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

Synthesis of metal-organic frameworks (MOFs): routes to various MOF topologies, morphologies, and composites.

Metal Organic Frameworks in Biomedicine Patricia Horcajada,* Ruxandra Gref, Tarek Baati, Phoebe K. Allan, Guillaume Maurin, Patrick Couvreur, G erard F erey, Russell E. Morris, and Christian Serre* Institut Lavoisier, UMR CNRS 8180, Universit e de Versailles St-Quentin en Yvelines, 45 Avenue des Etats-Unis, 78035 Versailles Cedex, France Facult e de Pharmacie, UMR CNRS 8612, Universit e Paris-Sud, 92296 Châtenay-Malabry Cedex, France Institut Charles Gerhardt Montpellier, UMR CNRS 5253, Universit e Montpellier 2, 34095 Montpellier cedex 05, France EaStChem School of Chemistry, University of St. Andrews Purdie Building, St Andrews, KY16 9ST U.K.

Metal-organic frameworks in biomedicine.

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Principles Of Fluorescence Spectroscopy

This review article presents the fundamental and practical aspects of water adsorption in Metal–Organic Frameworks (MOFs). The state of the art of MOF stability in water, a crucial issue to many applications in which MOFs are promising candidates, is discussed here. Stability in both gaseous (such as humid gases) and aqueous media is considered. By considering a non-exhaustive yet representative set of MOFs, the different mechanisms of water adsorption in this class of materials are presented: reversible and continuous pore filling, irreversible and discontinuous pore filling through capillary condensation, and irreversibility arising from the flexibility and possible structural modifications of the host material. Water adsorption properties of more than 60 MOF samples are reported. The applications of MOFs as materials for heat-pumps and adsorbent-based chillers and proton conductors are also reviewed. Some directions for future work are suggested as concluding remarks.

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Water adsorption in MOFs: fundamentals and applications

Nickel-catalyzed biaryl coupling of heteroarenes and aryl halides/triflates.

The one-pot postfunctionalization allows anchoring a molecular nickel complex into a mesoporous metal-organic framework (Ni@(Fe)MIL-101). It is generating a very active and reusable catalyst for the liquid-phase ethylene dimerization to selectively form 1-butene. Higher selectivity for 1-butene is found using the Ni@(Fe)MIL-101 catalyst than reported for molecular nickel diimino complexes.

/pdf/mof-supported-selective-ethylene-dimerization-single-site-5cxelxrgno.pdf

MOF-Supported Selective Ethylene Dimerization Single-Site Catalysts through One-Pot Postsynthetic Modification

A set of 15 metal–organic frameworks (MIL-53, MIL-68, MIL-125, UiO-66, ZIF) exhibiting different pore size, morphology, and surface chemistry is used to unravel the numerous behaviors of water adsorption at room temperature in this class of materials. Outstanding “S”-shaped (type V) adsorption isotherms are observed for MIL-68 type solids. We show that the underlying mechanism of water adsorption can be rationalized using a simple set of three parameters: the Henry constant (i.e. the slope of the adsorption pressure in the low pressure range), the pressure at which pore filling occurs, and the maximum water adsorption capacity. While the Henry constant and pore filling pressure mostly depend on the affinity of water for the surface chemistry and on pore size, respectively, these two parameters are correlated as they both reflect different aspects of the hydrophobicity–hydrophilicity of the material. For a given type of porous structure, the functionalization of the material by hydrophilic moieties such as hydrogen bonding groups (amine or aldehyde) systematically leads to an increase in the Henry constant concomitantly with a decrease in the pore filling pressure. As for the adsorption mechanism, we show that, for a given temperature, there is a critical diameter (Dc ∼ 20 A for water at room temperature) above which pore filling occurs through irreversible capillary condensation accompanied by capillary hysteresis loops. Below this critical diameter, pore filling is continuous and reversible unless the material exhibits some adsorption-induced flexibility.

Structure–property relationships of water adsorption in metal–organic frameworks

Novel nickel-based catalytic systems for the CH arylation of azoles with haloarenes and aryl triflates have been developed. We have established that Ni(OAc)2/bipy/LiOtBu serves as a general catalytic system for the coupling with aryl bromides and iodides as aryl electrophiles. For couplings with more challenging electrophiles, such as aryl chlorides and triflates, the Ni(OAc)2/dppf (dppf=1,1′-bis(diphenylphosphino)ferrocene) system was found to be effective. Thiazoles, benzothiazoles, oxazoles, benzoxazoles, and benzimidazoles can be used as the heteroarene coupling partner. Upon further investigation, we discovered a new protocol for the present coupling using Mg(OtBu)2 as a milder and less expensive alternative to LiOtBu. Attempts to reveal the mechanism of this nickel-catalyzed heterobiaryl coupling are also described. This newly developed methodology has been successfully applied to the syntheses of febuxostat (a xanthine oxidase inhibitor that is effective for the treatment of gout and hyperuricemia), tafamidis (effective for the treatment of TTR amyloid polyneuropathy), and texaline (a natural product having antitubercular activity).

Jérôme Canivet

Papers

Water adsorption in MOFs: fundamentals and applications

Nickel-catalyzed biaryl coupling of heteroarenes and aryl halides/triflates.

MOF-Supported Selective Ethylene Dimerization Single-Site Catalysts through One-Pot Postsynthetic Modification

Structure–property relationships of water adsorption in metal–organic frameworks

Nickel-catalyzed C-H arylation of azoles with haloarenes: scope, mechanism, and applications to the synthesis of bioactive molecules.