Theoretical investigation of the CO2 + OH- .fwdarw. HCO3- reaction in the gas and aqueous phases

Study of Amine Functionalized Mesoporous Carbon as CO2 Storage Materials

Carbon sequestration via the carbon capture and storage (CCS) method is one of the most useful methods of lowering CO2 emissions in the atmosphere. Ethylenediamine (EDA)- and triethylenetetramine (TETA)-modified mesoporous carbon (MC) has been successfully prepared as a CO2 storage material. The effect of various concentrations of EDA or TETA added to MC, as well as activated carbon (AC), on their CO2 adsorption capacity were investigated using high-purity CO2 as a feed and a titration method to quantitatively measure the amount of adsorbed CO2. The results showed that within 60 min adsorption time, MCEDA49 gave the highest CO2 capacity adsorption (19.68 mmol/g), followed by MC-TETA30 (11.241 mol/g). The improvement of CO2 adsorption capacity at low TETA loadings proved that the four amine functional groups in TETA gave an advantage to CO2 adsorption. TETA-functionalized MC has the potential to be used as a CO2 storage material at a low concentration. Therefore, it is relatively benign and friendly to the environment.

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.

Density Fluctuation in Aqueous Solutions and Molecular Origin of Salting-Out Effect for CO2

Using molecular dynamics simulation, we studied the density fluctuations and cavity formation probabilities in aqueous solutions and their effect on the hydration of CO₂. With increasing salt concentration, we report an increased probability of observing a larger than the average number of species in the probe volume. Our energetic analyses indicate that the van der Waals and electrostatic interactions between CO₂ and aqueous solutions become more favorable with increasing salt concentration, favoring the solubility of CO₂ (salting in). However, due to the decreasing number of cavities forming when salt concentration is increased, the solubility of CO₂ decreases. The formation of cavities was found to be the primary control on the dissolution of gas, and is responsible for the observed CO₂ salting-out effect. Our results provide the fundamental understanding of the density fluctuation in aqueous solutions and the molecular origin of the salting-out effect for real gas.

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.

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.

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. 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.

H2CO3 forms via HCO3- in water

According to the generally accepted picture of CO(2) dissolution in water, the formation of H(2)CO(3) proceeds in a single step that involves the attack of a water oxygen on the CO(2) carbon in concert with a proton transfer to a CO(2) oxygen. In the present work, a series of ab initio molecular dynamics simulations have been carried out along with the metadynamics technique which reveals a stepwise mechanism: the reaction of a water molecule with CO(2) yields HCO(3)(-) as an intermediate and a hydronium ion, whereas the protonation of the CO(2) moiety occurs in a separate step representing a well-defined activation barrier toward the H(2)CO(3) molecule. This alternative scenario was already taken into consideration decades ago, but subsequent experiments and calculations have given preference to the concerted mechanism. Employing extended periodic models of the CO(2)-water system that mimic the bulk aqueous environment, the present simulations yield the complete free energy profile of the stepwise mechanism and provide a detailed microscopic mechanism of the elementary steps. HCO(3)(-) formation is found to be the rate-determining step of the entire CO(2) hydration process.

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.

Hydroxycarbonyl anion (m/z 45), a diagnostic marker for alpha-hydroxy carboxylic acids

Collision-induced dissociation mass spectra of anions derived from alpha-hydroxy carboxylic acids (AHAs) show a diagnostic peak at m/z 45. Product ion spectra recorded from this m/z 45 ion confirm that it represents the hydroxycarbonyl anion [DIAGRAM: SEE TEXT], and not the formate anion [DIAGRAM: SEE TEXT] as sometimes described in the literature. For example, the formate anion is not only defiant to further fragmentation but is also unreactive toward CO2. In contrast, the hydroxycarbonyl anion easily fragments to produce a peak at m/z 17 for the hydroxyl anion, and also readily reacts with CO2 to produce a peak at m/z 61 for the bicarbonate anion. The hydrogen atom in the hydroxycarbonyl anion and that in the formate anion are not mobile within the skeletal framework of the ions, since the two ions did not manifest any interconversion under the conditions and time scales of our mass spectrometric experiments. The other significant product ion peak in the spectra of deprotonated AHAs represents a 46-Da loss. MS/MS data from appropriately deuteriated compounds confirmed that one hydrogen atom from the C-2 position, and the other from the hydroxy group are specifically removed for this loss of elements of formic acid. Moreover, the two oxygen atoms eliminated for the HCOOH loss originate exclusively from the carboxylate group.

Identification of Proton-Transfer Pathways in Human Carbonic Anhydrase II

We investigate the probable proton-transfer pathways from the surface of human carbonic anhydrase II into the active site cavity through His-64 that has been widely implicated as a key residue along the proton-transfer path. A recursive analysis of hydrogen-bonded clusters in the static crystallographic structure shows that there is no complete path through His-64 in either of its experimentally detected conformations. Side chain conformational fluctuation of His-64 from its outward conformation toward the active site is found to provide a crucial dynamic connectivity needed to complete the path coupled to local reorganization of the protein structure and hydration. The energy and free energy barriers along the detected pathway have been estimated to derive the mechanism of His-64 rotation toward the active site. We also investigate a dynamical connectivity map that highlights networks of disordered water molecules that may promote a direct (and probably transient) access of the solvent to the active site. Our studies reveal how such solvent access channels may be related to the putative proton shuttle mediated by His-64. The paths thus identified can be potentially used as reaction coordinates for further studies on the molecular mechanism of enzyme action.

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

We apply ab initio molecular dynamics (AIMD) to study the hydration structures of the carbon dioxide molecule and the bicarbonate and carbonate anions in liquid water. We also compute the free energy change associated with the nucleophilic attack of the hydroxide ion on carbon dioxide. CO2 behaves like a hydrophobic species and exhibits weak interactions with water molecules. The bicarbonate and carbonate ions are strongly hydrated and coordinate to an average of 6.9 and 8.7 water molecules, respectively. The energetics for the reaction in the gas phase are investigated using density functional theory and second-order Møller-Plesset perturbation theory (MP2) in conjunction with high-quality basis sets. Using umbrella sampling techniques, we compute the standard state, aqueous phase free energy difference associated with the reaction CO2+OH--->HCO3- after correcting AIMD energies with MP2 results. Our predictions are in good agreement with experiments. The hydration structures along the reaction coordinate, which give rise to a predicted 9.7 kcal/mol standard state free energy barrier, are further analyzed.

Molecular dynamics simulations of the mononuclear zinc-beta-lactamase from Bacillus cereus complexed with benzylpenicillin and a quantum chemical study of the reaction mechanism

Herein, we present results from MD simulations of the Michaelis complex formed between the B. cereus zinc-beta-lactamase enzyme and benzylpenicillin. The structural and dynamical effects induced by substrate-binding, the specific role of the conserved residues, and the near attack conformers of the Michaelis complex are discussed. Quantum chemical methods (HF/6-31G* and B3LYP/6-31G*) are also applied to study the hydrolysis reaction of N-methylazetidinone catalyzed by a monozinc system consisting of the side chains of the histidine residues (His86, His88, and His149) complexed with Zn-OH and the side chains of Asp90 and His210. From this model system, we built molecular-mechanics representations of the prereactive complex and transition state configurations docked into the active site. Linear-scaling semiempirical calculations coupled with a continuum solvent model were then performed on these static models. We propose that the experimental rate data for the B. cereus enzyme is compatible with a one-step mechanism for the hydrolysis of beta-lactam substrates in which His210 acts as a proton donor.