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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 37 records · Page 2
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Probing radical–molecule interactions with a second generation energy decomposition analysis of DFT calculations using absolutely localized molecular orbitals

Intermolecular interactions between radicals and closed-shell molecules are ubiquitous in chemical processes, ranging from the benchtop to the atmosphere and extraterrestrial space. While energy decomposition analysis (EDA) schemes for closed-shell molecules can be generalized for studying radical–molecule interactions, they face challenges arising from the unique characteristics of the electronic structure of open-shell species. In this work, we introduce additional steps that are necessary for the proper treatment of radical–molecule interactions to our previously developed unrestricted Absolutely Localized Molecular Orbital (uALMO)-EDA based on density functional theory calculations. A “polarize-then-depolarize” (PtD) scheme is used to remove arbitrariness in the definition of the frozen wavefunction, rendering the ALMO-EDA results independent of the orientation of the unpaired electron obtained from isolated fragment calculations. The contribution of radical rehybridization to polarization energies is evaluated. It is also valuable to monitor the wavefunction stability of each intermediate state, as well as their associated spin density profiles, to ensure the EDA results correspond to a desired electronic state. The examples suggest that this second generation uALMO-EDA is a useful tool for furthering one's understanding of both energetic and property changes associated with radical–molecule interactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Predicting Dexter Energy Transfer Interactions from Molecular Orbital Overlaps

Dexter energy transfer (DET), also known as spin forbidden energy transfer (e.g., 3 D 1 A → 1 D 3 A), is undergoing renewed interest because of its utility in energy science, photocatalysis, and biomedical imaging. The DET reactions enable exciton fission and fusion and have been recently used to facilitate nanoscale imaging of protein assemblies on cell surfaces. While DET and Förster energy transfer rates are often well described using Fermi’s golden rule, the donor–acceptor couplings for DET may be bridge-state-mediated and depend on the electronic structure of and interactions among the donor, bridge, and acceptor. We provide a simple approach to approximate DET couplings using a product of molecular orbital overlap factors. This approach may be used to guide the design of DET systems with targeted energy-transfer kinetics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Kβ X-ray Emission Spectroscopy of Cu(I)-Lytic Polysaccharide Monooxygenase: Direct Observation of the Frontier Molecular Orbital for H 2 O 2 Activation

Lytic polysaccharide monooxygenases (LPMOs) catalyze the degradation of recalcitrant carbohydrate polysaccharide substrates. These enzymes are characterized by a mononuclear Cu(I) active site with a three-coordinate T-shaped “His-brace” configuration including the N-terminal histidine and its amine group as ligands. Here, this study explicitly investigates the electronic structure of the d 10 Cu(I) active site in a LPMO using Kβ X-ray emission spectroscopy (XES). The lack of inversion symmetry in the His-brace site enables the 3d/p mixing required for intensity in the Kβ valence-to-core (VtC) XES spectrum of Cu(I)-LPMO. These Kβ XES data are correlated to density functional theory (DFT) calculations to define the bonding, and in particular, the frontier molecular orbital (FMO) of the Cu(I) site. These experimentally validated DFT calculations are used to evaluate the reaction coordinate for homolytic cleavage of the H 2 O 2 O–O bond and understand the contribution of this FMO to the low barrier of this reaction and how the geometric and electronic structure of the Cu(I)-LPMO site is activated for rapid reactivity with H 2 O 2 .

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Scrutinizing formally Ni IV centers through the lenses of core spectroscopy, molecular orbital theory, and valence bond theory

Nickel K- and L 2,3 -edge X-ray absorption spectra (XAS) are discussed for 16 complexes and complex ions with nickel centers spanning a range of formal oxidation states from II to IV. K-edge XAS alone is shown to be an ambiguous metric of physical oxidation state for these Ni complexes. Meanwhile, L 2,3 -edge XAS reveals that the physical d-counts of the formally Ni IV compounds measured lie well above the d 6 count implied by the oxidation state formalism. The generality of this phenomenon is explored computationally by scrutinizing 8 additional complexes. The extreme case of NiF 6 2- is considered using high-level molecular orbital approaches as well as advanced valence bond methods. The emergent electronic structure picture reveals that even highly electronegative F-donors are incapable of supporting a physical d 6 Ni IV center. The reactivity of Ni IV complexes is then discussed, highlighting the dominant role of the ligands in this chemistry over that of the metal centers.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Cartesian equivariant representations for learning and understanding molecular orbitals

Qualitative and quantitative orbital properties such as bonding/antibonding character, localization, and orbital energies are critical to how chemists understand reactivity, catalysis, and excited-state behavior. Despite this, representations of orbitals in deep learning models have been very underdeveloped relative to representations of molecular geometries and Hamiltonians. Here, we apply state-of-the-art equivariant deep learning architectures to the task of assigning global labels to orbitals, namely energies characterizations, given the molecular coefficients from Hartree–Fock or density functional theory. The architecture we have developed, the Cartesian Equivariant Orbital Network (CEONET), shows how molecular orbital coefficients are readily featurized as equivariant node features common to all graph-based machine-learned potentials. We find that CEONET performs well at predicting difficult quantitative labels such as the orbital energy and orbital entropy. Furthermore, we find that the CEONET representation provides an intuitive latent space for differentiating orbital character for the qualitative assignment of e.g. bonding or antibonding character. In addition to providing a useful representation for further integrating deep learning with electronic structure theory, we expect CEONET to be useful for automatizing and interpreting the results of advanced electronic structure methods such as complete active space self-consistent field theory. In particular, the ability of CEONET to infer multireference character via the orbital entropy paves the way toward the machine-learned selection of active spaces.

chemical reactions↗
DOE OSTI2024

Electronic structure and magnetic tendencies of trilayer La 4 Ni 3 O 10 under pressure: Structural transition, molecular orbitals, and layer differentiation

Motivated by the recent observation of superconductivity in the pressurized trilayer Ruddlesden-Popper (RP) nickelate La 4 Ni 3 O 10 , we explore its structural, electronic, and magnetic properties as a function of hydrostatic pressure from first-principles calculations. We find that an orthorhombic (monoclinic)-to-tetragonal transition under pressure takes place concomitantly with the onset of superconductivity. The electronic structure of La 4 Ni 3 O 10 can be understood using a molecular trimer basis wherein n molecular subbands arise as the d z 2 orbitals hybridize strongly along the c axis within the trilayer. The magnetic tendencies indicate that the ground state at ambient pressure is formed by nonmagnetic inner planes and stripe-ordered outer planes that are antiferromagnetically coupled along the c axis, resulting in an unusual ↑, 0, ↓ stacking that is consistent with the spin density wave model previously suggested by neutron diffraction. Such a state is destabilized at the pressure where superconductivity arises. Despite the presence of d z 2 states at the Fermi level, the d x 2 –y 2 orbitals also play a key role in the electronic structure of La4Ni3O10. Finally, this active role of the d x 2 –y 2 states in the low-energy physics of the trilayer RP nickelate, together with the distinct electronic behavior of the inner and outer planes, resembles the physics of multilayer cuprates.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

Electronic Properties of UN and UN – from Photoelectron Spectroscopy and Correlated Molecular Orbital Theory

In this work, the results of calculations of the properties of the anion UN – including electron detachment are described, which further expand our knowledge of this diatomic molecule. High-level electronic structure calculations were conducted for the UN and UN – diatomic molecules and compared to photoelectron spectroscopy measurements. The low-lying Ω states were obtained using multireference CASPT2 including spin-orbit effects up to ~20,000 cm –1 . At the Feller–Peterson–Dixon (FPD) level, the adiabatic electron affinity (AEA) of UN is estimated to be 1.402 eV and the vertical detachment energy (VDE) is 1.423 eV. The assignment of the UN excited states shows good agreement with the experimental results with a VDE of 1.424 eV. An Ω = 4 ground state was obtained for UN – which is mainly associated with the 3 H ΛS state. Thermochemical calculations estimate a bond dissociation energy (BDE) for UN – (U – + N) of 665.9 kJ/mol, ~15% larger than that of UN and UN + . The NBO analysis reveals U–N triple bonds for the UN, UN – , and UN + species.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

The role of SAXS and molecular simulations in 3D structure elucidation of a DNA aptamer against lung cancer

Aptamers are short, single-stranded DNA or RNA oligonucleotide molecules that function as synthetic analogs of antibodies and bind to a target molecule with high specificity. Aptamer affinity entirely depends on its tertiary structure and charge distribution. Therefore, length and structure optimization are essential for increasing aptamer specificity and affinity. Here, we present a general optimization procedure for finding the most populated atomistic structures of DNA aptamers. Based on the existed aptamer LC-18 for lung adenocarcinoma, a new truncated LC-18 (LC-18t) aptamer LC-18t was developed. A three-dimensional (3D) shape of LC-18t was reported based on small-angle X-ray scattering (SAXS) experiments and molecular modeling by fragment molecular orbital or molecular dynamic methods. Molecular simulations revealed an ensemble of possible aptamer conformations in solution that were in close agreement with measured SAXS data. The aptamer LC-18t had stronger binding to cancerous cells in lung tumor tissues and shared the binding site with the original larger aptamer. The suggested approach reveals 3D shapes of aptamers and helps in designing better affinity probes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Recent Developments in the General Atomic and Molecular Electronic Structure System

A discussion of many of the recently implemented features of GAMESS (General Atomic and Molecular Electronic Structure System) and LibCChem (the C++ CPU/GPU library associated with GAMESS) is presented. These features include fragmentation methods like the fragment molecular orbital, effective fragment potential and effective fragment molecular orbital methods, hybrid MPI/OpenMP approaches to Hartree-Fock and resolution of the identity second order perturbation theory. Many new coupled cluster theory methods have been implemented in GAMESS, as have multiple levels of density functional/tight binding theory. The role of accelerators, especially graphical processing units, is discussed in the context of the new features of LibCChem, as is the associated problem of power consumption as the power of computers increases dramatically. The process by which a complex program suite like GAMESS is maintained and developed is considered. Future developments are briefly summarized.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2025

Mechanistic Insights into the Demethylation of Lignin‐Derived Structures Using Protic Ionic Liquids: A Density Functional Theory Study

Lignin valorization is restricted by the stability of its methoxy groups, creating a critical need for efficient demethylation strategies. Here, in this study, density functional theory (DFT) is employed to dissect the mechanistic pathways of demethylation in lignin model compounds, guaiacol and syringol, using protic ionic liquids (PILs) that act as both solvent and catalyst. Conductor‐like Screening Model for Real Solvents (COSMO‐RS) analysis identifies monoethanolammonium acetate ([MEOA][Ace]) as the most promising medium, attributed to its strong hydrogen bonding network and solvation ability. By integrating implicit and explicit solvation models, it is revealed that an acid‐catalyzed hydrolytic mechanism governs demethylation, with PILs stabilizing crucial transition states and intermediates. Complementary electronic structure evaluations, including highest occupied molecular orbital–lowest unoccupied molecular orbital (HOMO‐LUMO) gap analysis, charge distribution, and electrostatic potential mapping, demonstrate how PILs lower energetic barriers and enhance reactivity. To simulate realistic environments, this study is extended to lignin dimer complexes with varying water content, uncovering how water‐bridged solvation reverses demethylation preference from guaiacyl to syringyl units. This mechanistic shift aligns with experimental observations showing faster S‐unit reactivity in hydrated systems. Together, these findings provide atomic‐level insight into lignin demethylation dynamics and highlight how tuning acid concentration in PILs can accelerate kinetics, enabling a rational pathway toward next‐generation biomass conversion technologies.

COSMO-RS↗
DOE OSTI2022

Copper(III) Metallacyclopentadienes via Zirconocene Transfer and Reductive Elimination to an Isolable Phenanthrocyclobutadiene

Despite the widespread use of copper catalysis for the formation of C–C bonds, debate about the mechanism persists. Reductive elimination from Cu(III) is often invoked as a key step, yet examples of its direct observation from isolable complexes remain limited to only a few examples. In this work, we demonstrate that incorporation of bulky mesityl (Mes) groups into the α-positions of a phenanthrene-appended zirconacyclopenta- diene, Cp 2 Zr(2,5-Mes 2 -phenanthro[9,10]C 4 ), enables efficient oxidative transmetalation to the corresponding, formal Cu(III) metallacyclopentadiene dimer. The dimer was quantitatively converted to a structurally analogous anionic monomer [ n Bu 4 N]- {Cl 2 Cu(2,5-Mes 2 -phenanthro[9,10]C 4 )} upon treatment with [ n Bu 4 N][Cl]. Both metallacycles undergo quantitative reductive elimination upon heating to generate phenanthrocyclobutadiene and a Cu(I) species. Due to the steric protection provided by the mesityl groups, this cyclobutadiene was isolated and thoroughly characterized to reveal antiaromaticity comparable to that of free cyclobutadiene, which imbues it with a small highest occupied molecular orbital–lowest unoccupied molecular orbital energy gap of 1.85 eV and accessible reduced and oxidized electronic states.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Spectroscopic Probe Molecule Selection Using Quantum Theory, First-Principles Calculations, and Machine Learning

Probe molecule vibrational spectra have a long history of being used to characterize materials including metals, oxides, metal-organic frameworks, and even human proteins. Furthermore, recent advances in machine learning have enabled computationally generated spectra to aid in detailed characterization of complex surfaces with probe molecules. Despite widespread use of probe molecules, the science of probe molecule selection is underdeveloped. Here, we develop physical concepts, including orbital interaction energy and the energy overlap integral, to explain and predict the ability of probe molecules to discriminate structural descriptors. We resolve the crystal orbital overlap population (COOP) to specific molecular orbitals and quantify their bonding character, which directly influences vibrational frequencies. Using only a single adsorbate calculation from density function theory (DFT), we compute the interaction energy of individual adsorbate molecular orbitals with adsorption site atomic orbitals across many different sites. Combining the molecular orbital resolved COOP and changes in orbital interaction energy enables probe molecule selection for improved discrimination of various sites. We demonstrate these concepts by comparing the predicted effectiveness of carbon monoxide (CO), nitric oxide (NO), and ethylene (C 2 H 4 ) to probe Pt adsorption sites. Finally, using a previously developed machine learning framework, we show that models trained on hundreds of thousand C 2 H 4 spectra, computed from DFT, which regress surface binding-type and generalized coordination number (GCN), outperform those trained using CO and NO spectra. Lastly, a python package, pDOS_overlap, for implementing the electron density based analysis on any combination of adsorbates and materials, is also made available.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2023

Graphically Contracted Function Construction with the Recursive Pairwise Merge Algorithm

A new implementation of a recursive pairwise merge algorithm to construct a GCF from a list of CSF expansion coefficients is presented. The essential new feature is the preallocation of some work arrays used within the intermediate steps of the merge procedure. This results in roughly an order of magnitude improvement in overall efficiency and also approximately eliminates a factor of n, the molecular orbital dimension, from the original implementation. Initial application of this merge procedure to a series of H m molecules shows that the GCF wave functions can be represented well both with delocalized canonical Hartree-Fock orbitals and with localized molecular orbitals. Finally, for a given wave function complexity, as measured by the average facet count, $\bar{\text {f}}$, the delocalized Hartree-Fock orbitals show smaller errors for small $\bar{\text {f}}$ values, while the localized orbitals show smaller errors for larger $\bar{\text {f}}$ values.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Synergistic Use of Pyridine and Selenophene in a Diketopyrrolopyrrole‐Based Conjugated Polymer Enhances the Electron Mobility in Organic Transistors

Abstract To achieve semiconducting materials with high electron mobility in organic field‐effect transistors (OFETs), low‐lying energy levels (the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO)) and favorable molecular packing and ordering are two crucial factors. Here, it is reported that the incorporation of pyridine and selenophene into the backbone of a diketopyrrolopyrrole (DPP)‐based copolymer produces a high‐electron‐mobility semiconductor, PDPPy‐Se. Compared with analogous polymers based on other DPP derivatives and selenophene, PDPPy‐Se features a lower LUMO that can decrease the electron transfer barrier for more effective electron injection, and simultaneously a lower HOMO that, however, can increase the hole transfer barrier to suppress the hole injection. Combined with thermal annealing at 240 °C for thin film morphology optimization to achieve large‐scale crystallite domains with tight molecular packing for effective charge transport along the conducting channel, OFET devices fabricated with PDPPy‐Se exhibit an n‐type‐dominant performance with an electron mobility (μ e ) as high as 2.22 cm 2 V −1 s −1 and a hole/electron mobility ratio (μ h /μ e ) of 0.26. Overall, this study demonstrates a simple yet effective approach to boost the electron mobility in organic transistors by synergistic use of pyridine and selenophene in the backbone of a DPP‐based copolymer.

Liu, Qian↗
DOE OSTI2022

Analysis of the Selective Flotation of Elemental Gold from Pyrite Using Diisobutyl Monothiophosphate

The gold contained in copper ores is an important resource for the gold industry. In some cases, elemental gold is present and can be recovered by selective flotation. It has been reported that the gold grade and recovery can be increased, without sacrificing the copper recovery, by replacing AERO 3477 (diisobutyl dithiophosphate (DTP)) with AERO 7249 (mixture of diisobutyl monothiophosphate (MTP) and diisobutyl dithiophosphate (DTP)) as the main collector. The fundamental understanding of the improvement in selectivity with the addition of MTP in the flotation of elemental gold from pyrite is limited and is the subject of this paper. In this regard, the hydrophobicity and selectivity of DTP and MTP in the flotation of pyrite and gold are compared and discussed. Density functional theory (DFT) was used to examine the electron density, reactivity, highest occupied molecular orbital (HOMO), and lowest unoccupied molecular orbital (LUMO) of the MTP and DTP collectors. The interaction energies for the adsorption of MTP and DTP from fresh pyrite, oxidized pyrite and gold surfaces were calculated and discussed with respect to the experimental results reported in the literature. Molecular dynamics simulation (MDS) was used to examine the adsorption state of MTP and DTP on the pyrite (100) and Au (111) surfaces.

58 GEOSCIENCES↗