Reaction Free Energy Research Articles

Operando Mössbauer Spectroscopic Tracking the Metastable State of Atomically Dispersed Tin in Copper Oxide for Selective CO2 Electroreduction.

Metastable state is the most active catalyst state that dictates the overall catalytic performance and rules of catalytic behaviors; however, identification and stabilization of the metastable state of catalyst are still highly challenging due to the continuous evolution of catalytic sites during the reaction process. In this work, operando 119Sn Mössbauer measurements and theoretical simulations were performed to track and identify the metastable state of single-atom Sn in copper oxide (Sn1-CuO) for highly selective CO2 electroreduction to CO. A maximum CO Faradaic efficiency of around 98% at -0.8 V (vs. RHE) over Sn1-CuO was achieved at an optimized Sn loading of 5.25 wt. %. Operando Mössbauer spectroscopy clearly identified the dynamic evolution of atomically dispersed Sn4+ sites in the CuO matrix that enabled the in situ transformation of Sn4+-O4-Cu2+ to a metastable state Sn4+-O3-Cu+ under CO2RR conditions. In combination with quasi in situ X-ray photoelectron spectroscopy, operando Raman and attenuated total reflectance surface enhanced infrared absorption spectroscopies, the promoted desorption of *CO over the Sn4+-O3 stabilized adjacent Cu+ site was evidenced. In addition, density functional theory calculations further verified that the in situ construction of Sn4+-O3-Cu+ as the true catalytic site altered the reaction path via modifying the adsorption configuration of the *COOH intermediate, which effectively reduced the reaction free energy required for the hydrogenation of CO2 and the desorption of the *CO, thereby greatly facilitating the CO2-to-CO conversion. This work provides a fundamental insight into the role of single Sn atoms on in situ tuning the electronic structure of Cu-based catalysts, which may pave the way for the development of efficient catalysts for high-selectivity CO2 electroreduction.

Theoretical Analysis of Metals Supported on Tungsten Oxide Nanowires (W18O49) for Water Dissociation Reaction

AbstractPt is the cause of the high total cost of fuel cells and electrolyzers, leading to difficult commercialization. Here, various types of metal atoms, i.e., Pt, Pd, Ni, Ir, Ag, and Rh, suitable for catalysts are used and supported by W18O49 nanowires for oxygen evolution reaction (OER) by the density functional theory (DFT) method. Four adsorbate molecules involved in OER were tested on adsorption energy: OH, O, OOH, and OO. Although the adsorption energy of these adsorbate molecules indicates that W18O49 has low adsorption energy, the Gibbs free energy diagram demonstrates that W18O49 has high OER reaction energy. Pt, Pd, Ni, and Rh have the lowest Gibbs energy to initiate the reaction and reasonable Gibbs free energy for other OER reactions. Bimetallic or trimetallic active sites can be developed along with selecting other metals with Pt, Pd, Rh, and Ni to reduce the Gibbs free energy difference for the decomposition of OH to O and OOH to H2O. Ag metal can also be applied as a second or third metal because Ag exhibits a relatively low Gibbs free energy difference in the O to OOH step. A selectivity study of each step on bimetallic and trimetallic active sites needs to be performed.

Deciphering the Primary Role of Au⋅⋅⋅H-X Hydrogen Bonding in Gold Catalysis.

Au⋅⋅⋅H-X (X=N or C) hydrogen bonding is gaining increasing interest, both in the study of its intrinsic nature and in their operability in different fields. While the role of these interactions has been studied in the stabilization of gold(I) complexes, their role during the minimum free energy reaction pathway of a given catalytic process remains unexplored. We report herein that complex [Au(C≡CPh)(pip)] (pip=piperidine) catalyses the A3 -coupling reaction for the synthesis of propargylamines, thanks to the ability of Au(I) to promote weak hydrogen bonding interactions with the reactants along the free energy profile. Density Functional Theory (DFT) calculations show that these Au⋅⋅⋅H-X interactions play a directing role in the catalysed A3 -coupling. Topological non-covalent interactions (NCI), interaction region indicator (IRI) and quantum theory of atoms in molecules (QTAIM) analysis in real space of the electron density provide a description of these interactions accurately.

Deciphering the Primary Role of Au⋅⋅⋅H−X Hydrogen Bonding in Gold Catalysis

AbstractAu⋅⋅⋅H−X (X=N or C) hydrogen bonding is gaining increasing interest, both in the study of its intrinsic nature and in their operability in different fields. While the role of these interactions has been studied in the stabilization of gold(I) complexes, their role during the minimum free energy reaction pathway of a given catalytic process remains unexplored. We report herein that complex [Au(C≡CPh)(pip)] (pip=piperidine) catalyses the A3‐coupling reaction for the synthesis of propargylamines, thanks to the ability of Au(I) to promote weak hydrogen bonding interactions with the reactants along the free energy profile. Density Functional Theory (DFT) calculations show that these Au⋅⋅⋅H−X interactions play a directing role in the catalysed A3‐coupling. Topological non‐covalent interactions (NCI), interaction region indicator (IRI) and quantum theory of atoms in molecules (QTAIM) analysis in real space of the electron density provide a description of these interactions accurately.

Exploring Unconventional Electrolytes to Tackle the Problem of Shuttling in Precipitation-Dissolution Battery Chemistries

A1-Triple I: Any galvanic cell functions by compartmentalizing, via the electron-blocking electrolyte, an exothermic chemical reaction into two redox half-reactions to force release of the reaction free energy as electrical energy. The conventional electrolyte is an ion-conductor shuttling the operative ions and preventing any other chemical exchange to maintain the integrity and reversibility of the electrodes. In overcoming the capacity ceiling of layered intercalation hosts, conversion reactions between low-cost chalcogens (sulfur, selenium, and oxygen) and alkali metals (lithium and sodium) have been investigated for decades. However, parasitic crossover of soluble polychalcogenides limit battery cycle life. We conceptualize that selective solute transport at the interface of partially miscible solvents can be utilized in designing organic electrolytes to suppress parasitic crossover in precipitation-dissolution battery chemistries. This talk will discuss successful concept-demonstration experiments and highlight intriguing physical phenomena within such electrolyte system under the dynamics of electrochemistry.

Towards Predicting Metal Extraction from Oxides with Machine-Learning Augmented First-Principles Calculations

The experimental characterization of high-temperature (electro)chemistry for the extraction of metals from their ores or spent electronics is challenging and requires specialized equipment. CALPHAD simulations can be an alternative but require assessed phase diagrams for the system of interest. On the other hand, first-principles calculations can provide robust estimates of many materials properties at zero Kelvin without experimental input, but simulating processes at high temperatures is computationally demanding and often too approximate. Here, we discuss the initial steps toward the efficient computational prediction of chemical reactions and process conditions using machine-learning augmented first-principles calculations. We show that a combination of zero-Kelvin density-functional theory (DFT) calculations and machine-learning models trained on temperature-dependent reaction-free energies allows predicting reduction temperatures of metal oxides (Garrido Torres et al., Nat. Commun. 12, 7012, 2021). An application to crystalline binary and ternary oxides demonstrates that the temperature dependence of the free energy can be cross-learned, removing the limitation to compounds that have previously been thermodynamically assessed. We also show recent progress in extending this approach to the prediction of melting temperatures.

In Silico Simulations Reveal Molecular Mechanism of Uranyl Ion Toxicity towards DNA-Binding Domain of PARP-1 Protein.

The molecular toxicity of the uranyl ion (UO22+) in living cells is primarily determined by its high affinity to both native and potential metal-binding sites that commonly occur in the structure of biomolecules. Recent advances in computational and experimental research have shed light on the structural properties and functional impacts of uranyl binding to proteins, organic ligands, nucleic acids, and their complexes. In the present work, we report the results of the computational investigation of the uranyl-mediated loss of DNA-binding activity of PARP-1, a eukaryotic enzyme that participates in DNA repair, cell differentiation, and the induction of inflammation. The latest experimental studies have shown that the uranyl ion directly interacts with its DNA-binding subdomains, zinc fingers Zn1 and Zn2, and alters their tertiary structure. Here, we propose an atomistic mechanism underlying this process and compute the free energy change along the suggested pathway. Our Quantum Mechanics/Molecular Mechanics (QM/MM) simulations of the Zn2-UO22+ complex indicate that the uranyl ion replaces zinc in its native binding site. However, the resulting state is destroyed due to the spontaneous internal hydrolysis of the U-Cys162 coordination bond. Despite the enthalpy of hydrolysis being +2.8 kcal/mol, the overall reaction free energy change is -0.6 kcal/mol, which is attributed to the loss of domain's native tertiary structure originally maintained by a zinc ion. The subsequent reorganization of the binding site includes the association of the uranyl ion with the Glu190/Asp191 acidic cluster and significant perturbations in the domain's tertiary structure driven by a further decrease in the free energy by 6.8 kcal/mol. The disruption of the DNA-binding interface revealed in our study is consistent with previous experimental findings and explains the loss of PARP-like zinc fingers' affinity for nucleic acids.

Assessing the Performance of Non-Equilibrium Thermodynamic Integration in Flavodoxin Redox Potential Estimation.

Flavodoxins are enzymes that contain the redox-active flavin mononucleotide (FMN) cofactor and play a crucial role in numerous biological processes, including energy conversion and electron transfer. Since the redox characteristics of flavodoxins are significantly impacted by the molecular environment of the FMN cofactor, the evaluation of the interplay between the redox properties of the flavin cofactor and its molecular surroundings in flavoproteins is a critical area of investigation for both fundamental research and technological advancements, as the electrochemical tuning of flavoproteins is necessary for optimal interaction with redox acceptor or donor molecules. In order to facilitate the rational design of biomolecular devices, it is imperative to have access to computational tools that can accurately predict the redox potential of both natural and artificial flavoproteins. In this study, we have investigated the feasibility of using non-equilibrium thermodynamic integration protocols to reliably predict the redox potential of flavodoxins. Using as a test set the wild-type flavodoxin from Clostridium Beijerinckii and eight experimentally characterized single-point mutants, we have computed their redox potential. Our results show that 75% (6 out of 8) of the calculated reaction free energies are within 1 kcal/mol of the experimental values, and none exceed an error of 2 kcal/mol, confirming that non-equilibrium thermodynamic integration is a trustworthy tool for the quantitative estimation of the redox potential of this biologically and technologically significant class of enzymes.

Metformin Impedes Oxidation of LDL In Vitro.

Metformin is the most commonly prescribed glucose-lowering drug for the treatment of type 2 diabetes. The aim of this study was to investigate whether metformin is capable of impeding the oxidation of LDL, a crucial step in the development of endothelial dysfunction and atherosclerosis. LDL was oxidized by addition of CuCl2 in the presence of increasing concentrations of metformin. The extent of LDL oxidation was assessed by measuring lipid hydroperoxide and malondialdehyde concentrations, relative electrophoretic mobilities, and oxidation-specific immune epitopes. Cytotoxicity of oxLDL in the vascular endothelial cell line EA.hy926 was assessed using the alamarBlue viability test. Quantum chemical calculations were performed to determine free energies of reactions between metformin and radicals typical for lipid oxidation. Metformin concentration-dependently impeded the formation of lipid hydroperoxides, malondialdehyde, and oxidation-specific immune epitopes when oxidation of LDL was initiated by addition of Cu2+. The cytotoxicity of oxLDL was reduced when it was obtained under increasing concentrations of metformin. The quantum chemical calculations revealed that only the reaction of metformin with hydroxyl radicals is exergonic, whereas the reactions with hydroperoxyl radicals or superoxide radical anions are endergonic. Metformin, beside its glucose-lowering effect, might be a suitable agent to impede the development of atherosclerosis and associated CVD. This is due to its capability to impede LDL oxidation, most likely by scavenging hydroxyl radicals.

Structural Determinants of Redox Conduction Favor Robustness over Tunability in Microbial Cytochrome Nanowires.

Structural determinants of a 103-fold variation in electrical conductivity for helical homopolymers of tetra-, hexa-, and octa-heme cytochromes (named Omc- E, S, and Z, respectively) from Geobacter sulfurreducens are investigated with the Pathways model for electron tunneling, classical molecular dynamics, and hybrid quantum/classical molecular mechanics. Thermally averaged electronic couplings for through-space heme-to-heme electron transfer in the "nanowires" computed with density functional theory are ≤0.015 eV. Pathways analyses also indicate that couplings match within a factor of 5 for all "nanowires", but some alternative tunneling routes are found involving covalent protein backbone bonds (Omc- S and Z) or propionic acid-ligating His H-bonds on adjacent hemes (OmcZ). Reorganization energies computed from electrostatic vertical energy gaps or a version of the Marcus continuum expression parameterized on the total (donor + acceptor) solvent-accessible surface area typically agree within 20% and fall within the range 0.48-0.98 eV. Reaction free energies in all three "nanowires" are ≤|0.28| eV, even though Coulombic interactions primarily tune the site redox energies by 0.7-1.2 eV. Given the conserved energetic parameters, redox conductivity differs by < 103-fold among the cytochrome "nanowires". Redox currents do not exceed 3.0 × 10-3 pA at a physiologically relevant 0.1 V bias, with the slowest electron transfers being on a (μs) timescale much faster than typical (ms) enzymatic turnovers. Thus, the "nanowires" are proposed to be functionally robust to variations in structure that provide a habitat-customized protein interface. The 30 pA to 30 nA variation in conductivity previously reported from atomic force microscopy experiments is not intrinsic to the structures and/or does not result from the physiologically relevant redox conduction mechanism.

Bridging semiempirical and abinitio QM/MM potentials by Gaussian process regression and its sparse variants for free energy simulation.

Free energy simulations that employ combined quantum mechanical and molecular mechanical (QM/MM) potentials at abinitio QM (AI) levels are computationally highly demanding. Here, we present a machine-learning-facilitated approach for obtaining AI/MM-quality free energy profiles at the cost of efficient semiempirical QM/MM (SE/MM) methods. Specifically, we use Gaussian process regression (GPR) to learn the potential energy corrections needed for an SE/MM level to match an AI/MM target along the minimum free energy path (MFEP). Force modification using gradients of the GPR potential allows us to improve configurational sampling and update the MFEP. To adaptively train our model, we further employ the sparse variational GP (SVGP) and streaming sparse GPR (SSGPR) methods, which efficiently incorporate previous sample information without significantly increasing the training data size. We applied the QM-(SS)GPR/MM method to the solution-phase SN2 Menshutkin reaction, NH3+CH3Cl→CH3NH3++Cl-, using AM1/MM and B3LYP/6-31+G(d,p)/MM as the base and target levels, respectively. For 4000 configurations sampled along the MFEP, the iteratively optimized AM1-SSGPR-4/MM model reduces the energy error in AM1/MM from 18.2 to 4.4 kcal/mol. Although not explicitly fitting forces, our method also reduces the key internal force errors from 25.5 to 11.1 kcal/mol/Å and from 30.2 to 10.3 kcal/mol/Å for the N-C and C-Cl bonds, respectively. Compared to the uncorrected simulations, the AM1-SSGPR-4/MM method lowers the predicted free energy barrier from 28.7 to 11.7 kcal/mol and decreases the reaction free energy from -12.4 to -41.9 kcal/mol, bringing these results into closer agreement with their AI/MM and experimental benchmarks.

Molecular Geometries and Vibrational Contributions to Reaction Thermochemistry Are Surprisingly Insensitive to the Choice of Basis Sets.

Calculation of molecular geometries and harmonic vibrational frequencies are pre-requisites for thermochemistry calculations. Contrary to conventional wisdom, this paper demonstrates that quantum chemical predictions of the thermochemistry of many gas and solution phase chemical reactions appear to be very insensitive to the choice of basis sets. For a large test set of 80 diverse organic and transition-metal-containing reactions, variations in reaction free energy based on geometries and frequencies calculated using a variety of double and triple-zeta basis sets from the Pople, Jensen, Ahlrichs, and Dunning families are typically less than 4 kJ mol-1, especially when the quasiharmonic oscillator correction is applied to mitigate the effects of low-frequency modes. Our analysis indicates that for many organic molecules and their transition states, high-level revDSD-PBEP86-D4 and DLPNO-CCSD(T)/(aug-)cc-pVTZ single-point energies usually vary by less than 2 kJ mol-1 on density functional theory geometries optimized using basis sets ranging from 6-31+G(d) to aug-pcseg-2 and aug-cc-pVTZ. In cases where these single-point energies vary significantly, indicating sensitivity of molecular geometries to the choice of basis set, there is often substantial cancellation of errors when the reaction energy or barrier is calculated. The study concludes that the choice of basis set for molecular geometry and frequencies, particularly those considered in this study, is not critical for the accuracy of thermochemistry calculations in the gas or solution phase.

Insight into the Mechanism Underlying Dehalococcoides mccartyi Strain CBDB1-Mediated B12-Dependent Aromatic Reductive Dehalogenation.

Anaerobic bacteria transform aromatic halides through reductive dehalogenation. This dehalorespiration is catalyzed by the supernucleophilic coenzyme vitamin B12, cob(I)alamin, in reductive dehalogenases. So far, the underlying inner-sphere electron transfer (ET) mechanism has been discussed controversially. In the present study, all 36 chloro-, bromo-, and fluorobenzenes and full-size cobalamin are analyzed at the quantum chemical density functional theory level with respect to a wide range of theoretically possible inner-sphere ET mechanisms. The calculated reaction free energies within the framework of CoI···X (X = F, Cl, and Br) attack rule out most of the inner-sphere pathways. The only route with feasible energetics is a proton-coupled two-ET mechanism that involves a B12 side-chain tyrosine (modeled by phenol) as a proton donor. For 12 chlorobenzenes and 9 bromobenzenes with experimental data from Dehalococcoides mccartyi strain CBDB1, the newly proposed PC-TET mechanism successfully discriminates 16 of 17 active from 4 inactive substrates and correctly predicts the observed regiospecificity to 100%. Moreover, fluorobenzenes are predicted to be recalcitrant in agreement with experimental findings. Conceptually, based on the Bell-Evans-Polanyi principle, the computational approach provides novel mechanistic insights and may serve as a tool for predicting the energetic feasibility of reductive aromatic dehalogenation.

Nucleophilic reactions with the novel 7-(chromon-3-yl)quinolino [3′,4′:5,6] pyrano[3,2-c]quinoline: Synthesis, biological and computational studies

Condensation reaction of 3-formylchromone (1) with 1-ethyl-4-hydroxyquinolin-2(1H)-one (2) in glacial acetic acid afforded the condensation product 4; in 1:2 molar ratio. Compound 4 was used as precursor for construction of some propenones linked pentacyclic quinolinopyranoquinoline. Ring opening of chromone moiety in compound 4 was achieved via reactions with a diversity of primary amines leading to propenone derivatives 5–7 and 11–13 in good yields (62–73%). All propanone derivatives exist in the E-configuration as deduced from their 1H NMR spectra. DFT/B3LYP functional was used with 6–311+G(d,p) basis sets for all theoretical calculations. Based on optimized geometry, the chemical potential (Pi), electronegativity (χ), hardness (η) and electrophilicity index (ω) are some of the global reactivity descriptors that were computed to predict the chemical reactivity of the studied compounds; where compound 13 has the highest softness and electrophilicity index (ω). Moreover, to determine the relative stability of compounds 1–4, the thermodynamic parameters such as enthalpy and free energies of the reactions were computed; where compound 4 has the lowest free energy of reaction (-439.61 kcal/mol), so its formation is spontaneous. By utilizing molecular electrostatic potential (MEP) and local-based descriptors in the form of condensed Fukui functions of the starting compound 4, the susceptible sites for electrophilic and nucleophilic attack were investigated. For compound 4, fk+ and Δfk values are more positive at C9 and C7 than other sites and these sites have more electrophilic characters. Therefore, nucleophilic attacks began at C9. On the other hand, the GIAO approximation was used to compute the 1H and 13C NMR chemical shift values in the ground state, of the present compounds, where a good agreement was observed between experimental and theoretical chemical shift results. Further, the calculated first hyperpolarizability of prepared compounds are found to be greater than that of urea. So, these compounds are ideal candidates for non-linear optical applications. The synthesized compounds were screened for their antimicrobial and anticancer activities showing variable inhibitory action. Compounds 5, 7 and 13 were more effective antimicrobial candidates against all tested microorganisms, while compound 13 was the most active against HepG-2 cell lines. Furthermore, a quantitative structure–activity relationship (QSAR) (relationship between DFT calculated descriptors and biological activities pIC50) model was built by applying multiple linear regression (MLR) on the synthesized compounds as anticancer agents. Moreover, Lipinski's rule of five indicates no problems with oral bioavailability of the prepared compounds.

Revisiting the scavenging activity of glutathione: Free radicals diversity and reaction mechanisms

Glutathione (GSH) is the most abundant low-molecular-mass thiolated compound in plants and animals, highly relevant in humans since it is one of the principal antioxidant agents capable of scavenging reactive oxygen species (ROS). In addition, it has a function in the immune system and in cell proliferation, and most recently it was discovered that it works against COVID-19. Considering the high flexibility of glutathione, with an atomic configuration and charge state susceptible to minimal changes in its chemical environment, it is of relevance to ascertain what is the scavenging capacity of each of the most probable glutathione species under physiological conditions. In order to find the site and mechanism that contributes the most to the antioxidant activity of GSH, density functional theory (DFT) calculations on multiple species of this molecule were performed in this work. Reactivity indexes, related to hydrogen atom transfer (HAT), single electron transfer-proton transfer (SET-PT), and sequential proton loss electron transfer (SPLET) mechanism were calculated for glutathione. In addition, Gibbs free energies of reaction (ΔG) were obtained for the reactions of GSH with several free radicals to confirm the thermochemical viability of each antioxidant mechanism and to avoid misleading conclusions in terms of considering energetically unfavorable reactions. The results confirm that HAT is the chemical route contributing the most to the antioxidant activity of GSH. However, at least for one radical of interest, SPLET should also be considered.

Temperature-dependent ethylene dissociative adsorption on ruthenium

The dissociative adsorption of ethylene onto Ru(111) at different temperatures was computed systematically at the first time. At 105 K, ethylene dissociative adsorption has the co-adsorbed CH2C*+2H* and CH3C*+H* as the first and second stable surface intermediates. At over 330 K, CH3C*+H* is converted back into CH2C* accompanied by H2 desorption and the subsequent dissociation of CH2C* into HCC*, HC*+C* and 2C*. The computed Arrhenius activation barriers of the dissociation of CH2CH2 (0.18 vs. 0.22 ± 0.04 eV) and CH3C (0.54 vs. 0.52 ± 0.04 eV) agree perfectly with the available experimental values, and CH3C* represents the most stable surface species. Under CO co-adsorption, the most stable surface species are the co-adsorbed CH3C*+H*+3CO*. It is found that CO co-adsorption promotes H2 desorption and stabilizes CH3C* by blocking the surface sites for dissociation and raises the dissociation barrier compared to the clean surface (0.78 vs 0.54 eV). Brønsted–Evans–Polanyi relationship between the activation Gibbs free energy barrier and reaction Gibbs free energy is found for CH2C*+2H*+nCO* = CH3C*+H*+nCO* and CH2C*+2H*+nCO* = HCC*+3H*+nCO* (n = 0–3). Ethylene adsorption has di-σ and π adsorption configurations in very close energy, and H2 has adsorption energy of about 0.90 eV.

Thermodynamic prediction of biogas production and combustion: The spontaneity and energy conversion efficiency from photosynthesis to combustion

Due to inappropriate energy consumption and subpar waste management, the growing population leads to an increase in energy demand and environmental damage. The creation of biogas enhances the management of organic waste and provides renewable energy. The production of biogas, which is a mixture of several gases, primarily methane and carbon dioxide, occurs during the four phases of aerobic digestion (AD). The four stages are hydrolysis, acidogenesis, acetogenesis, and methanogensis. Biogas comprises 50–70% Methane, 25–40% carbon dioxide and remaining traces of gases. In this paper, these biogas production processes are not thoroughly studied utilizing thermodynamic principles. Using thermodynamic criteria, this article analyses and assesses why the aerobic digesting process is spontaneous. Entropy, enthalpy, and Gibbs free energy of reactions during the various stages of the formation of biogas are examined. At Standard Temperature and Pressure Conditions (STP), the combined four phases of biogas formation are exothermic and spontaneous based on the analysis of Entropy, enthalpy, and Gibbs free energy of reactions from balanced equations at standard conditions of temperature and pressure. A unit mole of glucose is used to compare the energy released during photosynthesis with the energy released during biogas burning. Three moles of methane can be produced from decomposition of glucose. The combustion of three moles of methane yields 2406.876 kJ energy and if the same amount of moles of biogas (60% methane and 40% carbon dioxide) burns the energy yield is reduced to 1604.584 kJ. From the energy captured by photosynthesis i.e., 2808.1 kJ/mol 57.141% of the energy is recovered in the biogas combustion process. This efficiency reaches to 85.711% if pure methane is burned. As the separation of methane from biogas, mixture in actual plants is not economically feasible the combustion of methane gas the ideal limit of the efficiency.

Peptide-based metalloporphyrin catalysts: unveiling the role of the metal ion in indole oxidation

Over the last decades, much effort has been devoted to the construction of protein and peptide-based metalloporphyrin catalysts capable of promoting difficult transformations with high selectivity. In this context, mechanistic studies are fundamental to elucidate all the factors that contribute to catalytic performances and product selectivity. In our previous work, we selected the synthetic peptide-porphyrin conjugate MnMC6*a as a proficient catalyst for indole oxidation, promoting the formation of a 3-oxindole derivative with unprecedented selectivity. In this work, we have evaluated the role of the metal ion in affecting reaction outcome, by replacing manganese with iron in the MC6*a scaffold. Even though product selectivity is not altered upon metal substitution, FeMC6*a shows a lower substrate conversion and prolonged reaction times with respect to its manganese analogue. Experimental and theoretical studies have enabled us to delineate the reaction free energy profiles for both catalysts, indicating different thermodynamic limiting steps, depending on the nature of the metal ion.

A thermodynamic relationship between the chemical equilibrium constant and the dielectric properties of the reaction medium: Solvent mixtures and universal solvents.

We introduce a novel thermodynamic model oriented toward accurately predicting the effect of solvent polarity on chemical equilibrium. Our approach is based on the fundamental principles of thermodynamics of continuum medium and can be applied generally to estimate the Gibbs free energy contribution resulting from electrostatic interactions between the solvent and chemical species to the corresponding equilibrium constant in the solution phase. Using a set of assumptions, we have developed a practical calculation methodology that employs multivariate fitting to determine the dependence of 27 different reactions, including tautomerizations, dimerizations, and acid-base dissociations, on solvent polarity. From this approach, we estimated all the contributions to the Gibbs free energy of reaction in the solution phase of some of these processes, including the gas phase Gibbs free energy of reaction, the electrostatic (continuum) contribution to the solvation Gibbs free of the involved solutes and, even, the Gibbs free energy contribution due to specific (intramolecular) solute-solvent interactions, albeit indirectly.

N-Heterocyclic Carbene Formation in the Ionic Liquid [EMIM+][OAc-]: Elucidating Solvation Effects with Reactive Molecular Dynamics Simulations.

Recent experimental and theoretical work has debated whether N-heterocyclic carbenes (NHCs) are natively present in imidazolium-based ionic liquids (ILs) such as 1-ethyl-3-methylimidazolium acetate ([EMIM+][OAc-]) at room temperature. Because NHCs are powerful catalysts, determining their presence within imidazolium-based ILs is important, but experimental characterization is difficult due to the transient nature of the carbene species. Because the carbene formation reaction involves acid-base neutralization of two ions, ion solvation will largely dominate the reaction free energy and thus must be considered in any quantum chemical investigation of the reaction. To computationally study the NHC formation reaction, we develop physics-based, neural network reactive force fields to enable free energy calculations for the reaction in bulk [EMIM+][OAc-]. Our force field explicitly captures the formation of NHC and acetic acid by deprotonation of a EMIM+ molecule by acetate and in addition describes the dimerization of acetic acid and acetate. Using umbrella sampling, we compute reaction free energy profiles within the bulk IL and at the liquid/vapor interface to understand the influence of the environment on ion solvation and reaction free energies. Compared to reaction of the EMIM+/OAc- dimer in the gas phase, the bulk environment destabilizes formation of the NHC as expected due to the large ion solvation energies. Our simulations reveal a preference for the product acetic acid to share its proton with an acetate in solution and at the interface. We predict NHC content in bulk [EMIM+][OAc-] to be on the order of parts-per-million (ppm) levels, with order-of-magnitude enhancement of NHC concentration at the liquid/vapor interface. The interfacial enhancement of NHC content is due to both poorer solvation of the ionic reactants and solvophobic stabilization of the neutral NHC molecule at the liquid/vapor interface.