Yoshishige Okuno

Selective assembly on a surface of supramolecular aggregates with controlled size and shape

The realization of molecule-based miniature devices with advanced functions requires the development of new and efficient approaches for combining molecular building blocks into desired functional structures, ideally with these structures supported on suitable substrates. Supramolecular aggregation occurs spontaneously and can lead to controlled structures if selective and directional non-covalent interactions are exploited. But such selective supramolecular assembly has yielded almost exclusively crystals or dissolved structures; the self-assembly of absorbed molecules into larger structures, in contrast, has not yet been directed by controlling selective intermolecular interactions. Here we report the formation of surface-supported supramolecular structures whose size and aggregation pattern are rationally controlled by tuning the non-covalent interactions between individual absorbed molecules. Using low-temperature scanning tunnelling microscopy, we show that substituted porphyrin molecules adsorbed on a gold surface form monomers, trimers, tetramers or extended wire-like structures. We find that each structure corresponds in a predictable fashion to the geometric and chemical nature of the porphyrin substituents that mediate the interactions between individual adsorbed molecules. Our findings suggest that careful placement of functional groups that are able to participate in directed non-covalent interactions will allow the rational design and construction of a wide range of supramolecular architectures absorbed to surfaces.

Theoretical study of aryl-ring rotation in arylporphyrins

We carried out quantum chemical calculations for the aryl-ring rotations in phenylporphyrin and ortho-methoxyphenylporphyrin to determine the reaction path and the potential-energy barrier so that one can provide an insight into how such rotations can occur. It was found that along the reaction path, the structure changes from a planar porphyrin-ring at the stable state to a considerably distorted one at the transition state, and that the small potential-energy barrier, which is consistent with experiments, largely stems from the deformation of the porphyrin ring. An increase in the potential-energy barrier resulting from the substitution at the ortho position of the aryl group was also found to originate mainly from an additional deformation of the porphyrin ring at the transition state. These findings are in contrast with the calculated result for the aryl-ring rotation in the biphenyl, in which the direct steric hindrance between the aryl rings rather than the deformation makes large contributions to the overall potential energy barrier. We concluded that the deformation of the porphyrin ring is essential for the occurrence of the aryl-ring rotation in the arylporphyrins.

Microscopic description of nonadiabatic, nonequilibrium, and equilibrium solvations for solvated cluster reactions: (H2O)nCl−+CH3Cl→ClCH3+Cl−(H2O)n

A microscopic theory was presented for each of the nonadiabatic‐ and equilibrium‐solvation regimes in microsolvated cluster reactions to examine nonequilibrium‐solvation effects, and applied to the SN2 reactions: (H2O)nCl−+CH3Cl→ClCH3+Cl−(H2O)n for n=0–4. To have pictures for nonadiabatic and equilibrium solvations, the potential‐energy surface of the reacting system on the transition‐state region was described with effective normal coordinates defined in each of these solvation limits. The solute dynamics in each of these solvation limits was considered to be determined by the effective frequencies characterizing the motions along the corresponding normal coordinates, and a rate‐constant expression was approximately derived. Ab initio molecular‐orbital calculations were carried out for the microsolvated SN2 reactions, and the ratio of nonadiabatic‐ to equilibrium‐solvation rate constants was evaluated. It was found that the ratio provides a better approximate value of a transmission coefficient that corr...

Extended transition‐state theory and constant‐energy chemical‐reaction molecular‐dynamics method for liquid‐phase chemical reactions

An extension of transition‐state theory for liquid‐phase chemical reactions is presented. The effect of adding a second solvent water molecule on the proton‐transfer reaction in a formamidine–water (FW) cluster was studied. Ab initio molecular‐orbital calculations were performed for the formamidine–water–water (FWW) system to obtain the adiabatic potential‐energy surface. It was expressed in two coordinate systems: (i) the total normal‐coordinate system of the FWW system, and (ii) the composite normal‐coordinate system consisting of two normal‐coordinate systems of the isolated FW system and the isolated medium‐water molecule. In either of these two systems, the solvent effect can be categorized as either (i) an equilibrium solvation effect or (ii) a frictional effect. In this article, the former effect was investigated in detail and, in the total normal‐coordinate system, a frequency diagram was obtained by diagonalizing the Hessian matrix at successive geometries along intrinsic reaction coordinate and ...

Dendrimers for Optoelectronic Applications

This manuscript describes the dendritic macromolecules for optical and optoelectronic applications, particularly stimulated emission, laser emission, and nonlinear optics. Dendrimers have been designed and synthesized for these applications based on simple concepts. A core-shell structure, through the encapsulation of active units by dendritic branches, or a cone-shaped structure, through the step-by-step reactions of active units, can provide particular benefits for the optical high-gain media and nonlinear optical materials. It also described experimental results that support the methods presented for designing and fabricating functionalized dendrimers for optoelectronic applications, and theoretical results that reveal the intermolecular electronic effect of the dendritic structure.

A reaction-path Hamiltonian described with quasirectilinear vibrational coordinates constructed from a nonlinear combination of curvilinear internal coordinates: Application to examination of the reaction CH4+F→CH3+HF

The reaction-path Hamiltonian formulation reported in the preceding paper, where the Hamiltonian is described with quasirectilinear vibrational coordinates related nonlinearly to curvilinear internal coordinates, was applied to the examination of the reaction CH4+F→CH3+HF. For this reaction we made ab initio calculations and determined the harmonic vibrational frequencies along the reaction path by each of (1) a method using the new formulation, (2) the method of Miller et al. [J. Chem. Phys. 72, 99 (1980)], and (3) that of Truhlar et al. [J. Chem. Phys. 102, 3188 (1995)]. We found that the harmonic vibrational frequencies determined by the new method differ significantly from those determined by the other two methods in the region away from the stationary states. This difference is attributed to the limitations of the latter two methods. We concluded that the reaction-path Hamiltonian determined by the new method should be used to obtain an accurate picture of the reaction-path dynamics under the zero-an...

A reaction-path Hamiltonian described with quasirectilinear vibrational coordinates constructed from a nonlinear combination of curvilinear internal coordinates: Formulation

We present for a polyatomic reaction system a reaction-path Hamiltonian described with a reaction coordinate and quasirectilinear vibrational coordinates that are constructed from a nonlinear combination of curvilinear internal coordinates. To determine the vibrational coordinates we use a quasipotential-energy expression in which, in a Taylor-series expansion of the potential energy around the reaction path, the usual derivatives with respect to the internal coordinates are replaced by the corresponding covariant derivatives. The vibrational coordinates are determined so that (1) when the angular momentum is assumed to be zero, the respective expressions for the quasipotential energy and the kinetic energy have diagonal forms in the second-order terms and the first-order terms with respect to the vibrational coordinates in the internal configuration subspace perpendicular to the reaction path, and (2) the covariant second derivatives of the potential energy with respect to the vibrational coordinates coi...

Determining the conformation of a phenylene-linked porphyrin dimer by NMR spectroscopy and quantum chemical calculations

To determine the conformation of a substituted phenylene-linked porphyrin dimer, we observed the NMR spectra of this dimer and carried out quantum chemical calculations for an unsubstituted phenylene-linked porphyrin dimer. While the observed spectra could not establish the conformation, they did clarify the confirmation of the structural formula and demonstrate anomalously large chemical shifts of the pyrrole protons adjacent to the phenylene linker. The plane angles between the porphyrin and phenyl rings and between the two-porphyrin rings in the calculated stable structure were, respectively, 64.3 and 51.5°. The calculated proton chemical shifts for this structure were consistent with the observed ones. Moreover, the anomalously large chemical shifts of the pyrrole protons adjacent to the phenylene linker were found from the calculations for parts of the dimer to be caused by the remote porphyrin ring. These findings led us to the following conclusions: (1) The planes of the phenyl and two porphyrin rings were neither coplanar nor perpendicular to one another in the stable conformation of the phenylene-linked porphyrin dimer, and (2) a strong diamagnetic current of π electrons of the remote porphyrin ring resulted in magnetic deshielding on the pyrrole protons adjacent to the phenylene linker.

A quantum-mechanical/molecular-mechanical calculation method for molecules or molecular aggregates adsorbed on noble metal surfaces

Abstract We propose a quantum-mechanical/molecular-mechanical method to calculate characteristics including energies and stable structures for molecules or molecular aggregates adsorbed onto noble metal surfaces. In this method, on the one hand, quantum-chemical calculations for the adsorbate with image charges, which appear in the metal due to the electrostatic influence of the adsorbate on the metal, are made; therefore, the inductive interaction between the adsorbate and the surface is included in the calculations. On the other hand, analytical atom–atom potential functions are used to represent the repulsive and dispersive interactions between the surface and the adsorbate. We show that our method is useful for investigating physisorption on noble metal surfaces.

Dynamic transition state in the constant energy scheme CRMD simulation and the relative velocity correlation function

Abstract Chemical reaction molecular dynamics simulations are performed for the proton transfer reaction of the formamidine—water system with the constant energy scheme. The characteristic “cusp” appears similar to that which was observed previously in the hydrogen bonding correlation function for each trajectory in the constant temperature scheme simulations. Analysis using a relative velocity correlation function indicates that the cusp corresponds to the state where not only relative velocity but also relative acceleration disappears in at least one of two hydrogen bonds between the hydrogen and oxygen atoms. The cusp point is concluded to correspond to a “dynamic transition state”.