NMR-based reappraisal of the coordination of a metal ion at the pro-Rp oxygen of the A9/G10.1 site in a hammerhead ribozyme

In the identification of a metal-binding site within enzymes, kinetic analyses based on thio-effects and Cd(2+)-rescues are widely used. In those analyses, kinetic studies using a phosphorothioate have been discussed on the premise that the substitution by a sulfur atom does not change the conformation of a ribozyme. However, our present NMR structural analysis demonstrates the change of the conformation at the metal-binding site by Rp-sulfur but not by Sp-sulfur substitution and warns against incautious interpretations of thio-effects and rescue phenomena in kinetic studies using a phosphorothioate. Our analysis further demonstrates that, in solution, a Cd(2+) ion can interact with an Rp-phosphorothioate (in support of the controversial McKay's structure, Nature 1994, 372, 68-74) and with an Sp-phosphorothioate (in support of the controversial Scott's structure, Cell 1995, 81, 991-1002) at the metal-binding A9/G10.1 site and that, in the former case, the bound Cd(2+) ion can return the ribozyme to an active conformation and rescue its enzymatic activity.     

Identification of the metal ion binding site on an RNA motif from hammerhead ribozymes using (15)N NMR spectroscopy

An RNA oligomer, r(GGACGAGUCC), which mimics the metal ion-binding motif of hammerhead ribozymes, was shown to fold by itself into a conformation possessing a metal ion binding property which is similar to that of the intact ribozyme (Tanaka, et al. J. Am. Chem. Soc. 2000, 122, 11303-11310). To determine the metal ion-binding site of this motif at an atomic level, we synthesized a series of RNA oligomers which were selectively labeled with a (15)N-labeled guanosine at each of the four guanosine residues. The (15)N-chemical shift perturbation with Cd(II) ions by one-dimensional (1D) (15)N NMR spectra showed that the chemical shift of the N7 of the G7 residue, N7/G7, in the metal ion-binding motif was specifically perturbed. This is the first experimental evidence to prove that the N7/G7 binds with a Cd(II) ion.     

Tin(IV) Tetrachloride Complexes with Bis-(Dialkylamino)phosphoryl Fluoride: A Multinuclear (119Sn, 31P, 19F,and 1H) NMR Characterization in Solution

The two octahedral complexes SnCl₄·2(O)PF(NR₂)₂ (R = Me or Et) were prepared from reaction of SnCl₄ with the ligand (R₂N)₂P(O)F in anhydrous CHCl₃. The new adducts have been characterized by elemental analysis, IR, and multinuclear (¹¹⁹Sn, ³¹P, ¹⁹F, and ¹H) NMR spectroscopy. The NMR data show that the adducts exist in solution as a mixture of cis and trans isomers with markedly different proportions. When compared with previously described hexamethylphosphoramide (HMPA) and trimethylphosphate (TMPA) analogues, our results indicate that the cis isomer is the predominant species in solution. Low temperature ³¹P and ¹¹⁹Sn NMR spectra show that the compounds partially dissociate in dichloromethane.     

Electronic response of a (P,N)-based ligand on metal coordination

The reaction of [(THF)Li(Ph(2)PC(H)Py)] with ZnCl(2) in the presence of ZnO yields the zinc complex [Zn(3)(Ph(2)PC(H)Py)(4)O] (1). Deprotonation of the phosphane Ph(2)P(CH(2)Py) with [Fe(N(SiMe(3))(2))2] gives the iron complexes [(Ph(2)P(CH(2)Py))Fe(Ph(2)PC(H)Py)2] (2) and [Fe(Ph(2)PC(H)Py)(N(SiMe(3))(2))]2 (3), depending on the ratio of phosphane. The solid state structures of the metal complexes illustrate the coordination flexibility of the [Ph(2)C(H)Py](-)-anion. Depending on the electronic requirements of the coordinated metal the anion acts as a (P,N)-chelating amide or C-coordinating carbanion with the P- and N-heteroatoms as donor bases.     

Coordination environment of a site-bound metal ion in the hammerhead ribozyme determined by 15N and 2H ESEEM spectroscopy

Although site-bound Mg2+ ions have been proposed to influence RNA structure and function, establishing the molecular properties of such sites has been challenging due largely to the unique electrostatic properties of the RNA biopolymer. We have previously determined that, in solution, the hammerhead ribozyme (a self-cleaving RNA) has a high-affinity metal ion binding site characterized by a K(d,app) < 10 microM for Mn2+ in 1 M NaCl and speculated that this site has functional importance in the ribozyme cleavage reaction. Here we determine both the precise location and the hydration level of Mn2+ in this site using ESEEM (electron spin-echo envelope modulation) spectroscopy. Definitive assignment of the high-affinity site to the activity-sensitive A9/G10.1 region is achieved by site-specific labeling of G10.1 with 15N guanine. The coordinated metal ion retains four water ligands as measured by 2H ESEEM spectroscopy. The results presented here show that a functionally important, specific metal binding site is uniquely populated in the hammerhead ribozyme even in a background of high ionic strength. Although it has a relatively high thermodynamic affinity, this ion remains partially hydrated and is chelated to the RNA by just two ligands.     

Study of ion exchange selectivity of organic ions by using (31)P NMR spectroscopy

Ion exchange distribution of the phenylphosphoric acid has been studied on various types of chloride form strong base resins as a function of pH at 25 °C, at 0.1 M ionic strength. Equilibrium measurements were supplemented by the study of pH dependence of the ³¹P NMR spectra of the resin-phase phenylphosphate species. Equations were derived to describe the pH dependence of the overall distribution coefficient and the chemical shift of the resin-phase solute species. Experimental data were evaluated by using these model equations and the values of the individual distribution coefficients, ion exchange selectivity coefficients and the resin-phase ³¹P chemical shifts of the mono- and divalent ions have been calculated. Comparison of distribution data of the individual species corroborated the significance of the role of hydrophobic interaction in the selectivity of organic ion exchange processes. A well-defined correlation between the ion exchange selectivity and the resin-phase ³¹P NMR chemical shift data has been pointed out.     

Reaction of a cyclic triphosphenium ion with triflic acid and SnX2 (X = Br or Cl): A 31P NMR study

The di‐ium dication formed by triflic acid protonation of the cyclic triphosphenium ion derived from 1,4‐bis‐diphenylphosphinobutane, (dppb), and P₃(X = Br or Cl) decomposes via an acyclic dication bearing a  PHX group; this intermediate is reduced by SnX₂ in the presence of HX to yield a dication with a  PH₂ primary phosphane terminal group, which is comparatively stable. The structure of this species has been unequivocally confirmed by ³¹P solution‐state NMR spectroscopy. © 2007 Wiley Periodicals, Inc. Heteroatom Chem 18:609–612, 2007; Published online in Wiley InterScience ( www.interscience.wiley.com ). DOI 10.1002/hc.20302     

A ratiometric fluorescent metal ion indicator based on dansyl labeled poly(N-isopropylacrylamide) responds to a quenching metal ion

The fluorescence emission of poly(N-isopropylacrylamide) (PNIPAM) covalently tagged with a 5-(dimethylamino)naphthalene-1-sulfonyl (dansyl) fluorophore and an iminodiacetic acid (IDA) chelator changes with temperature and with Cu(II) complexation. Increasing the temperature above the lower critical solution temperature (LCST) causes the polymer to collapse from a coil to a compact globule. This changes the environment experienced by the fluorophore causing a shift in maximum emission wavelength from 546 to 508 nm and an increase in the ratio of emission intensity at 508 nm to emission intensity at 546 nm from 0.70 to almost 1.40. Metal ions can be sensed by working at a temperature where the uncomplexed polymer is in an expanded state due to the charges on the ligand. Complexation with a metal ion such as Cu(II) neutralizes the charges on the ligand causing the polymer to collapse. At 35 °C, the emission intensity maximum shifted from 535 to 510 nm as Cu(II) concentration was increased and the intensity ratio increased from 0.84 to 1.28. By decoupling complexation from fluorescence, we have prepared a ratiometric fluorescent indicator for a metal ion that normally quenches fluorescence. The affinity for Cu(II) was found to be thermally tunable. The log apparent formation constants for the indicator-Cu(II) complex were estimated as the half way point in the intensity ratio vs. pCu curve. The values were determined to be 4.3 at 35 °C and 3.2 at 34 °C respectively.     

Multinuclear (11B, 31P) MAS NMR spectroscopy of borophosphates

¹¹B and ³¹P MAS NMR spectroscopy of three borophosphates was used to monitor their phase composition via the isotropic chemical shifts. CaBPO₅ and BPO₄ represent nearly pure samples, SrBPO₅ contains β-Sr₂P₂O₇ as well as BPO₄ as impurities. The anisotropic chemical shift data provide additional information on the geometry and connectivity of the BO₄ and PO₄ building units. Received: 25 July 1996 / Revised: 19 August 1996 / Accepted: 23 August 1996     

Multinuclear (11B, 31P) MAS NMR spectroscopy of borophosphates

¹¹B and ³¹P MAS NMR spectroscopy of three borophosphates was used to monitor their phase composition via the isotropic chemical shifts. CaBPO₅ and BPO₄ represent nearly pure samples, SrBPO₅ contains β-Sr₂P₂O₇ as well as BPO₄ as impurities. The anisotropic chemical shift data provide additional information on the geometry and connectivity of the BO₄ and PO₄ building units. Received: 25 July 1996 / Revised: 19 August 1996 / Accepted: 23 August 1996     

Layered metal(IV) phosphonate materials: Solid‐state 1H, 13C, 31P NMR spectra and NMR relaxation

Multinuclear solid‐state NMR and powder X‐ray diffraction data collected for phosphonate materials Zr(O₃PC₆H₄PO₃) · 3.6H₂O and Sn(O₃PC₆H₄PO₃)_0.85(O₃POH)_0.30 · 3.09H₂O have resulted in the layered structure, where the phosphonic acids cross‐link the layers. The main structural motif (the 111 connectivity in the PO₃ group) has been established by determination of chemical shift anisotropy parameters for phosphorus nuclei in the phosphonate groups. An analysis of the variable‐temperature ³¹P T₁ measurements and the shapes of the phosphorus resonances in the ³¹P static NMR spectra have resulted in the dipolar mechanism of the phosphorus spin‐lattice relaxation, where the rotating phenylene rings reorient dipolar vectors P^…H as a driving force of the relaxation process. It has been found that water protons do not affect the ³¹P T₁ times. The activation energy of the phenylene rotation in both compounds has been determined as low as 12.5 kJ/mol. The interpretation of the phosphorus relaxation data has been independently confirmed by the measurements of ¹H T₁ times for protons of the phenylene rings.     

On phosphorus chemical shift anisotropy in metal (IV) phosphates and phosphonates: A 31P NMR experimental study

The phosphorus chemical shift anisotropies, ³¹PΔcs, and asymmetry parameters η were measured by the ³¹P{¹H} NMR experiments in static and low-frequency spinning samples of the zirconium phosphates and phosphonates and also in the mixed Zr (IV)/Sn (IV) phosphate/phosphonate material. The data obtained have shown a 111 connectivity in the HPO₄ and PO₃ groups, which does not change at modification and intercalation of the materials. The ³¹PΔcs values of the phosphonate groups (43–49 ppm) significantly surpass the values characterizing the HPO₄ groups (23–37 ppm). The ³¹P Δcs values obtained for the metal (IV) phosphates were discussed in terms of P-O distances. The ³¹P chemical shift anisotropy parameters can help at elucidation of local structures in phosphate and phosphonate materials.     

High-dimensional assembly depending on polyoxoanion templates, metal ion coordination geometries, and a flexible bis(imidazole) ligand

By introducing the flexible 1,1'-(1,4-butanediyl)bis(imidazole) (bbi) ligand into the polyoxovanadate system, five novel polyoxoanion-templated architectures based on [As(8)V(14)O(42)](4-) and [V(16)O(38)Cl](6-) building blocks were obtained: [M(bbi)(2)](2)[As(8)V(14)O(42)(H(2)O)] [M = Co (1), Ni (2), and Zn (3)], [Cu(bbi)](4)[As(8)V(14)O(42)(H(2)O)] (4), and [Cu(bbi)](6)[V(16)O(38)Cl] (5). Compounds 1-3 are isostructural, and they exhibit a binodal (4,6)-connected 2D structure with Schl?fli symbol (3(4) x 4(2))(3(4) x 4(4) x 5(4) x 6(3))(2), in which the polyoxoanion induces a closed four-membered circuit of M(4)(bbi)(4). Compound 4 exhibits an interesting 3D framework constructed from tetradentate [As(8)V(14)O(42)](4-) cluster anions and cationic ladderlike double chains. There exists a bigger M(8)(bbi)(6)O(2) circuit in 4. The 3D extended structure of 5 is composed of heptadentate [V(16)O(38)Cl](6-) anions and flexural cationic chains; the latter consists of six Cu(bbi) segments arranged alternately. It presents the largest 24-membered circuit of M(24)(bbi)(24) so far observed made of bbi molecules and transition-metal cations. Investigation of their structural relations shows the important template role of the polyoxoanions and the synergetic interactions among the polyoxoanions, transition-metal ions, and flexible ligand in the assembly process. The magnetic properties of compounds 1-3 were also studied.     

Effect of alkali metal coordination on gas-phase chemistry of the diphosphate ion: the MH(2)P(2)O(7) (-) ions

Systematic experimental and theoretical studies on anionic phosphate species in the gas phase are almost nonexistent, even though they could provide a benchmark for enhanced comprehension of their liquid-phase chemical behavior. Gaseous MH(2)P(2)O(7) (-) ions (M=Li, Na, K, Rb, Cs), obtained from electrospray ionization of solutions containing H(4)P(2)O(7) and MOH or M salts as a source of M(+) ions were structurally assayed by collisionally activated dissociation (CAD) mass spectrometry and theoretical calculations at the B3LYP/6-31+G* level of theory. The joint application of mass spectrometric techniques and theoretical methods allowed the MH(2)P(2)O(7) (-) ions to be identified as having a structure in which the linear diphosphate anion is coordinated to the M(+) ion (I) and provides information on gas-phase isomerization processes in the [PO(3)...MH(2)PO(4)](-) clusters II and the [P(2)O(6)...M...H(2)O](-) clusters IV. Studies of gas-phase reactivity by Fourier transform ion cyclotron resonance (FTICR) and triple quadrupole (TQ) mass spectrometry revealed that the MH(2)P(2)O(7) (-) ions react with selected nucleophiles by clustering, proton transfer and addition-elimination mechanisms. The influence of the coordination of alkali metal ions on the chemical behavior of pyrophosphate is discussed.     

1H, (19)F, and (31)P PGSE NMR diffusion studies on chiral organic salts: ion pairing and the dependence of a diffusion value on diastereomeric structure

1H, (19)F and (31)P pulsed field gradient spin-echo (PGSE) diffusion studies on chiral organic salts that contain hexacoordinate phosphate anions, namely tris(tetrachlorobenzenediolato)phosphate(V) (TRISPHAT) and bis(tetrachlorobenzenediolato)mono([1,1']binaphthalenyl-2,2'diolato)-phosphate(V) (BINPHAT), are reported. The first example of the dependence of a diffusion value on diastereomeric structure is presented. Marked solvent and concentration effects on the diffusion constants (D) of these salts are noted and the question of ion pairing is discussed.     

The pentacyanopyridine-4-aldoximeferrate(II) ion estimation of the ligand's coordination site

Summary Pyindine-4-aldoxime reacts with the aquopentacyanoferrate(II) ion by forming a complex compound of 1:1 molar ratio. ThepK _a value of the oxime group in the complex, the influence ofpH changes on its formation as well as IR data indicate the coordination of pyridine-4-aldoxime through the pyridine nitrogen.

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Das Pentacyanopyridin-4-aldoximferrat(II)-Ion. Bestimmung der Koordinationsstelle

Zusammenfassung Pyridin-4-aldoxim reagiert mit dem Aquopentacyanoferrat(II)-Ion und bildet einen Komplex mit dem Molarverhältnis 1:1. DerpK _a Wert der Oxim-Gruppe im Komplex, der Einfluß despH auf seine Bildung, wie auch die IR Daten weisen auf die Koordination des Pyridin-4-aldoxim über den Pyridin-Stickstoff hin.

     

Monitoring of the insecticide trichlorfon by phosphorus-31 nuclear magnetic resonance (31P NMR) spectroscopy

Trichlorfon is an organophosphorus insecticide, which is extensively being used for protection of fruit crops. Trichlorfon is a thermal labile compound, which cannot be easily determined by gas chromatography (GC) and has no suitable group for sensitive detection by high performance liquid chromatography (HPLC). In this study, a ³¹P nuclear magnetic resonance (³¹P NMR) has been described for monitoring of trichlorfon without any separation step. The quantitative works of ³¹P NMR spectroscopy has been performed in the presence of an internal standard (hexamethylphosphoramide). Limit of detection (LOD) for this method has been found to be 55 mg L⁻¹, without any sample preparation, and the linear working range was 150-5500 mg L⁻¹. Relative standard deviation (R.S.D.%) of the method for three replicates within and between days was obtained ≤9%. The average recovery efficiency was approximately 99-112%. This method was applied for monitoring trichlorfon in a commercial insecticide sample and tomato sample.     

Nature of the chemical bond formed with the structural metal ion at the A9/G10.1 motif derived from hammerhead ribozymes

We have studied the interaction between metal ions and the metal ion-binding motif in hammerhead ribozymes, as well as the functions of the metal ion at the motif, with heteronuclear NMR spectroscopy. In this study, we employed model RNA systems which mimic the metal ion-binding motif and the altered motif. In Co(NH3)6(III) titrations, we observed large 1H and 31P chemical shift perturbations for the motif and found that outer-sphere complexation of Co(NH3)6(III) is possible for this motif. From the reinvestigation of our previous 15N chemical shift data for Cd(II) binding, in comparison with those of organometallic compounds, we conclude that Cd(II) can form an inner-sphere complex with the nucleobase in the motif. Therefore, the A9/G10.1 site was found to accept both inner-sphere and outer-sphere complexations. The Mg(II) titration for a slightly different motif from the A9/G10.1 site (G10.1-C11.1 to A10.1-U11.1) revealed that its affinity to Mg(II) was drastically reduced, although the ribozyme with this altered motif is known to retain enzymatic activities. This observation suggests that the metal ion at these motifs is not a catalytic center of hammerhead ribozymes.