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All sourcesNASA NTRSDOE OSTI
NASA NTRS1988

Quantum mechanical algebraic variational methods for inelastic and reactive molecular collisions

The quantum mechanical problem of reactive or nonreactive scattering of atoms and molecules is formulated in terms of square-integrable basis sets with variational expressions for the reactance matrix. Several formulations involving expansions of the wave function (the Schwinger variational principle) or amplitude density (a generalization of the Newton variational principle), single-channel or multichannel distortion potentials, and primitive or contracted basis functions are presented and tested. The test results, for inelastic and reactive atom-diatom collisions, suggest that the methods may be useful for a variety of collision calculations and may allow the accurate quantal treatment of systems for which other available methods would be prohibitively expensive.

Schwenke, David W.↗
DOE OSTI2025

Convergent Protocols for Computing Protein–Ligand Interaction Energies Using Fragment-Based Quantum Chemistry

Fragment-based quantum chemistry methods offer a way to sidestep the steep nonlinear scaling of electronic structure calculations so that large molecular systems can be investigated using high-level methods. Here, we use fragmentation to compute protein–ligand interaction energies in systems with several thousand atoms, using a new software platform for managing fragment-based calculations that implements a screened many-body expansion. Convergence tests using a minimal-basis semiempirical method (HF-3c) indicate that two-body calculations, with single-residue fragments and simple hydrogen caps, are sufficient to reproduce interaction energies obtained using conventional supramolecular electronic structure calculations, to within 1 kcal/mol at about 1% of the computational cost. We also demonstrate that the HF-3c results are illustrative of trends obtained with density functional theory in basis sets up to augmented quadruple-ζ quality. Strategic deployment of fragmentation facilitates the use of converged biomolecular model systems alongside high-quality electronic structure methods and basis sets, bringing ab initio quantum chemistry to systems of hitherto unimaginable size. This will be useful for generation of high-quality training data for machine learning applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1994

Development of New Open-Shell Perturbation and Coupled-Cluster Theories Based on Symmetric Spin Orbitals

A new spin orbital basis is employed in the development of efficient open-shell coupled-cluster and perturbation theories that are based on a restricted Hartree-Fock (RHF) reference function. The spin orbital basis differs from the standard one in the spin functions that are associated with the singly occupied spatial orbital. The occupied orbital (in the spin orbital basis) is assigned the delta(+) = 1/square root of 2(alpha+Beta) spin function while the unoccupied orbital is assigned the delta(-) = 1/square root of 2(alpha-Beta) spin function. The doubly occupied and unoccupied orbitals (in the reference function) are assigned the standard alpha and Beta spin functions. The coupled-cluster and perturbation theory wave functions based on this set of "symmetric spin orbitals" exhibit much more symmetry than those based on the standard spin orbital basis. This, together with interacting space arguments, leads to a dramatic reduction in the computational cost for both coupled-cluster and perturbation theory. Additionally, perturbation theory based on "symmetric spin orbitals" obeys Brillouin's theorem provided that spin and spatial excitations are both considered. Other properties of the coupled-cluster and perturbation theory wave functions and models will be discussed.

Lee, Timothy J.↗
NASA NTRS1978

Theoretical study of collinear Be + FH/nu1/ yields BeF/nu2/ + H

The potential energy surface for collinear Be + FH yields BeF + H was studied at various levels of ab initio approximation. A final surface was obtained from a first order configuration interaction wave function, using the iterative orbital method and a medium-sized basis of Slater atomic functions. The exothermicity is computed to be 6 kcal/mole; the barrier height is predicted to be about 28 kcal/mole at a geometry where both internuclear separations are extended by about 0.4 bohr from their asymptotic equilibrium values. This surface differs qualitatively from simple LEPS models.

Schor, H.↗
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 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 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 OSTI2020

One-center close-coupling approach to two-center rearrangement collisions

Calculations of ionization and electron-capture cross sections in ion-atom collisions usually require solving the Schrödinger equation governing the collision system by expanding the total scattering wave function in a basis of target- and projectile-centered pseudostates. This approach leads to the two-center close-coupling equations which in some cases may become ill-conditioned due to the non-orthogonality of the underlying combined basis. Here we develop a technique which allows to accurately extract the necessary collision information, including that for the rearrangement channels, from the computationally more convenient one-center close-coupling equations which are built from only target-centered pseudostates. The robustness of the method is demonstrated by considering the proton-hydrogen scattering problem across a wide incident energy range. The developed method is then applied to study proton scattering on multielectron target of lithium. Here, the obtained results for the 2s → 2p excitation and the total electron-capture cross sections are in good agreement with corresponding experimental data. It is concluded that the presented technique could be a simpler alternative when integrated cross sections are required.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2021

A Systems Approach to Estimating the Uncertainty Limits of X-Ray Radiographic Metrology

Micro- and nanomanufacturing capabilities have rapidly expanded over the past decade to include complex three-dimensional (3D) structure fabrication; however, the metrology required to accurately assess these processes via part inspection and characterization has struggled to keep pace. X-ray computed tomography (CT) is considered an ideal candidate for providing the critically needed metrology on the smallest scales, especially internal features, or inaccessible regions. X-ray CT supporting micro- and nanomanufacturing often push against the poorly understood resolution and variation limits inherent to the machines, which can distort or hide fine structures. In this study, we have developed and experimentally verify a comprehensive analytical uncertainty propagation signal variation flow graph (SVFG) model for X-ray radiography in this work to better understand resolution and image variability limits on the small scale. The SVFG approach captures, quantifies, and predicts variations occurring in the system that limit metrology capabilities, particularly in the micro/nanodomain. This work is the first step to achieving full uncertainty modeling of CT reconstructions and provides insight into improving X-ray attenuation imaging systems. The SVFG methodology framework is applied to generate a complete basis set of functions describing the major sources of variation in radiographs. Five models are identified, covering variation in energy, intensity, length, blur, and position. Radiographic system experiments are defined to measure the parameters required by the SVFGs. Best practices are identified for these measurements. The SVFG models are confirmed via direct measurement of variation to predict variation within 30% on average.

47 OTHER INSTRUMENTATION↗
DOE OSTI2020

Time Domain Moment Tensor Inversion in Python

MTtime is a software tool developed for time domain inversion of complete seismic waveform data to obtain the seismic moment tensor. It supports both deviatoric and full moment tensor inversions as well as 1-D and 3-D basis Green's functions.

Chiang, Andrea↗
DOE OSTI2020

A Study of the Radiation Tolerance of CVD Diamond to 70 MeV Protons, Fast Neutrons and 200 MeV Pions

We measured the radiation tolerance of commercially available diamonds grown by the Chemical Vapor Deposition process by measuring the charge created by a 120 GeV hadron beam in a 50 μm pitch strip detector fabricated on each diamond sample before and after irradiation. We irradiated one group of samples with 70 MeV protons, a second group of samples with fast reactor neutrons (defined as energy greater than 0.1 MeV), and a third group of samples with 200 MeV pions, in steps, to (8.8±0.9) × 1015 protons/cm2, (1.43±0.14) × 1016 neutrons/cm2, and (6.5±1.4) × 1014 pions/cm2, respectively. By observing the charge induced due to the separation of electron–hole pairs created by the passage of the hadron beam through each sample, on an event-by-event basis, as a function of irradiation fluence, we conclude all datasets can be described by a first-order damage equation and independently calculate the damage constant for 70 MeV protons, fast reactor neutrons, and 200 MeV pions. We find the damage constant for diamond irradiated with 70 MeV protons to be 1.62±0.07(stat)±0.16(syst)× 10−18 cm2/(p μm), the damage constant for diamond irradiated with fast reactor neutrons to be 2.65±0.13(stat)±0.18(syst)× 10−18 cm2/(n μm), and the damage constant for diamond irradiated with 200 MeV pions to be 2.0±0.2(stat)±0.5(syst)× 10−18 cm2/(π μm). The damage constants from this measurement were analyzed together with our previously published 24 GeV proton irradiation and 800 MeV proton irradiation damage constant data to derive the first comprehensive set of relative damage constants for Chemical Vapor Deposition diamond. We find 70 MeV protons are 2.60 ± 0.29 times more damaging than 24 GeV protons, fast reactor neutrons are 4.3 ± 0.4 times more damaging than 24 GeV protons, and 200 MeV pions are 3.2 ± 0.8 more damaging than 24 GeV protons. We also observe the measured data can be described by a universal damage curve for all proton, neutron, and pion irradiations we performed of Chemical Vapor Deposition diamond. Finally, we confirm the spatial uniformity of the collected charge increases with fluence for polycrystalline Chemical Vapor Deposition diamond, and this effect can also be described by a universal curve.

36 MATERIALS SCIENCE↗
NASA NTRS1968

Application of a truncated normal failure distribution in reliability testing

Statistical truncated normal distribution function is applied as a time-to-failure distribution function in equipment reliability estimations. Age-dependent characteristics of the truncated function provide a basis for formulating a system of high-reliability testing that effectively merges statistical, engineering, and cost considerations.

Groves, C., Jr.↗
NASA NTRS1977

Variational calculations of vibrational properties of ozone

A variational method is used to obtain vibrational-rotational properties for ozone from an experimental quartic force field. Band positions, average structures, matrix elements for calculating infrared intensities, and effective rotational constants are reported for (O-16)3 and its O-18 isotopic species. Also, the degree to which the vibrational energies and properties are converged is investigated as a function of the basis set parameters and basis set size, and of the method of obtaining the Hamiltonian matrix elements. A convenient procedure for assigning the vibrational states is developed for variational vibrational wavefunction expansions.

Carney, G. D.↗
NASA NTRS1981

A hybrid method for improving MCSCF convergence

It has been found that the convergence problems for many ill conditioned single-configuration SCF calculations arise from mixing among only a small number of orbitals. This orbital set includes the highest closed, the partially filled, and (possibly) a few of the lowest virtual orbitals. The fact that convergence problems can be, in very large measure, linked to a small orbital set is used to design a hybrid MCSCF procedure in which these orbitals are treated using a second-order MCSCF method, while other mixings are treated with a lower-order method which avoids the time consuming integral transformation. Tests on BeO show that the hybrid method yields convergence even when the simple lower-order treatment diverges. The method is expected to facilitate determination of MCSCF wave functions for large basis problems and for the construction of potential energy surfaces.

Bauschlicher, C. W., Jr.↗
NASA NTRS1982

A discrete gust model for use in the design of wind energy conversion systems

A discrete gust model has been designed which includes an expression for the number of times per unit time thy wind exceeds a specific value. This expression, based on Rice's (1944, 1945) number-of-crossings model, assumes that the yearly mean wind speed is averaged over a period of 10 minutes to 1 (one) hour. Vertical and lateral coherence functions are the basis for a mathematical filter which isolates atmospheric disturbances of a characteristic size (e. g., those which would completely engulf a rotor). Predictions are calculated usising the given definition of cut-off frequency, then they are compared with actual data, showing that the model is reliable. The expression is provided in a format such that it may be used for engineering design calculations.

Frost, W.↗