Fine-tuning of boron complexes with cage-shaped ligand geometry: rational design of triphenolic ligand as a template for structure control

Boron complexes surrounded with organic cages were controlled precisely by a remote atom placed at the bottom of the cage. A replacement of the bottom tether atom (carbon or silicon) changed the characteristics (kinetic and thermodynamic factors) of boron complexes by geometric effects. A theoretical study shows that the bottom atoms also control eigenvalues of MO. This cage complex will provide a systematic template for fine-tuning of metal complexes to create various properties.     

Polarizable continuum model with the fragment molecular orbital-based time-dependent density functional theory

The polarizable continuum model (PCM) for describing the solvent effect was combined with the fragment molecular orbital-based time-dependent density functional theory (TDDFT). Several levels of the many-body expansion were implemented, and the importance of the many-body contributions to the singlet-excited states was discussed. To calibrate the accuracy, we performed a number of the model calculations using our method and the regular TDDFT in solution, applying them to phenol and polypeptides at the long-range corrected BLYP/6-31G* level. It was found that for systems up to 192 atoms the largest error in the excitation energy was 0.006 eV (vs. the regular TDDFT/PCM of the full system). The solvent shifts and the conformer effects were discussed, and the scaling was found to be nearly linear. Finally, we applied our method to the lowest singlet excitation of the photoactive yellow protein (PYP) in aqueous solution and determined the excitation energy to be in reasonable agreement with experiment. The excitation energy analysis provided the contributions of individual residues, and the main factors as well as their solvent shifts were determined.     

A study of comparability in amplified fragment length polymorphism profiling using a simple model system

A simple amplified fragment length polymorphism (AFLP) model, using the bacteriophage lambda genome, was developed to test the reproducibility of this technique in an international comparative study. Using either non-selective or selective primers, nine fragments or subsets of two or three fragments, respectively, were predicted using in silico software. Under optimized conditions, all predicted fragments were experimentally generated. The reproducibility of the AFLP model was tested by submitting both "unknown" DNA template that had been restricted and ligated with AFLP linkers (R/L mixture) and corresponding primer pairs to nine laboratories participating in the study. Participants completed the final PCR step and then used either slab gel electrophoresis or CE to detect the AFLP fragments. The predicted fragments were identified by the majority of participants with size estimates consistently up to 3 base pair (bp) larger for slab gel electrophoresis than for CE. Shadow fragments, 3 bp larger than the predicted fragments, were often observed by study participants and organizers. The nine AFLP fragments exhibited relative intensities ranging from less than 3% to 22% and, apart from the two weakest fragments, with a % CV of 16 to 25. Fragments containing the highest guanine-cytosine (GC) content of 50-56% showed the greatest stability in the AFLP profiles.     

A stroboscopic approach for fast photoactivation-localization microscopy with Dronpa mutants

The photophysical properties and photoswitching scheme of the reversible photoswitchable green fluorescent protein-like fluorescent proteins Dronpa-2 and Dronpa-3 were investigated by means of ensemble and single-molecule fluorescence spectroscopy and compared to those of the precursor protein Dronpa. The faster response to light and the faster dark recovery of the new mutants observed in bulk also hold at the single-molecule level. Analysis of the single-molecule traces allows us to extract the efficiencies and rate constants of the pathways involved in the forward and backward switching, and we find important differences when comparing the mutants to Dronpa. We rationalize our results in terms of a higher conformational freedom of the chromophore in the protein environment provided by the beta-can. This thorough understanding of the photophysical parameters has allowed us to optimize the acquisition parameters for camera-based sub-diffraction-limit imaging with these photochromic proteins. We show that Dronpa and its mutants are useful for fast photoactivation-localization microscopy (PALM) using common wide-field microscopy equipment, as individual fluorescent proteins can be localized several times. We provide a new approach to achieve fast PALM by introducing simultaneous two-color stroboscopic illumination.     

Determination of cadmium in grains by isotope dilution ICP–MS and coprecipitation using sample constituents as carrier precipitants

A coprecipitation method using sample constituents as carrier precipitants was developed that can remove molybdenum, which interferes with the determination of cadmium in grain samples via isotope dilution inductively coupled plasma mass spectrometry (ID-ICPMS). Samples were digested with HNO₃, HF, and HClO₄, and then purified 6 M sodium hydroxide solution was added to generate colloidal hydrolysis compounds, mainly magnesium hydroxide. Cadmium can be effectively separated from molybdenum because the cadmium forms hydroxides and adsorbs onto and/or is occluded in the colloid, while the molybdenum does not form hydroxides or adsorb onto the hydrolysis colloid. The colloid was separated by centrifugation and then dissolved with 0.2 M HNO₃ solution to recover the cadmium. The recovery of Cd achieved using the coprecipitation was >97%, and the removal efficiency of Mo was approximately 99.9%. An extremely low procedural blank (below the detection limit of ICPMS) was achieved by purifying the 6 M sodium hydroxide solution via Mg coprecipitation using Mg(NO₃)₂ solution. The proposed method was applied to two certified reference materials (NIST SRM 1567a wheat flour and SRM 1568a rice flour) and CCQM-P64 soybean powder. Good analytical results with small uncertainties were obtained for all samples. This method is simple and reliable for the determination of Cd in grain samples by ID-ICPMS. Figure Overview of a coprecipitation method using sample constituents     

Polymer brushes in nanopores surrounded by silicon-supported tris(trimethylsiloxy)silyl monolayers

A chemically grafted tris(trimethylsiloxy)silyl (tris(TMS)) monolayer on a silicon oxide substrate was used as a template for creating nanoclusters of polymer brushes. Polymer brushes were synthesized by surface-initiated polymerization of 2-methacryloyloxyethyl phosphorylcholine (MPC) and tert-butyl methacrylate (t-BMA) via atom transfer radical polymerization (ATRP) from alpha-bromoester groups tethered to the residual silanol groups on the silicon surface after generating a range of tris(TMS) coverage. CuBr/bpy and CuBr/PMDETA were used as the catalytic system for PMPC and Pt-BMA synthesis, respectively. The percentage of tris(TMS) coverage significantly influenced the thickness and morphology of the polymer brushes. Protrusions representing self-aggregation of PMPC brushes in nanopores as visualized by AFM analysis evidently suggested that PMPC brushes were distributed nanoscopically on the surface. The protrusion size and surface roughness corresponded quite well with the graft density of PMPC brushes. The fact that Pt-BMA brushes grown from nanopores were almost featureless implies that self-aggregation of PMPC brushes is truly a consequence of phase incompatibility between hydrophilic PMPC brushes and hydrophobic tris(TMS). The anti-fouling characteristic of PMPC brushes, inferred from plasma protein adsorption, was subsequently varied by controlling the surface coverage ratio between PMPC brushes and tris(TMS).     

Surface modification with well-defined biocompatible triblock copolymers Improvement of biointerfacial phenomena on a poly(dimethylsiloxane) surface

To improve interfacial phenomena of poly(dimethylsiloxane) (PDMS) as biomaterials, well-defined triblock copolymers were prepared as coating materials by reversible addition-fragmentation chain transfer (RAFT) controlled polymerization. Hydroxy-terminated poly(vinylmethylsiloxane-co-dimethylsiloxane) (HO–PV_lD_mMS–OH) was synthesized by ring-opening polymerization. The copolymerization ratio of vinylmethylsiloxane to dimethylsiloxane was 1/9. The molecular weight of HO–PV_lD_mMS–OH ranged from (1.43 to 4.44) × 10⁴, and their molecular weight distribution (M_w/M_n) as determined by size-exclusion chromatography equipped with multiangle laser light scattering (SEC-MALS) was 1.16. 4-Cyanopentanoic acid dithiobenzoate was reacted with HO–PV_lD_mMS–OH to obtain macromolecular chain transfer agents (macro-CTA). 2-Methacryloyloxyethyl phosphorylcholine (MPC) was polymerized with macro-CTAs. The gel-permeation chromatography (GPC) chart of synthesized polymers was a single peak and M_w/M_n was relatively narrow (1.3–1.6). Then the poly(MPC) (PMPC)–PV_lD_mMS–PMPC triblock copolymers were synthesized. The molecular weight of PMPC in a triblock copolymer was easily controllable by changing the polymerization time or the composition of the macro-CTA to a monomer in the feed. The synthesized block copolymers were slightly soluble in water and extremely soluble in ethanol and 2-propanol.

Surface modification was performed via hydrosilylation. The block copolymer was coated on the PDMS film whose surface was pretreated with poly(hydromethylsiloxane). The surface wettability and lubrication of the PDMS film were effectively improved by immobilization with the block copolymers. In addition, the number of adherent platelets from human platelet-rich plasma (PRP) was dramatically reduced by surface modification. Particularly, the triblock copolymer having a high composition ratio of MPC units to silicone units was effective in improving the surface properties of PDMS.

By selective decomposition of the Si–H bond at the surface of the PDMS substrate by irradiation with UV light, the coating region of the triblock copolymer was easily controlled, resulting in the fabrication of micropatterns. On the surface, albumin adsorption was well manipulated.     

Mechanical and dielectric studies of carrageenan sols and gels

The temperature dependence of the dynamic shear modulus, strain optical coefficient, DC conductivity, and complex dielectric spectrum of κ- and ι-carrageenan aqueous solutions with K, Ca, Cs, and Na were measured in order to clarify the formation process of the cross-linking region and the gel network structure. From the correlation analysis between the shear modulus and the strain optical coefficient, we found that the stress inducing unit orientation increases with decreasing temperature, which strongly suggests that the branching number in a cross-linking region increases with decreasing temperature, which depends on counterion species. In terms of the correlation parameters, an increasing scheme of the branching number depends on counterion species. Just below the coil-helix transition temperature, dielectric relaxation arises, with relaxation time ∼100μs and relaxation strength ∼10³. Dielectric relaxation can be assigned to the counterion fluctuation in the parallel direction to the helical axis. The fluctuation distance of the counterion estimated from the relaxation time increases sharply in the initial stage of gelation and gradually reaches a constant value. We concluded that the longitudinal length of the aggregated region increases sharply at the initial state of gelation while the number of helical molecules bundled in a cross-linking region increases successively with decreasing temperature.