Experimental Investigations on Adsorption of Reactive Toxic Dyes Using Hedyotis umbellate Activated Carbon

Hedyotis umbellate activated carbon (HUAC) was prepared by chemical and thermal activation. The adsorption behavior of Hedyotis umbellate activated carbon in aqueous basic green 4 (BG4) and acid fuchsin (AF) was investigated and characterized by UV-vis, FTIR, and FESEM. The possible mechanism of the adsorption of BG4 and AF dyes on the HUAC surface was framed. The influence of various adsorption control parameters like the initial dye concentration, pH, adsorbent dose, contact time, and temperature was studied. The data confirmed excellent BG4 removal of 97.94% at pH 10 and AF removal of 76.7% at pH 4. The experimental data were fitted using Langmuir, Freundlich, and Temkin isotherms to examine the adsorption mechanism. The adsorption data revealed monolayer adsorption of BG4 with the maximum capacity of 102.38 mg/g and multilayer adsorption of AF with the capacity of 139.33 mg/g. The kinetic data for different initial dye concentrations were computed using pseudofirst order, pseudosecond order, and intraparticle diffusion models. Thermodynamic parameters like Gibbs free energy change ∆ G 0 , enthalpy change ∆ H 0 , and entropy change ∆ S 0 were evaluated. From the values obtained, the negative values of ∆ G 0 and ∆ H 0 indicate that the adsorption of BG4 and AF by HUAC is spontaneous and exothermic.

dGPredictor: Automated fragmentation method for metabolic reaction free energy prediction and de novo pathway design

Group contribution (GC) methods are conventionally used in thermodynamics analysis of metabolic pathways to estimate the standard Gibbs free energy change (ΔrG′o) of enzymatic reactions from limited experimental measurements. However, these methods are limited by their dependence on manually curated groups and inability to capture stereochemical information, leading to low reaction coverage. Herein, we introduce an automated molecular fingerprint-based thermodynamic analysis tool called dGPredictor that enables the consideration of stereochemistry within metabolite structures and thus increases reaction coverage. dGPredictor has a higher prediction accuracy as compared to existing GC methods and can capture free energy changes for isomerase and transferase reactions, which exhibit no overall group changes. We also demonstrate dGPredictor’s ability to predict the Gibbs free energy change for novel reactions and seamless integration within de novo metabolic pathway design tools such as novoStoic. This enables performing a thermodynamic analysis for synthetic pathways, thus safeguarding against the inclusion of reaction steps with infeasible directionalities. To facilitate easy access to dGPredictor, we developed a graphical user interface to predict the standard Gibbs free energy change for reactions at various pH and ionic strengths. The tool allows customized user input of known metabolites as KEGG IDs and novel metabolites as InChI strings (https://github.com/maranasgroup/dGPredictor).Author summaryThe genome-scale metabolic networks consist of a large number of biochemical reactions interconnected in a complex system. The standard Gibbs free energy change is commonly used to check for the feasibility of enzyme-catalyzed reactions as thermodynamics plays a crucial role in pathway design for biochemical synthesis. The group contribution methods using expert-defined functional groups have been extensively used for estimating standard Gibbs free energy change with limited experimental measurements. However, current methods using functional groups have major issues that limit its ability to cover all the metabolites and reactions as well as the inability to consider stereochemistry leads to erroneous estimation of free energy that undergoes only stereochemical change such as isomerases. Here, we introduce a molecular fingerprint-based thermodynamic tool dGPredictor that enables stereochemistry in metabolites and thus improves the reaction coverage with higher prediction accuracy compared to current GC methods. It also allows the ability to predict free energy change for novel reactions which can aid the de novo metabolic pathway design tool to ensure the reaction feasibility. We apply and test our method on reactions in the KEGG database and isobutanol synthesis pathway. In addition, we provide an open-source user-friendly web interface to facilitate easy access for standard Gibbs free energy change of reactions at different physiological states.

Isothermal, Kinetic, and Thermodynamic Studies on the Adsorption of Molybdenum by a Nanostructured Magnetic Material

In this study, the magnetic 3-(trimethoxysilyl) propyl methacrylate (TMSPMA) – poly (4-vinylpyridine) (P4VP) was synthesized and characterized. Removal of Molybdenum (Mo) from aqueous solutions using prepared material as nanosorbent was investigated. The magnetic P4VP was prepared by copolymerization of P4VP with TMSPMA. The prepared adsorbent was characterized by various techniques including the X-ray powder diffraction (XRD), scanning electron microscopy (SEM), and Fourier-transform infrared spectroscopy (FTIR). The batch adsorption technique was applied and the effect of several important parameters such as pH of the aqueous solution, adsorbent dose, initial Mo(VI) concentration, contact time, and temperature was evaluated. Desorption behavior of Mo(VI) and the effect of foreign ions (Cd2+, Ca2+, Co2+, Fe3+, Ba2+ and Pt4+) in real samples were also investigated. Co (II) and Pt (IV) had a greater impact on the adsorption process than other foreign ions. The maximum capacity for Mo(VI) adsorption on the prepared adsorbent was 4.87 mg/g, which was obtained at a temperature of 40°C with an initial concentration of 10 mg/L of Mo(VI). The adsorption isotherms were best fitted with the Weber Van Vliet isotherm model. The kinetic data were fitted well with the pseudo-second-order equation with a high correlation coefficient (R2 > 0.99). Based on the negative standard Gibbs free energy change (ΔG° < 0) and the positive standard enthalpy change (ΔH° > 0), it was found that the adsorption was an endothermic and a spontaneous process in nature.

Thermodynamic Analysis of Moisture Adsorption of Taraxacum Officinale’ Powder

This work aims to model the adsorption isotherms and study the essential thermodynamic properties of Taraxacum Officinale’ powder during the moisture adsorption phenomenon at three temperatures 30, 40, and 50°C. The results have been determined by the application of the thermodynamics physical principles to the equilibrium data, which are experimentally measured. The estimated values of the isokinetic and harmonic temperatures and the Gibbs free energy change revealed that the sorption process is non-spontaneous and enthalpy driven.

Master curve of boosted diffusion for 10 catalytic enzymes

Molecular agitation more rapid than thermal Brownian motion is reported for cellular environments, motor proteins, synthetic molecular motors, enzymes, and common chemical reactions, yet that chemical activity coupled to molecular motion contrasts with generations of accumulated knowledge about diffusion at equilibrium. To test the limits of this idea, a critical testbed is the mobility of catalytically active enzymes. Sentiment is divided about the reality of enhanced enzyme diffusion, with evidence for and against. Here a master curve shows that the enzyme diffusion coefficient increases in proportion to the energy release rate—the product of Michaelis-Menten reaction rate and Gibbs free energy change (ΔG)—with a highly satisfactory correlation coefficient of 0.97. For 10 catalytic enzymes (urease, acetylcholinesterase, seven enzymes from the glucose cascade cycle, and one other), our measurements span from a roughly 40% enhanced diffusion coefficient at a high turnover rate and negativeΔGto no enhancement at a slow turnover rate and positiveΔG. Moreover, two independent measures of mobility show consistency, provided that one avoids undesirable fluorescence photophysics. The master curve presented here quantifies the limits of both ideas, that enzymes display enhanced diffusion and that they do not within instrumental resolution, and has possible implications for understanding enzyme mobility in cellular environments. The striking linear dependence of ΔGfor the exergonic enzymes (ΔG<0), together with the vanishing effect for endergonic enzyme (ΔG>0), are consistent with a physical picture in which the mechanism boosting the diffusion is an active one, utilizing the available work from the chemical reaction.

ProCaff: protein–carbohydrate complex binding affinity database

Motivation Protein–carbohydrate interactions perform several cellular and biological functions and their structure and function are mainly dictated by their binding affinity. Although plenty of experimental data on binding affinity are available, there is no reliable and comprehensive database in the literature. Results We have developed a database on binding affinity of protein–carbohydrate complexes, ProCaff, which contains 3122 entries on dissociation constant (Kd), Gibbs free energy change (ΔG), experimental conditions, sequence, structure and literature information. Additional features include the options to search, display, visualization, download and upload the data. Availability and implementation The database is freely available at http://web.iitm.ac.in/bioinfo2/procaff/. The website is implemented using HTML and PHP and supports recent versions of major browsers such as Chrome, Firefox, IE10 and Opera. Contact [email protected] Supplementary information Supplementary data are available at Bioinformatics online.