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At least 145 records · Page 8

Using X-ray free-electron lasers for spectroscopy of molecular catalysts and metalloenzymes

The metal centers in metalloenzymes and molecular catalysts are responsible for the rearrangement of atoms and electrons during complex chemical reactions, and they enable selective pathways of charge and spin transfer, bond breaking/making and the formation of new molecules. Mapping the electronic structural changes at the metal sites during the reactions gives a unique mechanistic insight that has been difficult to obtain to date. The development of X-ray free-electron lasers (XFELs) enables powerful new probes of electronic structure dynamics to advance our understanding of metalloenzymes. The ultrashort, intense and tunable XFEL pulses enable X-ray spectroscopic studies of metalloenzymes, molecular catalysts and chemical reactions, under functional conditions and in real time. In this Technical Review, we describe the current state of the art of X-ray spectroscopy studies at XFELs and highlight some new techniques currently under development. With more XFEL facilities starting operation and more in the planning or construction phase, new capabilities are expected, including high repetition rate, better XFEL pulse control and advanced instrumentation. For the first time, it will be possible to make real-time molecular movies of metalloenzymes and catalysts in solution, while chemical reactions are taking place.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Valence-to-core X-ray emission spectroscopy of vanadium oxide and lithiated vanadyl phosphate materials

In this work, we report valence-to-core (VTC) X-ray emission spectroscopy (XES) measurements and theoretical calculations of the electrochemical sequence ε-VOPO 4 , ε-LiVOPO 4 , ε-Li 2 VOPO 4 and the reference oxides V 2 O 3 , VO 2 , and V 2 O 5 . In our analysis of these results, we establish a framework for interrogating chemical bonding that is generally applicable to a wide range of systems, including complex, extended inorganic compounds. While this latter regime has garnered less focused application than, e.g. , metalloenzymes in many excellent catalysis studies, we show that the technique provides high utility in materials-focused energy storage research. Here, sensitivities to the local atomic structure and hybridization schemes are discussed in detail. Similarly, the effect of lithiation on oxidation, delocalization, and shifts in ligand valence energy levels are all readily apparent in the analyzed results. Finally, the TDDFT projections clearly reveal the directional dependencies of the valence band at each of the vanadium sites. Our results demonstrate laboratory-based X-ray spectroscopy instrumentation is a viable route for attaining well-resolved VTC-XES features for inorganic compounds of 3d transition metals, even for samples of limited quantity or suffering from sensitivity to the atmosphere. The experimental results are in good agreement with results produced by real-space Green's function and time-dependent density functional theory (TDDFT) methods, respectively. Hence, we propose that VTC-XES, when equipped with appropriate theoretical support, can be a valuable complement to X-ray absorption pre-edge features for more detailed characterization of a compound's electronic structure. We expect similar analyses will find application in a broad range of materials chemistry research and provide both fundamental and applied insights.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Physics-based reward driven image analysis in microscopy

The rise of electron microscopy has expanded our ability to acquire nanometer and atomically resolved images of complex materials. The resulting vast datasets are typically analyzed by human operators, an intrinsically challenging process due to the multiple possible analysis steps and the corresponding need to build and optimize complex analysis workflows. We present a methodology based on the concept of a Reward Function coupled with Bayesian Optimization, to optimize image analysis workflows dynamically. The Reward Function is engineered to closely align with the experimental objectives and broader context and is quantifiable upon completion of the analysis. Here, cross-section, high-angle annular dark field (HAADF) images of ion-irradiated (Y, Dy)Ba 2 Cu 3 O 7–δ thin-films were used as a model system. The reward functions were formed based on the expected materials density and atomic spacings and used to drive multi-objective optimization of the classical Laplacian-of-Gaussian (LoG) method. These results can be benchmarked against the DCNN segmentation. This optimized LoG* compares favorably against DCNN in the presence of the additional noise. We further extend the reward function approach towards the identification of partially-disordered regions, creating a physics-driven reward function and action space of high-dimensional clustering. We pose that with correct definition, the reward function approach allows real-time optimization of complex analysis workflows at much higher speeds and lower computational costs than classical DCNN-based inference, ensuring the attainment of results that are both precise and aligned with the human-defined objectives.

47 OTHER INSTRUMENTATION↗

Substitution Models of Protein Evolution with Selection on Enzymatic Activity

Abstract Substitution models of evolution are necessary for diverse evolutionary analyses including phylogenetic tree and ancestral sequence reconstructions. At the protein level, empirical substitution models are traditionally used due to their simplicity, but they ignore the variability of substitution patterns among protein sites. Next, in order to improve the realism of the modeling of protein evolution, a series of structurally constrained substitution models were presented, but still they usually ignore constraints on the protein activity. Here, we present a substitution model of protein evolution with selection on both protein structure and enzymatic activity, and that can be applied to phylogenetics. In particular, the model considers the binding affinity of the enzyme–substrate complex as well as structural constraints that include the flexibility of structural flaps, hydrogen bonds, amino acids backbone radius of gyration, and solvent-accessible surface area that are quantified through molecular dynamics simulations. We applied the model to the HIV-1 protease and evaluated it by phylogenetic likelihood in comparison with the best-fitting empirical substitution model and a structurally constrained substitution model that ignores the enzymatic activity. We found that accounting for selection on the protein activity improves the fitting of the modeled functional regions with the real observations, especially in data with high molecular identity, which recommends considering constraints on the protein activity in the development of substitution models of evolution.

Ferreiro, David↗

Magnetic anisotropy and two-dimensional short-range chemical ordering in Ba 1−𝑥 ⁢Na 𝑥 ⁢Fe 2 ⁢As 2

A true understanding of the properties of pnictide superconductors requires the development of high-quality materials and performing measurements designed to unravel their intrinsic properties and short-range nematic correlations which are often obscured by extrinsic effects such as poor crystallinity, inhomogeneity, domain formation, and twinning. Here, in this paper, we report the systematic growth of high-quality Na-substituted BaFe 2 As 2 single crystals and their characterization using pulsed magnetic fields x-ray diffraction and x-ray diffuse scattering. Analysis of the properties and compositions of the highest-quality crystals shows that their actual Na stoichiometry is about 50-60% of the nominal content and that the targeted production of crystals with specific compositions is accessible. We derived a reliable equation to estimate the Na stoichiometry based on the measured superconducting T c of these materials. Attempting to force spin reorientation and induce tetragonality, orthorhombic Ba 1-x Na x Fe 2 As 2 single crystals subjected to out-of-plane magnetic fields up to 31.4T are found to exhibit strong in-plane magnetic anisotropy demonstrated by the insufficiency of such high fields in manipulating the relative population of their twinned domains or in suppressing the orthorhombic order. Broad x-ray diffuse-intensity rods observed at temperatures between 30 and 300 K uncover short-range structural correlations. Local structure modeling together with 3D-Δ pair-distribution function mapping of real-space interatomic vectors show that the diffuse scattering arises from in-plane short-range chemical correlations of the Ba and Na atoms coupled with short-range atomic displacements within the same plane due to an effective size difference between the two atomic species.

36 MATERIALS SCIENCE↗

Nonresonant two-photon x-ray absorption in Cu

We present a real-space Green's function theory and calculations of two-photon x-ray absorption (TPA). Our focus is on nonresonant 𝐾-shell TPA in metallic Cu, which has been observed experimentally at intense x-ray free electron laser (XFEL) sources. The theory is based on an independent particle Green's function treatment of the Kramers-Heisenberg equation and an approximation for the sum over nonresonant intermediate states in terms of a static quadrupole transition operator. XFEL effects are modeled by a partially depleted 𝑑 band. This approach is shown to give results for 𝐾-shell TPA in quantitative agreement with XFEL experiment and with a Bethe-Salpeter equation approach. Furthermore, we also briefly discuss many-body corrections and TPA sum rules.

Approximation methods for many-body systems↗

Complexity in the medium-range order of gallium as a polyvalent liquid metal

Simplicity in chemical composition does not always translate into simplicity in the structures and dynamics of liquids and solids. Some elementary liquid metals, such as gallium, show unusual behaviors in thermodynamic and transport properties as a result of their complex atomic structure and dynamics. Here, in this work, we study the real-space atomic correlation function of liquid gallium by neutron scattering. In the pair-distribution function, there exist two kinds of medium-range order (MRO), characterized by oscillations beyond the first nearest neighbors. On the other hand, the first neighbor shell shows only one kind of bond. The two types of MRO are strongly overlapping in space and fluctuating in time. We propose that they are the basis for anomalous behavior of liquid gallium. This view challenges the current view that liquid gallium consists of fluctuating metallic and insulating domains. These findings shed light on the interpretation of similar microscopic anomalies observed in other semimetallic liquids.

Hua, Chengyun [Oak Ridge National Laboratory (ORNL↗

Advanced calculations of X-ray spectroscopies with FEFF10 and Corvus

The real-space Green's function code FEFF has been extensively developed and used for calculations of X-ray and related spectra, including X-ray absorption (XAS), X-ray emission (XES), inelastic X-ray scattering, and electron energy-loss spectra. The code is particularly useful for the analysis and interpretation of the XAS fine-structure (EXAFS) and the near-edge structure (XANES) in materials throughout the periodic table. Nevertheless, many applications, such as non-equilibrium systems, and the analysis of ultra-fast pump–probe experiments, require extensions of the code including finite-temperature and auxiliary calculations of structure and vibrational properties. To enable these extensions, we have developed in tandem a new version FEFF10 and new FEFF -based workflows for the Corvus workflow manager, which allow users to easily augment the capabilities of FEFF10 via auxiliary codes. This coupling facilitates simplified input and automated calculations of spectra based on advanced theoretical techniques. The approach is illustrated with examples of high-temperature behavior, vibrational properties, many-body excitations in XAS, super-heavy materials, and fits of calculated spectra to experiment.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

NSTX-U Machine Core Vacuum Seals Upgrade Design

The vacuum in the National Spherical Torus Experiment Upgrade (NSTX-U) is in the range of 2.66x10⁻⁶ Pa (2x 10⁻⁸ torr). To enhance vacuum seals and lower gas permeation in the NSTX-U and therefore ensuring operation safety and quality, the machine core vacuum seal design has been upgraded using double elastomeric seals and pumped interspaces (guard channels). In NSTX-U machine core, there are six major vacuum seals, including upper and lower vacuum vessel main flanges, upper and lower bellows flanges, and two in the ceramic isolation ring assembly that are mounted to the upper vacuum vessel main flange. The elastomeric seals are commercially available and customized fluorocarbon (Viton) O-rings. To ensure appropriate O-ring compression ratios for the vacuum seal, the O-ring grooves are customized with appropriate tolerances considering specific situations for each seal. In this upgrade, the vacuum in each interspace is designed to reach 13.33 Pa (0.1 torr), thus the overall pressure difference crossing each double O-ring seal is expected to be reduced by at least three orders of magnitude, and accordingly the overall rates of leakage and permeation will be lowered by three orders of magnitude. The corresponding pump-down times for each seal, at room temperature, are estimated at about 60 s. Additionally, the vacuum pumped interspaces will be able to function as a real-time leak monitor.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Center for Gas Separations (CGS)

The total energy consumption in the U.S. has been rising steadily for decades, and it currently amounts to ~98,000 TBtu/yr, with approximately 30% of this total attributable to the industrial sector. Reasonable estimates indicate that 45–55% of total industry energy consumption derives from chemical separations, and for example, over 120 TBtu/yr alone is used in carrying out olefin/paraffin separations via energy-intensive cryogenic distillation. Therefore, the pursuit of new, even radically different approaches to some of the most energy-intensive industrial separations processes is an imperative scientific pursuit for reducing energy consumption toward a more sustainable future. Adsorbent and membrane-based separations can require a fraction of the energy needed for distillation methods, and as such are considered promising solutions for balancing increasing energy demand in the U.S. with the need for a massive reduction in energy consumption. Although considerable research effort has been devoted to the design of materials capable of carrying out various gas separations, usually operating through size-selective, chemisorptive, or physisorptive mechanisms, it remains a great challenge to design materials that function adequately for real-world applications. Indeed, the chemical and physical differences between molecules in gas mixtures of interest are often small, and therefore it is necessary, through the use of nanoscience and synthetic chemistry, to engineer unprecedented molecular-level control in adsorbate–adsorbent interactions. The overarching mission of the Center for Gas Separations (CGS) was to discover fundamental innovations that have the potential to dramatically reduce the energy associated with critical gas separations. In particular, the CGS developed novel synthetic routes, guided by molecular chemistry principles, as well as advanced characterization and computational methods, that have enabled the discovery of new materials and membranes tailor-made to exhibit exceptional performance for a range of gas separations processes, as required in the clean use of fossil fuels and in reducing CO 2 emissions from industry. A challenge of this magnitude required the collaboration and synergy of a large team of researchers with expertise in materials synthesis, characterization, and computations. During the 11-year project period, the CGS created a range of new materials within the family of highly-tunable, porous solids known as metal–organic frameworks (MOFs). These new frameworks demonstrate novel mechanisms for key industrial gas separations, including revolutionary new cooperative adsorption processes that enable low-energy CO 2 and CO capture, and are capable of efficiently separating olefins from paraffins, O 2 from air, and the shape-selective separation of alkane isomers. In addition, the CGS developed new strategies for incorporating these materials into composite membranes toward highly efficient and selective membrane-based separations. As a testament to the success of the CGS, two start-up companies, Mosaic Materials,4 Inc. and Flux Technology, Inc., grew out of these research efforts, and these companies are seeking to commercialize MOF and composite membranes materials for key separations in industry, including large-scale CO 2 capture and hydrocarbon separations, respectively. Another company, framergy, Inc., licensed IP resulting from CGS research toward the commercialization of adsorbents for various energy-relevant applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Understanding the Behavioral Aspects of Rate Design

Consumer demand for electricity has often been thought of as homogenous and inelastic. However, consumers may have preferences for their electricity consumption that they have been unable to realize due to the structures of electricity rates, and historic methods of regulation. As ratemaking becomes more dynamic, consumers will have a newfound ability to realize these preferences. This paper conducts a review of this issue through the lenses of utility regulation, neoclassical economics, and behavioral economics. It surveys what aspects of consumer preferences and behavior have been well established for the electricity sector and identifies gaps that could be filled by future research. This analysis has implications for stakeholders looking to understand how households will function in transactive and real time pricing environments.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Instanton Effects in Euclidean vacuum, Real Time Production, and in the Light-front Wave Functions

Nontrivial topological structures of non-Abelian gauge fields were discovered in the 1970s. Instanton solutions, describing vacuum tunneling through topological barriers, have fermionic zero modes which are at the origin of ‘t Hooft effective Lagrangian. In the 1980s, instanton ensembles have been used to explain chiral symmetry breaking. In the 1990s, a large set of numerical simulations were performed deriving Euclidean correlation functions. The special role of scalar diquarks in nucleons and color superconductivity in dense quark matter has been elucidated. In these lectures, we discuss further developments of physics related to gauge topology. We show that the instanton–anti-instanton “streamline” configurations describe “sphaleron transitions” in high-energy collisions, which result in production of hadronic clusters with nontrivial topological/chiral charges. (They are not yet observed, but discussions of dedicated experiments at the LHC and RHIC are ongoing.) Another new direction is instanton effects in hadronic spectroscopy, both in the rest frame and on the light front. We will discuss their role in central and spin-dependent potentials, form factors and antiquark nuclear “sea”. Finally, we summarize the advances in the semiclassical theory of deconfinement, and chiral phase transitions at finite temperature, in QCD, and in some of its “deformed” versions.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Implementation of real‐time TDDFT for periodic systems in the open‐source PySCF software package

Abstract We present a new implementation of real‐time time‐dependent density functional theory (RT‐TDDFT) for calculating excited‐state dynamics of periodic systems in the open‐source Python‐based PySCF software package. Our implementation uses Gaussian basis functions in a velocity gauge formalism and can be applied to periodic surfaces, condensed‐phase, and molecular systems. As representative benchmark applications, we present optical absorption calculations of various molecular and bulk systems and a real‐time simulation of field‐induced dynamics of a (ZnO) 4 molecular cluster on a periodic graphene sheet. We present representative calculations on optical response of solids to infinitesimal external fields as well as real‐time charge‐transfer dynamics induced by strong pulsed laser fields. Due to the widespread use of the Python language, our RT‐TDDFT implementation can be easily modified and provides a new capability in the PySCF code for real‐time excited‐state calculations of chemical and material systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Real-Space Local Dynamics of Molten Inorganic Salts Using Van Hove Correlation Function

Molten inorganic salts are attracting resurgent attention because of their unique physicochemical properties, making them promising media for next-generation concentrating solar power systems and molten salt reactors. The dynamics of these highly disordered ionic media is largely studied by theoretical simulations, while the robust experimental techniques capable of observing local dynamics are not well-developed. To provide fundamental insights into the atomic-scale transport properties of molten salts, we report the real-space dynamics of molten magnesium chloride at high temperatures employing the Van Hove correlation function obtained by inelastic neutron scattering. Overall, our results directly depict the distance-dependent dynamics of a molten salt on the picosecond time scale. This study demonstrates the capability of the developed approach to describe the locally correlated- and self-dynamics in molten salts, significantly improving our understanding of the interplay between microscopic structural parameters and their dynamics that ultimately control physical properties of condensed matter in extreme environments.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Exploring Physics of Ferroelectric Domain Walls in Real Time: Deep Learning Enabled Scanning Probe Microscopy

The functionality of ferroelastic domain walls in ferroelectric materials is explored in real-time via the in situ implementation of computer vision algorithms in scanning probe microscopy (SPM) experiment. The robust deep convolutional neural network (DCNN) is implemented based on a deep residual learning framework (Res) and holistically nested edge detection (Hed), and ensembled to minimize the out-of-distribution drift effects. The DCNN is implemented for real-time operations on SPM, converting the data stream into the semantically segmented image of domain walls and the corresponding uncertainty. Further the pre-defined experimental workflows perform piezoresponse spectroscopy measurement on thus discovered domain walls, and alternating high- and low-polarization dynamic (out-of-plane) ferroelastic domain walls in a PbTiO 3 (PTO) thin film and high polarization dynamic (out-of-plane) at short ferroelastic walls (compared with long ferroelastic walls) in a lead zirconate titanate (PZT) thin film is reported. This work establishes the framework for real-time DCNN analysis of data streams in scanning probe and other microscopies and highlights the role of out-of-distribution effects and strategies to ameliorate them in real time analytics.

36 MATERIALS SCIENCE↗

Atomic Fingerprinting of Heteroatoms Using Noncontact Atomic Force Microscopy

We report immense strides have been made in increasing the resolution of scanning probe microscopy. Noncontact atomic force microscopy (n-AFM) now offers one the ability to characterize and visualize single molecules with subatomic resolution. Specifically, nc-AFM with a carbon monoxide (CO) functionalized tip has the ability to discriminate functional groups (–C≡C–, –CH 2 , –C$=$O, …), although discriminating atomic species often remains as an ongoing challenge. Here, real-space pseudopotentials constructed within density functional theory are employed to accurately simulate nc-AFM images of molecules containing heteroatoms (S, I, and N) within dibenzothiophene (DBT), 2-iodotriphenylene (ITP), acridine (ACR) and ferrous phthalocyanine (FePc). It is found that S and I atoms can be easily identified from C based on their unique features. For N atoms, a use of tip functionalization is proposed to effectively discriminate them from C atoms.

36 MATERIALS SCIENCE↗

Real-time coupled-cluster approach for the cumulant Green's function

Green’s function methods within many-body perturbation theory provide a general framework for treating electronic correlations in excited states. Here we investigate the cumulant form of the one-electron Green’s function based on the coupled-cluster equation of motion approach in an extension of our previous study. The approach yields a non-perturbative expression for the cumulant in terms of the solution to a set of coupled first order, non-linear differential equations. The method thereby adds non-linear corrections to traditional cumulant methods linear in the self energy. The approach is applied to the core-hole Green’s function and illustrated for a number of small molecular systems. For these systems we find that the non-linear contributions lead to significant improvements both for quasiparticle properties such as core-level binding energies, as well as the satellites corresponding to inelastic losses observed in photoemission spectra.

Vila, Fernando D.↗

Coordinate-based simulation of pair distance distribution functions for small and large molecular assemblies: implementation and applications

X-ray scattering has become a major tool in the structural characterization of nanoscale materials. Thanks to the widely available experimental and computational atomic models, coordinate-based X-ray scattering simulation has played a crucial role in data interpretation in the past two decades. However, simulation of real-space pair distance distribution functions (PDDFs) from small- and wide-angle X-ray scattering, SAXS/WAXS, has been relatively less exploited. This study presents a comparison of PDDF simulation methods, which are applied to molecular structures that range in size from β-cyclodextrin [1 kDa molecular weight (MW), 66 non-hydrogen atoms] to the satellite tobacco mosaic virus capsid (1.1 MDa MW, 81 960 non-hydrogen atoms). The results demonstrate the power of interpretation of experimental SAXS/WAXS from the real-space view, particularly by providing a more intuitive method for understanding of partial structure contributions. Furthermore, the computational efficiency of PDDF simulation algorithms makes them attractive as approaches for the analysis of large nanoscale materials and biological assemblies. The simulation methods demonstrated in this article have been implemented in stand-alone software, SolX 3.0 , which is available to download from https://12idb.xray.aps.anl.gov/solx.html.

Zuo, Xiaobing (ORCID:0000000201344804)↗