Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

Fast parallel algorithms for short-range molecular dynamics

J. Appl. Cryst.の発刊に際して

Although homogeneous gold catalysis was known previously, an exponential growth was only induced 12 years ago. The key findings which induce that rise of the field are discussed. This includes early reactions of allenes and furanynes and intermediates of these conversions as well as hydroarylation reactions. Other substrate types addressed are alkynyl epoxides and N-propargyl carboxamides. Important vinylgold intermediates, the transmetalation from gold to other transition metals, the development of new ligands for gold catalysis, and significant contributions from computational chemistry are other crucial points for the field highlighted here.

Gold-Catalyzed Organic Reactions

基礎講座 電気泳動(Electrophoresis)

N-Heterocyclic Carbenes in Late Transition Metal Catalysis

Readily available biphenyl derivatives containing an alkyne unit at one of their ortho-positions are converted into substituted phenanthrenes on exposure to catalytic amounts of either PtCl2, AuCl, AuCl3, GaCl3 or InCl3 in toluene. This 6-endo-dig cyclization likely proceeds through initial pi-complexation of the alkyne unit followed by interception of the resulting eta2-metal species by the adjacent arene ring. The reaction is inherently modular, allowing for substantial structural variations and for the incorporation of substituents at any site of the phenanthrene product. Moreover, it is readily extended to the heterocyclic series as exemplified by the preparation of benzoindoles, benzocarbazoles, naphthothiophenes, as well as bridgehead nitrogen heterocycles such as pyrrolo[1,2-a]quinolines. Depending on the chosen catalyst, biaryls bearing halo-alkyne units can either be converted into the corresponding 10-halo-phenanthrenes or into the isomeric 9-halo-phenanthrenes; in the latter case, the concomitant 1,2-halide shift is best explained by assuming a metal vinylidene species as the reactive intermediate. The scope of this novel method for the preparation of polycyclic arenes is illustrated by the total synthesis of a series of polyoxygenated phenanthrenes that are close relatives of the anticancer agent combretastatin A-4, as well as by the total synthesis of the aporphine alkaloid O-methyl-dehydroisopiline and its naturally occurring symmetrical dimer.

Synthesis of Phenanthrenes and Polycyclic Heteroarenes by Transition‐Metal Catalyzed Cycloisomerization Reactions

Exposure of enynes containing a hydroxyl group at one of the propargylic positions to catalytic amounts of either PtCl2 or (PPh3)AuCl/AgSbF6 results in a selective rearrangement with formation of bicyclo[3.1.0]hexan-3-one derivatives. The same products are obtained by a “one-pot” process on treatment of an alkynal with allylchlorodimethylsilane (4) and PtCl2 via a reaction cascade involving an initial platinum-catalyzed allylation followed by the cycloisomerization of the homoallylic alcohol formed in situ. This novel skeletal reorganization process was implemented into a concise total synthesis of the terpenes sabinone (18) and sabinol (19). Furthermore it is shown that conversion of the hydroxylated enynes into the corresponding acetates followed by reaction with a cationic gold catalyst formed from (PPh3)AuCl and AgSbF6 opens entry into isomeric products bearing the ketone function at the C-2 position of the bicyclo[3.1.0]hexane skeleton. The outcome of a deuterium labeling experiment and the analysis ...

Platinum- and Gold-Catalyzed Cycloisomerization Reactions of Hydroxylated Enynes

Readily available biphenyl derivatives containing an alkyne unit at one of their ortho positions are converted into substituted phenanthrenes upon exposure to catalytic amounts of either PtCl2, AuCl3, GaCl3, or InCl3 in toluene. This 6-endo-dig cyclization likely proceeds through initial π-coordination of the alkyne unit followed by interception of the resulting η2-metal complex by the adjacent arene ring. The reaction is inherently modular, allowing for substantial structural variations and for the incorporation of substituents at any site of the phenanthrene product except C-9. Moreover, the reaction is readily applied to the heterocyclic series as exemplified by the preparation of benzoindoles, naphthothiophenes as well as bridgehead nitrogen heterocycles.

Victor Mamane

Papers

Synthesis of Phenanthrenes and Polycyclic Heteroarenes by Transition‐Metal Catalyzed Cycloisomerization Reactions

Platinum- and Gold-Catalyzed Cycloisomerization Reactions of Hydroxylated Enynes

Flexible Synthesis of Phenanthrenes by a PtCl2-Catalyzed Cycloisomerization Reaction

Concise total synthesis of the aporphine alkaloid 7,7′-bisdehydro-O-methylisopiline by an InCl3 mediated cycloisomerization reaction

Homochiral metal-organic frameworks and their application in chromatography enantioseparations.