Calculations of Molecular Surface Area Changes with Docking of Host and Guest and Applications to Cyclodextrin Inclusion

A spectral displacement study of cyclodextrin/naphthenic acids inclusion complexes

The spectral displacement technique has been used to obtain 1:1 β-cyclodextrin (β-CD)/carboxylate anion equilibrium binding constants (K2) for some complex mixtures of naphthenic acids (NAs) and some examples of single-component NAs in aqueous solution. Three specific examples of single-component NAs were chosen with variable Z values as follows: 2-hexyldecanoic acid (Z = 0; S1), trans-4-pentylcyclohexanecarboxylic acid (Z = –2; S2), and dicyclohexylacetic acid (Z = –4; S3). The estimated K2 values for S1, S2, and S3 are as follows: 1.42 × 103 M–1, 52.2 × 104 M–1, and 13.1 × 104 M–1, respectively. The corresponding K2 values are 2.34 × 104 M–1 and 1.27 × 104 M–1 for commercial (Fluka) and industrial (Syncrude) sourced NAs, respectively. The magnitude of K2 for 1:1 complexes formed between β-CD and S1, S2, or S3 did not correlate with the degree of hydrogen deficiency (Z-series) but there was a correlation with the size of the guest molecules (n) examined in this study. The correlation between complex stability and the relative size of the lipophilic fragments of the guest molecule are related to the importance of the hydrophobic effect for inclusion of such carboxylic acid guest molecules within β-CD.

Advances in physical chemistry and pharmaceutical applications of cyclodextrins

Cyclodextrins (CDs) attract much attention for industrial applications and academic research. A few experimental methods for determination of the binding constant between CD and a guest molecule were reviewed critically. A hydrophile–hydrophobe matching model for host–guest docking was proposed for estimation of the binding constant and the solution structure of the complex. Rather detailed solution structures of CD complexes were determined by proton NMR spectroscopy, aided by calculations of molecular mechanics and surface areas, and were used to analyze the binding constants. The binding constants of CDs with multi-site guests were analyzed on the basis of their solution structures. The working mechanisms and physicochemical predictions in a few pharmaceutical applications of CDs were proposed on the basis of detailed solution structures and accurate binding constants.

Molecular Motions of .ALPHA.-Cyclodextrin on a Dodecyl Chain Studied by Molecular Dynamics Simulations

Motions of an alpha-cyclodextrin (alpha-CD) molecule on a dodecyl chain adopting the all-trans conformation were investigated in the presence of water by molecular dynamics simulations with CVFF force fields, where the trimethylammonium group of dodecyltrimethylammonium bromide (DTAB) is protruded outside the secondary hydroxyl rim of alpha-CD (the secondary-in structure). The alpha-CD molecule shuttled rapidly on the chain without decomplexation. This rapid motion is consistent with the NMR data. The plane formed by 6 O4 atoms of alpha-CD is most populated between the C6 and C7 atoms of DTAB. This structure is very close to that estimated by NMR. The alpha-CD molecule underwent a restricted rotation in a range of 60 degrees with regard to the plane of the dodecyl chain: this plane at the most population is middle between the two diagonal lines of the normal hexagon formed by 6 O4 atoms of alpha-CD. The published NMR data were reanalyzed in terms of the rotation angle, and a slightly better structure was obtained. The distortion of the alpha-CD cavity from the normal hexagon was decreased upon complex formation with DTAB. The deviation of the center of alpha-CD from the center of the dodecyl chain predicted by molecular dynamics simulations is consistent with the NMR data. The secondary-in structure is energetically more stable than the primary-in structure, as calculated by molecular mechanics with CVFF and Amber force fields. This result is consistent with the NMR data. Molecular dynamics simulations were also carried out for the primary-in structure. Some of the results are close to those of the secondary-in structure.

Stoichiometric and microenvironmental effects on hydrolysis of propantheline and oxyphenonium bromides in cyclodextrin solutions

The effects of alpha-, beta-, and gamma-cyclodextrins (CDs) on the basic hydrolysis of propantheline bromide (PB) and oxyphenonium bromide (OB) are analyzed in terms of the stoichiometry and microenvironments of their complexes. The rate constant of each species is evaluated with binding constant data for the 1:1, 1:2, and 2:1 complexes. The dielectric constant of the binding site of PB is estimated from the ultraviolet maximum wavelength in reference with the ethanol-water and dioxane-water systems. The energy-optimized structures of some complexes of PB with beta- and gamma-CD are obtained by molecular mechanics. Because the ester linkage of PB in the 1:1 complex with alpha-CD and in the 2:1 complex with gamma-CD is located near hydroxyls of the CD rim, these complexes catalyze the hydrolysis of PB. In contrast, the hydrolysis is inhibited by the formation of the 1:1 and 1:2 complexes of beta-CD and the 1:1 complex of gamma-CD because the ester linkage of PB is rather deeply incorporated into the CD cavities for these complexes. All the CDs inhibit the hydrolysis of OB. The rate constant of the 1:1 complex of OB and CD is in the decreasing order alpha-CD > gamma-CD > beta-CD. This order is consistent with that of the local dielectric constants of the binding sites.

[Software development for calculation of molecular surface area and its application to hydrophobic interaction]

A novel method of calculating the water-accessible molecular surface area from the number of points generated on the molecular surface was developed. This method yielded a molecular surface area with high accuracy and speed. The molecular surface area of lecithin shows an excellent linear correlation with the logarithm of the critical micelle concentration for many lecithins having different acyl chains. The solution structure of oxyphenonium bromide estimated from the molecular surface area approach was close to that obtained from NMR. Furthermore, the change of molecular surface area, delta S(HG), with docking of host and guest was defined and its calculation method was developed. Because both the host and the guest generally consist of hydrophilic and hydrophobic atomic groups, delta S(HG) was divided into such four terms as delta Soo(HG), delta Sow(HG), delta Swo(HG), and delta Sww(HG). For instance, delta Soo(HG) is the decrease in surface area with contact between the hydrophobic surfaces of the host and the guest. When the guest molecule was moved along the symmetry axis of cyclodextrin (CyD), the structure of a complex having the maximum value of delta Soo(HG) corresponds with the crystal structure. The solution structures of several inclusion systems were predicted by this method. For various systems including alpha-CyD, beta-CyD, gamma-CyD, and aromatic and aliphatic guests, the maximum values of delta Soo(HG) showed a good correlation with the logarithms of the binding constants. This relationship will be used for the prediction of the binding constants for CyD and other host-guest systems.