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

Crystalline metal-organic frameworks (MOFs) are formed by reticular synthesis, which creates strong bonds between inorganic and organic units. Careful selection of MOF constituents can yield crystals of ultrahigh porosity and high thermal and chemical stability. These characteristics allow the interior of MOFs to be chemically altered for use in gas separation, gas storage, and catalysis, among other applications. The precision commonly exercised in their chemical modification and the ability to expand their metrics without changing the underlying topology have not been achieved with other solids. MOFs whose chemical composition and shape of building units can be multiply varied within a particular structure already exist and may lead to materials that offer a synergistic combination of properties.

The Chemistry and Applications of Metal-Organic Frameworks

The long-standing challenge of designing and constructing new crystalline solid-state materials from molecular building blocks is just beginning to be addressed with success. A conceptual approach that requires the use of secondary building units to direct the assembly of ordered frameworks epitomizes this process: we call this approach reticular synthesis. This chemistry has yielded materials designed to have predetermined structures, compositions and properties. In particular, highly porous frameworks held together by strong metal-oxygen-carbon bonds and with exceptionally large surface area and capacity for gas storage have been prepared and their pore metrics systematically varied and functionalized.

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Reticular synthesis and the design of new materials

A critical review of the emerging field of MOF-based catalysis is presented. Discussed are examples of: (a) opportunistic catalysis with metal nodes, (b) designed catalysis with framework nodes, (c) catalysis by homogeneous catalysts incorporated as framework struts, (d) catalysis by MOF-encapsulated molecular species, (e) catalysis by metal-free organic struts or cavity modifiers, and (f) catalysis by MOF-encapsulated clusters (66 references).

Metal–organic framework materials as catalysts

Open metal–organic frameworks are widely regarded as promising materials for applications1,2,3,4,5,6,7,8,9,10,11,12,13,14,15 in catalysis, separation, gas storage and molecular recognition. Compared to conventionally used microporous inorganic materials such as zeolites, these organic structures have the potential for more flexible rational design, through control of the architecture and functionalization of the pores. So far, the inability of these open frameworks to support permanent porosity and to avoid collapsing in the absence of guest molecules, such as solvents, has hindered further progress in the field14,15. Here we report the synthesis of a metal–organic framework which remains crystalline, as evidenced by X-ray single-crystal analyses, and stable when fully desolvated and when heated up to 300?°C. This synthesis is achieved by borrowing ideas from metal carboxylate cluster chemistry, where an organic dicarboxylate linker is used in a reaction that gives supertetrahedron clusters when capped with monocarboxylates. The rigid and divergent character of the added linker allows the articulation of the clusters into a three-dimensional framework resulting in a structure with higher apparent surface area and pore volume than most porous crystalline zeolites. This simple and potentially universal design strategy is currently being pursued in the synthesis of new phases and composites, and for gas-storage applications.

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Design and synthesis of an exceptionally stable and highly porous metal-organic framework

The xenon-chlorine conundrum: van der Waals complex or linear molecule?

Ortho-metalated pyridine derivatives of the unsaturated rhenium cluster anion [Re3(.mu.-H)4(CO)10]-. Syntheses and x-ray crystal structures of the tetraethylammonium salts of the anions [Re3(.mu.-H)3(.mu.-.eta.2-NC5H4)(CO)10]- and [Re3(.mu.-H)3(.mu.-.eta.2-NC5H4)(CO)9(NC5H5)]-

Networks, Topologies, and Entanglements

Direct synthesis and structural characterization of a series of polar rare earth palladium germanides of R2Pd3Ge5 composition (R = La–Nd, Sm) is reported. The crystal structure of the Nd representative was determined by single-crystal X-ray diffraction analysis (U2Co3Si5-type, SG: Ibam, oI40, Z = 4, a = 10.1410(6), b = 12.0542(8), c = 6.1318(4) A, wR
 2 = 0.0306, 669 F
 2 values, 31 variables). The crystal structures of the other homologues were ensured by powder X-ray diffraction pattern analysis. A smooth variation of the cell dimensions is observed through the rare earth series. The structure of the studied compounds can be interpreted as consisting of a complex three-dimensional [Pd3Ge5]δ− network spaced by the rare earth cations. Within the concept of symmetry reduction, a Barnighausen tree is used to rationalize the related crystal structures of the RPd2Ge2, RPdGe3 and R2Pd3Ge5 ternary compounds, enriching the large family of the BaAl4 derivatives. Moreover, syntheses with metal fluxes were performed, some of which were successful to obtain large crystals of La2Pd3Ge5 (using Bi as solvent) and Nd2Pd3Ge5 (using Pb as solvent) stoichiometry.

/pdf/the-r2pd3ge5-r-la-nd-sm-germanides-synthesis-crystal-3wmaq7lzp3.pdf

The R2Pd3Ge5 (R = La–Nd, Sm) germanides: synthesis, crystal structure and symmetry reduction

Resonance scattering was applied for the first time to the class of solids with the AB2X2 stoichiometry. A few members of this family seem to violate the developed rules describing the structure−property relationship, and the source of ambiguity is often the experimental determination of the structure itself. As an example, the newly synthesized BaZn2Ge2 can in principle adopt either the ThCr2Si2 or the CaBe2Ge2 type structures, and conventional diffraction techniques do not allow discrimination between the two structure models. The resonance scattering method shows, however, that BaZn2Ge2 crystallizes in the ThCr2Si2 structure (tetragonal I4/mmm; a = 4.527(2) A c = 10.555(3) A, Z = 2), in agreement with theoretical analyses.

Davide M. Proserpio

Papers

The xenon-chlorine conundrum: van der Waals complex or linear molecule?

Ortho-metalated pyridine derivatives of the unsaturated rhenium cluster anion [Re3(.mu.-H)4(CO)10]-. Syntheses and x-ray crystal structures of the tetraethylammonium salts of the anions [Re3(.mu.-H)3(.mu.-.eta.2-NC5H4)(CO)10]- and [Re3(.mu.-H)3(.mu.-.eta.2-NC5H4)(CO)9(NC5H5)]-

Networks, Topologies, and Entanglements

The R2Pd3Ge5 (R = La–Nd, Sm) germanides: synthesis, crystal structure and symmetry reduction

Site Differentiation by Synchrotron Radiation Resonant Scattering: Case Study of BaZn2Ge2