Okimasa Okada

Study of the crystal structure of titanylphthalocyanine by Rietveld analysis and intermolecular energy minimization method

Rietveld analysis and intermolecular energy minimization were used to refine the crystal structure parameters of one of the polymorphs of titanylphthalocyanine (TiOPc), which is a highly photosensitive pigment used in electrophotography. The most probable crystal structure is proposed to be a monoclinic unit cell, space group P21/c. The unit cell parameters are a=1.385 nm, b=1.392 nm, c=1.514 nm and β=120.22°. There are four molecules per unit cell.

Low-Energy Electronic States Related to Contact Electrification of Pendant-Group Polymers: Photoemission and Contact Potential Difference Measurement

Low-energy electronic states, 3-6 eV below the vacuum level, relevant to contact electrification of pendant-group polymers were investigated by means of photoemission and contact potential difference (CPD) measurements under atmospheric conditions. As a result, it was shown that the thresholds of photoemission of the polymers are related to their highest occupied molecular orbital (HOMO) levels derived from modified neglect of diatomic overlap (MNDO) molecular orbital calculation, and that the thresholds exist near the energy corresponding to their work function inferred from CPD measurement. Furthermore, it was found that the contact electrification of the polymers is related to their threshold of photoemission. These results are interpreted in terms of a molecular ion model proposed by Duke et al. [Phys. Rev. B 18 (1978) 5717].

Study of the Crystal Structure of Titanylphthalocyanine by Rietveld Analysis. II

Rietveld analysis with the Monte Carlo method was used to estimate the crystal structure parameters of one of the polymorphs of titanylphthalocyanine (TiOPc). This polymorph is called TiOPc type C (C-TiOPc), and it is a low-photosensitive pigment used in electrophotograpy. In order to determine the relationship between crystal structure and photosensitivity, the crystal structure of C-TiOPc was estimated. The most probable crystal structure is a monoclinic unit cell, space group Cc: a=2.519 nm, b=0.385 nm, c=2.546 nm, β=90.3°, Z=4, dcalc.=1.54 g/cm3.

Roles of conserved basic amino acid residues and activation mechanism of the hyperthermophilic aspartate racemase at high temperature

X‐ray crystallography has revealed two similar α/β domains of the aspartate racemase from the hyperthermophilic archaeon, Pyrococcus horikoshii OT3. The active site is located in the cleft between the two domains where two cysteine residues face each other. This arrangement allows the substrate to enter the cleft and enables the two cysteine residues to act synergistically. However, the distance between their thiolates was estimated to be 9.6 Å, which is beyond the distance for cooperative action of them. We examined the molecular mechanism for the racemization reaction of this hyperthermophilic aspartate racemase by mutational analyses and molecular dynamics simulations. The mutational analyses revealed that Arg48 and Lys164 were essential for catalysis in addition to the putative catalytic cysteine residues. The molecular dynamics simulations revealed that the distance between the two active γ‐sulfur atoms of cysteine residues oscillate to periodically become shorter than the predicted cooperative distance at high temperature. In addition, the conformation of Tyr160, which is located at the entrance of the cleft and inhibits the entry of a substrate, changes periodically to open the entrance at 375 K. The opening of the gate is likely to be induced by the motion of the adjacent amino acid, Lys164. The entrance of an aspartate molecule was observed by molecular dynamics (MD) simulations driven by the force of the electrostatic interaction with Arg48, Lys164, and also Asp47. These results provide insights into the roles of amino acid residues at the catalytic site and also the activation mechanism of a hyperthermophilic aspartate racemase at high temperature. Proteins 2006.

Molecular dynamics studies of titanylphthalocyanine crystals

Molecular dynamics calculations have been used to study the stability of a titanylphthalocyanine (TiOPc) crystal called Y-form. This crystal is of interest as a photoconductive material. A Parrinello–Rahman molecular dynamics calculation and a rigid-molecule intermolecular potential have been used in this study. The proposed TiOPc Y-form crystal structure was found from powder X-ray diffraction analysis to be stable from 300 to 600 K, indicating that the crystal structure proposed is reasonable.

Molecular dynamics simulations for glutamate-binding and cleft-closing processes of the ligand-binding domain of GluR2

The gating of ion channel of ionotropic glutamate receptors is controlled by the structural change of the ligand-binding domain of GluR2. We examined the roles of residues in the glutamate-binding and cleft-closing mechanisms by molecular dynamics (MD) simulations. A glutamate entered the cleft deeply within the order of nanoseconds and the cleft locked the glutamate completely at 15 ns in an MD run. TYR450 seemed to regulate the orientation of the glutamate upon binding by cation-π interaction. A semi-open state was identified in the free energy profile evaluated with the structures on the spontaneously glutamate-bound and cleft-closed pathway by the unbiased MD simulations for the first time to our knowledge. In the semi-open state, the two sub-domains were bridged by two hydrogen bonds of GLU705 in the sub-domain 2 with TYR732 in the sub-domain 1 and with the glutamate bound to the sub-domain 1 until the transition to the closed state.

Phase transition and water molecules in titanylphthalocyanine phase Y crystal

We have performed several experiments and molecular dynamics calculations to investigate a phase transition of titanylphthalocyanine phase Y crystal and the behavior of water molecules in the crystal. We have shown that water is in the crystal as well as on its surface and the humidity dependence of the photosensitivity of the phase Y is due to the water on the surface. We propose a mechanism for the phase transition from the metastable phase Y to a stable phase I as follows. Water molecules on the surface detach as the crystal is heated to 100°C. At about 250°C water molecules in the crystal begin to jump from one space to another through channels connecting the spaces and as a result are expelled from the crystal. After the water molecules leave the spaces, the phase transition to phase I occurs by molecular rearrangement to shrink these spaces.

Molecular Dynamics Studies of Amorphous Poly(Tetrafluoroethylene)

Abstract Force field parameters for amorphous poly(tetrafiuoroethylene) (PTFE) and perfluoroalkanes for molecular simulations are developed using four perfluoroalkanes (C3F8, n-C4F10, n-C5F12 and n-C6F14) as reference molecules. Molecular dynamics calculations of the amorphous PTFE are performed under constant temperature and constant pressure conditions. Surprisingly, more than 6 ns calculations are needed to equilibrate the system. The calculated density and the structure factor are in good agreement with experiment. The concentration of the trans conformation of the backbone corresponds closely to that estimated from a Boltzmann distribution. The determined force field parameters are confirmed to reproduce the realistic amorphous structure of PTFE. The molecular motions of the backbones are investigated by tracing the time evolutions of the dihedral angles and several types of the conformational changes are observed.