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At least 19 records

Understanding the selectivity of nonsteroidal anti-inflammatory drugs for cyclooxygenases using quantum crystallography and electrostatic interaction energy

Quantum crystallography methods have been employed to investigate complex formation between nonsteroidal anti-inflammatory drugs (NSAIDs) and cyclooxygenase (COX) enzymes, with particular focus on the COX-1 and COX-2 isoforms. This study analyzed the electrostatic interaction energies of selected NSAIDs (flurbiprofen, ibuprofen, meloxicam and celecoxib) with the active sites of COX-1 and COX-2, revealing significant differences in binding profiles. Flurbiprofen exhibited the strongest interactions with both COX-1 and COX-2, indicating its potent binding affinity. Celecoxib and meloxicam showed a preference for COX-2, consistent with their known selectivity for this isoform, while ibuprofen showed comparable interaction energies with both isoforms, reflecting its nonselective inhibition pattern. Key amino-acid residues, including Arg120, Arg/His513 and Tyr355, were identified as critical determinants of NSAID selectivity and binding affinity. The findings highlight the complex interplay between interaction energy and selectivity, suggesting that while electrostatic interactions play a fundamental role, additional factors such as enzyme dynamics and the hydrophobic effect also contribute to the therapeutic efficacy and safety profiles of NSAIDs. These insights provide valuable guidance for the rational design of NSAIDs with enhanced therapeutic benefits and minimized adverse effects.

60 APPLIED LIFE SCIENCES

Convergent Protocols for Computing Protein–Ligand Interaction Energies Using Fragment-Based Quantum Chemistry

Fragment-based quantum chemistry methods offer a way to sidestep the steep nonlinear scaling of electronic structure calculations so that large molecular systems can be investigated using high-level methods. Here, we use fragmentation to compute protein–ligand interaction energies in systems with several thousand atoms, using a new software platform for managing fragment-based calculations that implements a screened many-body expansion. Convergence tests using a minimal-basis semiempirical method (HF-3c) indicate that two-body calculations, with single-residue fragments and simple hydrogen caps, are sufficient to reproduce interaction energies obtained using conventional supramolecular electronic structure calculations, to within 1 kcal/mol at about 1% of the computational cost. We also demonstrate that the HF-3c results are illustrative of trends obtained with density functional theory in basis sets up to augmented quadruple-ζ quality. Strategic deployment of fragmentation facilitates the use of converged biomolecular model systems alongside high-quality electronic structure methods and basis sets, bringing ab initio quantum chemistry to systems of hitherto unimaginable size. This will be useful for generation of high-quality training data for machine learning applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH

Interlayer coupling in two-dimensional MoS 2 and phosphorene bilayers: Benchmark quantum Monte Carlo study of interaction energies and quasiparticle band gaps

Using high-accuracy many-body quantum Monte Carlo (QMC) methods, we study the effect of interlayer coupling on the properties of two-dimensional freestanding bilayers (BLs) of MoS 2 and phosphorene. The properties of the two BL-materials are very different and largely determined by the interlayer interaction, which is purely van der Waals in MoS 2 and partially electronic/chemical in phosphorene, resulting in a modest layer-dependent property modulation in MoS 2 and strong modulation in phosphorene. Multireference and symmetry considerations are used to construct state-of-the-art accuracy QMC trial wave functions. We determine the quasiparticle band gaps for both materials, $Δ^{\textrm{qp}}_{Γ→\textrm{K}}$ = 2.45 ± 0.05 eV in BL-MoS 2 and $Δ^{\textrm{qp}}_{Γ→Γ}$=1.59 ±0.1eV in BL-phosphorene. In conclusion, these benchmark band-gap values make it possible to consolidate the interpretation of the widely scattered experimental and theory data.

Huang, Yongda [Slovak Academy of Sciences (SAS), B

Atomic ionization: sd energy imbalance and Perdew–Zunger self-interaction correction energy penalty in 3d atoms

To accurately describe the energetics of transition metal systems, density functional approximations (DFAs) must provide a balanced description of s- and d- electrons. One measure of this is the sd transfer error, which has previously been defined as E ( 3 d n − 1 4 s 1 ) − E ( 3 d n − 2 4 s 2 ) . Theoretical concerns have been raised about this definition due to its evaluation of excited-state energies using ground-state DFAs. A more serious concern appears to be strong correlation in the 4s 2 configuration. Here, we define a ground-state measure of the sd energy imbalance, based on the errors of s- and d-electron second ionization energies of the 3d atoms, that effectively circumvents the aforementioned problems. We find an improved performance as we move from the local spin density approximation (LSDA) to the Perdew-Burke-Ernzerhof (PBE) generalized gradient approximation (GGA) to the regularized and restored Strongly Constrained and Appropriately Normed (r 2 SCAN) meta-GGA for first-row transition metal atoms. However, we find large (∼2 eV) ground-state sd energy imbalances when applying a Perdew–Zunger 1981 self-interaction correction. This is attributed to an “energy penalty” associated with the noded 3d orbitals. A local scaling of the self-interaction correction to LSDA results in a balance of s- and d-errors.

Science & Technology - Other Topics

Energy-Screened Many-Body Expansion for Protein–Ligand Interactions: Examining Convergence for Metalloenzymes Through Seven–Body Interactions

Fragment-based quantum chemistry is a powerful strategy for calculating protein−ligand interaction energies using quantum chemistry methods. Rigorous convergence often requires hundreds of atoms in the protein binding-site model, especially if that model is constructed using distance-based criteria to select amino acid residues, while three- and four-body calculations exhibit instability related to combinatorial proliferation in the number of subsystem calculations. Here, we report an energy-based screening protocol for the many-body expansion applied to protein−ligand interactions, implemented in the open-source FRAGME∩T code. Using a combination of aggressive screening based on semiempirical quantum chemistry, with an improved graph-theoretical algorithm to eliminate unimportant subsystems, we are able to perform n-body calculations up to n = 7 using density functional theory in triple-ζ basis sets. Distance cutoffs further reduce the cost without compromising accuracy. Rapid and stable convergence of the many-body expansion is obtained by n = 4, for a pair of metalloenzymes in which a divalent ion coordinates directly to the ligand. As compared to previous results that relied solely on distance cutoffs, oscillations in the n-body corrections are reduced or eliminated, although residual errors remain in one case. This work demonstrates that benchmark-quality protein−ligand interaction energies can be systematically converged using a method with excellent parallel efficiency and scalability.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH

The kinetic analog of the pressure–strain interaction

Energy transport in weakly collisional plasma systems is often studied with fluid models and diagnostics. However, the applicability of fluid models is limited when collisions are weak or absent, and using a fluid approach can obscure kinetic processes that provide key insights into the physics of energy transport. Kinetic diagnostics retain all of the information in 3D-3V phase space and thereby reach beyond the insights of fluid models to elucidate the mechanisms responsible for collisionless energy transport. In this work, we derive the Kinetic Pressure–Strain (KPS): a kinetic analog of the pressure–strain interaction, which is the channel between flow energy density and internal energy density in fluid models. Through two case studies of electron Landau damping, we demonstrate that the KPS diagnostic can elucidate kinetic mechanisms that are responsible for energy transport in this channel, just as the related field–particle correlation is known to identify kinetic mechanisms of transport between electromagnetic field energy density and kinetic energy density in particle flows. In addition, we show that resonant electrons play a major role in transferring energy between fluid flows and internal energy during the process of Landau damping.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY

High-temperature quantum coherence of spinons in a rare-earth spin chain

Conventional wisdom dictates that quantum effects become unimportant at high temperatures. In magnets, when the thermal energy exceeds interactions between atomic magnetic moments, the moments are usually uncorrelated, and classical paramagnetic behavior is observed. This thermal decoherence of quantum spin behaviors is a major hindrance to quantum information applications of spin systems. Remarkably, our neutron scattering experiments on Yb chains in an insulating perovskite crystal defy these conventional expectations. We find a sharply defined spectrum of spinons, fractional quantum excitations of spin-1/2 chains, to persist to temperatures much higher than the scale of the interactions between Yb magnetic moments. The observed sharpness of the spinon continuum’s dispersive upper boundary indicates a spinon mean free path exceeding ≈ 35 inter-atomic spacings at temperatures more than an order of magnitude above the interaction energy scale. We thus discover an important and highly unique quantum behavior, which expands the realm of quantumness to high temperatures where entropy-governed classical behaviors were previously believed to dominate. Our results have profound implications for spin systems in quantum information applications operating at finite temperatures and motivate new developments in quantum metrology.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND

Theoretical tools for neutrino scattering: interplay between lattice QCD, EFTs, nuclear physics, phenomenology, and neutrino event generators

Maximizing the discovery potential of increasingly precise neutrino experiments will require an improved theoretical understanding of neutrino-nucleus cross sections over a wide range of energies. Low-energy interactions are needed to reconstruct the energies of astrophysical neutrinos from supernovae bursts and search for new physics using increasingly precise measurement of coherent elastic neutrino scattering. Higher-energy interactions involve a variety of reaction mechanisms including quasi-elastic scattering, resonance production, and deep inelastic scattering that must all be included to reliably predict cross sections for energies relevant to DUNE and other accelerator neutrino experiments. Refined nuclear interaction models in these energy regimes will also be valuable for other applications, such as measurements of reactor, solar, and atmospheric neutrinos. This manuscript discusses the theoretical status, challenges, required resources, and path forward for achieving precise predictions of neutrino-nucleus scattering and emphasizes the need for a coordinated theoretical effort involved lattice QCD, nuclear effective theories, phenomenological models of the transition region, and event generators.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS

Final state radiation from high and ultrahigh energy neutrino interactions

Charged leptons produced by high-energy and ultrahigh-energy neutrinos have a substantial probability of emitting prompt internal bremsstrahlung ν ℓ + N → ℓ + X + γ . This can have important consequences for neutrino detection. We discuss observable consequences at high- and ultrahigh-energy neutrino telescopes and the Large Hadron Collider’s (LHC’s) Forward Physics Facility. Logarithmic enhancements can be substantial (e.g., ∼ 20 % ) when either the charged lepton’s energy or the rest of the cascade is measured. We comment on final state radiation’s impacts on measuring the inelasticity distribution, ν / ν ¯ flux ratio, throughgoing muons, and double-bang signatures for high-energy neutrino observation. Furthermore, for ultrahigh-energy neutrino observation, we find that final state radiation increases the overall detectable energy by as much as 20%, affects flavor measurements, and decreases the energy of both Earth-emergent tau leptons and regenerated tau neutrinos. Many of these have significant impacts on measuring neutrino fluxes and spectra. Finally, for the LHC’s Forward Physics Facility, we find that final state radiation will impact future extractions of strange quark parton distribution functions. Final state radiation should be included in future analyses at neutrino telescopes and the Forward Physics Facility. Published by the American Physical Society 2025

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS

Dissociation of gas-phase anisole induced by low-energy electron interactions: understanding patterns of aromatic bond cleavage

Abstract In view of elucidating the fragmentation patterns of aromatic systems induced by low-energy electron interactions, dissociative electron attachment (DEA) to gas-phase anisole was performed. Anionic fragments resulting from this DEA process were detected by a quadrupole mass spectrometer, and ion yields of those fragments as a function of incident electron energy were rendered. Our study showed the formation of CH 3 − , HCC − , and OCH 3 − fragments, suggesting that various dissociation channels proceed out of DEA to anisole. We employed density functional theory to compute thermodynamic threshold energies for each potential dissociation channel. Those theoretical calculations supported the prediction that the CH 3 − and OCH 3 − fragments form via mechanisms of single-bond cleavage; the HCC − fragments may form through two-, three-, or four-body dissociation channels that entail hydrogen transfers and the cleavage of multiple aromatic bonds. The experimental resonance energies that form the CH 3 − , HCC − , and OCH 3 − fragments were 6.0 eV, 5.8 and 9.7 eV, and 9.8 eV, respectively. Given the classification of anisole as a monosubstituted aromatic species, our results explain generalizable patterns of electron-mediated dissociation in aromatic systems.

Finley, Jacob (ORCID:0009000606963352)

Toward an Understanding of Linear Scaling Relations through Energy Decomposition Analysis

The discovery of linear scaling relations has fundamentally changed the field of heterogeneous catalysis. The scaling relations have been rationalized based on the d-band theory, specifically a separation of sp and d electron contributions to adsorption energies. Within the framework of energy decomposition analysis, a full understanding of such a separation would require one to further break down the adsorption energy into distinct energy components such as electrostatics, polarization, charge transfer, and van der Waals interactions, and to examine the sp and d contributions to each of them. As a step in this direction, we analyzed the interaction energy between CH x (x = 1–4) adsorbates and fcc(100) transition metal surfaces (M = Cu, Ag, Au, Rh, and Pt), with the surfaces represented both as slabs in plane-wave density functional theory (pw-DFT) calculations and as atomic clusters in atomic-orbital basis density functional theory (ao-DFT) calculations. Through an absolutely localized molecular orbital (ALMO) based energy decomposition analysis of the ao-DFT adsorption energy, each of the interaction energy components (electrostatics, polarization, van der Waals, and charge transfer) was found to follow its own scaling relations, with an intricate interplay among these energy components yielding the overall scaling relations for the total adsorption energies. Using the recently introduced ALMO-based polarization and charge-transfer analysis schemes, we further dissected polarization into metal surface and adsorbate contributions, and charge transfer into metal → adsorbate and adsorbate → metal contributions. The contributions from the sp and d electrons of the metal to these terms were further quantified, and the dominant role of the metal d electrons was reaffirmed. These results shed light on how CHx adsorbates interact with metal surfaces and further reveal the physical origin of the scaling relations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH

Beyond Price Taker: Optimizing Integrated Energy Systems Considering Market/Grid Interactions

Integrated Energy Systems (IES) combine two or more processes to increase the efficiency, flexibility of operation, and the overall reliability. However, analyzing IESs in volatile electricity markets is challenging, since the volatility in electricity prices makes the conventional levelized cost-type analysis less realistic. This work presents two approaches to address the challenge: price-taker and a surrogates-based approach for incorporating market interactions. The price-taker approach formulates a multiperiod optimization problem that takes the time-varying electricity prices into account, and solves the optimization problem to determine the optimal operational schedule that maximizes the chosen economic metric. This approach is successfully applied to investigate the performance of flexible power and hydrogen co-production systems. The market surrogates approach trains a machine learning model to predict the market behavior as a function of the characteristics of the IES. The trained surrogate model is used to optimize the design and operation of the given IES in an electricity market. This approach is demonstrated on a case study involving a nuclear power plant retrofitted with a low-temperature electrolysis unit to co-produce power and hydrogen.

beyond price taker

Anion-dependent phase behavior of methylimidazolium-based ionic liquids mixed with water: Correlation between local molecular structure and mesoscale behaviors

The mesoscopic phase behavior of decylmethylimidazolium (C 10 mim) ionic liquids (ILs) bearing three monovalent anions—thiocyanate (SCN − ), nitrate (NO 3 − ), and chloride (Cl − )—mixed with water at relatively high IL contents (50–95 wt%) was investigated. Small-angle and wide-angle X-ray scattering (SAXS/WAXS) were employed to follow the evolution of both local and mesoscale structures across this composition range. In the absence of water, C 10 mimSCN and C 10 mimCl behaved as disordered liquids, whereas C 10 mimNO 3 spontaneously formed a hexagonally ordered cylindrical mesophase and displayed a sticky-solid macroscopic appearance. Upon addition of water, C 10 mimSCN remained a viscous liquid and only weakly ordered lamellar domains were observed. This limited ordering is attributed to the lack of hydrogen bonding and weak interaction energy between SCN − anions and C 10 mim + cations. In contrast, the trigonal-planar NO 3 − and point-like Cl − anions promoted the formation of well-defined hexagonal mesophases up to 35–45 wt% water. The formation of hydrogen bonding of the two anions with imidazolium ring protons likely enabled the creation of compact ion clusters that effectively exclude water molecules from the immediate vicinity of the IL aggregates. These findings demonstrate that the interaction energy between ion pairs dictate IL-water interactions and therefore control the transition from disordered liquids to ordered mesophases in IL/water mixtures with high IL contents. In conclusion, the combined SAXS/WAXS analysis reveals a correlation between local intermolecular structure and the emergence of mesoscopic order, providing a systematic framework for tailoring mesoscale structures in alkylimidazolium-based IL/water systems.

36 MATERIALS SCIENCE

Prediction of hydration energies of adsorbates at Pt(111) and liquid water interfaces using machine learning

Aqueous phase heterogeneous catalysis is important to various industrial processes, including biomass conversion, Fischer–Tropsch synthesis, and electrocatalysis. Accurate calculation of solvation thermodynamic properties is essential for modeling the performance of catalysts for these processes. Explicit solvation methods employing multiscale modeling, e.g., involving density functional theory and molecular dynamics have emerged for this purpose. Although accurate, these methods are computationally intensive. This study introduces machine learning (ML) models to predict solvation thermodynamics for adsorbates on a Pt(111) surface, aiming to enhance computational efficiency without compromising accuracy. In particular, ML models are developed using a combination of molecular descriptors and fingerprints and trained on previously published water–adsorbate interaction energies, energies of solvation, and free energies of solvation of adsorbates bound to Pt(111). These models achieve root mean square error values of 0.09 eV for interaction energies, 0.04 eV for energies of solvation, and 0.06 eV for free energies of solvation, demonstrating accuracy within the standard error of multiscale modeling. Feature importance analysis reveals that hydrogen bonding, van der Waals interactions, and solvent density, together with the properties of the adsorbate, are critical factors influencing solvation thermodynamics. Furthermore, these findings suggest that ML models can provide rapid and reliable predictions of solvation properties. This approach not only reduces computational costs but also offers insights into the solvation characteristics of adsorbates at Pt(111)–water interfaces.

Adsorption

Graphene oxide gluing layer enabling macroscale tribology applications of pristine graphene

In recent studies of two-dimensional (2D) nanomaterial-based solid lubricants, the importance of durability has been emerging for real engineering-scale applications. To achieve this, a transfer layer formation is essential to prevent the wear of the mechanical systems. However, it has been challenging for pristine graphene (PG) to induce a material transfer due to chemical inertness. In this study, we suggest an easy-to-process strategy to promote the huge material transfer of the PG onto the counterpart contacting material. We utilized graphene oxide (GO) as a gluing layer between the PG film and the counterpart contact surface to realize the superior tribological performance. The high interaction energy of the GO from its functional groups makes a contribution to the material transfer of PG, which is unveiled by a systematic analysis of the counterpart contact surface and the wear track. The huge solid transfer layer not only makes a wear-resistant contact interface between the transfer layer and the underlying film by densification and oxidation, but also reduces surface interaction energies, finally resulting in a significant improvement in durability.

graphene oxide (GO)