Structural and spectroscopic characterization of (mu-hydroxo or mu-oxo)(mu-peroxo)diiron(III) complexes: models for peroxo intermediates of non-heme diiron proteins

(mu-Hydroxo or oxo)(mu-1,2-peroxo)diiron(III) complexes having a tetradentate tripodal ligand (L) containing a carboxylate sidearm [Fe2(mu-OH or mu-O)(mu-O2)(L)2]n+ were synthesized as models for peroxo-intermediates of non-heme diiron proteins and characterized by various physicochemical measurements including X-ray analysis, which provide fundamental structural and spectroscopic insights into the peroxodiiron(III) complexes.     

The influence of polytypic structures on the M011-->M101 solid-solid phase transition of n-C36H74: an application of the oblique infrared transmission method

The molecular displacements on the M011-->M101 phase transition of n-hexatriacontane (n-C36H74) have been investigated with an IR microscope designed for the oblique infrared transmission method. It has been clarified that two polytypic structures of the M011 modification, single-layered structure (Mon) and double-layered one (Orth II), both transform to the M101 modification of single-layered structure with their respective mechanisms. On the M011(Mon)-->M101 transition, the inclination direction of molecular axis is changed by 90 degrees through an intermediate state in which the molecular chain is set perpendicular to the basal plane of the single crystal. On the other hand, a polymorphic-polytypic composite structural change on the M011(Orth II)-->M101 transition is accomplished through two kinds of molecular displacements occurring alternately along the stacking direction of molecular layers.     

Study of thermodynamic stabilities of polytypes of n-C36H74 by solubility measurements and incoherent inelastic neutron scattering

The thermodynamic properties of the two polytypes of n-hexatriacontane (n-C36H74), single-layered structure Mon and double-layered structure Orth II have been investigated by means of solubility measurements and incoherent inelastic neutron scattering. The solubility measurements reveal that Orth II is more stable than Mon by 1.2 kJ/mol because of the advantage of larger entropy. The neutron scattering measurements show that the vibrational modes of Orth II shift to the lower frequencies compared with those of Mon in the frequency region below 120 cm(-1). The advantage of Orth II in vibrational entropy due to the low-frequency shifts is estimated to be 9.6 J K(-1)/mol at 288 K under the harmonic approximation, which nearly agrees with the entropy difference of 6.8 J K(-1)/mol between Mon and Orth II determined by solubility measurements. These results suggest that the difference in vibrational entropy due to low-frequency modes mainly contributes to the relative thermodynamic stabilities of polytypic structures of long-chain compounds. From the frequency of methyl torsional mode, it is suggested that the cohesive force at the lamellar interface is stronger in Mon than in Orth II.     

Cascade Rearrangement of 5-Cyclopentylidenecyclooctanones

Acid-catalyzed rearrangement of 5-cyclopentylidenecyclooctanone derivatives 9a-c was examined to obtain polyspiropolyquinanes 11a-c, considered to have a unique helical structure, through cascade rearrangement pathways consisting of continuous transannular cyclization followed by successive 1,2-alkyl shifts. The substrates were prepared easily by use of the Wittig or McMurry reaction. Reaction of the 5-cyclopentylidenecyclooctanone (9a) with acid gave the expected dispirotriquinane ketone 11a in high yield. The precise mechanism was elucidated by a deuterium-labeling experiment. In the case of the ketone 9b, having another spiroannulated cyclopentane ring attached on 9a, the trispirotetraquiane 11b was not obtained but the bis-propellane-type tetrahydrofuran 25 was produced exclusively. The 5-(5'-cyclopentylidenecyclooctylidene)cyclooctanone (9c) afforded the polycyclic compounds 27-31, depending on the acid used, instead of the desired tetraspiropentaquinane 11c. The structures of the products were determined by NMR spectral data including 2D (13)C INADEQUATE spectra and X-ray crystallographic analyses. The unexpected rearrangement pathways are also discussed.     

Rapid oligosaccharide synthesis using a fluorous protective group

The Bfp-OH, a novel fluorous protecting reagent, was able to be easily prepared. The Bfp group was readily introduced to a carbohydrate, removed in high yield, and recyclable after cleavage. The use of the Bfp group made it possible to synthesize a pentasaccharide by minimal column chromatography purification. Each synthetic intermediate was able to be easily purified only by simple fluorous-organic solvent extraction and monitored by TLC, NMR, and MS.     

Camdas: An automated conformational analysis system using molecular dynamics

We present an automated conformational analysis program, CAMDAS (Conformational Analyzer with Molecular Dynamics And Sampling). CAMDAS performs molecular dynamics (MD) calculations for a target molecule and samples conformers from the trajectory of the MD. The program then evaluates the similarities between each of the sampled conformers in terms of the root- mean-square deviations of the atomic positions, clusters similar conformers, and finally prints out the clustered conformers. This MD-based conformational analysis is a broadly used method, and CAMDAS is intended to provide a convenient framework for the method. CAMDAS has the ability to find the representative conformers automatically from an arbitrarily given structure of the molecule. The accuracy of the program was examined using N- acetylalanine-N-methylamide, and the obtained result was consistent with that of the systematic search method. In the test calculation of cyclodecane, CAMDAS could identify most of the known conformers and their conformational enantiomers by examining only 5000 conformers. In addition, the potential-scaled method, which we have developed previously as an accelerating technique for MD, could find two additional conformers of cyclodecane that have not been reported. CAMDAS presents a convenient way to find the energetically possible conformers of a molecule, which is needed especially in the early stage of drug design.     

Synthesis of sodium-polystyrenesulfonate-grafted nanoparticles by core-cross-linking of block copolymer micelles

Sodium poly(styrenesulfonate)(polySSNa)-grafted polymer nanoparticles were synthesized by core-cross-linking of block copolymer micelles and subsequent chemical transformation. Block copolymers, poly(p-((1-methyl)silacyclobutyl)styrene-block-poly(neopentyl p-styrenesulfonate)s, polySBS-b-polySSPen, were synthesized by nitroxy-mediated living radical polymerization. The block copolymers formed micelles (R_h=15-23 nm, where R_h represents the hydrodynamic radius) with a polySBS core and polySSPen shell in acetone. The micelle core was cross-linked by ring-opening polymerization of silacyclobutyl groups in polySBS. Hydrolysis of the neopentyl groups provided polySSNa-grafted nanoparticles. The R_h of the particles before the hydrolysis ranged from 12 to 21 nm in acetone, while they varied to the range from 50 to 110 nm in water after the hydrolysis.     

Synthesis and Odor Evaluation of Stereoisomers of Imine Derivatives in Roasted Spotted Shrimp

All possible stereoisomers of imine derivatives 1 – 4 , which have the characteristic roast odor of seafood, were synthesized. As a result of odor evaluation of all isomers, we found that each isomer has a different and characteristic odor of roasted seafood.