Mechanistic Insights into the Dissociation and Decomposition of Carbonic Acid in Water via the Hydroxide Route: An Ab Initio Metadynamics Study

Prediction of the pKa's of Hydrated Metal Carbonates and Bicarbonates for Mg, Ca, Mn, Fe, Co, Ni, Cu, and Zn Dications

The gas- and aqueous-phase acidities of hydrated metal dication carbonates, bicarbonates, and hydroxide complexes M(CO3)(H2O)n for n = 1 to 3, M(HCO3)2, M(HCO3)2(H2O)2, M(HCO3)(OH), and M(HCO3)(H2O)2(OH) for M = Mg, Ca, Mn, Fe, Co, Ni, Cu, and Zn were calculated at the CCSD(T)/aug-cc-pwCVDZ/cc-pwCVDZ level in the gas phase and at the B3LYP/aug-cc-pVTZ/cc-pVTZ(-PP) level with the COSMO self-consistent reaction field (SCRF) method in the aqueous phase. The composite correlated molecular orbital theory G3(MP2) and G3(MP2)B3 methods were used to predict the pKa's of the Mg structures and cis-cis carbonic acid to provide additional benchmarks. Using values scaled to experiment for H2CO3, the pKa's of bicarbonate ligands in group 2 and transition-metal complexes were compared to carbonic acid to gauge the effect of the metal complex on the bicarbonate. The group 2 metal complexes M(HCO3)2 and M(HCO3)(OH) decreased the acidity of the bicarbonate ligands, whereas their dihydrates were even less acidic. The transition-metal di-bicarbonate and bicarbonate hydroxide complexes generally made the bicarbonate more acidic especially when reduction of the metal occurs consistent with electron donation from the ligands; this is accompanied by spin transfer which typically increases in the order Mn < Fe < Co < Ni < Cu. The transition-metal dihydrates were less acidic than carbonic acid. Using values scaled to experiment for hydrated metal dications, the pKa's of water coordinated to group 2 and transition-metal complexes were generally more acidic than the hydrated metal dications, with the exception of Ca bicarbonate dihydrate, Co carbonate, Ni di-bicarbonate dihydrate, and Cu bicarbonate hydroxide di-bicarbonate.

Chemistrees: Data-Driven Identification of Reaction Pathways via Machine Learning

We propose to analyze molecular dynamics (MD) output via a supervised machine learning (ML) algorithm, the decision tree. The approach aims to identify the predominant geometric features which correlate with trajectories that transition between two arbitrarily defined states. The data-driven algorithm aims to identify these features without the bias of human “chemical intuition”. We demonstrate the method by analyzing the proton exchange reactions in formic acid solvated in small water clusters. The simulations were performed with ab initio MD combined with a method to efficiently sample the rare event, path sampling. Our ML analysis identified relevant geometric variables involved in the proton transfer reaction and how they may change as the number of solvating water molecules changes.

Ab Initio Molecular Dynamics Simulations of the Influence of Lithium Bromide Salt on the Deprotonation of Formic Acid in Aqueous Solution

The deprotonation of formic acid is investigated using metadynamics in tandem with Born-Oppenheimer molecular dynamics simulations. We compare our findings for formic acid in pure water with previous studies before examining formic acid in aqueous solutions of lithium bromide. We carefully consider different definitions for the collective variable(s) used to drive the metadynamics, emphasizing that the variables used must include all of the possible reactive atoms in the system, in this case carboxylate oxygens and water hydrogens. This ensures that all the various possible proton exchange events can be accommodated and the collective variable(s) can distinguish the protonated and deprotonated states, even over rather long ab initio simulation runs (ca. 200-300 ps). Our findings show that the formic acid deprotonation barrier and the free energy of the deprotonated state are higher in concentrated lithium bromide, in agreement with the available experimental data for acids in salt solution. We show that the presence of Br^- in proximity to the formic acid hydroxyl group effectively inhibits deprotonation. Our study extends previous work on acid deprotonation in pure water and at air-water interfaces to more complex multicomponent systems of importance in atmospheric and marine chemistry.

The multiple dissociation constants of glutathione disulfide: interpreting experimental pH-titration curves with ab initio MD simulations

The hexapeptide glutathione disulfide (GSSG) has six ionizable groups with six associated dissociation constants. The experimentally measured pH-titration curve, however, does not exhibit the six corresponding equivalence points and bears little resemblance to standard textbook examples of acid-base pH-titration curves. The curve highlights the difficulties in determining multiple pKa values of polyprotic acids - typically proteins and peptides - from experiment. The six pKa values of GSSG can, however, be estimated using Car-Parrinello molecular dynamics (CPMD) simulations in conjunction with metadynamics sampling of the underlying free energy landscape of the dissociation reactions. Ab initio MD simulations were performed on a GSSG molecule solvated by 200 water molecules. Using the estimated pKa values the theoretical titration curve was calculated and found to be in good agreement with experiment. The results clearly highlight how dissociation constants estimated from ab initio MD simulations can facilitate the interpretation of the pH-titration curves of complex chemical and biological systems.

Characterization of a trans-trans Carbonic Acid-Fluoride Complex by Infrared Action Spectroscopy in Helium Nanodroplets

The high Lewis basicity and small ionic radius of fluoride promote the formation of strong ionic hydrogen bonds in the complexation of fluoride with protic molecules. Herein, we report that carbonic acid, a thermodynamically disfavored species that is challenging to investigate experimentally, forms a complex with fluoride in the gas phase. Intriguingly, this complex is highly stable and is observed in abundance upon nanoelectrospray ionization of an aqueous sodium fluoride solution in the presence of gas-phase carbon dioxide. We characterize the structure and properties of the carbonic acid–fluoride complex, F^–(H₂CO₃), and its deuterated isotopologue, F^–(D₂CO₃), by helium nanodroplet infrared action spectroscopy in the photon energy range of 390–2800 cm^–1. The complex adopts a C_2v symmetry structure with the carbonic acid in a planar trans–trans conformation and both OH groups forming ionic hydrogen bonds with the fluoride. Substantial vibrational anharmonic effects are observed in the infrared spectra, most notably a strong blue shift of the symmetric hydrogen stretching fundamental relative to predictions from the harmonic approximation or vibrational second-order perturbation theory. Ab initio thermostated ring-polymer molecular dynamics simulations indicate that this blue shift originates from strong coupling between the hydrogen stretching and bending vibrations, resulting in an effective weakening of the OH···F^– ionic hydrogen bonds.

Local initiation conditions for water autoionization

The pH of liquid water is determined by the infrequent process in which water molecules split into short-lived hydroxide and hydronium ions. This reaction is difficult to probe experimentally and challenging to simulate. One of the open questions is whether the local water structure around a slightly stretched OH bond is actually initiating the eventual breakage of this bond or whether this event is driven by a global ordering that involves many water molecules far away from the reaction center. Here, we investigated the self-ionization of water at room temperature by rare-event ab initio molecular dynamics and obtained autoionization rates and activation energies in good agreement with experiments. Based on the analysis of thousands of molecular trajectories, we identified a couple of local order parameters and show that if a bond stretch occurs when all these parameters are around their ideal range, the chance for the first dissociation step (double-proton jump) increases from [Formula: see text] to 0.4. Understanding these initiation triggers might ultimately allow the steering of chemical reactions.

Reaction Mechanism for Direct Proton Transfer from Carbonic Acid to a Strong Base in Aqueous Solution I: Acid and Base Coordinate and Charge Dynamics

Protonation by carbonic acid H2CO3 of the strong base methylamine CH3NH2 in a neutral contact pair in aqueous solution is followed via Car-Parrinello molecular dynamics simulations. Proton transfer (PT) occurs to form an aqueous solvent-stabilized contact ion pair within 100 fs, a fast time scale associated with the compression of the acid-base hydrogen-bond (H-bond), a key reaction coordinate. This rapid barrierless PT is consistent with the carbonic acid-protonated base pKa difference that considerably favors the PT, and supports the view of intact carbonic acid as potentially important proton donor in assorted biological and environmental contexts. The charge redistribution within the H-bonded complex during PT supports a Mulliken picture of charge transfer from the nitrogen base to carbonic acid without altering the transferring hydrogen's charge from approximately midway between that of a hydrogen atom and that of a proton.

How Acidic Is Carbonic Acid?

Carbonic, lactic, and pyruvic acids have been generated in aqueous solution by the transient protonation of their corresponding conjugate bases by a tailor-made photoacid, the 6-hydroxy-1-sulfonate pyrene sodium salt molecule. A particular goal is to establish the pK(a) of carbonic acid H2CO3. The on-contact proton transfer (PT) reaction rate from the optically excited photoacid to the carboxylic bases was derived, with unprecedented precision, from time-correlated single-photon-counting measurements of the fluorescence lifetime of the photoacid in the presence of the proton acceptors. The time-dependent diffusion-assisted PT rate was analyzed using the Szabo-Collins-Kimball equation with a radiation boundary condition. The on-contact PT rates were found to follow the acidity order of the carboxylic acids: the stronger was the acid, the slower was the PT reaction to its conjugate base. The pK(a) of carbonic acid was found to be 3.49 ± 0.05 using both the Marcus and Kiefer-Hynes free energy correlations. This establishes H2CO3 as being 0.37 pK(a) units stronger and about 1 pK(a) unit weaker, respectively, than the physiologically important lactic and pyruvic acids. The considerable acid strength of intact carbonic acid indicates that it is an important protonation agent under physiological conditions.

Ammonia as an efficient catalyst for decomposition of carbonic acid: a quantum chemical investigation

Electronic structure calculations using M06-2X, MP2 and CCSD(T) methods have been employed to show ammonia as an efficient catalyst for decomposition of carbonic acid.

Ab Initio MD Simulations of the Brønsted Acidity of Glutathione in Aqueous Solutions: Predicting pKa Shifts of the Cysteine Residue

The tripeptide glutathione (GSH) is one of the most abundant peptides and the major repository for nonprotein sulfur in both animal and plant cells. It plays a critical role in intracellular oxidative stress management by the reversible formation of glutathione disulfide with the thiol-disulfide pair acting as a redox buffer. The state of charge of the ionizable groups of GSH can influence the redox couple, and hence the pKa value of the cysteine residue of GSH is critical to its functioning. Here we report ab initio Car-Parrinello molecular dynamics simulations of glutathione solvated by 200 water molecules, all of which are considered in the simulation. We show that the free-energy landscape for the protonation-deprotonation reaction of the cysteine residue of GSH computed using metadynamics sampling provides accurate estimates of the pKa and correctly predicts the shift in the dissociation constant values as compared with the isolated cysteine amino acid.

Ab Initio Molecular Dynamics Simulations of Amino Acids in Aqueous Solutions: Estimating pKa Values from Metadynamics Sampling

Changes in the protonation and deprotonation of amino acid residues in proteins play a key role in many biological processes and pathways. Here, we report calculations of the free-energy profile for the protonation-deprotonation reaction of the 20 canonical α amino acids in aqueous solutions using ab initio Car-Parrinello molecular dynamics simulations coupled with metadynamics sampling. We show here that the calculated change in free energy of the dissociation reaction provides estimates of the multiple pKa values of the amino acids that are in good agreement with experiment. We use the bond-length-dependent number of the protons coordinated to the hydroxyl oxygen of the carboxylic and the amine groups as the collective variables to explore the free-energy profiles of the Bronsted acid-base chemistry of amino acids in aqueous solutions. We ensure that the amino acid undergoing dissociation is solvated by at least three hydrations shells with all water molecules included in the simulations. The method works equally well for amino acids with neutral, acidic and basic side chains and provides estimates of the multiple pKa values with a mean relative error, with respect to experimental results, of 0.2 pKa units.

Estimating successive pKa values of polyprotic acids from ab initio molecular dynamics using metadynamics: the dissociation of phthalic acid and its isomers

pKa values of polyprotic acids estimated from ab initio molecular dynamics computation of the change in free energy upon dissociation.

Solvation of CO2 in water: effect of RuBP on CO2 concentration in bundle sheath of C4 plants

An understanding of the temperature-dependence of solubility of carbon dioxide (CO2) in water is important for many industrial processes. Voluminous work has been done by both quantum chemical methods and molecular dynamics (MD) simulations on the interaction between CO2 and water, but a quantitative evaluation of solubility remains elusive. In this work, we have approached the problem by considering quantum chemically calculated total energies and thermal energies, and incorporating the effects of mixing, hydrogen bonding, and phonon modes. An overall equation relating the calculated free energy and entropy of mixing with the gas-solution equilibrium constant has been derived. This equation has been iteratively solved to obtain the solubility as functions of temperature and dielectric constant. The calculated solubility versus temperature plot excellently matches the observed plot. Solubility has been shown to increase with dielectric constant, for example, by addition of electrolytes. We have also found that at the experimentally reported concentration of enzyme RuBP in bundle sheath cells of chloroplast in C4 green plants, the concentration of CO2 can effectively increase by as much as a factor of 7.1-38.5. This stands in agreement with the observed effective rise in concentration by as much as 10 times.

Molecular dynamics simulations predict an accelerated dissociation of H2CO3 at the air–water interface

Ab initio molecular dynamics simulations of carbonic acid (H₂CO₃) at the air–water interface yield a lower dissociation barrier than in bulk water.

THE MECHANISM OF ACID-CATALYZED DECARBOXYLATION OF PYRROLE-2-CARBOXYLIC ACID: INSIGHTS FROM CLUSTER-CONTINUUM MODEL CALCULATIONS

The decarboxylation of pyrrole-2-carboxylic acid comprises the addition of water to the carboxyl group and the C–C bond cleavage leading to the protonated carbonic acid. Herein possible concerted and stepwise mechanisms for the C-protonated and O-protonated pathways were extensively investigated by using the cluster-continuum model. The calculated results indicate that the initial hydration or the nucleophilic attack of water at the carbonyl group of both C- and O-protonated derivatives is the rate-determining step for the overall reaction, and the O-protonated pathway will dominate the whole reaction. The predicted activation Gibbs energies for the overall reaction initialized by the O-protonated species fall in the range of 83.3 ∼ 123.0 kJ/mol, showing good agreement with experimental values of 91.6 ∼ 101.3 kJ/mol. On the basis of extensive calculations, the remarkable dependence of the predicted mechanisms and thermodynamic values on the number of explicit water molecules in the cluster-continuum model was discussed.

Revisiting the mechanism of neutral hydrolysis of esters: water autoionization mechanisms with acid or base initiation pathways

The mechanism of neutral hydrolysis of ester has long been explored by theoretical studies. However, reliable theoretical calculations show that the usual bifunctional catalysis mechanism reported by different authors cannot explain the experimental kinetics. An important advance was recently reported by Gunaydin and Houk, suggesting that ions are involved in the mechanism and the process initiates by water autoionization followed by protonation of the ester (W(AI)A mechanism). However, this mechanism does not explain the hydrolysis of activated esters. In this work, we have used ab initio calculations, continuum solvation models, and intrinsic reaction coordinate method to support the W(AI)A mechanism for normal ester. In the case of activated esters, the process can also be viewed as water autoionization with formation of hydroxide ion aided by a second water molecule acting as a general base (W(AI)B mechanism). This is the mechanism that was proposed by Jencks and Carriuolo 50 years ago. Our analysis point out that the usual method for exploring mechanisms, searching for saddle points, may not work for problems like the present one, since there are no saddle points on the reaction pathway. Rather, the formation of a pair of ions from a neutral species may have an asymptotic barrier. The approach used in this paper allows the calculation of the free energy profile and enable us to explain the mechanism and kinetics of the neutral hydrolysis of normal (methyl acetate) and activated (methyl trifluoroacetate) esters. In addition, the present study suggests that formation of a pair of ions should always be considered in reactions in aqueous solution.