Cubane Cluster Research Articles

Electronic and Structural Properties of the Double Cubane Iron-Sulfur Cluster

The double-cubane cluster (DCC) refers to an [Fe8S9] iron-sulfur complex that is otherwise only known to exist in nitrogenases. Containing a bridging µ2-S ligand, the DCC in the DCC-containing protein (DCCP) is covalently linked to the protein scaffold via six coordinating cysteine residues. In this study, the nature of spin coupling and the effect of spin states on the cluster’s geometry are investigated computationally. Using density functional theory (DFT) and a broken symmetry (BS) approach to study the electronic ground state of the system, we computed the exchange interaction between the spin-coupled spins of the four FeFe dimers contained in the DCC. This treatment yields results that are in excellent agreement with both computed and experimentally determined exchange parameters for analogously coupled di-iron complexes. Hybrid quantum mechanical (QM)/molecular mechanical (MM) geometry optimizations show that cubane cluster A closest to charged amino acid side chains (Arg312, Glu140, Lys146) is less compact than cluster B, indicating that electrons of the same spin in a charged environment seek maximum separation. Overall, this study provides the community with a fundamental reference for subsequent studies of DCCP, as well as for investigations of other [Fe8S9]-containing enzymes.

The FeIVO• oxyl unit as a key intermediate in water oxidation on the FeIIIhydroxide: DFT predictions

AbstractThe OO coupling process in water oxidation on the gamma FeOOH hydroxide catalyst is simulated by means of density functional theory using model iron cubane cluster Fe4O4(OH)4. A key reactive intermediate is proposed to be the HOFeIVO• oxyl unit with terminal oxo radical. The “initial” vertex FeIII(OH) moiety forms this intermediate at the calculated overpotential of 0.93 V by adding one water molecule and withdrawing two proton–electron pairs. The OO coupling goes via water nucleophilic attack on the oxyl oxygen to form the OO bond with a remarkably low barrier of 11 kcal/mol. This process is far more effective than alternative scenario based on direct interaction of two ferryl FeIVO sites (with estimated barrier of 36 kcal/mol) and is comparable with the coupling between terminal oxo center and three‐coordinated lattice oxo center (12 kcal/mol barrier). The process of hydroxylation of terminal oxygen inhibits the OO coupling. Nevertheless, being more effective for ferryl oxygen, the hydroxylation in fact enhances selectivity of the OO coupling initiated by the oxyl oxygen.

Hydrolysis of Element (White) Phosphorus under the Action of Heterometallic Cubane-Type Cluster {Mo3PdS4}.

Reaction of heterometallic cubane-type cluster complexes—[Mo3{Pd(dba)}S4Cl3(dbbpy)3]PF6, [Mo3{Pd(tu)}S4Cl3(dbbpy)3]Cl and [Mo3{Pd(dba)}S4(acac)3(py)3]PF6, where dba—dibenzylideneacetone, dbbpy—4,4′-di-tert-butyl-2,2′-bipyridine, tu—thiourea, acac—acetylacetonate, py—pyridine, with white phosphorus (P4) in the presence of water leads to the formation of phosphorous acid H3PO3 as the major product. The crucial role of the Pd atom in the cluster core {Mo3PdS4} has been established in the hydrolytic activation of P4 molecule. The main intermediate of the process, the cluster complex [Mo3{PdP(OH)3}S4Cl3(dbbpy)3]+ with coordinated P(OH)3 molecule and phosphine PH3, have been detected by 31P NMR spectroscopy in the reaction mixture.

Nitride-incorporated W-Fe-S double cubane clusters: terminal ligand substitutions and redox behaviors.

Structural mimicking of the nitrogenase FeMo cofactor has long been a challenge in synthetic inorganic chemistry and bioinorganic chemistry. This already very tough task had become even harder after the discovery of an interstitial light atom, which was later evidenced to be carbide. From a synthetic point of view, to introduce such a 2p atom into the core of a Fe-S cluster would have to overcome the coordination competition from overwhelming sulfide ligands. Recently, we have reported a controlled synthetic strategy named redox metathesis based on template-assisted structure design, and have successfully synthesized a couple of nitride-incorporated edge-bridged double cubane (N-EBDC) W-Fe-S clusters. In this work, we have systematically studied the terminal ligand substitutions of heteroleptic N-EBDC clusters, utilizing ethanethiolate, thiophenolate, p-thiocresolate, azide, and methoxide to replace the terminally bound chloride ligands. Structural analysis of this family of N-EBDC clusters reveals that different terminal ligands affect the fine structures of the cluster cores at different levels. Further studies by cyclic voltammetry indicate that these N-EBDC clusters with distinct terminal ligands exhibit different redox behaviors, furnishing in-depth information on the electronic structure of these clusters potentially related to their reactivity. This study provided useful information for the investigation of nitrogenase related Fe-S clusters toward structural and functional mimicking of the nitrogenase FeMo cofactor.

Luminescent Cu4I4-cubane clusters based on N-methyl-5,10-dihydrophenarsazines.

Two luminescent Cu4I4-cubane tetramers with N-methyl-10-(p-halogenophenyl)-5,10-dihydrophenarsazine ligands were synthesized and characterized by NMR spectroscopy, mass spectrometry, elemental analysis, and single-crystal X-ray diffraction analysis. The UV-Vis absorption and emission properties were studied and rationalized by DFT and time-dependent DFT calculations. The luminescence behavior was found to be rather different from that of recently reported tetranuclear copper iodide cubane clusters based on As,O-analogues - 10-(aryl)phenoxarsines. The crystalline powders of both complexes exhibit the temperature-dependent dual-band emission: the low-energy emission originates from the cluster-centered (3CC) triplet state, whereas the high-energy emission was attributed to the intraligand (3IL) triplet state.

Tetranuclear copper(ii) cubane complexes derived from self-assembled 1,3-dimethyl-5-(o-phenolate-azo)-6-aminouracil: structures, non-covalent interactions and magnetic property

A new doubly opened 4 + 2 Cu4O4 cubane cluster exhibits strong antiferromagnetic exchange coupling with J1 = −110.1 cm−1, and J2 = −27.1 cm−1.

Bridging Polyoxometalate-Based Mn4 Cubane Clusters with Inorganic Phosphates: Structural Transformation and Magnetic Properties.

The mixed-valent tetramanganese MnIII3MnIV (Mn4) cubane clusters have been at the forefront of molecular magnetism and biomimetic catalysis research for decades. Incorporating robust polyoxometalates to Mn4 cubanes significantly improves their stability and aqueous solubility, while providing a great platform for studying their deposition onto selected surfaces during device fabrication. In this work, we discovered that the terminal carboxylate ligands in these polyoxometalate-based [MnIII3MnIVO4] magnetic clusters can be partially or completely replaced by inorganic phosphate/polyphosphate groups. This replacement leads to oligomeric aggregates of the Mn4 clusters. The magnetic data of the monomeric and oligomeric Mn4 clusters suggested that the introduction of inorganic phosphate bridges may not alter the S = 9/2 ground state of individual Mn4 clusters, although different magnetic behaviors, especially at low temperatures, were observed primarily because of intercluster interactions.

Synthesis of Novel Tetra(µ3-Methoxo) Bridged with [Cu(II)-O-Cd(II)] Double-Open-Cubane Cluster: XRD/HSA-Interactions, Spectral and Oxidizing Properties.

A new double-open-cubane core Cd(II)-O-Cu(II) bimetallic ligand mixed cluster of type [Cl2Cu4Cd2(NNO)6(NN)2(NO3)2].CH3CN was made available in EtOH/CH3CN solution. The 1-hydroxymethyl-3,5-dimethylpyrazole (NNOH) and 3,5-dimethylpyrazole (NNH) act as N,O-polydentate anion ligands in coordinating the Cu(II) and Cd(II) centers. The structure of the cluster in the solid state was proved by XRD study and confirmed in the liquid state by UV-vis analysis. The XRD result supported the construction of two octahedral and one square pyramid geometries types around the four Cu(II) centers and only octahedral geometry around Cd(II) two centers. Interestingly, NNOH ligand acts as a tetra-µ3-oxo and tri-µ2-oxo ligand; meanwhile, the N-N in NNH acts as classical bidentate anion/neutral ligands. The interactions in the lattice were detected experimentally by the XRD-packing result and computed via Hirschfeld surface analysis (HSA). The UV-vis., FT-IR and Energy Dispersive X-ray (EDX), supported the desired double-open cubane cluster composition. The oxidation potential of the desired cluster was evaluated using a 3,5-DTB-catechol 3,5-DTB-quinone as a catecholase model reaction.

Ring-Shaped Polyoxometalate Built by {Mn 4 PW 9 } and PO 4 Units for Efficient Visible-Light-Driven Hydrogen Evolution

A novel mixed-valence, ring-shaped multinuclear Mn-containing polyoxometalate, [H2N(CH3)2]15NaH8-[MnIII3MnIV(μ3-O)3(OAc)PO4(B-α-PW9O34)]4·36H2O (1) was made and systematically characterized using v...

Single‐Crystal‐to‐Single‐Crystal Installation of Ln4(OH)4 Cubanes in an Anionic Metallosupramolecular Framework

AbstractPostsynthetic installation of lanthanide cubanes into a metallosupramolecular framework via a single‐crystal‐to‐single‐crystal (SCSC) transformation is presented. Soaking single crystals of K6[Rh4Zn4O(l‐cys)12] (K6[1]; l‐H2cys=l‐cysteine) in a water/ethanol solution containing Ln(OAc)3 (Ln3+=lanthanide ion) results in the exchange of K+ by Ln3+ with retention of the single crystallinity, producing Ln2[1] (2Ln) and Ln0.33[Ln4(OH)4(OAc)3(H2O)7][1] (3Ln) for early and late lanthanides, respectively. While the Ln3+ ions in 2Ln exist as disordered aqua species, those in 3Ln form ordered hydroxide‐bridged cubane clusters that connect [1]6− anions in a 3D metal‐organic framework through coordination bonds with carboxylate groups. This study shows the utility of an anionic metallosupramolecular framework with carboxylate groups for the creation of a series of metal cubanes that have great potential for various applications, such as magnetic materials and heterogeneous catalysts.

Single-Crystal-to-Single-Crystal Installation of Ln4 (OH)4 Cubanes in an Anionic Metallosupramolecular Framework.

Postsynthetic installation of lanthanide cubanes into a metallosupramolecular framework via a single-crystal-to-single-crystal (SCSC) transformation is presented. Soaking single crystals of K6 [Rh4 Zn4 O(l-cys)12 ] (K6 [1]; l-H2 cys=l-cysteine) in a water/ethanol solution containing Ln(OAc)3 (Ln3+ =lanthanide ion) results in the exchange of K+ by Ln3+ with retention of the single crystallinity, producing Ln2 [1] (2Ln ) and Ln0.33 [Ln4 (OH)4 (OAc)3 (H2 O)7 ][1] (3Ln ) for early and late lanthanides, respectively. While the Ln3+ ions in 2Ln exist as disordered aqua species, those in 3Ln form ordered hydroxide-bridged cubane clusters that connect [1]6- anions in a 3D metal-organic framework through coordination bonds with carboxylate groups. This study shows the utility of an anionic metallosupramolecular framework with carboxylate groups for the creation of a series of metal cubanes that have great potential for various applications, such as magnetic materials and heterogeneous catalysts.

Synthesis and structural characterization of the formato bridged Cu(ii) cubane: Crystallographic evidence of atmospheric CO2 fixation as formate in a tertranuclear Cu(II) cluster

Fixation of atmospheric carbon-di-oxide (CO2) by metal complexes continuously receives a great deal of attention from the viewpoint of environmental concerns. Herein, a novel tetranuclear copper (II) cluster [Cu4 μ3-(mph)4 μ2-(HCO2)2] (ClO4)2.CH2Cl2 (1), synthesized using Methyl(6-hydroxymethyl)picolinate ligand (Hmhp) and Cu(ClO4)2·6H2O in the presence of triethylamine base, is reported where atmospheric CO2 is serendipitously trapped in the form of formato-bridging ligand. The single X-ray structural elucidation of the complex 1 reveals a Cu4O4 cubane cluster stabilized by four peripheral mhp ligands, all of which display μ3-η1: η1: η3 binding mode (each bridging ligand link three Cu (II) ions). Moreover, the cubane core was supported by two bridging formate groups, resulted from the reduction of atmospheric CO2. The two formate ions exhibit μ2-η1: η1 binding mode, bridges two Cu(II) atoms. All the Cu(II) ions in the cubane core possess distorted octahedral coordination geometry (CuN1O5). Based on the observed Cu···Cu interactions in the Cu4O4 cubane core, 1 can be categorized under [2+2+2] type of classification. In addition to the synthesis and characterization of 1, a mechanistic hypothesis for the reduction of atmospheric CO2 to formate is also proposed to highlight the future potential of similar complexes in CO2 fixation/conversion.

Synthesis of novel Cubane [Ni4(O∩O)4(OCH3)4(OOH)4] cluster: XRD/HSA-interactions, spectral, DNA-binding, docking and subsequent thermolysis to NiO nanocrystals

Under liquid-state vibration ultrasonic mode, the Ni4(O∩O)4(OCH3)4(OOH)4 complex [O∩O-bidentate ligand = 4,4,4-trifluoro-1-phenylbutane-1,3-dione] was synthesized from metal precursor and ligand in 10% H2O2/MeOH media, as a novel [Ni4(μ3-O)4] cubane cluster. The XRD-structure of the desired cluster was unraveled that each Ni(II) metal center possesses a distorted octahedral geometry. Monitored thermal treatment to the tetranuclear metal cluster in an open atmosphere afforded nanocrystalline rod-shaped nickel oxide. Moreover, CHN-EA, FT-IR, conductivity measurement, UV–Vis., EDX, SEM, TG/DTA, and PXRD have confirmed the structure of the new cluster and NiO nanocrystals. The XRD-lattice interactions were explored to evaluate their role via computational Hirshfeld surface analysis. The molecular docking of the cluster with SS-DNA was estimated and demonstrated.

Interatomic Interactions in Heterometallic Cubane-Type Clusters with {Mo3S4M′} (M′ = Cu, Ni, Pd) Core

The electronic structure of heterometallic cubane-type clusters with core {Mo3S4M′} (M′ = Cu+, Ni0, Pd0) was investigated by the Atoms in Molecules and Electron Localization Function topological methods as well as Energy Decomposition Analysis. It was found that {Mo3S4Cu} and {Mo3S4M′} (M′= Ni, Pd) clusters have a different interaction between molybdenum and heterometallic atoms. In case of the complexes with Ni/Pd atom, the disynaptic basins on the Mo–M′ bonds were observed in contrast to the Cu containing complex. The complex formation between heterometallic fragments and trinuclear molybdenum complex {Mo3S4} were found to be hindered due to steric interactions. Nevertheless, the formation of the heterometallic cubane-type clusters occurs due to the multicenter and pair covalent interactions between Mo and M′ atoms.

Synthesis and XRD of Novel Ni4(µ3-O)4 Twist Cubane Cluster Using Three NNO Mixed Ligands: Hirshfeld, Spectral, Thermal and Oxidation Properties

A novel [Ni4(µ3-O)4] twisted cubane complex, Ni4Cl2(NN)2(ONN)2(NNO)2(H2O)2·2THF, was prepared from a crude mixture of three bidentate ligands. A mixture of ethyl 1-(hydroxymethyl)-3-methyl-1H-pyrazole-5-carboxylate (HONN) and ethyl 1-(hydroxyl-methyl)-5-methyl-1H-pyrazole-3-carboxylate (NNOH) were added to ethyl 3-methyl-1H-pyrazole-5-carboxylate (NNH) then mixed to NiCl2·6H2O solution under ambient conditions. Reaction progress was monitored via infrared and ultraviolet–visible spectroscopies and energy-dispersive X-ray spectroscopy was used to analyze the product. Reaction yields for cluster synthesis were very good. Single crystal structure determination for the cluster indicates a novel [Ni4(µ3-O)4] twisted cubane structure with octahedral geometry around each of the Ni(II) centers in Ni4Cl2(NN)2(ONN)2(NNO)2(H2O)2·2THF. The lattice is stabilized by hydrogen bonding and H– $$ \pi $$ stacking. Hirshfeld surface analysis (HSA) corroborates the single crystal structure determination results. The cluster displays significant thermal stability under open atmosphere conditions; it decomposes in three steps at high temperature. The cluster demonstrates promising results as a catalyst; it promoted the complete oxidation of catechol to o-Quinone in under mild conditions.

Isolation and Study of Ruthenium-Cobalt Oxo Cubanes Bearing a High-Valent, Terminal RuV-Oxo with Significant Oxyl Radical Character.

High-valent RuV-oxo intermediates have long been proposed in catalytic oxidation chemistry, but investigations into their electronic and chemical properties have been limited due to their reactive nature and rarity. The incorporation of Ru into the [Co3O4] subcluster via the single-step assembly reaction of CoII(OAc)2(H2O)4 (OAc = acetate), perruthenate (RuO4-), and pyridine (py) yielded an unprecedented Ru(O)Co3(μ3-O)4(OAc)4(py)3 cubane featuring an isolable, yet reactive, RuV-oxo moiety. EPR, ENDOR, and DFT studies reveal a valence-localized [RuV(S = 1/2)CoIII3(S = 0)O4] configuration and non-negligible covalency in the cubane core. Significant oxyl radical character in the RuV-oxo unit is experimentally demonstrated by radical coupling reactions between the oxo cubane and both 2,4,6-tri-tert-butylphenoxyl and trityl radicals. The oxo cubane oxidizes organic substrates and, notably, reacts with water to form an isolable μ-oxo bis-cubane complex [(py)3(OAc)4Co3(μ3-O)4Ru]-O-[RuCo3(μ3-O)4(OAc)4(py)3]. Redox activity of the RuV-oxo fragment is easily tuned by the electron-donating ability of the distal pyridyl ligand set at the Co sites demonstrating strong electronic communication throughout the entire cubane cluster. Natural bond orbital calculations reveal cooperative orbital interactions of the [Co3O4] unit in supporting the RuV-oxo moiety via a strong π-electron donation.

Synthesis, characterization and crystal structure of a novel tetranuclear Co(II) cubane cluster

A new tetranuclear Co(II) cubane cluster 1, [Co4(L1)4(L2)4]·4CH3CH2OH (HL1 = 2-Methylquinolin-8-ol, HL2 = t-Bu-COOH), has been synthesized and characterized by X-ray single crystal diffraction, FT-IR, TG/DSC, and elementary analysis. The data reveals that it has a very interesting structural motif consisting of a [Co4O4] core in the form of a cube with the Co and O occupying opposite corners. In the crystal structure of complex 1, the molecules are linked by intramolecular C−H···O hydrogen bonding interactions and Van der Waals forces, forming a three-dimensional network structure. Crystal data for complex 1: C60H68Co4N4O12, triclinic, space group P-1 (no. 2), with a = 12.0644(4), b = 12.0996(3), c = 20.2858(7) Å, α = 92.005(3)o, β = 92.182(3)°, γ = 97.943(3)°, Z = 2, V = 2928.25(16) Å3, T = 293 K, μ(MoKα) = 1.178 mm-1, Dcalc = 1.444 g/cm3, 16737 reflections measured (3.00° ≤ θ ≤ 28.53°), 9010 unique (Rint = 0.024, Rsigma = 0.0574) which were used in all calculations. The final R1 was 0.039 (I≥2σ(I)) and wR2 was 0.090 (all data).

Molecular Vibrations of an Oxygen-Evolving Complex and Its Synthetic Mimic.

Bio-inspired catalysis for artificial photosynthesis has been widely studied for decades, in particular, with the purpose of using bio-disposable and non-toxic metals as building blocks. The characterisation of such catalysts has been achieved by using different kinds of spectroscopic methods, from X-ray crystallography to NMR spectroscopy. An artificial Mn4 CaO4 cubane cluster with dangling Mn4 was synthesised in 2015 [Zhang et al. Science 2015, 348, 690-693]; this cluster showed many structural similarities to that of the natural oxygen-evolving complex. An accurate structural and spectroscopic comparison between the natural and artificial systems is highly relevant to understand the catalytic mechanism. Among data from different techniques, the differential FTIR spectra (Sn+1 -Sn ) of photosystem II are still lacking a complete interpretation. The availability of IR data of the artificial cluster offers a unique opportunity to assign absolute absorption spectra on a well-defined and easier to interpret analogous moiety. The present work aims to investigate the novel inorganic compound as a model system for an oxygen-evolving complex through measurement of its spectroscopic properties. The experimental results are compared with calculations by using a variety of theoretical methods (normal mode analysis, effective normal mode analysis) in the S1 state. We underline the similarities and the differences in the computational spectra based on atomistic models of Mn4 CaO5 and Mn4 CaO4 complexes.

Cobalt Cubane Clusters Based on Schiff Base: Synthesis, Characterization, Magnetic Properties and Hirshfeld Surface Analysis

Three cobalt cubane clusters with the composition of [Co4(L)4], (1, H2L is 1-{3-[(3,5-dibromo-2-hydroxy-benzylidene)-amino]-2-hydroxy-phenyl}-ethanone (H2DBHBA); 2, H2L is 1-{3-[(5-bromo-2-hydroxy-benzylidene)-amino]-2-hydroxy-phenyl}-ethanone (H2BHBA); 3, H2L is 1-{3-[(3,5-dichloro-2-hydroxy-benzylidene)-amino]-2-hydroxy-phenyl}-ethanone (H2DCHBA)), were prepared by the reaction of cobalt nitrate hexahydrate with 2-hydroxy-benzaldehyde ramification under solvothermal conditions. All the complexes were characterized by elemental analysis, infrared spectroscopy, and X-ray single-crystal diffraction. Complexes 1–3 have tetranuclear clusters with a cubane topology in which the metal ions and the oxygen atoms from the L ligands occupying the alternate vertices of the cubane. The {Co4O4} cores display dominant anitferromagnetic interactions owing to the μ3-O bridged binding modes. Hirshfeld surface analysis revealed that H···H, and C···X (X = Br or Cl) interactions were the dominant intermolecular interactions.

Preparation of Iron-Sulfur Cubane Nanoclusters and Their Immobilization on Functionalized Carbon Nanotubes.

With large surface area and versatile electronic behaviour, the composites of Fe₄S₄(SRS)₄ nanoclusters and functionalized carbon nanotubes (f-CNTs), are expected to catalyze the conversion of protons to hydrogen gas at lower electro-potentials with higher output than a platinum electrode. In search of a non-noble metal based catalytic material, we report for the first time, the isolation of unimolecular iron-sulfur cubane cluster, [Fe₄(μ-S)₄(mnt)₄], (1) (mnt = maleonitriledithiolate) as nanocubes (63×85×120 nm) in MeCN-EtOH (MeCN is acetonitrile, while EtOH is ethanol) solvents and bimolecular [NBu₄]₄[Fe₄(μ-S)₄(mnt)₄] as nanocuboctahedra (120×121×125 nm) in pure EtOH. The cubic shape of the nanocrystal reminds its geometrical relationship with a molecular cube and one of sides of the nanocube and nanocuboctahedron matches at 120 nm. The nanocubes of Fe₄S₄(SRS)₄ have been immobilized on f-CNTs and characterized by SEM and TEM methods which indicate that clusters of Fe₄S₄ of diameter (8-9 nm) interact with surfaces, sidewalls and tip of the f-CNTs. A ferrocene type of interaction could not be observed with f-CNTs, because nanoparticles are not found in CNT-inner cavity. The interaction could be either adsorption or hydrogen bonding interactions between -COOH/-OH groups of f-CNTs and N≡C terminals of iron-sulphur nanoclusters leading to immobilization of an iron-sulfur nanocluster on a single CNT molecule or the iron-sulfur nanoclusters can be entrapped between two CNT molecules.