Molecular modelling of the interactions of tetra-(4-N-methylpyridyl) porphin with TA and CG sites on DNA.

The molecular structure of the DNA-intercalating ligand tetra-(4-N-methylpyridyl) porphin has been determined by X-ray crystallography. The porphyrin has a precise centre of symmetry; the central core is planar, with the N-methylpyridyl groups inclined to it at angles of 66-72 degrees. Molecular modelling of this structure into TpA and CpG sites of intercalated DNA, has been performed, and approximate energetics calculated. It has been shown that only the CpG site can have full ligand intercalation, since the thymine methyl group sterically hinders such geometry at TpA sites. Modelling indicates the importance of electrostatic effects in the low-energy forms of intercalated and part-intercalated complexes at both sequences.     

Modelling of the binding specificity in the interactions of cationic porphyrins with DNA.

A theoretical investigation is performed of the complexes of a tetracationic porphyrin, tetra-(4-N-methylpyridyl)-porphyrin, (T4MPyP), with the hexanucleotides d(CGCGCG)2 and d(TATATA)2, considering the possibility of both the intercalative and the groove binding interactions. These computations demonstrate that T4MPyP manifests a significant preference for intercalation in its complex with d(CGCGCG)2 but for non intercalative binding in the minor groove in its complex with d(TATATA)2. Such a dual binding behaviour of T4MPyP as a function of the sequence to which it is attached is fully consistent with available experimental data. It demonstrates that intercalation and groove binding may be viewed as two potential wells on a continuous energy surface. In agreement with experiment, the computations indicate that in the here considered case the deepest well is associated with intercalation.     

Sorption of components from a mixture of essential oils by cryotextured cornstarches

Sorption by cryotextured cornstarches of components of the aqueous phase of a mixture of essential oils was studied by capillary gas chromatography. The amount of cryotexture-sorbed substances depended linearly on their concentration in the initial gel. The sorption of components from the mixture by starch polysaccharides was mainly associated with hydrophobic cooperative interactions, which resulted in the formation of supramolecular structures and inclusion complexes. The structure of the compounds was a major factor determining the degree of sorption. Sorption of monoterpene carbohydrates was the most pronounced. We revealed a synergistic increase in the degree of sorption from the mixture as compared to binding of individual compounds.     

DNA interaction and antiproliferative behavior of the water soluble platinum supramolecular squares [(en)Pt(N-N)]4(NO3)8 (en=ethylenediamine, N-N=4,4'-bipyridine or 1,4-bis(4-pyridyl)tetrafluorobenzene)

The interaction with DNA of two water soluble platinum supramolecular squares [(en)Pt(N-N)]4(NO3)8 (en=ethylenediamine, N-N=1,4-bis(4-pyridyl)tetrafluorobenzene, compound 1, N-N=4,4'-bipyridine, compound 2) has been studied by circular dichroism, electrophoretic mobility and atomic force microscopy. the two complexes drastically modify the second and tertiary structures of DNA, but compound 2 does it strongly due probably to its smaller size by comparison with compound 1 and its more suitable structural features for intercalation between base pairs. The two supramolecular squares were assayed against the HL-60 tumor cell line for 24 and 72 h. The IC50 values for 24 h are smaller than that of cisplatin for this time, however for 72 h the IC50 have higher values being the corresponding to compound 2 comparable to that of cisplatin. Apoptotic assays were also carried out for the compounds 1 and 2 against the tumor cell line.     

Sorption of Components from a Mixture of Essential Oils by Cryotextured Cornstarches

Sorption by cryotextured cornstarches of components of the aqueous phase of a mixture of essential oils was studied by capillary gas chromatography. The amount of cryotexture-sorbed substances depended linearly on their concentration in the initial gel. The sorption of components from the mixture by starch polysaccharides was mainly associated with hydrophobic cooperative interactions, which resulted in the formation of supramolecular structures and inclusion complexes. The structure of the compounds was a major factor determining the degree of sorption. Sorption of monoterpene hydrocarbons was the most pronounced. We revealed a synergistic increase in the degree of sorption from the mixture as compared to binding of individual compounds.__________Translated from Prikladnaya Biokhimiya i Mikrobiologiya, Vol. 41, No. 4, 2005, pp. 463–469.Original Russian Text Copyright © 2005 by Terenina, Misharina.     

Esterification of beta-chitin via intercalation by carboxylic anhydrides

beta-chitin is known to form intercalation complexes with aliphatic alcohols and amines. We found that it also forms complexes with carboxylic anhydrides. When the beta-chitin-acetic anhydride complex was heated to 105 degrees C, the hydroxyl groups of chitin were acetylated by a host-guest reaction, maintaining the host's crystal structure. Structures of complex and acetylated products were analyzed by X-ray diffraction, (13)C CP/MAS NMR, and infrared spectroscopy. The maximum degree of substitution (DS) was close to 1.0, suggesting regioselective esterification at the C6 position of chitin. Partially acetylated beta-chitin with a DS of 0.4 could incorporate various guest species that are difficult to be incorporated by original beta-chitin. In contrast, beta-chitin acetate with a DS of 1 lost the ability to form a complex. Intercalation complexes of beta-chitin with cyclic anhydrides (succinic and maleic) also underwent esterification by heating, and the products with a DS of approximately 1 dissolved in aqueous alkali, apparently as the result of the dissociation of introduced carboxyl groups. These phenomena are potentially useful in controlling the complexation ability of beta-chitin and the preparation of regioselectively esterified chitin derivatives.     

Complexation between triterpene glycosides of holothurians and cholesterol is the basis of lipid-saponin carriers of subunit protein antigens

The ability of some triterpene glycosides of holothurians: cucumarioside A2-2 from Cucumaria japonica, cucumarioside G1 from Cucumaria fraudatrix, frondoside A from Cucumaria frondosa, and holotoxin A1 from A postichopus japonicus to form lipid-saponin supramolecular complexes was studied. The formation of supramolecular cholesterol-glycosides complexes between cholesterol and these glycosides in water medium was observed by transmission electron microscopy. These complexes were considered as nanoparticles with different structure. Complexes formed by cholesterol with cucumarioside A2-2, holotoxin A1, and frondoside A are tubular nanoparticles. In contrast, complexes between cholesterol and cucumarioside G1 have different structured. The structure of nanoparticles formed in the presence of cucumarioside A2-2, holotoxin A1, and cucumarioside G1 was dependent on the ratio of cholesterol in the lipid-saponin system. On the other hand, frondoside A did not shown this tendency. In lipid-saponin systems with a similar molar ratio cholesterol-glycoside, the ordering of the supramolecular structure decreases in the following order: cucumarioside A2-2, holotoxin A1, frondoside A. A comparative analysis of the morphology of the supramolecular complexes and the peculiarities of the molecular structure of triterpene glycosides studied, demonstrated that the structure of supramolecular complexes formed depends on the branching and length of the glycoside carbohydrate chain. On the other hand, the formation of monomeric cholesterol-glycosides complexes depends on the peculiarities of the structure of aglycone. Thus, the possibility of the formation of a new type of antigen carries on the basis of marine triterpene glycosides was proved.     

Interactions of porphyrins and transfer RNA

The interactions of the free base porphyrin, tetra-(4N-methylpyridyl)porphyrin and its copper(II), manganese(III) and zinc(II) complexes with brewer's yeast type V phenylalaninyl tRNA were evaluated by UV-visible spectroscopy, circular dichroism and melting temperature studies over a range of magnesium ion concentrations and ionic strengths. Scatchard analysis of absorption spectra of the porphyrins in the presence of tRNA showed the free base, copper and zinc porphyrins to have binding constants of 7.3 X 10(7), 1.7 X 10(6) and 2.3 X 10(8), respectively; the manganese(III) complex did not demonstrate changes in its electronic spectra that enable the calculation of a binding constant. The results of the spectroscopic studies indicate a mode of binding for the free base, copper(II) and zinc(II) complexes that is neither intercalative nor simply outside electrostatic. The magnitude of the binding constants and the UV-visible results support intercalation, but the analyses of the thermal denaturation studies and the circular dichroism evaluations suggest that the porphyrins are associating at a single site in a fold of the tertiary structure of the tRNA close to several crucial hydrogen bonds, perhaps in the vicinity of the P10 loop. That the manganese(III) complex does not bind in this site points to constraints on the axial thickness of a molecule that may be accommodated in this locus.     

Experimental and theoretical study on the 1:1 supramolecular complexes of formamide with adrenaline

The electron transfer properties were investigated for supramolecular complexes of formamide (FA) with adrenaline (Ad) at graphite electrode and paraffine soaked graphite electrode using cyclic voltammetry (CV). The experimental results show that FA affected the electron transfer properties of Ad. The formed supramolecular complexes by hydrogen bond (H-bond) interaction between FA and Ad slowed down the diffusion ability of adrenaline, which makes it hard to donate electron and be oxidized. The H-bond interaction energies calculation for the supramolecular complexes of FA with Ad at MP2/6-311+G(d,p)//B3LYP/6-311+G(d,p) level have also been performed. The calculational results confirm the experimental fact that FA can form stable supramolecular complexes with Ad.     

Polar and hydrophobic effects on ester aminolysis in dimethyl sulfoxide

Aminolysis of various carboxyl-containing esters by several tetra-, tri-, and diamines was kinetically studied in dimethyl sulfoxide. Rates were measured in the presence or absence of added sulfuric acid with the amine concentration being much greater than the ester concentration. In some reactions, pseudo-first-order rate constants manifested saturation kinetic behavior with respect to the total amine concentration, indicating the formation of complexes between the amines and the esters. The complex formation was most efficient when the carboxyl group of the ester substrate was located at the meta position to the ester group. In addition, the complex formation was facilitated by hydrophobic amines. In order to explain the positional stereoselectivity and the hydrophobic effects observed in the kinetic study, a structure of the complex is proposed. In this structure of the complex, two nitrogen atoms of the amine are linked by an intramolecular hydrogen bond and then further interact with the two carbonyl oxygen atoms of the substrate. In addition, the hydrophobic interaction between the hydrophobic portion of the amine and the benzene ring of the substrate stabilizes the complex. Dimethyl sulfoxide accommodates both the polar and the hydrophobic interactions that are needed in the formation of the complex, mimicking the microenvironment of enzyme active sites.     

Effect of infrared laser radiation on sorption of dry cartilage and connective tissue preparations

Cartilaginous and connective tissues were exposed to a moderate-intensity IR laser treatment with IR radiometric temperature control. The isotherms of water sorption by dry preparations of intact and laser-treated tissues were obtained and calculated in terms of well known models. It was shown that the sorption capacity of a monolayer of tissues decreases with increasing temperature during laser treatment. Changes in the supramolecular structure of the extracellular matrix of tissues (loss of regularity) upon IR laser exposure are discussed.     

Binding of aliphatic aldehydes by cornstarch polysaccharides

Binding by cryotextured cornstarch of individual aliphatic aldehydes (C6-C10; saturated or unsaturated) and their mixtures from aqueous solutions has been studied using capillary gas chromatography. The amount of compounds absorbed by the cryotextures depended linearly on the concentration of aldehydes in the original gel. The majority of the compounds under study were bound irreversibly. Aldehydes with low molecular weight were better absorbed by the cryotextures than by granules of intact cornstarch. Data of IR spectrocopy demonstrated that binding to cornstarch polysaccharides decreased the conformational mobility of odorants. The appearance of binding isotherms depended of the extent of aldehyde sorption, suggesting the involvement of multiple mechanisms of binding. The formation of supramolecular complexes through cooperative hydrophobic interactions between aldehydes and cornstarch polysaccharides was the preferential mechanism of the sorption.     

Experimental and theoretical study on the supramolecular complexes of 15-crown-5 with adrenaline

The electron transfer properties of supramolecular complexes of 15-crown-5 (15C5) with protonated adrenaline (PAd⁺) at different electrodes using cyclic voltammetry (CV) have been investigated in the article. The experimental results show that 15C5 will affect the electron transfer properties of adrenaline. The formed supramolecular complexes by ion-dipole and hydrogen bond interaction between PAd⁺ and 15C5 will slow down the diffusion ability of adrenaline and make it hard to donate electron and be oxidized.The interaction energies and NPA calculations for the supramolecular complexes of 15C5 with PAd⁺ at B3LYP/6-31+G(d) level have been performed. The calculational results confirm the experimental fact that 15C5 can form stable supramolecular complexes with PAd⁺.     

Construction and Systematical Symmetric Studies of a Series of Supramolecular Clusters with Binary or Ternary Ammonium Triphenylacetates

Functions of clusters in nano or sub-nano scale significantly depend on not only kinds of their components but also arrangements, or symmetry, of their components. Therefore, the arrangements in the clusters have been precisely characterized, especially for metal complexes. Contrary to this, characterizations of molecular arrangements in supramolecular clusters composed of organic molecules are limited to a few cases. This is because construction of the supramolecular clusters, especially obtaining a series of the supramolecular clusters, is difficult due to low stability of non-covalent bonds compare to covalent bonds. From this viewpoint, utilization of organic salts is one of the most useful strategies. A series of the supramolecules could be constructed by combinations of a specific organic molecule with various counter ions. Especially, primary ammonium carboxylates are suitable as typical examples of supramolecules because various kinds of carboxylic acids and primary amines are commercially available, and it is easy to change their combinations. Previously, it was demonstrated that primary ammonium triphenylacetates using various kinds of primary amines specifically construct supramolecular clusters, which are composed of four ammoniums and four triphenylacetates assembled by charge-assisted hydrogen bonds, in crystals obtained from non-polar solvents. This study demonstrates an application of the specific construction of the supramolecular clusters as a strategy to conduct systematical symmetric study for clarification of correlations between molecular arrangements in supramolecules and kinds and numbers of their components. In the same way with binary salts composed of triphenylacetates and one kind of primary ammoniums, ternary organic salts composed of triphenylacetates and two kinds of ammoniums construct the supramolecular clusters, affording a series of the supramolecular clusters with various kinds and numbers of the components.     

Enhancement of chlorophyll a fluorescence yield, low-temperature F685/F730 fluorescence emission ratio, and electron transport rate by ether phospholipids (platelet activating factor and analogs) in isolated chloroplasts

Acetyl glyceryl ether phosphorylcholine (1-O-alkyl-2-acetyl-sn-glyceryl-3-phosphorylcholine; or platelet activating factor (PAF)), when incubated with chloroplasts or subchloroplast fractions derived from stroma or grana lamellae, induces a drastic increase in the low-temperature fluorescence emission ratio F685/F730 (77 degree K). The molecular structure requirement for the effect to be elicited is the ether bond and a long C chain at the C-1 position of glycerol, a short C chain at C-2 (or the lyso form), and a large polar head at C-3, the potent effector being PAF C-16. The effect is more pronounced in grana-derived fractions. PAF also induces an increase in the chlorophyll alpha fluorescence yield, enhances the association of chlorophyll in the supramolecular pigment-protein complexes of the thylakoid (especially those of Photosystem II), and enhances electron transfer from 1,5-diphenyl carbazide to 2,6-dichlorophenol. These effects are attributed to alteration of the Photosystem II unit organization via the incorporation/intercalation in the grana of the wedge-shaped PAF.     

A systematic study of ligand intermolecular interactions in crystals of copper(II) complexes of bidentate guanidino derivatives

The synthesis and X-ray structures of copper(II) complexes of the bidentate ligands, N-(4-oxo-5,5-diphenyl-4,5-dihydro-1H-imidazol-2-yl)-N′-phenylguanidino, 2-uanidinobenzimidazolo and N-(4-oxo-3-phenyl-1,3-diazaspiro[4.4]non-1-en-2-yl)guanidino, are reported. These complexes, which possess potential doublet (DA) or triplet (DAD) hydrogen bonding motifs, can form supramolecular structures based on synthons involving hydrogen bonding or phenyl embraces. The changes in supramolecular structure resulting from small changes in ligand structure, as well as from the use of different solvents for their crystallisation, are examined. The structures adopted are compared with others reported previously for complexes of related ligands.     

Binding of Aliphatic Aldehydes by Cornstarch Polysaccharides

Binding by cryotextured cornstarch of individual aliphatic aldehydes (C₆–C₁₀; saturated or unsaturated) and their mixtures from aqueous solutions has been studied using capillary gas chromatography. The amount of compounds sorbed by the cryotextures depended linearly on the concentration of aldehydes in the original gel. The majority of the compounds under study were bound irreversibly. Aldehydes with low molecular weight were better sorbed by the cryotextures than by granules of native cornstarch. Data of IR spectroscopy demonstrated that binding to cornstarch polysaccharides decreased the conformational mobility of odorants. The appearance of binding isotherms depended on the extent of sorption, suggesting the involvement of complex mechanisms of binding. The formation of supramolecular complexes through cooperative hydrophobic interactions between aldehydes and cornstarch polysaccharides was the preferential mechanism of the sorption.     

Synthesis, characterization and DNA binding and cleavage properties of ruthenium(II) complexes with various polypyridyls

Polypyridyl chlororuthenium(II) complexes have been synthesized and characterized. The binding mode of the complexes to DNA has been evaluated from the combined results of electronic absorption spectroscopy and viscosity measurement study. The results suggest that complexes 1, 2 and 3 bind to DNA via classical intercalation, electrostatic interaction and partial intercalation mode, respectively. Complex 2 shows less affinity for DNA. Cleavage of pUC19 DNA by complexes has been checked using gel electrophoresis. The data disclose that complex 1 has the highest cleaving ability.     

The complexation between holothurian triterpene glycosides and Chl as the basis for lipid-saponin carriers of subunit protein antigens

The ability of holothurian triterpene glycosides (cucumarioside A₂-2 from Cucumaria japonica, cucumarioside G₁ from C. fraudatrix, frondoside A from C. frondosa, and holotoxin A₁ from Apostichopus japonicus) to form supramolecular lipid-saponin complexes was studied. TEM demonstrated that all the studied compounds form supramolecular cholesterol-saponin complexes (nanoparticles) in aqueous medium. The complexes formed by cucumarioside A₂-2, holotoxin A₁, and frondoside A had a tubular structure and fundamentally differed in the structure from the particles produced by cucumarioside G₁. The morphology of the nanoparticles formed by cucumarioside A₂-2, holotoxin A₁, and cucumarioside G₁ changed depending on the fraction of cholesterol in the lipid-saponin system; however, this pattern was not observed for frondoside A. At the same molar fraction of cholesterol in the lipid-saponin system, cucumarioside A₂-2 formed the particles with the most pronounced tubular structure; the cholesterol-saponin complexes of holotoxin A₁ had a less pronounced tubular structure, whereas the structure of frondoside A particles was extremely heterogeneous. Comparative analysis of the morphology of the described supramolecular complexes and specific structural features of the glycosides demonstrated that the structure of the corresponding nanoparticles depended on the degree of branching of the carbohydrate moiety in the glycoside molecule and the complexation with cholesterol was determined by the specific features of aglycone structure. Thus, the feasibility of producing new generation antigen carriers using the complexes in question was proved.     

Interaction of DNA with actinocin amides containing cationoid centers in the amide groups

Complexes of DNA with actinocin derivatives containing ω-dialkylaminoalkyl groups in the1 and/or 9 positions of the chromophore were studied by spectrophotometric titration, circular dichroism, and viscometry. Induced circular dichroism (ICD) spectra of the DNA-ligand complexes were compared for the cases of the complexes of known structure established by other methods. It was shown that the presence of an isoelliptic point in the long-wavelength absorption band of the ICD spectra of the ligand under monomeric binding conditions could indicate intercalation of the actinocin chromophore into DNA. The separation of the cationoid center and the chromosphore upon elongation of the methylene chain increases the aggregability of the ligand pn the surface of the DNA double helix, which prevents the intercalation of the chromophore.