Toward Palau′amine: Hg(OTf)2‐Catalyzed Synthesis of the Cyclopentane Core

Catalytic cyclization : The Hg(OTf)₂‐catalyzed N‐selective cyclization of amide carbonyl moieties for the construction of a quaternary carbon center was developed. The Hg(OTf)₂‐catalyzed cyclization of cyclopentylidene alcohol with acylhydrazide afforded the desired cyclopenta[c]pyridazinone in good yield. The subsequent eight steps gave the functionalized cyclopentane with the correct stereochemistry that corresponds to the E ring of palau′amine (see scheme).

     

Conformational changes during apoplastocyanin folding observed by photocleavable modification and transient grating

A new method to investigate the initial protein folding dynamics is developed based on a pulsed laser light triggering method and a unique transient grating method. The side chain of the cysteine residue of apoplastocyanin (apoPC) was site-specifically modified with a 4,5-dimethoxy-2-nitrobenzyl derivative, where the CD and 2D NMR spectra showed that the modified apoPC was unfolded. The substituent was cleaved with a rate of about 400 ns by photoirradiation, which was monitored by the disappearance of the absorption band at 355 nm and the increase in the transient grating signal. After a sufficient time from the photocleavage reaction, the CD and NMR spectra showed that the native beta-sheet structure was recovered. Protein folding dynamics was monitored in the time domain with the transient grating method from a viewpoint of the molecular volume change and the diffusion coefficient, both of which reflect the global structural change, including the protein-water interaction. The observed volume decrease of apoPC with a time scale of 270 micros is ascribed to the initial hydrophobic collapse. The increase in the diffusion coefficient (23 ms) is considered to indicate a change from an intermolecular to an intramolecular hydrogen bonding network. The initial folding process of apoPC is discussed based on these observations.     

Open-loop and closed-loop control of dissociative ionization of ethanol in intense laser fields

The relative yield of the C-O bond breaking with respect to the C-C bond breaking in ethanol cation C2H5OH+ is maximized in intense laser fields (10(13)-10(15) Wcm2) by open-loop and closed-loop optimization procedures. In the open-loop optimization, a train of intense laser pulses are synthesized so that the temporal separation between the first and last pulses becomes 800 fs, and the number and width of the pulses within a train are systematically varied. When the duration of 800 fs is filled with laser fields by increasing the number of pulses or by stretching all pulses in a triple pulse train, the relative yield of the C-O bond breaking becomes significantly large. In the closed-loop optimization using a self-learning algorithm, the four dispersion coefficients or the phases of 128 frequency components of an intense laser pulse are adopted as optimized parameters. From these optimization experiments it is revealed that the yield ratio of the C-O bond breaking is maximized as far as the total duration of the intense laser field reaches as long as approximately 1 ps and that the intermittent disappearance of the laser field within a pulse does not affect the relative yields of the bond breaking pathways.     

N-linked oligosaccharide analysis of rat brain Thy-1 by liquid chromatography with graphitized carbon column/ion trap-Fourier transform ion cyclotron resonance mass spectrometry in positive and negative ion modes

We have previously described the site-specific glycosylation analysis of rat brain Thy-1 by LC/multistage tandem mass spectrometry (MS(n)) using proteinase-digested Thy-1. In the present study, detailed structures of oligosaccharides released from Thy-1 were elucidated by mass spectrometric oligosaccharide profiling using LC/MS with a graphitized carbon column (GCC-LC/MS). First, using model oligosaccharides, we improved the oligosaccharide profiling by ion trap mass spectrometry (IT-MS) coupled with Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS). Sequential scanning of a full MS(1) scan with FT-ICR-MS followed by data-dependent MS(n) with IT-MS in positive ion mode, and a subsequent full MS(1) scan with FT-ICR-MS followed by data-dependent MS(n) with IT-MS in negative ion mode enabled the monosaccharide composition analysis as well as profiling and sequencing of both neutral and acidic oligosaccharides in a single analysis. The improved oligosaccharide profiling was applied to elucidation of N-linked oligosaccharides from Thy-1 isolated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. It was demonstrated that Thy-1 possesses a significant variety of N-linked oligosaccharides, including Lewis a/x, Lewis b/y, and disialylated structure as a partial structure. Our method could be applicable to analysis of a small abundance of glycoproteins, and could become a powerful tool for glycoproteomics.     

Sensitive analysis of aconitine, hypaconitine, mesaconitine and jesaconitine in human body fluids and Aconitum tubers by LC/ESI-TOF-MS

The Aconitum species (Ranunculaceae) are widely distributed in northern Asia and North America. Their roots are popularly used in herbal medicines in China and Japan. Many cases of accidental, suicidal and homicidal intoxication with this plant have been reported; some of these were fatal because the toxicity of Aconitum is very high. It is thus important to detect and quantify Aconitum alkaloids in body fluids, with high sensitivity. We have developed a simple and sensitive method for measuring four kinds of Aconitum alkaloids (aconitine, hypaconitine, jesaconitine and mesaconitine) by LC/electrospray (ESI)-time-of-flight (TOF)-MS. For all of them, only molecular ions were observed at an orifice voltage of 75 V; at 135 V, base peaks corresponding to [M - 60 + H]+ ions were observed. These four compounds and methyllycaconitine (internal standard) in human plasma samples were purified by solid-phase extraction. The four extracted compounds were completely separated in mass chromatograms; the calibration curves showed good linearity in the range 10-300 ng/ml, and the detection limits were estimated to be 0.2-0.5 ng/ml. Using our method, we also determined the amounts of these compounds in tuber samples. The present method is applicable in clinical and forensic toxicology.     

Interactions between clusters of self-interstitial atoms via a conservative climb in BCC–Fe

We conduct kinetic Monte Carlo simulations for the conservative climb motion of a cluster of self-interstitial atoms (SIAs) towards another SIA cluster in BCC–Fe; the conservative climb velocity is inversely proportional to the fourth power of the distance between them, as per the prediction based on Einstein’s equation. The size of the climbing cluster significantly affects its conservative climb velocity, while the size of the cluster that originates the stress field does not. The activation energy for the conservative climb is considerably greater than that derived in previous studies and strongly dependent on the climbing cluster size. The results presented in this study are the atomistic evaluation of the behaviour of SIA clusters through three-dimensional motion, which cannot be achieved using molecular dynamics techniques alone.     

Peptidoglycan as Nod1 ligand; fragment structures in the environment, chemical synthesis, and their innate immunostimulation

Covering: up to 2011. This review focuses on the recent revealing of the immunostimulatory bacterial cell wall peptidoglycan (PGN) fragments as Nod1 ligands, especially a newly developed chemical synthesis of the partial structures, fragment structures in the environment and bacterial supernatant, and the immunostimulatory activities of the Nod1 ligands.     

A heme degradation enzyme, HutZ, from Vibrio cholerae

HutZ, one of the crucial proteins of the iron uptake system in Vibrio cholerae, was purified, which binds to heme at a stoichiometry of 1 : 1. In the presence of ascorbic acid, the HutZ-bound heme degrades via the same intermediates observed in heme oxygenase, suggesting that HutZ works as a heme degradation enzyme.     

Pd-catalyzed benzylic C-h amidation with benzyl alcohols in water: a strategy to construct quinazolinones

A novel method for the synthesis of 4-phenylquinazolinones via a palladium-catalyzed domino reaction of o-aminobenzamides with benzyl alcohols is developed. This protocol involves N-benzylation, benzylic C-H amidation, and dehydrogenation in water, which may play an important role in the smooth generation of the (η(3)-benzyl)palladium species by activation of the hydroxyl group of the benzyl alcohol.     

Atomically Precise Alloy Nanoclusters

Metal nanoclusters (NCs) have a particle size of about one nanometer, which makes them the smallest unit that can give a function to a substance. In addition, metal NCs possess physical and chemical properties that are different from those of the corresponding bulk metals. Metal NCs with such characteristics are expected to be important for use in nanotechnology. Research on the precise synthesis of metal NCs and elucidation of their physical/chemical properties and functions is being actively conducted. When metal NCs are alloyed, it is possible to obtain further various electronic and geometrical structures and functions. Thus, research on alloy NCs has become a hot topic in the study of metal NCs and the number of publications on alloy NCs has increased explosively in recent years. Such publications have provided much insight into the effects of alloying on the electronic structure and function of metal NCs. However, the rapid increase in knowledge has made it difficult for researchers (especially those new to the field) to grasp all of it. Therefore, in this review, we summarize the reported chemical composition, geometrical structure, electronic structure, and physical and chemical properties of Au_n−xM_x(SR)_m, Ag_n−xM_x(SR)_m, Au_n−xM_x(PR₃)_l(SR)_m, and Ag_n−xM_x(PR₃)_l(SR)_m (Au=gold, Ag=silver, M=heteroatom, PR₃=phosphine, and SR=thiolate) NCs. This review is expected to help researchers understand the characteristics of alloy NCs and lead to clear design guidelines to develop new alloy NCs with intended functions.