Nano Zinc Oxide Toxicity Varies With Age and Sex in Panagrellus redivivus.

ZnO NPs can adsorb onto soil particles and potentially enter groundwater. Nematodes and other soil microfauna are vital to the soil's health and nutrient cycles, yet they are seriously endangered by ZnO NPs. A dose-response study using Panagrellus redivivus was applied.

Aqueous Extracts of Organic Mulch Materials Have Nematicide and Repellent Effect on Infective Juveniles: A Laboratory Study.

While the nematicidal effectiveness of mulching against root-knot nematodes ( spp.) is calculated within organic crop protection, underlying mechanisms are not yet fully explored. Laboratory experiments were set up to determine whether mulch-derived substances cause mortality directly, or repel juveniles from crop rhizosphere.

The response of litter decomposition to extreme drought modified by plant species, plant part, and soil depth in a temperate grassland.

Plant litter decomposition is a key ecosystem process in carbon and nutrient cycling, and is heavily affected by changing climate. While the direct effects of drought on decomposition are widely studied, in order to better predict the overall drought effect, indirect effects associated with various drought-induced changes in ecosystems should also be quantified. We studied the effect of an extreme (5-month) experimental drought on decomposition, and if this effect varies with two dominant perennial grasses, plant parts (leaves vs.

Composted Municipal Green Waste Infused with Biocontrol Agents to Control Plant Parasitic Nematodes-A Review.

The last few years have witnessed the emergence of alternative measures to control plant parasitic nematodes (PPNs). We briefly reviewed the potential of compost and the direct or indirect roles of soil-dwelling organisms against PPNs. We compiled and assessed the most intensively researched factors of suppressivity.

Toxicity mitigation by N-acetylcysteine and synergistic toxic effect of nano and bulk ZnO to Panagrellus redivivus.

To better understand the nanosize-relevant toxic effects and underlying mechanisms, N-acetylcysteine (NAC), as a mitigation agent, an ionic form of Zn (ZnCl), and the binary mixture of ZnO with different particle sizes (15 nm and 140 nm), was used in toxicity assays with the nematode Panagrellus redivivus. The ZnCl concentrations were applied to show the amount of dissolved Zn ions present in the test system. Reactive oxygen species (ROS) measuring method was developed to fit the used test system.

Replacement of Oxygen by Sulfur in Small Organic Molecules. 3. Theoretical Studies on the Tautomeric Equilibria of the 2OH and 4OH-Substituted Oxazole and Thiazole and the 3OH and 4OH-Substituted Isoxazole and Isothiazole in the Isolated State and in Solution.

This follow-up paper completes the author's investigations to explore the in-solution structural preferences and relative free energies of all OH-substituted oxazole, thiazole, isoxazole, and isothiazole systems. The polarizable continuum dielectric solvent method calculations in the integral-equation formalism (IEF-PCM) were performed at the DFT/B97D/aug-cc-pv(q+(d))z level for the stable neutral tautomers with geometries optimized in dichloromethane and aqueous solution. With the exception of the predictions for the predominant tautomers of the 3OH isoxazole and isothiazole, the results of the IEF-PCM calculations for identifying the most stable tautomer of the given species in the two selected solvents agreed with those from experimental investigations.

Uptake and toxicity of nano-ZnO in the plant-feeding nematode, Xiphinema vuittenezi: the role of dissolved zinc and nanoparticle-specific effects.

Nanoparticulate ZnO is one of the most commonly applied nanomaterials. As ZnO is more soluble than many other oxide nanoparticles, its toxicity beyond the nanoparticle-specific effects can be attributed to the dissolved ionic zinc. The investigation of uptake and toxicity of nano-ZnO in the plant-feeding nematode, Xiphinema vuittenezi, which was used in previous studies as a biological model organism, was aimed.

Theoretical in-Solution Conformational/Tautomeric Analyses for Chain Systems with Conjugated Double Bonds Involving Nitrogen(s).

Conformational/tautomeric transformations for X=CH-CH=Y structures (X = CH2, O, NH and Y = NH) have been studied in the gas phase, in dichloromethane and in aqueous solutions. The paper is a continuation of a former study where s-cis/s-trans conformational equilibria were predicted for analogues. The s-trans conformation is preferred for the present molecules in the gas phase on the basis of its lowest internal free energy as calculated at the B97D/aug-cc-pvqz and CCSD(T)CBS (coupled-cluster singles and doubles with non-iterative triples extrapolated to the complete basis set) levels.

Competing intramolecular vs. intermolecular hydrogen bonds in solution.

A hydrogen bond for a local-minimum-energy structure can be identified according to the definition of the International Union of Pure and Applied Chemistry (IUPAC recommendation 2011) or by finding a special bond critical point on the density map of the structure in the framework of the atoms-in-molecules theory. Nonetheless, a given structural conformation may be simply favored by electrostatic interactions. The present review surveys the in-solution competition of the conformations with intramolecular vs.

Differential Induction of Cytoplasmic Vacuolization and Methuosis by Novel 2-Indolyl-Substituted Pyridinylpropenones.

Because many cancers harbor mutations that confer resistance to apoptosis, there is a need for therapeutic agents that can trigger alternative forms of cell death. Methuosis is a novel form of non-apoptotic cell death characterized by accumulation of vacuoles derived from macropinosomes and endosomes. Previous studies identified an indole-based chalcone, 3-(5-methoxy-2-methylindol-3-yl)-1-(4-pyridinyl)-2-propen-1-one (MOMIPP), that induces methuosis in human cancer cells.

In-solution conformational analysis of the XCYCH3 moiety for small esters and ethers with all combinations of X, Y = O, S.

Favorable steric and electrostatic fit of a ligand to a receptor is of central interest in theoretical drug design. This paper considers the effects of non-protic solvents, in comparison with the gas phase, on the preferred conformation of the XCYCH3 moiety of simple aliphatic esters and heterocyclic methyl ethers with all combinations of the X and Y atoms as oxygen and sulfur. An IEF-PCM/B97D/aug-cc-pv(t+d)z continuum dielectric solvent study in chloroform and acetonitrile explores the through-space polarization effect of the environment on the conformational preference, not affected by possible solute-solvent hydrogen bond formation.

Are the intramolecular O-H···F and O-H···Cl hydrogen bonds maintained in solution? A theoretical study.

The present case study aims at calculating the equilibrium conformer compositions for 2X-ethanol and 2X-phenol (X = F, Cl) in solution, and exploring the effect of the applied theoretical method and basis set on the obtained results, as well as considering the usefulness of the continuum solvent approach in comparison with the explicit solvent Monte Carlo model utilizing the free energy perturbation method. Gas-phase optimizations at the DFT/B97D/aug-cc-pvtz and ab initio MP2/aug-cc-pvtz levels predicted structures in good agreement with the available experimental data for three test molecules. Because in-solution geometries change only slightly according to the IEF-PCM continuum solvent calculations in carbon tetrachloride and water, the two theoretical levels were applied further on, and complete basis set (CBS) relative internal free energies were estimated for the conformers under study.

Theoretical study of the gauche-trans equilibrium with and without an intramolecular hydrogen bond for +H3NCH2CH2X systems (X = OH, NH2, COO-) in solution.

The gauche-trans conformational equilibrium has been studied for (+)H(3)NCH(2)CH(2)X systems (X = OH, NH(2), COO(-)) and for the neutral model of the simplest β-amino acid in aqueous solution and chloroform. Each structure exhibits an intramolecular hydrogen bond in the NCCX gauche conformation, which is necessarily disrupted in the local energy minimum trans form. Geometries were optimized at the IEF-PCM/B97D/aug-cc-pvtz level of theory and indicated that the solvent effect of chloroform vs.

Theoretical studies of the solvent effect on the conformation of the HO-C-C-X (X = F, NH2, NO2) moiety with competing intra- and intermolecular hydrogen bonds.

Theoretical calculations up to the ab initio IEF-PCM/CCSD(T)/CBS//IEF-PCM/B3LYP/6-311++G** and IEF-PCM/B97D/aug-cc-pvtz levels have been performed for 2X-ethanol and 2X-phenol systems with X = F, NH(2), NO(2) in chloroform and aqueous solution. The calculated relative free energies by means of the IEF-PCM continuum dielectric method do not differ very much at the DFT and ab initio levels. Application of explicit solvent models and the FEP/MC method for determining relative solvation free energies causes, however, large deviations in the predicted equilibrium compositions, although the predominant conformation for the solute is generally in agreement with that from the corresponding IEF-PCM calculations.

On the interaction of aliphatic amines and ammonium ions with carboxylic acids in solution and in receptor pockets.

Association energies of the acetate ion with cationic amines bearing one to three methyl groups were calculated in the range of -14 to -17 kcal/mol in aqueous solution by means of the IEF-PCM method at the CCSD(T)/CBS//MP2/aug-cc-pvdz and DFT/B97D/CBS//B97D/aug-cc-pvtz levels. The main stabilization factor for the association is the possibility for the formation of an ionic intermolecular hydrogen bond between the elements of the complex. For a quaternary ammonium ion, the favorable electrostatic interaction energy is the only driving force, and the stabilization energy for the complex is reduced to -4 kcal/mol.

Structure simulations for the 0.22 and 1 molar aqueous dimethylammonium chloride solutions.

Monte Carlo simulations have been performed for characterizing the 0.22 and 1 molar aqueous dimethylammonium chloride solutions at p = 1 atm and T = 310 K. On the basis of potential of mean force curves for the two systems with increasing concentrations, the N···N separations of about 8.

Combined ab initio/DFT and Monte Carlo calculation of relative standard chemical potentials in solution.

A method has been proposed for pure theoretical estimation of relative standard chemical potentials (1 mol/dm(3) standard state) and related K(c) equilibrium constants for tautomers/conformers dissolved in some solvents. The relative internal free energy could be obtained by means of in-solution ab initio/DFT methods. Using the free energy perturbation method for the transformation of the involved species, the solvation contribution to the relative standard chemical potential can be determined by considering 1 M solution models.

Theoretical studies of the in-solution isomeric protonation of non-aromatic six-member rings with two nitrogens.

For exploring the preferred site for hydrogen bond formation, theoretical calculations have been performed for a number of six-member, nonaromatic rings allowing for alternative protonation on the ring nitrogens. Gas-phase protonation studies for test molecules indicate that the B3LYP/aug-cc-pvtz and QCISD(T)(CBS) calculations approach the experimental values within about 1 kcal/mol with considerable improvement for relative enthalpies and free energies. Relative free energies calculated at the IEF-PCM/B3LYP/aug-cc-pvtz level predict favorable protonation on the tertiary rather than on the secondary nitrogen both in aqueous solution and in a dichloromethane solvent for saturated rings.

Molecular dynamics and Monte Carlo simulations for the structure of the aqueous trimethylammonium chloride solution in the 0.2-1 molar range.

Molecular dynamics and Monte Carlo simulations have been performed for characterizing the structure of the 0.2 and 1 molar aqueous trimethylammonium chloride solutions. Atomic charges were derived through the CHELPG and RESP fits to the molecular electrostatic potentials calculated for the cation in water at the IEF-PCM/B3LYP level using the 6-31G* and 6-311++G** basis sets.

Theoretical studies of salt-bridge formation by amino acid side chains in low and medium polarity environments.

Salt-bridge formation between Asp/Glu···Lys and Asp/Glu···Arg side chains has been studied by model systems including formic and acetic acids as proton donors and methylamine, guanidine, and methylguanidine as proton acceptors. Calculations have been performed up to the CCSD(T)(CBS)//MP2/aug-cc-pvtz level with formic acid proton donors. Complexes formed with acetic acid were studied at the CCSD(T)/aug-cc-pvdz//MP2/aug-cc-pvdz level.

The catalytic effect of water on the keto-enol tautomerism. Pyruvate and acetylacetone: a computational challenge.

The catalytic effect of explicit water molecules on the keto-enol tautomerism in a system of biological interest (enolpyruvate) has been investigated at the B3LYP/6-31++G** level by exploring the potential energy surface in the presence of 1 or 2 water molecules and comparing the energy profiles to the direct tautomerisation one. The water-assisted mechanisms turned out to be more favourable than the direct ones, in agreement with what occurred for the acetylacetone tautomerism in the presence of a single water molecule. To compare the behaviour of water in pyruvate and in acetylacetone, the two-water-assisted mechanism has been also examined for the latter at the B3LYP/6-31G* level.

Theoretical and experimental studies of the isomeric protonation in solution for a prototype aliphatic ring containing two nitrogens.

Theoretical calculations were carried out for studying the tautomeric protonation of N-methylpiperazine as a prototype six-member aliphatic ring containing a secondary and a tertiary nitrogen atom. The protonation was investigated in three solvents, water, acetonitrile, and dichloromethane. Calculations were performed up to the B3LYP/aug-cc-pvtz and QCISD(T)/CBS levels by applying the IEF-PCM polarizable continuum dielectric solvent model.

Ab initio study of hydrogen-bond formation between aliphatic and phenolic hydroxy groups and selected amino acid side chains.

Hydrogen bonding was studied in 24 pairs of isopropyl alcohol and phenol as one partner, and water and amino-acid mimics (methanol, acetamide, neutral and protonated imidazole, protonated methylalamine, methyl-guanidium cation, and acetate anion) as the other partner. MP2/6-31+G* and MP2/aug-cc-pvtz calculations were conducted in the gas phase and in a model continuum dielectric environment with dielectric constant of 15.0.

Monte Carlo structure simulations for aqueous 1,4-dioxane solutions.

Monte Carlo simulations in the NpT ensembles have been performed for the structure exploration of aqueous 1,4-dioxane solutions. Three different systems with all-atom dioxane:TIP4P water molar compositions of 2:500 (code:D2), 8:465 (D8), and 17:425 (D17) modeled solutions of 0.22, 0.

Theoretical Investigation of Tautomeric Equilibria for Isonicotinic Acid, 4-Pyridone, and Acetylacetone in Vacuo and in Solution.

Tautomeric equilibria have been theoretically calculated for isonicotinic acid (neutral and zwitterionic forms), the 4-pyridone/4-hydroxypyridine system, and the keto-enol transformation for acetylacetone in vacuo and in tetrahydrofuran, methanol, and water solvents. Solvent, basis set, and cavity model effects have been studied in the integral equation formalism for the polarizable continuum model (IEF-PCM)/B3LYP framework, as well as the effect of the procedure, CHELPG or RESP, applied in fitting atomic charges to the in-solution molecular electrostatic potential (ELPO). The in-solution optimized geometries obtained at the IEF-PCM/B3LYP/6-31G* and 6-311++G** levels differ moderately but deviate from their gas-phase counterparts.