Massively parallel implementation of 3D‐RISM calculation with volumetric 3D‐FFT

A new three‐dimensional reference interaction site model (3D‐RISM) program for massively parallel machines combined with the volumetric 3D fast Fourier transform (3D‐FFT) was developed, and tested on the RIKEN K supercomputer. The ordinary parallel 3D‐RISM program has a limitation on the number of parallelizations because of the limitations of the slab‐type 3D‐FFT. The volumetric 3D‐FFT relieves this limitation drastically. We tested the 3D‐RISM calculation on the large and fine calculation cell (2048³ grid points) on 16,384 nodes, each having eight CPU cores. The new 3D‐RISM program achieved excellent scalability to the parallelization, running on the RIKEN K supercomputer. As a benchmark application, we employed the program, combined with molecular dynamics simulation, to analyze the oligomerization process of chymotrypsin Inhibitor 2 mutant. The results demonstrate that the massive parallel 3D‐RISM program is effective to analyze the hydration properties of the large biomolecular systems. © 2014 Wiley Periodicals, Inc.     

An Improved Preparation of D‐Glyceraldehyde 3‐Phosphate and Its Use in the Synthesis of 1‐Deoxy‐D‐xylulose 5‐Phosphate

D ‐Glyceraldehyde 3‐phosphate (=D ‐GAP; 2 ) was prepared by an improved chemical method (Scheme 2), and it was then employed to synthesize 1‐deoxy‐D ‐xylulose 5‐phosphate (=DXP; 3 ) which is enzymatically one of the key intermediates in the MEP ( 4 ) terpenoid biosynthetic pathway (Scheme 1). The recombinant DXP synthase of Rhodobacter capsulatus was used to catalyze the condensation of D ‐glyceraldehyde 3‐phosphate ( 2 ) and pyruvate (=2‐oxopropanoate; 1 ) to produce the sugar phosphate 3 (Scheme 2). The simple two‐step chemoenzymatic route described affords DXP ( 3 ) with more than 70% overall yield and higher than 95% purity. The procedure may also be used for the synthesis of isotope‐labeled DXP ( 3 ) by using isotope‐labeled pyruvate.     

3D‐Printed Microfluidics

The advent of soft lithography allowed for an unprecedented expansion in the field of microfluidics. However, the vast majority of PDMS microfluidic devices are still made with extensive manual labor, are tethered to bulky control systems, and have cumbersome user interfaces, which all render commercialization difficult. On the other hand, 3D printing has begun to embrace the range of sizes and materials that appeal to the developers of microfluidic devices. Prior to fabrication, a design is digitally built as a detailed 3D CAD file. The design can be assembled in modules by remotely collaborating teams, and its mechanical and fluidic behavior can be simulated using finite‐element modeling. As structures are created by adding materials without the need for etching or dissolution, processing is environmentally friendly and economically efficient. We predict that in the next few years, 3D printing will replace most PDMS and plastic molding techniques in academia.     

Zr6STe2 – ein zirconiumreiches Sulfidtellurid mit einer Zr3Te‐Teilstruktur vom Re3B‐Typ

Zr₆STe₂ – a Zirconium‐rich Sulfide Telluride with a Zr₃Te Partial Structure of the Re₃B Type Zr₆STe₂ is accessible through the reduction of a mixture of ZrTe₂ and ZrS₂ with zirconium in fused tantalum tubes at 1520 K. The spatially averaged crystal structure of Zr₆STe₂ is described in the space group Cmcm, a = 377.81(4), b = 1156.4(1), c = 887.96(8), Z = 2, Pearson symbol oC18, 320 reflexions (I > 2σ(I)), 22 variables, R_w(I) = 0.088. Zr₆STe₂ crystallizes in a unique structure type, which can be seen as a filled Re₃B type structure. The tellurium atoms are surrounded by nine zirconium atoms situated at the vertices of a distorted, tricapped trigonal prism. The Zr₉Te tetrakaidecahedra are connected by common triangular prism faces parallel [100], edges approximately along [001] and common vertices along [010], thus forming a three‐dimensional tetrakaidecahedral network [Zr_9/3Te], which is decisively stabilized by homonuclear Zr–Zr‐interactions. The tetrakaidecahedra are arranged in such a way, that Zr₆ octahedra occur. The octahedra are arranged into layers by sharing edges parallel [100] and vertices along [001]. As a result of a distortion of the structure, every second octahedron is expanded to such an extent as to be able to smoothly accommodate sulfur atoms. According to the modulation of the diffraction intensities, the vacancy ordering in adjacent layers of octahedra occurs independently of each other.     

Neue [{Cp(CO)2Mo}2ESbCl]‐Cluster mit tetraedrischem Mo2SbE‐Gerüst (E = S,Se)

Reaction of [{Cp(CO)₃Mo}₂SbCl] with S₈ or Se₈ leads to the formation of cluster compounds [{Cp(CO)₂Mo}₂ESbCl] (E = S, Se). [{Cp(CO)₂Mo}₂SSbCl] crystallizes monoclinic, space group P2₁/n with a = 812.28(3), b = 855.65(4), c = 2441.01(9) pm and β = 90.149(3)°; [{Cp(CO)₂Mo}₂SeSbCl] · CH₂Cl₂ crystallizes triclinic, space group P$\bar{1}$ with a = 828.82(9), b = 1002.8(1), c = 1340.0(2) and α = 109.24(1), β = 100.87(1), γ = 96.81(1)°. For both compounds X‐ray crystal structure analysis reveals tetrahedral Mo₂SbE cluster cores with Sb–E bond lengths of 256.8(1) pm (E = S) and 265.3(1) (E = Se). According to the 18 electron rule the [{Cp(CO)₂Mo}₂ESbCl] clusters can be regarded as complexes of the 4 electron donator ESbCl that is coordinated “side‐on” to a {Cp(CO)₂Mo}₂ fragment.     

Neue Hexachalcogeno‐Hypodiphosphate der Erdalkalimetalle und des Europiums

New Hexachalcogeno‐Hypodiphosphates of Alkaline‐Earth Metals and Europium Six hexathio‐ and hexaseleno‐hypodiphosphates respectively with the formula M₂P₂X₆ (M = Ca, Sr, Eu, Ba; X = S, Se) were prepared by heating the elements at 750 °C (60 h) and their crystal structures were determined by single crystal X‐ray methods. Eu₂P₂S₆ (a = 9.396(2), b = 7.531(2), c = 6.593(2) Å, β = 91.48(2) °), Ba₂P₂S₆ (a = 9.966(1), b = 7.580(2), c = 6.737(2) Å, β = 91.17(3) °), Ca₂P₂Se₆ (a = 9.664(2), b = 7.519(2), c = 6.859(1) Å, β = 92.02(3) °), Sr₂P₂Se₆ (a = 9.844(2), b = 7.788(2), c = 6.963(1) Å, β = 91.50(3) °), Eu₂P₂Se₆ (a = 9.779(2), b = 7.793(2), c = 6.957(1) Å, β = 91.29(3) °), and Ba₂P₂Se₆ (a = 10.355(2), b = 7.862(2), c = 7.046(1) Å, β = 90.83(3) °) are isotypic and crystallize in the high temperature form of Sn₂P₂S₆ (P2₁/n; Z = 2). The discrete ethanlike (P₂X₆)^4— anions in staggered conformation are linked via X—M—X bonds to a three‐dimensional structure and in the course of this Ca²⁺, Sr²⁺, and Eu²⁺ are coordinated by 8 and Ba²⁺ by 8+1 S and Se atoms respectively. Susceptibility measurements of Eu₂P₂S₆ from 2 K to room temperature show Curie‐Weiss behavior with an experimental magnetic moment of 7.43(2) μ_B/Eu. No magnetic ordering was observed down to 2 K. A ¹⁵¹Eu Mössbauer spectrum at 77 K shows only one signal at an isomer shift of δ = —12.6(1) mm/s. The europium atoms in Eu₂P₂S₆ are therefore in a stable divalent oxidation state.     

2－脱氧－烟酰胺基－β－D－氨基葡萄糖的合成和表征

A new nicotinic acid derivative,2-deoxy-2-nicotinoylamido-β-D-glucopyranose, was synthesized with β-configuration exclusively. The structure and properties of the product were characterized by ^1H NMR, PT-IR, MS, DSC and polarimeter. The details of ^1H NMR spectrum and the mass spectrum proved that there are a great amount of hydrogen bonds in the product.     

Synthese und Struktur von RbHfF5, Rb2Zr3F12O und Rb2Hf3F12O — zwei Oxidfluoride mit zentraler trigonal‐planarer [M3O]‐Gruppe

Synthesis and Structure of RbHfF₅, Rb₂Zr₃F₁₂O and Rb₂Hf₃F₁₂O — two Oxydefluorides with Central Trigonal‐plane [M₃O] Group Colorless RbHfF₅ crystallizes isotypic with (NH₄)ZrF₅ and TlHfF₅ monoclinic, space group P2₁/c ‐ C_2h (No. 14) with a = 776.6, b = 789.6, c = 789.8 pm, and β = 120.52°. Also colorless Rb₂Zr₃F₁₂O crystallizes trigonal, space group R3¯m — D₃d (No. 166), with a = 771.9 and c = 2963.0 pm, isotypic is Rb₂Hf₃F₁₂O with a = 769.2 pm and c = 2986.1 pm. Both compounds are isotypic with Tl₂Zr₃F₁₂O.     

Ein Thiolato‐Zink‐Komplex mit einem Zn4O4‐Bicyclooctan‐Gerüst

A Thiolate‐Zinc Complex with a Zn₄O₄ Bicyclooctane Framework The reaction of diethyl zinc with 2,4,6‐triisopropyl thiophenol (HSR*) and N‐methyl‐2‐hydroxymethyl imidazole (ImCH₂OH) in methanol yields the complex Zn₄(SR*)₄ (ImCH₂O)₃(OMe) with terminal SR* and bridging ImCH₂O and MeO ligands. The structure of its Zn₄O₄ framework is that of a bicyclo[2.2.2]octane with Zn and O at the two apices.     

Na2ZrS3: Ein ternäres Sulfid des Zirconiums mit aufgefüllter AlCl3‐Struktur

Na₂ZrS₃: A Ternary Zirconium Sulfide with Stuffed AlCl₃‐type Structure Dark green, plate‐like single crystals of Na₂ZrS₃ (monoclinic, C2/m; a = 664.69(6), b = 1152.5(1), c = 695.48(7) pm, β = 108.78(1)°; Z = 4) are obtained along with pale yellow platelets of NaZr₂N₂SCl (trigonal, R3m; a = 363.56(3), c = 2951.2(4) pm; Z = 3) upon oxidation of zirconium metal with sulfur and sodium azide (NaN₃) in the presence of fluxing NaCl (molar ratio 7:6:2:3) in evacuated silica tubes at 850°C within three weeks. The crystal structure is best described as stuffed AlCl₃ type with all cations (Na⁺ and Zr⁴⁺) in octahedral coordination of the S^2– anions, which build up a cubic closest packed host lattice. The internuclear metal sulfur distances range from 276 to 296 pm for all three crystallographically different Na⁺ cations, and from 258 to 260 pm for Zr⁴⁺.     

Separation of D‐psicose and D‐fructose using simulated moving bed chromatography

Simulated moving bed (SMB) processes have been widely used in the sugar industries with ion‐exchange resin as a stationary phase. D ‐Psicose, a rare monosaccharide known as a valuable pharmaceutical substrate, was synthesized by the enzymatic conversion from D ‐fructose. The SMB process was adopted to separate D ‐psicose from D ‐fructose. Before the SMB experiment, the reaction mixture including D ‐psicose and D ‐fructose was treated by a deashing process to remove contaminants, such as buffers, proteins, and other organic materials. Four columns packed with Dowex 50WX4‐Ca²⁺ (200–400 mesh) ion‐exchange resins were used in the four‐zone SMB. Single‐step frontal analysis was performed to estimate the isotherm parameters of each monosaccharide. The operating conditions of the SMB process were determined based on the Equilibrium Theory. According to the simulation of the SMB process, the purity and yield of extract product (D ‐psicose) achieved were 99.04 and 97.46%, respectively and those of raffinate product (D ‐fructose) were 99.06 and 99.53%, respectively. Under the optimized operating condition, complete separation (extract purity = 99.36%, raffinate purity = 99.67%) was achieved experimentally.     

A 3D‐QSAR Study of Celebrex‐Based Pdk1 Inhibitors Using Comfa Method

A 3D‐QSAR study of celebrex‐based compounds of PDK1 inhibitors using comparative molecular field analysis (CoMFA) was carried out. The structures of the compounds were obtained using quantum chemistry calculation. CoMFA calculations for a number of grouped subsets of compounds gave q² values of correlation in the range from 0 to 0.8. The low q² values should be mainly due to the narrow span of biological activity. Calculations for several subsets of 11–13 compounds gave high q² values, with 0.5–0.8. Factors affecting the results of the calculations are discussed. Calculated results with high q² values suggest that further chemical modifications of the compounds could lead to enhanced activity and could be an aid in the design of celebrex‐based cancer drugs.     

ZrIV‐ und TaV‐Komplexe mit methanoverbrückten Bis(aryloxy)‐Liganden

Zr^IV and Ta^V Complexes with Methano‐Bridged Bis(aryloxy) Ligands The bis(aryloxy) ligand precursor compounds bis(2‐trimethylsiloxy‐5‐tbutylphenyl)methane (L–SiMe₃) and its bromoderivative (2‐trimethylsiloxy‐3‐bromo‐5‐tbutylphenyl)(2′‐trimethylsiloxy‐5′‐tbutylphenyl)methane (L^Br–SiMe₃) are prepared in analogy to the corresponding calixarenes in excellent yields. X‐ray structure analysis for L^Br–SiMe₃: space group P2₁/c, a = 12.462(7), b = 10.466(6), c = 23.315(14) Å, β = 105.02(4)°, V = 2937(3) ų, Z = 4. L–SiMe₃ and L^Br–SiMe₃ react with Zr^IV and Ta^V chlorides in very good yields forming di‐ and trinuclear complexes. From the reaction of CpZrCl₃ with L^Br–SiMe₃ in the ratio of 3 : 2 a Zr₃ complex ( 7 ) is obtained, with one L^Br ligand only, which Zr atoms are bridged by a μ₃‐oxygen. The X‐ray structure analysis of 7 (space group R 3, a = 33.23(6), c = 24.47(8) Å, V = 23405(128) ų, Z = 18) additionally reveals that one phenolato oxygen atom of the L^Br ligand is terminally bound to a distorted tetragonal‐pyramidal coordinated Zr atom, while the second phenolato oxygen atom of the L^Br ligand forms a bridge to another Zr atom with a distorted octahedral coordination. The third Zr atom is also found in a distorted octahedral coordination mode. The reactions of L–SiMe₃ and L^Br–SiMe₃ with CpTaCl₄ and TaCl₅ yield dinuclear Ta complexes with a bridging bis(aryloxy) ligand. NMR spectroscopic data point out that the coordination of the bis(aryloxy) ligands in the Ta complexes very much resembles that in the Zr₃‐complex with one terminal and one bridging phenolato oxygen atom. The Zr₃ and the Ta complexes L^BrTa₂Cp₂Cl₆ and LTa₂Cl₈ were tested with respect to their catalytic properties in olefin polymerisation reactions in the presence of MAO.     

Metall‐π‐Aren‐Wechselwirkungen in den Kristallstrukturen von zwei Lewis‐Donor‐freien Arylbis(cyclopentadienyl)lanthanoiden

Metal‐π‐Arene‐Interactions in the Solid‐State Structures of Two Lewis Donor‐Free Arylbis(cyclopentadienyl)lanthanoids Ar*Yb(C₅H₄Me)₂ ( 1 ) and Ar*SmCp₂ ( 2 ) (Ar* = 2,6‐Mes₂C₆H₃) have been obtained by the reaction of LiAr* with Yb(C₅H₄Me)₃ or SmCp₃ in toluene. Red crystals of 1 and orange crystals of 2 were characterized by X‐ray structure analysis. The lanthanoids are η⁵‐coordinated to the cyclopentadienyl ligands and η¹‐coordinated to the ipso carbon atom of the aryl groups. Additional π‐arene contacts to one mesityl group give rise to a different pyramidalisation of the metal centers, which depends on the size of the central lanthanoid atom.