Estimated effects of silicone glue on protein crystal growth

Silicone glue (modified silicone polymer) is widely used for both experiments involving inorganic crystal growth and those involving organic materials like proteins. This material is very useful for building a hand-made experiment setup or for fixing protein crystals to specific locations. Though silicone glue is regarded as harmful to proteins, no systematic verification was performed to investigate its impurity effects on protein crystal growth. We focused on and estimated the impurity effects of silicone glue on protein crystal growth.     

Epoxysilane rearrangement induced by a carbanion generated by conjugate addition of enolates of chloroacetate and alpha-chloroacetamides: formation of functionalized cyclopropane derivatives

[reaction: see text] Reaction of an enoate bearing an epoxysilane moiety at the alpha-position with lithium enolate of 2-chloroacetamide afforded highly functionalized cyclopropane derivatives via a tandem process that involves Michael addition, ring opening of the epoxide, Brook rearrangement, and intramolecular alkylation.     

An algebraic proof of the cyclic sum formula for multiple zeta values

We introduce an algebraic formulation of the cyclic sum formulas for multiple zeta values and for multiple zeta-star values. We also present an algebraic proof of cyclic sum formulas for multiple zeta values and for multiple zeta-star values by reducing them to Kawashima's relation.     

10 nm Spatial Resolution Fluorescence Imaging of Single Molecules by Near-Field Scanning Optical Microscopy Using a Tiny Aperture Probe

We demonstrate high-resolution fluorescence imaging of single molecules using near-field scanning optical microscopy (NSOM) with a tiny aperture probe for two different wavelengths in visible range in the illumination mode of operation. The spatial resolutions obtained at both excitation wavelengths were almost the same and the highest resolution realized was about 10 nm. To discuss the achievable resolution in aperture NSOM, we also employed a computer simulation by the finite-difference time-domain method for various aperture sizes and wavelengths. The resolution of 10 nm is predicted to be contributed by the single peak of localized near-field light around the rim of the aperture.     

A new mechanism for the addition of alcohols to disilenes revealed by DFT and ONIOM calculations

Density functional and ONIOM calculations of alcohol and phenol additions to two (tetramethyl and tetramesityl) disilenes were carried out. The dimer of MeOH adds to Me₂SiSiMe₂ more readily than the monomer. The trimer does not afford the adduct, but a zwitter-ionic intermediate. In the (CF₃OH)₂ addition to Me₂SiSiMe₂, H?Si bond formation is more advanced than O?Si bond formation in the transition state (TS). Addition of seven phenol derivatives to Me₂SiSiMe₂ was examined, and the dimer reactions were found to be superior to the monomer reaction regardless of the substituents on the benzene rings. (MeOH)₂ reacts also with Mes₂SiSiMes₂ favorably, and an isomer of the reactant-like complex (precursor) may afford an adduct of different stereochemistry via internal rotations. Generally, the dimer of the alcohol or phenol is the reactant toward the disilenes. Exceptionally, a monomer of p-(dimethylamino)phenol reacts with Mes₂SiSiMes₂ owing to steric congestion by the four mesityl groups.     

Regular and Black Hole Skyrmions with Axisymmetry

It has been known that a B=2 skyrmion is axially symmetric. We consider the Skyrme model coupled to gravity and obtain static axially symmetric regular and black hole solutions numerically. Computing the energy density of the skyrmion, we discuss the effect of gravity to the energy density and baryon density of the skyrmion.     

Is the Beckmann rearrangement a concerted or stepwise reaction? A computational study

[reaction: see text] RB3LYP calculations were performed on the Beckman rearrangement by the use of three substrates, acetone oxime (1), acetophenone oxime (2), and cyclohexanone oxime (3). Acidic solvents were modeled by H+ (CH3COOH)3 and H3O+ (H2O)6, and reaction paths were determined precisely. For 1, a two-step process involving a sigma-type cationic complex was obtained. For 2, a three-step process with pi- and sigma-type complexes was found in H+ (CH3COOH)3 and a two-step process involving a sigma-type cationic complex was obtained in H3O+ (H2O)6. However, for 3, a concerted process without pi and sigma complexes was calculated, which leads to the product, epsilon-caprolactam. Three different mechanisms were explained in terms of FMO theory.     

A DFT study of the hydrolysis of hydantoin

Density functional theory (DFT) calculations were made on the hydrolysis of hydantoin (2,4-imidazolidinedione). In the neutral hydrolysis, reacting systems composed of hydantoin and (H₂O)_n with n = 1+3, 2+3, 3+3, and 4+3 were adopted. Three water molecules (“+3”) participate in the in-plane hydrogen-bond circuit, and the n–3 = 1, 2, 3 or 4 water cluster works for the out-of-plane nucleophilic attack onto the carbonyl carbon of hydantoin. Transition states (TSs) involving bond interchanges prompted by proton transfers were determined. The reaction path with n = 3+3 containing N-carbamoyl glycine, N-carboxy glycine and three tetrahedral intermediates was found to be most likely. In the acid-catalyzed hydrolysis, a reacting system composed of hydantoin and H₃O⁺(H₂O)₇ was employed. Ten TSs and nine intermediates were obtained. N-carbamoyl glycine and N-carboxy glycine were confirmed to be detectable stable species. The product consists of glycine, carbonic acid (not CO₂), NH₄⁺, and (H₂O)₅. It has the exothermic energy, whereas the product in the neutral hydrolysis is of the endothermic one for all n values. For both neutral (n = 3+3) and acid-catalyzed hydrolyses, the rate-determining steps were calculated to be for formation of the tetrahedral intermediate, HOOC-CH₂-NH-C(OH)₂NH₂. The pattern of proton transfers along hydrogen bonds was carefully investigated.     

Synthetic approaches toward ecteinascidins. Part 2. Preparation of the ABCDE ring system of ecteinascidins having characteristic substituents in both benzene rings

A synthesis of an advanced ABCDE ring system (24c) having characteristic substituents in both benzene rings of ecteinascidin marine natural products is described based on our model studies.