Origin of Free Energy Barriers of Decarboxylation and the Reverse Process of CO2 Capture in Dimethylformamide and in Water

HEPOM: Using Graph Neural Networks for the Accelerated Predictions of Hydrolysis Free Energies in Different pH Conditions

Hydrolysis is a fundamental family of chemical reactions where water facilitates the cleavage of bonds. The process is ubiquitous in biological and chemical systems, owing to water's remarkable versatility as a solvent. However, accurately predicting the feasibility of hydrolysis through computational techniques is a difficult task, as subtle changes in reactant structure like heteroatom substitutions or neighboring functional groups can influence the reaction outcome. Furthermore, hydrolysis is sensitive to the pH of the aqueous medium, and the same reaction can have different reaction properties at different pH conditions. In this work, we have combined reaction templates and high-throughput ab initio calculations to construct a diverse data set of hydrolysis free energies. The developed framework automatically identifies reaction centers, generates hydrolysis products, and utilizes a trained graph neural network (GNN) model to predict ΔG values for all potential hydrolysis reactions in a given molecule. The long-term goal of the work is to develop a data-driven, computational tool for high-throughput screening of pH-specific hydrolytic stability and the rapid prediction of reaction products, which can then be applied in a wide array of applications including chemical recycling of polymers and ion-conducting membranes for clean energy generation and storage.

Tandem Mass Spectrometry of Perfluorocarboxylate Anions: Fragmentation Induced by Reactive Species Formed From Microwave Excited Hydrogen and Water Plasmas

RATIONALE

Polyfluoroalkyl substances (PFAS) like perfluorooctanoic acid have persistent environmental and physiological effects. This study investigates the degradation of CnF2n+1CO2 - (n = 1-7) with neutral radical fragmentation under oxygen attachment dissociation (OAD). Unique fragments absent from collision-induced dissociation (CID) are observed. Further, potential mechanisms are uncovered by density functional theory (DFT) calculations.

METHODS

From a standard mixture of PFAS, straight-chain perfluorinated carboxylic acids with carbon chain lengths of one to eight were separated via liquid chromatography and transferred to the gas phase via negative-mode electrospray ionisation. Each CnF2n+1CO2 - of interest was mass selected and fragmented via both CID and OAD in a quadrupole time-of-flight mass spectrometer. DFT optimisations of structures were performed at M06/6-31+g(d), and single point energy calculations were performed at M06-2X/aug-cc-pVTZ for C3F7CO2 -.

RESULTS

Decarboxylation was observed from both CID and OAD, but fluorine abstraction and hydroxyl addition only occurred with OAD. The DFT calculations suggest that C3F6 -• (m/z 150) is most likely formed from by H• attack onto a β- C-F bond, then loss of HF, finally decarboxylation. Further, C3F5O- (m/z 147) likely arises from C3F6 -• recombining with OH• to produce energised C3F6OH- ions, followed by α- or β- elimination of HF to give enolate and/or epoxide-type products.

CONCLUSIONS

OAD of C3F7CO2 - yields unique product ions C3F6 -• (m/z 150) and C3F5O- (m/z 147) absent from collision-induced dissociation. DFT calculations suggest an intricate pathway of H• attack onto a β C-F bond, then loss of HF, decarboxylation, recombination with OH•, and finally α- or β- elimination of HF to give the products.

Proton Transfer via π-Interactions from Pyridine Provides a Facilitated Route for Transfer of CO2 in Its Complex with a Carbanion

Aromatic π-interactions have been recognized as enhancing enzymatic catalytic processes, providing an efficient route to overcome entropic barriers. A nonenzymic analogue, a complex of protonated pyridine and a phenyl substituent in a thiamin conjugate, facilitates the departure of CO2 by protonation of a vicinal carbanion in a reactive complex. To evaluate the efficiency of the catalytic pathway from the π-associated proton donor, a system was assessed that produced measurable competition through the rates of formation of alternative products resulting from the same thiamin-derived carbanion. The barriers to competing pathways from the decarboxylation of p-(bromomethyl)-mandelylthiamin in the presence and absence of protonated pyridine were determined, establishing the efficiency of the vicinal proton transfer between π-associated species. The formation of the complex of CO2 and the co-formed carbanion also addresses the mechanism of the uncatalyzed exchange of 13CO2 into carboxyl groups discovered by Lundgren. Finally, microscopic reversibility implicates pyridine as a vicinal Brønsted base in thiamin-aldehyde adducts, producing carbanions that could incorporate dissolved CO2 into carboxyl groups.

Carboxylic Acid Salts as Dual-Function Reagents for Carboxylation and Carbon Isotope Labeling

The potassium salts of carboxylic acids are developed as efficient carboxylating agents through CO₂ exchange. We describe these carboxylates as dual-function reagents because they function as a combined source of CO₂ and base/metalating agent. By using the salt of a commercially available carboxylic acid, this protocol overcomes difficulties when using CO₂ gas or organometallic reagents, such as pressurized containers or strictly inert conditions. The reaction proceeds under mild conditions, does not require transition metals or other additives, and shows broad substrate scope. Through the preparation of several biologically important molecules, we show how this strategy provides an opportunity for isotope labeling with low equivalents of labeled CO₂ .

Aldol Cleavage in Water and the Power of Citrate Lyase as a Catalyst

Citrate lyase allows Klebsiella aerogenes to grow anaerobically on citrate as the sole carbon source. Arrhenius analysis of experiments at high temperatures indicates that citrate is cleaved nonenzymatically to acetate and oxaloacetate with a t_1/2 of 6.9 million years in neutral solution at 25 °C, while malate cleavage occurs even more slowly (t_1/2 = 280 million years). However, t_1/2 is only 10 days for the nonenzymatic cleavage of 4-hydroxy-2-ketoglutarate, indicating that the introduction of an α-keto group enhances the rate of aldol cleavage of malate by a factor of 10¹⁰. The aldol cleavages of citrate and malate, like the decarboxylation of malonate (t_1/2 = 180 years), are associated with a near-zero entropy of activation, and their extreme differences in rate reflect differences between their heats of activation. Citrate lyase enhances the rate of substrate cleavage 6 × 10¹⁵-fold, comparable in magnitude with the rate enhancement produced by OMP decarboxylase, although these enzymes are strikingly different in their mechanisms of action.

Adenylate Kinase-Catalyzed Reactions of AMP in Pieces: Specificity for Catalysis at the Nucleoside Activator and Dianion Catalytic Sites

The pressure to optimize the enzymatic rate acceleration for adenylate kinase (AK)-catalyzed phosphoryl transfer has led to the evolution of an induced-fit mechanism, where the binding energy from interactions between the protein and substrate adenosyl group is utilized to drive a protein conformational change that activates the enzyme for catalysis. The adenine group of adenosine contributes 11.8 kcal mol-1 to the total ≥14.7 kcal mol-1 adenosine stabilization of the transition state for AK-catalyzed phosphoryl transfer to AMP. The relative third-order rate constants for activation of adenylate kinase, by the C-5 truncated adenosine 1-(β-d-erythrofuranosyl)adenine (EA), for catalysis of phosphoryl transfer from ATP to phosphite dianion (HP, kcat/KHPKAct = 260 M-2 s-1), fluorophosphate (47 M-2 s-1), and phosphate (9.6 M-2 s-1), show that substitution of -F for -H and of -OH for -H at HP results, respectively, in decreases in the reactivity of AK for catalysis of phosphoryl transfer due to polar and steric effects of the -F and -OH substituents. The addition of a 5'-CH2OH to the EA activator results in a 3.0 kcal mol-1 destabilization of the transition state for AK-activated phosphoryl transfer to HP due to a steric effect. This is smaller than the 8.3 kcal mol-1 steric effect of the 5'-CH2OH substituent at OMP on HP-activated OMPDC-catalyzed decarboxylation of 1-(β-d-erythrofuranosyl)orotate. The 2'-OH ribosyl substituent shows significant interactions with the transition states for AK-catalyzed phosphoryl transfer from ATP to AMP and for adenosine-activated AK-catalyzed phosphoryl transfer from ATP to HP.

Taking the "F" out of forever chemicals

The right solvent mix breaks down perfluorinated organic acids.

Low-temperature mineralization of perfluorocarboxylic acids

Per- and polyfluoroalkyl substances (PFAS) are persistent, bioaccumulative pollutants found in water resources at concentrations harmful to human health. Whereas current PFAS destruction strategies use nonselective destruction mechanisms, we found that perfluoroalkyl carboxylic acids (PFCAs) could be mineralized through a sodium hydroxide-mediated defluorination pathway. PFCA decarboxylation in polar aprotic solvents produced reactive perfluoroalkyl ion intermediates that degraded to fluoride ions (78 to ~100%) within 24 hours. The carbon-containing intermediates and products were inconsistent with oft-proposed one-carbon-chain shortening mechanisms, and we instead computationally identified pathways consistent with many experiments. Degradation was also observed for branched perfluoroalkyl ether carboxylic acids and might be extended to degrade other PFAS classes as methods to activate their polar headgroups are identified.

Late-Stage Carbon-14 Labeling and Isotope Exchange: Emerging Opportunities and Future Challenges

Carbon-14 (¹⁴C) is a gold standard technology routinely utilized in pharmaceutical and agrochemical industries for tracking synthetic organic molecules and providing their metabolic and safety profiles. While the state of the art has been dominated for decades by traditional multistep synthetic approaches, the recent emergence of late-stage carbon isotope labeling has provided new avenues to rapidly access carbon-14-labeled biologically relevant compounds. In particular, the development of carbon isotope exchange has represented a fundamental paradigm change, opening the way to unexplored synthetic transformations. In this Perspective, we discuss the recent developments in the field with a critical assessment of the literature. We subsequently discuss research directions and future challenges within this rapidly evolving field.

Photochemistry of the pyruvate anion produces CO2, CO, CH3-, CH3, and a low energy electron

The photochemistry of pyruvic acid has attracted much scientific interest because it is believed to play critical roles in atmospheric chemistry. However, under most atmospherically relevant conditions, pyruvic acid deprotonates to form its conjugate base, the photochemistry of which is essentially unknown. Here, we present a detailed study of the photochemistry of the isolated pyruvate anion and uncover that it is extremely rich. Using photoelectron imaging and computational chemistry, we show that photoexcitation by UVA light leads to the formation of CO₂, CO, and CH₃⁻. The observation of the unusual methide anion formation and its subsequent decomposition into methyl radical and a free electron may hold important consequences for atmospheric chemistry. From a mechanistic perspective, the initial decarboxylation of pyruvate necessarily differs from that in pyruvic acid, due to the missing proton in the anion.

Pyruvic acid and its conjugate base, the pyruvate anion, are largely present in the atmosphere. Here the authors, using photoelectron imaging and quantum chemistry calculations, investigate the photochemistry of isolated pyruvate anions initiated by UVA radiation and report the formation of CO₂, CO, and CH₃⁻ further decomposing into CH₃ and a free electron.

Investigation on the Stoichiometry of Carbon Dioxide in Isotope-Exchange Reactions with Phenylacetic Acids

The functionalization of carbon dioxide (CO2) as a C1 building block has attracted enormous attention. Carboxylation reactions, in particular, are of major interest for applications in isotope labeling. Due to the inexpensive nature of CO2, information about its stoichiometric use is generally unavailable in the literature. Because of the rarity and limited availability of CO2 isotopomers, this parameter is of concern for applications in carbon-isotope labeling. We investigated the effects of the stoichiometry of labeled CO2 on carbon isotope exchange of phenyl­acetic acids. Both thermal and photocatalytic procedures were studied, providing insight into product outcome and isotope incorporation. Preliminary results on isotope-dilution effects of carbonate bases in photocatalytic carboxylation reactions have also been obtained.

Stability of a Monoethanolamine-CO2 Zwitterion at the Vapor/Liquid Water Interface: Implications for Low Partial Pressure Carbon Capture Technologies

The need to chemically convert CO₂ at the interface of aqueous amine solutions has become particularly relevant for the development and the broad distribution of cost-effective and near-future devices for direct air capture working at low (e.g., ambient) partial pressure. Here, we have determined the stability of a CO₂-monoethanolamine zwitterion and its chemical conversion into carbamate at the vapor/liquid water interface by first-principles molecular dynamics simulations coupled with a recently introduced enhanced sampling technique. Contrary to the bulk water case, our results show that both the zwitterion and carbamate ions are poorly stable at the vapor/amine aqueous interface, further stating the differences between the homogeneous and heterogeneous CO₂ chemical conversion. The design of novel and cost-effective capture systems, such as those offered by amine-based scrubbing solutions, working at low (e.g., ambient) CO₂ partial pressure should explore the use of novel solvents, different from aqueous mixtures, to overcome the limits of the current absorbents.

Oxidative cross-coupling processes inspired by the Chan-Lam reaction

The Cu-catalyzed oxidative cross-coupling of N- and O-nucleophiles with aryl boronic acids (the Chan-Lam reaction) remains among the most useful approaches to prepare aniline and phenol derivatives. The combination of high chemoselectivity, mild reaction conditions, and the ability to use simple Cu-salts as catalysts makes this process a valuable alternative to aromatic substitutions and Pd-catalyzed reactions of aryl electrophiles (Buchwald-Hartwig coupling). Despite the widespread use of Chan-Lam reactions in synthesis, the analogous carbon-carbon bond forming variant of this process had not been developed prior to our work. This feature article describes our discovery and application of Cu-catalyzed oxidative coupling reactions of activated methylene derivatives or carboxylic acids with nucleophiles including aryl boronic esters and amines.

Solvation Induction of Free Energy Barriers of Decarboxylation Reactions in Aqueous Solution from Dual-Level QM/MM Simulations

Carbon dioxide capture, corresponding to the recombination process of decarboxylation reactions of organic acids, is typically barrierless in the gas phase and has a relatively low barrier in aprotic solvents. However, these processes often encounter significant solvent-reorganization-induced barriers in aqueous solution if the decarboxylation product is not immediately protonated. Both the intrinsic stereoelectronic effects and solute-solvent interactions play critical roles in determining the overall decarboxylation equilibrium and free energy barrier. An understanding of the interplay of these factors is important for designing novel materials applied to greenhouse gas capture and storage as well as for unraveling the catalytic mechanisms of a range of carboxy lyases in biological CO₂ production. A range of decarboxylation reactions of organic acids with rates spanning nearly 30 orders of magnitude have been examined through dual-level combined quantum mechanical and molecular mechanical simulations to help elucidate the origin of solvation-induced free energy barriers for decarboxylation and the reverse carboxylation reactions in water.