Search NASA⌕ Search

SEARCH · Search NASA

Results for “electronic structure of atoms and molecules”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 451 records · Page 25
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Attosecond XUV probing of vibronic quantum superpositions in Br 2 +

Ultrafast laser excitation can create coherent superpositions of electronic states in molecules and trigger ultrafast flow of electron density on a few femtosecond timescale. While recent attosecond experiments have addressed real-time observation of these primary photochemical processes, the underlying roles of simultaneous nuclear motions and how they modify and disturb the valence electronic motion remain uncertain. In this work, we investigate coherent electronic-vibrational dynamics induced among multiple vibronic levels of ionic bromine (Br 2 + ), including both spin-orbit (X 2 Π 3/2,g – X 2 Π 1/2,g ) and valence (A 2 Π 3/2,u – 4 Σ 3/2,u ) electronic superpositions, using attosecond transient absorption spectroscopy. Decay, revival, and apparent frequency shifts of electronic coherences are measured via characteristic quantum beats on the Br-3d core-level absorption signals. Quantum-mechanical simulations attribute the observed electronic decoherence to broadened phase distributions of nuclear wave packets on anharmonic potentials. Molecular vibronic structure is further revealed to be imprinted as discrete progressions in electronic beat frequencies. These results provide a future basis to interpret complex charge-migration dynamics in polyatomic systems.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2023

Photodissociation of H 2 on Ag and Au Nanoparticles: Effect of Size and Plasmon versus Interband Transitions on Threshold Intensities for Dissociation

This Article provides new insights concerning the simulation of plasmon-driven chemical reactions using real-time TDDFT based on the tight-binding electronic structure code DFTB+, with applications to the dissociation of H 2 on octahedral silver and gold nanoparticles with 19–489 atoms. A new component of these calculations involves sampling a 300 K canonical ensemble to determine the distribution of possible outcomes of the calculations, and with this approach we are able to determine the threshold for dissociation as a function of laser intensity, wavelength, and nanocluster size. We show that the threshold intensity varies as an inverse power of nanocluster size, which makes it possible to extrapolate the results to sizes that are more typical of experimental studies. The intensities obtained from this extrapolation are around a factor of 100 above powers used in the pulsed experiments. This is a closer comparison of theory and experiment than has been obtained in previous real-time simulations, and the remaining discrepancy can be understood in terms of electromagnetic hot spots that are associated with cluster formation. Here, we also compare the influence of plasmon excitation versus interband excitation on reaction thresholds, revealing that for silver clusters plasmon excitation leads to lower thresholds, but for gold clusters interband excitation is more effective. Our study also includes an analysis of charge transfer to and from the H 2 molecule, and a determination of orbital populations during and after the pulse, showing the correlation between metal excitations and the location of the antibonding level of H 2 .

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2024

MolSym : A Python package for handling symmetry in molecular quantum chemistry

A consideration of the point group symmetry of molecules is often advantageous from a computational efficiency standpoint and sometimes necessary for the correct treatment of chemical physics problems. Many modern electronic structure software packages include a treatment of symmetry, but these are sometimes incomplete or unusable outside of that program’s environment. Therefore, we have developed the MolSym package for handling molecular symmetry and its associated functionalities to provide a platform for including symmetry in the implementation and development of other methods. Features include point group detection, molecule symmetrization, arbitrary generation of symmetry element sets and character tables, and symmetry adapted linear combinations of real spherical harmonic basis functions, Cartesian displacement coordinates, and internal coordinates. We present some of the advantages of using molecular symmetry as achieved by MolSym, particularly with respect to Hartree–Fock theory, and the reduction of finite difference displacements in gradient/Hessian computations. Furthermore, this package is designed to be easily integrated into other software development efforts and may be extended to further symmetry applications.

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

Perspective on Kramers symmetry breaking and restoration in relativistic electronic structure methods for open-shell systems

Without rigorous symmetry constraints, solutions to approximate electronic structure methods may artificially break symmetry. In the case of the relativistic electronic structure, if time-reversal symmetry is not enforced in calculations of molecules not subject to a magnetic field, it is possible to artificially break Kramers degeneracy in open shell systems. This leads to a description of excited states that may be qualitatively incorrect. Despite this, different electronic structure methods to incorporate correlation and excited states can partially restore Kramers degeneracy from a broken symmetry solution. For single-reference techniques, the inclusion of double and possibly triple excitations in the ground state provides much of the needed correction. Formally, however, this imbalanced treatment of the Kramers-paired spaces is a multi-reference problem, and so methods such as complete-active-space methods perform much better at recovering much of the correct symmetry by state averaging. Using multi-reference configuration interaction, any additional corrections can be obtained as the solution approaches the full configuration interaction limit. A recently proposed “Kramers contamination” value is also used to assess the magnitude of symmetry breaking.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2023

Accurate calculation of many-body energies in water clusters using a classical geometry-dependent induction model

We incorporate geometry-dependent distributed multipole and polarizability surfaces into an induction model that is used to describe the 3- and 4-body terms of the interaction between water molecules. The expansion is carried out up to hexadecapole with the multipoles distributed on the atom sites. Dipole-dipole, dipole-quadrupole, and quadrupole-quadrupole distributed polarizabilities are used to represent the response of the multipoles to an electric field. We compare the model against two large databases consisting of 43,844 3-body terms and 3,603 4-body terms obtained from high level ab initio calculations previously used to fit the MB-pol and q-AQUA interaction potentials. The classical induction model with no adjustable parameters reproduces the ab-initio 3- and 4-body terms contained in these teo Databases with a Root-Mean-Square-Error (RMSE) of 0.104/0.058 and a Mean-Absolute-Error (MAE) of 0.054/0.026 kcal/mol, respectively, results that are on a par with those obtained 1 by fitting the same data using tens of thousands of Permutationally Invariant Polynomials (PIPs). This demonstrates the accuracy of this physically motivated model in describing the 3- and 4-body terms in the interactions between water molecules with no adjustable parameters. The triple-dipole-dispersion energy was included in the 3-body energy and was found to be small but not quite negligible. The model represents a practical, efficient and transferable approach for obtaining accurate non-additive interactions for multi-component systems without the need of performing tens of thousands of high level electronic structure calculations and fitting them with tens of thousands of PIPs.

molecular analysis water, aqueous↗
DOE OSTI2021

Synchronous RNA conformational changes trigger ordered phase transitions in crystals

Time-resolved studies of biomacromolecular crystals have been limited to systems involving only minute conformational changes within the same lattice. Ligand-induced changes greater than several angstroms, however, are likely to result in solid-solid phase transitions, which require a detailed understanding of the mechanistic interplay between conformational and lattice transitions. Here we report the synchronous behavior of the adenine riboswitch aptamer RNA in crystal during ligand-triggered isothermal phase transitions. Direct visualization using polarized video microscopy and atomic force microscopy shows that the RNA molecules undergo cooperative rearrangements that maintain lattice order, whose cell parameters change distinctly as a function of time. The bulk lattice order throughout the transition is further supported by time-resolved diffraction data from crystals using an X-ray free electron laser. The synchronous molecular rearrangements in crystal provide the physical basis for studying large conformational changes using time-resolved crystallography and micro/nanocrystals.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Solid-to-plasma transition of polystyrene induced by a nanosecond laser pulse within the context of inertial confinement fusion

Laser Direct Drive (LDD) Inertial Confinement Fusion (ICF) involves irradiating a spherical target of thermonuclear fuel coated with an ablator, usually made of polystyrene. Laser energy absorption near the target surface leads to matter ablation, hydrodynamic shocks, and ultimately capsule implosion. The conservation of spherical symmetry is crucial for implosion efficiency, yet spatial modulations in laser intensity can induce nonuniformities, causing the laser imprint phenomenon. Understanding laser imprint, especially considering the initial solid state, is essential for advancing LDD ICF. A first microscopic model of solid-to-plasma transition was built in 2019, accounting for laser absorption in the solid state with a band structure based ionization model. This model has been improved to include chemical fragmentation and a more accurate description of electron collision frequency in various matter states. The latest development involves assessing the model reliability by comparing theoretical predictions with experimental observations. Despite the success of this approach, questions remain, leading to further investigations and observations under different irradiation conditions. This work presents an experiment with a nanosecond pulse, taking into account hydrodynamic effects, and measures transmission dynamics over the entire laser beam area to observe two-dimensional effects. As a result, the objective is to adapt the theoretical model, couple it with a hydrodynamic code, and observe additional effects related to the initial solid state.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2024

Vibrational Fermi Resonance in Atomically Thin Black Phosphorus

Fermi resonance is a phenomenon involving the hybridization of two coincidentally quasi-degenerate states that is observed in the vibrational or electronic spectra of molecules. Despite numerous examples in molecular systems, vibrational Fermi resonances in dispersive semiconducting systems remain largely unexplored due to the rarity of occurrence. Here we report a vibrational Fermi resonance in atomically thin black phosphorus. The Fermi resonance arises via anharmonic mixing of a fundamental Raman mode and a Davydov component of an infrared mode, leading to a doublet with mixed character. The extent of Fermi coupling can be modulated by the application of external biaxial strain. The consequences of Fermi hybridization are revealed by electronic resonance effects in the thickness-dependent and excitation-wavelength-dependent Raman spectrum, which is predicted by ab initio hybrid functional simulations including excitonic interactions. This work reveals new insight into electron–phonon coupling in black phosphorus and demonstrates a novel method for modulating Fermi resonances in 2D semiconductors.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2021

Polarizable Water Potential Derived from a Model Electron Density

A new empirical potential for efficient, large scale molecular dynamics simulation of water is presented. The HIPPO (Hydrogen-like Intermolecular Polarizable POtential) force field is based upon the model electron density of a hydrogen-like atom. This framework is used to derive and parametrize individual terms describing charge penetration damped permanent electrostatics, damped polarization, charge transfer, anisotropic Pauli repulsion, and damped dispersion interactions. Initial parameter values were fit to Symmetry Adapted Perturbation Theory (SAPT) energy components for ten water dimer configurations, as well as the radial and angular dependence of the canonical dimer. The SAPT-based parameters were then systematically refined to extend the treatment to water bulk phases. The final HIPPO water model provides a balanced representation of a wide variety of properties of gas phase clusters, liquid water, and ice polymorphs, across a range of temperatures and pressures. This water potential yields a rationalization of water structure, dynamics, and thermodynamics explicitly correlated with an ab initio energy decomposition, while providing a level of accuracy comparable or superior to previous polarizable atomic multipole force fields. The HIPPO water model serves as a cornerstone around which similarly detailed physics-based models can be developed for additional molecular species.

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

Rotational excitation and de-excitation of magnesium mono-sulphide (MgS) by He collisions

ABSTRACT Magnesium mono-sulphide (MgS) plays a crucial role in astrochemical processes, particularly in the interstellar medium (ISM), where metal-sulphur chemistry influences molecular formation and evolution. This work presents a detailed study of the rotational excitation and de-excitation of MgS through collisions with helium (He) atoms, the second most abundant species in the ISM after hydrogen, which includes both atomic (H) and molecular forms (H2). The focus on MgS–He collisions arises from He's high abundance, chemical inertness, and simpler electronic structure, which make it well suited for quantum scattering calculations. These characteristics establish He as an ideal candidate for initial studies, providing fundamental data for future investigations involving H2. The study uses quantum scattering methods to calculate the collisional rate coefficients over a broad temperature range. These rates are critical for interpreting observational data on MgS and predicting its abundance in space. The interaction potential between MgS and He is calculated using the rigid rotor approximation and the Jacobi coordinate system, employing the CCSD(T)-F12a/aug-cc-pVTZ method for accurate two-dimensional potential energy surface. The study explores the anisotropic nature of the MgS–He interaction, which favours odd Δj rotational transitions at low collision energies. The inelastic cross-sections for rotational transitions involving up to 16 rotational levels of MgS were computed up to 1000 cm−1, enabling the calculation of rate coefficients up to 150 K for Δj = ±1, ±2, and ± 3 rotational transitions. The results show that Δj = 1 transitions dominate at low temperatures, while Δj = 2 transitions become more significant at higher temperatures. This study provides valuable data for interpreting future astrophysical observations of MgS. The findings also propose new rotational transitions for MgS detection in space, enhancing our ability to track and study this molecule in various cosmic environments.

Hendaoui, Hamza (ORCID:0000000218641872)↗
DOE OSTI2024

Cholesky Decomposition-Based Implementation of Relativistic Two-Component Coupled-Cluster Methods for Medium-Sized Molecules

A Cholesky decomposition (CD)-based implementation of relativistic two-component coupled-cluster (CC) and equation-of-motion CC (EOM-CC) methods using an exact two-component Hamiltonian augmented with atomic-mean-field integrals (the X2CAMF scheme) is reported. Furthermore, the present CD-based implementation of X2CAMF-CC and EOM-CC methods employs atomic-orbital-based algorithms to avoid the construction of two-electron integrals and intermediates involving three and four virtual indices. The CD-based implementation extends the applicability of X2CAMF-CC and EOMCC methods to medium-sized molecules with the correlation of around 1000 spinors. Benchmark calculations for uranium-containing small molecules have been performed to assess the dependence of CC results with respect to the Cholesky threshold. A Cholesky threshold of 10 –4 is shown to maintain chemical accuracy. Example calculations to illustrate the capability of the CD-based relativistic CC methods are reported for the bond dissociation energy of the uranium hexafluoride molecule, UF 6 , with up to quadruple-zeta basis sets and the lowest excitation energy in solvated uranyl ion [UO 2 2+ (H 2 O) 12 ].

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

Predicting and Understanding Non-Covalent Interactions Using Novel Forms of Symmetry-Adapted Perturbation Theory

Although sometimes derided as “weak” interactions, non-covalent forces play a critical role in ligand binding and crystal packing and in determining the conformational landscape of flexible molecules. Symmetry-adapted perturbation theory (SAPT) provides a framework for accurate ab initio calculation of intermolecular interactions and furnishes a natural decomposition of the interaction energy into physically meaningful components: semiclassical electrostatics (rigorously obtained from monomer charge densities), Pauli or steric repulsion, induction (including both polarization and charge transfer), and dispersion. This decomposition helps to foster deeper understanding of non-covalent interactions and can be used to construct transferable, physics-based force fields. Separability of the SAPT interaction energy also provides the flexibility to construct composite methods, a feature that we exploit to improve the description of dispersion interactions. Furthermore, these are challenging to describe accurately because they arise from nonlocal electron correlation effects that appear for the first time at second order in perturbation theory but are not quantitatively described at that level.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2020

Surface chemical trapping of optical cycling centers

Quantum information processors based on trapped atoms utilize laser-induced optical cycling transitions for state preparation and measurement. These transitions consist of an electronic excitation from the ground to an excited state and a decay back to the initial ground state, associated with a photon emission. While this technique has been used primarily with atoms, it has also recently been shown to work for some divalent metal hydroxides ( e.g. SrOH) and alkoxides ( e.g. SrOCH 3 ). Additionally, this extension to molecules is possible because these molecules feature nearly isolated, atomic-like ground and first-excited electronic states centered on the radical metal atom. We theoretically investigate the extension of this idea to a larger scale by growing the alkyl group, R, beyond the initial methyl group, CH 3 , while preserving the isolated and highly vertical character of the electronic excitation on the radical metal atom, M. Theory suggests that in the limit as the size of the ligand carbon chain increases, it can be considered a functionalized diamond (or cubic boron nitride) surface. Several requirements must be observed for the cycling centers to function when bound to the surface. First, the surface must have a significant band gap that fully encapsulates both the ground and excited states of the cycling center. Second, while the surface lattice imposes strict limits on the achievable spacing between the SrO– groups, at high coverage, SrO– centers can interact, and show geometric changes and/or electronic state mixing. We show that the coverage of the diamond surface with SrO– cycling centers needs to be significantly sub-monolayer for the functionality of the cycling center to be preserved. Having the lattice-imposed spatial control of SrO– placements will allow nanometer-scale proximity between qubits and will eliminate the need for atom traps for localized cycling emitters. Our results also imply that a functionalization could be done on a scanning microscope tip for local quantum sensing or on photonic structures for optically-mediated quantum information processing.

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

Untangling the sequence of events during the S 2 → S 3 transition in photosystem II and implications for the water oxidation mechanism

In oxygenic photosynthesis, light-driven oxidation of water to molecular oxygen is carried out by the oxygen-evolving complex (OEC) in photosystem II (PS II). Recently, we reported the room-temperature structures of PS II in the four (semi)stable S-states, S 1 , S 2 , S 3 , and S 0 , showing that a water molecule is inserted during the S 2 → S 3 transition, as a new bridging O(H)-ligand between Mn1 and Ca. To understand the sequence of events leading to the formation of this last stable intermediate state before O 2 formation, we recorded diffraction and Mn X-ray emission spectroscopy (XES) data at several time points during the S 2 → S 3 transition. At the electron acceptor site, changes due to the two-electron redox chemistry at the quinones, Q A and Q B , are observed. At the donor site, tyrosine Y Z and His190 H-bonded to it move by 50 µs after the second flash, and Glu189 moves away from Ca. This is followed by Mn1 and Mn4 moving apart, and the insertion of O X (H) at the open coordination site of Mn1. This water, possibly a ligand of Ca, could be supplied via a “water wheel”-like arrangement of five waters next to the OEC that is connected by a large channel to the bulk solvent. XES spectra show that Mn oxidation (τ of ∼350 µs) during the S 2 → S 3 transition mirrors the appearance of O X electron density. This indicates that the oxidation state change and the insertion of water as a bridging atom between Mn1 and Ca are highly correlated.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Dial It Down: The Effect of Strongly Interacting Adsorbates on the BiAg 2 Rashba Surface State

Organic semiconductors interfaced with spin–orbit coupled materials offer a rich playground for fundamental studies of controlling spin dynamics in spintronic devices. The adsorbate–surface interactions at such interfaces play a key role in determining the valence electronic and spin structure and consequently, the device physics as well. Here we show that strong adsorbate–surface alloy interaction leads to weakening of the electronic coupling between the surface alloy atoms and quenches the spin–orbit coupled surface state, demonstrated for the case of the strong organic electron acceptor 2,7-dinitropyrene-4,5,9,10-tetrone (NO 2 –PyT, C 16 H 4 N 2 O 8 ) on the Rashba spin–orbit coupled surface alloy BiAg 2 /Ag(111). Furthermore, our findings demonstrate an important challenge associated with using molecular adsorbates to tailor the spin texture in BiAg 2 /Ag(111), and our work provides guidelines to consider while designing interfacial systems to engineer the spin texture in Rashba surface alloys.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Multifidelity Neural Network Formulations for Prediction of Reactive Molecular Potential Energy Surfaces

Here, this paper focuses on the development of multifidelity modeling approaches using neural network surrogates, where training data arising from multiple model forms and resolutions are integrated to predict high-fidelity response quantities of interest at lower cost. We focus on the context of quantum chemistry and the integration of information from multiple levels of theory. Important foundations include the use of symmetry function-based atomic energy vector constructions as feature vectors for representing structures across families of molecules and single-fidelity neural network training capabilities that learn the relationships needed to map feature vectors to potential energy predictions. These foundations are embedded within several multifidelity topologies that decompose the high-fidelity mapping into model-based components, including sequential formulations that admit a general nonlinear mapping across fidelities and discrepancy-based formulations that presume an additive decomposition. Methodologies are first explored and demonstrated on a pair of simple analytical test problems and then deployed for potential energy prediction for C 5 H 5 using B2PLYP-D3/6-311++G(d,p) for high-fidelity simulation data and Hartree–Fock 6-31G for low-fidelity data. For the common case of limited access to high-fidelity data, our computational results demonstrate that multifidelity neural network potential energy surface constructions achieve roughly an order of magnitude improvement, either in terms of test error reduction for equivalent total simulation cost or reduction in total cost for equivalent error.

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

Facile hermetic TEM grid preparation for molecular imaging of hydrated biological samples at room temperature

Abstract Although structures of vitrified supramolecular complexes have been determined at near-atomic resolution, elucidating in situ molecular structure in living cells remains a challenge. Here, we report a straightforward liquid cell technique, originally developed for real-time visualization of dynamics at a liquid-gas interface using transmission electron microscopy, to image wet biological samples. Due to the scattering effects from the liquid phase, the micrographs display an amplitude contrast comparable to that observed in negatively stained samples. We succeed in resolving subunits within the protein complex GroEL imaged in a buffer solution at room temperature. Additionally, we capture various stages of virus cell entry, a process for which only sparse structural data exists due to their transient nature. To scrutinize the morphological details further, we used individual particle electron tomography for 3D reconstruction of each virus. These findings showcase this approach potential as an efficient, cost-effective complement to other microscopy technique in addressing biological questions at the molecular level.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

The Hidden Path to the Resonance-Stabilized Fulvenallenyl Radical (C 7 H 5 ) via the Bimolecular Reaction of Tricarbon (C 3 , X 1 Σ g + ) with 1,3-Butadiene (C 4 H 6 ; X 1 A g )

Here, we report a novel bimolecular reaction pathway forming the resonance-stabilized fulvenallenyl radical (C 7 H 5 ) via the gas-phase reaction of tricarbon (C 3 , X 1 Σ g + ) with 1,3-butadiene (C 4 H 6 , X 1 A g ). Crossed molecular beam experiments combined with high-level electronic structures and statistical calculations reveal a rich potential energy surface. The reaction proceeds via tricarbon addition to a double bond of 1,3-butadiene, overcoming a 30 kJ mol –1 barrier, followed by ring closure, isomerizations (ring opening/closures, hydrogen shifts), and eventual hydrogen atom loss, yielding the fulvenallenyl radical (p1) almost exclusively via two dominant pathways. Considering the entrance barrier, this reaction may occur in high-temperature environments, like circumstellar envelopes of carbon stars, but is suppressed in colder regions such as molecular clouds and Titan’s atmosphere. These findings highlight the unexpected reactivity of small carbon clusters in shaping the molecular complexity of our universe, from the flicker of a flame to the death of a star.

Aromatic compounds↗