Molecular and structural basis of anti-DNA antibody specificity for pyrrolated proteins.

Anti-DNA antibodies (Abs), serological hallmarks of systemic lupus erythematosus (SLE) and markers for diagnosis and disease activity, show a specificity for non-nucleic acid molecules, such as N-pyrrolated proteins (pyrP) containing Nε-pyrrole-L-lysine (pyrK) residues. However, the detailed mechanism for the binding of anti-DNA Abs to pyrP remains unknown. In the present study, to gain structural insights into the dual-specificity of anti-DNA Abs, we used phage display to obtain DNA-binding, single-chain variable fragments (scFvs) from SLE-prone mice and found that they also cross-reacted with pyrP. It was revealed that a variable heavy chain (VH) domain is sufficient for the recognition of DNA/pyrP. Identification of an antigenic sequence containing pyrK in pyrP suggested that the presence of both pyrK and multiple acidic amino acid residues plays important roles in the electrostatic interactions with the Abs. X-ray crystallography and computer-predicted simulations of the pyrK-containing peptide-scFv complexes identified key residues of Abs involved in the interaction with the antigens. These data provide a mechanistic insight into the molecular basis of the dual-specificity of the anti-DNA Abs and provide a basis for therapeutic intervention against SLE.

Method for the Calculation of the Hamaker Constants of Organic Materials by the Lifshitz Macroscopic Approach with Density Functional Theory.

The Hamaker constants, which are coefficients providing quantitative information on intermolecular forces, were calculated for a number of different materials according to the Lifshitz theory via simple DFT calculations without any experimental measurements being performed. The physical properties (polarizability, dipole moment, molecular volume, and vibrational frequency) of organic molecules were calculated using the B3LYP density functional and the aug-cc-pVDZ basis set. Values for the Hamaker constants were obtained using the approximation of the Lorentz-Lorenz equation and Onsager's equation with these properties. It was found that, in the case of "nonassociative" materials, such as hydrocarbons, ethers, ketones, aldehydes, carboxylic acids, esters, nitriles, and hydrosilanes, and halides, the calculated Hamaker constants were similar in value to their experimentally determined counterparts. Moreover, with this calculation method, it is easy to create the molecular model and the CPU time can be shortened.

Hybrid cluster precursors of the LaZrO insulator for transistors: lowering the processing temperature.

Solution processing of ternary and multinary amorphous metal oxide insulators at processing temperatures below 250 °C remains challenging. Here, we report that the synthesis of a hybrid cluster structure, where the metal oxide core is coordinated by ligands and the different metal elements are incorporated into one core, is an effective strategy for the low-temperature processing of the ternary LaZrO insulator. Solvothermal treatment at 160-180 °C facilitated the development of a cluster structure. From the cluster precursor, high-performance insulating LaZrO films were obtained at 200 °C under the irradiation of ultraviolet light. The analysis data indicate that the solvothermal treatment led to structural unification of the metal oxide network and facilitated stabilization of the residual organic ingredients in UV annealing, which both contributed to the improved insulating properties of LaZrO. Together with a solution-processed channel, we have been able to fabricate LaZrO-based transistors at 200 °C. Though the channel material has not been optimized, the transistor have showed a low gate leakage current around 10 pA at an operating voltage of 15 V, an on/off ratio of near 106, a field-effect saturation mobility of 0.37 cm2 V-1 s-1, a subthreshold swing factor of 0.61 V decade-1.

Silicon deposition in nanopores using a liquid precursor.

Techniques for depositing silicon into nanosized spaces are vital for the further scaling down of next-generation devices in the semiconductor industry. In this study, we filled silicon into 3.5-nm-diameter nanopores with an aspect ratio of 70 by exploiting thermodynamic behaviour based on the van der Waals energy of vaporized cyclopentasilane (CPS). We originally synthesized CPS as a liquid precursor for semiconducting silicon. Here we used CPS as a gas source in thermal chemical vapour deposition under atmospheric pressure because vaporized CPS can fill nanopores spontaneously. Our estimation of the free energy of CPS based on Lifshitz van der Waals theory clarified the filling mechanism, where CPS vapour in the nanopores readily undergoes capillary condensation because of its large molar volume compared to those of other vapours such as water, toluene, silane, and disilane. Consequently, a liquid-specific feature was observed during the deposition process; specifically, condensed CPS penetrated into the nanopores spontaneously via capillary force. The CPS that filled the nanopores was then transformed into solid silicon by thermal decomposition at 400 °C. The developed method is expected to be used as a nanoscale silicon filling technology, which is critical for the fabrication of future quantum scale silicon devices.

Hybrid Cluster Precursors of the LaZrO Insulator for Transistors: Properties of High-Temperature-Processed Films and Structures of Solutions, Gels, and Solids.

In the solution processing of oxide electronics, the structure of metal-organic precursors in solution and their effect on processability and on the final structure and properties of the oxide have rarely been studied. We have observed that hybrid clusters, having inorganic cores coordinated by organic ligands, are the typical form of metal-organic precursor structures. For insulating ternary LaZrO, improved synthesis of the cluster precursor under solvothermal conditions led to low-temperature deposition of the film at 200 °C, as we will report in another paper. In the current paper, we first briefly show that solvothermal synthesis of the precursor resulted in significantly improved insulating properties (e.g., two orders lower leakage current) of high-temperature-annealed films, and then focus on the structural analysis of the cluster precursors and annealed solids and relate the results to the significant improvement of properties by solvothermal treatment of solutions. A change in the cluster core toward structural unification was brought about by solvothermal treatment, resulting in higher uniformity and higher stability of clusters. The final structure of the material maintained the features of the core structure in solution, even after annealing at high temperatures. These results demonstrate the key role played by designing cluster structure in solution.

Novel method to incorporate Si into monodispersed mesoporous carbon spheres.

Liquid silicon precursor is used as a silicon source and very simple and easy method for the incorporation of Si into mesoporous carbon spheres is presented. By using capillary condensation, the liquid precursor, Cyclopentasilane, penetrates into mesopores of carbon spheres homogeneously and subsequent heating brings the decomposition of the precursor and the formation of silicon inside meso-channels of carbon even though the decomposition is done much higher than the boiling point of the precursor. The homogeneous distribution of silicon is verified by EDX mapping of the composite as well as SEM observation of the calcined one. More than 45wt% of Si can be incorporated into mesopores by just one operation. The Si@mesoporous carbon composite works as an anode for a Lithium ion battery.

A bulk sub-femtoliter in vitro compartmentalization system using super-fine electrosprays.

The extreme miniaturization of biological and chemical assays in aqueous-droplet compartments enables spatiotemporal control for large-scale parallel experimentation and can thus permit new capabilities for "digitizing" directed molecular evolution methodologies. We report a remarkably facile bulk method to generate mega-scale monodisperse sub-femtoliter aqueous droplets by electrospray, using a prototype head with super-fine inkjet technology. Moreover, the electrostatic inkjet nozzle that injects the aqueous phase when immersed within an immiscible phase (an optimized oil/surfactant mixture) has the advantage of generating cell-like sub-femtoliter compartments for biomolecule encapsulation and successive biological and chemical reactions. Sub-femtoliter droplets of both liquid (water-in-oil, volumes ranging from 0.2 to 6.4 fL) and gel bead (agarose-in-oil, volume ranging from 0.3 to 15.6 fL) compartments with average sizes of 1.3 µm and 1.5 µm, respectively, were successfully generated using an inkjet nozzle at a speed of more than 10(5) droplets per second. We demonstrated the applicability of this system by synthesizing fluorescent proteins using a cell-free expression system inside electrosprayed sub-femtoliter droplets at an accelerated rate, thereby extending the utility of in vitro compartmentalization with improved analytical performance for a top-down artificial cellular system.

Direct Imprinting of Liquid Silicon.

A polymeric precursor solution for semiconducting silicon called "liquid silicon" was synthesized and directly imprinted to form well-defined and fine amorphous silicon patterns. The spin-coated film was cured and imprinted followed by annealing at 380 °C to complete the polymer-to-silicon conversion. A pattern with dimensions of several hundreds of nanometers or less was obtained on a substrate. We demonstrated that the curing step before imprinting is particularly important in the imprinting process. A curing temperature of 140-180 °C was found to be optimal in terms of the film's deformability and molding properties. Fourier transform infrared spectroscopy and thermal analysis clarified that the cross-linking of the polymer due to the 1,2-hydrogen shift reaction was induced exponentially with the release of a large amount of SiH4/H2 gases at temperatures between 140 and 220 °C, leading to the solidification of the film. Consequently, the film completely lost its deformability at higher temperatures. Despite a volume shrinkage as large as 53-56% during the polymer-to-silicon conversion, well-defined angular patterns were preserved. Fine silicon patterns were formed via the direct imprinting of liquid silicon with high resolution and high throughput, demonstrating the usefulness of this technique for the future manufacturing of silicon electronics.

Fabrication of high-quality amorphous silicon film from cyclopentasilane by vapor deposition between two parallel substrates.

Cyclopentasilane converts into amorphous silicon film between two parallel substrates under atmospheric pressure by thermal decomposition at 350-400 °C, which combines the advantages of high throughput with cost reduction and high quality film formation.

Pulse-heating ionization for protein on-chip mass spectrometry.

An on-chip pulse-heating ionization source for protein samples was developed for the realization of miniaturized mass spectrometry. A protein analyte was ionized on a chip by applying only thermal energy to the solid phase sample without a laser, high voltage, or heated ambient gases. A fabricated ionization source consisting of a Pt/Cr microheater (width: 30 µm; length: 100 µm) on a silicon substrate was coupled with a time-of-flight mass filter to analyze a protein sample of bovine serum albumin (BSA, M = 66 kDa). A singly charged BSA ion and other multiply charged BSA ions were generated in the presence of 2,5-dihydroxybenzoic acid as a matrix. To detect the singly charged BSA ion, the required surface energy density of 1.65 × 10(-2) µJ/µm(2) was applied to the microheater for 500 ns. The use of the 2,5-dihydroxyacetophenone matrix resulted in the generation of the multiply charged protein analyte, while the use of the sinapic acid matrix showed abundant peaks in the low m/z region.

Selected deposition of high-quality aluminum film by liquid process.

For generation of a fine aluminum pattern by conventional vacuum processing, it is necessary not only to use complex and costly instruments but also to perform an additional etching process, which may result in physical and chemical damage to the target film surface. Herein we report a simple solution process for the selected deposition of an Al pattern. Al is obtained from the decomposition of alane under dehydrogenation catalysis of a Pt nanocrystalline pattern on a substrate at ∼105-120 °C, while the self-decomposition of alane in solution is avoided in the presence of high-boiling-point amine. This deposited film generates Al crystals with a diameter of several hundred nanometers, following an epitaxial growth to a continual film. The obtained film shows high conductivity, with a resistivity close to that of bulk Al.

Deposition of platinum patterns by a liquid process.

In contrast to the traditional chemical vapor deposition technique under high vacuum, we introduce a deposition method in liquid to prepare Pt patterns on substrate near 100 °C by seed growth.

Preparation of large thermally stable platinum nanocubes by using solvent-thermal reaction.

We describe the synthesis of single-crystalline Pt nanocubes with a large diameter (around 35 nm) using a solvent-thermal reaction in a polarity-controlled mixture of 1-butanol, toluene, and N,N-dimethylformamide at 185 °C.

Spectral parameters and Hamaker constants of silicon hydride compounds and organic solvents.

Cyclopentasilane (CPS) and polydihydrosilane, which consist of hydrogen and silicon only, are unique materials that can be used to produce intrinsic silicon film in a liquid process, such as spin coating or an ink-jet method. Wettability and solubility of general organic solvents including the above can be estimated by Hamaker constants, which are calculated according to the Lifshitz theory. In order to calculate a Hamaker constant by the simple spectral method (SSM), it is necessary to obtain absorption frequency and function of oscillator strength in the ultraviolet region. In this report, these physical quantities were obtained by means of an optical method. As a result of examination of the relation between molecular structures and ultraviolet absorption frequencies, which were obtained from various liquid materials, it was concluded that ultraviolet absorption frequencies became smaller as electrons were delocalized. In particular, the absorption frequencies were found to be very small for CPS and polydihydrosilane due to sigma-conjugate of their electrons. The Hamaker constants of CPS and polydihydrosilane were successfully calculated based on the obtained absorption frequency and function of oscillator strength.

Soft-UV photolithography using self-assembled monolayers.

We report thiol-on-gold self-assembled monolayers (SAMs) that can be photodeprotected using soft UV irradiation (lambda = 365 nm) to yield CO(2)H functionalized surfaces complementing those reported previously, which yielded NH(2) functionalized surfaces. The photolysis of these SAMs were monitored using a combination of surface sensitive techniques. In the SAM environment the photodeprotection yields are lower than those obtained for equivalent reactions in dilute solution. The protected carboxylic acids SAMs are shown to have a low yield approximately 50% due to competing photoreduction reactions of the nitro group. The results from infrared studies show that, as the photolysis progresses, the long chain protected residues reorganize and shield the functional COOH groups, thereby reducing the hydrophilic character of the surface.

Solution-processed silicon films and transistors.

The use of solution processes-as opposed to conventional vacuum processes and vapour-phase deposition-for the fabrication of electronic devices has received considerable attention for a wide range of applications, with a view to reducing processing costs. In particular, the ability to print semiconductor devices using liquid-phase materials could prove essential for some envisaged applications, such as large-area flexible displays. Recent research in this area has largely been focused on organic semiconductors, some of which have mobilities comparable to that of amorphous silicon (a-Si); but issues of reliability remain. Solution processing of metal chalcogenide semiconductors to fabricate stable and high-performance transistors has also been reported. This class of materials is being explored as a possible substitute for silicon, given the complex and expensive manufacturing processes required to fabricate devices from the latter. However, if high-quality silicon films could be prepared by a solution process, this situation might change drastically. Here we demonstrate the solution processing of silicon thin-film transistors (TFTs) using a silane-based liquid precursor. Using this precursor, we have prepared polycrystalline silicon (poly-Si) films by both spin-coating and ink-jet printing, from which we fabricate TFTs with mobilities of 108 cm2 V(-1) s(-1) and 6.5 cm2 V(-1) s(-1), respectively. Although the processing conditions have yet to be optimized, these mobilities are already greater than those that have been achieved in solution-processed organic TFTs, and they exceed those of a-Si TFTs (< or = 1 cm2 V(-1) s(-1)).

A mixed-valence coordination polymer featuring two-dimensional ferroelectric order: {[Cu(I)4Cu(II)(Et2dtc)2Cl3][Cu(II)(Et2dtc)2]2(FeCl4)}n (Et2dtc- = diethyldithiocarbamate).

The first mixed-valence coordination polymer indicating ferroelectric properties, {[CuI4CuII(Et2dtc)2Cl3][CuII(Et2dtc)2]2(FeCl4)}n (Et2dtc- = diethyldithiocarbamate), has been synthesized and crystallographically characterized. This complex has a two-dimensional infinite square lattice structure, including both Cu(I) and Cu(II) ions, which is confirmed by XPS and SQUID measurements. In addition, the ferroelectric behaviors are revealed by the dielectric measurements with a LCR meter and a ferroelectric tester.

A mild photoactivated hydrophilic/hydrophobic switch.

Surface modification using light is one of the most powerful methods for controlling the physical and chemical properties offunctionalized surfaces. In this paper, we report on systems where soft UV irradiation (lambda = 365 nm) converts a "low" activity fluorocarbon to a "high" activity amine-functionalized surface. An amine-functionalized SAM (self-assembled monolayer) is first masked using a tertiary amine catalyzed reaction with an N-hydroxysuccinimidyl carbonyl reagent. This mild, room-temperature reaction introduces a hydrophobic photocleavable nitrobenzyl "protecting group" terminated with a fluorocarbon end-chain. UV irradiation (lambda = 365 nm) of this hydrophobic/fluorocarbon surface cleaves the nitrobenzyl residue, returning the surface to the original hydrophilic/amine-functionalized state. This provides a mild, generic method of producing surfaces with hydrophilic/hydrophobic patterns or patterned with amine functional residues. Two different protecting groups, one terminated with a single and the other with three fluorocarbon end chains, are compared. In the case of the more bulky protecting group, only a small proportion of the amine residues react, but the surface is equally hydrophobic and the amine residues equally well shielded from further reaction. Surfaces are characterized by X-ray photoelectron spectroscopy, ellipsometry, surface potential, and contact angle measurements. Images of the photopatterned SAMs were obtained using scanning electron microscopy.