Molecular dynamics study on the conformational flexibility and energetics in aqueous solution of methylated beta-cyclodextrins.

All possible methylated beta-cyclodextrins (CDs) with C7-symmetry have been studied by molecular dynamics simulations, in gas phase and in water solution. Energetic and structural information were obtained from the trajectory analysis. CD flexibility increases with degree of methylation, very likely due to the concomitant reduction of the intramolecular hydrogen bonds. Solvation-free energy was computed for each of the studied CDs using the MM/GBSA method. An analysis of radial distribution functions was used to determine distribution of solvent molecules around the O2, O3, and O6. The number of solvent molecules around these oxygens decreases with an increase in the degree of methylation. The DeltaS contribution from solvent thus becomes more positive when the degree of methylation increases and, consequently, the overall DeltaG in water diminishes.

Synthesis, structure, and inclusion capabilities of trehalose-based cyclodextrin analogues (cyclotrehalans).

Concise and efficient strategies toward the synthesis of D2h- and D3h-symmetric cyclodextrin analogues alternating alpha,alpha'-trehalose disaccharide subunits and pseudoamide segments (cyclotrehalans, CTs) are reported. The conformational properties of these cyclooligosaccharides are governed by the rigidity of the alpha,alpha'-trehalose disaccharide repeating unit and the partial double-bond character of the N-(C=X) linkages. In contrast to the typical concave-shaped cavity of cyclodextrins (CDs), CTs feature a convex-shaped hydrophobic cavity in which the beta-face of the monosaccharide subunits is oriented toward the inner side, as supported by NMR and modeling (molecular mechanics and dynamics) studies. In the case of cyclodimeric CTs (CT2s), the existence of intramolecular hydrogen bonds results in collapsed cavities, too small to allow the formation of inclusion complexes with organic molecules. Cyclotrimeric CTs (CT3s) display cavity sizes that are intermediate between those of alphaCD and betaCD, ideally suited for the complexation of complementary guests with ternary symmetry such as adamantane 1-carboxylate (AC). The higher flexibility of the pseudoamide bridges as compared with classical glycosidic linkages endow these glyconanocavities with some conformational adaptability properties, making them better suited than CDs for complexation of angular guests, as seen from comparative inclusion capability experiments against the fluorescent probes 6-p-toluidinonaphthalene-2-sulfonate (TNS; linear) and 8-anilinonaphthalene-1-sulfonate (ANS; angular).

Fine-tuning ligand-receptor design for selective molecular recognition of dicarboxylic acids.

The host-guest interaction between the hexaaza macrocyclic ligand 3,7,11,18,22,26-hexaazatricyclo[26.2.2.2]tetratriaconta-1(31),13(34),14,16(33),28(32),29-hexaene (P3) and three rigid dicarboxylic acids (isophthalic acid, H2is; phthtalic acid, H2ph; and terephthalic acid, H2te) has been investigated using potentiometric equilibrium methods and NMR spectroscopy including the measurement of intermolecular nuclear Overhauser effects (NOEs) and self-diffusion coefficients (D). Ternary complexes are formed in aqueous solution as a result of hydrogen bond formation and Coulombic interactions between the host and the guest. In the [(H6P3)(is)]4+ complex, those bonding interactions reach a maximum yielding a log K6R of 4.74. Competitive distribution diagrams and total species distribution diagrams are used to illustrate the main features of these systems. In particular, a selectivity of over 89% at p[H] = 5.0 is obtained for the complexation of the is versus the te substrates. The recognition capacity of P3 over dicarboxylic acids (da) is compared to the related hexaaza macrocycle Me2P3 (7,22-dimethyl-3,7,11,18,22,26-hexaazatricyclo[26.2.2.2]tetratriaconta-1(30),13,15,28,31,33-hexaene) that binds da with a lesser strength, and it is not selective. Theoretical calculations performed at molecular dynamics level have also been carried out and point out that the origin of selectivity is mainly due to the capacity of the P3 ligand receptor to adapt to the geometry of the dicarboxylic acid to form relatively strong hydrogen bonds.