Azuma Matsuura

Quantum wire and dot formation by chemical vapor deposition and molecular layer deposition of one‐dimensional conjugated polymer

Using the reaction between two types of molecules, I [terephthalaldehyde (TPA)] and II [p‐phenylenediamine (PPDA), 4,4’‐diaminodiphenyl ether (DDE), 4,4’‐diaminodiphenyl sulfide (DDS), or 1,4‐diaminodiphenylmethane (DDM)], we fabricate quantum wires and quantum dots by chemical vapor deposition. In the TPA/PPDA film, an exciton absorption peak occurs near 500 nm, indicating that long conjugated chains (quantum wire) are formed. In TPA/DDE, TPA/DDS, and TPA/DDM films, which have quantum dots consisting of three benzene rings separated by barriers of ‐O, ‐S‐, and ‐CH2‐ bonds, blue shifts of the absorption band occur due to an electron confinement. We also demonstrate molecular layer deposition of the TPA/PPDA film.

High-Level ab Initio Calculations To Improve Protein Backbone Dihedral Parameters.

We present new molecular mechanical dihedral parameters for the Ramachandran angles ϕ and ψ of a protein backbone based on high-level ab initio molecular orbital calculations for hydrogen-blocked or methyl-blocked glycine and alanine dipeptides. Fully relaxed 15° (ϕ, ψ) contour maps were calculated at the MP2/6-31G(d) level of theory. Finding out the lowest energy path for ϕ (or ψ) to change from -180° to 180° in the contour map, we performed a DF-LCCSD(T0)/Aug-cc-pVTZ//DF-LMP2/Aug-cc-pVTZ level calculation to get the torsional energy profiles of ϕ (or ψ). Molecular mechanical torsion profiles with AMBER force field variants significantly differed from the ab initio profiles, so we derived new molecular mechanical dihedral parameters of a protein backbone to fit the ab initio profiles.

Accurate evaluation of the absorption maxima of retinal proteins based on a hybrid QM/MM method

Here we improved our hybrid QM/MM methodology (Houjou et al. J Phys Chem B 2001, 105, 867) for evaluating the absorption maxima of photoreceptor proteins. The renewed method was applied to evaluation of the absorption maxima of several retinal proteins and photoactive yellow protein. The calculated absorption maxima were in good agreement with the corresponding experimental data with a computational error of <10 nm. In addition, our calculations reproduced the experimental gas‐phase absorption maxima of model chromophores (protonated all‐trans retinal Schiff base and deprotonated thiophenyl‐p‐coumarate) with the same accuracy. It is expected that our methodology allows for definitive interpretation of the spectral tuning mechanism of retinal proteins.

45.3: Tetra‐Substituted Pyrenes: New Class of Blue Emitter for Organic Light‐Emitting Diodes

We have developed a new class of highly-fluorescent blue emitter for organic light-emitting diodes (OLEDs) consisting of tetra-substituted pyrenes. From the analysis of the excited state diagrams of pyrene and its derivatives by molecular orbital calculations, we found that the new tetra-substituted pyrenes are highly fluorescent. OLEDs fabricated using the synthesized tetra-substituted pyrenes as emitters showed high efficiency and good color purity.

Force Driving Cu Diffusion into Interlayer Dielectrics.

The force driving Cu diffusion into insulators was investigated using a conventional Plasma enhanced chemical vapor deposition (CVD) film formed by Tetraethoxysilane (P-TEOS) and degassed P-TEOS films. The samples of degassed P-TEOS films with Cu electrodes kept in vacuum and N2 ambient show lower leakage currents than a sample kept in air and that of conventional P-TEOS. An interaction between O2 molecules included in films and atomic Cu was examined and it was found that an interaction between magnetic moments of atomic Cu and O2 molecules included in conventional P-TEOS film causes diffusion of Cu into the film.

Polyazomethine conjugated polymer film with second order nonlinear optical properties fabricated by electric‐field‐assisted chemical vapor deposition

We fabricated polyazomethine head‐to‐tail conjugated polymer films with second order nonlinear optical (NLO) properties using a dry‐processing technique, electric‐field‐assisted chemical vapor deposition (E‐CVD). Molecular orbital calculations show that the polyazomethine conjugated polymer chain, to which methoxy groups are attached as donors, has second order NLO susceptibility, β, 3–5 times larger than that of paranitroaniline. During film deposition the monomers were ordered by an electric field applied between slit‐type electrodes, and simultaneously polymerized. A channel waveguide for the TE mode of a He‐Ne laser beam was formed in a polymer film between the electrode gap. An electro‐optic (EO) effect in the polymer film was observed using a Mach–Zehnder interferometer. This indicates that head‐to‐tail conjugated polymers would be promising for second order NLO materials.

Docking study and binding free energy calculation of poly (ADP-ribose) polymerase inhibitors.

Recently, the massively parallel computation of absolute binding free energy with a well-equilibrated system (MP-CAFEE) has been developed. The present study aimed to determine whether the MP-CAFEE method is useful for drug discovery research. In the drug discovery process, it is important for computational chemists to predict the binding affinity accurately without detailed structural information for protein / ligand complex. We investigated the absolute binding free energies for Poly (ADP-ribose) polymerase-1 (PARP-1) / inhibitor complexes, using the MP-CAFEE method. Although each docking model was used as an input structure, it was found that the absolute binding free energies calculated by MP-CAFEE are well consistent with the experimental ones. The accuracy of this method is much higher than that using molecular mechanics Poisson-Boltzmann / surface area (MM / PBSA). Although the simulation time is quite extensive, the reliable predictor of binding free energies would be a useful tool for drug discovery projects.

Full-Quantum chemical calculation of the absorption maximum of bacteriorhodopsin: a comprehensive analysis of the amino acid residues contributing to the opsin shift

Herein, the absorption maximum of bacteriorhodopsin (bR) is calculated using our recently developed method in which the whole protein can be treated quantum mechanically at the level of INDO/S-CIS//ONIOM (B3LYP/6-31G(d,p): AMBER). The full quantum mechanical calculation is shown to reproduce the so-called opsin shift of bR with an error of less than 0.04 eV. We also apply the same calculation for 226 different bR mutants, each of which was constructed by replacing any one of the amino acid residues of the wild-type bR with Gly. This substitution makes it possible to elucidate the extent to which each amino acid contributes to the opsin shift and to estimate the inter-residue synergistic effect. It was found that one of the most important contributions to the opsin shift is the electron transfer from Tyr185 to the chromophore upon excitation. We also indicate that some aromatic (Trp86, Trp182) and polar (Ser141, Thr142) residues, located in the vicinity of the retinal polyene chain and the β-ionone ring, respectively, play an important role in compensating for the large blue-shift induced by both the counterion residues (Asp85, Asp212) and an internal water molecule (W402) located near the Schiff base linkage. In particular, the effect of Trp86 is comparable to that of Tyr185. In addition, Ser141 and Thr142 were found to contribute to an increase in the dipole moment of bR in the excited state. Finally, we provide a complete energy diagram for the opsin shift together with the contribution of the chromophore-protein steric interaction.

Selectively Aligned Polymer Film Growth on Obliquely Evaporated SiO2 Pattern by Chemical Vapor Deposition

Polyazomethin films were grown by chemical vapor deposition using terephthalaldehyde and p-phenylenediamine gases on SiO2 film patterned in a 10-µm-wide stripe. When the SiO2 film was obliquely evaporated on a quartz substrate by tilting the substrate along the y-axis, while polymer chain alignment was random on the quartz, the chain on the SiO2 film aligned along the y-axis, which induced birefringence and dichroism selectively on the stripe pattern. When the SiO2 stripe was formed on a SiO2 film deposited by tilting the substrate along the x-axis, the chain direction in the stripe region was at right angles to that in the surrounding region.