Publications

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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.

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Molecular diffusion coefficients calculated using molecular dynamics (MD) simulations suffer from finite-size (i.e., finite box size and finite particle number) effects. Results from finite-sized MD simulations can be upscaled to infinite simulation size by applying a correction factor. For self-diffusion of single-component fluids, this correction has been well-studied by many researchers including Yeh and Hummer (YH); for binary fluid mixtures, a modified YH correction was recently proposed for correcting MD-predicted Maxwell-Stephan (MS) diffusion rates. Here we use both empirical and machine learning methods to identify improvements to the finite-size correction factors for both self-diffusion and MS diffusion of binary Lennard-Jones (LJ) fluid mixtures. Using artificial neural networks (ANNs), the error in the corrected LJ fluid diffusion is reduced by an order of magnitude versus existing YH corrections, and the ANN models perform well for mixtures with large dissimilarities in size and interaction energies where the YH correction proves insufficient.

The molecular level origins for symmetry breaking in the excited state of symmetrical quadrupolar molecules, particularly in polar solvents, was investigated using time-dependent density functional theory approaches. Molecules of the form ADA (A/D electron accepting/donating respectively), have been shown to break their symmetry upon excitation, producing an intramolecular charge transfer event and permanent dipole. Current research indicates that polar solvents stabilize the charge transfer event thereby producing asymmetrical solvent dynamics on opposite ends of the molecules. In this work key structural features of the molecule were identified including (1) incorporation of cyano groups, (2) rotation of grafted phenyl rings, and (3) the length of the conjugated R group chain. More specifically, incorporation of cyano groups appears to decrease the magnitude of the dipole in the excited state, thereby indicating that solvent interactions at these groups do not stabilize the charge transfer. While the rotation of the phenyl groups appears to be necessary to break the symmetry of the excited state in the molecule.

The Spent Fuel and Waste Science and Technology (SFWST) Campaign of the U.S. Department of Energy (DOE) Office of Nuclear Energy (NE), Office of Spent Fuel & Waste Disposition (SFWD) is conducting research and development (R&D) on geologic disposal of spent nuclear fuel (SNF) and highlevel nuclear waste (HLW). A high priority for SFWST disposal R&D is to develop a disposal system modeling and analysis capability for evaluating disposal system performance for nuclear waste in geologic media. This report describes fiscal year (FY) 2020 advances of the Geologic Disposal Safety Assessment (GDSA) Framework and PFLOTRAN development groups of the SFWST Campaign. The common mission of these groups is to develop a geologic disposal system modeling capability for nuclear waste that can be used to probabilistically assess the performance of disposal options and generic sites. The capability is a framework called GDSA Framework that employs high-performance computing (HPC) capable codes PFLOTRAN and Dakota.

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Different machine learning (ML) methods were explored for the prediction of self-diffusion in Lennard-Jones (LJ) fluids. Using a database of diffusion constants obtained from the molecular dynamics simulation literature, multiple Random Forest (RF) and Artificial Neural Net (ANN) regression models were developed and characterized. The role and improved performance of feature engineering coupled to the RF model development was also addressed. The performance of these different ML models was evaluated by comparing the prediction error to an existing empirical relationship used to describe LJ fluid diffusion. It was found that the ANN regression models provided superior prediction of diffusion in comparison to the existing empirical relationships.

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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.

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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.

The degradation of a chemical warfare agent simulant using a catalytically active Zr-based metal-organic framework (MOF) as a function of different solvent systems was investigated. Complementary molecular modelling studies indicate that the differences in the degradation rates are related to the increasing size in the nucleophile, which hinders the rotation of the product molecule during degradation. Methanol was identified as an appropriate solvent for non-Aqueous degradation applications and demonstrated to support the MOF-based destruction of both sarin and soman.

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