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

A fundamental aim in the field of catalysis is the development of new modes of small molecule activation. One approach toward the catalytic activation of organic molecules that has received much attention recently is visible light photoredox catalysis. In a general sense, this approach relies on the ability of metal complexes and organic dyes to engage in single-electron-transfer (SET) processes with organic substrates upon photoexcitation with visible light.

Many of the most commonly employed visible light photocatalysts are polypyridyl complexes of ruthenium and iridium, and are typified by the complex tris(2,2′-bipyridine) ruthenium(II), or Ru(bpy)32+ (Figure 1). These complexes absorb light in the visible region of the electromagnetic spectrum to give stable, long-lived photoexcited states.1,2 The lifetime of the excited species is sufficiently long (1100 ns for Ru(bpy)32+) that it may engage in bimolecular electron-transfer reactions in competition with deactivation pathways.3 Although these species are poor single-electron oxidants and reductants in the ground state, excitation of an electron affords excited states that are very potent single-electron-transfer reagents. Importantly, the conversion of these bench stable, benign catalysts to redox-active species upon irradiation with simple household lightbulbs represents a remarkably chemoselective trigger to induce unique and valuable catalytic processes.






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Figure 1


Ruthenium polypyridyl complexes: versatile visible light photocatalysts.

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Visible Light Photoredox Catalysis with Transition Metal Complexes: Applications in Organic Synthesis

Department of Materials Science, University of Patras, 26504 Rio Patras, Greece, Theoretical and Physical Chemistry Institute, National Hellenic Research Foundation, 48 Vass. Constantinou Avenue, 116 35 Athens, Greece, Institut de Biologie Moleculaire et Cellulaire, UPR9021 CNRS, Immunologie et Chimie Therapeutiques, 67084 Strasbourg, France, and Dipartimento di Scienze Farmaceutiche, Universita di Trieste, Piazzale Europa 1, 34127 Trieste, Italy

Chemistry of Carbon Nanotubes

In this review, we highlight the use of organic photoredox catalysts in a myriad of synthetic transformations with a range of applications. This overview is arranged by catalyst class where the photophysics and electrochemical characteristics of each is discussed to underscore the differences and advantages to each type of single electron redox agent. We highlight both net reductive and oxidative as well as redox neutral transformations that can be accomplished using purely organic photoredox-active catalysts. An overview of the basic photophysics and electron transfer theory is presented in order to provide a comprehensive guide for employing this class of catalysts in photoredox manifolds.

Organic Photoredox Catalysis

Fenton chemistry encompasses reactions of hydrogen peroxide in the presence of iron to generate highly reactive species such as the hydroxyl radical and possibly others. In this review, the complex mechanisms of Fenton and Fenton-like reactions and the important factors influencing these reactions, from both a fundamental and practical perspective, in applications to water and soil treatment, are discussed. The review covers modified versions including the photoassisted Fenton reaction, use of chelated iron, electro-Fenton reactions, and Fenton reactions using heterogeneous catalysts. Sections are devoted to nonclassical pathways, by-products, kinetics and process modeling, experimental design methodology, soil and aquifer treatment, use of Fenton in combination with other advanced oxidation processes or biodegradation, economic comparison with other advanced oxidation processes, and case studies.

/pdf/advanced-oxidation-processes-for-organic-contaminant-546ow329vb.pdf

Advanced Oxidation Processes for Organic Contaminant Destruction Based on the Fenton Reaction and Related Chemistry

Surface chemistry is the topic of this tutorial review. It describes the electrochemical reduction of aryl diazonium salts on carbon, silicon or metals which leads to the formation of an aromatic organic layer covalently bonded to the surface. The method which permits such a modification is set forth. The proof for the existence of the organic layer is brought forward. The grafting mechanism and the covalent bonding between the surface and the aryl group are discussed. The formation of mono or multilayers depending on the experimental conditions is rationalized. Finally some examples of the possible uses of this reaction are given.

Attachment of organic layers to conductive or semiconductive surfaces by reduction of diazonium salts

Electrochemical reduction of a wide variety of aromatic diazonium salts on carbon electrodes (glassy carbon, highly oriented pyrolytic graphite) leads to the covalent attachment of the corresponding aromatic radicals The films thus deposited on glassy carbon surfaces require mechanical abrasion to be removed Cyclic voltammetry, X-ray photoelectron spectroscopy, polarization modulation IR reflection absorption spectroscopy, Auger spectroscopy, and Rutherford backscattering spectroscopy allow the characterization of the overlayer and an estimate of the surface coverage The latter can be controlled through diazonium concentration and electrolysis duration The mechanism of derivatization is discussed on the basis of the kinetic data obtained from cyclic voltammetry and preparative electrolysis This versatile method of surface modification may find applications in the field of carbon−epoxy composites as attested by the successful binding of grafted p-aminophenyl groups with epichlorhydrin

Covalent Modification of Carbon Surfaces by Aryl Radicals Generated from the Electrochemical Reduction of Diazonium Salts

Covalent Modification of Carbon Surfaces by Grafting of Functionalized Aryl Radicals Produced from Electrochemical Reduction of Diazonium Salts

Electrografting refers to the electrochemical reaction that permits organic layers to be attached to solid conducting substrates. This definition can be extended to reactions involving an electron transfer between the substrate to be modified and the reagent, but also to examples where a reducing or oxidizing reagent is added to produce the reactive species. These methods are interesting as they provide a real bond between the surface and the organic layer. Electrografting applies to a variety of substrates including carbon, metals and their oxides, but also dielectrics such as polymers. Since the 1980s several methods have been developed, either by reduction or oxidation, and some of them have reached an industrial stage. This critical review describes the methods that are used for electrografting, their mechanism, the formation and growth of the layers as well as their applications (742 references).

Electrografting: a powerful method for surface modification

4-NO2 and 4-Br benzenediazonium salts have been electrochemically reduced on H-terminated Si(111) electrodes. Electrochemical measurements evidence that the reaction results in a robust modification of Si(111) surfaces. XPS shows that organic films are monolayer thick and that covalent ≡SiAr bonding occurs, with no oxide at the interface. In the case of the Br salt, quantitative RBS measurements suggest that layers are (2×1) close-packed and assess their stability against several rinsing procedures including exposure to 40% HF. A mechanism of grafting is discussed.

Jean Pinson

Papers

Attachment of organic layers to conductive or semiconductive surfaces by reduction of diazonium salts

Covalent Modification of Carbon Surfaces by Aryl Radicals Generated from the Electrochemical Reduction of Diazonium Salts

Covalent Modification of Carbon Surfaces by Grafting of Functionalized Aryl Radicals Produced from Electrochemical Reduction of Diazonium Salts

Electrografting: a powerful method for surface modification

Electrochemical Formation of Close-Packed Phenyl Layers on Si(111)