Massively parallel algorithm and implementation of RI‐MP2 energy calculation for peta‐scale many‐core supercomputers

A new parallel algorithm and its implementation for the RI‐MP2 energy calculation utilizing peta‐flop‐class many‐core supercomputers are presented. Some improvements from the previous algorithm (J. Chem. Theory Comput. 2013, 9, 5373) have been performed: (1) a dual‐level hierarchical parallelization scheme that enables the use of more than 10,000 Message Passing Interface (MPI) processes and (2) a new data communication scheme that reduces network communication overhead. A multi‐node and multi‐GPU implementation of the present algorithm is presented for calculations on a central processing unit (CPU)/graphics processing unit (GPU) hybrid supercomputer. Benchmark results of the new algorithm and its implementation using the K computer (CPU clustering system) and TSUBAME 2.5 (CPU/GPU hybrid system) demonstrate high efficiency. The peak performance of 3.1 PFLOPS is attained using 80,199 nodes of the K computer. The peak performance of the multi‐node and multi‐GPU implementation is 514 TFLOPS using 1349 nodes and 4047 GPUs of TSUBAME 2.5. © 2016 Wiley Periodicals, Inc.     

First total synthesis of antimitotic compound, (+)-phomopsidin

[reaction: see text] The first total synthesis of (+)-phomopsidin has been achieved via a diastereoselective transannular Diels-Alder (TADA) reaction. Key steps in the synthesis include diastereoselective ynone reduction with (-)-alpha-pinene and 9-BBN, macrocyclization by E-selective intramolecular Horner-Wadsworth-Emmons (HWE) reaction, as well as carbometalation under Wipf's conditions, followed by HWE reaction at low temperature to selectively construct the (E)-1-methylpropenyl and (1E,2E)-4-carboxy-1,3-butadienyl substituents.     

The 3d←3p endothermic collisional population transfer of Li in He and Ar at 298 K

The 3p state of Li was excited in He and Ar buffer gases at room temperature (298 K) and the time profiles of sensitized fluorescence from the 3s and 3d states were measured. The 3d←3p endothermic population transfer rates determined from the pressure dependence of the time profiles were 6.5×10⁻¹¹ cm³ s⁻¹ for He and less than 10⁻³ cm³ s⁻¹ for Ar. The origin of this large difference between He and Ar is discussed in terms of non-adiabatic transitions between the 3p and 3d molecular states of the Li–He and Li–Ar molecules.     

Synthesis and characterization of exohedrally silylated M@C82 (M = Y and La)

The silylation of endohedral mono-metallofullerenes (Y@C(82) and La@C(82)) and isolation of the corresponding adducts by HPLC separation have been accomplished. The redox properties of the silylated mono-metallofullerene were first clarified by CV and DPV measurements, indicating that the bis-silylated mono-metallofullerenes have lower oxidation and higher reduction potentials than the parent mono-metallofullerenes. These results reveal that bis-silylation is very effective for producing the electronegatively mono-metallofullerene derivatives as well as empty fullerenes.     

Repetitive determination of chloride using the circulation of the reagent solution in closed flow-through system

The precipitation reaction of silver chloride (AgCl) is carried out in a large amount of ammonia (NH₃). This makes possible to adopt a closed-loop flow injection (FI) system and to determine chloride repetitively. A solution of 30 mmol l⁻¹ silver nitrate and 80 mmol l⁻¹ NH₃ in a single reservoir (250 ml) is continuously circulated through the flow cell at a flow rate of 2.0 ml ml⁻¹. The chloride containing sample (100 μl) was introduced into this reagent solution by means of six-way valve. AgCl precipitates formed in the sample zone are monitored spectrophotometrically (at 500 nm) in the flow system. After passing through the flow cell, the excess NH₃ in the circulating reagent solution dissolves AgCl precipitates and the stream then returns to the reservoir. Various variables of the FI system were optimized and a study of interfering ions was also carried out. A linear calibration graph was obtained from 3.0 to 30 mg l⁻¹ chloride. Two hundred repetitive injections of 5.0 mg l⁻¹ chloride into the circulating reagent solution have shown unchanged base-line and good reproducibility. The method was successfully applied to the determination of chloride in tap, natural and the reference waters.     

Stereochemistry of the nickel-catalyzed cross-coupling reaction of Grignard reagents with olefinic halides: stereospecific versus nonstereospecific-stereoselective reactions

The nickel-catalyzed cross-coupling reactions of Grignard reagents with monohalo-olefins proceed stereospecifically, while with 1,2-dihaloethylenes they proceed nonstereo-specifically to form cis-olefins stereoselectively in many cases.     

Chemoenzymatic synthesis of Park’s nucleotide: toward the development of high-throughput screening for MraY inhibitors

An efficient chemoenzymatic synthesis of UDP-N-acetylmuramyl-l-alanyl-γ-d-glutamyl-meso-diaminopimelyl-d-alanyl-d-alanine (Park’s nucleotide) is reported. UDP-MurNAc is efficiently synthesized by a minimum number of protecting strategies. One-pot amino acid ligation reactions catalyzed by MurC, D, E, and F enzymes are amenable to scale-up production.     

Repetitive determination of calcium ion and regeneration of a chromogenic reagent using chlorophosphonazo III and an ion exchanger in a circulatory flow injection system.

The spectrophotometric determination of Ca2+ with chlorophosphonazo III (CPN) has been carried out by a circulatory flow injection (FI) method. A cation-exchange mini-column for the on-line regeneration of the main reagent was incorporated in this FT system, allowing a repetitive determination of Ca2+. A solution of 4.0 x 10(-5) M CPN in a 0.05 M acetate buffer (pH 5.0) in a single reservoir (50 ml) was continuously circulated at a constant flow rate of 1.5 ml min(-1). Into the stream, an aliquot (20 microl) of a sample containing Ca2+ was quickly injected by means of a 6-way valve. The complex formed was monitored spectrophotometrically at 670 nm in the flow system. Then, the stream passed through a cation-exchange column, which was introduced after the flow-through cell. A successful ligand-exchange reaction of Ca2+ between the CPN reagent and a cation exchanger, as well as a simultaneous regeneration of the free reagent took place. The stream then returned to the reservoir. The regeneration and recycling of the CPN reagent allowed as many as 300 repetitive determinations of 2.5 mg l(-1) Ca2+ solutions with the same 50 ml circulating solution.     

Volumetric behavior and micelle formation of aqueous surfactant mixtures

A thermodynamic treatment of the volumetric behavior of surfactant mixtures in water have been developed on the basis of the thermodynamic treatment of mixed micelle by Motomura et al. Densities of aqueous solutions of mixtures of decyltrimethylammonium bromide (DeTAB) and dodecyltrimethylammonium bromide (DTAB) have been measured as a function of total molality at constant compositions. The apparent molar volumes of the mixtures have been derived from the density data and the mean partial molar volume of monomeric surfactant mixture V _t ^w , the molar volume of mixed micelle V^M/N _t ^M , the voluem of formation of mixed micelle _W ^M V, and the composition of surfactant in the mixed micelle have been evaluated. The V _t ^W , V^M/N _t ^M , and _W ^M V have been observed to depend on the composition. The linear dependence of V _t ^W and V^M/N _t ^M on the composition indicates that the mixing of DeTAB and DTAB is ideal both in the monomeric and micellar states. This has been confirmed further by the shape of the critical micelle concentration vs. composition curves.