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DOE OSTI2023

Elucidating the Role of Hydrogen Bonding in the Optical Spectroscopy of the Solvated Green Fluorescent Protein Chromophore: Using Machine Learning to Establish the Importance of High-Level Electronic Structure

Hydrogen bonding interactions with chromophores in chemical and biological environments play a key role in determining their electronic absorption and relaxation processes, which are manifested in their linear and multidimensional optical spectra. For chromophores in the condensed phase, the large number of atoms needed to simulate the environment has traditionally prohibited the use of high-level excited-state electronic structure methods. By leveraging transfer learning, we show how to construct machine-learned models to accurately predict the high-level excitation energies of a chromophore in solution from only 400 high-level calculations. Here, we show that when the electronic excitations of the green fluorescent protein chromophore in water are treated using EOM-CCSD embedded in a DFT description of the solvent the optical spectrum is correctly captured and that this improvement arises from correctly treating the coupling of the electronic transition to electric fields, which leads to a larger response upon hydrogen bonding between the chromophore and water.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2026

Nonlinear reversal of photoexcitation on the attosecond time scale improves ultrafast X-ray diffraction images

The complex refractive index of a material governs its light-matter interactions, with intense light fields enabling tailored nonlinear optical responses. In the X-ray regime, rapid photoionization limits the potential of nonlinear techniques by inducing irreversible electronic damage. Here we demonstrate that intense, sub-femtosecond X-ray pulses, shorter than typical Auger decay times, can partially reverse photoexcitation via stimulated emission near atomic resonances. By analyzing thousands of coherent diffraction patterns and ion spectra from neon nanoparticles exposed to sub-fs and 15-fs pulses, we observe enhanced X-ray diffraction alongside reduced energy absorption for sub-fs pulses. Theoretical modeling attributes this to dynamics akin to Rabi flopping that prolong the lifetime of resonant states and suppress electronic bleaching. These findings suggest that ultrashort, intense X-ray pulses enable active control of X-ray refractive index and damage pathways, opening avenues for improved high-resolution imaging and nonlinear spectroscopy in complex nanoscale systems.

Ulmer, Anatoli [Universität Hamburg (Germany)] (OR↗

DOE OSTI2023

Ionization disequilibrium in K- and L-shell ions

Time-gated Sc K-shell and Ge L-shell spectra are presented from a range of characterized thermodynamic states spanning ion densities of 1019–1020cm−3 and plasma temperatures around 2000 eV. For the higher densities studied and temperatures from 1000 to 3000 eV, the Sc and Ge x-ray emission spectra are consistent with steady-state calculations from the modern atomic kinetics model SCRAM. At the lower ion densities achieved through plasma expansion, however, the model calculations require a higher plasma temperature to reproduce the observed Ge spectrum. We attribute this to ionization disequilibrium of the Sc because the ionization time scales exceed the hydrodynamic timescale when the inferred temperatures diverge.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2020

Distinguishing electronic contributions of surface and sub-surface transition metal atoms in Ti-based MXenes

MXenes are a rapidly-expanding family of 2D transition metal carbides and nitrides that have attracted attention due to their excellent performance in applications ranging from energy storage to electromagnetic interference shielding. Numerous other electronic and magnetic properties have been computationally predicted, but not yet realized due to the experimental difficulty in obtaining uniform surface terminations (T x ), necessitating new design approaches for MXenes that are independent of surface groups. In this study, we distinguished the contributions of surface and sub-surface Ti atoms to the electronic structure of four Ti-based MXenes (Ti 2 CT x , Ti 3 C 2 T x , Cr 2 TiC 2 T x , and Mo 2 TiC 2 T x ) using soft x-ray absorption spectroscopy, revealing minimal changes in the spectral features between the parent MAX phase and its MXene when no surface Ti atoms are present in the MXene, such as Mo 2 TiC 2 T x and Cr 2 TiC 2 T x . In contrast, for MXenes with surface Ti atoms, here Ti 3 C 2 T x and Ti 2 CT x , the Ti L-edge spectra are significantly modified compared to their parent MAX phase compounds. First principles calculations provide similar trends in the partial density of states derived from surface and interior Ti atoms, corroborating the spectroscopic measurements. Furthermore, these results reveal that electronic states derived from sub-surface M-site layers are largely unperturbed by the surface groups, indicating a relatively short length scale over which the T x groups alter the nominal electron count associated with Ti atoms and suggesting that desired band features should be hosted by sub-surface M-sites that are electronically more robust than their surface M-site counterparts.

36 MATERIALS SCIENCE↗

DOE OSTI2021

Combined multiplet theory and experiment for the Fe 2p and 3p XPS of FeO and Fe 2 O 3

The Al K alpha, 1486.6eV, based XPS of Fe 2p and Fe 3p for Fe(III) in Fe 2 O 3 and Fe(II) in FeO are compared with theoretical predictions based on ab initio wavefunctions that accurately treat the final, core-hole, multiplets. The principal objectives of this comparison are to understand the multiplet structure and to evaluate the use of both the 2p and 3p spectra in determining oxidation state. In order to properly interpret the features of these spectra and to use the XPS to provide atomistic insights as well as atomic composition, it is necessary to understand the origin of the multiplet energies and intensities. The theoretical treatment takes into account the ligand field and spin-orbit splittings, the covalent mixing of ligand and Fe 3d orbitals, and the angular momentum coupling of the open shell electrons. These effects lead to the distribution of XPS intensity into a large number of final, ionic, states that are only partly resolved with energies spread over a wide range of binding energies, BEs. For this reason, it is necessary to record the Fe 2p and 3p XPS spectra over a wide energy range which includes all the multiplets in the theoretical treatment as well as additional shake satellites. We also evaluate the effects of differing assumptions concerning the extrinsic background subtraction, to be sure our experimental spectrum may be fairly compared to the theory. In this work, we conclude that the Fe 3p XPS provides an additional means for distinguishing Fe(III) and Fe(II) oxidation states beyond just using the Fe 2p spectrum. In particular, with the use of the Fe 3p XPS, the depth of the material probed is about 1.5 times greater than for the Fe 2p XPS. In addition, a new type of atomic many-body effect that involves excitations into orbitals that have Fe f,$\ell$=3, symmetry has been shown to be important for the Fe 3p XPS.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Advanced EXAFS analysis techniques applied to the L -edges of the lanthanide oxides

The unique properties of the lanthanide (Ln) elements make them critical components of modern technologies, such as lasers, anti-corrosive films and catalysts. Thus, there is significant interest in establishing structure–property relationships for Ln-containing materials to advance these technologies. Extended X-ray absorption fine structure (EXAFS) is an excellent technique for this task considering its ability to determine the average local structure around the Ln atoms for both crystalline and amorphous materials. However, the limited availability of EXAFS reference spectra of the Ln oxides and challenges in the EXAFS analysis have hindered the application of this technique to these elements. The challenges include the limited k-range available for the analysis due to the superposition of L-edges on the EXAFS, multielectron excitations (MEEs) creating erroneous peaks in the EXAFS and the presence of inequivalent absorption sites. Herein, we removed MEEs to model the local atomic environment more accurately for light Ln oxides. Further, we investigated the use of cubic and non-cubic lattice expansion to minimize the fitting parameters needed and connect the fitting parameters to physically meaningful crystal parameters. The cubic expansion reduced the number of fitting parameters but resulted in a statistically worse fit. The non-cubic expansion resulted in a similar quality fit and showed non-isotropic expansion in the crystal lattice of Nd 2 O 3 . In total, the EXAFS spectra and the fits for the entire set of Ln oxides (excluding promethium) are included. The knowledge developed here can assist in the structural determination of a wide variety of Ln compounds and can further studies on their structure–property relationships.

36 MATERIALS SCIENCE↗

DOE OSTI2021

Revealing the chemical environment of Cr, Fe, and Ni in high temperature-ultrafine precipitate strengthened steel subjected to low fluence neutron irradiation

High-temperature ultrafine-precipitate-strengthened (HT-UPS) steel has potential applications in advanced nuclear reactors as a structural material. However, little is currently known about its response to neutron irradiation. This research provides insight into the neutron irradiation-induced physicochemical changes of the major constituents in HT-UPS steels, including Fe, Cr, and Ni, using synchrotron X-ray absorption near edge structure (XANES) and diffraction. This study is the first known investigation using XANES to characterize HT-UPS steel to analyze the evolution of the atomic level chemistry. It was found that following irradiation, nucleation, ballistic dispersion, and/or coarsening of Cr 23 C 6 precipitates occurred at very low neutron irradiation fluences, from 0.003 displacements per atom (dpa) up to 0.3 dpa, at ~600°C, which were at least an order of magnitude lower than previous studies. Calculations of the angular momentum projections, partial density of states, and the XANES spectra confirmed the experimental findings of the Cr 23 C 6 precipitate evolution. In contrast, the local atomic structure around Fe and Ni atoms demonstrated irradiation resistance.

36 MATERIALS SCIENCE↗

DOE OSTI2021

Isotope Shifts of Radium Monofluoride Molecules

Isotope shifts of 223–226,228 Ra 19 F were measured for different vibrational levels in the electronic transition A 2 II 1/2 ←X 2 Σ + . The observed isotope shifts demonstrate the particularly high sensitivity of radium monofluoride to nuclear size effects, offering a stringent test of models describing the electronic density within the radium nucleus. Ab initio quantum chemical calculations are in excellent agreement with experimental observations. These results highlight some of the unique opportunities that short-lived molecules could offer in nuclear structure and in fundamental symmetry studies.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2021

ARES. V. No Evidence For Molecular Absorption in the HST WFC3 Spectrum of GJ 1132 b

We present a study on the spatially scanned spectroscopic observations of the transit of GJ 1132 b, a warm (∼500 K) super-Earth (1.13 R {sub ⊕}) that was obtained with the G141 grism (1.125–1.650 μm) of the Wide Field Camera 3 (WFC3) on board the Hubble Space Telescope. We used the publicly available Iraclis pipeline to extract the planetary transmission spectra from the five visits and produced a precise transmission spectrum. We analyzed the spectrum using the TauREx3 atmospheric retrieval code, with which we show that the measurements do not contain molecular signatures in the investigated wavelength range and are best fit with a flat-line model. Our results suggest that the planet does not have a clear primordial, hydrogen-dominated atmosphere. Instead, GJ 1132 b could have a cloudy hydrogen-dominated atmosphere, have a very enriched secondary atmosphere, be airless, or have a tenuous atmosphere that has not been detected. Due to the narrow wavelength coverage of WFC3, these scenarios cannot be distinguished yet, but the James Webb Space Telescope may be capable of detecting atmospheric features, although several observations may be required to provide useful constraints.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2025

Plasmonic Ag nanocomposite phosphate glasses produced via γ-ray irradiation as reduction route

This paper reports on the impact of γ-ray irradiation (10, 100 kGy) on melt-quenched Ag + -doped phosphate glass and the effects of subsequent thermal processing leading to the production of plasmonic Ag nanocomposites. The γ-irradiated glasses were characterized alongside the pristine by differential scanning calorimetry (DSC), Raman spectroscopy, electron paramagnetic resonance (EPR) spectroscopy, optical absorption, and photoluminescence (PL) spectroscopy. DSC characterization showed consistent glass transition temperatures (T g ) before and after γ-irradiation whereas the crystallization temperatures tended to decrease with increasing γ-ray dose. However, a lack of alteration of the glass network structure was supported by Raman spectroscopy. Room temperature EPR spectra clearly showed the formation of phosphorus oxygen hole center (POHC) defects in the undoped host, in addition to another doublet likely associated with a P 3 defect. The presence of paramagnetic silver species encompassing Ag 2+ and 107/109 Ag 0 atoms was also indicated in the silver-activated glass together with POHC defects. Optical absorption spectra were also consistent with the presence of various radiation-induced centers. Further analyzing the glass absorption edge via Tauc plots suggested the formation of electron center (EC) defects in γ-irradiated samples wherein the silver-doped glass exhibited decreasing band gap energies with increasing γ-ray dose. The PL characterization showed the silver-related radio-PL effect was induced exhibiting broad band emission with two maxima around 500 and 625 nm stemming from various molecular Ag$^{x+}_{n}$ clusters. Emission decay analyses revealed that the longer wavelength emission exhibited slower decay. The highest radiation dose of 100 kGy however resulted in weaker emission and faster decay kinetics attributed to energy transfer between the luminescent silver species and POHC defects. Finally subjecting the γ-irradiated Ag-doped glasses to heat treatment near the T g at 490 °C led to the development of the surface plasmon resonance of Ag nanoparticles (NPs) and the vanishing of the Ag$^{x+}_{n}$ clusters luminescence. In conclusion, the presence of the matrix-related EC defects was deemed accountable for the thermally induced reduction and consequent precipitation of Ag NPs making the plasmonic glasses attractive for photonic applications such as nonlinear optics.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Interpretation of Ir L-edge isotropic x-ray absorption spectra across the pressure-induced dimerization transition in hyper-honeycomb beta-Li2IrO3

The extended nature of atomic 5d orbitals, together with a relatively short ~ 3 °A Ir-Ir distance across edge-shared octahedra in honeycomb iridate lattices, leads to a tendency to disrupt the local, spin-orbit entangled jeff = 1 2 moments of Ir4+ ions in favor of dimerization and formation of molecular orbitals, especially upon lattice compression. The sensitivity of Ir L-edge spectroscopy to both spin-orbit entanglement in jeff states and quenching of orbital degrees of freedom in dimerized states, results in a peculiar evolution of x-ray absorption spectra across dimerization transitions including energy shifts in opposite direction for L3 and L2 leading absorption edges, and substantial changes in their isotropic branching ratio. We present a theoretical description of the evolution of 5d electronic states, and related x-ray absorption spectra, in going from the single ion to the dimerized limit. The calculations reproduce the experimental results for hyper-honeycomb β-Li2IrO3[1, 2] and shed light into the weakening of the coupling between spin and orbital degrees of freedom as the strength of dimerization increases. The results provide a basis for interpretation of L-edge xray absorption spectra in 5d systems where competition between formation of local jeff states and molecular orbitals is at play.

van Veenendaal, Michel↗

DOE OSTI2022

Enhanced analysis of experimental x-ray spectra through deep learning

X-ray spectroscopic data from high-energy-density laser-produced plasmas has long required thorough, time-consuming analysis to extract meaningful source conditions. There are often confounding factors due to rapidly evolving states and finite spatial gradients (e.g., the existence of multi-temperature, multi-density, multi-ionization states, etc.) that make spectral measurements and analysis difficult. Here, in this paper, we demonstrate how deep learning can be applied to enhance x-ray spectral data analysis in both speed and intricacy. Neural networks (NNs) are trained on ensemble atomic physics simulations so that they can subsequently construct a model capable of extracting plasma parameters directly from experimental spectra. Through deep learning, the models can extract temperature distributions as opposed to single or dual temperature/density fits from standard trial-and-error atomic modeling at a significantly reduced computational cost compared to traditional trial-and-error methods. These NNs are envisioned to be deployed with high repetition rate x-ray spectrometers in order to provide detailed real-time analysis of experimental spectra.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2025

OmniXAS: A universal deep-learning framework for materials x-ray absorption spectra

X-ray absorption spectroscopy (XAS) is a powerful characterization technique for probing the local chemical environment of absorbing atoms. However, analyzing XAS data presents significant challenges, often requiring extensive, computationally intensive simulations, as well as significant domain expertise. These limitations hinder the development of fast, robust XAS analysis pipelines that are essential in high-throughput studies and for autonomous experimentation. Here, we address these challenges with OmniXAS, a framework that contains a suite of transfer learning approaches for XAS prediction, each uniquely contributing to improved accuracy and efficiency, as demonstrated on the K-edge spectra database covering eight 3⁢d transition metals (Ti–Cu). The OmniXAS framework is built upon three distinct strategies. First, we use M3GNet [Nat. Comput. Sci. 2, 718 (2022)] to derive latent representations of the local chemical environment of absorption sites as input for XAS prediction, achieving significant improvements over conventional featurization techniques. Second, we employ a hierarchical transfer learning strategy, training a universal multitask model across elements before fine-tuning for element-specific predictions. Models based on this cascaded approach after elementwise fine-tuning outperform element-specific models by up to 69%. Third, we implement cross-fidelity transfer learning, adapting a universal model to predict spectra generated by simulation of a different fidelity with a much higher computational cost. This approach improves prediction accuracy by up to 11% over models trained on the target fidelity alone. Our approach significantly boosts the throughput of XAS modeling by orders of magnitude as compared to first-principles simulations and is extendable to XAS prediction for a broader range of elements. The proposed transfer learning framework is generalizable to enhance deep-learning models that target other properties in materials research.

36 MATERIALS SCIENCE↗

DOE OSTI2023

What do far-infrared spectra of solitary water in “water-in-solvent” systems reveal about water’s solvation and dynamics?

Classical molecular dynamics simulations of water in ionic and dipolar solvents were used to interpret the far-infrared (FIR) rotation/libration spectra of “solitary water” in terms of water’s rotational dynamics and interactions with solvents. Seven solvents represented by nonpolarizable all-atom force fields and a series of idealized variable-charge solvents were used to span the range of solvent polarities (hydrogen bonding) studied experimentally. Simulated spectra capture the solvent dependence observed, as well as the relationship between the frequencies of water libration (νL) and OH stretching bands (νOH). In more strongly interacting solvents, simulated νL are ∼20% higher than those of experiment. In all solvents, the simulated spectra are composites of rotational motions about the two axes perpendicular to water’s dipole moment, and the different frequencies of these two motions are responsible for the breadth of the libration band and the bimodal shape observed in halide ionic liquids. Simulations overestimate the separation of these two components in most solvents. The character of water rotational motions changes markedly with solvent polarity, from quasi-free rotation in nonpolar and weakly polar solvents to highly constrained libration in strongly hydrogen bonding environments. The changeover to librational motions dominating the spectrum occurs between solvents such as benzene (νL ∼ 250 cm−1) and acetonitrile (νL ∼ 400 cm−1). For solvents in the latter category, the mean frequency of the experimental FIR band provides a direct measure of mean-squared torques and, therefore, force constants associated with interactions constraining water’s librational motion.

Chemistry↗

DOE OSTI2021

D-Band EPR and ENDOR Spectroscopy of 15 N-Labeled Photosystem I

For billions of years, nature has optimized the photosynthetic machinery that converts light energy into chemical energy. Key primary reactions of photosynthesis occur in large membrane protein-cofactor complexes. The light-induced sequential electron transfer reactions occur through a chain of donor/acceptor cofactors embedded in the protein matrix resulting in a long-lived transmembrane charge-separated state. EPR is the method of choice to study electron transfer and the interaction of protein environment with redox-active cofactors. However, the spectra of organic cofactor radicals typically are not fully resolved and severely overlap at conventional X-band EPR. Even at Q-band EPR, this overlap is present and often a serious problem. As a result, there is a large variation of the reported EPR data and limited understanding of electronic structures of several redox-active cofactors. These serious problems can often be overcome by the excellent spectral resolution provided by high-frequency EPR (HF EPR). In this work, we study the electronic structure of the primary electron donor P 700 and the secondary electron acceptor A 1 of Photosystem I (PSI) using 130 GHz (D-band) EPR and Electron-Nuclear-Double-Resonance (ENDOR) spectroscopy. PSI was isotopically labeled with 15 N (I = $\frac{1/2}$) to avoid quadrupolar interactions in the most abundant nitrogen isotope 14 N (I = 1) and simplify the ENDOR spectra. ENDOR spectroscopy is central for determining the hyperfine coupling of nitrogen atoms of the two chlorophyll molecules comprising oxidized P 700 and the involvement of protein nitrogen atoms with reduced A 1 . While HF ENDOR of A 1 - allows identification of two nitrogen atoms, HF ENDOR of P 700 + still does not permit unique assignment of the recorded hyperfine couplings.

15N↗

DOE OSTI2021

Nonlocal and nonadiabatic Pauli potential for time-dependent orbital-free density functional theory

Time-dependent orbital-free density functional theory is an efficient ab initio method for calculating the electronic dynamics of large systems. In comparison to standard time-dependent density functional theory, it computes only a single electronic state regardless of system size, but it requires an additional time-dependent Pauli potential term. Herein we propose a nonadiabatic and nonlocal Pauli potential whose main ingredients are the time-dependent particle and current densities. Our calculations of the optical spectra of metallic and semiconductor clusters indicate that nonlocal and nonadiabatic time-dependent orbital-free density functional theory performs accurately for metallic systems and semiquantitatively for semiconductors. This paper opens the door to wide applicability of time-dependent orbital-free density functional theory for nonequilibrium electron and electron-nuclear dynamics of complex materials.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2022

Coexisting structural disorder and robust spin-polarization in half-metallic FeMnVAl

We report half-metallic ferromagnets (HMFs) are one of the most promising materials in the field of spintronics due to their unique band structure, consisting of one spin subband having metallic characteristics along with another subband with semiconductor-like behavior. In this work, we report the synthesis of a novel quaternary Heusler alloy—FeMnVAl—and we have studied the structural, magnetic, transport, and electronic properties complemented with first-principles calculations. Among different possible structurally ordered arrangements, the optimal structure is identified by theoretical energy minimization. The corresponding spin-polarized band-structure calculations indicate the presence of a half-metallic ferromagnetic ground state. A detailed and careful investigation of the x-ray diffraction data, Mössbauer spectra, and nuclear magnetic resonance spectra suggests the presence of site disorder between the Fe and Mn atoms in the stable ordered structure of the system. The magnetic susceptibility measurement clearly establishes a ferromagnetic-like transition below ~213 K. The Fe Mössbauer spectrometry measurements suggest that only the Mn spins could be responsible for the magnetic order, which is consistent with our theoretical calculation. Surprisingly, the density-functional-theory calculations reveal that the spin-polarization value is almost immunized (92.4% → 90.4%) from the Mn-Fe structural disorder, even when nonmagnetic Fe and moment-carrying Mn sites are entangled inseparably. The robustness of spin polarization and half-metallicity in the studied FeMnVAl compound comprising structural disorder is thus quite interesting and could provide a new direction to investigate and understand the exact role of disorders on spin polarization in this class of materials, beyond the available knowledge.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

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↗