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DOE OSTI2023

Natural Abundance Isotope Ratio Measurements of Organic Molecules Using 21 T FTICR MS

Subtle variations in stable isotope ratios at natural abundance are challenging to measure but can yield critical insights into biological, physical, and geochemical processes. Well established methods, particularly multi-collector, gas-source or plasma isotope ratio mass spectrometry (IRMS) are the gold standard for stable isotope measurement but inherent limitations in these approaches make them ill-suited to determining site-specific and multiply substituted isotopic abundances of all but a few compounds, or to characterizing mixtures or larger intact molecules. Additionally, Fourier transform mass spectrometry (FTMS), namely Orbitrap mass spectrometry, has recently demonstrated the ability to measure natural abundance isotope ratios with chemically informative accuracy and precision. Here, we report the first use of Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS) for the accurate (<1‰) and precise (<1‰ standard error) simultaneous determination of $δ$ 13 C and $δ$ 15 N in caffeine isotopologues and provide a discussion of the critical instrumental parameters necessary to make such measurements. Finally, we report the ability to make these measurements with online liquid chromatography, expanding the ability of this technique to explore mixtures in the future.

07 ISOTOPE AND RADIATION SOURCES↗

DOE OSTI2020

Development of Multiplexed Immuno-N-Terminomics to Reveal the Landscape of Proteolytic Processing in Early Embryogenesis of Drosophila melanogaster

Protein expression levels are regulated through both translation and degradation mechanisms. Levels of degradation intermediates, i.e., partially degraded proteins, cannot be distinguished from those of intact proteins by global proteomics analysis, which quantify total protein abundance levels. This study aimed to develop a tool for assessing the aspects of degradation regulation via proteolytic processing through a new multiplexed N-terminomics method involving selective isobaric labeling of protein N-termini and immunoaffinity capture of the labeled N-terminal peptides. Our method allows for not only identification or proteolytic cleavage sites, but also highly multiplexed quantification of proteolytic processing. In this paper, we profiled a number of potential cleavage sites by signal peptidase and provided experimental confirmation of predicted cleavage sites of signal peptide. Furthermore, the present method uniquely represents the landscape of proteomic proteolytic processing rate during early embryogenesis in Drosophila melanogaster, revealing the underlying mechanism of stringent decay regulation of zygotically expressed proteins during early stages of embryogenesis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Identifying Order and Disorder in Double Four-Membered Rings via Raman Spectroscopy during Crystallization of LTA Zeolite

Fluoride (F – ) has been essential for the synthesis of low-defect siliceous zeolites. It has been hypothesized that F – balances the positive charges from organic structure-directing agents (OSDAs) and stabilizes key building units during zeolite crystallization such as the double four-membered ring (D4R). However, due to the lack of characterization techniques for investigating medium-range structures, including rings and cages formed during zeolite crystallization, the roles of F – in stabilizing building units and maintaining local charge balance during zeolite assembly are not yet fully understood. Here, the crystallization of siliceous Linde type A (LTA) zeolite in the presence of F – was investigated using Raman spectroscopy and periodic density functional theory (DFT) calculations. We have discovered that the F – -filled double four-membered ring (F – /D4R) and the empty D4R exhibit rather distinct Raman features. Both the F – /D4R and empty D4R are formed in the LTA zeolite synthesized in the presence of F – using 1,2-dimethyl-3-(4-methylbenzyl) imidazolium as the OSDA. Observed Raman bands of the F – /D4R and empty D4R, along with predictive DFT calculations on LTA supercells, reveal an ordered distribution of these two D4R units in the final as-made LTA zeolite. The discovery of these distinct Raman signatures of F – /D4R and empty D4R units opens an interesting new window for studying defects in the D4R during zeolite formation. In particular, we have observed variation in Raman intensities of F – /D4R and empty D4R bands during LTA crystallization; periodic DFT calculations indicate that the observed Raman behavior is consistent with empty D4R units containing one or two Si vacancies surrounded by Q 3 Si—consistent also with solid-state nuclear magnetic resonance measurement. These defects appear to heal during further crystallization, leading to the formation of defect-free LTA zeolite crystals. Altogether, our results provide deeper understanding on the roles of F – in charge balancing and stabilizing intact D4R units during zeolite formation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Decoding the Gate Opening Mechanism of the Flexible Framework RPM3–Zn upon Hydrocarbon Inclusion

Although the existence of a gate-opening phenomenon in the flexible RPM3–Zn is well known, the actual mechanism remains a mystery. Here, we provide a full picture that unambiguously identifies and explains the gate-opening mechanism in RPM3–Zn upon exposure to various hydrocarbons—acetylene, ethylene, ethane, propane, and butane—by combining insights gained from calorimetry, adsorption isotherms, PXRD, in situ infrared spectroscopy, and ab initio simulations. We find that the key to gate opening in this framework is the stretching of a bond between an O and the Zn metal center (COO–Zn), acting as a “stabilizer”, which weakens the necessary support required for the structure to remain intact. Consequently, an increasing concentration of guest molecules exerts sufficient internal pressure to induce strong structural transformations in the unit cell shape and volume, thus triggering the gate opening. Here, our results are critical to understanding the gate opening in several other flexible frameworks and provide an opportunity to fine- tune hydrocarbon separation.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Tuning Optical and Electrical Properties of Vanadium Oxide with Topochemical Reduction and Substitutional Tin

Vanadium oxides are widely tunable materials, with many thermodynamically stable phases suitable for applications spanning catalysis to neuromorphic computing. The stability of vanadium in a range of oxidation states enables mixed-valence polymorphs of kinetically accessible metastable materials. Low-temperature synthetic routes to, and the properties of, these metastable materials are poorly understood and may unlock new optoelectronic and magnetic functionalities for expanded applications. In this work, we demonstrate topochemical reduction of α-V 2 O 5 to produce metastable vanadium oxide phases with tunable oxygen vacancies (>6%) and simultaneous substitutional tin incorporation (>3.5%). The chemistry is carried out at low temperature (65 °C) with solution-phase SnCl 2 , where Sn 2+ is oxidized to Sn 4+ as V 5+ sites are reduced to V 4+ during oxygen vacancy formation. Despite high oxygen vacancy and tin concentrations, the transformations are topochemical in that the symmetry of the parent crystal remains intact, although the unit cell expands. Band structure calculations show that these vacancies contribute electrons to the lattice, whereas substitutional tin contributes holes, yielding a compensation doping effect and control over the electronic properties. The SnCl 2 redox chemistry is effective on both solution-processed V 2 O 5 nanoparticle inks and mesoporous films cast from untreated inks, enabling versatile routes toward functional films with tunable optical and electronic properties. The electrical conductance rises concomitantly with the SnCl 2 concentration and treatment time, indicating a net increase in density of free electrons in the host lattice. This work provides a valuable demonstration of kinetic tailoring of electronic properties of vanadium–oxygen systems through top-down chemical manipulation from known thermodynamic phases.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Cell-Free Gene Expression: Methods and Applications

Cell-free gene expression (CFE) systems empower synthetic biologists to build biological molecules and processes outside of living intact cells. The foundational principle is that precise, complex biomolecular transformations can be conducted in purified enzyme or crude cell lysate systems. This concept circumvents mechanisms that have evolved to facilitate species survival, bypasses limitations on molecular transport across the cell wall, and provides a significant departure from traditional, cell-based processes that rely on microscopic cellular “reactors.” In addition, cell-free systems are inherently distributable through freeze-drying, which allows simple distribution before rehydration at the point-of-use. Furthermore, as cell-free systems are nonliving, they provide built-in safeguards for biocontainment without the constraints attendant on genetically modified organisms. These features have led to a significant increase in the development and use of CFE systems over the past two decades. Here, we discuss recent advances in CFE systems and highlight how they are transforming efforts to build cells, control genetic networks, and manufacture biobased products.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Distribution of Mn Oxidation States in Grassland Soils and Their Relationships with Soil Pores

Manganese (Mn) is known to be an active contributor to processing and cycling of soil organic carbon (C), yet the exact mechanisms behind its interactions with C are poorly understood. Plant diversity in terrestrial ecosystems drives feedback links between plant C inputs and soil pores, where the latter, in turn, impact the redox environment and Mn. This study examined associations between soil pores (>36 μm Ø) and Mn within intact soils from two grassland ecosystems, after their >6-year implementation in a replicated field experiment. In this work, we used μ-XRF imaging and XANES spectroscopy to explore spatial distribution patterns of Mn oxidation states, combined with X-ray computed microtomography and 2D zymography. A high plant diversity system (restored prairie) increased soil C and modified spatial distribution patterns of soil pores as compared to a single species system (monoculture switchgrass). In switchgrass, the abundance of oxidized and reduced Mn oxidation states varied with distance from pores consistently with anticipated O 2 diffusion, while in the soil from restored prairie, the spatial patterns suggested that biological activity played a greater role in influencing Mn distributions. Based on the findings, we propose a hypothesis that Mn transformations promote C gains in soils of high plant diversity grasslands.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

Molecular Design of Functional Polymers for Silica Scale Inhibition

Silica polymerization, which involves the condensation reaction of silicic acid, is a fundamental process with wide-ranging implications in biological systems, material synthesis, and scale formation. The formation of a silica-based scale poses significant technological challenges to energy-efficient operations in various industrial processes, including heat exchangers and water treatment membranes. Despite the common strategy of applying functional polymers for inhibiting silica polymerization, the underlying mechanisms of inhibition remain elusive. In this study, we synthesized a series of nitrogen-containing polymers as silica inhibitors and elucidated the role of their molecular structures in stabilizing silicic acids. Polymers with both charged amine and uncharged amide groups in their backbones exhibit superior inhibition performance, retaining up to 430 ppm of reactive silica intact for 8 h under neutral pH conditions. In contrast, monomers of these amine/amide-containing polymers as well as polymers containing only amine or amide functionalities present insignificant inhibition. Molecular dynamics simulations reveal strong binding between the deprotonated silicic acid and a polymer when the amine groups in the polymer are protonated. Notably, an extended chain conformation of the polymer is crucial to prevent proximity between the interacting monomeric silica species, thereby facilitating effective silica inhibition. Furthermore, the hydrophobic nature of alkyl segments in polymer chains disrupts the hydration shell around the polymer, resulting in enhanced binding with ionized silicic acid precursors compared to monomers. Finally, our findings provide novel mechanistic insights into the stabilization of silicic acids with functional polymers, highlighting the molecular design principles of effective inhibitors for silica polymerization.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Pretreatment of Biomass by Selected Type-III Deep Eutectic Solvents and Evaluation of the Pretreatment Effects on Hydrothermal Carbonization

Hydrothermal carbonization (HTC) is a novel thermochemical conversion that converts wet biomass into energy dense solid fuel. Residual moisture under subcritical conditions reacts with a lignin-cellulose-hemicellulose matrix with the major reactions being identified as dehydration and decarboxylation. Among other reaction parameters (e.g., temperature, time, pressure), biomass morphology often plays a key role in HTC. The hypothesis of this study was enhancing the porous structure of biomass without significantly affecting biopolymer composition would augment hydrothermal carbonization (HTC). To prove the hypothesis, two type-III deep eutectic solvents (DESs), namely choline chloride:urea (ChCl:Urea, 1:2 mol/mol) and methyltriphenylphosphonium bromide:ethylene glycol (MTPB:EG, 1:4 mol/mol), were studied to pretreat loblolly pine at room temperature and ambient pressure for 1 h. DES pretreatment shows swelling of the biomass, increasing the surface fiber-to-fiber gap length by 52% and 185% for ChCl:Urea and MPTB:EG pretreatments, respectively. The total pore volume remained intact (2.6 × 10 –3 cm 3 /g), although new small pores evolved, and existing pores were abated with DES pretreatment. Hydrochars prepared from DES pretreated loblolly pine showed a high O/C and H/C ratio resulting in a significant increase of energy content (up to 42%) and a decrease of mass yield (up to 50 wt %), indicating an enhancement of HTC severity due to the alteration of surface morphology by DES. Finally, a preliminary process economics revealed that integrated DES pretreatment-HTC would increase fixed capital investment but decrease the cost of operation and manufacturing than the standalone HTC process.

09 BIOMASS FUELS↗

DOE OSTI2019

Monomeric and Trimeric Thorium Chlorides Isolated from Acidic Aqueous Solution

Two thorium(IV) compounds, [Th(H 2 O) 4 Cl 4 ]·2 (HPy·Cl) ( 1 ) and (HPy) 3 [Th 3 (H 2 O) 2 Cl 10 (OH) 5 ]·4(HPy·Cl) ( 2 ) (HPy = pyridinium), were isolated from acidic aqueous solution. The compounds were synthesized at room temperature and subsequently characterized using single crystal X-ray diffraction along with Raman and IR spectroscopies. Whereas compound 1 is built from discrete mononuclear Th(H 2 O) 4 Cl 4 units, compound 2 consists of a novel hydroxo-bridged trimeric [Th 3 (OH) 5 ] 7+ core. Such species are largely absent from discussions of Th solution and solid-state chemistry and their isolation may be attributed to outer coordination sphere interactions that help stabilize the structural units; extensive hydrogen bonding and $π–π$ stacking interactions are present in 1 and 2 . Density functional theory calculations were performed to predict the respective vibrational frequencies of the structural units, and their relative stability was predicted at the correlated molecular theory level. Small-angle X-ray scattering analysis of [Th 3 (OH) 5 ] 7+ in water indicates that the trimeric structural unit remains intact and that it is indeed an important species that necessitates consideration in geochemical models and for design of Th materials from water.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2019

Utilizing Charge Effects and Minimizing Intramolecular Proton Rearrangement to Improve the Overpotential of a Thiosemicarbazonato Zinc HER Catalyst

The zinc(II) complex of diacetyl-2-(4-methyl-3-thiosemicarbazone)-3-(2-hydrazonepyridine), ZnL 1 (1), was prepared and evaluated as a precatalyst for the hydrogen evolution reaction (HER) under homogeneous conditions in acetonitrile. Complex 1 is protonated on the noncoordinating nitrogen of the hydrazonepyridine moiety to yield the active catalyst Zn(HL 1 )OAc (2) upon addition of acetic acid. Addition of methyl iodide to 1 yields the corresponding methylated derivative ZnL 2 I (3). In solution, partial dissociation of the coordinated iodide yields the cationic derivative 3'. Complexes 1–3 were characterized by 1 H NMR, FT-IR, and UV–visible spectroscopies. The solid-state structures of 2 and 3 were determined by single crystal X-ray diffraction. HER studies conducted in acetonitrile with acetic acid as the proton source yield a turnover frequency (TOF) of 7700 s –1 for solutions of 1 at an overpotential of 1.27 V and a TOF of 6700 s –1 for solutions of 3 at an overpotential of 0.56 V. For both complexes, the required potential for catalysis, E cat/2 , is larger than the thermodynamic reduction potential, E 1/2 , indicative of a kinetic barrier attributed to intramolecular proton rearrangement. The effect is larger for solutions of 1 (+440 mV) than for solutions of 3 (+160 mV). Controlled potential coulometry studies were used to determine faradaic efficiencies of 71 and 89% for solutions of 1 and 3, respectively. For both catalysts, extensive cycling of potential under catalytic conditions results in the deposition of a film on the glassy carbon electrode surface that is active as an HER catalyst. Analysis of the film of 3 by X-ray photoelectron spectroscopy indicates the complex remains intact upon deposition. A proposed ligand-centered HER mechanism with 1 as a precatalyst to 2 is supported computationally using density functional theory (DFT). All catalytic intermediates in the mechanism were structurally and energetically characterized with the DFT/B3LYP/6-311g(d,p) in solution phase using a polarizable continuum model (PCM). Finally, the thermodynamic feasibility of the mechanism is supported by calculation of equilibrium constants or reduction potentials for each proposed step.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2019

Inhibition of Inositol Polyphosphate Kinases by Quercetin and Related Flavonoids: A Structure–Activity Analysis

Dietary flavonoids inhibit certain protein kinases and phospholipid kinases by competing for their ATP-binding sites. These nucleotide pockets have structural elements that are well-conserved in two human small-molecule kinases, inositol hexakisphosphate kinase (IP6K) and inositol polyphosphate multikinase (IPMK), which synthesize multifunctional inositol phosphate cell signals. Herein, we demonstrate that both kinases are inhibited by quercetin and 16 related flavonoids; IP6K is the preferred target. Relative inhibitory activities were rationalized by X-ray analysis of kinase/flavonoid crystal structures; this detailed structure–activity analysis revealed hydrophobic and polar ligand/protein interactions, the degree of flexibility of key amino acid side chains, and the importance of water molecules. The seven most potent IP6K inhibitors were incubated with intact HCT116 cells at concentrations of 2.5 $μ$M; diosmetin was the most selective and effective IP6K inhibitor (>70% reduction in activity). Overall, our data can instruct on pharmacophore properties to assist the future development of inositol phosphate kinase inhibitors. Finally, we propose that dietary flavonoids may inhibit IP6K activity in cells that line the gastrointestinal tract.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Isolating the Contributions of Specific Network Sites to the Diffuse Vibrational Spectrum of Interfacial Water with Isotopomer-Selective Spectroscopy of Cold Clusters

Decoding the structural information contained in the interfacial vibrational spectrum of water requires understanding how the spectral signatures of individual water molecules respond to their local hydrogen bonding environments. In this study, we isolated the contributions for the five classes of sites that differ according to the number of donor (D) and acceptor (A) hydrogen bonds that characterize each site. These patterns were measured by exploiting the unique properties of the water cluster cage structures formed in the gas phase upon hydration of a series of cations M+·(H2O)n (M = Li, Na, Cs, NH4, CH3NH3, H3O, and n = 5, 20-22). This selection of ions was chosen to systematically express the A, AD, AAD, ADD, and AADD hydrogen bonding motifs. The spectral signatures of each site were measured using two-color, IR-IR isotopomer-selective photofragmentation vibrational spectroscopy of the cryogenically cooled, mass selected cluster ions in which a single intact H2O is introduced without isotopic scrambling, an important advantage afforded by the cluster regime. The resulting patterns provide an unprecedented picture of the intrinsic line shapes and spectral complexities associated with excitation of the individual OH groups, as well as the correlation between the frequencies of the two OH groups on the same water molecule, as a function of network site. The properties of the surrounding water network that govern this frequency map are evaluated by dissecting electronic structure calculations that explore how changes in the nearby network structures, both within and beyond the first hydration shell, affect the local frequency of an OH oscillator. The qualitative trends are recovered with a simple model that correlates the OH frequency with the network-modulated local electron density in the center of the OH bond.

Yang, Nan↗

DOE OSTI2021

Photodissociation and Infrared Spectroscopy of Uranium–Nitrogen Cation Complexes

Laser vaporization of uranium in a pulsed supersonic expansion of nitrogen is used to produce complexes of the form U + (N 2 ) n (n = 1–8). These ions are mass selected in a reflectron time-of-flight spectrometer and studied with visible and UV laser fixed-frequency photodissociation and with tunable infrared laser photodissociation spectroscopy. The dissociation patterns and spectroscopy of U + (N 2 ) n indicate that N 2 ligands are intact molecules and that there is no insertion chemistry resulting in UN + or NUN + . Fixed frequency photodissociation at 532 and 355 nm indicate that the U + –N 2 bond dissociation energy varies little with changing coordination. The photon energy and the number of ligands eliminated allow an estimate of the average U + –N 2 dissociation energy of 12 kcal/mol. Infrared bands are observed for these complexes near the N–N stretch vibration via elimination of N 2 molecules. These resonances are observed to be shifted about 130 cm–1 to the red from the free-N 2 frequency for complexes with n = 3–8. Density functional theory indicates that U + is most stable in the sextet state in these complexes and that N 2 molecules bind in end-on configurations. Furthermore, the fully coordinated complex is predicted to be U + (N 2 ) 8 , which has a cubic structure. The vibrational frequencies predicted by theory are consistently lower than those in the experiment, independent of the isomeric structure or spin state of the complexes. Despite its failure to reproduce the infrared spectra, theory provides an average U + –N 2 dissociation energy of 11.8 ± 0.5 kcal/mol, in good agreement with the value from the experiments.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2026

Photodissociation and Infrared Spectroscopy of U + (CO 2 ) n , UO + (CO 2 ) n , and UO 2+ (CO 2 ) n Cation-Molecular Complexes

Laser vaporization of uranium in a pulsed supersonic expansion of carbon dioxide is used to produce complexes of the form U + (CO 2 ) n , UO + (CO 2 ) n , and UO 2+ (CO 2 ) n . These ions are selected in a reflectron time-offlight mass spectrometer and studied with visible laser photodissociation and tunable infrared laser photodissociation spectroscopy in the region of the CO 2 antisymmetric stretch. The dissociation patterns and spectroscopy of these ions indicate that CO 2 ligands are intact molecules. Although reaction products that form oxide-carbonyl or oxalate species are predicted to be stable, there is no direct evidence in the frequency range studied for the formation of these species. There is no clear indication for the coordination numbers for singly charged uranium and its oxide complexes with CO 2 . However, there is strong support in the vibrational patterns for an eight-coordinate complex of the doubly charged UO 2+ species, i.e., UO 2+ (CO 2 ) 8 .

Cluster chemistry↗

DOE OSTI2020

Distinguishing Mesoscale Polar Order (Unidirectional vs Bidirectional) of Cellulose Microfibrils in Plant Cell Walls Using Sum Frequency Generation Spectroscopy

Cellulose in plant cell walls are synthesized as crystalline microfibrils with diameters of 3–4 nm and lengths of around 1–10 μm. These microfibrils are known to be the backbone of cell walls, and their multiscale three-dimensional organization plays a critical role in cell wall functions including plant growth and recalcitrance to degradation. The mesoscale organization of microfibrils over a 1–100 nm range in cell walls is challenging to resolve because most characterization techniques investigating this length scale suffer from low spatial resolution, sample preparation artifacts, or inaccessibility of specific cell types. Here, we report a sum frequency generation (SFG) study determining the mesoscale polarity of cellulose microfibrils in intact plant cell walls. SFG is a nonlinear optical spectroscopy technique sensitive to the molecular-to-mesoscale order of noncentrosymmetric domains in amorphous matrices. However, the quantitative theoretical model to unravel the effect of polarity in packing of noncentrosymmetric domains on SFG spectral features has remained unresolved. In this work, we show how the phase synchronization principle of the SFG process is used to predict the relative intensities of vibrational modes with different polar angles from the noncentrosymmetric domain axis. Applying this model calculation for the first time and employing SFG microscopy, we found that cellulose microfibrils in certain xylem cell walls are deposited unidirectionally (or biased in one direction) instead of the bidirectional polarity which was believed to be dominant in plant cell walls from volume-averaged characterizations of macroscopic samples. Here, with this advancement in SFG analysis, one can now determine the relative polarity of noncentrosymmetric domains such as crystalline biopolymers interspersed in amorphous polymer matrices, which will open opportunities to study new questions that have not been conceived in the past.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Hexagonal Lattices of HIV Capsid Proteins Explored by Simulations Based on a Thermodynamically Consistent Model

HIV capsid proteins (CAs) may self-assemble into a variety of shapes under in vivo and in vitro conditions. Here, we employed simulations based on a residue-level coarse-grained (CG) model with full conformational flexibility to investigate hexagonal lattices, which are the underlying structural pattern for CA aggregations. Facilitated by enhanced sampling simulations to rigorously calculate CA dimerization and polymerization affinities, we calibrated our model to reproduce the experimentally measured affinities. Here using the calibrated model, we performed unbiased simulations on several large systems consisting of 1512 CA subunits, allowing reversible binding and unbinding of the CAs in a thermodynamically consistent manner. In one simulation, a preassembled hexagonal CA sheet developed spontaneous curvatures reminiscent of those observed in experiments, and the edges of the sheet exhibited local curvatures larger than those of the interior. In other simulations starting with randomly distributed CAs at different concentrations, existing CA assemblies grew by binding free capsomeres to the edges and by merging with other assemblies. At high CA concentrations, rapid establishment of predominant aggregates was followed by much slower adjustments toward more regular hexagonal lattices, with increasing numbers of intact CA hexamers and pentamers being formed. Our approach of adapting a general CG model to specific systems by using experimental binding data represents a practical and effective strategy for simulating and elucidating intricate protein aggregations.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

High-Pressure Investigation of 2,4,6-Trinitro-3-bromoanisole (TNBA): Structural Determination and Piezochromism

Understanding phase transitions in energetic materials is crucial for developing predictive models of detonation. 2,4,6-Trinitro-3-bromoanisole (TNBA), an energetic material, was studied in its single-crystal form up to pressures of 45 GPa in a diamond anvil cell. The material was characterized by using X-ray, Raman, and optical transmission measurements. From single-crystal X-ray diffraction, the ambient structure of TNBA was determined which crystallizes in the P2 1 /c space group having four molecular units per unit cell. The X-ray data up to 9.2 GPa were fitted to a third-order Birch–Murnaghan equation of state by using the parameters K o = 13.2(2.4) GPa and K p = 5.1(1.4). Between 6.8 and 7.3 GPa, a phase transition was inferred in TNBA from concurrent fading of X-ray diffraction, disappearance of Raman peaks, increase in sample fluorescence, and discontinuous color change. The new phase was consistent with an amorphous state of at least partially intact molecules judging from the presence of higher-order Raman modes and irreversibility of the Raman spectra upon release. Piezochromism was observed with the translucent yellow TNBA gradually darkening and becoming opaque black at ~25 GPa. This correlated to the absorption edge gradually shifting to the red in the visible spectrum. Signs of two possible additional structural transitions were detected in the 32.4–41.0 GPa range as suggested by a jump in the absorption edge, the irreversible changes in the absorption spectrum upon release to ambient pressure, and by the lack of Raman modes in recovered samples. Here, the crystal and electronic structures of TNBA were also investigated up to 10 GPa by using DFT calculations and crystal structure prediction (CSP) simulations. In agreement with the experimentally observed transition at 7 GPa, the simulations at 10 GPa found a bevy of polymorphs lower in enthalpy and higher in density than P2 1 /c. The lowest calculated enthalpy structure was determined to be P2 1 2 1 2 1 , being in a different space group than the ambient experimental result.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗