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Special Issue "Advances in Chemical Crystallography: A Themed Issue Honoring Professor Alexandra M. Z. Slawin on the Occasion of Her 60th Birthday"

A special issue of Molecules (ISSN 1420-3049).

Deadline for manuscript submissions: closed (30 September 2021) | Viewed by 13791

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A printed edition of this Special Issue is available here.

Special Issue Editors

Prof. Dr. William T. A. Harrison
E-Mail Website
Guest Editor
Department of Chemistry, University of Aberdeen, Meston Walk, Aberdeen AB24 3UE, UK
Interests: synthetic and structural inorganic chemistry
Dr. R. Alan Aitken
E-Mail Website
Guest Editor
School of Chemistry, University of St Andrews North Haugh, St Andrews Fife KY16 9ST, UK
Interests: synthesis; synthetic use of flash vacuum pyrolysis; heterocyclic chemistry; reactive intermediates; organophosphorus; organosulfur; heavier main group chemistry
Dr. Paul Waddell
E-Mail Website
Guest Editor
Chemistry, School of Natural and Environmental Sciences, Newcastle University, Bedson Building, Newcastle upon Tyne NE1 7RU, UK
Interests: X-ray diffraction; spectroscopic techniques; structure-function relationships; optoelectronic materials; intermolecular interactions; physical properties; supramolecular environments

Special Issue Information

Dear Colleagues,

Molecules is delighted to host a Special Issue honouring Prof. Alexandra Slawin FRSE on her 60th birthday for her outstanding contributions to chemical crystallography, including teaching and instrumentation. Alex was educated at Imperial College London (BSc) and Loughborough University (PhD), and since 2004, she has been a Research Professor of Chemistry at the University of St Andrews (Scotland).  

The diffraction facility overseen by Prof. Slawin at St Andrews is amongst the finest in the world, with two rotating anode systems with state-of-the-art area detectors and a fully automated system, which was developed in house and allows non-experts to submit samples which are examined, measured, solved, refined and the results emailed to the researcher.

Alex’s productivity is legendary, and in a survey carried out by the Cambridge Structural Database in 2018, she was ranked 6th in the world for the number of datasets deposited in the CSD and the highest-ranked female. The Web of Science (November 2020) shows her to have 1362 publications, 38,470 citations and a Hirsch h-index of 86. Her papers cover numerous areas of chemistry, including porous materials, metal–organic frameworks, verifying organic mechanisms and total syntheses, main-group chemistry and materials chemistry, and her co-authors include three Nobel prize winners.  

It is a grave concern that crystallography (the most powerful and versatile characterisation technique available) is disappearing from many chemistry degrees, and one especially outstanding aspect of Alex’s activities is her commitment to teaching the practice and theory of the technique to undergraduates and the support that she offers to project students. She is fully committed to diversity and supporting the career development of women scientists.

We wish Alex a happy 60th birthday and many more years of productive and ground-breaking science!

Prof. Dr. William T. A. Harrison
Dr. R. Alan Aitken
Dr. Paul Waddell
Guest Editors

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Published Papers (14 papers)

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Research

Article
Rationalisation of Patterns of Competing Reactivity by X-ray Structure Determination: Reaction of Isomeric (Benzyloxythienyl)oxazolines with a Base
Molecules 2021, 26(24), 7690; https://doi.org/10.3390/molecules26247690 - 20 Dec 2021
Cited by 1 | Viewed by 911
Abstract
Three isomeric (benzyloxythienyl)oxazolines 9, 11 and 13 have been prepared and are found, upon treatment with a strong base, to undergo either Wittig rearrangement or intramolecular attack of the benzylic anion on the oxazoline function to give products derived from cleavage of [...] Read more.
Three isomeric (benzyloxythienyl)oxazolines 9, 11 and 13 have been prepared and are found, upon treatment with a strong base, to undergo either Wittig rearrangement or intramolecular attack of the benzylic anion on the oxazoline function to give products derived from cleavage of the initially formed 3-aminothienofuran products. This pattern of reactivity is directly linked to the distance between the two reactive groups as determined by X-ray diffraction, with the greatest distance in 11 leading to exclusive Wittig rearrangement, the shortest distance in 13 giving exclusively cyclisation-derived products, and the intermediate distance in 9 leading to both processes being observed. The corresponding N-butyl amides were also obtained in two cases and one of these undergoes efficient Wittig rearrangement leading to a thieno[2,3-c]pyrrolone product. Full article
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Article
A Comparison of Cysteine-Conjugated Nitroxide Spin Labels for Pulse Dipolar EPR Spectroscopy
Molecules 2021, 26(24), 7534; https://doi.org/10.3390/molecules26247534 - 13 Dec 2021
Cited by 2 | Viewed by 942
Abstract
The structure-function and materials paradigms drive research on the understanding of structures and structural heterogeneity of molecules and solids from materials science to structural biology. Functional insights into complex architectures are often gained from a suite of complementary physicochemical methods. In the context [...] Read more.
The structure-function and materials paradigms drive research on the understanding of structures and structural heterogeneity of molecules and solids from materials science to structural biology. Functional insights into complex architectures are often gained from a suite of complementary physicochemical methods. In the context of biomacromolecular structures, the use of pulse dipolar electron paramagnetic resonance spectroscopy (PDS) has become increasingly popular. The main interest in PDS is providing long-range nanometre distance distributions that allow for identifying macromolecular topologies, validating structural models and conformational transitions as well as docking of quaternary complexes. Most commonly, cysteines are introduced into protein structures by site-directed mutagenesis and modified site-specifically to a spin-labelled side-chain such as a stable nitroxide radical. In this contribution, we investigate labelling by four different commercial labelling agents that react through different sulfur-specific reactions. Further, the distance distributions obtained are between spin-bearing moieties and need to be related to the protein structure via modelling approaches. Here, we compare two different approaches to modelling these distributions for all four side-chains. The results indicate that there are significant differences in the optimum labelling procedure. All four spin-labels show differences in the ease of labelling and purification. Further challenges arise from the different tether lengths and rotamers of spin-labelled side-chains; both influence the modelling and translation into structures. Our comparison indicates that the spin-label with the shortest tether in the spin-labelled side-group, (bis-(2,2,5,5-Tetramethyl-3-imidazoline-1-oxyl-4-yl) disulfide, may be underappreciated and could increase the resolution of structural studies by PDS if labelling conditions are optimised accordingly. Full article
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Article
Synthetic and Structural Study of peri-Substituted Phosphine-Arsines
Molecules 2021, 26(23), 7222; https://doi.org/10.3390/molecules26237222 - 28 Nov 2021
Cited by 1 | Viewed by 965
Abstract
A series of phosphorus-arsenic peri-substituted acenaphthene species have been isolated and fully characterised, including single crystal X-ray diffraction. Reactions of EBr3 (E = P, As) with iPr2PAcenapLi (Acenap = acenaphthene-5,6-diyl) afforded the thermally stable peri-substitution supported donor–acceptor [...] Read more.
A series of phosphorus-arsenic peri-substituted acenaphthene species have been isolated and fully characterised, including single crystal X-ray diffraction. Reactions of EBr3 (E = P, As) with iPr2PAcenapLi (Acenap = acenaphthene-5,6-diyl) afforded the thermally stable peri-substitution supported donor–acceptor complexes, iPr2PAcenapEBr23 and 4. Both complexes show a strong P→E dative interaction, as observed by X-ray crystallography and 31P NMR spectroscopy. DFT calculations indicated the unusual As∙∙∙As contact (3.50 Å) observed in the solid state structure of 4 results from dispersion forces rather than metallic interactions. Incorporation of the excess AsBr3 in the crystal structure of 3 promotes the formation of the ion separated species [iPr2PAcenapAsBr]+Br 5. A decomposition product 6 containing the rare [As6Br8]2– heterocubane dianion was isolated and characterised crystallographically. The reaction between iPr2PAcenapLi and EtAsI2 afforded tertiary arsine (BrAcenap)2AsEt 7, which was subsequently lithiated and reacted with PhPCl2 and Ph2PCl to afford cyclic PhP(Acenap)2AsEt 8 and acyclic EtAs(AcenapPPh2)2 9. Full article
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Article
Synthesis of a Hexameric Magnesium 4-pyridyl Complex with Cyclohexane-like Ring Structure via Reductive C-N Activation
Molecules 2021, 26(23), 7214; https://doi.org/10.3390/molecules26237214 - 28 Nov 2021
Viewed by 689
Abstract
The reaction of [{(Arnacnac)Mg}2] (Arnacnac = HC{MeC(NAr)}2, Ar = 2,6-diisopropylphenyl, Dip, or 2,6-diethylphenyl, Dep) with 4-dimethylaminopyridine (DMAP) at elevated temperatures afforded the hexameric magnesium 4-pyridyl complex [{(Arnacnac)Mg(4-C5H4N)}6] [...] Read more.
The reaction of [{(Arnacnac)Mg}2] (Arnacnac = HC{MeC(NAr)}2, Ar = 2,6-diisopropylphenyl, Dip, or 2,6-diethylphenyl, Dep) with 4-dimethylaminopyridine (DMAP) at elevated temperatures afforded the hexameric magnesium 4-pyridyl complex [{(Arnacnac)Mg(4-C5H4N)}6] via reductive cleavage of the DMAP C-N bond. The title compound contains a large s-block organometallic cyclohexane-like ring structure comprising tetrahedral (Arnacnac)Mg nodes and linked by linear 4-pyridyl bridging ligands, and the structure is compared with other ring systems. [(Dipnacnac)Mg(DMAP)(NMe2)] was structurally characterised as a by-product. Full article
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Article
Solvothermal Synthesis of a Novel Calcium Metal-Organic Framework: High Temperature and Electrochemical Behaviour
Molecules 2021, 26(22), 7048; https://doi.org/10.3390/molecules26227048 - 22 Nov 2021
Cited by 1 | Viewed by 854
Abstract
The rapid growth in the field of metal-organic frameworks (MOFs) over recent years has highlighted their high potential in a variety of applications. For biological and environmental applications MOFs with low toxicity are vitally important to avoid any harmful effects. For this reason, [...] Read more.
The rapid growth in the field of metal-organic frameworks (MOFs) over recent years has highlighted their high potential in a variety of applications. For biological and environmental applications MOFs with low toxicity are vitally important to avoid any harmful effects. For this reason, Ca-based MOFs are highly desirable owing to their low cost and high biocompatibility. Useful Ca MOFs are still rare owing to the ionic character and large size of the Ca2+ ion tending to produce dense phases. Presented here is a novel Ca-based MOF containing 2,3-dihyrdoxyterephthalate (2,3-dhtp) linkers Ca(2,3-dhtp)(H2O) (SIMOF-4). The material undergoes a phase transformation on heating, which can be followed by variable temperature powder X-ray diffraction. The structure of the high temperature form was obtained using single-crystal X-ray diffraction. The electrochemical properties of SIMOF-4 were also investigated for use in a Na ion battery. Full article
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Article
Low-Dimensional Architectures in Isomeric cis-PtCl2{Ph2PCH2N(Ar)CH2PPh2} Complexes Using Regioselective-N(Aryl)-Group Manipulation
Molecules 2021, 26(22), 6809; https://doi.org/10.3390/molecules26226809 - 11 Nov 2021
Cited by 1 | Viewed by 517
Abstract
The solid-state behaviour of two series of isomeric, phenol-substituted, aminomethylphosphines, as the free ligands and bound to PtII, have been extensively studied using single crystal X-ray crystallography. In the first library, isomeric diphosphines of the type Ph2PCH2N(Ar)CH [...] Read more.
The solid-state behaviour of two series of isomeric, phenol-substituted, aminomethylphosphines, as the free ligands and bound to PtII, have been extensively studied using single crystal X-ray crystallography. In the first library, isomeric diphosphines of the type Ph2PCH2N(Ar)CH2PPh2 [1ae; Ar = C6H3(Me)(OH)] and, in the second library, amide-functionalised, isomeric ligands Ph2PCH2N{CH2C(O)NH(Ar)}CH2PPh2 [2ae; Ar = C6H3(Me)(OH)], were synthesised by reaction of Ph2PCH2OH and the appropriate amine in CH3OH, and isolated as colourless solids or oils in good yield. The non-methyl, substituted diphosphines Ph2PCH2N{CH2C(O)NH(Ar)}CH2PPh2 [2f, Ar = 3-C6H4(OH); 2g, Ar = 4-C6H4(OH)] and Ph2PCH2N(Ar)CH2PPh2 [3, Ar = 3-C6H4(OH)] were also prepared for comparative purposes. Reactions of 1ae, 2ag, or 3 with PtCl24-cod) afforded the corresponding square-planar complexes 4ae, 5ag, and 6 in good to high isolated yields. All new compounds were characterised using a range of spectroscopic (1H, 31P{1H}, FT–IR) and analytical techniques. Single crystal X-ray structures have been determined for 1a, 1b∙CH3OH, 2f∙CH3OH, 2g, 3, 4b∙(CH3)2SO, 4c∙CHCl3, 4d∙½Et2O, 4e∙½CHCl3∙½CH3OH, 5a∙½Et2O, 5b, 5c∙¼H2O, 5d∙Et2O, and 6∙(CH3)2SO. The free phenolic group in 1b∙CH3OH, 2f∙CH3OH,2g, 4b∙(CH3)2SO, 5a∙½Et2O, 5c∙¼H2O, and 6∙(CH3)2SO exhibits various intra- or intermolecular O–H∙∙∙X (X = O, N, P, Cl) hydrogen contacts leading to different packing arrangements. Full article
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Article
Azetidinium Lead Halide Ruddlesden–Popper Phases
Molecules 2021, 26(21), 6474; https://doi.org/10.3390/molecules26216474 - 27 Oct 2021
Viewed by 596
Abstract
A family of Ruddlesden–Popper (n = 1) layered perovskite-related phases, Az2PbClxBr4−x with composition 0 ≤ x ≤ 4 were obtained using mechanosynthesis. These compounds are isostructural with K2NiF4 and therefore adopt the idealised [...] Read more.
A family of Ruddlesden–Popper (n = 1) layered perovskite-related phases, Az2PbClxBr4−x with composition 0 ≤ x ≤ 4 were obtained using mechanosynthesis. These compounds are isostructural with K2NiF4 and therefore adopt the idealised n = 1 Ruddlesden–Popper structure. A linear variation in unit cell volume as a function of anion average radius is observed. A tunable bandgap is achieved, ranging from 2.81 to 3.43 eV, and the bandgap varies in a second-order polynomial relationship with the halide composition. Full article
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Article
Isothiourea-Catalyzed Enantioselective α-Alkylation of Esters via 1,6-Conjugate Addition to para-Quinone Methides
Molecules 2021, 26(21), 6333; https://doi.org/10.3390/molecules26216333 - 20 Oct 2021
Cited by 1 | Viewed by 895
Abstract
The isothiourea-catalyzed enantioselective 1,6-conjugate addition of para-nitrophenyl esters to 2,6-disubstituted para-quinone methides is reported. para-Nitrophenoxide, generated in situ from initial N-acylation of the isothiourea by the para-nitrophenyl ester, is proposed to facilitate catalyst turnover in this transformation. A [...] Read more.
The isothiourea-catalyzed enantioselective 1,6-conjugate addition of para-nitrophenyl esters to 2,6-disubstituted para-quinone methides is reported. para-Nitrophenoxide, generated in situ from initial N-acylation of the isothiourea by the para-nitrophenyl ester, is proposed to facilitate catalyst turnover in this transformation. A range of para-nitrophenyl ester products can be isolated, or derivatized in situ by addition of benzylamine to give amides at up to 99% yield. Although low diastereocontrol is observed, the diastereoisomeric ester products are separable and formed with high enantiocontrol (up to 94:6 er). Full article
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Article
Synthesis of Indoloquinolines: An Intramolecular Cyclization Leading to Advanced Perophoramidine-Relevant Intermediates
Molecules 2021, 26(19), 6039; https://doi.org/10.3390/molecules26196039 - 05 Oct 2021
Viewed by 702
Abstract
The bioactive natural product perophoramidine has proved a challenging synthetic target. An alternative route to its indolo[2,3-b]quinolone core structure involving a N-chlorosuccinimde-mediated intramolecular cyclization reaction is reported. Attempts to progress towards the natural product are also discussed with an unexpected deep-seated rearrangement of [...] Read more.
The bioactive natural product perophoramidine has proved a challenging synthetic target. An alternative route to its indolo[2,3-b]quinolone core structure involving a N-chlorosuccinimde-mediated intramolecular cyclization reaction is reported. Attempts to progress towards the natural product are also discussed with an unexpected deep-seated rearrangement of the core structure occurring during an attempted iodoetherification reaction. X-ray crystallographic analysis provides important analytical confirmation of assigned structures. Full article
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Article
Synthesis, Structural and Physicochemical Characterization of a Titanium(IV) Compound with the Hydroxamate Ligand N,2-Dihydroxybenzamide
Molecules 2021, 26(18), 5588; https://doi.org/10.3390/molecules26185588 - 15 Sep 2021
Viewed by 962
Abstract
The siderophore organic ligand N,2-dihydroxybenzamide (H2dihybe) incorporates the hydroxamate group, in addition to the phenoxy group in the ortho-position and reveals a very rich coordination chemistry with potential applications in medicine, materials, and physical sciences. The reaction of H2 [...] Read more.
The siderophore organic ligand N,2-dihydroxybenzamide (H2dihybe) incorporates the hydroxamate group, in addition to the phenoxy group in the ortho-position and reveals a very rich coordination chemistry with potential applications in medicine, materials, and physical sciences. The reaction of H2dihybe with TiCl4 in methyl alcohol and KOH yielded the tetranuclear titanium oxo-cluster (TOC) [TiIV4(μ-O)2(HOCH3)4(μ-Hdihybe)4(Hdihybe)4]Cl4∙10H2O∙12CH3OH (1). The titanium compound was characterized by single-crystal X-ray structure analysis, ESI-MS, 13C, and 1H NMR spectroscopy, solid-state and solution UV–Vis, IR vibrational, and luminescence spectroscopies and molecular orbital calculations. The inorganic core Ti4(μ-O)2 of 1 constitutes a rare structural motif for discrete TiIV4 oxo-clusters. High-resolution ESI-MS studies of 1 in methyl alcohol revealed the presence of isotopic distribution patterns which can be attributed to the tetranuclear clusters containing the inorganic core {Ti4(μ-O)2}. Solid-state IR spectroscopy of 1 showed the presence of an intense band at ~800 cm−1 which is absent in the spectrum of the H2dihybe and was attributed to the high-energy ν(Ti2μ-O) stretching mode. The ν(C=O) in 1 is red-shifted by ~10 cm−1, while the ν(N-O) is blue-shifted by ~20 cm−1 in comparison to H2dihybe. Density Functional Theory (DFT) calculations reveal that in the experimental and theoretically predicted IR absorbance spectra of the ligand and Ti-complex, the main bands observed in the experimental spectra are also present in the calculated spectra supporting the proposed structural model. 1H and 13C NMR solution (CD3OD) studies of 1 reveal that it retains its integrity in CD3OD. The observed NMR changes upon addition of base to a CD3OD solution of 1, are due to an acid–base equilibrium and not a change in the TiIV coordination environment while the decrease in the complex’s lability is due to the improved electron-donating properties which arise from the ligand deprotonation. Luminescence spectroscopic studies of 1 in solution reveal a dual narrow luminescence at different excitation wavelengths. The TOC 1 exhibits a band-gap of 1.98 eV which renders it a promising candidate for photocatalytic investigations. Full article
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Article
A Reusable Efficient Green Catalyst of 2D Cu-MOF for the Click and Knoevenagel Reaction
Molecules 2021, 26(17), 5296; https://doi.org/10.3390/molecules26175296 - 31 Aug 2021
Cited by 1 | Viewed by 1018
Abstract
[Cu(CPA)(BDC)]n (CPA = 4-(Chloro-phenyl)-pyridin-4-ylmethylene-amine; BDC = 1,4-benzenedicarboxylate) has been synthesized and structurally characterized by single crystal X-Ray diffraction measurement. The structural studies establish the copper (II) containing 2D sheet with (4,4) square grid structure. The square grid lengths are 10.775 and 10.769 [...] Read more.
[Cu(CPA)(BDC)]n (CPA = 4-(Chloro-phenyl)-pyridin-4-ylmethylene-amine; BDC = 1,4-benzenedicarboxylate) has been synthesized and structurally characterized by single crystal X-Ray diffraction measurement. The structural studies establish the copper (II) containing 2D sheet with (4,4) square grid structure. The square grid lengths are 10.775 and 10.769 Å. Thermal stability is assessed by TGA, and subsequent PXRD data establish the crystallinity. The surface morphology is evaluated by FE-SEM. The N2 adsorption−desorption analysis demonstrates the mesoporous feature (∼6.95 nm) of the Cu-MOF. This porous grid serves as heterogeneous green catalyst with superficial recyclability and thermal stability and facilitates organic transformations efficiently such as, Click and Knoevenagel reactions in the aqueous methanolic medium. Full article
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Article
Hydricity of 3d Transition Metal Complexes from Density Functional Theory: A Benchmarking Study
Molecules 2021, 26(13), 4072; https://doi.org/10.3390/molecules26134072 - 03 Jul 2021
Cited by 4 | Viewed by 1448
Abstract
A range of modern density functional theory (DFT) functionals have been benchmarked against experimentally determined metal hydride bond strengths for three first-row TM hydride complexes. Geometries were found to be produced sufficiently accurately with RI-BP86-D3(PCM)/def2-SVP and further single-point calculations with PBE0-D3(PCM)/def2-TZVP were found [...] Read more.
A range of modern density functional theory (DFT) functionals have been benchmarked against experimentally determined metal hydride bond strengths for three first-row TM hydride complexes. Geometries were found to be produced sufficiently accurately with RI-BP86-D3(PCM)/def2-SVP and further single-point calculations with PBE0-D3(PCM)/def2-TZVP were found to reproduce the experimental hydricity accurately, with a mean absolute deviation of 1.4 kcal/mol for the complexes studied. Full article
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Article
Synthesis and Single Crystal Structures of N-Substituted Benzamides and Their Chemoselective Selenation/Reduction Derivatives
Molecules 2021, 26(8), 2367; https://doi.org/10.3390/molecules26082367 - 19 Apr 2021
Viewed by 666
Abstract
A series of N-aryl-N-(2-oxo-2-arylethyl) benzamides and cinnamides has been prepared. The reaction of the benzamides with Woollins’ reagent, a highly efficient chemoselective selenation/reduction reagent, gave the corresponding N-aryl-N-(arylenethyl) benzoselenoamides in good yields. Five representative single crystal X-ray structures are discussed. Full article
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Article
[CrIII8NiII6]n+ Heterometallic Coordination Cubes
Molecules 2021, 26(3), 757; https://doi.org/10.3390/molecules26030757 - 02 Feb 2021
Cited by 1 | Viewed by 1416
Abstract
Three new heterometallic [CrIII8NiII6] coordination cubes of formulae [CrIII8NiII6L24(H2O)12](NO3)12 (1), [CrIII8NiII6L24(MeCN)7 [...] Read more.
Three new heterometallic [CrIII8NiII6] coordination cubes of formulae [CrIII8NiII6L24(H2O)12](NO3)12 (1), [CrIII8NiII6L24(MeCN)7(H2O)5](ClO4)12 (2), and [CrIII8NiII6L24Cl12] (3) (where HL = 1-(4-pyridyl)butane-1,3-dione), were synthesised using the paramagnetic metalloligand [CrIIIL3] and the corresponding NiII salt. The magnetic skeleton of each capsule describes a face-centred cube in which the eight CrIII and six NiII ions occupy the eight vertices and six faces of the structure, respectively. Direct current magnetic susceptibility measurements on (1) reveal weak ferromagnetic interactions between the CrIII and NiII ions, with JCr-Ni = + 0.045 cm−1. EPR spectra are consistent with weak exchange, being dominated by the zero-field splitting of the CrIII ions. Excluding wheel-like structures, examples of large heterometallic clusters containing both CrIII and NiII ions are rather rare, and we demonstrate that the use of metalloligands with predictable bonding modes allows for a modular approach to building families of related polymetallic complexes. Compounds (1)–(3) join the previously published, structurally related family of [MIII8MII6] cubes, where MIII = Cr, Fe and MII = Cu, Co, Mn, Pd. Full article
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