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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.

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At least 1,171 records · Page 65
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Mechanisms of Complete Dissociation of CO 2 on Iron Clusters

Dissociation of CO 2 on iron clusters was studied by using semilocal density functional theory and basis sets of triple-zeta quality. Fe 2 , Fe 4 , and Fe 16 clusters were selected as the representative host clusters. When searching for isomers of Fe n CO 2 , n=2, 4 and 16 corresponding to carbon dioxide attachment to the host clusters, its reduction to O and CO, and to the complete dissociation, it was found that the total spin magnetic moments of the lowest energy states of the isomers are often quenched with respect to those of initial reagents Fe n +CO 2 . Dissociation pathways of the Fe 2 +CO 2 , Fe 4 +CO 2 , and Fe 16 +CO 2 reactions contain several transition states separated by the local minima states; therefore, a natural question is where do the spin flips occur? Since lifetimes of magnetically excited states were shown to be of the order of 100 fs, the search for the CO 2 dissociation pathways was performed under the assumption that magnetic deexcitation may occur at the intermediate local minima. Two dissociation pathways were obtained for each Fe n +CO 2 reaction using the gradient-based methods. It was found that the Fe 2 +CO 2 reaction is endothermic with respect to both reduction and complete dissociation of CO 2 , whereas the Fe 4 +CO 2 and Fe 16 +CO 2 reactions are exothermic to both reduction and complete dissociation of carbon dioxide. Finally, the CO 2 reduction was found to be more favorable than its complete dissociation in the Fe 4 case.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1998

Atomization Energies of SO and SO2; Basis Set Extrapolation Revisted

The addition of tight functions to sulphur and extrapolation to the complete basis set limit are required to obtain accurate atomization energies. Six different extrapolation procedures are tried. The best atomization energies come from the series of basis sets that yield the most consistent results for all extrapolation techniques. In the variable alpha approach, alpha values larger than 4.5 or smaller than 3, appear to suggest that the extrapolation may not be reliable. It does not appear possible to determine a reliable basis set series using only the triple and quadruple zeta based sets. The scalar relativistic effects reduce the atomization of SO and SO2 by 0.34 and 0.81 kcal/mol, respectively, and clearly must be accounted for if a highly accurate atomization energy is to be computed. The magnitude of the core-valence (CV) contribution to the atomization is affected by missing diffuse valence functions. The CV contribution is much more stable if basis set superposition errors are accounted for. A similar study of SF, SF(+), and SF6 shows that the best family of basis sets varies with the nature of the S bonding.

Bauschlicher, Charles W., Jr.↗
DOE OSTI2013

Time-dependent density functional theory quantum transport simulation in non-orthogonal basis

Basing on the earlier works on the hierarchical equations of motion for quantum transport, we present in this paper a first principles scheme for time-dependent quantum transport by combining time-dependent density functional theory (TDDFT) and Keldysh's non-equilibrium Green's function formalism. This scheme is beyond the wide band limit approximation and is directly applicable to the case of non-orthogonal basis without the need of basis transformation. The overlap between the basis in the lead and the device region is treated properly by including it in the self-energy and it can be shown that this approach is equivalent to a lead-device orthogonalization. This scheme has been implemented at both TDDFT and density functional tight-binding level. Simulation results are presented to demonstrate our method and comparison with wide band limit approximation is made. Finally, the sparsity of the matrices and computational complexity of this method are analyzed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Efficient Total Chemical Synthesis of 13 C= 18 O Isotopomers of Human Insulin for Isotope-Edited FTIR

Isotope–edited two–dimensional Fourier transform infrared spectroscopy (2 D FTIR) can potentially provide a unique probe of protein structure and dynamics. However, general methods for the site–specific incorporation of stable 13 C= 18 O labels into the polypeptide backbone of the protein molecule have not yet been established. Here we describe, as a prototype for the incorporation of specific arrays of isotope labels, the total chemical synthesis—via a key ester insulin intermediate—of 97 % enriched [(1– 13 C= 18 O)Phe B24 ] human insulin: stable–isotope labeled at a single backbone amide carbonyl. The amino acid sequence as well as the positions of the disulfide bonds and the correctly folded structure were unambiguously confirmed by the X–ray crystal structure of the synthetic protein molecule. In vitro assays of the isotope labeled [(1– 13 C= 18 O)Phe B24 ] human insulin showed that it had full insulin receptor binding activity. Linear and 2 D IR spectra revealed a distinct red–shifted amide I carbonyl band peak at 1595 cm –1 resulting from the (1– 13 C= 18 O)Phe B24 backbone label. Furthermore, this work illustrates the utility of chemical synthesis to enable the application of advanced physical methods for the elucidation of the molecular basis of protein function.

2D IR spectra↗
DOE OSTI2024

A modified cosmic brane proposal for holographic Renyi entropy

We propose a new formula for computing holographic Renyi entropies in the presence of multiple extremal surfaces. Our proposal is based on computing the wave function in the basis of fixed-area states and assuming a diagonal approximation for the Renyi entropy. For Renyi index n ≥ 1, our proposal agrees with the existing cosmic brane proposal for holographic Renyi entropy. For n < 1, however, our proposal predicts a new phase with leading order (in Newton’s constant G) corrections to the cosmic brane proposal, even far from entanglement phase transitions and when bulk quantum corrections are unimportant. Recast in terms of optimization over fixed-area states, the difference between the two proposals can be understood to come from the order of optimization: for n < 1, the cosmic brane proposal is a minimax prescription whereas our proposal is a maximin prescription. We demonstrate the presence of such leading order corrections using illustrative examples. In particular, our proposal reproduces existing results in the literature for the PSSY model and high-energy eigenstates, providing a universal explanation for previously found leading order corrections to the n < 1 Renyi entropies.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2013

Solution structure and dynamics of C-terminal regulatory domain of Vibrio vulnificus extracellular metalloprotease

Highlights: Black-Right-Pointing-Pointer We have determined solution structures of vEP C-terminal regulatory domain. Black-Right-Pointing-Pointer vEP C-ter100 has a compact {beta}-barrel structure with eight anti-parallel {beta}-strands. Black-Right-Pointing-Pointer Solution structure of vEP C-ter100 shares its molecular topology with that of the collagen-binding domain of collagenase. Black-Right-Pointing-Pointer Residues in the {beta}3 region of vEP C-ter100 might be important in putative ligand/receptor binding. Black-Right-Pointing-Pointer vEP C-ter100 interacts strongly with iron ion. -- Abstract: An extracellular metalloprotease (vEP) secreted by Vibrio vulnificus ATCC29307 is a 45-kDa proteolytic enzyme that has prothrombin activation and fibrinolytic activities during bacterial infection. The action of vEP could result in clotting that could serve to protect the bacteria from the host defense machinery. Very recently, we showed that the C-terminal propeptide (C-ter100), which is unique to vEP, is involved in regulation of vEP activity. To understand the structural basis of this function of vEP C-ter100, we have determined the solution structure and backbone dynamics using multidimensional nuclear magnetic resonance spectroscopy. The solution structure shows that vEP C-ter100 is composed of eight anti-parallel {beta}-strands with a unique fold that has a compact {beta}-barrel formation which stabilized by hydrophobic and hydrogen bonding networks. Protein dynamics shows that the overall structure, including loops, is very rigid and stabilized. By structural database analysis, we found that vEP C-ter100 shares its topology with that of the collagen-binding domain of collagenase, despite low sequence homology between the two domains. Fluorescence assay reveals that vEP C-ter100 interacts strongly with iron (Fe{sup 3+}). These findings suggest that vEP protease might recruit substrate molecules, such as collagen, by binding at C-ter100 and that vEP participates in iron uptake from iron-withholding proteins of the host cell during infection.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Domain architecture and catalysis of the Staphylococcus aureus fatty acid kinase

Fatty acid kinase (Fak) is a two-component enzyme that generates acyl-phosphate for phospholipid synthesis. Fak consists of a kinase domain protein (FakA) that phosphorylates a fatty acid enveloped by a fatty acid binding protein (FakB). The structural basis for FakB function has been established, but little is known about FakA. Here, we used limited proteolysis to define three separate FakA domains: the amino terminal FakA_N, the central FakA_L, and the carboxy terminal FakA_C. The isolated domains lack kinase activity, but activity is restored when FakA_N and FakA_L are present individually or connected as FakA_NL. The X-ray structure of the monomeric FakA_N captures the product complex with ADP and two Mg 2+ ions bound at the nucleotide site. The FakA_L domain encodes the dimerization interface along with conserved catalytic residues Cys240, His282, and His284. AlphaFold analysis of FakA_L predicts the catalytic residues are spatially clustered and pointing away from the dimerization surface. Furthermore, the X-ray structure of FakA_C shows that it consists of two subdomains that are structurally related to FakB. Analytical ultracentrifugation demonstrates that FakA_C binds FakB, and site-directed mutagenesis confirms that a positively charged wedge on FakB meshes with a negatively charged groove on FakA_C. Finally, small angle X-ray scattering analysis is consistent with freely rotating FakA_N and FakA_C domains tethered by flexible linkers to FakA_L. These data reveal specific roles for the three independently folded FakA protein domains in substrate binding and catalysis.

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

Structural and biochemical basis for regiospecificity of the flavonoid glycosyltransferase UGT95A1

Glycosylation is a predominant strategy plants use to fine-tune the properties of small molecule metabolites to affect their bioactivity, transport, and storage. It is also important in biotechnology and medicine as many glycosides are utilized in human health. Small molecule glycosylation is largely carried out by family 1 glycosyltransferases. Here, we report a structural and biochemical investigation of UGT95A1, a family 1 GT enzyme from Pilosella officinarum that exhibits a strong, unusual regiospecificity for the 3'-O position of flavonoid acceptor substrate luteolin. We obtained an apo crystal structure to help drive the analyses of a series of binding site mutants, revealing that while most residues are tolerant to mutations, key residues M145 and D464 are important for overall glycosylation activity. Interestingly, E347 is crucial for maintaining the strong preference for 3'-O glycosylation, while R462 can be mutated to increase regioselectivity. The structural determinants of regioselectivity were further confirmed in homologous enzymes. Our study also suggests that the enzyme contains large, highly dynamic, disordered regions. We showed that while most disordered regions of the protein have little to no implication in catalysis, the disordered regions conserved among investigated homologs are important to both the overall efficiency and regiospecificity of the enzyme. This report represents a comprehensive in-depth analysis of a family 1 GT enzyme with a unique substrate regiospecificity and may provide a basis for enzyme functional prediction and engineering.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

Gaussian-windowed frame based method of moments formulation of surface-integral-equation for extended apertures

Scattering or coupling of electromagnetic beam-field at a surface discontinuity separating two homogeneous or inhomogeneous media with different propagation characteristics is formulated using surface integral equation, which are solved by the Method of Moments with the aid of the Gabor-based Gaussian window frame set of basis and testing functions. The application of the Gaussian window frame provides (i) a mathematically exact and robust tool for spatial-spectral phase-space formulation and analysis of the problem; (ii) a system of linear equations in a transmission-line like form relating mode-like wave objects of one medium with mode-like wave objects of the second medium; (iii) furthermore, an appropriate setting of the frame parameters yields mode-like wave objects that blend plane wave properties (as if solving in the spectral domain) with Green's function properties (as if solving in the spatial domain); and (iv) a representation of the scattered field with Gaussian-beam propagators that may be used in many large (in terms of wavelengths) systems.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2016

Determination of the stretch tensor for structural transformations

Structural transformations in crystalline solids are increasingly the basis of the functional behavior of materials. Both low hysteresis and reversibility of phase transformations have been linked to the satisfaction of the nongeneric conditions of compatibility between phases in diverse alloy systems. According to the Cauchy–Born rule, these conditions are expressed as properties of transformation stretch tensor. The transformation stretch tensor is difficult to measure directly due to the lack of knowledge about the exact transforming pathway during the structural change, and the complicating effects of microstructure. In this paper we give a rigorous algorithmic approach for determining the transformation stretch tensor from X-ray measurements of structure and lattice parameters. For some traditional and emerging phase transformations, the results given by the algorithm suggest unexpected transformation mechanisms.

42 ENGINEERING↗
DOE OSTI2017

Oxygen-Vacancy-Induced Midgap States Responsible for the Fluorescence and the Long-Lasting Phosphorescence of the Inverse Spinel Mg(Mg,Sn)O 4

Samples of inverse spinel Mg 2 SnO 4 were prepared using a ceramic method, their phosphorescence phenomenon was probed by optical measurements, and its cause was explored on the basis of density functional theory calculations for model structures of Mg 2 SnO 4 with oxygen vacancies VO. Mg 2 SnO 4 exhibits long-lasting luminescence at two different wavelength regions, peaking at ~498 and ~755 nm. A Sn-VO-Sn defect plus a Mg vacancy VMg away from the VO generates the empty midgap states, σSn-Sn and σSn-Sn*, localized at the Sn-VO-Sn defect, while an oxygen vacancy VO between adjacent Sn 4+ and Mg 2+ sites creates a filled midgap state Sn 2+ (5s 2 lone pair) lying below the σ Sn-Sn level. The long-lasting luminescence at two different wavelength regions and the up-conversion photostimulated luminescence observed for undoped Mg 2 SnO 4 are well explained by considering the σ Sn-Sn * level as the trapping level for a photogenerated electron.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

A Finite-Field Approach for GW Calculations beyond the Random Phase Approximation

In this work, we describe a finite-field approach to compute density response functions, which allows for efficient G0W0 and G0W0Γ0 calculations beyond the random phase approximation. The method is easily applicable to density functional calculations performed with hybrid functionals. Lastly, we present results for the electronic properties of molecules and solids and we discuss a general scheme to overcome slow convergence of quasiparticle energies obtained from G0W0Γ0 calculations, as a function of the basis set used to represent the dielectric matrix.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Clean and Convenient Tessellations for Number Counting Jastrow Factors

We introduce a basis of counting functions that, by cleanly tessellating three-dimensional space, allows real space number counting Jastrow factors to be straightforwardly applied to general molecular situations. Here, by exerting direct control over electron populations in local regions of space and encoding pairwise correlations between these populations, these Jastrow factors allow even very simple reference wave functions to adopt nodal surfaces well suited to many strongly correlated settings. Being trivially compatible with traditional Jastrow factors and diffusion Monte Carlo and having the same cubic per-sample cost scaling as a single determinant trial function, these Jastrow factors thus offer a powerful new route to the simultaneous capture of weak and strong electron correlation effects in a wide variety of molecular and materials settings. In multiple strongly correlated molecular examples, we show that even when paired with the simplest possible single determinant reference, these Jastrow factors allow quantum Monte Carlo to out-perform coupled cluster theory and approach the accuracy of traditional multireference methods.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Facile Electron Transfer to CO 2 during Adsorption at the Metal|Solution Interface

We estimate the rate of electron transfer to CO 2 at the Au (211)|water interface during adsorption in an electrochemical environment under reducing potentials. On the basis of density functional theory calculations at the generalized gradient approximation and hybrid levels of theory, we find electron transfer to the adsorbed *CO 2 to be very facile. This high rate of transfer is estimated by the energy distribution of the adsorbate-induced density of states as well as from the interaction between diabatic states representing neutral and negatively charged CO 2 . Up to 0.62 electrons is transferred to CO 2 , and this charge adiabatically increases with the bending angle to a lower limit of 137°. Finally, we conclude that this rate of electron transfer is extremely fast compared to the time scale of the nuclear degrees of freedom, that is, the adsorption process.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

Low-Energy Electronic Transition in SiB Rings

Five- and six-membered rings containing Si–B bonds were synthesized by salt metathesis of magnesium disilanides with tetramethylpiperidinyldichloroborane (TMPBCl 2 ). Materials were characterized by 1 H, 11 B, 13 C, and 29 Si NMR spectroscopy, as well as X-ray crystallography. Insights from crystallography facilitate conformational analysis of the cyclosilanes and elucidation of conformation-dependent optical properties. Furthermore, crystallography supports assignment of π character to the BN bond of the tetramethylpiperidinylborane fragment. The SiB rings possess unique optical properties compared to all silicon rings. A 350 nm electronic transition only observed in SiB rings is assigned to a σ–π* transition on the basis of density functional theory calculations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗