We study symmetry breaking in the mean field solutions to the 2 electron hydrogen molecule within... more We study symmetry breaking in the mean field solutions to the 2 electron hydrogen molecule within Kohn Sham (KS) local spin density function theory with Dirac exchange (the XLDA model). This simplified model shows behavior related to that of the (KS) spin density functional theory (SDFT) predictions in condensed and molecular systems. The Kohn Sham solutions to the constrained SDFT variation problem undergo spontaneous symmetry breaking as the relative strength of the non-convex exchange term increases. This results in the change of the molecular ground state from a paramagnetic state to an antiferromagnetic ground states and a stationary symmetric delocalized 1st excited state. We further characterize the limiting behavior of the minimizer when the strength of the exchange term goes to infinity. This leads to further bifurcations and highly localized states with varying character. The stability of the various solution classes is demonstrated by Hessian analysis. Finite element nume...
Background: Many important geochemical and biogeochemical reactions occur in the mineral/formatio... more Background: Many important geochemical and biogeochemical reactions occur in the mineral/formation water interface of the highly abundant mineral, goethite [α-Fe(OOH)]. Ab initio molecular dynamics (AIMD) simulations of the goethite α-FeOOH (100) surface and the structure, water bond formation and dynamics of water molecules in the mineral/aqueous interface are presented. Several exchange correlation functionals were employed (PBE96, PBE96 + Grimme, and PBE0) in the simulations of a (3 × 2) goethite surface with 65 absorbed water molecules in a 3D-periodic supercell (a = 30 Å, FeOOH slab ~12 Å thick, solvation layer ~18 Å thick). Results: The lowest energy goethite (100) surface termination model was determined to have an exposed surface Fe 3+ that was loosely capped by a water molecule and a shared hydroxide with a neighboring surface Fe 3+. The water molecules capping surface Fe 3+ ions were found to be loosely bound at all DFT levels with and without Grimme corrections, indicative that each surface Fe 3+ was coordinated with only five neighbors. These long bonds were supported by bond valence theory calculations, which showed that the bond valence of the surface Fe 3+ was saturated and surface has a neutral charge. The polarization of the water layer adjacent to the surface was found to be small and affected only the nearest water. Analysis by density difference plots and localized Boys orbitals identified three types of water molecules: those loosely bound to the surface Fe 3+ , those hydrogen bonded to the surface hydroxyl, and bulk water with tetrahedral coordination. Boys orbital analysis showed that the spin down lone pair orbital of the weakly absorbed water interact more strongly with the spin up Fe 3+ ion. These weakly bound surface water molecules were found to rapidly exchange with the second water layer (~0.025 exchanges/ps) using a dissociative mechanism. Conclusions: Water molecules adjacent to the surface were found to only weakly interact with the surface and as a result were readily able to exchange with the bulk water. To account for the large surface Fe-OH 2 distances in the DFT calculations it was proposed that the surface Fe 3+ atoms, which already have their bond valence fully satisfied with only five neighbors, are under-coordinated with respect to the bulk coordination.
Submitted for the MAR14 Meeting of The American Physical Society Parallel in time simulations usi... more Submitted for the MAR14 Meeting of The American Physical Society Parallel in time simulations using high level quantum chemistry methods and complex empirical potentials 1 ERIC BYLASKA, Pacific Northwest Natl Lab, JONATHAN WEARE, University Chicago, JOHN WEARE, UCSD-Algorithms that support parallel decomposition in the time dimension are presented and applied to conventional molecular dynamics (MD) models and ab initio molecular dynamics (AIMD) models of realistic complexity. The algorithms support convenient parallel implementation to achieve significant improvement in the simulation of high level (e.g. MP2) and excited state dynamics. Given a forward time integrator propagating the system from time t i (trajectory position and velocity x i = (r i , v i)) to t i+1 as x i+1 = f i (x i), the dynamics problem is transformed into a root finding problem, F = [x i − f (x (i−1)] i = 0, for the trajectory variables. The fixed point problem is unconditionally convergent and is solved iteratively using a variety of optimization techniques, including quasi-Newton and preconditioned quasi-Newton methods. The algorithm is parallelized by assigning a processor to each time-step entry in the columns of F(X). Less accurate but more efficient dynamical models based on simplified interactions or coarsening time-steps provide preconditioners for the root finding problem and lead to an algorithm similar to the parareal algorithm. 1 supported by ASCR Petascale Tools program and the BES Geosciences program of the
Due to space limitations, the Chemistry Department Computer Center put some of our software routi... more Due to space limitations, the Chemistry Department Computer Center put some of our software routines on an old disk. This disk subsequently crashed. Since the Center had failed to backup this space, the routines were lost. The Center acknowledges their error and has agreed to reimburse-the grant for the lost time. We are now negotiating the amount of time the lost routines represent. Fortunately, data files, input and output files, models and reports were not affected by this lost. The present assessment is that several fitting codes for creating TEQUIL models and GEOF'LUIDS models were lost. 11. TEQUIL MODELS, T c 350°C: The previous modifications to the fitting and equilibrium codes required to add many new species to the TEQUIL models were lost in the disk crash. These changes were necessary to add the aluminum species to the calcite model. Some of the lost upgrades have now been regenerated but we still need to reconstruct several important routines. We hope that most of this work will be completed by the end of May. We note that the recent work (see below) on developing 3-D capability for displaying phase diagrams generated by our TEQUIL models was not lost.
Gibbs ensemble Monte Carlo simulations of water vapor/liquid equilibrium (VLE) using the flexible... more Gibbs ensemble Monte Carlo simulations of water vapor/liquid equilibrium (VLE) using the flexible fixed charge RWK2 water-water potential are reported. The equilibrium densities, saturation pressures, and critical parameters calculated with this potential are in better agreement with experimental data than are values obtained from the SPC, MSPC/E, TIP4P, and TIP5P rigid fixed charge potentials as well as from polarizable interactions, such as those of the PPC, KJ, SPC/P, TIP4P/P, and SPCDP potentials. The agreement between predicted and experimental phase coexistence phase density versus temperature variation in the critical region is similar to that obtained from the SPC/E and the polarizable SPC-pol-1 potentials. However, the variation of the saturation pressure and heat of vaporization with temperature and the critical pressure predicted by the RWK2 potential are closer to experiment than predictions from SPC/E interaction and similar (for lower temperatures) to those of the MSPC/E potential. The water structure predictions of the RWK2 potential are substantially better than those from the SPC-pol-1 interaction. VLE data are not used to parametrize the RWK2 potential. Nevertheless, predictions for coexistence temperature versus phase density and saturation pressure versus temperature are similar to those of the recent potential of Errington and Panagiotopoulos (EP potential), which is adjusted to reproduce the VLE behavior of water. MD simulations using the RWK2 potential show much better agreement with the room-temperature liquid structure and second virial coefficient data than does the EP potential. Fixing the bond lengths and HOH angle in the RWK2 interaction at their isolated molecule minimum energy values leads to significant deterioration of the VLE predictions obtained.
Protein kinases catalyze the transfer of the γ-phosphoryl group of ATP to serine, threonine, and ... more Protein kinases catalyze the transfer of the γ-phosphoryl group of ATP to serine, threonine, and tyrosine residues in proteins, a process essential for cell signaling. Although there may be as many Figure 2. Time dependence of the bond distances between Ser-O and the Pγ of ATP (R1) and between Asp166-O and Ser-H (R2).
Parallel in time simulation algorithms are presented and applied to conventional molecular dynami... more Parallel in time simulation algorithms are presented and applied to conventional molecular dynamics (MD) and ab initio molecular dynamics (AIMD) models of realistic complexity. Assuming that a forward time integrator, f (e.g., Verlet algorithm), is available to propagate the system from time ti (trajectory positions and velocities xi = (ri, vi)) to time ti + 1 (xi + 1) by xi + 1 = fi(xi), the dynamics problem spanning an interval from t0…tM can be transformed into a root finding problem, F(X) = [xi − f(x(i − 1)]i = 1, M = 0, for the trajectory variables. The root finding problem is solved using a variety of root finding techniques, including quasi-Newton and preconditioned quasi-Newton schemes that are all unconditionally convergent. The algorithms are parallelized by assigning a processor to each time-step entry in the columns of F(X). The relation of this approach to other recently proposed parallel in time methods is discussed, and the effectiveness of various approaches to solvi...
Previously, we reported an equation of state (EOS) modeling approach that successfully calculated... more Previously, we reported an equation of state (EOS) modeling approach that successfully calculated the PVTX properties of supercritical fluid mixtures. The model is based on a corresponding states assumption applied to a highly accurate EOS for the reference CH 4 system. The CH 4 EOS was parameterized from 273 to 723 K and 1 to 3000 bar by using experimental PVT data. Molecular dynamics simulated PVT data were used to extend the parameterization in the CH 4 system to 2000 K and 20 kbar. Mixing in the H 2 O-CO 2-CH 4-N 2 system was successfully described by using a simple empirical mixing rule with only two temperature-and pressure-independent parameters for each binary mixture. Results indicated that PVTX properties in higher order systems could be reliably calculated without additional parameters. In this paper, by using experimental PVTX data in the H 2 O-CO 2-CH 4-N 2 system that were not used in the EOS parameterization, we show that the model predictions are accurate from just above the critical temperature for the least volatile component to 2000 K and from 0 to 100 kbar. We also show that our modeling approach can be extended to reliably calculate supercritical phase equilibria and other thermodynamic properties, such as fugacity and enthalpy, under high-temperature and-pressure conditions.
An equation of state (EOS) is developed for saltwater systems in the high temperature range. As a... more An equation of state (EOS) is developed for saltwater systems in the high temperature range. As an example of the applications, this EOS is parameterized for the calculation of density, immiscibility, and the compositions of coexisting phases in the CaCl 2-H 2 O and MgCl 2-H 2 O systems from 523 to 973 K and from saturation pressure to 1500 bar. All available volumetric and phase equilibrium measurements of these binaries are well represented by this equation. This EOS is based on a Helmholtz free energy representation constructed from a reference system containing hard-sphere and polar contributions plus an empirical correction. For the temperature and pressure range in this study, the electrolyte solutes are assumed to be associated. The water molecules are modeled as hard spheres with point dipoles and the solute molecules, MgCl 2 and CaCl 2 , as hard spheres with point quadrupoles. The free energy of the reference system is calculated from an analytical representation of the Helmholtz free energy of the hard-sphere contributions and perturbative estimates of the electrostatic contributions. The empirical correction used to account for deviations of the reference system predictions from measured data is based on a virial expansion. The formalism allows generalization to aqueous systems containing insoluble gases (CO 2 , CH 4), alkali chlorides (NaCl, KCl), and alkaline earth chlorides (CaCl 2 , MgCl 2). The program of this model is available as an electronic annex (see EA1 and EA2) and can also be downloaded at: http://www.geochem-model.org/programs.htm.
A model is developed for the prediction of H2S solubility in NaCl-bearing aqueous solutions up to... more A model is developed for the prediction of H2S solubility in NaCl-bearing aqueous solutions up to about 300 bar, 320°C and 6 m NaCI. Although many H2S solubility measurements have been published, most of them are limited to low pressures (just above water saturation pressure). In order to predict solubilities to higher pressures, we have developed an equation of state (EOS) for the H2S-H20 binary, which allows us to calculate chemical potentials of both H2S and H20 in liquid or in vapor phase. Below 350°C NaC1 has negligible effect on the vapor phase but has substantial effect on the activities of H2S in the liquid phase. Thiis salt effect is accounted for by specific ion interactions. Comparison of this model with all the available data indicates that predictions are within experimental uncertainty, even for pressures well above that covered by the data used for param~terization.
We present a molecular model for ferrous-ferric electron transfer in an aqueous solution and at i... more We present a molecular model for ferrous-ferric electron transfer in an aqueous solution and at interfaces that accounts for electronic polarizability and exhibits spontaneous cation hydrolysis, and allows estimation of pH dependence. In solution, the model predicts that the diabatic barrier to electron transfer increases with increasing pH, due to stabilization of the Fe 3+ by fluctuations in the number of hydroxide ions in its first coordination sphere, in much the same way as the barrier would increase with increasing dielectric constant in the Marcus theory. As expected, increasing pH reduces the potential of mean force between the ferrous and ferric ions in the model system. The magnitudes of the predicted increase in diabatic transfer barrier and the predicted decrease in the potential of mean force nearly cancel each other at the canonical transfer distance of 0.55 nm. Even though hydrolysis is allowed in our calculations, the distribution of reorganization energies has only one maximum and is Gaussian to an excellent approximation, giving a harmonic free energy surface in the reorganization energy F(∆E) with a single minimum. Evidently, fluctuations in hydrolysis state can be viewed on a continuum with other solvent contributions to the reorganization energy. There appears to be little justification for thinking of the transfer rate as arising from the contributions of different hydrolysis states.
Geochimica et Cosmochimica Acta Supplement, May 1, 2005
We present a molecular model for ferrous-ferric electron transfer in an aqueous solution and at i... more We present a molecular model for ferrous-ferric electron transfer in an aqueous solution and at interfaces that accounts for electronic polarizability and exhibits spontaneous cation hydrolysis, and allows estimation of pH dependence. In solution, the model predicts that the diabatic barrier to electron transfer increases with increasing pH, due to stabilization of the Fe 3+ by fluctuations in the number of hydroxide ions in its first coordination sphere, in much the same way as the barrier would increase with increasing dielectric constant in the Marcus theory. As expected, increasing pH reduces the potential of mean force between the ferrous and ferric ions in the model system. The magnitudes of the predicted increase in diabatic transfer barrier and the predicted decrease in the potential of mean force nearly cancel each other at the canonical transfer distance of 0.55 nm. Even though hydrolysis is allowed in our calculations, the distribution of reorganization energies has only one maximum and is Gaussian to an excellent approximation, giving a harmonic free energy surface in the reorganization energy F(∆E) with a single minimum. Evidently, fluctuations in hydrolysis state can be viewed on a continuum with other solvent contributions to the reorganization energy. There appears to be little justification for thinking of the transfer rate as arising from the contributions of different hydrolysis states.
The ability to predict the transport and transformations of contaminants within the subsurface is... more The ability to predict the transport and transformations of contaminants within the subsurface is critical for decisions on virtually every waste disposal option facing the Department of Energy (DOE), from remediation technologies such as in situ bioremediation to evaluations of the safety of nuclear waste repositories. With this fact in mind, the DOE has recently sponsored a series of workshops on the development of a Strategic Simulation Plan (SSP) on applications of high performance computing to national problems of significance to the DOE. One of the application areas selected was in the area of subsurface transport and environmental chemistry. Within the SSP on subsurface transport and environmental chemistry several areas were identified where applications of high performance computing could potentially significantly advance our knowledge of contaminant fate and transport. Within each of these areas molecular level simulations were specifically identified as a key capability necessary for the development of a fundamental mechanistic understanding of complex biogeochemical processes. This effort consists of a series of specific molecular level simulations and program development in four key areas of geochemistry/biogeochemistry (i.e., aqueous hydrolysis, redox chemistry, mineral surface interactions, and microbial surface properties). By addressing these four different, but computationally related, areas it becomes possible to assemble a team of investigators with the necessary expertise in high performance computing, molecular simulation, and geochemistry/biogeochemistry to make significant progress in each area. The specific targeted geochemical/biogeochemical issues include: Microbial surface mediated processes: the effects of lipopolysacchardies present on gramnegative bacteria. Environmental redox chemistry: Dechlorination pathways of carbon tetrachloride and other polychlorinated compounds in the subsurface. Mineral surface interactions: Describing surfaces at multiple scales with realistic surface functional groups Aqueous Hydrolysis Reactions and Solvation of Highly Charged Species: Understanding the formation of polymerized species and ore formation under extreme (Hanford Vadose Zone and geothermo) conditions. By understanding on a fundamental basis these key issues, it is anticipated that the impacts of this research will be extendable to a wide range of biogeochemical issues. Taken in total such an effort truly represents a "Grand Challenge" in molecular geochemistry and biogeochemistry.
We study symmetry breaking in the mean field solutions to the 2 electron hydrogen molecule within... more We study symmetry breaking in the mean field solutions to the 2 electron hydrogen molecule within Kohn Sham (KS) local spin density function theory with Dirac exchange (the XLDA model). This simplified model shows behavior related to that of the (KS) spin density functional theory (SDFT) predictions in condensed and molecular systems. The Kohn Sham solutions to the constrained SDFT variation problem undergo spontaneous symmetry breaking as the relative strength of the non-convex exchange term increases. This results in the change of the molecular ground state from a paramagnetic state to an antiferromagnetic ground states and a stationary symmetric delocalized 1st excited state. We further characterize the limiting behavior of the minimizer when the strength of the exchange term goes to infinity. This leads to further bifurcations and highly localized states with varying character. The stability of the various solution classes is demonstrated by Hessian analysis. Finite element nume...
Background: Many important geochemical and biogeochemical reactions occur in the mineral/formatio... more Background: Many important geochemical and biogeochemical reactions occur in the mineral/formation water interface of the highly abundant mineral, goethite [α-Fe(OOH)]. Ab initio molecular dynamics (AIMD) simulations of the goethite α-FeOOH (100) surface and the structure, water bond formation and dynamics of water molecules in the mineral/aqueous interface are presented. Several exchange correlation functionals were employed (PBE96, PBE96 + Grimme, and PBE0) in the simulations of a (3 × 2) goethite surface with 65 absorbed water molecules in a 3D-periodic supercell (a = 30 Å, FeOOH slab ~12 Å thick, solvation layer ~18 Å thick). Results: The lowest energy goethite (100) surface termination model was determined to have an exposed surface Fe 3+ that was loosely capped by a water molecule and a shared hydroxide with a neighboring surface Fe 3+. The water molecules capping surface Fe 3+ ions were found to be loosely bound at all DFT levels with and without Grimme corrections, indicative that each surface Fe 3+ was coordinated with only five neighbors. These long bonds were supported by bond valence theory calculations, which showed that the bond valence of the surface Fe 3+ was saturated and surface has a neutral charge. The polarization of the water layer adjacent to the surface was found to be small and affected only the nearest water. Analysis by density difference plots and localized Boys orbitals identified three types of water molecules: those loosely bound to the surface Fe 3+ , those hydrogen bonded to the surface hydroxyl, and bulk water with tetrahedral coordination. Boys orbital analysis showed that the spin down lone pair orbital of the weakly absorbed water interact more strongly with the spin up Fe 3+ ion. These weakly bound surface water molecules were found to rapidly exchange with the second water layer (~0.025 exchanges/ps) using a dissociative mechanism. Conclusions: Water molecules adjacent to the surface were found to only weakly interact with the surface and as a result were readily able to exchange with the bulk water. To account for the large surface Fe-OH 2 distances in the DFT calculations it was proposed that the surface Fe 3+ atoms, which already have their bond valence fully satisfied with only five neighbors, are under-coordinated with respect to the bulk coordination.
Submitted for the MAR14 Meeting of The American Physical Society Parallel in time simulations usi... more Submitted for the MAR14 Meeting of The American Physical Society Parallel in time simulations using high level quantum chemistry methods and complex empirical potentials 1 ERIC BYLASKA, Pacific Northwest Natl Lab, JONATHAN WEARE, University Chicago, JOHN WEARE, UCSD-Algorithms that support parallel decomposition in the time dimension are presented and applied to conventional molecular dynamics (MD) models and ab initio molecular dynamics (AIMD) models of realistic complexity. The algorithms support convenient parallel implementation to achieve significant improvement in the simulation of high level (e.g. MP2) and excited state dynamics. Given a forward time integrator propagating the system from time t i (trajectory position and velocity x i = (r i , v i)) to t i+1 as x i+1 = f i (x i), the dynamics problem is transformed into a root finding problem, F = [x i − f (x (i−1)] i = 0, for the trajectory variables. The fixed point problem is unconditionally convergent and is solved iteratively using a variety of optimization techniques, including quasi-Newton and preconditioned quasi-Newton methods. The algorithm is parallelized by assigning a processor to each time-step entry in the columns of F(X). Less accurate but more efficient dynamical models based on simplified interactions or coarsening time-steps provide preconditioners for the root finding problem and lead to an algorithm similar to the parareal algorithm. 1 supported by ASCR Petascale Tools program and the BES Geosciences program of the
Due to space limitations, the Chemistry Department Computer Center put some of our software routi... more Due to space limitations, the Chemistry Department Computer Center put some of our software routines on an old disk. This disk subsequently crashed. Since the Center had failed to backup this space, the routines were lost. The Center acknowledges their error and has agreed to reimburse-the grant for the lost time. We are now negotiating the amount of time the lost routines represent. Fortunately, data files, input and output files, models and reports were not affected by this lost. The present assessment is that several fitting codes for creating TEQUIL models and GEOF'LUIDS models were lost. 11. TEQUIL MODELS, T c 350°C: The previous modifications to the fitting and equilibrium codes required to add many new species to the TEQUIL models were lost in the disk crash. These changes were necessary to add the aluminum species to the calcite model. Some of the lost upgrades have now been regenerated but we still need to reconstruct several important routines. We hope that most of this work will be completed by the end of May. We note that the recent work (see below) on developing 3-D capability for displaying phase diagrams generated by our TEQUIL models was not lost.
Gibbs ensemble Monte Carlo simulations of water vapor/liquid equilibrium (VLE) using the flexible... more Gibbs ensemble Monte Carlo simulations of water vapor/liquid equilibrium (VLE) using the flexible fixed charge RWK2 water-water potential are reported. The equilibrium densities, saturation pressures, and critical parameters calculated with this potential are in better agreement with experimental data than are values obtained from the SPC, MSPC/E, TIP4P, and TIP5P rigid fixed charge potentials as well as from polarizable interactions, such as those of the PPC, KJ, SPC/P, TIP4P/P, and SPCDP potentials. The agreement between predicted and experimental phase coexistence phase density versus temperature variation in the critical region is similar to that obtained from the SPC/E and the polarizable SPC-pol-1 potentials. However, the variation of the saturation pressure and heat of vaporization with temperature and the critical pressure predicted by the RWK2 potential are closer to experiment than predictions from SPC/E interaction and similar (for lower temperatures) to those of the MSPC/E potential. The water structure predictions of the RWK2 potential are substantially better than those from the SPC-pol-1 interaction. VLE data are not used to parametrize the RWK2 potential. Nevertheless, predictions for coexistence temperature versus phase density and saturation pressure versus temperature are similar to those of the recent potential of Errington and Panagiotopoulos (EP potential), which is adjusted to reproduce the VLE behavior of water. MD simulations using the RWK2 potential show much better agreement with the room-temperature liquid structure and second virial coefficient data than does the EP potential. Fixing the bond lengths and HOH angle in the RWK2 interaction at their isolated molecule minimum energy values leads to significant deterioration of the VLE predictions obtained.
Protein kinases catalyze the transfer of the γ-phosphoryl group of ATP to serine, threonine, and ... more Protein kinases catalyze the transfer of the γ-phosphoryl group of ATP to serine, threonine, and tyrosine residues in proteins, a process essential for cell signaling. Although there may be as many Figure 2. Time dependence of the bond distances between Ser-O and the Pγ of ATP (R1) and between Asp166-O and Ser-H (R2).
Parallel in time simulation algorithms are presented and applied to conventional molecular dynami... more Parallel in time simulation algorithms are presented and applied to conventional molecular dynamics (MD) and ab initio molecular dynamics (AIMD) models of realistic complexity. Assuming that a forward time integrator, f (e.g., Verlet algorithm), is available to propagate the system from time ti (trajectory positions and velocities xi = (ri, vi)) to time ti + 1 (xi + 1) by xi + 1 = fi(xi), the dynamics problem spanning an interval from t0…tM can be transformed into a root finding problem, F(X) = [xi − f(x(i − 1)]i = 1, M = 0, for the trajectory variables. The root finding problem is solved using a variety of root finding techniques, including quasi-Newton and preconditioned quasi-Newton schemes that are all unconditionally convergent. The algorithms are parallelized by assigning a processor to each time-step entry in the columns of F(X). The relation of this approach to other recently proposed parallel in time methods is discussed, and the effectiveness of various approaches to solvi...
Previously, we reported an equation of state (EOS) modeling approach that successfully calculated... more Previously, we reported an equation of state (EOS) modeling approach that successfully calculated the PVTX properties of supercritical fluid mixtures. The model is based on a corresponding states assumption applied to a highly accurate EOS for the reference CH 4 system. The CH 4 EOS was parameterized from 273 to 723 K and 1 to 3000 bar by using experimental PVT data. Molecular dynamics simulated PVT data were used to extend the parameterization in the CH 4 system to 2000 K and 20 kbar. Mixing in the H 2 O-CO 2-CH 4-N 2 system was successfully described by using a simple empirical mixing rule with only two temperature-and pressure-independent parameters for each binary mixture. Results indicated that PVTX properties in higher order systems could be reliably calculated without additional parameters. In this paper, by using experimental PVTX data in the H 2 O-CO 2-CH 4-N 2 system that were not used in the EOS parameterization, we show that the model predictions are accurate from just above the critical temperature for the least volatile component to 2000 K and from 0 to 100 kbar. We also show that our modeling approach can be extended to reliably calculate supercritical phase equilibria and other thermodynamic properties, such as fugacity and enthalpy, under high-temperature and-pressure conditions.
An equation of state (EOS) is developed for saltwater systems in the high temperature range. As a... more An equation of state (EOS) is developed for saltwater systems in the high temperature range. As an example of the applications, this EOS is parameterized for the calculation of density, immiscibility, and the compositions of coexisting phases in the CaCl 2-H 2 O and MgCl 2-H 2 O systems from 523 to 973 K and from saturation pressure to 1500 bar. All available volumetric and phase equilibrium measurements of these binaries are well represented by this equation. This EOS is based on a Helmholtz free energy representation constructed from a reference system containing hard-sphere and polar contributions plus an empirical correction. For the temperature and pressure range in this study, the electrolyte solutes are assumed to be associated. The water molecules are modeled as hard spheres with point dipoles and the solute molecules, MgCl 2 and CaCl 2 , as hard spheres with point quadrupoles. The free energy of the reference system is calculated from an analytical representation of the Helmholtz free energy of the hard-sphere contributions and perturbative estimates of the electrostatic contributions. The empirical correction used to account for deviations of the reference system predictions from measured data is based on a virial expansion. The formalism allows generalization to aqueous systems containing insoluble gases (CO 2 , CH 4), alkali chlorides (NaCl, KCl), and alkaline earth chlorides (CaCl 2 , MgCl 2). The program of this model is available as an electronic annex (see EA1 and EA2) and can also be downloaded at: http://www.geochem-model.org/programs.htm.
A model is developed for the prediction of H2S solubility in NaCl-bearing aqueous solutions up to... more A model is developed for the prediction of H2S solubility in NaCl-bearing aqueous solutions up to about 300 bar, 320°C and 6 m NaCI. Although many H2S solubility measurements have been published, most of them are limited to low pressures (just above water saturation pressure). In order to predict solubilities to higher pressures, we have developed an equation of state (EOS) for the H2S-H20 binary, which allows us to calculate chemical potentials of both H2S and H20 in liquid or in vapor phase. Below 350°C NaC1 has negligible effect on the vapor phase but has substantial effect on the activities of H2S in the liquid phase. Thiis salt effect is accounted for by specific ion interactions. Comparison of this model with all the available data indicates that predictions are within experimental uncertainty, even for pressures well above that covered by the data used for param~terization.
We present a molecular model for ferrous-ferric electron transfer in an aqueous solution and at i... more We present a molecular model for ferrous-ferric electron transfer in an aqueous solution and at interfaces that accounts for electronic polarizability and exhibits spontaneous cation hydrolysis, and allows estimation of pH dependence. In solution, the model predicts that the diabatic barrier to electron transfer increases with increasing pH, due to stabilization of the Fe 3+ by fluctuations in the number of hydroxide ions in its first coordination sphere, in much the same way as the barrier would increase with increasing dielectric constant in the Marcus theory. As expected, increasing pH reduces the potential of mean force between the ferrous and ferric ions in the model system. The magnitudes of the predicted increase in diabatic transfer barrier and the predicted decrease in the potential of mean force nearly cancel each other at the canonical transfer distance of 0.55 nm. Even though hydrolysis is allowed in our calculations, the distribution of reorganization energies has only one maximum and is Gaussian to an excellent approximation, giving a harmonic free energy surface in the reorganization energy F(∆E) with a single minimum. Evidently, fluctuations in hydrolysis state can be viewed on a continuum with other solvent contributions to the reorganization energy. There appears to be little justification for thinking of the transfer rate as arising from the contributions of different hydrolysis states.
Geochimica et Cosmochimica Acta Supplement, May 1, 2005
We present a molecular model for ferrous-ferric electron transfer in an aqueous solution and at i... more We present a molecular model for ferrous-ferric electron transfer in an aqueous solution and at interfaces that accounts for electronic polarizability and exhibits spontaneous cation hydrolysis, and allows estimation of pH dependence. In solution, the model predicts that the diabatic barrier to electron transfer increases with increasing pH, due to stabilization of the Fe 3+ by fluctuations in the number of hydroxide ions in its first coordination sphere, in much the same way as the barrier would increase with increasing dielectric constant in the Marcus theory. As expected, increasing pH reduces the potential of mean force between the ferrous and ferric ions in the model system. The magnitudes of the predicted increase in diabatic transfer barrier and the predicted decrease in the potential of mean force nearly cancel each other at the canonical transfer distance of 0.55 nm. Even though hydrolysis is allowed in our calculations, the distribution of reorganization energies has only one maximum and is Gaussian to an excellent approximation, giving a harmonic free energy surface in the reorganization energy F(∆E) with a single minimum. Evidently, fluctuations in hydrolysis state can be viewed on a continuum with other solvent contributions to the reorganization energy. There appears to be little justification for thinking of the transfer rate as arising from the contributions of different hydrolysis states.
The ability to predict the transport and transformations of contaminants within the subsurface is... more The ability to predict the transport and transformations of contaminants within the subsurface is critical for decisions on virtually every waste disposal option facing the Department of Energy (DOE), from remediation technologies such as in situ bioremediation to evaluations of the safety of nuclear waste repositories. With this fact in mind, the DOE has recently sponsored a series of workshops on the development of a Strategic Simulation Plan (SSP) on applications of high performance computing to national problems of significance to the DOE. One of the application areas selected was in the area of subsurface transport and environmental chemistry. Within the SSP on subsurface transport and environmental chemistry several areas were identified where applications of high performance computing could potentially significantly advance our knowledge of contaminant fate and transport. Within each of these areas molecular level simulations were specifically identified as a key capability necessary for the development of a fundamental mechanistic understanding of complex biogeochemical processes. This effort consists of a series of specific molecular level simulations and program development in four key areas of geochemistry/biogeochemistry (i.e., aqueous hydrolysis, redox chemistry, mineral surface interactions, and microbial surface properties). By addressing these four different, but computationally related, areas it becomes possible to assemble a team of investigators with the necessary expertise in high performance computing, molecular simulation, and geochemistry/biogeochemistry to make significant progress in each area. The specific targeted geochemical/biogeochemical issues include: Microbial surface mediated processes: the effects of lipopolysacchardies present on gramnegative bacteria. Environmental redox chemistry: Dechlorination pathways of carbon tetrachloride and other polychlorinated compounds in the subsurface. Mineral surface interactions: Describing surfaces at multiple scales with realistic surface functional groups Aqueous Hydrolysis Reactions and Solvation of Highly Charged Species: Understanding the formation of polymerized species and ore formation under extreme (Hanford Vadose Zone and geothermo) conditions. By understanding on a fundamental basis these key issues, it is anticipated that the impacts of this research will be extendable to a wide range of biogeochemical issues. Taken in total such an effort truly represents a "Grand Challenge" in molecular geochemistry and biogeochemistry.
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