The indexing process, that is determination of unit-cell parameters, is the first important stage of the crystal structure determination from powder diffraction data (SDPD). Accurate Bragg positions (2θ or d values) of 10∼20 peaks picked up by peak-search from low 2θ angle side are indispensable for determination of lattice constants with hkl indices. Subsequently, space group can be estimated according to systematic absences based on obtained lattice constants. Integral intensities of each reflection are tentatively extracted by the whole powder pattern fitting i.e. the Le Bail or Pawley methods. Crystal structure of small organic molecule can be solved by the direct method or the charge flipping algorithm. In this report, the brief summary about indexing and whole pattern fitting was described. Furthermore, some practical examples of SDPD of small organic molecules by the direct method (EXPO2009) and the charge flipping (Superflip) were demonstrated.
The crystal structure determination from powder diffraction (SDPD) has attracted wide interests for its huge potential to accelerate a design, synthesis, and characterization of the materials in the fields of nano- and bio- technologies. One of the most important progresses of the SDPD is the development of the direct-space strategy. In this report, SDPD by direct-space strategy has been described. Fundamental aspects of the strategy have been demonstrated with some examples. Global optimization methods within direct-space strategy such as Grid Search, Simulated Annealing, and Genetic Algorithm have been described including detailed methodologies.
Crystal structures of two protein complexes that work through large quaternary changes were determined. The structures of giant hemoglobin of an invertebrate reveal completely different manners of molecular assembly and cooperative mechanisms of invertebrate hemoglobin. The structures of V1-ATPase reveal another rotation mechanism of rotary ATPase/synthase superfamily.
Charge density analysis by single-crystal X-ray diffraction using high-energy synchrotron radiation reveals molecular structure of C60 fullerene containing lithium atom, Li@C60. Weak charge density peaks of the lithium atom are clearly reconstructed near the centers of six-membered rings of the C60 cage. The molecular structure of Li@C60 is quite different from that of C60 fullerene containing a gas molecule at the cage center such as H2@C60. The existence of electrostatic attractive interaction between a Li+ cation and SbCl6− anions through the C60 cage is suggested from the crystal structure.
Tail anchored proteins, defined by a single transmembrane domain at C-terminus, are post-translationally inserted into the membrane by Get3 ATPase. Here we report the crystal structure of Get3 in ADP-bound and nucleotide free forms. Get3 forms an open dimer conformation, in which two subunits are linked by a Zn2+ ion. Together with the biochemical studies, we propose the ATP independent TA protein binding, and the membrane insertion by conformational change of Get3 coupled with ATP hydrolysis.
Genetic Algorithm (GA) applied to ab initio structure determination from synchrotron powder diffraction is described. It seems to have an advantage over other real space methods for ab initio structure determination because of the existence of schema theorem. As an example, the case of Prednisolone Succinate is shown in some detail. Future development of GA in crystallography is briefly described.
The formation of a triangular lattice of the topological spin textures (skyrmions) is suggested by recent neutron scattering studies on B20-type helical magnets. We have observed the real-space image of the skyrmion lattice in Fe0.5Co0.5Si by Lorentz transmission electron microscopy. Besides the perfect hexagonal arrangement of skyrmions, we have observed the disordered or isolated skyrmions as well as the coexistence with helical spin order. Furthermore, we have found that the skyrmion lattice is quite stable over a wide temperature region in a thin crystal plate with its thickness smaller than the skyrmion lattice constant.
Spherical aberration correctors recently developed for transmission electron microscopes (TEM) and scanning TEM (STEM) have enabled direct imaging of single molecules and atoms at low electron acceleration voltages. Here, we review some recent studies on carbon nanotubes (CNTs) and fullerene nanopeapods using aberration-corrected TEM/STEM operated at 120 kV or lower voltages. Local structures of individual CNTs are visualized in details including various defects such as atomic vacancies and so-called Stone-Wales defects. Atomic-level structures of fullerene molecules inside CNTs are unambiguously visualized. Single atoms of lanthanides and calcium in nanopeapods are identified by using STEM-EELS operated at 60 kV.