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Many important chemical processes involve reactivity and dynamics in complex solutions. Gaining a fundamental understanding of these reaction mechanisms is a challenging goal that requires advanced computational and experimental approaches. However, important techniques such as molecular simulation have limitations in terms of scales of time, length, and system complexity. Furthermore, among the currently available solvation models, there are very few designed to describe the interaction between the molecular scale and the mesoscale. To help address this challenge, here, we establish a novel hybrid approach that couples first-principles plane-wave density functional theory with classical density functional theory (cDFT). In this approach, a region of interest described by ab initio molecular dynamics (AIMD) interacts with the surrounding medium described using cDFT to arrive at a self-consistent ground state. cDFT is a robust but efficient mesoscopic approach to accurate thermodynamics of bulk electrolyte solutions over a wide concentration range (up to 2M concentrations). Benchmarking against commonly used continuum models of solvation, such as SMD, as well as experiments, demonstrates that our hybrid AIMD–cDFT method is able to produce reasonable solvation energies for a variety of molecules and ions. With this model, we also examined the solvent effects on a prototype SN2 reaction of the nucleophilic attack of a chloride ion on methyl chloride in the solution. The resulting reaction pathway profile and the solution phase barrier agree well with experiment, showing that our AIMD/cDFT hybrid approach can provide insight into the specific role of the solvent on the reaction coordinate. [ABSTRACT FROM AUTHOR]

An efficient and accurate approach for calculating exact exchange and other two-electron integrals has been developed for periodic electronic structure methods. Traditional approaches used for integrating over the Brillouin zone in band structure calculations, e.g. trapezoidal or Monkhorst-Pack, are not accurate enough for two-electron integrals. This is because their integrands contain multiple singularities over the double integration of the Brillouin zone, which with simple integration methods lead to very inaccurate results. A common approach to this problem has been to replace the Coulomb interaction with a screened Coulomb interaction that removes singularities from the integrands in the two-electron integrals, albeit at the inelegance of having to introduce a screening factor which must precomputed or guessed. Instead of introducing screened Coulomb interactions in an ad hoc way, the method developed in this work derives an effective screened potential using a Filon-like integration approach that is based only on the lattice parameters. This approach overcomes the limitations of traditionally defined screened Coulomb interactions for calculating two-electron integrals, and makes chemistry many-body calculations tractable in periodic boundary conditions. This method has been applied to several systems for which conventional DFT methods do not work well, including the reaction pathways for the addition of H2 to phenol and Au 20 − nanoparticle, and the electron transfer of a charge trapped state in the Fe(II) containing mica, annite. [ABSTRACT FROM AUTHOR]

Results of ab initio molecular dynamics (AIMD) simulations (density functional theory+PBE96) of the dynamics of waters in the hydration shells surrounding the Zn2+ ion (T≈300 K, ρ≈1 gm/cm3) are compared to simulations using a combined quantum and classical molecular dynamics [AIMD/molecular mechanical (MM)] approach. Both classes of simulations were performed with 64 solvating water molecules (∼15 ps) and used the same methods in the electronic structure calculation (plane-wave basis set, time steps, effective mass, etc.). In the AIMD/MM calculation, only six waters of hydration were included in the quantum mechanical (QM) region. The remaining 58 waters were treated with a published flexible water-water interaction potential. No reparametrization of the water-water potential was attempted. Additional AIMD/MM simulations were performed with 256 water molecules. The hydration structures predicted from the AIMD and AIMD/MM simulations are found to agree in detail with each other and with the structural results from x-ray data despite the very limited QM region in the AIMD/MM simulation. To further evaluate the agreement of these parameter-free simulations, predicted extended x-ray absorption fine structure (EXAFS) spectra were compared directly to the recently obtained EXAFS data and they agree in remarkable detail with the experimental observations. The first hydration shell contains six water molecules in a highly symmetric octahedral structure is (maximally located at 2.13–2.15 Å versus 2.072 Å EXAFS experiment). The widths of the peak of the simulated EXAFS spectra agree well with the data (8.4 Å2 versus 8.9 Å2 in experiment). Analysis of the H-bond structure of the hydration region shows that the second hydration shell is trigonally bound to the first shell water with a high degree of agreement between the AIMD and AIMD/MM calculations. Beyond the second shell, the bonding pattern returns to the tetrahedral structure of bulk water. The AIMD/MM results emphasize the importance of a quantum description of the first hydration shell to correctly describe the hydration region. In these calculations the full d10 electronic structure of the valence shell of the Zn2+ ion is retained. The simulations show substantial and complex charge relocation on both the Zn2+ ion and the first hydration shell. The dipole moment of the waters in the first hydration shell is 3.4 D (3.3 D AIMD/MM) versus 2.73 D bulk. Little polarization is found for the waters in the second hydration shell (2.8 D). No exchanges were seen between the first and the second hydrations shells; however, many water transfers between the second hydration shell and the bulk were observed. For 64 waters, the AIMD and AIMD/MM simulations give nearly identical results for exchange dynamics. However, in the larger particle simulations (256 waters) there is a significant reduction in the second shell to bulk exchanges. [ABSTRACT FROM AUTHOR]

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 with very well-known results from x-ray data. The average U==O bond length was found to be 1.77 Å. The first hydration shell contained five trigonally coordinated water molecules that were equatorially oriented about the O–U–O axis with the hydrogen atoms oriented away from the uranium atom. The five waters in the first shell were located at an average distance of 2.44 Å (2.46 Å, 122 water simulation). The second hydration shell was composed of distinct equatorial and apical regions resulting in a peak in the U–O radial distribution function at 4.59 Å. The equatorial second shell contained ten 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 a way as to have their protons pointed toward the cation. While the number of apical waters varied greatly, an average of five to six waters was found in this region. Many water transfers into and out of the equatorial and apical second solvation shells were observed to occur on a picosecond time scale via dissociative mechanisms. Beyond these shells, the bonding pattern substantially returned to the tetrahedral structure of bulk water. [ABSTRACT FROM AUTHOR]

Car-Parrinello molecular dynamics (CPMD) simulations have been used to examine the hydration structures, coordination energetics, and the first hydrolysis constants of Pu3+, Pu4+, PuO2+, and PuO22+ ions in aqueous solution at 300 K. The coordination numbers and structural properties of the first shell of these ions are in good agreement with available experimental estimates. The hexavalent PuO22+ species is coordinated to five aquo ligands while the pentavalent PuO2+ complex is coordinated to four aquo ligands. The Pu3+ and Pu4+ ions are both coordinated to eight water molecules. The first hydrolysis constants obtained for Pu3+ and PuO22+ are 6.65 and 5.70, respectively, all within 0.3 pH unit of the experimental values (6.90 and 5.50, respectively). The hydrolysis constant of Pu4+, 0.17, disagrees with the value of -0.60 in the most recent update of the Nuclear Energy Agency Thermochemical Database (NEA-TDB) but supports recent experimental findings. The hydrolysis constant of PuO2+, 9.51, supports the experimental results of Bennett et al. [Radiochim. Acta 1992, 56, 15]. A correlation between the pKa of the first hydrolysis reaction and the effective charge of the plutonium center was found. [ABSTRACT FROM AUTHOR]

Results of ab initio molecular dynamics (AIMD), quantum mechanics/molecular mechanics (QM/MM), and classical molecular dynamics (CMD) simulations of Cm3+ in liquid water at a temperature of 300 K are reported. The AIMD simulation was based on the Car-Parrinello MD scheme and GGA-PBE formulation of density functional theory. Two QM/ MM simulations were performed by treating Cm3+ and the water molecules in the first shell quantum mechanically using the PBE (QM/MM-PBE) and the hybrid PBEO density functionals (QM/MM-PBEO). Two CMD simulations were carried out using ab initio derived pair plus three-body potentials (CMD-3B) and empirical Lennard-Jones pair potential (CMD-LJ). The AÍMD and QM/MM-PBE simulations predict average first shell hydration numbers of 8, both of which disagree with recent experimental EXAFS and TRLFS value of 9. On the other hand, the average first shell hydration numbers obtained in the QM/MM-PBEO and CMD simulations was 9, which agrees with experiment. All the simulations predicted an average first shell and second shell Cm-O bond distance of 2.49-2.53 Å and 4.67-4.75 Å respectively, both of which are in fair agreement with corresponding experimental values of 2.45-2.48 and 4.65 Å. The geometric arrangement of the 8-fold and 9-fold coordinated first shell structures corresponded to the square antiprism and tricapped trigonal prisms, respectively. The second shell hydration number for AIMD QM/MM-PBE, QM/MM-PBEO, CMD-3B, and CMD-LJ, were 15.8, 17.2, 17.7, 17.4, and 16.4 respectively, which indicates second hydration shell overcoordination compared to a recent EXAFS experimental value of 13. Save the EXAFS spectra CMD-LJ simulation, all the computed EXAFS spectra agree fairly well with experiment and a clear distinction could not be made between configurations with 8-fold and 9-fold coordinated first shells. The mechanisms responsible for the first shell associative and dissociative ligand exchange in the classical simulations have been analyzed. The first shell mean residence time was predicted to be on the nanosecond time scale. The computed diffusion constants of Cm3+ and water are in good agreement with experimental data. [ABSTRACT FROM AUTHOR]

Abstract: Density functional and correlated molecular orbital calculations (MP2) are carried out on B(OH)3·nH2O clusters (n =0, 6, 32), and ·nH2O (n =0, 8, 11, 32) to estimate the equilibrium distribution of 10B and 11B isotopes between boric acid and borate in aqueous solution. For the large 32-water clusters, multiple conformations are generated from ab initio molecular dynamics simulations to account for the effect of solvent fluctuations on the isotopic fractionation. We provide an extrapolated value of the equilibrium constant α 34 for the isotope exchange reaction 10B(OH)3(aq)+ (aq)= 11B(OH)3(aq)+ (aq) of 1.026–1.028 near the MP2 complete basis set limit with 32 explicit waters of solvation. With some exchange-correlation functionals we find potentially important contributions from a tetrahedral neutral B(OH)3·H2O Lewis acid–base complex. The extrapolations presented here suggest that DFT calculations give a value for 103lnα 34 about 15% higher than the MP2 calculations. [Copyright &y& Elsevier]

Many different degradation reactions of chlorinated hydrocarbons are possible in natural groundwaters. 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 are 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 [ABSTRACT FROM AUTHOR]

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 solving the root finding problem is tested. We demonstrate that more efficient dynamical models based on simplified interactions or coarsening time-steps provide preconditioners for the root finding problem. However, for MD and AIMD simulations, such preconditioners are not required to obtain reasonable convergence and their cost must be considered in the performance of the algorithm. The parallel in time algorithms developed are tested by applying them to MD and AIMD simulations of size and complexity similar to those encountered in present day applications. These include a 1000 Si atom MD simulation using Stillinger-Weber potentials, and a HCl + 4H2O AIMD simulation at the MP2 level. The maximum speedup (serial execution timeparallel execution time) obtained by parallelizing the Stillinger-Weber MD simulation was nearly 3.0. For the AIMD MP2 simulations, the algorithms achieved speedups of up to 14.3. The parallel in time algorithms can be implemented in a distributed computing environment using very slow transmission control protocol/Internet protocol networks. Scripts written in Python that make calls to a precompiled quantum chemistry package (NWChem) are demonstrated to provide an actual speedup of 8.2 for a 2.5 ps AIMD simulation of HCl + 4H2O at the MP2/6-31G* level. Implemented in this way these algorithms can be used for long time high-level AIMD simulations at a modest cost using machines connected by very slow networks such as WiFi, or in different time zones connected by the Internet. The algorithms can also be used with programs that are already parallel. Using these algorithms, we are able to reduce the cost of a MP2/6-311++G(2d,2p) simulation that had reached its maximum possible speedup in the parallelization of the electronic structure calculation from 32 s/time step to 6.9 s/time step. [ABSTRACT FROM AUTHOR]

The article focuses on the study about the ab initio calculation of isotopic fractionation in B(OH)3(aq) and BOH4-(aq). Intricately, researchers take a new approach to estimating alpha34 for aqueous species using ab nitio molecular dynamics (AIMD). They then conclude that the AIMD method allows an important connection to be made between the measured anharmonic vibrational spectrum and the measured fractionation factor.

The Car--Parrinello-based molecular dynamics (CPMD) method was used to investigate the ion-pairing behavior between Cl⁻ and Al3+ ions in an aqueous A1Cl³ solution containing 63 water molecules. A series of constrained simulations was carried out at 300 K for up to 16 ps each, with the internuclear separation (rAl-Cl) between the Al3+ ion and one of the Cl⁻ ions held constant. The calculated potential of mean force (PMF) of the Al3+--Cl⁻ ion pair shows a global minimum at rAl-Cl = 2.3 A corresponding to a contact ion pair (CIP). Two local minima assigned to solvent-separated ion pairs (SSIPs) are identified at rAl-Cl = 4.4 and 6.0 A. The positions of the free energy minima coincide with the hydration-sheD intervals of the Al3+ cation, suggesting that the Cl⁻ ion is inclined to reside in regions with low concentrations of water molecules, that is, between the first and second hydration shells of Al3+ and between the second shell and the bulk. A detailed analysis of the solvent structure around the Al3+ and Cl⁻ ions as a function of rAl-Cl is presented. The results are compared to structural data from X-ray measurements and unconstrained CPMD simulations of single Al3+ and Cl⁻ ions and A1Cl³ solutions. The dipole moments of the water molecules in the first and second hydration shells of Al3+ and in the bulk region and those of Cl⁻ ions were calculated as a function of rAl-Cl. Major changes in the electronic structure of the system were found to result from the removal of Cl⁻ from the first hydration shell of the Al3+ cation. Finally, two unconstrained CPMD simulations of aqueous A1Cl³ solutions corresponding to CIP and SS1P configurations were performed (17 ps, 300 K). Only minor structural changes were observed in these systems, confirming their stability. [ABSTRACT FROM AUTHOR]

Ab initio molecular dynamics simulations at 300 K, based on density functional theory, are performed to study the hydration shell geometries, solvent dipole, and first hydrolysis reaction of the uranium(IV) (U4+) and uranyl(V) (UO2+) ions in aqueous solution. The solvent dipole and first hydrolysis reaction of aqueous uranyl(VI) (UO22+) are also probed. The first shell of U4+ is coordinated by 8-9 water ligands, with an average U-O distance of 2.42 Å. The average first shell coordination number and distance are in agreement with experimental estimates of 8-11 and 2.40-2.44 Å, respectively. The simulated EXAFS of U4+ matches well with recent experimental data. The first shell of UO2+ is coordinated by five water ligands in the equatorial plane, with the average U═Oax and U-O distances being 1.85 Å and 2.54 Å, respectively. Overall, the hydration shell structure of UO2+ closely matches that of UO22+, except for small expansions in the average U═Oax and U-O distances. Each ion strongly polarizes their respective first-shell water ligands. The computed acidity constants (pKa) of U4+ and UO22+ are 0.93 and 4.95, in good agreement with the experimental values of 0.54 and 5.24, respectively. The predicted pKa value of UO2+ is 8.5. [ABSTRACT FROM AUTHOR]

This paper reports molecular dynamics simulations of the magnetite (001)-water interface, both in pure water and in the presence of a 2.3 molal solution of NaClO4. The simulations are carried out using a potential model designed to allow the protonation states of the surface functional groups to evolve dynamically through the molecular dynamics trajectory. The primary structural quantities investigated are the populations of the surface functional groups, the distribution of electrolyte in the solution, and the surface hydrogen bonding relationships. The surface protonation states are dominated by extensive hydrolysis of interfacial water molecules, giving rise to a dipolar surface dominated by FeOH2+-OH2-OH− arrangements. Triply coordinated, more deeply buried, surface sites are inert, probably due to the relative lack of solvent in their vicinity. The electrolyte distribution is oscillatory, arranging preferentially in layers defined by the solvating water molecules. The presence of electrolyte has a negligible effect on the protonation states of the surface functional groups. Steady-state behavior is obtained for the protonation states of the surface functional groups and hydrogen-bonding network. Although the overall structure of the electrolyte distribution is fairly well established, the electrolyte distribution has not fully equilibrated, as evidenced by the asymmetry in the distribution from the top to the bottom of the slab. [Copyright &y& Elsevier]

The characterization of trace elements in minerals using extended X-ray absorption fine structure (EXAFS) spectroscopy constitutes a first step toward understanding how impurities and contaminants interact with the host phase and the environment. However, limitations to EXAFS interpretation complicate the analysis of trace concentrations of impurities that are distributed across multiple phases in a heterogeneous system. Ab initio molecular dynamics (AIMD)-informed EXAFS analysis was employed to investigate the immobilization of trace uranium associated with nanophase iron (oxyhydr)oxides, a model system for the geochemical sequestration of radiotoxic actinides. The reductive transformation of ferrihydrite [Fe(OH)3] to nanoparticulate iron oxyhydroxide minerals in the presence of uranyl (UO2)2+(aq) resulted in the preferential incorporation of U into goethite (α-FeOOH) over lepidocrocite (γ-FeOOH), even though reaction conditions favored the formation of excess lepidocrocite. This unexpected result is supported by atomically resolved transmission electron microscopy. We demonstrate how AIMD-informed EXAFS analysis lifts the strict statistical limitations and uncertainty of traditional shell-by-shell EXAFS fitting, enabling the detailed characterization of the local bonding environment, charge compensation mechanisms, and oxidation states of polyvalent impurities in complex multiphase mineral systems. [ABSTRACT FROM AUTHOR]

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 control 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. However, we also show how our method for pK a prediction could be improved using ab initio molecular dynamics simulations of solvated surfaces. [Copyright &y& Elsevier]