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

Nitrogen heterocycles are among the most significant structural components of pharmaceuticals. Analysis of our database of U.S. FDA approved drugs reveals that 59% of unique small-molecule drugs contain a nitrogen heterocycle. In this review we report on the top 25 most commonly utilized nitrogen heterocycles found in pharmaceuticals. The main part of our analysis is divided into seven sections: (1) three- and four-membered heterocycles, (2) five-, (3) six-, and (4) seven- and eight-membered heterocycles, as well as (5) fused, (6) bridged bicyclic, and (7) macrocyclic nitrogen heterocycles. Each section reveals the top nitrogen heterocyclic structures and their relative impact for that ring type. For the most commonly used nitrogen heterocycles, we report detailed substitution patterns, highlight common architectural cores, and discuss unusual or rare structures.

Analysis of the Structural Diversity, Substitution Patterns, and Frequency of Nitrogen Heterocycles among U.S. FDA Approved Pharmaceuticals

Arsenic removal from water/wastewater using adsorbents—A critical review

Hydrogel delivery systems can leverage therapeutically beneficial outcomes of drug delivery and have found clinical use. Hydrogels can provide spatial and temporal control over the release of various therapeutic agents, including small-molecule drugs, macromolecular drugs and cells. Owing to their tunable physical properties, controllable degradability and capability to protect labile drugs from degradation, hydrogels serve as a platform in which various physiochemical interactions with the encapsulated drugs control their release. In this Review, we cover multiscale mechanisms underlying the design of hydrogel drug delivery systems, focusing on physical and chemical properties of the hydrogel network and the hydrogel-drug interactions across the network, mesh, and molecular (or atomistic) scales. We discuss how different mechanisms interact and can be integrated to exert fine control in time and space over the drug presentation. We also collect experimental release data from the literature, review clinical translation to date of these systems, and present quantitative comparisons between different systems to provide guidelines for the rational design of hydrogel delivery systems.

/pdf/designing-hydrogels-for-controlled-drug-delivery-3k03j5j2j9.pdf

Designing hydrogels for controlled drug delivery.

Arsenic derived from natural sources occurs in groundwater in many countries, affecting the health of millions of people. The combined effects of As(V) reduction and diagenesis of iron oxide minerals on arsenic mobility are investigated in this study by comparing As(V) and As(III) sorption onto amorphous iron oxide (HFO), goethite, and magnetite at varying solution compositions. Experimental data are modeled with a diffuse double layer surface complexation model, and the extracted model parameters are used to examine the consistency of our results with those previously reported. Sorption of As(V) onto HFO and goethite is more favorable than that of As(III) below pH 5−6, whereas, above pH 7−8, As(III) has a higher affinity for the solids. The pH at which As(V) and As(III) are equally sorbed depends on the solid-to-solution ratio and type and specific surface area of the minerals and is shifted to lower pH values in the presence of phosphate, which competes for sorption sites. The sorption data indicate tha...

Comparison of arsenic(V) and arsenic(III) sorption onto iron oxide minerals: implications for arsenic mobility.

Methods of soil analysis. Part 3 - chemical methods.

https://pubag.nal.usda.gov/download/27113/PDF

Mechanisms of Arsenic Adsorption on Amorphous Oxides Evaluated Using Macroscopic Measurements, Vibrational Spectroscopy, and Surface Complexation Modeling.

To more fully understand the potential for transport of nitroaromatic compounds in soils and subsoils, the adsorption of a series of para- and meta-substituted nitrobenzenes (SNBs) by K-smectite clay was measured. Adsorption isotherms were fit to the Freundlich equation, and the resultant Freundlich adsorption coefficients (log(Kf)) were positively correlated with the Hammett substituent constant (r2 = 0.80). This relationship and a positive reaction constant (ρ = 1.15) indicate that the adsorption reaction is favored by electron-withdrawing substituents. These results are consistent with an electron donor (smectite)−acceptor (substituted nitrobenzene) mechanism offered previously. However, quantum calculations did not reveal any systematic relationship between the Hammett constant and the electron density on the aromatic ring, which would explain a donor−acceptor relationship. Rather, electron density donated by a second substituent on nitrobenzene appears to be appropriated by the nitro group leaving ri...

Mechanisms for the adsorption of substituted nitrobenzenes by smectite clays.

Soil organic matter (SOM) is often considered the dominant sorptive phase for organic contaminants and pesticides in soil-water systems. This is evidenced by the widespread use of organic-matter-normalized sorption coefficients (K(OM)) to predict soil-water distribution of pesticides, an approach that ignores the potential contribution of soil minerals to sorption. To gain additional perspective on the potential contributions of clays and SOM to pesticide retention in soils, we measured sorption of seven pesticides by a K-saturated reference smectite clay (SWy-2) and SOM (represented by a muck soil). In addition, we measured the adsorption of atrazine by five different K-saturated smectites and Ca-saturated SWy-2. On a unit mass basis, the K-SWy-2 clay was a more effective sorbent than SOM for 4,6-dinitro-o-cresol (DNOC), dichlobenil, and carbaryl of the seven pesticides evaluated, of which, DNOC was sorbed to the greatest extent. Atrazine was sorbed to a similar extent by K-SWy-2 and SOM. Parathion, diuron, and biphenyl were sorbed to a greater extent by SOM than by K-SWy-2. Atrazine was adsorbed by Ca-SWy-2 to a much lesser extent than by K-SWy-2. This appears to be related to the larger hydration sphere of Ca(2+) (compared to that of K(+)) which shrinks the effective size of the adsorption domains between exchangeable cations, and which expands the clay layers beyond the apparently optimal spacing of approximately 12.2 A for sorption of aromatic pesticide structures. Although a simple relation between atrazine adsorption by different K-smectites and charge properties of clay was not observed, the highest charge clay was the least effective sorbent; a higher charge density would result in a loss of adsorption domains. These results indicate that for certain pesticides, expandable soil clays have the potential to be an equal or dominant sorptive phase when compared to SOM for pesticide retention in soil.

Potential contributions of smectite clays and organic matter to pesticide retention in soils.

This chapter on surface and interface chemistry of clay minerals follows a bottom-up approach. It starts with the properties of surface oxygens and hydrogens as influenced by chemical composition and structure. Then, three types of surfaces are described: surfaces with a permanent charge, neutral siloxane surfaces and hydroxyl surfaces. The remaining part of the chapter is devoted to a discussion of the interaction of these surfaces with water, dye molecules, and transition metal ion complexes with emphasis on chiral clay minerals and proteins. The chapter ends with the synthesis of hybrid films, consisting of alternating layers of clay minerals and cationic polyelectrolytes, amphiphilic alkylammonium cations, amphiphilic cationic dyes, or cationic proteins. These films are discussed in the light of the preparation of advanced functional materials.

Cliff T. Johnston

Papers

Methods of soil analysis. Part 3 - chemical methods.

Mechanisms of Arsenic Adsorption on Amorphous Oxides Evaluated Using Macroscopic Measurements, Vibrational Spectroscopy, and Surface Complexation Modeling.

Mechanisms for the adsorption of substituted nitrobenzenes by smectite clays.

Potential contributions of smectite clays and organic matter to pesticide retention in soils.

Surface and Interface Chemistry of Clay Minerals