Autonomous DNA computing machine based on photochemical gate transition

We report the construction of a one-pot autonomous DNA computing machine based on photochemical gate transition (photocleavage, hybridization, and photoligation), and we performed binary digit additions using this machine. In our method, both photochemical DNA manipulations previously reported, photoligation via 5-carboxyvinyldeoxyuridene (cvU) containing ODN and photocleavage via carbazole-modified ODN, were employed. The binary digit additions were autonomously carried out by one-time irradiation at 366 nm in the single test tube. The fluorescence readout by the DNA chip was in good agreement with the correct answer of binary digit additions. We believe that this system is easily applicable to correlation analysis between SNPs as well as other binary digit processing, such as subtraction.     

In situ direct sampling mass spectrometric study on formation of polycyclic aromatic hydrocarbons in toluene pyrolysis

The gas-phase reaction products of toluene pyrolysis with and without acetylene addition produced in a flow tube reactor at pressures of 8.15-15.11 Torr and temperatures of 1136-1507 K with constant residence time (0.56 s) have been detected in an in situ direct sampling mass spectrometric study by using a vacuum ultraviolet single-photon ionization time-of-flight mass spectrometry technique. Those products range from methyl radical to large polycyclic aromatic hydrocarbons (PAHs) of mass 522 amu (C(42)H(18)) including smaller species, radicals, polyynes, and PAHs, together with ethynyl, methyl, and phenyl PAHs. On the basis of observed mass spectra, the chemical kinetic mechanisms of the formation of products are discussed. Especially, acetylene is mixed with toluene to understand the effect of the hydrogen abstraction and acetylene addition (HACA) mechanism on the formation pathways of products in toluene pyrolysis. The most prominent outputs of this work are the direct detection of large PAHs and new reaction pathways for the formation of PAHs with the major role of cyclopenta-fused radicals. The basis of this new reaction route is the appearance of different sequences of mass spectra that well explain the major role of aromatic radicals mainly cyclopenta fused radicals of PAHs resulting from their corresponding methyl PAHs, with active participation of c-C(5)H(5), C(6)H(5), C(6)H(5)CH(2) ,and C(9)H(7) in the formation of large PAHs. The role of the HACA only seemed important for the formation of stable condensed PAHs from unstable primary PAHs with zigzag structure (having triple fusing sites) in one step by ring growth with two carbon atoms.     

Synthesis of well-defined polystyrene with multi-functional end groups utilizing cyclotriphosphazene

Telechelic polystyrenes with five benzyl chloride moieties at the polymer end (PSt-E) were prepared by coupling reaction of polystyryllithium with hexakis(4-chloromethyl-phenoxy)cyclotriphosphazene ( 4 ). The coupling reaction occurs almost quantitatively and unfavorable side reactions were not operative. When a mole ratio [ 4 ]/[sec-BuLi] = 9.3 was used, polystyrenes with cyclophosphazene carrying five benzyl chloride moieties at the polymer end (PSt-E) were obtained in more than 90% yield, which have narrow and predictable molecular weights (M _w/M _n = 1.05). A star shaped polystyrene with phosphazene core could also be prepared by using excess polystyryl anions.     

Shallow surface etching of organic and inorganic compounds by electrospray droplet impact

The electrospray droplet impact (EDI) was applied to bradykinin, polyethylene terephthalate (PET), SiO₂/Si, and indium phosphide (InP). It was found that bradykinin deposited on the stainless steel substrate was ionized/desorbed without the accumulation of radiation products. The film thickness desorbed by a single collisional event was found to be less than 10 monolayers. In the EDI mass spectra for PET, several fragment ions were observed but the XPS spectra did not change with prolonged cluster irradiation. The etching rate for SiO₂ by EDI was measured to be ∼0.2 nm/min. The surface roughness of InP etched by EDI was found to be one order of magnitude smaller than that etched by 3 keV Ar⁺ for about the same etching depths. EDI is capable of shallow surface etching with little damage left on the etched surface.     

Electrospray droplet impact/secondary ion mass spectrometry: cluster ion formation

The electrospray droplets that are sampled through an orifice into the vacuum chamber are accelerated by 10 kV and impact on the stainless steel substrate. The mass and the kinetic energy of electrospray droplets are roughly estimated to be a few 10(6) u and approximately 10(6) eV, respectively. The molecular ion M(+.) and the protonated molecule [M+H](+) are observed as secondary ions for chrysene and coronene deposited on the metal substrate (no matrix used). The ionization may take place in the shock wave generated by the high-momentum coherent collision between the droplet projectile and the solid sample. Cluster ions of H(+)(H(2)O)(n) and CF(3)COO(-)(H(2)O)(n), with n up to approximately 150, were observed as secondary ions formed by the electrospray droplet impact ionization (EDI) for 10(-2) M trifluoroacetic acid (TFA) aqueous solution. This indicates that the charged droplets that collide with the metal substrate with the kinetic energy of approximately 10(6) eV do not vaporize completely but are disintegrated into many tiny microdroplets. The ion signal intensity anomalies (i.e. magic numbers) were observed for the cluster ions of H(3)O(+)(H(2)O)(n) and CF(3)COO(-)(H(2)O)(n) for 10(-2) M TFA aqueous solution and of Cs(+)(H(2)O)(n), I(-)(H(2)O)(n), Cs(+)(CsI)(n), and I(-)(CsI)(n) for 10(-2) M CsI aqueous solution.     

Mass spectrometric monitoring of oxidation of aliphatic C6–C8 hydrocarbons and ethanol in low pressure oxygen and air plasmas

Experimental and theoretical studies on the oxidation of saturated hydrocarbons (n‐hexane, cyclohexane, n‐heptane, n‐octane and isooctane) and ethanol in 28 Torr O₂ or air plasma generated by a hollow cathode discharge ion source were made. Ions corresponding to [M + 15]⁺ and [M + 13]⁺ in addition to [M ? H]⁺ and [M ? 3H]⁺ were detected as major ions where M is the sample molecule. The ions [M + 15]⁺ and [M + 13]⁺ were assigned as oxidation products, [M ? H + O]⁺ and [M ? 3H + O]⁺, respectively. By the tandem mass spectrometry analysis of [M ? H + O]⁺ and [M ? 3H + O]⁺, H₂O, olefins (and/or cycloalkanes) and oxygen‐containing compounds were eliminated from these ions. Ozone as one of the terminal products in the O₂ plasma was postulated as the oxidizing reagent. As an example, the reactions of C₆H₁₄^+? with O₂ and of C₆H₁₃⁺ (CH₃CH₂CH⁺CH₂CH₂CH₃) with ozone were examined by density functional theory calculations. Nucleophilic interaction of ozone with C₆H₁₃⁺ leads to the formation of protonated ketone, CH₃CH₂C(=OH⁺)CH₂CH₂CH₃. In air plasma, [M ? H + O]⁺ became predominant over carbocations, [M ? H]⁺ and [M ? 3H]⁺. For ethanol, the protonated acetic acid CH₃C(OH)₂⁺ (m/z 61.03) was formed as the oxidation product. The peaks at m/z 75.04 and 75.08 are assigned as protonated ethyl formate and protonated diethyl ether, respectively, and that at m/z 89.06 as protonated ethyl acetate. Copyright © 2016 John Wiley & Sons, Ltd.     

Mechanism and control of periodic surface nanostructure formation with femtosecond laser pulses

Fundamental mechanism of femtosecond-laser-induced periodic surface nanostructure formation has been investigated under the condition using superimposed multiple shots at lower fluence than the single-pulse ablation threshold. With increasing the shot number of low-fluence fs-laser pulses, the periodic nanostructure develops through the bonding structure change of target material, the nanoscale ablation with optical near-fields induced around the high curvatures, and the excitation of surface plasmon polaritons (SPPs) to create the nano-periodicity in the surface structure. It is confirmed that non-thermal interaction at the surface plays the crucial role in the nanostructure formation. Based on the mechanism, we have demonstrated that the periodic nanostructure formation process can be controlled to fabricate a homogeneous nanograting on the target surface, using a two-step ablation process in air. The experimental results obtained represent exactly the nature of a single spatial standing SPP wave mode that generates periodically enhanced near-fields for the nanograting formation. The calculated results for a model target reproduce well the nanograting period and explain the characteristic properties observed in the experiment.     

Glutinoin, a novel antioxidative ellagitannin from Alnus glutinosa cones with glutinoic acid dilactone moiety

The crude aqueous ethanol extract of the cones of Alnus glutinosa (L.) Gaertn. (Betulaceae; black alder, European alder) was obtained and further partitioned between water and various organic phases. The active water and butanol phases were subjected to assay-guided (DPPH) fractionation using repetitive RP HPLC until individual compounds were isolated. Their antioxidative activities, measured as SC?? values, were evaluated. The chemical structures of the isolated compounds were elucidated with the help of mass spectroscopy, (1)H NMR technique, UV spectroscopy, and chemical approaches. One novel ellagitannin, glutinoin (2), along with two known compounds, pedunculagin (1) and praecoxin D (3), were isolated and found to contribute to antioxidative activity of the A. glutinosa cones extract. The activities (SC??) of 1-3 were evaluated as 0.95 (1), 1.00 (2) and 1.01?μg?mL?1 (3). The scavenging effects of glutinoin (2) and praecoxin D (3) were reported for the first time.