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DOE OSTI2025

Coarse-grained simulation of colloidal self-assembly, cation exchange, and rheology in Na/Ca smectite clay gels

Knowledge Gap: The aggregation of clay minerals—layered silicate nanoparticles—strongly impacts fluid flow, solute migration, and solid mechanics in soils, sediments, and sedimentary rocks. Experimental and computational characterization of clay aggregation is inhibited by the delicate water-mediated nature of clay colloidal interactions and by the range of spatial scales involved, from 1 nm thick platelets to flocs with dimensions up to micrometers or more. Simulations: Using a new coarse-grained molecular dynamics (CGMD) approach, we predicted the microstructure, dynamics, and rheology of hydrated smectite (more precisely, montmorillonite) clay gels containing up to 2,000 clay platelets on length scales up to 0.1 μm. Further, simulations investigated the impact of simulation time, platelet diameters (6 to 25nm), and the ratio of Na to Ca exchangeable cations on the assembly of tactoids (i.e., stacks of parallel clay platelets) and larger aggregates (i.e., assemblages of tactoids). We analyzed structural features including tactoid size and size distribution, basal spacing, counterion distribution in the electrical double layer, clay association modes, and the rheological properties of smectite gels. Findings: Our results demonstrate new potential to characterize and understand clay aggregation in dilute suspensions and gels on a scale of thousands of particles with explicit representation of counterion clouds and with accuracy approaching that of all-atom molecular dynamics (MD) simulations. For example, our simulations predict the strong impact of Na/Ca ratio on clay tactoid formation and the shear-thinning rheology of clay gels.

42 ENGINEERING↗

DOE OSTI2022

Resolving Salt-Induced Agglomeration of Laponite Suspensions Using X-ray Photon Correlation Spectroscopy and Molecular Dynamics Simulations

Linking the physics of the relaxation behavior of viscoelastic fluids as they form arrested gel states to the underlying chemical changes is essential for developing predictive controls on the properties of the suspensions. In this study, 3 wt.% laponite suspensions are studied as model systems to probe the influence of salt-induced relaxation behavior arising from the assembly of laponite nanodisks. X-ray Photon Correlation Spectroscopy (XPCS) measurements show that laponite suspensions prepared in the presence of 5 mM concentrations of CaCl2, MgCl2 and CsCl salts accelerate the formation of arrested gel states, with CaCl2 having a significant impact followed by CsCl and MgCl2 salts. The competing effects of ion size and charge on relaxation behavior are noted. For example, the relaxation times of laponite suspensions in the presence of Mg2+ ions are slower compared to Cs+ ions despite the higher charge, suggesting that cation size dominates in this scenario. The faster relaxation behavior of laponite suspensions in the presence of Ca2+ ions compared to Cs+ ions shows that a higher charge dominates the size of the ion. The trends in relaxation behavior are consistent with the cluster formation behavior of laponite suspensions and the electrostatic interactions predicted from MD simulations. Charge balance is achieved by the intercalation of the cations at the negatively charged surfaces of laponite suspensions. These studies show that the arrested gel state of laponite suspensions is accelerated in the presence of salts, with ion sizes and charges having a competing effect on relaxation behavior.

36 MATERIALS SCIENCE↗

NASA NTRSDate not supplied

Characterizing Porous and Nonporous Phenolic Resins from Molecular Dynamics Simulations

Phenolic resins are an important component of many ablative heat shield materials, which protect spacecrafts from the extreme temperatures reached during atmospheric entry. Examples include the high-density Heritage Carbon Phenolic (HCP) used in the Pioneer-Venus and Galileo missions, as well as the low-density Phenolic Impregnated Carbon Ablator (PICA) used in the Mars Science Laboratory and Mars 2020 missions. Additionally, recent developments within NASA have produced the mid-density Heatshield for Extreme Entry Environment Technology (HEEET) and its derivative 3D Woven Mid-Density Carbon Phenolic (3MDCP). Unlike the nonporous phenolic in HCP, PICA and HEEET/3MDCP are fabricated by infusing preforms with diluted phenolic formulations to obtain a lower density porous matrix. Despite the importance of the phenolic phase to the material response during entry, the variation in properties of porous and nonporous phenolic is not well understood. Here, we present an investigation of porous and nonporous phenolic resins using molecular dynamics (MD) simulations. Resin cure is mimicked in the simulations through the inclusion of representative reaction templates to generate accurate models of the complex crosslinked structures. To create porous models, explicit solvent molecules are included during the cure simulations. We observe nanoscale separation of the phenolic and solvent phases, which results in significant differences in the final structures of porous and nonporous models. In addition to a quantitative assessment of the network structure and porosity, we elucidate the effects of the phenolic formulation on the final material properties. These results are compared with experimental data as appropriate.

phenolic↗

DOE OSTI2022

Virtual texture analysis to investigate the deformation mechanisms in metal microstructures at the atomic scale

Understanding the deformation behavior of metallic materials at high strain rates requires the characterization of plasticity contributors such as twins, phase transformed regions, and dislocations. However, predicting the contributions from phase transformation and twinning relies on a complete understanding of the selection of variants for various loading orientations and the evolution of their volume fractions. This manuscript presents a new virtual texture (VirTex) analysis approach to characterize phase transformation and twinning variants in deformed microstructures generated using molecular dynamics (MD) simulations. Furthermore, the VirTex method involves the construction of a rotation matrix to calculate the angle/axis pairs and misorientation angles for each atom in the microstructure. Any changes in the orientation angle from angle/axis pairs and/or structure types are analyzed to determine the nucleation and evolution of variants in the microstructure. The study uses shock deformed single-crystal Fe, Ta, and Cu to analyze the variant selections for phase transformation or twinning or both in BCC and FCC systems. In addition, the VirTex analysis is able to characterize the phase transformation and twinning variants in nanocrystalline Fe and Ta microstructures. Besides characterizing variants, orientation mapping also provides an accelerated and on-the-fly approach for quantifying twin fractions in MD microstructures.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Evaluation of 6-OxP-CD, an Oxime-based cyclodextrin as a viable medical countermeasure against nerve agent poisoning: Experimental and molecular dynamic simulation studies on its inclusion complexes with cyclosarin, soman and VX

The ability of the cyclodextrin-oxime construct 6-OxP-CD to bind and degrade the nerve agents Cyclosarin (GF), Soman (GD) and S -[2-[Di(propan-2-yl)amino]ethyl] O -ethyl methylphosphonothioate (VX) has been studied using 31 P-nuclear magnetic resonance (NMR) under physiological conditions. While 6-OxP-CD was found to degrade GF instantaneously under these conditions, it was found to form an inclusion complex with GD and significantly improve its degradation (t 1/2 ~ 2 hrs) relative over background (t 1/2 ~ 22 hrs). Consequently, effective formation of the 6-OxP-CD:GD inclusion complex results in the immediate neutralization of GD and thus preventing it from inhibiting its biological target. In contrast, NMR experiments did not find evidence for an inclusion complex between 6-OxP-CD and VX, and the agent’s degradation profile was identical to that of background degradation (t 1/2 ~ 24 hrs). As a complement to this experimental work, molecular dynamics (MD) simulations coupled with Molecular Mechanics-Generalized Born Surface Area (MM-GBSA) calculations have been applied to the study of inclusion complexes between 6-OxP-CD and the three nerve agents. These studies provide data that informs the understanding of the different degradative interactions exhibited by 6-OxP-CD with each nerve agent as it is introduced in the CD cavity in two different orientations (up and down). For its complex with GF, it was found that the oxime in 6-OxP-CD lies in very close proximity (P GF …O Oxime ~ 4–5 Å) to the phosphorus center of GF in the ‘down GF ’ orientation for most of the simulation accurately describing the ability of 6-OxP-CD to degrade this nerve agent rapidly and efficiently. Further computational studies involving the center of masses (COMs) for both components (GF and 6-OxP-CD) also provided some insight on the nature of this inclusion complex. Distances between the COMs (ΔCOM) lie closer in space in the ‘down GF ’ orientation than in the ‘up GF ’ orientation; a correlation that seems to hold true not only for GF but also for its congener, GD. In the case of GD, calculations for the ‘down GD ’ orientation showed that the oxime functional group in 6-OxP-CD although lying in close proximity (P GD …O Oxime ~ 4–5 Å) to the phosphorus center of the nerve agent for most of the simulation, adopts another stable conformation that increase this distance to ~ 12–14 Å, thus explaining the ability of 6-OxP-CD to bind and degrade GD but with less efficiency as observed experimentally (t 1/2 ~ 4 hr. vs. immediate). Lastly, studies on the VX:6-OxP-CD system demonstrated that VX does not form a stable inclusion complex with the oxime-bearing cyclodextrin and as such does not interact in a way that is conducive to an accelerated degradation scenario. Collectively, these studies serve as a basic platform from which the development of new cyclodextrin scaffolds based on 6-OxP-CD can be designed in the development of medical countermeasures against these highly toxic chemical warfare agents.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2026

Mechanism of Tyrosine-Driven Deprotonation in Photosystem II Revealed by Multiscale Simulations

Photosystem II (PSII) drives light-induced water oxidation via stepwise redox transitions of its oxygen-evolving complex (OEC), a Mn 4 Ca cluster advancing through five intermediate S-states (S 0 –S 4 ). The S 2 → S 3 transition involves a redox event in which a Mn ion donates an electron to the redox-active tyrosine YZ, coupled to deprotonation of an OEC-bound water ligand─yet the underlying coupling mechanism remains unresolved. Time-resolved serial femtosecond crystallography (TR-SFX) has revealed transient electron density shifts near the redox-active tyrosine Y Z , interpreted as sequential oxidation and reduction, with reduction initiating ∼1 μs after excitation and substantially progressed by 30 μs. However, this interpretation conflicts with kinetics from photothermal beam deflection (PBD), time-resolved X-ray absorption spectroscopy (TR-XAS), and electron paramagnetic resonance (EPR), which place electron transfer at 190–400 μs and proton transfer around 30 μs. Here, we reconcile these discrepancies using quantum mechanics/molecular mechanics (QM/MM) and molecular dynamics (MD) simulations. We show that oxidation of P680 and Y Z breaks the symmetry of the nearby hydrogen bonds involving water molecule W4, displacing Y Z and replicating the TR-SFX features of Y Z and Q165 observed at 1 μs. This local perturbation propagates through a hydrogen-bond network, transmitting the electrostatic signal from Y Z to the E65-E312 dyad and triggering redox-coupled deprotonation via the Cl1 channel. By 30 μs, the hydrogen-bond symmetry is restored through deprotonation of W2 (or alternatively W1), reproducing the disappearance of TR-SFX density differences around Y Z and Q165 without requiring Y Z reduction. Our proposed mechanism also gives molecular insights into the O6* density, assigning it to water reorganization rather than a discrete Ca-bound hydroxide species. Here, our results reveal a detailed atomistic mechanism linking Y Z oxidation to long-range proton release and suggest a functional role for the nearby Cl – ion in proton transfer. More broadly, this study underscores the importance of hydrogen-bond dynamics in mediating redox-driven proton transport and demonstrates how integrative simulations can resolve mechanistic ambiguities.

Deprotonation↗

DOE OSTI2020

Evaluation of Nuclear Spent Fuel Disposal in Clay-Bearing Rock - Process Model Development and Experimental Studies

The DOE R&D program under the Spent Fuel Waste Science Technology (SFWST) campaign has made key progress in modeling and experimental approaches towards the characterization of chemical and physical phenomena that could impact the long-term safety assessment of heat-generating nuclear waste disposition in deep clay/shale/argillaceous rock. International collaboration activities such as heater tests and postmortem analysis of samples recovered from these have elucidated key information regarding changes in the engineered barrier system (EBS) material exposed to years of thermal loads. Chemical and structural analyses of sampled bentonite material from such tests has as well as experiments conducted on these are key to the characterization of thermal effects affecting bentonite clay barrier performance and the extent of sacrificial zones in the EBS during the thermal period. Thermal, hydrologic, and chemical data collected from heater tests and laboratory experiments has been used in the development, validation, and calibration of THMC simulators to model near-field coupled processes. This information leads to the development of simulation approaches (e.g., continuum vs. discrete) to tackle issues related to flow and transport at various scales of the host-rock and EBS design concept. Consideration of direct disposal of large capacity dual-purpose canisters (DPCs) as part of the back-end SNF waste disposition strategy has generated interest in improving our understanding of the effects of elevated temperatures on the EBS design. This is particularly important for backfilled repository concepts where temperature plays a key role in the EBS behavior and long-term performance. This report describes multiple R&D efforts on disposal in argillaceous geologic media through development and application of coupled THMC process models, experimental studies on clay/metal/cement barrier and host-rock (argillite) material interactions, molecular dynamic (MD) simulations of water transport during (swelling) clay dehydration, first-principles studies of metaschoepite (UO 2 corrosion product) stability, and advances in thermodynamic plus surface complexation database development. Drift-scale URL experiments provides key data for testing hydrological-chemical (HC) model involving strong couplings of fluid mixing and barrier material chemical interactions. The THM modeling focuses on heater test experiments in argillite rock and gas migration in bentonite as part of international collaboration activities at underground research laboratories (URLs). In addition, field testing at an URL involves in situ analysis of fault slip behavior and fault permeability. Pore-scale modeling of gas bubble migration is also being investigated within the gas migration modeling effort. Interaction experiments on bentonite samples from heater test under ambient and elevated temperatures permit the evaluation of ion exchange, phase stability, and mineral transformation changes that could impact clay swelling. Advances in the development, testing, and implementation of a spent nuclear fuel (SNF) degradation model coupled with canister corrosion focus on the effects of hydrogen gas generation and its integration with Geologic Disposal Safety Assessment (GDSA). GDSA integration activities includes evaluation of groundwater chemistries in shale formations.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2021

The solution structures of higher-order human telomere G-quadruplex multimers

Human telomeres contain the repeat DNA sequence 5'-d(TTAGGG), with duplex regions that are several kilobases long terminating in a 3' single-stranded overhang. The structure of the single-stranded overhang is not known with certainty, with disparate models proposed in the literature. We report here the results of an integrated structural biology approach that combines small-angle X-ray scattering, circular dichroism (CD), analytical ultracentrifugation, size-exclusion column chromatography and molecular dynamics simulations that provide the most detailed characterization to date of the structure of the telomeric overhang. We find that the single-stranded sequences 5'-d(TTAGGG)n, with n = 8, 12 and 16, fold into multimeric structures containing the maximal number (2, 3 and 4, respectively) of contiguous G4 units with no long gaps between units. The G4 units are a mixture of hybrid-1 and hybrid-2 conformers. In the multimeric structures, G4 units interact, at least transiently, at the interfaces between units to produce distinctive CD signatures. Global fitting of our hydrodynamic and scattering data to a worm-like chain (WLC) model indicates that these multimeric G4 structures are semi-flexible, with a persistence length of ~34 Å. Investigations of its flexibility using MD simulations reveal stacking, unstacking, and coiling movements, which yield unique sites for drug targeting.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

Third-body stabilization of supercritical CO 2 in CO oxidation: development and application of a ReaxFF force field for the CO/O/CO 2 system

Supercritical CO 2 (scCO 2 ) plays a crucial role as a solvent in separation processes, advanced power cycles, and materials processing. Nonetheless, the atomistic comprehension of how the dense scCO 2 matrix influences the fundamental reaction of carbon monoxide (CO) is still insufficiently explored. Experimental studies and molecular dynamics (MD) simulations frequently fail to detect the highly reactive, transient intermediates, such as atomic oxygen (O), that drive these reactions. Here, to address this issue, we have developed a novel ReaxFF reactive force field for the CO 2 /CO/O system. The force field parameters were calibrated using density functional theory and second-order Møller-Plesset calculations to model CO 2 crystal properties, intermolecular interactions, bond dissociation curves, and reaction energy barriers. The force field reproduces the cohesive energy of the CO 2 crystal, the pressure characteristics of bulk scCO 2 , the equation-of-state behavior over a wide pressure–density range, the pressure dependence of the C–O bond length under compression, and the structural properties of liquid and scCO 2 , as documented by experiments, ab-initio MD, and prominent non-reactive models. The force field was subsequently applied to study the CO + O → CO 2 reaction. In a dilute environment, the reaction is inefficient as the newly formed CO 2 rapidly dissociates due to excess kinetic and potential energy acquired from the exothermic reaction. Conversely, in a dense scCO 2 environment, the surrounding matrix acts as an efficient third body, stabilizing the emerging CO2 product via molecular collisions. Statistical analysis confirms an average excess energy dissipation of 133.9 ± 3.6 kcal/mol over 112.4 ± 17.9 ps. Kinetic energy decomposition reveals that ∼ 92% of the excess kinetic energy is stored in internal (rotational and vibrational) degrees of freedom. This ReaxFF force field establishes a mechanistic foundation for third-body stabilization in dense reactive environments.

Chowdhury, Emdadul Haque [Pennsylvania State Univ.↗

DOE OSTI2020

A comparative study of the effectiveness of empirical potentials for molecular dynamics simulations of borosilicate glasses

Despite their practical importance, atomistic modeling of B 2 O 3 containing glasses have been challenging due to the lack of reliable empirical potentials. Fortunately, a few recent developments have shown promises to simulate these glasses where the boron coordination has complex and non-linear dependence on glass composition. This work aims to provide an evaluation of the effectiveness of three recently developed potentials by a systematic study of a series (~20) of sodium borosilicate glasses with constant K (ratio of [SiO 2 ]/[B 2 O 3 ]) =2 and varying R (ratio of [Na 2 O]/[B 2 O 3 ] ranging from 0.1 to 4) values and several sodium boroaluminosilicate glasses. A comparative assessment was established on the basis of the short- and medium-range structure features, such as boron N 4 values, total correlation functions, bond angle distribution, oxygen speciation, and mechanical properties using experimental or well-established models as criteria. Furthermore, this work provides insights on the choices of empirical potentials for MD simulations of borosilicate glasses and gives directions of future potential development and refining.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2020

Ions Tune Interfacial Water Structure and Modulate Hydrophobic Interactions at Silica Surfaces

The structure and ultrafast dynamics of the electric double layer (EDL) are central to chemical reactivity and physical properties at solid/aqueous interfaces. While the Gouy–Chapman–Stern model is widely used to describe EDLs, it is solely based on the macroscopic electrostatic attraction of electrolytes for the charged surfaces. Structure and dynamics in the Stern layer are, however, more complex because of competing effects due to the localized surface charge distribution, surface–solvent–ion correlations, and the interfacial hydrogen bonding environment. Here, we report combined time-resolved vibrational sum frequency generation (TR-vSFG) spectroscopy with ab initio DFT-based molecular dynamics simulations (AIMD/DFT-MD) to get direct access to the molecular-level understanding of how ions change the structure and dynamics of the EDL. We show that innersphere adsorbed ions tune the hydrophobicity of the silica–aqueous interface by shifting the structural makeup in the Stern layer from dominant water–surface interactions to water–water interactions. This drives an initially inhomogeneous interfacial water coordination landscape observed at the neat interface toward a homogeneous, highly interconnected in-plane 2D hydrogen bonding (2D-HB) network at the ionic interface, reminiscent of the canonical, hydrophobic air–water interface. This ion-induced transformation results in a characteristic decrease of the vibrational lifetime (T 1 ) of excited interfacial O–H stretching modes from T 1 ~ 600 fs to T 1 ~ 250 fs. Hence, we propose that the T 1 determined by TR-vSFG in combination with DFT-MD simulations can be widely used for a quantitative spectroscopic probe of the ion kosmotropic/chaotropic effect at aqueous interfaces as well as of the ion-induced surface hydrophobicity.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Rotational and translational diffusion of liquid n-hexane: EFP-based molecular dynamics analysis

Molecular Dynamics (MD) simulations based on the Effective Fragment Potential (EFP) method are utilized to provide a comprehensive assessment of diffusion in liquid n-hexane. We decompose translational diffusion into components along and orthogonal to the long axis of the molecule. Rotational diffusion is decomposed into tumbling and spinning motions about this axis. Our analysis yields four corresponding diffusion coefficients which are related to diagonal entries in the complete 6 × 6 diffusion tensor accounting for the three rotational and three translational degrees of freedom and for the potential coupling between them. However, coupling between different degrees of freedom is expected to be minimal for a natural choice of the molecular body-fixed axis, so then off-diagonal entries in the tensor are negligible. This expectation is supported by a hydrodynamic analysis of the diffusion tensor which treats the liquid surrounding the molecule being tracked as a viscous continuum. Thus, the EFP MD analysis provides a comprehensive characterization of diffusion and also reveals expected shortcomings of the hydrodynamic treatment, particularly for rotational diffusion, when applied to neat liquids.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2022

Assessing models of force-dependent unbinding rates via infrequent metadynamics

Protein–ligand interactions are crucial for a wide range of physiological processes. Many cellular functions result in these non-covalent “bonds” being mechanically strained, and this can be integral to proper cellular function. Broadly, two classes of force dependence have been observed—slip bonds, where the unbinding rate increases, and catch bonds, where the unbinding rate decreases. Despite much theoretical work, we cannot predict for which protein–ligand pairs, pulling coordinates, and forces a particular rate dependence will appear. Here, we assess the ability of MD simulations combined with enhanced sampling techniques to probe the force dependence of unbinding rates. We show that the infrequent metadynamics technique correctly produces both catch and slip bonding kinetics for model potentials. We then apply it to the well-studied case of a buckyball in a hydrophobic cavity, which appears to exhibit an ideal slip bond. Finally, we compute the force-dependent unbinding rate of biotin–streptavidin. Here, the complex nature of the unbinding process causes the infrequent metadynamics method to begin to break down due to the presence of unbinding intermediates, despite the use of a previously optimized sampling coordinate. Allowing for this limitation, a combination of kinetic and free energy computations predicts an overall slip bond for larger forces consistent with prior experimental results although there are substantial deviations at small forces that require further investigation. Furthermore, this work demonstrates the promise of predicting force-dependent unbinding rates using enhanced sampling MD techniques while also revealing the methodological barriers that must be overcome to tackle more complex targets in the future.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Insights on the dissolution of water in an albite melt at high pressures and temperatures from a direct structural analysis

The water dissolution mechanism in silicate melts under high pressures is not well understood. Here we present the first direct structure investigation of a water-saturated albite melt to monitor the interactions between water and the network structure of silicate melt at the molecular level. In situ high-energy X-ray diffraction was carried out on the NaAlSi 3 O 8 -H 2 O system at 800 °C and 300 MPa, at the Advanced Photon Source synchrotron facility. The analysis of the X-ray diffraction data was augmented with classical Molecular Dynamics simulations of a hydrous albite melt, incorporating accurate water-based interactions. The results show that metal–oxygen bond breaking at the bridging sites occurs overwhelmingly at the Si site upon reaction with H 2 O, with subsequent Si–OH bond formation and negligible Al–OH formation. Furthermore, we see no evidence for the dissociation of the Al 3+ ion from the network structure upon breaking of the Si–O bond in the hydrous albite melt. The results also indicate that the Na + ion is an active participant in the modifications of the silicate network structure of the albite melt upon water dissolution at high P–T conditions. We do not find evidence for the Na + ion dissociating from the network structure upon depolymerization and subsequent formation of NaOH complexes. Instead, our results show that the Na + ion persists as a structure modifier with a shift away from Na–BO bonding to an increase in the extent of Na-NBO bonding, in parallel with pronounced depolymerization of the network. Our MD simulations show that the Si–O and Al–O bond lengths are expanded by about 6% in the hydrous albite melt compared to those of the dry melt at high P–T conditions. The changes in the network silicate structure of a hydrous albite melt at high pressure and temperature, as revealed in this study, must be considered in the advancement of water dissolution models of hydrous granitic (or alkali aluminosilicate) melts.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Mechanisms of ion irradiation induced ordering in amorphous TiO 2 nanotubes: Effects of ion mass and energy

Here, amorphous TiO 2 nanotubes were irradiated in-situ in a transmission electron microscope (TEM) with Kr + ions at energies of 46 keV, 150 keV, and 1 MeV and with 46 keV Xe + ions, to investigate the structural and morphological evolution of the nanotubes under irradiation. At all irradiation conditions, amorphous TiO 2 nanotubes exhibited significant morphological instability, and tended to undergo volumetric swelling with increasing ion counts, often until collapse of the original nanotube structure. Molecular dynamics (MD) simulations confirmed that irradiation-induced defects can explain the observed swelling. Structurally, nanotubes remain amorphous following all Kr + irradiation conditions, but irradiation with 46 keV Xe + leads to the formation of anatase nanocrystallites. Importantly, through systematically varying ion energy and ion species, we try to elucidate the influence of nuclear and electronic stopping power on ion irradiation induced changes. By contextualizing these results within the existing literature, we propose that the observed changes in TiO 2 nanotube morphology and structure could be due to a competition between two mechanisms: (1) disorder-induced swelling and (2) irradiation-induced amorphous-to-crystalline transformation.

36 MATERIALS SCIENCE↗

DOE OSTI2025

Dynamic Metal–Support Interaction Dictates Cu Nanoparticle Sintering on Al 2 O 3 Surfaces

Nanoparticle sintering remains a critical challenge in heterogeneous catalysis. In this work, we present a unified deep potential (DP) model based on the Perdew–Burke–Ernzerhof approximation of density functional theory for Cu nanoparticles on three Al 2 O 3 surfaces (γ-Al 2 O 3 (100), γ-Al 2 O 3 (110), and α-Al 2 O 3 (0001)). Using DP-accelerated simulations, we reveal that the nanoparticle size-mobility relationship strongly depends on the supporting surface. The diffusion of nanoparticles on the two γ-Al 2 O 3 surfaces is almost independent of the size of the nanoparticle, while the diffusion on α-Al 2 O 3 (0001) decreases rapidly with increasing size. Interestingly, nanoparticles with fewer than 55 atoms diffuse several times faster on α-Al 2 O 3 (0001) than on γ-Al 2 O 3 (100) at 800 K while expected to be more sluggish based on their larger binding energy at 0 K. The diffusion on α-Al 2 O 3 (0001) is facilitated by dynamic metal–support interaction (MSI), where Al atoms move out of the surface plane to optimize contact with the nanoparticle and relax back to the plane as the nanoparticle moves away. In contrast, the MSI on γ-Al 2 O 3 (100) and on γ-Al 2 O 3 (110) is dominated by more stable and directional Cu–O bonds, consistent with the limited diffusion observed on these surfaces. Our extended MD simulations provide insight into the sintering processes, showing that the dispersity of the nanoparticles strongly influences the coalescence driven by nanoparticle diffusion. We observed that the coalescence of Cu 13 nanoparticles on α-Al 2 O 3 (0001) can occur in a short time (10 ns) at 800 K even with an initial internanoparticle distance increased to 3 nm, while the coalescence on the two γ-Al 2 O 3 surfaces are inhibited significantly by increasing the initial internanoparticle distance. These findings demonstrate that the dynamics of the supporting surface is crucial to understanding the sintering mechanism and offer guidance for designing sinter-resistant catalysts by engineering the support morphology.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS1991

Macromolecular recognition: Structural aspects of the origin of the genetic system

Theoretical simulation of prebiotic chemical processes is an invaluable tool for probing the phenomenon of evolution of life. Using computational and modeling techniques and guided by analogies from present day systems we, seek to understand the emergence of genetic apparatus, enzymatic catalysis and protein synthesis under prebiotic conditions. In one possible scenario, the RNA enzymatic reaction plays a key role in the emergence of the self-replicating and offers a clue to the onset of enzymatic catalysis prior to the existence of the protein biosynthetic machinery. Our ultimate goal is to propose a simple RNA segment which contains the specificity and catalytic activity of the contemporary RNA enzyme and which could emerge in a primordial chemical environment. To understand the mechanism of ribozyme catalyzed reactions, ab initio and semi-empirical (ZINDO) programs were used to investigate the reaction path of transphosphorylation. A special emphasis was placed on the possible catalytic and structural roles played by the coordinated magnesium cation. Both the inline and adjacent mechanisms of transphosphorylation have been studied. Another important aspect of this reaction is the identity of the functional groups which are essential for the acid base catalysis. The structural characteristics of the target helices, particularly a possible role of G center dot T pair, is under examination by molecular dynamics (MD) simulation technique. Modeling of the ancestral aminoacyl-tRNA synthetases (aRS) may provide important clues to the emergence of the genetic code and the protein synthetic machinery. Assuming that the catalytic function evolved before the elements of specific recognition of a particular amino acid, we are exploring the minimal structural requirements for the catalysis of tRNA aminoacylation. The molecular modeling system SYBYL was used for this study based on the high resolution crystallographic structures of the present day tyrosyl-adenylate:tyrRS and tRNA(Gln): ATP:glnRS complexes. The trinucleotide CCA of the 3'-end tRNA is placed into the active site pocket of tyrRS, based on the scheme of interaction between tRNA(Gln) and glnRS, and upon the stereochemistry of the tyrRS:tRNA:Tyr-AMP transition state. This provides a model of the non-specific recognition of a tRNA's 3'-end by an aRS, which might be similar to that of the ancestral aRS's. In the next step, modeling of the rest of the acceptor stem of tRNA (Tyr) with tyrRS is carried out.

Rein, Robert↗

DOE OSTI2025

Nanoscale Miscibility in In Situ Polymerized Hybrid Electrolytes Speeds Up Ion Dynamics and Enables Stable Cycling of Li Metal Batteries

While the potential use of copolymerized electrolytes in Li metal batteries is subject to intense investigation, the fundamental understanding of the nanoscale domain formation and its effect on Li + transport is still lacking. In this study, we investigated the correlation between the Li + transport mechanism and the miscibility of monomers in polymer blend electrolytes derived from the in situ copolymerization of methyl methacrylate (MMA) and vinylene carbonate (VC) in the presence of polyethylene glycol dimethyl ether (PEGDME) plasticizer and bis(trifluoromethanesulfonyl)imide (LiTFSI) salt. The addition of a polar short chain plasticizer reduced the dynamic and structural heterogeneities of the electrolyte. Small-angle X-ray scattering (SAXS) measurements and coarse-grained molecular dynamics (MD) simulations were used to investigate the nanoscale structure of the electrolytes. The distribution of relaxation times corresponding to the three distinct diffusion mechanisms of the free and interfacial Li + ions at the copolymer/plasticizer and electrolyte/SEI boundaries was analyzed in a broad temperature range to elucidate the Li + transport mechanism. Furthermore, the chemical composition of the SEI and the contribution of a ceramic lithium lanthanum zirconium oxide (LLZO, Li 7 La 3 Zr 2 O 12 ) phase on the interfacial resistance, salt degradation, and SEI stability were studied by X-ray photoelectron spectroscopy (XPS) depth profile analysis and electrochemical testing.

Li metal↗