Changes In Chemical Environment Research Articles

Facile Construction of pH- and Redox-Responsive Micelles from a Biodegradable Poly(β-hydroxyl amine) for Drug Delivery.

Here we demonstrate a type of pH and reduction dual-sensitive biodegradable micelles, which were self-assembled by a cationic polymer in an aqueous solution. Due to tumor cells or tissues showing low pH and high reduction concentration, these micelles possessed specific tumor targetability and maximal drug-release controllability inside tumor cells upon changes in physical and chemical environments, but presented good stability at physiological conditions. CCK-8 assay showed that the DOX-loaded micelles had a similar cytotoxicity for MCF-7 tumor cells as free DOX, and blank micelles had a very low cytotoxicity to the cells. Fluorescent microscopy observation revealed that the drug-loaded micelles could be quickly internalized by endosomes to inhibit cancer cell growth. These results indicated these biodegradable micelles, as a novel and effective pH- and redox-responsive nanocarrier, have a potential to improve drug delivery and enhance the antitumor efficacy.

AtomicChargeCalculator: interactive web-based calculation of atomic charges in large biomolecular complexes and drug-like molecules.

BackgroundPartial atomic charges are a well-established concept, useful in understanding and modeling the chemical behavior of molecules, from simple compounds, to large biomolecular complexes with many reactive sites.Results This paper introduces AtomicChargeCalculator (ACC), a web-based application for the calculation and analysis of atomic charges which respond to changes in molecular conformation and chemical environment. ACC relies on an empirical method to rapidly compute atomic charges with accuracy comparable to quantum mechanical approaches. Due to its efficient implementation, ACC can handle any type of molecular system, regardless of size and chemical complexity, from drug-like molecules to biomacromolecular complexes with hundreds of thousands of atoms. ACC writes out atomic charges into common molecular structure files, and offers interactive facilities for statistical analysis and comparison of the results, in both tabular and graphical form.ConclusionsDue to high customizability and speed, easy streamlining and the unified platform for calculation and analysis, ACC caters to all fields of life sciences, from drug design to nanocarriers. ACC is freely available via the Internet at http://ncbr.muni.cz/ACC.Electronic supplementary materialThe online version of this article (doi:10.1186/s13321-015-0099-x) contains supplementary material, which is available to authorized users.

A Fundamental Assessment of Graphite Nanoplatelet Effects on Progress of Alkali-Silica Reactions

Graphite nanoplatelets were used to control alkali-silica reactions in concrete by enhancing the barrier qualities of cementitious binders and providing local reinforcing effects against the damaging expansive phenomena. Nuclear magnetic resonance (NMR) spectroscopy was used to monitor the changes in chemical environment that reflect upon alkali-silica reactivity. Laboratory experiments were conducted to evaluate the effects of graphite nanoplatelets on alkali-silica reactions (ASRs). Reactive flint aggregates were used to induce ASR. The ²⁹Si MAS NMR spectroscopy technique was employed for evaluating the changes in chemical environment by monitoring different silicate tethrahedra (Qⁿ) as a basis to quantify the progress of ASR in concrete materials prepared with and without graphite nanoplatelets. Quantitative evaluations of different Qⁿ species present in anhydrous cement, calcium silicate hydrate (C-S-H), and ASR products indicated that introduction of graphite nanoplatelets lowered the degree of polymerization of silicate tetrahedral in C-S-H. The reduction in the breakdown of the networked structure of silicate tetrahedra under accelerated ASR indicates that graphite nanoplatelets reduce the extent of ASRs.

E. coli DH5α cell response to a sudden change in microfluidic chemical environment.

Motile bacteria respond to changing chemical environment by moving towards or away from a particular location. Bacterial migration under chemical gradient is one of the most studied areas in biomedical field. In this work we looked into how bacterial cells respond to sudden change in the microfluidic chemical environment. E. coli DH5α cells were subjected to an attractant gradient (0.1 mM sorbitol--attractant to E. coli cells) and after 120 min the same cells were exposed to an inhibitor (0.1 mM NiSO4) gradient in the same microfluidic device. Our studies revealed that when the E. coli DH5α cells were exposed to 0.1 mM sorbitol, they showed faster chemotaxis towards the attractant (0.1 mM sorbitol) and achieved steady state by 60 min. When we replaced 0.1 mM sorbitol with 0.1 mM NiSO4 in the device we found that that the E. coli DH5α cells started responding to change in chemical environment within 10 min and achieved steady state at the end of 60 min. This shows that the bacterial cells respond to change in local chemical environment is within few minutes.

Role of Confinement in Localized Corrosion

In context of localized corrosion, the dissolution of metallic species into a bulk electrolyte solution will produce negligible changes in the concentration of a bulk solution (Refer Fig. 1a). However, if the immediate environment is confined and has limited electrolyte with respect to the metal surface area - as would be the case for a crevice, environmentally assisted cracking, or a deep pit - the limited amount of dissolved species produced as a result of anodic dissolution would be adequate to change the chemical composition (i.e. concentration) of the confined solution as shown in Fig. 1a. Should the change in chemical environment be adequately adverse, these primary reaction products will lead to secondary reactions within the confined space, thus accelerating corrosion damage. This research explores the quantitative effect of confinement on chemical reactivity of metals susceptible to pitting and stress corrosion cracking (SCC). To investigate the effects of confinement, a simulated crevice was created by maintaining a tight spacing between the polished surface of a flat pH probe and the metal test specimen, as shown in Fig. 1b. The pH probe and the solution are held against the sample by an inert polyethylene fixture. Sensitized AA5083 was chosen as the test material because of its susceptibility to SCC as a result of intergranular precipitates of Al2Mg3 known as β-phase. The electrolyte was pH neutral 0.1 M sodium chloride solution. Exposing AA5083 to neutral-pH NaCl solution under confinement in free corrosion conditions triggered a spontaneous localized alkaline corrosion, which resulted in a gradual evolution of the pH from 6.9 to roughly 9. At this higher pH value, the passivation film was damaged and hydrogen evolution that promotes the increase in pH was observed as the counter-reaction to aluminum oxidation. This research presents the effect of different ratios of metal surface area to electrolyte volume on the reaction kinetics, as characterized by the evolution of the solution pH with time. Surface area to volume ratios ranged from 4 cm2/ml to 100 cm2/ml. The results are supported with microscopic analysis and EIS studies. Figure 1

Investigation of LiMn2O4-Li2NiF4 Solid Solutions As Electrode Materials for Lithium-Ion Batteries

Lithium ion batteries play a very important role in consumer electronics as the component where energy stored. However, today’s lithium ion batteries are not suitable for widespread application in electric vehicles due to the high cost required to achieve desired levels of energy density and life.1 Improvements in energy density (cell voltage and/or storage capacity) are still sought for these applications. Given the high capacity of graphite-based negative electrodes, the focus is placed on increasing performance at the positive electrode. Today, the most popular positive electrode materials are layered LiMO2 (M = Co, Mn, Ni), spinel LiM 2O4 (M = Mn, Ni), and olivine LiMPO4 (M = Fe, Co, Mn).2, 3 LiM 2O4 and its derivatives are widely used in current electric vehicles mainly because of their robust framework with fast ionic diffusion and low cost. In this work, we explore the possibility of raising their voltage of operation by incorporating Li2NiF4 into the LiMn2O4 lattice to form a solid solution of LiMn2O4-Li2NiF4 by taking the advantage of their structural similarity. The reaction between the two components is complex. Apart from single phase samples, core-shell structures could also be obtained by varying the ratio of two components as well as reaction duration. An example of this competition is provided by LiMn2O4-20% Li2NiF4, as shown by the different elemental distributions from energy dispersive spectroscopy (EDS) elemental maps in Figure 1, indicating solid solution and core-shell structures, respectively. The local chemical environment change of oxygen, fluorine and transition metals has been investigated by X-ray absorption spectroscopy. The electrochemical performance of the phase-pure LiMn2O4-Li2NiF4solid solutions will also be presented. ADDIN EN.REFLIST 1. R. V. Noorden, Nature, 50726-28 (2014). 2. J. M. Tarascon and M. Armand, Nature, 414359-367 (2001). 3. B. L. Ellis, K. T. Lee, and L. F. Nazar, Chem. Mater., 22691-714 (2010). Figure 1

A dispenser-reactor apparatus applied for in situ XAS monitoring of Pt nanoparticle formation.

In situ time-resolved X-ray absorption spectroscopy (XAS) measurements collected at the Pt L3-edge during the synthesis of Pt nanoparticles (NPs) in aqueous solution are reported. A specially designed dispenser-reactor apparatus allowed for monitoring changes in the XAS spectra from the earliest moments of Pt ions in solution until the formation of metallic nanoparticles with a mean diameter of 4.9 ± 1.1 nm. By monitoring the changes in the local chemical environment of the Pt atoms in real time, it was possible to observe that the NPs formation kinetics involved two stages: a reduction-nucleation burst followed by a slow growth and stabilization of NPs. Subsequently, the synthesized Pt NPs were supported on activated carbon and characterized by synchrotron-radiation-excited X-ray photoelectron spectroscopy (XPS), X-ray diffraction (XRD) and extended X-ray absorption fine structure (EXAFS). The supported Pt NPs remained in the metallic chemical state and with a reduced size, presenting slight lattice parameter contraction in comparison with the bulk Pt values.

Relative importance of soil physico-chemical characteristics and plant species identity to the determination of soil microbial community structure

The structure of soil microbial communities is affected by biotic and abiotic environmental factors, such as plant community composition and soil chemical characteristics, among others. However, little is known about the relative importance of these factors on soil microbial community structure. The objective of this study was to verify which factor, soil chemical characteristics or plant species identity, is more important to the determination of soil microbial community structure. For this, a factorial experiment with four soil chemical conditions and five plant species were set in a greenhouse. After 80 days of cultivation, the rhizospheric soil microbial community structure was accessed by a multiplex T-RFLP, and the mycorrhizal colonization of roots and plant shoot dry mass were estimated. Plant species showed similar growth responses to different soil chemical conditions, but exhibited different patterns in the control of root mycorrhizal colonization. A principal component analysis (PCA) was performed using the T-RFLP data set and showed that soil chemical condition is the main factor defining the structure of soil microbial community. Archaeal and bacterial communities showed to be more sensitive to changes in the soil chemical environment, suggesting a greater importance of these microbial groups in plant adaptation.

Start-up strategies in manure-fed biogas reactors: Process parameters and methanogenic communities

Four start-up strategies were assayed in 75 dm3 continuous stirred-tank reactors to select the optimal conditions for the start-up of the demonstration BIO4GAS® plant. Two reactors were completely filled with manure and their temperature increased from 20 to 37 °C at either a slow or fast rate. The other two reactors were started at 37 °C with a seed sludge from a stably operating plant and their load (cattle manure) increased at a low or high rate. Reactor performance was monitored for 35 days. The composition and abundance of the methanogenic communities was determined using a phylogenetic microarray and quantitative PCR. All reactors performed successfully in terms of biogas production and experienced a steady start-up, with pH values above 7.3 and VFA/alkalinity ratios below 0.3, denoting stability. Similar methanogenic loads (averaging 5 × 107 g-1 of 16S rRNA gene copies) were detected in the cattle manure and seed sludge, however the methanogenic diversity was higher in the manure with dominance of Methanosarcina and subdominance of Methanocorpusculum and Methanobrevibacter. Starting-up the reactors with an initial full load of manure and progressively increasing the temperature entailed less changes in the sludge chemical environment and in the dynamics of the dominant methanogens. Using a rate of temperature increase of 0.61 K d−1 proved better than1.21 K d−1 with a methane yield of 103.8 dm3 kg−1 VS and a COD mass removal efficiency of 28.3%. The diverse methanogenic community in the manure easily adapted to reactor upsets due to forced overload conditions.

Protein folding and binding can emerge as evolutionary spandrels through structural coupling

Binding interactions between proteins and other molecules mediate numerous cellular processes, including metabolism, signaling, and gene regulation. These interactions often evolve in response to changes in the protein's chemical or physical environment (such as the addition of an antibiotic). Several recent studies have shown the importance of folding stability in constraining protein evolution. Here we investigate how structural coupling between folding and binding--the fact that most proteins can only bind their targets when folded--gives rise to an evolutionary coupling between the traits of folding stability and binding strength. Using a biophysical and evolutionary model, we show how these protein traits can emerge as evolutionary "spandrels" even if they do not confer an intrinsic fitness advantage. In particular, proteins can evolve strong binding interactions that have no functional role but merely serve to stabilize the protein if its misfolding is deleterious. Furthermore, such proteins may have divergent fates, evolving to bind or not bind their targets depending on random mutational events. These observations may explain the abundance of apparently nonfunctional interactions among proteins observed in high-throughput assays. In contrast, for proteins with both functional binding and deleterious misfolding, evolution may be highly predictable at the level of biophysical traits: adaptive paths are tightly constrained to first gain extra folding stability and then partially lose it as the new binding function is developed. These findings have important consequences for our understanding of how natural and engineered proteins evolve under selective pressure.

Millisecond single-molecule localization microscopy combined with convolution analysis and automated image segmentation to determine protein concentrations in complexly structured, functional cells, one cell at a time.

We present a single-molecule tool called the CoPro (concentration of proteins) method that uses millisecond imaging with convolution analysis, automated image segmentation and super-resolution localization microscopy to generate robust estimates for protein concentration in different compartments of single living cells, validated using realistic simulations of complex multiple compartment cell types. We demonstrate its utility experimentally on model Escherichia coli bacteria and Saccharomyces cerevisiae budding yeast cells, and use it to address the biological question of how signals are transduced in cells. Cells in all domains of life dynamically sense their environment through signal transduction mechanisms, many involving gene regulation. The glucose sensing mechanism of S. cerevisiae is a model system for studying gene regulatory signal transduction. It uses the multi-copy expression inhibitor of the GAL gene family, Mig1, to repress unwanted genes in the presence of elevated extracellular glucose concentrations. We fluorescently labelled Mig1 molecules with green fluorescent protein (GFP) via chromosomal integration at physiological expression levels in living S. cerevisiae cells, in addition to the RNA polymerase protein Nrd1 with the fluorescent protein reporter mCherry. Using CoPro we make quantitative estimates of Mig1 and Nrd1 protein concentrations in the cytoplasm and nucleus compartments on a cell-by-cell basis under physiological conditions. These estimates indicate a ∼4-fold shift towards higher values in the concentration of diffusive Mig1 in the nucleus if the external glucose concentration is raised, whereas equivalent levels in the cytoplasm shift to smaller values with a relative change an order of magnitude smaller. This compares with Nrd1 which is not involved directly in glucose sensing, and which is almost exclusively localized in the nucleus under high and low external glucose levels. CoPro facilitates time-resolved quantification of protein concentrations in single functional cells, and enables the distributions of concentrations across a cell population to be measured. This could be useful in investigating several cellular processes that are mediated by proteins, especially where changes in protein concentration in a single cell in response to changes in the extracellular chemical environment are subtle and rapid and may be smaller than the variability across a cell population.

The role of Ag in (Ag,Cu)2ZnSnS4 thin film for solar cell application

Recently, Ag incorporation into Cu(In,Ga)Se2 structure was found to benefit the solar cell performance. However, (Ag,Cu)2ZnSnS4 used as the solar cell absorber is not widely reported even though Ag2ZnSnS4 has shown much better photocatalysts activity for H2 evolution than Cu2ZnSnS4. In this paper, (Ag,Cu)2ZnSnS4 thin film solar cell was synthesized through sulfurization of Ag/Zn/Cu/Sn metallic stacked layers. In order to understand the actual role of Ag in the Cu2ZnSnS4 structure, the changing chemical environment, microstructure and intragrain defect due to the Ag incorporation, were studied by X-ray photoelectron spectroscopy and transmission electron microscopy. After sulfurization, Ag is uniformly distributed in the absorber and is incorporated into Cu2ZnSnS4 crystal structure but no obvious change of the Cu2ZnSnS4 chemical environment is detected. A large density of voids is formed at the Cu2ZnSnS4/Mo interface and some of these voids are found to be coated with CdS which is believed to be detrimental to Cu2ZnSnS4 device performance. In contrast, Ag incorporation reduces the size and amount of voids and thus effectively eliminates CdS deposited at back contact region. Moreover, fewer planar defects and Cu vacancies are formed in the (Ag,Cu)2ZnSnS4 sample than Cu2ZnSnS4 sample as suggested by electron diffraction patterns. Therefore, improved solar cell performance should result from the formation of (Ag,Cu)2ZnSnS4 structure.

Study on the microstructure of cement-based piezoelectric ceramic composites

In this paper, a study is presented on the microstructure of a cement-based PZT (Lead Zirconate Titanate) piezoelectric ceramic composite. A mechanism is proposed for chemical bonding between piezoelectric ceramic particles and cement material in the composite. The microstructure of the composite, as well as chemical bonding at the ceramic–cement interface is investigated using XRD, IR and XPS. Experimental results indicate that Ti–O in the ceramic particles links to Si–O in the cement paste via bridging oxygen, forming a Ti–O⋯Si–O bonding. And the change of chemical environment takes place for all of Ti, Si, Ca and Zr for cement-based piezoelectric ceramic composites. One prominent result pertaining to chemical reactions at the interface between ceramic particles and cement paste shows that Ti diffuses into the cement paste via Ti–O⋯Si–O bonding.

Stabilization of alkali earth metal cations in Na-4-mica

Na-4-mica, a highly charged swelling mica, has suffered from insufficient understanding of some fundamental features such as partial layer collapse and rearrangement of interlayered cations and layers during exchange reaction. This study focuses on elucidating the changes in chemical environments of divalent cations and in layered structure during the exchange reaction with divalent cations. Cation exchange reaction with a series of alkali earth cations led to significant changes in both XRD pattern and IR spectra. The extent of cation exchange reaction depended highly and systematically on cation size and hydration energy. Exchange reaction with Mg2+ and Ca2+ led to highly hydrated phases whereas that with Sr2+ to anhydrous phase and that with Ba2+ to remarkable degradation of layered structure. The hydrated divalent cations could be quickly stabilized in interlayer space in spite of localized incompatibility of both lattice and charge through formation of interstratified phases having various ratios of Na+/M2+ and Na+/H3O+. Therefore, divalent cations could be stably accommodated either in hydrated or anhydrous state within the cavities, preferably around crystal edges to obstruct their further uptake.

Observing Pt nanoparticle formation at the atomic level during polyol synthesis.

This study investigated the synthesis of platinum nanoparticles (Pt NPs) in ethylene glycol using low cost and low toxicity chemicals as reducing (ascorbic acid) and stabilizing agents (polyvinylpyrrolidone and sodium citrate). By monitoring the changes in the local chemical environment of the Pt atoms in real time by in situ dispersive X-ray absorption spectroscopy, it is observed that the NP formation kinetics involved three different stages within 3 h 30 min of the reaction: a reduction-nucleation burst, followed by diffusion-limited Ostwald ripening growth and subsequent stabilization of the NPs. The resulting Pt NPs were analyzed by transmission electron microscopy and X-ray diffraction, revealing a monodisperse average size distribution of 2.7 ± 0.5 nm, characterized by highly crystalline and stable Pt clusters, showing no significant aging for at least nine months.

A High‐Performance Microbial Battery Based on the Chemotactic Biofilm of a Motile Microaerophilic Bacterium

AbstractMotile bacteria adapt themselves to changes in chemical environment by a stochastic mechanism called chemotaxis, which plays a major role in many bacterial processes. We report here for the first time that the preferential migration of bacteria across a nutrient gradient can be harnessed to generate useful electric power. The chemotactic battery demonstrated in the present work involves a nutrient‐localized anode toward which bacteria activated by starvation migrate and generate electricity by oxidation of the nutrient molecules. The chemotactic battery yields a significant power density (25±2 W m−2). Systematic investigation on biofilm morphology and electroactivity reveals significant differences between chemotactic and non‐chemotactic configurations. In addition, the chemotactic setup has also been integrated in the anode chamber of a microbial fuel cell to improve microbial biofilm properties. Thus the results of the study could be used to design miniature microbial batteries for portable applications as well as to improve the performance of microbial fuel cells.

Novel high-pressure crystal structures of boron trifluoride

This study systematically investigated the high-pressure crystal structures of solid trifluoride (BF 3 ) using first principle structure searches and several high-pressure phases were predicted. We found that the coordination of B atoms increased from 3 to 4 at 11 GPa, and to 6 at 160 GPa, while all the F atoms were bridge bonding at a sufficiently high pressure, from terminal bonding. Further calculations of the electronic properties showed that solid BF 3 remained insulating up to the highest pressure considered, i.e., 300 GPa. Phonon calculations indicated that all the predicted structures of BF 3 are dynamically stable under high pressure. These results show that pressure plays an important role in the changing chemical environments of elements, thereby improving our understanding of the evolution of structure and bonding with compression in other molecular systems, particularly in other boron trihalides. • We predicted several novel high-pressure phases of solid BF 3 . • We examined the electronic properties of solid BF 3 up to 300 GPa. • The predicted BF 3 structures are dynamically stable at high pressure. • The coordination of the B atoms in BF 3 is 6 at 160 GPa.

The Investigation of Sequence-dependent Interaction of Messenger RNA Binding to Carbon Nanotube

To investigate carbon nanotubes (CNTs) as gene delivery vehicles, it is essential to characterize their interactions with mRNA. Messenger RNA is a powerful tool for controlling the expression of genes in biomedical applications. In the present report, we study the interactions of single-walled CNT with three codons of mRNA(UGC,GAC,CAG) by using MM, AM1,HF and DFT (B3LYP) methods with STO-3G and 3-21G basis sets in gas phase. To estimate the stability of Nanotubes- mRNA complexes total energy of the systems were determined. The varieties of obtained energy data suggest the relation between the stability of complexes as this order: CAG > GAC > UGC. According to the ability of NMR in providing detailed information about the structure and chemical environment of molecules, this technique has been carried out by supposing gauge-included atomic orbital (GIAO). Considering on the calculated results of NMR chemical shift consist of σiso, σaniso, Δσ, δ and η that are very sensitive to small changes in molecular geometry and chemical environments and the results of energy reveal that the characteristic's variety and the stability of these complexes is depend on the specific mrna base and nucleotide sequences. We can predict that diseases with special mutation and gene sequences are the better aim for special kinds of treatment. Current observations will allow the implementation of new strategies in the development of CNT: mRNA complexes as effective gene therapy.

Strength failure and crack coalescence behavior of sandstone containing single pre-cut fissure under coupled stress, fluid flow and changing chemical environment

In order to study the strength failure and crack coalescence characteristics of cracked rocks, uniaxial compression experiments were conducted on cylindrical sandstone specimens, sampled from Longyou Grottoes of Zhejiang Province, China, with a single pre-cut crack soaking in different chemical solutions. Based on the results of uniaxial compressive test under different chemical solutions and velocities of flow, the effect of strength and deformation characteristics and main modes of crack coalescence for cracked rocks under chemical corrosion were analyzed. The results show that the pH value and velocity of the chemical solutions both have great influence on the sandstone sample’s uniaxial compressive strength and deformation characteristics. Cracked sandstone samples are tension-destructed under uniaxial compression, and the crack propagation directions are consistent with the loading direction. The phenomena of crack initiation, propagation and coalescence of sandstone are well observed. Four different crack types are identified based on the crack propagation mechanism by analyzing the ultimate failure modes of sandstone containing a single pre-cut fissure. The failure process of specimen in air is similar with the specimen under chemical solutions, however, the initial time of crack occuring in specimen under chemical solutions is generally earlier than that in the natural specimen, and the crack propagation and coalescence process of specimen under chemical solutions are longer than those of the natural specimen due to softening of structure of rock caused by hydro-chemical action. Immersion velocity of flow and chemical solutions does not have influence on the ultimate modes of crack coalescence.

Monitoring conformational changes in the NDM-1 metallo-β-lactamase by 19F NMR spectroscopy.

The New Delhi metallo-β-lactamase (NDM-1) is involved in the emerging antibiotic resistance problem. Development of metallo-β-lactamases (MBLs) inhibitors has proven challenging, due to their conformational flexibility. Here we report site-selective labeling of NDM-1 with 1,1,1-trifluoro-3-bromo acetone (BFA), and its use to study binding events and conformational changes upon ligand–metal binding using 19F NMR spectroscopy. The results demonstrate different modes of binding of known NDM-1 inhibitors, including l- and D-captopril by monitoring the changing chemical environment of the active-site loop of NDM-1. The method described will be applicable to other MBLs and more generally to monitoring ligand-induced conformational changes.