Transition State Analysis Research Articles

Reaction Pathway Analysis of PET Deconstruction via Methanolysis and Tertiary Amine Catalysts.

Polyethylene terephthalate (PET) is a type of polymer frequently used in plastic packaging that significantly adds the amount of plastic waste found in landfills. One of the ways to recover valuable raw materials from postconsumer plastic is by depolymerizing PET into its monomeric constituents, which are dimethyl terephthalate (DMT) and ethylene glycol. PET depolymerization is often done in methanolysis with the help of acidic or base catalysts. Tertiary amine is one of the most attractive base catalysts for PET depolymerization in methanolysis since it does not lead to the generation of potentially environmentally harmful waste, unlike metal-based catalysts. However, the mechanism by which tertiary amines catalyze PET depolymerization in methanolysis remains unexplored. Developing a detailed mechanistic understanding of this process is important for improving plastic upcycling since it opens the possibility of employing various cheaper and more environmentally friendly reaction conditions. Using density functional theory and transition state analysis, we show that in the presence of tertiary amine catalysts, methanolysis of PET consists of multiple discrete-step reactions rather than a single concerted step. Furthermore, by comparing our calculations to recent experimental results, we were able to rationalize the DMT yield from the depolymerization process by relating it to charge polarization within tertiary amine catalysts, thus opening a pathway to identify atomic descriptors for future catalyst design.

Systematic simulations and analysis of transition states using committor functions.

Systematic simulations and analysis of transition states using committor functions.

Exploring the bonding and extraction separation effects of N donor ligands with different skeletons on Am(III) and Eu(III)

Designing ligands for effective separation of actinide(III)/lanthanide(III) is one of the key issues in the treatment of spent nuclear fuel. However, due to the chemical similarity of trivalent actinides and lanthanides, their separation faces a great challenge in the reprocessing of spent nuclear fuel. Nitrogen donor extractants are considered as promising reagents for separation of trivalent actinides and lanthanides. To the best of our knowledge, the pre-organized structure of the ligand has a strong influence on the extraction separation capacity. In this work, we designed four N-donor ligands (L1 and L2 with pyridine and bipyridine skeletons, respectively, and L3 and L4 both with phenanthroline skeletons) with different pre-organized structures and investigated their selective extraction for Am(III) and Eu(III) by using scalar relativistic density functional theory (DFT). The absolute minimum ESP values of these ligands and the higher HOMO level suggest that the ligand L2 may have a stronger affinity for Am(III)/Eu(III) ions than other ligands. The three average bond lengths of each complex indicate that the Am(III) and Eu(III) ions have larger bond lengths with N2 atoms than with N1 atoms. Various theoretical approaches have been used to evaluate the properties of the four ligands as well as the coordination structures, bonding properties and thermodynamic properties of the complexes of the four ligands with Am(III) and Eu(III). The WBIs, QTAIM, NBO, DOS and EDA analysis indicate that the metal–ligand bonds are mainly ionic in character, the Am-N bond has more covalency than the Eu-N bond because the Am 5f orbitals are more involved in bonding with ligand than Eu 4f orbitals. According to the extended transition state and natural orbital chemical valence theory (ETS-NOCV) analysis, electrons are obviously transferred from the lone pair of the ligand N atom to the hybrid s, d and f orbitals of the metal ion. The thermodynamic results show that the four ligands can coordinate well with the Am and Eu ions, and also have suitable separation capacity for Am and Eu. Among the four ligands, the L2 and L3 ligands have the strongest coordination ability for metals and the best extraction separation effect for Am and Eu. It can be seen that the bridging skeleton of the ligand and the number of N atoms on the five-membered ring and also different organic solvents have obvious effects on the extraction and separation capacity of the ligand. This study provides a theoretical basis for the efficient separation of Am(III)/Eu(III) by adjusting the preorganization level of ligands, and provides a theoretical basis for the design and screening of ligands by preorganization.

Highly enantioselective carbene-catalyzed δ-lactonization via radical relay cross-coupling

An N-heterocyclic carbene (NHC) catalyzed enantioselective cyclisation and trifluoromethylation of olefins with cinnamaldehydes via radical relay cross-coupling in the presence of Togni reagent is reported and δ-lactones tolerated with stereogenic centers at β- and γ-positions are obtained in moderate to high yields and with high enantioselectivities. Further computational studies explain that the radical cross-coupling step is the key to determining the enantioselectivity. Energy analysis of key transition states and intermediates also provides a reasonable explanation for the difficulty of diastereoselective control. DFT calculations also reveal that the hydrogen-bonding interaction plays a vital role in the promotion of this chemistry.

Photocatalytic chloride-to-chlorine conversion by ionic iron in aqueous aerosols: a combined experimental, quantum chemical, and chemical equilibrium model study

Abstract. Prior aerosol chamber experiments show that the ligand-to-metal charge transfer absorption in iron(III) chlorides can lead to the production of chlorine (Cl2/Cl). Based on this mechanism, the photocatalytic oxidation of chloride (Cl−) in mineral dust–sea spray aerosols was recently shown to be the largest source of chlorine over the North Atlantic. However, there has not been a detailed analysis of the mechanism that includes the aqueous formation equilibria and the absorption spectra of the iron chlorides nor has there been an analysis of which iron chloride is the main chromophore. Here we present the results of experiments measuring the photolysis of FeCl3 ⋅ 6H2O in specific wavelength bands, an analysis of the absorption spectra of FeCln3-n (n=1 … 4) made using density functional theory, and the results of an aqueous-phase model that predicts the abundance of the iron chlorides with changes in pH and iron concentrations. Transition state analysis is used to determine the energy thresholds of the dissociations of the species. Based on a speciation model with conditions extending from dilute water droplets and acidic seawater droplets to brine and salty crust, as well as the absorption rates and dissociation thresholds, we find that FeCl2+ is the most important species for chlorine production for a wide range of conditions. The mechanism was found to be active in the range of 400 to 530 nm, with a maximum around 440 nm. We conclude that iron chlorides will form in atmospheric aerosols from the combination of iron(III) cations with chloride and that they will be activated by sunlight, generating chlorine (Cl2/Cl) from chloride (Cl−) in a process that is catalytic in both chlorine and iron.

Mechanistic insight into the degradation of sulfadiazine by electro-Fenton system: Role of different reactive species

Sulfadiazine (SDZ), a widely used effective antibiotic, is resistant to conventional biological treatment, which is concerning since untreated SDZ discharge can pose a significant environmental risk. Electro-Fenton (EF) technology is a promising advanced oxidation technology for efficiently removing SDZ. However, due to the limitations of traditional experimental methods, there is a lack of in-depth study on the mechanism of ·OH-dominated SDZ degradation in EF process. In this study, an EF system was established for SDZ degradation and the transformation products (TPs) were detected by mass spectrometry. Dynamic thermodynamic, kinetic and wave function analysis of reactants, transition states and intermediates were proposed by density functional theory calculations, which was applied to elucidate the underlying mechanism of SDZ degradation. Experimental results showed that amino, benzene, and pyrimidine sites in SDZ were oxidized by ·OH, producing TPs through hydrogen abstraction and addition reactions. ·OH was kinetically more likely to attack SDZ- than SDZ. Fe(IV) dominated the single-electron transfer oxidation reaction of SDZ, and the formed organic radicals can spontaneously generate the de-SO2 product via Smiles rearrangement. Toxicity experiments showed the toxicity of SDZ and TPs can be greatly reduced. The results of this study promote the understanding of SDZ degradation mechanism in-depth. Environmental ImplicationSulfadiazine (SDZ) is one of the antibiotics widely used around the world. However, it has posed a significant environmental risk due to its overuse and cannot be efficiently removed by traditional treatment methods. The lack of in-depth study on SDZ degradation mechanism under reactive species limits the improvement of SDZ degradation efficiency. Therefore, this work focused on SDZ degradation mechanism in-depth under electro-Fenton system through reactive species investigation, mass spectrometry analysis, and theoretical calculation. The results in this study can provide a theoretical basis for improving the SDZ degradation efficiency which will contribute to solving SDZ pollution problems.

Enantioselective Sulfonimidamide Acylation via a Cinchona Alkaloid-Catalyzed Desymmetrization: Scope, Data Science, and Mechanistic Investigation.

Methods to access chiral sulfur(VI) pharmacophores are of interest in medicinal and synthetic chemistry. We report the desymmetrization of unprotected sulfonimidamides via asymmetric acylation with a cinchona-phosphinate catalyst. The desired products are formed in excellent yield and enantioselectivity with no observed bis-acylation. A data-science-driven approach to substrate scope evaluation was coupled to high throughput experimentation (HTE) to facilitate statistical modeling in order to inform mechanistic studies. Reaction kinetics, catalyst structural studies, and density functional theory (DFT) transition state analysis elucidated the turnover-limiting step to be the collapse of the tetrahedral intermediate and provided key insights into the catalyst-substrate structure-activity relationships responsible for the origin of the enantioselectivity. This study offers a reliable method for accessing enantioenriched sulfonimidamides to propel their application as pharmacophores and serves as an example of the mechanistic insight that can be gleaned from integrating data science and traditional physical organic techniques.

Transition State Analysis of Key Steps in Dual Photoredox-Cobalt-Catalyzed Elimination of Alkyl Bromides.

A combination of inter- and intramolecular 13C kinetic isotope effects and density functional theory analysis is used to evaluate the key mechanistic events of sequentially operating catalytic cycles in the dual photoredox-cobalt-catalyzed elimination of alkyl bromides. The results point to a mechanism proceeding via irreversible halogen-atom transfer (XAT) from the alkyl halide, resulting in an alkyl radical, which undergoes hydrogen-atom transfer (HAT) to a Co(II) intermediate to deliver the product olefin. Alternative pathways involving nucleophilic substitution by a Co(I) species and by β-hydride elimination are discounted based on the poor agreement of experimental and predicted 13C KIEs. This mechanistic understanding is used to evaluate the origins of regioselectivity in the elimination step for an unsymmetrical alkyl halide catalyzed by electronically and sterically distinct cobaloxime catalysts. This study represents the experimental validation of the key features of the transition state structure of XAT by α-aminoalkyl radicals, an important class of atom transfer reactions that generate carbon-centered radicals from alkyl and aryl halides. Furthermore, it illustrates the power of 13C KIEs in probing complex mechanisms in metallaphotoredox catalysis.

Structural EEG signal analysis for sleep apnea classification.

Diagnosing the sleep apnea can be critical in preventing the person having sleep disorder from unhealthy results. The aim of this study is to obtain a sleep apnea scoring approach by comparing parametric and non-parametric power spectral density (PSD) estimation methods from EEGsignals recorded from different brain regions (C4-M1 and O2-M1) for transient signal analysis of sleep apnea patients. Power Spectral Density (PSD) methods (Burg, Yule-Walker, periodogram, Welch and multi-taper) are examined for the detection of apnea transition states including pre-apnea, intra-apnea and post-apnea together with statistical methods. In the experimental studies, EEG recordings available in the database were analyzed with PSD methods. Results showed that there are statistically significant differences between parametric and non-parametric methods applied for PSD analysis of apnea transition states in delta, theta, alpha and beta bands. Moreover, it was also revealed that PSD of EEG signals obtained from C4-M1 and O2-M1 channels were also found statistically different as proved by classification using the K-nearest neighbour (KNN) method. It was concluded that not only applying different PSD methods, but also EEG signals from different brain regions provided different statistical results in terms of apnea transition states as obtained from KNN classification.

Chemorheological Kinetic Modeling of Uncatalyzed Hydroxyl‐Terminated Polybutadiene and Isophorone Diisocyanate

AbstractCatalysts are often employed to enable nonisothermal reaction kinetic studies when tracking cure progression of polyurethane reactions. However, when quickly reacting, catalyzed materials are prepared through mixing followed by the addition of fillers or additives, subsequent processing of the partially reacted material becomes difficult. Here, chemorheology is used to track changes in viscoelastic properties of uncatalyzed polybutadiene‐diisocyanate reactions for multiple days, which quantifies the degree of cure during polymerization. Viscosity profiles are accurately captured by the two‐stage Arrhenius model (r2>0.95), and conversion progress is adequately represented by the Kamal–Sourour model (r2>0.76). Transition state analysis via Wynne–Jones–Eyring–Evans theory (WJEE) reveals the presence of an associative mechanism according to entropic and enthalpic activation energies ΔS# = −96.9 J K−1 and ΔH# = 36.4 kJ, respectively. These rheokinetic modeling results align with Fourier transform infrared spectroscopy findings. To the knowledge, no rheokinetic studies have tracked cure progress of this uncatalyzed system for the extended timeframe presented here. The cure profile also presents unique viscosity growth, representative of molecular weight buildup, compared to catalyzed systems. This finding emphasizes the novelty of applying previously developed chemorheological models to multiday thermosetting reactions within a flow field in a manner that is generalizable to many long‐term curing systems.

From covalent transition states in chemistry to noncovalent in biology: from β- to Φ-value analysis of protein folding.

Solving the mechanism of a chemical reaction requires determining the structures of all the ground states on the pathway and the elusive transition states linking them. 2024 is the centenary of Brønsted's landmark paper that introduced the β-value and structure-activity studies as the only experimental means to infer the structures of transition states. It involves making systematic small changes in the covalent structure of the reactants and analysing changes in activation and equilibrium-free energies. Protein engineering was introduced for an analogous procedure, Φ-value analysis, to analyse the noncovalent interactions in proteins central to biological chemistry. The methodology was developed first by analysing noncovalent interactions in transition states in enzyme catalysis. The mature procedure was then applied to study transition states in the pathway of protein folding - 'part (b) of the protein folding problem'. This review describes the development of Φ-value analysis of transition states and compares and contrasts the interpretation of β- and Φ-values and their limitations. Φ-analysis afforded the first description of transition states in protein folding at the level of individual residues. It revealed the nucleation-condensation folding mechanism of protein domains with the transition state as an expanded, distorted native structure, containing little fully formed secondary structure but many weak tertiary interactions. A spectrum of transition states with various degrees of structural polarisation was then uncovered that spanned from nucleation-condensation to the framework mechanism of fully formed secondary structure. Φ-analysis revealed how movement of the expanded transition state on an energy landscape accommodates the transition from framework to nucleation-condensation mechanisms with a malleability of structure as a unifying feature of folding mechanisms. Such movement follows the rubric of analysis of classical covalent chemical mechanisms that began with Brønsted. Φ-values are used to benchmark computer simulation, and Φ and simulation combine to describe folding pathways at atomic resolution.

Theoretical Research on the Reduction of CO2 with H2S on Pyrite FeS2 Surfaces

Understanding the reduction of CO2 and the origin and evolution of early life on Earth is an important research endeavor. Pyrite, due to its semiconductor properties, is believed to play a pivotal role as a reactant or catalyst in converting reducing gases, such as CO2, into organic matter. In this study, we employed density functional theory (DFT) to investigate the reduction of CO2 in the presence of H2S on the surface of pyrite. Our findings reveal that the presence of sulfur vacancies enhances the adsorption of H2S and CO2 molecules onto the pyrite surface. Interestingly, we observed the generation of the HCOOH molecule on the defective pyrite surface. Additionally, the transition state analysis indicates that H2S and CO2 molecules require the overcoming of an energy barrier (Ea) of 36.93 kJ/mol to form the HCOOH molecule. This study sheds light on the role of pyrite in the early creation of life on Earth by elucidating its impact on the reduction of carbon dioxide.

Multicomponent and Metal‐Free Diels–Alder/Aromatization Approach to the Stereospecific Synthesis of E‐(Hetero)Stilbenes and Diarylacetylenes

AbstractHerein, we present a novel and metal‐free approach to the stereospecific synthesis of E‐stilbenes. Starting from substituted 6‐arylhexa‐3,5‐dien‐2‐ones, a multicomponent enolacetylation/intermolecular Diels–Alder reaction was performed using ethyl acetate as a green solvent. The obtained cycloadducts were then oxidized without purification to produce the stilbenic products in good yields up to 67 % and with complete (E)‐stereospecificity and regioselectivity. Moreover, heterostilbenes were synthetized using this approach, displaying the potential applications of this protocol in pharmaceutical and material sciences. The proposed methodology was further extended to the synthesis of diarylacetylenes, furnishing a new metal‐free synthetic access to this important class of compounds. Furthermore, DFT calculations were performed confirming a concerted [4+2] reaction mechanism of the key ring‐forming step. At last, the energetic analysis of the possible transition states helps to shed some light on the experimentally observed total regio‐ and chemoselectivity.

Linear Free Energy Relationships and Transition State Analysis of CO2 Reduction Catalysts Bearing Second Coordination Spheres with Tunable Acidity.

In molecular catalysts, protic functional groups in the secondary coordination sphere (SCS) work in conjunction with an exogenous acid to relay protons to the active site of electrochemical CO2 reduction; however, it is not well understood how the acidity of the SCS and exogenous acid together determine the kinetics of catalytic turnover. To evaluate the relative contributions of proton transfer driving forces, we synthesized a series of modular iron tetraphenylporphyrin electrocatalysts bearing SCS amides of tunable pKa (17.6 to 20.0 in dimethyl sulfoxide (DMSO)) and employed phenols of variable acidity (15.3 to 19.1) as exogenous acids. This system allowed us to (1) evaluate contributions from proton transfer driving forces associated with either the SCS or exogenous acid and (2) obtain mechanistic insights into CO2 reduction as a function of pKa. A series of linear free-energy relationships show that kinetics become increasingly sensitive to variations in SCS pKa when more acidic exogenous acids are used (0.82 ≥ Brønsted α ≥ 0.13), as well as to variations in exogenous acid pKa when SCS acidity is increased (0.62 ≥ Brønsted α ≥ 0.32). An Eyring analysis suggests that the rate-determining transition state becomes more ordered with decreasing SCS acidity, which is consistent with the proposal that SCS acidity modulates charge accumulation and solvation at the rate-limiting transition state. Together, these insights enable the optimization of activation barriers as a function of both SCS and exogenous acid pKa and can further guide the rational design of electrocatalytic systems wherein contributions from all participants in a proton relay are considered.

Nonlinear optical properties, structural and transition state analyses of ionic liquids: DFT and DFT-D2/D3 studies

This paper includes the structural properties, transition state analysis and NLO properties of the ionic liquids in quantum chemical calculations. Hydrogen bond geometries calculated by B3LYP and ωB97XD approaches have been compared with the crystallographic data in the literature. Transition state analysis have been carried out using Synchronous Transit-Guided Quasi-Newton (STQN) method with QST2 option and Density Functional Theory. Forms according to the positions of the proton on hydrogen bond axes and transition states have been evaluated by relative energy scanning. Interactions between anions and cations in ionic liquids optimizations have been studied by CP approach with D2 and D3 versions of Grimme’s dispersion correction. Electric dipole moments, dipole polarizability, first and second dipole hyper polarizability and important components have been calculated, statically and dynamically for ionic liquids. Effective and stable structures in terms of NLO have been evaluated. In addition, B3LYP and ωB97XD functionals approaches have been tested considering Grimme’s D2/D3 dispersion models for lithium interactions with bis(trifluoromethanesulfonyl)amide and methylsulfonate anions.

Selective Functionalisation of 5-Methylcytosine by Organic Photoredox Catalysis.

The epigenetic modification 5-methylcytosine plays a vital role in development, cell specific gene expression and disease states. The selective chemical modification of the 5-methylcytosine methyl group is challenging. Currently, no such chemistry exists. Direct functionalisation of 5-methylcytosine would improve the detection and study of this epigenetic feature. We report a xanthone-photosensitised process that introduces a 4-pyridine modification at a C(sp3 )-H bond in the methyl group of 5-methylcytosine. We propose a reaction mechanism for this type of reaction based on density functional calculations and apply transition state analysis to rationalise differences in observed reaction efficiencies between cyanopyridine derivatives. The reaction is initiated by single electron oxidation of 5-methylcytosine followed by deprotonation to generate the methyl group radical. Cross coupling of the methyl radical with 4-cyanopyridine installs a 4-pyridine label at 5-methylcytosine. We demonstrate use of the pyridination reaction to enrich 5-methylcytosine-containing ribonucleic acid.

Selective Functionalisation of 5-Methylcytosine by Organic Photoredox Catalysis.

The epigenetic modification 5-methylcytosine plays a vital role in development, cell specific gene expression and disease states. The selective chemical modification of the 5-methylcytosine methyl group is challenging. Currently, no such chemistry exists. Direct functionalisation of 5-methylcytosine would improve the detection and study of this epigenetic feature. We report a xanthone-photosensitised process that introduces a 4-pyridine modification at a C(sp3)-H bond in the methyl group of 5-methylcytosine. We propose a reaction mechanism for this type of reaction based on density functional calculations and apply transition state analysis to rationalise differences in observed reaction efficiencies between cyanopyridine derivatives. The reaction is initiated by single electron oxidation of 5-methylcytosine followed by deprotonation to generate the methyl group radical. Cross coupling of the methyl radical with 4-cyanopyridine installs a 4-pyridine label at 5-methylcytosine. We demonstrate use of the pyridination reaction to enrich 5-methylcytosine-containing ribonucleic acid.

Transition-State Analysis Reveals Unexpected Coordination-Specific Reactivity That Drives Alkene Dimerization by Sulfated Metal–Organic Frameworks

Transition-State Analysis Reveals Unexpected Coordination-Specific Reactivity That Drives Alkene Dimerization by Sulfated Metal–Organic Frameworks

Theoretical insights into the reversible CO2 absorption by ethylene glycol/KOH/boric acid low temperature transition mixture

The Low Temperature Transition Mixture (LTTM) formed by ethylene glycol, potassium hydroxide and boric acid experimentally demonstrated to reversibly absorb carbon dioxide (see J. Mol. Liq. 340 (2021) 117180). In this paper, we study the speciation of the components and the absorption/desorption mechanism by Density Functional Theory, providing reasonable hypotheses to explain all the experimental facts for which it was not possible to provide a satisfactory explanation. In addition, we used the recently developed Extended Transition State-Natural Orbitals for Chemical Valence (ETS-NOCV) analysis of concerted transition states (cTS), in order to isolate and quantitatively evaluate the relative importance and asynchrony of all the concurrent molecular events embedded in the cTS.

One-pot production of 5-methylfurfural (5-MF) and enhanced dewaterability of waste activated sludge by hydrothermal treatment with natural deep eutectic solvents (NADES): Experimental and theoretical studies

Natural deep eutectic solvents (NADES) coupled with hydrothermal treatment was innovatively proposed to process waste activated sludge for sustainable production of 5-methylfurfural (5-MF) and enhanced dewaterability. The yield of 5-MF up to 11.54 kg/t volatile solids (VS) with a NADES dosage of 2.0 mL, hydrothermal temperature of 180 °C and holding time of 30 min. The decreased capillary suction time (CST) and bound water content indicated that NADES with hydrothermal treatment substantially improved the dewaterability of sludge. The variations of sludge physicochemical properties and extracellular polymeric substances (EPS) compositions revealed that NADES disrupted the structure of sludge biopolymers. Density functional theory (DFT) calculations indicated that NADES weakened the hydrogen bond strength between EPS components, and thus promoted the solubilization of proteins and polysaccharides. Besides, transition state analysis showed that NADES also lowered the energy barrier of polypeptide hydrolysis and carbohydrates dehydration reactions for the production of 5-MF.