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All sourcesNASA NTRSDOE OSTI
NASA NTRSDate not supplied

REACTER: A Versatile Tool for Large-Scale Reactive Molecular Dynamics

Accurately describing reactive events over long length and time scales remains a grand challenge of computational materials science. REACTER is a general protocol for modeling chemical reactions using classical force fields, and is implemented in the popular molecular dynamics software LAMMPS. REACTER has a growing user base and has been used as a model-building tool for a variety of materials, including thermoplastics, thermosets, glassy materials and composites. The method has also been applied to accelerated modeling of reversible chemical reactions, such as the formation of electrochemical components for batteries. Recently, the REACTER protocol has received some major upgrades to enhance its ability to predict when reactions occur and to make it easier to use. Force field parameters can now be automatically assigned to newly created bonds, angles and other interactions. Advanced reaction constraints have also been added, including an Arrhenius constraint to enforce an effective activation energy, a root-mean-square-deviation option for complex geometrical constraints, and a constraint based on the total potential energy of the atoms involved in a reactive site. This potential energy constraint allows for the accurate reproduction of DFT-based tight-binding (DFTB3) predicted bond dissociation curves for mechanically induced bond breaking.

polymer simulations, molecular dynamics↗
NASA NTRS1958

Extreme Speeds and Thermodynamic States in Supersonic Flight

The increasing importance of high-speed flow leads to similar problems in various fields of research which are summarized in what follows. Typical of all cases is the conversion of high kinetic energy into extreme thermodynamic states with temperatures of several thousand degrees, frequently connected with dissociation and ionization of the gas involved. There is also a characteristic small sensitivity to the processes discussed in the case of gases of low molecular weight (light gases). The penetration of meteors into the atmosphere of the earth at astronomical speeds results in temperatures higher than those of the surface of the sun. Such temperatures may be produced in shock tubes, with light gases used as the driving gas. For supersonic fighters the problem of propulsion is less difficult to solve than the problem of large heating, on the surface and in the combustion chamber. Finally, for the space-travel rocket, astronomical speeds have to be reached which require the lightest possible gases as propellants. Here again, dissociation processes in the combustion chamber are of considerable importance.

Oswatitsch, Klaus↗
NASA NTRS1982

Effective photodissociation cross sections for molecular oxygen and nitric oxide in the Schumann-Runge bands

Accurate calculations of the atmospheric opacity and the photodissociation rate of molecular oxygen in the Schumann-Runge bands (175-205) are necessary for modeling chemistry in the terrestrial upper atmosphere. The present investigation is concerned with a single simple parameterization of effective cross sections which can be used to calculate both O2 opacity and dissociation rates. Use is made of a zenith angle dependent factor which accounts for variations shown in detailed calculations. The conducted analysis is based on the results of Frederick and Hudson (1980). Attention is given to molecular oxygen effective cross sections and nitric oxide effective cross sections. It is found that the depth of the atmosphere to which solar radiation in the 175-200 nm spectral region penetrates is a sensitive function of the rotational line widths in the Schumann-Runge bands. The oscillator strength for each band measures the cross section integrated over the band while the line width determine how the absorption is distributed in wavenumber.

Allen, M.↗
DOE OSTI2025

Internally Catalyzed Hydrogen Atom Transfer (I-CHAT)—A New Class of Reactions in Combustion Chemistry

The current paradigm of low-T combustion and autoignition of hydrocarbons is based on the sequential two-step oxygenation of fuel radicals. The key chain-branching occurs when the second oxygenation adduct (OOQOOH) is isomerized releasing an OH radical and a key ketohydroperoxide (KHP) intermediate. The subsequent homolytic dissociation of relatively weak O–O bonds in KHP generates two more radicals in the oxidation chain leading to ignition. Based on the recently introduced intramolecular “catalytic hydrogen atom transfer” mechanism (J. Phys. Chem. 2024, 128, 2169), abbreviated here as I-CHAT, we have identified a novel unimolecular decomposition channel for KHPs to form their classical isomers—enol hydroperoxides (EHP). The uncertainty in the contribution of enols is typically due to the high computed barriers for conventional (“direct”) keto–enol tautomerization. Remarkably, the I-CHAT dramatically reduces such barriers. The novel mechanism can be regarded as an intramolecular version of the intermolecular relay transfer of H-atoms mediated by an external molecule following the general classification of such processes (Catal. Rev.-Sci. Eng. 2014, 56, 403). Here, we present a detailed mechanistic and kinetic analysis of the I-CHAT-facilitated pathways applied to n-hexane, n-heptane, and n-pentane models as prototype molecules for gasoline, diesel, and hybrid rocket fuels. We particularly examined the formation kinetics and subsequent dissociation of the γ-enol-hydroperoxide isomer of the most abundant pentane-derived isomer γ-C5-KHP observed experimentally. To gain molecular-level insight into the I-CHAT catalysis, we have also explored the role of the internal catalyst moieties using truncated models. All applied models demonstrated a significant reduction in the isomerization barriers, primarily due to the decreased ring strain in transition states. In addition, the longer-range and sequential H-migration processes were also identified and illustrated via a combined double keto–enol conversion of heptane-2,6-diketo-4-hydroperoxide as a potential chain-branching model. To assess the possible impact of the I-CHAT channels on global fuel combustion characteristics, we performed a detailed kinetic analysis of the isomerization and decomposition of γ-C5-KHP comparing I-CHAT with key alternative reactions—direct dissociation and Korcek channels. Calculated rate parameters were implemented into a modified version of the n-pentane kinetic model developed earlier using RMG automated model generation tools (ACS Omega, 2023, 8, 4908). Simulations of ignition delay times revealed the significant effect of the new pathways, suggesting an important role of the I-CHAT pathways in the low-T combustion of large alkanes.

Biochemistry & Molecular Biology↗
DOE OSTI2021

High-resolution Near-infrared Spectroscopy of Diffuse Sources around MWC 1080

To reveal the origins of diffuse Hα emissions observed around the Herbig star MWC 1080, we have performed a high-resolution near-infrared (NIR) spectroscopic observation using the Immersion Grating Infrared Spectrograph. In the NIR H and K bands, we detected various emission lines (six hydrogen Brackett lines, seven H{sub 2} lines, and an [Fe ii] line) and compared their spatial locations with the optical (Hα and [S ii]) and radio ({sup 13}CO and CS) line maps. The shock-induced H{sub 2} and [Fe ii] lines indicate the presence of multiple outflows, consisting of at least three associated young stars in this region. The kinematics of H{sub 2} and [Fe ii] near the northeast (NE) cavity edge supports the idea that the NE main outflow from MWC 1080A is the blueshifted one with a low inclination angle. The H{sub 2} and [Fe ii] lines near the southeast molecular region newly reveal that additional highly blueshifted outflows originate from other young stars. The fluorescent H{sub 2} lines were found to trace photodissociation regions formed on the cylindrical surfaces of the main outflow cavity, which are expanding outward with a velocity of about 10–15 km s{sup −1}. For the Hα emission, we identify its components associated with two stellar outflows and two young stars in addition to the dominant component of MWC 1080A scattered by dust. We also report a few faint Hα features located ∼0.4 pc away in the southwest direction from MWC 1080A, which lie near the axes of the NE main outflow and one of the newly identified outflows.

74 ATOMIC AND MOLECULAR PHYSICS↗
NASA NTRS1991

Observations of forbidden Si II (35 microns) and Si I (25 microns) in Orion - Evidence of a wind shock near IRc2

Forbidden Si II and Si I line emission from Orion's BN-KL was measured using a cryogenic grating spectrometer aboard NASA's Kuiper Airborne Observatory. It is believed that the bulk of the forbidden Si II emission in Orion originates in photodissociated gas at the interface between the H II region and its parent molecular cloud. There is, however, a twofold enhancement in forbidden Si II emission near IRc2, which is attributed to fast dissociative J-shock where the wind from IRc2 impact slower moving material. Model fits suggest a silicon gas-phase depletion near ITc2 of 0.3-1.0 relative to solar. The spatial distribution of the forbidden Si II emission has a centralized peak.

Haas, Michael R.↗
NASA NTRS1997

Characteristics of an Electron Cyclotron Resonance Plasma Source for the Production of Active Nitrogen Species in III-V Nitride Epitaxy

A simple analysis is provided to determine the characteristics of an electron cyclotron resonance (ECR) plasma source for the generation of active nitrogen species in the molecular beam epitaxy of III-V nitrides. The effects of reactor geometry, pressure, power, and flow rate on the dissociation efficiency and ion flux are presented. Pulsing the input power is proposed to reduce the ion flux.

Meyyappan, Meyya↗
DOE OSTI2025

Charge regulation effects on colloidal mixture nanoparticles

Changes in pH within a system containing dissociable sites affect the protonation and deprotonation of these groups, thereby influencing their physical properties. In response, the system modifies their surface charge, affecting electrostatic interactions, aggregation, stability, and structural behavior. Although the pH can be tuned in experiments, it is difficult to model this phenomenon using simulations or theoretical approaches. Here, we perform hybrid Monte Carlo-molecular dynamics simulations to model charge regulation effects in an equimolar colloidal charged system. We compare charge regulation effects with those of a system in which the charges of colloidal nanoparticles are not dissociable. The comparison between the two cases modifies the phase diagram, and it changes the volume fraction where a percolation network of nanoparticles is found. Charge regulation is found to destroy network formation, as the charge in the nanoparticles is modified because of the cooperativity dependency of the degree of charge dissociation sites among the nanoparticles favoring cluster formation. Furthermore, our work suggests that the ionic and/or electronic conductivity in functionalized nanoparticles can be modified by changing pH values. It also guides the experimental design of oppositely charged nanoparticles as inks for 3D printing processes.

Classical statistical mechanics↗
NASA NTRS2003

Molecular Carbon in the Galaxy: Laboratory and Observational Studies

In a collaboration with the Mats Larsson group from Stockholm, we carried out a new measurement of the rate of dissociative recombination of H(sup *, sub j), using a new pulsed supersonic beam source of rotationally cold H(sup *, sub j). This source was first designed and characterized in our lab by IR cavity ringdown spectroscopy, determining a rotationaYtranslationa1 temperature of 20-60K, depending on conditions. This new source was then taken to Stockholm for the recombination rate studies at the CRYRING storage ring. The recombination rate constant measured against temperature yields values consistent with the most recent calculations, whereas previous experimental measurements varied over a range of 10(exp 4) and were poor agreement with theory. This is a crucial achievement for understanding the ion chemistry of diffuse clouds. Moreover, this result in combination with recent observations implies a greatly enhanced (factor of 40) cosmic ray ionization rate in a diffuse cloud (zeta Persei) relative to previous studies. The implications of this are discussed in our recent Nature paper. An enhanced cosmic-ray flux towards zeta Persei inferred from a laboratory study of the H(sup *, sub j)-e(sup -) recombination rate.

Saykally, Richard James↗
DOE OSTI2020

Dissociation of salts in water under pressure

The investigation of salts in water at extreme conditions is crucial to understanding the properties of aqueous fluids in the Earth. We report first principles (FP) and classical molecular dynamics simulations of NaCl in the dilute limit, at temperatures and pressures relevant to the Earth's upper mantle. Similar to ambient conditions, we observe two metastable states of the salt: the contact (CIP) and the solvent-shared ion-pair (SIP), which are entropically and enthalpically favored, respectively. We find that the free energy barrier between the CIP and SIP minima increases at extreme conditions, and that the stability of the CIP is enhanced in FP simulations, consistent with the decrease of the dielectric constant of water. The minimum free energy path between the CIP and SIP becomes smoother at high pressure, and the relative stability of the two configurations is affected by water self-dissociation, which can only be described properly by FP simulations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1992

Development of a new model for vibration-dissociation coupling in nitrogen

A new model for vibration-dissociation coupling is derived using knowledge obtained from a simulation of the vibrational relaxation of heated nitrogen by collisional processes. This bilevel model is based on the assumption that nitrogen can be represented by two molecular species. The vibrational energy relaxation is represented by a modified form of the Landau-Teller equation. The effects of the bilevel model on a typical hypervelocity flowfield computation are examined and compared to the Park TTv model. Specifically, it is found that the bilevel model exhibits a decreased dissociation rate. This is believed to be due to the inhibition of dissociation by nonequilibrium vibrational relaxation.

Landrum, D. B.↗
DOE OSTI2025

Irreversible oxygen poisoning: Modeling the initial water dissociation kinetics on δ-Pu(111) and δ-Pu(100) through density functional theory

In this work, the initial kinetics of water dissociation on two facets of δ-plutonium, δ-Pu(111) and δ-Pu(100), are explored through density functional theory in order to understand how water dissociation occurs on these facets. We explored the dissociation of water via the formation of hydroxyls, atomic hydrogen, and atomic oxygen species on each facet. We calculate low energetic barriers for water to split to adsorbed hydrogen and hydroxyl species at 0.19 eV for δ-Pu(111) and 0.07 eV for δ-Pu(100). The hydroxyl has a barrier of 0.64 and 0.37 eV to cleave the hydrogen–oxygen bond on δ-Pu(111) and δ-Pu(100), respectively. Due to the highly exergonic adsorption free energy of atomic oxygen of −2.10 eV, the metallic surfaces are found to be fully covered in oxygen, even with the inclusion of oxygen lateral interactions. When combined with the reaction thermodynamics, this free energy of adsorption forms a molecular oxygen desorption barrier greater than 9.51 eV (918 kJ/mol). These results, combined with simulated temperature programed desorption spectra, indicate that oxygen formed via water dissociation on δ-Pu (111) and (100) facets induces an irreversible poison that prevents further reaction of water directly on metallic plutonium surfaces, most likely due to the strong hybridization of the Pu and O valence states. Therefore, these results imply that another mechanism is responsible for the continuously experimentally measured water dissociation, which is most likely due to the Pu oxide.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Activation of CO 2 by Actinide Cations (Th + , U + , Pu + , and Am + ) as Studied by Guided Ion Beam and Triple Quadrupole Mass Spectrometry

Reactions of CO 2 with Th+ have been studied using guided ion beam tandem mass spectrometry (GIBMS) and with An + (An + = Th + , U + , Pu + , and Am + ) using triple quadrupole inductively coupled plasma mass spectrometry (QQQ-ICP-MS). Additionally, the reactions ThO + + CO and ThO + + CO 2 were examined using GIBMS. Modeling the kinetic energy dependent GIBMS data allowed determination of bond dissociation energies (BDEs) for D o (Th + -O) and D o (OTh + -O) that are in reasonable agreement with previous GIBMS measurements. The QQQ-ICP-MS reactions were studied at higher pressures where multiple collisions between An + and the neutral CO 2 occur. As a consequence, both AnO + and AnO 2 + products were observed for all An + except Am + , where only AmO + was observed. Here, the relative abundances of the observed monoxides compared to the dioxides are consistent with previous reports of the AnO n + (n = 1, 2) BDEs. Comparison of the periodic trends of the group 4 transition metal, lanthanide (Ln), and actinide atomic cations in reactions with CO 2 (a formally spin-forbidden reaction for most M + ground states), and O 2 (a spin unrestricted reaction) indicate that spin conservation plays a minor role, if any, for the heavier An + metals. Further correlation of Ln + and An + + CO 2 reaction efficiencies with the promotion energy (E p ) to the first electronic state with two valence d-electrons (E p (5d 2 ) for Ln + and E p (6d 2 ) for An + ) indicates that the primary limitation in the activation of CO 2 is the energetic cost to promote from the electronic ground state of the atomic metal ion to a reactive state.

bond activation↗
DOE OSTI2020

Preserving Symmetry and Degeneracy in the Localized Orbital Scaling Correction Approach

Symmetry is a fundamental concept that plays a critical role in many chemical and physical phenomena and processes, which highlights the importance of theoretical methods to correctly handle symmetry. The recently developed localized orbital scaling correction (LOSC1) shows great improvement on the description of band gaps, photoemission spectra, and dissociation limits of cationic species. However, issues remain with LOSC1 in dealing with the symmetry and degeneracy of electronic states, which are also relevant to other methods using localization. In this work, we utilize a new method that deals with the physical-space and the energy-space localization on an equal footing. The resulting localized orbitals, i.e., orbitalets, are able to maintain more symmetry and the desired state degeneracy, which is important in calculating the electronic structure of both molecules and periodic bulk systems. Furthermore, the curvature matrix is redefined to improve potential energy curves for systems with stretched bonds, while retaining the correct dissociation limits. This new approach, termed LOSC2, includes only two fitting parameters. It maintains accuracy similar to that of LOSC1 over many properties, while overcoming LOSC1’s deficiencies in symmetry and degeneracy. Our tests have shown that LOSC2 orbitalets possess the full- or subgroup of molecular symmetry if allowed, which preserves the state degeneracy. Tests on differently sized planar annulenes, odd-numbered allenes, and triphenylene again verify that LOSC2 is able to maintain the state degeneracy, while LOSC1 cannot. Finally, all the tests demonstrate the advantage of LOSC2 in the calculation of molecular systems and its potential for application to periodic bulk systems.

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

Terpolymer Donor with Inside Alkyl Substituents on Thiophene π ‐Bridges toward Thiazolothiazole A 2 ‐Unit Enables 18.21% Efficiency of Polymer Solar Cells

Abstract PM6 is a widely used D–A copolymer donor in the polymer solar cells (PSCs). Incorporating second electron‐withdrawing (A 2 ) units into PM6 backbone by ternary D–A 1 –D–A 2 random copolymerization strategy is an effective approach to further improve its photovoltaic performance. Here, the authors synthesize the PM6‐based terpolymers by introducing thiazolothiazole as the A 2 units connecting with thiophene π‐bridges attaching alkyl substituent towards the A 2 unit (PMT‐CT) or towards D‐unit (PMT‐FT), and study the effect of the alkyl substituent position on the photovoltaic performance of them. Two terpolymers PMT‐FT‐10 and PMT‐CT‐10 are obtained by incorporating 10% A 2 units in the terpolymers. The film of PMT‐CT‐10 shows slightly up‐shifted highest occupied molecular orbital (HOMO) energy levels while better co‐planar structure than that of PMT‐FT‐10. Meanwhile, the PMT‐CT‐10:Y6 blend film exhibits better molecular packing properties, more proper phase separation and more balanced hole and electron mobilities, which are beneficial to more efficient exciton dissociation, efficient charge transport and weaker bimolecular recombination. Consequently, the PMT‐CT‐10 based PSCs obtain the highest power conversion efficiency of 18.21%. The results indicate that side chain position on the thiophene π‐bridges influence the device performance of the terpolymer donors, and PMT‐CT‐10 is a high efficiency polymer donor for the PSCs.

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

CFM-ID 4.0: More Accurate ESI MS/MS Spectral Prediction and Compound Identification

In the field of metabolomics, mass spectrometry (MS) is the method most commonly used for identifying and annotating metabolites. As this typically involves matching a given MS spectrum against an experimentally acquired reference spectral library, this approach is limited by the coverage and size of such libraries (which typically number in the thousands). These experimental libraries can be greatly extended by predicting the MS spectra of known chemical structures (which number in the millions) to create computational reference spectral libraries. To facilitate the generation of predicted spectral reference libraries we developed CFM-ID, a computer program that can accurately predict ESI-MS/MS spectrum for a given compound structure. CFM-ID is one of the best-performing methods for compound-to-mass-spectrum prediction, and also one of the top tools for in silico mass-spectrum-to-compound identification. This work improves CFM-ID’s ability to predict ESI-MS/MS spectra from compounds by: (1) learning parameters from features based on the molecular topology, (2) adding a new approach to ring cleavage that models such cleavage as a sequence of simple chemical bond dissociations and (3) expanding its hand-written rule-based predictor to cover more chemical classes, including acylcarnitines, acylcholines, flavonols, flavones, flavanones, and flavonoid glycosides. We demonstrate that this new version of CFM-ID (version 4.0) is significantly more accurate than previous CFM-ID versions, in terms of both EI-MS/MS spectral prediction and compound identification. CFM-ID 4.0 is available at http://cfmid4.wishartlab.com/ as a webservice and docker images can be downloaded at https://hub.docker.com/r/wishartlab/cfmid

Wang, Fei↗
NASA NTRS1983

NMR (Nuclear Magnetic Resonance) and macromolecular migration in a melt or in concentrated solutions

The purpose of this paper is to analyze the migration process of long polymer molecules in a melt or in concentrated solutions as it may be observed from the dynamics of the transverse magnetization of nuclear spins linked to these chains. The low frequency viscoelastic relaxation of polymer systems is known to be mainly controlled by the mechanism of dissociation of topological constraints excited on chains and which are called entanglements. This mechanism exhibits a strong dependence upon the chain molecular weight. These topological constraints also govern the diffusion process of polymer chains. So, the accurate description of the diffusion motion of a chain may be a convenient way to characterize disentanglement processes necessarily involved in any model proposed to explain viscoelastic effects.

Addad, J. P. C.↗