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At least 667 records · Page 37
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

From bulk to surface: Structure and dynamics of amorphous alumina from deep potential molecular dynamics

Understanding the atomic-scale structure and dynamics of amorphous oxide surfaces is essential for interpreting their chemical reactivity, mechanical stability, and interfacial behavior, yet direct experimental characterization remains challenging. We employ Deep Potential (DP) molecular dynamics to generate large-scale, ab initio -quality models of amorphous Al 2 O 3 bulk glasses and melt-quenched free surfaces, enabling a quantitative analysis of both structure and relaxation dynamics with statistical confidence inaccessible to direct ab initio simulation. The trained DP model reproduces experimental liquid and glass structure, captures the cooling-rate dependence of the bulk glass transition, and corrects systematic biases in the polyhedral populations predicted by widely used classical force fields. At the free surface, mass density recovers to bulk values over ~10 Å, while local coordination requires a slightly wider subsurface region to fully converge. The outermost layer is oxygen-enriched, exhibits altered polyhedral connectivity with contracted Al–O bonds, and hosts a broad population of under-coordinated motifs (notably AlO 3 and OAl 2 ) whose abundances are governed by glass stability. These under-coordinated surface motifs exhibit distinct vibrational signatures and occur as locally paired Lewis acid and Brønsted base sites consistent with bond-valence compensation, yet remain spatially dispersed rather than aggregating into extended clusters. Despite this pronounced structural heterogeneity, surface relaxation and the glass-transition temperature remain comparable to their bulk counterparts, suggesting that the disordered surface is kinetically stable once formed. Together, these results establish a molecular-level picture of amorphous alumina surfaces and demonstrate the capability of machine-learned potentials to resolve structure–property relationships in disordered oxide interfaces.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

First Principles Nonadiabatic Excited-State Molecular Dynamics in NWChem

Computational simulation of non-adiabatic molecular dynamics is an indispensable tool for understanding complex photoinduced processes such as internal conversion, energy transfer, charge separation, and spatial localization of excitons, to name a few. Here, we report an implementation of the fewest-switches surface hopping algorithm in the NWChem computational chemistry program. Here the surface hopping method is combined with linear-response time-dependent density functional theory calculations of adiabatic excited state potential energy surfaces. To treat quantum transitions between arbitrary electronic Born{Oppenheimer states, we have implemented both numerical and analytical differentiation schemes for derivative non-adiabatic couplings. A numerical approach for the time-derivative non-adiabatic couplings together with an analytical method for calculating non-adiabatic coupling vectors is an efficient combination for surface hopping approaches. Additionally, electronic decoherence schemes and a state reassigned unavoided crossings algorithm are also implemented to improve the accuracy of the simulated dynamics and to handle trivial unavoided crossings. We apply our code to study the ultrafast decay of photoexcited benzene, including a detailed analysis of the potential energy surface, population decay time scales, and vibrational coordinates coupled to the excitation dynamics. The development presented in this work is a baseline for future implementations of more sophisticated frameworks for simulating of non-adiabatic molecular dynamics in NWChem.

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

Cellular Phosphate Sensing and Anion Binding by an Azacrown‐Calixpyrrole Hybrid

A hybrid receptor-sensor for anions originating from the merging of positively charged ammonium moieties for electrostatic attraction/stronger binding of azacrowns with directionality of calixpyrrole hydrogen bond donors for selectivity is investigated. As demonstrated this hybrid receptor-sensor shows a remarkable selectivity for orthophosphate even in the presence of other phosphates and anions found in cellular materials (K assoc H 2 PO 4 − >H 2 P 2 O 7 2− >AMP − ≫ADP 2− or ATP 3− over halides, nitrate, or hydrogen sulfate; all Na + salts in water) but also cellular polyphosphate or phospholipids. This selectivity is harnessed in a real-time monitoring of cell lysis by lysozyme, which releases orthophosphate and other phosphates and anions from the cells. This sensitive (LOD 0.4 μM) fluorescence-based microscale method compares favorably with the state-of-the-art techniques but can easily be practiced in a high-throughput screening (HTS) manner. The anion binding and selectivity in aqueous solutions were investigated by NMR and put in context with phosphate binding of the parent calix[4]pyrrole. The microscopic understanding of anion binding by the hybrid receptor was then obtained from a combination of density functional theory (DFT), classical molecular dynamics (MD) with explicit water solvation, and ab initio MD (AIMD) simulations. Correlating the NMR and fluorescence binding data with studies of solvation of the receptor, phosphate anion, and the resulting complex confirms the binding is largely driven by entropic component (TΔS) associated with receptor and anion desolvation.

Anions↗
DOE OSTI2024

Molecular Dynamics Simulation of Complex Reactivity with the Rapid Approach for Proton Transport and Other Reactions (RAPTOR) Software Package

Simulating chemically reactive phenomena such as proton transport on nanosecond to microsecond and beyond time scales is a challenging task. Ab initio methods are unable to currently access these time scales routinely, and traditional molecular dynamics methods feature fixed bonding arrangements that cannot account for changes in the system’s bonding topology. The Multiscale Reactive Molecular Dynamics (MS-RMD) method, as implemented in the Rapid Approach for Proton Transport and Other Reactions (RAPTOR) software package for the LAMMPS molecular dynamics code, offers a method to routinely sample longer time scale reactive simulation data with statistical precision. RAPTOR may also be interfaced with enhanced sampling methods to drive simulations toward the analysis of reactive rare events, and a number of collective variables (CVs) have been developed to facilitate this. Key advances to this methodology, including GPU acceleration efforts and novel CVs to model water wire formation are reviewed, along with recent applications of the method which demonstrate its versatility and robustness.

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

Computational Insights into Malononitrile-Based Carbanions for CO 2 Capture

Although anionic N and O sites have been widely used in chemisorption of CO 2 , carbanions are much less explored for CO 2 capture. Here, in this study, we employ ab initio calculations and quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) simulations to examine the interaction between CO 2 and the malononitrile carbanion, [CH(CN) 2 ] – . We have explored the potential energy surface of CO 2 binding by scanning the C–C distance between CO 2 and the central C site of the carbanion. We find that CO 2 prefers to bind to the nitrile group physically rather than to form a C–C bond via the carboxylation reaction at the sp 2 C site. Moreover, the two –CN groups can attract two CO 2 molecules at equal strength. The presence of an alkali metal ion enhances both physical and chemical interactions of CO 2 with the malononitrile carbanion. QM/MM MD simulations further confirm the preference of physical interaction in the condensed ionic liquid phase with a phosphonium cation. Our findings suggest that ionic liquids based on the malononitrile carbanion may have a high CO 2 solubility for carbon capture.

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

Low-index mesoscopic surface reconstructions of Au surfaces using Bayesian force fields

Metal surfaces have long been known to reconstruct, significantly influencing their structural and catalytic properties. Many key mechanistic aspects of these subtle transformations remain poorly understood due to limitations of previous simulation approaches. Using active learning of Bayesian machine-learned force fields trained from ab initio calculations, we enable large-scale molecular dynamics simulations to describe the thermodynamics and time evolution of the low-index mesoscopic surface reconstructions of Au (e.g., the Au(111)-‘Herringbone,’ Au(110)-(1 × 2)-‘Missing-Row,’ and Au(100)-‘Quasi-Hexagonal’ reconstructions). This capability yields direct atomistic understanding of the dynamic emergence of these surface states from their initial facets, providing previously inaccessible information such as nucleation kinetics and a complete mechanistic interpretation of reconstruction under the effects of strain and local deviations from the original stoichiometry. We successfully reproduce previous experimental observations of reconstructions on pristine surfaces and provide quantitative predictions of the emergence of spinodal decomposition and localized reconstruction in response to strain at non-ideal stoichiometries. A unified mechanistic explanation is presented of the kinetic and thermodynamic factors driving surface reconstruction. Furthermore, we study surface reconstructions on Au nanoparticles, where characteristic (111) and (100) reconstructions spontaneously appear on a variety of high-symmetry particle morphologies.

36 MATERIALS SCIENCE↗
DOE OSTI2021

A Chemical Dynamics Study of the Reaction of the Methylidyne Radical (CH, X 2 Π) with Dimethylacetylene (CH 3 CCCH 3 , X 1 A 1g )

The gas-phase reaction of the methylidyne (CH; X 2 Π) radical with dimethylacetylene (CH 3 CCCH 3 ; X 1 A 1g ) was studied at a collision energy of 20.6 kJ mol -1 under single collision conditions with experimental results merged with ab initio calculations of the potential energy surface (PES) and ab initio molecule dynamics (AIMD) simulations. Here, the crossed molecular beams experiment reveals that the reaction proceeds barrierless via indirect scattering dynamics through long-lived C 5 H 7 reaction intermediate(s) ultimately dissociating to C 5 H 6 isomers along with atomic hydrogen with atomic hydrogen predominantly released from the methyl groups as verified by replacing the methylidyne with the D1-methylidyne reactant. AIMD simulations reveal that the reaction dynamics are statistical leading predominantly to p28 (1-methyl-3-methylene-cyclopropene, 13 %) and p8 (1-penten-3-yne, 81 %) plus atomic hydrogen with a significant amount of available energy being channeled into the internal excitation of the polyatomic reaction products.

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

Ultrafast Events in Electrocyclic Ring-Opening Reactions

Electrocyclic reactions are characterized by the concerted formation and cleavage of multiple σ and π bonds in a molecular system and have been extensively studied since they were introduced by Robert Burns Woodward and Roald Hoffmann in 1965. Recent advances and the integration of time-resolved experiments and nonadiabatic quantum molecular dynamics simulations have transformed the traditional understanding of electrocyclic reactions beyond the Woodward–Hoffmann rules. In this review, we focus on recent studies of 1,3-cyclohexadiene and two of its derivatives, α-phellandrene and α-terpinene, to shed light on the underlying mechanisms of electrocyclic photochemical reactions. We highlight recent progress in ultrafast electron diffraction techniques and the simulation approach of ab initio multiple spawning. Together, these approaches can elucidate molecular structure dynamics from femtosecond to picosecond timescales as well as nuclear and electronic responses at conical intersections.

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

Iodine recombination in xenon solvent: Clusters in the gas to liquid-like state transition

Supercritical fluids (SCFs) have attracted significant attention as solvents for chemical reactions due to their unique properties, such as high diffusivity, low viscosity, and tunable solvation properties. These properties profoundly influence reaction kinetics and are often attributed to the formation of molecular clusters within SCFs. To study the effect of supercritical solvent on chemical reactivity and dynamics of reactions, one needs to understand the dynamics of clusters in supercritical fluid. Extensive experiments on the photodissociation and recombination of iodine in supercritical fluids served as a model system for understanding these effects. Experimental studies have been complemented by theoretical and computational investigations, which mostly employ Monte Carlo or empirical molecular dynamics simulations. However, computational studies using non-reactive force fields and ab initio approaches present challenges in capturing reactive processes at larger scales within supercritical fluids. Here, in this work, we developed the ReaxFF parameters by training against quantum mechanics data. ReaxFF reactive force field based molecular dynamics simulations were performed, studying the dynamics of a xenon solvent and cage effect at different thermodynamic conditions for the iodine recombination reaction. We show that the conditions near the critical point are the optimal conditions to study the cage effect. We show that the average lifetime of xenon clusters ranging between 5 and 11 ps is comparable to iodine geminate recombination. Our simulation results of iodine recombination in xenon solvent demonstrate the higher probability of iodine molecule formation in the presence of xenon clusters. Finally, we show that the supercritical condition exhibits the highest recombination rate for iodine atoms.

Cage effect↗
DOE OSTI2025

High Radiation Resistance in the Binary W‐Ta System Through Small V Additions: A New Paradigm for Nuclear Fusion Materials

Abstract Refractory High‐Entropy Alloys (RHEAs) are promising candidates for structural materials in nuclear fusion reactors, where W‐based alloys are currently leading. Fusion materials must withstand extreme conditions, including i) severe radiation damage from energetic neutrons, ii) embrittlement due to H and He ion implantation, and iii) exposure to high temperatures and thermal gradients. Recent RHEAs, such as WTaCrV and WTaCrVHf, have shown superior radiation tolerance and microstructural stability compared to pure W, but their multi‐element compositions complicate bulk fabrication and limit practical use. In this study, it is demonstrated that reducing alloying elements in RHEAs is feasible without compromising radiation tolerance. Herein, two Highly Concentrated Refractory Alloys (HCRAs) − W 53 Ta 44 V 3 and W 53 Ta 42 V 5 (at.%) − were synthesized and investigated. We found that small V additions significantly influence the radiation response of the binary W–Ta system. Experimental results, supported by ab‐initio Monte Carlo simulations and machine‐learning‐driven molecular dynamics, reveal that minor variations in V content enhance Ta–V chemical short‐range order (CSRO), improving radiation resistance in the W 53 Ta 42 V 5 HCRA. By focusing on reducing chemical complexity and the number of alloying elements, the conventional high‐entropy alloy paradigm is challenged, suggesting a new approach to designing simplified multi‐component alloys with refractory properties for thermonuclear fusion applications.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2020

Thickness and strain dependence of piezoelectric coefficient in BaTiO 3 thin films

We explore the thickness dependence of the converse piezoelectric coefficient (d 33 ) in epitaxial thin films of BaTiO 3 (BTO) grown on (001) SrTiO 3 substrates. Piezoresponse force microscope was performed using an atomic force microscope equipped with an interferometric displacement sensor allowing direct quantification of electromechanical coupling coefficients in BTO free from unwanted background contributions. We find that 80-nm-thick films exhibit a d 33 of ~20.5pm/V, but as the thickness is reduced, the d 33 reduces to less than 2 pm/V for a 10 nm film. To explain the atomistic origin of the effect, we performed molecular dynamics simulations with a recently developed ab initio-derived reactive force field, constructed using the ReaxFF framework. Simulations predict that under applied electric fields thin films of BaTiO 3 show an increasing thickness, with compressive strain, of the region screening the depolarization-field. This study confirms quantitatively the drop in piezoelectric performance in BTO ultrathin films and again highlights the importance of the screening mechanisms when films approach the ultrathin limits in dictating the functional behaviors.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Thermodynamics of Liquid Uranium from Atomistic and Ab Initio Modeling

We present thermodynamic properties for liquid uranium obtained from classical molecular dynamics (MD) simulations and the first-principles theory. The coexisting phases method incorporated within MD modeling defines the melting temperature of uranium in good agreement with the experiment. The calculated melting enthalpy is in agreement with the experimental range. Classical MD simulations show that ionic contribution to the total specific heat of uranium does not depend on temperature. The density of states at the Fermi level, which is a crucial parameter in the determination of the electronic contribution to the total specific heat of liquid uranium, is calculated by ab initio all electron density functional theory (DFT) formalism applied to the atomic configurations generated by classical MD. The calculated specific heat of liquid uranium is compared with the previously calculated specific heat of solid γ-uranium at high temperatures. The liquid uranium cannot be supercooled below T sc ≈ 800 K or approximately about 645 K below the calculated melting point, although, the self-diffusion coefficient approaches zero at T D ≈ 700 K. Uranium metal can be supercooled about 1.5 times more than it can be overheated. The features of the temperature hysteresis are discussed.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Structural dynamics of laser-ionized cis-stilbene studied by ultrafast electron diffraction

Stilbene has been a model system for studying photoisomerization upon absorption of a UV photon. Although the dynamics of the first excited state have been investigated in great detail, the structural dynamics of cationic states remains largely experimentally unexplored. In this study, the dynamics following ionization via absorption of two UV photons was captured using ultrafast electron diffraction. cis-stilbene (CS) was optically pumped with 267 nm ultraviolet light with two different pump fluences and probed with 3.7 MeV electrons. We compare our experimental results to ab-initio multiple spawning simulations for single-photon excitation and molecular dynamics simulations for ionization in order to separate the contributions from the two channels. We found that with a fluence of 170 mJ cm −2 both the single and two-photon channels are present, while with higher fluence of 280 mJ cm −2 the two-photon channel dominates. We did not observe isomerization of the CS cation and found the main structural motion a to be a vibration of the phenyl rings about the central C–C bond.

74 ATOMIC AND MOLECULAR PHYSICS↗
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 OSTI2023

Evaluating the active site-substrate interplay between x-ray crystal structure and molecular dynamics in chorismate mutase

Designing realistic quantum mechanical (QM) models of enzymes is dependent on reliably discerning and modeling residues, solvents, and cofactors important in crafting the active site microenvironment. Interatomic van der Waals contacts have previously demonstrated usefulness toward designing QM-models, but their measured values (and subsequent residue importance rankings) are expected to be influenceable by subtle changes in protein structure. Using chorismate mutase as a case study, this work examines the differences in ligand-residue interatomic contacts between an x-ray crystal structure and structures from a molecular dynamics simulation. Select structures are further analyzed using symmetry adapted perturbation theory to compute ab initio ligand-residue interaction energies. The findings of this study show that ligand-residue interatomic contacts measured for an x-ray crystal structure are not predictive of active site contacts from a sampling of molecular dynamics frames. In addition, the variability in interatomic contacts among structures is not correlated with variability in interaction energies. However, the results spotlight using interaction energies to characterize and rank residue importance in future computational enzymology workflows.

Chemistry↗
DOE OSTI2023

Characterizing the Mechanisms of Ca and Mg Carbonate Ion-Pair Formation with Multi-Level Molecular Dynamics/Quantum Mechanics Simulations

The carbonate minerals of Ca and Mg are abundant throughout the lithosphere and have recently garnered significant research interest as possible long-term carbon sinks in the sequestration of atmospheric carbon dioxide. Nonetheless, an understanding of the atomic-level processes comprising their mineralization remains limited. Furthermore, we characterize and contrast the mechanisms of contact ion-pair formation in aqueous Ca and Mg carbonate systems, which represents the most fundamental step leading to the formation of their mineral solids. Utilizing multilevel embedded correlated wavefunction-based ab initio molecular dynamics/quantum mechanics simulations, we characterize not only the dynamics of these processes but also factors arising from the electronic structure of the involved species, revealing further details of the fundamentally different mechanisms for the interconversion between the contact ion-pairs and solvent-shared ion-pairs of Ca versus Mg carbonate.

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

Dissipative ground state preparation in ab initio electronic structure theory

Dissipative engineering is a powerful tool for quantum state preparation, and has drawn significant attention in quantum algorithms and quantum many-body physics in recent years. In this work, we introduce a novel approach using the Lindblad dynamics to efficiently prepare the ground state for general ab initio electronic structure problems on quantum computers, without variational parameters. These problems often involve Hamiltonians that lack geometric locality or sparsity structures, which we address by proposing two generic types of jump operators for the Lindblad dynamics. Type-I jump operators break the particle number symmetry and should be simulated in the Fock space. Type-II jump operators preserves the particle number symmetry and can be simulated more efficiently in the full configuration interaction space. For both types of jump operators, we prove that in a simplified Hartree-Fock framework, the spectral gap of our Lindbladian is lower bounded by a universal constant. For physical observables such as energy and reduced density matrices, the convergence rate of our Lindblad dynamics with Type-I jump operators remains universal, while the convergence rate with Type-II jump operators only depends on coarse grained information such as the number of orbitals and the number of electrons. To validate our approach, we employ a Monte Carlo trajectory-based algorithm for simulating the Lindblad dynamics for full ab initio Hamiltonians, demonstrating its effectiveness on molecular systems amenable to exact wavefunction treatment.

Quantum chemistry↗
DOE OSTI2023

Computational insights into the interaction of water with the UiO-66 metal–organic framework and its functionalized derivatives

The UiO-66 metal–organic framework (MOF) has been identified as a promising hydrophilic material for water harvesting. Recent studies show that its water uptake ability at low relative humidity (RH) can be improved by incorporating hydrophilic functional groups into the framework. In this work, we provide computational insights into the adsorption of water in UiO-66 and its functionalized derivatives to reveal the role played by different adsorption sites and functional groups in the adsorption mechanism. We started by developing molecular models for UiO-66, UiO-66-NH 2 , UiO-66-OH, and UiO-66-(OH) 2 compatible with the MB-pol data-driven many-body potential of water. We then benchmarked these models against ab initio data. Here we used these models to perform molecular dynamics simulations and calculate radial distribution functions, IR spectra, and two-dimensional density distribution maps for water in the MOFs. These results consistently show that the μ 3 -OH sites are the preferential interaction sites for water in UiO-66 and all its variants, and the formation of localised water clusters inside the octahedral pores is responsible for the abrupt step in the experimental adsorption isotherms. Furthermore, the presence of functional groups in the framework allows water to cluster in the octahedral pores at lower RH, thus making the MOF a more efficient water harvester. Overall, this study provides molecular-level insights into the pore filling process of UiO-66 and its functionalized derivatives, which are needed for the design of efficient water harvesting materials based on MOFs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗