Response surface and DFT protocols for improvement of the adsorption process of lignocellulosic-based biomass for the removal of basic dyes.

Jatobá-do-cerrado fruit shells, archetypical of lignocellulosic-based biomass, were used as an adsorbent to remove crystal violet (CV) and methylene blue (MB) from water. The adsorbent was characterized using various techniques, and kinetic studies showed dye adsorption followed second-order kinetics. An experimental design investigated the effects of pH and temperature on removal efficiency, with a quadratic model fitting the data best. The results suggest pH influences MB's adsorption capacity more than temperature and at 25 °C and pH 8, MB had a desirability value of 0.89, with 95 % removal efficiency. For CV, temperature had a greater influence, with a desirability value of 0.874 at 25 °C and pH 10, and 95 % removal efficiency. Adsorption isotherm studies revealed maximum adsorption capacities of 123.0 mg·g-1 and 113.0 mg·g-1 for CV and MB, respectively. Experimental thermodynamic parameters indicated an endothermic and spontaneous process which it was supported by quantum chemistry calculations. The protocols developed confirmed the potential for adsorbing CV and MB dyes in water, achieving over 73.1 and 74.4 mg g-1 dyes removal.

Reply to the 'Comment on "Topography of the Free Energy Landscape on the Claisen-Schmidt Condensation: Solvent and Temperature Effect in the Rate-Controlling Step"' by N. D. Coutinho, H. G. Machado, V. H. Carvalho-Silva and W. A. da Silva, Phys. Chem. Chem. Phys., 2021, 23, 6738.

In the Comment on our paper on the description of the Gibbs Free energy profile of Claisen-Schmidt condensation, it is claimed that our calculations are flawed due to inconsistencies with experimental isotope effects in aqueous acetonitrile. In this Reply, we presented rigorous arguments, ambiguities in the Comment and new calculations confirming the consistency of our results: (i) small differences in the relative energetic barriers in both experimental and theoretical curves make the assignment of the rate-limiting step debatable, making the concept of RCS questionable; (ii) it is shown how the misinterpretation of the elementary steps and of the overall processes rate constants led the Comment to incorrect conclusions about the behavior of the inverse isotopic effect; (iii) neglect in the Comment of the inverse kinetic isotope effect in step R2 due to the hybridization conversion, and of the inverse equilibrium isotopic effect for step R1 to describe an overall iKIE > 1, (iv) an erroneous suggestion in the Comment that the disagreement between experimental kinetic parameters is due to the fact that acetonitrile is not used in previous experimental works, when contradictorily the literature recommends it as being indispensable to allow kinetic accuracy; and (v) new calculations improved by explicit-implicit hybrid treatment again ensure that step R4, and not step R5, can assume the role of RCS in protic solvents. Recognizing that questioning is an excellent path for promoting understanding, we hope that the answers provided here will help to clarify and expand the pertinent topics under discussion.

"pySiRC": Machine Learning Combined with Molecular Fingerprints to Predict the Reaction Rate Constant of the Radical-Based Oxidation Processes of Aqueous Organic Contaminants.

We developed a web application structured in a machine learning and molecular fingerprint algorithm for the automatic calculation of the reaction rate constant of the oxidative processes of organic pollutants by •OH and SO4•- radicals in the aqueous phase-the pySiRC platform. The model development followed the OECD principles: internal and external validation, applicability domain, and mechanistic interpretation. Three machine learning algorithms combined with molecular fingerprints were evaluated, and all the models resulted in high goodness-of-fit for the training set with R2 > 0.931 for the •OH radical and R2 > 0.916 for the SO4•- radical and good predictive capacity for the test set with Rext2 = Qext2 values in the range of 0.639-0.823 and 0.767-0.824 for the •OH and SO4•- radicals. The model was interpreted using the SHAP (SHapley Additive exPlanations) method: the results showed that the model developed made the prediction based on a reasonable understanding of how electron-withdrawing and -donating groups interfere with the reactivity of the •OH and SO4•- radicals. We hope that our models and web interface can stimulate and expand the application and interpretation of kinetic research on contaminants in water treatment units based on advanced oxidative technologies.

Efficiency of water treatment with crushed shell of jatobá-do-cerrado (Hymenaea stigonocarpa) fruit to adsorb Cu(II) and Ni(II) ions: experimental and quantum chemical assessment of the complexation process.

The shell surrounding fruits of the jatobá-do-cerrado tree, in its natural state, was modified by the addition of HNO3 and NaOH and used as an adsorbent in the removal of Cu(II) and Ni(II) from aqueous solutions. The untreated (JIN) and chemically modified (JCT) fruit shell samples were characterized by Fourier transform infrared (FTIR) spectroscopy, scanning electron microscopy (SEM), thermogravimetric analysis (TGA), and X-ray diffraction. Their efficiency as adsorbents in the removal of Cu(II) and Ni(II) ions from aqueous solutions was studied under different conditions of pH (2-9) and it was observed that the optimal pH for Cu (II) adsorption was 5.5 and for Ni (II) it was 6.0. The adsorption isotherms were obtained at different temperatures (298, 308, 318 K) and the qmax values ranged from 33.96 to 41.00 mg g-1. The adsorbents presented higher selectivity toward Cu ions (II). The thermodynamic analysis results suggest that the adsorption process studied is of a physical nature. Supported by quantum mechanical calculations, the interaction sites of the ion-cellulose and ion-lignin complexes were identified, evidencing the central role of water molecules in stabilization of the complexes. The experimental and theorical results indicate that JIN and JCT have good potential for the adsorption of Cu(II) and Ni(II) ions and are thus promising materials for the removal of other metal ions in aqueous systems.

Topography of the free energy landscape of Claisen-Schmidt condensation: solvent and temperature effects on the rate-controlling step.

Recent studies have found that hydroxide elimination and the C[double bond, length as m-dash]C bond formation step in base-promoted aldol condensation have a strong influence on the overall rate of the reaction, in contrast to the well-accepted first enolization or C-C bond formation step. Here, applying theoretical models to the prototypical reaction of chalcone formation, the complete free energy profile of Claisen-Schmidt condensation is assessed, revealing how a protic solvent and a slight increase in temperature can induce the second enolization as the rate-controlling step (RCS). It is also observed: i) the nonexistence of a step with a much higher energetic barrier than the others, making the concept of RCS debatable; and ii) that the overall inverse kinetic isotopic effect does not exclude second enolization as a RCS in protic continuum medium. We expect that these results can expand the understanding of the decisive role of physicochemical factors on the choose of the RCS in the aldol condensation.

Nucleophilic substitution vs elimination reaction of bisulfide ions with substituted methanes: exploration of chiral selectivity by stereodirectional first-principles dynamics and transition state theory.

Control of molecular orientation is emerging as crucial for the characterization of the stereodynamics of kinetics processes beyond structural stereochemistry. The special role played in chiral discrimination phenomena has been particularly emphasized by Aquilanti and collaborators after their extensive probes of experimental control of molecular alignment and orientation. In this work, the manifestation of the Aquilanti mechanism has been demonstrated for the first time in first-principles molecular dynamics simulations: stationary points characterized on potential energy surfaces have been calculated for the study of chemical reactions occurring between the bisulfide anion HS- and oriented prototypical chiral molecules CHFXY (where X = CH3 or CN and Y = Cl or I). The important reaction channels are those corresponding to bimolecular nucleophilic substitution (SN2) and to bimolecular elimination (E2): their relative role has been assessed and alternative pathways due to the mirror forms of the oriented chiral molecule are revealed by the different reactivity of the two enantiomers of CHFCNI in SN2 reaction.

Kinetics of low-temperature transitions and a reaction rate theory from non-equilibrium distributions.

This article surveys the empirical information which originated both by laboratory experiments and by computational simulations, and expands previous understanding of the rates of chemical processes in the low-temperature range, where deviations from linearity of Arrhenius plots were revealed. The phenomenological two-parameter Arrhenius equation requires improvement for applications where interpolation or extrapolations are demanded in various areas of modern science. Based on Tolman's theorem, the dependence of the reciprocal of the apparent activation energy as a function of reciprocal absolute temperature permits the introduction of a deviation parameter d covering uniformly a variety of rate processes, from those where quantum mechanical tunnelling is significant and d < 0, to those where d > 0, corresponding to the Pareto-Tsallis statistical weights: these generalize the Boltzmann-Gibbs weight, which is recovered for d = 0. It is shown here how the weights arise, relaxing the thermodynamic equilibrium limit, either for a binomial distribution if d > 0 or for a negative binomial distribution if d < 0, formally corresponding to Fermion-like or Boson-like statistics, respectively. The current status of the phenomenology is illustrated emphasizing case studies; specifically (i) the super-Arrhenius kinetics, where transport phenomena accelerate processes as the temperature increases; (ii) the sub-Arrhenius kinetics, where quantum mechanical tunnelling propitiates low-temperature reactivity; (iii) the anti-Arrhenius kinetics, where processes with no energetic obstacles are rate-limited by molecular reorientation requirements. Particular attention is given for case (i) to the treatment of diffusion and viscosity, for case (ii) to formulation of a transition rate theory for chemical kinetics including quantum mechanical tunnelling, and for case (iii) to the stereodirectional specificity of the dynamics of reactions strongly hindered by the increase of temperature.This article is part of the themed issue 'Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces'.