1H NMR Analysis of Heteroassociation of Caffeine with Mitoxanthrone in Aqueous Solution

Heteroassociation of caffeine (CAF) with the antibiotic mitoxanthrone (novatrone, NOV) in aqueous solution was studied by one-dimensional (1D) and two-dimensional (2D) ¹H NMR spectroscopy (500 MHz). The concentration and temperature dependences of the proton chemical shifts of the molecules in aqueous solution have been measured. The equilibrium constants of heteroassociation between CAF and NOV and the limiting proton chemical shifts of the aromatic ligands of the associates have been determined. The most plausible structure of the 1:1 CAF–NOV heterocomplex in aqueous solution was inferred from the calculated values of the induced proton chemical shifts and quantum-mechanical screening curves for CAF and NOV. The thermodynamic parameters of the formation of the CAF–NOV heterocomplex have been calculated. The relatively high heteroassociation constant (K = 256 ± 31 M^–1, T = 318 K), the positive value of entropy for heteroassociation [ S = 15.3 ± 4.0 J/(moleK)], and the structural features of the chromophore of the novatrone molecule indicate that hydrophobic interactions play a significant role in stabilization of the CAF–NOV heterocomplex.     

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.     

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.     

Investigation of the association of aromatic dyestuff molecules in aqueous solution by1H NMR

We have studied experimentally the proton chemical shifts of the molecules of Acridine Orange and proflavine in aqueous solution as a function of the.concentration of the aromatic ligands. A method is proposed for determining the chemical shifts of the protons in associations from the observed concentration dependence of the proton chemical shifts of dyestuff molecules in solution, which can be used at fairly high concentrations of the interacting molecules. The association constants of the dyestuff molecules and the proton chemical shifts in the association have been calculated. The proton shifts obtained have been used toether with a model of the ring currents to determine the most probable structure for the 1:1 molecular complexes of Acridine Organce and proflavine in aqueous solution.Sevastopol Institute for Instrument Construction. Translated from Teoreticheskaya i Éksperimental'naya Khimiya, No. 1, pp. 83–89, January–February, 1991. Original article submitted February 2, 1988.     

Structural and Thermodynamic Analysis of Self-Association of Phenanthridine Dyes in Aqueous Solution by 1H NMR Spectroscopy

Self-association of phenanthridine dyes (ethidium monoazide EMB and ethidium diazide EDC) in aqueous solution was studied by one- and two-dimensional ¹H NMR (500 MHz). 2D-TOCSY and 2D-ROESY experiments were used for signal assignment of the dye protons. The concentration and temperature dependences of the chemical shifts of the nonexchangeable protons of EMB and EDC in aqueous solution have been measured. The experimental results were analyzed based on the infinitely dimensional noncooperative and cooperative models of self-association of molecules. The cooperativity parameter, the equilibrium constants, and the enthalpies and entropies of self-association of the dyes were calculated along with the limiting chemical shifts of EMB and EDC protons in the associates. The cooperativity parameter 1 indicates that association of phenanthridine dye molecules in aqueous solution is not a cooperative process. The presence of azido groups in the phenanthridine chromophore diminishes the equilibrium constant and the enthalpy of formation of dye aggregates in aqueous solution. The most plausible structures of EMB and EDC dimers in aqueous solution were derived from the induced proton chemical shifts of the dyes. In the dimer complexes of EMB and EDC, the distances between the planes of the aromatic chromophores are longer than those in the dimer of ethidium bromide due to electrostatic repulsion of the dipole azido groups in the phenanthridine chromophores of the dyes.     

Structural and thermodynamic analysis of heteroassociation of daunomycin and flavin mononucleotide molecules in water by <Superscript>1</Superscript>H NMR spectroscopy

Heteroassociation of the antitumor antibiotic daunomycin (DAU) with flavin mononucleotide (FMN) has been investigated by one-and two-dimensional ¹H NMR spectroscopy (500 MHz) in a water solution to determine the molecular mechanism of the combined action of the antibiotic and vitamin in the FMN-DAU system. The equilibrium constants of the reactions, induced proton chemical shifts, and thermodynamic parameters (ΔH, ΔS) of heteroassociation were determined from the concentration and temperature dependences of the proton chemical shifts in the interacting aromatic molecules. Analysis of the results indicate that heterocomplexes of riboflavin mononucleotide and daunomycin are formed due to stacking interactions between aromatic chromophores. The most probable spatial structure of the 1:1 DAU-FMN heterocomplex was determined by the molecular dynamics method using the X-PLOR program and the results of the analysis of the induced proton chemical shifts in molecules. Calculation of the relative content of self-and hetero-complexes of daunomycin for different values of the ratio (r) between the concentrations of flavin mononucleotide and daunomycin demonstrated that for r > 3, the contribution of DAU-FMN heterocomplexes to the equilibrium distribution of associates in aqueous solution is dominant. It is concluded that the aromatic molecules of vitamins, in particular, riboflavin, can form energetically strong heteroassociates with antitumor antibiotics in water solution and can thereby affect their medical and biological activity.     

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     

Complexation of the antibiotic daunomycin with desoxytetraribonucleoside triphosphate 5’-d(CpGpCpG) in aqueous solution

This paper presents the results of our study of the complexation of the antibiotic daunomycin with desoxytetranucleotide 5’-d(CpGpCpG) in aqueous salt solution by one- and two-dimensional (2D-TOCSY and 2D-NOESY)¹H NMR spectroscopy (500 MHz). The concentration and temperature dependences of the proton chemical shifts of molecules were measured and used to calculate the equilibrium reaction constants, the relative contents of different types of complex as functions of concentration and temperature, the limiting values of the proton chemical shifts of daunomycin in various complexes, and the thermodynamic parameters of complexation δH and δS. It is concluded that the triplet nucleotide sequences are the preferable sites at which daunomycin is attached. The binding of the second daunomycin molecule to both single-stranded and duplex forms of tetramer is markedly anticooperative. This is explained by the presence in the antibiotic of a positively charged amino sugar residue creating steric hindrances for the attachment of the second antibiotic molecule to the short tetranucleotide sequence. The most plausible spatial structure of the 1:2 complex of antibiotic with desoxytetranucleotide is constructed using the calculated values of the induced proton chemical shifts of daunomycin and 2D-NOE data. Translated fromZhurnal Strukturnoi Khimii, Vol.40, No. 2, pp. 276–286, March–April, 1999.     

Analysis by Means of <Superscript>1</Superscript>H NMR Spectroscopy of Heteroassociaion in Water Solution of Antitumor Antibiotics Daunomycin and Actinomycin D

Heteroassociation of aromatic antitumor antibiotics daunomycin (DAU) and actinomycin D (AMD) was investigated using 1D and 2D ¹H NMR spectroscopy (at 500 MHz) and molecular mechanics procedure with the goal of establishing the mechanism of the combined action of antibiotics in the system AMD-DAU. The experimental data were processed applying a modified statistical and thermodynamic model of the molecules heteroassociation. Proceeding from this model the values were obtained of induced proton chemical shifts, equilibrium constant and thermodynamic parameters of complexing reaction between DAU and AMD. By means of molecular mechanics with the use of X-PLOR software and of the analysis results of the induced proton chemical shifts in the molecules the most probable spatial structure, 1:1, was established for the heterocomplex of DAU and AMD. Heterocomplexes of daunomycin and actinomycin D form due to stacking interaction between the aromatic chromophores with possible additional stabilization of the complexes by an intermolecular hydrogen bond.     

Investigation of the self-association of proflavine and acridine orange molecules in aqueous solution by 1H NMR

The chemical shifts of the protons in the proflavine and acridine orange molecules in aqueous solution were measured by ¹H NMR spectroscopy. The equilibrium constants for the association of the molecules and the chemical shifts of the protons in the monomers and associates were obtained from the concentration dependence of the proton chemical shifts. The most probable structures for the dimers of the dyes were calculated on the basis of the obtained chemical shifts, and a comparative analysis was made.Translated from Teoreticheskaya i Éksperimental'naya Khimiya, Vol. 23, No. 3, pp. 373–376, May–June, 1987.     

H NMR investigation of the self-association of ethidium homodimer and its complexation with propidium iodide in aqueous solution

The self-association of a bis-intercalator, ethidium homodimer (EBH), and its hetero-association with phenanthridine dye, propidium iodide (PI), have been studied by 1D and 2D ¹H NMR spectroscopy using the analysis of proton chemical shifts changes in aqueous solution as a function of concentration and temperature. Experimental results have shown that dynamic equilibrium in solution includes different conformational states of EBH molecules: folded (F) and unfolded (U) forms, a dimer form (F₂) where an aromatic chromophore of one of EBH molecules is inserted (intercalated) between the linked chromophores of the other homodimer molecule and a trimer complex (F₃) with two partitially intercalated aromatic chromophores between the chromophores of the folded EBH molecule. It has been found that EBH associates with propidium iodide forming 1:1 complex, where PI is inserted between the chromophores of the folded form, and 1:2 complex resulting from intercalation of PI into F₂ EBH dimer. Thermodynamical parameters of EBH self-association and complexation between EBH and PI have been determined and conclusions about the nature of the physical forces responsible for the formation of intermolecular complexes have been made.     

Investigation of the structures of associates of the acridine dye proflavin with deoxytetranucleotides in aqueous solution by 1H NMR spectroscopy

A comparative investigation was made of the complex formation of proflavin with isomeric CG-containing self-complementary deoxytetraribonucleoside triphosphates in aqueous solution by ¹H NMR spectroscopy (500 MHz). Two-dimensional homogeneous 2M-COSY and 2M-NOESY spectroscopy was used for complete assignment of the proton signals of the molecules in solutions and for qualitative analysis of the nature of the reaction of the dye with the tetranucleotides. The concentration dependences of the proton chemical shift of the molecules were measured. The equilibrium constants of the reactions, the relative content of associates of various types, and the limiting values of the chemical shifts of the dye protons in the complex were determined according to the proposed models of complex formation. A comparative analysis was made of the characteristics of binding of the dye to tetranucleotides with various sequences of nitrogen bases and the structural characteristics of the molecular complexes formed in solution.Translated from Teoreticheskaya i Eksperimental'naya Khimiya, Vol. 28, Nos. 5–6, pp. 424–429, September–December, 1992.     

1H NMR study of self-association of actinomycin D in an aqueous solution

This paper presents the results of a proton magnetic resonance study (500 MHz) of self-association of actinomycin D (AMD) antibiotic in an aqueous solution. The equailibrium constants and thermo-dynamic parameters (ΔH, ΔS) of molecular association as well as the limiting values of proton chemical shifts of associate molecules were determined from the concentration and temperature dependences of¹H NMR chemical shifts of AMD. The results were analyzed using dimeric and infinite-dimensional cooperative models of molecular self-association. The value of the cooperativity parameter indicates that AMD self-association is anticooperative, i.e., formation of aggregates larger than dimers is energetically unfavorable. The values of induced proton chemical shifts were used to determine the most probable mutual orientation of chromophores in AMD structure. Sevastopol State Technical University. Berkbeck College, London University. Translated fromZhurnal Struktumoi Khimii, Vol. 36, No. 1, pp. 81–88, January–February, 1995. Translated by L. Smolina     

<Superscript>1</Superscript>H NMR Study of Heteroassociation of Ethidium Homodimer and Propidium Iodide in Water

1D and 2D ¹H NMR spectroscopy (500 MHz) was used to study heteroassociation of the bifunctional intercalator ethidium homodimer (EBH) with a phenanthridine dye propidium iodide (PI) in an aqueous salt (0.1 mol/l NaCl). A physical model of equilibrium between various associated forms of ethidium homodimer and propidium in solution is suggested, the most probable forms being 1:1 and 1:2 complexes of PI with the EBH monomer and dimer. The chemical shifts of the EBH molecule in heterocomplexes, as well as the equilibrium constants and the thermodynamic parameters (enthalpy, entropy) of heteroassociations, were calculated from the concentration and temperature dependences of the proton chemical shifts. It is concluded that the propidium molecule is built (intercalated) into the EBH monomer and dimer to form 1:1 and 1:2 complexes mainly stabilized by dispersive and hydrophobic interactions.Original Russian Text Copyright © 2004 by A. N.Veselkov, M. P. Evstigneev, S. A. Hernandez, O. V. Rogova, D. A. Veselkov, and D. B. Davies__________Translated from Zhurnal Strukturnoi Khimii, Vol. 45, No. 5, pp. 837–843, September–October, 2004.     

Equilibrium transformations of meso-methylated thiacarbocyanine in aqueous solutions

Equilibrium processes of dimerization and H*- and J-aggregation of 3,3′-di-(γ-sulfopropyl)-5,5′-dichloro-9-methylthiacarbocyanine (TCC) in aqueous solutions have been investigated, and the thermodynamic parameters of the processes have been calculated. At least seven equilibrium forms of TCC have been found in aqueous solution for the first time. The absorption bands of the dye have been attributed to various forms (M, D, H*, and J) with allowance for existence of stereoisomers. The aggregation numbers for J- and H*-aggregates have calculated from the dependence of the absorption spectra on the dye concentration in solutions. It has been shown that the TCC aggregates consisting of a large number of molecules are formed by the “block” mechanism via intermediate steps of the formation of dimers, J- or H*-tetramers, octamers, etc.     

Spectrophotometric investigation of the hetero-association of caffeine and thiazine dye in aqueous solution

The self-association of thiazine dye, Methylene Blue (MB), and its hetero-association with Caffeine (CAF), were studied in aqueous solution by means of spectrophotometry in the visible range of spectrum. Concentration and temperature dependences of molar absorption of the interacting molecules were used to analyse dynamic equilibrium in solution in terms of two-component model of molecular hetero-association. The magnitudes of equilibrium dimerization and hetero-association constants as well as thermodynamic parameters, enthalpy and entropy, were determined. The calculation of the fraction of different types of associates in the mixed solution, containing Methylene Blue and Caffeine, was done. It was concluded that the hetero-association of Methylene Blue and Caffeine molecules results in lower effective concentration of the dye in solution, which may account for the alteration of its biological activity.     

Accurate prediction of proton chemical shifts. I. Substituted aromatic hydrocarbons

Forty‐five proton chemical shifts in 14 aromatic molecules have been calculated at several levels of theory: Hartree–Fock and density functional theory with several different basis sets, and also second‐order Møller–Plesset (MP2) theory. To obtain consistent experimental data, the NMR spectra were remeasured on a 500 MHz spectrometer in CDCl₃ solution. A set of 10 molecules without strong electron correlation effects was selected as the parametrization set. The calculated chemical shifts (relative to benzene) of 29 different protons in this set correlate very well with the experiment, and even better after linear regression. For this set, all methods perform roughly equally. The best agreement without linear regression is given by the B3LYP/TZVP method (rms deviation 0.060 ppm), although the best linear fit of the calculated shifts to experimental values is obtained for B3LYP/6‐311++G**, with an rms deviation of only 0.037 ppm. Somewhat larger deviations were obtained for the second test set of 4 more difficult molecules: nitrobenzene, azulene, salicylaldehyde, and o‐nitroaniline, characterized by strong electron correlation or resonance‐assisted intramolecular hydrogen bonding. The results show that it is possible, at a reasonable cost, to calculate relative proton shieldings in a similar chemical environment to high accuracy. Our ultimate goal is to use calculated proton shifts to obtain constraints for local conformations in proteins; this requires a predictive accuracy of 0.1–0.2 ppm. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1887–1895, 2001     

A 1H NMR study of hydrogen bonding and complexation processes of trimethylacetic acid in acetone

The carboxyl proton chemical shifts of trimethylacetic acid, which was dissolved in acetone and in binary mixtures of acetone and cyclohexane, have been measured as a function of concentration at temperatures of 0, +15, +30, +45 and +60 °C. The results obtained for the system studied, using the equilibrium constant method for interpretation of experimental data, indicate that the molecular association through hydrogen bonds occurs as a monomer-cyclic dimer-1:1 complex equilibrium process in the low concentration range (up to 0·08 mol fraction). The equilibrium constants of complexation and dimerization, the chemical shifts of the acid in the complex, and the thermodynamic parameters of complexation and dimerization have been calculated.     

自由能微扰法研究系列烷基芳基磺酸盐的胶束化焓-熵补偿现象

为了研究不同结构的表面活性剂分子在水溶液中的胶束化焓-熵补偿现象, 采用自由能微扰(FEP)法计算了系列烷基芳基磺酸盐的溶剂化自由能, 并根据胶团化过程的质量作用模型讨论了相关热力学性质. 结果表明: 自由能微扰法得到的溶剂化自由能大小与用传统热力学表面张力法测定的吉布斯自由能相近, 能够用于比较不同结构的烷基芳基磺酸盐间胶束化能力; 烷基芳基磺酸盐在水溶液中的胶束化过程是自发进行的, 且存在焓-熵补偿现象, 补偿温度范围均在(302±2) K; 随着分子结构中芳环向长烷基链中间位置移动, 胶束化能力和胶束的稳定性均下降; 而随着芳环上短烷基链或长烷基链碳数的增加, 形成胶束的能力与稳定性均提高.     

Tricarbonyltechnetium(I) and tricarbonylrhenium(I) complexed with N-methyl-2-pyridinecarboxyamide as potential radiopharmaceuticals: a computational study

The electronic and thermodynamic properties of the ‘2 + 1’ tricarbonyltechnetium(I) and -rhenium(I) mixed ligand complexes with N-methylpyridine-2-carboxyamide (MPCA) as a bidentate ligand and chloride, water, or tert-butyl-3-isocyanopropanoate (BCP), were investigated within the framework of Density Functional Theory. The atomic charges of all complexes, polarization of the CO groups, as well as the effect of transfer of π-electron density between the ligands through the metal were calculated and compared. The free energies of the reaction of formation of the isocyanide complexes in aqueous solution were calculated based on calculated total free energies in aqueous solution of the products and the substrates. The dissociation energies of the complexes were also determined in order to rationalize the experimentally observed higher resistance of the rhenium compared to the technetium complexes in the challenge experiments with the standard sulfur-containing amino acids.