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.     

Structures of TMC-95A-D: novel proteasome inhibitors from Apiospora montagnei sacc. TC 1093

Four novel proteasome inhibitors, TMC-95A-D (1-4) have been isolated from the fermentation broth of Apiospora montagnei Sacc. TC 1093, isolated from a soil sample. All of the molecular formulas of 1-4 were established as C(33)H(38)N(6)O(10) by high-resolution FAB-MS. Their planar structures were determined on the basis of extensive analyses of 1D and 2D NMR, and degradation studies. Compounds 1-4 have the same planar structures to each other, and are unique highly modified cyclic peptides containing L-tyrosine, L-aspargine, highly oxidized L-tryptophan, (Z)-1-propenylamine, and 3-methyl-2-oxopentanoic acid units. The absolute configuration at C-11 and C-36 of 1-4 was determined based on chiral TLC and HPLC analyses of their chemical degradation products. The ROESY analysis along with (1)H-(1)H coupling constants clarified the absolute stereochemistry at C-6, -7, -8, and -14 of the cyclic moieties. These studies revealed the relationships of 1-4 to be diastereomers at C-7 and C-36.     

Isoscalar magnetic moments and the role of the δ-hole excitation

Expectation values of the total spinS of nucleons in nuclei are very quenched. This quenching is shown to be hardly explained by the mixture of-hole states. The quenching thus provides the best evidence for the role of non-central parts of the nucleon-nucleon interaction, especially the tensor interaction.     

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.     

Effect of molecular orientation distribution and crystallinity on the measurement of the crystal lattice modulus of nylon 6 by x-ray diffraction

The crystal lattice modulus of nylon 6 (-type) was measured by x-ray diffraction using nylon 6 films drawn up to five times. The measured crystal lattice modulus was 173–175 GPa for all specimens whose crystallinity and the Young's modulus were beyond 46% and 3.75 GPa, respectively. These results indicate that a state of homogenous stress can be achieved. In contrast, the values were scattered for the speciments whose crystallinity and Young's modulus are less than the above values. To study the origin, a numerical calculation of the crystal lattice modulus, as measured by x-ray diffraction, was carried out by considering effects on the orientation factors of molecular chains and crystallinity. In this calculation, a previously introduced model was employed, in which oriented crystalline layers are surrounded by oriented amorphous phases so that the strains of the two phases at the boundary are identical. The theoretical results calculated by the introduced model indicated that the crystal lattice modulus by x-ray diffraction is almost equal to the intrinsic crystal modulus if the morphology of the test specimen can be represented as a series model. In contrast, if a parallel model is more appropriate, the difference between the measured modulus and the intrinsic value can be pronounced. Such morphological dependence was found to be less pronounced with increasing high degree of molecular orientation and crystallinity.     

Production of micron-sized monodispersed composite polymer particles by seeded polymerization utilizing the dynamic swelling method

 In order to develop the seeded polymerization technique utilizing the dynamic swelling method (DSM) proposed by authors for the production of micron-sized mono-dispersed “composite” polymer particles consisting of two kinds of polymers, the seeded polymerization for the dispersion of ethyl methacry-late (EMA)-swollen PS particles prepared utilizing DSM was carried out. Monodispersed PS/poly(ethyl methacrylate) (PEMA) composite particles having 7 μm in diameter were produced by the addition of NaCl to lower the solubility of EMA in medium and by the addition of CuCl₂ as a water-soluble inhibitor to depress the by-production of submicron-sized PEMA particles. Received: 16 July 1996 Accepted: 10 October 1996     

Novel ring transformation reactions of xanthine derivatives

The novel ring transformation reactions were found in the reactions of 1,3,7,9-tetra-alkyl-8,9-dihydroxanthines and acetylenic compounds. The reaction of the dihydroxanthine with DMAD gave a propellane type compound and with methyl propiolate afforded the similar type compound and a pyrimido[4,5-b]diazepine derivative. The mechanism of these reactions was also discussed.