The Aqueous Ca2+ System,in Comparison with Zn2+, Fe3 +, and Al3 +: An Ab Initio Molecular Dynamics Study

Herein, we report on the structure and dynamics of the aqueous Ca²⁺ system studied by using ab initio molecular dynamics (AIMD) simulations. Our detailed study revealed the formation of well‐formed hydration shells with characteristics that were significantly different to those of bulk water. To facilitate a robust comparison with state‐of‐the‐art X‐ray absorption fine structure (XAFS) data, we employ a 1st principles MD‐XAFS procedure and directly compare simulated and experimental XAFS spectra. A comparison of the data for the aqueous Ca²⁺ system with those of the recently reported Zn²⁺, Fe³⁺, and Al³⁺ species showed that many of their structural characteristics correlated well with charge density on the cation. Some very important exceptions were found, which indicated a strong sensitivity of the solvent structure towards the cation′s valence electronic structure. Average dipole moments for the 2nd shell of all cations were suppressed relative to bulk water.     

Parallel implementation of γ‐point pseudopotential plane‐wave DFT with exact exchange

Semi‐local functionals commonly used in density functional theory (DFT) studies of solids usually fail to reproduce localized states such as trapped holes, polarons, excitons, and solitons. This failure is ascribed to self‐interaction which creates a Coulomb barrier to localization. Pragmatic approaches in which the exchange correlation functionals are augmented with small amount of exact exchange (hybrid‐DFT, e.g., B3LYP and PBE0) have shown to promise in rectifying this type of failure, as well as producing more accurate band gaps and reaction barriers. The evaluation of exact exchange is challenging for large, solid state systems with periodic boundary conditions, especially when plane‐wave basis sets are used. We have developed parallel algorithms for implementing exact exchange into pseudopotential plane‐wave DFT program and we have implemented them in the NWChem program package. The technique developed can readily be employed in Γ‐point plane‐wave DFT programs. Furthermore, atomic forces and stresses are straightforward to implement, making it applicable to both confined and extended systems, as well as to Car‐Parrinello ab initio molecular dynamic simulations. This method has been applied to several systems for which conventional DFT methods do not work well, including calculations for band gaps in oxides and the electronic structure of a charge trapped state in the Fe(II) containing mica, annite. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

One-electron-transfer reactions of polychlorinated ethylenes: concerted and stepwise cleavages

Reaction barriers were calculated by using ab initio electronic structure methods for the reductive dechlorination of the polychlorinated ethylenes: C2Cl4, C2HCl3, trans-1,2-C2H2Cl2, cis-1,2-C2H2Cl2, 1,1-C2H2Cl2 and C2H3Cl. Concerted and stepwise cleavages of R-Cl bonds were considered. Stepwise cleavages yielded lower activation barriers than concerted cleavages for the reduction of C2Cl4, C2HCl3, and trans-1,2-C2H2Cl2 for strong reducing agents. However, for typical ranges of reducing strength concerted cleavages were found to be favored. Both gas-phase and aqueous-phase calculations predicted C2Cl4 to have the lowest reaction barrier. Additionally, the reduction of C2HCl3 was predicted to show selectivity toward formation of cis-1,2-C2HCl2* over the formation of trans-1,2-C2HCl2*, and 1,1-C2HCl2* radicals.     

Structure and hydrolysis of the U(IV), U(V), and U(VI) aqua ions from ab initio molecular simulations

Ab initio molecular dynamics simulations at 300 K, based on density functional theory, are performed to study the hydration shell geometries, solvent dipole, and first hydrolysis reaction of the uranium(IV) (U(4+)) and uranyl(V) (UO(2)(+)) ions in aqueous solution. The solvent dipole and first hydrolysis reaction of aqueous uranyl(VI) (UO(2)(2+)) are also probed. The first shell of U(4+) is coordinated by 8-9 water ligands, with an average U-O distance of 2.42 ?. The average first shell coordination number and distance are in agreement with experimental estimates of 8-11 and 2.40-2.44 ?, respectively. The simulated EXAFS of U(4+) matches well with recent experimental data. The first shell of UO(2)(+) is coordinated by five water ligands in the equatorial plane, with the average U═O(ax) and U-O distances being 1.85 ? and 2.54 ?, respectively. Overall, the hydration shell structure of UO(2)(+) closely matches that of UO(2)(2+), except for small expansions in the average U═O(ax) and U-O distances. Each ion strongly polarizes their respective first-shell water ligands. The computed acidity constants (pK(a)) of U(4+) and UO(2)(2+) are 0.93 and 4.95, in good agreement with the experimental values of 0.54 and 5.24, respectively. The predicted pK(a) value of UO(2)(+) is 8.5.     

Equatorial and apical solvent shells of the UO2 2+ ion

First principles molecular dynamics simulations of the hydration shells surrounding UO(2)(2+) ions are reported for temperatures near 300 K. Most of the simulations were done with 64 solvating water molecules (22 ps). Simulations with 122 water molecules (9 ps) were also carried out. The hydration structure predicted from the simulations was found to agree with very well-known results from x-ray data. The average U=O bond length was found to be 1.77 A. The first hydration shell contained five trigonally coordinated water molecules that were equatorially oriented about the O-U-O axis with the hydrogen atoms oriented away from the uranium atom. The five waters in the first shell were located at an average distance of 2.44 A (2.46 A, 122 water simulation). The second hydration shell was composed of distinct equatorial and apical regions resulting in a peak in the U-O radial distribution function at 4.59 A. The equatorial second shell contained ten water molecules hydrogen bonded to the five first shell molecules. Above and below the UO(2)(2+) ion, the water molecules were found to be significantly less structured. In these apical regions, water molecules were found to sporadically hydrogen bond to the oxygen atoms of the UO(2)(2+), oriented in such a way as to have their protons pointed toward the cation. While the number of apical waters varied greatly, an average of five to six waters was found in this region. Many water transfers into and out of the equatorial and apical second solvation shells were observed to occur on a picosecond time scale via dissociative mechanisms. Beyond these shells, the bonding pattern substantially returned to the tetrahedral structure of bulk water.     

Free energies for degradation reactions of 1,2,3-trichloropropane from ab initio electronic structure theory

Electronic structure methods were used to calculate the gas and aqueous phase reaction energies for reductive dechlorination (i.e., hydrogenolysis), reductive β-elimination, dehydrochlorination, and nucleophilic substitution by OH? of 1,2,3-trichloropropane. The thermochemical properties ΔH(f)°(298.15 K), S°(298.15 K, 1 bar), and ΔG(S)(298.15 K, 1 bar) were calculated by using ab initio electronic structure calculations, isodesmic reactions schemes, gas-phase entropy estimates, and continuum solvation models for 1,2,3-trichloropropane and several likely degradation products: CH3?CHCl?CH2Cl, CH2Cl?CH2?CH2Cl, C?H2?CHCl?CH2Cl, CH2Cl?C?H?CH2Cl, CH2═CCl?CH2Cl, cis-CHCl═CH?CH2Cl, trans-CHCl═CH?CH2Cl, CH2═CH?CH2Cl, CH2Cl?CHCl?CH2OH, CH2Cl?CHOH?CH2Cl, CH2═CCl?CH2OH, CH2═COH?CH2Cl, cis-CHOH═CH?CH2Cl, trans-CHOH═CH?CH2Cl, CH(═O)?CH2?CH2Cl, and CH3?C(═O)?CH2Cl. On the basis of these thermochemical estimates, together with a Fe(II)/Fe(III) chemical equilibrium model for natural reducing environments, all of the reactions studied were predicted to be very favorable in the standard state and under a wide range of pH conditions. The most favorable reaction was reductive β-elimination (ΔG(rxn)° ≈ ?32 kcal/mol), followed closely by reductive dechlorination (ΔG(rxn)° ≈ ?27 kcal/mol), dehydrochlorination (ΔG(rxn)° ≈ ?27 kcal/mol), and nucleophilic substitution by OH? (ΔG(rxn)° ≈ ?25 kcal/mol). For both reduction reactions studied, it was found that the first electron-transfer step, yielding the intermediate C?H2?CHCl?CH2Cl and the CH2Cl?C?H?CH2Cl species, was not favorable in the standard state (ΔG(rxn)° ≈ +15 kcal/mol) and was predicted to occur only at relatively high pH values. This result suggests that reduction by natural attenuation is unlikely.     

Ab initio electronic structure study of one-electron reduction of polychlorinated ethylenes

Polychlorethylene radicals, anions, and radical anions are potential intermediates in the reduction of polychlorinated ethylenes (C(2)Cl(4), C(2)HCl(3), trans-C(2)H(2)Cl(2), cis-C(2)H(2)Cl(2), 1,1-C(2)H(2)Cl(2), C(2)H(3)Cl). Ab initio electronic structure methods were used to calculate the thermochemical properties, (298.15 K), S degrees (298.15 K,1 bar), and DeltaG(S)(298.15 K, 1 bar) of 37 different polychloroethylenyl radicals, anions, and radical anion complexes, C(2)H(y)Cl(3)(-)(y)(*), C(2)H(y)Cl(3)(-)(y)(-), and C(2)H(y))Cl(4)(-)(y)(*)(-) for y = 0-3, for the purpose of characterizing reduction mechanisms of polychlorinated ethylenes. In this study, 8 radicals, 7 anions, and 22 radical anions were found to have stable structures, i.e., minima on the potential energy surfaces. This multitude of isomers for C(2)H(y)Cl(4)(-)(y)(*)(-) radical anion complexes are pi*, sigma*, and -H...Cl(-) structures. Several stable pi* radical anionic structures were obtained for the first time through the use of restricted open-shell theories. On the basis of the calculated thermochemical estimates, the overall reaction energetics (in the gas phase and aqueous phase) for several mechanisms of the first electron reduction of the polychlorinated ethylenes were determined. In almost all of the gas-phase reactions, the thermodynamically most favorable pathways involve -H...Cl(-) complexes of the C(2)H(y)Cl(4)(-)(y)(*)(-) radical anion, in which a chloride ion is loosely bound to a hydrogen of a C(2)H(x)Cl(2)(-)(x))(*) radical. The exception is for C(2)Cl(4), in which the most favorable anionic structure is a loose sigma* radical anion complex, with a nearly iso-energetic pi* radical anion. Solvation significantly changes the product energetics with the thermodynamically most favorable pathway leading to C(2)H(y)Cl(3)(-)(y)(*) + Cl(-). The results suggest that a higher degree of chlorination favors reduction, and that reduction pathways involving the C(2)H(y)Cl(3)(-)(y)(-) anions are high energy pathways.