Fabrication of Uniaxially Aligned Silica Nanogrooves with Sub-5 nm Periodicity on Centimeter-Scale Si Substrate Using Poly(dimethylsiloxane) Stamps.

The large-area fabrication of aligned nanopatterns with sub-5 nm feature size is crucial for developing nanodevices. Highly ordered nanostructures fabricated through molecular self-assembly exhibit substantial potential for sub-5 nm patterning techniques. Previously, we had reported the fabrication of silica nanogrooves with sub-5 nm periodicity on a Si substrate by using the outermost surfaces of cylindrical surfactant micelles as a template. However, uniaxial alignment of nanogrooves on the entire substrate surface has not yet been achieved. In this study, uniaxially aligned silica nanogrooves were prepared on the entire surface of a Si substrate (2 cm × 2 cm) by utilizing a poly(dimethylsiloxane) (PDMS) stamp with a striped pattern. The PDMS stamp was placed on the surface of a surfactant thin film precoated on the substrate, although the stamp was not in direct contact with the substrate as in the case of the soft nanoimprint technique. The substrate was then exposed to water vapor, during which cylindrical micelles were aligned in the direction of the guide. Subsequently, by exposing the substrate to an NH3-water vapor mixture, the outermost surfaces of the aligned micelles facing the substrate were replicated with soluble silicate species. The formation of uniaxially aligned nanogrooves on the entire surface of the centimeter-scale substrate was verified by scanning electron microscopy observations and grazing-incidence small-angle X-ray scattering analysis. Thus, herein we provide a simple large-area fabrication method for uniaxially aligned nanopatterns with ultrafine pitch.

Selective Removal of B800 Bacteriochlorophyll a from Light-Harvesting Complex 2 of the Purple Photosynthetic Bacterium Phaeospirillum molischianum.

The selective removal of B800 bacteriochlorophyll (BChl) a from light-harvesting complex 2 (LH2) in purple photosynthetic bacteria is a clue about elucidation of the mechanism for the transfer of energy from these pigments to B850 BChl a and their roles in the LH2 protein structure. We demonstrated that the kinetics of the removal of B800 BChl a from two representative LH2 proteins derived from Phaeospirillum molischianum and Rhodoblastus acidophilus differed significantly, in contrast to the calculated binding enthalpy. These results may be interpreted as changes in the local structure near B800 BChl a with respect to the geometries of the original crystal structures upon removal of B800 BChl a. Despite the difficulty of removing B800 BChl a from molischianum-LH2, we prepared the molischianum-LH2 protein lacking B800 BChl a by combination of two detergents, n-dodecyl ß-d-maltoside and n-octyl ß-d-glucoside, under acidic conditions. Spectral and atomic force microscopy analyses indicated that the absence of B800 BChl a had little effect on the local structure in the vicinity of B850 BChl a and the circular arrangement in this protein. These results suggest that the hydrophobic domain near B850 BChl a is rigid and plays a major role in the structural formation of molischianum-LH2.

Formation of Concentric Silica Nanogrooves Guided by the Curved Surface of Silica Particles.

The flexible control of nanopatterns by a bottom-up process at the nanometer scale is essential for nanofabrication with a finer pitch. We have previously reported that for the fabrication of linear nanopatterns with sub-5 nm periodicity on Si substrates the outermost surfaces of assembled micelles facing the substrates can be replicated with soluble silicate species generated from the Si substrates under basic conditions. In this study, concentrically arranged nanogrooves with a sub-5 nm periodicity were prepared on Si substrates by replicating the outermost surfaces of bent micelles guided by silica particles. The Si substrates, where silica particles and surfactants films were deposited, were exposed to an NH3-water vapor mixture. During the vapor treatment, cylindrical micelles became arranged in concentric patterns centered on the silica particles, and their outermost surfaces facing the substrates were replicated by soluble silicate species on the Si substrates. The thinness of the surfactant film on the substrate is crucial for the formation of concentric silica nanogrooves because the out-of-plane orientations of the micelles are suppressed at the interface. Surprisingly, the domains of the concentric silica nanogrooves spread to much larger areas than the maximum cross-sectional areas of the particles, and the size of the domains increased linearly with the radii of the particles. The extension of concentric nanogrooves is discussed on the basis of the orientational elastic energies of the micelles around one silica particle. This study of the formation of bent nanogrooves guided by the outlines of readily deposited nanoscale objects provides a new nanostructure-guiding process.

Reversible Changes in the Structural Features of Photosynthetic Light-Harvesting Complex 2 by Removal and Reconstitution of B800 Bacteriochlorophyll a Pigments.

Light-harvesting complex 2 (LH2) is an integral membrane protein in purple photosynthetic bacteria. This protein possesses two types of bacteriochlorophyll (BChl) a, termed B800 and B850, which exhibit lowest-energy absorption bands (Qy bands) around 800 and 850 nm. These BChl a pigments in the LH2 protein play crucial roles not only in photosynthetic functions but also in folding and maintaining its protein structure. We report herein the reversible structural changes in the LH2 protein derived from a purple photosynthetic bacterium, Rhodoblastus acidophilus, induced by the removal of B800 BChl a (denoted as B800-free LH2) and the reconstitution of exogenous BChl a. Atomic force microscopy observation clearly visualized the nonameric ring structure of the B800-free LH2 with almost the same diameter as the native LH2. Size exclusion chromatography measurements indicated a considerable decrease in the size of the protein induced by the removal of B800 BChl a. The protein size was almost recovered by the insertion of BChl a pigments into the B800 binding sites. The decrease in the LH2 size would mainly originate from the shrinkage of the B800 binding sites perpendicular to the macrocycle of B800 BChl a without deformation of the circular arrangement. The reversible changes in the LH2 structure induced by the removal and reconstitution of B800 BChl a will be helpful for understanding the structural principle and the folding mechanism of photosynthetic pigment-protein complexes.

Determination of the Molar Extinction Coefficients of the B800 and B850 Absorption Bands in Light-harvesting Complexes 2 Derived from Three Purple Photosynthetic Bacteria Rhodoblastus acidophilus, Rhodobacter sphaeroides, and Phaeospirillum molischianum by Extraction of Bacteriochlorophyll a.

The molar extinction coefficients of light-harvesting complex 2 (LH2) have been ambiguous in spite of its fame and wide utilization. Herein we determine the molar extinction coefficients of the LH2 proteins derived from the three purple photosynthetic bacteria Rhodoblastus acidophilus, Rhodobacter sphaeroides and Phaeospirillum molischianum at 298 K by direct extraction of bacteriochlorophyll (BChl) a from the lyophilized proteins, followed by estimation of BChl a amounts from their electronic absorption spectra.

Introduction of perfluoroalkyl chain into the esterifying moiety of bacteriochlorophyll c in the green sulfur photosynthetic bacterium Chlorobaculum tepidum by pigment biosynthesis.

The green sulfur photosynthetic bacterium Chlorobaculum (Cba.) tepidum was grown in liquid cultures containing perfluoro-1-decanol, 1H,1H,2H,2H-heptadecafluoro-1-decanol [CF3(CF2)7(CH2)2OH] or 1H,1H-nonadecafluoro-1-decanol [CF3(CF2)8CH2OH], to introduce rigid and fluorophilic chains into the esterifying moiety of light-harvesting bacteriochlorophyll (BChl) c. Exogenous 1H,1H,2H,2H-heptadecafluoro-1-decanol was successfully attached to the 17(2)-carboxy group of bacteriochlorophyllide (BChlide) c in vivo: the relative ratio of the unnatural BChl c esterified with this perfluoroalcohol over the total BChl c was 10.3%. Heat treatment of the liquid medium containing 1H,1H,2H,2H-heptadecafluoro-1-decanol with ß-cyclodextrin before inoculation increased the relative ratio of the BChl c derivative esterified with this alcohol in the total BChl c in Cba. tepidum. In a while, 1H,1H-nonadecafluoro-1-decanol was not attached to BChlide c in Cba. tepidum, which was grown by its supplementation. These results suggest that the rigidity close to the hydroxy group of the esterifying alcohol is not suitable for the recognition by the BChl c synthase called BchK in Cba. tepidum. The unnatural BChl c esterified with 1H,1H,2H,2H-heptadecafluoro-1-decanol participated in BChl c self-aggregates in chlorosomes.

In Vitro Enzymatic Activities of Bacteriochlorophyll a Synthase Derived from the Green Sulfur Photosynthetic Bacterium Chlorobaculum tepidum.

The activity of an enzyme encoded by the CT1610 gene in the green sulfur photosynthetic bacterium Chlorobaculum tepidum, which was annotated as bacteriochlorophyll (BChl) a synthase, BchG (denoted as tepBchG), was examined in vitro using the lysates of Escherichia coli containing the heterologously expressed enzyme. BChl a possessing a geranylgeranyl group at the 17-propionate residue (BChl aGG) was produced from bacteriochlorophyllide (BChlide) a and geranylgeranyl pyrophosphate in the presence of tepBchG. Surprisingly, tepBchG catalyzed the formation of BChl a bearing a farnesyl group (BChl aF) as in the enzymatic production of BChl aGG, indicating loose recognition of isoprenoid pyrophosphates in tepBchG. In contrast to such loose recognition of isoprenoid substrates, BChlide c and chlorophyllide a gave no esterifying product upon being incubated with geranylgeranyl or farnesyl pyrophosphate in the presence of tepBchG. These results confirm that tepBchG undoubtedly acts as the BChl a synthase in Cba. tepidum. The enzymatic activity of tepBchG was higher than that of BchG of Rhodobacter sphaeroides at 45 °C, although the former activity was lower than the latter below 35 °C.

Pheophytinization kinetics of chlorophyll c under weakly acidic conditions: effects of acrylic acid residue at the 17-position.

Pheophytinization of chlorophyll (Chl) c1, which was isolated from the diatom Chaetoceros gracilis, was kinetically analyzed under weakly acidic conditions, and was compared with that of protochlorophyllide (PChlide) a and chlorophyllide (Chlide) a. Chl c1 possessing a trans-acrylic acid residue at the 17-position exhibited slower pheophytinization kinetics than PChlide a and Chlide a, both of which possessed a propionic acid residue at the same position. The difference in pheophytinization properties between Chl c1 and (P)Chlide a was ascribable to the electronegativity of the 17-substituent in Chl c1 larger than that of (P)Chlide a due to the C17(1)-C17(2) double bond with the conjugated 17(2)-carboxy group in Chl c1. Demetalation kinetics of PChlide a was slower than that of Chlide a, which originated from the effect of the π-macrocyclic structures.