Activation energy of photosynthetic oxygen evolution: An attempt at theoretical analysis

In this study, a first attempt is made to calculate theoretically the activation energies of the different steps of water oxidation. The analysis has led to the following conclusions about the process mechanism: (1) the barrier produced by the repulsion of unbound O-atoms during their mutual approach may be partly surmounted at the expense of the binding energy of water molecules by manganese ions; (2) the concerted transfer of electrons and protons involving the participation of bases stronger than water improves essentially the process energetics; (3) multi-electron steps require the use of several one-electron acceptors; (4) four-electron oxidation of water in a single elementary act is unlikely: (5) the most likely reaction path is the rate-determining two-electron water oxidation to hydrogen peroxide (the possibility of this process occurring in two consecutive one-electron steps is not clear), followed by two fast oxidation steps of H₂O₂ to HO₂ and further to O₂.     

Accurate ab initio binding energies of alkaline earth metal clusters

The effects of basis set superposition error (BSSE) and core-correlation on the electronic binding energies of alkaline earth metal clusters Y(n) (Y = Be, Mg, Ca; n = 2-4) at the Moller-Plesset second-order perturbation theory (MP2) and the single and double coupled cluster method with perturbative triples correction (CCSD(T)) levels are examined using the correlation consistent basis sets cc-pVXZ and cc-pCVXZ (X = D, T, Q, 5). It is found that, while BSSE has a negligible effect for valence-electron-only-correlated calculations for most basis sets, its magnitude becomes more pronounced for all-electron-correlated calculations, including core electrons. By utilizing the negligible effect of BSSE on the binding energies for valence-electron-only-correlated calculations, in combination with the negligible core-correlation effect at the CCSD(T) level, accurate binding energies of these clusters up to pentamers (octamers in the case of the Be clusters) are estimated via the basis set extrapolation of ab initio CCSD(T) correlation energies of the monomer and cluster with only the cc-pVDZ and cc-pVTZ sets, using the basis set and correlation-dependent extrapolation formula recently devised. A comparison between the CCSD(T) and density functional theory (DFT) binding energies is made to identify the most appropriate DFT method for the study of these clusters.     

Density functional theory study of water activation and COads + OHads reaction on pure platinum and bimetallic platinum/ruthenium nanoclusters

A density functional theory study of the elementary steps that lead to the removal of CO(ads(Pt)) over alloyed and sequentially deposited Pt/Ru bimetallic nanoclusters is presented. The reaction energies and activation barriers for the H2O(ads(Ru)) dissociation and CO(ads(Pt)) + OH(ads(Ru)) reaction are estimated in solid-gas interface and in a microsolvated environment to determine which surface morphology is more tolerant to COads poisoning. On the basis of the energetics, the sequentially deposited Pt/Ru nanocluster is predicted to be a much more promising anode catalyst than the alloy cluster surface in fuel cell applications.     

Modeling hydrogen evolution from the Fe4S4 and Fe8S9X (X = N,C) clusters. Can a Fe?S high‐spin cluster serve as a surrogate for the FeMo cofactor?

A high-spin model of nitrogenase with a Fe(8)S(9)X(+) cluster (X = nitrogen or carbon) is used to test a mechanism for molecular hydrogen production, which is known to accompany ammonia production. The reaction proceeds with a series of protonation-reduction (PR) steps which are considered to be spontaneous if the calculated hydrogen-cluster bond energy exceeds 35-40 kcal/mol. The novel features of this mechanism include the opening of the cluster when one of the bridging sulfides undergoes two PR steps and the direct participation of the central atom when it undergoes a PR step. After the sixth PR step, a cluster is formed which has a low barrier for loss of molecular hydrogen in an exothermic reaction step. The central atom (nitrogen or carbon) has only a minor effect on the reaction steps.     

Theoretical investigation of reaction mechanisms of alkaline hydrolysis of 2,3,6-trinitro-β-d-glucopyranose as a monomer of nitrocellulose

The 2,3,6-trinitro-β-d-glucopyranose as a monomer of nitrocellulose in the ⁴C₁ chair conformation was selected for the alkaline hydrolysis of nitrocellulose within S_N2 framework in the gas phase and in the bulk water solution. Both the direct and angular attacks of OH^? in the hydrolysis reactions were considered. Geometries were optimized at the B3LYP/6-311G(d,p) level both in the gas phase and in bulk water solution. Effect of bulk water solution was modeled using the PCM approach. Nature of potential energy surfaces of the local minima and transition states was ascertained through harmonic vibrational frequency analysis. Intrinsic reaction coordinate calculations were also performed to validate the computed transition state structures. Effect of electron correlation on computed energies was considered at the MP2/cc-pVTZ//B3LYP/6-311G(d,p) level. It was found that the angular attack of OH^? in the hydrolysis reaction will require significantly larger activation energy than the direct attack. Computed transition states correspond to the structure where the presence of hydrogen bonds between the OH^? and various sites of nitrocellulose was the necessary stabilizing factor. The ring breaking through the C–O ring bond was not found to be the first step in the alkaline hydrolysis reactions. It was predicted that alkaline hydrolysis would be driven by the addition–elimination (substitution) reaction starting at the C3 site and will progress in the C2 → C6 direction. Entropy of system in water solution will have profound effect on alkaline hydrolysis reaction of nitrocellulose.     

Computational insight on the chalcone formation mechanism by the Claisen–Schmidt reaction

New insight of the formation mechanism of chalcones is presented in the current study. Ab initio calculations were applied in studying the mechanistic pathways for the base‐catalyzed Claisen–Schmidt condensation for obtaining chalcones (1,3‐diphenyl‐2‐propen‐1‐ons). The energies of the stationary points along the reaction coordinate were obtained at two levels of theory—MP2/6‐31 + G(d,p) and SCS‐MP2/6‐31 + G(d,p). The role of water in the reaction mechanisms is examined. The theoretical results show that the process is catalyzed by an ancillary water molecule. The reaction mechanism, proposed in this study, consists of two reactions—an activation of the acetophenone by a removal of proton is followed by the attack of the formed acetophenone anion to the aromatic aldehyde, which through few steps leads to the formation of the final product—chalcone. The first reaction proceeds very fast in one step while the second reaction goes through four steps and three intermediate complexes before the formation of the final product.     

On the nature of solubilized water clusters in aerosol OT/alkane solutions. A study of the formation of hydrated electrons and 1,8-anilinonaphthalene sulphonate fluorescence

The pulse radiolysis of dioctyl sulphosuccinate (aerosol-OT) H₂O/heptane solutions leads to formation of hydrated electrons in the aqueous core of the inverted aerosol-OT micelles. The hydrated electrons are produced via direct interaction of the radiation with the aqueous regions and scavenging of electrons formed initially in the hydrocarbon phase by the water bubbles. The scavenging efficiency decreases with decreasing radius of the water cluster. Hydrated electrons are not formed below a critical size of the solubilized water particles.The quantum yield and wavelength of the maximum of the aniline-naphthalene sulphonate (ANS) fluorescence are strongly dependent on the water content of aerosol-OT inverted micelles. The fluorescence behavior indicates an increase of polarity with increasing cluster radius. The polarity of very large water clusters (r ≈ 73 Å) is still lower than that of bulk water. Water which is bound to Na⁺ counterions cannot effectively participate in the solvation of the dipolar ANS excited states.     

Structures and reaction mechanisms of glycerol dehydration over H-ZSM-5 zeolite: a density functional theory study

The initial stage of glycerol conversion over H-ZSM-5 zeolite has been investigated using density functional theory (DFT) calculations on an embedded cluster model consisting of 128 tetrahedrally coordinated atoms. It is found that glycerol dehydration to acrolein and acetol proceeds favourably via a stepwise mechanism. The formation of an alkoxide species upon the first dehydration requires the highest activation energy (42.5 kcal mol(-1)) and can be considered as the rate determining step of the reaction. The intrinsic activation energies for the first dehydration are virtually the same for both acrolein and acetol formation, respectively, suggesting the competitive removal of the primary and secondary OH groups. A high selectivity to acrolein at moderate temperatures can be attributed to the selective activation of the stronger adsorption mode of glycerol through the secondary OH group and the kinetically favoured subsequent consecutive steps. In addition, the less reactive nature of acrolein relative to acetol precludes it from being converted to other products upon conversion to glycerol. In accordance with typical endothermic reactions, the forward rate constant for glycerol dehydration significantly increases with increasing reaction temperature.     

Theoretical study on the oxidation mechanism of thiourea by hydrogen peroxide with water and hydroxyl assistance

This article presents a theoretical study on the oxidation reaction of thiourea by hydrogen peroxide in water or alkaline solutions using density functional and ab initio theories. This work also focuses on the analysis of the thermodynamic and kinetic properties of the predicted oxidation mechanism of thiourea using density functional and ab initio theories. The calculated results show that the activation energies, activation enthalpies, and activation Gibbs free energies of the reaction decreased and the releasable reaction energies, enthalpies and Gibbs free energies increased with the cooperation of water or hydroxyl anion. We conclude that the oxidation reaction of thiourea by hydrogen peroxide in water or alkaline solutions was easier and more completed than that in the gas state. The calculated results are consistent with the experiments.     

Calculation of solvation free energies of charged solutes using mixed cluster/continuum models

We derive a consistent approach for predicting the solvation free energies of charged solutes in the presence of implicit and explicit solvents. We find that some published methodologies make systematic errors in the computed free energies because of the incorrect accounting of the standard state corrections for water molecules or water clusters present in the thermodynamic cycle. This problem can be avoided by using the same standard state for each species involved in the reaction under consideration. We analyze two different thermodynamic cycles for calculating the solvation free energies of ionic solutes: (1) the cluster cycle with an n water cluster as a reagent and (2) the monomer cycle with n distinct water molecules as reagents. The use of the cluster cycle gives solvation free energies that are in excellent agreement with the experimental values obtained from studies of ion-water clusters. The mean absolute errors are 0.8 kcal/mol for H(+) and 2.0 kcal/mol for Cu(2+). Conversely, calculations using the monomer cycle lead to mean absolute errors that are >10 kcal/mol for H(+) and >30 kcal/mol for Cu(2+). The presence of hydrogen-bonded clusters of similar size on the left- and right-hand sides of the reaction cycle results in the cancellation of the systematic errors in the calculated free energies. Using the cluster cycle with 1 solvation shell leads to errors of 5 kcal/mol for H(+) (6 waters) and 27 kcal/mol for Cu(2+) (6 waters), whereas using 2 solvation shells leads to accuracies of 2 kcal/mol for Cu(2+) (18 waters) and 1 kcal/mol for H(+) (10 waters).     

Quantum chemical simulation of propylene oxidation on Ag<Subscript>20</Subscript>

The adsorption of atomic oxygen and the mechanism of propylene (C₃H₆) oxidation to oxide (C₃H₆O) on an Ag₂₀ tetrahedral cluster were studied using density functional theory. The effects of cluster structure and active site structure on the mechanism of this reaction were considered. The oxidation of C₃H₆ can occur both on an edge and at the apex of the silver cluster. The C₃H₆O formation steps on the cluster edge are characterized by lower activation energies.     

Alkaline hydrolysis of ethylene phosphate: an ab initio study by supermolecule model and polarizable continuum approach

The alkaline hydrolysis reaction of ethylene phosphate (EP) has been investigated using a supermolecule model, in which several explicit water molecules are included. The structures and single-point energies for all of the stationary points are calculated in the gas phase and in solution at the B3LYP/6-31++G(df,p) and MP2/6-311++G(df,2p) levels. The effect of water bulk solvent is introduced by the polarizable continuum model (PCM). Water attack and hydroxide attack pathways are taken into account for the alkaline hydrolysis of EP. An associative mechanism is observed for both of the two pathways with a kinetically insignificant intermediate. The water attack pathway involves a water molecule attacking and a proton transfer from the attacking water to the hydroxide in the first step, followed by an endocyclic bond cleavage to the leaving group. While in the first step of the hydroxide attack pathway the nucleophile is the hydroxide anion. The calculated barriers in aqueous solution for the water attack and hydroxide attack pathways are all about 22 kcal/mol. The excellent agreement between the calculated and observed values demonstrates that both of the two pathways are possible for the alkaline hydrolysis of EP.     

On the dissolution processes of Na2I+ and Na3I2+ with the association of water molecules: mechanistic and energetic details

The sequential association energies for one through six water molecules clustering to Na(2)I(+), as well as one and two water molecules clustering to Na(3)I(2)(+), are measured. The association energies show a pairwise behavior, indicating a symmetric association of water molecules to the linear Na(2)I(+) and Na(3)I(2)(+) ions. This pairwise behavior is well reproduced by Density Functional Theory (DFT) calculations. DFT calculations also suggest that a significant separation of charge for the Na-I ion pair occurs when four or more water molecules cluster to a single sodium center. Two different solvent-separated ion pairs have been identified with the DFT calculations. Experiments also show that the dissolution processes, loss of a neutral NaI unit, occurs when six or more water molecules have been added to Na(2)I(+) cluster. However, one or two water molecules are able to detach an NaI unit from the Na(3)I(2)(+) cluster. The difference in solubility of the Na(2)I(+) and Na(3)I(2)(+) ions is due to the difference in the energies required to lose an NaI unit from these two species. The experiment also confirms that the loss of a neutral NaI unit, instead of an Na(+) ion, occurs during the dissolution processes of Na(3)I(2)(+). The microsolvation schemes proposed to explain our experimental observations are supported by DFT and phase space theory (PST) calculations.     

Interaction energy of a water molecule with a single-layer graphitic surface modeled by hydrogen- and fluorine-terminated clusters

In ab initio calculations a finite graphitic cluster model is often used to approximate the interaction energy of a water molecule with an infinite single-layer graphitic surface (graphene). In previous studies, the graphitic cluster model is a collection of fused benzene rings terminated by hydrogen atoms. In this study, the effect of using fluorine instead of hydrogen atoms for terminating the cluster model is examined to clarify the role of the boundary. The interaction energy of a water molecule with the graphitic cluster was computed using ab initio methods at the MP2 level of theory and with the 6-31G(d = 0.25) basis set. The interaction energy of a water molecule with graphene is estimated by extrapolation of two series of increasing size graphitic cluster models (C(6n2)H(6n) and C(6n2)F(6n), n = 1-3). Two fixed orientations of water molecule are considered: (a) both hydrogen atoms of water pointing toward the cluster (mode A) and (b) both hydrogen atoms of water pointing away from the cluster (mode B). The interaction energies for water mode A are found to be -2.39 and -2.49 kcal/mol for C(6n2)H(6n) and C(6n2)F(6n) cluster models, respectively. For water mode B, the interaction energies are -2.32 and -2.44 kcal/mol for C(6n2)H(6n) and C(6n2)F(6n) cluster models, respectively.     

Theoretical study of the oxygen exchange in uranyl hydroxide. An old riddle solved?

A multistep mechanism for the experimentally observed oxygen exchange [Inorg. Chem. 1999, 38, 1456] of UO2(2+) cations in highly alkaline solutions is suggested and probed computationally. It involves an equilibrium between [UO2(OH)4](2-) and [UO2(OH)5](3-), followed by formation of the stable [UO3(OH)3 x H2O](3-) intermediate that forms from [UO2(OH)5](3-) through intramolecular water elimination. The [UO3(OH)3 x H2O](3-) intermediate facilitates oxygen exchange through proton shuttling, retaining trans-uranyl structures throughout, without formation of the cis-uranyl intermediates proposed earliar. Alternative cis-uranyl pathways have been explored but were found to have activation energies that are too high. Relativistic density functional theory (DFT) has been applied to obtain geometries and vibrational frequencies of the different species (reactants, intermediates, transition states, products) and to calculate reaction paths. Two different relativistic methods were used: a scalar four-component all-electron relativistic method and the zeroeth-order regular approximation. Calculations were conducted for both gas phase and condensed phase, the latter treated using the COSMO continuum model. An activation energy of 12.5 kcal/mol is found in solution for the rate-determining step, the reaction of changing the four-coordinated uranyl hydroxide to the five-coordinated one. This compares favorably to the experimental value of 9.8 +/- 0.7 kcal/mol. Activation energies of 7.8 and 5.1 kcal/mol are found for the hydrogen transfer between equatorial and axial oxygens through a water molecule in [UO3(OH)3 x H2O](3-) in the gas phase and condensed phase, respectively. Contrary to previously proposed mechanisms that resulted in high activation barriers, we find energies that are low enough to facilitate the reaction at room temperature. For the activation energies, two approximate DFT methods, B3LYP and PBE, are compared. The differences in activation energies are only about 1-2 kcal/mol for these methods.     

Dissociative photodetachment dynamics of the iodide-aniline cluster

The photodetachment dynamics of the iodide-aniline cluster, I-(C6H5NH2), were investigated using photoelectron-photofragment coincidence spectroscopy at several photon energies between 3.60 and 4.82 eV in concert with density functional theory calculations. Direct photodetachment from the solvated I- chromophore and a wavelength-independent autodetachment process were observed. Autodetachment is attributed to a charge-transfer-to-solvent reaction in which incipient continuum electrons photodetached from I- are temporarily captured by the nascent neutral iodine-aniline cluster configured in the anion geometry. Subsequent dissociation of the neutral cluster removes the stabilization, leading to autodetachment of the excess electron. The dependence of the dissociative photodetachment (DPD) and autodetachment dynamics on the final spin-orbit electronic state of the iodine fragment is characterized. The dissociation dynamics of the neutral fragments correlated with autodetached electrons were found to be identical to the DPD dynamics of the I atom product spin-orbit state closest to threshold at a given photon energy, lending support to the proposed sequential mechanism.     

Interactions of water and methanol with a mixture of copper and zinc metals: a theoretical <Emphasis Type="Italic">ab initio</Emphasis> study

Ab initio cluster quantum chemical calculations at the Hartree–Fock and second-order Møller–Plesset perturbation theory levels were carried out to mimic the interactions of water and methanol with a mixture of Cu and Zn metals. It was shown that both molecular and dissociative adsorption of methanol on a mixture of Cu and Zn metal catalyst are preferred over the corresponding adsorptions of water. Estimated transition-state structures for dissociation of methanol into CH·₃ and OH· lie about 9.0 and 22.0 kcal/mol higher compared to the dissociated (forward reaction) and molecular adsorption (reverse reaction) complexes, respectively. Based on distinct radicals' bond energies with the active sites of the catalyst considered, it is suggested that hydrogen molecules could be formed through a chain of homogeneous reactions of methyl radicals released into the gas phase with the water and/or methanol molecules.     

MICELLAR CATALYSIS OF COMPOSITE REACTIONS I MICELLAR EFFECT ON THE CONSECUTIVE FIRST ORDER REACTION

The micellar catalytic model (or the consecutive first order reaction has been proposed in this paper. It was applied to the alkaline hydrolysis of dimethyl phthalate in micellar solutions of surfactants (CTAB, SDS and Triton X-100), and the alkaline hydrolysis of bis (2,4-dinitrophenyl) posphate in CTAB micellar solution. Rate constants obtained in micellar phase indicate that the two steps of alkaline hydrolysis of dimethyl phthalate are both inhibited by all of the surfactants investigated. CTAB micelle exhibits a greater catalytic effect on the alkaline hydrolysis of bis (2, 4-dinitrophenyl) phosphate. this may be arised from the local concentration effect of hydroxide ion in CTAB micellar phase. Nevertheless. the second order rate constant of bis-(2, 4-dinitrophenyl) phosphate in the micellar phase is smaller than that in the bulk phase.     

Can an α-anomer of the trinitro form of D-glucopyranose be more easily hydrolyzed in alkaline environment than the β-anomer? A detailed theoretical analysis

Comprehensive computational investigations of detailed alkaline hydrolysis reaction pathways of the α-anomeric form of nitrocellulose monomer (2,3,6-trinitro-α-D-glucopyranose) in the (4)C(1) chair conformation within the S(N)2 framework in the gas phase and in bulk water solution are reported. Geometries of reactant complexes, transition states, intermediates, and completely denitrated product were optimized at the density functional theory (DFT) level using the B3LYP functional and the 6-311G(d,p) basis set both in the gas phase and in the bulk water solution. The effect of bulk water was modeled using the polarizable continuum model (PCM) approach. The nature of the potential energy surface of the local minima and transition states was ascertained through vibrational frequency analysis. Intrinsic reaction coordinate (IRC) calculations were also performed to validate the computed transition state structures. Effect of electron correlation on computed energies was considered through a single point energy calculation at the MP2 level using the cc-pVTZ basis set. It was revealed that the presence of hydrogen bonds between the attacking OH(-) ion and various hydrogen bond donating sites (including CH sites) of monomer was necessary for stabilization of the transition state. It was revealed that the α-anomer will be more reactive than the β-anomer with regard to the denitration reaction. The role of entropy and the denitration ability of various sites are also discussed.     

Mechanism of the hydration of carbon dioxide: direct participation of H2O versus microsolvation

Thermochemical parameters of carbonic acid and the stationary points on the neutral hydration pathways of carbon dioxide, CO 2 + nH 2O --> H 2CO 3 + ( n - 1)H 2O, with n = 1, 2, 3, and 4, were calculated using geometries optimized at the MP2/aug-cc-pVTZ level. Coupled-cluster theory (CCSD(T)) energies were extrapolated to the complete basis set limit in most cases and then used to evaluate heats of formation. A high energy barrier of approximately 50 kcal/mol was predicted for the addition of one water molecule to CO 2 ( n = 1). This barrier is lowered in cyclic H-bonded systems of CO 2 with water dimer and water trimer in which preassociation complexes are formed with binding energies of approximately 7 and 15 kcal/mol, respectively. For n = 2, a trimeric six-member cyclic transition state has an energy barrier of approximately 33 (gas phase) and a free energy barrier of approximately 31 (in a continuum solvent model of water at 298 K) kcal/mol, relative to the precomplex. For n = 3, two reactive pathways are possible with the first having all three water molecules involved in hydrogen transfer via an eight-member cycle, and in the second, the third water molecule is not directly involved in the hydrogen transfer but solvates the n = 2 transition state. In the gas phase, the two transition states have comparable energies of approximately 15 kcal/mol relative to separated reactants. The first path is favored over in aqueous solution by approximately 5 kcal/mol in free energy due to the formation of a structure resembling a (HCO 3 (-)/H 3OH 2O (+)) ion pair. Bulk solvation reduces the free energy barrier of the first path by approximately 10 kcal/mol for a free energy barrier of approximately 22 kcal/mol for the (CO 2 + 3H 2O) aq reaction. For n = 4, the transition state, in which a three-water chain takes part in the hydrogen transfer while the fourth water microsolvates the cluster, is energetically more favored than transition states incorporating two or four active water molecules. An energy barrier of approximately 20 (gas phase) and a free energy barrier of approximately 19 (in water) kcal/mol were derived for the CO 2 + 4H 2O reaction, and again formation of an ion pair is important. The calculated results confirm the crucial role of direct participation of three water molecules ( n = 3) in the eight-member cyclic TS for the CO 2 hydration reaction. Carbonic acid and its water complexes are consistently higher in energy (by approximately 6-7 kcal/mol) than the corresponding CO 2 complexes and can undergo more facile water-assisted dehydration processes.