Binding Isotherms Research Articles

Synthesis, recognition properties and drug release behavior of diltiazem‐imprinted chitosan‐based biomaterials

AbstractIn this study, we prepared diltiazem (DTZ)‐imprinted biomaterials for TDDS using chitosan, PVA, plasticizers, and sulfosuccinic acid. DTZ and the prepared biomaterials were characterized using field emission scanning electron microscopy, Fourier transform infrared, and 1H nuclear magnetic resonance. DTZ recognition properties were confirmed by the binding isotherm, Scatchard plot analysis, the adsorption of materials with structures similar to DTZ, selectivity factor (α), and the imprinting‐induced promotion of binding (IPB). Results revealed that adsorbed amount (Q) of DTZ‐imprinted biomaterials was 1.63–2.53 times higher than that of non‐imprinted biomaterials. In addition, it could be verified that DTZ‐imprinted biomaterials have a binding site for DTZ according to Scatchard plot analysis. Furthermore, the results of α and IPB indicated that the recognition capacity of the prepared DTZ‐imprinted biomaterials is superior to that non‐imprinted biomaterials. DTZ release properties were evaluated under various pH buffers and artificial skin. Results indicated that the DTZ release in buffers at low pH was faster than that in buffers at high pH. The DTZ release using artificial skin was continuous over 20 days. Furthermore, the DTZ release profile in the buffer followed the pseudo‐Fickian diffusion mechanism, whereas the profile in the artificial skin test followed a non‐Fickian diffusion mechanism.

Site heterogeneity and broad surface-binding isotherms in modern catalysis: Building intuition beyond the Sabatier principle

Learning the science of heterogeneous catalysis and electrocatalysis always starts with the simple case of a flat, uniform surface with an ideal adsorbate. It has of course been recognized for a century that real catalysts are more complicated. For the increasingly complex catalysts of the 21st century, this Perspective argues that surface heterogeneity and non-ideal binding isotherms are central features, and their implications need to be incorporated in current thinking. A variety of systems are described herein where catalyst complexity leads to broad, non-Langmuirian surface isotherms for the binding of hydrogen atoms – and this occurs even for ideal, flat Pt(111) surfaces. Modern catalysis employs nanoscale materials whose surfaces have substantial step, edge, corner, impurity, and other defect sites, and they increasingly have both metallic and non-metallic elements MnXm, including metal oxides, chalcogenides, pnictides, carbides, doped carbons, etc. The surfaces of such catalysts are often not crystal facets of the bulk phase underneath, and they typically have a variety of potential active sites. Catalytic surfaces in operando are often non-stoichiometric, amorphous, dynamic, and impure, and often vary from one part of the surface to another. Understanding of the issues that arise at such nanoscale, multi-element catalysts is just beginning to emerge. Yet these catalysts are widely discussed using Brønsted/Bell-Evans-Polanyi (BEP) relations, volcano plots, Tafel slopes, the Butler-Volmer equation, and other linear free energy relations (LFERs), which all depend on the implicit assumption that the active sites are “similar” and that surface adsorption is close to ideal. These assumptions underly the ubiquitous intuition based on the Sabatier Principle, that the fastest catalysis will occur when key intermediates have free energies of adsorption that are not too strong nor too weak. Current catalysis research often aims to minimize the complexity of non-ideal isotherms through experimental and computational design (e.g., the use of single crystal surfaces), and these studies are the foundation of the field. In contrast, this Perspective argues that the heterogeneity of binding sites and binding energies is an inherent strength of these catalysts. This diversity makes many nanoscale catalysts inherently a high-throughput screen wrapped in a tiny package. Only by making the heterogeneity part of the foundation of catalysis models, sorting the types of active sites and dissecting non-ideal binding isotherms, will modern catalysis learn to harness the inherent diversity of real catalysts. Controlling and exploiting diversity rather than avoiding it will help to optimize complex modern catalysts and catalytic conditions.

OpenHW3 – An open-source, low-cost temperature-controlled orbital shaker

The current lack of standardized testing methods to assess the binding isotherms of ions in cement and concrete research leads to uncontrolled variability in these results. In this study, an open-source and low-cost apparatus, named OpenHW3, is proposed to accurately measure the binding isotherms of ions in various cementitious material systems. OpenHW3 provides two main options, a temperature-controlled orbital shaker, as well as an option to retrofit a commercial orbital shaker for temperature control. The effectiveness of these device options is validated via comparison with conventional binding isotherms experiments. The binding isotherm results were comparable to conventional Waterbath shakers, while providing more reliable results compared to horizontal commercial shakers. It also provided accurate temperature control between 25 °C and 75 °C. The results here are critical for allowing open access to scientific equipment, and providing high-quality binding isotherm data for reliable service life models of urban infrastructure assets throughout the world.

Presenting a new fluorescent probe, methyl(10-phenylphenanthren-9-yl)sulfane sensitive to the polarity and rigidity of the microenvironment: applications toward microheterogeneous systems.

A molecule, methyl(10-phenylphenanthren-9-yl)sulfane (MPPS), with a straightforward structure, has been synthesized, characterized, and explored as a new fluorescent probe for microheterogeneous systems. The photophysical properties of MPPS have been studied through experimental and theoretical calculations using the range-separated hybrid functional CAM-B3LYP in conjunction with a 6-311++g(d,p) basis set. Theoretical calculations show that the freely rotating phenyl ring forms a 94° dihedral angle with the phenanthrene ring in the ground state. Experimentally found two absorption bands correspond to the n → π* and π → π* transitions supported by the frontier molecular orbital calculations. Two excited singlet states, E-1 and E-2 (the former being more stable than the latter in the gas phase), exist with dihedral angles between the phenyl and phenanthrene rings as 142° and 133°, respectively, in the gas phase. Two emitting states in a condensed medium of varying polarities are supported by the steady-state fluorescence and fluorescence intensity decay data. Emission energies, fluorescence intensities, and excited singlet state lifetimes change with the polarity of the solvents. To support that the free rotation in the molecule is responsible for these changes, the fluorescence properties of another molecule, methyl(10-(o-tolyl)phenanthren-9-yl)sulfane (MTPS), with restricted rotation of the substituted benzene, i.e., o-tolyl ring have been studied. The fast-intensity decay component of MPPS is ascribed to the conformer in the E-1 state. The molecule has proved to be an excellent polarity probe explored to determine the critical micelle concentrations (cmc) values of different surfactants, which agree well with the literature reports. Different regions of binding isotherm (specific, non-cooperative, cooperative, and massive binding) of a gemini surfactant, 12-6-12,2Br- with bovine serum albumin (BSA) have been successfully demonstrated by the steady-state and time-resolved fluorescence and fluorescence anisotropic properties of MPPS. Docking results show that MPPS resides in the hydrophobic pocket of BSA. The fluorescence quenching of BSA by MPPS reveals the location of Trp residues of BSA. Thus, a polarity and molecular rigidity-sensitive fluorescent molecule, MPPS has been presented here that can potentially be used to monitor the changes in the microenvironment of biomolecules in different processes.

Maximizing the Accuracy of Equilibrium Dissociation Constants for Affinity Complexes: From Theory to Practical Recommendations.

The equilibrium dissociation constant (Kd) is a major characteristic of affinity complexes and one of the most frequently determined physicochemical parameters. Despite its significance, the values of Kd obtained for the same complex under similar conditions often exhibit considerable discrepancies and sometimes vary by orders of magnitude. These inconsistencies highlight the susceptibility of Kd determination to large systematic errors, even when random errors are small. It is imperative to both minimize and quantitatively assess the systematic errors inherent in Kd determination. Traditionally, Kd values are determined through nonlinear regression of binding isotherms. This analysis utilizes three variables: concentrations of two reactants and a fraction R of unbound limiting reactant. The systematic errors in Kd arise directly from systematic errors in these variables. Therefore, to maximize the accuracy of Kd, this study thoroughly analyzes the sources of systematic errors within the three variables, including (i) non-additive signals to calculate R, (ii) mis-calibrated experimental instruments, (iii) inaccurate calibration parameters, (iv) insufficient incubation time, (v) unsaturated binding isotherm, (vi) impurities in the reactants, and (vii) solute adsorption onto surfaces. Through this analysis, we illustrate how each source contributes to inaccuracies in the determination of Kd and propose strategies to minimize these contributions. Additionally, we introduce a method for quantitatively assessing the confidence intervals of systematic errors in concentrations, a crucial step toward quantitatively evaluating the accuracy of Kd. While presenting original findings, this paper also reiterates the fundamentals of Kd determination, hence guiding researchers across all proficiency levels. By shedding light on the sources of systematic errors and offering strategies for their mitigation, our work will help researchers enhance the accuracy of Kd determination, thereby making binding studies more reliable and the conclusions drawn from such studies more robust.

Simulation of chloride diffusion tests in cement paste and mortar made with CEM II and CEM VI cements

We developed a simplified coupled model to simulate the chloride ingress of cement paste and mortar fabricated with CEM II/C-M (S-LL) and CEM VI (S-V) cements. Diffusion of chloride, calcium, sodium, potassium, sulphate and hydroxyl ions is considered, resulting in a set of coupled mass balance equations. Source and sink terms are introduced to represent the dissolution/precipitation processes due to leaching, and interactions between free chloride and hydrated phases are considered through binding isotherm curves. Electrodiffusion phenomenon is introduced through a modified Poisson equation to enforce local electroneutrality. The model is applied to simulate bulk diffusion tests with exposure solutions containing NaCl, and NaCl + KOH to reduce leaching. The main features observed experimentally are correctly reproduced: a higher chloride content is predicted for the materials made with CEM II binder, and a much clearer peaking behavior near the exposed surface is predicted in the case of NaCl exposure.

Modelling chloride diffusion in concrete with carbonated surface layer

Due to the demand for carbon neutrality, concrete carbonation has been reconsidered as an interesting topic because of its potential for capturing carbon dioxide (CO2) from the atmosphere. Concrete carbonation can significantly modify the chemical and microstructure properties of concrete and thus will have important effects on chloride diffusion. This paper presents a chloride diffusion model in which the concrete cover is divided into three different zones, each with their own defined porosity and chloride binding isotherm. The first is the fully carbonated concrete near the surface, where the porosity and chloride binding isotherm can be obtained from the experimental data of fully carbonated concrete. The second is the uncarbonated concrete near the reinforcement, where the porosity and chloride binding isotherm can be obtained from the experimental data of normal concrete. The third is the transition zone between the fully carbonated and uncarbonated concretes, where the porosity and chloride binding isotherm can be assumed to vary continuously from the carbonated concrete to uncarbonated concrete. To validate the present model, a comparison of the present model with published experimental results is provided, which demonstrates the importance of considering different zones in the chloride diffusion model when the concrete has a carbonated layer near the surface.

Macromolecular Crowding Effect on Chitosan-Hyaluronic Acid Complexation and the Activity of Encapsulated Catalase.

The associative phase separation of charged biomacromolecules plays a key role in many biophysical events that take place in crowded intracellular environments. Such natural polyelectrolyte complexation and phase separation often occur at nonstoichiometric charge ratios with the incorporation of bioactive proteins, which is not studied as extensively as those complexations at stoichiometric ratios. In this work, we investigated how the addition of a crowding agent (polyethylene glycol, PEG) affected the complexation between chitosan (CS) and hyaluronic acid (HA), especially at nonstoichiometric ratios, and the encapsulation of enzyme (catalase, CAT) by the colloidal complexes. The crowded environment promoted colloidal phase separation at low charge ratios, forming complexes with increased colloidal and dissolution stability, which resulted in a smaller size and polydispersity (PDI). The binding isotherms revealed that the addition of PEG greatly enhanced the ion-pairing strength (with increased ion-pairing equilibrium constant Ka from 4.92 × 104 without PEG to 1.08 × 106 with 200 g/L PEG) and switched the coacervation from endothermic to exothermic, which explained the promoted complexation and phase separation. At the stoichiometric charge ratio, the enhanced CS-HA interaction in crowded media generated a more solid-like coacervate phase with a denser network, slower chain relaxation, and higher modulus. Moreover, both crowding and complex encapsulation enhanced the activity and catalytic efficiency of CAT, represented by a 2-fold increase in catalytic efficiency (Kcat/Km) under 100 g/L PEG crowding and CS-HA complex encapsulation. This is likely due to the lower polarity in the microenvironment surrounding the enzyme molecules. By a systematic investigation of both nonstoichiometric and stoichiometric charge ratios under macromolecular crowding, this work provided new insights into the complexation between natural polyelectrolytes in a scenario closer to an intracellular environment.

Time-dependent concrete chloride diffusion coupled with nonlinear chloride binding: An analytical study

Both the temporal dependence of chloride diffusion coefficient and the effect of nonlinear chloride binding substantially affect the behavior of concrete chloride diffusion. This study develops an exact chloride diffusion solution that accommodates the above two factors by introducing a simplified but reasonably realistic nonlinear chloride binding isotherm. The introduction of this isotherm makes it possible to achieve an analytical solution to a highly nonlinear chloride diffusion equation that involves a free chloride concentration dependent dimensionless factor which reflects the effect of chloride binding. First, a time-dependent chloride diffusion model incorporating the introduced isotherm is established with the corresponding exact solution derived. The proposed solution is successfully validated against two existing analytical solutions and a numerical solution. Parametric study is conducted using the proposed solution to investigate how the parameters regarding chloride ingress influence the corrosion initiation time, and results show that the increase of the initial effective chloride diffusivity or the before-ingress age decreases the corrosion initiation time bringing an acceleration of a different level to chloride diffusion while the increase of the age factor prolongs the corrosion initiation time decelerating chloride diffusion to some extent, and as each of the three nonlinear chloride binding associated parameters (i.e., the deflection-point concentration, the former slope and the latter slope) increases, the corrosion initiation time rises and the retardation effect on chloride diffusion is enhanced to a various extent. Lastly, to demonstrate the practical validity of the proposed solution, the solution is applied to reproducing a reported chloride diffusion test, and it turns out that our solution reproduces the diffusion test reasonably well, justifying its practical validity.

Probing the potential of mercury removal by covalently immobilized phycobiliproteins onto the surface of chitosan beads

Mercury emissions represent a significant risk to the environment and human health. Mercury is persistent and can circulate in the environment for thousands of years, which is why treating this toxic metal is important. Chitosan polymer is easily obtainable, and it has good mercury adsorption characteristics. This study aimed to improve its capabilities to absorb mercury by immobilizing phycobiliproteins (PBPs) onto the surface of chitosan beads (chitosan–PBPs). Phycobiliproteins, light-harvesting proteins from algae and cyanobacteria, have several industrially essential applications. These proteins can bind heavy metals with high affinities. Protein extracts obtained from both Arthrospira platensis, with C-phycocyanin (C-PC) as the primary protein, and Porphyra yezoensis, with R-phycocyanin (R-PC) and R-phycoerythrin (R-PE) as the dominant PBPs, were covalently immobilized onto chitosan beads. Beads with immobilized PBPs were characterized by scanning electron microscopy and Fourier transform infrared spectroscopy. Binding analysis showed that, on average, each chitosan bead weighed 20 mg and immobilized 63.54 μg of PBPs from Spirulina and 44.12 μg of PBPs from Porphyra. Immobilized proteins were still in their native state, with no visible color change months after immobilization. Chitosan–PBPs and chitosan alone were tested for mercury adsorption at pH 4 and pH 7 by atomic absorption spectroscopy. The tested concentration range of mercury was from 1 to 70 ppm. Affinity, calculated using Henry's binding isotherm, of chitosan–PBPs for mercury was twice as much higher at both pH values than chitosan alone. Furthermore, chitosan-PBP beads were able to absorb more mercury than chitosan alone. These results showed that the covalent immobilization of PBPs onto chitosan improves its mercury adsorption characteristics and creates a more efficient eco-friendly adsorbent to potentially remove mercury ions in the tested concentration range from polluted waters.

Chloride binding by layered double hydroxides (LDH/AFm phases) and alkali-activated slag pastes: an experimental study by RILEM TC 283-CAM

Chloride binding by the hydrate phases of cementitious materials influences the rate of chloride ingress into these materials and, thus, the time at which chloride reaches the steel reinforcement in concrete structures. Chloride binding isotherms of individual hydrate phases would be required to model chloride ingress but are only scarcely available and partly conflicting. The present study by RILEM TC 283-CAM ‘Chloride transport in alkali-activated materials’ significantly extends the available database and resolves some of the apparent contradictions by determining the chloride binding isotherms of layered double hydroxides (LDH), including AFm phases (monosulfate, strätlingite, hydrotalcite, and meixnerite), and of alkali-activated slags (AAS) produced with four different activators (Na2SiO3, Na2O·1.87SiO2, Na2CO3, and Na2SO4), in NaOH/NaCl solutions at various liquid/solid ratios. Selected solids after chloride binding were analysed by X-ray diffraction, and thermodynamic modelling was applied to simulate the phase changes occurring during chloride binding by the AFm phases. The results of the present study show that the chloride binding isotherms of LDH/AFm phases depend strongly on the liquid/solid ratio during the experiments. This is attributed to kinetic restrictions, which are, however, currently poorly understood. Chloride binding by AAS pastes is only moderately influenced by the employed activator. A steep increase of the chloride binding by AAS occurs at free chloride concentrations above approx. 1.0 M, which is possibly related to chloride binding by the C–(N–)A–S–H gel in the AAS.

A New Methodological Approach to Study the Interaction of Humic Acids, Minerals and Polyvalent Cations in Soil

ABSTRACT A new methodological approach of humic acid (HA) extraction is applied to study soil samples with contrasting management regimes: natural vegetation (NV) and agricultural (A). This innovative approach involves a modification of the Swift’s method, wherein several steps HCl/HF are replaced by a single-step HCl/HF. This modification enabled us to investigate the ability of HA to retain inorganic constituents. The carbon content was significantly higher in soils under NV (19.8–27.3 g C kg−1) than under A (11.2–13.4 g C kg−1). The same pattern was observed for the HA content. The new methodology revealed that HA from NV soils had a much higher capacity to retain inorganics (ash contents in HA from 12.3–28.3%) than in A soils (ash content in HA from 1.6–2.6%). Similar results were found for Ca+Al+Fe contents in the HA (3.7–2.5 meq g−1 in HA from NV soils; 2.2–.9 meq g−1 in HA from A soils). Some differences were observed in IR spectra, mainly an intense band at around 1050 cm−1 of HA from NV that reflects the high ash content of the HA and its capacity of retaining inorganic material. Ca binding isotherms of HA also showed that the HA differed significantly in their ability to retain inorganic components when extracted. Humic acid from NV was more efficient in retaining metal ions and minerals than HA from A soils. All results point to a better contact between organic and inorganic matter in NV soils, and this contact contributes to the stabilization of organic matter.

Innovative approaches to suppress non-specific adsorption in molecularly imprinted polymers for sensing applications

Molecularly imprinted polymers (MIPs) are synthetic antibodies developed to bind selectively with specific molecules. They function through a particular recognition process involving their cavities and functional groups. Nevertheless, functional groups located outside these cavities are the main cause of non-specific molecule binding, thus reducing the effectiveness of MIPs in sensing applications. This work focused on enhancing the selectivity and performance of MIPs through electrostatic modification with surfactants. The study investigates the use of two surfactants, namely sodium dodecyl sulfate (SDS) and cetyl trimethyl ammonium bromide (CTAB), to eliminate non-specific adsorption in MIPs. The binding isotherms of the target molecule sulfamethoxazole (SMX) on MIPs and non-imprinted polymers (NIPs) were analyzed, showing higher adsorption capacity of MIPs due to the specific cavities. The modification with SDS or CTAB effectively eliminated non-specific adsorption in MIPs. The kinetic adsorption behavior further demonstrated the efficacy of MIP+--SDS/CTAB in the selective adsorption of SMX. Calibration curves showcase the methodology's analytical capabilities, achieving low limit of detection for SMX 6 ng mL−1 using MIP +-SDS. The stability study confirmed that the developed MIP +/--SDS/CTAB remains stable even at high temperatures, demonstrating its suitability for on-site applications. The methodology was successfully applied to detect SMX in milk and water samples, achieving promising recoveries. Overall, the electrostatic modification of MIPs with surfactants emerges as a valuable strategy for enhancing selectivity and performance in target molecule recognition and detection.

Musketeer: a software tool for the analysis of titration data.

Musketeer is a powerful open-source software tool for the analysis of titration data, featuring a simple cross-platform graphical interface for importing data directly from UV-vis, fluorescence and NMR spectrometers, or from spreadsheets. The fast data analysis algorithm can be used to obtain equilibrium constants for simple binding isotherms, as well as for more complicated systems with multiple competing equilibria. Applications of Musketeer for the analysis of a range of different supramolecular and biomolecular systems are illustrated, including titrations with multiple spectroscopically active species, competitive binding assays, denaturation experiments, optimisation of concentrations as variables. The software also includes a number of tools that can be used to select the binding isotherm that represents the best model to describe a dataset.

Modulating the ion-transfer electrochemistry of perfluorooctanoate with serum albumin and β-cyclodextrin.

Per- and polyfluoroalkyl substances (PFAS) are durable synthetic pollutants that persist in the environment and resist biodegradation. Ion-transfer electrochemistry at aqueous-organic interfaces is a simple strategy for the detection of ionised PFAS. Herein, we investigate the modulation of the ion transfer voltammetry of perfluorooctanoate (PFOA) at liquid-liquid micro-interface arrays by aqueous phase bovine serum albumin (BSA) or β-cyclodextrin (β-CD) and examine the determination of association constants for these binding interactions. By tracking the ion transfer current due to ionised, uncomplexed PFOA as a function of BSA or β-CD concentration, titration curves are produced. Fitting of a binding isotherm to these data provides the association constants. The association constant of PFOA with the BSA determined in this way was ca. 105 M-1 assuming a 1 : 1 binding. Likewise, the association constant for PFOA with β-CD was ca. 104 M-1 for a 1 : 1 β-CD-PFOA complex. Finally, the simultaneous effect of both BSA and β-CD on the ion transfer voltammetry of PFOA was studied, showing clearly that PFOA bound to BSA is released (de-complexed) upon addition of β-CD. The results presented here show ion transfer voltammetry as a simple strategy for the study of molecular and biomolecular binding of ionised PFAS and is potentially useful in understanding the affinity of different PFAS with aqueous phase binding agents such as proteins and carbohydrates.

Coordination-cage binding and catalysed hydrolysis of organophosphorus chemical warfare agent simulants.

The use of organophosphorus chemical warfare agents still remains an ongoing global threat. Here we investigate the binding of small-molecule organic guests including phosphate esters, sulfonate esters, carbonate esters and a sulfite ester - some of which act as simulants for organophosphorus chemical warfare agents - in the cavity of a water-soluble coordination cage. For several of these guest species, binding constants in the range 102 to 103 M-1 were determined in water/DMSO (98 : 2 v/v) solution, through a combination of fluorescence and 1H NMR spectroscopy, and subsequent fitting of titration data to a 1 : 1 binding isotherm model. For three cage/guest complexes crystallographic structure determinations were possible: in two cases (with guests phenyl methanesulfonate and phenyl propyl carbonate) the guest lies inside the cavity, forming a range of CH⋯O hydrogen-bonding interactions with the cage interior surface involving CH groups on the cationic cage surface that act as H-bond donors and O atoms on the guests that act as H-bond acceptors. In a third case, with the guest 4-nitrophenyl-methanesulfonate, the guest lies in the spaces outside a cage cavity between cages and forms weak CH⋯O interactions with the cage exterior surface: the cavity is occupied by a network of H-bonded water molecules, though this guest does show cavity binding in solution. For the isomeric guests 4-nitrophenyl-methanesulfonate and 4-nitrophenyl methyl sulfite, hydrolysis in water/DMSO (98 : 2 v/v) could be monitored colorimetrically via appearance of the 4-nitrophenolate anion; both showed accelerated hydrolysis rates in the presence of the host cage with second-order rate constants for the catalysed reactions in the range 10-3 to 10-2 M-1 s-1 at pH 9. The typical rate dependence on external pH and the increased reaction rates when chloride ions are present (which can bind inside the cavity and displace other cavity-bound guests) imply that the catalysed reaction actually occurs at the external surface of the cage rather than inside the cavity.

In vivo-like nearest neighbor parameters improve prediction of fractional RNA base-pairing in cells.

We conducted a thermodynamic analysis of RNA stability in Eco80 artificial cytoplasm, which mimics in vivo conditions, and compared it to transcriptome-wide probing of mRNA. Eco80 contains 80% of Escherichia coli metabolites, with biological concentrations of metal ions, including 2 mM free Mg2+ and 29 mM metabolite-chelated Mg2+. Fluorescence-detected binding isotherms (FDBI) were used to conduct a thermodynamic analysis of 24 RNA helices and found that these helices, which have an average stability of -12.3 kcal/mol, are less stable by ΔΔGo37 ∼1 kcal/mol. The FDBI data was used to determine a set of Watson-Crick free energy nearestneighbor parameters (NNPs), which revealed that Eco80 reduces the stability of three NNPs. This information was used to adjust the NN model using the RNAstructure package. The in vivo-like adjustments have minimal effects on the prediction of RNA secondary structures determined in vitro and in silico, but markedly improve prediction of fractional RNA base pairing in E. coli, as benchmarked with our in vivo DMS and EDC RNA chemical probing data. In summary, our thermodynamic and chemical probing analyses of RNA helices indicate that RNA secondary structures are less stable in cells than in artificially stable in vitro buffer conditions.

Chemical Protein Unfolding - A Simple Cooperative Model.

Chemical unfolding with guanidineHCl or urea is a common method to study the conformational stability of proteins. The analysis of unfolding isotherms is usually performed with an empirical linear extrapolation method (LEM). A large positive free energy is assigned to the native protein, which is usually considered to be a minimum of the free energy. The method thus contradicts common expectations. Here, we present a multistate cooperative model that addresses specifically the binding of the denaturant to the protein and the cooperativity of the protein unfolding equilibrium. The model is based on a molecular statistical-mechanical partition function of the ensemble, but simple solutions for the calculation of the binding isotherm and the associated free energy are presented. The model is applied to 23 published unfolding isotherms of small and large proteins. For a given denaturant, the binding constant depends on temperature and pH but shows little protein specificity. Chemical unfolding is less cooperative than thermal unfolding. The cooperativity parameter σ is at least 2 orders of magnitude larger than that of thermal unfolding. The multistate cooperative model predicts zero free energy for the native protein, which becomes strongly negative beyond the midpoint concentration of unfolding. The free energy to unfold a cooperative unit corresponds exactly to the diffusive energy of the denaturant concentration gradient necessary for unfolding. The temperature dependence of unfolding isotherms yields the denaturant-induced unfolding entropy and, in turn, the unfolding enthalpy. The multistate cooperative model provides molecular insight and is as simple to apply as the LEM but avoids the conceptual difficulties of the latter.

Selective adsorption and special recognition of roxarsone (ROX) from water by utilizing novel core-shell magnetic molecularly imprinted polymers

To eliminate environmental risk that induced from organoarsenic feed additive ROX, and enhance special selectivity and recognizability of this micro-polluted aromatic organoarsenicals compound in complex aqueous as well. Novel core-shell magnetic molecularly imprinted polymers (MMIPs) were successfully synthesized through the surface imprinting technology, which circumvented the drawbacks of traditional method such as the deep embedding of the imprinting sites and incomplete elution of the target molecule. Owing to its imprinting effect, the obtained MMIPs displayed excellent behavior and performance for ROX removal compared with magnetic non-imprinted polymers (MNIPs), the binding isotherms of ROX for both MMIPs and MNIPs were better fitted by Langmuir model, and two types of binding sites (specific and non-specific adsorption sites) existed on the surface of MMIPs. The removal efficiency of ROX by MMIPs remained unchanged along with a broad pH range (3.0–10.0), whereas pH seriously affected the ROX removal efficiency of MNIPs. The better uptake of ROX by MMIPs co-existed with competitive substances and two other organic/inorganic arsenic compounds (p-ASA/As(V)) confirmed the high binding selectivity and special recognizability for its target pollutant. Finally, the application in different spiked real water samples and continuous flow tests further demonstrated MMIPs were the promising candidates and of the potential application future to selectively remove this trace pollutant in different water bodies.

Physical and chemical chloride binding characteristics of the hydration products for phosphoaluminate cement

Phosphoaluminate cement (PAC) has the potential to prepare the anti-corrosive coatings for rebar due to with high compactness and resistance to chloride. Whereas, the reports of the binding type, its ratio and binding capacity of PAC for chloride ions are not found up to now. Thus, the chloride binding performance of PAC hydration products, as well as the binding isotherms and kinetic models, were investigated in this work. The experimental results showed that the binding capacity of the fully hydrated sample reached 21.03 mg/g in 0.56 mol/L NaCl solution. Up to 80 % of this total was non-water-soluble chloride, dominated by the chemical binding of calcium hydroaluminates (i.e., C(A,P)H10 and C2(A,P)H8). The water-soluble chloride at 20 ℃ accounted for only 20 % and was mainly adsorbed physically by Al(OH)3 and Fe(OH)3 gels. The whole chloride binding process of hydration products was well described using Freundlich isotherm and Elovich kinetic models. Its non-water-soluble bound chloride was more suitable for D-R isotherm and Elovich kinetic models, while the water-soluble bound chloride was more applicable to Freundlich isotherm and PSO kinetic models. These data will offer theoretical support for the rational use of PAC in constructions exposed to high chloride environments, such as the ocean.