1H NMR study of complexation of ethidium bromide with single-stranded noncomplementary desoxytetranucleotide 5′-d(GpApApG) in aqueous solution

Complication of the ethidium bromide dye (3,8-diamino-6-phenyl-5-ethylphenanthridine) with single-stranded noncomplementary desaxytetranucleotide 5′-d(GpApApG) in aqueous salt solution was studied by one- and two-dimensional¹H NMR (500 and 600 MHz). The concentration dependences of the proton chemical shifts of the reactant molecules were measured at different temperatures (T₁ = 298 K, T₂ = 308 K). Investigations of self-association of the tetranucleotide showed that duplices can hardly form in solution. Therefore, dye complexes with single-stranded tetranucleotide play a major role in the equilibrium in solution; this makes it possible to analyze the specifics of interactions of aromatic ligands with single-stranded DNA. Various schemes of complexation are discussed; the equilibrium constants and the limiting values of the proton chemical shifts of ethidium bromide in the complexes are determined. The constants of dye binding to the single-stranded tetranucleotide 5′-d(GAAG) involving only purine bases is approximately an order of magnitude lower than the constants of ethidium bromide complexation with desaxytetranucleotide monomers whose sequences contain alternating types of base in the chain. The relative contents of complexes of different types are analyzed, and peculiarities of dynamic equilibrium, depending on the ratio of concentrations between the dye and the tetranucleotide, are revealed. Based on the data obtained it is concluded that the binding between ethidium bromide and the single-stranded nucleotide is sequence-specific. The estimated values of the induced chemical shifts of the dye protons are used to establish the most probable structures of the 1:1 and 2:1 complexes of ethidium bromide with single-stranded desaxytetranucleotide. Translated fromZhumal Struktumoi Khimii, Vol. 39, No. 5, pp. 808–820, September–October, 1998. This work was supported by INTAS grant NUD 7200.     

Coordination properties of N,O-carboxymethyl chitosan (NOCC). Synthesis and equilibrium studies of some metal ion complexes. Ternary complexes involving Cu(II) with (NOCC) and some biorelevant ligand

In the present study, the acid-base equilibria of N,O-carboxymethy chitosan abbreviated as (NOCC), is investigated. The complex formation equilibria with the metal ions Cu^(II), Ni^(II), Co^(II), Mn^(II), and Zn^(II) are investigated potentiometrically. The stability constant values of the binary and ternary complexes formed in solution were determined and the binding centers of the ligands were assigned. The relationships between the properties of the studied central metal ions as ionic radius, electronegativity, atomic number, and ionization potential, and the stability constants of the formed complexes were investigated in an effort to give information about the nature of chemical bonding in complexes and make possible the calculation of unknown stability constants. Cu^(II), Ni^(II), and U^(VI) complexes with NOCC are isolated as solid complexes and characterized by conventional chemical and physical methods. The structures of the isolated solid complexes are proposed on the basis of the spectral and magnetic studies. The ternary copper(II) complexes involving NOCC and various biologically relevant ligands containing different functional groups, as amino acids and DNA constituents are investigated. The stability constants of the complexes are determined and the concentration distribution diagrams of the complexes are evaluated.     

Multiple Multidentate Halogen Bonding in Solution,in the Solid State,and in the (Calculated) Gas Phase

The binding properties of neutral halogen‐bond donors (XB donors) bearing two multidentate Lewis acidic motifs toward halides were investigated. Employing polyfluorinated and polyiodinated terphenyl and quaterphenyl derivatives as anion receptors, we obtained X‐ray crystallographic data of the adducts of three structurally related XB donors with tetraalkylammonium chloride, bromide, and iodide. The stability of these XB complexes in solution was determined by isothermal titration calorimetry (ITC), and the results were compared to X‐ray analyses as well as to calculated binding patterns in the gas phase. Density functional theory (DFT) calculations on the gas‐phase complexes indicated that the experimentally observed distortion of the XB donors during multiple multidentate binding can be reproduced in 1:1 complexes with halides, whereas adducts with two halides show a symmetric binding pattern in the gas phase that is markedly different from the solid state structures. Overall, this study demonstrates the limitations in the transferability of binding data between solid state, solution, and gas phase in the study of complex multidentate XB donors.     

Hydrogen Bonding versus Halogen Bonding: Spectroscopic Investigation of Gas-Phase Complexes Involving Bromide and Chloromethanes

Hydrogen bonding and halogen bonding are important non-covalent interactions that are known to occur in large molecular systems, such as in proteins and crystal structures. Although these interactions are important on a large scale, studying hydrogen and halogen bonding in small, gas-phase chemical species allows for the binding strengths to be determined and compared at a fundamental level. In this study, anion photoelectron spectra are presented for the gas-phase complexes involving bromide and the four chloromethanes, CH₃Cl, CH₂Cl₂, CHCl₃, and CCl₄. The stabilisation energy and electron binding energy associated with each complex are determined experimentally, and the spectra are rationalised by high-level CCSD(T) calculations to determine the non-covalent interactions binding the complexes. These calculations involve nucleophilic bromide and electrophilic bromine interactions with chloromethanes, where the binding motifs, dissociation energies and vertical detachment energies are compared in terms of hydrogen bonding and halogen bonding.     

1H NMR spectroscopic investigation of β-cyclodextrin inclusion compounds with parecoxib

The inclusion complexes of β-CD and parecoxib [PRB] in aqueous solution were investigated using ¹H NMR spectroscopic study revealed the existence of four different equilibria for 1:1 inclusion complexes in which both the aromatic rings of the guest are tightly held by the host cavity. The NMR spectra of the PRB studied in the presence of β-CD are fully assigned and interpreted by means of COSY spectrum for the unambiguous assignment of guest aromatic ring protons. The parallel interpretation of β-CD chemical shift changes and dipolar contacts, with the aid of 2D ROESY, allows the mode of binding to be established for four possible structures of 1:1 PRB-β-CD inclusion complexes.     

1H NMR study of the interaction between ethidium bromide and self-complementary and self-complementary deoxytetranucleotide 5′-d(CpGpCpG) in an aqueous solution

Complexation of the ethidium bromide (3,8-diamino-6-phenyl-5-ethylphenanthridine) dye with self-complementary deoxytetraribonucleoside triphosphate 5′-d(CpGpCpG) in a water-salt solution is studied by one- and two-dimensional¹H NMR spectroscopy (500 MHz). Two-dimensional PMR spectroscopy (2D-COSY and 2D-NOESY) is used for the full assignment of proton signals of the molecules in the solution and for the qualitative analysis of the interaction between ethidium bromide and the tetranucleotide. The concentration dependences of the proton chemical shifts of the molecules at a fixed temperature (T=308 K) are measured. Different schemes of the formation of the dye complexes with the tetranucleotide, taking into account various molecular associations in the solution are considered. The equilibrium constants of the reactions and the limiting chemical shifts of ethidium bromide protons in the complexes are determined. The relative contents of different complexes in the solution are analyzed, and the dynamic equilibrium is studied as a function of the dye-tetranucleotide ratio in the solution. The data obtained suggest that ethidium bromide (like the acridine dye proflavine) is intercalated predominantly into the pyrimidine-purine sections (CG sites) of the tetranucleotide duplex. However, ethidium bromide is intercalated on the side of the narrow slot of the duplex, while proflavine intercalation occurs through the broad slot of the double helix. The most likely structures of the 1∶2 and 2∶2 dye-tetranucleotide complexes in the solution are constructed using the calculated values of the induced chemical shifts of ethidium bromide protons and 2D NOESY spectroscopy data. Sevastopol State Technical University. Berkbeck College, London University. Translated fromZhurnal Strukturnoi Khimii, Vol. 37, No. 1, pp. 75–87, January–February, 1996. Translated by I. Izvekova     

N-Heterocyclic carbene adducts of orthopalladated triarylphosphite complexes

Carbene adducts of orthopalladated triarylphosphite complexes have been synthesised and characterised. The structures of three of these complexes were determined by single-crystal X-ray analysis. The complexes are active in the Suzuki coupling of a range of aryl bromide substrates.     

Analysis of the interaction of ethidium bromide with a DNA octamer 5’-d(GpApCpApTpGpTpC) in aqueous solution using1H NMR data

Complexation of a phenanthridine dye ethidium bromide with a desoxyoligonucleotide 5’-d(GpApCpAp-TpGpTpC) in aqueous salt solution is studied by one- and two-dimensional¹H NMR spectroscopy. Two-dimensional correlated homonuclear PMR spectroscopy (2D-TOCSY and 2D-N0ESY) was used for complete assignment of the proton signals of molecules in solution and for qualitative analysis of the character of interaction between ethidium bromide and desoxyoctanucleotide. The concentration dependences of the proton chemical shifts of the molecules were measured at three temperatures (T₁ = 298 K, T₂ = 308 K, and T₃ = 318 K); the temperature dependences were measured in the temperature range 278–358 K. Different schemes of dye complexation with an octamer duplex involving different molecular associates in solution are considered. The equilibrium constants of the reactions, the corresponding thermodynamic parameters (δH⁰, δS₀), and the limiting values of the chemical shifts of ethidium bromide protons in the complexes are determined. The relative contents of complexes of different types in solution (dye complexes with desoxyoctanucleotide in duplex form) are analyzed, and peculiarities of the dynamic equilibrium depending on the ratio of dye and octamer concentrations and temperature are established. The most probable structures of the 1:2 and 2:2 intercalated complexes corresponding to dye intercalation into the pyrimidine-purine sites of the desoxyoctanucleotide duplex are derived using the calculated values of the induced proton chemical shifts of ethidium bromide and two-dimensional PMR data. Translated fromZhurnal Strukturnoi Khimii, Vol.40, No. 2, pp. 265–275, March–April, 1999.     

Coordination properties of hydralazine Schiff base Synthesis and equilibrium studies of some metal ion complexes

In the present study, a new ligand is prepared by condensation of hydralazine (1-Hydralazinophthalazine) with 2-butanon-3-oxime. The acid-base equilibria of the schiff-base and the complex formation equilibria with the metal ions as Cu(II), Ni(II), Co(II), Cd(II), Mn(II) and Zn(II) are investigated potentiometrically. The stability constants of the complexes are determined and the concentration distribution diagrams of the complexes are evaluated. The effect of metal ion properties as atomic number, ionic radius, electronegativity and ionization potential are investigated. The isolated solid complexes are characterized by conventional chemical and physical methods. The potential coordination sites are assigned using the i.r. and (1)H NMR spectra. The structures of the isolated solid complexes are proposed on the basis of the spectral and magnetic studies.     

Calix[4]pyrrole: a new ion-pair receptor as demonstrated by liquid-liquid extraction

Solvent-extraction studies provide confirming evidence that meso-octamethylcalix[4]pyrrole acts as an ion-pair receptor for cesium chloride and cesium bromide in nitrobenzene solution. The stoichiometry of the interaction under extraction conditions from water to nitrobenzene was determined from plots of the cesium distribution ratios vs cesium salt and receptor concentration, indicating the formation of an ion-paired 1:1:1 cesium:calix[4]pyrrole:halide complex. The extraction results were modeled to evaluate the equilibria inherent to the solvent-extraction system, with either chloride or bromide. The binding energy between the halide anion and the calix[4]pyrrole was found to be about 7 kJ/mol larger for cesium chloride than for the cesium bromide. The ion-pairing free energies between the calix[4]pyrrole-halide complex and the cesium cation are nearly the same within experimental uncertainty for either halide, consistent with a structural model in which the Cs+ cation resides in the calix bowl. These results are unexpected since nitrobenzene is a polar solvent that generally leads to dissociated complexes in the organic phase when used as a diluent in extraction studies of univalent ions. Control studies involving nitrate revealed no evidence of ion pairing for CsNO3 under conditions identical to those where it is observed for CsCl and CsBr.     

Platinum-modified adenines: unprecedented protonation behavior revealed by NMR spectroscopy and relativistic density-functional theory calculations

Two novel Pt(IV) complexes of aromatic cytokinins with possible antitumor properties were prepared by reaction of selected aminopurines with K(2)PtCl(6). The structures of both complexes, 9-[6-(benzylamino)purine] pentachloroplatinate (IV) and 9-[6-(furfurylamino)purine] pentachloroplatinate (IV), were characterized in detail by using two-dimensional NMR spectroscopy ((1)H, (13)C, (15)N, and (195)Pt) in solution and CP/MAS NMR techniques in the solid state. We report for the first time the X-ray structure of a nucleobase adenine derivative coordinated to Pt(IV) via the N9 atom. The protonation equilibria for the complexes in solution were characterized by using NMR spectroscopy (isotropic chemical shifts and indirect nuclear spin-spin coupling constants) and the structural conclusions drawn from the NMR analysis are supported by relativistic density-functional theory (DFT) calculations. Because of the presence of the Pt atom, hybrid GGA functionals and scalar-relativistic and spin-orbit corrections were employed for both the DFT calculations of the molecular structure and particularly for the NMR chemical shifts. In particular, the populations of the N7-protonated and neutral forms of the complexes in solution were characterized by correlating the experimental and the DFT-calculated NMR chemical shifts. In contrast to the chemical exchange process involving the N7-H group, the hydrogen atom at N3 was determined to be unexpectedly rigid, probably because of the presence of the stabilizing intramolecular interaction N3-H···Cl. The described methodology combining the NMR spectroscopy and relativistic DFT calculations can be employed for characterizing the tautomeric and protonation equilibria in a large family of transition-metal-modified purine bases.     

Non-steroidal antiinflammatory drug-copper(II) complexes: structure and biological perspectives

Copper(II) complexes with the non-steroidal antiinflammatory drug mefenamic acid in the presence of aqua or nitrogen donor heterocyclic ligands (2,2'-bipyridine, 1,10-phenanthroline, 2,2'-bipyridylamine or pyridine) have been synthesized and characterized. The crystal structures of [(2,2'-bipyridine)bis(mefenamato)copper(II)], 2, [(2,2'-bipyridylamine)bis(mefenamato)copper(II)], 4, and [bis(pyridine)bis(methanol)bis(mefenamato)copper(II)], 5, have been determined by X-ray crystallography. UV study of the interaction of the complexes with calf-thymus DNA (CT DNA) has shown that the complexes can bind to CT DNA and [bis(aqua)tetrakis(mefenamato)dicopper(II)] exhibits the highest binding constant to CT DNA. The cyclic voltammograms of the complexes in the presence of CT DNA solution have shown that the complexes can bind to CT DNA by the intercalative binding mode verified also by DNA solution viscosity measurements. Competitive studies with ethidium bromide (EB) indicate that the complexes can displace the DNA-bound EB suggesting strong competition with EB. Mefenamic acid and its complexes exhibit good binding propensity to human or bovine serum albumin protein having relatively high binding constant values. All the compounds have been tested for their antioxidant and free radical scavenging activity as well as for their in vitro inhibitory activity against soybean lipoxygenase showing significant activity.     

Binding of anthraquinone dyes by polyion complexes consisting of a piperidinium cationic polymer and various polyanions in aqueous solution

The extent of binding of 1-amino-4-alkylaminoanthraquinone-2-sulfonates (alkyl?methyl, ethyl, propyl, and butyl), which have different chemical structures from methyl orange derivatives, by polyion complexes consisting of a piperidinium cationic polymer and various polyanions such as sodium poly acrylate, poly methacrylate, poly styrenesulfonate, carboxymethylcellulose, and dextran sulfate, was measured in an aqueous solution. The effect of alkyl group of the anthraquinone dye on the binding behavior was investigated. Also, the resultant binding characteristics were compared with those previously observed with methyl orange and its homologs. These polyion complexes exhibited very strong binding affinity toward the anthraquinone dye. The polyion complex of the polycation and sodium poly styrenesulfonate bound the dye noncooperatively and the binding process was athermal. The first binding constant accompanying the binding is of the order of 10⁵–10⁶. In contrast, the polyion complexes composed of the polycation and the other polyanions exhibited strong cooperative binding and the binding process was exothermic. The possible mode of binding is discussed.     

Interaction of Zn(II) with quinolone drugs: structure and biological evaluation

Zinc complexes with the third-generation quinolone antibacterial drugs levofloxacin and sparfloxacin have been synthesized and characterized. The deprotonated quinolones act as bidentate ligands coordinated to zinc ion through the pyridone and a carboxylato oxygen atom. The crystal structures of [bis(aqua)bis(levofloxacinato)zinc(II)], 1, and [bis(sparfloxacinato)(1,10-phenanthroline)zinc(II)], 3, have been determined by X-ray crystallography. The biological activity of the complexes has been evaluated by examining their ability to bind to calf-thymus DNA (CT DNA) by UV spectroscopy and viscosity measurements. UV studies of the interaction of the complexes with DNA have revealed that they can bind to CT DNA probably by the intercalative binding mode which has also been verified by DNA solution viscosity measurements. The DNA binding constants have been also calculated. A competitive study with ethidium bromide (EB) showed that the complexes exhibit the ability to displace the DNA-bound EB indicating that they bind to DNA in strong competition with EB for the intercalative binding site. The interaction of the complexes with human and bovine serum albumin proteins has been studied by fluorescence spectroscopy showing that the complexes exhibit good binding propensity to these proteins having relatively high binding constant values. The biological properties of the complexes have been evaluated in comparison to the previously reported Zn(II) complexes with the first- and second-generation quinolones oxolinic acid and enrofloxacin.     

Recognition of anions by protonated methylazacalixpyridines

Methylazacalixpyridines are a unique kind of macrocyclic molecules that are able to self-regulate their conformations to best fit the guests. They had shown good recognition to both neutral molecules such as diols and fullerenes and cations. After protonation, the conformation of methylazacalixpyridines became more flexible and could serve as receptors for anions. In the solution, the protonated methylazacalix[2]pyridine[2]arene formed complexes with halides yielding biding constants of 79 (mol/L)⁻¹ for chloride, 10 (mol/L)⁻¹ for bromide, and 79 (mol/L)⁻¹ for iodide, respectively. The crystal structures of the complexes between protonated methylazacalix[4]pyridine (MACP-4), methylazacalix[2]pyridine[2]arene (MACP-2-A-2), and iodide anion showed a multiple interaction mode including electrostatic attraction, hydrogen bonding, and anion-π interaction     

Bridged bis(beta-cyclodextrin)s possessing coordinated metal center(s) and their inclusion complexation behavior with model substrates: enhanced molecular binding ability by multiple recognition.

To investigate quantitatively the cooperative binding ability of several beta-cyclodextrin oligomers bearing single or multiligated metal center(s), the inclusion complexation behavior of four bis(beta-cyclodextrin)s (2-5) linked by 2,2'-bipyridine-4,4'-dicarboxy tethers and their copper(II) complexes (6-9) with representative dye guests, i.e., methyl orange (MO), acridine red (AR), rhodamine B (RhB), ammonium 8-anilino-1-naphthalenesulfonic acid (ANS), and sodium 6-(p-toludino)-2-naphthalenesulfonate (TNS), have been examined in aqueous solution at 25 degrees C by means of UV-vis, circular dichroism, fluorescence, and 2D NMR spectroscopy. The results obtained indicate that bis(beta-cyclodextrin)s 2-5 can associate with one or three copper(II) ion(s) producing 2:1 or 2:3 bis(beta-cyclodextrin)-copper(II) complexes. These metal-ligated oligo(beta-cyclodextrin)s can bind two model substrates to form intramolecular 2:2 host-guest inclusion complexes and thus significantly enhance the original binding abilities of parent beta-cyclodextrin and bis(beta-cyclodextrin) toward model substrates through the cooperative binding of two guest molecules by four tethered cyclodextrin moieties, as well as the additional binding effect supplied by ligated metal center(s). Host 6 showed the highest enhancement of the stability constant, up to 38.3 times for ANS as compared with parent beta-cyclodextrin. The molecular binding mode and stability constant of substrates by bridged bis- and oligo(beta-cyclodextrin)s 2-9 are discussed from the viewpoint of the size/shape-fit interaction and molecular multiple recognition between host and guest.     

Mutual induced fit in cyclodextrin-rocuronium complexes

The binding of rocuronium bromide to 6-perdeoxy-6-per(4-carboxyphenyl)thio-gamma-cyclodextrin sodium salt, displays biphasic behaviour characteristic of the formation of a binary and 2 : 1 ternary guest-host complex in aqueous solution. Thermodynamic and structural data on this sequential complexation process can be rationalised within a single model involving switching of the conformational equilibria of both the rocuronium bromide and cyclodextrin molecules. Isothermal titration calorimetry (ITC), NMR and fluorescence experiments in solution, together with X-ray crystallography and molecular modelling, suggest that in order to induce encapsulation both rocuronium bromide and the modified cyclodextrin undergo conformational changes. Ring A of rocuronium bromide 'switches' from the more sterically encumbered chair to the sterically less demanding twist-boat, whilst the modified cyclodextrin "opens" its cavity to allow the steroid to enter. The recognition and mutual induced fit between cyclodextrin and steroid represents a classic example of dynamic host-guest chemistry.     

Synthesis and X-ray Structures of Novel Macrocycles and Macrobicycles Containing N,N-Di(pyrrolylmethyl)-N-methylamine Moiety: Preliminary Anion Binding Study

The [2 + 2] Schiff base condensation reactions between the newly synthesized dialdehyde, N,N-di(α-formylpyrrolyl-α-methyl)-N-methylamine), and ethylenediamine or p-phenylenediamine dihydrochloride readily afforded the 30- and 34-membered large size macrocycles in very high yields. Subsequent reduction reactions of these macrocycles with NaBH(4) gave the corresponding saturated macrocyclic hexaamines in good yields. The analogous reaction of the new dialdehyde with a triamine molecule afforded the [3 + 2] Schiff base macrobicycle in high yield, which was then reduced by reaction with NaBH(4) to give the saturated macrobicycle. All these compounds were characterized by spectroscopic methods. The anion binding properties of the saturated macrocycles having the ethylene and the phenylene linkers in CDCl(3) were studied by NMR titration methods. Although they have similar pyrrolic and amine NH groups their binding properties are different and interesting, owing to the conformational flexibility or rigidness rendered by the ethylene or phenylene groups, respectively. The macrocycle having the ethylene linkers binds anions in a 1:1 fashion, while the other receptor having the phenylene linkers prefers to bind anions in a sequential 1:2 fashion and has a multiple equilibria between a 1:1 and a 1:2 complexes, as shown by their binding constants, curve fittings by EQNMR, and Job plots. The X-ray structures of the 1:2 methanol, the aqua and the benzoate anion complexes of the macrocycles show two cavities in which the guests are bound, correlating with the high affinity found for the formation of stable 1:2 complexes in solution. The X-ray structure showed that the macrobicycle Schiff base adopts an eclipsed paddle-wheel shaped conformation and exhibits an out-out configuration at the bridgehead nitrogen atoms.     

A comparative study of aluminum(III), gallium(III), indium(III), and thallium(III) binding to human serum transferrin

Group 13 cations exhibit an essentially similar chemical behavior in aqueous solution. Under physiological conditions these cations exist as metal complexes. They are known to bind tightly to human serum transferrin in the blood. Here, the numerous published studies on the interactions of Group 13 metals with transferrin are reviewed, particular attention being given to the comparative analysis of the binding constants and to the kinetics and mechanisms of metal ion uptake and release. The structural and functional information obtained on these metallotransferrins by advanced physicochemical methods, such as NMR spectroscopy, is presented in light of the recent crystal structures of ferric- and apotransferrin. The biological consequences of binding of aluminum(III), gallium(III) and indium(III) to transferrin are discussed in relation to the relevant roles played by these metal ions in pharmacology and toxicology.     

Estimation of Pitzer's ion interaction parameters for electrolytes involved in complex formation using a chemical equilibrium model

Pitzer's ion interaction model has been widely accepted for calculating the thermodynamic properties for electrolytes at high ionic strength. For weak electrolytes, a better estimation can be obtained by combining the model with chemical equilibria. The method of calculation is to treat each individual species as a single, separated ion. The concentration of each ion will be constrained by the mass balance equation and its activity will be guarded by the stability constants. Including chemical equilibria in Pitzer's model provides not only a better estimation of the thermodynamic properties of weak electrolytes but also a better understanding of the equilibrium among the complexes. The results may be used for correcting the effect from high ionic strength solution when determining the stability constants. When considering chemical equilibria, some of the parameters reported by Pitzer may have to be reestimated. The method of estimation and comparison between final results are presented. The binary system of HF, and the ternary systems of CuCl₂ in NaCl and in HCl are used for demonstration.