Porphyrin synthesis in water provides new expanded porphyrins with direct bipyrrole linkages: isolation and characterization of two heptaphyrins

The use of water for the porphyrin cyclization changes the products completely. Scandium-catalyzed aqueous condensation between pentafluorobenzaldehyde and pyrrole and subsequent oxidation provides novel expanded porphyrins with direct bipyrrole linkages, of which two novel heptaphyrins have been characterized by X-ray analyses.     

Electron hydration dynamics in water clusters: A direct ab initio molecular dynamics approach

Electron attachment dynamics of excess electron in water cluster (H2O)n (n = 2 and 3) have been investigated by means of full-dimensional direct ab initio molecular dynamics (MD) method at the MP26-311++G(d,p) level. It was found that the hydrogen bond breaking due to the excess electron is an important process in the first stage of electron capture in water trimer. Time scale of electron localization and hydrogen bond breaking were determined by the direct ab initio MD simulation. The initial process of hydration in water cluster is clearly visualized in the present study. In n = 3, an excess electron is first trapped around the cyclic water trimer with a triangular form, where the excess electron is equivalently distributed on the three water molecules at time zero. After 50 fs, the excess electron is concentrated into two water molecules, while the potential energy of the system decreases by -1.5 kcal/mol from the vertical point. After 100 fs, the excess electron is localized in one of the water molecules and the potential energy decreases by -5.3 kcal/mol, but the triangular form still remained. After that, one of the hydrogen bonds in the triangular form is gradually broken by the excess electron, while the structure becomes linear at 100-300 fs after electron capture. The time scale of hydrogen bond breaking due to the excess electron is calculated to be about 300 fs. Finally, a dipole bound state is formed by the linear form of three water molecules. In the case of n = 2, the dipole bound anion is formed directly. The mechanism of electron hydration dynamics was discussed on the basis of theoretical results.     

A facile and practical method of preparing optically active α-monosubstituted cycloalkanones by thermodynamically controlled deracemization

Racemic 2-monosubstituted cycloalkanones were converted to R-isomers when TADDOLs (e.g., 1a, b) were used as host molecules in alkaline aqueous MeOH. The efficiency of this thermodynamically controlled deracemization was strongly influenced by the mixture ratio of the solvent, H₂O/MeOH. Based on this finding, an improved method of preparing (R)-2-monosubstituted cycloalkanones with higher optical purity was developed. For example, (R)-2-(4-methylbenzyl)cyclohexanone (5) was obtained in 85% yield with 98% ee, when a 1:1 mixture of H₂O/MeOH was used as the solvent in the presence of 1a.     

Parallel Fock matrix construction with distributed shared memory model for the FMO‐MO method

A parallel Fock matrix construction program for FMO‐MO method has been developed with the distributed shared memory model. To construct a large‐sized Fock matrix during FMO‐MO calculations, a distributed parallel algorithm was designed to make full use of local memory to reduce communication, and was implemented on the Global Array toolkit. A benchmark calculation for a small system indicates that the parallelization efficiency of the matrix construction portion is as high as 93% at 1,024 processors. A large FMO‐MO application on the epidermal growth factor receptor (EGFR) protein (17,246 atoms and 96,234 basis functions) was also carried out at the HF/6‐31G level of theory, with the frontier orbitals being extracted by a Sakurai‐Sugiura eigensolver. It takes 11.3 h for the FMO calculation, 49.1 h for the Fock matrix construction, and 10 min to extract 94 eigen‐components on a PC cluster system using 256 processors. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

Photocontrolled Translational Motion of a Microscale Solid Object on Azobenzene‐Doped Liquid‐Crystalline Films

On the move : Irradiation of azobenzene‐doped liquid crystalline films with UV/Vis light results in the photocontrolled translational motion of microscale solid object on the surface, which occurs through cis–trans isomerization of the azobenzene unit. Irradiation with an Ar⁺ laser (488 nm) resulted in precise control of the translational motion so that the particle always moved away from the irradiation position (see picture).

     

Zwitterionic Corroles: Regioselective Nucleophilic Pyridination of a Doubly Linked Biscorrole

Pyridine attacks : Nucleophilic addition of pyridine derivatives to a doubly linked corrole, which is a stable singlet biradical species, occurs at the bay area with high regioselectivity to provide zwitterionic dimers (see picture; Ar=C₆F₅). Charge transfer between the anionic corrole and the pyridinium groups induces effective fluorescence quenching of the corrole dimer, which can be utilized for selective fluoride ion recognition.

     

Functional cDNA expression cloning: pushing it to the limit

The 1970s and the following decade are the era of the birth and early development of recombinant DNA technologies, which have entirely revolutionized the modern life science by providing tools that enable us to know the structures of genes and genomes and to dissect their components and understand their functions at the molecular and submolecular levels. One major objective of the life sciences is to achieve molecular and chemical understandings of the functions of genes and their encoded proteins, which are responsible for the manifestation of all biological phenomena in organisms. In the early 1980s, I developed, together with Paul Berg, a new technique that enables the cloning of full-length complementary DNAs (cDNAs) on the basis of their functional expression in a given cell of interest. I review the development, application and future implications in the life sciences of this gene-cloning technique.     

Interaction of dopant atoms with stacking faults in silicon

The width of a stacking fault ribbon bound by a pair of partial dislocations in silicon crystals was unchanged when boron and gallium atoms of p-type dopant were agglomerated nearby the ribbon by annealing, even though the width increased when n-type dopant atoms were agglomerated as previously reported [Y. Ohno, Y. Tokumoto, I. Yonenaga, Thin Solid Films, accepted for publication]. The origin of the width-increase in n-type crystals was proposed as the reduction of the stacking fault energy, from 58±5 down to 46±5 mJ/m², due to an electronic interaction between the ribbon and the n-type dopant atoms, and the interaction energy was estimated to be 0.15±0.05 eV. On the other hand, the interaction of p-type dopant atoms with stacking faults was not detected.