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

All cyanobacteria, algae, and plants use a similar water-oxidizing catalyst for water oxidation. This catalyst is housed in Photosystem II, a membrane-protein complex that functions as a light-driven water oxidase in oxygenic photosynthesis. Water oxidation is also an important reaction in artificial photosynthesis because it has the potential to provide cheap electrons from water for hydrogen production or for the reduction of carbon dioxide on an industrial scale. The water-oxidizing complex of Photosystem II is a Mn–Ca cluster that oxidizes water with a low overpotential and high turnover frequency number of up to 25–90 molecules of O2 released per second. In this Review, we discuss the atomic structure of the Mn–Ca cluster of the Photosystem II water-oxidizing complex from the viewpoint that the underlying mechanism can be informative when designing artificial water-oxidizing catalysts. This is followed by consideration of functional Mn-based model complexes for water oxidation and the issue of Mn com...

Manganese Compounds as Water-Oxidizing Catalysts: From the Natural Water-Oxidizing Complex to Nanosized Manganese Oxide Structures

Modeling and simulation of cement hydration kinetics and microstructure development

Following Nature's lessons, today chemists can cross the boundary of the small molecule world to construct multifunctional and highly complex molecular nano-objects up to protein size and even cell-like nanosystems showing responsive sensing. Impressive examples emerge from studies of the solutions of some oxoanions of the early transition metals especially under reducing conditions which enable the controlled linking of metal-oxide building blocks. The latter are available from constitutional dynamic libraries, thus providing the option to generate multifunctional unique nanoscale molecular systems with exquisite architectures, which even opens the way towards adaptive and evolutive (Darwinian) chemistry. The present review presents the first comprehensive report of current knowledge (including synthesis aspects not discussed before) regarding the related giant metal-oxide clusters mainly of the type {Mo57M′6} (M′ = FeIII, VIV) (torus structure), {M72M′30} (M = Mo, M′ = VIV, CrIII, FeIII, MoV), {M72Mo60} (M = Mo, W) (Keplerates), {Mo154}, {Mo176}, {Mo248} (“big wheels”), and {Mo368} (“blue lemon”) – all having the important transferable pentagonal {(M)M5} groups in common. These discoveries expanded the frontiers of inorganic chemistry to the mesoscopic world, while there is probably no collection of discrete inorganic compounds which offers such a versatile chemistry and the option to study new phenomena of interdisciplinary interest. The variety of different properties of the sphere- and wheel-type metal-oxide-based clusters can directly be related to their unique architectures: The spherical Keplerate-type capsules having 20 crown-ether-type pores and tunable internal functionalities allow the investigation of confined matter as well as that of sphere-surface-supramolecular and encapsulation chemistry – including related new aspects of the biologically important hydrophobic effects – but also of nanoscale ion transport and separation. The wheel-type molybdenum-oxide clusters exhibiting complex landscapes do not only have well-defined reaction sites but also show unprecedented adaptability regarding the integration of various kinds of matter. Applications in different fields, e.g. in materials science and catalysis including those in small spaces, investigated by several groups, are discussed while possible directions for future work are outlined.

From linking of metal-oxide building blocks in a dynamic library to giant clusters with unique properties and towards adaptive chemistry

The ubiquity of aqueous solutions in contact with charged surfaces and the realization that the molecular-level details of water–surface interactions often determine interfacial functions and properties relevant in many natural processes have led to intensive research. Even so, many open questions remain regarding the molecular picture of the interfacial organization and preferential alignment of water molecules, as well as the structure of water molecules and ion distributions at different charged interfaces. While water, solutes and charge are present in each of these systems, the substrate can range from living tissues to metals. This diversity in substrates has led to different communities considering each of these types of aqueous interface. In this Review, by considering water in contact with metals, oxides and biomembranes, we show the essential similarity of these disparate systems. While in each case the classical mean-field theories can explain many macroscopic and mesoscopic observations, it soon becomes apparent that such theories fail to explain phenomena for which molecular properties are relevant, such as interfacial chemical conversion. We highlight the current knowledge and limitations in our understanding and end with a view towards future opportunities in the field. What do a rock in a river, a red blood cell in our body and the electrodes inside a car battery have in common? Charged surfaces in contact with water. Although a unified approach to study such a variety of systems is not available yet, the current understanding — even with its limitations — paves the road to the development of new concepts and techniques.

/pdf/water-at-charged-interfaces-fan1z241aq.pdf

Water at charged interfaces

Large aqueous oxide ions as minerals! Minerals dissolve by repeated ligand exchange reactions and geochemists use polyoxometalate ions to establish structure-reactivity relations for environmentally important functional groups. Here, for example, are plotted the dissolution rates of two classes of minerals against rates of solvent exchanges around the corresponding aquo ions.Geochemists and environmental chemists make predictions about the fate of chemicals in the shallow earth over enormously long times. Key to these predictions is an understanding of the hydrolytic and complexation reactions at oxide mineral surfaces that are difficult to probe spectroscopically. These minerals are usually oxides with repeated structural motifs, like silicate or aluminosilicate polymers, and they expose a relatively simple set of functional groups to solution. The geochemical community is at the forefront of efforts to describe the surface reactivities of these interfacial functional groups and some insights are being acquired by using small oligomeric oxide molecules as experimental models. These small nanometer-size clusters are not minerals, but their solution structures and properties are better resolved than for minerals and calculations are relatively well constrained. The primary experimental data are simple rates of steady oxygen-isotope exchanges into the structures as a function of solution composition that can be related to theoretical results. There are only a few classes of large oxide ions for which data have been acquired and here we review examples and illustrate the general approach, which also derives directly from the use of model clusters to understand for the active core of metalloenzymes in biochemistry.

Minerals as Molecules—Use of Aqueous Oxide and Hydroxide Clusters to Understand Geochemical Reactions

The structure of water and its dynamics affect a number of fundamental properties of an interface. Yet, these properties are often inaccessible experimentally and computational studies including solvent are comparatively few. Here, we estimate the structure and kinetics of water exchange of aqueous barium ions and barium ions within the {001} barite surface using molecular dynamics and the reactive flux method. For the aqueous ion, the Ba−O distance to water in the first hydration shell was found to be 280 pm with a coordination number of 8.3, and the best estimate of the exchange rate constant is 4.8 × 109 s-1, closely matching experimental estimates. For the barite surface, the first shell water distance was 282 pm, with a coordination number of 0.9 and the best estimate of the rate constant for exchange is 1.7 × 1010 s-1, 3.5 times faster than that of the aqueous ion.

Structure and Dynamics of Water on Aqueous Barium Ion and the {001} Barite Surface

The activation volume of water exchange around Li+ (aq) was determined from reactive flux calculations using molecular dynamics simulations with a classical force field. The barrier height for exchange decreases with pressure, giving a negative activation volume, in agreement with the current paradigm for inferring exchange mechanism from activation volume. However, it is also demonstrated that pressure-dependent transmission effects make a significant contribution to the overall activation volume. These calculations indicate that small activation volumes should not be regarded as mechanistically indicative because of the potential contributions from transmission effects.

Molecular dynamics calculation of the activation volume for water exchange on Li

The surface morphology of the {100} face growth hillock of potassium dihydrogen phosphate (KDP) is examined through first-principles calculations and using periodic-bonded-chain (PBC) theory. KDP, or archerite ([K, NH 4 ]H 2 PO 4 ), is used extensively in industry and is an excellent model for more complicated materials that have considerable ionic and hydrogen bonding as part of their structure. Here, we have calculated the gas-phase detachment energies of KH 2 PO 4 growth units adsorbed to steps oriented normal to the [010] and [001] PBC directions. The detachment energies of growth units adsorbed to the two different terminations of the {010}-facing step are +4.2 and +4.5 eV, and detachment from the {001}-facing step is +3.8 eV. Detachment from the {010}-facing step is more unfavorable, indicating that the adsorbed species will be less labile and the step will advance more quickly than the {001}-facing step. The relative detachment energies are qualitatively consistent with experimentally observed fast and slow step velocities on the {100} growth hillock. Detachment energies of growth units adsorbed subsequently to the {010}-facing step are similar, but detachment of a second growth unit from the {001}-facing step is much more unfavorable, +5.1 eV. The increase in detachment energy indicates that the high rate of detachment of the initial KH 2 PO 4 unit from the {001}-facing step may limit the advance of the step, whereas the second growth unit detaches much more slowly. To explain this behavior, we propose that the first growth unit adsorbed to the {001 }-facing step has a higher lability because of the lack of hydrogen bonds to the step edge. This study provides a qualitative picture of how crystal structure may control growth morphology of KDP and emphasizes the importance of anisotropic hydrogen bonding in the system.

The growth morphology of the {100} surface of KDP (archerite) on the molecular scale

We carried out a series of molecular dynamics simulations of the hydrolysis of a model trivalent metal ion in aqueous solution. We use a dissociative model for water and examine the spontaneous speciation of M3+ into M(OH)n(3-n)+ (n =1,4) both in neutral solution and as a function of added protons and hydroxide ions. The species distributions in neutral solution correspond reasonably well with those expected for real trivalent metal ions at neutral pH. However, the change in the species distributions as a function of either added protons or hydroxide ions is much less than expected with very large concentrations of protons or hydroxide ions required to shift the species equilibria in either direction. The influence of added protons and hydroxide ions on the species distributions appears to be proportional to the average charge of the hydrolysis couples, being highest for the 3+/2+ couple and lowest for the 1+/0 and 0/1- couples. Proton exchange rates vary with proton/hydroxide ion concentration giving a minimum at intermediate values ([H+]≈ 0.166) with increasing rates at both lower and higher pH.

A molecular dynamics investigation of the titration of a trivalent aqueous ion

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