A nanocarbon film electrode as a platform for exploring DNA methylation

We describe the quantitative nonlabel electrochemical detection of both cytosine (C) and methylcytosine (mC) in oligonucleotides using newly developed nanocarbon film electrodes. The film consists of nanocrystalline sp2 and sp3 mixed bonds formed by employing the electron cyclotron resonance (ECR) sputtering method. We successfully used this film to develop a simple electrochemical DNA methylation analysis technique based on the measurement of the differences between the oxidation currents of C and mC since our ECR nanocarbon film electrode can directly measure all DNA bases more quantitatively than conventional glassy carbon or boron-doped diamond electrodes. The excellent properties of ECR nanocarbon film electrodes result from the fact that they have a wide potential window while maintaining the high electrode activity needed to oxidize oligonucleotides electrochemically. Proof-of-concept experiments were performed with synthetic oligonucleotides including different numbers of C and mC. This film allowed us to perform both C- and mC-positive assays solely by using the electrochemical oxidation of oligonucleotides without bisulfite or labeling processes.     

Comparison of Electrochemical and Surface Plasmon Resonance Immunosensor Responses on Single Thin Film

This paper reports results obtained when comparing an electrochemical enzyme immunosensor and a surface plasmon resonance (SPR) based immunosensor on the same gold surface installed in an electrochemical SPR flow cell. Simultaneous electrochemical and SPR measurements were performed on a gold surface modified with multilayers of poly‐L ‐lysine and poly‐styrenesulfonate assembled with the layer‐by‐layer method. First, we obtained the SPR response induced by the formation of an immunocomplex from the shift in the SPR angle by injecting an anti tumor necrosis factor‐α antibody solution labeled with alkaline phosphatase into the flow cell containing the multilayer modified with tumor necrosis factor‐α. Then we compared this SPR result with that obtained for the electrochemical oxidation current of p‐aminophenol catalyzed by alkaline phosphatase from p‐aminophenolphosphate on the same gold film. We compared the two immunosensor responses obtained using the different measurement principles and found that there was a high correlation efficient of 0.973 between them. This was because we were able to immobilize the immunoreagents with good stability and without losing the transport of the enzyme product in the multilayer whose thickness we easily controlled with nanometer scale accuracy. We also report that the detection limit of our electrochemical immunosensor after optimization was around 100 pg/mL (0.4 pM), which is one of the lowest values yet reported for an electrochemical immunosensor.     

Variational calculation of second-order reduced density matrices by strong N-representability conditions and an accurate semidefinite programming solver

The reduced density matrix (RDM) method, which is a variational calculation based on the second-order reduced density matrix, is applied to the ground state energies and the dipole moments for 57 different states of atoms, molecules, and to the ground state energies and the elements of 2-RDM for the Hubbard model. We explore the well-known N-representability conditions (P, Q, and G) together with the more recent and much stronger T1 and T2(') conditions. T2(') condition was recently rederived and it implies T2 condition. Using these N-representability conditions, we can usually calculate correlation energies in percentage ranging from 100% to 101%, whose accuracy is similar to CCSD(T) and even better for high spin states or anion systems where CCSD(T) fails. Highly accurate calculations are carried out by handling equality constraints and/or developing multiple precision arithmetic in the semidefinite programming (SDP) solver. Results show that handling equality constraints correctly improves the accuracy from 0.1 to 0.6 mhartree. Additionally, improvements by replacing T2 condition with T2(') condition are typically of 0.1-0.5 mhartree. The newly developed multiple precision arithmetic version of SDP solver calculates extraordinary accurate energies for the one dimensional Hubbard model and Be atom. It gives at least 16 significant digits for energies, where double precision calculations gives only two to eight digits. It also provides physically meaningful results for the Hubbard model in the high correlation limit.     

The movement of a water droplet on a gradient surface prepared by photodegradation

A hydrophobic to hydrophilic gradient surface was prepared using the tuned photodegradation of an alkylsilane self-assembled monolayer (SAM) using irradiation of vacuum ultraviolet light (wavelength=172 nm). The water contact angle on the photodegraded SAM surface was adjusted using the intensity and time photoirradiation parameters. The formation of a gradient was confirmed by fluorescent labeling. The water drop moved from the hydrophobic to hydrophilic surface with a velocity that depended on the gradient. The higher the gradient, the faster the water moved. For the first time, we have prepared a gradient surface using photodegradation where the movement of a water drop was regulated by the degree of gradation. Considering that the photodegradation technique can be applied to various surfaces and to lithography, this technique will be useful for various material surfaces.     

Heterogeneous Pd/C-catalyzed ligand-free, room-temperature Suzuki-Miyaura coupling reactions in aqueous media

A mild and efficient ligand-free Suzuki-Miyaura coupling reaction catalyzed by heterogeneous Pd/C was developed. Aryl bromides and triflates undergo the cross-coupling with aryl boronic acids in excellent yields without the presence of any additives in aqueous media at room temperature. Aryl vinyl boronic acids are also applicable to this coupling reaction and provide the trans-stilbene derivatives in high yields. The application of wet-type Pd/C to the coupling reaction was achieved without any loss of activity under aerobic conditions, and the reuse of Pd/C is feasible for a fifth run without significant loss of activity. Inductively coupled plasma (ICP) mass-spectrometric analysis of the filtrate from the reaction mixture of 4-bromonitrobenzene with phenylboronic acid demonstrated that the palladium metal hardly leached into the solution within the limits of the detector (<1 ppm), thus suggesting that the present Suzuki-Miyaura reaction proceeded by heterogeneous catalysis.     

Phase-ordering kinetics of the liquid-liquid transition in single-component molecular liquids

Recently it has been revealed that even a single-component liquid can have more than two liquid states. The transition between these liquid states is called the "liquid-liquid transition." Most known liquid-liquid transitions occur at temperatures and pressures which are difficult to access experimentally, so the physical nature of the transition, particularly the kinetics, has remained elusive. However, the recent discovery of liquid-liquid transitions in molecular liquids opens up a possibility to study the kinetics in detail. Here, we report the first phase field simulation on the kinetics of a liquid-liquid transition and its direct comparison with experimental results of the molecular liquids. Both nucleation-growth-type and spinodal-decomposition-type liquid-liquid transformation observed experimentally are well reproduced by numerical simulation based on a two-order-parameter model of liquid that regards the liquid-liquid transition as the cooperative formation of locally favored structures. Thus, phase field calculations may allow us to predict the kinetics of liquid-liquid transitions and the resulting spatiotemporal change of various physical properties of the liquid, such as density and refractive index.     

Heat‐Induced Morphological Transformation of Supramolecular Nanostructures by Retro‐Diels–Alder Reaction

Controlling the morphology of supramolecular nanostructures in response to external stimuli is an important challenge in the development of functional soft materials. Here we show that a morphological transformation from 2D nanosheets to a network of 1D nanofibers is triggered by heating, which induces molecular conversion of a bolaamphiphile to a hydrogelator by means of a retro‐Diels–Alder reaction, thereby producing a new heat‐set supramolecular hydrogel. We anticipate that our design will be a starting point for more sophisticated supramolecular systems that integrate the thermodynamics of molecular assembly and the kinetics of chemical reactions to create complex supramolecular nanostructures.     

Microbial degradation of physiologically active peptides by strain B-9

The reaction of some physiologically active peptides with bacterial strain B-9 has been investigated. Bradykinin, β-endorphin, and [Leu(5)]enkephalin were quickly degraded, with half-lives of <5 min. Somatostatin, substance P, and angiotensin I were degraded relatively smoothly, with half-lives of 10 min to 1 h, whereas oxytocin and insulin were slowly degraded, with half-lives of 1 and 4 days, respectively. Vasopressin was barely degraded, with a half-life of >7 days. Linearized vasopressin, prepared by the reductive cleavage of the disulfide bond followed by alkylation with iodoacetamide, was degraded significantly faster than intact vasopressin, with a half-life of 2.5 h. A loop formed by disulfide bond formation was regarded as one of the degradation-resistant factors. Hydrolysis of the peptides in this study took place through cleavage of various peptide bonds, and the strain B-9 may bear similarities to the neutral endopeptidase in terms of its broad selectivity.