Target Self‐Enhanced Selectivity in Metal‐Specific DNAzymes

Highly selective recognition of metal ions by rational ligand design is challenging, and simple metal binding by biological ligands is often obscured by nonspecific interactions. In this work, binding‐triggered catalysis is used and metal selectivity is greatly increased by increasing the number of metal ions involved, as exemplified in a series of in vitro selected RNA‐cleaving DNAzymes. The cleavage junction is modified with a glycyl–histidine‐functionalized tertiary amine moiety to provide multiple potential metal coordination sites. DNAzymes that bind 1, 2, and 3 Zn²⁺ ions, increased their selectivity for Zn²⁺ over Co²⁺ ions from approximately 20‐, 1000‐, to 5000‐fold, respectively. This study offers important insights into metal recognition by combining rational ligand design and combinatorial selection, and it provides a set of new DNAzymes with excellent selectivity for Zn²⁺ ions.     

Molecular Simulations of Human and Mouse Aβ1–16 at Different pH Values: Structural Characteristics toward Understanding Cu2+‐Coordinated Amyloid Beta Spheres

As the main sequence responsible for metal ion coordination in the amyloid beta (Aβ) peptide, Aβ_1–16 plays a key role in the understanding of the aggregation of Aβ induced by Cu²⁺ ions. There is no consensus on the nature of the coordination sphere of the Cu²⁺–Aβ complex so far due to the amorphous conformation of the Aβ_1–16 peptide itself and the pH dependence of Cu²⁺–Aβ coordination. The simulation reported here reveals that human Aβ_1–16 monomer has a U‐shape morphology, which is preserved at any pH. This morphology accommodates Cu²⁺ ions with several binding sites and is also the basis for establishing a center‐distance statistical method (CDSM). Based on this CDSM, specific histidine residues for a Cu²⁺‐coordinated sphere are identified and the corresponding accurate pH range is established, indicating that the CDSM can be used as a reference to predict the potential coordination sites of metal ions in other amorphous peptides. By contrast, mouse Aβ_1–16 monomer has a more open and random morphology than human Aβ_1–16 due to the differences of three sequence positions. These mutations not only reduce the number of binding sites required by a stable Cu²⁺‐binding sphere but also diminish the capacity to generate salt bridges compared to the human peptide. These observations offer insights into the roles of three residues that differ in the mouse Aβ_1–16 and perhaps into the reasons mice seldom develop Alzheimer's disease.     

Single Crystal‐to‐Single Crystal Site‐Selective Postsynthetic Metal Exchange in a Zn–MOF Based on Semi‐Rigid Tricarboxylic Acid and Access to Bimetallic MOFs

The metal ions in a neutral Zn–MOF constructed from tritopic triacid H₃L with inherent concave features, rigid core, and peripheral flexibility are found to exist in two distinct SBUs, that is, 0D and 1D. This has allowed site‐selective postsynthetic metal exchange (PSME) to be investigated and reactivities of the metal ions in two different environments in coordination polymers to be contrasted for the first time. Site‐selective transmetalation of Zn ions in the discrete environment is shown to occur in a single crystal‐to‐single crystal (SCSC) fashion, with metal ions such as Fe³⁺, Ru³⁺, Cu²⁺, Co²⁺, etc., whereas those that are part of 1D SBU sustain structural integrity, leading to novel bimetallic MOFs, which are inaccessible by conventional approaches. To the best of our knowledge, site‐selective postsynthetic exchange of an intraframework metal ion in a MOF that contains metal ions in discrete as well as polymeric SBUs is heretofore unprecedented.     

Synthesis, coordination properties, and analytical applications of mixed donor macrocycles containing the 1,10-phenanthroline sub-unit

The coordination properties towards different metal ions of a new class of mixed N/S-, and N/S/O-donor macrocycles containing the 1,10-phenanthroline sub-unit in the cyclic framework are reviewed. The conformational constraints imposed by the heteroaromatic fragment onto the aliphatic portion of the ring determine the coordination mode of these ligands which can stabilise low-valent Ni⁺, Pd⁺, Pt⁺, and Rh⁺ metal complexes. Structural and thermodynamic aspects of the coordination chemistry of these ligands are considered together with possible applications as building blocks in the synthesis of multi-centred systems, and as template in the construction of extended polyiodide networks. However, solution studies demonstrate the inability of these ligands to work as selective and specific fluorescent chemosensors for heavy transition and post-transition metal ions and the formation constants evaluated for the formation of 1:1 complexes with Pb²⁺, Cd²⁺, Hg²⁺, Cu²⁺, and Ag⁺ in acetonitrile are of the same order of magnitude. Nevertheless, some of these macrocyles are extremely effective to recognise Cu²⁺ or Ag⁺ over the other metal ions in transport processes, and have been successfully used as neutral ionophore in the construction of PVC-based ionselective electrodes and supported liquid membranes for analytical detection and separation, respectively, of these metal ions.     

New Mechanistic Insight into Stepwise Metal‐Center Exchange in a Metal–Organic Framework Based on Asymmetric Zn4 Clusters

Herein, a mechanism of stepwise metal‐center exchange for a specific metal–organic framework, namely, [Zn₄(dcpp)₂(DMF)₃(H₂O)₂]_n (H₄dcpp=4,5‐bis(4′‐carboxylphenyl)phthalic acid), is disclosed for the first time. The coordination stabilities between the central metal atoms and the ligands as well as the coordination geometry are considered to be dominant factors in this stepwise exchange mechanism. A new magnetic analytical method and a theoretical model confirmed that the exchange mechanism is reasonable. When the metathesis reaction occurs between Cu^II ions and framework Zn^II ions, the magnetic exchange interaction of each pair of Cu^II centers gradually strengthens with increasing amount of framework Cu^II ions. By analyzing the changes of coupling constants in the Cu‐exchanged products, it was deduced that Zn4 and Zn3 are initially replaced, and then Zn1 and Zn2 are replaced later. The theoretical calculation further verified that Zn4 is replaced first, Zn3 next, then Zn1 and Zn2 last, and the coordination stability dominates the Cu/Zn exchange process. For the Ni/Zn and Co/Zn exchange processes, besides the coordination stability, the preferred coordination geometry was also considered in the stepwise‐exchange behavior. As Ni^II and Co^II ions especially favor octahedral coordination geometry in oxygen‐ligand fields, Ni^II ions and Co^II ions could only selectively exchange with the octahedral Zn^II ions, as was also confirmed by the experimental results. The stepwise metal‐exchange process occurs in a single crystal‐to‐single crystal fashion.     

Nitrogen centered inverse coordination complexes. A survey of molecular topologies

Abstract

Inverse coordination is an emerging novel chemical concept describing the formation of metal complexes in which the arrangement of acceptor and donor sites is opposite to that occurring in conventional coordination complexes. Inverse coordination complexes are formed around a non-metal species as central atom (ion or small molecule) surrounded by a number of metal atoms (ions) connected or not by internal bridging (intramolecular) linkers. This article illustrates the diversity of species described under this concept with structures in which the coordination center is nitrogen (mono- and poly-nitrogen moieties).     

Supramolecular hydrogen‐bonding patterns in the organic–inorganic hybrid compound bis(4‐amino‐5‐chloro‐2,6‐dimethylpyrimidinium) tetrathiocyanatozinc(II)–4‐amino‐5‐chloro‐2,6‐dimethylpyrimidine–water (1/2/2)

Zinc thiocyanate complexes have been found to be biologically active compounds. Zinc is also an essential element for the normal function of most organisms and is the main constituent in a number of metalloenzyme proteins. Pyrimidine and aminopyrimidine derivatives are biologically very important as they are components of nucleic acids. Thiocyanate ions can bridge metal ions by employing both their N and S atoms for coordination. They can play an important role in assembling different coordination structures and yield an interesting variety of one‐, two‐ and three‐dimensional polymeric metal–thiocyanate supramolecular frameworks. The structure of a new zinc thiocyanate–aminopyrimidine organic–inorganic compound, (C₆H₉ClN₃)₂[Zn(NCS)₄]·2C₆H₈ClN₃·2H₂O, is reported. The asymmetric unit consist of half a tetrathiocyanatozinc(II) dianion, an uncoordinated 4‐amino‐5‐chloro‐2,6‐dimethylpyrimidinium cation, a 4‐amino‐5‐chloro‐2,6‐dimethylpyrimidine molecule and a water molecule. The Zn^II atom adopts a distorted tetrahedral coordination geometry and is coordinated by four N atoms from the thiocyanate anions. The Zn^II atom is located on a special position (twofold axis of symmetry). The pyrimidinium cation and the pyrimidine molecule are not coordinated to the Zn^II atom, but are hydrogen bonded to the uncoordinated water molecules and the metal‐coordinated thiocyanate ligands. The pyrimidine molecules and pyrimidinium cations also form base‐pair‐like structures with an R₂²(8) ring motif via N—H…N hydrogen bonds. The crystal structure is further stabilized by intermolecular N—H…O, O—H…S, N—H…S and O—H…N hydrogen bonds, by intramolecular N—H…Cl and C—H…Cl hydrogen bonds, and also by π–π stacking interactions.     

Divergent Coordination Chemistry: Parallel Synthesis of [2×2] Iron(II) Grid‐Complex Tauto‐Conformers

The coordination of iron(II) ions by a homoditopic ligand L with two tridentate chelates leads to the tautomerism‐driven emergence of complexity, with isomeric tetramers and trimers as the coordination products. The structures of the two dominant [Fe^II₄ L ₄]⁸⁺ complexes were determined by X‐ray diffraction, and the distinctness of the products was confirmed by ion‐mobility mass spectrometry. Moreover, these two isomers display contrasting magnetic properties (Fe^II spin crossover vs. a blocked Fe^II high‐spin state). These results demonstrate how the coordination of a metal ion to a ligand that can undergo tautomerization can increase, at a higher hierarchical level, complexity, here expressed by the formation of isomeric molecular assemblies with distinct physical properties. Such results are of importance for improving our understanding of the emergence of complexity in chemistry and biology.     

Capture of CO2 by a Cationic Nickel(I) Complex in the Gas Phase and Characterization of the Bound,Activated CO2 Molecule by Cryogenic Ion Vibrational Predissociation Spectroscopy

We describe a systematic method for the preparation and spectroscopic characterization of a CO₂ molecule coordinated to an activated bisphenoidal nickel(I) compound containing a tetraazamacrocyclic ligand in the gas phase. The resulting complex was then structurally characterized by using mass‐selected vibrational predissociation spectroscopy. The results indicate that a highly distorted CO₂ molecule is bound to the metal center in an η²‐C,O coordination mode, thus establishing an efficient and rational method for the preparation of metal‐activated CO₂ for further studies using ion chemistry techniques.     

Capture of CO2 by a Cationic Nickel(I) Complex in the Gas Phase and Characterization of the Bound,Activated CO2 Molecule by Cryogenic Ion Vibrational Predissociation Spectroscopy

We describe a systematic method for the preparation and spectroscopic characterization of a CO₂ molecule coordinated to an activated bisphenoidal nickel(I) compound containing a tetraazamacrocyclic ligand in the gas phase. The resulting complex was then structurally characterized by using mass‐selected vibrational predissociation spectroscopy. The results indicate that a highly distorted CO₂ molecule is bound to the metal center in an η²‐C,O coordination mode, thus establishing an efficient and rational method for the preparation of metal‐activated CO₂ for further studies using ion chemistry techniques.     

Construction of Insulin 18‐mer Nanoassemblies Driven by Coordination to Iron(II) and Zinc(II) Ions at Distinct Sites

Controlled self‐assembly (SA) of proteins offers the possibility to tune their properties or to create new materials. Herein, we present the synthesis of a modified human insulin (HI) with two distinct metal‐ion binding sites, one native, the other abiotic, enabling hierarchical SA through coordination with two different metal ions. Selective attachment of an abiotic 2,2′‐bipyridine (bipy) ligand to HI, yielding HI–bipy, enabled Zn^II‐binding hexamers to SA into trimers of hexamers, [[HI–bipy]₆]₃, driven by octahedral coordination to a Fe^II ion. The structures were studied in solution by small‐angle X‐ray scattering and on surfaces with AFM. The abiotic metal ligand had a higher affinity for Fe^II than Zn^II ions, enabling control of the hexamer formation with Zn^II and the formation of trimers of hexamers with Fe^II ions. This precise control of protein SA to give oligomers of oligomers provides nanoscale structures with potential applications in nanomedicine.     

Carbonic Anhydrase‐Mimetic Bolaamphiphile Self‐Assembly for CO2 Hydration and Sequestration

A biomimetic catalyst was prepared through the self‐assembly of a bolaamphiphilic molecule with histidine moieties for the sequestration of carbon dioxide. The histidyl bolaamphiphilic molecule bis(N‐α‐amidohistidine)‐1,7‐heptane dicarboxylate has been synthesized and self‐assembled to produce analogues of the active sites of carbonic anhydrase (CA) after association with Zn²⁺ ions. Spectroscopic analysis demonstrated the coordination of the Zn²⁺ ions with histidine imidazole moieties, which is the core conformation of CA active sites. The Zn‐associated self‐assembly worked as a CA‐mimetic catalyst that shows catalytic activity for CO₂ hydration. Evaluation of the kinetics of using para‐nitrophenylacetate revealed that the kinetic parameters of the CA‐mimetic catalyst were maximized at the optimal Zn concentration and that excess Zn ions resulted in deteriorated catalytic activity. The performance of the CA‐mimetic catalyst was enhanced by changing the pH value and temperature of the reaction, which implies that the hydrolysis of the substrate is the rate‐determining step. The catalyst‐assisted sequestration of CO₂ was demonstrated by CaCO₃ precipitation upon the addition of Ca²⁺ ions. This study offers an easy way to prepare enzyme analogues for CO₂ sequestration through the self‐assembly of bolaamphiphile molecules with designer biochemical moieties.     

Overcoming Statistical Complexity: Selective Coordination of Three Different Metal Ions to a Ligand with Three Different Coordination Sites

In general, it is difficult to selectively introduce different metal ions at specific positions of a cluster‐like structure. This is mainly due to statistical problems as well as the reversibility of the formation of coordination bonds. To overcome this statistical problem, we used a carefully designed ligand, H₆L, which can accommodate three different kinds of metal ions in three types of coordination sites. The complex [LNiZn₂La]³⁺, which contains three different metals, was quantitatively obtained by a stepwise procedure, but different products were obtained when the metal ions were added in a different order. However, equilibration studies indicated that this complex was almost solely formed among 54 (=3×3×₃H₂) possible products upon heating; the formation efficiency (ca. 100 %) was significantly higher than the statistical probability (2.47 %). Such carefully designed ligands should be useful for the synthesis multimetallic systems, which are of interest because of the interplay between the different metals.     

Transition metals as electron traps. II. Structures,energetics and electron transfer dissociations of ternary Co,Ni and Zn–peptide complexes in the gas phase

Transition metal cations Co²⁺, Ni²⁺ and Zn²⁺ form 1 : 1 : 1 ternary complexes with 2,2′‐bipyridine (bpy) and peptides in aqueous methanol solutions that have been studied for tripeptides GGG and GGL. Electrospray ionization of these solutions produced singly charged [Metal(bpy)(peptide ? H)]⁺ and doubly charged [Metal(bpy)(peptide)]²⁺ ions (Metal = metal ion) that underwent charge reduction by glancing collisions with Cs atoms at 50 and 100 keV collision energies. Electron transfer to [Metal(bpy)(peptide)]²⁺ ions was less than 4.2 eV exoergic and formed abundant fractions of non‐dissociated charge‐reduced intermediates. Charge‐reduced [Metal(bpy)(peptide)]⁺ ions dissociated by the loss of a hydrogen atom, ammonia, water and ligands that depended on the metal ion. The Ni and Co complexes mainly dissociated by the elimination of ammonia, water, and the peptide ligand. The Zn complex dissociated by the elimination of ammonia and bpy. A sequence‐specific fragment was observed only for the Co complex. Electron transfer to [Metal(bpy)(peptide ? H)]⁺ was 0.6–1.6 eV exoergic and formed intermediate radicals that were detected as stable anions after a second electron transfer from Cs. [Metal(bpy)(peptide ? H)] neutrals and their anions dissociated by the loss of bpy and peptide ligands with branching ratios that depended on the metal ion. Optimized structures for several spin states, electron transfer and dissociation energies were addressed by combined density functional theory and Møller–Plesset perturbational calculations to aid interpretation of experimental data. The experimentally observed ligand loss and backbone cleavage in charge‐reduced [Metal(bpy)(peptide)]⁺ complexes correlated with the dissociation energies at the present level of theory. The ligand loss in ⁺CR^? spectra showed overlap of dissociations in charge‐reduced [Metal(bpy)(peptide ? H)] complexes and their anionic counterparts which complicated spectra interpretation and correlation with calculated dissociation energies. Copyright © 2009 John Wiley & Sons, Ltd.     

Signal‐Induced Release of Guests from a Photolatent Metal–Phenolic Supramolecular Cage and Its Hybrid Assemblies

The coordination chemistry of plant polyphenols and metal ions can be used for coating various substrates and for creating modular superstructures. We herein explored this chemistry for the controlled release of guests from mesoporous silica nanoparticles (MSNs). The selective adsorption of tannic acids (TAs) on MSN silica walls opens the MSN mesoporous channels without disturbing mass transport. The channel may be closed by the coordination of TA with Cu^II ions. Upon exposure to light, photolysis of Trojan horse guests (photoacid generators, PAGs) leads to acid generation, which enables the release of payloads by decomposing the outer coordination shell consisting of TA and Cu^II. We also fabricated a modular assembly of MSNs on glass substrates. The photoresponsive release characteristics of the resulting film are similar to those of the individual MSNs. This method is a fast and facile strategy for producing photoresponsive nanocontainers by non‐covalent engineering of MSN surfaces that should be suitable for various applications in materials science.     

[Fe19] “Super‐Lindqvist” Aggregate and Large 3D Interpenetrating Coordination Polymer from Solvothermal Reactions of [Fe2(OtBu)6] with Ethanol

The syntheses, crystal structures, and physical properties of [HFe₁₉O₁₄(OEt)₃₀] and {Fe₁₁(OEt)₂₄}_∞ are reported. [HFe₁₉O₁₄(OEt)₃₀] has an octahedral shape. Its core with a central Fe metal ion surrounded by six μ₆‐oxo ligands is arranged in the rock salt structure. {Fe₁₁(OEt)₂₄}_∞ is a mixed‐valence coordination polymer in which Fe^III metal ions form three 3D interpenetrating (10,3)‐b nets. The arrangement of the Fe^III ions can also be compared to that of Si ions in α‐ThSi₂. Thus, the described structures are at the interface between molecular and solid‐state chemistry.     

Physico‐Chemical Studies on Cu(II) Complexes of Acrylate Chelating Polymers

Abstract

Metal chelating polymers containing amide and carboxylic groups were prepared by gamma‐radiation polymerization of acrylic acid (AA) monomers in the presence of polyacrylamide (PAM). The resins obtained were loaded by copper ions and characterized by FT‐IR spectroscopy, electron spin resonance (ESR), thermogravimetric analysis (TGA), and differential scanning calorimetery (DSC). The IR spectra indicated a lower frequencies shift in the carbonyl bands due to copper ion chelation with carbonyl groups in the polymer resins. Also, the IR spectra reveal a splitting in the band at 3600–3200?cm^?1 that due to the coordination of the NH and OH groups with copper ions. The ESR spectrum was anisotropic with hyperfine structure having the following values 2.3808 and 2.07218 for g _∥ and g _⊥, respectively. These spectra for copper ions have square planar coordination with two nitrogen and two oxygen atoms. TGA and DSC studies show that radiation crosslinking and complexation with copper ion increase the thermal stability of PAM–AA resins. Meanwhile, resin complexes with copper ion showed a higher thermal stability than pure resin. The increase in thermal stability may be correlated with the metal ions coordination with NH and OH groups; this coordination prevents the splitting of ammonia and water molecules. Also, the metal ions providing a coordination crosslink between polymer chains could increase thermal stability.     

Engineering Multifunctional DNA Hybrid Nanospheres through Coordination‐Driven Self‐Assembly

Developing simple and general approaches for the synthesis of nanometer‐sized DNA materials with specific morphologies and functionalities is important for various applications. Herein, a novel approach for the synthesis of a new set of DNA‐based nanoarchitectures through coordination‐driven self‐assembly of Fe^II ions and DNA molecules is reported. By fine‐tuning the assembly, Fe–DNA nanospheres of precise sizes and controlled compositions can be produced. The hybrid nanoparticles can be tailored for delivery of functional DNA to cells in vitro and in vivo with enhanced biological function. This highlights the potential of metal ion coordination as a tool for directing the assembly of DNA architectures, which conceptualizes a new pathway to expand the repertoire of DNA‐based nanomaterials. This methodology will advance both the fields of DNA nanobiotechnology and metal–ligand coordination chemistry.     

Regulated Incorporation of Two Different Metal Ions into Programmed Sites in a Duplex by DNA Polymerase Catalyzed Primer Extension

Metal‐mediated base pairs formed by the coordination of metal ions to natural or artificial bases impart unique chemical and physical properties to nucleic acids and have attracted considerable interest in the field of nanodevices. Ag^I ions were found to mediate DNA polymerase catalyzed primer extension through the formation of a C–Ag^I–T base pair, as well as the previously reported C–Ag^I–A base pair. The comparative susceptibility of dNTPs to Ag^I‐mediated enzymatic incorporation into the site opposite cytosine in the template was shown to be dATP>dTTP?dCTP. Furthermore, two kinds of metal ions, Ag^I and Hg^II, selectively mediate the incorporation of thymidine 5′‐triphosphate into sites opposite cytosine and thymine in the template, respectively. In other words, the regulated incorporation of different metal ions into programmed sites in the duplex by DNA polymerase was successfully achieved.     

Rotationally Active Ligands: Dialing‐Up the Co‐conformations of a [2]Rotaxane for Metal Ion Binding

A novel [2]rotaxane was constructed that has a bidentate N,N′‐chelate as part of a rigid, H‐shaped axle and a 24‐membered crown ether macrocycle containing six ether O‐atoms and an olefinic group as the wheel. This unique topology produces a ligand with the ability to dial‐up different donor sets for complexation to metal ions by simply rotating the wheel about the axle. The solution and solid‐state structures of the free ligand and complexes with Li⁺ and Cu⁺ show how the ligand adopts different rotational co‐conformations for each. The Li⁺ ion uses the N,N′‐chelate and O‐donors while the Cu⁺ center is coordinated to both O‐donors and the olefinic group. This concept of rotationally active ligands should be possible with a wide variety of donor sets and could find broad application in areas of coordination chemistry, such as catalysis and metal sequestration.