Tokyo Chemical Industry Research Articles

DigiMOF: A Database of Metal-Organic Framework Synthesis Information Generated via Text Mining.

The vastness of materials space, particularly that which is concerned with metal-organic frameworks (MOFs), creates the critical problem of performing efficient identification of promising materials for specific applications. Although high-throughput computational approaches, including the use of machine learning, have been useful in rapid screening and rational design of MOFs, they tend to neglect descriptors related to their synthesis. One way to improve the efficiency of MOF discovery is to data-mine published MOF papers to extract the materials informatics knowledge contained within journal articles. Here, by adapting the chemistry-aware natural language processing tool, ChemDataExtractor (CDE), we generated an open-source database of MOFs focused on their synthetic properties: the DigiMOF database. Using the CDE web scraping package alongside the Cambridge Structural Database (CSD) MOF subset, we automatically downloaded 43,281 unique MOF journal articles, extracted 15,501 unique MOF materials, and text-mined over 52,680 associated properties including the synthesis method, solvent, organic linker, metal precursor, and topology. Additionally, we developed an alternative data extraction technique to obtain and transform the chemical names assigned to each CSD entry in order to determine linker types for each structure in the CSD MOF subset. This data enabled us to match MOFs to a list of known linkers provided by Tokyo Chemical Industry UK Ltd. (TCI) and analyze the cost of these important chemicals. This centralized, structured database reveals the MOF synthetic data embedded within thousands of MOF publications and contains further topology, metal type, accessible surface area, largest cavity diameter, pore limiting diameter, open metal sites, and density calculations for all 3D MOFs in the CSD MOF subset. The DigiMOF database and associated software are publicly available for other researchers to rapidly search for MOFs with specific properties, conduct further analysis of alternative MOF production pathways, and create additional parsers to search for additional desirable properties.

Controlled Growth Interface of Charge Transfer Salts of Nickel-7,7,8,8-Tetracyanoquinodimethane on Surface of Graphdiyne

Controlled Growth Interface of Charge Transfer Salts of Nickel-7,7,8,8-Tetracyanoquinodimethane on Surface of Graphdiyne

Bidirectional Light-Driven Ion Transport through Porphyrin Metal–Organic Framework-Based van der Waals Heterostructures via pH-Induced Band Alignment Inversion

Bidirectional Light-Driven Ion Transport through Porphyrin Metal–Organic Framework-Based van der Waals Heterostructures via pH-Induced Band Alignment Inversion

Breath Acetone Analysis Using a Porous Glass Sensor Developed By Impregnating with 4-Nitrophenylhydrazine

Introduction High concentrations of acetone are typically detected in the air exhaled by patients suffering from diabetes [1]. Therefore, breath acetone analysis is expected to be a non-invasive diagnosis or monitoring method for patients suffering from diabetes, and this method can replace blood tests. Generally, gaseous acetone detection is conducted via gas chromatography/mass spectrometry (GC/MS) [2]. Although this method provides results with low uncertainties, it requires large equipment. Therefore, it does not meet the requirements of clinical applications, which include cost effectiveness and user friendliness. We have previously developed an analytical chip for the simple detection of gaseous acetone using porous glass impregnated with 4-nitrophenylhydrazine (4-NPH) [3]. Porous glass has the advantages of small size, resistance to organic solvents, and large surface area (specific surface area: 200 m2 g−1). The developed chip could detect acetone in 3 h by a passive method that include hanging acetone in a bag containing gaseous acetone. In this study, we evaluated the applicability of chip for the analysis of breath samples and investigated a method to detect gaseous acetone in a short time by combining the chip with an active method. Method Preparation of the analytical chip Porous glass sheets (thickness = 1 mm, Vycor#7930, Corning Co., USA) with an average pore diameter of 4 nm were cut into 8 mm × 8 mm chips and used as a substrate. The porous glass was cleaned with acetone and ethanol using an ultrasonic cleaner (ASU-3, As One Co., Japan), then soaked in 6 mol L−1 hydrochloric acid for 2 h, and finally dried in a nitrogen atmosphere for >20 h. Subsequently, 4-NPH (0.0492 g, Tokyo Chemical Industry Co., Japan) and concentrated HCl (100 µL) were dissolved in methanol (25 mL). The porous glass was soaked in the 4-NPH-methanol solution (1.26 × 10−2 mol L−1) for 24 h and dried in a nitrogen atmosphere for 24 h. Exposure to gaseous acetone To prepare an acetone atmosphere of arbitrary concentration and relative humidity of 50% at 25 °C in a sampling bag, an acetone–water solution (80 µL) and deionized water (498 µL) were injected into a bag filled with 50 L of dry nitrogen. The bag was left to stand at 25 °C for 24 h to volatilize the acetone–water solution. The resulting acetone atmospheres occupied volumes of 50 L at several concentrations (i.e., 1.06, 2.65, 5.30, and 10.6 ppm). Subsequently, the analytical chip was placed in a sensor holder, and the acetone atmosphere flowed through the sensor holder at a gas flow rate of 2.0 L min−1 using a pump (MP-∑300NⅡ, SHIBATA SCIENTIFIC TECHNOLOGY Co., Japan) for an arbitrary time (10, 30, 60, 120, and 300 s). Results and Conclusions The analytical chip exhibited an absorption peak at 314 nm due to its impregnation with 4-NPH. After exposure to an acetone atmosphere, a new absorption peak appeared at 390 nm. This peak can be attributed to the production of 4-NPH derivative (Acetone-4-NPH) resulting from the reaction between 4-NPH and acetone inside the chip. It was found that the absorbance at 390 nm increased with an increase in the acetone concentration or exposure time. The 3 h exposure to 1 L of acetone atmosphere (1.06, 5.30, and 10.6 ppm) by a passive method showed an absorbance difference at 390 nm of 0.322, 1.20, and 2.04, respectively. In contrast, when exposed to an acetone atmosphere (1.06, 5.30, and 10.6 ppm) at a gas flow rate of 2.0 L min−1 for 30 s, it was 0.0183, 0.0540, and 0.133, respectively. The calculated acetone concentration of the 1 L breath samples suggested that the results obtained using analytical chip agreed with those obtained via gas chromatography with a probability of approximately 60%. Additionally, the chip worked cumulatively and could detect gaseous acetone of 1 ppm in 300 s by the active method of using a pump. Based on a kinetic analysis of the reaction between 4-NPH and acetone, the rate constant of the reaction between these two species was calculated as 3.0 × 10−5 ppm−1 min−1.

Application of Nanocarbons Modified with Anthraquinone Polycondensation Polymer to Electrochemical Double Layer Capacitance

Carbon-based fine particles have been widely used as fillers for enhancing the reinforcement for bulk materials. In addition, the excellent physical stability and unique chemical properties of these fine particles expand their potential utility in electroconductive materials, carriers for catalysis, packing materials such as pigment and colorant for inks, paints, and resins. Recently, it was reported that one-pot polymerization of 1.5-dihydoroxynaphtalene (DHN) and 1,3,5-1,3,5-trimethyl-1,3,5-triazinane(TA) in ethanol or other related solvents without any additives, and subsequent calcination at relatively enables us to control the diameter of the resultant particle in the range of submicron to a couple of microns. In this study we report that the nano carbons modified with an anthraquinone polycondensation polymer prepared by this one-pot polymerization method using an aromatic hydrocarbon with OH groups and TA function as an electrochemical double layer capacitors (EDLC).Anthraquinone derivatives having two OH groups and 1,3,5-trimethyl-1,3,5-triazinane (TA) were purchased from Tokyo Chemical Industry Co., Ltd. and used as received. Carbon black powders (DENKA Black) and mineral oil were purchased from DENKA Co. Ltd. and Sigma, respectively. Cyclic voltammetry (CV) and potential step chronocoulometry were performed with a ALS model 621 electrochemical analyzer. A platinum plate and Ag/AgCl (KCl sat.) were used as a counter and reference electrode, respectively.CV in 0.1 M HClO4 at a bare carbon black (CB) electrode shows very small charging current without redox waves. In contrast, at the CB modified with anthraquinone condensation polymer (AQP), redox waves of anthraquinone moieties associated with a large charging current. The capacitance calculated from CV depended on the kind and concentration of the supporting electrolyte used, the kind of carbon black, and modification conditions of the AQP. The capacitance of 1.34 F cm-2 was obtained at the AQP modified CB (DENKA Black HS-100) in 0.1 M HClO4. This modification method is very simple, versatile, and effective for modifying nanocarbons.

Preventive Effect of High-Dose Digestive Enzyme Management on Development of Nonalcoholic Fatty Liver Disease after Pancreaticoduodenectomy: A Randomized Controlled Clinical Trial

Nonalcoholic fatty liver disease (NAFLD) is a complication of pancreaticoduodenectomy (PD). We conducted a randomized clinical trial to determine if high-dose digestive enzymes prevented the development of NAFLD after PD. This parallel-group, nonblinded, multicenter study enrolled patients undergoing elective PD at Shinshu University School of Medicine, from June 2011 to April 2017. Patients were randomly assigned to receive normal-dose (Excelase: 3.0 g/day [Meiji Seika Pharma Holdings Co, Ltd]) or high-dose digestive enzyme treatment (Excelase: 3.0 g/day; Pancreatin [Tokyo Chemical Industry Co Ltd]: 3.0 g/day; Berizym [Kyowa Pharmaceutical Industry Co Ltd]: 3.0 g/day; and Toughmac-E [Ono Pharmaceutical Co, Ltd]: 3.0 g/day) within 1 week after surgery. Because patients in the control group switched interventions upon receiving a diagnosis of NAFLD, intention-to-treat analysis was used. The primary endpoint was incidence of NAFLD within 1 year, and the secondary endpoints were the incidences of NAFLD at 1, 3, 6, and 12 months and the rate of improvement in NAFLD with high-dose transfer in the control group. The secondary analysis comprised assessment of risk factors for the development of NAFLD. Eighty-four patients were randomly assigned (42 per group), 80 of whom were finally analyzed (39 normal-dose, 41 high-dose). The incidence of NAFLD was significantly lower in the high-dose (8 of 41) compared with the normal-dose (25 of 39) patients (p<0.001). Multivariate analysis identified normal-dose (odds ratio [OR] 14.65, p<0.001), total protein ≤ 6.5g/dL (OR 9.01, p= 0.018), pre-albumin ≤ 22.0 mg/dL (OR 7.71, p= 0.018), and pancreatic function diagnostic test ≤ 70% (OR 6.66, p= 0.009) as independent risk factors. There were no adverse effects. The model was accurate (c-index=0.92) and reliable (Hosmer-Lemeshow test p= 0.32). High-dose administration of digestive enzymes significantly reduced the onset of NAFLD after PD compared with normal-dose administration. Registration number: UMIN000005595 (http://www.umin.ac.jp/ctr/).

A droplet-generator-on-a-chip actuated by ECF (electro-conjugate fluid) micropumps

The traditional power sources for generating droplets are bulky devices such as syringe pumps, constant pressure systems and so on, resulting in difficult integration with other microfluidic components. To overcome this limitation, we propose and develop a droplet generator with its power sources on a chip (22 × 21 × ~ 1 mm). The compact droplet generator consists of two ECF (electro-conjugate fluid) micropumps, a T-junction channel geometry made of SU-8, a water chamber and three I/O ports. In our methodology, the two ECF micropumps are used to pump the continuous phase fluid (oil) directly and the dispersed phase fluid (water) indirectly on a chip. ECF is a kind of functional and dielectric oil, which can generate a strong and active ECF jet when its corresponding electrodes are applied to high DC voltages. Our ECF micropump is composed of triangular prism and silt electrode pairs (TPSEs) and is able to control flow rates precisely on a chip. In our device, the water in oil droplet is formed by the T-junction geometry. Using MEMS technology, we successfully fabricate the droplet-generator-on-a-chip. Span 80 and dibutyl decanedioate (DBD, Tokyo Chemical Industry Co., Ltd) are used as the surfactant and one type of ECF, respectively. Prior to the characteristic experiments of the T-junction generator, we investigate viscosity, electrical conductivity and relative permittivity of the mixtures of DBD and Span 80 at different concentrations (0 wt%, 1 wt%, 3 wt% and 5 wt%). We also research the impact of the mixtures on the performance of ECF micropumps and the wettability of SU-8 fluidic channels. After that, we confirm the flow pattern diagrams of two-phase fluids, the generated droplet diameter and the droplet production rate for our droplet-generator. Therefore, our droplet generator powered by ECF micropumps can realize the droplet generation on a chip.

Simultaneous Synthesis of Vitamins D2, D4, D5, D6, and D7 from Commercially Available Phytosterol, β-Sitosterol, and Identification of Each Vitamin D by HSQC NMR.

We succeeded in simultaneously synthesizing the vitamin D family, vitamins D2, D4, D5, D6, and D7, from β-sitosterol, which is sold as a commercially available reagent from Tokyo Chemical Industry Co., Ltd. It is officially sold as a mixture of four phytosterols {β-sitosterol (40–45%), campesterol (20–30%), stigmasterol, and brassicasterol}. Owing to this, we anticipated that, using this reagent, various vitamin D analogs could be synthesized simultaneously. We also synthesized vitamin D3 from pure cholesterol and analyzed and compared all vitamin D analogs (D2, D3, D4, D5, D6, and D7) by HSQC NMR. We succeeded in clearly demonstrating the difference in the NMR chemical shifts for each vitamin D analog.

Teruaki Mukaiyama

Teruaki Mukaiyama, 91, died on Nov. 17, 2018, in Tokyo. “Professor Mukaiyama is best known for developing the Mukaiyama aldol addition. He also achieved a total synthesis of Taxol. He won numerous awards, including the American Chemical Society Award for Creative Work in Synthetic Organic Chemistry in 2006. He devoted his life to research in organic synthesis, and he asked a similar attitude of his students. Apart from research, he was very supportive and generous toward them. This was how he nurtured 54 professors in academia. All of them loved him from the bottom of their hearts.”—Masahiro Murakami, former student Most recent title: Research adviser, Tokyo Chemical Industry Education: BSc, synthetic organic chemistry, Tokyo Institute of Technology, 1948; PhD, synthetic organic chemistry, University of Tokyo, 1957; honorary degree, synthetic organic chemistry, Technical University of Munich, 1976 Survivors: Son, Taketo Mukaiyama To recognize your late loved one or colleague, submit obituary

(Invited) Elucidating the Micro Phase-Separation of Mixed Kappa and Iota Carrageenan Gels Using Multiple Particle Tracking

Carrageenan is a family of linear sulfated polysaccharides extracted from seaweeds. Among the different types of carrageenan, kappa carrageenan (KC) and iota carrageenan (IC) are widely used in industries due to its gelling behavior. Because of its importance in industries, KC and IC as well as its mixtures have been extensively studied using different methods. However, it is still unclear whether mixed KC:IC undergo a phase separated network structure of IC-rich and KC-rich or interpenetrated network structure. In this report, the network structure and gelation mechanism of KC, IC and its mixture were elucidated using multiple particle tracking. Sodium-type κ- and ι- carrageenan powder was purchased from Tokyo Chemical Industry Co., Ltd. (Tokyo, Japan). All samples were dialyzed against NaCl solution and subsequently against deionized water, to obtain Na+ type carrageenan solutions. Samples were prepared by diluting carrageenan and KCl solutions and heated for 30 min at 70 °C under vigorous stirring. The prepared solutions were mixed using vortex to obtain 1.5% w/w carrageenan with 10 mM KCl and heated at 90 °C for 20 min. Fluorescently labelled 0.1 μm particles (Green, ThermoScientific) were added at a concentration of ~0.01% (v/w) at 90 °C and stirred for another 5 min to assure homogenous dispersion. Mixture of KC and IC was prepared at different volume fraction of IC. Movies of the diffusing particles were recorded at a frame rate of 7.5 frames per second for 110 seconds. In cooling experiments, particle tracking was performed at different sample temperatures from 50 °C to 10 °C. In storage experiments, hot solutions of carrageenan were cooled down from 50 °C to 5 °C at a rate of 1 °C/min in a temperature-controlled incubator to form a gel. The gelled sample was stored at 5 °C prior to experiment and particle tracking was performed at 5 °C. Particle tacking was implemented in Mathematica 10 (Wolfram Research, Inc., USA). The temperature dependence of the mean square displacement (MSD) of particles in KC, IC and mixed KC:IC gels were carried out to quantify the dynamics of the evolving network structure on cooling as shown in Figure 1. In mixed KC:IC, a two-step decrease in MSD was observed. The onset of the observed decrease is close to the decrease in pure KC and IC gels. This trend is consistent with the observed increase in the viscoelastic modulus in dynamic viscoelasticity measurements. The decrease in the MSD with decreasing temperature is due to the steric hindrance created by the formation of clusters of IC and KC chain aggregates. This suggests that KC and IC chains formed aggregates independently on cooling. In pure carrageenan, IC gels formed weak entanglement among clusters of IC chain that allowed diffusion of particles through crevices of the entangled clusters while KC gels rapidly formed thick aggregates of interconnected clusters that confined the particles. On the other hand, in mixed KC:IC, the presence of IC clusters decreased the mobility of KC chains at low temperature thus slowed the formation of stable clusters of KC. With storage time, a broad distribution of MSD was observed for the mixed gels. This suggests that an inhomogeneous solution was formed as KC and IC clusters continue to rearrange to form a stable network. The degree of heterogeneity in the mixed gels is reflected in the corresponding van Hove distribution of particle displacement and the distribution of MSD as a function of slope. In the van Hove distribution, a bimodal Gaussian form with a broad and narrow Gaussian width fit well on the distribution suggests a mobile and immobile fraction of particle at each mixing ratios. In the distribution of MSD as a function of slope, the mobile and immobile particles were identified and clustered accordingly. This suggests that the presence of mobile particles was due to the existence of IC-rich domains that allowed diffusion of particles and the immobile particles was due to the confinement of particles in KC-rich domains as shown in the graphical representation in Figure 1. This is consistent with the proposed gelation mechanism of a local phase separation into IC-rich and KC-rich domains. As the volume fraction of IC was increased, the number of mobile particles increased consequently and suggests a phase transition from a sea-island (80%KC:20%IC) to a bi-continuous (50%KC:50%IC) to an island-sea (30%KC:70%IC) network structure is likely to occur. Figure 1

Determination of Nitrate Ion Concentration in Fresh Vegetable Juices Using Ion-Pair Ultra Performance Liquid Chromatography (IP-UPLC)

Determination of Nitrate Ion Concentration in Fresh Vegetable Juices Using Ion-Pair Ultra Performance Liquid Chromatography (IP-UPLC)

Analysis of Ion Transport in Solution Electrolytes for Electrochemical Capacitors

In recent years, electric double layer capacitors (EDLCs) have attracted much attention not only for small electric devices as smart phone and tablet PC, but also for large power sources in electric vehicles. The advantage of EDLCs is a high-rate capability and good cycleability, which are due to the fast charge/discharge mechanism by using electric double layer regardless of Faradaic reaction with electrodes. Also, lithium ion capacitors (LICs) with Faradaic reaction electrodes such as graphite anode on the one side have been intensively developed to solve the small energy density of EDLCs. The performances of capacitors (EDLCs and LICs) strongly depend on the electrolyte properties, i.e. the ionic conductivity and electrochemical stability. In this study, we separately measured self-diffusion coefficients D of ions and solvent in the solution electrolytes for EDLCs and LICs by a pulse gradient spin-echo (PGSE) NMR. The viscosity and ionic conductivity were also examined to discuss the relationship with D values. Moreover, the interactions between ions and ion-solvent were evaluated from the DFT calculations.1 M solutions of (C2H5)4NBF4(TEABF4) and LiBF4 in propylene carbonate (PC) were obtained from Kishida Chemical Co, Ltd. TEAPF6 (99%, Aldrich), TEATfO (98%, Wako Pure Chemicals) and (C2H5)3CH3NBF4 (TEMABF4) (98%, Tokyo Chemical Industry Co., Ltd.) were used as supporting salts, and dissolved in PC (Wako Pure Chemicals) as a solvent in an Ar-filled dry box to prepare their 1 M solutions. The solution electrolytes were subjected to the PGSE-NMR for measuring the D values of cations (Li+(7Li), TEA+(1H), TEMA+(1H)), anions (BF4 -(9F), PF6 -(9F)) and solvent (PC(1H)) [1]. The viscosity and ionic conductivity of electrolytes were evaluated by a viscometer (anton paar) and an AC impedance analyzer (Bio-Logic), respectively. The interaction energies between cation-anion and ion-solvent were estimated by DFT calculations with Gaussian09.Fig. 1 plots the D values of ions at 30oC against the ion radius, where the D value of Li+ was also plotted at the point of solvated radius by PC [2]. For the EDLC electrolytes, the smaller size of anions (BF4 -, PF6 -, TfO-) showed relatively higher D values than the larger cations (TEA+, TEMA+). In addition, as for the kind of cation and anion, smaller size of TEMA+ and BF4 - were also exhibited a higher D values than the other larger ions. These facts indicate that there is a clear dependence of ion radius for the EDLC electrolytes. As a result, it was found that the TEMABF4 was the best supporting salt among them. On the other hand, for the LIC electrolytes smaller size of Li+ exhibited lower D value than the larger BF4 -. Moreover, considering the solvated radius of Li+ by PC suggested the reasonable results on the transport behaviors as well as the EDLC electrolytes. This implies that Li+ in the LIC electrolytes was strongly solvated by PC, and suppressed the smooth transport compared with BF4 -. In contrast, the PC solvation of TEA+ in the EDLC electrolytes is suggested to be weaker than that of Li+ in the LIC ones. Fig. 2 shows the concentration dependence of D values of ions in the representative electrolytes for EDLC (TEABF4/PC) and LIC (TEABF4/PC) at 30oC. For all the concentration, the EDLC electrolyte exhibited higher D values than the LIC one, and the trend observed in Fig. 1 was not changed by the concentration. For both electrolytes, the D values became higher with a decrease in the concentration. This is due to a decrease in the viscosity of electrolytes. In addition, for the LIC electrolyte, promotion of the dissociation of LiBF4 salt was also suggested to enhance the D values. To elucidate the detail, ion radius against PC (r ion/r PC) in the solution electrolytes at 30oC were estimated by using the Stokes-Einstein equation (Fig. 3) [1]. The r ion/r PC values of Li+ and BF4 - for the LIC electrolyte were higher than those of ions in the EDLC electrolytes. This implies that Li+ in the LIC electrolyte strongly interacts with PC and BF4 - to form large solvated ions and ion pairs, respectively. Especially in comparison of the r ion/r PC value of BF4 -, it was found that the LiBF4 was more difficult to dissociate in PC than the TEABF4 and the dissociation of LiBF4 was promoted by the decrease in the concentration. Further analysis of Dvalues and comparison with the other parameters of viscosity, ionic conductivity, etc. will be discussed in the meeting.This study was supported by JST “A Tenure-track Program” from MEXT, Japan.[1] M. Saito et al., s in ACEPS-7, 2P-32 (2013). [2] M. Ue, J. Electrochem. Soc., 141, 3336 (1994).

オルセイン染色の実態調査結果と標準化への試み

Copper deposition of periportal hepatocytes indicates chronic cholestasis and it is regarded as a very important histological finding to diagnose primary biliary cirrhosis (PBC) and define its stage. Orcein stain makes copper-binding protein visible clearly and sensitively. However, there are variations in orcein staining results every institutions. In order to generalize and standardize staining method, we surveyed the methods of orcein stain at 11 institutions including our laboratory. Consequently, there were differences in staining result according to the kinds of orcein reagents and reducers. As for staining of copper-binding protein, combination of orcein reagent manufactured by Merck or Tokyo Chemical Industry and 1.5 to 3%oxalic acid as reducer is recommended.

Development of a Novel Composite Material with Carbon Nanotubes Assisted by Self-Assembled Peptides Designed in Conjunction with β-Sheet Formation

A novel composite material is developed with single-walled carbon nanotubes (SWCNTs) and artificially designed peptides, and its chemical and physicochemical characteristics are evaluated with an aim toward biomedical application. The peptides were designed to form a β-sheet structure that would be suitable for wrapping SWCNTs. The complex of SWCNTs and peptide (SWCNT-peptide) showed good dispersibility in aqueous media and was considerably stable even in the absence of an excess amount of peptide in the media. The formation of SWCNT-peptide was confirmed by its performance in water, atomic force microscopy and transmission electron microscopy observation, and molecular modeling. The possibility of introducing various functions to SWCNT-peptide was also demonstrated by several methods, such as introduction of special amino acids, chemical modification, and additional complex formation based on electrostatic interaction. These results suggest the potential of the SWCNT-peptide complex as a molecular platform on which a desirable structure and/or function can be constructed for biomedical and industrial application.

Nanosecond Bias-Free Mach–Zehnder Electro-Optic Switch Based on Dye-Doped Polymer DR1/SU-8 and Microstrip Line Electrode

A bias-free Mach–Zehnder interferometer electro-optic switch is demonstrated with a dye-doped polymer Disperse Red 1 (Tokyo Chemical Industry, Co., LTD, Tokyo, Japan)/SU-8 (MicroChem Corp., Newton, Massachusetts, USA) and microstrip line electrode. The device is carefully designed and optimized for bias-free function and high-speed switching using the three-dimensional beam-propagation method and extended point-matching method, and the switch is seriously fabricated by a wet-etching technique and inductively coupled plasma etching technique for good control of dimension parameters. The measured rise time and fall time at 1,550 nm are both at the level of ~10 ns. Owing to the bias-free function and nanosecond response speed, this switch exhibits potential applications of high-speed optical routing and exchanging.

Large-Ordered Striped Phase of Didodecyl Sulfide Self-Assembled Monolayers on Au(111)

Alkanethiol self-assembled monolayers (SAMs) on metal surfaces are key elements for the fabrication of functional organic layers and devices in the broad fields of nanotechnology and biotechnology. However, it was found that alkanethiol SAMs were usually composed of structural defects such as domain boundaries and vacancy islands (VIs), which make them more amenable to oxidation. Compared to alkanethiols, thioethers (RSR') are more robust to oxidation, and their chemical structures with various alkyl chains can be modified readily by a simple synthetic method. Therefore, SAMs prepared using thioethers provide a very useful means for tuning the characteristics of metal surfaces. Despite these advantages, there have only been a limited number of papers involving the formation and structure of thioether SAMs on gold surfaces. It has been revealed that dioctadecyl sulfides (DODS, CH3(CH2)17S(CH2)17CH3) at the initial growth stage form SAMs with striped phases in which the molecular backbones are oriented parallel to the surface, whereas DODS SAMs formed after long immersion have two mixed phases containing closely packed and loosely packed standing-up phases where the molecular backbones are oriented perpendicular to the surface. High-resolution scanning tunneling microscopy (STM) observation revealed that the SAMs of dimethyl sulfides (DMS, CH3SCH3) with the shortest alkyl chains on Cu(111) have a herringbone-like packing structure, whereas dibutyl sulfides (DBS, CH3(CH2)3S(CH2)3CH3) with slightly larger alkyl chains form striped phases. From these results, we assumed that the formation of dialkyl sulfide SAMs strongly depends on van der Waals interactions between alkyl chains. So far, there no data has been reported on the formation and structure of didodecyl sulfides (DDS, CH3(CH2)11S(CH2)11CH3) with medium alkyl chains from a molecular-scale perspective. In this paper, we report the first STM results showing that the adsorption of DDS molecules at 70 oC generating long-range ordered SAMs with a 7.5 × √3 striped phase with VIs-free surfaces. Dodecanethiol (DDT, CH3(CH2)11SH) and DDS were purchased from Tokyo Chemical Industry (Tokyo, Japan). DDT and DDS SAMs were prepared by dipping the Au(111) substrate in 1 mM ethanol solutions of corresponding compounds at room temperature for 24 h. To understand the effect of solution temperature on the formation of DDS SAMs, the SAMs were prepared at 70 C for 1 h. STM images were obtained using a NanoScope E (Veeco, Santa Barbara, CA, USA) with a commercial Pt/Ir (80:20) tip under ambient conditions. The STM images in Figure 1 show remarkable structural differences in the formation of ordered domains and VIs (dark holes) for DDT and DDS SAMs on Au(111) formed after 24 h immersion at room temperature. Figure 1(a) shows a typical packing structure of DDT SAMs with a c(4 × 2) superlattice formed at saturation coverage. DDT SAMs were mainly composed of ordered phases with three domain orientations (Regions A, B, and C) separated by domain boundaries. The proportion of the VI areas to the total surface area was measured to be approximately 8%-12%, values which are similar to those observed from other alkanethiol SAMs. Unlike DDT SAMs, Figure 1(b) shows that the DDS SAMs have two mixed phases: the ordered phase with three domain orientations (Regions A, B, and C) and the disordered phase (Region D). The existence of three domain orientations for DDS SAMs on Au(111) means that the formation of SAMs was influenced by interactions between the sulfide atoms and gold surfaces. On the other hand, DDS SAMs contained few VIs comprising a small (23%) area fraction of the total surface area. The presence of disordered phases and a smaller VI fraction for DDS SAMs can be attributed to the weaker interactions between the sulfide atoms and gold surfaces compared to those between the sulfur atoms of thiols and gold surfaces for DDT SAMs. This finding is consistent with a previous result for the SAMs of DODS with long alkyl chains of 18 carbon units. The ordered domains have a row structure with an inter-row distance of 1.59 ± 0.03 nm, which is nearly half of the entire

Apo- and Cellopentaose-bound Structures of the Bacterial Cellulose Synthase Subunit BcsZ

Cellulose, a very abundant extracellular polysaccharide, is synthesized in a finely tuned process that involves the activity of glycosyl-transferases and hydrolases. The cellulose microfibril consists of bundles of linear β-1,4-glucan chains that are synthesized inside the cell; however, the mechanism by which these polymers traverse the cell membrane is currently unknown. In Gram-negative bacteria, the cellulose synthase complex forms a trans-envelope complex consisting of at least four subunits. Although three of these subunits account for the synthesis and translocation of the polysaccharide, the fourth subunit, BcsZ, is a periplasmic protein with endo-β-1,4-glucanase activity. BcsZ belongs to family eight of glycosyl-hydrolases, and its activity is required for optimal synthesis and membrane translocation of cellulose. In this study we report two crystal structures of BcsZ from Escherichia coli. One structure shows the wild-type enzyme in its apo form, and the second structure is for a catalytically inactive mutant of BcsZ in complex with the substrate cellopentaose. The structures demonstrate that BcsZ adopts an (α/α)(6)-barrel fold and that it binds four glucan moieties of cellopentaose via highly conserved residues exclusively on the nonreducing side of its catalytic center. Thus, the BcsZ-cellopentaose structure most likely represents a posthydrolysis state in which the newly formed nonreducing end has already left the substrate binding pocket while the enzyme remains attached to the truncated polysaccharide chain. We further show that BcsZ efficiently degrades β-1,4-glucans in in vitro cellulase assays with carboxymethyl-cellulose as substrate.

Drosophila Evaluates and Learns the Nutritional Value of Sugars

Living organisms need to search for and ingest nutritional chemicals, and gustation plays a major role in detecting and discriminating between chemicals present in the environment. Using Drosophila as a model organism, we asked whether animals have the ability to evaluate the nutritional value of sugars. In flies, chemosensilla on the tarsi and labellum are the gustatory organs used to discriminate between edible and nonedible compounds [1, 2]. We noticed that Drosophila do not assign nutritional values to all sweet chemicals. D-arabinose is sweet to flies, but it provides them with no nutrition. By contrast, the sugar alcohol D-sorbitol is not sensed as sweet, but flies can live on it. We performed behavioral and electrophysiological measurements to confirm these gustatory and feeding responses. We found that Drosophila can learn the nutritional value of nonsweet D-sorbitol when it is associated with an odor cue. The learning process involved the synapsin molecule, suggesting that a neuronal mechanism is involved. We propose that Drosophila uses neural machinery to detect, evaluate, and learn the nutritional value of foods after ingestion.

Structural and Biochemical Elucidation of Mechanism for Decarboxylative Condensation of β-Keto Acid by Curcumin Synthase

The typical reaction catalyzed by type III polyketide synthases (PKSs) is a decarboxylative condensation between acyl-CoA (starter substrate) and malonyl-CoA (extender substrate). In contrast, curcumin synthase 1 (CURS1), which catalyzes curcumin synthesis by condensing feruloyl-CoA with a diketide-CoA, uses a β-keto acid (which is derived from diketide-CoA) as an extender substrate. Here, we determined the crystal structure of CURS1 at 2.32 Å resolution. The overall structure of CURS1 was very similar to the reported structures of type III PKSs and exhibited the αβαβα fold. However, CURS1 had a unique hydrophobic cavity in the CoA-binding tunnel. Replacement of Gly-211 with Phe greatly reduced the enzyme activity. The crystal structure of the G211F mutant (at 2.5 Å resolution) revealed that the side chain of Phe-211 occupied the hydrophobic cavity. Biochemical studies demonstrated that CURS1 catalyzes the decarboxylative condensation of a β-keto acid using a mechanism identical to that for normal decarboxylative condensation of malonyl-CoA by typical type III PKSs. Furthermore, the extender substrate specificity of CURS1 suggested that hydrophobic interaction between CURS1 and a β-keto acid may be important for CURS1 to use an extender substrate lacking the CoA moiety. From these results and a modeling study on substrate binding, we concluded that the hydrophobic cavity is responsible for the hydrophobic interaction between CURS1 and a β-keto acid, and this hydrophobic interaction enables the β-keto acid moiety to access the catalytic center of CURS1 efficiently.

Curcuminoid Biosynthesis by Two Type III Polyketide Synthases in the Herb Curcuma longa

Curcuminoids found in the rhizome of turmeric, Curcuma longa, possess various biological activities. Despite much attention regarding the biosynthesis of curcuminoids because of their pharmaceutically important properties and biosynthetically intriguing structures, no enzyme systems have been elucidated. Here we propose a pathway for curcuminoid biosynthesis in the herb C. longa, which includes two novel type III polyketide synthases. One of the type III polyketide synthases, named diketide-CoA synthase (DCS), catalyzed the formation of feruloyldiketide-CoA by condensing feruloyl-CoA and malonyl-CoA. The other, named curcumin synthase (CURS), catalyzed the in vitro formation of curcuminoids from cinnamoyldiketide-N-acetylcysteamine (a mimic of the CoA ester) and feruloyl-CoA. Co-incubation of DCS and CURS in the presence of feruloyl-CoA and malonyl-CoA yielded curcumin at high efficiency, although CURS itself possessed low activity for the synthesis of curcumin from feruloyl-CoA and malonyl-CoA. These findings thus revealed the curcumin biosynthetic route in turmeric, in which DCS synthesizes feruloyldiketide-CoA, and CURS then converts the diketide-CoA esters into a curcuminoid scaffold.