Anastasia O. Lantushenko

Profiles of equilibrium constants for self-association of aromatic molecules

Analysis of the noncovalent, noncooperative self-association of identical aromatic molecules assumes that the equilibrium self-association constants are either independent of the number of molecules (the EK-model) or change progressively with increasing aggregation (the AK-model). The dependence of the self-association constant on the number of molecules in the aggregate (i.e., the profile of the equilibrium constant) was empirically derived in the AK-model but, in order to provide some physical understanding of the profile, it is proposed that the sources for attenuation of the equilibrium constant are the loss of translational and rotational degrees of freedom, the ordering of molecules in the aggregates and the electrostatic contribution (for charged units). Expressions are derived for the profiles of the equilibrium constants for both neutral and charged molecules. Although the EK-model has been widely used in the analysis of experimental data, it is shown in this work that the derived equilibrium constant, K(EK), depends on the concentration range used and hence, on the experimental method employed. The relationship has also been demonstrated between the equilibrium constant K(EK) and the real dimerization constant, K(D), which shows that the value of K(EK) is always lower than K(D).

Relation between structure and enthalpy for stacking interactions of aromatic molecules

An approximately linear correlation has been found between the enthalpy of complexation and the area of overlap of the chromophores using published structural and thermodynamical data on the self- and hetero-association of aromatic molecules measured under similar solution conditions. This finding is consistent with the assumption that short-range van-der-Waals forces dominate over other contributions to the enthalpy of stacking of aromatic molecules. It provides a ‘model-independent’ approach for a priori estimation of the enthalpy of aromatic–aromatic stacking interactions from knowledge of the structural properties or vice versa.

Hexamer Oligonucleotide Topology and Assembly Under Solution Phase NMR and Theoretical Modeling Scrutiny

The entire family of noncomplementary hexamer oligodeoxyribonucleotides d(GCXYGC) (X and Y = A, G, C, or T) were assessed for topological indicators and equilibrium thermodynamics using a priori molecular modeling and solution phase NMR spectroscopy. Feasible modeled hairpin structures formed a basis from which solution structure and equilibria for each oligonucleotide were considered. ¹H and ³¹P variable temperature-dependent (VT) and concentration-dependent NMR data, NMR signal assignments, and diffusion parameters led to d(GCGAGC) and d(GCGGGC) being understood as exceptions within the family in terms of self-association and topological character. A mean diffusion coefficient D(298 K) = (2.0 ± 0.07) × 10⁻¹⁰ m² s⁻¹ was evaluated across all hexamers except for d(GCGAGC) (D(298 K) = 1.7 × 10⁻¹⁰ m² s⁻¹) and d(GCGGGC) (D(298 K) = 1.2 × 10⁻¹⁰ m² s⁻¹). Melting under VT analysis (T(m) = 323 K) combined with supporting NMR evidence confirmed d(GCGAGC) as the shortest tandem sheared GA mismatched duplex. Diffusion measurements were used to conclude that d(GCGGGC) preferentially exists as the shortest stable quadruplex structure. Thermodynamic analysis of all data led to the assertion that, with the exception of XY = GA and GG, the remaining noncomplementary oligonucleotides adopt equilibria between monomer and duplex, contributed largely by monomer random-coil forms. Contrastingly, d(GCGAGC) showed preference for tandem sheared GA mismatch duplex formation with an association constant K = 3.9 × 10⁵M⁻¹. No direct evidence was acquired for hairpin formation in any instance although its potential existence is considered possible for d(GCGAGC) on the basis of molecular modeling studies.

The Self-Association of Antibiotic Actinocyl-bis(3-dimethylaminopropylamine) in Aqueous Solution: A 1H NMR Analysis

The self-association of the synthetic antibiotic actinocyl-bis(3-dimethylaminopropylamine) was studied in aqueous solution by one- and two-dimensional 1H NMR spectroscopy at 500 MHz. The two-dimensional homonuclear correlation NMR techniques (TOCSY and ROESY) were used to completely assign all the proton signals of the antibiotic and to quantitatively analyze the mutual arrangement of the antibiotic molecules in their aggregates. The concentration and temperature dependences of proton chemical shifts were used to determine the equilibrium constants and the thermodynamic parameters (ΔH and ΔS) of the self-association, as well as the limiting values of proton chemical shifts in associates. The experimental results were analyzed using both the indefinite noncooperative and cooperative models of the molecular self-association. The calculated value of the cooperativity coefficient (σ ≈ 1.1) for our synthetic antibiotic confirmed a substantially lower anticooperative effect at the aggregation of its molecules in comparison with that of the antitumor antibiotic actinomycin D (σ ≈ 1.5). We calculated the most favorable structure of the dimeric associate of the synthetic antibiotic in aqueous solution and found that, like in the actinomycin D dimer, the antiparallel orientation of the phenoxazone chromophore planes of interacting molecules is characteristic of its dimer.

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

AbstractSelf-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 H NMR analysis of complexation of hydrotropic agents nicotinamide and caffeine with aromatic biologically active molecules in aqueous solution

\sigma

Quantitation of the molecular mechanisms of biological synergism in a mixture of DNA-acting aromatic drugs

≈ 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.

On the origin of the decrease in stability of the DNA hairpin d(GCGAAGC) on complexation with aromatic drugs

The heteroassociation of caffeine (CAF) and the synthetic antibiotic actinocyl-bis(3-dimethylaminopropylamine) (ACT) was studied in aqueous solution by one- and two-dimensional 1H NMR spectroscopy at 500 MHz. The equilibrium reaction constants, thermodynamic parameters (ΔH and ΔS) of ACT heteroassociation with CAF, the limiting values of proton chemical shifts of their molecules in the heteroassociation complex, and the spatial structure of the ACT–CAF complex were determined from the experimental dependences of proton chemical shifts of the aromatic molecules on concentration and temperature. The parameters of CAF heteroassociation with the phenoxazone antibiotic actinomycin D and its synthetic analogue ACT were comparatively analyzed and conclusions were made on the crucial role of stacking interactions of the chromophores of CAF and the phenoxazone antibiotics in the formation of the heterocomplexes in aqueous solution.