Masaaki Shiono

Phytochemistry: structure of the blue cornflower pigment.

The same anthocyanin pigment makes roses red but cornflowers blue, a phenomenon that has so far not been entirely explained. Here we describe the X-ray crystal structure of the cornflower pigment, which reveals that its blue colour arises from a complex of six molecules each of anthocyanin and flavone, with one ferric iron, one magnesium and two calcium ions. We believe that this tetrametal complex may represent a previously undiscovered type of supermolecular pigment.

Ab initio structure determination of quasicrystals by density modification method

A novel density modification method has been applied to phase reconstruction of X-ray single crystal data of quasicrystals. This is based on the low electron density elimination (LDE) method that is an ab initio structure determination method for crystal in the real space. The location, size and shape of the occupation domains for quasicrystals in the n-dimensional (nD) unit cell are obtained without any model structure. Therefore, the LDE method can be a substitute for the direct method for quasicrystals as nD crystals. The structure solution can easily be found in the trial sets (normally 100 sets) and is confirmed by the subsequent analysis. The result is used as a crude starting model for constructing a detailed structure model of quasicrystals. The solutions of several quasicrystals (i-AlPdMn, i-ZnMgHo and i-CdYb) are exemplified. The reliability and limitations of the algorithm to retrieve the quasicrystalline structures will also be discussed.

Ab initio structure determinations by direct-space methods: tests of low-density elimination

The low-density elimination method, which was developed for phase extension and refinement, has been investigated regarding its power to solve crystal structures starting from completely random phase sets. The method employs a multi-solution strategy. Low-symmetry structures are easily solvable where phase restrictions are only applied to a few reflections. Even with high-symmetry structures, a reasonable solution was obtained regarding centric reflections as general reflections. It is also shown that the structure of a small protein ribonuclease Ap1 is solvable if the positions of the five S atoms in the protein are known.

Caged and clustered structures of endothelin inhibitor BQ123, cyclo(-d-Trp-d-Asp−-Pro-d-Val-Leu-)\cdotNa+, forming five and six coordination bonds between sodium ions and peptides

BQ123 is a cyclic pentapeptide and a potent endothelin-1 inhibitor. The crystal structure of the BQ123 sodium salt was determined as the first example of an endothelin inhibitor. Four independent molecules and many solvent molecules were found in the asymmetric unit; the total weight was about 3000 Da. The precise structure including the solvent molecules was determined using high-resolution data collected on a synchrotron source. Sodium ions formed unique structures with five and six coordination bonds and their forms were distinguished into three classes. An ion was sandwiched by two BQ123 molecules. This peptide-sodium (2:1) complex showed a cage-like structure and octahedral coordination was observed. Sodium ions also formed a cluster composed of hydrated water molecules and peptides. Two sodium ions were contained in this cluster, making five coordination bonds. Despite having the same coordination numbers, these ions were distinguishable by differences in the polyhedra. One was trigonal bipyramidal (having six planes) and the other was square pyramidal (having five planes). Both shapes were very similar to each other, although the synchrotron data clearly revealed slight geometrical differences.

Structure of icosahedral Zn-Mg-Ho quasicrystals determined by a density modification method

Abstract The structure of icosahedral Zn60Mg31Ho9 quasicrystal has been determined, by means of ab initio structure determination, by applying a novel density modification method (low density elimination method) within a framework of 6D description. The suggested Ho sites in the 3D structure obtained as a section of resulting 6D electron density are consistent with the results of magnetic diffuse scattering.

Ab initio structure solutions of quasicrystals by a Density modification method

Abstract A unique and powerful density modification method for solving multi-dimensional crystal structures has been developed. The method is an extension of the Low Density Elimination (LDE) method1,2,3. The LDE method was made applicable to multi-dimensional crystal structures and applied to several quasicrystals including an unknown structure. Tests on the X-ray single crystal data of icosahedral AlPdMn4 and synthetic data of decagonal AlNiCo quasicrystals suggests that the multi-dimensional LDE method can easily solve quasicrystal structures starting from completely random phases. The procedure has also been applied to an unknown structure of icosahedral ZnMgHo quasicrystal. Multi-solution strategy was employed and 28 resultant maps clearly showed the positions and shapes of occupation domains. We were convinced by analyzing the map that the 28 results were the solutions.

Unique sodium-caged structure of a potent endothelin-1 inhibitor: crystal structure of BQ123 sodium salt, cyclo(-D-Trp-D-Asp−-Pro-D-Val-Leu-)·Na+

The crystal structure of cyclo(D-Trp-D-Asp−-Pro-D-Val-Leu-)·Na+, a potent endothelin-1 antagonist, showed four conformational isomers and two Na+-caged structures in pairs.