Engineering, The University of Edinburgh, King's Buildings, West Mains Road, Edinburgh, Scotland EH9 3FD, UK.
| | - Christine M Beavers
- Advanced Light Source, 1 Cyclotron Road, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
- Department of Earth & Planetary Sciences, University of California, Santa Cruz, 1156 High Street Santa Cruz, CA 95064, USA.
- Present address: Diamond Light Source, STFC Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Harwell Oxford, Didcot OX11 0QX, UK.
| | - Claire L Hobday
- Centre for Science at Extreme Conditions and EaStCHEM School of Chemistry, The University of Edinburgh, King's Buildings, West Mains Road, Edinburgh, Scotland EH9 3FD, UK.
| | - Konstantin V Kamenev
- Centre for Science at Extreme Conditions and School of Engineering, The University of Edinburgh, King's Buildings, West Mains Road, Edinburgh, Scotland EH9 3FD, UK.
| | - Earl F O'Bannon
- Advanced Light Source, 1 Cyclotron Road, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
- Department of Earth & Planetary Sciences, University of California, Santa Cruz, 1156 High Street Santa Cruz, CA 95064, USA.
- Present address: Physical and Life Sciences, Physics Division, Lawrence Livermore National Laboratory, Livermore, CA 94551, USA.
| | - Javier Ruiz-Fuertes
- Dpto. DCITIMAC, Facultad de Ciencias, Universidad de Cantabria, 39005 Santander, Spain.
| | - Simon J Teat
- Advanced Light Source, 1 Cyclotron Road, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
| | - Rafael Valiente
- Dpto. Física Aplicada, Facultad de Ciencias, Universidad de Cantabria-IDIVAL, 39005 Santander, Spain.
| | - Simon Parsons
- Centre for Science at Extreme Conditions and EaStCHEM School of Chemistry, The University of Edinburgh, King's Buildings, West Mains Road, Edinburgh, Scotland EH9 3FD, UK.
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23
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Bortoluzzi M, Castro J. Dibromomanganese(II) complexes with hexamethylphosphoramide and phenylphosphonic bis(diamide) ligands. J COORD CHEM 2019. [DOI: 10.1080/00958972.2018.1560430] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Marco Bortoluzzi
- Dipartimento di Scienze Molecolari e Nanosistemi, Università Ca’ Foscari Venezia, Mestre (VE), Italy
- CIRCC, Bari, Italy
| | - Jesús Castro
- Departamento de Química Inorgánica, Universidade de Vigo, Facultade de Química, Edificio de Ciencias Experimentais, Galicia, Spain
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24
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Akbari Afkhami F, Mahmoudi G, White JM, Lipkowski J, Konyaeva IA, Safin DA. Möbius-like metal chelates constructed from CdHal2 (Hal = Cl, Br, I) and benzilbis(pyridin-2-yl)methylidenehydrazone. Inorganica Chim Acta 2019. [DOI: 10.1016/j.ica.2018.09.082] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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25
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Afkhami FA, Mahmoudi G, Khandar AA, White JM, Konyaeva IA, Safin DA. Metal chelates constructed from CdHal2 (Hal = Cl, Br, I) and 1,2-diphenyl-1,2-bis((phenyl(pyridin-2-yl)methylene)hydrazono)ethane. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2018.09.036] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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26
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Milovanović MR, Andrić JM, Medaković VB, Djukic JP, Zarić SD. Investigation of interactions in Lewis pairs between phosphines and boranes by analyzing crystal structures from the Cambridge Structural Database. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2018; 74:255-263. [PMID: 29927388 DOI: 10.1107/s2052520618003736] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 03/04/2018] [Indexed: 06/08/2023]
Abstract
The interactions between phosphines and boranes in crystal structures have been investigated by analyzing data from the Cambridge Structural Database (CSD). The interactions between phosphines and boranes were classified into three types; two types depend on groups on the boron atom, whereas the third one involves frustrated Lewis pairs (FLPs). The data enabled geometric parameters in structures to be compared with phosphine-borane FLPs with classical Lewis pairs. Most of the crystal structures (78.1%) contain BH3 as the borane group. In these systems, the boron-phosphorus distance is shorter than systems where the boron atom is surrounded by groups other than hydrogen atoms. The analysis of the CSD data has shown that FLPs have a tendency for the longest boron-phosphorus distance among all phosphine-borane pairs, as well as different other geometrical parameters. The results show that most of the frustrated phosphine-borane pairs found in crystal structures are bridged ones. The minority of non-bridged FLP structures contain, beside phosphorus and boron atoms, other heteroatoms (O, N, S for instance).
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Affiliation(s)
- Milan R Milovanović
- Faculty of Chemistry, University of Belgrade, Studentski trg 12-16, Belgrade, 11000, Serbia
| | - Jelena M Andrić
- Innovation Center, Department of Chemistry, Studentski trg 12-16, Belgrade, 11000, Serbia
| | - Vesna B Medaković
- Faculty of Chemistry, University of Belgrade, Studentski trg 12-16, Belgrade, 11000, Serbia
| | - Jean Pierre Djukic
- Institut de Chimie de Strasbourg, UMR 7177 CNRS, Université de Strasbourg, 4, rue Blaise Pascal, Strasbourg, 67000, France
| | - Sneǽana D Zarić
- Faculty of Chemistry, University of Belgrade, Studentski trg 12-16, Belgrade, 11000, Serbia
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27
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Mahmoudi G, Afkhami FA, Castiñeiras A, García-Santos I, Gurbanov A, Zubkov FI, Mitoraj MP, Kukułka M, Sagan F, Szczepanik DW, Konyaeva IA, Safin DA. Quasi-aromatic Möbius Metal Chelates. Inorg Chem 2018; 57:4395-4408. [DOI: 10.1021/acs.inorgchem.8b00064] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Ghodrat Mahmoudi
- Department of Chemistry, Faculty of Science, University of Maragheh, 55181-83111 Maragheh, Iran
| | - Farhad A. Afkhami
- Young Researchers and Elite Club, Tabriz Branch, Islamic Azad University, 51579-44533Tabriz, Iran
| | - Alfonso Castiñeiras
- Departamento de Química Inorgánica, Facultad de Farmacia, Universidad de Santiago de Compostela, E-15782 Santiago de Compostela, Spain
| | - Isabel García-Santos
- Departamento de Química Inorgánica, Facultad de Farmacia, Universidad de Santiago de Compostela, E-15782 Santiago de Compostela, Spain
| | - Atash Gurbanov
- Department of Chemistry, Baku State University, Z. Xalilov Str. 23, AZ1148, Baku, Azerbaijan
- Centro de Química Estrutural, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049−001 Lisboa, Portugal
| | - Fedor I. Zubkov
- Organic Chemistry Department, Faculty of Science, Peoples’ Friendship University of Russia (RUDN University), 6 Miklukho-Maklaya Street, Moscow 117198, Russian Federation
| | - Mariusz P. Mitoraj
- Department of Theoretical Chemistry, Faculty of Chemistry, Jagiellonian University, R. Gronostajowa 2, 30-387 Cracow, Poland
| | - Mercedes Kukułka
- Department of Theoretical Chemistry, Faculty of Chemistry, Jagiellonian University, R. Gronostajowa 2, 30-387 Cracow, Poland
| | - Filip Sagan
- Department of Theoretical Chemistry, Faculty of Chemistry, Jagiellonian University, R. Gronostajowa 2, 30-387 Cracow, Poland
| | - Dariusz W. Szczepanik
- Department of Theoretical Chemistry, Faculty of Chemistry, Jagiellonian University, R. Gronostajowa 2, 30-387 Cracow, Poland
| | - Irina A. Konyaeva
- Limited Liability Company “NIOST”, Kuzovlevski trakt 2, 634067 Tomsk, Russian Federation
- Department of Technology of Organic Substances and Polymer Materials, National Research Tomsk Polytechnic University, 43 Lenin Avenue, 634050 Tomsk, Russian Federation
| | - Damir A. Safin
- Institute of Chemistry, University of Tyumen, Perekopskaya Street 15a, 625003 Tyumen, Russian Federation
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28
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Lo Presti L. On the significance of weak hydrogen bonds in crystal packing: a large databank comparison of polymorphic structures. CrystEngComm 2018. [DOI: 10.1039/c8ce00674a] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Weak hydrogen bonds control initial molecular recognition modes, but the structure is determined by the interactions among larger supramolecular assemblies.
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Affiliation(s)
- Leonardo Lo Presti
- Department of Chemistry
- Università degli Studi di Milano
- Milano
- Italy
- Centre for Materials Crystallography
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29
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McKenzie J, Hunter CA. Competitor analysis of functional group H-bond donor and acceptor properties using the Cambridge Structural Database. Phys Chem Chem Phys 2018; 20:25324-25334. [DOI: 10.1039/c8cp05470c] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The CSD can be used to obtain a reliable quantitative ranking of the H-bond properties of organic functional groups provided each crystal structure is individually analysed as the result of a competition between all of the functional groups present for H-bond formation.
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Affiliation(s)
- James McKenzie
- Department of Chemistry
- University of Cambridge
- Cambridge CB2 1EW
- UK
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30
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Zhang Q, Xu Z, Shi J, Zhu W. Underestimated Halogen Bonds Forming with Protein Backbone in Protein Data Bank. J Chem Inf Model 2017. [DOI: 10.1021/acs.jcim.7b00235] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Qian Zhang
- Department
of Computer Science and Technology, East China Normal University, Shanghai 200241, China
| | - Zhijian Xu
- CAS
Key Laboratory of Receptor Research, Drug Discovery and Design Center,
Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Jiye Shi
- UCB Biopharma SPRL, Chemin du Foriest, B-1420 Braine-l′Alleud, Belgium
| | - Weiliang Zhu
- CAS
Key Laboratory of Receptor Research, Drug Discovery and Design Center,
Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
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31
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Taylor R. The hydrogen bond between N—H or O—H and organic fluorine: favourable yes, competitive no. ACTA CRYSTALLOGRAPHICA SECTION B-STRUCTURAL SCIENCE CRYSTAL ENGINEERING AND MATERIALS 2017; 73:474-488. [DOI: 10.1107/s2052520617005923] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 04/19/2017] [Indexed: 12/26/2022]
Abstract
A study was made ofX—H...F—C interactions (X= N or O) in small-molecule crystal structures. It was primarily based on 6728 structures containingX—H and C—F and no atom heavier than chlorine. Of the 28 451 C—F moieties in these structures, 1051 interact withX—H groups. However, over three-quarters of these interactions are either the weaker components of bifurcated hydrogen bonds (so likely to be incidental contacts) or occur in structures where there is a clear insufficiency of good hydrogen-bond acceptors such as oxygen, nitrogen or halide. In structures where good acceptors are entirely absent, there is about a 2 in 3 chance that a givenX—H group will donate to fluorine. Viable alternatives areX—H...π hydrogen bonds (especially to electron-rich aromatics) and dihydrogen bonds. The average H...F distances ofX—H...F—C interactions are significantly shorter for CR3F (R= C or H) and Csp2—F acceptors than for CRF3. TheX—H...F angle distribution is consistent with a weak energetic preference for linearity, but that of H...F—C suggests a flat energy profile in the range 100–180°.X—H...F—C interactions are more likely when the acceptor is Csp2—F or CR3F, and when the donor is C—NH2. They also occur significantly more often in structures containing tertiary alcohols or solvent molecules, or withZ′ > 1,i.e.when there may be unusual packing problems. It is extremely rare to findX—H...F—C interactions in structures where there are several unused good acceptors. When it does happen, there is often a clear reason,e.g.awkwardly shaped molecules whose packing isolates a donor group from the good acceptors.
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32
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Groom CR, Cole JC. The use of small-molecule structures to complement protein-ligand crystal structures in drug discovery. Acta Crystallogr D Struct Biol 2017; 73:240-245. [PMID: 28291759 PMCID: PMC5349436 DOI: 10.1107/s2059798317000675] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 01/13/2017] [Indexed: 11/10/2022] Open
Abstract
Many ligand-discovery stories tell of the use of structures of protein-ligand complexes, but the contribution of structural chemistry is such a core part of finding and improving ligands that it is often overlooked. More than 800 000 crystal structures are available to the community through the Cambridge Structural Database (CSD). Individually, these structures can be of tremendous value and the collection of crystal structures is even more helpful. This article provides examples of how small-molecule crystal structures have been used to complement those of protein-ligand complexes to address challenges ranging from affinity, selectivity and bioavailability though to solubility.
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Affiliation(s)
- Colin R. Groom
- Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, England
| | - Jason C. Cole
- Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, England
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33
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Higham J, Henchman RH. Locally adaptive method to define coordination shell. J Chem Phys 2017; 145:084108. [PMID: 27586905 DOI: 10.1063/1.4961439] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
An algorithm is presented to define a particle's coordination shell for any collection of particles. It requires only the particles' positions and no pre-existing knowledge or parameters beyond those already in the force field. A particle's shell is taken to be all particles that are not blocked by any other particle and not further away than a blocked particle. Because blocking is based on two distances and an angle for triplets of particles, it is called the relative angular distance (RAD) algorithm. RAD is applied to Lennard-Jones particles in molecular dynamics simulations of crystalline, liquid, and gaseous phases at various temperatures and densities. RAD coordination shells agree well with those from a cut-off in the radial distribution function for the crystals and liquids and are slightly higher for the gas.
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Affiliation(s)
- Jonathan Higham
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom and School of Chemistry, The University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Richard H Henchman
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom and School of Chemistry, The University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
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Brock CP. High- Z′ structures of organic molecules: their diversity and organizing principles. ACTA CRYSTALLOGRAPHICA SECTION B STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2016; 72:807-821. [DOI: 10.1107/s2052520616017297] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 10/27/2016] [Indexed: 04/11/2023]
Abstract
A list has been compiled of 284 well determined organic structures having more than four crystallographically independent molecules or formula units (i.e. Z′ > 4). Another 22 structures were rejected because the space group or unit cell was probably misassigned; the rate for that type of error is then only 7%. The space-group frequencies are unusual; half the structures are in Sohncke groups, partly because the fraction of enantiopure structures of resolvable enantiomers is higher than for lowerZ′ structures. Careful investigation of the 284 structures has shown that they are very diverse; no simple classification can describe them all. Organizing principles have, however, been recognized for almost all of them. The most common features are simple modulations and hydrogen-bonded aggregates; only 14% of the structures have neither. In 50% of the structuresnmolecules are related by a pseudotranslation that would be a crystallographic translation but for small molecular displacements and rotations. In 70% of the structures there are aggregates (e.g. n-mers, columns or layers) held together by strong intermolecular interactions; those aggregates usually have approximate local symmetry. Because then-fold modulations and then-mers often haven<Z′, 85% of the structures withZ′ > 5 have several features that combine to give the highZ′ value. The number of different molecular conformations is usually small,i.e.one or two in 84% of the structures. More exotic packing features, such as ordered faults and alternating layers of different types, are found inca30% of the structures. A very few structures are so complex that it is difficult to understand how the crystals could have formed.
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The Bright Future of Unconventional σ/π-Hole Interactions. Chemphyschem 2015; 16:2496-517. [DOI: 10.1002/cphc.201500314] [Citation(s) in RCA: 475] [Impact Index Per Article: 52.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Indexed: 01/25/2023]
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Seth SK, Lee VS, Yana J, Zain SM, Cunha AC, Ferreira VF, Jordão AK, de Souza MCBV, Wardell SMSV, Wardell JL, Tiekink ERT. Crystallographic and computational study of 1-(arylamino)-1,2,3-triazole-4-carbohydrazides. CrystEngComm 2015. [DOI: 10.1039/c4ce02175d] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The influence of substituents on the formation of supramolecular synthons is described.
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Affiliation(s)
| | | | - Janchai Yana
- Department of Chemistry, Faculty of Science and Technology
- Chiang Mai Rajabhat University
- Chiang Mai 50300, Thailand
| | | | - Anna C. Cunha
- Universidade Federal Fluminense
- Departamento de Química Orgânica
- Instituto de Química
- Outeiro de São João Baptista
- 24020-141 Niterói, Brazil
| | - Vitor F. Ferreira
- Universidade Federal Fluminense
- Departamento de Química Orgânica
- Instituto de Química
- Outeiro de São João Baptista
- 24020-141 Niterói, Brazil
| | - Alessandro K. Jordão
- Universidade Federal Fluminense
- Departamento de Química Orgânica
- Instituto de Química
- Outeiro de São João Baptista
- 24020-141 Niterói, Brazil
| | - Maria C. B. V. de Souza
- Universidade Federal Fluminense
- Departamento de Química Orgânica
- Instituto de Química
- Outeiro de São João Baptista
- 24020-141 Niterói, Brazil
| | | | - James L. Wardell
- Centro de Desenvolvimento Tecnológico em Saúde (CDTS)
- Fundação Oswaldo Cruz, (FIOCRUZ)
- Casa Amarela
- Campus de Manguinhos
- Rio de Janeiro, Brazil
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Taylor R, Allen FH, Cole JC. Quantifying the symmetry preferences of intermolecular interactions in organic crystal structures. CrystEngComm 2015. [DOI: 10.1039/c5ce00035a] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Many intermolecular interactions show preferences for particular crystallographic symmetries and the extent to which this is the case is quantifiable.
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Affiliation(s)
- Robin Taylor
- Cambridge Crystallographic Data Centre
- Cambridge CB2 1EZ, UK
| | - Frank H. Allen
- Cambridge Crystallographic Data Centre
- Cambridge CB2 1EZ, UK
| | - Jason C. Cole
- Cambridge Crystallographic Data Centre
- Cambridge CB2 1EZ, UK
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Otero-de-la-Roza A, Luaña V, Tiekink ERT, Zukerman-Schpector J. Unraveling Interactions in Molecular Crystals Using Dispersion Corrected Density Functional Theory: The Case of the Epoxydihydroarsanthrene Molecules. J Chem Theory Comput 2014; 10:5010-9. [DOI: 10.1021/ct500832g] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- A. Otero-de-la-Roza
- National Institute for Nanotechnology, National Research Council of Canada, 11421 Saskatchewan Drive, Edmonton, Alberta, Canada T6G 2M9
| | - Víctor Luaña
- Departamento
de Química Física y Analítica, Facultad de Química, Universidad de Oviedo, 33006 Oviedo, Asturias, Spain
| | | | - Julio Zukerman-Schpector
- Laboratório
de Cristalografía Estereodinâmica e Modelagem Molecular,
Departamento de Química, Universidade Federal de São Carlos, São
Carlos, SP 13565−905, Brazil
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Reis SG, Del Águila-Sánchez MA, Guedes GP, Ferreira GB, Novak MA, Speziali NL, López-Ortiz F, Vaz MGF. Synthesis, crystal structures and magnetic behaviour of four coordination compounds constructed with a phosphinic amide-TEMPO radical and [M(hfac)2] (M = Cu(II), Co(II) and Mn(II)). Dalton Trans 2014; 43:14889-901. [PMID: 25177845 DOI: 10.1039/c4dt01444h] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
In the present work we describe the synthesis, crystal structures and magnetic properties of four coordination compounds obtained by assembling a new phosphinic amide containing the TEMPO moiety, 1-piperidinyloxy-4-[(diphenylphosphinyl)amino]-2,2,6,6-tetramethyl radical (dppnTEMPO), with [M(hfac)2] building blocks (M = Cu(II), Co(II), Mn(II)). The crystal structures of the coordination compounds revealed the usefulness of the functionalized radical to provide discrete or extended architectures. In the copper compound () the ligand is coordinated through the oxygen atom of the NP[double bond, length as m-dash]O linkage to the metal, which exists in a square pyramidal or octahedral geometry. For the cobalt and manganese complexes (), both the phosphinic amide and the nitroxide oxygen atoms are involved in the coordination to the metal leading to one dimensional systems. In the cobalt complex () an interesting spin topology in the zig-zag chain was obtained due to the oxygen atom of the phosphinic amide group being μ2 coordinated to two cobalt(ii) ions. The magnetic behaviour of the coordination compounds shows overall antiferromagnetic interactions involving the metal ion and the organic radical. DFT calculations were performed in order to assign the main path for the magnetic interactions.
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Affiliation(s)
- Samira G Reis
- Instituto de Química, Universidade Federal Fluminense, 24020-141 Niterói, RJ, Brazil.
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Abstract
Consistent van der Waals radii are deduced for Ne-Xe, based on the noble gas···oxygen intermolecular distances found in gas phase structures. The set of radii proposed is shown to provide van der Waals distances for a wide variety of noble gas···element atom pairs that represent properly the distribution of distances both in the gas phase and in the solid state. Moreover, these radii show a smooth periodic trend down the group which is parallel to that shown by the halogens.
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Affiliation(s)
- Jürgen Vogt
- Chemical Information Systems, University of Ulm , 89069 Ulm, Germany
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