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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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All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

InteraChem: Virtual Reality Visualizer for Reactive Interactive Molecular Dynamics

Interactive molecular dynamics in virtual reality (IMD-VR) simulations provide a digital molecular playground for students as an alternative or complement to traditional molecular modeling kits or 2D illustrations. Previous IMD-VR studies have used molecular mechanics to enable simulations of macromolecules such as proteins and nanostructures for the classroom setting with considerable success. Here, we present the InteraChem molecular visualizer, intended for reactive IMD-VR simulation using semiempirical and ab initio methods. InteraChem visualizes not only the molecular geometry but also (1) isosurfaces such as molecular orbitals and electrostatic potentials and (2) two-dimensional graphs of time-varying simulation quantities such as kinetic/potential energy, internal coordinates, and user-applied force. Additionally, InteraChem employs speech recognition to facilitate user interaction and introduces a novel “atom happiness” visualization using emojis to indicate the energetic feasibility of a particular bonding arrangement. Furthermore, we include a set of accompanying exercises that we have used to teach chemical reactivity in small molecular systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Imaging Three-Dimensional Molecular Structure and Dynamics with Multiparticle Covariance and Cumulant Coulomb Explosion Analysis

Coulomb explosion imaging (CEI) provides a direct means of imaging molecular geometry by correlating fragment ion momenta following the fragmentation of a molecular polycation. Here, we demonstrate the use of three-body covariance and four-body cumulant analysis to extract three-dimensional (3D) structural information from the X-ray-induced Coulomb explosion of tert-butyl iodide (C4H9I). Site-selective ionization at the iodine 4d edge with intense femtosecond soft X-ray pulses from an X-ray free-electron laser (XFEL) enables rapid charge buildup and molecular breakup. By correlating ionic fragments in the molecular frame, we isolate complete dissociation channels and reveal subtle structural changes, such as umbrella-type motion of the branched alkyl chain, during the ionization process. Comparison with point-charge simulations of the Coulomb explosion shows close agreement, validating the approach. Furthermore, these results establish covariance/cumulant mapping as a powerful strategy for imaging complex three-dimensional molecular structures and point the way toward time-resolved CEI using both XFEL and tabletop sources for capturing ultrafast structural dynamics.

Imaging↗
DOE OSTI2026

Dataset for Role of electron correlation on the adenine dimer interaction for non-equilibrium geometries: a benchmark Quantum Monte Carlo study

Datasets for the calculations reported in "Role of electron correlation on the adenine dimer interaction for non-equilibrium geometries: A benchmark Quantum Monte Carlo study" by L. Washburn, A. Sedova, P. R. C. Kent. J. Chem. Phys. (2026) 165 (5): 054118. https://doi.org/10.1063/5.0332651. Includes the molecular geometries, QMCPACK, PySCF, and ORCA inputs and outputs, analysis scripts and files needed to reproduce all the figures and tables.

59 BASIC BIOLOGICAL SCIENCES↗
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 OSTI2025

Enhanced Ion Transport and Molecular Packing Stability in Asymmetric 2D Nanostructured π‐Conjugated Thieno[3,2‐b]Thiophene‐Based Liquid Crystal

Organic semiconductors based on liquid crystal (LC) molecules have attracted increasing interest. Here, in this work, two linear LCs based on 2,5‐bis(thien‐2‐yl)thieno[3,2‐b]thiophene (BTTT) mesogen are designed and synthesized, including BTTT/dEO3 with two symmetrically attached tri(ethylene oxide) groups and BTTT/mEO6 with one asymmetrically attached hexa(ethylene oxide) group. These two molecules have comparable functional‐group compositions but different molecular geometries, leading to their moderately different material performances. Both LCs show smectic mesophases with relatively low transition temperatures as confirmed by differential scanning calorimetry and polarized optical microscopy. A combination of experimental grazing incidence wide‐angle X‐ray scattering and molecular dynamics (MD) simulations reveals a herringbone packing motif of BTTT segments in both LCs while a smaller molecular tilt angle in BTTT/mEO6. Ionic conductivities are measured by doping LCs with different amounts of ionic dopants, lithium bis(trifluoromethanesulfonyl)imide (LiTFSI). BTTT/mEO6 shows better smectic phase stability to higher LiTFSI doping ratios. Both LCs exhibit similar ionic conductivities in the smectic phases, but BTTT/mEO6 outperforms BTTT/dEO3 by a factor of three in the amorphous phase at higher temperatures. MD simulations, performed to examine the ion solvation environment, reveal that BTTT/mEO6 is more efficient in coordinating Li‐ions and screening their interactions with TFSI‐ions which further promote ionic transport.

grazing incidence wide-angle X-ray scattering↗
DOE OSTI2025

Method-independent cusps for atomic orbitals in quantum Monte Carlo

Here, we present an approach for augmenting Gaussian atomic orbitals with correct nuclear cusps. Like the atomic orbital basis set itself and unlike previous cusp corrections, this approach is independent of the many-body method used to prepare wave functions for quantum Monte Carlo. Once the basis set and molecular geometry are specified, the cusp-corrected atomic orbitals are uniquely specified, regardless of which density functionals, quantum chemistry methods, or subsequent variational Monte Carlo optimizations are employed. We analyze the statistical improvement offered by these cusps in a number of molecules and find them to offer similar advantages as molecular-orbital-based approaches while remaining independent of the choice of many-body method.

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

Development of a scalar-based geometric parameterization approach for the crystal structure landscape of dithienylethene-based crystalline solids

Dithienylethenes (DTEs) are a promising class of organic photoswitches that can be used to create crystalline solids with properties controlled by light. However, the ability of DTEs to adopt multiple conformations, only one of which is photoactive, complicates the rational design of these materials. Herein, the synthesis and structural characterization of 19 crystalline solids containing a single DTE molecule are described. A novel D – D analysis of the molecular geometries obtained from rotational potential energy surface calculations and the ensemble of experimental structures were used to construct a crystal landscape for DTE. Of the 19 crystal structures, 17 contained photoinactive DTE rotamers and only 2 were photoactive. These results highlight the challenges associated with the design of these materials. Overall, the D – D analysis described herein provides rapid, effective and intuitive means of linking the molecular structure to photoactivity that could be applied more broadly to afford a general strategy for producing photoactive diarylethene-based crystalline solids.

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

Computing molecular excited states on a D-Wave quantum annealer

Abstract The possibility of using quantum computers for electronic structure calculations has opened up a promising avenue for computational chemistry. Towards this direction, numerous algorithmic advances have been made in the last five years. The potential of quantum annealers, which are the prototypes of adiabatic quantum computers, is yet to be fully explored. In this work, we demonstrate the use of a D-Wave quantum annealer for the calculation of excited electronic states of molecular systems. These simulations play an important role in a number of areas, such as photovoltaics, semiconductor technology and nanoscience. The excited states are treated using two methods, time-dependent Hartree–Fock (TDHF) and time-dependent density-functional theory (TDDFT), both within a commonly used Tamm–Dancoff approximation (TDA). The resulting TDA eigenvalue equations are solved on a D-Wave quantum annealer using the Quantum Annealer Eigensolver (QAE), developed previously. The method is shown to reproduce a typical basis set convergence on the example $$\hbox {H}_2$$ H 2 molecule and is also applied to several other molecular species. Characteristic properties such as transition dipole moments and oscillator strengths are computed as well. Three potential energy profiles for excited states are computed for $$\hbox {NH}_3$$ NH 3 as a function of the molecular geometry. Similar to previous studies, the accuracy of the method is dependent on the accuracy of the intermediate meta-heuristic software called qbsolv.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2021

Photoionization of endohedral molecules: N 2 @C 60

Calculations of the photoionization of the nitrogen $1σ_g$, $1σ_u$, and $2σ_g$, states of the N 2 @C 60 molecule are performed at the density functional theory (DFT) level taking full account of the molecular geometry of both N 2 and the C 60 . In this work, the results show that cross sections are sensitive to the parity of the final channels, with a complex interplay between the native $σ_u$ resonance in free N 2 and confinement resonances. A quite different behavior is obtained for the asymmetry parameters.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2022

Zinc-based cyclens containing pyridine and cross-bridges: X-ray and DFT structures, Lewis acidity, gas-phase acidity, and p K a values

Herein it is well known that catalytic centers containing the zinc(II) ion can act as both Lewis and Bronsted-Lowry acids. In addition to coordination number, the Zn coordination geometry can also strongly impact the acidity of the active site, no matter what measure of acidity is considered. Herein, we report the first pentacoordinate, zinc-ammonia complex containing a pyridine based tetraazamacrocycle, [(pyclen)Zn(NH 3 )](PF 6 ) 2 , that has applications in Lewis acid catalysis. From this structure, we obtain binding energies and acidities for a series of related pyclen and cross-bridged cyclen type tetraazamacrocycles comprising the pentacoordinate N 4 Zn(II)–OH 2 entity, collectively referred to as [(R-cyclen)Zn–OH 2 ] 2+ . Results from gas- and aqueous-phase density functional theory (M05-2X) and ab initio (MP2) calculations reported herein demonstrate that molecular geometry has a substantial influence on both the Zn–OH x binding strengths and the deprotonation energy of coordinated H 2 O, but not necessarily in a predicable way. While generally more constrained N–Zn–N coordination leads to greater Zn–OH 2 binding energies (Lewis acidities), the corresponding Lewis acidities of the complexes don’t always correlate with the Zn–OH 2 bond lengths nor the (Bronsted) acidity of the coordinated H 2 O. Additionally, the order of the Lewis acid strength of the [(R-cyclen)Zn(II)] complexes changes as the basic –OH 2 ligand is replaced with its –OH counterpart.

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

Replacing Pyridine with Pyrazine in Molecular Cobalt Catalysts: Effects on Electrochemical Properties and Aqueous H2 Generation

Four new molecular Co(II)tetrapyridyl complexes were synthesized and evaluated for their activity as catalysts for proton reduction in aqueous environments. The pyridine groups around the macrocycle were substituted for either one or two pyrazine groups. Single crystal X-ray analysis shows that the pyrazine groups have minimal impact on the Co(II)–N bond lengths and molecular geometry in general. X-band EPR spectroscopy confirms the Co(II) oxidation state and the electronic environment of the Co(II) center are only very slightly perturbed by the substitution of pyrazine groups around the macrocycle. The substitution of pyrazine groups has a substantial impact on the observed metal- and ligand-centered reduction potentials as well as the overall H2 catalytic activity in a multimolecular system using the [Ru(2,2′-bipyridine)3]Cl2 photosensitizer and ascorbic acid as a sacrificial electron donor. The results reveal interesting trends between the H2 catalytic activity for each catalyst and the driving force for electron transfer between either the reduced photosensitizer to catalyst step or the catalyst to proton reduction step. The work presented here showcases how even the difference of a single atom in a molecular catalyst can have an important impact on activity and suggests a pathway to optimize the photocatalytic activity and stability of molecular systems.

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

Solution–Doped Donor–Acceptor Copolymers Based on Diketopyrrolopyrrole and 3, 3'–Bis (2–(2–(2–Methoxyethoxy) Ethoxy) ethoxy)–2, 2'–Bithiophene Exhibiting Outstanding Thermoelectric Power Factors with p –Dopants

The design of polymeric semiconductors exhibiting high electrical conductivity (σ) and thermoelectric power factor (PF) will be vital for flexible large-area electronics. In this work, four polymers based on diketopyrrolopyrrole (DPP), 2,3-dihydrothieno[3,4-b][1,4]dioxine (EDOT), thieno[3,2-b]thiophene (TT), and 3, 3'-bis (2-(2-(2-methoxyethoxy) ethoxy) ethoxy)-2, 2'-bithiophene (MEET) are investigated as side-chains, with the MEET polymers newly synthesized for this study. These polymers are systematically doped with tetrafluorotetracyanoquinodimethane ( F 4 TCNQ), CF3SO3H, and the synthesized dopant Cp(CN) 3 -(COOMe) 3 , differing in geometry and electron affinity. The DPP-EDOT-based polymer containing MEET as side-chains exhibits the highest conductivity (σ) ≈700 S cm–1 in this series with the acidic dopant (CF 3 SO 3 H). This polymer also shows the lowest oxidation potential by cyclic voltammetry (CV), the strongest intermolecular interactions evidenced by differential scanning calorimetry (DSC), and has the most oxygen-based functionality for possible hydrogen bonding and ionic screening. Other polymers exhibit high σ ≈300–500 S cm–1 and power factor up to 300 µW m –1 K –2 . The mechanism of conductivity is predominantly electronic, as validated by time-dependent conductance studies and transient thermo voltage monitoring over time, including for those doped with the acid. Furthermore, these materials maintain significant thermal stability and air stability over ≈6 weeks. Density functional theory calculations reveal molecular geometries and inform about frontier energy levels. Raman spectroscopy, in conjunction with scanning electron microscopy (SEM-EDS) and x-ray diffraction, provides insight into the solid-state microstructure and degree of phase separation of the doped polymer films. Infrared spectroscopy enables this study to further quantify the degree of charge transfer from polymer to dopant.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Deep Learning Coordinate-Free Quantum Chemistry

Computing quantum chemical properties of small molecules and polymers can provide insights valuable to physicists, chemists and biologists when designing new materials, catalysts, biological probes and drugs. Deep learning can compute quantum chemical properties accurately in a fraction of the time required by commonly used methods such as density functional theory (DFT). However, many of these deep learning architectures require energy minimized molecular geometries as input, which is also computationally expensive, and decreasing the reproducibility and throughput of these methods. In this study, we demonstrate that accurate quantum chemical computations can be performed without optimized geometries by operating in the coordinate-free domain using deep learning on graph encodings. Furthermore, we also find that the choice of graph-encoding architecture substantially affects the performance of these methods. The Wave architecture outperforms graph convolution architectures, particularly on complex molecules. Furthermore, the structures of these graph encoding architectures provide an opportunity to probe an important, outstanding question in quantum mechanics: What types of quantum chemical properties can be represented by local-variable models? We find that Wave, a local-variable model, is more accurately calculates quantum chemical properties. Graph convolutional architectures require global variables, and are not as effective as as Wave. We anticipate that coordinate-free, deep-learning models of quantum chemistry will become valuable tools in chemistry and biology, enabling researchers to rapidly screen chemical databases or identify new molecules using automated, de-novo design algorithms.

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

Proton-detected 15 N- 1 H dipolar coupling/ 1 H chemical shift correlation experiment for the measurement of NH distances in biological solids under fast MAS solid-state NMR

Measurement of distances from dipolar couplings is essential for structural characterization, refinement and validation using the solid-state nuclear magnetic resonance (ssNMR) spectroscopy. Particularly, knowledge about NH dipolar interactions in biological solids is important for understanding the hydrogen (H)-bonding interactions, molecular geometry and spin dynamics. In this regard, we have proposed a proton-detected two-dimensional (2D) 15 N- 1 H dipolar coupling/ 1 H chemical shift correlation experiment using the C-symmetry based windowless recoupling of chemical shift anisotropy (ROCSA) in combination with the DIPSHIFT pulse-based method for the measurement of short NH distances in the isotopically labeled and naturally abundant biological solids at fast magic angle spinning (MAS) rates (40–70 kHz). Our proposed method results in undistorted recoupled 15 N- 1 H dipolar coupling powder lineshapes that are free from the recoupled 1 H CSA contributions under the 15 N evolution, a feature that is essential for the measurement of NH distances with improved accuracy (± 500 Hz in terms of the NH dipolar couplings). The pulse sequence developed in the present study is also insensitive to the 1H–1H homonuclear dipolar interactions, relaxation effects owing to its constant-time implementation, and t1-noise from the fluctuations in the MAS.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2026

Spatial Mapping of Valence Excited-State Landscapes Using Time-Resolved Shake-Down Spectroscopy

Time-resolved X-ray photoelectron spectroscopy (XPS) is used to track the photodissociation dynamics of 2-iodothiophene following 262 nm excitation. The transient XPS features include both direct ionization of the initially populated excited states and pronounced satellite peaks arising from shake-down processes. While the direct ionization signals exhibit only minimal energy shifts during C−I bond cleavage, the shake-down transitions undergo a substantial, 5 eV, shift over the reaction coordinate. By correlating these shifts with simulated C−I bond lengths, a direct structural mapping is established that reveals the exceptional sensitivity of shake-down channels to molecular geometry. These results demonstrate that shake-down transitions provide a new and powerful probe of ultrafast structural dynamics.

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

Quantum Monte Carlo Benchmarking of Molecular Adsorption on Graphene-Supported Single Pt Atom

The precise understanding of adsorption energetics and molecular geometry at catalytic sites is fundamental for advancing catalysis, particularly under the constraints of resource efficiency and environmental sustainability. Here, this study benchmarks the performance of density functional theory (DFT) calculations against diffusion Monte Carlo (DMC) calculations for adsorption properties of small gas molecules relevant to CO oxidation—namely O 2 , CO, CO 2 , and atomic oxygen—on a single Pt atom supported by pristine graphene. Our findings reveal that DMC calculations provide a significantly different landscape of adsorption energetics compared to DFT results. Notably, DFT predicts different lowest-energy configurations and spin states, particularly for O 2 , which suggests potential discrepancies in predicting the catalytic behavior. Furthermore, this study identifies the critical issue of CO poisoning, highlighted by the large disparity between the DMC adsorption energies of O 2 (−1.23(2) eV) and CO (−3.37(1) eV), which can inhibit the catalytic process. These results emphasize the necessity for more sophisticated computational approaches in catalysis research, aiming to refine the prediction accuracy of reaction mechanisms and to enhance the design of more effective catalysts.

Ahn, Jeonghwan [University of Illinois at Urbana-C↗
DOE OSTI2024

Spin-Dependent Stereochemistry: A Nonadiabatic Quantum Dynamics Case Study of S + H 2 → SH + H Reaction

We study the spin-dependent stereodynamics of the S + H 2 → SH + H reaction by using full-dimensional quantum dynamics calculations with zero total nuclear angular momentum along the triplet 3 A" states and singlet 1 A' states. We find that the interplay between the electronic spin direction and the molecular geometry has a measurable influence on the singlet–triplet intersystem crossing reaction probabilities. Our results show that for some incident scattering angles in the body-fixed frame, the relative difference in intersystem crossing reaction probabilities (as determined between spin up and spin down initial states) can be as large as 15%. Furthermore, our findings are an ab initio demonstration of spin-dependent nonadiabatic dynamics, which we hope will shine light as far as understanding the chiral-induced spin selectivity effect.

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

Femtosecond Core-Level Spectroscopy Reveals Involvement of Triplet States in the Gas-Phase Photodissociation of Fe(CO) 5

Excitation of iron pentacarbonyl [Fe(CO) 5 ], a prototypical photocatalyst, at 266 nm causes the sequential loss of two CO ligands in the gas phase, creating catalytically active, unsaturated iron carbonyls. Despite numerous studies, major aspects of its ultrafast photochemistry remain unresolved because the early excited-state dynamics have so far eluded spectroscopic observation. This has led to the long-held assumption that ultrafast dissociation of gas-phase Fe(CO) 5 proceeds exclusively on the singlet manifold. Herein, we present a combined experimental–theoretical study employing ultrafast extreme ultraviolet transient absorption spectroscopy near the Fe M 2,3 -edge, which features spectral evolution on 100 fs and 3 ps time scales, alongside high-level electronic structure theory, which enables characterization of the molecular geometries and electronic states involved in the ultrafast photodissociation of Fe(CO) 5 . We assign the 100 fs evolution to spectroscopic signatures associated with intertwined structural and electronic dynamics on the singlet metal-centered states during the first CO loss and the 3 ps evolution to the competing dissociation of Fe(CO) 4 along the lowest singlet and triplet surfaces to form Fe(CO) 3 . Calculations of transient spectra in both singlet and triplet states as well as spin–orbit coupling constants along key structural pathways provide evidence for intersystem crossing to the triplet ground state of Fe(CO) 4 . Finally, our work presents the first spectroscopic detection of transient excited states during ultrafast photodissociation of gas-phase Fe(CO) 5 and challenges the long-standing assumption that triplet states do not play a role in the ultrafast dynamics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗