Novel canonical coding method for representation of three-dimensional structures

A new canonical coding method for representation of three-dimensional structures, CAST (CAnonical representation of STereochemistry), is described. CAST canonically codes stereochemistry around an atom in a molecule. The same CAST notations are given for atoms of molecules in the same conformation. The CAST code is based on the dihedral angles of four atoms that are uniquely defined by a molecular tree structure. CAST has successfully represented similarities and differences between several conformers.     

Recent progress of high-power negative ion beam development for fusion plasma heating

A negative-ion-based neutral beam injector (N-NBI) has been constructed for JT-60U. The N-NBI is designed to inject 500 keV, 10 MW neutral beams using two ion sources, each producing a 500 keV, 22 A D⁻ ion beam. In the preliminary experiment using one ion source, a D⁻ ion beam of 13.5 A has been successfully accelerated with an energy of 400 keV (5.4 MW) for 0.12 s at an operating pressure of 0.22 Pa. This is the highest D⁻ beam current and power in the world. Co-extracted electron current was effectively suppressed to the ratio of Ie/I_D⁻ < 1. The highest energy beam of 460 keV, 2.4 A, 0.44 s has also been obtained. To realize 1 MeV class NBI system for ITER (International Thermonuclear Experimental Reactor), demonstration of ampere class negative ion beam acceleration up to 1 MeV is an important mile stone. To achieve the mile stone, a prototype accelerator and a 1 MV, 1 A test facility called MeV Test Facility (MTF) were constructed. Up to now, an H⁻ ion beam was accelerated up to the energy of 805 keV with an acceleration drain current of 150 mA for 1 s in a five stage electrostatic multi-aperture accelerator.     

The structure of enopeptins A and B, novel depsipeptide antibiotics

The structures of enopeptins A and B, novel depsipeptide antibiotics with 1,3,5,7,9-decapentaene-1,10-dicarboxylic acid and 2-amino-3-hydroxycyclopent-2-enone in a side chain, were determined by chemical and spectroscopic means.     

Epoxyquinol A, a highly functionalized pentaketide dimer with antiangiogenic activity isolated from fungal metabolites

A unique pentaketide dimer structure of a novel fungal metabolite with antiangiogenic activity, designated as epoxyquinol A (1), was determined on the basis of NMR spectral data as well as the X-ray crystallographic analysis. 1 inhibits the endothelial migration induced by vascular endothelial growth factor (ED100 = 3 mug/mL).     

Representation of molecular configurations by CAST coding method

A configurational CAST (CAnonical representation of STereochemistry) coding method, which represents relative and absolute configuration, is described. The configurational CAST codes are constructed by canonical rotation of the dihedral angles of the input structure before the CAST codes are assigned. Using the configurational CAST, configurational differences can be distinguished independently of conformational differences. Representation of enantiomers is also achieved by a mirror image conversion method. The CAST representation shows the distinctive characteristics of several diastereomers and conformers that were examined. The method clearly represents the differences in configurations. Applications to organic molecules having complex stereochemistry are also demonstrated.     

CAST/CNMR: highly accurate C NMR chemical shift prediction system considering stereochemistry

Accurate, practical prediction of ¹³C NMR chemical shifts has been achieved with a new system, CAST/CNMR, taking account of stereochemistry. The CAST/CNMR system has solved the critical problem of the accurate distinction of differences and similarities in stereochemical structures around a specific carbon, which has not yet been achieved by any other database-oriented system for prediction of ¹³C NMR chemical shifts. CAST/CNMR uses a three-dimensional structural database together with a ¹³C NMR spectral database. Absolute/relative configurational and conformational structural information are described by the CAST (CAnonical-representation of STereochemistry) coding method. This paper provides an overview of the CAST/CNMR system, and describes its application to two natural products as examples.     

Synthesis of All Stereoisomers of Monomeric Spectomycin A1/A2 and Evaluation of Their Protein SUMOylation-Inhibitory Activity

A synthetic methodology to access all possible stereoisomers of spectomycin A1 (SMA1) and A2 (SMA2) has been established through late-stage diversification. The key reaction for the construction of all four diastereomers is an intramolecular cyclization based on the umpolung of π-allyl palladium species with bis(pinacolato)diborane (B₂(pin)₂). Silyl group assisted direct benzylic oxidation of each isomer enabled construction of the fragile β-hydroxytetralone skeleton to provide the SMAs. The relative and absolute stereochemistry of SMA2 was also determined, and the absolute stereochemistry of SMA1 was extrapolated based on the optical rotation of SMA2. The axial chirality of SMAs is discussed based on circular dichroism spectra and DFT calculations, and it is concluded that the M isomer is predominant in solution. Biochemical assessment of all isomers in vitro revealed that the C9 hydroxyl group and dimeric structure were both important for protein SUMOylation-inhibitory activity.     

Oxygenation of Trimethylsilylallenes Readily Obtainable from Organoboranes. Syntheses of 1-Trimethylsilyl-1-alkyn-3-ones and 1-Trimethylsilyl-1-alkyn-3-ols

Abstract

Recently we have reported that the reaction of sodium methoxide with ate-complexes (1) readily prepared from trimethyl-silylpropargyl phenyl ether and organoboranes gives trimethyl-silylallenes (2) selectively (eq. 1).¹ In an attempt to find a new synthetic application of such silylallenes (2), the oxidation of 2 was examined. Although the usual oxidants such as m-chloro-perbenzoic acid were found to be unsuitable for the oxidation of the silylallenes, it was discovered that 2 was autoxidized at room temperature to propargylic hydroperoxide (3) (eq. 2). For example, the acidified starch-iodine test² strongly suggested the presence of the organic hydroperoxide in the reaction mixture obtained from 1,2-heptadienyltrimethylsilane (2, R=Bu) and oxygen. The hydroperoxide (3, R=Bu) was isolated in a 40% yield by distillation, 45–48 [ddot]C/0.1 mmHg. In the infrared spectrum, the OH stretching frequency appears at 3430 cm^?1 and the C°C at 2180 cm,^?1     

Detection of oxygen addition peaks for terpendole E and related indole–diterpene alkaloids in a positive‐mode ESI‐MS

This report describes that a regular positive electrospray ionization mass spectrometry (MS) analysis of terpendoles often causes unexpected oxygen additions to form [M + H + O]⁺ and [M + H + 2O]⁺, which might be a troublesome in the characterization of new natural analogues. The intensities of [M + H + O]⁺ and [M + H + 2O]⁺ among terpendoles were unpredictable and fluctuated largely. Simple electrochemical oxidation in electrospray ionization was insufficient to explain the phenomenon. So we studied factors to form [M + H + O]⁺ and [M + H + 2O]⁺ using terpendole E and natural terpendoles together with some model indole alkaloids. Similar oxygen addition was observed for 1,2,3,4‐tetrahydrocyclopent[b]indole, which is corresponding to the substructure of terpendole E. In tandem MS experiments, a major fragment ion at m/z 130 from protonated terpendole E was assigned to the substructure containing indole. When the [M + H + O]⁺ was selected as a precursor ion, the ion shifted to m/z 146. The same 16 Da shift of fragments was also observed for 1,2,3,4‐tetrahydrocyclopent[b]indole, indicating that the oxygen addition of terpendole E took place at the indole portion. However, the oxygen addition was absent for some terpendoles, even whose structure resembles terpendole E. The breakdown curves characterized the tandem MS features of terpendoles. Preferential dissociation into m/z 130 suggested the protonation tendency at the indole site. Terpendoles that are preferentially protonated at indole tend to form oxygen addition peaks, suggesting that the protonation feature contributes to the oxygen additions in some degrees. © 2014 The Authors. Journal of Mass Spectrometry published by John Wiley & Sons, Ltd.     

A new method to improve validity range of Lie canonical perturbation theory: with a central focus on a concept of non-blow-up region

Validity ranges of Lie canonical perturbation theory (LCPT) are investigated in terms of non-blow-up regions. We investigate how the validity ranges depend on the perturbation order in two systems, one of which is a simple Hamiltonian system with one degree of freedom and the other is a HCN molecule. Our analysis of the former system indicates that non-blow-up regions become reduced in size as the perturbation order increases. In case of LCPT by Dragt and Finn and that by Deprit, the non-blow-up regions enclose the region inside the separatrix of the Hamiltonian, but it may not be the case for LCPT by Hori. We also analyze how well the actions constructed by these LCPTs approximate the true action of the Hamiltonian in the non-blow-up regions and find that the conventional truncated LCPT does not work over the whole region inside the separatrix, whereas LCPT by Dragt and Finn without truncation does. Our analysis of the latter system indicates that non-blow-up regions do not necessarily cover the whole regions inside the HCN well. We propose a new perturbation method to improve non-blow-up regions and validity ranges inside them. Our method is free from blowing up and retains the same normal form as the conventional LCPT. We demonstrate our method in the two systems and show that the actions constructed by our method have larger validity ranges than those by the conventional and our previous methods proposed in Teramoto and Komatsuzaki (J Chem Phys 129:094302, 2008; Phys Rev E 78:017202, 2008).