Periodic density functional theory calculations of bulk and the (010) surface of goethite

<p>Abstract</p> <p>Background</p> <p>Goethite is a common and reactive mineral in the environment. The transport of contaminants and anaerobic respiration of microbes are significantly affected by adsorption and reduction reactions involving goethite. An understanding of the mineral-water interface of goethite is critical for determining the molecular-scale mechanisms of adsorption and reduction reactions. In this study, periodic density functional theory (DFT) calculations were performed on the mineral goethite and its (010) surface, using the Vienna <it>Ab Initio </it>Simulation Package (VASP).</p> <p>Results</p> <p>Calculations of the bulk mineral structure accurately reproduced the observed crystal structure and vibrational frequencies, suggesting that this computational methodology was suitable for modeling the goethite-water interface. Energy-minimized structures of bare, hydrated (one H₂O layer) and solvated (three H₂O layers) (010) surfaces were calculated for 1 × 1 and 3 × 3 unit cell slabs. A good correlation between the calculated and observed vibrational frequencies was found for the 1 × 1 solvated surface. However, differences between the 1 × 1 and 3 × 3 slab calculations indicated that larger models may be necessary to simulate the relaxation of water at the interface. Comparison of two hydrated surfaces with molecularly and dissociatively adsorbed H₂O showed a significantly lower potential energy for the former.</p> <p>Conclusion</p> <p>Surface Fe-O and (Fe)O-H bond lengths are reported that may be useful in surface complexation models (SCM) of the goethite (010) surface. These bond lengths were found to change significantly as a function of solvation (i.e., addition of two extra H₂O layers above the surface), indicating that this parameter should be carefully considered in future SCM studies of metal oxide-water interfaces.</p

Transferable Reactive Force Fields: Extensions of ReaxFF-<i>lg</i> to Nitromethane

Transferable ReaxFF-<i>lg</i> models of nitromethane that predict a variety of material properties over a wide range of thermodynamic states are obtained by screening a library of ∼6600 potentials that were previously optimized through the Multiple Objective Evolutionary Strategies (MOES) approach using a training set that included information for other energetic materials composed of carbon, hydrogen, nitrogen, and oxygen. Models that best match experimental nitromethane lattice constants at 4.2 K and 1 atm are evaluated for transferability to high-pressure states at room temperature and are shown to better predict various liquid- and solid-phase structural, thermodynamic, and transport properties as compared to the existing ReaxFF and ReaxFF-<i>lg</i> parametrizations. Although demonstrated for an energetic material, the library of ReaxFF-<i>lg</i> models is supplied to the scientific community to enable new research explorations of complex reactive phenomena in a variety of materials research applications

Transferable Reactive Force Fields: Extensions of ReaxFF-<i>lg</i> to Nitromethane

Transferable ReaxFF-<i>lg</i> models of nitromethane that predict a variety of material properties over a wide range of thermodynamic states are obtained by screening a library of ∼6600 potentials that were previously optimized through the Multiple Objective Evolutionary Strategies (MOES) approach using a training set that included information for other energetic materials composed of carbon, hydrogen, nitrogen, and oxygen. Models that best match experimental nitromethane lattice constants at 4.2 K and 1 atm are evaluated for transferability to high-pressure states at room temperature and are shown to better predict various liquid- and solid-phase structural, thermodynamic, and transport properties as compared to the existing ReaxFF and ReaxFF-<i>lg</i> parametrizations. Although demonstrated for an energetic material, the library of ReaxFF-<i>lg</i> models is supplied to the scientific community to enable new research explorations of complex reactive phenomena in a variety of materials research applications

Coarse-grain modelling using an equation-of-state many-body potential: application to fluid mixtures at high temperature and high pressure

<p>A many-body, coarse-grain model, termed the product gas mixture model, is presented that accurately describes the thermodynamic behaviour of molecular mixtures. The coarse-grain model is developed by first approximating the mixture as a van der Waals one-fluid, and subsequently applying an exponential-6 equation-of-state to describe the forces and energies between particles in the spirit of the many-body model pioneered by Pagonabarraga and Frenkel. Isothermal dissipative particle dynamics simulations are carried out at thermochemical states that occur during decomposition of a prototypical energetic material, RDX (1,3,5-trinitro-1,3,5-triazinane). The product gas mixture model performance is assessed by comparing to an explicit-molecule model and a hard-core coarse-grain model based on the exponential-6 pair potential. Overall, the many-body, coarse-grain model is shown to accurately capture the structural and thermodynamic properties for the wide variety of thermochemical states considered, while the hard-core coarse-grain model cannot. The many-body, coarse-grain model overcomes the issues of transferability, scaling consistency and unphysical ordered phase behaviour that often afflict coarse-grain models. While specific thermochemical conditions related to RDX decomposition are considered, the results are generally applicable to the thermodynamic behaviour of other fluid mixtures at both moderate and extreme conditions.</p

Aqueous divalent metal-nitrate interactions: hydration versus ion pairing.

Nitrate aqueous solutions, Mg(NO(3))(2), Ca(NO(3))(2), Sr(NO(3))(2), and Pb(NO(3))(2), are investigated using Raman spectroscopy and free energy profiles from molecular dynamics (MD) simulations. Analysis of the in-plane deformation, symmetric stretch, and asymmetric stretch vibrational modes of the nitrate ions reveal perturbation caused by the metal cations and hydrating water molecules. Results show that Pb(2+) has a strong tendency to form contact ion pairs with nitrate relative to Sr(2+), Ca(2+), and Mg(2+), and contact ion pair formation decreases with decreasing cation size and increasing cation charge density: Pb(2+) \u3e Sr(2+) \u3e Ca(2+) \u3e Mg(2+). In the case of Mg(2+), the Mg(2+)-OH(2) intermolecular modes indicate strong hydration by water molecules and no contact ion pairing with nitrate. Free energy profiles provide evidence for the experimentally observed trend and clarification between solvent-separated, solvent-shared, and contact ion pairs, particularly for Mg(2+) relative to other cations

Maximum Entropy Theory of Multiscale Coarse-Graining via Matching Thermodynamic Forces: Application to a Molecular Crystal (TATB)

The MSCG/FM (multiscale coarse-graining via force-matching) approach is an efficient supervised machine learning method to develop microscopically informed coarse-grained (CG) models. We present a theory based on the principle of maximum entropy (PME) enveloping the existing MSCG/FM approaches. This theory views the MSCG/FM method as a special case of matching the thermodynamic forces from the extended ensemble described by the set of thermodynamic (relevant) system coordinates. This set may include CG coordinates, the stress tensor, applied external fields, and so forth, and may be characterized by nonequilibrium conditions. Following the presentation of the theory, we discuss the consistent matching of both bonded and nonbonded interactions. The proposed PME formulation is used as a starting point to extend the MSCG/FM method to the constant strain ensemble, which together with the explicit matching of the bonded forces is better suited for coarse-graining anisotropic media at a submolecular resolution. The theory is demonstrated by performing the fine coarse-graining of crystalline 1,3,5-triamino-2,4,6-trinitrobenzene (TATB), a well-known insensitive molecular energetic material, which exhibits highly anisotropic mechanical properties

Maximum Entropy Theory of Multiscale Coarse-Graining via Matching Thermodynamic Forces: Application to a Molecular Crystal (TATB)

The MSCG/FM (multiscale coarse-graining via force-matching) approach is an efficient supervised machine learning method to develop microscopically informed coarse-grained (CG) models. We present a theory based on the principle of maximum entropy (PME) enveloping the existing MSCG/FM approaches. This theory views the MSCG/FM method as a special case of matching the thermodynamic forces from the extended ensemble described by the set of thermodynamic (relevant) system coordinates. This set may include CG coordinates, the stress tensor, applied external fields, and so forth, and may be characterized by nonequilibrium conditions. Following the presentation of the theory, we discuss the consistent matching of both bonded and nonbonded interactions. The proposed PME formulation is used as a starting point to extend the MSCG/FM method to the constant strain ensemble, which together with the explicit matching of the bonded forces is better suited for coarse-graining anisotropic media at a submolecular resolution. The theory is demonstrated by performing the fine coarse-graining of crystalline 1,3,5-triamino-2,4,6-trinitrobenzene (TATB), a well-known insensitive molecular energetic material, which exhibits highly anisotropic mechanical properties

Generalized Energy-Conserving Dissipative Particle Dynamics with Mass Transfer. Part 2: Applications and Demonstrations

We present the second part of a two-part paper series intended to address a gap in computational capability for coarse-grain particle modeling and simulation, namely, the simulation of phenomena in which diffusion via mass transfer is a contributing mechanism. In part 1, we presented a formulation of a dissipative particle dynamics method to simulate interparticle mass transfer, termed generalized energy-conserving dissipative particle dynamics with mass transfer (GenDPDE-M). In the GenDPDE-M method, the mass of each mesoparticle remains constant following the interparticle mass exchange. In part 2 of this series, further verification and demonstrations of the GenDPDE-M method are presented for mesoparticles with embedded binary mixtures using the ideal gas (IG) and van der Waals (vdW) equation-of-state (EoS). The targeted readership of part 2 is toward practitioners, where applications and practical considerations for implementing the GenDPDE-M method are presented and discussed, including a numerical discretisztion algorithm for the equations-of-motion. The GenDPDE-M method is verified by reproducing the particle distributions predicted by Monte Carlo simulations for the IG and vdW fluids, along with several demonstrations under both equilibrium and non-equilibrium conditions. GenDPDE-M can be generally applied to multi-component mixtures and to other fundamental EoS, such as the Lennard-Jones or Exponential-6 models, as well as to more advanced EoS models such as Statistical Associating Fluid Theory

Parameterizing Complex Reactive Force Fields Using Multiple Objective Evolutionary Strategies (MOES): Part 2: Transferability of ReaxFF Models to C–H–N–O Energetic Materials

The Multiple Objective Evolutionary Strategies (MOES) algorithm was used to parametrize force fields having the form of the reactive models ReaxFF (van Duin, A. C. T.; Dasgupta, S.; Lorant, F.; Goddard, W. A. <i>J. Phys. Chem. A</i> <b>2001</b>, <i>105</i>, 9396) and ReaxFF-<i>lg</i> (Liu, L.; Liu, Y.; Zybin, S. V.; Sun, H.; Goddard, W. A. <i>J. Phys. Chem. A</i> <b>2011</b>, <i>115</i>, 11016) in an attempt to produce equal or superior ambient state crystallographic structural results for cyclotrimethylene trinitramine (RDX). Promising candidates were then subjected to molecular dynamics simulations of five other well-known conventional energetic materials to assess the degree of transferability of the models. Two models generated through the MOES search were shown to have performance better than or as good as ReaxFF-<i>lg</i> in describing the six energetic systems modeled. This study shows that MOES is an effective and efficient method to develop complex force fields