Molecular structure of an organic photocatalist, 9-mesityl-10-methylacrinium cation, at a photo-induced electron-transferred state was directly observed by a pump-probe single crystal X-ray structure analysis. Observed photo-induced structural changes were the bending of the N-methly group and the positional change of perchrolate anion, which co-exists in the crystal. Those structural changes respectively represented the reduction of the 10-methylacridinium cation and the oxidation of the mesitylene by photo-induced electron transfer. The dyhedral angle betweem 10-methylacridinium and mesitylene moieties at the electron-transferred state was almost identical with the ground one. This is a clear evidence for restriction of intramolecular back electron transfer and long-lived character of the electron-transferred state. The observed geometrical features will provide a solid basis for designing a novel artificital photosynthetic system.
This account describes the development of direct observation of unstable species and chemical reactions in single crystals by X-rays. The methodology was developed by three steps: utilization of 1) the crystal packing of target molecules, 2) a void of a cage compound (a prison cell approach), and 3) a pore of coordination networks (a crystalline molecular flask approach). Using these strategies, we succeeded in observing radical, nitrene, carbene, a 2+2 reaction, condensation reactions, imine, hemiaminal, and so on. Noteworthy is that, using a porous coordination network as a nano-meter sized flask, various chemical reactions can be directly observed by X-rays. The crystalline molecular flask concept can be a general method to observe many kinds of chemical processes.
Time-resolved X-ray absorption spectra was conducted to investigate transient structure change in the triplet metal-to-ligand charge transfer (3MLCT) state of ruthenium(II)-tris-2,2'-bipyridine ([RuII(bpy)3]2+). The results obtained by visible (400 nm) and UV (267 nm) excitation indicates that electrostatic interaction between the oxidized Ru atom and the reduced bipyridine ligand are the dominant factors affecting the Ru-N bond contraction. The EXAFS analysis of the 3MLCT state shows decrease of Ru-N distance and increase of Debye-Waller (DW) factor. An increase of the DW factor suggests that fast and localized structural distortions due to electron hopping exist in the 3MLCT excited state.
This review introduces pedal motion of molecules in crystals, where a pair of benzene rings in a molecule move like the pedals of a bicycle. The pedal motion brings about conformational interconversions, which result in disordered crystal structures. This type of molecular motion takes place in a wide range of compounds. This review describes how to investigate molecular motions using X-ray diffraction analysis, especially focusing on disorder analysis as a function of temperature.
The combination of small-angle X-ray solution scattering (SAXS) experiments and molecular dynamics (MD) simulations is now becoming a powerful tool to study protein dynamics in solution at an atomic resolution. We have developed a method called MD-SAXS, in which this combination is used with explicit evaluation of X-ray scattering from water molecules hydrating protein molecules. This method offers a link between low-resolution structural information from SAXS and the three-dimensional high-resolution structure. The study using MD-SAXS method revealed the importance of intrinsic dynamics of DNA-binding protein EcoO109I in its function.
The mechanistic analysis and visualization of solid-state reactions of unsaturated carboxylic acid derivatives and the polymer crystals therefrom are described. We revealed a change in the crystal structures during the solid-state polymerization and the EZ isomerization of muconates on the basis of the results of X-ray single crystal structure analysis as well as powder X-ray diffraction measurements. We also describe the visualization of the processes of crystal phase transition and an intercalation reaction using the monomer and polymer crystals of unsaturated carboxylic acid derivatives.
Described are the nonporous but yet gas-sorbing molecular crystals of nitrogen-bridged calixarene analogues (azacalixarenes) that have recently emerged as a new calixarene family. Single crystals of cyclic tetramer with nonporous crystal architecture exhibited the highly selective uptake of carbon dioxide, and its sorption state was successfully visualized at an atomic level by means of X-ray crystallography. Cyclic pentamer yielded two polymorphs both with nonporous crystal structures; one polymorph was truly nonporous to all of the examined gases, whereas another one showed the selective capture of carbon dioxide. Here we report the solid-gas sorption behavior and mechanism in the nonporous molecular crystals of this new calixarene family.
We visualized the course of nucleotidyl transfer reaction by human DNA polymerase η (Pol η) using time resolved protein crystallography. The reaction was initiated by exposing Pol η-DNA-dATP crystals to 1 mM Mg2+ at pH 7.0 and stopped at various time points by freezing. The substrates and two Mg2+ ions are aligned for reaction within 40 s. Transient electron densities indicate that deprotonation and an accompanying C2'-endo to C3'-endo conversion of the nucleophile 3'-OH are rate limiting. A third Mg2+ ion, which arrives with the new bond and stabilizes the intermediate state, may be an unappreciated feature of the two-metal-ion mechanism.
Neutron crystallography enables us to identify the accurate hydrogen positions in proteins, which play important roles in many chemical reactions in living system. Here we show our results of neutron structure determination of enzymes in complex with its inhibitors which corresponds to transition state analogues. Neutron structure analysis elucidated the detail catalytic reaction of each enzyme by direct observation of hydrogen atoms. Furthermore we would like to introduce a new neutron beam line for neutron structural biology planned at MLF in J-PARC.
Molecular reactions involving proteins take place at a variety of hierarchical spatial levels, ranging from Å to sub-μm scales, e.g., local chemical reactions inside protein molecules, tertiary structural changes of whole molecules, and association-and-dissociation of ensembles of multiple molecules. Because of the absence of techniques to observe all of these reactions coincidentally, it is important to choose an adequate method for investigating the molecular events occurring at each level of the spatial hierarchy. In this paper, I describe the tertiary structural changes and the local structure of hydrogen bonding network of the light-sensor protein, photoactive yellow protein (PYP), investigated by neutron/X-ray joint crystallography and wild-angle solution scattering experiments, respectively. Furthermore, based on these results, the interdependency among the molecular events at the different spatial hierarchies will be discussed.
Photochromism is reversible change of color by photoirradiation. In recent years, photochromic compounds have been attracting considerable attention of the chemists because of their potential application in optical memory media and optical switching devices etc. However, photochromic property such as the lifetime of the colored species depends on the crystal structure of the compounds, therefore it is difficult to control. Here we designed new hybrid cobalt complexes with photochromic compounds and show the dynamical change of the color fading rate of photochromic compounds by structural change with photoisomerization of alkyl group of the complexes in the crystalline-state.
Exposure of 4-methoxyazachalcone (1) with a head-to-head orientation to HCl gas produced the corresponding HCl salt with a head-to-tail stacked arrangement, which was confirmed by PXRD experiments. A plausible mechanism for the reorientation was proposed, in which cation-π interaction plays a key role during the processes. Irradiation of the produced salt afforded synHT dimer in high regio- and stereoselectivities, thus showing the effectiveness of the cascade process in crystals. Photodimerization of styrylpyridine (5) and 5·HCl·2H2O was also investigated. While 5 was photo-stable, irradiation of 5·HCl·2H2O gave synHT dimer in high selectivity. X-ray structural analysis of 5·HCl·2H2O clarified that water molecules assist the assembly of the molecules in a head-to-tail and face-to-face fashion through N-H⋅⋅⋅O hydrogen bonds in combination with cation-π interactions between the pyridinium and aromatic rings. Dehydration of 5·HCl·2H2O produced anhydrous 5·HCl, which was also photo-stable. This was rehydrated to produce 5·HCl·2H2O by exposure to H2O vapor.
Molecular rearrangement and reactions occur between crystals spontaneously or by mechanical methods by way of molecular diffusion, cleavage and creation of hydrogen bonds or formation of co-ordination bonds, while retaining the memory of original crystal structures. Therefore, crystals thus formed in the solid state are often different from those obtained from conventional solution crystallization. Photocyclization of 2-(o-substuted-arylthio)-3-methyl-2-cyclohexene-1-ones within a crystal is influenced by external heavy-atom effect, and affords unique reaction products. By placing reactant molecules in a different environment by way of co-crystal formation, we could switch reaction pathways and hence product distribution in the solid state.
Recently, crystalline metal complexes with regular nanochannel structures have been extensively studied. The characteristic features of these metal complexes are controllable channel structures approximating molecular dimensions, designable pore surface functionality, and flexible frameworks responsive to guest molecules. Owing to these advantages, successful applications range from molecular storage/separation to heterogeneous catalysts. In particular, use of their tunable nanochannels for polymer chemistry can allow precision polymer synthesis and unique polymer confinement. This review article discusses promising approaches to multiple controls of polymer structures, analysis systems for low-dimensional polymer assemblies, and the construction of functional polymer nanohybrid materials.
In recent years, protein crystals receive much attention in the filed of nanobiomaterial sciences because they consist of highly ordered protein assemblies with unique nano reaction environments. Therefore, protein crystals have been utilized as nanosized porous materials for application in separation processes, heterogeneous catalysis, drug delivery, and so on. These crystals are able to capture and deposit metal ions and metal complexes within solvent channels because the amino acid side chains responsible for coordinating the metal ions are periodically aligned on the surface of solvent channels of the crystal lattices. Here, we elucidate accumulation process of metals by X-ray crystallographic analysis of protein crystals containing metal complexes or ions and apply to catalytic reactions and preparation of magnetic materials.