High‐Resolution Crystal Structure of a Silver(I)–RNA Hybrid Duplex Containing Watson–Crick‐like C?Silver(I)?C Metallo‐Base Pairs

Metallo‐base pairs have been extensively studied for applications in nucleic acid‐based nanodevices and genetic code expansion. Metallo‐base pairs composed of natural nucleobases are attractive because nanodevices containing natural metallo‐base pairs can be easily prepared from commercially available sources. Previously, we have reported a crystal structure of a DNA duplex containing T Hg^II T base pairs. Herein, we have determined a high‐resolution crystal structure of the second natural metallo‐base pair between pyrimidine bases C Ag^I C formed in an RNA duplex. One Ag^I occupies the center between two cytosines and forms a C Ag^I C base pair through N3 Ag^I N3 linear coordination. The C Ag^I C base pair formation does not disturb the standard A‐form conformation of RNA. Since the C Ag^I C base pair is structurally similar to the canonical Watson–Crick base pairs, it can be a useful building block for structure‐based design and fabrication of nucleic acid‐based nanodevices.     

Crystal Structure of Metallo DNA Duplex Containing Consecutive Watson–Crick‐like T–HgII–T Base Pairs

The metallo DNA duplex containing mercury‐mediated T–T base pairs is an attractive biomacromolecular nanomaterial which can be applied to nanodevices such as ion sensors. Reported herein is the first crystal structure of a B‐form DNA duplex containing two consecutive T–Hg^II–T base pairs. The Hg^II ion occupies the center between two T residues. The N3‐Hg^II bond distance is 2.0 Å. The relatively short Hg^II‐Hg^II distance (3.3 Å) observed in consecutive T–Hg^II–T base pairs suggests that the metallophilic attraction could exist between them and may stabilize the B‐form double helix. To support this, the DNA duplex is largely distorted and adopts an unusual nonhelical conformation in the absence of Hg^II. The structure of the metallo DNA duplex itself and the Hg^II‐induced structural switching from the nonhelical form to the B‐form provide the basis for structure‐based design of metal‐conjugated nucleic acid nanomaterials.     

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.     

A Novel DNA Helical Wire Containing HgII‐Mediated T:T and T:G Pairs

Numerous applications of metal‐mediated base pairs (metallo‐base‐pairs) to nucleic acid based nanodevices and genetic code expansion have been extensively studied. Many of these metallo‐base‐pairs are formed in DNA and RNA duplexes containing Watson–Crick base pairs. Recently, a crystal structure of a metal–DNA nanowire with an uninterrupted one‐dimensional silver array was reported. We now report the crystal structure of a novel DNA helical wire containing Hg^II‐mediated T:T and T:G base pairs and water‐mediated C:C base pairs. The Hg‐DNA wire does not contain any Watson–Crick base pairs. Crystals of the Hg‐DNA wire, which is the first DNA wire structure driven by Hg^II ions, were obtained by mixing the short oligonucleotide d(TTTGC) and Hg^II ions. This study demonstrates the potential of metallo‐DNA to form various structural components that can be used for functional nanodevices.     

A Highly Stabilizing Silver(I)‐Mediated Base Pair in Parallel‐Stranded DNA

The first parallel‐stranded DNA duplex with Hoogsteen base pairing that readily incorporates an Ag⁺ ion into an internal mispair to form a metal‐mediated base pair has been created. Towards this end, the highly stabilizing 6 FP ‐Ag⁺‐ 6 FP base pair comprising the artificial nucleobase 6‐furylpurine ( 6 FP ) was devised. A combination of temperature‐dependent UV spectroscopy, CD spectroscopy, and DFT calculations was used to confirm the formation of this base pair. The nucleobase 6 FP is capable of forming metal‐mediated base pairs both by the Watson–Crick edge (i.e. in regular antiparallel‐stranded DNA) and by the Hoogsteen edge (i.e. in parallel‐stranded DNA), depending on the oligonucleotide sequence and the experimental conditions. The 6 FP ‐Ag⁺‐ 6 FP base pair within parallel‐stranded DNA is the most strongly stabilizing Ag⁺‐mediated base pair reported to date for any type of nucleic acid, with an increase in melting temperature of almost 15 °C upon the binding of one Ag⁺ ion.     

Highly Stable Double‐Stranded DNA Containing Sequential Silver(I)‐Mediated 7‐Deazaadenine/Thymine Watson–Crick Base Pairs

The oligonucleotide d(TX)₉, which consists of an octadecamer sequence with alternating non‐canonical 7‐deazaadenine (X) and canonical thymine (T) as the nucleobases, was synthesized and shown to hybridize into double‐stranded DNA through the formation of hydrogen‐bonded Watson–Crick base pairs. dsDNA with metal‐mediated base pairs was then obtained by selectively replacing W‐C hydrogen bonds by coordination bonds to central silver(I) ions. The oligonucleotide I adopts a duplex structure in the absence of Ag⁺ ions, and its stability is significantly enhanced in the presence of Ag⁺ ions while its double‐helix structure is retained. Temperature‐dependent UV spectroscopy, circular dichroism spectroscopy, and ESI mass spectrometry were used to confirm the selective formation of the silver(I)‐mediated base pairs. This strategy could become useful for preparing stable metallo‐DNA‐based nanostructures.     

A DNA Structure Containing AgI‐Mediated G:G and C:C Base Pairs

Metal‐mediated base pairs have been extensively utilized in many research fields, including genetic‐code extension, novel therapeutics development, and nanodevice design. Compared to other cations, Ag^I is more flexible in pairing with natural base pairs. Herein, we present a DNA structure containing two C‐Ag^I‐C pairs and the first reported G‐Ag^I‐G pair in a short 8mer DNA strand. This structure not only provides detailed insight into these Ag^I‐mediated base‐pairing patterns in DNA, but also represents the first nonhelical DNA structure driven by heavy‐metal ions, thus further contributing to the structural diversity of DNA. This unique complex structure is highly sequence‐dependent, thus implying functional potentials as a new DNA aptamer that can bind and recognize silver ions. These results not only advance our understanding of the interactions between Ag^I and nucleobases, but also provide a unique structural component for the rational design of new DNA nanodevices.     

Contiguous metal-mediated base pairs comprising two Ag(I) ions

The incorporation of transition‐metal ions into nucleic acids by using metal‐mediated base pairs has proved to be a promising strategy for the site‐specific functionalization of these biomolecules. We report herein the formation of Ag⁺‐mediated Hoogsteen‐type base pairs comprising 1,3‐dideaza‐2′‐deoxyadenosine and thymidine. By defunctionalizing the Watson–Crick edge of adenine, the formation of regular base pairs is prohibited. The additional substitution of the N3 nitrogen atom of adenine by a methine moiety increases the basicity of the exocyclic amino group. Hence, 1,3‐dideazaadenine and thymine are able to incorporate two Ag⁺ ions into their Hoogsteen‐type base pair (as compared with one Ag⁺ ion in base pairs with 1‐deazaadenine and thymine). We show by using a combination of experimental techniques (UV and circular dichroism (CD) spectroscopies, dynamic light scattering, and mass spectrometry) that this type of base pair is compatible with different sequence contexts and can be used contiguously in DNA double helices. The most stable duplexes were observed when using a sequence containing alternating purine and pyrimidine nucleosides. Dispersion‐corrected density functional theory calculations have been performed to provide insight into the structure, formation and stabilization of the twofold metalated base pair. They revealed that the metal ions within a base pair are separated by an Ag???Ag distance of about 2.88 Å. The Ag–Ag interaction contributes some 16 kcal mol^?1 to the overall stability of the doubly metal‐mediated base pair, with the dominant contribution to the Ag–Ag bonding resulting from a donor–acceptor interaction between silver 4d‐type and 4s orbitals. These Hoogsteen‐type base pairs enable a higher functionalization of nucleic acids with metal ions than previously reported metal‐mediated base pairs, thereby increasing the potential of DNA‐based nanotechnology.     

Structure Determination of an AgI‐Mediated Cytosine–Cytosine Base Pair within DNA Duplex in Solution with 1H/15N/109Ag NMR Spectroscopy

The structure of an Ag^I‐mediated cytosine–cytosine base pair, C–Ag^I–C, was determined with NMR spectroscopy in solution. The observation of 1‐bond ¹⁵N‐¹⁰⁹Ag J‐coupling (¹J(¹⁵N,¹⁰⁹Ag): 83 and 84 Hz) recorded within the C–Ag^I–C base pair evidenced the N3–Ag^I–N3 linkage in C–Ag^I–C. The triplet resonances of the N4 atoms in C–Ag^I–C demonstrated that each exocyclic N4 atom exists as an amino group (?NH₂), and any isomerization and/or N4–Ag^I bonding can be excluded. The 3D structure of Ag^I–DNA complex determined with NOEs was classified as a B‐form conformation with a notable propeller twist of C–Ag^I–C (?18.3±3.0°). The ¹⁰⁹Ag NMR chemical shift of C‐Ag^I‐C was recorded for cytidine/Ag^I complex (δ(¹⁰⁹Ag): 442 ppm) to completed full NMR characterization of the metal linkage. The structural interpretation of NMR data with quantum mechanical calculations corroborated the structure of the C–Ag^I–C base pair.     

Redox Sorption and Recovery of Silver Ions as Silver Nanocrystals on Poly(aniline‐co‐5‐sulfo‐2‐anisidine) Nanosorbents

Poly[aniline(AN)‐co‐5‐sulfo‐2‐anisidine(SA)] nanograins with rough and porous structure demonstrate ultrastrong adsorption and highly efficient recovery of silver ions. The effects of five key factors—AN/SA ratio, Ag^I concentration, sorption time, ultrasonic treatment, and coexisting ions—on Ag^I adsorbability were optimized, and AN/SA (50/50) copolymer nanograins were found to exhibit much stronger Ag^I adsorption than polyaniline and all other reported sorbents. The maximal Ag^I sorption capacity of up to 2034 mg g^?1 (18.86 mmol g^?1) is the highest thus far and also much higher than the maximal Hg‐ion sorption capacity (10.28 mmol g^?1). Especially at ≤2 mM Ag^I, the nanosorbents exhibit ≥99.98 % adsorptivity, and thus achieve almost complete Ag^I sorption. The sorption fits the Langmuir isotherm well and follows pseudo‐second‐order kinetics. Studies by IR, UV/Vis, X‐ray diffraction, polarizing microscopy, centrifugation, thermogravimetry, and conductivity techniques showed that Ag^I sorption occurs by a redox mechanism mainly involving reduction of Ag^I to separable silver nanocrystals, chelation between Ag^I and ? NH? /? N?/? NH₂/ ? SO₃H/? OCH₃, and ion exchange between Ag^I and H⁺ on ? SO₃^?H⁺. Competitive sorption of Ag^I with coexisting Hg, Pb, Cu, Fe, Al, K, and Na ions was systematically investigated. In particular, the copolymer nanoparticles bearing many functional groups on their rough and porous surface can be directly used to recover and separate precious silver nanocrystals from practical Ag^I wastewaters containing Fe, Al, K, and Na ions from Kodak Studio. The nanograins have great application potential in the noble metals industry, resource reuse, wastewater treatment, and functional hybrid nanocomposites.     

Bifunctional Ion‐Selective Electrode Based on C60‐Cryptand 22 for Silver and Iodine Ions

Fullerence C60‐cryptand 22 was prepared and successfully applied as the electric carrier in the PVC electrode membrane of a bifunctional ion‐selective electrode for cations, e.g., Ag⁺ ions as well as anions, e.g., I^? ions. The bifunctional ion‐selective electrode based on C60‐cryptand 22 can be applied as a Silver (Ag⁺) ion selective electrode with an internal electrode solution of 10^?3 M AgNO₃ in water (pH = 6.3), or as an Iodide (I^?) ion selective electrode with an acidic internal electrode solution of 10^?4 M KI_(aq) (pH = 2) in which the cryptand 22 is protonated, and the C60‐cryptand 22 is changed to C60‐Cryptand22–H⁺ and becomes an anionic electro‐carrier to absorb the I^? ion. The Ag⁺ ion selective electrode based on C60‐cryptand 22 gave a linear response with a near‐Nernstian slope (59.5 mV decade^?1) within the concentration range 10^?1‐10^?3 M Ag⁺_(aq). The Ag⁺ ion electrode exhibited comparatively good selectivity for silver ions, over other transition‐metal ions, alkali and alkaline earth metal ions. The Ag⁺ ion selective electrode with good stability and reproducibility was successfully used for the titration of Ag⁺_(aq) with Cl^? ions. The Iodide (I^?) Ion selective electrode based on protonated C60–cryptand22‐H⁺ also showed a linear response with a nearly Nernstian slope (58.5 mV decade^?1) within 10^?1 ‐ 10^?3 M I^? _(aq) and exhibited good selectivity for I^? ions and had small selectivity coefficients (10^?2–10^?3) for most of other anions, e.g., F^? , OH^?, CH₃COO^?, SO₄^2?, CO₃^2?, CrO₄^2?, Cr₂O₇^2? and PO₄^3? ions.     

Unusual NH Activation of 2‐Aminopyrimidine: Supramolecular Assembly into an AgI Metal–Organic Framework

A rare example of coordination at the amino group of NH₂pym (2‐aminopyrimidine) relevant to N? H activation is described that leads to a novel Ag^I–imide 3D metal–organic framework (MOF). The coordination of Ag^I to NH₂pym produced an electron‐withdrawing effect and thus increased its acidity, which facilitated the N? H activation and the subsequent formation of the Ag–imide bond. A cooperative metalation/deprotonation process for the N? H activation of NH₂pym is suggested. Interestingly, photoluminescence of 1 is switched on at the low temperature of 77 K.     

Self‐Assembly of a Au16 Ring via Metal–Metal Bonding Interactions

Metal–metal bonding interactions have been employed as an efficient strategy to generate a number of unique gold(I) metallo‐macrocycles with fascinating functions. The self‐assembly, crystal structure and emission property of novel nest‐like tetramer 1₄ , namely, {[Au₄(μ‐dppm)₂(μ‐dctp^2?)](BF₄)₂}₄ ? (CH₃CN)₂ (dppm=bis(diphenylphosphino)methane, dctp^2?=N,N′‐bis(dicarbodithioate)‐2,11‐diaza[3.3]paracyclophane) is reported. The complex has been characterized by single‐crystal X‐ray diffraction analysis, ¹H NMR spectroscopy, ¹³C NMR spectroscopy, and CSI‐MS spectrometry. The aggregate demonstrates the sixteen gold(I) atoms are arranged in a ring with a circumference of 50.011(68) Å generated by Au^I???Au^I attractions. UV/visible and luminescence spectroscopy revealed that this Au^I???Au^I bonded metallo‐macrocycle exhibited yellow phosphorescence.     

Rhodium(I)‐Catalyzed Cycloisomerization of Benzylallene‐Alkynes through CH Activation

The efficient Rh^I‐catalyzed cycloisomerization of benzylallene‐alkynes produced the tricyclo[9.4.0.0^3,8]pentadecapentaene skeleton through a C? H bond activation in good yields. A plausible reaction mechanism proceeds via oxidative addition of the acetylenic C? H bond to Rh^I, an ene‐type cyclization to the vinylidenecarbene–Rh^I intermediate, and an electrophilic aromatic substitution with the vinylidenecarbene species. It was proposed based on deuteration and competition experiments.     

Unusual Nitrile–Nitrile and Nitrile–Alkyne Coupling of FcCN and FcCCCN

The reactions of the Group 4 metallocene alkyne complexes, [Cp*₂M(η²‐Me₃SiC₂SiMe₃)] ( 1 a : M=Ti, 1 b : M=Zr, Cp*=η⁵‐pentamethylcyclopentadienyl), with the ferrocenyl nitriles, Fc?C?N and Fc?C?C?C?N (Fc=Fe(η⁵‐C₅H₅)(η⁵‐C₅H₄)), is described. In case of Fc?C?N an unusual nitrile–nitrile C?C homocoupling was observed and 1‐metalla‐2,5‐diaza‐cyclopenta‐2,4‐dienes ( 3 a , b ) were obtained. As the first step of the reaction with 1 b , the nitrile was coordinated to give [Cp*₂Zr(η²‐Me₃SiC₂SiMe₃)(N?C‐Fc)] ( 2 b ). The reactions with the 3‐ferrocenyl‐2‐propyne‐nitrile Fc?C?C?C?N lead to an alkyne–nitrile C?C coupling of two substrates and the formation of 1‐metalla‐2‐aza‐cyclopenta‐2,4‐dienes ( 4 a , b ). For M=Zr, the compound is stabilized by dimerization as evidenced by single‐crystal X‐ray structure analysis. The electrochemical behavior of 3 a , b and 4 a , b was investigated, showing decomposition after oxidation, leading to different redox‐active products.     

N‐Methyl‐2, 2'‐Dipicolylamine Complexes as Potential Models for Metal‐Mediated Base Pairs

Metal‐mediated base pairs can be used to insert metal ions into nucleic acids at precisely defined positions. As structural data on the resulting metal‐modified DNA are scarce, appropriate model complexes need to be synthesized and structurally characterized. Accordingly, the molecular structures of nine transition metal complexes of N‐methyl‐2, 2'‐dipicolylamine (dipic) are reported. In combination with an azole‐containing artificial nucleoside, this tridentate ligand had recently been used to generate metal‐mediated base pairs (Chem. Commun. 2011 , 47, 11041–11043). The Pd^II and Pt^II complexes reported here confirm that the formation of planar complexes (as required for a metal‐mediated base pair) comprising N‐methyl‐2, 2'‐dipicolylamine is possible. Two Hg^II complexes with differing stoichiometry indicate that a planar structure might also be formed with this metal ion, even though it is not favored. In the complex [Ag₂(dipic)₂](ClO₄)₂, the two Ag^I ions are located close to one another with an Ag ··· Ag distance of 2.9152(3) Å, suggesting the presence of a strong argentophilic interaction.     

Unprecedented Efficient Structure Controlled Phosphorescence of Silver(I) Clusters Stabilized by Carba‐closo‐dodecaboranylethynyl Ligands

{Ag₂(12‐C≡C‐closo‐1‐CB₁₁H₁₁)}_n and selected pyridine ligands have been used for the synthesis of photostable Ag^I clusters that, with one exception, exhibit for Ag^I compounds unusual room‐temperature phosphorescence. Extraordinarily intense phosphorescence was observed for a distorted pentagonal bipyramidal Ag^I₇ cluster that shows an unprecedented quantum yield of Φ=0.76 for Ag^I clusters. The luminescence properties correlate with the structures of the central Ag^I_n motifs as shown by comparison of the emission properties of the clusters with different numbers of Ag^I ions, different charges, and electronically different pyridine ligands.     

Metal–Organic Frameworks (MOFs) of a Cubic Metal Cluster with Multicentered MnIMnI Bonds

MOFs with both multicentered metal–metal bonds and low‐oxidation‐state (LOS) metal ions have been underexplored hitherto. Here we report the first cubic [Mn^I₈] cluster‐based MOF ( 1 ) with multicentered Mn^I? Mn^I bonds and +1 oxidation state of manganese (Mn^I or Mn(I)), as is supported by single‐crystal structure determination, XPS analyses, and quantum chemical studies. Compound 1 possesses the shortest Mn^I? Mn^I bond of 2.372 Å. Theoretical studies with density functional theory (DFT) reveal extensive electron delocalization over the [Mn^I₈] cube. The 48 electrons in the [Mn^I₈] cube fully occupy half of the 3d‐based and the lowest 4s‐based bonding orbitals, with six electrons lying at the nonbonding 3d‐orbitals. This bonding feature renders so‐called cubic aromaticity. Magnetic properties measurements show that 1 is an antiferromagnet. This work is expected to inspire further investigation of cubic metal–metal bonding, MOF materials with LOS metals, and metalloaromatic theory.     

Stable Copper(I)‐Mediated Base Pairing in DNA

A GNA (glycol nucleic acid) functionalized nucleoside analogue containing the artificial nucleobase 1H‐imidazo[4,5‐f][1,10]phenanthroline (P) was used to form a copper(I)‐mediated base pair within a DNA duplex. The geometrical constraints imposed by the artificial nucleobase play a pivotal role in this unprecedented stabilization of copper(I) in aqueous medium via metal‐mediated base pairing. The formation of the copper(I)‐mediated base pair was investigated by temperature‐dependent UV spectroscopy and CD spectroscopy. The metal‐mediated base pair stabilizes the DNA oligonucleotide duplex by 23 °C. A redox chemistry approach confirmed that this base pair formation was due to the incorporation of copper(I) into the duplex. This first report of a copper(I)‐mediated base pair adds metal‐based diversity to the field and consequently opens up the range of possible applications of metal‐modified nucleic acids.     

Cation–Cation Pairing by NCH⋅⋅⋅O Hydrogen Bonds

The pairing of ions of opposite charge is a fundamental principle in chemistry, and is widely applied in synthesis and catalysis. In contrast, cation–cation association remains an elusive concept, lacking in supporting experimental evidence. While studying the structure and properties of 4‐oxopiperidinium salts [OC₅H₈NH₂]X for a series of anions X^? of decreasing basicity, we observed a gradual self‐association of the cations, concluding in the formation of an isolated dicationic pair. In 4‐oxopiperidinium bis(trifluoromethylsulfonyl)amide, the cations are linked by N? H???O?C hydrogen bonds to form chains, flanked by hydrogen bonds to the anions. In the tetra(perfluoro‐tert‐butoxy)aluminate salt, the anions are fully separated from the cations, and the cations associate pairwise by N? C? H???O?C hydrogen bonds. The compounds represent the first genuine examples of self‐association of simple organic cations based merely on hydrogen bonding as evidenced by X‐ray structure analysis, and provide a paradigm for an extension of this class of compounds.