Ab Initio Molecular Dynamics Study of Carbon Dioxide and Bicarbonate Hydration and the Nucleophilic Attack of Hydroxide on CO2

The Structure of Carbon Dioxide at the Air-Water Interface and its Chemical Implications

The efficient reduction of CO2 into valuable products is a challenging task in an international context marked by the climate change crisis and the need to move away from fossil fuels. Recently, the use of water microdroplets has emerged as an interesting reaction media where many redox processes which do not occur in conventional solutions take place spontaneously. Indeed, several experimental studies in microdroplets have already been devoted to study the reduction of CO2 with promising results. The increased reactivity in microdroplets is thought to be linked to unique electrostatic solvation effects at the air-water interface. In the present work, we report a theoretical investigation on this issue for CO2 using first-principles molecular dynamics simulations. We show that CO2 is stabilized at the interface, where it can accumulate, and that compared to bulk water solution, its electron capture ability is larger. Our results suggest that reduction of CO2 might be easier in interface-rich systems such as water microdroplets, which is in line with early experimental data and indicate directions for future laboratory studies. The effect of other relevant factors which could play a role in CO2 reduction potential is discussed.

Adsorption of CO32-/HCO3- on a quartz surface: cluster formation, pH effects, and mechanistic aspects

Soluble inorganic carbon is an important component of a soil carbon pool, and its fate in soils, sediments, and underground water environments has great effects on many physiochemical and geological processes. However, the dynamical processes, behaviors and mechanism of their adsorption by soil active components, such as quartz, are still unclear. The aim of this work is to systematically address the anchoring mechanism of CO₃^2- and HCO₃^- on a quartz surface at different pH values. Three pH values (pH 7.5, pH 9.5 and pH 11) and three carbonate salt concentrations (0.07, 0.14 and 0.28 M) are considered, and molecular dynamics methods are used. The results indicate that the pH value regulates the adsorption behavior of CO₃^2- and HCO₃^- on the quartz surface by affecting the CO₃^2-/HCO₃^- ratio and the surface charge of quartz. In general, both HCO₃^- and CO₃^2- ions were able to adsorb on the quartz surface and the adsorption capacity of CO₃^2- is higher than that of HCO₃^-. HCO₃^- ions tended to uniformly distribute in an aqueous solution and contact the quartz surface in the form of single molecules instead of clusters. In contrast, CO₃^2- ions were mainly adsorbed as clusters which became larger as the concentration increased. Na⁺ ions were essential for the adsorption of HCO₃^- and CO₃^2-, because some of the Na⁺ and CO₃^2- ions spontaneously associated together to form clusters, promoting the clusters to be adsorbed on the quartz surface through cationic bridges. The local structures and dynamics trajectory of CO₃^2- and HCO₃^- showed that the anchoring mechanism of carbonate solvates on quartz involved H-bonds and cationic bridges, which changed in relation to the concentration and pH values. However, the HCO₃^- ions mainly adsorbed on the quartz surface via H-bonds while the CO₃^2- ions tended to be adsorbed through cationic bridges. These results may help in understanding the geochemical behavior of soil inorganic carbon and further the processes of the Earth's carbon chemical cycle.

The intrinsically disordered region from PP2C phosphatases functions as a conserved CO2 sensor

Carbon dioxide not only plays a central role in the carbon cycle, but also acts as a crucial signal in living cells. Adaptation to changing CO₂ concentrations is critical for all organisms. Conversion of CO₂ to HCO₃^- by carbonic anhydrase and subsequent HCO₃^--triggered signalling are thought to be important for cellular responses to CO₂ (refs. ^1-3). However, carbonic anhydrases are suggested to transduce a change in CO₂ rather than be a direct CO₂ sensor^4,5, the mechanism(s) by which organisms sense CO₂ remain unknown. Here we demonstrate that a unique group of PP2C phosphatases from fungi and plants senses CO₂, but not HCO₃^-, to control diverse cellular programmes. Different from other phosphatases, these PP2Cs all have an intrinsically disordered region (IDR). They formed reversible liquid-like droplets through phase separation both in cells and in vitro, and were activated in response to elevated environmental CO₂ in an IDR-dependent manner. The IDRs in PP2Cs are characterized by a sequence of polar amino acids enriched in serine/threonine, which provides CO₂ responsiveness. CO₂-responsive activation of PP2Cs via the serine/threonine-rich IDR-mediated phase separation represents a direct CO₂ sensing mechanism and is widely exploited.

Space-Resolved OH Vibrational Spectra of the Hydration Shell around CO2

The CO2 molecule is weakly bound in water. Here we analyze the influence of a dissolved CO2 molecule on the structure and OH vibrational spectra of the surrounding water. From the analysis of ab initio molecular dynamics simulations (BLYP-D3) we present static (structure, coordination, H-bonding, tetrahedrality) and dynamical (OH vibrational spectra) properties of the water molecules as a function of distance from the solute. We find a weakly oscillatory variation ("ABBA") in the 'solution minus bulk water' spectrum. The origin of these features can largely be traced back to solvent-solute hard-core interactions which lead to variations in density and tetrahedrality when moving from the solute's vicinity out to the bulk region. The high-frequency peak in the solute-affected spectra is specifically analyzed and found to originate from both water OH groups that fulfill the geometric H-bond criteria, and from those that do not (dangling ones). Effectively, neither is hydrogen-bonded.

Quantitative Kinetic Model of CO2 Absorption in Aqueous Tertiary Amine Solvents

Aqueous tertiary amine solutions are increasingly used in industrial CO₂ capture operations because they are more energy-efficient than primary or secondary amines and demonstrate higher CO₂ absorption capacity. Yet, tertiary amine solutions have a significant drawback in that they tend to have lower CO₂ absorption rates. To identify tertiary amines that absorb CO₂ faster, it would be efficacious to have a quantitative and predictive model of the rate-controlling processes. Despite numerous attempts to date, this goal has been elusive. The present computational approach achieves this goal by focusing on the reaction of CO₂ with OH^- forming HCO₃^-. The performance of the resulting model is demonstrated for a consistent experimental data set of the absorption rates of CO₂ for 24 different aqueous tertiary amine solvents. The key to the new model's success is the manner in which the free energy barrier for the reaction of CO₂ with OH^- is evaluated from the differences among the solvation free energies of CO₂, OH^-, and HCO₃^-, while the pK_a of the amines controls the concentration of OH^-. These solvation energies are obtained from molecular dynamics simulations. The experimental value of the free energy of reaction of CO₂ with pure water is combined with information about measured rates of absorption of CO₂ in an aqueous amine solvent in order to calibrate the absorption rate model. This model achieves a relative accuracy better than 0.1 kJ mol^-1 for the free energies of activation for CO₂ absorption in aqueous amine solutions and 0.07 g L^-1 min^-1 for the absorption rate of CO₂. Such high accuracies are necessary to predict the correct experimental ranking of CO₂ absorption rates, thus providing a quantitative approach of practical interest.

Carbon dioxide, bicarbonate and carbonate ions in aqueous solutions under deep Earth conditions

We investigate the effect of pressure, temperature and acidity on the composition of water-rich carbon-bearing fluids under thermodynamic conditions that correspond to the Earth's deep crust and upper mantle. Our first-principles molecular dynamics simulations provide mechanistic insight into the hydration shell of carbon dioxide, bicarbonate and carbonate ions, and into the pathways of the acid/base reactions that convert these carbon species into one another in aqueous solutions. At temperatures of 1000 K and higher, our simulations can sample the chemical equilibrium of these acid/base reactions, thus allowing us to estimate the chemical composition of diluted carbon dioxide and (bi)carbonate ions as a function of acidity and thermodynamic conditions. We find that, especially at the highest temperature, the acidity of the solution is essential to determine the stability domain of CO₂vs. HCO₃^-vs. CO₃^2-.

Application of dynamic current density for increased concentration factors and reduced energy consumption for concentrating ammonium by electrodialysis

Ammonium (NH₄⁺) can be recovered from water for fertiliser production or even energy production purposes. Because NH₄⁺ recovery is more effective at increased concentrations, electrodialysis (ED) can be used to concentrate NH₄⁺ from side streams, such as sludge reject water, and simultaneously achieve high NH₄⁺ removal efficiencies. However, the effect of osmosis and back-diffusion increases when the NH₄⁺ concentration gradient between the diluate and the concentrate stream increases, resulting in a limitation of the concentration factor and an increase in energy consumption for NH₄⁺ removal. In this study, we showed that operation at dynamic current density (DCD) reduced the effect of osmosis and back-diffusion, due to a 75% decrease of the operational run time, compared to operation at a fixed current density (FCD). The concentration factor increased from 4.5 for an FCD to 6.7 for DCD, while the energy consumption of 90% NH₄⁺ removal from synthetic sludge reject water at DCD remained stable at 5.4 MJ·kg-N^-1.

Understanding Carbamate Formation Reaction Thermochemistry of Amino Acids as Solvents for Postcombustion CO2 Capture

The carbamate stability constant for a data set of 10 amino acids, having potential for being postcombustion CO₂ capture (PCC) solvents, has been calculated using various implicit and explicit solvation shell models. This work also includes an extensive study of gas-phase free energy and enthalpy for the amino acid carbamate formation reaction with the Hartree Fock method, density functional methods [B3LYP/6-311++G(d,p)], and composite methods (G3MP2B3, G3MP2, CBS-QB3, and G4MP2). Ideal PCC solvent properties require finding a profitable tradeoff between various thermodynamic and system optimization parameters. Benchmark gaseous-phase and solution-phase thermodynamic properties given in this work can help in making informed decisions when choosing promising PCC solvents. The temperature dependency of the carbamate stability constant of amino acids is predicted using PCM and SM8T implicit solvation models. PCC is a temperature swing absorption-desorption process, and the high-temperature sensitivity of the ln K_c^AmCOO- value is of vital importance in attaining cost-efficient processes.

Molecular Hydration of Carbonic Acid: Ab Initio Quantum Chemical and Density Functional Theory Investigation

Molecular hydration of carbonic acid (H₂CO₃) is investigated in terms of bonding patterns in H₂CO₃···(H₂O) _n [ n = 1-4] hydrogen-bonded clusters within ab initio quantum chemical and density functional theory (DFT) frameworks. Successive addition of water molecules to H₂CO₃···H₂O entails elongation of O-H (hydroxyl) bond as well as contraction of specific intermolecular hydrogen bonds signifying hydration of carbonic acid; these structural features get markedly enhanced under the continuum solvation framework. A comparison between the structurally similar clusters H₂CO₃···(H₂O) _n and HCOOH···(H₂O) _n [ n = 1-3] brings out the structural stability of the former. The present investigation in conjunction with the binding energy behavior of approaching water molecule(s) should serve as a precursor for pathways exploring aqueous dissociation of H₂CO₃ for larger clusters, as well as development of force-field potentials for acid dissociation process.

Versatile electrification of two-dimensional nanomaterials in water

The recent emergence of nanofluidics has highlighted the exceptional properties of graphene and its boron-nitride counterpart as confining nanomaterials for water and ion transport. Surprisingly, ionic transport experiments have unveiled a consequent electrification of the water/carbon surfaces, with a contrasting response for its water/boron-nitride homologue. In this paper, we report free energy calculations based on ab initio molecular dynamics simulations of hydroxide OH^- ions in water near graphene and hexagonal boron nitride (h-BN) layers. Our results disclose that both surfaces get charged through hydroxide adsorption, but two strongly different mechanisms are evidenced. The hydroxide species shows weak physisorption on the graphene surface while it exhibits also strong chemisorption on the h-BN surface. Interestingly OH^- is shown to keep very fast lateral dynamics and interfacial mobility within the physisorbed layer on graphene. Taking into account the large ionic surface conductivity, an analytic transport model allows to reproduce quantitatively the experimental data.

Structure, Dynamics, and Hydration Free Energy of Carbon Dioxide in Aqueous Solution: A Quantum Mechanical/Molecular Mechanics Molecular Dynamics Thermodynamic Integration (QM/MM MD TI) Simulation Study

The solvation of carbon dioxide in solution represents a key step for the capture and fixation CO₂ in nature, which may be further influenced by the formation of (bi)carbonate species and/or the formation of CO₂ clusters in solution. The latter processes are strongly dependent on the exact environment of the liquid state (e.g., pH value, solvated ions, etc.) and may interfere with the experimental determination of structural, dynamical, and thermodynamic properties. In this work a hybrid quantum mechanical/molecular mechanical (QM/MM) simulation approach at correlated ab initio level of theory resolution-of-identity second-order Møller-Plesset Perturbation Theory (RI-MP2) has been applied in the framework of thermodynamic integration (TI) to study structure, dynamics, and the hydration free energy of a single carbon dioxide molecule in aqueous solution. A detailed analysis of the individual QM/MM potential energy contributions demonstrate that the overall potential remains highly consistent over the entire sampling phase and that no artificial contributions are influencing the determination of the hydration free energy. The latter value of 0.01 ± 0.92 kcal/mol was found in very good agreement with the values of 0.06 and 0.24 kcal/mol obtained via quasi-chemical theory and experimental measurements, respectively. In order to obtain detailed information about the C- and O _C-water interaction, conically restricted regions with respect to the main axis of the CO₂ molecule have been employed in structural analysis. The presented data not only provide detailed information about the hydration properties of CO₂ but act as a critical validation of the simulation technique, which will be beneficial in the study of nonaqueous solvents such as pure and aqueous NH₃ solutions, which have been suggested as potential candidates to capture CO₂ from anthropogenic sources.

Solvation effects on the vibrational modes in hydrated bicarbonate clusters

Harmonic analysis and ab initio molecular dynamics simulations reveal the solvation effects on the vibrational modes of HCO₃⁻(H₂O)_n.

CO2 Hydration Shell Structure and Transformation

The hydration-shell of CO₂ is characterized using Raman multivariate curve resolution (Raman-MCR) spectroscopy combined with ab initio molecular dynamics (AIMD) vibrational density of states simulations, to validate our assignment of the experimentally observed high-frequency OH band to a weak hydrogen bond between water and CO₂. Our results reveal that while the hydration-shell of CO₂ is highly tetrahedral, it is also occasionally disrupted by the presence of entropically stabilized defects associated with the CO₂-water hydrogen bond. Moreover, we find that the hydration-shell of CO₂ undergoes a temperature-dependent structural transformation to a highly disordered (less tetrahedral) structure, reminiscent of the transformation that takes place at higher temperatures around much larger oily molecules. The biological significance of the CO₂ hydration shell structural transformation is suggested by the fact that it takes place near physiological temperatures.

Examining the structural evolution of bicarbonate–water clusters: insights from photoelectron spectroscopy, basin-hopping structural search, and comparison with available IR spectral studies

Combining NIPES, theoretical calculations and available IR spectra allows us to identify the minimum energy structures that best fit the experiments.

Ab Initio Studies of Calcium Carbonate Hydration

Ab initio simulations of large hydrated calcium carbonate clusters are challenging due to the existence of multiple local energy minima. Extensive conformational searches around hydrated calcium carbonate clusters (CaCO3·nH2O for n = 1-18) were performed to find low-energy hydration structures using an efficient combination of Monte Carlo searches, density-functional tight binding (DFTB+) method, and density-functional theory (DFT) at the B3LYP level, or Møller-Plesset perturbation theory at the MP2 level. This multilevel optimization yields several low-energy structures for hydrated calcium carbonate. Structural and energetics analysis of the hydration of these clusters revealed a first hydration shell composed of 12 water molecules. Bond-length and charge densities were also determined for different cluster sizes. The solvation of calcium carbonate in bulk water was investigated by placing the explicitly solvated CaCO3·nH2O clusters in a polarizable continuum model (PCM). The findings of this study provide new insights into the energetics and structure of hydrated calcium carbonate and contribute to the understanding of mechanisms where calcium carbonate formation or dissolution is of relevance.

Interplay between water uptake, ion interactions, and conductivity in an e-beam grafted poly(ethylene-co-tetrafluoroethylene) anion exchange membrane

We demonstrate that the true hydroxide conductivity in an e-beam grafted poly(ethylene-co-tetrafluoroethylene) [ETFE] anion exchange membrane (AEM) is as high as 132 mS cm(-1) at 80 °C and 95% RH, comparable to a proton exchange membrane, but with very much less water present in the film. To understand this behaviour we studied ion transport of hydroxide, carbonate, bicarbonate and chloride, as well as water uptake and distribution. Water uptake of the AEM in water vapor is an order of magnitude lower than when submerged in liquid water. In addition (19)F pulse field gradient spin echo NMR indicates that there is little tortuosity in the ionic pathways through the film. A complete analysis of the IR spectrum of the AEM and the analyses of water absorption using FT-IR led to conclusion that the fluorinated backbone chains do not interact with water and that two types of water domains exist within the membrane. The reduction in conductivity was measured during exposure of the OH(-) form of the AEM to air at 95% RH and was seen to be much slower than the reaction of CO2 with OH(-) as the amount of water in the film determines its ionic conductivity and at relative wet RHs its re-organization is slow.

On the origin of preferred bicarbonate production from carbon dioxide (CO2) capture in aqueous 2-amino-2-methyl-1-propanol (AMP)

The strong interaction between AMP and H₂O is found to promote bicarbonate production while suppressing carbamate formation.

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.

CO(2) incorporation in hydroxide and hydroperoxide containing water clusters--a unifying mechanism for hydrolysis and protolysis

The reactions of CO2 with anionic water clusters containing hydroxide, OH(-)(H2O)n, and hydroperoxide, HO2(-)(H2O)n, have been studied in the isolated state using a mass spectrometric technique. The OH(-)(H2O)n clusters were found to react faster for n = 2,3, while for n >3 the HO2(-)(H2O)n clusters are more reactive. Insights from quantum chemical calculations revealed a common mechanism in which the decisive bicarbonate-forming step starts from a pre-reaction complex where OH(-) and CO2 are separated by one water molecule. Proton transfer from the water molecule to OH(-) then effectively moves the hydroxide ion motif next to the CO2 molecule. A new covalent bond is formed between CO2 and the emerging OH(-) in concert with the proton transfer. For larger clusters, successive proton transfers from H2O molecules to neighbouring OH(-) are required to effectively bring about the formation of the pre-reaction complex, upon which bicarbonate formation is accomplished according to the concerted mechanism. In this manner, a general mechanism is suggested, also applicable to bulk water and thereby to CO2 uptake in oceans. Furthermore, this mechanism avoids the intermediate H2CO3 by combining the CO2 hydrolysis step and the protolysis step into one. The general mechanistic picture is consistent with low enthalpy barriers and that the limiting factors are largely of entropic nature.

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.

Carbon Dioxide Migration Pathways in Proteins

Some of the most important biological processes, such as carbon fixation, are dependent on protein-gas interactions. The motion of CO2 through the enzyme phosphoenolpyruvate carboxykinase was investigated using extensive all-atom molecular dynamics simulations. Three discrete migration pathways were located, suggesting the protein directs the movement of CO2. The chemical nature of these pathways is discussed, as are their biotechnological ramifications.

Predicting the acidity constant of a goethite hydroxyl group from first principles

Accurate predictions of the acid-base behavior of hydroxyl groups at mineral surfaces are critical for understanding the trapping of toxic and radioactive ions in soil samples. In this work, we apply ab initio molecular dynamics (AIMD) simulations and potential-of-mean-force techniques to calculate the pK(a) of a doubly protonated oxygen atom bonded to a single Fe atom (Fe(I)OH(2)) on the goethite (101) surface. Using formic acid as a reference system, pK(a) = 7.0 is predicted, suggesting that isolated, positively charged groups of this type are marginally stable at neutral pH. Similarities and differences between AIMD and the more empirical multi-site complexation methodology are highlighted, particularly with respect to the treatment of hydrogen bonding with water and proton sharing among surface hydroxyl groups. We also highlight the importance of an electronic structure method that can accurately predict transition metal ion properties for goethite pK(a) calculations.

Photodetachment of Isolated Bicarbonate Anion: Electron Binding Energy of HCO3(.)

We report the first direct photodetachment photoelectron spectroscopy of HCO3(-) in the gas phase under low-temperature conditions. The observed photoelectron spectra are complicated due to excitations of manifolds in both vibrational and electronic states. A long and single vibrational progression with a frequency of 530 ± 20 cm(-1) is partially resolved in the threshold of the T = 20 K, 266 nm spectrum. The adiabatic electron detachment energy (ADE) of HCO3(-), or, in other words, the electron affinity (EA) of neutral HCO3, is experimentally determined from the (0,0) transition to be 3.680 ± 0.015 eV. The computed values of the Franck-Condon integral and intensity are favorable for observing the (0,0) transition. High-level ab initio calculations at the CCSD(T) level of theory produce an estimated anharmonic frequency of 546 cm(-1) for HCO3 and a value of 3.79 eV for the (0,0) transition, both in good agreement with the experimentally determined values.

Cobalt-porphyrin catalyzed electrochemical reduction of carbon dioxide in water. 1. A density functional study of intermediates

The reduction of carbon dioxide by cobalt porphyrins is thought to be a multistep reaction with several possible intermediates and reaction pathways. We here investigate a number of possible intermediates in this reaction using density functional theory, including both hybrid (B3LYP) and pure (PBE and BP86) functionals. Optimum structures are located, and harmonic vibrational frequencies and thermal corrections are computed for the low-lying electronic states for all intermediates. Free energies of solvation are predicted for all species, providing a reaction profile in the aqueous phase, which enables identification of likely pathways. Finally, the reaction energy for the binding of carbon dioxide to the cobalt porphine cation is determined in the gas phase and in solution.

Cobalt-porphyrin catalyzed electrochemical reduction of carbon dioxide in water. 2. Mechanism from first principles

We apply first principles computational techniques to analyze the two-electron, multistep, electrochemical reduction of CO(2) to CO in water using cobalt porphyrin as a catalyst. Density functional theory calculations with hybrid functionals and dielectric continuum solvation are used to determine the steps at which electrons are added. This information is corroborated with ab initio molecular dynamics simulations in an explicit aqueous environment which reveal the critical role of water in stabilizing a key intermediate formed by CO(2) bound to cobalt. By use of potential of mean force calculations, the intermediate is found to spontaneously accept a proton to form a carboxylate acid group at pH < 9.0, and the subsequent cleavage of a C-OH bond to form CO is exothermic and associated with a small free energy barrier. These predictions suggest that the proposed reaction mechanism is viable if electron transfer to the catalyst is sufficiently fast. The variation in cobalt ion charge and spin states during bond breaking, DFT+U treatment of cobalt 3d orbitals, and the need for computing electrochemical potentials are emphasized.

Comprehensive study of the hydration and dehydration reactions of carbon dioxide in aqueous solution

The reversible interactions of dissolved CO(2) with H(2)O and OH(-) to form H(2)CO(3) and HCO(3)(-) in aqueous solution have been investigated using spectrophotometric stopped-flow measurements. The progress of the reactions was monitored via indicators coupled to the pH changes during the reactions. The study, involving global analysis of the complete data set, spanned the temperature range 6.6-42.8 degrees C and resulted in the evaluation of all rate and equilibrium constants as well as activation parameters for the kinetic data and the reaction enthalpies and entropies for the equilibrium constants.