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All sourcesNASA NTRSDOE OSTI
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↗
DOE OSTI2020

The energetics and dynamics of confinement in flexible frameworks and molecular confinement

Porous frameworks form the chemical and structural basis for critical technologies in separations, catalysis, nuclear waste containment and biomedical applications. Hundreds of zeolites and metal organic frameworks (MOFs) have been synthesized, and their ability to separate and store hydrogen, methane and carbon dioxide has been investigated both experimentally and theoretically. Nevertheless, a fundamental and systematic molecular-level understanding of the thermodynamic and structural factors governing the stability and guest-host interactions in these materials lags behind focused studies of specific systems. Because the guest molecules interact with each other and with the host framework, molecular confinement is a finely balanced and complex phenomenon. The ability of the guest molecules to bind and diffuse through the pores is determined by the nature of the host framework which, in turn, responds to the nature and concentration of guest molecules and to pressure and temperature. The work explores how framework flexibility, tailored by structure, composition, temperature and pressure, is a general phenomenon, similar in nature but variable in extent, in both zeolites and MOFs and is part of a free energy landscape in which framework-guest interactions, pressure, and temperature result in changes in framework geometry and, in some cases, phase transitions. These subtle and/or pronounced changes in lattice geometry, energetics, and dynamics can play a decisive role in confinement and in differentiating the binding of molecules of similar size. The free energy landscape created by these structural changes links polymorphism, amorphization, “breathing,” “gate opening” and confinement. Specifically, the generality of such behavior arises from commonalities in lattice dynamics and energetics of frameworks containing a combination of strong rigid bonds and weaker more flexible deformation modes. Identifying and describing these common and collective phenomena is the focus of the research on a selected group of zeolites and MOFs. Structural studies using X-ray and neutron diffraction explore the mechanical functionality of these important materials, specifically how framework materials respond to changes in temperature, pressure and guest loading. These structural studies are combined with calorimetric measurements, using techniques uniquely developed in the participating laboratories, of heats of formation, heat capacities and entropies, and guest-host interactions. The experimental thermodynamic studies are complemented by inelastic neutron scattering studies of the lattice dynamics related both to framework vibrations and to guest-host interactions. The report below summarizes the work done at UC Davis, which is complemented by work done at BYU (Woodfield) and Virginia Tech (Ross).

36 MATERIALS SCIENCE↗
DOE OSTI2022

The energetics and dynamics of confinement in flexible frameworks and molecular confinement

Porous frameworks form the chemical and structural basis for critical technologies in separations, catalysis, nuclear waste containment and biomedical applications. Hundreds of zeolites and metal organic frameworks (MOFs) have been synthesized, and their ability to separate and store hydrogen, methane and carbon dioxide has been investigated both experimentally and theoretically. Nevertheless, a fundamental and systematic molecular-level understanding of the thermodynamic and structural factors governing the stability and guest-host interactions in these materials lags behind focused studies of specific systems. Because the guest molecules interact with each other and with the host framework, molecular confinement is a finely balanced and complex phenomenon. The ability of the guest molecules to bind and diffuse through the pores is determined by the nature of the host framework which, in turn, responds to the nature and concentration of guest molecules and to pressure and temperature. The work explores how framework flexibility, tailored by structure, composition, temperature and pressure, is a general phenomenon, similar in nature but variable in extent, in both zeolites and MOFs and is part of a free energy landscape in which framework-guest interactions, pressure, and temperature result in changes in framework geometry and, in some cases, phase transitions. These subtle and/or pronounced changes in lattice geometry, energetics, and dynamics can play a decisive role in confinement and in differentiating the binding of molecules of similar size. The free energy landscape created by these structural changes links polymorphism, amorphization, “breathing,” “gate opening” and confinement. Specifically, the generality of such behavior arises from commonalities in lattice dynamics and energetics of frameworks containing a combination of strong rigid bonds and weaker more flexible deformation modes. Identifying and describing these common and collective phenomena is the focus of the research on a selected group of zeolites and MOFs. Structural studies using X-ray and neutron diffraction explore the mechanical functionality of these important materials, specifically how framework materials respond to changes in temperature, pressure and guest loading. These structural studies are combined with calorimetric measurements, using techniques uniquely developed in the participating laboratories, of heats of formation, heat capacities and entropies, and guest-host interactions. The experimental thermodynamic studies are complemented by inelastic neutron scattering studies of the lattice dynamics related both to framework vibrations and to guest-host interactions. This research was a collaboration between UC Davis (A. Navrotsky) BYU (B. Woodfield) and Virginia Tech (N. Ross).

36 MATERIALS SCIENCE↗
DOE OSTI2025

Nature of molybdenum carbide surfaces for catalytic hydrogen dissociation using machine-learned potentials: an ensemble-averaged perspective

Molybdenum carbides with an electronic structure similar to noble metals have gained attention as a promising low-cost catalyst for biomass valorization and the hydrogen evolution reaction. However, our fundamental understanding of the catalyst surface and how different phases of these catalysts behave at varying reaction conditions is limited to ground state density functional theory calculations as ab initio molecular dynamics (AIMD) is computationally prohibitive at relevant length and time scales. Here, in this work, we train a multi-atomic cluster expansion (MACE) machine-learned interatomic potentials (MLIP) to study hydrogen dissociation and dynamics over Mo, δ-MoC, α-Mo 2 C, and β-Mo 2 C surfaces at varying temperatures and hydrogen partial pressures. Our simulations identify unique and different molecular and atomic hydrogen adsorption sites on different surfaces that do not depend on the temperature. At low hydrogen pressures, the surface coverage is monolayer, which transitions to two-layer adsorption at higher pressures. We find that atomic hydrogen diffusion and recombinations are preferred over molybdenum atom hollow sites, while the diffusion over carbon-terminated facets was negligible, signifying particularly strong C–H interactions. In contrast, molecular hydrogen adsorption occurs mostly atop Mo or the bridging sites. At a comparable hydrogen loading, β-Mo 2 C (001) is the most active surface for hydrogen dissociation reaction. This work provides insights into the dynamic nature of the hydrogen dissociation chemistry and the diversity of hydrogen adsorption sites on molybdenum carbides.

08 HYDROGEN↗
DOE OSTI2021

Oxygen Electrocatalysis on Mixed-Metal Oxides/Oxyhydroxides: From Fundamentals to Membrane Electrolyzer Technology

Catalyzing the oxygen evolution reaction (OER) is important for key energy-storage technologies, particularly water electrolysis and photoelectrolysis for hydrogen fuel production. Under neutral-to-alkaline conditions, first-row transition-metal oxides/(oxy)hydroxides are the fastest-known OER catalysts and have been the subject of intense study for the past decade. Critical to their high performance is the intentional or accidental addition of Fe to Ni/Co oxides that convert to layered (oxy)hydroxide structures during the OER. Unraveling the role that Fe plays in the catalysis and the molecular identity of the true “active site” has proved challenging, however, due to the dynamics of the host structure and absorbed Fe sites as well as the diversity of local structures in these disordered active phases. In this Account, we highlight our work to understand the role of Fe in Ni/Co (oxy)hydroxide OER catalysts. We first discuss how we characterize the intrinsic activity of the first-row transition-metal (oxy)hydroxide catalysts as thin films by accounting for the contributions of the catalyst-layer thickness (mass loading) and electrical conductivity as well as the underlying substrate’s chemical interactions with the catalyst and the presence of Fe species in the electrolyte. We show how Fe-doped Ni/Co (oxy)hydroxides restructure during catalysis, absorb/desorb Fe, and in some cases degrade or regenerate their activity during electrochemical testing. We highlight the relevant techniques and procedures that allowed us to better understand the role of Fe in activating other first-row transition metals for OER. We find several modes of Fe incorporation in Ni/Co (oxy)hydroxides and show how those modes correlate with activity and durability. We also discuss how this understanding informs the incorporation of earth-abundant transition-metal OER catalysts in anion-exchange-membrane water electrolyzers (AEMWE) that provide a locally basic anode environment but run on pure water and have advantages over the more-developed proton-exchange-membrane water electrolyzers (PEMWE) that use platinum-group-metal (PGM) catalysts. We outline the key issues of introducing Fe-doped Ni/Co (oxy)hydroxide catalysts at the anode of the AEMWE, such as the oxidative processes triggered by Fe species traveling through the polymer membrane, pH-gradient effects on the catalyst stability, and possibly limited catalyst utilization in the compressed stack configuration. We also suggest possible mitigation strategies for these issues. Lastly, we summarize remaining challenges including the long-term stability of Fe-doped Ni/Co (oxy)hydroxides under OER conditions and the lack of accurate models of the dynamic active surface that hinder our understanding of, and thus ability to design, these catalysts.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Enhanced Oxide Reduction by Hydrogen at Cuprous Oxide–Copper Interfaces near Ascending Step Edges

We report that understanding the dynamic processes involved in the interaction of hydrogen with oxides is of fundamental importance in catalysis. This paper probes the reduction of Cu 2 O-‘29’ surfaces by hydrogen at room temperature combining in situ ambient pressure scanning tunneling microscopy (STM), X-ray photoelectron spectroscopy (XPS), and density functional theory (DFT) calculations. Reduction of the atomic layer thin Cu 2 O film is observed to be preferentially initiated2 at step edges and terrace defects, where perfect Cu 2 O(111) terraces are found to be stable towards hydrogenation under the same conditions. After a long induction period, regions of partially reduced Cu 2 O-‘29’ and metallic Cu co-exist before the surface is fully reduced to Cu(111). The reduction rate strongly depends on the nature of nearby Cu step edges. We propose a mechanism for the reduction of Cu 2 O-‘29’ by hydrogen where free copper atoms from ascending metallic step edges facilitate the formation of active ensembles for H 2 dissociation and transfer H to the edges of Cu2O regions

08 HYDROGEN↗
DOE OSTI2026

Theoretical Insights into Reaction-Induced Transformation and Tuning of Catalytic Behavior in Heterogenous Catalysis

Reaction-induced transformations in heterogenous catalysis represent diverse phenomena that challenge traditional views of static catalyst surfaces. From surface adsorbate dynamics, atomic rearrangements, to composition and phase transitions, these processes reveal the profound differences between idealized model systems under ultrahigh vacuum and the complex, evolving interfaces that govern real catalytic behaviors under reaction conditions. Here, this perspective reviews recent theoretical efforts to provide atomic-level mechanistic insights into significant reaction-induced transformations and their impact on catalytic activity and selectivity. It underscores the need for an integrated framework that combines predictive simulations with operando characterization to uncover active sites and mechanisms under realistic operating conditions. Achieving this requires accelerating existing simulations to fully capture diverse reaction-induced surface dynamics, enabling scalable and accurate modeling of catalysts as condition-dependent, dynamically evolving systems. Such approaches are critical to bridge the gap between theory and practice, offering a pathway to more impactful and predictive catalyst design.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2024

A modular and extensible CHARMM-compatible model for all-atom simulation of polypeptoids

Peptoids (N-substituted glycines) are a class of sequence-defined synthetic peptidomimetic polymers with applications including drug delivery, catalysis, and biomimicry. Classical molecular simulations have been used to predict and understand the conformational dynamics of single chains and their self-assembly into morphologies including sheets, tubes, spheres, and fibrils. The CGenFF-NTOID model based on the CHARMM General Force Field has demonstrated success in accurate all-atom molecular modeling of peptoid structure and thermodynamics. Extension of this force field to new peptoid side chains has historically required reparameterization of side chain bonded interactions against ab initio data. This fitting protocol improves the accuracy of the force field but is also burdensome and precludes modular extensibility of the model to arbitrary peptoid sequences. In this work, we develop and demonstrate a Modular Side Chain CGenFF-NTOID (MoSiC-CGenFF-NTOID) as an extension of CGenFF-NTOID employing a modular decomposition of the peptoid backbone and side chain parameterizations, wherein arbitrary side chains within the large family of substituted methyl groups (i.e., –CH 3 , –CH 2 R, –CHRR', and –CRR'R") are directly ported from CGenFF. We validate this approach against ab initio calculations and experimental data to develop a MoSiC-CGenFF-NTOID model for all 20 natural amino acid side chains along with 13 commonly used synthetic side chains and present an extensible paradigm to efficiently determine whether a novel side chain can be directly incorporated into the model or whether refitting of the CGenFF parameters is warranted. We make the model freely available to the community along with a tool to perform automated initial structure generation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Probing the influence of ion-pairing on ligand-field excited-state dynamics

Exploration of the photophysical and photochemical properties of transition metal complexes has driven ground-breaking advancements in solar energy conversion technologies, including photoredox catalysis. While significant research has been devoted to understanding excited state properties of second- and third-row transition metal complexes, earth-abundant first-row metal complexes have received comparatively little attention in this context until very recently. In particular, the role of ion-pairing – which has been identified as a potentially significant factor for Ir(III)-based photosensitizers – has not been examined with regard to its influence on the ligand-field excited states that dominate much of first-row photophysics. A key challenge in studying ion-pair interactions lies in quantifying the extent and nature of ion-pairing, particularly in non-aqueous media where the vast majority of photophysical studies are performed. Cobalt(III) polypyridyl complexes provide an attractive platform to address such questions due to their demonstrated potential for applications in photoredox catalysis involving ligand-field excited states. In the present study, we prepared a cobalt(III) polypyridyl complex, [Co(4,4′-OMebpy) 3 ](BAr F 4 ) 3 (where 4,4′-OMebpy is 4,4′-dimethoxy-2,2′-bipyridine and BAr F 4 is tetrakis(3,5-bis(trifluoromethyl)-phenyl)borate) to probe ion-pairing in non-aqueous solutions. Specifically, analysis of data acquired from both variable-temperature diffusion ordered spectroscopy (DOSY) NMR and 1-D rotating-frame nuclear Overhauser effect (ROE) experiments allowed us to identify and differentiate between solvent-separated ion pairs in high-dielectric media and contact ion pairs in a low-dielectric solvent. Time-resolved absorption spectroscopy was then used to measure ground-state recovery dynamics under these varying conditions of ion-pairing, the results of which revealed an increase in excited-state lifetime for contact ion-pairs that we suggest arises from a reduction in outer-sphere reorganization energy relative to conditions which favored solvent-separated ion pairs. We believe this study demonstrates that one can leverage broadly available NMR-based methods to understand ion-pairing in non-aqueous solutions, which in turn can provide a microscopic picture of intermolecular interactions that can impact the photophysical properties of transition metal-based chromophores.

Ghosh, Atanu [Michigan State University, East Lans↗
DOE OSTI2020

The energetics and dynamics of confinement in flexible frameworks and molecular confinement

This project is part of an ongoing and long-term collaboration among Alexandra Navrotsky (who moved recently from UC Davis to Arizona State University), Nancy Ross at Virginia Tech, and Brian Woodfield at Brigham Young University (BYU) on the thermodynamics and lattice dynamics of nanophase and porous materials. Navrotsky emphasizes energetics of formation and guest molecule sorption by ambient and high temperature calorimetry, Woodfield contributes cryogenic heat capacity measurements, and Ross uses inelastic neutron scattering, X-ray and neutron diffraction, and high pressure studies to probe lattice dynamics and phase transitions. Porous frameworks form the chemical and structural basis for critical technologies in separations, catalysis, nuclear waste containment and biomedical applications. Hundreds of zeolites and metal organic frameworks (MOFs) have been synthesized, and their ability to separate and store hydrogen, methane and carbon dioxide has been investigated both experimentally and theoretically. Nevertheless, a fundamental and systematic molecular-level understanding of the thermodynamic and structural factors governing the stability and guest-host interactions in these materials lags behind focused studies of specific systems. Because the guest molecules interact with each other and with the host framework, molecular confinement is a finely balanced and complex phenomenon. The ability of the guest molecules to bind and diffuse through the pores is determined by the nature of the host framework which, in turn, responds to the nature and concentration of guest molecules and to pressure and temperature. The work explores how framework flexibility, tailored by structure, composition, temperature and pressure, is a general phenomenon, similar in nature but variable in extent, in both zeolites and MOFs and is part of a free energy landscape in which framework-guest interactions, pressure, and temperature result in changes in framework geometry and, in some cases, phase transitions. These subtle and/or pronounced changes in lattice geometry, energetics, and dynamics can play a decisive role in confinement and in differentiating the binding of molecules of similar size.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Machine-Learned Force Field for Molecular Dynamics Simulations of Nonequilibrium Ammonia Synthesis on Iron Catalysts

Ammonia (NH 3 ) is one of the most important industrial chemicals. The conventional NH 3 synthesis method-the Haber–Bosch process-converts atmospheric nitrogen (N 2 ) into NH 3 using H 2 with an iron (Fe) catalyst. However, this process requires high pressures (100–200 atm) and temperatures (700–800 K) near thermal equilibrium. Recently, Fe-based nanocatalysts have been reported to produce promising NH 3 yields under atmospheric pressures and temperature-modulated nonequilibrium conditions. Understanding the mechanism of nonequilibrium catalysis with programmed temperature variation could help to optimize this fully electrified and less energy-intensive process. Although reactive molecular dynamics (RMD) simulations can be a useful tool to model nonequilibrium catalytic processes, they require the development of accurate force fields (i.e., interatomic potentials). Here, we present a machine-learned (ML) force field within the Deep Potential MD (DPMD) framework, trained using periodic density functional theory (DFT) calculations, to model NH 3 synthesis on Fe catalysts with various surface adsorbates such as *N, *H, *N 2 , *H 2 , *NH, *NH 2 , and *NH 3 . Here, we generated the DFT data from static models of elementary reactions on the most stable (110) surface of body-centered cubic Fe, which then were augmented by data from constant number of particles–volume–temperature (NVT) DFT-MD trajectories at various temperatures. Finally, we utilized the fully optimized ML force field to investigate reaction dynamics at an Fe(110) surface at linearly increasing temperatures using NVT-DPMD simulations. Our simulations indicate that pulsed temperature ramping could prove favorable for NH3 synthesis. For example, we conducted ramping under multiple sets of conditions: (i) from 900 to 1200 K over periods of 0.1–0.3 ns for Fe surfaces precovered with N or NH along with H; and (ii) from 300 to 600 K over 0.1–0.3 ns for Fe surfaces precovered with NH 3 . While our simulations so far are limited to short time scales (very rapid heating), these observations shed light on the mechanism of the high NH 3 synthesis rate achieved in a novel temperature-modulated nonequilibrium catalytic reactor using pulsed heating and cooling.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Dynamic Evolution of Palladium Single Atoms on Anatase Titania Support Determines the Reverse Water–Gas Shift Activity

Research interest in single-atom catalysts (SACs) has been continuously rising. However, the lack of understanding of the dynamic behaviors of SACs during applications hinder catalyst development and mechanistic understanding. Herein, we report on the evolution of active sites over Pd/TiO 2 -anatase SAC (Pd 1 /TiO 2 ) in the reverse water-gas shift (rWGS) reaction. Combining kinetics, in-situ characterization, and theory, we show that at T ≥ 350 °C, the reduction of TiO 2 by H 2 alters the coordination environment of Pd, creating Pd sites with partially cleaved Pd-O interfacial bonds and a unique electronic structure that exhibit high intrinsic rWGS activity through the carboxyl pathway. The activation by H 2 is accompanied by the partial sintering of single Pd atoms (Pd 1 ) into disordered, flat, ~1 nm diameter clusters (Pd n ). The highly active Pd sites in the new coordination environment under H 2 are eliminated by oxidation, which, when performed at high temperature, also re-disperses Pd n and facilitates the reduction of TiO 2 . In contrast, Pd 1 sinters into crystalline, ~5 nm particles (Pd NP ) during CO treatment, deactivating Pd 1 /TiO 2 . During the rWGS reaction, the two Pd evolution pathways co-exist. The activation by H 2 dominates, leading to the increasing rate with time-on-stream, and steady-state Pd active sites similar with the ones formed under H 2 . Finally, this work demonstrates how the coordination environment and nuclearity of metal sites on a SAC evolve during catalysis and pre-treatments, and how their activity is modulated by these behaviors. These insights on SAC dynamics and structure-function relationship are valuable to mechanistic understanding and catalyst design.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Environmental Contributions to Proton Sharing in Protein Low-Barrier Hydrogen Bonds

Hydrogen bonds (H-bonds) are central to biomolecular structure and dynamics. Although H-bonds are typically characterized by well-defined proton positions, proton delocalization has been proposed to play a role in facilitating enzyme catalysis and allostery in some systems. Experimentally locating protons is difficult, hampering the study of proton mobility in H-bonds. We used neutron crystallography, atomic resolution X-ray bond length analysis, and large quantum mechanics/molecular mechanics-Born–Oppenheimer molecular dynamics (QM/MM-BOMD) simulations to comprehensively characterize the shared proton/deuteron in a Glu–Asp low-barrier hydrogen bond (LBHB) in the bacterial protein YajL that is a conventional H-bond in the homologous disease-associated human protein DJ-1. X-ray bond length analysis of protiated and perdeuterated DJ-1 and YajL shows no significant effect of deuteron substitution on these carboxylic acid-carboxylate H-bonds but does reveal an effect at the active site glutamic acid near a cysteine thiolate. Residues in an H-bonded network that might favor LBHB formation in YajL were interrogated by the mutation of homologous residues in DJ-1. A distal DJ-1 substitution increases proton delocalization in the Glu–Asp H-bond, demonstrating that mutations within extended H-bond networks can modulate proton transfer barriers in carboxylic acid-carboxylate H-bonds. In addition, proton mobility in the H-bond is correlated with dimer-spanning motions in the QM/MM-BOMD simulations of YajL and DJ-1. Our results show that proton delocalization can be tuned using combined bioinformatic, structural, and computational information, opening the possibility of using engineered proton delocalization as a probe of H-bonding environments and as a tool to test hypotheses about LBHB function.

Lin, Jiusheng [University of Nebraska, Lincoln, NE↗
DOE OSTI2021

Hydration structure of flat and stepped MgO surfaces

We investigate the solvation structure of flat and stepped MgO(001) in neutral liquid water using ab initio molecular dynamics based on a hybrid density functional with dispersion corrections. Our simulations show that the MgO surface is covered by a densely packed layer of mixed intact and dissociated adsorbed water molecules in a planar arrangement with strong intermolecular H-bonds. The water dissociation fractions in this layer are >20% and >30% on the flat and stepped surfaces, respectively. Slightly above the first water layer, we observe metastable OH groups perpendicular to the interface, similar to those reported in low temperature studies of water monolayers on MgO. Here, these species receive hydrogen bonds from four nearby water molecules in the first layer and have their hydrophobic H end directed toward bulk water, while their associated protons are bound to surface oxygens. The formation of these OH species is attributed to the strong basicity of the MgO surface and can be relevant for understanding various phenomena from morphology evolution and growth of (nano)crystalline MgO particles to heterogeneous catalysis.

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 OSTI2020

Probing Pore Size and Connectivity in Porous Silicas Using 13C MAS NMR Spectroscopy of Supercritical Methane

Measuring the pore size and pore-size distributions and exploring the fluid-exchange dynamics between different types of pores in porous materials remains a significant experimental challenge but is critical to understanding catalysis, chromatography, nutrient cycling, and a whole range of geochemical phenomena, including shale gas and tight gas extraction. Here, we present the results of 1D 13 C NMR and 2D exchange spectroscopy (EXSY) NMR investigations of a porous silica using supercritical methane (scCH 4 ) as a direct probe of pore size and fluid exchange between pore types. The results show that the 13 C chemical shift of scCH 4 adsorbed in nanometer-scale silica pores becomes more negative with increasing pore diameter, in agreement with trends reported for gas hydrates, zeolites, MOFs, and clays and other microporous (<10 nm pores) geochemical materials. These 13 C chemical shifts follow a natural log–linear trend with pore size in the vacuum-dried porous silicas studied here, allowing one to predict pore size based on the 13 C chemical shift in dry silica nanopores. The EXSY and 1D 13 C NMR results both show that CH 4 exchanges between pore and bulk fluid environments over rate scales from 0.01 to 1 kHz in vacuum-dried samples and that exchange dynamics must be considered when interpreting 13 C NMR of pore-adsorbed CH 4 . Introducing H 2 O to the system causes the 13 C chemical shift to become more negative with increasing H 2 O content as a result of H 2 O preferentially filling small pores, forcing CH 4 to occupy larger pores that are better connected to the bulk environment. Likewise, the 1D 13 C data show a decreased distribution of exchange rates between pore-adsorbed and bulk CH 4 in the presence of H 2 O.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Applying deep learning methods to develop new models of molecular charge transfer, nonadiabatic dynamics, and nonlinear spectroscopy in the condensed phase

Photon- and field-induced charge transfer has central importance in the generation and storage of electricity, the novel properties of materials, photo-induced catalysis, and electro-optic activity (e.g., photovoltaic cells, fuel cells, and organic chromophores for use in optical fibers and light-emission diodes). These non-equilibrium electronic and chemical transformations are probed by ultrafast, nonlinear spectroscopies. Accurate simulations play a crucial role in our ability to understand, optimize, and control these transformations. This project applies modern deep learning and machine learning (ML) methods to dramatically improve models of electronic dynamics, electronic-nuclear dynamics, and spectroscopic measurements for improved simulations of chemistry in complex environments, far from equilibrium phenomena, and processes in extreme environments, such as materials exposed to strong or resonant fields. This project develops accurate neural net models that go beyond predictive capability to also provide new insight into the fundamental physics underlying electron and nuclear dynamics. To achieve its objectives, this project explores and develops customized versions of high-capacity deep learning algorithms/models. These techniques are developed with an emphasis on fundamental chemical insight, not just predictive accuracy, to assist the development of the next generation of quantum simulation methods.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Dynamic Behavior of Platinum Atoms and Clusters in the Native Oxide Layer of Aluminum Nanocrystals

Strong metal–support interactions (SMSIs) are well-known in the field of heterogeneous catalysis to induce the encapsulation of platinum (Pt) group metals by oxide supports through high temperature H 2 reduction. However, demonstrations of SMSI overlayers have largely been limited to reducible oxides, such as TiO 2 and Nb 2 O 5 . In this report we show that the amorphous native surface oxide of plasmonic aluminum nanocrystals (AlNCs) exhibits SMSI-induced encapsulation of Pt following reduction in H 2 in a Pt structure dependent manner. Reductive treatment in H 2 at 300 °C induces the formation of an AlO x SMSI overlayer on Pt clusters, leaving Pt single-atom sites (Ptiso) exposed available for catalysis. The remaining exposed Pt iso species possess a more uniform local coordination environment than has been observed on other forms of Al 2 O 3 , suggesting that the AlO x native oxide of AlNCs presents well-defined anchoring sites for individual Pt atoms. This observation extends our understanding of SMSIs by providing evidence that H 2 -induced encapsulation can occur for a wider variety of materials and should stimulate expanded studies of this effect to include nonreducible oxides with oxygen defects and the presence of disorder. It also suggests that the single-atom sites created in this manner, when combined with the plasmonic properties of the Al nanocrystal core, may allow for site-specific single-atom plasmonic photocatalysis, providing dynamic control over the light-driven reactivity in these systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗