Rhenium(I)-Based Heteroleptic Pentagonal Toroid-Shaped Metallocavitands: Self-Assembly and Molecular Recognition Studies

A family of neutral, heteroleptic, dinuclear M₂LL'-type pentagonal toroid-shaped metallomacrocycles (1-8) were synthesized using flexible ditopic N donors (Lⁿ = L¹-L²), rigid bis-chelating ligands (H₂-L' = H₂-E), and Re₂(CO)₁₀ in a one-pot solvothermal self-assembly approach. The ligands and the metallomacrocycles were characterized using ATR-IR, electrospray ionization mass spectrometry, nuclear magnetic resonance, ultraviolet-visible, and emission spectroscopy methods. The molecular structures of 1, 2, 4, 6, and 7 were confirmed by an X-ray diffraction study and are similar to those of calix[5]arene. The cyclic inner cavities of the metallomacrocycles accommodate toluene/mesitylene/acetone/chlorobenzene as guest molecules that are stabilized by cumulative C-H···π and π···π interactions with the cyclic framework of metallomacrocycle. The photophysical properties of the ligands and the metallomacrocycles were studied. The host-guest recognition properties of metallocavitands 1, 2, 7, and 8 as a model host with phenol and nitrobenzene derivatives as guest molecules were studied by emission spectroscopy methods.

Coupling 6-chloro-3-methyluracil with copper: structural features, theoretical analysis, and biofunctional properties

As nucleobases in RNA and DNA, uracil and 5-methyluracil represent a recognized class of bioactive molecules and versatile ligands for coordination compounds with various biofunctional properties. In this study, 6-chloro-3-methyluracil (Hcmu) was used as an unexplored building block for the self-assembly generation of a new bioactive copper(II) complex, [Cu(cmu)₂(H₂O)₂]·4H₂O (1). This compound was isolated as a stable crystalline solid and fully characterized in solution and solid state by a variety of spectroscopic methods (UV-vis, EPR, fluorescence spectroscopy), cyclic voltammetry, X-ray diffraction, and DFT calculations. The structural, topological, H-bonding, and Hirshfeld surface features of 1 were also analyzed in detail. The compound 1 shows a distorted octahedral {CuN₂O₄} coordination environment with two trans cmu^- ligands adopting a bidentate N,O-coordination mode. The monocopper(II) molecular units participate in strong H-bonding interactions with water molecules of crystallization, leading to structural 0D → 3D extension into a 3D H-bonded network with a tfz-d topology. Molecular docking and ADME analysis as well as antibacterial and antioxidant activity studies were performed to assess the bioactivity of 1. In particular, this compound exhibits a prominent antibacterial effect against Gram negative (E. coli, P. aeruginosa) and positive (S. aureus, B. cereus) bacteria. The obtained copper(II) complex also represents the first structurally characterized coordination compound derived from 6-chloro-3-methyluracil, thus introducing this bioactive building block into a family of uracil metal complexes with notable biofunctional properties.

Coordination capacity of cytosine, adenine and derivatives towards open-paddlewheel diruthenium compounds

[Ru₂Cl₂(DPhF)₃] (DPhF = diphenylformamidinate) links preferentially to the junctions of RNA (ribonucleic acid) structures, although the bonding mode is not known. In order to clarify this question the reactions between [Ru₂Cl₂(DPhF)₃] and cytosine (Hcyto), cytidine (Hcyti), cytidine 2',3'-cyclic monophosphate sodium salt (NacCMP), adenine (Hade), adenosine (Haden) and adenosine 3',5'-cyclic monophosphate (HcAMP) have been carried out. In the resultant complexes, cyto (cytosinate), cyti (cytidinate), cCMP (cytidine 2',3'-cyclic monophosphate monoanion), ade (adeninate), aden (adenosinate) and cAMP (deprotonated adenosine 3',5'-cyclic monophosphate) are bonded to the diruthenium unit as N,N'-bridging ligands, as confirmed by the solution of the crystal structures of [RuCl(DPhF)₃(cyto)] and [RuCl(DPhF)₃(ade)] by X-ray diffraction. The axial positions of the diruthenium species are still available for additional interactions with other residues that could explain its preference towards RNA junctions.

Rhenium(i) based irregular pentagonal-shaped metallacavitands

Neutral ditopic flexible N-donor ligands (Ln = bis(4-(naphtho[2,3-d]imidazol-1-ylmethyl)phenyl)methane, L1 bis(4-(benzimidazol-1-ylmethyl)phenyl)methane, L2 or bis(4-(2-nonylbenzimidazol-1-ylmethyl)phenyl)methane, L3) possessing a bis(4-methylphenyl)methane spacer with two imidazolyl donor units were designed and synthesized. The ligands were utilized to develop metallacavitands analogous to irregular pentagonal-shaped metallacavitands with larger cavities. The metallacavitands 1-4 were assembled from Re2(CO)10, a rigid bis-chelating donor (1,4-dihydroxy-9,10-anthraquinone or chloranilic acid) and Lnvia a solvothermal approach. The ligands and the metallacavitands were characterized by analytical and spectroscopic methods. The molecular structures of 1 and 4 were further confirmed by single crystal X-ray diffraction analysis which revealed that a toluene molecule resides in the hydrophobic cavity. Ln and 1-4 are emissive in DMSO at room temperature. The internal cavity of the metallacavitand acts as a host for aromatic guest molecules. The host-guest interaction properties of 1 with anthracene, naphthalene, nitrobenzene, 2-nitrotoluene, 4-nitrotoluene and 2,4-dinitrotoluene were studied by an emission spectroscopic method.

Crystal structures of bis-[2-(pyridin-2-yl)phenyl-κ(2) N,C (1)]rhodium(III) complexes containing an aceto-nitrile or monodentate thyminate(1-) ligand

The crystal structures of bis-[2-(pyridin-2-yl)phen-yl]rhodium(III) complexes with the metal in an octahedral coordination containing chloride and aceto-nitrile ligands, namely (OC-6-42)-aceto-nitrile-chlorido-bis-[2-(pyridin-2-yl)phenyl-κ(2) N,C (1)]rhodium(III), [RhCl(C11H8N)2(CH3CN)] (1), thyminate(1-) and methanol, namely (OC-6-42)-methanol(5-methyl-2,4-dioxo-1,2,3,4-tetrahydro-pyrimidin-1-ido-κN (1))bis-[2-(pyridin-2-yl)phenyl-κ(2) N,C (1)]rhodium(III), [Rh(C11H8N)2(C5H5N2O2)(CH3OH)]·CH3OH·0.5H2O (2), and thy-min-ate(1-) and ethanol, namely (OC-6-42)-ethanol(5-methyl-2,4-dioxo-1,2,3,4-tetra-hydro-pyrimidin-1-ido-κN (1))bis[2-(pyridin-2-yl)phenyl-κ(2) N,C (1)]rhodium(III), [Rh(C11H8N)2(C5H5N2O2)(C2H5OH)]·C2H5OH (3), are reported. The aceto-nitrile complex, 1, is isostructural with the Ir(III) analog. In complexes 2 and 3, the monodeprotonated thyminate (Hthym(-)) ligand coordinates to the Rh(III) atom through the N atom, and the resulting Rh-N(Hthym) bond lengths are relatively long [2.261 (2) and 2.252 (2) Å for 2 and 3, respectively] as compared to the Rh-N bonds in the related thyminate complexes. In each of the crystals of 2 and 3, the complexes are linked via a pair of inter-molecular N-H⋯O hydrogen bonds between neighbouring Hthym(-) ligands, forming an inversion dimer. A strong intra-molecular O-H⋯O hydrogen bond between the thyminate(1-) and alcohol ligands in mutually cis positions to each other is also observed.

Topology of metallacalix[4]arenes with uracil and cytosine ligands: favorable and unfavorable assemblies

A single isomer of many topologically possible ones! The experimentally isolated metallacalix[4]arenes based on pyrimidine nucleobases are the energetically more favorable.

Thyminate(2-)-bridged cyclic tetranuclear rhodium(III) complexes formed by a template of a sodium, calcium or lanthanoid ion

In the thyminate(2-)-bridged tetranuclear Cp*Rh(III) complexes incorporating a Na(+), Ca(2+) or Ln(3+) cation, homochiral aggregation of four Rh(III) centres was achieved to form metallacalix[4]arene-type clusters. The thyminate(2-) bridged two Rh(III) and the third metal ion with a μ3-1κN(1):2κ(2)N(3),O(2):3κO(2) mode in the Na(+) and Ca(2+) complexes, while in the Ln(3+) analogues it exhibited a different bridging mode, μ3-1κN(1):2κ(2)N(3),O(4):3κO(2).

Simultaneous co-ordination of three cytosine ligands displaying different binding sites around the copper centres

The reaction of copper with 1,10-phenanthroline and cytosine forms a novel polymeric structure with two different cytosine binding modes coordinated to copper centers. Also the polymeric complex has mixed coordination geometry around the metal centers.

The importance of peripheral sequences in determining the metal selectivity of an in vitro-selected Co(2+) -dependent DNAzyme

DNAzymes are catalytically active DNA molecules that use metal cofactors for their enzymatic functions. While a growing number of DNAzymes with diverse functions and metal selectivities have been reported, the relationships between metal ion selectivity, conserved sequences and structures responsible for selectivity remain to be elucidated. To address this issue, we report biochemical assays of a family of previously reported in vitro selected DNAzymes. This family includes the clone 11 DNAzyme, which was isolated by positive and negative selection, and the clone 18 DNAzyme, which was isolated by positive selection alone. The clone 11 DNAzyme has a higher selectivity for Co(2+) over Pb(2+) compared with clone 18. The reasons for this difference are explored here through phylogenetic comparison, mutational analysis and stepwise truncation. A novel DNAzyme truncation method incorporated a nick in the middle of the DNAzyme to allow for truncation close to the nicked site while preserving peripheral sequences at both ends of the DNAzyme. The results demonstrate that peripheral sequences within the substrate binding arms, most notably the stem loop, loop II, are sufficient to restore its selectivity for Co(2+) over Pb(2+) to levels observed in clone 11. A comparison of these sequences' secondary structures and Co(2+) selectivities suggested that metastable structures affect metal ion selectivity. The Co(2+) selectivity of the clone 11 DNAzyme showed that the metal ion binding and selectivities of small, in vitro selected DNAzymes may be more complex than previously appreciated, and that clone 11 may be more similar to larger ribozymes than to other small DNAzymes in its structural complexity and behavior. These factors should be taken into account when metal-ion selectivity is required in rationally designed DNAzymes and DNAzyme-based biosensors.