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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 379 records · Page 21
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DOE OSTI2020

Coupled Cluster Study of the Interactions of AnO 2 , AnO 2 + , and AnO 2 2+ (An = U, Np) with N 2 and CO

We report thermochemical and spectroscopic properties for actinyl complexes involving UO 2 2+/1+/0 and NpO 2 2+/1+/0 with N 2 and CO, together with the UO 2 -O 2 , UO 2 + -O 2 , and UO 2 + -NO complexes, have been studied for the first time using an accurate composite coupled cluster approach. Two general bonding motifs were investigated, end-on (η 1 ) and side-on (η 2 ) relative to the metal center of the actinyls. For end-on CO complexes, both C-coordinated (An-C) and O-coordinated (An-O) structures were examined, with the former always being lower in energy. All of the η 1 complexes were calculated to be stable, with dissociation energies ranging from 2 to 36 kcal/mol, except for that of UO 2 + -O 2 (the η 1 orientation for UO 2 + -NO was not amenable to single reference coupled cluster). In agreement with a previous study, the η 2 structure for UO 2 + -O 2 was calculated to be relatively strongly bound, by 22.3 kcal/mol in this work. The closely related NO complex, however, had a calculated dissociation energy of just 4.0 kcal/mol. The binding energy of O 2 to neutral UO 2 in a η 2 orientation was calculated to be very strong, 75.4 kcal/mol, and strongly resembled a UO 2 + (O 2 – ) complex at equilibrium. The N–N and C–O bonds were found to be somewhat activated for all the side-on (η 2 ) neutral An(IV) complexes, with stretching frequencies of N 2 or CO being red-shifted by as much as 480 cm –1 with a 0.06 Å bond length elongation. Dissociation energies for the η 1 complexes are strongly correlated with the extent of electron transfer from ligand to actinyl. The nature of bonding in the actinyl complexes is examined using natural resonance theory (NRT). The correlation between bonding motif and small molecule activation is in agreement with experiments in condensed phases.

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DOE OSTI2021

Mass Spectrometry Adduct Calculator

We describe the Mass Spectrometry Adduct Calculator (MSAC), an automated Python tool to calculate the adduct ion masses of a parent molecule. Here, adduct refers to a version of a parent molecule [M] that is charged due to addition or loss of atoms and electrons resulting in a charged ion, e.g. [M+H] + . MSAC includes a database of 2,341 potential ions and their mass-to-charge ratios (m/z) as extracted from the NIST/EPA/NIH Mass Spectral Library (NIST17), the Global Natural Products Social Molecular Networking Public Spectral Libraries (GNPS), and MassBank of North America (MoNA). The calculator relies on user-selected subsets of the combined database to calculate expected m/z for adducts of molecules supplied as formulas This tool is intended to help researchers create identification libraries to collect evidence for the presence of molecules in mass spectrometry data. While the included adduct database focuses on adducts typically detected during liquid chromatography-mass spectrometry analyses, users may supply their own lists of adducts and charge states for calculating expected m/z. We also analyzed statistics on adducts from spectra contained in the three selected mass spectral libraries. MSAC is freely available at https://github.com/pnnl/MSAC.

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DOE OSTI2021

Permutationally Invariant Polynomial Expansions with Unrestricted Complexity

A general strategy is presented for constructing and validating permutationally invariant polynomial (PIP) expansions for chemical systems of any stoichiometry. Demonstrations are made for three categories of gas-phase dynamics and kinetics: collisional energy-transfer trajectories for predicting pressure-dependent kinetics, three-body collisions for describing transient van der Waals adducts relevant to atmospheric chemistry, and nonthermal reactivity via quasiclassical trajectories. In total, 30 systems are considered with up to 15 atoms and 39 degrees of freedom. Permutational invariance is enforced in PIP expansions with as many as 13 million terms and 13 permutationally distinct atom types by taking advantage of petascale computational resources. The quality of the PIP expansions is demonstrated through the systematic convergence of in-sample and out-of-sample errors with respect to both the number of training data and the order of the expansion, and these errors are shown to predict errors in the dynamics for both reactive and nonreactive applications. Here, the parallelized code distributed as part of this work enables the automation of PIP generation for complex systems with multiple channels and flexible user-defined symmetry constraints and for automatically removing unphysical unconnected terms from the basis set expansions, all of which are required for simulating complex reactive systems.

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DOE OSTI2022

The Effect of Geometry, Spin, and Orbital Optimization in Achieving Accurate, Correlated Results for Iron–Sulfur Cubanes

Iron–sulfur clusters comprise an important functional motif in the catalytic centers of biological systems, capable of enabling important chemical transformations at ambient conditions. This remarkable capability derives from a notoriously complex electronic structure that is characterized by a high density of states that is sensitive to geometric changes. The spectral sensitivity to subtle geometric changes has received little attention from correlated, large active space calculations, owing partly to the exceptional computational complexity for treating these large and correlated systems accurately. Here, to provide insight into this aspect, we report the first Complete Active Space Self Consistent Field (CASSCF) calculations for different geometries of the [Fe(II/III) 4 S 4 (SMe) 4 ] -2 clusters using two complementary, correlated solvers: spin-pure Adaptive Sampling Configuration Interaction (ASCI) and Density Matrix Renormalization Group (DMRG). We find that the previously established picture of a double-exchange driven magnetic structure, with minute energy gaps (<1 mHa) between consecutive spin states, has a weak dependence on the underlying geometry. However, the spin gap between the singlet and the spin state 2S + 1 = 19, corresponding to a maximal number of Fe-d electrons being unpaired and of parallel spin, is strongly geometry dependent, changing by a factor of 3 upon slight deformations that are still within biologically relevant parameters. The CASSCF orbital optimization procedure, using active spaces as large as 86 electrons in 52 orbitals, was found to reduce this gap compared to typical mean-field orbital approaches. Our results show the need for performing large active space calculations to unveil the challenging electronic structure of these complex catalytic centers and should serve as accurate starting points for fully correlated treatments upon inclusion of dynamical correlation outside the active space.

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DOE OSTI2023

Møller–Plesset and Density-Fixed Adiabatic Connections for a Model Diatomic System at Different Correlation Regimes

In recent years, adiabatic connection (AC) interpolations developed within density functional theory (DFT) have been found to provide good performances in the calculation of interaction energies when used with Hartree–Fock (HF) ingredients. The physical and mathematical reasons for such unanticipated performance have been clarified, to some extent, by studying the strong-interaction limit of the Møller–Plesset (MP) AC. In this work, we calculate both the MP and the DFT AC integrand for the asymmetric Hubbard dimer, which allows for a systematic investigation of different correlation regimes by varying two simple parameters in the Hamiltonian: the external potential, Δv, and the interaction strength, U. Notably, we find that, while the DFT AC integrand appears to be convex in the full parameter space, the MP integrand may change curvature twice. Furthermore, we discuss different aspects of the second-order expansion of the correlation energy in each AC, and we demonstrate why the derivative of the λ-dependent density in the MP AC at λ = 0 (i.e., at the HF density) is zero in the model. Concerning the strong-interaction limit of both ACs in the Hubbard dimer setting, we show that the asymptotic value of the MP AC, W ∞ HF , is lower than (or equal to) its DFT analogue, W ∞ KS , if the two are compared at a given density, just like in real space. Furthermore, we also show that this is not always the case if the two quantities are compared at a given external potential.

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DOE OSTI2023

Excited State Properties of Point Defects in Semiconductors and Insulators Investigated with Time-Dependent Density Functional Theory

Here, we present a formulation of spin-conserving and spin-flip hybrid time-dependent density functional theory (TDDFT), including the calculation of analytical forces, which allows for efficient calculations of excited state properties of solid-state systems with hundreds to thousands of atoms. We discuss an implementation on both GPU- and CPU-based architectures along with several acceleration techniques. We then apply our formulation to the study of several point defects in semiconductors and insulators, specifically the negatively charged nitrogen-vacancy and neutral silicon-vacancy centers in diamond, the neutral divacancy center in 4H silicon carbide, and the neutral oxygen-vacancy center in magnesium oxide. Our results highlight the importance of taking into account structural relaxations in excited states in order to interpret and predict optical absorption and emission mechanisms in spin defects.

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DOE OSTI2021

Density-Functional Tight-Binding Parameters for Bulk Zirconium: A Case Study for Repulsive Potentials

Density-functional tight-binding (DFTB) parameters are presented for the simulation of the bulk phases of zirconium. Electronic parameters were obtained using a band structure fitting strategy, while two-center repulsive potentials were created by particle swarm optimization. As objective functions for the repulsive potential fitting, we employed the Birch–Murnaghan equations of state for hexagonal close-packed (HCP), body-centered cubic (BCC) and ω phases of Zr from density-functional theory (DFT). When fractional atomic coordinates are not allowed to change in the generation of the equation-of-state curves, long-range repulsive DFTB potentials are able to almost perfectly reproduce equilibrium structures, relative DFT energies of the bulk phases, and bulk moduli. However, the same potentials lead to artifacts in the DFTB potential energy surfaces when atom positions in the unit cell are allowed to fully relax during the change of unit cell parameters. Finally, conventional short-range repulsive DFTB potentials, while inferior in their ability to reproduce DFT bulk energetics, are able to correctly reproduce the qualitative shape of the DFT potential energy surfaces, including the location of global minima, and can therefore be considered more transferable.

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DOE OSTI2021

Electrostatics, Charge Transfer, and the Nature of the Halide–Water Hydrogen Bond

Binary halide–water complexes X – (H 2 O) are examined by means of symmetry-adapted perturbation theory, using charge-constrained promolecular reference densities to extract a meaningful charge-transfer component from the induction energy. As is known, the X – (H 2 O) potential energy surface (for X = F, Cl, Br, or I) is characterized by symmetric left and right hydrogen bonds separated by a C 2v -symmetric saddle point, with a tunneling barrier height that is <2 kcal/mol except in the case of F – (H 2 O). Our analysis demonstrates that the charge-transfer energy is correspondingly small (<2 kcal/mol except for X = F), considerably smaller than the electrostatic interaction energy. Nevertheless, charge transfer plays a crucial role determining the conformational preferences of X – (H 2 O) and provides a driving force for the formation of quasi-linear X··· H–O hydrogen bonds. Here, charge-transfer energies correlate well with measured O–H vibrational redshifts for the halide–water complexes and also for OH – (H 2 O) and NO 2 – (H 2 O), providing some indication of a general mechanism.

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DOE OSTI2021

Bond Dissociation Energies in Heavy Element Chalcogen and Halogen Small Molecules

Thermodynamic properties including bond dissociation energies, heats of formation, and gas phase acidities for the hydrides and dimers of chalcogens and halogens: H 2 Y, HX, Y 2 and X 2 for Y = Se, Te, At and X = Br, I, and At have been predicted using the Feller-Peterson-Dixon composite correlated molecular orbital theory approach. A full 4-component CCSD(T) approach was used to calculate the spin-orbit effects on thermodynamic properties, except for Se 2 where the AoC-DHF value was used due to strong multireference effects in Se 2 for the SO calculations. The calculated results show that the At 2 bond dissociation energy is quite small, 19.5 kcal/mol, with much of the low bond energy due to spin orbit effects. H 2 Po is not predicted to be stable to dehydrogenation to Po + H 2 in terms of the free energy at 298 K. In the gas phase, HAt is predicted to be a stronger acid than H 2 SO 4 . Here, the current results provide insights into potential difficulties in the actual experimental observation of such species for heavy elements.

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DOE OSTI2021

General Design Rules for Bimetallic Platinum(II) Complexes

A series of platinum(II) bimetallic complexes were studied to investigate the effects of ligands on both the geometric and electronic structure. Modulating the Pt-Pt distance through the bridging ligand architecture was found to dictate the nature of the lowest energy electronic transitions, localized in one-half of the molecule or delocalized across the entire molecule. By reducing the separation between the platinum atoms, the lowest energy electronic transitions will be dominated by the metal-metal-to-ligand charge transfer transition. Conversely, by increasing the distance between the platinum atoms, the lowest electronic transition will be largely localized metal-to-ligand charge transfer or ligand centered in nature. Additionally, the cyclometalating ligands were observed to have a noticeable stabilizing effect on the triplet excited states as the conjugation increased, arising from geometric reorientation and increased electron delocalization of the ligands. Furthermore, such stabilization of the triplet state energy has been shown to alter the excited state potential energy landscape as well as the excited state trajectory.

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DOE OSTI2020

Molecular Simulation of Covalent Bond Dynamics in Liquid Silicon

Many atomic liquids can form transient covalent bonds reminiscent of those in the corresponding solid states. These directional interactions dictate many important properties of the liquid state, necessitating a quantitative, atomic-scale understanding of bonding in these complex systems. A prototypical example is liquid silicon, wherein transient covalent bonds give rise to local tetrahedral order and consequent nontrivial effects on liquid-state thermodynamics and dynamics. To further understand covalent bonding in liquid silicon, and similar liquids, we present an ab initio-simulation-based approach for quantifying the structure and dynamics of covalent bonds in condensed phases. Through the examination of structural correlations among silicon nuclei and maximally localized Wannier function centers, we develop a geometric criterion for covalent bonds in liquid Si. We use this to monitor the dynamics of transient covalent bonding in the liquid state and estimate a covalent bond lifetime. We compare covalent bond dynamics to other processes in liquid Si and similar liquids and suggest experiments to measure the covalent bond lifetime.

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DOE OSTI2021

Nonadiabatic Molecular Dynamics Study of the Relaxation Pathways of Photoexcited Cyclooctatetraene

In the current study, we present nonadiabatic (NAMD) and adiabatic molecular dynamics simulations of the transition-state dynamics of photoexcited cyclooctatetraene (COT). The equilibrium-state structure and absorption spectra are analyzed using the semiempirical Austin Model 1 potential. The NAMD simulations are obtained by a surface-hopping algorithm. We analyzed in detail an active excited to ground state relaxation pathway accompanied by an S 2 /S 3 (D 2d ) → S 1 (D 8h ) → S o (D 4h ) → S o (D 2d ) double-bond shifting mechanism. The simulated excitation lifetime is in good agreement with experiment. The first excited singlet state S1 plays a crucial role in the photochemistry. Here, the obtained critical molecular conformations, energy barrier, and transition-state lifetime results will provide a basis for further investigations of the bond-order inversion and photoswitching process of COT.

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DOE OSTI2025

Deriving the Landauer Principle From the Quantum Shannon Entropy

We derive an expression to determine the equilibrium probability distribution of a quantum state in contact with a noisy thermal environment that formally separates contributions from quantum and classical forms of probabilistic uncertainty. A statistical mechanical interpretation of this probability distribution enables us to derive an expression for the minimum free energy costs for arbitrary (reversible or irreversible) quantum state changes. In conclusion, based on this derivation, we demonstrate that–in contrast to classical systems–the free energy required to erase or reset a qubit depends sensitively on both the fidelity of the target state and on the physical properties of the environment, such as the number of quantum bath states, due primarily to the entropic effects of system-bath entanglement.

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DOE OSTI2020

The Role of Ligand–Ligand Interactions in Multimodal Ligand Conformational Equilibria and Surface Pattern Formation

Multimodal chromatography uses multiple modes of interaction such as charge, hydrophobic, or hydrogen bonding to separate proteins. Recently, we used molecular dynamics (MD) simulations to show that ligands immobilized on surfaces can interact and associate with neighboring ligands to form hydrophobic and charge patches, which may have important implications for the nature of protein–surface interactions. Here, we study interfacial systems of increasing complexity—from a single immobilized multimodal ligand to high density surfaces—to better understand how ligand behavior is affected by the presence of a surface and the presence of other ligands in the vicinity, and how this behavior scales to larger systems. Furthermore, we find that tethering a ligand to a surface restricts its conformations to a subset of those observed in free solution, yet the ligand maintains flexibility in the plane of the surface and can form contacts with neighboring ligands. We find that although the formation of a contact between two neighboring ligands is slightly unfavorable, three neighboring ligands exhibit a preference for the formation of a fully connected cluster. To explore how these trends in ligand association extend to a larger surface with high density of ligands, we performed coarse-grained Monte Carlo (MC) simulations of a 132-ligand surface using ligand interactions parametrized based on free energies obtained from the three-ligand MD simulations. Despite their simplicity, the coarse-grained simulations qualitatively capture the cluster size distribution of ligands observed in detailed MD simulations. Quantitative differences between the two suggest opportunities for improvements in the coarse-grained energy function for efficient predictions of cluster and pattern formations. Our approach presents a promising route to the engineering of multimodal patterns for future chromatographic resin design.

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DOE OSTI2022

Random Knotting in Fractal Ring Polymers

Many ring polymer systems of physical and biological interest exhibit both pronounced topological effects and nontrivial self-similarity, but the relationship between these two phenomena has not yet been clearly established. Here, we use theory and simulation to formulate such a connection by studying a fundamental topological property—the random knotting probability—for ring polymers with varying fractal dimension, d f . Using straightforward scaling arguments, we generalize a classic mathematical result, showing that the probability of a trivial knot decays exponentially with chain size, N, for all fractal dimensions: P 0 (N) ∝ exp(–N/N 0 ). However, no such simple considerations can account for the dependence of the knotting length, N 0 , on d f , necessitating a more involved analytical calculation. This analysis reveals a complicated double-exponential dependence, which is well supported by numerical data. By contrast, functional forms typical of simple scaling theories fail to adequately describe the observations. These findings are equally valid for two-dimensional ring polymer systems, where “knotting” is defined as the intersection of any two segments.

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