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At least 631 records · Page 35

Potential energy surfaces for atomic oxygen reactions: Formation of singlet and triplet biradicals as primary reaction products with unsaturated organic molecules

The experimental study of the interaction of atomic oxygen with organic polymer films under LEO conditions has been hampered by the inability to conduct detailed experiments in situ. As a result, studies of the mechanism of oxygen atom reactions have relied on laboratory O-atom sources that do not fully reproduce the orbital environment. For example, it is well established that only ground electronic state O atoms are present at LEO, yet most ground-based sources are known to produce singlet O atoms and molecules and ions in addition to O(3P). Engineers should not rely on such facilities unless it can be demonstrated either that these different O species are inert or that they react in the same fashion as ground state atoms. Ab initio quantum chemical calculations have been aimed at elucidating the biradical intermediates formed during the electrophilic addition of ground and excited-state O atoms to carbon-carbon double bonds in small olefins and aromatic molecules. These biradicals are critical intermediates in any possible insertion, addition and elimination reaction mechanisms. Through these calculations, we will be able to comment on the relative importance of these pathways for O(3P) and O(1D) reactions. The reactions of O atoms with ethylene and benzene are used to illustrate the important features of the mechanisms of atomic oxygen reaction with unsaturated organic compounds and polymeric materials.

Jaffe, Richard L.↗

Dispensing targets for ion beam particle generators

A target for dispensing high energy protons or neutrons or ionized atoms or ionized molecules is provided which comprises a container for the target gas, which is at atmospheric or higher pressure. The container material can release the target gas in the spot where the container is heated above a predetermined temperature by the impact of an ion beam where protons or neutrons are desired, or by electrons where ionized atoms or molecules are desired. On the outside of the container, except for the region where the beam is to impact, there is deposited a layer of a metal which is imperious to gaseous diffusion. A further protective coating of a material is placed over the layer of metal, except at the region of the ion impact area in order to adsorb any unreacted gas in the vacuum in which the target is placed, to thereby prevent reduction of the high vacuum, as well as contamination of the interior of the vacuum chamber.

Miller, C. G.↗

A Comparison of the Accuracy of Different Functionals

The errors in the computed geometries, zero-point energies, and atomization energies of molecules containing only first and second row atoms are compared for several levels of theory, including Hartree-Fock, second-order Moller-Plesset perturbation theory (MP2), and density functional theory (DFT) using five different functionals, including two hybrid functionals. The 6-31G* and 6-311+G(3df,2p) basis set are used. Overall, the B3LYP hybrid functional yields the best results.

Bauschlicher, Charles W., Jr.↗

Production of carbon, sulfur, and CS in Comet West

Results from ultraviolet spectrographic observations of Comet West (1975n) in the 1620-3960 A wavelength range are presented. Objective grating imagery of the comet reveals for the first time emission from sulfur atoms and CS molecules as well as previously observed lines or bands in carbon atoms and CO(+), CO2(+) and OH molecules. Some evidence exists for emission in the C2 Mulliken bands and in the CO Cameron bands. On the basis of the observations, production rates of C (ground state), C(1D), S, and CS are inferred to be 3.8 x 10 to the 29th per sec, 4.4 x 10 to the 29th per sec, 1.7 x 10 to the 28th per sec, and greater than approximately 3.1 x 10 to the 27th per sec, respectively.

Smith, A. M.↗

Simplified Modeling of Oxidation of Hydrocarbons

A method of simplified computational modeling of oxidation of hydrocarbons is undergoing development. This is one of several developments needed to enable accurate computational simulation of turbulent, chemically reacting flows. At present, accurate computational simulation of such flows is difficult or impossible in most cases because (1) the numbers of grid points needed for adequate spatial resolution of turbulent flows in realistically complex geometries are beyond the capabilities of typical supercomputers now in use and (2) the combustion of typical hydrocarbons proceeds through decomposition into hundreds of molecular species interacting through thousands of reactions. Hence, the combination of detailed reaction- rate models with the fundamental flow equations yields flow models that are computationally prohibitive. Hence, further, a reduction of at least an order of magnitude in the dimension of reaction kinetics is one of the prerequisites for feasibility of computational simulation of turbulent, chemically reacting flows. In the present method of simplified modeling, all molecular species involved in the oxidation of hydrocarbons are classified as either light or heavy; heavy molecules are those having 3 or more carbon atoms. The light molecules are not subject to meaningful decomposition, and the heavy molecules are considered to decompose into only 13 specified constituent radicals, a few of which are listed in the table. One constructs a reduced-order model, suitable for use in estimating the release of heat and the evolution of temperature in combustion, from a base comprising the 13 constituent radicals plus a total of 26 other species that include the light molecules and related light free radicals. Then rather than following all possible species through their reaction coordinates, one follows only the reduced set of reaction coordinates of the base. The behavior of the base was examined in test computational simulations of the combustion of heptane in a stirred reactor at various initial pressures ranging from 0.1 to 6 MPa. Most of the simulations were performed for stoichiometric mixtures; some were performed for fuel/oxygen mole ratios of 1/2 and 2.

Bellan, Josette↗

Pt-Assisted Carbon Remediation of Mo2C Materials for CO Disproportionation

Using the CO disproportionation (Boudouard) reaction as a probe reaction, an in-depth analysis of temperature-programmed pulse response data shows that the addition of Pt to Mo2C mitigates deactivation of Mo active sites by acting as a carbon collector. CO2 production on Mo2C and Pt/Mo2C materials is dependent on both the activation energy and the CO surface concentration. Detailed plane-wave density functional theory calculations of the CO adsorption and disproportion reactions on Mo2C-supported Pt nanoparticles (NPs) are reported. The Mo2C was modeled by the ß-Mo2C (100) surface, and the Pt/Mo2C interface was modeled by the addition of 12 Pt atoms to the Mo2C (100) surface (12Pt@Mo2C). The potential energy surfaces of the Boudouard reaction were calculated on pure Mo2C, 12Pt@Mo2C, and Pt (111) surfaces. CO dissociation readily occurs on the Mo2C (100) surface, but not on the Pt (111) surface, with the former being exothermic and the latter being endothermic. At the Pt/Mo2C interface, CO dissociation is still exothermic, but with a larger energy barrier. The Boudouard reaction takes place on the Mo2C region, where CO2 is formed from a surface O atom dissociated from one CO molecule in reaction with another CO molecule, leaving one C atom on the surface. C adsorption is preferential on the Pt site in comparison to the Mo site. The supported Pt domains can collect the remaining C atoms, facilitating further CO2 formation on the active Mo sites. A Bader charge analysis shows that the surface metal-carbon bond is a mixture of covalent and ionic bonds, whereas the surface metal-oxygen bond is ionic. Electron localization function (ELF) and partial charge density calculations agree well with the Bader charge analysis. These computational results are consistent with experimental observations of the interaction of CO with Mo2C nanotube supported Pt domains in the transient regime under far from equilibrium conditions. The Boudouard reaction is an important side reaction, and the unexpected role found for Pt as a carbon collector, with Mo serving as a disproportionation site, provides a unique vantage point for understanding carbon and coke formation on catalytic materials.

Pt-assisted carbon remediation, Pt/Mo2C interface,↗

Theoretical research program to predict the properties of molecules and clusters containing transition metal atoms

The primary focus of this research has been the theoretical study of transition metal (TM) chemistry. A major goal of this work is to provide reliable information about the interaction of H atoms with iron metal. This information is needed to understand the effect of H atoms on the processes of embrittlement and crack propagation in iron. The method in the iron hydrogen studies is the cluster method in which the bulk metal is modelled by a finite number of iron atoms. There are several difficulties in the application of this approach to the hydrogen iron system. First the nature of TM-TM and TM-H bonding for even diatomic molecules was not well understood when these studies were started. Secondly relatively large iron clusters are needed to provide reasonable results.

Walch, S.↗

Characterization of Cosmic Grain Analogs Formed at Low Temperature from Small Hydrocarbon Precursors in the NASA Ames COSmIC Facility

Here, we present the results of the first solid-phase ex situ analysis of cosmic grain analogs produced at low temperature (<200 K) in the NASA Ames COsmic SImulation Chamber (COSmIC) from small hydrocarbon precursors, methane (CH4) and acetylene (C2H2), seeded in an argon supersonic jet expansion and submitted to a plasma discharge. The plasma-induced chemical reactions, initiated between the precursor molecules and their atomic and molecular fragments, radicals and ions, produce larger molecules and eventually solid particles that are collected in situ under controlled conditions. Scanning electron microscopy (SEM) imaging was used to provide insight on the morphology and growth structure of the grains produced in COSmIC, and to investigate how the precursors used to produce the grains affect these parameters. This SEM study has shown that under identical experimental conditions with fixed physical and chemical parameters (precursor density, temperature, energy, and reaction time), heavier precursors in the initial mixture produce larger grains and in larger quantity, most likely as a result of a more complex chemistry: most of the grains produced in the Ar/CH4 (95:5) gas mixture ranged from 15 to 385 nm in diameter with an average density of 2.1 grains per sq.μm, while the grains produced in the Ar/C2H2 (95:5) gas mixture ranged from 40 to 650 nm with a density of 3.5 grains per sq.μm. Changes in the morphology were also observed, with grains produced from acetylene (C2H2) precursors tending to be more spherical than grains produced from methane (CH4) precursors. This change in morphology could be associated with different stages of growth formation at low temperature from a more "planar" growth at first, followed by coagulation into more spherical particles. This study demonstrates that the COSmIC experimental setup can be used to investigate carbon grain formation from small gas-phase molecular precursors at low temperature (<200 K), i.e., under a temperature regime that is representative of the dust condensation zone and outer region of circumstellar envelopes.

Ella Sciamma-O'Brien↗

QM7-X, a comprehensive dataset of quantum-mechanical properties spanning the chemical space of small organic molecules

We introduce QM7-X, a comprehensive dataset of 42 physicochemical properties for ≈4.2 million equilibrium and non-equilibrium structures of small organic molecules with up to seven non-hydrogen (C, N, O, S, Cl) atoms. To span this fundamentally important region of chemical compound space (CCS), QM7-X includes an exhaustive sampling of (meta-)stable equilibrium structures—comprised of constitutional/structural isomers and stereoisomers, e.g., enantiomers and diastereomers (including cis-/trans- and conformational isomers)—as well as 100 non-equilibrium structural variations thereof to reach a total of ≈4.2 million molecular structures. Computed at the tightly converged quantum-mechanical PBE0+MBD level of theory, QM7-X contains global (molecular) and local (atom-in-a-molecule) properties ranging from ground state quantities (such as atomization energies and dipole moments) to response quantities (such as polarizability tensors and dispersion coefficients). By providing a systematic, extensive, and tightly-converged dataset of quantum-mechanically computed physicochemical properties, we expect that QM7-X will play a critical role in the development of next-generation machine-learning based models for exploring greater swaths of CCS and performing in silico design of molecules with targeted properties.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Attosecond X-Ray Core-Level Chronoscopy of Aromatic Molecules

Attosecond photoemission or photoionization delays are a unique probe of the structure and the electronic dynamics of matter. However, the spectral congestion of valence photoelectron spectra sets fundamental limits to the complexity of systems that can be studied, and the delocalization of valence electron wave functions blurs the spatial origin of the photoelectron wave packet. Using attosecond x-ray pulses from LCLS, we demonstrate the key advantages of measuring core-level delays: The photoelectron spectra remain atomlike, the measurements become element specific, and the observed scattering dynamics originate from a pointlike source when multicenter interference effects are negligible. We exploit these unique features to reveal the effects of changing functional groups (C-H vs N) and symmetry on attosecond scattering dynamics by measuring and calculating the photoionization delays between N−1⁢𝑠 and C−1⁢𝑠 core shells of a series of aromatic azabenzene molecules. Remarkably, the delays increase with the number of nitrogen atoms in the molecule and reveal multiple resonances. We identify two previously unknown mechanisms regulating the associated attosecond dynamics, namely the enhanced confinement of the trapped wave function with the replacement of C-H groups by N atoms and the decrease of the coupling strength among the photoemitted partial waves with increasing symmetry. This study demonstrates the unique opportunities opened by measurements of core-level photoionization delays for unraveling attosecond electron dynamics in complex matter.

Ji, Jia-Bao [Eidgenoessische Technische Hochschule↗

Ultraviolet studies of the interstellar gas

Sounding-rocket and satellite UV observations of interstellar gas clouds are reviewed with major attention given to Copernicus observations of interstellar absorption lines. Analysis of typical absorption-line data is outlined, and observations are reviewed for atomic hydrogen as well as interstellar H2, HD, and CO molecules. Investigations of atomic abundances in H I regions are summarized, measurements of atomic deuterium abundances in the interstellar gas are examined, and the properties of ionized interstellar gas are described. Theoretical analyses of the physical state of the interstellar gas are summarized with respect to ionization by energetic radiation, cool H I clouds, and the intercloud medium. The data obtained thus far are shown to indicate mean temperatures of about 80 K, particle densities between 10 and 1000 per cu cm, and a depletion of heavy elements that becomes greatly enhanced with increasing condensation temperature for those H I regions with strong H2 lines.

Spitzer, L., Jr.↗

Unraveling Spatio-Temporal Chemistry Evolution in Laser Ablation Plumes and Its Relation to Initial Plasma Conditions

The chemistry evolution in a laser ablation plume depends strongly on its initial physical conditions. In this article, we investigate the impact of plasma generation conditions on the interrelated phenomena of expansion dynamics, plasma chemistry, and physical conditions. Plasmas are produced from a uranium metal target in air using nanosecond, femtosecond, and femtosecond filament-assisted laser ablation. Time-resolved two-dimensional spectral imaging was performed for evaluating the spatio-temporal evolu-tion of atoms, diatoms, polyatomic molecules, and nanoparticles in situ. Emission spectral features reveal that molecular formation occurs at early times in both femtosecond and filament ablation plumes, although with different temporal decay. In contrast, mo-lecular formation is found to occur at much later times in nanosecond plasma evolution. Spectral modeling is used to infer tem-poral behavior of plasma excitation temperature, and results highlighted that nanosecond plume temperatures decay rapidly while plumes generated by filament ablation show slowest decay. In this work, we find U atoms and UO molecules co-exist in ultrafast laser produced plasmas even at early times after plasma onset owing to favorable temperatures for molecular formation. Regardless of irradiation conditions, plume emission features showed presence of higher oxides (i.e. UxOy), although with different temporal histories. Our study provides insight into the impact of plasma generation conditions on chemistry evolution in plasmas produced from traditional focused femtosecond, nanosecond, and filament-assisted laser ablation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Breaking covalent bonds in the context of the many-body expansion (MBE). I. The purported “first row anomaly” in XH n (X = C, Si, Ge, Sn; n = 1–4)

We present a new, novel implementation of the Many-Body Expansion (MBE) to account for the breaking of covalent bonds, thus extending the range of applications from its previous popular usage in the breaking of hydrogen bonds in clusters to molecules. A central concept of the new implementation is the in situ atomic electronic state of an atom in a molecule that casts the one-body term as the energy required to promote it to that state from its ground state. The rest of the terms correspond to the individual diatomic, triatomic, etc., fragments. Its application to the atomization energies of the XH n series, X = C, Si, Ge, Sn and n = 1–4, suggests that the (negative, stabilizing) 2-B is by far the largest term in the MBE with the higher order terms oscillating between positive and negative values and decreasing dramatically in size with increasing rank of the expansion. The analysis offers an alternative explanation for the purported “first row anomaly” in the incremental H n–1 X–H bond energies seen when these energies are evaluated with respect to the lowest energy among the states of the XH n molecules. Due to the “flipping” of the ground/first excited state between CH 2 ( 3 B 1 ground state, 1 A 1 first excited state) and XH 2 , X = Si, Ge, Sn ( 1 A 1 ground state, 3 B 1 first excited state), the overall picture does not exhibit a “first row anomaly” when the incremental bond energies are evaluated with respect to the molecular states having the same in situ atomic states.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Ionization of Free and Confined Atoms and Ions (Final Technical Report)

Over the almost 22-year duration of this theoretical research project, a great deal of progress has been made in the understanding of the ionization of free and confined atomic and molecular systems along with a recent particular emphasis upon studies of the ultrafast time-delay phenomenon in the photoemission process. Our methods have emphasized the role of many-body interactions and relativistic effects in the various processes we have studied. The advances that we have made over the course of this project have been in the areas nondipole effects in the photoionization process, inner-shell photoemission from negative atomic ions, excited state photoionization of neutral atoms and positive atomic ions, Cooper minima in quadrupole photoionization, relativistic interaction in the photoionization of atoms and negative atomic ions, photoionization of the fullerene molecule C 60 along with the photoionization of atomic and molecular systems confined in the C 60 molecule, confinement resonances in endohedral atom photoemission, interchannel coupling effects in photoionization, Wigner time delay in free and confined atoms and ions, angular effects in Wigner time delay in atomic photoionization, photoionization of superheavy atoms and the influence of core relaxation on the photoionization of atomic systems, among others. In the course of this project, we have had extensive collaboration with experimentalists where we have explained the physics of numerous measurements and pointed the way to new laboratory investigations with our calculations. We have also collaborated with a number of theorists as well. Thus, owing to these many collaborations with scientists not funded by DOE, we have leveraged the DOE support rather considerably. To illustrate the depth and breadth of the theoretical investigations, listed below are the 138 refereed and invited publications that cite DOE support. These publications detail the many contributions made over the period of this project.

74 ATOMIC AND MOLECULAR PHYSICS↗

Applying the ATOM drug discovery platform to small-molecule antivirals (Annual Report)

The objective of this project is to advance our understanding of the ML approaches needed to find the most potent inhibitor through an AI guided search that simultaneously optimizes for limited off-target safety activity and desirable pharmacokinetics (PK) properties. The methods will be tested for inhibiting SARS-CoV-2 activity through inhibition of the main protease as a demonstration, but the methodology will be developed to apply to any biothreat target using a small-molecule protein binding-based intervention, with limited experimental data. Computational experiments are conducted using our ATOM generative molecular design (GMD) loop software, which is the implementation of our AI/ML drug design pipeline.

59 BASIC BIOLOGICAL SCIENCES↗

Atom Equivalent Energies for the Rapid Estimation of the Heat of Formation of Explosive Molecules from Density Functional Tight Binding Theory

Atom equivalent energies have been derived from which the gas-phase heat of formation of explosive molecules can be estimated from fast, semiempirical density functional tight binding total energy calculations. The root-mean-square deviation and maximum deviation of the heats of formation from the experimental values for the set of 45 energetic molecules compiled by Byrd and Rice [ J. Phys. Chem. A, 2006, 110, 1005–1013] are 10.4 and 25.5 kcal/mol, respectively, using 4 atom equivalent energies and 7.4 and 15.0 kcal/mol, respectively, using 7 atom equivalent energies. These errors are around a factor of 2–3 larger than those obtained from density functional theory calculations but are smaller than those obtained from other semiempirical electronic structure methods. Heats of formation calculated with density functional tight binding theory using the 4 and 7 atom equivalent energies, the Byrd and Rice scheme, and the atom pair contribution method for a new set of 531 energetic molecules that contain only carbon, hydrogen, nitrogen, and oxygen are provided.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗