Synthesis of meso-fluorotetrabenzoporphyrins

Fluorination of quadruply bicyclo[2.2.2]octadiene-fused porphyrin (CP) with 1-chloromethyl-4-fluoro-1,4-diazoniabicyclo[2.2.2]octane bis(tetrafluoroborate) (Selectfluor) occurred at the meso positions to give a mixture of various meso-fluorinated CPs, which were separated and then quantitatively transformed to the corresponding meso-fluorinated tetrafluorobenzoporphyrins (BPs) at 240 °C for 30 min. X-ray analysis of the mono-fluoro BPs revealed that the BP skeleton remained flat, which is crucial for retaining aggregation behavior similar to that of the parent BP, thus producing highly crystalline BP derivatives.     

Designing of interference pattern in ultra-short pulse laser processing

We have studied material processing by using an interfering ultra-short pulse laser. In this process, an interference pattern is transferred to material surface, and a periodic structure can be generated in a single shot of laser irradiation. Here, it is well known that the period of the interference pattern can be controlled by correlation angle and wavelength. In addition, a composite, doubled in density or designed interference pattern can be formed by controlling the phase shift and variation of amplitude between the interfering laser beams. In this paper, basic patterns of interference are summarized in the case of four-beam correlation.     

Radiation effects in ionic solids

Current development of the research of radiation damage in ionic solids is reviewed. Emphasis is placed on the correlation between elementary radiation damage processes and the atomic and electronic structures of the materials. Both the radiation damage induced by electronic excitation and by elastic collision are treated. For the former two crucial processes, the self-trapping of excitons and the formation of stable Frenkel pairs from the self-trapped excitons in several materials, is discussed in terms of the structures of materials. Deficiency in the available data on the knock-on threshold energies are pointed out. Available information of Frenkel pairs produced by electronic and elastic encounters is surveyed. Possible models of defect clustering are summarized and existing information on clustering is discussed on their basis.     

Highly enantioselective fluorescent recognition of mandelic acid derivatives by chiral salen macrocycles

Calixarene-like chiral salen macrocycles can be used for the enantioselective fluorescent recognition of mandelic acid derivatives. It was observed that one enantiomer of mandelic acid causes a 28-fold increase in the fluorescence intensity of a chiral salen macrocycle, whereas the other enantiomer causes only a 14-fold fluorescence enhancement. This highly enantioselective fluorescent response makes chiral salen macrocycles useful for the enantioselective fluorescent recognition of some mandelic acid derivatives.     

Assessment and acceleration of binding energy calculations for protein–ligand complexes by the fragment molecular orbital method

In the field of drug discovery, it is important to accurately predict the binding affinities between target proteins and drug applicant molecules. Many of the computational methods available for evaluating binding affinities have adopted molecular mechanics‐based force fields, although they cannot fully describe protein–ligand interactions. A noteworthy computational method in development involves large‐scale electronic structure calculations. Fragment molecular orbital (FMO) method, which is one of such large‐scale calculation techniques, is applied in this study for calculating the binding energies between proteins and ligands. By testing the effects of specific FMO calculation conditions (including fragmentation size, basis sets, electron correlation, exchange‐correlation functionals, and solvation effects) on the binding energies of the FK506‐binding protein and 10 ligand complex molecule, we have found that the standard FMO calculation condition, FMO2‐MP2/6‐31G(d), is suitable for evaluating the protein–ligand interactions. The correlation coefficient between the binding energies calculated with this FMO calculation condition and experimental values is determined to be R = 0.77. Based on these results, we also propose a practical scheme for predicting binding affinities by combining the FMO method with the quantitative structure–activity relationship (QSAR) model. The results of this combined method can be directly compared with experimental binding affinities. The FMO and QSAR combined scheme shows a higher correlation with experimental data (R = 0.91). Furthermore, we propose an acceleration scheme for the binding energy calculations using a multilayer FMO method focusing on the protein–ligand interaction distance. Our acceleration scheme, which uses FMO2‐HF/STO‐3G:MP2/6‐31G(d) at R_int = 7.0 Å, reduces computational costs, while maintaining accuracy in the evaluation of binding energy. © 2015 Wiley Periodicals, Inc.     

Faithful PCR Amplification of an Unnatural Base‐Pair Analogue with Four Hydrogen Bonds

In vitro replication of an unnatural imidazopyridopyridine:naphthyridine base pair, (i.e., ImN^N:NaO^O), having four hydrogen bonds was investigated. Kinetic studies of single‐nucleotide insertion revealed that ImN^N and NaO^O were recognized as complementary bases by an exonuclease‐deficient Klenow fragment with higher specificity and efficiency than two previously described pairs (ImN^O:NaO^N and ImO^N:NaN^O) because of higher thermal and thermodynamic stabilities and the DAAD:ADDA (D=donor, A=acceptor) hydrogen‐bonding pattern of the ImN^N:NaO^O pair. Faithful polymerase chain reaction (PCR) amplification of a DNA fragment containing the ImN^N:NaO^O pair was achieved by using DNA polymerases possessing 3′→5′ exonuclease activity (≈99.5 % per doubling).     

Lagrange multiplier and singular limit of double obstacle problems for the Allen–Cahn equation with constraint

We study the properties of the Lagrange multiplier for an Allen–Cahn equation with a double obstacle potential. Here, the dynamic boundary condition, including the Laplace–Beltrami operator on the boundary, is investigated. We then establish the singular limit of our system and clarify the limit of the solution and the Lagrange multiplier of our problem. We present remarks on a trace problem as well as on the Neumann boundary condition. Moreover, we describe a numerical experiment for a problem with Neumann boundary condition using the Lagrange multiplier. Copyright © 2016 John Wiley & Sons, Ltd.     

Enhanced surface sensitivity in secondary ion mass spectrometric analysis of organic thin films using size‐selected Ar gas‐cluster ion projectiles

A size‐selected argon (Ar) gas‐cluster ion beam (GCIB) was applied to the secondary ion mass spectrometry (SIMS) of a 1,4‐didodecylbenzene (DDB) thin film. The samples were also analyzed by SIMS using an atomic Ar⁺ ion projectile and X‐ray photoelectron spectroscopy (XPS). Compared with those in the atomic‐Ar⁺ SIMS spectrum, the fragment species, including siloxane contaminants present on the sample surface, were enhanced several hundred times in the Ar gas‐cluster SIMS spectrum. XPS spectra during beam irradiation indicate that the Ar GCIB sputters contaminants on the surface more effectively than the atomic Ar⁺ ion beam. These results indicate that a large gas‐cluster projectile can sputter a much shallower volume of organic material than small projectiles, resulting in an extremely surface‐sensitive analysis of organic thin films. Copyright © 2010 John Wiley & Sons, Ltd.     

Contributions of 3D Printed Fracture Networks to Development of Flow and Transport Models

Transport in Porous Media - Conventional experiments using natural rock samples have trouble in observing rock structures and controlling fracture properties. Taking advantage of 3D printing...