Ab initio molecular dynamics simulations of Aluminum solvation

The solvation of Al and its hydrolyzed species in water clusters has been studied by means of ab initio molecular dynamics simulations. The hexa-hydrate aluminum ion formed a stable complex in the finite temperature cluster simulation of one aluminum ion and 16 waters. The average dipole moment of strongly polarized hydrated water molecules in the first solvation shell of the hexa-hydrate aluminum ion was found to be 5.02 Debye. The deprotonated hexa-hydrate complex evolves into a tetra-coordinated aluminate ion with two water molecules in the second solvation shell forming hydrogen bonds to the hydroxyl groups in agreement with the observed coordination.Comment: 12 pages in Elsevier LaTeX, 5 figures in Postscript, 2 last figures are in color, submitted to Chemical Physics Letter

Advancing Inclusion in the Geosciences: An Overview of the NSF-GOLD Program

Here we report on five pilot projects working to develop effective professional development aimed at improving diversity, equity, and inclusion within the geosciences. All five projects were funded by the NSF GEO Opportunities for Leadership in Diversity (GOLD) program, which was designed to bring together geoscientists and social scientists to create innovative pilot programs for preparing and empowering geoscientists as change agents for increasing diversity. Each project has different objectives and applies different combinations of methods, but focuses on professional development, bystander intervention training, and the formation of new networks in the pursuit of systemic, institutional change. This article describes the origins, aims, and activities of these projects, and reflects on lessons learned to date. These projects are still ongoing, but in their first two years they have received more interest than anticipated and more demand than can be fulfilled, suggesting an unserved need in the field. We have also found that teams with varied backgrounds, experiences, and expertise are vital to overcoming common struggles in facing inequalities. Coaching from experts in diversity, equity, and inclusion keeps the teams motivated, particularly when many team members are accustomed to typical scientific research. Finally, institutional change requires time to catalyze, develop, and institutionalize, highlighting the importance of sustained effort over years

Chemically specifi C multiscale modeling of clay-polymer nanocomposites reveals intercalation dynamics, tactoid self-assembly and emergent materials properties

A quantitative description is presented of the dynamical process of polymer intercalation into clay tactoids and the ensuing aggregation of polymerentangled tactoids into larger structures, obtaining various characteristics of these nanocomposites, including clay-layer spacings, out-of-plane clay-sheet bending energies, X-ray diffractograms, and materials properties. This model of clay-polymer interactions is based on a three-level approach, which uses quantum mechanical and atomistic descriptions to derive a coarse-grained yet chemically specifi c representation that can resolve processes on hitherto inaccessible length and time scales. The approach is applied to study collections of clay mineral tactoids interacting with two synthetic polymers, poly(ethylene glycol) and poly(vinyl alcohol). The controlled behavior of layered materials in a polymer matrix is centrally important for many engineering and manufacturing applications. This approach opens up a route to computing the properties of complex soft materials based on knowledge of their chemical composition, molecular structure, and processing conditions.This work was funded in part by the EU FP7 MAPPER project (grant number RI-261507) and the Qatar National Research Fund (grant number 09–260–1–048). Supercomputing time was provided by PRACE on JUGENE (project PRA044), the Hartree Centre (Daresbury Laboratory) on BlueJoule and BlueWonder via the CGCLAY project, and on HECToR and ARCHER, the UK national supercomputing facility at the University of Edinburgh, via EPSRC through grants EP/F00521/1, EP/E045111/1, EP/I017763/1 and the UK Consortium on Mesoscopic Engineering Sciences (EP/L00030X/1). The authors are grateful to Professor Julian Evans for stimulating discussions during the course of this project. Data-storage and management services were provided by EUDAT (grant number 283304)

Activated carbons of varying pore structure eliminate the bioavailability of 2,3,7,8-tetrachlorodibenzo-p-dioxin to a mammalian (mouse) model

The use of activated carbon (AC) as an in situ sorbent amendment to sequester polychlorinated-dibenzo-p-dioxins and furans (PCDD/Fs) present in contaminated soils and sediments has recently gained attention as a novel remedial approach. This remedy could be implemented at much lower cost while minimizing habitat destruction as compared to traditional remediation technologies that rely on dredging/excavation and landfilling. Several prior studies have demonstrated the ability of AC amendments to reduce pore water concentrations and hence bioaccumulation of PCDD/Fs in invertebrate species. However, our recent study was the first to show that AC had the ability to sequester 2,3,7,8‑tetrachlorodibenzo‑p‑dioxin (TCDD) in a form that eliminated bioavailability to a mammalian (mouse) model. Here we show that three commercially available ACs, representing a wide range of pore size distributions, were equally effective in eliminating the bioavailability of TCDD based upon two sensitive bioassays, hepatic induction of cyp1A1 mRNA and immunoglobulin M antibody-forming cell response. These results provide direct evidence that a wide range of structurally diverse commercially available ACs may be suitable for use as in situ sorbent amendments to provide a cost-effective remedy for PCDD/F contaminated soils and sediments. Potentially, adaption of this technology would minimize habitat destruction and be protective of ecosystem and human health

Synthesis and evaluation of Fe3O4-impregnated activated carbon for dioxin removal

Polychlorinated dibenzo-p-dioxins and -furans (PCDD/PCDFs) are highly toxic organic pollutants in soils and sediments which persist over timescales that extend from decades to centuries. There is a growing need to develop effective technologies for remediating PCDD/Fs-contaminated soils and sediments to protect human and ecosystem health. The use of sorbent amendments to sequester PCDD/Fs has emerged as one promising technology. A synthesis method is described here to create a magnetic activated carbon composite (AC-Fe3O4) for dioxin removal and sampling that could be recovered from soils using magnetic separation. Six AC-Fe3O4 composites were evaluated (five granular ACs (GACs) and one fine-textured powder AC(PAC)) for their magnetization and ability to sequester dibenzo-p-dioxin (DD). Both GAC/PAC and GAC/PAC-Fe3O4 composites effectively removed DD from aqueous solution. The sorption affinity of DD for GAC-Fe3O4 was slightly reduced compared to GAC alone, which is attributed to the blocking of sorption sites. The magnetization of a GAC-Fe3O4 composite reached 5.38 emu/g based on SQUID results, allowing the adsorbent to be easily separated from aqueous solution using an external magnetic field. Similarly, a fine-textured PAC-Fe3O4 composite was synthesized with a magnetization of 9.3 emu/g

Bioavailability of clay-adsorbed dioxin to Sphingomonas wittichii RW1 and its associated genome-wide shifts in gene expression

Polychlorinated dibenzo-p-dioxins and dibenzofurans are a group of chemically-related pollutants categorically known as dioxins. Some of their chlorinated congeners are among the most hazardous pollutants that persist in the environment. This persistence is due in part to the limited number of bacteria capable of metabolizing these compounds, but also to their limited bioavailability in soil. We used Sphingomonas wittichii strain RW1 (RW1), one of the few strains able to grow on dioxin, to characterize its ability to respond to and degrade clay-bound dioxin. We found that RW1 grew on and completely degraded dibenzo-p-dioxin (DD) intercalated into the smectite clay saponite (SAP). To characterize the effects of DD sorption on RW1 gene expression, we compared transcriptomes of RW1 grown with either free crystalline DD or DD intercalated clay, i.e. sandwiched between the clay interlayers (DDSAP). Free crystalline DD appeared to cause greater expression of toxicity and stress related functions. Genes coding for heat shock proteins, chaperones, as well as genes involved in DNA repair, and efflux were up-regulated during growth on crystalline dioxin compared to growth on intercalated dioxin. In contrast, growth on intercalated dioxin up-regulated genes that might be important in recognition and uptake mechanisms, as well as surface interaction/attachment/biofilm formation such as extracellular solute-binding protein and LuxR. These differences in gene expression may reflect the underlying adaptive mechanisms by which RW1 cells sense and deploy pathways to access dioxin intercalated into clay. These data show that intercalated DD remains bioavailable to the degrading bacterium with implications for bioremediation alternatives

Periodic Density Functional Theory Investigation of the Uranyl Ion Sorption on Three Mineral Surfaces: A Comparative Study

Canister integrity and radionuclides retention is of prime importance for assessing the long term safety of nuclear waste stored in engineered geologic depositories. A comparative investigation of the interaction of uranyl ion with three different mineral surfaces has thus been undertaken in order to point out the influence of surface composition on the adsorption mechanism(s). Periodic DFT calculations using plane waves basis sets with the GGA formalism were performed on the TiO2(110), Al(OH)3(001) and Ni(111) surfaces. This study has clearly shown that three parameters play an important role in the uranyl adsorption mechanism: the solvent (H2O) distribution at the interface, the nature of the adsorption site and finally, the surface atoms’ protonation state

CATMoS: Collaborative Acute Toxicity Modeling Suite.

BACKGROUND: Humans are exposed to tens of thousands of chemical substances that need to be assessed for their potential toxicity. Acute systemic toxicity testing serves as the basis for regulatory hazard classification, labeling, and risk management. However, it is cost- and time-prohibitive to evaluate all new and existing chemicals using traditional rodent acute toxicity tests. In silico models built using existing data facilitate rapid acute toxicity predictions without using animals. OBJECTIVES: The U.S. Interagency Coordinating Committee on the Validation of Alternative Methods (ICCVAM) Acute Toxicity Workgroup organized an international collaboration to develop in silico models for predicting acute oral toxicity based on five different end points: Lethal Dose 50 (LD50 value, U.S. Environmental Protection Agency hazard (four) categories, Globally Harmonized System for Classification and Labeling hazard (five) categories, very toxic chemicals [LD50 (LD50≤50mg/kg)], and nontoxic chemicals (LD50>2,000mg/kg). METHODS: An acute oral toxicity data inventory for 11,992 chemicals was compiled, split into training and evaluation sets, and made available to 35 participating international research groups that submitted a total of 139 predictive models. Predictions that fell within the applicability domains of the submitted models were evaluated using external validation sets. These were then combined into consensus models to leverage strengths of individual approaches. RESULTS: The resulting consensus predictions, which leverage the collective strengths of each individual model, form the Collaborative Acute Toxicity Modeling Suite (CATMoS). CATMoS demonstrated high performance in terms of accuracy and robustness when compared with in vivo results. DISCUSSION: CATMoS is being evaluated by regulatory agencies for its utility and applicability as a potential replacement for in vivo rat acute oral toxicity studies. CATMoS predictions for more than 800,000 chemicals have been made available via the National Toxicology Program's Integrated Chemical Environment tools and data sets (ice.ntp.niehs.nih.gov). The models are also implemented in a free, standalone, open-source tool, OPERA, which allows predictions of new and untested chemicals to be made. https://doi.org/10.1289/EHP8495

Molecular dynamics simulation of humic substances

© 2014, Orsi. Humic substances (HS) are complex mixtures of natural organic material which are found almost everywhere in the environment, and particularly in soils, sediments, and natural water. HS play key roles in many processes of paramount importance, such as plant growth, carbon storage, and the fate of contaminants in the environment. While most of the research on HS has been traditionally carried out by conventional experimental approaches, over the past 20 years complementary investigations have emerged from the application of computer modeling and simulation techniques. This paper reviews the literature regarding computational studies of HS, with a specific focus on molecular dynamics simulations. Significant achievements, outstanding issues, and future prospects are summarized and discussed