Synthesis and cationic selectivity studies of novel calix[4]arene derivatives containing heteroatom at the lower rim

A series of calixarene derivatives 2―5 containing heteroatom at the lower rim have been synthesized. 1H NMR studies and crystallographic structures demonstrated that the calix[4]arene derivatives adopted cone conformations. Their cationic binding abilities and selectivities towards heavy and tran- sition metal ions have been evaluated by solvent extraction of aqueous metal picrates. The obtained results indicated that the introduction of nitrogen, sulfur, and/or phosphor atoms to the calix[4]arene framework could effectively enhance their binding ability and selectivity for heavy and transition metal ions, such as Pb2 or Ag .     

Synthesis and characterization of linear molecular assembly of crystalline calix[4]arenes dithianes

A family of six new variously substituted calix[4]arene dithianes has been prepared from respective formyl and acetyl derivatives. Shorter reaction time, mild conditions, and facile isolation of desired products are attractive features of the described method. The new 1,2-dithiane derivatives have been characterized by ¹H NMR, ¹³C NMR spectroscopy, and FABMS analysis. The crystal structure of one of the acetyl calix[4]arene dithiane was determined by X-ray diffraction analysis, which revealed a dithiane capped linear molecular organization. Preliminary evaluation of bis (dithiane) calix[4]arene derivatives as molecular receptor for transition metal ions has revealed strong interaction with Hg²⁺ in 1:1 stoichiometry.     

Direct NMR detection of alkali metal ions bound to G-quadruplex DNA

We describe a general multinuclear (1H, 23Na, 87Rb) NMR approach for direct detection of alkali metal ions bound to G-quadruplex DNA. This study is motivated by our recent discovery that alkali metal ions (Na+, K+, Rb+) tightly bound to G-quadruplex DNA are actually "NMR visible" in solution (Wong, A.; Ida, R.; Wu, G. Biochem. Biophys. Res. Commun. 2005, 337, 363). Here solution and solid-state NMR methods are developed for studying ion binding to the classic G-quadruplex structures formed by three DNA oligomers: d(TG4T), d(G4T3G4), and d(G4T4G4). The present study yields the following major findings. (1) Alkali metal ions tightly bound to G-quadruplex DNA can be directly observed by NMR in solution. (2) Competitive ion binding to the G-quadruplex channel site can be directly monitored by simultaneous NMR detection of the two competing ions. (3) Na+ ions are found to locate in the diagonal T4 loop region of the G-quadruplex formed by two strands of d(G4T4G4). This is the first time that direct NMR evidence has been found for alkali metal ion binding to the diagonal T4 loop in solution. We propose that the loop Na+ ion is located above the terminal G-quartet, coordinating to four guanine O6 atoms from the terminal G-quartet and one O2 atom from a loop thymine base and one water molecule. This Na+ ion coordination is supported by quantum chemical calculations on 23Na chemical shifts. Variable-temperature 23Na NMR results have revealed that the channel and loop Na+ ions in d(G4T4G4) exhibit very different ion mobilities. The loop Na+ ions have a residence lifetime of 220 micros at 15 degrees C, whereas the residence lifetime of Na+ ions residing inside the G-quadruplex channel is 2 orders of magnitude longer. (4) We have found direct 23Na NMR evidence that mixed K+ and Na+ ions occupy the d(G4T4G4) G-quadruplex channel when both Na+ and K+ ions are present in solution. (5) The high spectral resolution observed in this study is unprecedented in solution 23Na NMR studies of biological macromolecules. Our results strongly suggest that multinuclear NMR is a viable technique for studying ion binding to G-quadruplex DNA.     

Solid‐state NMR and EPR Spectroscopy of Mn2+‐Substituted ATP‐Fueled Protein Engines

Paramagnetic metal ions deliver structural information both in EPR and solid‐state NMR experiments, offering a profitable synergetic approach to study bio‐macromolecules. We demonstrate the spectral consequences of Mg²⁺/ Mn²⁺ substitution and the resulting information contents for two different ATP:Mg²⁺‐fueled protein engines, a DnaB helicase from Helicobacter pylori active in the bacterial replisome, and the ABC transporter BmrA, a bacterial efflux pump. We show that, while EPR spectra report on metal binding and provide information on the geometry of the metal centers in the proteins, paramagnetic relaxation enhancements identified in the NMR spectra can be used to localize residues at the binding site. Protein engines are ubiquitous and the methods described herein should be applicable in a broad context.     

Ion Interactions with a New Ditopic Naphthalimide‐Based Receptor: A Photophysical,NMR and Theoretical (DFT) Study

A new multi‐component chemosensor system comprising a naphthalimide moiety as fluorophore is designed and developed to investigate receptor–analyte binding interactions in the presence of metal and non‐metal ions. A dimethylamino moiety is utilized as receptor for metal ions and a thiourea receptor, having acidic protons, for binding anions. The system is characterized by conventional analytical methods. The absorption and fluorescence spectra of the system consist of a broad band typical for an intramolecular charge transfer (ICT). The effects of various metal‐ion additives on the spectral behavior of the present sensor system are examined in acetonitrile. It is found that among the metal ions studied, alkali/alkaline earth‐metal ions and transition‐metal ions modulate the absorption and fluorescence spectra of the system. As an additional feature, the anion signaling behavior of the system in acetonitrile is studied. A decrease in fluorescence efficiency of the system is observed upon addition of fluoride and acetate anions. Fluorescence quenching is most effective in the case of fluoride ions. This is attributed to the enhancement of the photoinduced electron transfer from the anion receptor to the fluorophore moiety. Hydrogen‐bond interactions between the acidic NH protons of the thiourea moiety and the F^? anions are primarily attributed to the fluoride‐selective signaling behavior. Interestingly, a negative cooperativity for the binding event is observed when the interactions of the system are studied in the presence of both Zn²⁺ and F^? ions. NMR spectroscopy and theoretical calculations are also carried out to better understand the receptor–analyte binding.     

酰氨基硫脲类新型分子钳受体的合成及其对氟离子的识别性能研究

本文设计并高产率合成了三种新型阴离子识别受体化合物,它们对F-的识别选择性较卤素其他阴离子的高。其对F-的识别性能通过紫外—可见光谱和核磁共振氢谱进行了检测,光谱数据表明,在DMSO溶液中受体与F-通过氢键相互作用形成1:1配合物。与以前我们报道的受体化合物相比,由于此类分子钳受体化合物具有更多的阴离子识别位点,因此具有更好地阴离子识别性能。     

3‐Mercapto‐2,6‐Pyridinedicarboxylic Acid: A Small Lanthanide‐Binding Tag for Protein Studies by NMR Spectroscopy

Paramagnetic effects from lanthanide ions present powerful tools for protein studies by nuclear magnetic resonance (NMR) spectroscopy provided that the lanthanide can be site‐specifically and rigidly attached to the protein. A new, particularly small and rigid lanthanide‐binding tag, 3‐mercapto‐2,6‐pyridinedicarboxylic acid (3MDPA), was synthesized and attached to two different proteins via a disulfide bond. The complexes of the N‐terminal domain of the E. coli arginine repressor (ArgN) with seven different paramagnetic lanthanide ions and Co²⁺ were analyzed in detail by NMR spectroscopy. The magnetic susceptibility anisotropy (Δχ) tensors and metal position were determined from pseudocontact shifts. The 3MDPA tag generated very different Δχ tensor orientations compared to the previously studied 4‐mercaptomethyl‐DPA tag, making it a highly complementary and useful tool for protein NMR studies.     

Coordination chemistry of a terpyridine-tris(pyrazolyl) ditopic ligand

A new ditopic ligand, 4'-(4-(2,2,2-tris(1H-pyrazol-1-ido)ethoxymethyl)phenyl)-2,2':6',2'-terpyridine (pzt), has been prepared and its coordination chemistry studied. Metal ions with a preference for octahedral geometry form ML(2) complexes that are readily isolated and characterised, with the metal ion being bound to the terpyridine sites of both ligands. Other metal ions bind to the terpyridine site of just one ligand. In the case of silver(i), a dinuclear M(2)L(2) complex has been isolated in which each silver ion is coordinated to the terpyridine site of one ligand and to a single pyrazolyl donor group from the second ligand. Evidence for binding of metal ions to the tris(pyrazolyl) binding site was obtained by electrospray mass spectrometry and NMR techniques. The free ligand and three metal complexes, including the disilver complex, have been characterised by X-ray crystallographic techniques.     

Competitive binding exchange between alkali metal ions (K+, Rb+, and Cs+) and Na+ ions bound to the dimeric quadruplex [d(G4T4G4)]2: a 23Na and 1H NMR study

A comparative study of the competitive cation exchange between the alkali metal ions K⁺, Rb⁺, and Cs⁺ and the Na⁺ ions bound to the dimeric quadruplex [d(G₄T₄G₄)]₂ was performed in aqueous solution by a combined use of the ²³Na and ¹H NMR spectroscopy. The titration data confirm the different binding affinities of these ions for the G‐quadruplex and, in particular, major differences in the behavior of Cs⁺ as compared to the other ions were found. Accordingly, Cs⁺ competes with Na⁺ only for the binding sites at the quadruplex surface (primarily phosphate groups), while K⁺ and Rb⁺ are also able to replace sodium ions located inside the quadruplex. Furthermore, the ¹H NMR results relative to the CsCl titration evidence a close approach of Cs⁺ ions to the phosphate groups in the narrow groove of [d(G₄T₄G₄)]₂. Based on a three‐site exchange model, the ²³Na NMR relaxation data lead to an estimate of the relative binding affinity of Cs⁺ versus Na⁺ for the quadruplex surface of 0.5 at 298 K. Comparing this value to those reported in the literature for the surface of the G‐quadruplex formed by 5′‐guanosinemonophosphate and for the surface of double‐helical DNA suggests that topology factors may have an important influence on the cation affinity for the phosphate groups on DNA. Copyright © 2009 John Wiley & Sons, Ltd.     

Molecular Tweezers for Dicarboxylic Acids Based on a Saddle-Shaped Metallomacrocyclic Platform

A new metal containing molecular receptor was prepared from a 15-membered nickel(II) macrocyclic cyclidene platform and two cyclic tetramine (cyclen) recognition cites. In the saddle shaped conformation of the platform, the cyclen receptors are positioned for ditopic binding of difunctional substrates. NMR titration experiments demostrate that the molecule binds dicarboxylic acids in DMSO with apparent equilibrium constants ranging from 10 to 10⁴ M^-1. Incusion of dicarboxylates into the protonated macrocyclic host is shape-selective, with cis-1,2-dicarboxylates (succinate, maleate, and o-phthalate) being the best guests.     

Accurate analysis of Mg2+ binding to RNA: From classical methods to a novel iterative calculation procedure

Mg²⁺ acts as a catalytic cofactor in many ribozymes and specifically bound divalent metal ions have been implicated in the stabilization of structural motifs that are essential for RNA folding. The accurate calculation of intrinsic affinity constants of M²⁺ to specific binding sites in nucleic acids is therefore of high importance. Methods classically applied to determine the affinity constants of metal ions to RNAs are summarized in the first part of this review, e.g. hydrolytic cleavage experiments, equilibrium dialysis, and spectroscopic techniques like EPR and NMR. However, the fact that several binding sites of similar affinities are often present in a single RNA molecule is mostly neglected. The most immediate consequence of several binding sites is that less than the total amount of M²⁺ is available to bind to a particular binding site at a given total concentration. We have recently introduced a new iterative procedure that tackles this problem and have developed a rapid calculation tool (ISTAR) that is available from the authors. Here, we explain this procedure in detail under different assumptions and illustrate how the intrinsic affinity constants for Mg²⁺ to a short RNA hairpin, a minimal domain 6 from the group II intron Sc.ai5γ, change. We use ISTAR to calculate intrinsic affinities and to validate a particular binding stoichiometry by judging the quality of the fit to the experimental data for a given model. This is important since weak coordination sites exhibiting similar binding affinities, and being thus in direct competition to each other, are a characteristic feature of nucleic acids. With ISTAR these binding affinities can be calculated more accurately within minutes and we can gain a better understanding of these crucial metal ion–nucleic acid interactions.     

Chelation Ion Chromatography on DMSO Impregnated Silica Gel-G Layers: Specific Separation of Cd2+, W6+, and Zr4+ from Transitional Metal Ions

Abstract

Chelation ion chromatography of metal ions on DMSO impregnated silica gel-G layers in ether; DMSO: 1M HNO₃ (1:1); n-butanol: acetone: HNO₃ (6:6:1) and di-isopropyl ether: DMSO: THF systems having varying compositions, was performed. The zero R_f for a number of cations is explained in terms of precipitation and strong adsorption. It was possible to separate Cd²⁺, W⁶⁺, Zr⁴⁺, Zn²⁺ and VO²⁺ from numerous metal ions. A number of analytically important binary and ternary separations were also achieved and were found useful in synthetic alloy analysis.     

Synthesis of nucleobase-calix[4]arenes via click chemistry and evaluation of their complexation with alkali metal ions and molecular assembly

In this study, calix[4]arene derivatives (11–14) bearing a single nucleobase (adenine, thymine, cytosine or guanine) were synthesised via click chemistry. The complexation ability of the synthesised derivatives with alkali metal ions was measured using MALDI-TOF mass spectrometry, and their molecular assembly in CDCl₃ was determined using ¹H NMR. Calix[4]arene derivatives (11–14) formed 1:1 complexes with all alkali metal ions and the rank order for the complexation selectivity was Rb⁺ > Cs⁺ > K⁺ ? Na⁺ > Li⁺. The attachment of nucleobase at the upper rim of calix[4]arene had little effect on its complexation selectivity for alkali metal ions. Thymine-, adenine- and guanine-calix[4]arenes formed self-assembled structures in CDCl₃ via base–base interactions. In addition, adenine-calix[4]arene (11) bound to thymine-calix[4]arene (12) to form a discrete species via Hoogsteen hydrogen bonding.     

Perimidine-based synthetic receptors for determination of copper(II) in water solution

Perimidine-based chelators 1 and 2 were prepared, and their structures were confirmed by ¹H and ¹³C NMR, MS spectroscopy and elemental analysis. These compounds were studied as specific synthetic receptors for the recognition of transition metal ions. They exhibited high affinity and selectivity towards Cu(II) ions. The conditional binding constants, linear dynamic range and detection limit were determined by UV–vis spectroscopy. These parameters demonstrated high potential of the prepared synthetic receptors for the recognition and determination of Cu(II) ions. The minimum detectable concentrations of Cu(II) ions for the synthetic receptors 1 and 2 were 270 and 75 nM (R ² = 0.9915 and 0.9964) in aqueous medium (water/DMSO; 99:1 (v/v)), respectively.     

Carbon-13 NMR spectroscopy of the biological pigments luteoskyrin and rugulosin and some polyhydroxyanthraquinone analogues

The bianthraquinonic biological pigments luteoskyrin and rugulosin and five polyhydroxyanthraquinone derivatives are studied by carbon-13 NMR in DMSO solution. Peak assignment for the fourteen carbon atoms of these compounds is achieved by proton spin decoupling and by investigating the effect of ionisation of the hydroxyl groups upon the carbon chemical shifts. Carbon chemical shifts in the planar hydroxyanthraquinones can be rationalised in terms of conjugation and intramolecular hydrogen bonding. The latter is responsible for the relative acidity of the hydroxyl groups in the analogues, and for the different conformations proposed for luteoskyrin and rugulosin. Tautomeric equilibria occur in DMSO and water–DMSO solutions for the anionic species [LS]^2? and [RG]^2?. This can account for the binding of luteoskyrin and rugulosin to nucleic acids.     

Syntheses and metal ions recognition of dendritic calix[n]arenes (n = 6,8) amide derivative

Dendritic p-t-butylcalix[n]arene amide derivatives with terminal amino groups of the first and second generations were synthesized by using divergent methods from ammonolysis of ethyl calixarylacetate with 1,6-diaminohexane and Michael addition of methyl acrylate. Their structures were confirmed by IR, ¹H NMR. The recognition properties of these amide derivatives for several kinds of metal ions were studied with UV-Vis spectroscopy. The results showed a great affinity for soft Ag⁺ and UO₂ ²⁺ ions and formed 1:2 or 1:3 stoichiometric complexes. Translated from Chinese Journal of Applied Chemistry, 2006, 23(3) (in Chinese)     

Two Histidines in an α‐Helix: A Rigid Co2+‐Binding Motif for PCS Measurements by NMR Spectroscopy

Pseudocontact shifts (PCS) generated by paramagnetic metal ions present valuable long‐range information in the study of protein structural biology by nuclear magnetic resonance (NMR) spectroscopy. Faithful interpretation of PCSs, however, requires complete immobilization of the metal ion relative to the protein, which is difficult to achieve with synthetic metal tags. We show that two histidine residues in sequential turns of an α‐helix provide a binding site for a Co²⁺ ion, which positions the metal ion in a uniquely well‐defined and predictable location. Exchange between the bound and free cobalt is slow on the timescale defined by chemical shifts, but the NMR resonance assignments are nonetheless readily transferred from the diamagnetic to the paramagnetic NMR spectrum by an I_zS_z‐exchange experiment. The double‐histidine‐Co²⁺ motif offers a straightforward, inexpensive, and convenient way of generating precision PCSs in proteins.     

Binding of metal ions by polyethylenimine and its derivatives

Measurements have been made of the binding of divalent metal ions, Cu²⁺, Ni²⁺, Co²⁺, and Zn²⁺ ions, by polyethylenimine (PEI) and its acetyl or alkyl derivatives by the equilibriumdialysis technique. These metal ions, in particular the Cu²⁺ ion, exhibited tremendously remarkable binding affinity toward PEI. The extent of complexation of the polymer with the metal ions was decreased markedly by acetylation or alkylation of the polymer. PEI with no primary amine showed an appreciable decrease in its affinity for the metal ion. These results indicate the participation of the primary amine of the polymer in the formation of the complex. A cooperative binding isotherm was observed in PEI–metal ion complex formation, suggesting swelling or conformational change of the polymer induced by this coordination process. Binding of the Cu²⁺ ion by PEI was found to be essentially independent of temperature over the range 5–35°C.     

A molecular switch based on acid and base promoted, cation governed binding in a crown ether threaded rotaxane

A rotaxane, containing both oligo ethylene glycol and secondary ammonium cation binding sites for a threaded crown ether, has been prepared. ¹H NMR spectroscopy has been used to show that the crown ether moiety in the rotaxane undergoes acid-base and alkali metal cation dependent switch from binding at the ammonium cation position to cooperative binding to the metal cation at the oligo ethylene glycol site.     

Synthesis of Tripodal Naphthylacetamide Derivatives

A tripodal naphthylacetamide derivative (I and II) used as anew enhancement fluorescence chemical sensor for detection of transition metal ions has been synthesized in this work. Two new derivatives were prepared in good yields according to the proposed method. The products were characterized by elemental analysis, ¹H NMR spectra, and mass spectrometry (MS).