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DOE OSTI2021

Evolution of standardization and dissemination of cryo-EM structures and data jointly by the community, PDB, and EMDB

Cryogenic electron microscopy (cryo-EM) methods began to be used in the mid-1970s to study thin and periodic arrays of proteins. Following a half-century of development in cryo-specimen preparation, instrumentation, data collection, data processing and modeling software, cryo-EM has become a routine method for solving structures from large biological assemblies to small biomolecules at near to true atomic resolution. This review explores the critical roles played by the Protein Data Bank (PDB) and Electron Microscopy Data Bank (EMDB) in partnership with the community to develop the necessary infrastructure to archive cryo-EM maps and associated models. Public access to cryo-EM structure data has in turn facilitated better understanding of structure-function relationships and advancement of image processing and modeling tool development. The partnership between the global cryo-EM community and PDB and EMDB leadership has synergistically shaped the standards for metadata, one-stop deposition of maps and models, and validation metrics to assess the quality of cryo-EM structures. The advent of cryo-electron tomography (cryo-ET) for in situ molecular cell structures at a broad resolution range and their correlations with other imaging data introduces new data archival challenges in terms of data size and complexity in the years to come.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

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↗

DOE OSTI2024

AlphaFold -assisted structure determination of a bacterial protein of unknown function using X-ray and electron crystallography

Macromolecular crystallography generally requires the recovery of missing phase information from diffraction data to reconstruct an electron-density map of the crystallized molecule. Most recent structures have been solved using molecular replacement as a phasing method, requiring an a priori structure that is closely related to the target protein to serve as a search model; when no such search model exists, molecular replacement is not possible. New advances in computational machine-learning methods, however, have resulted in major advances in protein structure predictions from sequence information. Methods that generate predicted structural models of sufficient accuracy provide a powerful approach to molecular replacement. Taking advantage of these advances, AlphaFold predictions were applied to enable structure determination of a bacterial protein of unknown function (UniProtKB Q63NT7, NCBI locus BPSS0212) based on diffraction data that had evaded phasing attempts using MIR and anomalous scattering methods. Using both X-ray and micro-electron (microED) diffraction data, it was possible to solve the structure of the main fragment of the protein using a predicted model of that domain as a starting point. The use of predicted structural models importantly expands the promise of electron diffraction, where structure determination relies critically on molecular replacement.

molecular replacement↗

DOE OSTI2020

Electron transfer calculations between edge sharing octahedra in hematite, goethite, and annite

A key reaction underlying the charge transport in iron containing oxides, clays, micas is the Fe$^{2+}$-Fe$^{3+}$ exchange reaction between edge-sharing iron octahedra. These reactions facilitate conduction in these minerals by the thermally-activated hopping of small polarons across the lattice. Depending on the mineral and local charge state the small polaron can either encase an electron or hole. The probability for conduction of small polarons depends strongly on the height and adiabicity of the reaction barrier, with larger and more diabatic barriers yielding slow conduction associated with either weak coupling or a large prerequisite rearrangement of the lattice during charge transport. To model these reactions, a first principle electron transfer (ET) method was developed to model the small polaron hopping between the edge-sharing octahedra sites in hematite ($e^{-}$ polaron), goethite ($e^{-}$ polaron), and annite ($h^{+}$ polaron) bulk structures. The ET method is based on electronic structure methods (i.e., plane-wave Density Functional Theory) capable of performing calculations with periodic cells and large size systems efficiently while at the same time being accurate enough to be used in the estimation of the electron-transfer coupling matrix element, $V_{AB}$, and the electron transfer transmission factor, $\kappa_{el}$. Additionally, the calculations confirmed the existence of small polarons in all three minerals, and the reactions were predicted to be strongly adiabatic. It was found that transfer of a hole in the octahedral layer of annite had an adiabatic barrier of $0.311$ eV, and the transfer of an extra electron in hematite and goethite had adiabatic barriers of $0.242$ eV and $0.232$ eV respectively. The electronic coupling parameters,$V_{AB}$, were found to be $0.188$ eV, $0.196$ eV, and $0.102$ eV respectively for hematite, goethite, and annite. While similar bonding topologies pertain, the underlying basis for the differences is the subtle differences in local structures.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Critical role of structural order in bipolar redox-active molecules for organic redox flow batteries

Bipolar redox-active molecules (BRMs) have been suggested as a means to address crossover related issues in all-organic redox flow batteries (RFBs). In such species, electron donors (anolytes) and electron acceptors (catholytes) are linked by a chain, and the same chemical composition is used in both anode and cathode compartments to reduce chemical gradients and unbalanced ion transport. The resultant RFBs resemble the aqueous vanadium RFBs, but offer greater design flexibility and potentially more favorable electrochemical and physicochemical properties. Yet the complex trade-offs in these properties have been a complication. Here we developed a fundamental rubric to uncover the likely origins in the performance metrics of these BRMs that are salient for their use in RFBs. Methylene linked phenothiazine and phthalimide moieties were employed as model BRMs and variations in their properties and molecular conformations were evaluated by systematically varying the methylene linker. Our results revealed that even minimalistic changes in the linker length resulted in dramatic oscillations in the solubility and stability. Using crystallography, quantum chemistry, and molecular dynamics, we clarify that the seemingly fluctuating behavior is due to (1) the inter- and intra-molecular charge transfer between the donor and acceptor through bond or/and through space; (2) the formation of distinctive packing/clustering motifs. Both interactions are strongly dependent on the molecular conformation. As these structural factors modify the electronic structure of both electroactive functional groups and do not change monotonically, the structure–property response in BRMs is often complex. Finally, accordingly, these behaviors need to be taken into account in developing BRMs and knowledge of these structural factors will allow the more rational design of BRMs for grid-scale energy storage.

25 ENERGY STORAGE↗

DOE OSTI2022

Complexation of Astatine(III) with Ketones: Roles of NO 3 – Counterion and Exploration of Possible Binding Modes

Ketones have been proven effective in extracting astatine(III) from aqueous solvents. Previous theoretical studies suggested a mechanism where the “sp 2 ” lone pair on the carbonyl oxygen donates electron density into the π system of the AtO + molecular cation to form a dative-type bond. In this study, co-extraction of NO 3 – as AtO(NO 3 )·(O=CR 1 R 2 ) species into the organic phase appears to be a key factor. Adjusting the electronic properties of the ketone, by having an aryl group instead of an alkyl group in the alpha position of the ketone, increased the electron density on C=O, increased the bond strength between the ketone and AtO + , and in turn increased the extraction of 211 At into the organic phase. Extraction with diketones shows dependence on the bridging distance between the two carbonyl moieties, where a C 3 or longer bridge results in a 10-fold increase in extraction into the organic phase. Furthermore, DFT calculations show the longer bridge allows for the chelation of AtO(NO 3 ) by either the second carbonyl or the phenyl ring.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

N -Arylimide Molecular Balances: A Comprehensive Platform for Studying Aromatic Interactions in Solution

Noncovalent interactions of aromatic surfaces play a key role in many biological processes and in determining the properties and utility of synthetic materials, sensors, and catalysts. However, the study of aromatic interactions has been challenging because these interactions are usually very weak and their trends are modulated by many factors such as structural, electronic, steric, and solvent effects. Recently, N-arylimide molecular balances have emerged as highly versatile and effective platforms for studying aromatic interactions in solution. These molecular balances can accurately measure weak noncovalent interactions in solution via their influence on the folded–unfolded conformational equilibrium. The structure (i.e., size, shape, π-conjugation, and substitution) and nature (i.e., element, charge, and polarity) of the π-surfaces and interacting groups can be readily varied, enabling the study of a wide range of aromatic interactions. These include aromatic stacking, heterocyclic aromatic stacking, and alkyl–π, chalcogen–π, silver–π, halogen–π, substituent–π, and solvent–π interactions. The ability to measure a diverse array of aromatic interactions within a single model system provides a unique perspective and insights as the interaction energies, stability trends, and solvent effects for different types of interactions can be directly compared. Some broad conclusions that have emerged from this comprehensive analysis include: (1) The strongest aromatic interactions involve groups with positive charges such as pyridinium and metal ions which interact with the electrostatically negative π-face of the aromatic surface via cation–π or metal–π interactions. Attractive electrostatic interactions can also form between aromatic surfaces and groups with partial positive charges. (2) Electrostatic interactions involving aromatic surfaces can be switched from repulsive to attractive using electron-withdrawing substituents or heterocycles. These electrostatic trends appear to span many types of aromatic interactions involving a polar group interacting with a π-surface such as halogen–π, chalcogen–π, and carbonyl–π. (3) Nonpolar groups form weak but measurable stabilizing interactions with aromatic surfaces in organic solvents due to favorable dispersion and/or solvophobic effects. Furthermore, a good predictor of the interaction strength is provided by the change in solvent-accessible surface area. (4) Solvent effects modulate the aromatic interactions in the forms of solvophobic effects and competitive solvation, which can be modeled using solvent cohesion density and specific solvent–solute interactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Reactivity of the Hydrated Electron

Hydrated electrons are created in virtually every radiation environment and in many photochemical or electrochemical environments where liquid water is present, so their reaction products and reaction rate constants are naturally important in applications. Thanks to the strong optical absorbance of (e - ) aq , these rate constants are easy to measure, and a large database has been accumulated. It is not generally appreciated that no working theory of hydrated electron reaction rates presently exists. We discuss key experimental observations of hydrated electron reactions in the context of recent progress in theoretical and simulation developments toward understanding them, made possible by ever increasing computational power.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Influence of shape resonances on the angular dependence of molecular photoionization delays

Characterizing time delays in molecular photoionization as a function of the ejected electron emission direction relative to the orientation of the molecule and the light polarization axis provides unprecedented insights into the attosecond dynamics induced by extreme ultraviolet or X-ray one-photon absorption, including the role of electronic correlation and continuum resonant states. Here, we report completely resolved experimental and computational angular dependence of single-photon ionization delays in NO molecules across a shape resonance, relying on synchrotron radiation and time-independent ab initio calculations. The angle-dependent time delay variations of few hundreds of attoseconds, resulting from the interference of the resonant and non-resonant contributions to the dynamics of the ejected electron, are well described using a multichannel Fano model where the time delay of the resonant component is angle-independent. Comparing these results with the same resonance computed in e-NO + scattering highlights the connection of photoionization delays with Wigner scattering time delays.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2026

Diabatization with Electrostatic Embedding for Studying Photophysics in Organic Molecular Crystals

Highly emissive organic molecular crystals find applications in several areas, such as organic electronics, solar cells, and sensors. Understanding the excited-state mechanisms underlying these applications is essential for optimizing and controlling them effectively. Exciton models coupled with nonadiabatic dynamics, particularly quantum dynamics, provide crucial insights into photochemical and photophysical processes in molecular crystals. Nevertheless, there remains a lack of general tools and automated workflows to facilitate such simulations. In this paper, we present a computational strategy to investigate the photoactivated dynamics of organic molecular crystals, bridging methodologies traditionally used for molecular systems and materials science, with a particular focus on the interplay between local excitations and charge transfer (CT) processes. We have implemented an interface between the fromage and Overdia programs, enabling the construction of vibronic Hamiltonians for molecular crystals within an excited-state ONIOM(QM:QM′) framework, incorporating long-range electrostatics through a RESP-based Ewald summation. Fragment-based diabatization provides a route to quantum dynamics simulations in weak-to-intermediate coupling regimes. The method was applied to the photophysics of dibenzo[g,p]chrysene (DBC) crystals using time-dependent DFT. The fromage/ Overdia interface was employed to compute the couplings of local excitations and CT states for 18 unique DBC dimers in the crystal and to quantify the influence of electrostatic embedding, which was found to be modest (10−20%). Simulations on π-stacked dimers reproduced the small red shift observed experimentally from solution to crystal, attributed to electronic interactions among fixed monomers rather than crystal electrostatics. Quantum dynamics simulations revealed ultrafast population transfer from bright local excitations to CT states. This approach establishes a robust framework linking molecular and solid-state excited-state dynamics, with potential applications for studying excitations, defects, and impurities in molecular crystals.

Crystals↗

DOE OSTI2024

Above-threshold ionization at laser intensity greater than 10 20 W / cm 2

Here we present experimental observation of above-threshold ionization (ATI) electrons produced by ionization of the neon K shell in a laser field where intensity exceeds 10 20 W/cm 2 . An array of plastic scintillating calorimeter detectors was used to measure the high-energy electrons at four angles in the laser forward direction. Coarse energy resolution was obtained using aluminum filters of several thicknesses to block lower-energy electrons. A threshold intensity around 2×10 20 W/cm 2 is observed for production of energetic ATI electrons in the laser forward direction, with maximum electron energy exceeding 10 MeV. L-shell electrons with energies <1.4 MeV are scattered farther forward along the laser direction than expected. We present comparisons of the measured total electron energies to the predictions of Monte Carlo models employing the ADK-PPT ionization model and the Augst barrier suppression ionization model.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2023

Reaction Chemistry at Discrete Organometallic Fragments on Black Phosphorus

Abstract Black phosphorus (bP) is a two‐dimensional van der Waals material unique in its potential to serve as a support for single‐site catalysts due to its similarity to molecular phosphines, ligands quintessential in homogeneous catalysis. However, there is a scarcity of synthetic methods to install single metal centers on the bP lattice. Here, we demonstrate the functionalization of bP nanosheets with molecular Re and Mo complexes. A suite of characterization techniques, including infrared, X‐ray photoelectron and X‐ray absorption spectroscopy as well as scanning transmission electron microscopy corroborate that the functionalized nanosheets contain a high density of discrete metal centers directly bound to the bP surface. Moreover, the supported metal centers are chemically accessible and can undergo ligand exchange transformations without detaching from the surface. The steric and electronic properties of bP as a ligand are estimated with respect to molecular phosphines. Sterically, bP resembles tri(tolyl)phosphine when monodentate to a metal center, and bis(diphenylphosphino)propane when bidentate, whereas electronically bP is a σ‐donor as strong as a trialkyl phosphine. This work is foundational in elucidating the nature of black phosphorus as a ligand and underscores the viability of using bP as a basis for single‐site catalysts.

Mitra, Kendahl L. Walz↗

DOE OSTI2023

Reaction Chemistry at Discrete Organometallic Fragments on Black Phosphorus

Chemistry↗

DOE OSTI2022

SAXS-guided unbiased coarse-grained Monte Carlo simulation for identification of self-assembly nanostructures and dimensions

Recent studies have shown that solvated amphiphiles can form nanostructured self-assemblies called dynamic binary complexes (DBCs) in the presence of ions. Since the nanostructures of DBCs are directly related to their viscoelastic properties, it is important to understand how the nanostructures change under different solution conditions. However, it is challenging to obtain a three-dimensional molecular description of these nanostructures by utilizing conventional experimental characterization techniques or thermodynamic models. To this end, we combined the structural data from small angle X-ray scattering (SAXS) experiments and thermodynamic knowledge from coarse-grained Monte Carlo (CGMC) simulations to identify the detailed three-dimensional nanostructure of DBCs. Specifically, unbiased CGMC simulations are performed with SAXS-guided initial conditions, which aids us to sample accurate nanostructures in a computationally efficient fashion. As a result, an elliptical bilayer nanostructure is obtained as the most probable nanostructure of DBCs whose dimensions are validated by scanning electron microscope (SEM) images. Then, utilizing the obtained molecular model of DBCs, here we could also explain the pH tunability of the system. Overall, our results from SAXS-guided unbiased CGMC simulations highlight that using potential energy combined with SAXS data, we can distinguish otherwise degenerate nanostructures resulting from the inherent ambiguity of SAXS patterns.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Mass-selected ion–molecule cluster beam apparatus for ultrafast photofragmentation studies

We describe an apparatus for investigating the excited-state dissociation dynamics of mass-selected ion–molecule clusters by mass-resolving and detecting photofragment-ions and neutrals, in coincidence, using an ultrafast laser operating at high repetition rates. The apparatus comprises a source that generates ion–molecule clusters, a time-of-flight spectrometer, and a mass filter that selects the desired anions, and a linear-plus-quadratic reflectron mass spectrometer that discriminates the fragment anions after the femtosecond laser excites the clusters. The fragment neutrals and anions are then captured by two channeltron detectors. The apparatus performance is tested by measuring the photofragments: I – , CF 3 I – , and neutrals from photoexcitation of the ion–molecule cluster CF 3 I·I – using femtosecond UV laser pulses with a wavelength of 266 nm. Here, the experimental results are compared with our ground state and excited state electronic structure calculations as well as the existing results and calculations, with particular attention to the generation mechanism of the anion fragments and dissociation channels of the ion–molecule cluster CF 3 I·I – in the charge-transfer excited state.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗

DOE OSTI2022

A crossed molecular beams and computational study on the unusual reactivity of banana bonds of cyclopropane (c-C 3 H 6 ; X 1 A$^{'}_{1}$ ) through insertion by ground state carbon atoms (C( 3 P j ))

The mechanism and chemical dynamics of the reaction of ground electronic state atomic carbon C( 3 P j ) with cyclopropane c-C 3 H 6 (X 1 A$^{'}_{1}$) have been explored by combining crossed molecular beams experiments with electronic structure calculations of the pertinent triplet C 4 H 6 potential energy surface and statistical computations of product branching ratios under single-collision conditions. The experimental findings suggest that the reaction proceeds via indirect scattering dynamics through triplet C 4 H 6 reaction intermediate(s) leading to C 4 H 5 product(s) plus atomic hydrogen via a tight exit transition state, with the overall reaction exoergicity evaluated as 231 ± 52 kJ mol –1 . The calculations indicate that C( 3 P j ) can easily insert into one of the three equivalent C–C ‘banana’ bonds of cyclopropane overcoming a low barrier of only 2 kJ mol –1 following the formation of a van der Waals reactant complex stabilized by 15 kJ mol –1 . The carbon atom insertion into one of the six C–H bonds is also feasible via a slightly higher barrier of 5 kJ mol –1 . Here, these results highlight an unusual reactivity of cyclopropane's banana C–C bonds, which behave more like unsaturated C–C bonds with a π-character than saturated σ C–C bonds, which are known to be generally unreactive toward the ground electronic state atomic carbon such as in ethane (C 2 H 6 ). The statistical theory predicts the overall product branching ratios at the experimental collision energy as 50% for 1-butyn-4-yl, 33% for 1,3-butadien-2-yl, i-C 4 H 5 , and 11% for 1,3-butadien-1-yl, n-C 4 H 5 , with i-C 4 H 5 (230 kJ mol –1 below the reactants) favored by the C–C insertion providing the best match with the experimentally observed reaction exoergicity. The C( 3 P j ) + c-C 3 H 6 reaction is predicted to be a source of C 4 H 5 radicals under the conditions where its low entrance barriers can be overcome, such as in planetary atmospheres or in circumstellar envelopes but not in cold molecular clouds. Both i- and n-C 4 H 5 can further react with acetylene eventually producing the first aromatic ring and hence, the reaction of the atomic carbon with c-C 3 H 6 can be considered as an initial step toward the formation of benzene.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Dynamics of resonant low-energy electron attachment to ethanol-producing hydroxide anions

Here, the dynamics of dissociative electron attachment to ethanol is experimentally investigated at the Feshbach resonance formed with incident electron energies near 9.5 eV. Highly differential laboratory-frame momentum distributions of OH – fragments are measured for a series of energies spanning the resonance width, using the velocity-map-imaging technique. The OH – kinetic-energy distribution indicates that the C-O breaking dissociation process could either be a three-body dissociation or a two-body dissociation with significant rovibrational excited fragments. The small, but significant, anisotropy in the OH – angular distribution provides signatures of the molecular symmetry of the associated resonant state under the axial recoil approximation, which assumes the dissociation is much faster than any rotation of the dissociation axis. Within these assumptions, the 9.5-eV Feshbach resonance can be assigned to the electronic transition from the ($10a'$) orbital with its ground-state C s symmetry to the empty ($4a''$) level, involving the simultaneous electron attachment. This dynamics could be a model for C-O dissociation in larger alcohols and ethers.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2025

Solvated Electrons Have Multiple Personalities in Molten Salts

P-Crosscut: Solvated Electrons Have Multiple Personalities in Molten Salts [EFRC – MSEE] Alejandro Ramos-Ballesteros;1 Hung H. Nguyen;2 Kazuhiro Iwamatsu;3 Santanu Roy;4 Vyacheslav Bryantsev;4 Michael E. Woods;1 Ruchi Gakhar;1 Phillip Halstenberg;4 Bobby Layne;5 Jay A. LaVerne;6 Claudio J. Margulis:2* and James F. Wishart5* 1Idaho National Laboratory; 2The University of Iowa; 3Hunter College; 4Oak Ridge National Laboratory; 5Brookhaven National Laboratory; 6University of Notre Dame Abstract: The solvated (eS–) is a powerful reducing agent and one of the primary products of molten salt radiolysis. In these extreme high-temperature environments, the eS– can initiate cascades of redox processes that significantly alter the physical and chemical properties of a molten salt, posing challenges for molten salt reactor (MSR) performance and longevity. Consequently, mastering the fundamental behavior of the eS– could enable the design of specific molten salt mixtures with tailored Lewis acidities for controlling the speciation and chemical reactivity of the eS–, thereby mitigating its overall impact on MSR technologies. Here, we use time-resolved electron pulse radiolysis techniques for determining chemical kinetics and transient absorption spectra, combined with ab initio molecular dynamics simulations to explore the influence of multivalent metal cations on the fundamental speciation and distribution of eS– coordination environments.

38 - RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCL↗