Kazuaki Aburaya

X-ray diffraction study of a pseudo single crystal prepared from a crystal belonging to point group 2

A pseudo single crystal (a composite of matrix resin and powder crystallites, wherein the individual crystallites are aligned three-dimensionally) was prepared from a powder of sucrose, and its X-ray diffraction pattern was studied. A powder of sucrose crystals suspended in a UV-curable resin precursor was subjected to magnetic alignment in order to align the individual crystallites three-dimensionally, and then the resin precursor was photopolymerized to maintain this orientation. The pseudo single crystal thus obtained produced a well resolved X-ray diffraction profile that is similar to that produced by a twin crystal. The origin of the twin orientation was explained in terms of the interplay between the symmetry of magnetic susceptibility axes and the crystal symmetry (point group 2) of sucrose. The crystal structure of sucrose solved using the pseudo single crystal was in excellent agreement with that solved using a single crystal.

Flexible host frameworks with diverse cavities in inclusion crystals of bile acids and their derivatives

We have systematically investigated structures and properties of inclusion crystals of bile acids and their derivatives. These steroidal compounds form diverse host frameworks having zero-, one- and two-dimensional cavities, causing various inclusion behaviors towards many organic compounds. The diverse host frameworks exhibit the following guest-dependent flexibility. First, the frameworks mainly depend on the included guests in size and shape. The size-dependence is quantitatively estimated by the parameter PCcavity, which is the volume ratio of a guest molecule to a host cavity. The resulting values of PCcavity lie in the range of 42-76%. Second, each of the host frameworks has its own range of the values. Some guests can employ two different frameworks with the boundary values, explaining formation of polymorphic crystals. Third, the host frameworks are selected by host-guest interactions through weak hydrogen bonds, such as NH/pi and CH/O. The weak hydrogen bonds play an important role for various selective inclusion processes. Fourth, the host frameworks are dynamically exchangeable, resulting in intercalation and polymerization in the cavities. These static and dynamic structures of the frameworks demonstrate great potential of crystalline organic inclusion compounds as functional materials.

Single crystal structure analysis via magnetically oriented microcrystal arrays

X-ray single crystal structure analysis was performed on three-dimensional magnetically oriented microcrystal arrays (3D-MOMAs) of L-alanine, 1,3,5-triphenyl benzene, and cellobiose. A 3D-MOMA is a composite in which powdery microcrystals are aligned three dimensionally. Microcrystals suspended in a UV-curable monomer were subjected to a time dependent magnetic field, followed by consolidation of the monomer to fix the 3D alignment of the microcrystals. The structures determined from X-ray diffractometry of the three 3D-MOMAs were in excellent agreement with those of the corresponding single crystals reported in the literature, demonstrating the usefulness of the 3D-MOMA technique for single crystal structure analyses in circumstances where a large single crystal is not available.

Guest-induced inversion of an asymmetric host layer in inclusion crystals of cholic acid

Cholic acid, a typical asymmetric host, forms inclusion crystals with six 1,2,3-trisubstituted benzenes and five 1,2,4-trisubstituted benzenes as guests. All the eleven crystals have a bilayer structure composed of hydrophilic and lipophilic layers. The guest molecules are included in one-dimensional (1-D) cavities within the lipophilic layers, where the host molecules array in an antiparallel mode. On the other hand, in the absence of host–guest hydrogen bonds, the host arrangements in the hydrophilic layers change depending on the guest shape; 1,2,3- and 1,2,4-trisubstituted benzenes give the parallel and antiparallel arrangements that are categorized into shv and shv# patterns, respectively. The former crystals have a size-fit relationship between the guest molecule and the host cavity lesser than usual inclusion crystals involving the latter crystals. Therefore, the shape-fit relationship plays an important role in the formation of the host arrangements with the shv pattern. Moreover, the crystal structures of cholic acid with 1,2,3-trisubstituted benzenes are similar to those of deoxycholic acid with the identical guests. This is a rare example that hosts with a different number of hydroxyl groups in their molecular structure form an isomorphous crystal structure.

Excellent enantio-selective enclathration of (2R,3S)-3-methyl-2-pentanol in channel-like cavity of 3-epideoxycholic acid, interpreted by the four-location model for chiral recognition

Pure (2R,3S)-3-methyl-2-pentanol is resolved from the racemates by a steroidal host; the interpretation of the recognition mechanism based on the crystal structure reveals that CH/O interaction between the host and guest plays a decisive role in enantio-selective enclathration of the small aliphatic secondary alcohol.

Single-crystal structure determination from microcrystalline powders (∼5 μm) by an orientation attachment mountable on an in-house X-ray diffractometer

An X-ray attachment that can realize single-crystal X-ray diffraction patterns from microcrystalline powders is proposed. Single-crystal diffraction data are acquired in situ and analyzed using conventional computer software to determine the crystal structure of the microcrystals. The performance of the attachment is demonstrated using L-alanine microcrystals (∼5 μm).

Dependence of the enantioselectivity on reversion of layer directions in cholamide inclusion compounds

Cholamide includes 2,2-dimethyl-3-hexanol with high enantioselectivity, which is derived from reversion of layer direction due to a methyl group added to 2-methyl-3-hexanol.

X-Ray Diffraction from Magnetically Oriented Microcrystal Suspension

A three dimensionally magnetically oriented microcrystal array (3D-MOMA) is attractive to determination of a crystal structure as well as a molecular structure because it does not require a single crystal with sufficient size and quality for diffraction studies. We have developed a novel method to fabricate 3D-MOMA and determined several crystal structures using the 3D-MOMAs[1],[2]. However, the structure determination through MOMA requires a solidification treatment with UV curable monomer prior to X-ray diffraction experiment. We have developed a new X-ray diffractometer equipped with a magnetic field generator, which makes it possible to collect diffraction data without the solidification treatment. In this poster, we describe X-ray diffraction analyses of a magnetically oriented microcrystal suspension (MOMS) of L-alanine without the solidification treatment. A suspension of L-alanine microcrystals was poured in a glass capillary and rotated at a constant speed in a magnetic circuit attached in the X-ray diffractometer. Then, diffraction images were collected every 60 seconds. In the initial phase, the diffraction pattern showed a broad shape similar to that from a powder sample. As time goes on, diffraction patterns have gradually changed to single-crystal like patterns. After 2 hours, the shape of diffraction spots became as sharp as that of a single crystal. This observation shows that the microcrystals are oriented in the same direction. Owing to the improvement of the magnetic circuit and X-ray diffractometer, the quality of the diffraction has been greatly improved compared to that reported previously[3]. Further details of the analyses will be shown in the poster.

One instrument to answer to all your challenges? Cu/Mo, small crystals and more...

Today’s most interesting samples rarely make our jobs easy for us. Unfortunately many of the systems that we want to study crystallise as very tiny crystals. This can be particularly true of pharmaceuticals but is a widespread difficulty in many areas of chemistry and materials where we repeatedly face these challenges. Constant pressure to deliver high quality results and extract as much information as possible are coupled with pressures to do so both cost and time efficiently. The combination of the Rigaku MicroMax 007HF generator with the RAPID II unique curved, large area image plate detector already provides a hugely flexible tool to address many of these challenges. Advances in optics now mean that this powerful combination of generator and detector can be used with both Mo and Cu radiation (or Cu and Cr) on the same instrument, just by swapping the rapidly interchangeable targets. The image plate is highly sensitive for all these wavelengths providing for high quality data without compromise. The extremely large active area of the detector (-60 to 144°) allows a massive solid angle of data to be collected in a single exposure; ideal for fast high resolution Cu data for absolute configuration determination and equally for very high resolution data with Mo radiation. The exceptional low noise and wide dynamic range also suit the long exposure times often necessary for very tiny crystals – even with a brilliant source without saturation or excessive noise problems. This single instrument is so versatile that it can replace several others – for single crystal diffraction studies (both small and macromolecular) at both wavelengths as well as powder diffraction. Results of studies using this new dual wavelength capability system will be presented.

Chiral recognition in cholamide crystals: four-location model for hydrogen and stereogenic carbon

bioactivities, antifungal bioactivities and inhibitor activities against viruses. In the past few years, we have pursued investigations on the new thiourea derivatives. As a continuation of these studies, N-(2,2diphenylacetyl)-N’-(naphthalen-1yl)-thiourea (PANT) has been synthesized and characterized by elemental analysis, IR spectroscopy and H-NMR spectroscopy. The crystal and molecular structure of the title compound has been determined from single crystal X-ray diffraction data. It crystallizes in the triclinic space group P-1, Z = 2 with a = 10.284(2) Å, b = 10.790(2) Å, c = 11.305(2) Å, α= 64.92(3) °, β= 89.88(3) °, γ= 62.99(3) °, V = 983.7(3) Å and Dcalc = 1.339 Mg/m. The molecular structure, vibrational frequencies and infrared intensities of PANT were calculated by the HartreeFock and Density Functional Theory methods (BLYP and B3LYP) using 6-31G(d) basis set. The calculated geometric parameters were compared to the corresponding X-ray structure of the title compound. We obtained 22 stable conformers for the title compound; however the Conformer 1 is approximately 9.53 kcal/mol more stable than the Conformer 22. The comparison of the theoretical and experimental geometry of the title compound shows that the X-ray parameters fairly well reproduce the geometry of the Conformer 17. The harmonic vibrations computed of this compound by the B3LYP/631G(d) method are in a good agreement with the observed IR spectral data. Theoretical vibrational spectra of the title compound were interpreted by means of PEDs using VEDA 4 program. A general better performance of the investigated methods was calculated by PAVF 1.0 program.