(SR/RS)-cyclohexanyl PNAs: conformationally preorganized PNA analogues with unprecedented preference for duplex formation with RNA

PNA oligomers H-GTAGATCAT-lys-NH2 with cis-(1S,2R/1R,2S)-cyclohexyl-T (III) in the backbone form PNA:RNA duplexes with Tm approximately 30-50 degrees C higher than that of PNA:DNA duplexes. In comparison, cis-(1S,2R/1R,2S)-cyclopentyl PNA-T (IV) form highly stable duplexes with both RNA and DNA without discrimination.     

Zirconium(IV) complexes of oxydiacetic acid in aqueous solution and in the solid state as studied by multinuclear NMR and X-ray crystallography

The structures of complexes of Zr(IV) and oxydiacetate (ODA2-) in aqueous solutions of pH 0-7 were investigated with the use of 1H, 13C, and 17O NMR spectroscopy. Equilibria of mononuclear [Zr(oda)]2+, [Zr(oda)2], and [Zr(oda)3]2- complexes have been observed. In all complexes ODA2- is bound in a tridentate fashion through the two carboxylate groups and the ether oxygen. No di- or oligonuclear species containing ODA2- were observed. An excess of free Zr(IV) remains in solution, probably as a result of weak electrostatic interactions between negatively charged Zr-ODA complexes or free ODA2- and a positively charged cyclic tetranuclear hydroxy zirconium complex. CP-MAS 13C NMR spectra of solid compounds isolated from the samples indicated that the structures of the [Zr(oda)2] and [Zr(oda)3]2- complexes in solution are similar to those in the solid state. This is corroborated by the single-crystal X-ray structure of Na2[Zr(oda)3] x 5.5 H2O, which was obtained from a solution containing exclusively the [Zr(oda)3]2- complex. In this structure Zr(IV) is nine-coordinate with the three ODA2- ligands bound in a tricapped trigonal prismatic geometry. The negative charge of this [Zr(oda)3]2complex is balanced by two Na+ ions, one of which is on a center of symmetry between delta and lambda enantiomers of [Zr(oda)3]2-. This Na+ is octahedrally coordinated to six (non Zr(IV)-bound) carboxylate oxygen atoms of six different [Zr(oda)3]2- units.     

Thermogravimetric studies of dipyridinium complexes of cerium(IV), thorium(IV) and zirconium(IV)

The TG curves of dipyridinium complexes of Ce(IV), Th(IV) and Zr(IV) have been reported. The mode of decomposition of the cerium and thorium complexes is broadly comparable but the decomposition of Zr complex shows some variation.     

Coordination-driven inversion of handedness in ligand-modified PNA

Peptide nucleic acid (PNA) is a synthetic analogue of DNA, which has the same nucleobases as DNA but typically has a backbone based on aminoethyl glycine (Aeg). PNA forms duplexes by Watson Crick hybridization. The Aeg-based PNA duplexes adopt a chiral helical structure but do not have a preferred handedness because they do not contain a chiral center. An L-lysine situated at the C-end of one or both strands of a PNA duplex causes the duplex to preferably adopt a left-handed structure. We have introduced into the PNA duplexes both a C-terminal L-lysine and one or two PNA monomers that have a γ-(S)-methyl-aminoethyl glycine backbone, which is known to induce a preference for a right-handed structure. Indeed, we found that in these duplexes the γ-methyl monomer exerts the dominant chiral induction effect causing the duplexes to adopt a right-handed structure. The chiral PNA monomer had a 2,2':6',2'-terpyridine (Tpy) ligand instead of a nucleobase and PNA duplexes that contained one or two Tpys formed [Cu(Tpy)(2)](2+) complexes in the presence of Cu(2+). The CD spectroscopy studies showed that these metal-coordinated duplexes were right-handed due to the chiral induction effect exerted by the S-Tpy PNA monomer(s) except for the cases when the [Cu(Tpy)(2)](2+) complex was formed with Tpy ligands from two different PNA duplexes. In the latter case, the metal complex bridged the two PNA duplexes and the duplexes were left-handed. The results of this study show that the preferred handedness of a ligand-modified PNA can be switched as a consequence of metal coordination to the ligand. This finding could be used as a tool in the design of functional nucleic-acid based nanostructures.     

Template-synthesized DNA nanotubes

There is considerable interest in DNA-functionalized nanotubes with proposed applications that include use as gene delivery vehicles, in DNA-assisted separation and assembly of carbon nanotubes, and in nanotube-based DNA sensing and separations. In all of these previous cases, the DNA molecules were attached to a nanotube composed of a second material, typically carbon; however, it might also be advantageous to have nanotubes composed entirely, or predominately, of DNA itself. We describe here a template synthesis method for preparing such DNA nanotubes. The synthetic strategy builds on prior work, where we used Mallouk's layer-by-layer alpha,omega-diorganophosphonate (alpha,omega-DOP) Zr(IV) chemistry to deposit layered alpha,omega-DOP/Zr(IV) nanotubes along the pore walls of an alumina template membrane. The DNA nanotubes described here have an outer skin of one or more of these alpha,omega-DOP/Zr(IV) layers, to provide structural integrity, surrounding an inner core of multiple double-stranded DNA layers held together by hybridization between the layers. The DNA molecules comprising these nanotubes can be varied at will, and the DNA can be released from the nanotube by melting of the DNA duplexes comprising the nanotubes.     

Development of thiol-responsive amide bond cleavage device and its application for peptide nucleic acid-based DNA releasing system

To develop a thiol-responsive DNA-releasing system, a thiol-responsive amino acid capable of inducing an amide bond cleavage in the presence of a thiol was developed. It was successfully combined with peptide nucleic acid (PNA), and thiol-induced release of DNA from the thiol-responsive PNA/DNA complex was observed.     

Chiral bispyridylamide metal complexes as catalysts for the enantioselective addition of TMSCN to aldehydes

The use of (1R,2R)-N,N′-bis(2-pyridinecarboxyamido)-1,2-diphenylethane metal complexes as catalysts for the enantioselective addition of trimethylsilyl cyanide to aldehydes is described. Enantioselectivities up to 70% ee were obtained with a Ti(IV) catalyst. Complexes with Zr(IV), Sc(III), Yb(III) and Cu(II) afforded less selective catalysts. For the Zr(IV) complex, a rate and selectivity enhancement was observed when adding 0.5 equiv. of water with respect to the catalyst. Studies of the metal complexes involved in the reaction were carried out by means of ¹H NMR spectroscopy. A Zr complex was shown by X-ray crystallography to exhibit distorted octahedral coordination, with the four nitrogen atoms of the doubly deprotonated ligand essentially in one plane.     

Templated metal catalysis for single nucleotide specific DNA sequence detection

A catalytic DNA-templated reaction of hydrolysis of an ester group in an N-modified peptide nucleic acid, which is activated by a Cu2+ complex-PNA, has been discovered and optimized. Both the ester-containing PNA and the metal complex PNA bind neighboring sites on a template DNA. This brings the reacting groups (the ester and the Cu2+ complex) in proximity to each other and accelerates the hydrolysis of the ester approximately 500 times in comparison with its hydrolysis in the absence of the template. The hydrolysis reaction provides >10(2)-fold kinetic discrimination between DNAs that are different from each other at a single nucleotide position. Natural enzyme T4 DNA ligase is slightly less selective. On the basis of this reaction a fully homogeneous and sensitive assay for sequence-specific DNA detection has been developed (10 fmol DNA). Identification of one of four DNAs (variation at one position) can be done in a single experiment. Since the Cu2+ ion is tightly bound in an associate containing the ester PNA, the metal complex PNA, and the template DNA, application of this method in buffers containing other Cu2+-binding ligands, e.g., PCR buffer and physiological buffer, is possible.     

(2S,5R/2R,5S)-Aminoethylpipecolyl aepip-aegPNA chimera: synthesis and duplex/triplex stability

This article reports the design and facile synthesis of novel chiral six-membered PNA analogues (2S,5R/2R,5S)-1-(N-Boc-aminoethyl)-5-(thymin-1-yl)pipecolic acid, aepipPNA IV that upon incorporation into standard aegPNA sequences effected stabilization of complexes with complementary target DNA. Substitution of aegPNA unit by the designed monomer at the C-terminus was more effective than substitution at N-terminus. The stabilizing behaviour improved with degree of substitution and was found to be dependent on their relative positions in the sequence. The six-membered piperidine ring in the design may freeze the rigid chair conformations and the relative stereochemistry of the substituents may in effect direct the complex formation with DNA/RNA by sequence-specific nucleobase recognition. In the present aepipPNA analogues, the l-trans stereochemical disposition of the substituents seems to lead to the favorable pre-organization of the PNA oligomers for complex formation with DNA. The results reported here further expand the repertoire of cyclic PNA analogues.     

Metal binding to ligand-containing peptide nucleic acids

The substitution of nucleobases in nucleic acid duplexes with ligands that have high affinity for transition metal ions creates metal-binding sites at specific locations within the duplexes. Several studies on the incorporation of metal ions into DNA and peptide nucleic acid (PNA) duplexes have suggested that the stability constant of the metal complex formed within the duplexes is a primary determinant of the thermal stability of the duplexes. To understand this relationship, we have synthesized two PNA monomers that carry the same ligand, namely 8-hydroxyquinoline, but have this ligand attached differently to the PNA backbone. The PNA monomers have been incorporated into PNA duplexes. UV and CD spectroscopy and calorimetric studies of the 8-hydroxyquinoline-PNA duplexes showed that the effect of the stability of the metal complex on the PNA duplexes was significantly modulated by the steric relationship between the complex and the duplex. This information is useful for the construction of hybrid inorganic-nucleic acid nanostructures.     

"Oxidative addition" to a Zirconium(IV) redox-active ligand complex

A strategy to enable reactivity analogous to oxidative addition is presented for d(0) transition-metal complexes. The reaction of the redox-active ligand 2,4-di-tert-butyl-6-tert-butylamidophenolate (ap) with ZrCl(4)(THF)(2) affords the new complex Zr(IV)(ap)(2)(THF)(2). This compound is formally zirconium(IV) and contains no d electrons; however, exposure of Zr(IV)(ap)(2)(THF)(2) to chlorine gas results in swift chlorine addition at the zirconium metal center via one-electron oxidation of each ap ligand. The diradical product, Zr(IV)Cl(2)(isq)(2) (isq = 2,4-di-tert-butyl-6-tert-butyliminosemiquinone), has been characterized by X-ray crystallography, electron paramagnetic resonance spectroscopy, and SQUID magnetometery.     

Condition dependence of Zr electrochemical reactions and morphological evolution of Zr deposits in molten salt

This work presents a comprehensive study for the electrochemical behaviors of zirconium in LiCl-KCl eutectic.The effects of stirring,temperature and Zr concentration on the electrode reactions,the ZrCl_4 sublimation from the melt,microcosmic morphologies of Zr deposits(ZrCl and Zr)obtained at different potential and temperature have been investigated.The behaviors of Zr(Ⅳ),on a large concentration range from 0.13%to 2.28%in melt,show a multiple-step reaction involving Zr(Ⅳ),Zr(Ⅱ),ZrCl and Zr species.Temperature plays a crucial role on the changes of Zr(IV)reduction behavior on the solid electrode.The Zr(Ⅳ)/ZrCl couple is more easily observed at lower temperature and gradually diminishes with the increase of temperature.The Zr(Ⅳ)/Zr(Ⅱ)and Zr(Ⅱ)/Zr reactions are predominant on the W electrode at higher temperatures.At 673 K,a layered structure of insoluble ZrCl formed by potentiostatic electrolyses at 1.1 V was visualized by scanning electron microscopy-energy dispersive X-ray(SEM-EDS),while only Zr metal particles was observed at higher temperature than 773 K.An evolution of the Zr-based structure and size corresponding to the ZrCl and Zr metal based on different potentiostatic electrolysis was observed.The average particle size of the Zr metalparticles increases with the increase of temperature.     

Layer by layer assembly of DNA film via Zr(IV) ion and its intercalation property

In order to study the molecular recognition ability of DNA and different behavior of dyes incorporated into the base pairs, DNA molecule was assembled layer by layer via a Zr(IV) ion. The UV absorption spectra showed the uniform layer assembly of the DNA film. The fabricated DNA film was water-insoluble and maintained the native B-form structure. UV and CD measurements showed that the DNA film could intercalate ethidium bromide (EtBr).     

Sonochemical synthesis and characterization of nano-sized zirconium(IV) complex: new precursor for the preparation of pure monoclinic and tetragonal zirconia nanoparticles

In this study, synthesis and characterization of two polymorphs of a new nano-sized zirconium(IV) complex, [ZrO(dmph)I₂] (1), {dmph = 2,9-dimethyl-1,10-phenanthroline (neocuproine)}, have been investigated in two different solvents. The reaction between zirconyl nitrate pentahydrate and potassium iodide with dmph as a ligand under ultrasonic irradiation in methanol and mono-ethylene glycol (MEG) leads to the formation of the nano-sized Zr(IV) complex. Characterization of the Zr(IV) complex has been performed using scanning electron microscopy (SEM), X-ray powder diffraction (XRD), Fourier transform infrared (FT-IR) spectroscopy and elemental analysis. The thermal stability of the compound 1 has been studied by thermal gravimetric and differential thermal analyses. Particle sizes of the compound 1 have been decreased after thermal treatments in an autoclave. Pure monoclinic (m) and tetragonal (t) zirconia (ZrO₂) nanoparticles were readily synthesized from thermal decomposition of the Zr(IV) complex as a new precursor in presence of methanol and MEG as solvents, respectively. Zirconium oxide was characterized by FT-IR, XRD, and SEM to depict the phase and morphology. The results showed that, pure zirconia was produced with particle size about 59 nm and crystal system was monoclinic when methanol was used as a solvent during complexation process. On the other hand, particle sizes of zirconia with tetragonal structure were significantly reduced to about 39 nm, when MEG was used as solvent.     

Application of trans-[ZrO(curcumin)2(H2O)]·H2O in coloration of cotton fibers

Research on Chemical Intermediates - A novel six-coordinate complex of Zr(IV) with curcumin ligand was synthesized and characterized by thermogravimetric analysis, elemental analysis and...     

Simultaneous determination of Zr(IV) and Hf(IV) by CE using precolumn complexation with a [PW(11)O(39)](7-) ligand

A CE method was developed for the simultaneous determination of Zr(IV) and Hf(IV) at trace levels. A lacunary Keggin-type [PW(11)O(39)](7-) ligand reacted quantitatively with a mixture of trace amounts of Zr(IV) and Hf(IV) to form the so-called ternary Keggin-type anions [P(Zr(IV)W(11))O(40)](5-) and [P(Hf(IV)W(11))O(40)](5-) in 0.010 M monochloroacetate buffer (pH 2.2). Since both ternary anions possessed different electrophoretic mobilities and high molar absorptivities in the UV region, Zr(IV) and Hf(IV) were determined simultaneously with direct UV detection at 258 nm. Each peak height was linearly dependent on the concentration of Zr(IV) or Hf(IV) in the range of 5.0x10(-7)-1.0x10(-5) M; a detection limit of 2x10(-7) M was achieved. The utility of the proposed CE method was demonstrated for the simultaneous determination of Zr(IV) and Hf(IV) in natural water samples with satisfactory results.     

Label‐Free Bioelectronic Detection of Point Mutation by Using Peptide Nucleic Acid Probes

An electrochemical hybridization biosensor based on peptide nucleic acid (PNA) probes with a label‐free protocol is described. The detection of PNA‐DNA and DNA‐DNA hybridizations were accomplished based on the oxidation signal of guanine by using differential pulse voltammetry (DPV) at carbon paste electrode (CPE). It was observed that the oxidation signals of guanine obtained from the PNA and DNA probe modified CPEs were higher than those obtained from the PNA‐DNA and DNA‐DNA hybrid modified CPEs due to the accessible unbound guanine bases. The detection of hybridization between PNA probe and point mutation containing DNA target sequences was clearly observed due to the difference of the oxidation signals of guanine bases, because the point mutation was guanine nearly at the middle of the sequence. The effect of the DNA target concentration on the hybridization signal was also observed. The PNA probe was also challenged with excessive and equal amount of noncomplementary DNA and also mixtures of point mutation and target DNA.     

Trace determination of zirconium by adsorptive anodic stripping voltammetry of its complex with alizarin violet using a glassy carbon electrode modified with acetylene black-dihexadecyl hydrogen phosphate composite film

We report on a novel electrochemical method for the sensitive determination of trace zirconium (Zr) at a glassy carbon electrode modified with a film of acetylene black containing dihexadecyl hydrogen phosphate and in the presence of alizarin violet (AV). The method is based on the preconcentration of the Zr(IV)-AV complex at a potential of ?200?mV (vs. SCE). The adsorbed complex is then oxidized, producing a response with a peak potential of 526?mV. Compared to the poor electrochemical signal at the unmodified GCE, the electrochemical response of Zr(IV)-AV complex is greatly improved, as confirmed by the significant increase in peak current. The effects of experimental conditions on the oxidation current were studied and a calibration plot established. The oxidation current is linearly related to the Zr(IV) concentration in the 8.0?pM to 10?nM concentration range (c_AV?=?0.2???M) and 10?nM ~0.6???M (c_AV?=?2.0???M), and the detection limit (S/N?=?3) is as low as 4.0?pM for a 3-min accumulation time. The method was successfully employed to the determination of zirconium in standard ore samples.

Facing unexpected reactivity paths with Zr(IV)-pyridylamido polymerization catalysts

This work provides original insights to the better understanding of the complex structure-activity relationship of Zr(IV)-pyridylamido-based olefin polymerization catalysts and highlights the importance of the metal-precursor choice (Zr(NMe(2))(4) vs. Zr(Bn)(4)) to prepare precatalysts of unambiguous identity. A temperature-controlled and reversible σ-bond metathesis/protonolysis reaction is found to take place on the Zr(IV)-amido complexes in the 298-383 K temperature range, changing the metal coordination sphere dramatically (from a five-coordinated tris-amido species stabilized by bidentate monoanionic {N,N(-)} ligands to a six-coordinated bis-amido-mono-amino complexes featured by tridentate dianionic {N(-),N,C(-)} ligands). Well-defined neutral Zr(IV)-pyridylamido complexes have been prepared from Zr(Bn)(4) as metal source. Their cationic derivatives [Zr(IV) N(-),N,C(-)}Bn](+)[B(C(6)F(5))(4)](-) have been successfully applied to the room-temperature polymerization of 1-hexene with productivities up to one order of magnitude higher than those reported for the related Hf(IV) state-of-the-art systems. Most importantly, a linear increase of the poly(1-hexene) M(n) values (30-250 kg mol(-1)) has been observed upon catalyst aging. According to that, the major active species (responsible for the increased M(n) polymer values) in the aged catalyst solution, has been identified.     

Modeling of synergistic solvent extraction of Zr(IV) / HCl / TOA+Cyanex 921 system using statistical analysis and neural network

Multi-linear regression analysis (MLR), radial basis function (RBF) and multilayer perceptron (MLP) of artificial neural network (ANN) with five inputs (temperature, concentrations of HCl, TOA, Cyanex 921, Zr (IV) and percentage of extraction (%E)) as only output were employed for the construction of models. It was observed that ANN (RBF and MLP) performed better as compared to the MLR model. Based on the models proposed, the extraction of Zr(IV) could be predicted under variable experimental conditions of concentrations of HCl, TOA (Tri-n-octylamine), Cyanex 921 (Tri-n-octyl phosphineoxide), Zr(IV) and temperature. The nonlinear and complex relation between the percentage of extraction and operating variables have been determined using two and three layered feed forward neural network with back-propagation of error learning algorithm. Uncertainties in data have been determined in terms of statistical parameters such as root mean-squared error and R-squared values to check the efficiency of the model for prediction.