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DOE OSTI2025

Including Physics-Informed Atomization Constraints in Neural Networks for Reactive Chemistry

Machine learning interatomic potentials (MLIPs) have emerged as powerful tools for investigating atomistic systems with high accuracy and a relatively low computational cost. However, a common and unaddressed challenge with many current neural network (NN) MLIP models is their limited ability to accurately predict the relative energies of systems containing isolated or nearly isolated atoms, which appear in various reactive processes. To address this limitation, we present a mathematical technique for modifying any existing atom-centered NN architecture to account for the energies of isolated atoms. The result produces a consistent prediction of the atomization energy (AE) of a system using minimal constraints on the model. Using this technique, we build a model architecture that we call hierarchically interacting particle neural network (HIP-NN)-AE, an AE-constrained version of the HIP-NN, as well as ANI-AE, the AE-constrained version of the accurate NN engine for molecular energies (ANI). Our results demonstrate AE consistency of AE-constrained models, which drastically improves the AE predictions for the models. We compare the AE-constrained approach to unconstrained models as well as models from the literature in other scenarios, such as bond dissociation energies, bond dissociation pathways, and extensibility tests. These results show that the constraints improve the model performance in some of these tasks and do not negatively affect the performance on any tasks. The AE constraint approach thus offers a robust solution to the challenges posed by isolated atoms in energy prediction tasks.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2021

Comparison of water nanodroplet properties on different graphite-based substrates

The molecular structure and dynamics of water differ considerably at various interfaces. We compare the interfacial water structure–property relationship on three different carbon substrates, namely, amorphous carbon, compressed expanded natural graphite, and pure graphite by utilizing atomistic molecular dynamics simulations. The effect of different substrates on the structural and dynamical properties of water can readily be observed. Here, the density distributions parallel and normal to the substrates show oblate droplet structures. The normal to the substrate water distribution shows a strong hydration layer at the interface that does not vary with substrates. However, the disparity in the structure and dynamics on three different substrates shows that the surface morphologies of the substrates are critical for determining nanoscale water properties. Furthermore, it is observed that the formation of an interfacial water layer or the hydration layer is a direct consequence of both water “confinement” at the nanoscale and “attraction” between water molecules and the carbon substrates.

42 ENGINEERING↗

DOE OSTI2020

First-Principles Modeling of the Repassivation of Corrosion Resistant Alloys: Part II. Surface Adsorption Isotherms for Alloys and the Chloride Susceptibility Index

Quantitatively predicting the corrosion resistance of alloys is vital to the design and application of the next generation of superior corrosion resistant alloys (CRAs). Here, the Chloride Susceptibility Index (CSI), a scientifically based quantitative descriptor for repassivation tendency of CRAs, is proposed as a metric constructed through combining atomistically resolved information regarding adsorption and alloy surface composition with environmental conditions such as applied potential, temperature, pH, and Cl – concentration. Using this method, the response of CRAs to relevant environments can be predicted. CSI is determined by: (1) estimation of thermoequilibrium surface coverages of O and Cl by a Langmuir isotherm model using adsorption energies of different species (O, Cl, OH, H 2 O) obtained from DFT. (2) determination of CSI by integrating Cl surface coverage over a realistic window of applied potentials, thereby incorporating the effect of Cl surface coverage and electrochemical environment simultaneously. A series of Ni-Cr-X alloys was used as an example to develop and validate the method through studying the effect of different alloy solutes X on chloride resistance. Here, the trends and relations predicted by CSI are in qualitative agreements with experimental observations. Moreover, a quantitative correlation is found between CSI and the repassivation potential.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Predicting Small Molecule Transfer Free Energies by Combining Molecular Dynamics Simulations and Deep Learning

Accurately predicting small molecule partitioning and hydrophobicity is critical in the drug discovery process. There are many heterogeneous chemical environments within a cell and entire human body. For example, drugs must be able to cross the hydrophobic cellular membrane to reach their intracellular targets, and hydrophobicity is an important driving force for drug–protein binding. Atomistic molecular dynamics (MD) simulations are routinely used to calculate free energies of small molecules binding to proteins, crossing lipid membranes, and solvation but are computationally expensive. Machine learning (ML) and empirical methods are also used throughout drug discovery but rely on experimental data, limiting the domain of applicability. We present atomistic MD simulations calculating 15,000 small molecule free energies of transfer from water to cyclohexane. This large data set is used to train ML models that predict the free energies of transfer. We show that a spatial graph neural network model achieves the highest accuracy, followed closely by a 3D-convolutional neural network, and shallow learning based on the chemical fingerprint is significantly less accurate. A mean absolute error of ~4 kJ/mol compared to the MD calculations was achieved for our best ML model. We also show that including data from the MD simulation improves the predictions, tests the transferability of each model to a diverse set of molecules, and show multitask learning improves the predictions. This work provides insight into the hydrophobicity of small molecules and ML cheminformatics modeling, and our data set will be useful for designing and testing future ML cheminformatics methods.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Extemporaneous Mechanochemistry: Shock-Wave-Induced Ultrafast Chemical Reactions Due to Intramolecular Strain Energy

We report regions of energy localization referred to as hotspots are known to govern shock initiation and the run-to-detonation in energetic materials. Mounting computational evidence points to accelerated chemistry in hotspots from large intramolecular strains induced via the interactions between the shock wave and microstructure. However, definite evidence mapping intramolecular strain to accelerated or altered chemical reactions has so far been elusive. From a large-scale reactive molecular dynamics simulation of the energetic material 1,3,5-triamino-2,4,6-trinitrobenzene, we map decomposition kinetics to molecular temperature and intramolecular strain energy prior to reaction. Both temperature and intramolecular strain are shown to accelerate chemical kinetics. A detailed analysis of the atomistic trajectory shows that intramolecular strain can induce a mechanochemical alteration of decomposition mechanisms. The results in this paper could inform continuum-level chemistry models to account for a wide range of mechanochemical effects.

36 MATERIALS SCIENCE↗

DOE OSTI2021

Ion correlations drive charge overscreening and heterogeneous nucleation at solid–aqueous electrolyte interfaces

Significance Ion distributions at charged solid–water interfaces, referred to as the electrical double layer (EDL), are poorly understood at high ion concentrations, in part due to the lack of molecular-scale descriptions of the interactions between adsorbed hydrated ions. Here, direct visualization of the salinity-dependent evolution of EDL structure reveals molecular origins of nonclassical transformation of the EDL, in which charge overscreening and heterogeneous nucleation are driven by ion–ion correlations at the interfaces. This manifestation of the atomistic basis of nonclassical behaviors provides a much-needed understanding of the impact of ion cooperativity at charged interfaces for the development of predictive models for element transport in natural environments and advanced technologies for material growth and synthesis in saline environments.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Topologically derived dislocation theory for twist and stretch moiré superlattices in bilayer graphene

In this work, we develop a continuum dislocation description of twist and stretch moiré superlattices in two-dimensional material bilayers. The continuum formulation is based on the topological constraints introduced by the periodic dislocation network associated with the moiré structure. The approach is based on solving analytically for the structural distortion and displacement fields that satisfy the topological constraints and that minimize the total energy. The total energy is described by both the strain energy of each individual distorted layer and a Peierls-Nabarro-like interfacial contribution arising from stacking disregistry. The dislocation core emerges naturally within the formalism as a result of the competition between the two contributions. The approach presented here captures the structure and energetics of twist and stretch moiré superlattices of dislocations with arbitrary direction and character, without assuming an analytical solution a priori and while accounting naturally for dislocation-dislocation image interactions. In comparisons to atomistic simulations using classical potentials, the maximum structure deviation is 6%, while the maximum line energy deviation is 0.019 eV/Å. Several applications of our model are shown, including predicting the variation of structure with twist angle and describing dislocation line tension and junction energies.

36 MATERIALS SCIENCE↗

DOE OSTI2021

Modeling of Peptides with Classical and Novel Machine Learning Force Fields: A Comparison

The replacement of classical force fields (FFs) with novel neural-network-based frameworks is an emergent topic in molecular dynamics (MD) simulations. In contrast to classical FFs, which have proven their capability to provide insights into complex soft matter systems at an atomistic resolution, the machine learning (ML) potentials have yet to demonstrate their applicability for soft materials. However, the underlying philosophy, which is learning the energy of an atom in its surrounding chemical environment, makes this approach a promising tool. In particular for the exploration of novel chemical compounds, which have not been considered in the original parametrization of classical FFs. In this article, we study the performance of the ANI-2x ML model and compare the results with those of two classical FFs, namely, CHARMM27 and the GROMOS96 43a1 FF. We explore the performance of these FFs for bulk water and two model peptides, trialanine and a 9-mer of the α-aminoisobutyric acid, in vacuum and water. The results for water describe a highly ordered water structure, with a structure similar to those using ab initio molecular dynamics simulations. The energy landscape of the peptides described by Ramachandran maps show secondary structure basins similar to those of the classical FFs but differ in the position and relative stability of the basins. Details of the sampled structures show a divergent performance of the different models, which can be related either to the short-ranged nature of the ML potentials or to shortcomings of the underlying data set used for training. These findings highlight the current state of the applicability of ANI-2x ML potential for MD simulations of soft matter systems. Simultaneously, they provide insights for future improvements of current ML potentials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Electronic and Geometric Contributors to Hydrogen Binding in Uranium Oxide Grain Boundaries

Hydrogen induced corrosion of uranium, which leads to the formation of toxic and pyrophoric UH 3 , raises significant safety concerns for long-term storage of nuclear materials. Previous work suggests hydrogen diffuses through the grain boundaries (GBs) of the passivating oxide layer to initiate hydriding reactions. However, the atomistic mechanisms underlying this phenomenon and the structural factors that control its initiation are not well understood. To address this knowledge gap, here we use a high-throughput density functional theory (DFT) workflow to investigate the adsorption of H and H 2 in the defective bulk UO 2 . Specifically, we have exhaustively investigated the adsorption of H (107 sites) and H 2 (26 sites) in three different coincident site lattice (CSL) GBs: Σ3, Σ5, and Σ9. Compared to the binding energies in pristine UO 2 , we observe significantly stronger hydrogen adsorption at these GB sites. Interestingly, we find that the trends in H and H 2 adsorption vary considerably across the three GB models. In particular, while a small number of sites in Σ5 and Σ9 show exothermic adsorption of H and H 2 , respectively, no such sites are found in Σ3. These results provide fundamental atomistic insights that could guide the development of future corrosion mitigation strategies for the storage of nuclear materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

CHARMM-GUI Bicelle Builder : An Extension of Membrane Builder for Modeling and Simulation of Bicelle Systems

Membrane mimetics, such as detergent micelles, nanodiscs, and amphipol complexes, which can provide membrane-like environments while retaining small and soluble features, have been utilized to study membrane proteins. A bicelle, composed of varying lipids and detergents, is a useful membrane mimetic because the lipid-to-detergent ratio, the q-value, can be adjusted to alter the properties of the aggregate, including the thickness and size of the bicelle. However, building a bicelle model for modeling and simulation studies requires nontrivial efforts, even for experts. We introduce CHARMM-GUI Bicelle Builder, a web-based platform that can generate various all-atom bicelle systems via a graphical user interface with all available lipids and detergents in Membrane Builder. To illustrate and validate Bicelle Builder with practical systems, we have modeled and simulated pure bicelles consisting of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) lipids with 1,2-dihexanoyl-sn-glycero-3-phosphocholine (C6DHPC) detergents and protein–bicelle complexes, composed of DMPC with C6DHPC, foscholine-10 (FOS10), and lysophosphatidylcholine-12 (LPC12) detergents. Our simulation results indicate that Bicelle Builder can generate reliable and robust bicelle models with and without proteins that retain DMPC bilayer characteristics. Bicelle Builder is expected to help researchers better understand not only bicelles themselves but also atomistic-level structures of protein–bicelle complexes that are often difficult to access through experimental approaches.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Trends in oxygenate/hydrocarbon selectivity for electrochemical CO (2) reduction to C 2 products

The electrochemical conversion of carbon di-/monoxide into commodity chemicals paves a way towards a sustainable society but it also presents one of the great challenges in catalysis. Herein, we present the trends in selectivity towards specific dicarbon oxygenate/hydrocarbon products from carbon monoxide reduction on transition metal catalysts, with special focus on copper. We unveil the distinctive role of electrolyte pH in tuning the dicarbon oxygenate/hydrocarbon selectivity. The understanding is based on density functional theory calculated energetics and microkinetic modeling. We identify the critical reaction steps determining selectivity and relate their transition state energies to two simple descriptors, the carbon and hydroxide binding strengths. The atomistic insight gained enables us to rationalize a number of experimental observations and provides avenues towards the design of selective electrocatalysts for liquid fuel production from carbon di-/monoxide.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Mechanistic roles of metal- and ligand-protonated species in hydrogen evolution with [Cp*Rh] complexes

Protonation reactions involving organometallic complexes are ubiquitous in redox chemistry and often result in the generation of reactive metal hydrides. However, some organometallic species supported by η 5 -pentamethylcyclopentadienyl (Cp*) ligands have recently been shown to undergo ligand-centered protonation by direct proton transfer from acids or tautomerization of metal hydrides, resulting in the generation of complexes bearing the uncommon η 4 -pentamethylcyclopentadiene (Cp*H) ligand. Here, time-resolved pulse radiolysis (PR) and stopped-flow spectroscopic studies have been applied to examine the kinetics and atomistic details involved in the elementary electron- and proton-transfer steps leading to complexes ligated by Cp*H, using Cp*Rh(bpy) as a molecular model (where bpy is 2,2′-bipyridyl). Stopped-flow measurements coupled with infrared and UV-visible detection reveal that the sole product of initial protonation of Cp*Rh(bpy) is [Cp*Rh(H)(bpy)] + , an elusive hydride complex that has been spectroscopically and kinetically characterized here. Tautomerization of the hydride leads to the clean formation of [(Cp*H)Rh(bpy)] + . Variable-temperature and isotopic labeling experiments further confirm this assignment, providing experimental activation parameters and mechanistic insight into metal-mediated hydride-to-proton tautomerism. Spectroscopic monitoring of the second proton transfer event reveals that both the hydride and related Cp*H complex can be involved in further reactivity, showing that [(Cp*H)Rh] is not necessarily an off-cycle intermediate, but, instead, depending on the strength of the acid used to drive catalysis, an active participant in hydrogen evolution. Identification of the mechanistic roles of the protonated intermediates in the catalysis studied here could inform design of optimized catalytic systems supported by noninnocent cyclopentadienyl-type ligands.

08 HYDROGEN↗

DOE OSTI2025

Status Report on Design of In-situ Thermomechanical Testing at LANSCE

Nuclear fuel encounters severe thermomechanical environments in which its mechanical response is determined by its microstructure, temperature and stress level histories. Simulating the response of such microstructures is crucial for predicting both performance and transient fuel mechanical responses and experimental verification of such predictions is therefore of great interest. While most of the deformation in a nuclear fuel rod occurs in the cladding, deformation of the fuel itself is still of interest with deformation mechanisms at operating temperature and above including creep, swelling, cracking as well as pellet-clad interaction. Characterization of these properties and understanding of the underlying deformation phenomena at operating or excursion temperatures is therefore of great importance for development and ultimately licensing of improved and novel nuclear fuel forms. Diffraction techniques offer unique insight on the atomistic (e.g. crystal structure) and microstructure (e.g. phase transformations, texture, defects) length scales and have a long history of providing unique data to inform relevant deformation models that enable the required predictive capabilities. For example, dislocations lead to diffraction peak broadening that can be characterized to estimate the dislocation density and study the role of dislocations on the deformation while measuring lattice strains allows to studie load sharing in two phase materials. In this report the requirements for a sample environment for high temperature deformation of nuclear fuels are defined. The HIPPO neutron time-of-flight diffractometer at LANSCE will host this sample environment and is also described. This instrument covers diffraction angles from 140° to 40° and is also equipped with an event-mode neutron imaging detector system, enabling energy-resolved neutron imaging in parallel with the diffraction that could measure sample temperature from Doppler broadening of neutron absorption resonances or measure pore densities from changes in the attenuation. Designs of devices to characterize thermomechanical properties of nuclear fuel without diffraction are also considered to guide the design. While this report is focused on applications for nuclear fuels, the device can also characterize cladding, moderator or structural materials and therefore contribute to other fields of research and development for advanced reactors. The temperatures planned to be reached are above 2000℃, thus enabling characterization of LWR reactor fuels under accident scenarios but also reaching temperatures of fuels developed for nuclear thermal propulsion and providing opportunities to characterize those. In conjunction with the energy-resolved neutron imaging detector, this setup would allow to measure neutron cross-sections at high temperatures, filling a gap towards development of reactors operating at high temperatures.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2021

Molecular Dynamics Simulations of a Catalytic Multivalent Peptide–Nanoparticle Complex

Molecular modeling of a supramolecular catalytic system is conducted resulting from the assembling between a small peptide and the surface of cationic self-assembled monolayers on gold nanoparticles, through a multiscale iterative approach including atomistic force field development, flexible docking with Brownian Dynamics and µs-long Molecular Dynamics simulations. Self-assembly is a prerequisite for the catalysis, since the catalytic peptides do not display any activity in the absence of the gold nanocluster. Atomistic simulations reveal details of the association dynamics as regulated by defined conformational changes of the peptide due to peptide length and sequence. Our results show the importance of a rational design of the peptide to enhance the catalytic activity of peptide–nanoparticle conjugates and present a viable computational approach toward the design of enzyme mimics having a complex structure–function relationship, for technological and nanomedical applications.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Improving the Accuracy of Atomistic Simulations of the Electrochemical Interface

Atomistic simulation of the electrochemical double layer is an ambitious undertaking, requiring quantum mechanical description of electrons, phase space sampling of liquid electrolytes, and equilibration of electrolytes over nanosecond time scales. All models of electrochemistry make different trade-offs in the approximation of electrons and atomic configurations, from the extremes of classical molecular dynamics of a complete interface with point-charge atoms to correlated electronic structure methods of a single electrode configuration with no dynamics or electrolyte. Here, we review the spectrum of simulation techniques suitable for electrochemistry, focusing on the key approximations and accuracy considerations for each technique. Additionally, we discuss promising approaches, such as enhanced sampling techniques for atomic configurations and computationally efficient beyond density functional theory (DFT) electronic methods, that will push electrochemical simulations beyond the present frontier.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Kinetic Growth of Multicomponent Microcompartment Shells

An important goal of systems and synthetic biology is to produce high value chemical species in large quantities. Microcompartments, which are protein nanoshells encapsulating catalytic enzyme cargo, could potentially function as tunable nanobioreactors inside and outside cells to generate these high value species. Modifying the morphology of microcompartments through genetic engineering of shell proteins is one viable strategy to tune cofactor and metabolite access to encapsulated enzymes. However, this is a difficult task without understanding how changing interactions between the many different types of shell proteins and enzymes affect microcompartment assembly and shape. Here, we use multiscale molecular dynamics and experimental data to describe assembly pathways available to microcompartments composed of multiple types of shell proteins with varied interactions. As the average interaction between the enzyme cargo and the multiple types of shell proteins is weakened, the shell assembly pathway transitions from (i) nucleating on the enzyme cargo to (ii) nucleating in the bulk and then binding the cargo as it grows to (iii) an empty shell. Atomistic simulations and experiments using the 1,2-propanediol utilization microcompartment system demonstrate that shell protein interactions are highly varied and consistent with our multicomponent, coarse-grained model. Furthermore, our results suggest that intrinsic bending angles control the size of these microcompartments. Altogether, our simulations and experiments provide guidance to control microcomparmtent size and assembly by modulating the interactions between shell proteins.

defects↗

DOE OSTI2021

A theoretical calculation of stacking fault energy of Ni alloys: The effects of temperature and composition

Combining cluster expansion (CE) method with one dimensional axial Ising model, this work investigated the effects of alloying elements and configurational variations due to temperature on the stacking fault energy (SFE) of FCC Ni binary alloys. Ensembles of large numbers of atomistic structures, each with more than ~400 atoms, were generated to consider sufficient long-range chemical disorder and temperature effects due to configurational entropy. Here, a Monte Carlo Metropolis algorithm was used to generate these structures, whose energies were then evaluated based on the effective cluster interactions obtained from CE. As a baseline, this work had shown the SFE of pure Ni and Al to be 127 mJ/m 2 and 137 mJ/m 2 , respectively, which agreed with the experimental values of 125 mJ/m 2 and 150 mJ/m 2 reported in the literature. Additions of Al, Ti, Cr and Co to pure Ni were found to decrease the SFE to different extents. Although temperature does not strongly influence the SFE of the FCC Ni-Al and Ni-Cr binary alloys, it can lead to significant changes to the SFE of the FCC Ni-Ti and Ni-Co alloys. While effects of temperature and composition on SFE observed in this work were calculated from binary Ni alloys, the general trends are nonetheless expected to be valid in the γ phase of multicomponent Ni superalloys.

36 MATERIALS SCIENCE↗

DOE OSTI2022

High-pressure hydrogen decompression in sulfur crosslinked elastomers

High-pressure storage and cyclic (de)pressurization of hydrogen gas is known to result in degradation and failure of gas canisters, hoses, linings, and O-rings as the relatively small hydrogen molecule can readily permeate most materials. Hence, identifying material compositions that are less susceptible to hydrogen-induced damage is of significant importance to the hydrogen energy infrastructure. Here, we use classical atomistic molecular dynamics simulations to study hydrogen exposed ethylene-propylene-diene monomer (EPDM) rubber, an elastomer typically used in O-rings. We make chemical modifications to the model by adjusting the crosslink density and report on gas solubility, diffusivity, and molecular restructuring in response to rapid decompression. Our simulations indicate that increases in crosslink density can reduce volumetric expansion during decompression and result in smaller free volume pore sizes. However, these favorable properties for sealing materials come with a tradeoff. At pressure, crosslinks introduce extra free volume, providing potential sites for gas localization, the precursor to cavitation-induced failure.

08 HYDROGEN↗