Dialkynylpyrenes: strongly fluorescent, environment-sensitive DNA building blocks

Two isomeric dialkynylpyrene phosphoramidites and their incorporation into oligonucleotides are described. The pyrene units closely resemble the well-known perylene bisimide dye PDI with regard to the ability to self-organize within a DNA duplex. In addition, dialkynylpyrenes exhibit significant monomer and remarkably strong excimer fluorescence. The dialkynylpyrene building blocks are promising candidates for applications in diagnostic tools, such as excimer-based molecular beacons, as well as for novel DNA-based materials with special optical properties.     

Photochromic DNA having fluorescent protein-inspired nucleosides

Molecular switches controlled by light stimuli can be applicable to the variety of the biological application. In this study, skeletal structures of a chromophore of fluorescent protein were applied as aglycones of newly designed photochromic nucleosides, “Fluorescent protein-inspired nuceloside: FIN”. Phosphoramidite units of the photochromic nucleosides having imidazolinone derivatives with benzylidene or 3-pyridilidene groups were successfully synthesized for FIN-containing ODNs. Thermodynamic studies of the FIN-containing ODNs revealed that photo-irradiation with specific wavelength induced stability change of the duplexes.     

Novel trifunctional building blocks for fluorescent polymers

[reaction: see text] Herein, we describe the synthesis of fluorescent 2-(arylsulfonyl)methacrylates and its polymers. These novel trifunctional monomers, possessing a fluorescent arylsulfonyl (ArSO(2)) group, an alkyl group (R), and a polymerizable olefin, serve as useful building blocks for functionalized fluorescent polymers.     

New fluorescent chemosensors for metal ions in solution

After a brief introduction on the main transduction mechanisms for metal ion detection by fluorescence, this paper reviews ligand molecules containing fluorophores synthesized and employed in metal ions sensing in solution in the last few years. With the aim of making more readable the paper we have organized it by dividing the subject first for type of fluorophore, then type of metal ion. Because of many acronyms a glossary has been inserted.     

Metal triangles as building blocks in metal cluster chemistry

Many trinuclear metal clusters have structures based on isolated metal triangles with either single bonds (e.g.,M ₃(CO)₁₂ whereM = Fe, Ru, Os) or double bonds (e.g., Re₃ Cl ₁₂ ^3– ) along each edge of the triangle. Individual metal triangles can be joined in the following ways to form more complicated triangulated networks: (1) Bridging an edge of a triangle with a new vertex to give rafts in which adjacent triangles share edges; (2) Bridging a vertex of a triangle with a new edge to give bowties in which adjacent triangles share vertices; (3) Capping a triangular face with a new vertex to give a chain of tetrahedra in which adjacent tetrahedra share faces. Such triangulated metal networks are particularly common in osmium carbonyl chemistry and in mixed osmium/platinum carbonyl derivatives. Platinum triangles of the type Pt₃L₆ are analogous to cyclopropenyl rings and can form sandwiches with one or two mercury atoms in the center such as the mercuric derivative Hg[Pt.₃(µ₂-2,6-Me₂C₆H₃NC)₃] (2,6-Me₂C₆H₃NC)₃]₂ and the mercurous derivative Hg₂[Pt₃(µ₂-CO)₃L₃]₂. Platinum triangles can also be stacked in the absence of filling to give [Pt₃(µ₂-CO)₃(CO)₃] _n ^2– (n=2, 3, 4, 5, 6, 10). Metal triangles also form the faces of metal deltahera of which the octahedron, bicapped square antiprism, and icosahedron are found in globally delocalized transition metal clusters.This article is dedicated to Prof. L. F. Dahl in recognition of his many seminal contributions to metal cluster chemistry.     

A new fluorescent calix crown ether: synthesis and complex formation with alkali metal ions

We synthesised a new N-benzylaza-21-crown-7 ether 5 with a dihydroxy coumarin as a fluorescence sensor and investigated the binding behaviour towards alkali metal cations in methanol by fluorescence titrations. The association constants are within one order of magnitude, with the exception of sodium. Potassium is the preferred binding partner (K(Na)=330 M(-1); K(K)=8600 M(-1); K(Rb)=8200 M(-1); K(Cs)=4400 M(-1)). The corresponding aza-21-crown-7 ether (6) was attached by a methylene unit to a resorcarene to give fluorescent calix crown ether 12. The binding abilities of the calix crown ether towards alkali metal ions in methanol have also been investigated, and an increasing complex stability, distinct for potassium and rubidium in comparison with 5, was found: K(Na)=440 M(-1); K(K)=110,000 M(-1); K(Rb)=63,000 M(-1); K(Cs)=20,000 M(-1). Like bis(crown ether)s, a cooperative complexation of the crown ether and the cavitand scaffold can be assumed. The proposed complex geometry is supported by Kohn-Sham DFT calculations for the potassium and caesium complexes.     

Transition metal vinylidene complexes as supramolecular building blocks: nucleobase-mediated self-assembly of crystals with hexagonal symmetry

Reaction of the ruthenium half sandwich compound RuCl(eta(5)-C(5)H(5))(PPh(3))(2) with the uracil (Ur) substituted alkyne HC[triple bond, length as m-dash]CUr in the presence of halide scavengers NH(4)X (X = PF(6), BF(4), OTf) results in the formation of the vinylidene complexes [Ru([double bond, length as m-dash]C[double bond, length as m-dash]CHUr)(eta(5)-C(5)H(5))(PPh(3))(2)][X] which crystallize in the hexagonal space group P6(3)/m. The hexagonal symmetry inherent to the system is due to the formation of a hydrogen bonded array mediated by the two sets of donor-acceptor units on the uracil, resulting in the formation of a cyclic "rosette" containing six ruthenium cations. In solution the (1)H and (31)P{(1)H} NMR spectra of the vinylidene complexes are both concentration and temperature dependent, in accord with the presence of monomer-dimer equilibria in which the rate of rotation of the vinylidene group is fast on the NMR timescale in the monomeric species, but slow in the dimers. The isoelectronic molybdenum-containing vinylidene complex [Mo(eta(7)-C(7)H(7))(dppe)([double bond, length as m-dash]C[double bond, length as m-dash]CHUr)][BF(4)] (dppe = 1,2-bis(diphenylphosphino)ethane) has also been prepared, but forms symmetric dimers in the solid state.     

Early metal di- and tricyanometalates: Useful building blocks for constructing magnetic clusters

Treatment of mer-VCl3(THF)3 with KTp [Tp = hydridotris(3,5-dimethylpyrazol-1-yl)borate], followed by [NEt4]CN in acetonitrile, affords [NEt4][(Tp)V(III)(CN)3].H2O (1.H2O); aerobic oxidation affords [NEt4][(Tp)V(IV)(O)(CN)2] (2). Subsequent treatment of 2 with Mn(II)(OTf)2 (OTf = trifluoromethanesulfonate) and 2,2'-bipyridine affords {[(Tp)V(O)(CN)2]2[Mn(II)(bipy)2]2[OTf]2}.2MeCN (3). Magnetic measurements indicate that 1-3 exhibit S = 1, (1/2), and 4 spin ground states, respectively.     

Click synthesized dianthryl-TTFV: an efficient fluorescent turn-on probe for transition metal ions

Tetrathiafulvalene vinylogue (TTFV) was functionalized with two anthryl fluorophores via Cu(I)-catalyzed alkyne-azide [3 + 2] cycloaddition, forming a dianthryl-TTFV hybrid to show fluorescent turn-on sensing behaviour for Cu(2+), Fe(2+), and Cd(2+) ions in THF with remarkably low detection limit down to the sub-ppm level.     

Tetraimine macrocyclic transition metal complexes as building blocks for molecular devices

The synthetic strategy initiated by Busch and further developed in recent years resulted in an impressive variety of new azamacrocyclic ligand superstructures. In this contribution, we have reviewed papers containing general synthetic strategies, structural and electronic properties and results of electrochemical studies for a long series of neutral and charged macrocyclic tetraimine complexes of transition metals leading to a new type of homo- and heteronuclear[2]catenanes as examples of switchable molecular machines. The whole series consists of neutral and charged mono-, bis- and trismacrocycles and appropriate reference neutral molecules and many of their derivatives. The bismacrocyclic moieties are constructed from simpler tetraazamacrocyclic fragments. When two of them are linked through polymethylene chains, they form face-to-face biscyclidenes—rectangular box-like moieties. They can host some small guest molecules (water, π-electron-donating compounds) and are stabilized by hydrogen bonds with solvent molecules or a shell of neighboring counterions. Neutral thiol derivatives are used as recognition sites of monolayers self-assembled on electrode surfaces to be employed in devices based on donor–acceptor interactions.Our catenanes consist of bismacrocyclic transition metal complexes linked by aliphatic chains and interlocked with a substituted crown ether. We have proved that under external stimuli – electrochemical pulses – the heteronuclear catenane exhibits controlled intramolecular relocation of the crown ether between two positions. The relocation is possible due to π?π interactions between the aromatic fragments of the crown ether and the transition metal (Ni, Cu) coordinating macrocyclic rings.Our model tetraimine complexes of transition metals can also be used to solve the problem of controlling directional relative movement of molecular fragments present in complex supramolecules. On the way to this aim we have synthesized trismacrocyclic derivatives which are now appropriately modified to serve as components of complex catenanes.     

Decaborane thiols as building blocks for self-assembled monolayers on metal surfaces

Three nido-decaborane thiol cluster compounds, [1-(HS)-nido-B(10)H(13)] 1, [2-(HS)-nido-B(10)H(13)] 2, and [1,2-(HS)(2)-nido-B(10)H(12)] 3 have been characterized using NMR spectroscopy, single-crystal X-ray diffraction analysis, and quantum-chemical calculations. In the solid state, 1, 2, and 3 feature weak intermolecular hydrogen bonding between the sulfur atom and the relatively positive bridging hydrogen atoms on the open face of an adjacent cluster. Density functional theory (DFT) calculations show that the value of the interaction energy is approximately proportional to the number of hydrogen atoms involved in the interaction and that these values are consistent with a related bridging-hydrogen atom interaction calculated for a B(18)H(22)·C(6)H(6) solvate. Self-assembled monolayers (SAMs) of 1, 2, and 3 on gold and silver surfaces have been prepared and characterized using X-ray photoelectron spectroscopy. The variations in the measured sulfur binding energies, as thiolates on the surface, correlate with the (CC2) calculated atomic charge for the relevant boron vertices and for the associated sulfur substituents for the parent B(10)H(13)(SH) compounds. The calculated charges also correlate with the measured and DFT-calculated thiol (1)H chemical shifts. Wetting-angle measurements indicate that the hydrophilic open face of the cluster is directed upward from the substrate surface, allowing the bridging hydrogen atoms to exhibit a similar reactivity to that of the bulk compound. Thus, [PtMe(2)(PMe(2)Ph)(2)] reacts with the exposed and acidic B-H-B bridging hydrogen atoms of a SAM of 1 on a gold substrate, affording the addition of the metal moiety to the cluster. The XPS-derived stoichiometry is very similar to that for a SAM produced directly from the adsorption of [1-(HS)-7,7-(PMe(2)Ph)(2)-nido-7-PtB(10)H(11)] 4. The use of reactive boron hydride SAMs as templates on which further chemistry may be carried out is unprecedented, and the principle may be extended to other binary boron hydride clusters.     

Functional isocyanide metal complexes as building blocks for supramolecular materials: hydrogen-bonded liquid crystals

Gold, palladium and platinum complexes with an unusual isocyanide ligand containing a carboxylic acid function, [AuCl(CNC(6)H(4)COOH)], cis-[MI(2)(CNC(6)H(4)COOH)(2)] and trans-[MI(2)(CNC(6)H(4)COOH)(2)] (M = Pd, Pt) have been isolated. The carboxylic acid group of the coordinated isocyanide acts as a hydrogen donor for hydrogen-bonding and three series of stable hydrogen-bonded liquid crystalline metal complexes have been prepared with decyloxystilbazole. Although all the metal acid derivatives used are not mesomorphic, and decyloxystilbazole only shows an ordered Smectic E phase, four out of the five hydrogen-bonded decyloxystilbazole complexes studied display enantiotropic smectic A or nematic mesophases. The single crystal X-ray diffraction structure of trans-[PdI(2)(CNC(6)H(4)COOH)(2)].C(4)H(8)O(2) has been determined and confirms the formation of a supramolecular array in the solid state supported by hydrogen-bonding.     

Boronic acid-substituted metal complexes: versatile building blocks for the synthesis of multimetallic assemblies

Polypyridyl complexes of Ru(II) and Ir(III) incorporating a boronic acid substituent undergo cross-coupling with bromo-substituted complexes, and a sequential coupling-bromination-coupling strategy permits the controlled synthesis of a luminescent Y-shaped heterometallic assembly, in which efficient energy transfer to the terminus occurs.     

A porphyrin-related macrocycle from carbazole and pyridine building blocks: synthesis and metal coordination

In this communication, we report the synthesis of a novel porphyrin-related macrocycle. The core modifications result in aromatic building blocks connected exclusively via aryl-aryl bonds. The concept of synthesis permits the formation of a cavity similar to that of a porphyrin combined with the ability to bind metal ions to provide neutral metal complexes.     

含硫氮杂套索冠醚的合成及应用研究

合成了一系列分别带有香豆素基和α—萘胺基套索冠醚，用紫外光谱法测定了 这些套索冠醚与Cu^2+，Pb^2+，Cd^2+，Hg^2+，Cr^3+，Ni^2+，Mg^2+，Zn^2+金属 离子的络合作用，及所形成络合物的λmax及摩尔消光系数ε，发现其中一些化合 物对Pb^2+，Hg^2+，Cr^3+金属离子具有较高的灵敏度和选择性．     

Benzoderivatives of nucleic acid bases as modified DNA building blocks

The tautomeric properties of benzoderivatives of the canonical nucleic acid bases have been studied by using different computational approaches. Attention has been paid to the impact of the benzene group in altering the tautomeric preferences of the canonical bases both in the gas phase and in aqueous solution. To this end, relative solvation free energies of the tautomers determined from Self-Consistent Reaction Field continuum calculations and Monte Carlo-Free Energy Perturbation are combined with gas-phase tautomerization free energies determined from quantum mechanical calculations. The results provide a detailed picture of the tautomeric preferences of the benzoderivatives of nucleic acid bases. This information is used to examine the recognition properties of the preferred tautomers of the benzo-fused derivatives, paying particular attention to the ability to form Watson-Crick hydrogen-bonding and stacking interactions as well as to the hydrophobic nature of the modified bases. The implications of present results on the potential use of benzo-fused bases as potential building blocks in modified DNA duplexes are examined.     

Azadibenzophospholes: functional building blocks with pronounced electron-acceptor character

A series of azadibenzophospholes with varying location of the nitrogen center has been synthesized and comprehensively characterized. In the context of the study, suitably brominated phenylpyridine precursors were accessed via Suzuki-Miyaura cross-coupling for the first time. Despite being nonfluorescent, X-ray crystallographic studies of two azadibenzophosphole oxides revealed planar conjugated scaffolds with high degree of π-conjugation. The P-oxidized species were found to show desirable reversible reduction features that support promising electron-accepting properties of the materials. The presence of the nitrogen as well as phosphorus centers within the scaffold allowed for further functionalization with transition metals, as well as methyl groups that result in altered absorption and redox features for the materials. Subsequent bromination of the scaffold selectively occurred at the exocyclic P-phenyl group, as confirmed via X-ray crystallography. This halogenation allowed for further modification of the system via catalytic cross-coupling with pyridine.     

Tetra- and octalactam macrocycles and catenanes with exocyclic metal coordination sites: versatile building blocks for supramolecular chemistry

The synthesis of a new tetralactam macrocycle and the simultaneous formation of catenanes and larger octalactam macrocycles is reported. These species bear 2,2'-biquinoline moieties suitably positioned to bind a metal center at the outer periphery of the macrocycles. (1)H NMR chemical shifts permit the unambiguous distinction of transoid and cisoid conformations of the biquinoline moiety, thereby allowing an unequivocal identification of the catenane and octalactam structures, despite the fact that both have the same elemental composition and bear identical structural subunits. With the aid of an anion template effect, rotaxanes can be prepared from the smaller tetralactam macrocycle. These reveal significantly altered requirements in terms of the stopper size as compared to previously reported tetralactam wheels. Several copper(I)-mediated dimers and a (bpy)(2)Ru(II) complex (bpy=2,2'-bipyridine) have been synthesized from the tetralactam macrocycle and the rotaxanes. The anion binding abilities of the tetralactam macrocycle and its (bpy)(2)Ru(II) complex in DMSO have been compared by (1)H NMR titration experiments, which revealed significantly enhanced binding by the metal complex. Mass spectrometry has been used to study the potential formation of larger assemblies of copper(I) and the catenane built-up from two tetralactam macrocycles. Indeed, a 2:2 complex was identified. In contrast, the octalactam macrocycle of the same elemental composition yields only 1:1 complexes, with the Cu(I) ion connecting its two biquinoline moieties in the center of a figure-eight-shaped molecule. Molecular modeling studies support the structural assignments made.     

Rational design of hetero-ring-expanded guanine analogs with enhanced properties for modified DNA building blocks

The properties and modes of recognition of physiological DNAs associated with the four natural nucleobases might be extended, in principle, by the design of non-natural nucleobase derivatives. The goal is an expansion of the genetic alphabet, with the possible outcome of producing new DNAs with improved physical or biological properties. In this work, a new series of hetero-ring-expanded guanine analogs are proposed, and their relevant structural characteristics and electronic properties are determined by density functional theory. The stabilities of the decamer DNA duplexes (dn.dC)10 (where n represents the corresponding expanded guanine analog designed here) are also examined, using molecular dynamics. The simulations show that the designed motifs can form stable DNA-like structures. We determined the pairing energies for the Watson-Crick (WC) hydrogen-bonded dimers between the expanded G-analogs and the natural C, and found that the pairing energies are close to those of the natural GC pair. The calculated adiabatic ionization potentials (IPs) of the size-expanded guanine analogs and their base pairs, and the corresponding vertical ionization potentials, show that some are distinctly smaller than the corresponding natural versions. The HOMO-LUMO energy gaps for most of the size-expanded guanine analogs and their WC base pairs are considerably lower than those of the corresponding natural base and base pairs. Thus, the expanded G bases may be considered as DNA genetic motifs, and they may serve as building blocks for potential biological applications and the development of molecular electronic devices.