Effect Of Chemical Environment Research Articles

Structural equation model was used to evaluate the effects of soil chemical environment, fertility and enzyme activity on eucalyptus biomass.

This paper aims to reveal the effects of multi-generational succession of eucalyptus on soil fertility, organic structure and biological properties. Soil samples were collected from eucalyptus plantations of different stand ages (5, 11, 17 and 21 years old) in a typical area in south Asia, soil organic fraction structure and content characteristics were investigated using Fourier transform infrared (FTIR), and structural equation modelling (SEM) was used to explore influences of soil fertility, enzyme activity and organic fraction on stand biomass. FTIR analysis showed that 11 infrared absorption peaks existed in the soils of this study area, attributed to silicates, aromatics, carbonate ions, sugars, esters, polysaccharides, aliphatic hydrocarbons and phenolic alcohols. Combined with the results of peak area integration, the content of esters, aromatics and phenolic alcohols was significantly higher in 17- and 21-year-old stand soils than in control soils. The results of SEM showed that organic components were negatively related (p < 0.01) to enzyme activity and biomass, with standardized coefficients of 0.53 and 0.49, respectively. In summary, multi-generation succession of eucalyptus trees can change the structure of soil organic functional group composition and promote the enrichment of aromatic and phenolic alcohol functional groups. Such changes can directly inhibit the increase in eucalyptus biomass and indirectly negatively affect biomass by inhibiting enzyme activity.

Piperazine ring toxicity in three novel anti-breast cancer drugs: an in silico and in vitro metabolic bioactivation approach using olaparib as a case study.

The metabolic activation of small-molecule drugs into electrophilic reactive metabolites is widely recognized as an indicator of idiosyncratic adverse drug reactions (IADRs). Three novel anti-breast cancer drugs containing piperazine rings, ribociclib (Kisqali®, RCB), abemaciclib (Verzenio®, ABC), and olaparib (Lynparza®, OLP), were selected to study the effect of different chemical environment on the piperazine ring activation using in silico and in vitro metabolic experiments. ABC and RCB were previously studied and we noticed the piperazine ring in ABC could be strongly bioactivated generating more reactive intermediates than piperazine ring in RCB. OLP was further used as a case study to show the power of in silico software to predict the piperazine ring activation that was approved using in vitro experiments. Initially, predictions of susceptible sites in the metabolism and reactivity pathways were performed using the StarDrop P450 model and XenoSite reactivity tool, respectively. Later, in vitro OLP metabolites were characterized based on rat liver microsomes (RLMs) using KCN (trapping agent) using LC-MS/MS. The main goal of the current study was to answer the question of whether the presence of a piperazine ring in the chemical structure should be always considered a structural alert. Piperazine ring in RBC and ABC was bioactivated through a metabolic sequence that involves the hydroxylation of α-carbon to the tertiary nitrogen atoms of the piperazine ring. In the case of OLP, no cyano adduct was formed due to the presence of two carbonyl groups attached to the two nitrogen atoms of the piperazine ring (neutral amide groups). From the results, piperazine ring in certain cases should not be considered as a structural alert as in the case of OLP due to the presence of two electron withdrawing group that stops the proposed toxicity. Also blocking the bioactive center (α-carbon) using steric hindrances such as methyl group, also the isosteric replacement of α-carbon hydrogen with fluoro atom can aid in reducing the toxic side effects of ABC and RCB. These experiments were done in vitro through incubation with RLMs in the presence of KCN. Also, the results are supported by data generated from in silico software. In the future, drug discovery studies using this concept could be undertaken, allowing for the development of new drugs with reasonable safety profiles. Overall, in vitro RLMs incubations and in silico experiments were able to predict successfully that the piperazine ring should not always be considered a structural alert.

Structures and conformational dynamics of DNA minidumbbells in pyrimidine-rich repeats associated with neurodegenerative diseases

Expansions of short tandem repeats (STRs) are associated with approximately 50 human neurodegenerative diseases. These pathogenic STRs are prone to form non-B DNA structure, which has been considered as one of the causative factors for repeat expansions. Minidumbbell (MDB) is a relatively new type of non-B DNA structure formed by pyrimidine-rich STRs. An MDB is composed of two tetraloops or pentaloops, exhibiting a highly compact conformation with extensive loop-loop interactions. The MDB structures have been found to form in CCTG tetranucleotide repeats associated with myotonic dystrophy type 2, ATTCT pentanucleotide repeats associated with spinocerebellar ataxia type 10, and the recently discovered ATTTT/ATTTC repeats associated with spinocerebellar ataxia type 37 and familial adult myoclonic epilepsy. In this review, we first introduce the structures and conformational dynamics of MDBs with a focus on the high-resolution structural information determined by nuclear magnetic resonance spectroscopy. Then we discuss the effects of sequence context, chemical environment, and nucleobase modification on the structure and thermostability of MDBs. Finally, we provide perspectives on further explorations of sequence criteria and biological functions of MDBs.

Point defect properties of the VCrMnFe0.33 multi-principal alloy from first-principles calculations

We performed first-principles calculations to explore the point defect formation and migration properties and the corresponding chemical environment effects for a bcc VCrMnFe 0.33 multi-principal alloy. The results indicate that the vacancy formation energies vary with local environment, and vacancies favor Mn-rich surroundings. The exchange between vacancies and V atoms presents lower energy barriers due to the large atomic size of V. Moreover, interstitial calculations found that [110] direction dumbbells take up more than 93%, suggesting a slow defect diffusion. The large V interstitials can substitute neighboring atoms and leave the squeezed atom forming dumbbells with its surroundings. Our investigation indicates that this low-activation multi-principal alloy may exhibit promising irradiation resistance due to its special defect properties. All data generated or analyzed during this study are included in this published article.

Extraction processes reduce polyphosphate ion migration, dispersion and diffusion as detected with gel electrophoresis and 31 P DOSY NMR.

Inorganic polyphosphates (polyPs) have been identified in eukaryotic and prokaryotic cells alike. Various extraction methods have been optimized as a necessary step before identification and measurement of these polymers. Three commercially available sodium polyP glasses were either dissolved or dissolved and extracted by two commonly used polyP extraction techniques - perchloric acid or buffered phenol-chloroform. The products were separated by polyacrylamide gel electrophoresis (PAGE), stained with toluidine blue O, and the migration results quantitatively compared. Both extraction processes reduced the relative migration distances of the peak and leading edges, and the stained band lengths, suggesting reduced polyP migration and dispersion. 31 P diffusion-ordered spectroscopy nuclear magnetic resonance confirmed that polyP extraction by perchloric acid or phenol-chloroform processes reduced polyP diffusion coefficients and suggested hydrolytic degradation with stronger end-chain signals. Reduced polyP diffusivity after extraction makes possible an overestimation of synthetic polyP chain length assignment when compared to unextracted polyP ladders with PAGE. The mechanism(s) for reduced synthetic polyP diffusion after extraction and intracellular chemical environment effects on migration are not known.

Nanoscale visualization of metallic electrodeposition in a well-controlled chemical environment

Liquid phase transmission electron microscopy (TEM) provides a useful means to study a wide range of dynamics in solution with near-atomic spatial resolution and sub-microsecond temporal resolution. However, it is still a challenge to control the chemical environment (such as the flow of liquid, flow rate, and the liquid composition) in a liquid cell, and evaluate its effect on the various dynamic phenomena. In this work, we have systematically demonstrated the flow performance of an in situ liquid TEM system, which is based on ‘on-chip flow’ driven by external pressure pumps. We studied the effects of different chemical environments in the liquid cell as well as the electrochemical potential on the deposition and dissolution behavior of Cu crystals. The results show that uniform Cu deposition can be obtained at a higher liquid flow rate (1.38 μl min−1), while at a lower liquid flow rate (0.1 μl min−1), the growth of Cu dendrites was observed. Dendrite formation could be further promoted by in situ addition of foreign ions, such as phosphates. The generality of this technique was confirmed by studying Zn electrodeposition. Our direct observations not only provide new insights into understanding the nucleation and growth but also give guidelines for the design and synthesis of desired nanostructures for specific applications. Finally, the capability of controlling the chemical environment adds another dimension to the existing liquid phase TEM technique, extending the possibilities to study a wide range of dynamic phenomena in liquid media.

1-Methyl-1H-1,2,4-triazole as the main marker of 1,1-dimethylhydrazine exposure in plants.

With their wide application in chemical industry, human health and environmental toxic effects of hydrazines arise extensive concerns. Although hydrazine exposure is known to lead to inhibition of seed germination and seedling growth in plants, there are few reports about the mechanism of oxidation or transformation ways of hydrazines in plant tissue. In this research, garden cress (Lepidium sativum L.) and zucchini (Cucurbita pepo L.) were used as model plant objects to study 1,1-dimethylhydrazine exposure in vitro using the GC-MS system. The seed germination and plant growth experiments were carried out in Petri dishes using an aqueous media. Among the detected 1,1-dimethylhydrazine transformation products in plant tissues, 1-methyl-1H-1,2,4-triazole had the highest intensity and reproducibility. In our research, 1-methyl-1H-1,2,4-triazole formed at all contaminant concentrations in an extremely short period. This preliminary study determined 1,1-dimethylhydrazine environment contamination by detecting 1-methyl-1H-1,2,4-triazole in combination with other transformation products.

Effect of changing chemical environment on physical properties of maize root mucilage

AimsHigh viscosity, low surface tension and hydrophobicity are specific properties of maize root mucilage which contribute to modulate the spatial configuration of the liquid phase in soil pores. Several processes in the rhizosphere, in particularly nutrient absorption, root exudation and microbial activity, may cause strong temporal variations in the chemistry of the soil solution of the rhizosphere. Although the physical properties of maize root mucilage have been repeatedly measured in the last years, their variation upon a changing chemical environment and understanding of the chemical mechanisms governing these properties remain unexplored.MethodsWe investigated how flow and surface properties of maize root mucilage varied by changes in pH, calcium chloride (CaCl2) and lecithin concentrations.ResultsThe physical properties of mucilage can strongly vary depending on the environmental conditions. Low surface tension of maize root mucilage at pH7 was increased by addition of calcium. Upon pH change and lecithin addition, hydrophobic mucilage turned hydrophilic. High Ca concentration above 0.83 mmol Ca (g dry mucilage)−1, the addition of 167 μg lecithin (g dry mucilage)−1 and a pH rise to 9 decreased the viscosity of mucilage.ConclusionSuch variations strongly suggest that the role of mucilage in hydraulic processes in the rhizosphere depends on changes of solutes concentration and composition, which themselves vary according to plant growth and soil water content. It seems that mucilage can best serve as a hydraulic bridge only under certain chemical environments, whose spatio-temporal occurrence in the changing rhizosphere remains to be defined.

Effect of the local chemical environment on oxidation resistance mechanisms in AlNbTiZr refractory high entropy alloys: A first-principles study

The present study is dedicated to the effect of local chemical environment on structure and properties of oxygen adsorption on AlNbTiZr surface from first-principle investigation. The adsorption energy results illustrate that the most stable adsorption sites are those with high content Ti, mainly due to its highest t 2g states near Fermi level. The stronger O-Al than O-Ti interaction will cause outward diffusion of Al, which explains the high concentration Al in oxide layer of AlNbTiZr experimentally. More importantly, Ti atom weakens the O-Al interaction, and thereby may weaken the stability of Al-containing oxides. Consequently, it is necessary to control experimentally by different processing methods to decrease the occurrence of Ti-Ti arrangement on the surface to improve oxidation resistance of AlNbTiZr.

Ab initio prediction of vacancy energetics in HCP Al-Hf-Sc-Ti-Zr high entropy alloys and the subsystems

We perform ab initio density-functional-theory (DFT) calculations to investigate the vacancy formation and migration energies in HCP Al-Hf-Sc-Ti-Zr high entropy alloys (HEAs) and their subsystems from binaries to quinaries. For the vacancy formation properties, we utilize the special quasi-random structure approach in conjunction with a statistical analysis, from which temperature-dependent formation Gibbs energies as well as averaged atomic environments can be extracted. We show that the temperature-dependent vacancy formation Gibbs energy due to configurational excitations has a negative configurational entropy contribution. For the vacancy migration barriers, obtained from the nudged elastic band method, we apply the local cluster expansion technique to the kinetically resolved activation barriers to explore extended vacancy migration phase spaces. The local chemical environment effect and general trends in terms of the “high entropy” effect are analyzed.

Elucidating molecular mechanisms of two-dimensional chemical reactions

Elucidating molecular mechanisms of two-dimensional chemical reactions

Chemical environment effects on the electrochemical performance and thermal stability of PdCu3 nanoparticles in HER cathodic electrodes

The need for diversification of the worldwide industrial matrix encourages the use of cleaner and renewable electrical power sources, such as hydrogen fuel cells. Water electrolysis for H2 production is an efficient process but it demands the development of resourceful, low-cost electrocatalysts for the hydrogen evolution reaction (HER). This work aims to apply carbon supported PdCu3 nanoparticles as electrocatalysts in HER, seeking to understand the influence of atomic chemical environment changes on their activities. Since thermal treatments affect chemical bonds, thus electrodes produced with these nanocatalysts are heated either in air or under vacuum. XPS (X-ray photoelectron spectroscopy) yields precise information on metallic sites evolution, and our analyses infer that thermal treatment in air favours the formation of Pd–O bonds and a strong Cu oxidation. Concomitantly, these electrodes achieve the highest exchange current density and improved catalytic activity. In contrast, the electrodes treated in vacuum form Cu–F bonds and exhibit low activity. These findings strongly indicate that our methodology leads to economically viable copper rich Pd–Cu electrodes, whereas the presence of CuO on the nanoparticles surfaces is a key factor for their improved activity owing to Cu leaching and/or CuO metallization mechanism during HER, and consequent Pd-enrichment of the nanoparticles.

Towards molecular understanding of local chemical environment effects in electro- and photocatalytic CO2 reduction

Towards molecular understanding of local chemical environment effects in electro- and photocatalytic CO2 reduction

Stability, electronic structures, and band alignment of two-dimensional IIA -IV- N2 materials

Structural and phonon properties, formation and cohesive energies, and electronic structures of ${\mathrm{II}}_{A}$-IV-${\mathrm{N}}_{2}$ (where ${\mathrm{II}}_{\mathrm{A}}=\mathrm{Be}$ or Mg; $\mathrm{IV}=\mathrm{Si}$, Ge, or Sn) monolayers with a graphenelike planar structure are systematically studied. Stability and property evolution with the variation of constituent group ${\mathrm{II}}_{A}$ and group IV elements are revealed. Dynamical and elastic stability of ${\mathrm{II}}_{A}$-IV-${\mathrm{N}}_{2}$ monolayers is justified by phonon and elasticity calculations, respectively. Their wide band gaps ranging from 3.32 to 5.61 eV are predicted by the $GW$ method on top of density functional calculations. The fat-band analysis and charge-density calculation of selected eigenstates unveil the effect of chemical environment and elemental substitution on electronic states near the band-gap region. The quasi-free-electron state and the parabolic dispersion of the lowest conduction band are advantageous for electron transport in electronic applications. A close examination of the band alignment and structural similarity between monolayers of ${\mathrm{II}}_{A}$-IV-${\mathrm{N}}_{2}$ compounds and III nitrides indicates that it is possible to form type-I or type-II heterostructures and alloy systems composed of monolayers of ${\mathrm{II}}_{A}$-IV-${\mathrm{N}}_{2}$ compounds and III nitrides. The findings in this work will promote research aiming at the synthesis, characterization, and application of novel two-dimensional materials, alloys, and heterostructures.

Single Molecule Investigation of Nanoconfinement Hydrophobicity in Heterogeneous Catalysis.

Nanoconfinement imposes physical constraints and chemical effects on reactivity in nanoporous catalyst systems. In the present study, we lay the groundwork for quantitative single-molecule measurements of the effects of chemical environment on heterogeneous catalysis in nanoconfinement. Choosing hydrophobicity as an exemplary chemical environmental factor, we compared a range of essential parameters for an oxidation reaction on platinum nanoparticles (NPs) confined in hydrophilic and hydrophobic nanopores. Single-molecule experimental measurements at the single particle level showed higher catalytic activity, stronger adsorption strength, and higher activation energy in hydrophobic nanopores than those in hydrophilic nanopores. Interestingly, different dissociation kinetic behaviors of the product molecules in the two types of nanopores were deduced from the single-molecule imaging data.

The effect of local chemical environment on the energetics of stacking faults and vacancy platelets in [formula omitted]-zirconium

The onset of breakaway irradiation growth in Zr and its alloys has been correlated with the nucleation and growth of faulted vacancy c-loops on basal planes. One theory for c-loop stabilization at high fluence is the reduction in stacking fault energy by solute or impurity segregation. This hypothesis is investigated through density functional theory calculations of the binding energy of Fe, Sn, Nb, Cr, and Ni to basal extrinsic, basal intrinsic or prismatic stacking faults in α-Zr. By means of a thermodynamic model, the ab initio binding energies have been correlated to segregation profiles and modified SFEs. Sn and Fe are shown to be tightly bound to basal stacking faults with only a weak interaction towards prismatic stacking faults. The corresponding segregation to faulted basal c-loops significantly reduces their formation energies and has the potential to stabilize these defects in the matrix. Based on the DFT calculations presented here, Nb, Cr, and Ni do not have a considerable effect on faulted c-loop formation energies. The binding energies of Fe, Sn, Nb, Cr, Ni, and H to a 19-vacancy platelet were additionally calculated to confirm the behavior of these elements with a nucleating c-loop defect. Fe and Cr in particular show strong binding to the periphery of this high-energy structure and correspondingly reduce the nucleation barrier for a vacancy c-loops.

Effect of Surrounding Chemical Environment on Adsorption and Accumulation of Serum Protein onto Octacalcium Phosphate Crystals

Effect of Surrounding Chemical Environment on Adsorption and Accumulation of Serum Protein onto Octacalcium Phosphate Crystals

Dissolution of olivines from steel and copper slags in basic solution

This study explores the effect of aqueous chemical environment on the dissolution rate of the minerals γ-C2S and fayalite, identified as primary phases of ladle furnace steel slag and copper slag. γ-C2S and fayalite were exposed to solutions of NaOH and Ca(OH)2, chosen to mimic the pore solutions of alkali-activated and Portland-cement based binders. While both from the olivine mineral group, γ-C2S and fayalite displayed opposing dissolution trends with respect to pH. The rates of γ-C2S dissolution were observed to decrease with higher pH, while fayalite dissolution rates increased with pH, and both relationships were described via empirical functions of the form R = k ∙ aH+n. The contrasting dependence of dissolution rate on pH for both minerals was attributed to the formation of chemically distinct surface layers on both minerals during dissolution. These results have significance for blending of slags with high olivine contents in binders with a range of aqueous chemical environments.

Total Internal Reflection Transient Absorption Microscopy: An Online Detection Method for Microfluidics.

Microreactors have garnered widespread attention for their tunability and precise control of synthetic parameters to efficiently produce target species. Despite associated advances, a lack of online detection and optimization methods has stalled the progression of microfluidic reactors. Here we employ and characterize a total internal reflection transient absorption microscopy (TIRTAM) instrument to image excited state dynamics on a continuous flow device. The experiments presented demonstrate the capability to discriminate between different chromophores as well as in differentiating the effects of local chemical environments that a chromophore experiences. This work presents the first such online transient absorption measurements and provides a new direction for the advancement and optimization of chemical reactions in microfluidic devices.

Chemical environment and magnetic moment effects on point defect formations in CoCrNi-based concentrated solid-solution alloys

Atomic investigation of point defects is the basis for exploring the mechanisms underlying the macro performance of materials under irradiation. Owing to the complex local disordered chemical environments and unique site-to-site lattice distortions, there have been few related studies on high-entropy alloys (HEAs). In this work, we applied ab initio calculations to systemically characterize the chemical environment and magnetic moment effects on point defect formations in three equimolar alloys, namely: CoCrNi, CoCrNiFe, and CoCrNiFeMn. These calculations were based on investigations of a large number of statistical atomic sites. An appropriate method applying similar atomic environments (SAEs) and an efficient approach using Widom-type substitution techniques were employed to achieve results that were reliable. It was found that the vacancy formation energies (VFEs) were conspicuously larger in the CoCrNiFeMn HEA than in the CoCrNi or CoCrNiFe alloys. The local chemical environment—in particular, the number of first-nearest neighbor (1nn) Ni and Cr atoms—is the key factor affecting the VFE, as vacancies prefered Ni-rich and Cr-poor environments. Interstitial defects were primarily dominated by Co and Mn. Finally, the point defect formation energies were found to be negatively correlated with the anti-magnetic moment changes in 1nn atoms. Our results indicate that the low vacancy generation in HEAs is important for their enhanced irradiation resistance and that the local anti-magnetic moments influences of the constituent elements on the VFEs provide guidance for the design of advanced radiation-resistant HEAs.