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Shunsaku Kimura

Publications and source records attributed to Shunsaku Kimura.

13 recordsLinked to original sources
PubMed2006

Helix triangle: unique peptide-based molecular architecture.

We here report a unique cyclic peptide structure, "helix triangle", as a unique example of peptide-based molecular architecture. The cyclic peptide is designed to have a triangular shape in which three 9mer helical peptide units make the sides and three pyrene derivatives make the apexes. The helical peptide units are ideally linear, and the pyrene units are ideal 60 degrees angular components. The yield of the cyclic peptide was relatively high despite its large cycle size. Absorption and fluorescence spectroscopy revealed that the three pyrene units do not interact with each other electronically, and circular dichroism spectroscopy indicated that the helical peptide units take 3(10)-helical conformation. Geometry optimization by the semi-empirical molecular orbital method gave a triangular structure with 3(10)-helices as the plausible molecular structure. To gain more information on the geometry and demonstrate one example of its self-assemblies, the monolayer of the cyclic peptide was prepared at the air/water interface, and its surface pressure-molecular area isotherm was studied. The isotherm indicated formation of a stable monolayer and suggested that the cyclic peptide actually takes the triangular structure predicted by the geometry optimization. The monolayer was then transferred onto a substrate and characterized by various methods. Ellipsometry and infrared reflection-absorption spectroscopy confirmed that the cyclic peptide has horizontal orientation to the surface in the monolayer. Furthermore, absorption and fluorescence spectroscopy showed that the isolated electronic properties of the pyrene units are intact even in a condensed state in the monolayer.

Air↗
PubMed2006

Parallel assembly of dipolar columns composed of a stacked cyclic tri-beta-peptide.

A novel cyclic trimer of a beta-amino acid, trans-2-aminocyclohexylcarboxylic acid, was synthesized and its conformation and ability to form assemblies investigated. FT-IR and NMR measurements and computational calculations showed that this cyclic tri-beta-peptide has a C3-symmetric conformation with trans amide groups. A notable feature of the conformation is a vertical and parallel orientation of the three amide groups to the cyclic skeleton. The cyclic tri-beta-peptide was crystallized from a solution in trifluoroacetic acid-methanol (or trifluoroacetic acid-water) to yield a rod-shaped molecular assembly, as observed by TEM. The electron crystallography of the rod-shaped assembly both in suspension and in ultrathin cross-section revealed that the cyclic tri-beta-peptides were stacked up to form molecular columns, and that a two-fold screw symmetry operation along the column direction was present in the unit cell, which contained two cyclic tri-beta-peptides. This indicates that all the amide groups are oriented in the same direction. Since any two molecular columns are staggered by a quarter of a c-axis length and aligned parallel to each other, the dipole moments of the columns are aligned to enhance the strength additively in the whole assembly.

Crystallization↗
PubMed2006

Columnar assembly of cyclic beta-amino acid functionalized with pyranose rings.

A novel cyclic trimer and tetramer of protected beta-glycamino acids were synthesized and investigated on conformation and assembly formation. A characteristic point of these cyclic beta-glycamino acids is their better solubility than other cyclic beta-amino acids due to the pyranose rings. Thus, the assembling process of the cyclic molecules could be examined by CD or NMR spectroscopy. FT-IR and NMR measurements and geometry optimization revealed a highly symmetric and planar conformation for each cyclic beta-peptide with all-trans amide groups. The amide groups in the cyclic peptides took a vertical orientation against the cyclic skeleton to be suitably arranged for intermolecular hydrogen bonds, which should promote formation of molecular assembly in a columnar structure through molecular stacking. These cyclic beta-peptides were successfully crystallized to yield rod-shaped molecular assemblies in nanometer sizes. Evidence for the columnar structure in the crystals was obtained by electron diffraction analysis, which showed a layer spacing of ca. 4.8 A. Interestingly, the molecular assembly of the cyclic trimer showed a high aspect ratio, width less than 40 nm, and length more than 2 mum, suggesting stable molecular stacking in the column.

Amino Acids↗
PubMed2005

Electron transfer in metal-molecule-metal junction composed of self-assembled monolayers of helical peptides carrying redox-active ferrocene units.

Electronic properties of three kinds of helical peptides with or without redox-active ferrocene units were investigated by using scanning tunneling microscopy under ultrahigh vacuum. The currents through the helical peptides carrying ferrocene units at the molecular terminals became significantly larger than that through a reference peptide without any ferrocene units. On the other hand, ferrocene units in the middle of the peptide chain did not affect the current-voltage characteristics. These results indicate that the ferrocene units near the metal electrode should play an important role for efficient electron transfer between the metal and the peptide molecules, which process is one of the rate-determining steps for characterizing molecular conductance in metal-molecule-metal junction.

Electrons↗
PubMed2005

pH-controlled switching of photocurrent direction by self-assembled monolayer of helical peptides.

A novel molecular system, where the photocurrent direction can be reversibly switched by changing the pH of the solution, was prepared on gold from helical peptides carrying a photosensitizer and a carboxyl group at the terminal. Upon photoexcitation of the photosensitizer in an aqueous solution containing an electron donor and acceptor at pH 10, the monolayer generated an anodic photocurrent due to enhancement of the dipole moment by a carboxylate anion, while it generated an opposite cathodic photocurrent at pH 3.4

Hydrogen-Ion Concentration↗
PubMed2005

Effects of dipole moment, linkers, and chromophores at side chains on long-range electron transfer through helical peptides.

Octadecapeptides carrying a ferrocene moiety at the molecular terminal were self-assembled on gold, and long-range electron transfer from the ferrocene moiety to gold was investigated by electrochemical methods. Effects on electron transfer of dipole moment of helical peptides, linkers connecting the peptide to gold, and chromophores introduced into the side chains were discussed. Cyclic voltammetry of the monolayers in an aqueous solution revealed that long-range electron transfer over 40 A occurred along the peptide molecule. Chronoamperometry showed that the long-range electron transfer should be ascribed to a hopping mechanism with use of amide groups as hopping sites. Electron transfer through the long peptide was not significantly accelerated by the dipole moment. However, the linker remarkably affected electron transfer depending on whether it was a methylene chain or a phenylene group, suggesting that local electron transfer between gold and the peptides should be the slowest step to determine the overall rate. Pyrenyl groups introduced into the side chains in the middle of the peptide molecule did not noticeably change electron transfer, probably because pyrenyl groups were too distant to allow direct electron transfer between them. Electrostatic potential profiles across the peptide monolayers were also calculated to explain reasonably the several interesting features in the present peptide systems.

Cross-Linking Reagents↗
PubMed2005

Molecular rectification of a helical peptide with a redox group in the metal-molecule-metal junction.

A helical hexadecapeptide immobilized on gold via a thiophenyl group at the N-terminal was analyzed by scanning tunneling microscopy under ultrahigh vacuum to obtain the I-V response at a molecular level. The attenuation factor of the electron transfer through the hexadecapeptide was determined by applying the Simons model to the I-V response to show better molecular conductance of the hexadecapeptide than dodecanethiol. Chemical modification at the C-terminal of the hexadecapeptide with a ferrocene unit, on the other hand, brought about significant changes in the I-V response, where the helical peptide became more conductive at the negative bias voltage. The molecular rectification behavior is due to the ferrocene unit regulating the direction of the electron transfer at the metal-molecule junction.

Aminoisobutyric Acids↗
PubMed2005

Enzymatic polymerization behavior using cellulose-binding domain deficient endoglucanase II.

A mutant enzyme, EGII(core), in which the cellulose-binding domain was deleted from endoglucanase II from Trichoderma viride, was expressed in yeast, and the secreted enzyme was examined for the enzymatic polymerization to obtain artificial cellulose. EGII(core) polymerized beta-cellobiosyl fluoride to afford crystalline cellulose of type II. Comparison of the polymerization behavior of EGII(core) with that of EGII revealed the following: i) the crystalline product obtained with EGII(core) was stable in the polymerization solution, although the product was readily hydrolyzed in the presence of EGII; ii) the turnover number of EGII(core) was as high as that of EGII; iii) EGII(core) produced highly crystalline cellulose. EGII(core) is therefore advantageous for enzymatic polymerization.

Cellobiose↗
PubMed2004

Formation of gold nanoparticles in microreactor composed of helical peptide assembly in water.

A novel microreactor was prepared by self-assembly of an amphiphilic block copolymer composed of a hydrophobic helical peptide unit with a naphthyl group at the C terminal and a hydrophilic poly(ethylene glycol) unit. The copolymer formed a self-assembly in water, taking a vesicular structure. Noticeably, when the copolymer was dispersed in an Au(3+) aqueous solution, gold nanoparticles were formed without addition of any reducing reagent. The naphthyl groups, which are located at the inner surface of the vesicular assembly, promoted the reduction of Au(3+) ions with accompanying pH decrease.

Cations↗
PubMed2004

Efficient photocurrent generation by self-assembled monolayers composed of 3 10-helical peptides carrying linearly spaced naphthyl groups at the side chains.

Self-assembled monolayers (SAMs) were prepared on a gold substrate from a 310-helical peptide carrying three naphthyl groups at the side chain (SSN3B) or from the reference peptides carrying no or one naphthyl group. The 310-helical conformation of SSN3B in solution was confirmed by 1H NMR spectroscopy and geometry optimization. Cyclic voltammetry and infrared absorption-reflection spectroscopy showed vertical molecular orientation and a well-packed structure in the SSN3B SAM. Anodic photocurrent was successfully generated by the SSN3B SAM in the presence of triethanolamine, and the current intensity was found to be much larger than those by the other SAMs from peptides carrying one naphthyl group. It was therefore concluded that the linearly spaced naphthyl groups along the helical axis act as photosensitizer and electron-hopping site to promote photocurrent generation remarkably.

Aminoisobutyric Acids↗
PubMed2004

A molecular photodiode system that can switch photocurrent direction.

We prepared a molecular photodiode system in which the photocurrent direction can be switched by choosing the wavelength of an irradiating light. The molecular system is composed of two types of helical peptides that carry different chromophores and have different directions of dipole moments when they are immobilized on gold. The mixed, self-assembled monolayer generated an anodic photocurrent when one of the two chromophores was photoexcited, whereas the photocurrent switched to being cathodic when the other chromophore was photoexcited. The opposite current response arises from the dipole moment of each helical peptide, which accelerates electron transfer in the same direction.

Journal Article↗
PubMed2003

Long-range electron transfer over 4 nm governed by an inelastic hopping mechanism in self-assembled monolayers of helical peptides.

Well-ordered self-assembled monolayers (SAMs) were prepared on gold from helical peptides carrying a ferrocene (Fc) moiety at the N- or C-terminal end, and long-range electron transfer (ET) from Fc to gold was investigated. Electrochemical studies revealed that an inelastic hopping mechanism dominated over the superexchange mechanism in the ET reactions in the present SAMs and the dipole moment of the helix accelerated the ET reactions probably due to the lowering of the barrier height between the gold surface and peptide layer.

Disulfides↗