2009. "Computational Nanoscience with NWChem." Journal of Computational and Theoretical Nanoscience 6(6 SP ISS):1297-1304. Abstract The NWChem software as been used to examine many nanoscale systems and their properties over the years. In this paper, an overiew of the general capabilities of NWChem is given as well as more specific details on the planewave and Gaussian based density functional codes usually used for nanoscale investigations. Examples are given of the scientific literature using NWChem, as well as two case studies: 1) Band gaps in oxides using exact-exchange based exchange-correlation functionals with the planewave DFT module, 2) Optical properties of chromophores using the Gaussian based DFT module.
2009. "Gaussian Basis Set and Planewave Relativistic Spin-Orbit Methods in NWChem." Journal of Chemical Theory and Computation 5(3):491-499. doi:10.1021/ct8002892 Abstract Relativistic spin-orbit density functional theory (DFT) methods have been implemented in the molecular Gaussian DFT and pseudopotential plane-wave DFT modules of the NWChem electronic-structure program. The Gaussian basis set implementation is based upon the zeroth-order regular approximation (ZORA) while the planewave implementation uses spin-orbit pseudopotentials that are directly generated from the atomic Dirac-Kohn-Sham wavefunctions or atomic ZORA-Kohn-Sham wavefunctions. Compared to solving the full Dirac equation these methods are computationally efficient, but robust enough for a realistic description of relativistic effects such as spin-orbit splitting, molecular orbital hybridization, and core effects. Both methods have been applied to a variety of small molecules, including I$_{\text{2}}$, IF, HI, Br$_{\text{2}}$, Bi$_{\text{2}}$, AuH, and Au$_{\text{2}}$, using various exchange-correlation functionals. Our results are in good agreement with experiment and previously reported calculations.
2009. "Adaptive Finite Element Method for Solving the Exact Kohn-Sham Equation of Density Functional Theory." Journal of Chemical Theory and Computation 5(4):937-948. doi:10.1021/ct800350j Abstract Results of the application of an adaptive finite element (FE) based solution using the FETK library of M. Holst to Density Functional Theory (DFT) approximation to the electronic structure of atoms and molecules are reported. The severe problem associated with the rapid variation of the electronic wave functions in the near singular regions of the atomic centers is treated by implementing completely unstructured simplex meshes that resolve these features around atomic nuclei. This concentrates the computational work in the regions in which the shortest length scales are necessary and provides for low resolution in regions for which there is no electron density. The accuracy of the solutions significantly improved when adaptive mesh refinement was applied, and it was found that the essential difficulties of the Kohn-Sham eigenvalues equation were the result of the singular behavior of the atomic potentials. Even though the matrix representations of the discrete Hamiltonian operator in the adaptive finite element basis are always sparse with a linear complexity in the number of discretization points, the overall memory and computational requirements for the solver implemented were found to be quite high. The number of mesh vertices per atom as a function of the atomic number Z and the required accuracy e (in atomic units) was esitmated to be v (e;Z) = 122:37 * Z2:2346 /1:1173 , and the number of floating point operations per minimization step for a system of NA atoms was found to be 0(N3A*v(e,Z0) (e.g. Z=26, e=0.0015 au, and NA=100, the memory requirement and computational cost would be ~0.2 terabytes and ~25 petaflops). It was found that the high cost of the method could be reduced somewhat by using a geometric based refinement strategy to fix the error near the singularities.
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.
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.
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.
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.
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.
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,
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.
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.
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.
2005. "Kinetic Evidence for Five-Coordination in AlOH(aq)2+ Ion." Science 308(5727):1450-1453. Abstract In dilute aqueous solution, AlIII exists almost entirely as the octahedral Al(H2O)63+ ion at pH <3.0 and as tetrahedral Al(OH)4– ion at pH > 7, while in the biochemically and geochemically critical pH range 4.3-7.0 other hydrolytic species such as AlOH(aq)2+exist that are traditionally assumed to be hexacoordinate. We show, however, from the kinetics of proton- and water exchange on aqueous AlIII, supported by Car-Parrinello simulations, that a five-coordinate Al(H2O)4OH2+ ion is important under ambient conditions. In water, AlIII differs strikingly from other trivalent metal ions.
2005. "Defect Properties in GaN: Ab Initio and Empirical Potential Calculations." Materials Science Forum 475-479(1-5):3087-3090. Abstract The defect properties and atomic configurations in GaN have been comparatively investigated using density functional theory (DFT) and molecular dynamics method with two representative potentials. The DFT calculations show that the relaxation of vacancies is generally small, but the relaxation around antisite defects is large. The N interstitials, starting from any possible configurations, eventually relax into a N+-N<11-20 > split interstitial. In the case of Ga interstitials, the most stable configuration is a Ga octahedral interstitial, but the Ga+-Ga<11-20 > split interstitial can bridge the gap between non-bounded Ga atoms. The formation energies of vacancies and antisite defects obtained using the Stillinger-Weber potential (SW) are in reasonable agreement with those obtained by DFT calculations, whereas the Tersoff-Brenner (TB) potential better describes the behavior of N interstitials.
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 —HCl- 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.
2004. "Diversity of Contaminant Reduction Reactions by Zero-Valent Iron: Role of the Reductate." Environmental Science and Technology 38(1):139-147 . Abstract Abstract The reactions of 8 model contaminants with 9 types of granular Fe(0) were studied in batch experiments using consistent experimental conditions. The model contaminants (herein referred to as “reductates†because they were reduced by the iron metal) included cations (Cu2+), anions (CrO42-; NO3-; and 5,5’,7,7’-indigotetrasulfonate), and neutral species (2-chloroacetophenone; 2,4,6-trinitrotoluene; carbon tetrachloride; and trichloroethene). The diversity of this range of reductates offers a uniquely broad perspective on the reactivity of Fe(0). Rate constants for disappearance of the reductates vary over as much as 4 orders of magnitude for particular reductates (due to differences in the 9 types of iron) but differences among the reductates were even larger, ranging over almost 7 orders of magnitude. Various ways of summarizing the data all suggest that relative reactivities with Fe(0) varies in the order: Cu2, I4S > 2CAP, TNT > CT, Cr6 > TCE > NO3. Although the reductate has the largest effect on disappearance kinetics, more subtle differences in reactivity due to the type of Fe(0) suggests that removal of Cr6 and NO3 (the inorganic anions) involves adsorption to oxides on the Fe(0), whereas the disappearance kinetics of all other types of reductants is favored by reduction on comparatively oxide-free metal. Correlation analysis of the disappearance rate constants using descriptors of the reductates calculated by molecular modeling (energies of the lowest unoccupied molecular orbitals, LUMO, highest occupied molecular orbitals, HOMO, and HOMO-LUMO gaps) showed that reactivities generally increase with decreasing ELUMO and increasing EGAP (and, therefore, increasing chemical hardness h).
2004. "Wannier Orbitals and Bonding Properties of Interstitial and Antisite Defects in GaN." Applied Physics Letters 85(23):5565-5567. Abstract Intrinsic interstitial and antisite defects in GaN have been studied using density functional theory (DFT), and their configurations, electronic structures and bonding properties have been characterized using the Wannier function. All N interstitial configurations eventually transform into N-N split interstitials, between which two π orbitals exist. The relaxation of a Ga antisite defect also leads to the formation of a N-N split configuration; however, its local Wannier orbitals are remarkably different from the N-N split interstitial. The different local Wannier orbitals around Ga interstitial configurations demonstrate that Ga interstitials are critical defects in GaN. The electronic orbitals of the Ga octahedral interstitial is, for example, greatly delocalized, and there are no covalent bonds formed between the interstitial and the surrounded atoms. The most striking feature is that Ga-Ga split interstitials can bridge the gap between non-bonded Ga atoms, thereby leading to a chain of four metallic-like-bonded Ga atoms in GaN, which may exhibit novel quantum properties.
2004. "Intrinsic Defect Properties in GaN Calculated By Ab Initio and Empirical Potential Methods." Physical Review. B, Condensed Matter and Materials Physics 70(24):245208-1-245208-8. doi:10.1103/PhysRevB.70.245208 Abstract Density functional theory (DFT) has been used to investigate the formation, properties, and atomic configurations of vacancies, antisite defects and interstitials in GaN, and the DFT results are compared with those calculated by molecular dynamics (MD) simulations using two representative potentials. The DFT calculations reveal that the relaxation of vacancies is generally small, but the relaxation around antisite defects is large, especially for the Ga antisite that is not stable and converts to a N+-N<0001> split interstitial plus a Ga vacancy at the original site. The N interstitials, starting from all possible sites, eventually relax into a N+-N<11-20> split interstitial. In the case of Ga interstitials, the most stable configuration is a Ga octahedral interstitial, but the energy difference among all the interstitials is small. The Ga+-Ga<11-20> split interstitial can bridge the gap between non-bonded Ga atoms, thereby leading to a chain of four Ga atoms along the <11-20> direction in GaN. The formation energies of vacancies and antisite defects obtained using the Stillinger-Weber potential (SW) are in reasonable agreement with those obtained by DFT calculations, whereas the Tersoff-Brenner (TB) potential better describes the behavior of N interstitials. In the case of Ga interstitials, the most stable configuration predicted by the TB-model is a Ga+-N<11-20> split interstitial; while for the SW-model the Ga tetrahedral configuration is more stable, which is in contrast to DFT results.
2004. "The Energetics of the Hydrogenolysis, Dehydrohalogenation, and Hydrolysis of 4,4'-Dichloro-diphenyl-trichloroethane from Ab Initio Electronic Structure Theory." Journal of Physical Chemistry A 108(27):5883-5893. Abstract Electronic structure methods were used to calculate the aqueous reaction energies for hydrogenolysis, dehydrochlorination, and nucleophilic substitution by OH- of 4,4¢-DDT. Thermochemical properties ¢Hf° (298.15 K), S° (298.15 K, 1 bar), ¢GS (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 a series of DDT type structures (p-C6H4Cl)2-CH-CCl3, (p-C6H4Cl)2-CH-CCl2¥, (p-C6H4Cl)2-CHCHCl2, (p-C6H4Cl)2-CdCCl2, (p-C6H4Cl)2-CH-CCl2OH, (p-C6H4Cl)2-CH-CCl(dO), and (p-C6H4-Cl)2-CH-COOH. On the basis of these thermochemical estimates, the overall aqueous reaction energetics of hydrogenolysis, dehydrochlorination, and hydrolysis of 4,4¢-DDT were estimated. The results of this investigation showed that the dehydrochlorination and hydrolysis reactions have strongly favorable thermodynamics in the standard state, as well as under a wide range of pH conditions. For hydrogenolysis with the reductant aqueous Fe(II), the thermodynamics are strongly dependent on pH, and the stability region of the (p-C6H4Cl)2-CH-CCl2¥(aq) species is a key to controlling the reactivity in hydrogenolysis. These results illustrate the use of ab initio electronic structure methods to identify the potentially important environmental degradation reactions by calculation of the reaction energetics of a potentially large number of organic compounds with aqueous species in natural waters.
2003. "Calculations of the Electronic Structure of 3d Transition Metal Dimers with Projector Augmented Plane Wave Method." Journal of Chemical Physics 119(12):5955-5964. Abstract The projected augmented plane wave (PAW) method provides an all-electron implementation of plane wave basis set in density-functional calculations. It allows an accurate treatment of systems throughout the periodic table while preserving the efficiency required for applications to first principles molecular dynamics simulations. In this article we report a comprehensive comparison of structural and energetic properties of 3d transition metal dimmers predicted by PAW and various local basis set methods. The bond energies, distances, and vibrational frequencies for the lowest lying multiplet states are calculated with both PAW as well local basis method using NWChem. Our results demonstrate that PAW calculations deliver the same level of accuracy as local basis set methods.
2003. "Molecular simulation of the magnetite-water interface." Geochimica et Cosmochimica Acta 67(5):1001-1016. Abstract Molecular simulation of the magnetite-water interface
2003. "Ab initio investigation of the structures of NaOH hydrates and their Na+ and OH- coordination polyhedra." American Mineralogist 88(2-3):436-449. Abstract Ab initio investigation of the structures of NaOH hydrates and their Na+ and OH- coordination polyhedra
2003. "Energy Dependence of Vitreous B2O3 On Boroxol Ring Concentration." Physics and Chemistry of Glasses 44(3):174-177. Abstract Total energy calculations of borate glass samples with fixed fraction of boroxol rings are carried out using density function theory. In this work, the method of preparation of the samples is described and preliminary results are presented. This work suggests that initial structures may strongly affect simulation results, although further work is needed.
2003. "NWChem for Materials Science." Computational Materials Science 28(2):209-221. Abstract This paper focuses on describing the computational chemistry software, NWChem, and its use in materials science research. The current functionalities and capabilities are outlined, as well as future features. Specific computational examples are given to show the flexibility and usefulness of NWChem to answering materials science problems.
2002. "Parallel Implementation of the Projector Augmented Plane Wave Method for Charged Systems." Computer Physics Communications 143(1):11-28. Abstract The parallel implementation of the projector augmented plane wave (PAW) method with the applications to several transition metal complexes is presented. A unique aspect of our PAW code is that it can treat both charged and neutral cluster systems. We discuss how this can be achieved via accurate numerical treatment of the Coulomb Greens function with free space boundary conditions. The strategy for parallelizing of the PAW code is based on distributing the plane wave basis across processors. This is a most versatile approach and is easily implemented using a parallel three-dimensional Fast Fourier Trasformation (FFT). We report parallel performance analysis of our program as well as three-dimensional FFT's and discuss large-scale parallelization issues of the PAW code. Using a series of transition metal monoxides and dioxides, as well as two iron aqueous complexes, it is shown that a free space PAW code can give structural parameters and energies in good agreement with more traditional Gaussian based methods. PACS-1996 number(s): 71.15.a, 71.15.H, 71.15.p, 41.20.C
2002. "One-Electron Reduction of Substituted Chlorinated Methanes as Determined from Ab Initio Electronic Structure Theory." Journal of Physical Chemistry A 106(47):11581-11593. Abstract Substituted chloromethyl radicals and anions are potential intermediates in the reduction of substituted chlorinated methanes (CHxCl3-xL, with L- ) F-, OH-, SH-, NO3 -, HCO3 - and x ) 0-3). Thermochemical properties, ¢H°f (298.15 K), S°(298.15 K,1 bar), and ¢GS(298.15 K, 1 bar), were calculated by using ab initio electronic structure methods for the substituted chloromethyl radicals and anions: CHyCl2-yL¥ and CHyCl2-yL-, for y ) 0-2. In addition, thermochemical properties were calculated for the aldehyde, ClHCO, and the gemchlorohydrin anions, CCl3O-, CHCl2O-, and CH2ClO-. The thermochemical properties of these additional compounds were calculated because the nitrate-substituted compounds, CHyCl2-y(NO3)¥ and CHyCl2-y(NO3)-, were not stable, with all levels of ab initio theory leading to highly dissociated complexes. On the basis of these thermochemical estimates, the overall reaction energetics (in the gas phase and aqueous phase) for several mechanisms of the first electron reduction of the substituted chlorinated methanes were predicted. In almost all of the cases, the thermodynamically most favorable pathway resulted in loss of Cl-. The exception was for the reduction of the nitrate-substituted chlorinated methanes CHxCl3-x(NO3). On reduction, these compounds were shown to readily decompose into a Cl- anion, NO2 ¥ gas, and an aldehyde. In addition, the results of this study suggest that a higher degree of chlorination corresponds to a more favorable reduction. Relative to the nonsubstituted chlorinated methanes, the thermodynamic results suggest the CHxCl3-xF, CHxCl3-xOH, and CHxCl3-x(HCO3) compounds are moderately more difficult to reduce, the CHxCl3-xSH compounds are moderately less difficult to reduce, and the CHxCl3-x(NO3) compounds are substantially more favorable to reduce. These results demonstrate that ab initio electronic structure methods can be used to calculate the reduction potentials of organic compounds to help identify the potentially important environmental degradation reactions.
2001. "The Cs/K Exchange in Muscovite Interlayers: An Ab Initio Treatment." Clays and Clay Minerals 49(6):500-513. Abstract The Cs/K Exchange in Muscovite Interlayers: An Ab Initio Treatment
2001. "Native Defect Properties in Beta-SiC: Ab Initio and Empirical Potential Calculations." Nuclear Instruments and Methods in Physics Research. Section B, Beam Interactions with Materials and Atoms 180(1-4):286-292. Abstract There is considerable ambiguity about the formation of native defects and their clusters in SiC, since different empirical potential gives different results, particular related to the stability of interstitial configurations. Ab intio pseudopotential methods are used to study the formation and properties of native defects in beta-SiC. The results are compared with those calculated by molecular dynamics (MD) using a Tersoff potential, where the various cut-off distances found in the literature are employed. The formation energy of vacancies and antisite defects obtained by ab initio calculations are in good agreement with those given by the Tersoff potential, regardless of the cut-off distances, but there is a disparity for interstitials between the two methods, depending on the cut-off distances used in the Tersoff potential. The present results, however, provide guidelines for evaluating the quality and fit of empirical potentials for large-scale simulations of irradiation damage (displacement cascades) and point defect migration (recombination or annealing) in SiC.
2001. "Ab Initio and Empirical Potential Studies of Defect Properties in 3C-SiC." Physical Review. B, Condensed Matter 64(24):245208, 1-7. Abstract Density functional theory (DFT) is used to study the formation and properties of native defects in 3C-SiC. The extensive calculations have been carried out to determine the formation of point defects and the stability of self interstitials. Although there is a good agreement in the formation of vacancies and antisite defects between the present study and previous calculations, a large disparity appears in the formation of self interstitials. It is found that the most stable configuration of interstitials is the C-C dumbbell along the <100> direction at a C site, with a formation energy of 3.16 eV. The present DFT results are also compared with those calculated by molecular dynamics (MD) simulations using the Tersoff potentials, with parameters obtained from the literature. The formation energy of vacancies and antisite defects obtained by MD calculations are in good agreement with those obtained by DFT calculations. However, the MD calculations yield different results for interstitials energies and structures that depend on the cut-off distances used in the Tersoff potentials. The results provide guidelines for evaluating the quality and fit of empirical potentials for large-scale simulations of irradiation damage and defect migration processes in SiC.
2000. "Ab initio molecular dynamics simulations of aluminum ion solvation in water clusters." Chemical Physics Letters 322:447-453.
2000. "High Performance Computational Chemistry: An Overview of NWChem a Distributed Parallel Application." Computer Physics Communications 128(1 - 2):260 - 283. Abstract NWChem is the software package for computational chemistry on massively parallel computing systems developed by the High Performance Computational Chemistry Group for the Environmental Molecular Sciences Laboratory. The software provides a variety of modules for quantum mechanical and classical mechanical simulation. This article describes the design and some implementation details of the overall NWChem architecture. This architecture facilitates rapid development and portability of fully distributed application modules. We also delineate some of the functionality within NWChem and show performance of a few of the modules within NWChem.
2000. "The Free Energies of Reactions of Chlorinated Methanes with Aqueous Monovalent Anions: Applications of ab initio Electronic Structure Theory." Journal of Physical Chemistry A 104(3):610-617. Abstract The presence of different anionic species in natural waters can significantly alter the degradation rates of chlorinated methanes and other organic compounds. Favorable reaction energetics is a necessary feature of these nucleophilic substitution reactions that can result in the degradation of the chlorinated methanes. In this study, ab initio electronic structure theory is used to evaluate the free energies of reaction of a series of monovalent anionic species (OH-, SH-, NO3 -, HCO3 -, HSO3 -, HSO4 -, H2PO4 -, and F-) that can occur in natural waters with the chlorinated methanes, CCl4, CCl3H, CCl2H2, and CClH3. The results of this investigation show that nucleophilic substitution reactions of OH-, SH-, HCO3 -, and F- are significantly exothermic for chlorine displacement, NO3 - reactions are slightly exothermic to thermoneutral, HSO3 - reactions are slightly endothermic to thermoneutral and HSO4 -, and H2PO4 - reactions are significantly endothermic. In the case of OH-, SH-, and F- where there are limited experimental data, these results agree well with experiment. The results for HCO3 - are potentially important given the near ubiquitous occurrence of carbonate species in natural waters. The calculations reveal that the degree of chlorination, with the exception of substitution of OH-, does not have a large effect on the Gibbs free energies of the substitution reactions. These results demonstrate that ab initio electronic structure methods can be used to calculate the reaction energetics of a potentially large number of organic compounds with other aqueous species in natural waters and can be used to help identify the potentially important environmental degradation reactions.
2000. "From Small to Large Behavior: The Transition from the Aromatic to the Peierls Regime in Carbon Rings." Journal of Chemical Physics 113(15):6096-6106. Abstract From small to large behavior: The transition from the aromatic to the Peierls regime in carbon rings