Noncovalent Interaction of Uridine 5′-Monophosphate with Adenosine, Cytidine, and Thymidine, as well as Adenosine 5′-Monophosphate and Cytidine 5′-Monophosphate in Aqueous Solution

Adduct formation has been studied in the systems of uridine 5′-monophosphate (UMP) with adenosine (Ado), cytidine (Cyd), thymidine (Thd), adenosine 5′-monophosphate (AMP), and cytidine 5′-monophosphate (CMP) by the potentiometric method with computer analysis of the data and ¹³C and ³¹P NMR spectroscopic measurements. It has been established that in the complexes identified, ion–dipole and dipole–dipole interactions occur with the positive reaction centers being protonated nitrogen atoms N(3) of UMP or Thd, and at low pH values, endocyclic nitrogen atoms of the other nucleosides and nucleotides, as e.g., in (UMP)H₂(Ado). The negative reaction centers are the high-electron density atoms N(1) and N(7) from Ado or AMP and N(3) from Cyd or CMP, and the phosphate group of the nucleotides studied, which already undergo partial deprotonation at low pH values. The NMR results have established the presence of noncovalent stacking-type interactions in certain molecular complexes, e.g., (UMP)H₂(AMP). The sites of ion–dipole or dipole–dipole interactions are generated as a result of deprotonation of the nucleosides and nucleotides in the pH range of formation of molecular complexes. Analysis of the equilibrium constants of the reaction allowed a determination of the effectiveness of the phosphate groups and donor atoms of heterocyclic rings in the process of molecular complex formation.     

Interference of Copper(II) ions with Non-covalent Interactions in Uridine or Uridine 5′-Monophosphate Systems with Adenosine,Cytidine, Thymidine and their Monophosphates in Aqueous Solution

Coordination reactions of copper(II) ions and their effect on non-covalent interactions in uridine (Urd) or uridine 5′-monophosphate (UMP) systems with nucleosides (Ado, Cyd, Thd) and nucleotides (AMP and CMP) in aqueous solutions have been studied. At high pH the effective coordination centers are deprotonated N(3) atoms from Urd and Thd, whereas at low pH, the N(3) atoms of pyrimidine nucleosides are blocked for coordination and the metallation sites are endocyclic nitrogen atoms from Ado, Cyd, AMP and CMP. Moreover, at low pH, the main reaction center in nucleotide solutions is the phosphate group. The NMR study has proven the occurrence of non-covalent ion-dipole interactions and stacking interactions in the systems considered. Introduction of a copper ion in the majority of systems causes the disappearance of weak interactions between ligands. The structures of the complexes in solution have been inferred from the equilibrium study: an analysis of the pH range of their occurrence with respect to the pH range of deprotonation of particular groups in the compounds studied, using Vis, EPR and ¹³C as well as ³¹P NMR spectral analysis.     

Ternary Complexes of La(III), Ce(III), Pr(III) or Er(III) with Adenosine 5′-mono, 5′-di,and 5′-triphosphate as Primary Ligands and some Biologically Important Zwitterionic Buffers as Secondary Ligands

Equilibrium constant measurements have been performed potentiometrically at (25±0.1) °C and an ionic strength I=0.1 mol⋅dm⁻³ KNO₃ for the interaction of La(III), Ce(III), Pr(III) and Er(III) with the purine nucleotides adenosine 5′-mono, 5′-di, and 5′-triphosphate and with the biologically relevant secondary ligand zwitterionic buffers 3-(cyclohexyl amino)-1-propanesulfonic acid (CAPS), 3-(cyclohexylamino)-2-hydroxy-1-propane sulfonic acid (CAPSO), N-tris(hydroxymethyl)methyl-3-aminopropanesulfonic acid (TAPS), 3-[N-bis(hydroxyethyl)amino]-2-hydroxypropanesulfonic acid (DIPSO), N,N-bis(2-hydroxyethyl)glycine (BICINE), and N-(2-acetamido)-2-iminodiacetic acid (ADA) in a 1:1:1 ratio. The formation of various 1:1:1 normal and protonated mixed-ligand complex species was inferred from the potentiometric pH titration curves. The experimental conditions were selected such that self-association of the purine nucleotides and their complexes was negligibly small; that is, the monomeric normal and protonated ternary complexes were studied. Initial estimates of the formation constants of the resulting species and the acid dissociation constants of adenosine 5′-mono-, 5′-di-, and 5′-triphosphate and the zwitterionic buffer secondary ligands were refined with the Superquade computer program. In some Ln(III) mixed-ligand systems, interligand interactions between the coordinating ligands, possibly involving H-bond formation, have been found to be the most important factors in deciding the stability of the mixed-ligand complexes in solutions. The thermodynamic ΔG° values of the monomeric normal and protonated ternary complexes were calculated and discussed.     

Synthesis,spectroscopic and thermal properties of Pt(II) complexes of some polydentate ligands

The new tetradentate symmetrical (2R,2′S)-1,1′-piperazine-1,4-diyldipropane-2-thiol) (L¹), (2S)-1-[bis(2-aminoethyl)amino]propan-2-ol) (L²), and 2-{(E)-[((1R,2S)-2-{[(1Z)-(2-hydroxy phenyl)methylene]amino}cyclohexyl)imino]methyl}phenol (L³) ligands were synthesized and characterized on the basis of FT-IR, ¹H, ¹³C NMR, EI mass, and elemental analysis. Three commercially available ligands, (2,2′-[ethane-1,2-diylbis(thio)]diethanol (L⁴), 2,2′-dithiodiethanenamine (L⁵), and (2,2′-[ethane-1,2-diyldi(imino)] diethanol (L⁶), were also studied. Pt(II) complexes were characterized by FTIR, elemental analysis and thermal methods. Thermal behaviors of these complexes were investigated in the range 10–1000 °C. Magnetic properties were also studied, and the all complexes were found to be diamagnetic. The structures consist of the monomeric units in which the Pt(II) atoms exhibit square planar geometry. N,N′-bis(salicylidene)-1,2-cyclohexane has been synthesized and characterized by X-ray single crystal diffraction measurement. The ligand crystallizes in monoclinic crystal system and space group, Cc.     

Equilibrium and spectroscopic studies of ternary cadmium(II) and mercury(II) complexes with CMP and triamines

Formation of ternary Cd(II) and Hg(II) complexes with cytidine 5′-monophosphate (CMP) and triamines has been studied. Complexes M(CMP)(H _x PA) and M(CMP)(PA) (M?=?Cd, Hg; PA?=?polyamine) were detected and overall stability constants and equilibrium constants for their formation determined. The mode of coordination in the complexes has been proposed on the basis of the equilibrium and ¹³C, ³¹P NMR and IR studies. In the Hg(II) systems, metalation involves the donor endocyclic N(3) atom, the CMP phosphate group and nitrogen donor atoms of PA. Relative to the Hg/CMP binary systems, the presence of a polyamine in ternary systems does not change the metal–nucleotide mode of coordination. In ternary systems including Hg(II) ions, the occurrence of noncovalent interactions has not been detected. Cd(II) ions form molecular complexes as well as protonated species. Introduction of a polyamine to the Cd/CMP system changes the coordination mode of the nucleotide. The phosphate group of CMP is inactive in binary complexes (metalation by the N(3) atom) but is involved in coordination in heteroligand species. In contrast to other polyamines studied, in the system including 1,7-diamino-4-azaheptane (3,3-tri), the phosphate group of CMP in Cd(CMP)(H3,3-tri) does not participate in metalation but is engaged in intramolecular noncovalent interactions that stabilize the complex.     

Estimation of the Effectiveness of the Phosphate Group in Binary Phosphoserine/Biogenic Amine Systems in Aqueous Solution

Adduct formation in the binary systems of O-phospho-L-serine with biogenic amines (putrescine, spermidine or spermine) has been investigated. The overall stability constants of the adducts and the equilibrium constants of their formation have been determined using computer analysis of potentiometric data. Ion-ion interactions have been established to occur in the identified molecular complexes. The potential reaction centers are phosphate, carboxylate and amine groups from phosphorylated serine as well as the –NH₃⁺ and –NH₂⁺– groups from polyamine. The pH range of adduct formation is found to coincide with that in which the polyamine is protonated (positive reaction center) and the phosphoserine is partly or totally deprotonated (negative reaction center). The stability of the molecular complexes formed in the studied systems depends on the acid-base character of the substrates and on the structure of the reacting molecules. Sites of interactions in the bioligands have been deduced on the basis of the results of the equilibrium study and analysis of the changes in the positions of signals in the ¹³C and ³¹P NMR spectra.     

Isoflavone glycosides from the bark of Amorpha fruticosa

Four known isoflavone glucosides have been isolated from the bark of Amorpha fruticosa, which is a traditional remedy plant, for the first time. They were elucidated as 3′-hydroxy-4′-methoxyisoflavone-7-O-β-D-glucopyranoside (1), 4′,6-dimethoxyisoflavone-7-O-β-D-glucopyranoside (2), 4′-methoxyisoflavone-7-O-β-D-glucopyranoside (3), and 3′,5-dihydroxy-4′-methoxyisoflavone-7-O-β-D-glucopyranoside (4), based on the UV, FT-IR, EIMS, FABMS, HREIMS, and NMR (¹H and ¹³C, DEPT, COSY, NOESY, HMQC, and HMBC) data. Published in Khimiya Prirodnykh Soedinenii, No. 4, pp. 336–338, July–August, 2006.     

Crystal structural characterization of three chlorosalicylato titanocene compounds

Abstract  Three chlorosalicylato titanocene compounds, namely [(MeCp)₂Ti(O,O′)(OCC₆H₃-5-Cl)]₂ (1), [(MeCp)₂Ti(O,O′)(OCC₆H₂-3,5-Cl₂)] (2) and [(MeCp)₂Ti(O,O′)(OCC₆H-3,5,6-Cl₃)] (3) have been synthesized via the reaction of (MeCp)₂TiCl₂ [MeCp = η⁵-(CH₃)C₅H₄] with the corresponding substituted chlorosalicylic acids in aqueous-organic systems in high yields and characterized by elemental analysis, IR and ¹H NMR spectra. Single-crystal X-ray diffraction analysis shows that geometries at titanium (IV) atoms are distorted tetrahedrons and the exhibited frameworks are constructed through weak interactions, which are H-bonding, π–π stacking and C–H···π interactions. Additional weak interactions, such as Cl···Cl interactions in compound 1, are also present, which help to form and stabilize crystalline materials. It is noticeable that the discriminating framework structures of three compounds due to their weak interactions existing conspicuous changes which result from the number of chlorine atoms on substituted chlorosalicylates. Graphical Abstract  Three to four coordinated chlorosalicylato titanocene compounds, [(MeCp)₂Ti(O,O′)(OCC₆H₃-5-Cl)]₂ (1), [(MeCp)₂Ti(O,O′)(OCC₆H₂-3,5-Cl₂)] (2) and [(MeCp)₂Ti(O,O′)(OCC₆H-3,5,6-Cl₃)] (3) have been synthesized in aqueous-organic system in high yields. Single-crystal X-ray diffraction analysis shows that geometries at titanium (IV) atoms are distorted tetrahedrons and the exhibited frameworks are constructed through weak interactions. The number of chlorine atoms on substituted chlorosalicylates has an effect on their framework structures.      

Equilibrium and NMR Studies of Noncovalent Interactions in Binary Systems: Uridine,Adenosine, Cytidine and Thymidine,and Adenosine (or Cytidine) 5′-Monophosphate in Aqueous Solution

The molecular complex formation reactions of uridine (Urd) with adenosine (Ado), cytidine (Cyd), thymidine (Thd), adenosine 5-monophosphate (AMP) and cytidine 5-monophosphate (CMP) have been studied at 20°C. It was found that the main positive noncovalent centers of ion–dipole and dipole–dipole type interactions are the protonated N(3) atoms of Urd, whereas the negative centers are the endocyclic atoms of the bases characterized by high electron density from the second molecule involved in the reaction. Moreover, NMR results indicate the occurrence of stacking in the complex (Urd)H(Cyd), whereas in the complex, (Urd)H₂(Thd), it is the only type of interaction. Deprotonation of the latter species brings about a change in the character of the reaction and ion–dipole interactions have been detected in the adduct, (Urd)H(Thd). Interestingly, no involvement of the phosphate groups in the formation of AMP and CMP adducts has been evidenced and the main centers of the reactions were found to be the N(7)and N(1) atoms of AMP, or the N(3) atoms of CMP and Urd. Moreover, in the Urd/CMP system the NMR results suggest stacking-type interactions.     

Isolation and characterization of a new flavone diglucoside from <Emphasis Type="Italic">Salix denticulata</Emphasis>

A new flavone diglucoside named 7,3′-dihydroxy-4′-methoxyflavone-5-O-β-D-glucopyranosyl (6″ → 1‴)-β-D-glucopyranoside (1), along with four known flavonoids, luteolin (2), isoquercetin (3), catechin (4), and diosmetin (5), has been isolated and characterized from Salix denticulata. The structure of the new flavone diglucoside was characterized by means of high field 1D and 2D NMR and MS spectral analysis.     

Another two novel ceramides from <Emphasis Type="Italic">Zephyranthes candida</Emphasis>

From the the bulbs of Zephyranthes candida (Amaryllidaceae), another two novel ceramides have been isolated and identified. The structures of the two novel compounds were established as (2S,3S,4R,21E,2′R)2-[N-(2′-hydroxynonadecanoyl)-N-(1′′,2′′-dihydroxyethyl)amino]-21-hexacosene-1,3,4-triol, named zephyranamide C (1), and 1,3,4,5,6-pentahydroxy-2-(2′-hydroxyhexacosanoyl-amino)-18-(E)-tetracosene, named zephyranamide D (2). Their structures and stereochemistries were elucidated by spectral techniques including ¹H NMR, ¹³C NMR, as well as HSQC, HMBC, DEPT, and COSY.     

Spectroscopic study of protonation of oligonucleotides containing adenine and cytosine

Acidobasic properties of purine and pyrimidine bases (adenine, cytosine) and relevant nucleosides (adenosine, cytidine) were studied by means of glass-electrode potentiometry and the respective dissociation constants were determined under given experimental conditions (I = 0.1 M (NaCl), t = (25.0 ± 0.1) °C): adenine (pK _HL = 9.65 ± 0.04, pK _H2L = 4.18 ± 0.04), adenosine (pK _H2L = 3.59 ± 0.05), cytosine (pK _H2L = 4.56 ± 0.01), cytidine (pK _H2L = 4.16 ± 0.02). In addition, thermodynamic parameters for bases: adenine (ΔH ⁰ = (−17 ± 4) kJ mol⁻¹, ΔS ⁰ = (23 ± 13) J K⁻¹ mol⁻¹), cytosine (ΔH ⁰ = (−22 ± 1) kJ mol⁻¹, ΔS ⁰ = (13 ± 5) J K⁻¹ mol⁻¹) were calculated. Acidobasic behavior of oligonucleotides (5′CAC-CAC-CAC3′ = (CAC)₃, 5′AAA-CCC-CCC3′ = A₃C₆, 5′CCC-AAA-CCC3′ = C₃A₃C₃) was studied under the same experimental conditions by molecular absorption spectroscopy. pH-dependent spectral datasets were analyzed by means of advanced chemometric techniques (EFA, MCR-ALS) and the presence of hemiprotonated species concerning (C⁺-C) a non-canonical pair (i-motif) in titled oligonucleotides was proposed in order to explain experimental data obtained according to literature.     

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.     

Investigations of the extraction equilibrium of ternary ion-association complexes of thallium(III) with ditetrazolium salts,neo-tetrazolium chloride and nitrobluetetrazolium chloride

The extraction equilibrium of ternary ion-association complexes formed between the tetrachloro complexes of thallium(III) and ditetrazolium salts, neotetrazolium chloride (NTC)[2,2′,5,5′-tetraphenyl-3-3′-(p-biphenylene)ditetrazolium chloride] and nitrobluetetrazolium chloride (NBT)[3,3′-dianizole-4,4′-bis-2-(4-nitrophenyl-5-phenyltetrazolium chloride], has been studied. As a result, the extraction constants, the distribution constants, the association constants, the distribution coefficients of thallium(III) and the extraction indicators R, have been calculated. The results have been evaluated statistically. The relative standard deviations S_r have been calculated at a statistical certainty of 95%. The ratio ditetrazolium salts/TlCl ₄ ⁻ =1∶2 has been confirmed once again.     

Non-Covalent Interaction in Binary Thymidine/Polyamine Systems in Aqueous Solution

Results of equilibrium and NMR spectral studies have shown the formation of molecular complexes in the systems of thymidine with polyamines—ethylenediamine, 1,3-diaminopropane, putrescine, 3-aza-1,5-diaminopentane, 3-aza-1,6-diaminohexane, 4-aza-1,7-diaminoheptane, spermidine, 4,8-diaza-1,11-diaminoundecane or spermine. The overall stability constants of the adducts and the equilibrium constants of their formation have been determined. Relative to adenosine or cytidine, the pH range of complex formation is shifted towards higher values, which is a consequence of a significantly higher basicity of thymine and corresponds well with the assumed model of ion-ion or ion-dipole interactions. The pH range of adduct formation is found to coincide with that in which the polyamine is protonated and the thymidine deprotonated. The -NH₃⁺ groups from polyamine and the N(3) atom from thymidine have been identified as the centers of noncovalent interactions. The stability of the molecular complexes formed in the studied systems depends on the acid-base character of the substrates and on the structure of the reacting molecules.     

Fluxional rearrangement in congested ruthenium(II) complexes containing pyrimidine- and/or pyridine-based dithioether ligands

The solvento species obtained by the treatment of cis-RuCl₂(N,N-L)₂ [L = di-2-pyridyl sulfide (dps), di-2-pyrimidyl sulfide (dprs)] with AgPF₆, reacted with dithioethers L′ [L′ = 2,6-bis(2-pyridylthiomethyl)pyridine (pytmp), 2,6-bis(2-pyrimidylthiomethyl)pyridine (prtmp) and 2,6-bis{2-(4-methyl)pyrimidylthiomethyl} pyridine (mprtmp)] to afford the compounds [Ru(N,N-L)₂(N,S-L′)][PF₆]₂. The ¹H NMR spectra indicate that L′ is chelated through S and N atoms with the formation of a four-membered ring. As a consequence, the ruthenium and sulfur atoms are stereogenic centers with ∆ and Λ and (R) and (S) configurations, respectively. NMR spectra, at low temperatures, show that two invertomers, of similar abundance, as enantiomeric couples ∆S, ΛR and ∆R, ΛS are present. In the methylene region, four AB systems are observed that in both the species contain two non-equivalent methylene groups. Variable-temperature NMR spectra and EXSY experiments show that the sulfur inversion produces an exchange between the invertomers. The one-dimensional band-shape analysis of the exchanging methylene signals showed that the energy barriers for the process are in the 43–52 kJ mol⁻¹ range. The possible mechanisms of the sulfur inversion are discussed.     

Equilibrium and <Superscript>1</Superscript>H NMR Kinetic Study of the Reactions of Dichlorido [S-Methyl-L-Cysteine(N,S)]Platinum(II) Complex with Some Relevant Biomolecules

The formation equilibria of the [Pt(SMC)(H₂O)₂]⁺ complex with some biologically relevant ligands such as L-methionine (L-met) and glutathione (GSH) were studied. The stoichiometry and stability constants of the formed complexes are reported, and the concentration distribution of the various complex species has been evaluated as a function of pH. The reaction between [PtCl₂(SMC)] and guanosine-5′-monophosphate (5′-GMP) was studied by ¹H NMR spectroscopy. The NMR spectra indicated that first step is the hydrolysis of the [PtCl₂(SMC)] complex and second step is the substitution of an aqua ligand, either in the cis or trans position with guanosine-5′-monophosphate in molar ratio 1:1. The values of rate constant showed faster substitution of coordinated H₂O in the trans position to the S donor atom of S-methyl-L-cysteine, whereas the slower reaction was assigned to the displacement of the cis coordinated aqua molecule. This is due to the strong trans labilization effect of coordinated sulfur. Electronic Supplementary Material  The online version of this article () contains supplementary material, which is available to authorized users.     

Binding of Benzyltrimethylammonium Bromide and its Alkyldimethylbenzylammonium Homologues by β-Cyclodextrin in Water

The binding constants, K′, for the reaction between some alkyldimethylbenzylammonium bromide homologues (alkyl = methyl, ethyl, propyl, butyl, hexyl, decyl, and dodecyl, respectively) and β-cyclodextrin in water at 25.0 ± 0.1 ^∘C have been determined, by applying the spectral displacement technique with phenolphthalein as the displacing anion. It has been shown that the ln K′ values increase linearly with the number of carbon atoms in the alkyl chain for the salts whose alkyl chain has at least four carbon atoms. The ln K′ values estimated for the parent compound benzyltrimetylammonium bromide and its two nearest homologues are distinctly lower than might be expected by extrapolation of the linear relation found for the higher homologues. Assuming that it is the organic cation that undergoes association with β-cyclodextrin, then one may suppose that a change occurs in the mode of inclusion of the cation upon passing to higher homologues. In the case of the lighter homologues, it is the phenylene group that undergoes inclusion. This model of inclusion is confirmed by analysis of rotating-frame overhauser effect spectroscopy (ROESY) spectra.     

Laws of complex formation in a series of azo-substituted pyrocatechol derivatives and their tin(II) complexes

Physicochemical properties of new reagents, azo-substituted pyrocatechol derivatives and their tin(II) complexes, are studied. The acid-base properties of the hydroxy groups (pK′_i, pK″_i), parameters of complex formation reactions (pH, temperature, time), and instability constants of the complexes formed (pK _i) are determined. Quantitative correlations between the dissociation constants (pK′_a) of the functional analytical group, and the electronic Hammett constant σ for a substituent (pK′_a-pH₅₀ of the complex formation reaction), as well as between pK′_a and instability constants of the complexes (pK _a), are established. The quantitative correlations established allow the prediction of the physicochemical properties of the reagents and tin(II) complexes with new reagents of this class with the same functional analytical group (FAG) but other substituents.     

New glycosidic and other constituents from hulls of <Emphasis Type="Italic">Oryza sativa</Emphasis>

Three new compounds, 4-hydroxymethylene-7-(9,9,13-trimethylcyclohexyl)-heptanyl-3′,7′,7′-trimethylcyclohexa-2′,4′-dien-1′-oate (1), 1-(n-hexadec-7-enoxy)-6-(n-octadecanoxy)-β-D-glucopyranoside (2), and (Z)-12-hydroxy-9-octadecenoic acid-12-β-D-glucopyranoside (3), along with the known compound hexacosanoic acid (4), were isolated and identified from the rice hulls of Oryza sativa. Their structures were elucidated by 1D and 2D NMR spectroscopic techniques (¹H-¹H COSY, ¹H-¹³C HETCOR, DEPT) aided by EIMS, FABMS, HRFABMS, and IR spectra. Published in Khimiya Prirodnykh Soedinenii, No. 4, pp. 344–347, July–August, 2007.