EMSL: Eric Bylaska's Publications

Bylaska EJ, M Dupuis, and PG Tratnyek. 2008. "One-Electron-Transfer Reactions of Polychlorinated Ethylenes: Concerted and Stepwise Cleavages." Journal of Physical Chemistry A 112(16):3712-3721. Abstract Reaction barriers were calculated by using ab initio electronic structure methods for the reductive dechlorination of the polychlorinated ethylenes: C2CL4, C2Cl4, C2HCl3, trans-1,2-C2H2Cl2, cis-1,2-C2H2Cl2, 1,1-C2H2Cl2, and C2HCl3. 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 via 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 have a significant amount of selectivity of cis-1,2-C2HCl2 over the corresponding reactions leading to the trans-1,2-C2HCl2, and 1,1-C2HCl2 radicals. These results illustrate how ab initio electronic structure methods, by providing experimentally inaccessible thermodynamics properties and activation energies, are able to sort out possible reactions mechanisms of reactions that have broad relevance in environmental chemistry.

Nichols P, EJ Bylaska, GK Schenter, and WA De Jong. 2008. "Equatorial and Apical Solvent Shells of the UO₂²⁺ Ion." Journal of Chemical Physics 128(12):124507. doi:10.1063/1.2884861 Abstract First principles molecular dynamics simulations of the hydration shells surrounding UO₂²⁺ 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 very well known results from X-ray data. The average U=O bond length was found to be 1.77Å . 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 2.44Å (2.46Å - 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 4.59Å. The equatorial second shell contained 10 water molecules hydrogen-bonded to the five first shell molecules. Above and below the UO₂²⁺ 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 UO₂²⁺; oriented in such way as to have their protons pointed towards the cation. While the number of apical waters varied greatly, an average of 5-6 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 (ps) time scale via dissociative mechanisms. Beyond these shells, the bonding pattern substantially returned to the tetrahedral structure of bulk water.

Valiev M, EJ Bylaska, M Dupuis, and PG Tratnyek. 2008. "Combined Quantum Mechanical and Molecular Mechanics Studies of the Electron-Transfer Reactions Involving Carbon Tetrachloride in Solution." Journal of Physical Chemistry A 112(12):2713-2720. doi:10.1021/jp7104709 Abstract The reductive dechlorination of carbon tetrachloride, CC₄, was investigated using combined high level quantum mechanical and molecular mechanics (QM/MM) approach. The first electron transfer process was assumed to proceed by a concerted electron transfer-bond breaking mechanism, and reaction barriers for the first electron reduction were estimated by using the crossing point of the free energy profiles of CCl₃-Cl and CCl₃-Cl•- as a function of the CCl₃-Cl distance. The results of these calculations showed that the activation barriers for this reaction are reachable under a wide range of reduction potentials. In the gas-phase, the barrier to reduction varied from 0.8 kcal/mol for reducing agent with a -5 kcal/mol work function to 24.7 kcal/mol for a reducing agent with a 40 kcal/mol work function at the CCSD(T)/aug-cc-pVDZ level. In the aqueous phase, QM/MM calculations at the CCSD(T)/aug-cc-pVDZ level predicted that the barrier to reduction varied from 0.7 kcal/mol to 35.2 kcal/mol for -2.32 V and 0.93 V reduction potentials respectively. COSMO continuum solvation calculations were also performed for comparison. For strong reducing agents (EH < -1.5V) very little difference was seen between the QM/MM and COSMO activation barriers. For weak reducing agents (EH > 0V) the activation barriers differed by as much as 6 kcal/mol between the QM/MM and COSMO calculations. These results demonstrate that ab initio electronic structure methods coupled with explicit molecular mechanics representation of the aqueous environment offer an efficient and accurate way to calculate the free energy reaction barriers for dissociative electron transfer reactions of organochlorine compounds to identify the potentially important environmental degradation processes.

Bylaska EJ, M Valiev, JR Rustad, and JH Weare. 2007. "Structure and Dynamics of the Hydration Shells of the Al3+ Ion ." Journal of Chemical Physics 126(10):Art.no.104505. Abstract First principles simulations of the hydration shells surrounding Al3+ ions are reported for temperatures near 300oC. The predicted six waters in the octahedral first hydration shell were found to be trigonally coordinated via hydrogen-bonds to 12 second shell waters in agreement with the putative structure used to analyze the X-ray data, but in disagreement with results reported from conventional molecular dynamics using two- and three-body potentials. Bond lengths and angles of the water molecules in the first and second hydration shell and the average radii of these shells also agreed very well with the results of the X-ray analysis. Water transfers into and out of the 2nd solvation shell were observed to occur on a picosecond (ps) time scale via a dissociative mechanism. Beyond the second shell the bonding pattern substantially returned to the tetrahedral structure of bulk water. Most of the simulations were done with 64 solvating waters (20 ps). Limited simulations with 128 waters (5 ps) were also carried out. Results agreed as to the general structure of the solvation region and were essentially the same for the first and second shell. However, there were differences in hydrogen-bonding and Al-O radial distribution function in the region just beyond the second shell. At the end of the second shell a nearly zero minimum in the Al-O radial distribution was found for the 128 water system. This minimum is less pronounced minimum was found for the 64 water system, which may indicate that sizes larger than 64 may be required to reliably predict behavior in this region,

Du J, LR Corrales, K Tsemekhman, and EJ Bylaska. 2007. "Electron, hole and exciton self-trapping in germanium doped silica glass from DFT calculations with self-interactions correction." Nuclear Instruments and Methods in Physics Research. Section B, Beam Interactions with Materials and Atoms 255(1 (SP ISS)):188-194. Abstract We performed density functional theory (DFT) calculations of electron, hole and exciton self-trapping in germanium doped silica glass to understand the refractive index change in these glasses induced by UV irradiation. The local structure relaxation and excess electron density distribution upon trapping of the above species were calculated. The results show that both trapped exciton and electron are highly localized on germanium ion and, to some extent, on its oxygen neighbors. Exciton self-trapping is found to lead to the formation of Ge E’ center and non-bridging hole center. Electron trapping changes the GeO4 tetrahedron structure into trigonal bi-pyramid with the majority of the excess electron density located along the equatorial line. Self-trapped hole is localized on bridging oxygen ions that are not coordinated to germanium atoms and leads to elongation of the Si-O bonds and change of the Si-O-Si bond angles. We did comparative study of standard DFT vs. DFT with a hybrid PBE0 exchange and correlation functional. The results show that the two methods give qualitatively similar relaxed structure and charge distribution for the electron and exciton trapping in germanium doped silica glass; however, only using the PBE0 functional reproduces the hole self-trapping. This research is supported by the Divisions of Chemical Science, Office of Basic Energy Sciences, US Department of Energy. This research was performed in part using the Molecular Science Computing Facility in the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL) at the Pacific Northwest National Laboratory (PNNL). The EMSL is funded by DOE’s Office of Biological and Environmental Research. The pacific Northwest National Laboratory is operated by Battelle for the US Department of Energy.

Gao F, J Du, EJ Bylaska, M Posselt, and WJ Weber. 2007. "Ab Initio Atomic Simulations of Antisite Pair Recovery in Cubic Silicon Carbide." Applied Physics Letters 90(22):Art. No. 221915. doi:10.1063/1.2743751 Abstract The thermal stability of an antisite pair in 3C-SiC is studied using ab initio molecular dynamics within the framework of density functional theory. The lifetime of the antisite pair configuration is calculated for temperatures between 1800 and 2250 K, and the effective activation energy for antisite pair recombination is determined to be 2.52 eV. The recombination energy path and static energy barrier are also calculated using the nudged elastic band method, along with the dimer method to accurately locate the transition states. The consistency of the results suggests that the antisite pair cannot be correlated with the DI photoluminescence center, as proposed by previously theoretical interpretations. An extended exchange mechanism is found for the antisite pair recombination, and this may be a dominant mechanism for antisite pair recombination and diffusion of impurities in compound semiconductors.

Bickmore BR, KM Rosso, CJ Tadanier, EJ Bylaska, and D Doud. 2006. "Bond-valence methods for pKa prediction. II. Bond-valence, electrostatic, molecular geometry, and solvation effects ." Geochimica et Cosmochimica Acta 70(16):4057-4071. doi:10.1016/j.gca.2006.06.006 Abstract In a previous contribution, we outlined a method for predicting (hydr)oxy-acid and oxide surface acidity constants based on three main factors: bond valence, Me–O bond ionicity, and molecular shape. Here electrostatics calculations and ab initio molecular dynamics simulations are used to qualitatively show that Me–O bond ionicity controls the extent to which the electrostatic work of proton removal departs from ideality, bond valence controls the extent of solvation of individual functional groups, and bond valence and molecular shape controls local dielectric response. These results are consistent with our model of acidity, but completely at odds with other methods of predicting acidity constants for use in multisite complexation models. In particular, our ab initio molecular dynamics simulations of solvated monomers clearly indicate that hydrogen bonding between (hydr)oxo-groups and water molecules adjusts to obey the valence sum rule, rather than maintaining a fixed valence based on the coordination of the oxygen atom as predicted by the standard MUSIC model.

Bylaska EJ. 2006. "Estimating The Thermodynamics And Kinetics Of Chlorinated Hydrocarbon Degradation." Theoretical Chemistry Accounts 116(1-3):281-296. doi:10.1007/s00214-005-0042-8 Abstract Many different degradation reactions of chlorinated hydrocarbons are possible in natural ground waters. In order to identify which degradation reactions are important, a large number of possible reaction pathways must be sorted out. Recent advances in ab initio electronic structure methods have the potential to help identify relevant environmental degradation reactions by characterizing the thermodynamic properties of all relevant contaminant species and intermediates for which experimental data is usually not available, as well as provide activation energies for relevant pathways. In this paper, strategies based on ab initio electronic structure methods for estimating thermochemical and kinetic properties of reactions with chlorinated hydrocarbons are presented. Particular emphasis is placed on strategies that are computationally fast and can be used for large organochlorine compounds such as 4,4’-DDT.

Bylaska EJ, K Tsemekhman, and F Gao. 2006. "New Development of Self-Interaction Corrected DFT for Extended Systems Applied to the Calculation of Native Defects in 3C-SiC." Physica Scripta T124:86-90. Abstract We recently have developed a framework for implementing a scaled self-interaction corrected density functional theory (DFT-SIC) into pseudopotential plane-wave DFT. The technique implements the original method due to Perdew and Zunger by direct minimization of the DFT-SIC total energy functional. By using maximally localized Wannier functions, DFT-SIC calculation can be carried out efficiently even for extended systems. Using this new development the formation energies of defects in 3C-SiC were calculated and compared to more standard DFT calculations. Differences of up to 1eV were seen between DFT and DFT-SIC calculations of the formation energies. When compared to DFT, DFT-SIC produced less stable vacancies and silicon interstials, more stable antisites and carbon interstitials. The most favorable interstitials were found to be C interstitials in a C+-C<100> dumbbell configuration, with the formation energy of 5.91eV with DFT and 5.65 eV with DFT-SIC. Si interstitials were not as stable as C interstitials. The most favorable Si interstitial was found to be Si tetrahedral surrounded by four C atoms, with a formation energy of 7.65eV with DFT and 8.71eV with DFT-SIC.

Bylaska EJ, M Dupuis, and PG Tratnyek. 2005. "Ab Initio Electronic Structure Study of One-Electron Reduction Of Polychlorinated Ethylenes ." Journal of Physical Chemistry A 109(26):5905-5916. Abstract Polychlorethylene radicals, anions, and radical anions are potential intermediates in the reduction of polychlorinated ethylenes (C2Cl4, C2HCl3, trans-C2H2Cl2, cis-C2H2Cl2, 1,1-C2H2Cl2, C2H3Cl). Ab initio electronic structure methods were used to calculate the thermochemical properties, Hof(298.15K), So(298.15K,1 bar),GS(298.15K, 1 bar) of 37 different polychloroethylene-yl radicals, anions, and radical anion complexes: C2HyCl3-y•, C2HyCl3-y-, and C2HyCl4-y-• for y = 0,1,2,3 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 C2HyCl4-y-• radical anion complexes are *, *, and -H…Cl- structures. Several stable * 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 C2HyCl4-y-• radical anion, in which a chloride ion is loosely bound to a hydrogen of a C2HxCl2-x• radical. The exception is for C2Cl4, in which the most favorable anionic structure is a loose * radical anion complex, with a nearly iso-energetic * radical anion. Solvation significantly changes the product energetics with the thermodynamically most favorable pathway leads to C2HyCl3-y• + Cl-. The results suggest that a higher degree of chlorination favors reduction, and that reduction pathways involving the C2HyCl3-y- anions are high energy pathways.