Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “Reactive molecular dynamics”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 235 records · Page 13
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Theoretical Investigation of the Oxygen Reduction Reaction over Platinum Catalysts Supported by Multi-Edged Vertically Aligned Carbon Nanofiber for Electrocatalyst Preparation

Vertically aligned carbon nanofibers (VACNFs) are promising supports for oxygen reduction reaction (ORR) electrocatalysts in fuel cells. Although experimentally these catalytic systems have shown great potential, there is lack of molecular understanding of the catalytic sites and reaction mechanisms. This work investigated the origin of the ORR reactivities of the platinum catalysts on multi-edged VACNFs (Pt/VACNF) using a multiscale modeling approach combining Density Functional Theory (DFT) and classical Molecular Dynamics (MD) simulations. Based on the ReaxFF potential, here all nanoscale Pt particles (Pt 55 , P 100 , and Pt 147 ) are stabilized by the open edges located axially along the VACNF walls. The calculated first-shell coordination numbers, CN, of surface Pt atoms are 6.63, 7.27, and 7.85, respectively, suggesting that the percentage of low coordination sites increases as the particle size decreases. The adsorption energies of OOH, O, and OH on Pt-55 were systematically probed using DFT calculations. These adsorption energies retain a linear correlation against the generalized coordination numbers ($\overline{CN}$). For Pt nanoparticles supported on VACNF, we found that the OOH and OH bind stronger than on Pt (111) by 0.14 and 0.17 eV, respectively, which can hinder the ORR activity with lower limiting potential than Pt (111). Our theoretical prediction is in good agreement with the linear sweeping voltammetry that revealed a left shift of the half-wave potential.

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

Adsorption, Orientation, and Speciation of Amino Acids at Air–Aqueous Interfaces for the Direct Air Capture of CO 2

Amino acids make up a promising family of molecules capable of direct air capture (DAC) of CO 2 from the atmosphere. Under alkaline conditions, CO 2 reacts with the anionic form of an amino acid to produce carbamates and deactivated zwitterionic amino acids. The presence of the various species of amino acids and reactive intermediates can have a significant effect on DAC chemistry, the role of which is poorly understood. In this study, all-atom molecular dynamics (MD) based computational simulations and vibrational sum frequency generation (vSFG) spectroscopy studies were conducted to understand the role of competitive interactions at the air–aqueous interface in the context of DAC. We find that the presence of potassium bicarbonate ions, in combination with the anionic and zwitterionic forms of amino acids, induces concentration and charge gradients at the interface, generating a layered molecular arrangement that changes under pre- and post-DAC conditions. In parallel, an enhancement in the surface activity of both anionic and zwitterionic forms of amino acids is observed, which is attributed to enhanced interfacial stability and favorable intermolecular interactions between the adsorbed amino acids in their anionic and zwitterionic forms. The collective influence of these competitive interactions, along with the resulting interfacial heterogeneity, may in turn affect subsequent capture reactions and associated rates. Finally, these effects underscore the need to consider dynamic changes in interfacial chemical makeup to enhance DAC efficiency and to develop successful negative emission and storage technologies.

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

Using enzymes to tame nitrogen-centred radicals for enantioselective hydroamination

The formation of C–N bonds—of great importance to the pharmaceutical industry—can be facilitated enzymatically using nucleophilic and nitrene transfer mechanisms. However, neither natural nor engineered enzymes are known to generate and control nitrogen-centred radicals, which serve as valuable species for C–N bond formation. Here we use flavin-dependent ‘ene’-reductases with an exogenous photoredox catalyst to selectively generate amidyl radicals within the protein active site. These enzymes are engineered through directed evolution to catalyse 5-exo, 6-endo, 7-endo, 8-endo, and intermolecular hydroamination reactions with high levels of enantioselectivity. Mechanistic studies suggest that radical initiation occurs via an enzyme-gated mechanism, where the protein thermodynamically activates the substrate for reduction by the photocatalyst. Molecular dynamics studies indicate that the enzymes bind substrates using non-canonical binding interactions, which may serve as a handle to further manipulate reactivity. Furthermore, this approach demonstrates the versatility of these enzymes for controlling the reactivity of high-energy radical intermediates and highlights the opportunity for synergistic catalyst strategies to unlock previously inaccessible enzymatic functions.

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

Ultrafast optical modulation of vibrational strong coupling in ReCl(CO) 3 (2,2-bipyridine)

Polaritons – hybrid light-matter states formed from the strong coupling of a bright molecular transition with a confined photonic mode – may offer new opportunities for optical control of molecular behavior. Vibrational strong coupling (VSC) has been reported to impact ground-state chemical reactivity, but its influence on electronic excited-state dynamics remains unexplored. Here, we take a first step towards excited-state VSC by demonstrating optical modulation of the ReCl(CO) 3 (bpy), (bpy = 2,2-bipyridine) complex under VSC using femtosecond ultraviolet (UV)-pump/infrared (IR)-probe spectroscopy. We establish ground-state VSC of ReCl(CO) 3 (bpy) in a microfluidic Fabry-Pérot cavity equipped with indium tin oxide (ITO)-coated mirrors. ITO is effectively dichroic as it is reflective in the IR and transmissive in the UV-visible and therefore minimizes optical interference. Excitation with UV pump light drives ReCl(CO) 3 (bpy) into a manifold of electronic excited states that subsequently undergo non-radiative relaxation dynamics. We probe the transient response of the strongly-coupled system in the mid-IR, observing both Rabi contraction and cavity-filtered excited-state absorption signatures. We reconstruct the intrinsic response of intracavity molecules from the transient cavity transmission spectra to enable quantitative comparison with extracavity control experiments. We report no changes in the excited-state dynamics of ReCl(CO) 3 (bpy) under ground-state VSC. However, we do observe significant amplification of transient vibrational signals due to classical cavity-enhanced optical effects. This effort lays the groundwork to pursue direct excited-state VSC aimed at modulating photochemical reactivity.

cavity-enhanced spectroscopy↗
DOE OSTI2021

Carbon fiber synthesis from pitch: Insights from ReaxFF based molecular dynamics simulations

Despite the potential to lowering fabrication costs of pitch-based carbon fiber (CF) compared to polyacrylonitrile-based CF, large scale utilization is currently limited by the complexity in manufacturing. This is mainly due to the lack of consistency between the pitch structure/chemistry and CF properties under different processing conditions. Here, we employed full atomistic simulations based on reactive force fields to investigate the conversion of pitch precursors to CFs. Additionally, it was found that at the carbonization stage, the consumption rates of precursors, gas formations, and solid yields (carbonized CFs) are all dependent on the composition and arrangement of molecular moieties in the precursor. Specifically, precursors with sp 3 carbons in the cata-condensed core area have limited decomposition pathways (i.e., limited reaction sites), which leads to the formation of carbonized CFs with similar compositions. Furthermore, carbonized CFs possess distinct structural characteristics, and finally lead to the formation of CFs with different moduli. By analyzing CF crystallinity and elemental composition, general rationales are proposed for the selection of optimal precursors and processing conditions, and thus shed lights on parameter screening during industrial CF synthesis. For instance, inclusion of sp 3 carbons in cata- condensed rings can be preferred over the presence of sp 3 carbons on side chains.

01 COAL, LIGNITE, AND PEAT↗
DOE OSTI2026

A High-Fidelity Molecular Model of the Cu(111) Repeating Unit

Dynamic processes at surfaces are central to heterogeneous catalysis, but their atomistic mechanism(s) can prove difficult to elucidate due to variations in material structure and the corresponding impact on reactivity. Moreover, disparities between reaction conditions and those employed for spectroscopic characterization at surfaces can inhibit detailed understanding of catalysis-relevant chemistries. Herein, we substantiate the so-called “cluster-surface” analogy by leveraging a low-valent tricopper architecture ( 1 ) as a model system for small molecule activation at Cu(111). Two reaction classes are explored: the adsorption of carbon monoxide (CO) and the dissociative adsorption of dihydrogen (H 2 ). These processes serve as an ideal testbed to compare the reactivity of a molecular cluster ( 1 ) to that of a heterogeneous surface, as both reactions have empirical data from measurements performed on crystalline Cu(111). Cluster 1 reversibly binds CO. Variable temperature NMR analysis with 13 CO reveals a favorable enthalpy but large negative entropy (−5.1 kcal × mol –1 and −22.9 cal × mol –1 × K –1 , respectively) for CO binding, affording a process that is marginally endergonic at room temperature (ΔG ads (298.15 K) = 1.7 ± 0.5 kcal × mol –1 ). Similarly, analogous to a Cu(111) surface, 1 is shown to oxidatively add (chemisorb) H 2 . Kinetic parameters were determined for this process and the activation enthalpy (8.4 ± 0.5 kcal × mol –1 ) closely mirrors that established for H 2 binding at the Cu(111) facet (6.0 to 12.4 kcal × mol –1 ). Together, these results showcase that a trinuclear cluster can reproduce the small molecule binding and activation energetics of a bulk crystalline surface, setting the stage for studying less-defined surface processes in an atomically precise molecular setting.

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

Effect of an oxide layer on high velocity impact of tantalum particles characterized using molecular dynamics

Micro-cold spray, also commonly referred to as the aerosol deposition method or vacuum kinetic spraying, is a process for depositing nanostructured films of metals and ceramics by impacting solid nanoparticles at high velocity onto a substrate at room temperature and at low pressures. Tantalum films deposited by micro-cold spray are desirable because tantalum is non-reactive to certain molten metals and can therefore serve as a non-reactive barrier coating. However, unlike most other metals deposited by micro-cold spray, tantalum quickly forms an oxide layer when exposed to air. In the deposition of films using traditional cold spray with much larger particles, native oxides must fracture for particle–substrate bonding to occur. Furthermore, the fraction of the particle that is oxidized in micro-cold spray and the strain rates experienced by the particles upon impact are both much larger than in cold spray, suggesting that the role of the oxide on film deposition may be distinct. The effect of this oxide layer on particle deformation and adherence to a substrate under high strain rates is studied using molecular dynamics simulations. The effect of oxide layer thickness, particle diameter, and impact velocity are examined.

42 ENGINEERING↗
DOE OSTI2022

Simulations of graphite boronization: A molecular dynamics study of amorphization resulting from bombardment

The molecular dynamics code LAMMPS was used to simulate the bombardment of a graphite structure by atomic boron with impact energies ranging from 50–250 eV. The transient structural evolution, penetration depth, and amorphous layer thickness were analyzed. Simulations show that larger impact energies lead to a greater volume of amorphization and penetration of boron, but that the growth rate of the amorphous layer decreases with increasing fluence. Furthermore, the change in surface chemistry of the amorphized structures was studied using the ReaxFF formalism, which found that the amorphization process introduces dangling bonds thus increasing reactivity in the amorphous region.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2020

Emerging investigator series: ion diffusivities in nanoconfined interfacial water films contribute to mineral carbonation thresholds

The dynamics and reactivity of nanoconfined fluids play critical roles across a wide range of environmental and technological systems, though reaction mechanisms and kinetics are not well understood. Here, the carbonation kinetics of forsterite (Mg 2 SiO 4 ) exposed to 90 atm supercritical carbon dioxide at 35–65 °C and 85–100% relative humidity (RH) was monitored with in situ X-ray diffraction, and partner molecular dynamics simulations were used to describe the free energy landscape of Mg 2+ adsorption and diffusion on forsterite surfaces covered in water films 3–10 monolayers thick. The collective findings reveal how decreasing the water film thickness by ~1.4 monolayers, from ~0.92 to ~0.64 nm, inhibited reaction rates by up to 97%, promoted anhydrous Mg-carbonate (magnesite, MgCO 3 ) precipitation, and more than doubled the apparent activation energy of carbonation. The transport simulations suggest that four monolayers are required to enable sufficiently facile Mg 2+ diffusion, helping explain previously observed water film thickness-dependent reactivity thresholds.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Oxidation of Silicon Carbide with Atomic Oxygen through the Passive-to-Active Transition

The inelastic and reactive scattering dynamics of O( 3 P) atoms on a 6H-silicon carbide (SiC) surface were investigated as a function of temperature with a molecular beam-surface scattering technique that employed a rotatable mass spectrometer detector. One set of experiments used a pulsed hyperthermal beam that produced ~8 km s –1 O atoms, and another set of experiments used a continuous beam that contained O atoms with a nominal velocity of ~2 km s –1 . When exposed to the relatively low-flux, pulsed hyperthermal O-atom beam, a passive oxide layer on the SiC that formed at lower temperatures decomposed as the temperature increased above 1673 K. Instead of entering an active oxidation regime, a graphitic layer formed on the surface and largely protected the underlying SiC from incoming O atoms. Investigation of the oxide decomposition without O-atom bombardment revealed volatile Si and SiO products at the moment that the oxide decomposed, implying that Si sublimation occurs concurrently with oxide decomposition. In the experiment with the continuous (higher flux) O-atom beam, volatile SiO and CO products were observed after the passive oxide decomposed, indicating that active oxidation was reached. Finally, the results of this study provide evidence for the importance of Si sublimation within the active oxidation regime. Above the passive-to-active transition temperature, Si sublimation is an ongoing process, and continuous active oxidation will only occur if sufficient oxygen reacts with the surface to produce SiO more quickly than a graphitic layer can form. Thus, accurate models of SiC ablation by atomic oxygen must account for multiple competing mechanisms that depend on the surface temperature and incident O-atom flux.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Tailored computational approaches to interrogate heavy element chemistry and structure in condensed phase

In this chapter we are presenting a brief review of the challenges encountered in the study of 4f and 5f block elements in the condensed phase. Their recovery, use in molten salt reactors and other interesting applications necessitate the use of molecular dynamics and large-scale models that take into account both the electronic structure and relativistic corrections. Sampling the multitude of electronic and atomic configurational states is at the heart of reliable predictions of structure, reactivity, dynamics and transport of heavy metals in complex environments. We present three examples that combine lanthanide elements with large scale models: i) our recent developments of a versatile adaptive learning method that enables global optimization in high dimensional spaces, ii) results of computed pKa values of lanthanide aqua complexes, and iii) structure and computed EXAFS of heavy elements in molten salts. The latter two employ our recently-optimized lanthanide pseudo-potentials and companion basis sets for condensed phase ab initio molecular dynamics.

Nguyen, Manh Thuong↗
DOE OSTI2021

Vapor-phase self-assembly for generating thermally stable single-atom catalysts

Preparation of thermally stable metal single-atom catalysts (SACs) is a challenge in heterogeneous catalysis, especially on conventional supports that provide a weak metal-support interaction. In this work, we report that a modified support MgAl 2 O 4 can stabilize Pt single atoms by a mechanism of vapor-phase self-assembly in a high-temperature treatment (800°C, air). The experimental results on the formation mechanism and the structure are validated by DFT and ab initio molecular dynamics simulations. We infer that stable triangular K 3 O 3 structures help stabilize Pt single atoms at high temperatures in oxidizing conditions, exhibiting excellent reactivity for methane oxidation. The obtained Pt/K/MgAl 2 O 4 SAC presents excellent stability in methane oxidation after steam treatment at elevated temperatures, whereas the Pt/MgAl 2 O 4 nanocatalyst suffers from rapid deactivation due to Pt nanoparticle growth. Now this work paves the way for preparing thermally stable and highly active SACs using conventional high-surface-area supports, despite the weak metal-support interaction.

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

Source of Rate Acceleration for Carbocation Cyclization in Biomimetic Supramolecular Cages

The results of quantum chemical and molecular dynamics calculations reveal that polyanionic gallium-based cages accelerate cyclization reactions of pentadienyl alcohols as a result of substrate cage interactions, preferential binding of reactive conformations of substrate/H 3 O + pairs, and increased substrate basicity. However, the increase in basicity dominates. Here, experimental structure–activity relationship studies in which the metal vertices and overall charge of the cage are varied confirm the model derived via calculations.

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

Complexion dictated thermal resistance with interface density in reactive metal multilayers

Multilayers composed of aluminum (A1) and platinum (Pt) exhibit a non-monotonic trend in thermal resistance with bilayer thickness as measured by time domain thermoreflectance. The thermal resistance initially increases with reduced bilayer thickness only to reach a maximum and then decrease with further shrinking of the multilayer period. These observations are attributed to the evolving impact of an intermixed amorphous complexion approximately 10 nm in thickness, which forms at each boundary between Al- and Pt-rich layers. Scanning transmission electron microscopy combined with energy dispersive X-ray spectroscopy find that the elemental composition of the complexion varies based on bilayer periodicity as does the fraction of the multilayer composed of this interlayer. These variations in complexion mitigate boundary scattering within the multilayers as shown by electronic transport calculations employing density functional theory and non-equilibrium Green's functions on amorphous structures obtained via finite temperature molecular dynamics. The lessening of boundary scattering reduces the total resistance to thermal transport leading to the observed non-monotonic trend thereby highlighting the central role of complexion on thermal transport within reactive metal multilayers.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Stochastic Constrained Extended System Dynamics for Solving Charge Equilibration Models

In this work, we present a new stochastic extended Lagrangian molecular dynamics solution to charge equilibration that eliminates self-consistent field (SCF) calculations, thus eliminating the computational bottleneck in solving the charge distribution with standard SCF solvers. By formulating both charges and chemical potential as latent variables and introducing a holonomic constraint that satisfies charge conservation, the SC-XLMD method accurately reproduces thermodynamic, dynamic, and structural properties within the framework of ReaxFF for a bulk water system and highly reactive RDX molecules simulated at high temperature. The SC-XLMD method shows excellent computational performance and is available in the publicly available LAMMPS package.

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

Confinement Effects on Proton Transfer in TiO 2 Nanopores from Machine Learning Potential Molecular Dynamics Simulations

Improved understanding of proton transfer in nanopores is critical for a wide range of emerging applications, yet experimentally probing mechanisms and energetics of this process remains a significant challenge. To help reveal details of this process, we developed and applied a machine learning potential derived from first-principles calculations to examine water reactivity and proton transfer in TiO 2 slit-pores. Here, we find that confinement of water within pores smaller than 0.5 nm imposes strong and complex effects on water reactivity and proton transfer. Although the proton transfer mechanism is similar to that at a TiO 2 interface with bulk water, confinement reduces the activation energy of this process, leading to more frequent proton transfer events. This enhanced proton transfer stems from the contraction of oxygen–oxygen distances dictated by the interplay between confinement and hydrophilic interactions. Our simulations also highlight the importance of the surface topology, where faster proton transport is found in the direction where a unique arrangement of surface oxygens enables the formation of an ordered water chain. In a broader context, our study demonstrates that proton transfer in hydrophilic nanopores can be enhanced by controlling pore size, surface chemistry, and topology.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Thermal conductivity tensor of γ and ε -hexanitrohexaazaisowurtzitane as a function of pressure and temperature

Using reverse non-equilibrium molecular dynamics simulations, we have determined the dependences on temperature and pressure of the thermal conductivity tensors for the monoclinic γ and ε polymorphs of hexanitrohexaazaisowurtzitane (HNIW or CL20). In this work, a recently developed non-reactive force field [X. Bidault and S. Chaudhuri, RSC Adv. 9, 39649–39661 (2019)], designed to study polymorphism and phase transitions in CL20, is employed. The effects of temperature and pressure are investigated between 200 and 500 K and up to 0.5 GPa for γ-CL20 and 2 GPa for ε-CL20. In order to obtain the full thermal conductivity tensor, $κ_{ij}$, for the monoclinic crystals, four distinct heat propagation directions are used. We find that $κ_{ij}$ for both polymorphs is more isotropic than for other energetic molecular crystals, including α- and γ-RDX, β-HMX, and PETN, with a maximum difference of 9.8% between orientations observed at 300 K and 0 GPa for γ-CL20 and a maximum difference of 4.8% for ε-CL20. The average thermal conductivity, $\bar{κ}$, of ε-CL20 is 6.4% larger than that of γ-CL20 at 300 K and 0 GPa. Analytic linear functions of the inverse temperature and the pressure are provided, which fit the data well and can be used to predict the thermal conductivity of both polymorphs for any orientation, pressure, and temperature in and around the fitting range. Our predictions agree reasonably well with the limited available experimental data, for which the polymorph type is unknown.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Equilibrium-gated pattern formation: How molecular dissociation thermodynamics drive emergent behavior in dissipative polymeric systems

Emergent patterns in biological systems arise through dissipative processes that balance reaction and transport phenomena, producing highly functional properties from self-regulating mechanisms. Synthetic fabrication, by contrast, often relies on user-controlled, multistep methods that lack the self-organizing capabilities of natural systems. Inspired by nature, we sought chemical systems that integrate strongly coupled reaction and transport phenomena, identifying frontal ring-opening metathesis polymerization (FROMP) as a method capable of creating diverse forms and functions through reactive processing. By employing discrete molecular initiators, FROMP allows precise control of key reaction steps—inhibition, initiation, and propagation. Using an integrated computational and experimental framework, we uncover how near-equilibrium inhibition dynamics, coupled with far-from-equilibrium reaction kinetics, drive pattern formation in frontally polymerized synthetic materials. We propose the concept of equilibrium-gated pattern formation, demonstrating how initiator chemistry can be tuned to achieve programmable macroscale properties. Our study reveals a surprising insight: Emergent behavior in FROMP systems arises from the inhibition-dominated regime of resin composition, expanding prior observations that such behavior is confined to a narrow compositional space near the boundary between front quenching and uniform front propagation. We identify a broader compositional window, far from the quenching regime, where emergent behavior reliably manifests. This expanded design space significantly enhances the operational flexibility of reactive systems and their capacity for self-organization. Furthermore, these insights provide a roadmap for designing bioinspired materials with self-organizing capabilities, unlocking possibilities in synthetic manufacturing.

Architected Polymers↗