Effect-based monitoring of two rivers under urban and agricultural influence reveals a range of biological activities in sediment and water extracts.

Chemical contaminants, such as pesticides, pharmaceuticals and industrial compounds are ubiquitous in surface water and sediment in areas subject to human activity. While targeted chemical analysis is typically used for water and sediment quality monitoring, there is growing interest in applying effect-based methods with in vitro bioassays to capture the effects of all active contaminants in a sample. The current study evaluated the biological effects in surface water and sediment from two contrasting catchments in Aotearoa New Zealand, the highly urbanised Whau River catchment in Tamaki Makaurau (Auckland) and the urban and mixed agricultural Koreti (New River) Estuary catchment. Two complementary passive sampling devices, Chemcatcher for polar chemicals and polyethylene (PED) for non-polar chemicals, were applied to capture a wide range of contaminants in water, while composite sediment samples were collected at each sampling site. Bioassays indicative of induction of xenobiotic metabolism, receptor-mediated effects, genotoxicity, cytotoxicity and apical effects were applied to the water and sediment extracts. Most sediment extracts induced moderate to strong estrogenic and aryl hydrocarbon (AhR) activity, along with moderate toxicity to bacteria. The water extracts showed similar patterns to the sediment extracts, but with lower activity. Generally, the polar Chemcatcher extracts showed greater estrogenic activity, photosynthesis inhibition and algal growth inhibition than the non-polar PED extracts, though the PED extracts showed greater AhR activity. The observed effects in the water extracts were compared to available ecological effect-based trigger values (EBT) to evaluate the potential risk. For the polar extracts, most sites in both catchments exceeded the EBT for estrogenicity, with many sites exceeding the EBTs for AhR activity and photosynthesis inhibition. Of the wide range of endpoints considered, estrogenic activity, AhR activity and herbicidal activity appear to be the primary risk drivers in both the Whau and Koreti Estuary catchments.

Quantum Chemistry Common Driver and Databases (QCDB) and Quantum Chemistry Engine (QCEngine): Automation and interoperability among computational chemistry programs.

Community efforts in the computational molecular sciences (CMS) are evolving toward modular, open, and interoperable interfaces that work with existing community codes to provide more functionality and composability than could be achieved with a single program. The Quantum Chemistry Common Driver and Databases (QCDB) project provides such capability through an application programming interface (API) that facilitates interoperability across multiple quantum chemistry software packages. In tandem with the Molecular Sciences Software Institute and their Quantum Chemistry Archive ecosystem, the unique functionalities of several CMS programs are integrated, including CFOUR, GAMESS, NWChem, OpenMM, Psi4, Qcore, TeraChem, and Turbomole, to provide common computational functions, i.e., energy, gradient, and Hessian computations as well as molecular properties such as atomic charges and vibrational frequency analysis. Both standard users and power users benefit from adopting these APIs as they lower the language barrier of input styles and enable a standard layout of variables and data. These designs allow end-to-end interoperable programming of complex computations and provide best practices options by default.

Recent developments in the general atomic and molecular electronic structure system.

A discussion of many of the recently implemented features of GAMESS (General Atomic and Molecular Electronic Structure System) and LibCChem (the C++ CPU/GPU library associated with GAMESS) is presented. These features include fragmentation methods such as the fragment molecular orbital, effective fragment potential and effective fragment molecular orbital methods, hybrid MPI/OpenMP approaches to Hartree-Fock, and resolution of the identity second order perturbation theory. Many new coupled cluster theory methods have been implemented in GAMESS, as have multiple levels of density functional/tight binding theory. The role of accelerators, especially graphical processing units, is discussed in the context of the new features of LibCChem, as it is the associated problem of power consumption as the power of computers increases dramatically. The process by which a complex program suite such as GAMESS is maintained and developed is considered. Future developments are briefly summarized.

Application of a semi-empirical dispersion correction for modeling water clusters.

The Grimme-D3 semi-empirical dispersion energy correction has been implemented for the original effective fragment potential for water (EFP1), and for systems that contain water molecules described by both correlated ab initio quantum mechanical (QM) molecules and EFP1. Binding energies obtained with these EFP1-D and QM/EFP1-D methods were tested using 27 benchmark species, including neutral, protonated, deprotonated, and auto-ionized water clusters and nine solute-water binary complexes. The EFP1-D and QM/EFP1-D binding energies are compared with those obtained using fully QM methods: second-order perturbation theory, and coupled cluster theory, CCSD(T), at the complete basis set (CBS) limit. The results show that the EFP1-D and QM/EFP1-D binding energies are in good agreement with CCSD(T)/CBS binding energies with a mean absolute error of 5.9 kcal/mol for water clusters and 0.8 kcal/mol for solute-water binary complexes. © 2018 Wiley Periodicals, Inc.

Acute waterborne cadmium toxicity in the estuarine pulmonate mud snail, Amphibola crenata.

Freshwater pulmonate snails are sensitive to trace metals, but to date, the sensitivity of estuarine pulmonate snails to these important environmental toxicants is undescribed. Using the estuarine mud snail Amphibola crenata, effects of a 48-h exposure to waterborne cadmium (Cd) were investigated. The 48-h median lethal concentration (LC50) was 50.4 mg L-1, a value higher than that previously reported for any gastropod mollusc. Cadmium levels in the tissues of mud snails were highest in the viscera (digestive gland and gonad), with the foot muscle and remaining tissue compartment (kidney, mantle, remaining digestive tissues and heart) displaying significantly lower concentrations. Over a Cd exposure concentration range of 0-32 mg L-1, Amphibola exhibited reduced oxygen consumption and elevated ammonia excretion in response to increasing Cd, the latter effect likely reflecting a switch to protein metabolism. This finding was supported by a declining oxygen: nitrogen ratio (O:N) as exposure Cd concentration increased. Other energy imbalances were noted, with a decrease in tissue glycogen (an effect strongly correlated with Cd burden in the viscera and foot muscle) and an elevated haemolymph glucose observed. An increase in catalase activity in the visceral tissues was recorded, suggestive of an effect of Cd on oxidative stress. The magnitude of this effect was correlated with tissue Cd burden. The induction of antioxidant defence mechanisms likely prevented an increase in levels of lipid peroxidation, which were unchanged relative to Cd exposure concentration in all measured tissues.

ParFit: A Python-Based Object-Oriented Program for Fitting Molecular Mechanics Parameters to ab Initio Data.

A newly created object-oriented program for automating the process of fitting molecular-mechanics parameters to ab initio data, termed ParFit, is presented. ParFit uses a hybrid of deterministic and stochastic genetic algorithms. ParFit can simultaneously handle several molecular-mechanics parameters in multiple molecules and can also apply symmetric and antisymmetric constraints on the optimized parameters. The simultaneous handling of several molecules enhances the transferability of the fitted parameters. ParFit is written in Python, uses a rich set of standard and nonstandard Python libraries, and can be run in parallel on multicore computer systems. As an example, a series of phosphine oxides, important for metal extraction chemistry, are parametrized using ParFit. ParFit is in an open source program available for free on GitHub ( https://github.com/fzahari/ParFit ).

Mature leaf concentrate of Sri Lankan wild type Carica papaya Linn. modulates nonfunctional and functional immune responses of rats.

BACKGROUND: The leaf concentrate of Carica papaya is a traditionally acclaimed immunomodulatory remedy against numerous diseases; nonetheless comprehensive scientific validation of this claim is limited. The present study thus investigated the immunomodulatory potential of Carica papaya mature leaf concentrate (MLCC) of the Sri Lankan wild type cultivar using nonfunctional and functional immunological assays. METHODS: Wistar rats (N = 6/ group) were orally gavaged with 3 doses (0.18, 0.36 and 0.72 ml/100g body weight) of the MLCC once daily for 3 consecutive days. Selected nonfunctional (enumeration of immune cells and cytokine levels) and functional (cell proliferation and phagocytic activity) immunological parameters, and acute toxic effects were determined using standard methods. Effect of the MLCC (31.25, 62.5, 125, 250, 500 and 1000 µg/ml) on ex vivo proliferation of bone marrow cells (BMC) and splenocytes (SC), and in vitro phagocytic activity of peritoneal macrophages (PMs), and their corresponding cytokine responses were evaluated. The phytochemical profile of the MLCC was established using liquid chromatography-mass spectrometry (LS-MS) and Gas chromatography-mass spectrometry (GC-MS). RESULTS: Counts of rat platelets, total leukocytes, lymphocyte and monocyte sub populations, and BMCs were significantly augmented by oral gavage of the MLCC (p < 0.05). The highest MLCC dose tested herein significantly reduced pro inflammatory cytokines, Interleukin 6 (IL-6) and Tumor Necrosis Factor α (TNF α) levels of rats (p < 0.05). The in vivo phagocytic index of rat PMs significantly increased by oral gavage of all three doses of the MLCC (p < 0.05). In vitro phagocytic activity of rat PMs were enhanced by the MLCC and triggered a Th1 biased cytokine response. The MLCC at low concentrations elicited ex vivo proliferation of BMC (31.25 µg/ml) and SC (31.25 and 62.5 µg/ml) respectively. Conversely, high concentrations (500 and 1000 µg/ml) exhibited cytotoxicity of both BMC and SC with significant modulation of cytokines. Chemical profile of the MLCC revealed the presence of several immunomodulatory compounds. The oral gavage of the MLCC was found to be safe in terms of both hepatic and renal toxicities. CONCLUSION: The present study established that the mature leaf concentrate (MLCC) of Carica papaya Sri Lankan wild type cultivar is orally active, safe and effectively modulates nonfunctional and functional immunological parameters of rats that unequivocally corroborate the traditional medical claims.

Conformations of Organophosphine Oxides.

The conformations of a series of organophosphine oxides, OP(CH3)2R, where R = methyl, ethyl, isopropyl, tert-butyl, vinyl, and phenyl, are predicted using the MP2/cc-pVTZ level of theory. Comparison of potential energy surfaces for rotation about P-C bonds with crystal structure data reveals a strong correlation between predicted location and energetics of minima and histograms of dihedral angle distributions observed in the solid state. In addition, the most stable conformers are those that minimize the extent of steric repulsion between adjacent rotor substituents, and the torsional barriers tend to increase with the steric bulk of the rotating alkyl group. MM3 force field parameters were adjusted to fit the MP2 results, providing a fast and accurate model for predicting organophosphine oxides shapes-an essential part of understanding the chemistry of these compounds. The predictive power of the modified MM3 model was tested against MP2/cc-pVTZ conformations for triethylphosphine oxide, OP(CH2CH3)3, and triphenylphosphine oxide, OP(Ph)3.

Assessment of Amphibola crenata as a bioindicator of estuarine trace element pollution using biochemical and physiological endpoints.

To assess its utility as a bioindicator of estuarine contamination, Amphibola crenata, a pulmonate mud snail, was collected from 17 estuaries in New Zealand. Whole-body soft tissue trace element concentrations were measured via quadrupole inductively coupled plasma mass spectrophotometer (Q-ICP-MS) and were found to be significantly positively correlated with sediment trace element profiles for arsenic, copper and lead. Snails from polluted estuaries generally displayed higher ammonia excretion rates, elevated whole-body soft tissue catalase activity and lipid peroxidation compared to snails from reference sites. Across all sites haemolymph glucose was positively correlated with the tissue burdens of arsenic, copper, nickel and zinc, while haemolymph protein was negatively correlated with arsenic, cadmium and zinc soft tissue concentrations, indicative of altered energy metabolism associated with trace element contamination. Overall, sites were distinguishable by application of the array of measures employed. Our findings suggest that gastropods have significant value as bioindicators of estuarine health.

Solvent induced shifts in the UV spectrum of amides.

Solvent effects on the electronic spectra of formamide and trans-N-methylacetamide are studied using four different levels of theory: singly excited configuration interaction (CIS), equations of motion coupled-cluster theory with singles and doubles (EOM-CCSD), completely renormalized coupled-cluster theory with singles and doubles with perturbative triple excitations (CR-EOM-CCSD(T)), and time-dependent density functional theory (TDDFT), employing small clusters of water molecules. The simulated electronic spectrum is obtained via molecular dynamics simulations with 100 waters modeled with the effective fragment potential method and exhibits a blue-shift and red-shift, respectively, for the n → π* and πnb → π* vertical excitation energies, in good agreement with the experimental electronic spectra of amides.

Physiological and biochemical responses of the estuarine pulmonate mud snail, Amphibola crenata, sub-chronically exposed to waterborne cadmium.

Physiological and biochemical responses of the pulmonate mud snail, Amphibola crenata, to waterborne cadmium (Cd) were investigated to determine the mechanisms of toxicity and impacts of a 21-d Cd exposure. Mud snails were exposed to nominal Cd concentrations of 0, 0.2, 4 and 8 mg L - 1 and bioaccumulation, whole animal physiological (oxygen consumption, ammonia excretion and oxygen:nitrogen), and tissue level biochemical (catalase activity, lipid peroxidation, glycogen, glucose and protein) endpoints were measured every 7 days. At the two highest Cd exposure concentrations complete mortality was observed over 21-d. In surviving animals, oxygen consumption declined and ammonia excretion rate increased with Cd exposure concentration and duration. The increased ammonia excretion likely reflected enhanced protein metabolism as suggested by a reduced oxygen:nitrogen (O:N). Increasing waterborne Cd concentration and exposure time led to increasing metal accumulation in all tissues. The snail viscera showed the highest Cd accumulation. Both catalase activity and lipid peroxidation in the viscera significantly increased with Cd exposure concentration and time, whereas, the foot muscle and remaining tissues (kidney, mantle, remaining digestive tissues and heart) showed increased catalase activity and lipid peroxidation at higher Cd concentrations (4 and 8 mg L - 1), suggestive of an effect of Cd on oxidative stress. Over the course of 21 days, Cd exposure resulted in significantly lower levels of glycogen in viscera relative to Cd-free controls, reflecting an increased energy demand. Haemolymph glucose rose initially and then fell with increased exposure duration, while haemolymph protein generally exhibited an increased concentration in Cd-exposure groups, reflecting the changes in energy substrates noted for somatic tissues. These results suggest that the physiological and biochemical responses of A. crenata to Cd are conserved relative to other aquatic animals, and were tissue-specific, dose- and time-dependant.

Anharmonicity of weakly bound Li(+)-(H2)n (n = 1-3) complexes.

The anharmonicity of Li(+)-(H(2))(n) (n = 1, 2, and 3) complexes is studied using the vibrational self-consistent field (VSCF) approach. The H-H stretching frequency shifts of Li(+)-(H(2))(n) complexes are calculated with the coupled-cluster method including all single and double excitations with perturbative triples (CCSD(T)) level of theory with the cc-pVTZ basis set. The calculated IR active H-H stretching frequency in Li(+)-H(2), Li(+)-(H(2))(2) and Li(+)-(H(2))(3) is red-shifted by 121, 109, and 96-99 cm(-1), respectively, relative to that of isolated H(2). The calculated red shifts and their trends are in good agreement with the available experimental data.

The relationship between population attributes of the mud snail Amphibola crenata and sediment contamination: A multi-estuary assessment.

This study assessed the potential of the New Zealand mud snail Amphibola crenata to act as a bioindicator of contaminated estuarine sediment. Seventeen sites with varying contaminant burdens were identified within six New Zealand regions. Attributes (population density, individual length distribution and individual dry weight condition index) were measured for field-collected A. crenata, and related to measurements of sediment trace metals and nutrients. Population density of the mud snail was relatively high in sites with elevated nutrients and organic matter. The length distribution of A. crenata showed significant regional and site-specific variations. Minimum, mean, and median shell length of A. crenata were positively correlated with sediment cadmium and zinc concentration. Overall, the sites were able to be distinguished by A. crenata population attributes and the sediment metal and nutrient content. These results suggest that A. crenata population information has potential value for assessing estuarine sediment metal and nutrient contamination.

Anharmonicity of weakly bound M(+)-H2 complexes.

The anharmonicity of weakly bound complexes is studied using the vibrational self-consistent field (VSCF) approach for a series of metal cation dihydrogen (M(+)-H(2)) complexes. The H-H stretching frequency shifts of M(+)-H(2) (M(+) = Li(+), Na(+), B(+), and Al(+)) complexes are calculated with the coupled-cluster method including all single and double excitations with perturbative triples (CCSD(T)) level of theory with the cc-pVTZ basis set. The calculated H-H stretching frequency of Li(+)-H(2), B(+)-H(2), Na(+)-H(2), and Al(+)-H(2) is red-shifted by 121, 202, 74, and 62 cm(-1), respectively, relative to that of unbound H(2). The calculated red shifts and their trends are in good agreement with the available experimental and previously calculated data. Insight into the observed trends is provided by symmetry adapted perturbation theory (SAPT).

Implementation of the analytic energy gradient for the combined time-dependent density functional theory/effective fragment potential method: application to excited-state molecular dynamics simulations.

Excited-state quantum mechanics/molecular mechanics molecular dynamics simulations are performed, to examine the solvent effects on the fluorescence spectra of aqueous formaldehyde. For that purpose, the analytical energy gradient has been derived and implemented for the linear-response time-dependent density functional theory (TDDFT) combined with the effective fragment potential (EFP) method. The EFP method is an efficient ab initio based polarizable model that describes the explicit solvent effects on electronic excitations, in the present work within a hybrid TDDFT/EFP scheme. The new method is applied to the excited-state MD of aqueous formaldehyde in the n-π* state. The calculated π*→n transition energy and solvatochromic shift are in good agreement with other theoretical results.

Molecular Recognition at Mineral Interfaces: Implications for the Beneficiation of Rare Earth Ores.

Ce-bastnäsite is the single largest mineral source for light rare-earth elements. In view of the growing industrial importance of rare-earth minerals, it is critical to develop more efficient methods for separating the valuable rare-earth-containing minerals from the surrounding gangue. In this work, we employ a combination of periodic density functional theory (DFT) and molecular mechanics (MM) calculations together with the de novo molecular design program HostDesigner to identify bis-phosphinate ligands that preferentially bind to the (100) Ce-bastnäsite surface rather than the (104) calcite surface. DFT calculations for a simple phosphinate ligand were employed to qualitatively understand key behaviors involved in ligand-metal, ligand-solvent, and solvent-metal interactions. These insights were then used to guide the search for flexible, rigid, and semirigid hydrocarbon linkers to identify candidate bis-phosphinate ligands with the potential to bind preferentially to Ce-bastnäsite. Among the five most promising bis-phosphinate ligands suggested by theoretical studies, three ligands were synthesized and their adsorption characteristics to bastnäsite (100) interfaces were characterized using vibrational sum-frequency (vSFG) spectroscopy, attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy, and isothermal titration calorimetry (ITC). The efficacy of the selective interfacial molecular binding was demonstrated by identifying a bis-phosphinate ligand capable of providing an overall higher surface coverage of alkyl groups relative to a monophosphinate ligand. The results highlight the interplay between adsorption binding strength and maximum surface coverage in determining ligand efficiency to render the mineral surface hydrophobic. DFT calculations further indicate that all tested ligands have higher affinity for Ce-bastnäsite than for calcite. This is consistent with the ITC data showing stronger adsorption enthalpy to bastnäsite than to calcite, making these ligands promising candidates for selective flotation of Ce-bastnäsite.

Sono-photocatalytic production of hydrogen by interface modified metal oxide insulators.

Dielectric oxide materials are well-known insulators that have many applications in catalysis as well as in device manufacturing industries. However, these dielectric materials cannot be employed directly in photochemical reactions that are initiated by the absorption of UV-Vis photons. Despite their insensitivity to solar energy, dielectric materials can be made sono-photoactive even for low energy IR photons by modifications of the interfacial properties of dielectric materials by noble metals and metal oxides. In this investigation, by way of interface modification of dielectric MgO nanoparticles by Ag metal and Ag2O nanoparticles, IR photon initiated sono-photocatalytic activity of MgO is reported. The observed photocatalytic activity is found to be the synergic action of both IR light and sonication effect and sonication assisted a multi-step, sub-bandgap excitation of electrons in the MgO is proposed for the observed catalytic activity of Ag/Ag2O coated MgO nanoparticles. Our investigation reveals that other dielectric materials such as silver coated SiO2 and Al2O3 also exhibit IR active sono-photocatalytic activity.

Metal and polymer-mediated synthesis of porous crystalline hydroxyapatite nanocomposites for environmental remediation.

This study was focused on the preparation of metal and polymer-mediated porous crystalline hydroxyapatite (HAp) nanocomposites for environmental applications. Four different nano HAp systems were synthesized, namely, microwave irradiated HAp (M1), Zn doped HAp (M2), Mg-doped HAp (M3) and sodium alginate incorporated HAp (M4), and characterized using X-ray diffraction (XRD), Fourier transform infra-red spectroscopy, scanning electron microscopy, transmission electron microscopy, atomic force microscopy, nuclear magnetic resonance (NMR), X-ray fluorescence, thermogravimetric analysis and Brunauer-Emmett-Teller (BET) analyses. Systems M1-M4 showed morphologies similar to coral shapes, polymer-like interconnected structures, sponges and feathery mycelium assemblies. Using XRD, selected area electron diffraction patterns and 1H and 31P CP/MAS solid-state NMR studies, crystallinity variation was observed from highest to lowest in the order of M4 > M1 > M3 > M2. Surface area estimates using BET isotherm reflected the highest surface area for M3, and M1 > M2 > M4. Four systems of M1-M4 were used as potential adsorbent materials for the removal of metal containing azo dye from aqueous system. Adsorption data were correlated to Freundlich and Langmuir isotherm models. According to the results, the highest capacity of 212.8 mg g-1 was exhibited by M4 having mycelium like morphology with alginate groups. This study highlights the possibility of developing HAp nanocomposites for the effective removal of dye contaminants in the environment.

pH responsive controlled release of anti-cancer hydrophobic drugs from sodium alginate and hydroxyapatite bi-coated iron oxide nanoparticles.

Developing a drug carrier system which could perform targeted and controlled release over a period of time is utmost concern in the pharmaceutical industry. This is more relevant when designing drug carriers for poorly water soluble drug molecules such as curcumin and 6-gingerol. Development of a drug carrier system which could overcome these limitations and perform controlled and targeted drug delivery is beneficial. This study describes a promising approach for the design of novel pH sensitive sodium alginate, hydroxyapatite bilayer coated iron oxide nanoparticle composite (IONP/HAp-NaAlg) via the co-precipitation approach. This system consists of a magnetic core for targeting and a NaAlg/HAp coating on the surface to accommodate the drug molecules. The nanocomposite was characterized using FT-IR spectroscopy, X-ray diffraction, scanning electron microscopy, transmission electron microscopy and thermogravimetric analysis. The loading efficiency and loading capacity of curcumin and 6-gingerol were examined. In vitro drug releasing behavior of curcumin and 6-gingerol was studied at pH 7.4 and pH 5.3 over a period of seven days at 37°C. The mechanism of drug release from the nanocomposite of each situation was studied using kinetic models and the results implied that, the release is typically via diffusion and a higher release was observed at pH 5.3. This bilayer coated system can be recognized as a potential drug delivery system for the purpose of curcumin and 6-gingerol release in targeted and controlled manner to treat diseases such as cancer.

In-situ formation of supramolecular aggregates between chitin nanofibers and silver nanoparticles.

Chitin and chitin derivatives have gained significant research interest over the years due to a number of beneficial properties that can be exploited in various application fields. Particularly, interactions between their nanostructures and other nanomaterials are of great interest. In situ photo-reduction of AgCl in chitin nanofiber aqueous dispersions resulted in significant loss of colloidal stability of both chitin nanofibers (CNF) and silver nanoparticles. UV-vis spectroscopy was used to characterize the extinction profiles of in-situ prepared CNF and several silver nanoparticle mixtures over the reaction steps. High resolution TEM characterization of the resulting structures indicated the presence of the aggregated form of nanofiber and nanoparticles. Energy filtered TEM analysis confirmed the existence of both CNF and silver nano particles in the aggregate, with silver in its chemically reduced state (Ag(0)). FT-IR, and 13C solid state NMR revealed the presence of strong interactions between Ag and CNF through hydroxyl and carbonyl moieties of the CNF structure. It was concluded that these interactions led to the formation of a supramolecular aggregate in the in-situ mixture as a result of wrapping of CNF around photo-reduced silver nanoparticles which resulted in the colloidal instability.