Understanding the adsorption of isolated metal cations from water on to mineral surfaces is critical for toxic waste retention and cleanup in the environment. Heterogeneous nucleation of metal oxyhydroxides and other minerals on material surfaces is key to crystal growth and dissolution. The link connecting these two areas, namely cation dimerization and polymerization, is far less understood. In this work we apply ab initio molecular dynamics calculations to examine the coordination structure of hydroxide-bridged Cu(II) dimers, and the free energy changes associated with Cu(II) dimerization on silica surfaces. The dimer dissociation pathway involves sequential breaking of two Cu2+-OH− bonds, yielding three local minima in the free energy profiles associated with 0-2 OH− bridges between the metal cations, and requires the design of a (to our knowledge) novel reaction coordinate for the simulations. Cu(II) adsorbed on silica surfaces are found to exhibit stronger tendency towards dimerization than when residing in water. Cluster-plus-implicit-solvent methods yield incorrect trends if OH− hydration is not correctly depicted. The predicted free energy landscapes are consistent with fast equilibrium times (seconds) among adsorbed structures, and favor Cu2+ dimer formation on silica surfaces over monomer adsorption.
Tracer gases, whether they are chemical or isotopic in nature, are useful tools in examining the flow and transport of gaseous or volatile species in the underground. One application is using detection of short-lived argon and xenon radionuclides to monitor for underground nuclear explosions. However, even chemically inert species, such as the noble gases, have bene observed to exhibit non-conservative behavior when flowing through porous media containing certain materials, such as zeolites, due to gas adsorption processes. This report details the model developed, implemented, and tested in the open source and massively parallel subsurface flow and transport simulator PFLOTRAN for future use in modeling the transport of adsorbing tracer gases.
The structural and dynamical properties of nanoconfined solutions can differ dramatically from those of the corresponding bulk systems. Understanding the changes induced by confinement is central to controlling the behavior of synthetic nanostructured materials and predicting the characteristics of biological and geochemical systems. A key outstanding issue is how the molecular-level behavior of nanoconfined electrolyte solutions is reflected in different experimental, particularly spectroscopic, measurements. This is addressed here through molecular dynamics simulations of the OH stretching infrared (IR) spectroscopy of NaCl, NaBr, and NaI solutions in isotopically dilute HOD/D 2 O confined in hydroxylated amorphous silica slit pores of width 1–6 nm and pH [Formula: see text]. In addition, the water reorientation dynamics and spectral diffusion, accessible by pump–probe anisotropy and two-dimensional IR measurements, are investigated. The aim is to elucidate the effect of salt identity, confinement, and salt concentration on the vibrational spectra. It is found that the IR spectra of the electrolyte solutions are only modestly blue-shifted upon confinement in amorphous silica slit pores, with both the size of the shift and linewidth increasing with the halide size, but these effects are suppressed as the salt concentration is increased. This indicates the limitations of linear IR spectroscopy as a probe of confined water. However, the OH reorientational and spectral diffusion dynamics are significantly slowed by confinement even at the lowest concentrations. The retardation of the dynamics eases with increasing salt concentration and pore width, but it exhibits a more complex behavior as a function of halide.
Structural properties of the anionic surfactant dioctyl sodium sulfosuccinate (AOT or Aerosol-OT) adsorbed on the mica surface were investigated by molecular dynamics simulation, including the effect of surface loading in the presence of monovalent and divalent cations. The simulations confirmed recent neutron reflectivity experiments that revealed the binding of anionic surfactant to the negatively charged surface via adsorbed cations. At low loading, cylindrical micelles formed on the surface, with sulfate head groups bound to the surface by water molecules or adsorbed cations. Cation bridging was observed in the presence of weakly hydrating monovalent cations, while sulfate groups interacted with strongly hydrating divalent cations through water bridges. The adsorbed micelle structure was confirmed experimentally with cryogenic electronic microscopy, which revealed micelles approximately 2 nm in diameter at the basal surface. At higher AOT loading, the simulations reveal adsorbed bilayers with similar surface binding mechanisms. Adsorbed micelles were slightly thicker (2.2–3.0 nm) than the corresponding bilayers (2.0–2.4 nm). Upon heating the low loading systems from 300 K to 350 K, the adsorbed micelles transformed to a more planar configuration resembling bilayers. The driving force for this transition is an increase in the number of sulfate head groups interacting directly with adsorbed cations.
The ability to predict transport properties of liquids quickly and accurately will greatly improve our understanding of fluid properties both in bulk and complex mixtures, as well as in confined environments. Such information could then be used in the design of materials and processes for applications ranging from energy production and storage to manufacturing processes. As a first step, we consider the use of machine learning (ML) methods to predict the diffusion properties of pure liquids. Recent results have shown that Artificial Neural Networks (ANNs) can effectively predict the diffusion of pure compounds based on the use of experimental properties as the model inputs. In the current study, a similar ANN approach is applied to modeling diffusion of pure liquids using fluid properties obtained exclusively from molecular simulations. A diverse set of 102 pure liquids is considered, ranging from small polar molecules (e.g., water) to large nonpolar molecules (e.g., octane). Self-diffusion coefficients were obtained from classical molecular dynamics (MD) simulations. Since nearly all the molecules are organic compounds, a general set of force field parameters for organic molecules was used. The MD methods are validated by comparing physical and thermodynamic properties with experiment. Computational input features for the ANN include physical properties obtained from the MD simulations as well as molecular properties from quantum calculations of individual molecules. Fluid properties describing the local liquid structure were obtained from center of mass radial distribution functions (COM-RDFs). Feature sensitivity analysis revealed that isothermal compressibility, heat of vaporization, and the thermal expansion coefficient were the most impactful properties used as input for the ANN model to predict the MD simulated self-diffusion coefficients. The MD-based ANN successfully predicts the MD self-diffusion coefficients with only a subset (2 to 3) of the available computationally determined input features required. A separate ANN model was developed using literature experimental self-diffusion coefficients as model targets. Although this second ML model was not as successful due to a limited number of data points, a good correlation is still observed between experimental and ML predicted self-diffusion coefficients.
Predicting the diffusion coefficient of fluids under nanoconfinement is important for many applications including the extraction of shale gas from kerogen and product turnover in porous catalysts. Due to the large number of important variables, including pore shape and size, fluid temperature and density, and the fluid-wall interaction strength, simulating diffusion coefficients using molecular dynamics (MD) in a systematic study could prove to be prohibitively expensive. Here, we use machine learning models trained on a subset of MD data to predict the self-diffusion coefficients of Lennard-Jones fluids in pores. Our MD data set contains 2280 simulations of ideal slit pore, cylindrical pore, and hexagonal pore geometries. We use the forward feature selection method to determine the most useful features (i.e., descriptors) for developing an artificial neutral network (ANN) model with an emphasis on easily acquired features. Our model shows good predictive ability with a coefficient of determination (i.e., R2) of ∼0.99 and a mean squared error of ∼2.9 × 10-5. Finally, we propose an alteration to our feature set that will allow the ANN model to be applied to nonideal pore geometries.
The objective of this project was to eliminate and/or render bulk agent unusable by a threat entity via neutralization and/or polymerization of the bulk agent using minimal quantities of additives. We proposed the in situ neutralization and polymerization of bulk chemical agents (CAs) by performing reactions in the existing CA storage container via wet chemical approaches using minimal quantities of chemical based materials. This approach does not require sophisticated equipment, fuel to power generators, electricity to power equipment, or large quantities of decontaminating materials. By utilizing the CA storage container as the batch reactor, the amount of logistical resources can be significantly reduced. Fewer personnel are required since no sophisticated equipment needs to be set up, configured, or operated. Employing the CA storage container as the batch reactor enables the capability to add materials to multiple containers in a short period of time as opposed to processing one container at a time for typical batch reactor approaches. In scenarios where a quick response is required, the material can be added to all the CA containers and left to react on its own without intervention. Any attempt to filter the CA plus material solution will increase the rate of reaction due to increased agitation of the solution.
As a general-purpose force field for molecular simulations of layered materials and their fluid interfaces, Clayff continues to see broad usage in atomistic computational modeling for numerous geoscience and materials science applications due to its (1) success in predicting properties of bulk nanoporous materials and their interfaces, (2) transferability to a range of layered and nanoporous materials, and (3) simple functional form which facilitates incorporation into a variety of simulation codes. Here, we review applications of Clayff to model bulk phases and interfaces not included in the original parameter set and recent modifications for modeling surface terminations such as hydroxylated nanoparticle edges. We conclude with a discussion of expectations for future developments.
We present a combined molecular dynamics (MD) simulation and X-ray absorption fine structure (XAFS) spectroscopic investigation of aqueous iron adsorption on nanoconfined amorphous silica surfaces. The simulation models examine the effects of pore size, pH (surface charge), iron valency, and counter-ion (chloride or hydroxide). The simulation methods were validated by comparing the coordination environment of adsorbed iron with coordination numbers and bond lengths derived from XAFS. In the MD models, nanoconfinement effects on local iron coordination were investigated by comparing results for unconfined silica surfaces and in confined domains within 2 nm, 4 nm, and 8 nm pores. Experimentally, coordination environments of iron adsorbed onto mesoporous silica with 4 nm and 8 nm pores at pH 7.5 were investigated. The effect of pH in the MD models was included by simulating Fe(ii) adsorption onto negatively charged SiO2surfaces and Fe(iii) adsorption on neutral surfaces. The simulation results show that iron adsorption depends significantly on silica surface charge, as expected based on electrostatic interactions. Adsorption on a negatively charged surface is an order of magnitude greater than on the neutral surface, and simulated surface coverages are consistent with experimental results. Pore size effects from the MD simulations were most notable in the adsorption of Fe(ii) at deprotonated surface sites (SiO−), but adsorption trends varied with concentration and aqueous Fe speciation. The coordination environment of adsorbed iron varied significantly with the type of anion. Considerable ion pairing with hydroxide anions led to the formation of oligomeric surface complexes and aqueous species, resulting in larger iron hydroxide clusters at higher surface loadings.
Water in nano-scale confining environments is a key element in many biological, material, and geological systems. The structure and dynamics of the liquid can be dramatically modified under these conditions. Probing these changes can be challenging, but vibrational spectroscopy has emerged as a powerful tool for investigating their behavior. A critical, evolving component of this approachis a detailed understanding of the connection between spectroscopic features and molecular-level details. In this paper, this issue is addressed by using molecular dynamics simulations to simulate the linear infrared (IR) and Raman spectra for isotopically dilute HOD in D2O confined inhydroxylated amorphous silica slit pores. The effect of slit-pore width and hydroxyl density on thesilica surface on the vibrational spectra is also investigated. The primary effect of confinement is a blueshift in the frequency of OH groups donating a hydrogen bond to the silica surface. Thisappears as a slight shift in the total (measurable) spectra but is clearly seen in the distance-based IR and Raman spectra. Analysis indicates that these changes upon confinement are associated withtheweaker hydrogen-bond accepting properties of silica oxygens compared to water molecules.
González, Rafael I.; Rojas-Nunez, Javier; Valencia, Felipe J.; Munoz, Francisco; Baltazar, Samuel E.; Allende, Sebastián; Rogan, José; Valdivia, Juan A.; Kiwi, Miguel; Ramírez, Ricardo; Greathouse, Jeffery A.
Imogolite is a fascinating inorganic nanotube that is found in nature or synthesized in a laboratory. The synthesis process is carried out in liquid media, and leads to the formation of almost monodisperse diameter nanotubes. Here we investigate, employing classical molecular dynamics simulations, the interaction of water and imogolite for nanotubes of several radii. We established that water penetrates the pores of N = 9 and larger nanotubes, and adopts a coaxial arrangement in it. Also, while water molecules can diffuse along the center of the nanotube, the molecules next to the inner imogolite walls have very low mobility. At the outer nanotube wall, an increase of water density is observed, this effect extends up to 1 nm, beyond which water properties are bulk-like. Both phenomena are affected by the imogolite curvature.
Classical molecular dynamics (MD) simulations were performed to provide a conceptual understanding of the amorphous-crystalline interface for a candidate negative thermal expansion (NTE) material, ZrW2O8. Simulations of pressure-induced amorphization at 300 K indicate that an amorphous phase forms at pressures of 10 GPa and greater, and this phase persists when the pressure is subsequently decreased to 1 bar. However, the crystalline phase is recovered when the slightly distorted 5 GPa phase is relaxed to 1 bar. Simulations were also performed on a two-phase model consisting of the high-pressure amorphous phase in direct contact with the crystalline phase. Upon equilibration at 300 K and 1 bar, the crystalline phase remains unchanged beyond a thin layer of disrupted structure at the crystalline-amorphous interface. Differences in local atomic structure at the interface are quantified from the simulation trajectories.
Here we report molecular level details regarding the adsorption of sarin (GB) gas in a prototypical zirconium-based metal-organic framework (MOF, UiO-66). By combining predictive modeling and experimental spectroscopic techniques, we unambiguously identify several unique bindings sites within the MOF, using the P=O stretch frequency of GB as a probe. Remarkable agreement between predicted and experimental IR spectrum is demonstrated. As previously hypothesized, the undercoordinated Lewis acid metal site is the most favorable binding site. Yet multiple sites participate in the adsorption process; specifically, the Zr-chelated hydroxyl groups form hydrogen bonds with the GB molecule, and GB weakly interacts with fully coordinated metals. Importantly, this work highlights that subtle orientational effects of bound GB are observable via shifts in characteristic vibrational modes; this finding has large implications for degradation rates and opens a new route for future materials design.
This report describes the potential of a novel class of materials--a-ZrW 2 0 8 , Zr 2 WP 2 0 12 , and related compounds that contract upon amorphization as possible radionuclide waste-forms. The proposed ceramic waste-forms would consist of zoned grains, or sintered ceramics with center- loaded radionuclides and barren shells. Radiation-induced amorphization would result in core shrinkage but would not fracture the shells or overgrowths, maintaining isolation of the radionuclide. In this report, we have described synthesis techniques to produce phase-pure forms of the materials, and how to fully densify those materials. Structural models for the materials were developed and validated using DFPT approaches, and radionuclide substitution was evaluated; U(IV), Pu(IV), Tc(IV) and Tc(VII) all readily substitute into the material structures. MD modeling indicated that strain associated with radiation-induced amorphization would not affect the integrity of surrounding crystalline materials, and these results were validated via ion beam experimental studies. Finally, we have evaluated the leach rates of the barren materials, as determined by batch and flow-through reactor experiments. ZrW 2 0 8 leaches rapidly, releasing tungstate while Zr is retained as a solid oxide or hydroxide. Tungsten release rates remain elevated over time and are highly sensitive to contact times, suggesting that this material will not be an effective waste-form. Conversely, tungsten releases rates from Zr2WP2012 rapidly drop, show little dependence on short-term changes in fluid contact time, and in over time, become tied to P release rates. The results presented here suggest that this material may be a viable waste-form for some hard-to-handle radionuclides such as Pu and Tc. ACKNOWLEDGEMENTS The authors acknowledge the contributions to this report from Sandia National Laboratories researchers Steven Meserole, Mark Rodriguez, Clay Payne, Tim Boyle, Nate Padilla, Khalid Hattar, Anthony Monterrosa, Trevor Clark, and Daniel Perry.
A molecular-scale understanding of the transition between hydration states in clay minerals remains a challenging problem because of the very fast stepwise swelling process observed from X-ray diffraction (XRD) experiments. XRD profile modeling assumes the coexistence of multiple hydration states in a clay sample to fit the experimental XRD pattern obtained under humid conditions. While XRD profile modeling provides a macroscopic understanding of the heterogeneous hydration structure of clay minerals, a microscopic model of the transition between hydration states is still missing. Here, for the first time, we use molecular dynamics simulation to investigate the transition states between a dry interlayer, one-layer hydrate, and two-layer hydrate. We find that the hydrogen bonds that form across the interlayer at the clay particle edge make an important contribution to the energy barrier to interlayer hydration, especially for initial hydration.
The phonon, infrared, and Raman spectroscopic properties of zirconium tungsten phosphate, Zr2(WO4)(PO4)2 (space group Pbcn, IT No. 60; Z = 4), have been extensively investigated using density functional perturbation theory (DFPT) calculations with the Perdew, Burke, and Ernzerhof exchange-correlation functional revised for solids (PBEsol) and validated by experimental characterization of Zr2(WO4)(PO4)2 prepared by hydrothermal synthesis. Using DFPT-simulated infrared, Raman, and phonon density-of-state spectra combined with Fourier transform infrared and Raman measurements, new comprehensive and extensive assignments have been made for the spectra of Zr2(WO4)(PO4)2, resulting in the characterization of its 29 and 34 most intense IR- and Raman-active modes, respectively. DFPT results also reveal that ν1(PO4) symmetric stretching and ν3(PO4) antisymmetric stretching bands have been interchanged in previous Raman experimental assignments. Negative thermal expansion in Zr2(WO4)(PO4)2 appears to have very limited impact on the spectral properties of this compound. This work shows the high accuracy of the PBEsol exchange-correlation functional for studying the spectroscopic properties of crystalline materials using first-principles methods.
Toward the development of classical force fields for the accurate modeling of clay mineral-water systems, we have extended the use of metal-O-H (M-O-H) angle bending terms to describe surface Si-O-H bending for hydrated kaolinite edge structures. Kaolinite, comprising linked octahedral Al and tetrahedral Si sheets, provides a rigorous test by combining aluminol and silanol groups with water molecules in hydrated edge structures. Periodic density functional theory and classical force fields were used with molecular dynamics to evaluate the structure, dynamics, hydrogen bonding, and power spectra for deriving optimum bending force constants and optimal equilibrium angles. Cleavage energies derived from density functional theory molecular dynamics calculations indicate the relative stabilities of both AC 1 and AC 2 edge terminations of kaolinite where Si-OH and Al-(OH 2 ) or Si-OH, Al-OH, and Al-(OH 2 ) groups exist, respectively. Although not examined in this study, the new Si-O-H angle bending parameter should allow for improved modeling of hydroxylated surfaces of silica minerals such as quartz and cristobalite, as well as amorphous silica-based surfaces and potentially those of other silicate and aluminosilicate phases.
Observation of vibrational properties of phyllosilicate edges via a combined molecular modeling and experimental approach was performed. Deuterium exchange was utilized to isolate edge vibrational modes from their internal counterparts. The appearance of a specific peak within the broader D2O band indicates the presence of deuteration on the edge surface, and this peak is confirmed with the simulated spectra. These results are the first to unambiguously identify spectroscopic features of phyllosilicate edge sites.
We use molecular simulations to provide a conceptual understanding of a crystalline-amorphous interface for a candidate negative thermal expansion (NTE) material. Specifically, classical molecular dynamics (MD) simulations were used to investigate the temperature and pressure dependence on structural properties of ZrW2O8. Polarizability of oxygen atoms was included to better account for the electronic charge distribution within the lattice. Constant-pressure simulations of cubic crystalline ZrW2O8 at ambient pressure reveal a slight NTE behavior, characterized by a small structural rearrangement resulting in oxygen sharing between adjacent WO4 tetrahedra. Periodic quantum calculations confirm that the MD-optimized structure is lower in energy than the idealized structure obtained from neutron diffraction experiments. Additionally, simulations of pressure-induced amorphization of ZrW2O8 at 300 K indicate that an amorphous phase forms at pressures greater than 10 GPa, and this phase persists when the pressure is decreased to 1 bar. Simulations were performed on a hybrid model consisting of amorphous ZrW2O8 in direct contact with the cubic crystalline phase. Upon equilibration at 300 K and 1 bar, the crystalline phase remains unchanged beyond a thin layer of disrupted structure at the amorphous interface. Detailed analysis reveals the transition in metal coordination at the interface.
Appropriate waste-forms for radioactive materials must isolate the radionuclides from the environment for long time periods. To accomplish this typically requires low waste-form solubility, to minimize radionuclide release to the environment. However, radiation eventually damages most waste-forms, leading to expansion, crumbling, increased exposed surface area, and faster dissolution. We have evaluated the use of a novel class of materials-ZrW2O8, Zr2P2WO12 and related compounds-that contract upon amorphization. The proposed ceramic waste-forms would consist of zoned grains, or sintered ceramics with center-loaded radionuclides and barren shells. Radiation-induced amorphization would result in core shrinkage but would not fracture the shells or overgrowths, maintaining isolation of the radionuclide. We have synthesized these phases and have evaluated their leach rates. Tungsten forms stable aqueous species at neutral to basic conditions, making it a reliable indicator of phase dissolution. ZrW2O8 leaches rapidly, releasing tungstate while Zr is retained as a solid oxide or hydroxide. Tungsten release rates remain elevated over time and are highly sensitive to contact times, suggesting that this material will not be an effective waste-form. Conversely, tungsten release rates from Zr2P2WO12 rapidly drop and are tied to P release rates; we speculate that a low-solubility protective Zr-phosphate leach layer forms, slowing further dissolution.
We have investigated cubic zirconium tungstate (ZrW2O8) using density functional perturbation theory (DFPT), along with experimental characterization to assess and validate computational results. Cubic zirconium tungstate is among the few known materials exhibiting isotropic negative thermal expansion (NTE) over a broad temperature range, including room temperature where it occurs metastably. Isotropic NTE materials are important for technological applications requiring thermal-expansion compensators in composites designed to have overall zero or adjustable thermal expansion. While cubic zirconium tungstate has attracted considerable attention experimentally, a very few computational studies have been dedicated to this well-known NTE material. Therefore, spectroscopic, mechanical and thermodynamic properties have been derived from DFPT calculations. A systematic comparison of the calculated infrared, Raman, and phonon density-of-state spectra has been made with Fourier transform far-/mid-infrared and Raman data collected in this study, as well as with available inelastic neutron scattering measurements. The thermal evolution of the lattice parameter computed within the quasi-harmonic approximation exhibits negative values below the Debye temperature, consistent with the observed negative thermal expansion characteristics of cubic zirconium tungstate, α-ZrW2O8. These results show that this DFPT approach can be used for studying the spectroscopic, mechanical and thermodynamic properties of prospective NTE ceramic waste forms for encapsulation of radionuclides produced during the nuclear fuel cycle.
The adsorption of chemical warfare agents and their simulants by Zr (UiO-66) and rare-earth (Y, UiO-66-DOBDC analog)-based metal-organic frameworks (MOFs) is explored here using density functional theory. In particular, we investigate the role of linker functional group (OH, H) and metal atom identity on the binding energies of organophosphorous compounds. Commonly used cluster approximations for MOF secondary building units and various optimization constraints are compared with three-dimensional periodic results. An in-depth scan of potential binding sites and orientations reveals little effect due to metal identity, whereas the effect of linker functionalization depends on the substrate. This finding strongly suggests that full linkers and functional groups should be included in cluster models. Importantly, defect sites show considerably improved binding of organophosphorous compounds as compared to ideal clusters. Favorable binding is also demonstrated at two additional adsorption sites, ZrOH and μ3-OH, that likely play a role in the initial adsorption process. The results presented here portray the importance of including full three-dimensional pore structures in the adsorption process of organophosphorous compounds in MOFs; a critical first step in the degradation of these harmful chemicals.
Nanoporous materials such as metal-organic frameworks (MOFs) have attractive properties for selective capture of chemical warfare agents (CWAs). For obvious reasons, most research on adsorption of CWAs is performed with simulant molecules rather than real agents. This paper examines how effectively common CWA simulants mimic the adsorption properties of sarin and soman. To this end, we perform molecular simulations in the dilute adsorption limit for four simulants [dimethyl methylphosphonate (DMMP), diethyl chlorophosphate (DCP), diisopropyl fluorophosphate, and dimethyl p-nitrophenyl phosphate (DMNP)] and sarin and soman in a set of 2969 MOFs with experimentally known crystal structures. To establish the robustness of the conclusions with respect to the force field used in these simulations, each system was examined with two independent force fields, a "generic" force field and a density functional theory (DFT)-derived force field we established based on extensive dispersion-corrected DFT calculations of adsorption in the well-known MOF UiO-66. Our results show that when judging the performance of adsorbents using the heat of adsorption, DCP and DMMP are the best simulants for the adsorption of sarin, while DMNP is the best simulant for soman. The adsorption properties of DCP or DMMP show a strong correlation with sarin over a range of MOFs, but the correlation between DMNP and soman is considerably weaker. Comparisons of results with both force fields indicate that our main conclusions are robust with respect to the force field used to define adsorbate-MOF interactions.
The adsorption equilibrium constants of monovalent and divalent cations to material surfaces in aqueous media are central to many technological, natural, and geochemical processes. Cation adsorption-desorption is often proposed to occur in concert with proton transfer on hydroxyl-covered mineral surfaces, but to date this cooperative effect has been inferred indirectly. This work applies density functional theory-based molecular dynamics simulations of explicit liquid water/mineral interfaces to calculate metal ion desorption free energies. Monodentate adsorption of Na+, Mg2+, and Cu2+ on partially deprotonated silica surfaces are considered. Na+ is predicted to be unbound, while Cu2+ exhibits binding free energies to surface SiO- groups that are larger than those of Mg2+. The predicted trends agree with competitive adsorption measurements on fumed silica surfaces. As desorption proceeds, Cu2+ dissociates one of the H2O molecules in its first solvation shell, turning into Cu2+(OH-)(H2O)3, while Mg remains Mg2+(H2O)6. The protonation state of the SiO- group at the initial binding site does not vary monotonically with cation desorption.
Cubic zirconium tungstate (α-ZrW2O8), a well-known negative thermal expansion material, has been investigated within the framework of density functional perturbation theory (DFPT), combined with experimental characterization to assess and validate computational results. Using combined Fourier transform infrared measurements and DFPT calculations, new and extensive assignments were made for the far-infrared (<400 cm−1) spectrum of α-ZrW2O8. A systematic comparison of DFPT-simulated infrared, Raman, and phonon density-of-state spectra with Fourier transform far-/mid-infrared and Raman data collected in this study, as well as with available inelastic neutron scattering measurements, shows the superior accuracy of the PBEsol exchange-correlation functional over standard PBE calculations for studying the spectroscopic properties of this material.
Molecular tracers that can be selectively placed underground and uniquely identified at the surface using simple on-site spectroscopic methods would significantly enhance subsurface fluid monitoring capabilities. To ensure their widespread utility, the solubility of these tracers must be easily tuned to oil-or water-wet conditions as well as reducing or eliminating their propensity to adsorb onto subsurface rock and/or mineral phases. In this work, molecular dynamics simulations were used to investigate the relative solubilities and mineral surface adsorption properties of three candidate tracer compounds comprising Mg-salen derivatives of varying degrees of hydrophilic character. Simulations in water-toluene liquid mixtures indicate that the partitioning of each Mg-salen compound relative to the interface is strongly influenced by the degree of hydrophobicity of the compound. Simulations of these complexes in fluid-filled mineral nanopores containing neutral (kaolinite) and negatively charged (montmorillonite) mineral surfaces reveal that adsorption tendencies depend upon a variety of parameters, including tracer chemical properties, mineral surface type, and solvent type (water or toluene). Simulation snapshots and averaged density profiles reveal insight into the solvation and adsorption mechanisms that control the partitioning of these complexes in mixed liquid phases and nanopore environments. This work demonstrates the utility of molecular simulation in the design and screening of molecular tracers for use in subsurface applications.
The porosity of clay aggregates is an important property governing chemical reactions and fluid flow in low-permeability geologic formations and clay-based engineered barrier systems. Pore spaces in clays include interlayer and interparticle pores. Under compaction and dewatering, the size and geometry of such pore spaces may vary significantly (sub-nanometer to microns) depending on ambient physical and chemical conditions. Here we report a molecular dynamics simulation method to construct a complex and realistic clay-like nanoparticle aggregate with interparticle pores and grain boundaries. The model structure is then used to investigate the effect of dewatering and water content on micro-porosity of the aggregates. The results suggest that slow dewatering would create more compact aggregates compared to fast dewatering. Furthermore, the amount of water present in the aggregates strongly affects the particle-particle interactions and hence the aggregate structure. Detailed analyses of particle-particle and water-particle interactions provide a molecular-scale view of porosity and texture development of the aggregates. The simulation method developed here may also aid in modeling the synthesis of nanostructured materials through self-assembly of nanoparticles.
Low-salinity water flooding, a method of enhanced oil recovery, consists of injecting low ionic strength fluids into an oil reservoir in order to detach oil from mineral surfaces in the underlying formation. Although highly successful in practice, the approach is not completely understood at the molecular scale. Molecular dynamics simulations have been used to investigate the effect of surface protonation on the adsorption of an anionic crude oil component on clay mineral edge surfaces. A set of interatomic potentials appropriate for edge simulations has been applied to the kaolinite (010) surface in contact with an aqueous nanopore. Decahydro-2-napthoic acid in its deprotonated form (DHNA-) was used as a representative resin component of crude oil, with monovalent and divalent counterions, to test the observed trends in low-salinity water flooding experiments. Surface models include fully protonated (neutral) and deprotonated (negative) edge sites, which require implementation of a new deprotonation scheme. The surface adsorptive properties of the kaolinite edge under neutral and deprotonated conditions have been investigated for low and high DHNA- concentrations with Na+ and Ca2+ as counterions. The tendency of DHNA- ions to coordinate with divalent (Ca2+) rather than monovalent (Na+) ions greatly influences adsorption tendencies of the anion. Additionally, the formation of net positively charged surface sites due to Ca2+ at deprotonated sites results in increased DHNA- adsorption. Divalent cations such as Ca2+ are able to efficiently bridge surface sites and organic anions. Replacing those cations with monovalent cations such as Na+ diminishes the bridging mechanism, resulting in reduced adsorption of the organic species. A clear trend of decreased DHNA- adsorption is observed in the simulations as Ca2+ is replaced by Na+ for deprotonated surfaces, as would be expected for oil detachment from reservoir formations following a low-salinity flooding event.
Molecular simulations of the adsorption of representative organic molecules onto the basal surfaces of various clay minerals were used to assess the mechanisms of enhanced oil recovery associated with salinity changes and water flooding. Simulations at the density functional theory (DFT) and classical levels provide insights into the molecular structure, binding energy, and interfacial behavior of saturate, aromatic, and resin molecules near clay mineral surfaces. Periodic DFT calculations reveal binding geometries and ion pairing mechanisms at mineral surfaces while also providing a basis for validating the classical force field approach. Through classical molecular dynamics simulations, the influence of aqueous cations at the interface and the role of water solvation are examined to better evaluate the dynamical nature of cation-organic complexes and their coadsorption onto the clay surfaces. The extent of adsorption is controlled by the hydrophilic nature and layer charge of the clay mineral. All organic species studied showed preferential adsorption on hydrophobic mineral surfaces. However, the anionic form of the resin (decahydro-2-naphthoic acid), expected to be prevalent at near-neutral pH conditions in petroleum reservoirs, readily adsorbs to the hydrophilic kaolinite surface through a combination of cation pairing and hydrogen bonding with surface hydroxyl groups. Analysis of cation-organic pairing in both the adsorbed and desorbed states reveals a strong preference for organic anions to coordinate with divalent calcium ions rather than monovalent sodium ions, lending support to current theories regarding low-salinity water flooding.
First-principles molecular dynamics simulations were used to investigate the dissociation of sarin (GB) on the calcium silicate hydrate (CSH) mineral tobermorite (TBM), a surrogate for cement. CSH minerals (including TBM) and amorphous materials of similar composition are the major components of Portland cement, the binding agent of concrete. Metadynamics simulations were used to investigate the effect of the TBM surface and confinement in a microscale pore on the mechanism and free energy of dissociation of GB. Our results indicate that both the adsorption site and the humidity of the local environment significantly affect the sarin dissociation energy. In particular, sarin dissociation in a low-water environment occurs via a dealkylation mechanism, which is consistent with previous experimental studies.
An open pored metal-organic framework (MOF) with oxygen selectivity at exceptionally high temperatures is confirmed by synthesis, sorption, and synchrotron structural analyses. The large-pore MIL-100 framework with access to the metal center (e.g., Sc and Fe) resulted in preferential O2 over N2 gas uptake at temperatures ranging from 77 K to ambient temperatures (258, 298, and 313 K). Most notably, Sc-MIL-100 shows exceptional O2 sorption; pair distribution function analyses indicate that this is due to distortions in the framework owing to the size of Sc atoms, in particular in the trimer metal cluster. Experimental studies also correlate very well with GCMC simulations, confirming more favorable O2-framework interactions at pressures up to 1 bar, due to the close proximity of O2 to the high density of metal centers in the small tetrahedral cages. Both materials maintain their crystallinity upon gas adsorption cycling, are regenerable, and show exceptional promise for use in energy efficient oxygen purification processes, such as Pressure Swing Adsorption.
The separation of oxygen from nitrogen using metal-organic frameworks (MOFs) is of great interest for potential pressure-swing adsorption processes for the generation of purified O2 on industrial scales. This study uses ab initio molecular dynamics (AIMD) simulations to examine for the first time the pure-gas and competitive gas adsorption of O2 and N2 in the M2(dobdc) (M = Cr, Mn, Fe) MOF series with coordinatively unsaturated metal centers. Effects of metal, temperature, and gas composition are explored. This unique application of AIMD allows us to study in detail the adsorption/desorption processes and to visualize the process of multiple guests competitively binding to coordinatively unsaturated metal sites of a MOF.
The diffusion of water and ions in the interlayer region of smectite clay minerals represents a direct probe of the type and strength of clay-fluid interactions. Interlayer diffusion also represents an important link between molecular simulation and macroscopic experiments. Here we use molecular dynamics simulation to investigate trends in cation and water diffusion in montmorillonite interlayers, looking specifically at the effects of layer charge, interlayer cation and cation charge (sodium or calcium), water content, and temperature. For Na-montmorillonite, the largest increase in ion and water diffusion coefficients occurs between the one-layer and two-layer hydrates, corresponding to the transition from inner-sphere to outer-sphere surface complexes. Calculated activation energies for ion and water diffusion in Na-montmorillonite are similar to each other and to the water hydrogen bond energy, suggesting the breaking of water-water and water-clay hydrogen bonds as a likely mechanism for interlayer diffusion. A comparison of interlayer diffusion with that of bulk electrolyte solutions reveals a clear trend of decreasing diffusion coefficient with increasing electrolyte concentration, and in most cases the interlayer diffusion results are nearly coincident with the corresponding bulk solutions. Trends in electrical conductivities computed from the ion diffusion coefficients are also compared.
Oxy-fuel combustion is a well-known approach to improve the heat transfer associated with stationary energy processes. Its overall penetration into industrial and power markets is constrained by the high cost of existing air separation technologies for generating oxygen. Cryogenic air separation is the most widely used technology for generating oxygen but is complex and expensive. Pressure swing adsorption is a competing technology that uses activated carbon, zeolites and polymer membranes for gas separations. However, it is expensive and limited to moderate purity O₂ . MOFs are cutting edge materials for gas separations at ambient pressure and room temperature, potentially revolutionizing the PSA process and providing dramatic process efficiency improvements through oxy-fuel combustion. This LDRD combined (1) MOF synthesis, (2) gas sorption testing, (3) MD simulations and crystallography of gas siting in pores for structure-property relationship, (4) combustion testing and (5) technoeconomic analysis to aid in real-world implementation.
Organic dyes such as methylene blue (MB) are often used in the characterization of clays and related minerals, but details of the adsorption mechanisms of such dyes are only partially understood from spectroscopic data, which indicate the presence of monomers, dimers, and higher aggregates for varying mineral surfaces. A combination of quantum (density functional theory) and classical molecular simulation methods was used to provide molecular detail of such adsorption processes, specifically the adsorption of MB onto kaolinite basal surfaces. Slab models with vacuum-terminated surfaces were used to obtain detailed structural properties and binding energies at both levels of theory, while classical molecular dynamics simulations of aqueous pores were used to characterize MB adsorption at infinite dilution and at higher concentration in which MB dimers and one-dimensional chains formed. Results for the neutral MB molecules are compared with those for the corresponding cation. Simulations of the aqueous pore indicate preferred adsorption on the hydrophobic siloxane surface, while charge-balancing chloride ions adsorb at the aluminol surface. At infinite dilution and in the gas-phase models, MB adsorbs with its primary molecular plane parallel to the siloxane surface to enhance hydrophobic interactions. Sandwiched dimers and chains are oriented perpendicular to the surface to facilitate the strong hydrophobic intermolecular interactions. Compared with quantum results, the hybrid force field predicts a weaker MB adsorption energy but a stronger dimerization energy. The structure and energetics of adsorbed MB at infinite dilution are consistent with the gas-phase binding results, which indicate that monomer adsorption is driven by strong interfacial forces rather than by the hydration properties of the dye. These results inform spectroscopic studies of MB adsorption on mineral surfaces while also revealing critical areas for development of improved hybrid force fields.
Here, we describe the homogeneous substitution of Mn, Fe, and Co at various levels into a prototypical metal-organic framework (MOF), namely Cu-BTC (HKUST-1), and the effect of that substitution on preferential gas sorption. Using a combination of density functional theory (DFT) calculations, postsynthetic metal substitutions, materials characterization, and gas sorption testing, we demonstrate that the identity of the metal ion has a quantifiable effect on their oxygen and nitrogen sorption properties at cryogenic temperatures. An excellent correlation is found between O2/N2 selectivities determined experimentally at 77 K and the difference in O2 and N2 binding energies calculated from DFT modeling data: Mn > Fe &-apcode; Co 蠑 Cu. Room temperature gas sorption studies were also performed and correlated with metal substitution. The Fe-exchanged sample shows a significantly higher nitrogen isosteric heat of adsorption at temperatures close to ambient conditions (273-298 K) as compared to all other metals studied, indicative of favorable interactions between N2 and coordinatively unsaturated Fe metal centers. Interestingly, differences in gas adsorption results at cryogenic and room temperatures are evident; they are explained by comparing experimental results with DFT binding energies (0 K) and room temperature Grand Canonical Monte Carlo simulations.
Computational screening of metal-organic framework (MOF) materials for selective oxygen adsorption from air could lead to new sorbents for the oxyfuel combustion process feedstock streams. A comprehensive study on the effect of MOF metal chemistry on gas binding energies in two common but structurally disparate metal-organic frameworks has been undertaken. Dispersion-corrected density functional theory methods were used to calculate the oxygen and nitrogen binding energies with each of fourteen metals, respectively, substituted into two MOF series, M2(dobdc) and M3(btc)2. The accuracy of DFT methods was validated by comparing trends in binding energy with experimental gas sorption measurements. A periodic trend in oxygen binding energies was found, with greater oxygen binding energies for early transition-metal-substituted MOFs compared to late transition metal MOFs; this was independent of MOF structural type. The larger binding energies were associated with oxygen binding in a side-on configuration to the metal, with concomitant lengthening of the O-O bond. In contrast, nitrogen binding energies were similar across the transition metal series, regardless of both MOF structural type and metal identity. Altogether, these findings suggest that early transition metal MOFs are best suited to separating oxygen from nitrogen, and that the MOF structural type is less important than the metal identity.
Molecular dynamics simulations were used to investigate trends in noble gas (Ar, Kr, Xe) diffusion in the metal-organic frameworks HKUST-1 and ZIF-8. Diffusion occurs primarily through inter-cage jump events, with much greater diffusion of guest atoms in HKUST-1 compared to ZIF-8 due to the larger cage and window sizes in the former. We compare diffusion coefficients calculated for both rigid and flexible frameworks. For rigid framework simulations, in which the framework atoms were held at their crystallographic or geometry optimized coordinates, sometimes dramatic differences in guest diffusion were seen depending on the initial framework structure or the choice of framework force field parameters. When framework flexibility effects were included, argon and krypton diffusion increased significantly compared to rigid-framework simulations using general force field parameters. Additionally, for argon and krypton in ZIF-8, guest diffusion increased with loading, demonstrating that guest-guest interactions between cages enhance inter-cage diffusion. No inter-cage jump events were seen for xenon atoms in ZIF-8 regardless of force field or initial structure, and the loading dependence of xenon diffusion in HKUST-1 is different for rigid and flexible frameworks. Diffusion of krypton and xenon in HKUST-1 depends on two competing effects: the steric effect that decreases diffusion as loading increases, and the “small cage effect” that increases diffusion as loading increases. Finally, a detailed analysis of the window size in ZIF-8 reveals that the window increases beyond its normal size to permit passage of a (nominally) larger krypton atom.
Anthropogenic activities have led to an increased concentration of uranium on the Earth’s surface and potentially in the subsurface with the development of nuclear waste repositories. Uranium is soluble in groundwater, and its mobility is strongly affected by the presence of clay minerals in soils and in subsurface sediments. We use molecular dynamics simulations to probe the adsorption of aqueous uranyl (UO22+) ions onto the basal surface of muscovite, a suitable proxy for typically ultrafine-grained clay phases. Model systems include the competitive adsorption between potassium counterions and aqueous ions (0.1 M and 1.0 M UO2Cl2 , 0.1 M NaCl). We find that for systems with potassium and uranyl ions present, potassium ions dominate the adsorption phenomenon. Potassium ions adsorb entirely as inner-sphere complexes associated with the ditrigonal cavity of the basal surface. Uranyl ions adsorb in two configurations when it is the only ion species present, and in a single configuration in the presence of potassium. Finally, the majority of adsorbed uranyl ions are tilted less than 45° relative to the muscovite surface, and are associated with the Si4Al2 rings near aluminum substitution sites.