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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 937 records · Page 52
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Deciphering the Solvent Effect for the Solvation Structure of Ca 2+ in Polar Molecular Liquids

Although the crystal structures for many inorganic compounds are readily available, researchers are still working hard to understand the relations between the structures and chemical properties of solutions because most of the chemical reactions take place in solutions. A huge amount of effort has been put toward modeling the ion solvation structure from the perspectives of both experiments and theories. In this study, the solvation structures of Ca 2+ ions in aqueous and alcoholic solutions at different concentrations were carefully evaluated by Ca K-edge X-ray absorption near-edge structure (XANES) and extended X-ray absorption fine structure (EXAFS) analyses. Further, density functional theory (DFT) calculations were also performed to correlate the results with the experimental data and then further extended to other similar systems. It was found that the number of coordinating solvent molecules decreases with increasing Ca 2+ concentration and increasing solvent molecule sizes. From the EXAFS data, it was observed that the first solvation shell of Ca 2+ splits into two Ca-O distances in a methanol solution and the counter ion Cl - might also be within the first shell at high concentrations. For the first time, the effects of solvents with different polarities and sizes on the ion solvation environment were systematically evaluated.

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

Structural, Electrical, and Electromechanical Properties of Inverse Hybrid Perovskites from First-Principles: The Case of (CH 3 NH 3 ) 3 OI

Inverse-hybrid perovskites (IHPs) with large polarization have recently been predicted from first-principles computations. Here, we use one representative from the IHP class of materials, (CH 3 NH 3 ) 3 OI (MA3OI), to propose a route to the first-principles prediction of structural and electrical properties, such as polarization, polarization reversibility, and the associated coercive field for hybrid organic–inorganic perovskites. The route relies on the construction of the polarization reversal path that models experimental measurements. Such a path was found to play an important role in the ground-state search as well as in the identification of competing structural variations. The latter is believed to be the origin of the structural disorder that is characteristic of hybrid organic–inorganic perovskites. The application of such an approach to MA3OI leads to the prediction of several structural variations that are expected to result in a structurally disordered phase above 766 K and of the polar ground state with a polarization of 25.3 μC/cm 2 that is reversible with the application of an electric field. The upper estimate for the coercive field associated with homogeneous polarization reversal is 6.9 GV/m. The piezoelectric constants of MA3OI are predicted to be an order of magnitude smaller in comparison with a prototypical inorganic ferroelectric PbTiO 3 ; however, the low symmetry of the MA3OI structure yields finite values for all components of the piezoelectric tensor. The polarization in MA3OI is tunable by the epitaxial strain (11.5% change under 5% epitaxial strain), although less so as compared with PbTiO 3 .

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

Electronic Structure of Excitons in Hematite Fe 2 O 3

We present a computational study of the electronic structure of excitons in hematite Fe 2 O 3 using density functional theory (DFT) and time-dependent DFT theory. Excitons resulting from solar light absorption are precursors to photogenerated charge carriers, which are the active species in solar-to-fuel redox conversions. Upon vertical excitation, the lowest energy exciton is found to have a multideterminantal wave function, describing an electron excited from O 2p states to Fe 3d states of the nearest basal plane, possibly supporting a recent XUV-derived exciton structure with a radius of a single Fe–O bond. Subsequently, the exciton self-traps into stable electron–hole pair structures whose wave functions are well-approximated by single excitations conveniently labeled “HOMO–LUMO”. Self-trapping yields electron–hole pair structures whereby the electron state (electron polaron-like) is separated from the hole state (hole polaron-like) by 3, 5, 7, 9, ... basal planes in structures referred to as Exc-3, Exc-5, Exc-7, Exc-9, ... The natural transition orbitals (electron–hole states) exhibit a strong “localized” character. The hole state is best described as a (FeO 6 ) + octahedral moiety carrying ~0.65 h + charge, and overall ~70% of the hole is assigned to O 2p atomic states, mostly on the four (4) equatorial O atoms of the moiety. The electron state is best described as a (FeFe) – moiety carrying ~0.80 e – charge in Fe 3d atomic states. The lattice distortions around the hole site exhibit Fe–O bond shortening due to the removal of electron density from an orbital state with O–Fe–O antibonding character. The electron site shows Fe–Fe distance shortening due to excess electron density added to an orbital state with in-phase Fe–Fe interactions. Furthermore, these excitonic structures with increasing electron–hole separation can be viewed as the onset of exciton separation into isolated electrons and hole polarons.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Coverage-Dependent Adsorption of Hydrogen on Fe(100): Determining Catalytically Relevant Surface Structures via Lattice Gas Models

Hydrogen adatoms are a critical surface species for several reactions catalyzed by Fe surfaces such as Fischer–Tropsch synthesis, ammonia synthesis, and the hydrodeoxygenation of biomass-derived oxygenates. Parameterizing the energetics for H/Fe in terms of both coverage and configuration space can significantly aid in the development of multiscale models as well as provide atomic level insight into the dominant surface structures present under realistic reaction conditions. Here, we construct a lattice gas model for H/Fe(100), where the lateral interactions are determined from first-principles using density functional theory. Using 950 symmetrically unique H/Fe(100) configurations, we generate a cluster expansion with a predictive accuracy in terms of surface energy of 3.8 meV/site over a coverage range from 0 to 3 monolayers. Ten electronic ground state structures are identified from this thorough scan (including the structures at 0 and 3 monolayers), which were subsequently used to generate ab initio phase diagrams under a range of temperatures and pressures. Under reaction conditions typical of Fischer–Tropsch synthesis, ammonia synthesis, and biomass oxygenate hydrodeoxygenation, we find that the 1.0 monolayer structure is dominant. Furthermore, examination of the total H–H lateral interactions for the H/Fe(100) electronic ground state structures shows that H/Fe(100) can be accurately modeled via a mean-field ideal lattice gas model for coverages less than 1.0 monolayers. Altogether, this work enables the incorporation of H–H lateral interactions on Fe(100) into multiscale models, via either mean-field or site-dependent techniques, and provides atomic insight into the catalytically relevant H/Fe(100) structures for a range of heterogeneous reactions.

09 BIOMASS FUELS↗
DOE OSTI2021

Disconnection-Mediated Transition in Segregation Structures at Twin Boundaries

Twin boundaries play an important role in the thermodynamics, stability, and mechanical properties of nanocrystalline metals. Understanding their structure and chemistry at the atomic scale is key to guide strategies for fabricating nanocrystalline materials with improved properties. In this work, we report an unusual segregation phenomenon at gold-doped platinum twin boundaries, which is arbitrated by the presence of disconnections, a type of interfacial line defect. By using atomistic simulations, we show that disconnections containing a stacking fault can induce an unexpected transition in the interfacial-segregation structure at the atomic scale, from a bilayer, alternating-segregation structure to a trilayer, segregation-only structure. This behavior is found for faulted disconnections of varying step heights and dislocation characters. Supported by a structural analysis and the classical Langmuir–McLean segregation model, we reveal that this phenomenon is driven by a structurally induced drop of the local pressure across the faulted disconnection accompanied by an increase in the segregation volume.

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

Prediction and Experimental Verification of Electrolyte Solvation Structure from an OMol25-Trained Interatomic Potential

A molecular-level understanding of electrolyte solvation structure and ion–ion correlations is critical to developing next-generation battery chemistries. Atomistic simulation capabilities with sufficient accuracy, speed, and transferability to deliver reliable structural insights while avoiding arduous system-specific reparameterization are thus highly desirable. Machine learning interatomic potentials (MLIPs) trained on large, chemically diverse data sets are revolutionizing computational chemistry, enabling molecular dynamics simulations of battery electrolytes with near-DFT accuracy over 10,000× faster than DFT. While previous MLIP training data sets with suitable elemental coverage for electrolytes have been based on inorganic materials, the Open Molecules 2025 (OMol25) data set provides large-scale molecular DFT MLIP training data with broad elemental coverage and specifically samples tens of millions of electrolyte configurations. Here, we integrate computational modeling with experimental validation to systematically assess the ability of large-scale MLIPs pretrained on materials data or on OMol25 to accurately resolve nanoscale structural organization and ion-solvation characteristics in Na-ion battery electrolytes across diverse physicochemical conditions and compositional regimes. We find that the OMol25-trained Universal Model of Atoms (UMA-OMol) predicts experimentally measured densities and X-ray structure factors in substantially better agreement compared to state-of-the-art models trained only on inorganic materials data. Using UMA-OMol, we further analyze systematic trends in solvation structure as a function of cation identity, anion chemistry, salt concentration, and solvent topology. We observe that increasing system temperature amplifies the heterogeneity within the solvation environment, perturbing cation–solvent interactions and promoting the formation of contact ion pairs (CIPs). Moreover, subtle variations in the solvent topology of glyme-based electrolytes cause pronounced changes in ion correlations and solvation structure. The experimental agreement and microscopic insights shown here position OMol25-trained MLIPs as a practical route to predictive, high-throughput electrolyte simulations beyond the limits of classical force fields and direct DFT molecular dynamics, serving as a powerful tool for accelerating the design of next-generation Na-ion battery electrolytes and beyond.

MLIPs↗
DOE OSTI2025

Chemistry and Interfacial Structure Promoting Quasi-van der Waals Epitaxial Growth of WS 2 Nanosheets on Sapphire for Prospective Application in Field-Effect Transistors

How do chemical and structural modifications to the supporting crystal surface affect the subsequent van der Waals (vdW) or quasi(Q)-vdW epitaxial growth of 2D nanocrystals? Developing an atomic-scale picture of such an interfacial system is crucial for understanding its impact on the physical and chemical properties of the supported 2D materials. The elucidation of the interfacial structure and chemistry needed to promote the Q-vdW epitaxial growth of 2D tungsten disulfide (WS 2 ) nanocrystals contributes to the growth mechanism understanding, thus pushing forward the integration of such atomically thin semiconductors toward real field-effect transistor applications. In addition to an atomic-force microscopy top view, we showcase a combination of X-ray techniques for a top-to-bottom investigation of the complexities of the buried interface structures. Furthermore, this approach uses X-ray photoelectron spectroscopy, X-ray standing wave excited X-ray fluorescence, and crystal truncation rod scattering to produce a highly resolved chemical-state-specific 3D atomic map for the extended interface structure of WS 2 /α-Al 2 O 3 (001). Employing these detailed analysis methods, along with density functional theory to further refine the picoscale structure, we demonstrate how two different types of interface engineering during the pregrowth stage lead to significant differences in the chemical and structural modifications to the terminal surface of c-face sapphire, which in turn leads to substantial differences in the submonolayer growth of supported WS 2 2D nanocrystals in terms of lateral domain sizes, epitaxial registry, vdW gaps, and stability.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Thermally Induced Structural Transitions in Epoxy Thermoset Polymer Networks and Their Spectroscopic Responses

The polymer network structure of epoxy thermosets plays a significant role in its final material properties. However, the effects of mild thermal exposure on these network structures are poorly studied. In this work, wide-angle X-ray scattering was used to investigate the polymer network structure of two epoxy thermosets: homopolymerized bisphenol A (BPA) epoxy resin and BPA epoxy resin cured with a polyether amine hardener (BPA/T-403). Using density functional theory and wide-angle X-ray scattering, insights into the polymer network structure were obtained. Diffraction features were determined to originate from hardener-to-hardener molecular distance, perpendicular π–π stacking of aromatic p-phenylene rings, and the average carbon–carbon distance in the polymer. Thermal exposure was found to permanently alter these structural features for both thermosets, with an increase in the π–π stacking distance. Homopolymerized BPA had an additional decrease in the hardener-to-hardener distance. These structural alterations were found to be detectable using Fourier transform infrared spectroscopy and Raman spectroscopy, with changes in the hardener-to-hardener distance having the largest variations in the resulting spectra specifically at the aromatic and ether frequencies.

36 MATERIALS SCIENCE↗
DOE OSTI2020

In Situ Phosphatizing of Triphenylphosphine Encapsulated within Metal–Organic Frameworks to Design Atomic Co 1 –P 1 N 3 Interfacial Structure for Promoting Catalytic Performance

The engineering coordination environment offers great opportunity in performance tunability of isolated metal single-atom catalysts. For the most popular metal–N x (MN x ) structure, the replacement of N atoms by some other atoms with relatively weak electronegativity has been regarded as a promising strategy for optimizing the coordination environment of an active metal center and promoting its catalytic performance, which is still a challenge. Herein, we proposed a new synthetic strategy of an in situ phosphatizing of triphenylphosphine encapsulated within metal–organic frameworks for designing atomic Co 1 –P 1 N 3 interfacial structure, where a cobalt single atom is costabilized by one P atom and three N atoms (denoted as Co-SA/P-in situ). In the acidic media, the Co-SA/P-in situ catalyst with Co 1 –P 1 N 3 interfacial structure exhibits excellent activity and durability for the hydrogen evolution reaction (HER) with a low overpotential of 98 mV at 10 mA cm –2 and a small Tafel slope of 47 mV dec –1 , which are greatly superior to those of catalyst with Co 1 –N 4 interfacial structure. We discover that the bond-length-extended high-valence Co 1 –P 1 N 3 atomic interface structure plays a crucial role in boosting the HER performance, which is supported by in situ X-ray absorption fine structure (XAFS) measurements and density functional theory (DFT) calculation. With this work, we hope to promote the development of high performance metal single-atom catalysts.

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

High-Resolution XFEL Structure of the Soluble Methane Monooxygenase Hydroxylase Complex with its Regulatory Component at Ambient Temperature in Two Oxidation States

Soluble methane monooxygenase (sMMO) is a multicomponent metalloenzyme that catalyzes the conversion of methane to methanol at ambient temperature using a nonheme, oxygen-bridged dinuclear iron cluster in the active site. Structural changes in the hydroxylase component (sMMOH) containing the diiron cluster caused by complex formation with a regulatory component (MMOB) and by iron reduction are important for the regulation of O 2 activation and substrate hydroxylation. Structural studies of metalloenzymes using traditional synchrotron-based X-ray crystallography are often complicated by partial X-ray-induced photoreduction of the metal center, thereby obviating determination of the structure of the enzyme in pure oxidation states. Here, microcrystals of the sMMOH:MMOB complex from Methylosinus trichosporium OB3b were serially exposed to X-ray free electron laser (XFEL) pulses, where the ≤35 fs duration of exposure of an individual crystal yields diffraction data before photoreduction-induced structural changes can manifest. Merging diffraction patterns obtained from thousands of crystals generates radiation damage-free, 1.95 Å resolution crystal structures for the fully oxidized and fully reduced states of the sMMOH:MMOB complex for the first time. The results provide new insight into the manner by which the diiron cluster and the active site environment are reorganized by the regulatory protein component in order to enhance the steps of oxygen activation and methane oxidation. Furthermore, this study also emphasizes the value of XFEL and serial femtosecond crystallography (SFX) methods for investigating the structures of metalloenzymes with radiation sensitive metal active sites.

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

Tailoring Hierarchical Structure and Rare Earth Affinity of Compositionally Identical Polymers via Sequence Control

Macromolecule sequence, structure, and function are inherently intertwined. While well-established relationships exist in proteins, they are more challenging to define for synthetic polymer nanoparticles due to their molecular weight, sequence, and conformational dispersities. Furthermore, to explore the impact of sequence on nanoparticle structure, we synthesized a set of 16 compositionally identical, sequence-controlled polymers with distinct monomer patterning of dimethyl acrylamide and a bioinspired, structure-driving di(phenylalanine) acrylamide (FF). Sequence control was achieved through multiblock polymerizations, yielding unique ensembles of polymer sequences which were simulated by kinetic Monte Carlo simulations. Systematic analysis of the global (tertiary- and quaternary-like) structure in this amphiphilic copolymer series revealed the effect of multiple sequence descriptors: the number of domains, the hydropathy of terminal domains, and the patchiness (density) of FF within a domain, each of which impacted both chain collapse and the distribution of single- and multichain assemblies. Furthermore, both the conformational freedom of chain segments and local-scale, β-sheet-like interactions were sensitive to the patchiness of FF. To connect sequence, structure, and target function, we evaluated an additional series of nine sequence-controlled copolymers as sequestrants for rare earth elements (REEs) by incorporating a functional acrylic acid monomer into select polymer scaffolds. We identified key sequence variables that influence the binding affinity, capacity, and selectivity of the polymers for REEs. Collectively, these results highlight the potential of and boundaries of sequence control via multiblock polymerizations to drive primary sequence ensembles hierarchical structures, and ultimately the functionality of compositionally identical polymeric materials.

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

Structural Insights into the Mechanism of a Polyketide Synthase Thiocysteine Lyase Domain

Polyketide synthases (PKSs) are renowned for the structural diversity of the polyketide natural products they produce, but sulfur-containing functionalities are rarely installed by PKSs. We previously characterized thiocysteine lyase (SH) domains involved in the biosynthesis of the leinamycin (LNM) family of natural products, exemplified by LnmJ-SH and guangnanmycin (GnmT-SH). Here we report a detailed investigation into the PLP-dependent reaction catalyzed by the SH domains, guided by a 1.8 Å resolution crystal structure of GnmT-SH. A series of elaborate substrate mimics were synthesized to answer specific questions garnered from the crystal structure and from the biosynthetic logic of the LNM family of natural products. Here, through a combination of bioinformatics, molecular modeling, in vitro assays, and mutagenesis, we have developed a detailed model of acyl carrier protein (ACP)-tethered substrate-SH, and interdomain interactions, that contribute to the observed substrate specificity. Comparison of the GnmT-SH structure with archetypical PLP-dependent enzyme structures revealed how Nature, via evolution, has modified a common protein structural motif to accommodate an ACP-tethered substrate, which is significantly larger than any of those previously characterized. Overall, this study demonstrates how PLP-dependent chemistry can be incorporated into the context of PKS assembly lines and sets the stage for engineering PKSs to produce sulfur-containing polyketides.

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

Role of backbone strain in de novo design of complex α/β protein structures

Abstract We previously elucidated principles for designing ideal proteins with completely consistent local and non-local interactions which have enabled the design of a wide range of new αβ-proteins with four or fewer β-strands. The principles relate local backbone structures to supersecondary-structure packing arrangements of α-helices and β-strands. Here, we test the generality of the principles by employing them to design larger proteins with five- and six- stranded β-sheets flanked by α-helices. The initial designs were monomeric in solution with high thermal stability, and the nuclear magnetic resonance (NMR) structure of one was close to the design model, but for two others the order of strands in the β-sheet was swapped. Investigation into the origins of this strand swapping suggested that the global structures of the design models were more strained than the NMR structures. We incorporated explicit consideration of global backbone strain into the design methodology, and succeeded in designing proteins with the intended unswapped strand arrangements. These results illustrate the value of experimental structure determination in guiding improvement of de novo design, and the importance of consistency between local, supersecondary, and global tertiary interactions in determining protein topology. The augmented set of principles should inform the design of larger functional proteins.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Cryo-EM structures of Uba7 reveal the molecular basis for ISG15 activation and E1-E2 thioester transfer

ISG15 plays a crucial role in the innate immune response and has been well-studied due to its antiviral activity and regulation of signal transduction, apoptosis, and autophagy. ISG15 is a ubiquitin-like protein that is activated by an E1 enzyme (Uba7) and transferred to a cognate E2 enzyme (UBE2L6) to form a UBE2L6-ISG15 intermediate that functions with E3 ligases that catalyze conjugation of ISG15 to target proteins. Despite its biological importance, the molecular basis by which Uba7 catalyzes ISG15 activation and transfer to UBE2L6 is unknown as there is no available structure of Uba7. Here, we present cryo-EM structures of human Uba7 in complex with UBE2L6, ISG15 adenylate, and ISG15 thioester intermediate that are poised for catalysis of Uba7-UBE2L6-ISG15 thioester transfer. Our structures reveal a unique overall architecture of the complex compared to structures from the ubiquitin conjugation pathway, particularly with respect to the location of ISG15 thioester intermediate. Our structures also illuminate the molecular basis for Uba7 activities and for its exquisite specificity for ISG15 and UBE2L6. Altogether, our structural, biochemical, and human cell-based data provide significant insights into the functions of Uba7, UBE2L6, and ISG15 in cells.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Structural characterization of a GNAT family acetyltransferase from Elizabethkingia anophelis bound to acetyl-CoA reveals a new dimeric interface

General control non-repressible 5 (GCN5)-related N-acetyltransferases (GNATs) catalyse the acetylation of a diverse range of substrates, thereby orchestrating a variety of biological processes within prokaryotes and eukaryotes. GNAT enzymes can catalyze the transfer of an acetyl group from acetyl coenzyme A to substrates such as aminoglycoside antibiotics, amino acids, polyamines, peptides, vitamins, catecholamines, and large macromolecules including proteins. Although GNATs generally exhibit low to moderate sequence identity, they share a conserved catalytic fold and conserved structural motifs. In this current study we characterize the high-resolution X-ray crystallographic structure of a GNAT enzyme bound with acetyl-CoA from Elizabethkingia anophelis , an important multi-drug resistant bacterium. The tertiary structure is comprised of six α-helices and nine β-strands, and is similar with other GNATs. We identify a new and uncharacterized GNAT dimer interface, which is conserved in at least two other unpublished GNAT structures. This suggests that GNAT enzymes can form at least five different types of dimers, in addition to a range of other oligomers including trimer, tetramer, hexamer, and dodecamer assemblies. The high-resolution structure presented in this study is suitable for future in-silico docking and structure–activity relationship studies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

A novel hardmask-to-substrate pattern transfer method for creating 3D, multi-level, hierarchical, high aspect-ratio structures for applications in microfluidics and cooling technologies

Abstract This letter solves a major hurdle that mars photolithography-based fabrication of micro-mesoscale structures in silicon. Conventional photolithography is usually performed on smooth, flat wafer surfaces to lay a 2D design and subsequently etch it to create single-level features. It is, however, unable to process non-flat surfaces or already etched wafers and create more than one level in the structure. In this study, we have described a novel cleanroom-based process flow that allows for easy creation of such multi-level, hierarchical 3D structures in a substrate. This is achieved by introducing an ultra-thin sacrificial silicon dioxide hardmask layer on the substrate which is first 3D patterned via multiple rounds of lithography. This 3D pattern is then scaled vertically by a factor of 200–300 and transferred to the substrate underneath via a single shot deep etching step. The proposed method is also easily characterizable—using features of different topographies and dimensions, the etch rates and selectivities were quantified; this characterization information was later used while fabricating specific target structures. Furthermore, this study comprehensively compares the novel pattern transfer technique to already existing methods of creating multi-level structures, like grayscale lithography and chip stacking. The proposed process was found to be cheaper, faster, and easier to standardize compared to other methods—this made the overall process more reliable and repeatable. We hope it will encourage more research into hybrid structures that hold the key to dramatic performance improvements in several micro-mesoscale devices.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2024

Multi-omics analysis reveals the dynamic interplay between Vero host chromatin structure and function during vaccinia virus infection

The genome folds into complex configurations and structures thought to profoundly impact its function. The intricacies of this dynamic structure-function relationship are not well understood particularly in the context of viral infection. To unravel this interplay, here we provide a comprehensive investigation of simultaneous host chromatin structural (via Hi-C and ATAC-seq) and functional changes (via RNA-seq) in response to vaccinia virus infection. Over time, infection significantly impacts global and local chromatin structure by increasing long-range intra-chromosomal interactions and B compartmentalization and by decreasing chromatin accessibility and inter-chromosomal interactions. Local accessibility changes are independent of broad-scale chromatin compartment exchange (~12% of the genome), underscoring potential independent mechanisms for global and local chromatin reorganization. While infection structurally condenses the host genome, there is nearly equal bidirectional differential gene expression. Despite global weakening of intra-TAD interactions, functional changes including downregulated immunity genes are associated with alterations in local accessibility and loop domain restructuring. Therefore, chromatin accessibility and local structure profiling provide impactful predictions for host responses and may improve development of efficacious anti-viral counter measures including the optimization of vaccine design.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Determination of excited state molecular structures from time-resolved gas-phase X-ray scattering

We present a comprehensive investigation of a recently introduced method to determine transient structures of molecules in excited electronic states with sub-ångstrom resolution from time-resolved gas-phase scattering signals. The method, which is examined using time-resolved X-ray scattering data measured on the molecule N-methylmorpholine (NMM) at the Linac Coherent Light Source (LCLS), compares the experimentally measured scattering patterns against the simulated patterns corresponding to a large pool of molecular structures to determine the full set of structural parameters. In addition, we examine the influence of vibrational state distributions and find the effect negligible within the current experimental detection limits, despite that the molecules have a comparatively high internal vibrational energy. Here, the excited state structures determined using three structure pools generated using three different computational methods are in good agreement, demonstrating that the procedure is largely independent of the computational chemistry method employed as long as the pool is sufficiently expansive in the vicinity of the sought structure and dense enough to yield good matches to the experimental patterns.

74 ATOMIC AND MOLECULAR PHYSICS↗