Development and assessment of isatin hydrazone-functionalized/ion-imprinted cellulose adsorbent for gadolinium (III) removal.

It is of tremendous economic and environmental significance to obtain a powerful adsorbent for the extraction of Gd3+ from wastewater. Adsorbents derived from cellulosic materials functionalized with specific chelators show great promise for the removal of heavy metal ions from wastewater. The selectivity of these sorbents for metal ions is, however, still rather poor. Here, we present a technique for trapping Gd3+ ions from wastewater by synthesizing Gd3+ ion-imprinted polymers based on isatinhydrazone-functionalized cellulose (Gd-ISH-CE). Not only did isatinhydrazone work as a tridentate ligand to directly provide ligand vacancies and build hierarchy pores on Gd-ISH-CE, but it also enabled cross-linking through the epichlorohydrine cross-linker thanks to its very effective NH2 functionalization. The as-prepared Gd-ISH-CE with ISH functionality shows a high adsorption capacity of 275 mg/g and a rapid equilibration time of 30 min for Gd3+ due to its plentiful binding sites and hierarchical pore structure. Furthermore, Gd-ISH-CE shows very selective capture of Gd3+ over competing ions. By integrating the benefits of ion-imprinting and chelator functionalization methodologies in an effortless manner, this study presents a practical approach to the development of superior materials for Gd3+ recovery.

Highly stretchable, elastic, antimicrobial conductive hydrogels with environment-adaptive adhesive property for health monitoring.

HYPOTHESIS: Development of soft conductive materials has enabled the promising future of wearable electronics for motion sensing. However, conventional soft conductive materials typically lack robust adhesive and on-demand removable properties for a target substrate. Therefore, it is believed that the integration of superior mechanical properties, electrical conductivity, and tunable adhesive properties into hydrogels would support and improve their reliable sensing performance. EXPERIMENTS: A hydrogel ionic conductor composed of cationic micelles crosslinked in the polyacrylamide (PAM) network was designed and fabricated. The viscoelastic, mechanical, adhesion, electrical, and antimicrobial properties of the hydrogel were systematically characterized. FINDINGS: The developed ionic conductor possesses a range of desirable properties including mechanical performances such as excellent stretchability (>1100%), toughness, elasticity (recovery from 1000% strain), conductivity (2.72 S·m-1), and antimicrobial property, owing to the multiple non-covalent supramolecular interactions (e.g., hydrogen bonding, hydrophobic, and π-π/cation-π interactions) present in the cross-linked network. Meanwhile, the developed hydrogel is incorporated with different stimuli-responsive polymers and exhibits a tunable adhesive property (triggerable attachment and on-demand removable capabilities) in adapt to the surrounding environmental conditions (i.e., pH, temperature). With all these significant features, the resulting hydrogel ionic conductor serves as a proof-of-concept motion-sensing system with excellent sensitivity and enhanced reliability for the detection of a wide range of motions.

Cost-effective microabsorbance detection based nanoparticle immobilized microfluidic system for potential investigation of diverse chemical contaminants present in drinking water.

The measurement of the concentration of different heavy-metal ions present in the water environments is becoming increasingly essential as water-pollution concerns worsen. The optical sensor has become a good platform for detecting heavy-metal-ion concentration due to its compact size; chemical inertness; and anti-electromagnetic interference. Here, we propose to fabricate a simple and cost-effective microfluidic device for the detection of aqueous-heavy-metal ions such as lead(II), chromium(III) and mercury(II) using an optical-micro-absorbance-spectroscopy/LSPR based principle. Firstly, a disposable-PDMS-micro-device with a rectangular "Z-shaped microfluidic channel" integrated with micro-lens-structure and optical-fibre-coupler-structure was fabricated via cost-effective soft-lithography-technique using a microfabricated SU8 master. Further, the synthesized-Silver-Nanoparticles were also immobilized inside the microchannel structure in some of the micro-devices for nanoparticle-based-sensing studies. The real-time presence of heavy metal ions in the minuscule sample volume was analyzed by passing different-sample concentrations intermittently through the abovementioned microfluidic structure and measuring the bulk-micro-absorbance across its enhanced optical path length coupler-structure. The results specify that the fabricated micro-device can be easily utilized for label-free detection of a minimum of 0.5 ppb for all the aforesaid sample-heavy metal ions. The absorbance-change observed per unit concentration-change of Lead ion, mercury ion and chromium ion (from 0.001 to ∼50 µg/ml) is found on average-1.8 × 10-2 ΔA/µg/ml, 1.1 × 10-2 ΔA/µg/ml, 4.2 × 10-3 ΔA/µg/ml, respectively. For silver nanoparticle-based studies, the absorbance-change observed per unit concentration change of aforesaid heavy-metal-ions (i.e. the sensitivity) was found on average ∼2 times higher in comparison to simple micro-absorbance-based studies. Additionally, the micro-device has a capability for simplistic incessant(real-time)investigation, a preset-analyte-quantity-interface, and management over the injected analyte-evaporation.

Dinucleotides as simple models of the base stacking-unstacking component of DNA 'breathing' mechanisms.

Regulatory protein access to the DNA duplex 'interior' depends on local DNA 'breathing' fluctuations, and the most fundamental of these are thermally-driven base stacking-unstacking interactions. The smallest DNA unit that can undergo such transitions is the dinucleotide, whose structural and dynamic properties are dominated by stacking, while the ion condensation, cooperative stacking and inter-base hydrogen-bonding present in duplex DNA are not involved. We use dApdA to study stacking-unstacking at the dinucleotide level because the fluctuations observed are likely to resemble those of larger DNA molecules, but in the absence of constraints introduced by cooperativity are likely to be more pronounced, and thus more accessible to measurement. We study these fluctuations with a combination of Molecular Dynamics simulations on the microsecond timescale and Markov State Model analyses, and validate our results by calculations of circular dichroism (CD) spectra, with results that agree well with the experimental spectra. Our analyses show that the CD spectrum of dApdA is defined by two distinct chiral conformations that correspond, respectively, to a Watson-Crick form and a hybrid form with one base in a Hoogsteen configuration. We find also that ionic structure and water orientation around dApdA play important roles in controlling its breathing fluctuations.

Metal-phenolic network coated cellulose foams for solar-driven clean water production.

Solar-driven water steam generation is a promising strategy for seawater desalination and wastewater purification. However, oil contaminants commonly exist in real water resources, which drives us to design and fabricate photothermal materials with high efficient water steam generation and outstanding anti-oil-fouling ability. Herein, we developed a metal-phenolic network-coated cellulose foam (Fe3+/TA@CF), which exhibits not only superb hydrophilicity and underwater lipophobicity, but also achieves high water evaporation rate of ∼1.3 kg m-2 h-1 even in oil-polluted seawater under one sun illumination. In addition, Fe3+/TA@CF is demonstrated to be both anti-oil-fouling and anti-salt-fouling, which benefits to long-term evaporation in practical utilizations. Metal ions and oil contaminants in the condensed water vapor are almost eliminated after purification. We believe that this low-cost, biodegradable Fe3+/TA@CF paves a way for rationally designing and fabricating high-performance evaporator for oil contaminated water purification.

Role of a complex of two proteins in alleviating sodium ion stress in an economic crop.

An economically valuable woody plant species tree bean (Cajanus cajan (L.) Millsp.) is predominantly cultivated in tropical and subtropical areas and is regarded as an important food legume (or pulse) crop that is facing serious sodium ion stress. NAM (N-acetyl-5-methoxytryptamine) has been implicated in abiotic and biotic stress tolerance in plants. However, the role of NAM in sodium ion stress tolerance has not been determined. In this study, the effect of NAM was investigated in the economically valuable woody plant species, challenged with stress at 40 mM sodium ion for 3 days. NAM-treated plants (200 µM) had significantly higher fresh weight, average root length, significantly reduced cell size, increased cell number, and increased cytoskeleton filaments in single cells. The expression pattern of one of 10 Tree bean Dynamic Balance Movement Related Protein (TbDMP), TbDMP was consistent with the sodium ion-stress alleviation by NAM. Using TbDMP as bait, Dynamic Balance Movement Related Kinase Protein (TbDBK) was determined to interact with TbDMP by screening the tree bean root cDNA library in yeast. Biochemical experiments showed that NAM enhanced the interaction between the two proteins which promoted resist sodium ion stress resistance. This study provides evidence of a pathway through which the skeleton participates in NAM signaling.

Chemical Dosimetry in the "Water Window": Ferric Ions and Hydroxyl Radicals Produced by Intense Soft X Rays.

A standard Fricke dosimeter was used to measure the absorbed dose via the oxidation yields of Fe3+ ions in an aqueous environment induced by soft X rays within the "water window" spectral range. We also exploited the property of a neutral solution containing terephthalic acid as a tool for selective detection of OH radicals. Both dosimetric systems were irradiated using the experimental pulsed laser-plasma soft X-ray source as well as conventional 1.25-MeV gamma rays. Radiation chemical yields of Fe3+ ions and OH radicals were determined to be (5.13 ± 0.94) × 10-1 µmol·J-1 (4.95 ± 0.91 100eV-1) and (2.33 ± 0.35) × 10-2 µmol·J-1 (0.23 ± 0.03 100eV-1), respectively. Measurements were supported by Monte Carlo simulations to estimate the linear energy transfer of the water window radiation. The simulation results are in good agreement with expected linear energy transfer of ions inducing the same Fe3+ ion and OH radical radiation chemical yield.

Role of metallic core for the stability of virus-like particles in strongly coupled electrostatics.

Electrostatic interactions play important roles in the formation and stability of viruses and virus-like particles (VLPs) through processes that often involve added, or naturally occurring, multivalent ions. Here, we investigate the electrostatic or osmotic pressure acting on the proteinaceous shell of a generic model of VLPs, comprising a charged outer shell and a metallic nanoparticle core, coated by a charged layer and bathed in an aqueous electrolyte solution. Motivated by the recent studies accentuating the role of multivalent ions for the stability of VLPs, we focus on the effects of multivalent cations and anions in an otherwise monovalent ionic solution. We perform extensive Monte-Carlo simulations based on appropriate Coulombic interactions that consistently take into account the effects of salt screening, the dielectric polarization of the metallic core, and the strong-coupling electrostatics due to multivalent ions. We specifically study the intricate roles these factors play in the electrostatic stability of the model VLPs. It is shown that while the insertion of a metallic nanoparticle by itself can produce negative, inward-directed, pressure on the outer shell, addition of only a small amount of multivalent counterions can robustly engender negative pressures, enhancing the VLP stability across a wide range of values for the system parameters.

Adduct ion formation as a tool for the molecular structure assessment of ten isomers in traveling wave and trapped ion mobility spectrometry.

RATIONALE: The separation of isomeric compounds with major differences in their physiochemical and pharmacokinetic properties is of particular importance in pharmaceutical R&D. However, the structural assessment and separation of these compounds with current analytical techniques and methods are still a challenge. In this study, we describe strategies to separate the various structural and stereo-isomers. METHODS: The separation of ten structural and stereo-isomers was investigated using Trapped and Travelling Wave ion mobility spectrometry (TIMS and TWIMS). Different strategies including adduct ion formation with Na, Li, Ag and Cs as well as fragmentation before and after the ion mobility cell were applied to separate the isomeric compounds. RESULTS: All the counter ions (in particular Na) strongly coordinated with the test analytes in all the IMS systems. The highest resolving power was achieved for the sodium and lithium adducts using TIMS-time-of-flight (TOF). However, some separation was attained on a Synapt HDMS system with its unique potential to monitor the ion mobility of the product ions. The elution order of the adduct ions was the same in all instruments, in which, unexpectedly, the para-substituted isomer of the [M + Na]+ species had the lowest collision cross section followed by the meta- and ortho-isomers. CONCLUSIONS: The formation of adduct ions could facilitate the separation of structural and even stereo-isomers by generating different molecular conformations. In addition, fragmenting isomers before or after the ion mobility cell is a valuable strategy to separate and also to assess the structures of adducts and different conformers.

Na+-binding modes involved in thrombin's allosteric response as revealed by molecular dynamics simulations, correlation networks and Markov modeling.

The monovalent sodium ion (Na+) is a critical modulator of thrombin. However, the mechanism of thrombin's activation by Na+ has been widely debated for more than twenty years. Details of the linkage between thrombin and Na+ remain vague due to limited temporal and spatial resolution in experiments. In this work, we combine microsecond scale atomic-detailed molecular dynamics simulations with correlation network analyses and hidden Markov modeling to probe the detailed thermodynamic and kinetic picture of Na+-binding events and their resulting allosteric responses in thrombin. We reveal that ASP189 and ALA190 comprise a stable Na+-binding site (referred as "inner" Na+-binding site) along with the previously known one (referred as "outer" Na+-binding site). The corresponding newly identified Na+-binding mode introduces significant allosteric responses in thrombin's regulatory regions by stabilizing selected torsion angles of residues responsive to Na+-binding. Our Markov model indicates that the bound Na+ prefers to transfer between the two Na+-binding sites when an unbinding event takes place. These results suggest a testable hypothesis of a substrate-driven Na+ migration (ΔG ∼ 1.7 kcal mol-1) from the "inner" Na+-binding site to the "outer" one during thrombin's catalytic activities. The binding of a Na+ ion at the "inner" Na+-binding site should be inferred as a prerequisite for thrombin's efficient recognition to the substrate, which opens a new angle for our understanding of Na+-binding's allosteric activation on thrombin and sheds light on detailed processes in thrombin's activation.

Vertical Ionization Energies and Electron Affinities of Native and Damaged DNA Bases, Nucleotides, and Pairs from Density Functional Theory Calculations: Model Assessment and Implications for DNA Damage Recognition and Repair.

To assess the effect of an 8-oxoguanine (8OG) defect base on the vertical ionization energies (VIEs) and electron affinities (VEAs) of DNA, density functional theory calculations were carried out for native and defect DNA bases and nucleotides, as well as for larger fragments containing one or multiple pairs. Absolute values of VIE and VEA under implicit solvation did not converge as a function of model size even up to the largest systems taken into consideration (3 base pairs/2 nucleotide pairs). Nonetheless, a consistent trend was observed for the relative difference in the VIE of native and damaged DNA showing that the defect was lowering the VIE by -0.1 eV for the largest fragments. This strongly suggests that the presence of 8OG makes the DNA more easily oxidizable and is in line with experimental evidence that a defect region can act as a sink of oxidative damage. In contrast, relative differences in VEA were very small and varied inconsistently around 0.01 eV. This seems to indicate that insertion of 8OG has a negligible effect on the electron capturing properties of DNA. Similar conclusions can be drawn by the adiabatic IEs and EAs computed for some of the larger fragments. Analysis of the hole and excess electron distributions was consistent with the above trends. The findings presented here support the possibility that a mechanism based on hole transport through DNA may be efficiently employed by the cell for the detection of defect bases.

Sequencing batch biosorption of micropollutants from aqueous effluents by rapeseed waste: Experimental assessment and statistical modelling.

Rapeseed (RS) waste was used for sequential biosorption from aqueous solutions of two target micropollutants: lead ions and Reactive blue 19 (Rb19) dye, through an integrated approach, combining experimental assessment and statistical modeling. In both cases of sequential biosorption, a pseudo-second order kinetic model fitted the biosorption data well. Intraparticle diffusion proved to be the rate-limiting step in the sequential retention of both micropollutants. A selective desorption of metal ions and anionic dye at pH 2.5 and 10.5, respectively was observed. The quadratic models generated by response surface methodology (RSM) adequately described the sequential biosorption process and the desorption process, respectively. XPS and FTIR analysis indicated the mechanisms involved in the retention of target pollutants.

Cost-Efficient Graphitic Carbon Nitride as an Effective Photocatalyst for Antibiotic Degradation: An Insight into the Effects of Different Precursors and Coexisting Ions, and Photocatalytic Mechanism.

In this study, the photocatalytic activity of graphitic carbon nitride (g-C3 N4 ) synthesized via different precursors (urea, thiourea, and dicyandiamide) is investigated in the degradation process of tetracycline. Owing to the efficient charge separation and transfer, prolonged radiative lifetime of charge, large surface area, and nanosheet morphology, the urea-derived g-C3 N4 exhibits superior photocatalytic activity for tetracycline degradation under visible-light irradiation. This performance can compare with that of most reported g-C3 N4 -based composite photocatalysts. Through the time-circle degradation experiment, the urea-derived g-C3 N4 is found to have an excellent photocatalytic stability. The presence of NO3 - , CH3 COO- , Cl- and SO4 2- ions with the concentration of 10 mm inhibits the photocatalytic activity of urea-derived g-C3 N4 , where this inhibitory effect is more obvious for Cl- and SO4 2- ions. For the coexisting Cu2+ , Ca2+ , and Zn2+ ions, the Cu2+ ion exhibits a significantly higher inhibitory effect than Ca2+ and Zn2+ ions for tetracycline degradation. However, both the inhibitory and facilitating effects are observed in the presence of Fe3+ ion with different concentration. The h+ , . OH and . O2 - radicals are confirmed as major oxidation species and a possible photocatalytic mechanism is proposed in a urea-derived g-C3 N4 reaction system. This study is of important significance to promote the large-scale application of g-C3 N4 photocatalysts in antibiotic wastewater purification.

QSAR Development for Plasma Protein Binding: Influence of the Ionization State.

PURPOSE: This study explored several strategies to improve the performance of literature QSAR models for plasma protein binding (PPB), such as a suitable endpoint transformation, a correct representation of chemicals, more consistency in the dataset, and a reliable definition of the applicability domain. METHODS: We retrieved human fraction unbound (Fu) data for 670 compounds from the literature and carefully checked them for consistency. Descriptors were calculated taking account of the ionization state of molecules at physiological pH (7.4), in order to better estimate the affinity of molecules to blood proteins. We used different algorithms and chemical descriptors to explore the most suitable strategy for modeling the endpoint. SMILES (simplified molecular input line entry system)-based string descriptors were also tested with the CORAL software (CORelation And Logic). We did an outlier analysis to establish the models to use (or not to use) in case of well recognized families. RESULTS: Internal validation of the selected models returned Q2 values close to 0.60. External validation also gave r2 values always greater than 0.60. The CORAL descriptor based model for √fu was the best, with r2 0.74 in external validation. CONCLUSIONS: Performance in prediction confirmed the robustness of all the derived models and their suitability for real-life purposes, i.e. screening chemicals for their ADMET profiling. Optimization of descriptors can be useful in order to obtain the correct results with a ionized molecule.

Explicit ions/implicit water generalized Born model for nucleic acids.

The ion atmosphere around highly charged nucleic acid molecules plays a significant role in their dynamics, structure, and interactions. Here we utilized the implicit solvent framework to develop a model for the explicit treatment of ions interacting with nucleic acid molecules. The proposed explicit ions/implicit water model is based on a significantly modified generalized Born (GB) model and utilizes a non-standard approach to define the solute/solvent dielectric boundary. Specifically, the model includes modifications to the GB interaction terms for the case of multiple interacting solutes-disconnected dielectric boundary around the solute-ion or ion-ion pairs. A fully analytical description of all energy components for charge-charge interactions is provided. The effectiveness of the approach is demonstrated by calculating the potential of mean force for Na+-Cl- ion pair and by carrying out a set of Monte Carlo (MC) simulations of mono- and trivalent ions interacting with DNA and RNA duplexes. The monovalent (Na+) and trivalent (CoHex3+) counterion distributions predicted by the model are in close quantitative agreement with all-atom explicit water molecular dynamics simulations used as reference. Expressed in the units of energy, the maximum deviations of local ion concentrations from the reference are within k B T. The proposed explicit ions/implicit water GB model is able to resolve subtle features and differences of CoHex distributions around DNA and RNA duplexes. These features include preferential CoHex binding inside the major groove of the RNA duplex, in contrast to CoHex biding at the "external" surface of the sugar-phosphate backbone of the DNA duplex; these differences in the counterion binding patters were earlier shown to be responsible for the observed drastic differences in condensation propensities between short DNA and RNA duplexes. MC simulations of CoHex ions interacting with the homopolymeric poly(dA·dT) DNA duplex with modified (de-methylated) and native thymine bases are used to explore the physics behind CoHex-thymine interactions. The simulations suggest that the ion desolvation penalty due to proximity to the low dielectric volume of the methyl group can contribute significantly to CoHex-thymine interactions. Compared to the steric repulsion between the ion and the methyl group, the desolvation penalty interaction has a longer range and may be important to consider in the context of methylation effects on DNA condensation.

Evaluation of Ca2+ Binding Sites in Tacrolimus by Infrared Multiple Photon Dissociation Spectroscopy.

Tacrolimus (TAC) is an efficient immunosuppressant used in organ transplantation procedures. There is an intrinsic correlation between TAC and Ca2+ because of the dependence of its action mechanism on calcium and calcineurin, and the role of ion coordination on TAC identification and quantitation. To depict the Ca2+ binding sites in TAC, this work carried out gas-phase vibrational infrared multiple photon dissociation spectroscopy of [Ca(TAC)]2+ and of three other TAC mimetic molecules (probes 1-3). Density functional theory (DFT) and Monte Carlo (MC) simulations were also used to support the experimental data assignment, and natural bond orbital (NBO) analysis was carried out to depict the coordination sphere. PM3 and B3LYP/6-31G(d) levels of theory displayed similar trends during the MC simulations, suggesting that PM3 is a viable alternative to more expensive DFT calculations, at least during the conformational analysis step. Infrared spectroscopy of the [Ca(probe X)1]2+ and [Ca(probe X)3]2+ ( X = 1-3) complexes allowed for a useful guide for building guess geometries and for the band assignment of the [Ca(TAC)]2+ complex. Nevertheless, the MC approach was particularly useful for exploring the potential energy surface. The lowest energy conformation for [Ca(TAC)]2+ was found by MC simulations and is 32.92 kJ mol-1 lower in energy than the one found by comparing the results obtained for Ca2+ coordination in probes, despite the calculated spectra being virtually identical. Both approaches are good ways to depict the coordination sites, and these results suggest that using small molecules as models is a reliable approach to depict the geometry or coordination sites of extensive ions, yielding a robust correlation between experimental and theoretical spectra. Furthermore, MC survey produced a lower energy conformation with a good match to the experimental results. Both methods depict the Ca2+ coordination sphere as a hexacoordinated environment where the main coordination centers are carbonyl groups.

Critical assessment of polymeric nanostructures used as colorimetric ions probes.

In this study the effect of nature of nanostructural materials used as colorimetric optical probes on the analytical performance of the resulting sensors is compared. Different effects related to the nanoprobe materials - probe structure and properties: surface charge and stability, but also effects related to the analyte - receptor interactions - complex formation kinetics and transport of ions from the sample to the probe were taken into account. Presence of charge on the nanostructural colorimetric sensor effectively hinders ions exchange between the probe and the sample, leading to a linear dependence of absorbance on logarithm of analyte concentration changes. Interestingly, both anionic and cationic micelles are offering linear dependence on logarithm of concentration, covering 2 logarithmic units. Nanostructures, e.g. prepared from amphiphilic polymer Pluronic F127, lead to absorbance dependence on concentration observed in rather narrow concentration range. In this respect crosslinked poly(maleic anhydride-alt-1-octadecene) nanostructures of pH tunable surface charge, due to the presence of carboxyl and amine group on the surface, seem an attractive alternative, offering also the lowest detection limits among tested systems. This system is stable even in the presence of high concentration of background electrolyte in the sample and offers the lowest detection limit, what makes it useful as e.g. indicator for titration. Generally from the results obtained it follows that inert complexes, hindering ion transport to the probe, can be used to expose a linear dependence of the optical signal on logarithm of concentration, whereas for labile complexes formed sigmoidal type dependences of higher sensitivity over limited concentration range are obtained.

Rapid Ion Mobility Separations of Bile Acid Isomers Using Cyclodextrin Adducts and Structures for Lossless Ion Manipulations.

Bile acids (BAs) constitute an important class of steroid metabolites often displaying changes associated with disease states and other health conditions. Current analyses for these structurally similar compounds are limited by a lack of sensitivity and long separation times with often poor isomeric resolution. To overcome these challenges and provide rapid analyses for the BA isomers, we utilized cyclodextrin adducts in conjunction with novel ion mobility (IM) separation capabilities provided by structures for lossless ion manipulations (SLIM). Cyclodextrin was found to interact with both the tauro- and glyco-conjugated BA isomers studied, forming rigid noncovalent host-guest inclusion complexes. Without the use of cyclodextrin adducts, the BA isomers were found to be nearly identical in their respective mobilities and thus unable to be baseline resolved. Each separation of the cyclodextrin-bile acid host-guest inclusion complex was performed in less than 1 s, providing a much more rapid alternative to current liquid chromatography-based separations. SLIM provided capabilities for the accumulation of larger ion populations and IM peak compression that resulted in much higher resolution separations and increased signal intensities for the BA isomers studied.

Genotoxic Assessment of Different Sizes of Iron Oxide Nanoparticles and Ionic Iron in Earthworm (Eisenia hortensis) Coelomocytes by Comet Assay and Micronucleus Test.

The current study was designed to evaluate genotoxicity of different sizes of iron oxide nanoparticles (IONPs) and ionic iron using coelomocytes of the earthworms Eisenia hortensis. Earthworms were exposed to different series of IONPs and ionic iron concentrations to find the respective LC50 of the chosen chemicals. LC50 for < 50, <100 nm and the ionic iron of IONPs were 500, 200, 250 µg/mL respectively. Concentrations of LC50/2 (250, 100, 125 µg/mL for < 50, <100 nm and the ionic iron respectively) and LC50 for 48 h were used to perform the comet assay and micronucleus test. Statistically significant (p < 0.05) increase in DNA and chromosomal damage was observed for all sizes of IONPs and ionic iron. In the comet assay system, the greatest genotoxicity was observed in the treatments with < 100 nm IONPs, whereas the greatest numbers of micronuclei and binucleate cells were observed in the treatments with ionic iron. It was concluded that different types of nanoparticles (i.e. sizes, shapes) may have different genotoxic potencies in different assays with E. hortensis earthworms.

Biomolecular Simulations under Realistic Macroscopic Salt Conditions.

Biomolecular simulations are typically performed in an aqueous environment where the number of ions remains fixed for the duration of the simulation, generally with either a minimally neutralizing ion environment or a number of salt pairs intended to match the macroscopic salt concentration. In contrast, real biomolecules experience local ion environments where the salt concentration is dynamic and may differ from bulk. The degree of salt concentration variability and average deviation from the macroscopic concentration remains, as yet, unknown. Here, we describe the theory and implementation of a Monte Carlo osmostat that can be added to explicit solvent molecular dynamics or Monte Carlo simulations to sample from a semigrand canonical ensemble in which the number of salt pairs fluctuates dynamically during the simulation. The osmostat reproduces the correct equilibrium statistics for a simulation volume that can exchange ions with a large reservoir at a defined macroscopic salt concentration. To achieve useful Monte Carlo acceptance rates, the method makes use of nonequilibrium candidate Monte Carlo (NCMC) moves in which monovalent ions and water molecules are alchemically transmuted using short nonequilibrium trajectories, with a modified Metropolis-Hastings criterion ensuring correct equilibrium statistics for an ( Δµ, N, p, T) ensemble to achieve a ∼1046× boost in acceptance rates. We demonstrate how typical protein (DHFR and the tyrosine kinase Src) and nucleic acid (Drew-Dickerson B-DNA dodecamer) systems exhibit salt concentration distributions that significantly differ from fixed-salt bulk simulations and display fluctuations that are on the same order of magnitude as the average.