Structure Determination from Powder Diffraction data (SDPD) technique for organic and organo-metallic molecular crystals has been developed since 1990s, and is now widely used. The X-ray powder diffraction data has a difficulty in extraction of correct intensity data from overlapping diffraction peaks, however, the development of direct space method overcomes the difficulty, leading to the progress of this area. The SDPD technique was composed of the indexing, intensity extraction, initial structure solution, structure refinement steps and each of them requires very careful treatments. This technique is usually used for crystal structure determination of powdery crystals, and also phase transition and crystalline-state reaction are examined by SDPD technique because single crystallinity is lost in such phenomena.
Techniques to prepare the sample and strategies to measure powder X-ray diffraction data for ab initio crystal structure analysis of organic and organometallic compound are shown together with an introduction to typical optics of powder X-ray diffractometry.
The phytohormone abscisic acid (ABA) plays a key role in the rapid adaptation of plants to environmental stresses such as drought and high salinity. Accumulated ABA in plant cells promotes stomatal closure in guard cells and transcription of stress-tolerant genes. Our understanding of ABA responses dramatically improved by the discovery of both PYR/PYL/RCAR as a soluble ABA receptor and inhibitory complex of a protein phospatase PP2C and a protein kinase SnRK2. Moreover, several structural analyses of PYR/PYL/RCAR revealed the mechanistic basis for the regulatory mechanism of ABA signaling, which provides a rational framework for the design of alternative agonists in future.
Metal complexes with tripodal hexadentate ligands containing three bidentate arms have a pair of optical isomers, that is Δ form and Λ form. We have prepared the metal complexes with two types of tripodal ligands. The complexes are not only mononuclear ones but also multinuclear and self-assembled supramolecular ones. Here, we describe the structures and properties with the emphasis on chirality-related features of them.
The crystal structures of manganese complexes with tridentate, tetradentate, pentadentate, hexadentate, and dodecadentate ligands with oxygen and nitrogen donors are described. Reactions of these ligands with manganese salts afforded mononuclear (MnII, MnIII, and MnIV), dinuclear (MnII2, MnIII2, and MnIIMnIII), trinuclear (MnIII3), and tetranuclear (MnII2MnIII2 and MnIII4) complexes. As for MnII complexes, octahedral, trigonal prismatic, capped trigonal prismatic, and square antiprismatic geometries were found depending on the combination of the organic and anionic ligands. In the case of MnIII complexes, the Jahn-Teller distortions due to the high-spin d4 electronic configuration were observed as elongated or compressed octahedral geometries. An octahedral geometry was confirmed for the Mn (IV) complexes.
Many achiral organic compounds can crystallize in chiral form to generate the chirality in solid-state. We have investigated the asymmetric autocatalysis with amplification of enantiomeric excess using these crystal formed from achiral compounds as an origin of chirality. When the enantioselective addition of diisopropylzinc to pyrimidine-5-carbaldehyde was performed in the presence of chiral crystal, 5-pyrimidyl alkanol was formed in highly enantioselective manner. The absolute configuration of resulting pyrimidyl alkanol was well controlled by the crystal chirality of achiral organic compounds.
Autotaxin (ATX), also known as Enpp2, is a secreted lysophospholipase D that hydrolyzes lysophosphatidylcholine to generate lysophosphatidic acid (LPA), a lipid mediator that activates G-protein coupled receptors to evoke various cellular responses. We solved the crystal structures of mouse ATX alone and in complex with LPAs with different acyl-chain lengths and saturations. The structures reveal a multidomain architecture that may maintain the structure of the hydrophobic pocket, in which the respective LPA molecules are accommodated in distinct conformations. Moreover, our data suggest that the produced LPAs are transferred from the catalytic pocket to cognate receptors through a hydrophobic channel.
X-ray crystallographic analysis of a metalloprotein requires knowing the electronic state of the metal center, if one wants to elucidate the exact function and/or reaction mechanism. As an example, we show our recent structural analysis of the heme oxygenase reaction intermediate which is involved in the third step of the heme degradation reaction. The reaction intermediate was crystallized under anaerobic condition, and the obtained crystals were frozen into liquid nitrogen. The absorption spectra of the single crystal before and after X-ray irradiation were compared with that of the frozen solution in 100 K cold nitrogen stream. The determined structure offers the first solid evidence for the presence of a water cluster in the distal pocket of this catalytically critical intermediate. This structure combined with the QM/MM calculation supports our proposal that the biliverdin is produced via Fe-OOH verdoheme intermediate.