Cluster Ligands Research Articles

Assembly of BF4−, PF6−, ClO4− and F− with trinuclear copper(i) acetylide complexes bearing amide groups: structural diversity, photophysics and anion binding properties

Trinuclear copper(i) acetylide complexes 1·BF4–4·BF4, 1·PF6, 1·ClO4 and 4·F exhibit structural diversity with different anions and R groups on “Cu3 cluster ligands”.

Sequence-function relationships in folding upon binding.

Folding coupled to binding is ubiquitous in biology. Nevertheless, the relationship of sequence to function for protein segments that undergo coupled binding and folding remains to be determined. Specifically, it is not known if the well-established rules that govern protein folding and stability are relevant to ligand-linked folding transitions. Upon small ligand biotinoyl-5'-AMP (bio-5'-AMP) binding the Escherichia coli protein BirA undergoes a disorder-to-order transition that results in formation of a network of packed hydrophobic side chains. Ligand binding is also allosterically coupled to protein association, with bio-5'-AMP binding enhancing the dimerization free energy by -4.0 kcal/mol. Previous studies indicated that single alanine replacements in a three residue hydrophobic cluster that contributes to the larger network disrupt cluster formation, ligand binding, and allosteric activation of protein association. In this work, combined equilibrium and kinetic measurements of BirA variants with alanine substitutions in the entire hydrophobic network reveal large functional perturbations resulting from any single substitution and highly non-additive effects of multiple substitutions. These substitutions also disrupt ligand-linked folding. The combined results suggest that, analogous to protein folding, functional disorder-to-order linked to binding requires optimal packing of the relevant hydrophobic side chains that contribute to the transition. The potential for many combinations of residues to satisfy this requirement implies that, although functionally important, segments of homologous proteins that undergo folding linked to binding can exhibit sequence divergence.

Substrate-induced radical formation in 4-hydroxybutyryl coenzyme A dehydratase from Clostridium aminobutyricum.

4-Hydroxybutyryl-coenzyme A (CoA) dehydratase (4HBD) from Clostridium aminobutyricum catalyzes the reversible dehydration of 4-hydroxybutyryl-CoA to crotonyl-CoA and the irreversible isomerization of vinylacetyl-CoA to crotonyl-CoA. 4HBD is an oxygen-sensitive homotetrameric enzyme with one [4Fe-4S](2+) cluster and one flavin adenine dinucleotide (FAD) in each subunit. Upon the addition of crotonyl-CoA or the analogues butyryl-CoA, acetyl-CoA, and CoA, UV-visible light and electron paramagnetic resonance (EPR) spectroscopy revealed an internal one-electron transfer to FAD and the [4Fe-4S](2+) cluster prior to hydration. We describe an active recombinant 4HBD and variants produced in Escherichia coli. The variants of the cluster ligands (H292C [histidine at position 292 is replaced by cysteine], H292E, C99A, C103A, and C299A) had no measurable dehydratase activity and were composed of monomers, dimers, and tetramers. Variants of other potential catalytic residues were composed only of tetramers and exhibited either no measurable (E257Q, E455Q, and Y296W) hydratase activity or <1% (Y296F and T190V) dehydratase activity. The E455Q variant but not the Y296F or E257Q variant displayed the same spectral changes as the wild-type enzyme after the addition of crotonyl-CoA but at a much lower rate. The results suggest that upon the addition of a substrate, Y296 is deprotonated by E455 and reduces FAD to FADH·, aided by protonation from E257 via T190. In contrast to FADH·, the tyrosyl radical could not be detected by EPR spectroscopy. FADH· appears to initiate the radical dehydration via an allylic ketyl radical that was proposed 19 years ago. The mode of radical generation in 4HBD is without precedent in anaerobic radical chemistry. It differs largely from that in enzymes, which use coenzyme B12, S-adenosylmethionine, ATP-driven electron transfer, or flavin-based electron bifurcation for this purpose.

Octahedral clusters with mixed inner ligand environment: Self-assembly, modification and isomerism

Octahedral cluster complexes of transition metals are associated with halogen or chalcogen inner ligands to form edge-bridged {M6(μ2-X)12} or face-capped {M6(μ3-X)8} cluster cores. The partial exchange of X atoms leading to mixed inner ligand environment invokes a distortion of metallic cluster, reduction of symmetry as well as an isomerism of the cluster cores. This review summarizes preparation methods of mixed ligand cluster complexes with the general formulas [{M6(μ2-X)12}L6] n or [{M6(μ3-X)8}L6] n and their structural features.

Monitoring the solid-state electrochemistry of Cu(2,7-AQDC) (AQDC = anthraquinone dicarboxylate) in a lithium battery: coexistence of metal and ligand redox activities in a metal-organic framework.

By adopting a facile synthetic strategy, we obtained a microporous redox-active metal-organic framework (MOF), namely, Cu(2,7-AQDC) (2,7-H2AQDC = 2,7-anthraquinonedicarboxylic acid) (1), and utilized it as a cathode active material in lithium batteries. With a voltage window of 4.0-1.7 V, both metal clusters and anthraquinone groups in the ligands exhibited reversible redox activity. The valence change of copper cations was clearly evidenced by in situ XANES analysis. By controlling the voltage window of operation, extremely high recyclability of batteries was achieved, suggesting the framework was robust. This MOF is the first example of a porous material showing independent redox activity on both metal cluster nodes and ligand sites.

Synthesis, Structures, and Magnetic Properties of Three Series of Discrete or 1D Compounds based on Pyramidal [LnCu4] (Ln = Gd and Dy) Cluster and Formate Ligand

AbstractWith formate as ligand, one discrete dragonfly‐like 3d–4f cluster showing beautiful pyramidal metal skeleton, [GdCu4(HCOO)5(μ3‐OH)4(NO3)2(H2O)7](H2O) (1Gd), was obtained by a self‐assembly reaction of Gd(NO3)3, Cu(NO3)2, and formate ligand. The two nitrates could be treated as the “wings” of the “dragonfly”, and the formate with a free oxygen atom could be regarded as the “tail”. When using perchlorate instead of nitrate, two series of 1D compounds based on the similar pyramidal [LnCu4] unit, linear {[GdCu4(HCOO)5(μ3‐[OH)4(H2O)8](ClO4)2(H2O)2}n (2Gd) and zigzag {[LnCu4Na2(HCOO)4(μ3‐OH)4(H2O)9(ClO4)5](H2O)2}n [Ln = Gd, (3Gd); Dy, (3Dy)] were synthesized by controlling the formate amount. They used μ5‐η1:η4 formate or [Na2(ClO4)4]2– unit as connectors to link the neighboring [LnCu4] units together, respectively. Magnetic analyses reveal that these four compounds all show ferromagnetic interactions, and 3Dy displays slow relaxation of the magnetization.

Nanoparticle tension probes patterned at the nanoscale: impact of integrin clustering on force transmission.

Herein we aimed to understand how nanoscale clustering of RGD ligands alters the mechano-regulation of their integrin receptors. We combined molecular tension fluorescence microscopy with block copolymer micelle nanolithography to fabricate substrates with arrays of precisely spaced probes that can generate a 10-fold fluorescence response to pN-forces. We found that the mechanism of sensing ligand spacing is force-mediated. This strategy is broadly applicable to investigating receptor clustering and its role in mechanotransduction pathways.

Alkali/alkaline earth metal and solvents-regulated construction of novel heterometallic coordination polymers based on a semirigid ligand and tetranuclear metal clusters

Five novel three-dimensional (3D) heterometallic coordination polymers, [ZnCa(dcppa)(DMF)2]n (1), [ZnCa(dcppa)(DMA)2]n (2), [ZnBa(dcppa)(DMF)2]n (3), [ZnBa(dcppa)(DMA)2]n (4), and [ZnNa(dcppa)(DMF)]n·n(Me2NH2)·n(H2O)2 (5) (Me2NH2+=dimethylammonium cation; DMA=N,N-dimethylacetamide; DMF=N,N-dimethylformamide; H4dcppa=3-(3′,5′-dicarboxylphenoxy) phthalic acid), have been hydrothermally synthesized and structurally characterized with the aid of single-crystal X-ray diffraction. Complexes 1–5 are heterometallic Zn/M (M=Ca, Ba, Na) coordination polymers constructed from a semirigid H4dcppa ligand and tetranuclear metal clusters. Topological analyses show that 1/3/4 and 2/5 exhibit complicated 3D framework that could be simplified into binodal (3,6)-connected rtl nets and binodal (3,6)-connected flu nets, respectively. Unlike 1–4, 5 features a unique 3D anionic framework with Me2NH2+ cations occupying the voids. From the viewpoint of crystal structure diversity and comparison, our results further prove that the coordination modes of metal ions and ligands play indispensable roles in the construction of the final crystal structure. Moreover, the thermal stability and solid-state luminescence properties of 1–5 have also been investigated at room temperature.

How and Why Do Cluster Size, Charge State, and Ligands Affect the Course of Metal‐Mediated Gas‐Phase Activation of Methane?

AbstractRecent progress in the gas‐phase activation of methane is discussed. We demonstrate that cluster size, charge state, and ligands crucially affect both the reactivity and selectivity of metal‐mediated bond activation processes. We outline the important role that relativistic effects and spin densities play and discuss the paradigm of two‐state reactivity in thermal reactions. State‐of‐the‐art mass‐spectrometry based experiments, in conjunction with electronic structure calculations, permit identification of the elementary steps at a strictly molecular level and thus allow to uncover mechanistic features for four types of reactions: (i) metal‐mediated dehydrogenation of methane, (ii) ligand‐switch processes of the type ML + CH4 → M(CH3) + HL, (iii) hydrogen‐atom abstraction as the crucial step in the oxidative coupling of methane, and (iv) the mechanism of the challenging CH4→CH3OH conversion.

A family of octahedral rhenium cluster complexes trans-[{Re6Q8}(PPh3)4X2] (Q = S or Se, X = Cl, Br or I): Preparation and halide-dependent luminescence properties

Four new octahedral rhenium cluster complexes trans-[{Re6Q8}(PPh3)4X2] (Q=S, Se; X=Cl, I) were synthesized by reaction of cesium salts of cluster anions [{Re6Q8}X6]4−/3− with molten triphenylphosphine. The compounds were characterized by elemental and X-ray structural analyses. Emission spectra and photophysical characteristics for all new compounds and earlier described trans-[{Re6Q8}(PPh3)4Br2] were obtained showing a dependence of the emission maximum wavelength, quantum yield and lifetime values from cluster ligand environment.

Electronic Effect Related to the Nonuniform Distribution of Ionic Charges in Metal‐Cluster Chalcogenide Halides

Recently, it was shown that the bond valence model is a unique tool to describe the lattice strains in (TM)6 chalcogenide halides (TM = transition metal). Three different phenomena that result in valence violations were identified: (1) a steric conflict between countercations and the cluster–ligand framework, (2) a steric conflict between small (TM)6 clusters and large coordination polyhedra around the cluster or the so-called matrix effect, and (3) nonuniform distribution of the anion valences (bond valence sums) around the clusters. This paper shows that the model is valid for a wide family of cluster compounds with different nuclearities. On the basis of the separation of the steric and electronic effects in the calculation procedure, the unusual distribution of the anion valences in the cluster compounds was assigned to the nonuniform spreading of ionic charges. Thus, stabilization mechanisms in cluster compounds were explained by simple electrostatic interactions.

RGD-conjugated rod-like viral nanoparticles on 2D scaffold improve bone differentiation of mesenchymal stem cells.

Viral nanoparticles have uniform and well-defined nano-structures and can be produced in large quantities. Several plant viral nanoparticles have been tested in biomedical applications due to the lack of mammalian cell infectivity. We are particularly interested in using Tobacco mosaic virus (TMV), which has been demonstrated to enhance bone tissue regeneration, as a tunable nanoscale building block for biomaterials development. Unmodified TMV particles have been shown to accelerate osteogenic differentiation of adult stem cells by synergistically upregulating bone morphogenetic protein 2 (BMP2) and integrin-binding bone sialoprotein (IBSP) expression with dexamethasone. However, their lack of affinity to mammalian cell surface resulted in low initial cell adhesion. In this study, to increase cell binding capacity of TMV based material the chemical functionalization of TMV with arginine-glycine-aspartic acid (RGD) peptide was explored. An azide-derivatized RGD peptide was “clicked” to tyrosine residues on TMV outer surface via an efficient copper(I) catalyzed azide-alkyne cycloaddition (CuAAC) reaction. The ligand spacing is calculated to be 2–4 nm, which could offer a polyvalent ligand clustering effect for enhanced cell receptor signaling, further promoting the proliferation and osteogenic differentiation of bone marrow-derived mesenchymal stem cells (BMSCs).

CO adsorption on Fe N (N = 1-4) transition metal clusters: a density functional theory study

The structures and stabilities of the Fe N (CO)m (N = 1-4, m = 1-5) clusters have been theoretically studied at the density functional theory (DFT) and ab initio levels of theory. In particular, the energetic, structural and vibrational frequencies of carbon monoxide (CO) chemisorptions on iron clusters are studied and compared with those of nitric oxide (NO) and ammonia (NH 3 ) adsorption. While the C-O and N-O bond lengths and vibrational frequencies strongly depend on cluster size and ligand population, the N-H bond length and vibrational frequency are independent on both cluster size and ligand population. For a particular Fe N cluster, the vibrational frequency increases as the ligand population increases. On the other hand, keeping the number of ligands fixed, the vibrational frequency decreases significantly with the Fe N cluster size. NO and CO being strong field ligands in the spectrochemical series, we have seen red shift of the vibrational frequencies with both cluster size and ligand population. As NH3 is a weak field ligand, we do not observe any variation. We have also observed that the HOMO-LUMO gap of both Fe N (CO) m and Fe N (NO) m clusters strongly depends on N and m. For Fe N (NH 3 ) m cluster, HOMO-LUMO gap decreases as more NH 3 molecules are adsorbed on the metal centre.

Pathogen‐induced lipid coalescence in the host membrane causes downstream activation of Rho GTPase (99.3)

We recently discovered a family of bacterial adhesins (Multivalent Adhesion Molecules, MAMs) which mediate initial contact between pathogen and host cells during infection. MAMs are composed of tandem arrays of six to seven mammalian cell entry (mce) domains, each recognizing a phosphatidic acid lipid ligand in the host cell membrane. We utilized bacteriomimetic tools to reconstruct the process of pathogen adhesion to host cells independent of other bacterial components and virulence factors. This revealed that MAMs, through binding to phosphatidic acid ligands with high affinity, induce lipid coalescence in the host cell membrane. Clustering of phosphatidic acid ligands triggers downstream activation of the small GTPase RhoA and actin rearrangements. In vivo infection studies with Vibrio parahaemolyticus demonstrated that MAM‐triggered RhoA activation facilitates breaching of a polarized epithelial cell layer by the pathogen. This is an unprecedented mechanism utilized by a bacterial pathogen to manipulate host cells and facilitate infection.Grant Funding Source: This work was supported by an EMBO fellowship (ALTF 938‐2011).

Pathogen‐induced lipid coalescence in the host membrane causes downstream activation of Rho GTPase (LB229)

We recently discovered a family of bacterial adhesins (Multivalent Adhesion Molecules, MAMs) which mediate initial contact between pathogen and host cells during infection. MAMs are composed of tandem arrays of six to seven mammalian cell entry (mce) domains, each recognizing a phosphatidic acid lipid ligand in the host cell membrane. We utilized bacteriomimetic tools to reconstruct the process of pathogen adhesion to host cells independent of other bacterial components and virulence factors. This revealed that MAMs, through binding to phosphatidic acid ligands with high affinity, induce lipid coalescence in the host cell membrane. Clustering of phosphatidic acid ligands triggers downstream activation of the small GTPase RhoA and actin rearrangements. In vivo infection studies with Vibrio parahaemolyticus demonstrated that MAM‐triggered RhoA activation facilitates breaching of a polarized epithelial cell layer by the pathogen. This is an unprecedented mechanism utilized by a bacterial pathogen to manipulate host cells and facilitate infection.Grant Funding Source: This work was supported by an EMBO fellowship (ALTF 938‐2011).

Assembly of Two Flexible Metal–Organic Frameworks with Stepwise Gas Adsorption and Highly Selective CO2 Adsorption

[Co3(bpydc)2(HCOO)2H2O]·2DMF (JLU-Liu3) and [Zn3(bpydc)2(HCOO)2]·H2O·DMF (JLU-Liu4), two kinds of chiral flexible metal–organic frameworks, have been synthesized using 2,2′-bipyridyl-5,5′-dicarboxylate ligand (H2bpydc) and trinuclear clusters. The two materials reveal ant topology and exhibit uncommon stepwise N2 and CO2 adsorption behaviors with large hysteresis loops. The three-dimensional frameworks of JLU-Liu3 and JLU-Liu4 undergo structural transformation upon the removal of the guest molecules in the pores, which is indicated by the shift of powder X-ray diffraction peaks and the alteration of the peak intensity. These two flexible metal organic frameworks can be switched between the unique “closed” and “opened” forms via the removal of guest molecules. Moreover, after activation, both samples show high selective CO2 uptake over N2 and CH4.

Three transition metal complexes constructed from a rigid 2,2′-bipyridine-3,3′,6,6′-tetracarboxylic acid ligand: Syntheses, structures and their fluorescence properties

Three complexes, {[Cd(bptcH2)(H2O)]·H2O}n (1), {[Cu(bptc)0.5(H2O)]·H2O}n (2), {[Co2(bptc)(H2O)6]·3H2O}n (3) (bptcH4=2,2′-bipyridine-3,3′,6,6′-tetracarboxylic acid) have been synthesized by self-assembly of the rigid bptcH4 ligand and corresponding transition metal salts. The structural analysis indicates that complex 1 displays a two-dimensional (2D) puckered sheet with (44·62) topology built from 4-connecting Cd3N2(OOC)3 cluster and bridging ligand bptcH22−. Complex 2 features a one-dimensional (1D) double-stranded chain made up 4-connecting bptc4− and Cu4N2(OOC)4 cluster. Complex 3 also exhibits a 2D grid with (44·62) topology, similar to that of complex 1. In addition, the fluorescence properties of complexes 1 and 3 have also been explored.

A balanced procedure for the treatment of cluster–ligand interactions on gold phosphine systems in catalysis

Ligand-protected metal clusters are difficult to describe within density functional theory due to the need to treat the electronic structure of the cluster, possible charge transfer between the ligands and the cluster, and weak ligand-ligand interactions in a balanced manner. We demonstrate the use of an appropriate, stepwise benchmarking process that accounts for the nonadditivity of these different contributions to stability and catalytic activity. We consider both open- and closed-shell clusters, differently charged systems, and ligands of increasing complexity for gold phosphine systems. The use of a dispersion correction to density functional calculations was found to be crucial for both structure optimization and the calculation of binding energies. We find that PBE-D3 performs well with a variation in energetics of 0.7-10.9 kcal/mol, PBE0-D3 better with 0.0-3.3 kcal/mol, and B2PLYP-D3 the best with 0.2-2.4 kcal/mol, when compared to the best available benchmark [CCSD(T) or SCS-MP2]. Our systematic procedure clarifies that these functionals all give accurate results for certain cases, but for the total performance over a range of interactions, they perform in accordance with Jacob's ladder.

Synthesis and Characterization of a New Type of Highnuclear Lanthanide – Cobalt Carboxylate Cluster Complex

A new heteronuclear Ln-Co carbonyl cluster, Ce4Yb2(μ3-L)4(CF3COO)8(DMF)6Co (L=(CO)6Co2CC(COO)2-), has been synthesized by reaction of (CO)6Co2CC(COOH)2 with Ce (OOCCF3)32H2O and Yb (OOCCF3)32H2O. The cluster structure was characterized by single-crystal X-ray diffraction and IR. The crystal is monoclinic crystal system and C2/c space group. X-ray analysis revealed that the heterometallic cluster belonged to a rare class of Ln-Co carbonyl cluster bridged by carboxylate groups of carbonyl cluster ligands. The cluster was monometric unit and exhibited cage-like configuration.

Carbohydrate-Lectin Recognition of Sequence-Defined Heteromultivalent Glycooligomers

Multivalency as a key principle in nature has been successfully adopted for the design and synthesis of artificial glycoligands by attaching multiple copies of monosaccharides to a synthetic scaffold. Besides their potential in various applied areas, e.g. as antiviral drugs, for the vaccine development and as novel biosensors, such glycomimetics also allow for a deeper understanding of the fundamental aspects of multivalent binding of both artificial and natural ligands. However, most glycomimetics so far neglect the purposeful arranged heterogeneity of their natural counterparts, thus limiting more detailed insights into the design and synthesis of novel glycomimetics. Therefore, this work presents the synthesis of monodisperse glycooligomers carrying different sugar ligands at well-defined positions along the backbone using for the first time sequential click chemistry and stepwise assembly of functional building blocks on solid support. This approach allows for straightforward access to sequence-defined, multivalent glycooligomers with full control over number, spacing, position, and type of sugar ligand. We demonstrate the synthesis of a set of heteromultivalent oligomers presenting mannose, galactose, and glucose residues. All heteromultivalent structures show surprisingly high affinities toward Concanavalin A lectin receptor in comparison to their homomultivalent analogues presenting the same number of binding ligands. Detailed studies of the ligand/receptor interaction using STD-NMR and 2fFCS indeed indicate a change in binding mechanism for trivalent glycooligomers presenting mannose or combinations of mannose and galactose residues. We find that galactose residues do not participate in the binding to the receptor, but they promote steric shielding of the heteromultivalent glycoligands and thus result in an overall increase in affinity. Furthermore, the introduction of nonbinding ligands seems to suppress receptor clustering of multivalent ligands. Overall these results support the importance of heteromultivalency specifically for the design of novel glycoligands and help to promote a fundamental understanding of multivalent binding modes.