The dimeric complex of cyclomaltoheptaose with 1,14-tetradecanedioic acid. Comparison with related complexes.

The structure of the complex of cyclomaltoheptaose (beta-cyclodextrin, betaCD) with 1,14-tetradecanedioic acid has been determined and refined to a final R=0.0693 based on 9824 observed reflections. Each diacid molecule threads through two betaCD monomers arranged in dimers thus, forming a [3]pseudorotaxane. The end carboxylic groups of adjacent dimers, far apart and fully hydrated, are associated indirectly through water molecules. The positioning of the carboxylic groups with respect to the betaCD dimer and the H-bonds with water molecules are very similar to these of the corresponding complexes of the diacids with 12 and 13 carbon atoms. The bending in the middle of the aliphatic chain is more prominent, compared to that of the corresponding guests with less carbon atoms, thus the end carboxylic groups stay in the same height of the primary faces of the betaCD dimeric complex. As a consequence of the present structure, more close contacts are observed between calculated H-atoms of the guest and O-atoms of the host inside the cavity. This bending is allowed by the width of the betaCD dimer cavity at the secondary interface region.

Structure of the complex of beta-cyclodextrin with beta-naphthyloxyacetic acid in the solid state and in aqueous solution.

The structure of the complex of beta-cyclodextrin (cyclomaltoheptaose) with beta-naphthyloxyacetic acid was studied in solid state by X-ray diffraction and in aqueous solution by 1H NMR spectroscopy. The complex crystallizes in the channel mode, space group C2, with a stoichiometry of 2:1; two beta-cyclodextrin molecules related by a twofold crystal axis form dimers, in the cavity of which one guest molecule is found on average. The above stoichiometry indicates one guest per beta-CD dimer statistically oriented over two positions or two guest molecules in pi-pi interactions in half of the beta-CD dimers and the rest of the beta-CD dimers empty. In addition, occupancy of 0.5 for the guest per every beta-CD dimer is in accord with the occupancy of the two disordered primary hydroxyls. These two hydroxyl groups, to which the carboxylic oxygen atoms of the guest are hydrogen bonded, point towards the interior of the beta-CD cavity. In aqueous solution, the 1H NMR spectroscopic study indicated that there is a mixture of complexes with host-guest stoichiometries both 1:1 and 2:1.

Non-covalent interactions in the crystallization of the enantiomers of 1,7-dioxaspiro.

The enantiomers of racemic olive fly sex pheromone 1,7-dioxaspiro[5.5]undecane (1) have been isolated by crystallization with enantiospecific cyclodextrin hosts: (S)-(1) crystallizes with heptakis(2,3,6-tri-O-methyl)-beta-cyclodextrin (TMbetaCD) and (R)-(1) with hexakis(2,3,6-tri-O-methyl)-alpha-cyclodextrin (TMalphaCD). The crystal structure of TMbetaCD/(S)-(1) from synchrotron radiation data at 100 K, determined for the first time, proves that TMbetaCD crystallizes with only the (S)-enantiomer from the racemic mixture. Comparison with the 100 K structure of TMalphaCD/(R)-(1) redetermined with synchrotron data has provided insight into the interactions between each of the hosts with the corresponding enantiomeric guests. Owing to the high resolution of the data and the unusually high quality of the crystals, localization of the H atoms has been achieved, a rare accomplishment for cyclodextrin X-ray structures. This made possible, apart from the geometry of the complexes, the detailed description of a five-membered-ring water cluster with very well ordered hydrogen bonding. The enantiospecificity exhibited by the described systems reveals the subtle differences of the weak intermolecular forces involved in the selective binding of the two optical antipodes by the two hosts. The binding geometry in the two complexes is different, but it is effected in both by numerous host-guest C-H.O interactions, resulting from induced fit of the hosts toward each of the enantiomeric guests. In TMalphaCD/(R)-(1) two of these H.O host-guest distances, directed toward the acetal O atoms defining the chirality of the guest, are much shorter than the rest and also shorter than all the H.O distances in TMbetaCD/(S)-(1). Moreover, (R)-(1) interacts not only with the enclosing host, but with other hosts in the crystal lattice, in contrast to (S)-(1) in the TMbetaCD/(S)-(1) complex which is isolated inside channels formed by the host molecules. The above differences are reflected in the much higher binding constant of TMalphaCD/(R)-(1) compared with that of TMbetaCD/(S)-(1) ( approximately 6800 and approximately 935 M(-1), respectively), determined by NMR in aqueous solution, and the ability of TMalphaCD to selectively precipitate (R)-(1) from racemic (1) in much higher yield than TMbetaCD precipitates (S)-(1).

The crystal structure of the inclusion complex of cyclomaltoheptaose (beta-cyclodextrin) with 4-tert-butyltoluene.

The crystal of the 1:1 complex of 4-tert-butyltoluene with cyclomaltoheptaose (beta-cyclodextrin, beta CD) is triclinic P1 with a = 15.562(2), b = 15.564(4), c = 15.835(3) A, alpha = 102.11(2), beta = 102.15(1), gamma = 103.64(2) degrees, V = 3505(1) A3, and Z = 2. The two independent beta CD molecules in the asymmetric unit form a dimer by hydrogen bonding involving HO-3, which accommodates two molecules of the guest. The hydrophobic guests are enclosed completely in the beta CD cavities with the tert-butyl groups in the hydrophobic region beneath the primary hydroxyl groups. The aromatic rings have two orientations and their toluene methyl moieties could not be located but were calculated to be at the interface of the two monomers. The dimers form channels along the c axis. The inter-dimer space is filled with 17 molecules of water distributed over 25 sites. A dense network of hydrogen bonds is formed, involving the beta CD hydroxyl groups and water molecules.

The crystal structure of the inclusion complex of cyclo-maltoheptaose (beta-cyclodextrin) with 3,3-dimethylbutylamine.

The crystal of the 1:1 complex of 3,3-dimethylbutylamine with cyclomaltoheptaose (beta CD, beta-cyclodextrin) is monoclinic C2 with a = 19.187(9), b = 24.56(1), c = 15.893(7) A, beta = 108.77(4) degrees, V = 7091 A3, and Z = 4. Two beta CD molecules, held together by intermolecular hydrogen bonds involving HO-3, form dimers, in the cavities of which two 3,3-dimethylbutylamine and two water molecules are accommodated. The guest molecule is completely enclosed in the cavity. The amino group is located at the secondary-hydroxyl-group side, and is hydrogen-bonded to the entrapped water molecules. The dimers form channels along the c axis. The inter-dimer space is filled with 10.7 water molecules that are distributed over 14 sites, and there is a dense network of hydrogen bonds involving the water molecules and the beta CD hydroxyl groups.

The folding and quaternary structure of trimeric 2-keto-3-deoxy-6-phosphogluconic aldolase at 3.5-A resolution.

An X-ray crystallographic structure determination has been carried out on 2-keto-3-deoxy-6-phosphogluconic (KDPG) aldolase at 3.5-A resolution using the multiple isomorphous replacement method with three heavy atom derivatives along with anomalous dispersion contributions from two of the derivatives. Crystals grown from ammonium sulfate-phosphate buffered (pH 3.5) solutions were: cubic, a= 103.40 (4) A, space group P213. KDPG aldolase consists of trimeric heterologous assemblages utilizing crystallographic threefold symmetry. The overall profile of the oligomeric structure viewed down the threefold axis resembles that of a ship propeller while the subunits are approximate irregular oblate ellipsoids (25 X 45 X 45 A). The folding of most of the polypeptide chain was traced unambiguously. Secondary structural features consist of nine helical regions (75 residues, 35%) and a pair of two parallel chains. The subunit contains a long empty channel which is about 9 X 9 X 30 A with one of the pair of parallel chains forming part of the wall. Three mercury binding sites are located in this channel. These might correspond to the two readily accessible and one of the two buried cysteine residues of each subunit. The channel terminates with another cavity of about 8 X 10 X 25 A near the surface of the oligomeric structure. The regions of the subunits near the threefold axis are characterized by a high degree of secondary structural organization and these make close intersubunit contacts. Quarternary interactions are due mainly to side-chain interactions of helices.