Computational chemistry on Fujitsu vector-parallel processors: Development and performance of applications software

In this and a preceding paper, we provide an introduction to the Fujitsu VPP range of vector-parallel supercomputers and to some of the computational chemistry software available for the VPP. Here, we consider the implementation and performance of seven popular chemistry application packages. The codes discussed range from classical molecular dynamics to semiempirical and ab initio quantum chemistry. All have evolved from sequential codes, and have typically been parallelised using a replicated data approach. As such they are well suited to the large-memory/fast-processor architecture of the VPP. For one code, CASTEP, a distributed-memory data-driven parallelisation scheme is presented. (C) 2000 Published by Elsevier Science B.V. All rights reserved.

Geochemistry of volcanic rocks of ODP Holes 126-792E and 126-793B

The Izu-Bonin forearc basement volcanic rocks recovered from Holes 792E and 793B show the same phenocrystic assemblage (i.e., plagioclase, two pyroxenes, and Fe-Ti oxides ±olivine), but they differ in the crystallization sequence and their phenocryst chemistry. All the igneous rocks have suffered low-grade hydrothermal alteration caused by interaction with seawater. As a result, only clinopyroxenes, plagioclases, and oxides have preserved their primary igneous compositions. The Neogene olivine-clinopyroxene diabasic intrusion (Unit II) recovered from Hole 793B differs from the basement basaltic andesites because it lacks Cr-spinels and contains abundant titanomagnetites (Usp38.5-46.4) and uncommon FeO-rich (FeO = 29%) spinels. It displays petrological and geochemical similarities to the Izu Arc volcanoes and, thus, can be considered as related to Izu-Bonin Arc magmatic activity. The titanomagnetites (Usp28.5-33) in the calc-alkaline andesitic fragments of the Oligocene volcaniclastic breccia in Hole 793B (Unit VI) represent an early crystallization phase. The Plagioclase phenocrysts enclosed in these rocks show oscillatory zoning and are less Ca-rich (An78.6-67.8) than the plagioclase phenocrysts of the diabase sill and the basement basaltic andesites. Their clinopyroxenes are Fe-rich augites (Fs ? 19.4; FeO = 12%) and thus, differ significantly from the clinopyroxenes of the Hole 793B arc-tholeiitic igneous rocks. The 30-32 Ma porphyritic, two-pyroxene andesites recovered from Hole 792E are very similar to the andesitic clasts of the Neogene breccia recovered in Hole 793B (Unit VI). Both rocks have the same crystallization sequence, and similar chemistry of the Fe-Ti oxides, clinopyroxenes, and plagioclases: that is, Ti-rich (Usp25.5-30.4) magnetites, Fe-rich augites, and intensely oscillatory zoned plagioclases with bytownitic cores (An86-63) and labradorite rims (An73-68). They display a calc-alkaline differentiation trend (Taylor et al., this volume). So, the basement highly porphyritic andesites recovered at Hole 792E, and the Hole 793B andesitic clasts of Unit VI show the same petrological and geochemical characteristics, which are that of calc-alkaline suites. These Oligocene volcanic rocks represent likely the remnants of the Izu-Bonin normal arc magmatic activity, before the forearc rifting and extension. The crystallization sequence in the basaltic andesites recovered from Hole 793B is olivine-orthopyroxene-clinopyroxene-plagioclase-Fe-Ti oxides, indicating a tholeiitic differentiation trend for these volcanic rocks. Type i is an olivine-and Cr-spinel bearing basaltic andesite whereas Type ii is a porphyritic pyroxene-rich basaltic andesite. The porphyritic plagioclase-rich basaltic andesite (Type iii) is similar, in most respects, to Type ii lavas but contains plagioclase phenocrysts. The last, and least common lava is an aphyric to sparsely phyric andesite (Type iv). Cr-spinels, included either in the olivine pseudomorphs of Type i lavas or in the groundmass of Type ii lavas, are Cr-rich and Mg-rich. In contrast, Cr-spinels included in clinopyroxenes and orthopyroxenes (Types i and ii lavas) show lower Cr* and Mg* ratios and higher aluminium contents. Orthopyroxenes from all rock types are Mg-rich enstatites. Clinopyroxenes display endiopsidic to augitic compositions and are TiO2 and Al2O3 depleted. All the crystals exhibit strong zoning patterns, usually normal, although, reverse zoning patterns are not uncommon. The plagioclases show compositions within the range of An90-64. The Fe-Ti oxides of the groundmass are TiO2-poor (Usp16-17). The Hole 793B basaltic andesites show, like the Site 458 bronzites from the Mariana forearc, intermediate features between arc tholeiites and boninites: (1) Cr-spinel in olivine, (2) presence of Mg-rich bronzite, Ca-Mg-rich clinopyroxenes, and Ca-plagioclase phenocrysts, and (3) transitional trace element depletion and epsioln-Nd ratios between arc tholeiites and boninites. Thus, the forearc magmatism of the Izu-Bonin and Mariana arcs, linked to rifting and extension, is represented by a depleted tholeiitic suite that displays boninitic affinities.

Direct synthesis of methanol by partial oxidation of methane with oxygen over cobalt modified mesoporous H-ZSM-5 catalyst

Peer reviewed

Lasting mantle scars lead to perennial plate tectonics

R.N.P. and P.J.H. are grateful for funding from an NSERC Discovery Grant. Computations were performed on the GPC supercomputer at the SciNet HPC Consortium. SciNet is funded by the Canada Foundation for Innovation under the auspices of Compute Canada, the Government of Ontario, Ontario Research Fund—Research Excellence and the University of Toronto. Numerical calculations were done using a modified version of the SOPALE (2000) software. The SOPALE modelling code was originally developed by Philippe Fullsack at Dalhousie University with Chris Beaumont and his Geodynamics group.

Application of Inelastic Neutron Scattering to the Methanol-to-Gasoline Reaction Over a ZSM-5 Catalyst

Peer reviewed

Understanding the twist-bend nematic phase: the characterisation of 1-(4-cyanobiphenyl-4'-yloxy)-6-(4-cyanobiphenyl-4'-yl) hexane (CB6OCB) and comparison with CB7CB

Acknowledgements The FFTEM data were obtained at the (Cryo) TEM facility at the Liquid Crystal Institute, Kent State University, supported by the Ohio Research Scholars Program Research Cluster on Surfaces in Advanced Materials. ODL acknowledges the support of NSF DMR-1410378 grant. The authors are grateful for financial support from MINECO/FEDER MAT2015-66208-C3-2-P and from the Gobierno Vasco (GI/IT-449-10)

Crystal structure of 1-benzylsulfonyl-1,2,3,4-tetrahydroquinoline

Peer reviewed

Determination of 210Po content of vietnamese tobacco samples

Smoking is one of the leading causes of preventable death. In recent years, numerous countries have initiated the prohibition of smoking in restaurants, workplaces and public spaces. The Vietnamese government intends to follow the precautions against public smoking as well. Over and above the number of some hazardous chemical components found in tobacco, ²¹⁰Po isotope content could enhance the probability of the development of lung cancer. In this study 14 Vietnamese tobacco products (commercial cigarettes and pipe tobacco) ²¹⁰Po activity concentration were determined using PIPS semiconductor alpha spectrometry. The results showed that the 210Po activity concentration of the investigated samples varied between 7.40 ± 1.09 - 128.64 ± 11.22 mBq g^-1. The average ²¹⁰Po content of commercial cigarettes was 15.5 mBq g^-1, whilst the average of pipe tobacco was 20.4 mBq g^-1. To estimate the risk of inhalation of ²¹⁰Po isotopes originating as a result of smoking, dose estimations were carried out. © Versita Sp. z o.o.

Total Synthesis of the GRP78-Downregulatory Macrolide (+)-Prunustatin A, the Immunosuppressant (+)-SW-163A, and a JBIR- 04 Diastereoisomer That Confirms JBIR-04 Has Nonidentical Stereochemistry to (+)-Prunustatin A

A unified total synthesis of the GRP78-downregulator(+)-prunustatin A and the immunosuppressant(+)-SW-163A based upon [1 + 1 + 1 + 1]-fragment condensationand macrolactonization between O(4) and C(5) is hereindescribed. Sharpless asymmetric dihydroxylation was used toset the C(2) stereocenter present in both targets. In like fashion,coupling of the (+)-prunustatin A macrolide amine with benzoicacid furnished a JBIR-04 diastereoisomer whose NMR spectradid not match those of JBIR-04, thus confirming that it hasdifferent stereochemistry than (+)-prunustatin A.

Highlights from Faraday Discussion: Designing New Heterogeneous Catalysts, London, UK, April 2016

The Faraday Discussion on the design of new heterogeneous catalysts took place from 4-6 April 2016 in London, United Kingdom. It brought together world leading scientists actively involved in the synthesis, characterisation, modelling and testing of solid catalysts, attracting more than one hundred delegates from a broad spectrum of backgrounds and experience levels-academic and industrial researchers, experimentalists and theoreticians, and students. The meeting was a reflection of how big of an impact the ability to control and design catalysts with specific properties for particular processes can potentially have on the chemical industry, environment, economy and society as a whole. In the following, we give an overview of the topics covered during this meeting and briefly highlight the content of each presentation.

Acid-mediated topological control in a functionalized foldamer

Induced conformational change provides a powerful mechanism to modulate the structure and function of molecules. Here we describe the synthesis of chiral, surface-functionalized oligomeric pyridine/imidazolidin-2-one foldamers, and interrogate their acid-mediated transition between linear and helical topologies.

Ion-mediated conformational switches

Molecular switches are ubiquitous in Nature and provide the basis of many forms of transport and signalling. Single synthetic molecules that change conformation, and thus function, reversibly in a stimulus-dependent manner are of great interest not only to chemists but society in general; myriad applications exist in storage, display, sensing and medicine. Here we describe recent developments in the area of ion-mediated switching.

β-Strand mimetic foldamers rigidified through dipolar repulsion

Many therapeutically relevant protein-protein interactions contain hot-spot regions on secondary structural elements, which contribute disproportionately to binding enthalpy. Mimicry of such α-helical regions has met with considerable success, however the analogous approach for the β-strand has received less attention. Presented herein is a foldamer for strand mimicry in which dipolar repulsion is a central determinant of conformation. Computation as well as solution- and solid-phase data are consistent with an ensemble weighted almost exclusively in favor of the desired conformation.

Catalytic enantioselective electrocyclic cascades

A catalytic enantioselective electrocyclic cascade leads to the construction of topologically complex systems comprising multiple rings with up to three stereocentres. This phase-transfer catalysed process offers a new strategy for the rapid and enantioselective generation of complex products bearing all-carbon quaternary stereogenic centres. © 2012 The Royal Society of Chemistry.

Asymmetric electrocyclic reactions

This critical review offers an overview of asymmetric electrocyclic processes, where diastereo- or enantioselectivity is a consequence of the influence of a chiral component (be it substrate or catalyst) on the electrocyclic bond-forming process (195 references). © 2011 The Royal Society of Chemistry.