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At least 1,531 records · Page 85

Maximum Entropy Theory of Multiscale Coarse-Graining via Matching Thermodynamic Forces: Application to a Molecular Crystal (TATB)

The MSCG/FM (multiscale coarse-graining via force-matching) approach is an efficient supervised machine learning method to develop microscopically informed coarse-grained (CG) models. Here we present a theory based on the principle of maximum entropy (PME) enveloping the existing MSCG/FM approaches. This theory views the MSCG/FM method as a special case of matching the thermodynamic forces from the extended ensemble described by the set of thermodynamic (relevant) system coordinates. This set may include CG coordinates, the stress tensor, applied external fields, and so forth, and may be characterized by nonequilibrium conditions. Following the presentation of the theory, we discuss the consistent matching of both bonded and nonbonded interactions. The proposed PME formulation is used as a starting point to extend the MSCG/FM method to the constant strain ensemble, which together with the explicit matching of the bonded forces is better suited for coarse-graining anisotropic media at a submolecular resolution. The theory is demonstrated by performing the fine coarse-graining of crystalline 1,3,5-triamino-2,4,6-trinitrobenzene (TATB), a well-known insensitive molecular energetic material, which exhibits highly anisotropic mechanical properties.

1,3,5-triamino-2,4,6-trinitrobenzene↗

Equipartition and the Temperature of Maximum Density of TIP4P/2005 Water

Here, we simulate TIP4P/2005 water in the temperature range of 257 to 318 K with time-steps δ = 0.25, 0.50, 1.00, 2.00, and 4.00 fs. The density–temperature behavior obtained using 0.25 or 0.50 fs is in excellent agreement with each other but differs from those obtained using time steps that have been shown earlier to lead to a breakdown of equipartition. For δt = 0.25 or 0.50 fs, the temperature of maximum density (TMD) is 277.15 K and the density value is in close agreement with experiments. For δt = 1.00 fs, the TMD is 277.15 K, but the density value is shifted higher. For the other time steps considered here, the TMD is shifted to progressively lower values for longer time steps, a trend that holds for different thermostat/barostat combinations. Enhancing the water–water dispersion interaction, as has been recommended for simulating disordered proteins in TIP4P/2005, degrades the description of the liquid–vapor phase envelope. We present a simple physically transparent explanation that highlights the separation of the time scales between translational and rotational motion. We also develop a metric, χ, that we term the equipartition anomaly, to detect equipartition violations in simulations that include molecules that are treated as rigid objects. Calculating χ is shown to be straightforward and sensitive to equipartition violations. A key takeaway from this study is that using sufficiently short time steps (≤0.5 fs) to preserve equipartition is essential for obtaining meaningful liquid water properties and for producing reliable simulation data, as correct ensemble sampling is fundamental to ensure reproducibility across codes and simulation algorithms.

Asthagiri, Dilipkumar N. [Oak Ridge National Labor↗

Spin Decoherence in VOPc@graphene Nanoribbon Complexes

Carbon nanoribbons or nanographene qubit arrays can facilitate quantum-to-quantum transduction between light, charge, and spin, making them an excellent testbed for fundamental science in quantum coherent systems and for the construction of higher-level qubit circuits. Here, in this work, we study spin decoherence due to coupling with a surrounding nuclear spin bath of an electronic molecular spin of a vanadyl phthalocyanine (VOPc) molecule integrated onto an armchair-edged graphene nanoribbon (GNR). Density functional theory (DFT) is used to obtain ground-state atomic configurations. Decay of spin coherence in Hahn echo experiments is then simulated using the cluster correlation expansion method with a spin Hamiltonian involving hyperfine and electric field gradient tensors calculated from DFT. We find that the decoherence time T 2 is anisotropic with respect to magnetic field orientation and determined only by the hydrogen nuclear spins on both VOPc and GNR. Large electron spin echo envelope modulation (ESEEM) due to nitrogen and vanadium nuclear spins is present at specific field ranges and can be completely suppressed by tuning the magnetic field. The relation between these field ranges and the hyperfine interactions is analyzed. The effects of interactions with the nuclear quadrupole moments are also studied, validating the applicability and limitations of the spin Hamiltonian when they are disregarded.

Hamiltonians↗

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↗

Enhancing Top-Down Proteomics of Brain Tissue with FAIMS

Proteomic investigations of Alzheimer’s and Parkinson’s disease have provided valuable insights into neurodegenerative disorders. Thus far, these investigations have largely been restricted to bottom-up approaches, hindering the degree to which one can characterize a protein’s “intact” state. Top-down proteomics (TDP) overcomes this limitation, however it is typically limited to observing only the most abundant proteoforms and of a relatively small size. Therefore, offline fractionation techniques are commonly used to reduce sample complexity, limiting throughput. A higher throughput alternative is online fractionation, such as gas phase high-field asymmetric waveform ion mobility spectrometry (FAIMS). Using a high complexity sample derived from Alzheimer’s disease brain tissue, we describe how the addition of FAIMS to TDP can robustly improve the depth of proteome coverage. For example, implementation of FAIMS at -50 compensation voltage (CV) more than doubled the mean number of non-redundant proteoforms observed (1,833 ± 17, n = 3), compared to without (754 ± 35 proteoforms). We also found FAIMS can influence the transmission of proteoforms and their charge envelopes based on their size. Importantly, FAIMS enabled the identification of intact amyloid beta (Aß) proteoforms, including the aggregation-prone Aß1-42 variant which is strongly linked to Alzheimer’s disease.

59 BASIC BIOLOGICAL SCIENCES↗

Carbon-Sequestration Straw Cellulose-Aerogel Gradient Thermal Insulation Material

Green superinsulation materials are essential for net-zero sustainable building envelopes. Realizing such potential is indispensable for simultaneously achieving carbon-sequestration and superinsulation performance. Here, we report the synthesis of a water glass-based silica aerogel exhibiting a thermal conductivity of 17.2 mW/m·K and a high porosity of 92%. Here, we used carbon-sequestration wheat straw fiber to create a gradient cellulose-aerogel composite to improve mechanical stability. The as-prepared gradient composite exhibits a thermal conductivity of 27.1 mW/m·K and a flexural modulus of 824 MPa, while exhibiting superhydrophobicity (water contact angle of 135.4°) for the development of green building insulation materials.

36 MATERIALS SCIENCE↗

Band-edge Engineering to Eliminate Radiation-Induced Defect States in Perovskite Scintillators

Under radiative environments such as extended hard X- or γ-rays, degradation of scintillation performance is often due to irradiation-induced defects. To overcome the effect of deleterious defects, novel design mitigation strategies are needed to identify and design more resilient materials. The potential for band-edge engineering to eliminate the effect of radiation-induced defect states in rare-earth-doped perovskite scintillators is explored, taking Ce 3+ -doped LuAlO 3 as a model material system, using density functional theory (DFT)-based DFT + U and hybrid Heyd–Scuseria–Ernzerhof (HSE) calculations. Furthermore, from spin-polarized hybrid HSE calculations, the Ce 3+ activator ground-state 4f position is determined to be 2.81 eV above the valence band maximum in LuAlO 3 . Except for the oxygen vacancies which have a deep level inside the band gap, all other radiation-induced defects in LuAlO 3 have shallow defect states or are outside the band gap, that is, relatively far away from either the 5d 1 or the 4f Ce 3+ levels. Finally, we examine the role of Ga doping at the Al site and found that LuGaO 3 has a band gap that is more than 2 eV smaller than that of LuAlO 3 . Specifically, the lowered conduction band edge envelopes the defect gap states, eliminating their potential impact on scintillation performance and providing direct theoretical evidence for how band-edge engineering could be applied to rare-earth-doped perovskite scintillators.

36 MATERIALS SCIENCE↗

Light-Induced Transformation of Virus-Like Particles on TiO 2

Titanium dioxide (TiO 2 ) shows significant potential as a self-cleaning material to inactivate severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and prevent virus transmission. This study provides insights into the impact of UV-A light on the photocatalytic inactivation of adsorbed SARS-CoV-2 virus-like particles (VLPs) on a TiO 2 surface at the molecular and atomic levels. X-ray photoelectron spectroscopy, combined with density functional theory calculations, reveals that spike proteins can adsorb on TiO 2 predominantly via their amine and amide functional groups in their amino acids blocks. We employ atomic force microscopy and grazing-incidence small-angle X-ray scattering (GISAXS) to investigate the molecular-scale morphological changes during the inactivation of VLPs on TiO 2 under light irradiation. Notably, in situ measurements reveal photoinduced morphological changes of VLPs, resulting in increased particle diameters. These results suggest that the denaturation of structural proteins induced by UV irradiation and oxidation of the virus structure through photocatalytic reactions can take place on the TiO 2 surface. The in situ GISAXS measurements under an N 2 atmosphere reveal that the virus morphology remains intact under UV light. This provides evidence that the presence of both oxygen and UV light is necessary to initiate photocatalytic reactions on the surface and subsequently inactivate the adsorbed viruses. The chemical insights into the virus inactivation process obtained in this study contribute significantly to the development of solid materials for the inactivation of enveloped viruses.

36 MATERIALS SCIENCE↗

In-Situ Atomic-Scale Revelation of Amorphous Metallic Iron Formation during Hydrogen-Driven Reduction of Iron Oxides

The transition to hydrogen as a green reductant in metal production is critical for decarbonizing the metallurgical industry, yet atomic-scale mechanisms governing reduction pathways and phase evolution remain unresolved. Using in-situ environmental transmission electron microscopy, we identify a hidden pathway that reveals dynamic formation of amorphous metallic iron (Fe) during the hydrogen-driven reduction of ferrous oxides of Fe 3 O 4 and FeO. Real-time imaging uncovers three coexisting transformation routes: (i) Fe 3 O 4 → FeO, (ii) Fe 3 O 4 → amorphous Fe, and (iii) FeO → amorphous Fe. The resulting amorphous Fe exhibits fluid-like mobility, enabling its rapid aggregation and crystallization into core-shell nanostructures, with a crystalline core enveloped by an amorphous shell. Complementary ab initio molecular dynamics simulations trace the amorphous Fe formation to interfacial strain at the metal/oxide interfaces, where large lattice mismatches destabilize the metal lattice during initial metallization. This interplay between thermodynamics and kinetics governs phase evolution: thermodynamics favors a self-limiting amorphous Fe overlayer, while rapid oxide reduction kinetics drives amorphous overgrowth. Our findings demonstrate that amorphous intermediates bypass rate-limiting crystalline steps, providing mechanistic insights to optimize H 2 -based processes for sustainable steelmaking. In conclusion, these insights bridge the gap between macroscopic process engineering and atomic-scale dynamics, with broader implications for catalysis and nanostructured material synthesis, where oxide reduction pathways critically shape functional phases and microstructures.

36 MATERIALS SCIENCE↗

Direct Visualization of Laser-Induced Coalescence and Alloying of Au into Ag Nanowires

Noble metal nanocomposites with controlled morphology and composition have been largely useful in a wide variety of applications like catalysis, plasmonics, and biological applications. Herein, we show pulsed-laser-assisted fabrication of beaded Au-Ag nanowires with a variety of morphologies and compositions via coalescence and alloying of Au nanoparticles (NP) into a Ag nanowire (NW). Direct visualization of the evolution process with in situ laser heating transmission electron microscopy (ILH-TEM) leads to unambiguous insights into the mechanism of formation for the first time. Ag, being a soft material, melts at the surface to bridge the gap between the NP-NW, forming a cup-like morphology underneath the Au NP via capillary action. Progressive laser irradiation leads to wetting of the Au NP with Ag, forming an envelope around the NP. This is associated with the formation of a valley in Ag NW around the NP, which flattens gradually by partial embedding of the NP. Interdiffusion of Au into Ag and vice versa sets in at this stage, leading to the depletion of Au from the Au-rich NP region. Prolonged irradiation leads to gradual intermixing of Au-Ag forming beaded Au-doped Ag nanowires with homogeneous composition. Such a step-by-step understanding of the coalescence and alloying process has implications in nanowelding, which holds the future in designing efficient transparent conductors and printed electronics.

Isik, Tugba↗

Decontamination of SARS-CoV-2 and Other RNA Viruses from N95 Level Meltblown Polypropylene Fabric Using Heat under Different Humidities

In March of 2020, the World Health Organization declared a pandemic of coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The pandemic led to a shortage of N95-grade filtering facepiece respirators (FFRs), especially surgical-grade N95 FFRs for protection of healthcare professionals against airborne transmission of SARS-CoV-2. We and others have previously reported promising decontamination methods that may be applied to the recycling and reuse of FFRs. In this study we tested disinfection of three viruses, including SARS-CoV-2, dried on a piece of meltblown fabric, the principal component responsible for filtering of fine particles in N95-level FFRs, under a range of temperatures (60–95 °C) at ambient or 100% relative humidity (RH) in conjunction with filtration efficiency testing. We found that heat treatments of 75 °C for 30 min or 85 °C for 20 min at 100% RH resulted in efficient decontamination from the fabric of SARS-CoV-2, human coronavirus NL63 (HCoV-NL63), and another enveloped RNA virus, chikungunya virus vaccine strain 181/25 (CHIKV-181/25), without lowering the meltblown fabric’s filtration efficiency.

60 APPLIED LIFE SCIENCES↗

Thickness- and Twist-Angle-Dependent Interlayer Excitons in Metal Monochalcogenide Heterostructures

Interlayer excitons, or bound electron-hole pairs whose constituent quasiparticles are located in distinct stacked semiconducting layers, are being intensively studied in heterobilayers of two dimensional semiconductors. They owe their existence to an intrinsic type-II band alignment between both layers that convert these into p-n junctions. Here, we unveil a pronounced interlayer exciton (IX) in heterobilayers of metal monochalcogenides, namely gamma-InSe on epsilon-GaSe, whose pronounced emission is adjustable just by varying their thicknesses given their number of layers dependent direct bandgaps. Time-dependent photoluminescense spectroscopy unveils considerably longer interlayer exciton lifetimes with respect to intralayer ones, thus confirming their nature. The linear Stark effect yields a bound electron-hole pair whose separation d is just (3.6 ± 0.1) Å with d being very close to d Se = 3.4 Å which is the calculated interfacial Se separation. The envelope of IX is twist angle dependent and describable by superimposed emissions that are nearly equally spaced in energy, as if quantized due to localization induced by the small moiré periodicity. Furthermore, these heterostacks are characterized by extremely flat interfacial valence bands making them prime candidates for the observation of magnetism or other correlated electronic phases upon carrier doping.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Low-Voltage Haze Tuning with Cellulose-Network Liquid Crystal Gels

Being key components of the building envelope, glazing products with tunable optical properties are in great demand because of their potential for boosting energy efficiency and privacy features while enabling the main function of allowing natural light indoors. However, windows and skylights with electric switching of haze and transparency are rare and often require high voltages or electric currents, as well as not fully meet the stringent technical requirements for glazing applications. Here, by introducing a predesigned gel material we describe an approach dubbed “Haze-Switch” that involves low-voltage tuning of the haze coefficient in a broad range of 2–90% while maintaining high visible-range optical transmittance. The approach is based on a nanocellulose fiber gel network infiltrated by a nematic liquid crystal, which can be switched between polydomain and monodomain spatial patterns of optical axis via a dielectric coupling between the nematic domains and the applied external electric field. By utilizing a nanocellulose network of nanofibers ~10 nm in diameter we achieve <10 V dielectric switching and <2% haze in the clear state, as needed for applications in window products. Finally, we characterize physical properties relevant to window and smart glass technologies, like the color rendering index, haze coefficient, and switching times, demonstrating that our material and envisaged products can meet the stringent requirements of the glass industry, including applications such as privacy windows, skylights, sunroofs, and daylighting.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Resolving Nonequilibrium Shape Variations among Millions of Gold Nanoparticles

Nanoparticles, exhibiting functionally relevant structural heterogeneity, are at the forefront of cutting-edge research. Now, high-throughput single-particle imaging (SPI) with X-ray free-electron lasers (XFELs) creates opportunities for recovering the shape distributions of millions of particles that exhibit functionally relevant structural heterogeneity. To realize this potential, three challenges have to be overcome: (1) simultaneous parametrization of structural variability in real and reciprocal spaces; (2) efficiently inferring the latent parameters of each SPI measurement; (3) scaling up comparisons between 10 5 structural models and 10 6 XFEL-SPI measurements. Here, we describe how we overcame these three challenges to resolve the nonequilibrium shape distributions within millions of gold nanoparticles imaged at the European XFEL. These shape distributions allowed us to quantify the degree of asymmetry in these particles, discover a relatively stable “shape envelope” among nanoparticles, discern finite-size effects related to shape-controlling surfactants, and extrapolate nanoparticles’ shapes to their idealized thermodynamic limit. Ultimately, these demonstrations show that XFEL SPI can help transform nanoparticle shape characterization from anecdotally interesting to statistically meaningful.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Force-Triggered, Biobased Sealants for Prefabricated Building Components: Toward Improved Efficiency and Performance

The prefabricated building construction industry has made extensive progress in expediting the manufacture of prefabricated components at off-site plants. However, the sealing of joints between these components, which is crucial to ensuring the weatherproofing of the assembly, still represents a labor-intensive, on-site effort that relies on the manual installation of tapes and caulks. Here, to reduce work at the jobsite and improve the airtightness and waterproofness of building envelopes, we developed a sealant that can be installed at the plant on prefab components and have the curing reaction triggered at the jobsite by using microencapsulation technology to separate the reactive agents. A series of force-triggered, high-strength, and fast-curing sealants derived from biobased feedstocks were developed, which consist of a biobased epoxy agent encapsulated in a polymer shell, embedded in a biobased amine curing agent. The shell of the microcapsules allows an effective separation of the reactive species in the one-part sealant, allowing shelf stability to an otherwise fast-curing system as well as improving the hydrophobicity of the whole system. When force activates and breaks the microcapsules, the highly reactive epoxy and amine mix and cure, exhibiting peel strength values of up to 143 ppi (pounds per inch). The hydrophobicity of the sealants allows them to retain up to 94% of the original peel strength after complete submersion in water for 24 h, showcasing the water resistivity of the sealant system. The open-air shelf stability of the sealant complex is demonstrated by the obtention of peel strength values of ∼16 ppi when triggering the curing reaction even after being exposed 8 months to open air and humidity. The successful on-demand triggering of curing reactions and the shelf stability provide efficacy of these force-triggered sealants for installation on prefabricated components, storage for months prior to delivery, and assembly at a jobsite. These force-triggered biobased sealants for prefabricated buildings can result in lower installation time and cost and better performance than tapes and caulks at the jobsite.

biobased↗

Robust Synthetic Biology Toolkit to Advance Carboxysome Study and Redesign

Carboxysomes are polyhedral protein organelles that microorganisms use to facilitate carbon dioxide assimilation. They are composed of a modular protein shell that envelops an enzymatic core mainly composed of physically coupled Rubisco and carbonic anhydrase. While the modular construction principles of carboxysomes make them attractive targets as customizable metabolic platforms, their size and complexity can be a hindrance. In this work, we design and validate a plasmid set, the pXpressome toolkit, in which α-carboxysomes are robustly expressed and remain intact and functional after purification. We tested this toolkit by introducing mutations that influence carboxysome structure and performance. We find that deletion of vertex-capping genes results in formation of larger carboxysomes, while deletion of facet forming genes produces smaller particles, suggesting that adjusting the ratio of these proteins can rationally affect morphology. Through a series of fluorescently labeled constructs, we observe that this toolkit leads to more uniform expression and better cell health than previously published carboxysome expression systems. Overall, the pXpressome toolkit facilitates the study and redesign of carboxysomes with robust performance and improved phenotype uniformity. The pXpressome toolkit will support efforts to remodel carboxysomes for enhanced carbon fixation or serve as a platform for other nanoencapsulation goals.

59 BASIC BIOLOGICAL SCIENCES↗

A Theory-Guided X-ray Absorption Spectroscopy Approach for Identifying Active Sites in Atomically Dispersed Transition-Metal Catalysts

Atomically dispersed supported metal catalysts offer new properties and the benefits of maximized metal accessibility and utilization. The characterization of these materials, however, remains challenging. Using atomically dispersed platinum supported on crystalline MgO (chosen for its well-defined bonding sites) as a prototypical example, we demonstrate in this work how systematic density functional theory calculations for assessing all the potentially stable platinum sites, combined with automated analysis of extended X-ray absorption fine structure (EXAFS) spectra, leads to unbiased identification of isolated, surface-enveloped platinum cations as the catalytic species for CO oxidation. The catalyst has been characterized by atomic-resolution imaging and EXAFS and high-energy resolution fluorescence detection X-ray absorption near edge spectroscopy. The proposed platinum sites are in agreement with experiment. This theory-guided workflow leads to rigorously determined structural models and provides a more detailed picture of the structure of the catalytically active site than what is currently possible with conventional EXAFS analyses. As this approach is efficient and agnostic to the metal, support, and catalytic reaction, we posit that it will be of broad interest to the materials characterization and catalysis communities.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Tuning the Type 1 Reduction Potential of Multicopper Oxidases: Uncoupling the Effects of Electrostatics and H-Bonding to Histidine Ligands

In multicopper oxidases (MCOs), the type 1 (T1) Cu accepts electrons from the substrate and transfers these to the trinuclear Cu cluster (TNC) where O 2 is reduced to H 2 O. The T1 potential in MCOs varies from 340 to 780 mV, a range not explained by the existing literature. Here, this study focused on the ~350 mV difference in potential of the T1 center in Fet3p and Trametes versicolor laccase (TvL) that have the same 2His1Cys ligand set. A range of spectroscopies performed on the oxidized and reduced T1 sites in these MCOs shows that they have equivalent geometric and electronic structures. However, the two His ligands of the T1 Cu in Fet3p are H-bonded to carboxylate residues, while in TvL they are H-bonded to noncharged groups. Electron spin echo envelope modulation spectroscopy shows that there are significant differences in the second-sphere H-bonding interactions in the two T1 centers. Redox titrations on type 2-depleted derivatives of Fet3p and its D409A and E185A variants reveal that the two carboxylates (D409 and E185) lower the T1 potential by 110 and 255–285 mV, respectively. Density functional theory calculations uncouple the effects of the charge of the carboxylates and their difference in H-bonding interactions with the His ligands on the T1 potential, indicating 90–150 mV for anionic charge and ~100 mV for a strong H-bond. Finally, this study provides an explanation for the generally low potentials of metallooxidases relative to the wide range of potentials of the organic oxidases in terms of different oxidized states of their TNCs involved in catalytic turnover.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗