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At least 1,693 records · Page 94

Automated Computational Thermochemistry for Butane Oxidation: A Prelude to Predictive Automated Combustion Kinetics

arge-scale implementation of high level computational theoretical chemical kinetics offers the prospect for dramatically improving the fidelity of combustion chemical modeling. As a first step toward this goal, we developed a procedure for automatically generating the thermochemical data for combustion of an arbitrary fuel. The procedure begins by producing a list of combustion relevant species from a specification of the fuel and combustion conditions of interest. Then, for each element in the list of species, the procedure determines an internal coordinate z-matrix description of its structure, the optimal torsional configuration via Monte Carlo sampling, key rovibrational properties for that optimal geometry (including anharmonic corrections from torsional mappings and/or vibrational perturbation theory), and high level estimates of the electronic and zero-point energies via arbitrarily defined composite methods. This dataset is then converted first to partition functions, then to thermodynamic properties, and finally to NASA polynomial representations of the data. The end product is an automatically generated database of electronic structure results and thermochemical data including representations in a format appropriate for combustion simulations. The utility and functioning of this predictive automated computational thermochemistry (PACT) software package is illustrated through application to the automated generation of thermochemical data for the combustion of n-butane. Butane is chosen for this demonstration as its species list is of reasonably manageable size for debugging level computations, while still presenting most of the key challenges that need to be surmounted in the consideration of larger fuels. Furthermore, its low temperature chemistry is representative of that oc-curring with larger alkanes.

Keceli, Murat↗

Technetium incorporation into goethite (α-FeOOH): An atomic-scale investigation

During the processing of low-activity radioactive waste to generate solid waste forms (e.g., glass), technetium-99 (Tc) is of concern because of its volatility. A variety of materials are under consideration to capture Tc from waste streams, including the iron oxyhydroxide, goethite (α-FeOOH), which was experimentally shown to sequester Tc(IV). This material could ultimately be incorporated into glass or other low-temperature waste form matrices. However, questions remain regarding the incorporation mechanism for Tc(IV) in goethite, which has implications for predicting the long-term stability of Tc in waste forms under changing conditions. Here, quantum-mechanical calculations were used to evaluate the energy of five different charge-compensated Tc(IV) incorporation scenarios in goethite. The two most stable incorporation mechanisms involve direct substitution of Tc(IV) onto Fe(III) lattice sites and charge balancing either by removing one nearby H+ (i.e., within 5 Å), or by creating an Fe(III) vacancy when substituting 3 Tc(IV) for 4 Fe(III), with the former being preferred over the latter relative to gas-phase ions. When corrections for hydrated references phases are applied, the Fe(III)-vacancy mechanism becomes more energetically competitive. Calculated incorporation energies and optimized bond-lengths are presented. Proton movement is observed to satisfy under-coordinated bonds surrounding vacancies in the goethite structure.

atomic-scale modeling↗

Pronounced Pressure Dependence of Electronic Transitions for Americium Compared to Isomorphous Neodymium and Samarium Mellitates

The mellitate ion is relevant in spent nuclear fuel processing and is utilized as a surrogate for studying the interactions of f elements with humic acids. A wealth of different coordination modes gives the potential for diverse structural chemistry across the actinide series. In this study, an americium mellitate, 243 Am 2 [(C 6 (COO – ) 6 ](H 2 O) 8 ·2H 2 O (1-Am), has been synthesized and characterized using structural analysis and spectroscopy at ambient and elevated pressures. 1-Am was then compared to isomorphous neodymium (1-Nd) and samarium (1-Sm) mellitates via bond-length analysis and pressure dependence of their Laporte-forbidden f → f transitions. Results show that the pressure dependence of the f → f transitions of 1-Am is significantly greater than that observed in 1-Nd and 1-Sm, with average shifts of 21.4, 4.7, and 3.6 cm –1 /GPa, respectively. Finally, this greater shift found in 1-Am shows further evidence that the 5f orbitals are more affected than the 4f orbitals when pressure is applied to isostructural compounds.

Actinides↗

Cis-Divacant Octahedral Fe(II) in a Dimensionally Reduced Family of 2-(Pyridin-2-yl)pyrrolide Complexes

Four-coordinate transition metal complexes can adopt a diverse array of coordination geometries, with square planar and tetrahedral coordination being the most prevalent. Previously, we reported the synthesis of a trinuclear Fe(II) complex, Fe 3 TPM 2 , supported by a three-fold symmetric 2-pyridylpyrrolide ligand (i.e., tris(5-(pyridin-2-yl)-1H-pyrrol-2-yl)methane), that featured a rare cis-divacant octahedral (CDO) geometry at each Fe(II) center. Here, a series of truncated 2-pyridylpyrrolide ligands is described that support mono- and binuclear Fe(II) complexes that also exhibit CDO geometries. Metallation of tetradentate ligand bis(5-(pyridin-2-yl)-1H-pyrrol-2-yl)methane (H 2 BPM) in THF results in a binuclear complex Fe 2 (BPM) 2 (THF) 2 in which both Fe(II) ions are octahedrally coordinated. The coordinated THF solvent ligands are labile: THF dissociation leads to Fe 2 (BPM) 2 , which features five-coordinate Fe(II) ions. The Fe–Fe distance in these binuclear complexes can be elongated by ligand methylation. Metalation of bis(5-(6-methylpyridin-2-yl)-1H-pyrrol-2-yl)methane (H 2 BPM Me ) in THF leads to the formation of four-coordinate, CDO Fe(II) centers in Fe(BPM Me ) 2 . Further ligand truncation affords bidentate ligands 2-(1H-pyrrol-2-yl)pyridine (PyrPyrrH) and 2-methyl-6-(1H-pyrrol-2-yl)pyridine (Pyr Me PyrrH). Metalation of these ligands in THF affords six-coordinate complexes Fe(PyrPyrr) 2 (THF) 2 and Fe(Pyr Me Pyrr) 2 (THF) 2 . Dissociation of labile solvent ligands provides access to fourcoordinate Fe(II) complexes. Ligand disproportionation at Fe(PyrPyrr) 2 results in the formation of Fe(PyrPyrr) 3 and Fe(0). Ligand methylation suppresses this disproportionation and enables isolation of Fe(Pyr Me Pyrr) 2 , which is rigorously CDO. Complete ligand truncation, by separating the 2-pyridylpyrrolide ligands into the constituent monodentate pyridyl and pyrrolide donors, affords Fe(Pyr) 2 (Pyrr) 2 in which the Fe(II) is tetrahedrally coordinated. Computational analysis indicates that the potential energy surface that dictates the coordination geometry in this family of four-coordinate complexes is fairly flat in the vicinity of CDO coordination. Furthermore, these synthetic studies provide the structural basis to explore the implications of CDO geometry on Fe-catalyzed reactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Monomeric and Trimeric Thorium Chlorides Isolated from Acidic Aqueous Solution

Two thorium(IV) compounds, [Th(H 2 O) 4 Cl 4 ]·2 (HPy·Cl) ( 1 ) and (HPy) 3 [Th 3 (H 2 O) 2 Cl 10 (OH) 5 ]·4(HPy·Cl) ( 2 ) (HPy = pyridinium), were isolated from acidic aqueous solution. The compounds were synthesized at room temperature and subsequently characterized using single crystal X-ray diffraction along with Raman and IR spectroscopies. Whereas compound 1 is built from discrete mononuclear Th(H 2 O) 4 Cl 4 units, compound 2 consists of a novel hydroxo-bridged trimeric [Th 3 (OH) 5 ] 7+ core. Such species are largely absent from discussions of Th solution and solid-state chemistry and their isolation may be attributed to outer coordination sphere interactions that help stabilize the structural units; extensive hydrogen bonding and $π–π$ stacking interactions are present in 1 and 2 . Density functional theory calculations were performed to predict the respective vibrational frequencies of the structural units, and their relative stability was predicted at the correlated molecular theory level. Small-angle X-ray scattering analysis of [Th 3 (OH) 5 ] 7+ in water indicates that the trimeric structural unit remains intact and that it is indeed an important species that necessitates consideration in geochemical models and for design of Th materials from water.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Quantum Chemical Characterization of Factors Affecting the Neutral and Radical-Cation Newman–Kwart Reactions

Details of the electronic and geometric structures of stationary points along the reaction coordinate of the Newman Kwart rearrangement, which transforms an O- arylthiocarbamate to an S-arylcarbamothioate, are examined using quantum chemical methods for a large number of compounds considering both the thermal reactions of uncharged substrates as well as the corresponding reactions of radical cation substrates generated under photoredox conditions. The uncharged mechanism, which has intrinsically high 298 K free energies of activation (in excess of 30 kcal.mol -1 ), has the character of nucleophilic aromatic substitution and is thus accelerated by electron-withdrawing substituents on the aromatic ring. The radical cationic mechanism, by contrast, has 298 K free energies of activation that are typically below 20 kcal.mol -1 , and is accelerated by electron donating substituents on the aromatic ring, which stabilize the hole character that is transferred to this fragment from the thiocarbamate fragment as the reaction proceeds. Opportunities to further accelerate the radical cation reaction are revealed by computational assessment of alternative amino groups for the thiocarbamate functionality.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Controlling Gold Nanoclusters by Diphospine Ligands

We report the synthesis and structure determination of a new Au22 nanocluster coordinated by six bidentate diphosphine ligands: 1,8-bis(diphenylphosphino) octane (L8 for short). Single crystal x-ray crystallography and electrospray ionization mass spectrometry show that the cluster assembly is neutral and can be formulated as Au22(L8)6. The Au22 core consists of two Au11 units clipped together by four L8 ligands, while the additional two ligands coordinate to each Au11 unit in a bidentate fashion. Eight gold atoms at the interface of the two Au11 units are not coordinated by any ligands. Four short gold-gold distances (2.64?2.65 Å) are observed at the interface of the two Au11 clusters as a result of the clamping force of the four clipping ligands and strong electronic interactions. The eight uncoordinated surface gold atoms in the Au22(L8)6 nanocluster are unprecedented in atom-precise gold nanoparticles and can be considered as potential in-situ active sites for catalysis.

Environmental Molecular Sciences Laboratory↗

Scope and Mechanism of Cooperativity at the Intersection of Organometallic and Supramolecular Catalysis

Here, the scope and mechanism of the microenvironment-catalyzed C(sp 3 )-C(sp 3 ) reductive elimination from transition metal complexes [Au(III), Pt(IV)] is explored. Experiments detailing the effect of structural perturbation of neutral and anionic spectator ligands, reactive alkyl ligands, solvent, and catalyst structure are disclosed. Indirect evidence for a coordinatively unsaturated encapsulated cationic intermediate is garnered via observation of several inactive donor-arrested inclusion complexes, including a crystallographically characterized encapsulated Au(III) cation. Finally, based on stoichiometric experiments under catalytically relevant conditions, a detailed mechanism is outlined for the dual supramolecular and platinum-catalyzed C-C coupling between methyl iodide and tetramethyltin. Determination of major platinum species present under catalytic conditions and subsequent investigation of their chemistry reveals an unexpected interplay between cis-trans isomerism and the supramolecular catalyst in a Pt(II)/Pt(IV) cycle, as well as several off-cycle reactions.

36 MATERIALS SCIENCE↗

Tailoring the Selective Oxidation of Hydroxyl-Containing Compounds via Precisely Tuning the Hydrogen-Bond Strength of Catalyst H-Bond Acceptors

The unique performance of the enzyme is mainly achieved via weak interactions between the “outer coordination sphere” and the substrate. Inspired by this process, we developed 3D encapsulated-structure catalysts with hydrogen-bond engineering on the shell, which mimics the “outer coordination sphere” of an enzyme. Various hydrogen bond acceptors (C=O, S=O, and N–O groups) are imparted in the shell. Concentration-dependent 1H NMR, inverse-phase gas Chromatography (IGC) measurements, and DFT calculations underscore that the hydrogen bond strength between the acceptor groups and alcohol follows the order of C=O < S=O < N–O. The hydroxyl compound oxidation rate vs the hydrogen bond strength follows a volcano behavior, reminiscent of Sabatier’s principle. The performance variation among catalysts is attributed to the adsorption strength of the substrate. The proposed bioinspired design principle expands the scope of encapsulated catalysts, enabling fine regulation of catalytic activity through precise microenvironment control via weak interactions with substrates.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Atom-by-atom fabrication with electron beams

Assembling matter atom-by-atom into functional devices is the ultimate goal of nanotechnology. The possibility of achieving this goal is intrinsically dependent on the ability to visualize matter at the atomic level, induce and control atomic-scale motion, facilitate and direct chemical reactions, and coordinate and guide fabrication processes towards desired structures atom-by-atom. In this Perspective, we summarize recent progress in chemical transformations, material alterations and atomic dynamics studies enabled by the converged, atomic-sized electron beam of an aberration-corrected scanning transmission electron microscope. We discuss how such top-down observations have led to the concept of controllable, beam-induced processes and then of bottom-up, atom-by-atom assembly via electron-beam control. Finally, the progress in this field, from electron-beam-induced material transformations to atomically precise doping and multi-atom assembly, is reviewed, as are the associated engineering, theoretical and big-data challenges.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

Evaluation of Attractive Interactions in the Second Coordination Sphere of Iron Complexes Containing Pendant Amines

The interactions between pendant amines in the second coordination sphere and ligands in the first coordination sphere are important for understanding the structures and reactivity of complexes containing PR2NR'2 ligands, which have been shown to be highly active H2 oxidation/production catalysts. A series of [Fe(PPh2NBn2)2(X)(Y)]n+ complexes have been prepared and structurally characterized. These complexes have two different ligands with which the pendant amines of the diphosphine ligand can interact. The solid state structure of cis-Fe(PPh2NBn2)2Cl2 reveals that the six-membered rings adjacent to the P atoms are in a boat confirmation, resulting in close N•••P distances that suggests the P atoms have a greater affinity for the lone pair of electrons on the N atom than chloride ligands. Similarly, boat conformations are observed for both rings adjacent to the hydride ligands of trans-[HFe(PPh2NBn2)2(CH3CN)]+ and trans-HFe(PPh2NBn2)2Cl, resulting in short N•••H distances. Spectroscopic and computational studies of trans-[HFe(PPh2NBn2)2(CO)]+, trans-[HFe(PPh2NBn2)(PPh2NBn2H)(CO)]2+, and trans-[HFe(PPh2NBn2)2(H2)]+ indicate the complexes are more stable when the pendant amines in boat conformations are adjacent to the hydride ligand. These data suggest an attractor ordering of H- > CO > H2 > PR3 > Cl- ~ CH3CN. This work was supported by the Center for Molecular Electrocatalysis, an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences. Pacific Northwest National Laboratory (PNNL) is operated by Battelle for the U.S. DOE. Computations were performed using the Cascade supercomputer at the Environmental Molecular Sciences Laboratory, a National Scientific User Facility sponsored by the DOE’s Office of Biological and Environmental Research and located at PNNL.

Liao, Qian↗

WIND-ACCRETION DISKS IN WIDE BINARIES, SECOND-GENERATION PROTOPLANETARY DISKS, AND ACCRETION ONTO WHITE DWARFS

Mass transfer from an evolved donor star to its binary companion is a standard feature of stellar evolution in binaries. In wide binaries, the companion star captures some of the mass ejected in a wind by the primary star. The captured material forms an accretion disk. Here, we study the evolution of wind-accretion disks, using a numerical approach which allows us to follow the long-term evolution. For a broad range of initial conditions, we derive the radial density and temperature profiles of the disk. In most cases, wind accretion leads to long-lived stable disks over the lifetime of the asymptotic giant branch donor star. The disks have masses of a few times 10{sup -5}-10{sup -3} M {sub Sun }, with surface density and temperature profiles that follow broken power laws. The total mass in the disk scales approximately linearly with the viscosity parameter used. Roughly, 50%-80% of the mass falling into the disk accretes onto the central star; the rest flows out through the outer edge of the disk into the stellar wind of the primary. For systems with large accretion rates, the secondary accretes as much as 0.1 M {sub Sun }. When the secondary is a white dwarf, accretion naturally leads to nova and supernova eruptions. For all types of secondary star, the surface density and temperature profiles of massive disks resemble structures observed in protoplanetary disks, suggesting that coordinated observational programs might improve our understanding of uncertain disk physics.

79 ASTRONOMY AND ASTROPHYSICS↗

Connecting X-ray and infrared variability among young stellar objects: ruling out potential sources of disk fluctuations

Variability in the infrared emission from disks around pre-main-sequence stars over the course of days to weeks appears to be common, but the physical cause of the changes in disk structure are not constrained. Here we present coordinated monitoring of one young cluster with the Spitzer and Chandra space telescopes aimed at studying the physical source of the variability. In fall 2011 we obtained 10 epochs of Chandra ACIS photometry over a period of 30 days with a roughly 3 day cadence contemporaneous with 20 epochs of Spitzer [3.6], [4.5] photometry over 40 days with a roughly 2 day cadence of the IC 348 cluster. This cadence allows us to search for week- to month-long responses of the infrared emission to changes in the high-energy flux. We find no strong evidence for a direct link between the X-ray and infrared variability on these timescales among 39 cluster members with circumstellar disks. There is no significant correlation between the shape of the infrared and X-ray light curves or between the sizes of the X-ray and infrared variability. Among the stars with an X-ray flare, none showed evidence of a correlated change in the infrared photometry on timescales of days to weeks following the flare. This lack of connection implies that X-ray heating of the planet-forming region of the disk is not significant, although we cannot rule out rapid or instantaneous changes in infrared emission.

79 ASTRONOMY AND ASTROPHYSICS↗

Updated resources for exploring experimentally-determined PDB structures and Computed Structure Models at the RCSB Protein Data Bank

The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB, RCSB.org), the US Worldwide Protein Data Bank (wwPDB, wwPDB.org) data center for the global PDB archive, provides access to the PDB data via its RCSB.org research-focused web portal. We report substantial additions to the tools and visualization features available at RCSB.org, which now delivers more than 227000 experimentally determined atomic-level three-dimensional (3D) biostructures stored in the global PDB archive alongside more than 1 million Computed Structure Models (CSMs) of proteins (including models for human, model organisms, select human pathogens, crop plants and organisms important for addressing climate change). In addition to providing support for 3D structure motif searches with user-provided coordinates, new features highlighted herein include query results organized by redundancy-reduced Groups and summary pages that facilitate exploration of groups of similar proteins. Newly released programmatic tools are also described, as are enhanced training opportunities.

Burley, Stephen K.↗

Revisiting metastable immiscibility in SiO 2 –Al 2 O 3 : Structure and phase separation of supercooled liquids and glasses

Understanding and controlling liquid–liquid phase separation in aluminosilicates is crucial for optimizing glass properties. However, the metastable nature of aluminosilicates’ phase separation has made it difficult to study experimentally, and uncertainty persists regarding the compositional and temperature extents of the miscibility gap. Here, we present new experimental evidence that suggests a consolute temperature between 1440 and 1590°C and endmember compositions of 7 and 62 mol.% Al 2 O 3 for the phase-separated glasses. Using containerless melt processing, deeply supercooled liquids over the 0–60 mol.% Al 2 O 3 range are probed with in situ small- and wide-angle X-ray scattering, which simultaneously reveals changes in nanoscale density heterogeneity and atomic structure. Correlations between phase separation and atomic coordination environments are compared for liquids and glasses. Pair distribution function analysis shows mean O–(Si + Al) coordination increases with Al 2 O 3 content and decreases with temperature.

36 MATERIALS SCIENCE↗

Amorphization in extreme deformation of the CrMnFeCoNi high-entropy alloy

Ever-harsher service conditions in the future will call for materials with increasing ability to undergo deformation without sustaining damage while retaining high strength. Prime candidates for these conditions are certain high-entropy alloys (HEAs), which have extraordinary work-hardening ability and toughness. By subjecting the equiatomic CrMnFeCoNi HEA to severe plastic deformation through swaging followed by either quasi-static compression or dynamic deformation in shear, we observe a dense structure comprising stacking faults, twins, transformation from the face-centered cubic to the hexagonal close-packed structure, and, of particular note, amorphization. The coordinated propagation of stacking faults and twins along {111} planes generates high-deformation regions, which can reorganize into hexagonal packets; when the defect density in these regions reaches a critical level, they generate islands of amorphous material. These regions can have outstanding mechanical properties, which provide additional strengthening and/or toughening mechanisms to enhance the capability of these alloys to withstand extreme loading conditions.

36 MATERIALS SCIENCE↗

Site Identity and Importance in Cosubstituted Bixbyite In2O3

The bixbyite structure of In2O3 has two nonequivalent, 6-coordinate cation sites and, when Sn is doped into In2O3, the Sn prefers the “b-site” and produces a highly conductive material. When divalent/tetravalent cation pairs are cosubstituted into In2O3, however, the conductivity increases to a lesser extent and the site occupancy is less understood. We examine the site occupancy in the MgxIn2−2xSnxO3 and ZnxIn2−2xSnxO3 systems with high resolution X-ray and neutron diffraction and density functional theory computations, respectively. In these sample cases and those that are previously reported in the MxIn2−2xSnxO3 (M = Cu, Ni, or Zn) systems, the solubility limit is greater than 25%, ensuring that the b-site cannot be the exclusively preferred site as it is in Sn:In2O3. Prior to this saturation point, we report that the M2+ cation always has at least a partial occupancy on the d-site and the Sn4+ cation has at least a partial occupancy on the b-site. The energies of formation for these configurations are highly favored, and prefer that the divalent and tetravalent substitutes are adjacent in the crystal lattice, which suggests short range ordering. Diffuse reflectance and 4-point probe measurements of MgxIn2−xSnxO3 demonstrate that it can maintain an optical band gap >2.8 eV while surpassing 1000 S/cm in conductivity. Understanding how multiple constituents occupy the two nonequivalent cation sites can provide information on how to optimize cosubstituted systems to increase Sn solubility while maintaining its dopant nature, achieving maximum conductivity.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗