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At least 127 records · Page 7

Molecular dynamics simulations of inelastic x-ray scattering from shocked copper

By taking the spatial and temporal Fourier transforms of the coordinates of the atoms in molecular dynamics simulations conducted using an embedded-atom-method potential, we calculate the inelastic scattering of x rays from copper single crystals shocked along [001] to pressures of up to 70 GPa. Above the Hugoniot elastic limit, we find that the copious stacking faults generated at the shock front introduce strong quasi-elastic scattering (QES) that competes with the inelastic scattering signal, which remains discernible within the first Brillouin zone; for specific directions in reciprocal space outside the first zone, the QES dominates the inelastic signal overwhelmingly. The synthetic scattering spectra we generate from our Fourier transforms suggest that energy resolutions of order 10 meV would be required to distinguish inelastic from quasi-elastic scattering within the first Brillouin zone of shock-loaded copper. We further note that high-resolution inelastic scattering also affords the possibility of directly measuring particle velocities via the Doppler shift. These simulations are of relevance to future planned inelastic scattering experiments at x-ray Free Electron Laser facilities.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Imaging Wavepackets in Real-Space & Disentangling Ultrafast Solvation Dynamics with High-Energy Ultrafast X-ray Scattering

The microscopic information of solute and solute-solvent motions can be measured using ultrafast diffuse x-ray scattering, and compared to molecular dynamics simulations, as demonstrated in studies of solvated molecular systems done in X-ray free-electron lasers. However, for the typical photon energies used in these experiments, the photon momentum transfer range was limited to lower Q values where the signals arising from different parts of the studied system overlap significantly. Recently, this limitation was greatly alleviated by extending the photon energy at the Linac Coherent Light-Source (LCLS), significantly increasing the accessible momentum transfer range. This improvement is transformative for ultrafast diffuse x-ray scattering measurements, enabling for the first time to disentangle the solute scattering difference signal, that persists to higher Q values, from the bulk solvent and solute-solvent cross-terms difference signals. In addition, it enhances the prediction ability of modeling and simulation methods such as the hybrid QM/MM approach. The extended Q range also opens the way to resolve in real-space details regarding coherent wavepackets motions beyond their center-of-mass positions. Here, we present the first results on high-energy (18keV) diffuse x-ray scattering in solution, demonstrating high fidelity time-resolved scattering and analysis of the photoexcited model photocatalysts PtPOP ([Pt2(POP)4]4-), and IrDimen ([Ir2(dimen)4]2+) in several solvents. These complexes provide ideal systems for demonstrating the ability of high-Q ultrafast scattering and QM/MM simulations to decompose ultrafast solvation dynamics into specific changes in the solute-solvent pair distribution function with a particular focus on how electronically excited states change the interaction between the solvent and photo-catalytically active metal sites. We introduce an approach to further utilize the high-energy capability and demonstrate a single-shot ultra-wide-angle X-ray Scattering modality using two perpendicular detectors, spanning a scattering angle range of more than 100 degrees, allowing to extend the accessible momentum transfer range up to Q~14 Å-1. We develop a model-free method to invert the x-ray scattering signals and enable the recovery of multiple pair-density motions that happen simultaneously, allowing us to directly measure in real-space nuclear wavepacket motions. . [1] Natan, Adi. "Real-Space Inversion and Super-Resolution of Ultrafast X-ray Scattering using Natural Scattering Kernels." arXiv preprint arXiv:2107.05576 (2021)

Natan, Adi↗

X‐ray scattering reveals disordered linkers and dynamic interfaces in complexes and mechanisms for DNA double‐strand break repair impacting cell and cancer biology

Abstract Evolutionary selection ensures specificity and efficiency in dynamic metastable macromolecular machines that repair DNA damage without releasing toxic and mutagenic intermediates. Here we examine non‐homologous end joining (NHEJ) as the primary conserved DNA double‐strand break (DSB) repair process in human cells. NHEJ has exemplary key roles in networks determining the development, outcome of cancer treatments by DSB‐inducing agents, generation of antibody and T‐cell receptor diversity, and innate immune response for RNA viruses. We determine mechanistic insights into NHEJ structural biochemistry focusing upon advanced small angle X‐ray scattering (SAXS) results combined with X‐ray crystallography (MX) and cryo‐electron microscopy (cryo‐EM). SAXS coupled to atomic structures enables integrated structural biology for objective quantitative assessment of conformational ensembles and assemblies in solution, intra‐molecular distances, structural similarity, functional disorder, conformational switching, and flexibility. Importantly, NHEJ complexes in solution undergo larger allosteric transitions than seen in their cryo‐EM or MX structures. In the long‐range synaptic complex, X‐ray repair cross‐complementing 4 (XRCC4) plus XRCC4‐like‐factor (XLF) form a flexible bridge and linchpin for DNA ends bound to KU heterodimer (Ku70/80) and DNA‐PKcs (DNA‐dependent protein kinase catalytic subunit). Upon binding two DNA ends, auto‐phosphorylation opens DNA‐PKcs dimer licensing NHEJ via concerted conformational transformations of XLF‐XRCC4, XLF–Ku80, and LigIV BRCT –Ku70 interfaces. Integrated structures reveal multifunctional roles for disordered linkers and modular dynamic interfaces promoting DSB end processing and alignment into the short‐range complex for ligation by LigIV. Integrated findings define dynamic assemblies fundamental to designing separation‐of‐function mutants and allosteric inhibitors targeting conformational transitions in multifunctional complexes.

59 BASIC BIOLOGICAL SCIENCES↗

Investigation into the transport properties of planetary interiors through inelastic X-ray scattering experiments and quantum molecular dynamics (Final Technical Report)

This was a two-year research project for the period 08/15/2018 - 08/14/2020 conducted at the University of Nevada, Reno using Pronghorn, a newly built high-performance cluster located at the University. The short-term project goal was to provide computational support for the experimental campaigns at LCLS through data analysis of previous and upcoming scheduled experiments, along with performing state-of-the-art atomistic simulations of dense plasmas. The longer-term goal was to create a new computational high energy density physics group located at the University of Nevada, Reno. Guided by results from past and future high-resolution scattering experiments, we aimed to research and develop non-equilibrium and non-adiabatic atomistic simulations of dense plasmas that went beyond the Born-Oppenheimer approximation

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Interfacial Reactivity and Speciation Emerging from Na-Montmorillonite Interactions with Water and Formic Acid at 200 °C: Insights from Reactive Molecular Dynamics Simulations, Infrared Spectroscopy, and X-ray Scattering Measurements

Reactive organic fluid - mineral interactions at elevated temperatures contribute to the evolution of planetary matter. One of the less studied but important transformations in this regard involves the reactions of formic acid with naturally occurring clays such as sodium montmorillonite. To advance a mechanistic understanding of these interactions, we use ReaxFF reactive molecular dynamics simulations in conjunction with infrared (IR) spectroscopy and X-ray scattering experiments to investigate the speciation behavior of water-formic acid mixtures on sodium montmorillonite interfaces at 473 K and 1 atm. Using a newly developed reactive forcefield, we show that the experimental IR spectra of unreacted and reacted mixture can be accurately reproduced by ReaxFF/MD. We further benchmark the simulation predictions of sodium carbonate and bicarbonate formation in the clay interlayers using Small and Wide-Angle X-ray Scattering measurements. Subsequently, leveraging the benchmarked forcefield, we interrogate the pathway of speciation reactions with emphasis on carbonate, formate, and hydroxide groups elucidating the energetics, transition states, intermediates, and preferred products. Further, we also delineate the differences in reactivities and catalytic effects of clay edges, facets, and interlayers owing to their local chemical environments, which have far reaching consequences in their speciation behavior. The experimental and simulation approaches described in this study and the transferable forcefields can be applied translationally to advance the science of clay-fluid interactions for several applications including subsurface fluid storage and recovery and clay-pollutant dynamics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Stochastic exciton-scattering theory of optical line shapes: Renormalized many-body contributions

Spectral line shapes provide a window into the local environment coupled to a quantum transition in the condensed phase. In this paper, we build upon a stochastic model to account for non-stationary background processes produced by broad-band pulsed laser stimulation, as distinguished from those for stationary phonon bath. In particular, we consider the contribution of pair-fluctuations arising from the full bosonic many-body Hamiltonian within a mean-field approximation, treating the coupling to the system as a stochastic noise term. Herein, using the Itô transformation, we consider two limiting cases for our model, which lead to a connection between the observed spectral fluctuations and the spectral density of the environment. In the first case, we consider a Brownian environment and show that this produces spectral dynamics that relax to form dressed excitonic states and recover an Anderson–Kubo-like form for the spectral correlations. In the second case, we assume that the spectrum is Anderson–Kubo like and invert to determine the corresponding background. Using the Jensen inequality, we obtain an upper limit for the spectral density for the background. The results presented here provide the technical tools for applying the stochastic model to a broad range of problems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Relaxation dynamics of deformed polymer nanocomposites as revealed by small-angle scattering and rheology

Here, the relaxation dynamics of polystyrene (PS)/silica nanocomposites after a large step deformation are studied by a combination of small-angle scattering techniques and rheology. Small-angle X-ray scattering measurements and rheology show clear signatures of nanoparticle aggregation that enhances the mechanical properties of the polymer nanocomposites (PNCs) in the linear viscoelastic regime and during the initial phase of stress relaxation along with accelerated relaxation dynamics. Small-angle neutron scattering experiments under the zero-average-contrast condition reveal, however, smaller structural anisotropy in the PNCs than that in the neat polymer matrix, as well as accelerated anisotropy relaxation. In addition, the degrees of anisotropy reduction and relaxation dynamics acceleration increase with increasing nanoparticle loading. These results are in sharp contrast to the prevailing viewpoint of enhanced molecular deformation as the main mechanism for the mechanical enhancement in PNCs. Furthermore, the observed acceleration of stress relaxation and reduction in structural anisotropy point to two types of nonlinear effects in the relaxation dynamics of PNCs at large deformation.

36 MATERIALS SCIENCE↗

In-situ Investigations on Gold Nanoparticles Stabilization Mechanisms in Biological Environments Containing HSA

Nanoparticles (NPs) developments advance innovative biomedical applications. However, complex interactions and the low colloidal stability of NPs in biological media restrict their widespread utilization. The influence of NPs properties on the colloidal stability for gold NPs with 5 and 40 nm in diameter with two surface modifications, methoxy-polyethylene glycol-sulfhydryl (PEG) and citrate, in NaCl and human serum albumin (HSA) protein solution, is investigated. This study is based on small-angle X-ray scattering (SAXS) methods allowing the in-situ monitoring of interactions in physiological conditions. The PEG coating provides high colloidal stability for NPs of both sizes. For 5 nm NPs in NaCl solution, a stable 3D self-assembled body-centered cubic (BCC) arrangement is detected with an interparticle distance of 20.7 ± 0.1 nm. In protein solution, this distance increases to 21.9 ± 0.1 nm by protein penetration inside the ordered structure. For citrate-capped NPs, a different mechanism is observed. The protein particles attach to the NPs surfaces, and an appropriate concentration of proteins results in a stable suspension. Cryogenic transmission electron microscopy (Cryo-TEM), UV–visible spectroscopy, and dynamic light scattering (DLS) support the SAXS results. The findings will pave the way to design and synthesize NPs with controlled behaviors in biomedical applications.

36 MATERIALS SCIENCE↗

Optically Induced Anisotropy in Time-Resolved Scattering: Imaging Molecular-Scale Structure and Dynamics in Disordered Media with Experiment and Theory

Time-resolved scattering experiments enable imaging of materials at the molecular scale with femtosecond time resolution. However, in disordered media they provide access to just one radial dimension thus limiting the study of orientational structure and dynamics. Here we introduce a rigorous and practical theoretical framework for predicting and interpreting experiments combining optically induced anisotropy and time-resolved scattering. Using impulsive nuclear Raman and ultrafast x-ray scattering experiments of chloroform and simulations, we demonstrate that this framework can accurately predict and elucidate both the spatial and temporal features of these experiments.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

How Do Ionic Liquids “Fold” Ionenes? Computational and Experimental Analysis of Imidazolium Polymers Based on Ether and Alkyl Chain Variations Dissolved in an Ionic Liquid

Molecular dynamics (MD) simulations and complementary experiments are used here to understand the inter- and intramolecular structure and conformational properties of ionenes (i.e., cationic polymers formed from condensation reactions) dissolved in an ionic liquid (IL), 1-ethyl-3-methylimidazolium bistriflimide [C 2 mim + ][Tf 2 N - ]. The simulated structural properties are benchmarked against experimental analyses of these same polymers, mainly using dynamic light scattering (DLS) experiments. Four different imidazolium ionenes are considered, corresponding to variations in the chemistry and structure of the repeat units including: (1) poly (decylimidazolium) (PD 10 ); (2) poly (tetraethyleneglycolimidazolium) (PE 10 ); (3) alternating copolymer (P(ED) 5 ); and (4) a block copolymer (PE 5 D 5 ). Detailed computational analyses of the polymer structure and conformational properties were performed, including the radius of gyration, end-to-end distance, torsional distributions, and site-site and spatial distribution functions. Overall, there is a competition between intramolecular associations between the imidazolium groups and the ether sites in the polymers versus the intermolecular interactions of the polymer imidazolium groups with the surrounding anion molecules. The polymer with only ether linkages (PE 10 ) results in the most intramolecular interactions, leading to significant coiling behavior and chain contraction. These strong interactions reduce chain flexibility, but they also result in much more linear chain configurations and alignment of the imidazolium groups. The polymer structure is strongly affected as the concentration of alkyl groups is increased, and we find that the polymer architecture (alternating versus block copolymer) also has an important influence. Furthermore, these detailed observations are important for understanding the connection between the molecular design of imidazolium polymers and their emergent structural properties, which could lead to unique opportunities for creating polymer composites.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Scalable Synthesis of Ti 3 C 2 T x MXene

Scaling the production of synthetic 2D materials to industrial quantities has faced significant challenges due to synthesis bottlenecks whereby few have been produced in large volumes. These challenges typically stem from bottom‐up approaches limiting the production to the substrate size or precursor availability for chemical synthesis and/or exfoliation. In contrast, MXenes, a large class of 2D transition metal carbides and/or nitrides, are produced via a top‐down synthesis approach. The selective wet etching process does not have similar synthesis constraints as some other 2D materials. The reaction occurs in the whole volume; therefore, the process can be readily scaled with reactor volume. Herein, the synthesis of 2D titanium carbide MXene (Ti 3 C 2 T x ) is studied in two batch sizes, 1 and 50 g, to determine if large‐volume synthesis affects the resultant structure or composition of MXene flakes. Characterization of the morphology and properties of the produced MXene using scanning electron microscopy, X‐ray diffraction, dynamic light scattering, Raman spectroscopy, X‐ray photoelectron spectroscopy, UV–visible spectroscopy, and conductivity measurements show that the materials produced in both batch sizes are essentially identical. This illustrates that MXenes experience no change in structure or properties when scaling synthesis, making them viable for further scale‐up and commercialization.

Shuck, Christopher E.↗

Titanium Dioxide Nanomaterial Ink Production Through Laser Ablation Synthesis in Solution for Printed Electronics Applications

Flexible and printed electronics have become increasingly popular as they make possible the production of flexible, low-cost, multifunction devices that are unachievable through traditional manufacturing methods. The printed films are significantly impacted and thus limited by the existing ink production process. Herein, an alternate technique of generating high-quality titanium dioxide (TiO 2 ) nanoparticle ink compatible with aerosol jet printing using laser ablation synthesis in solution (LASiS) is showcased. Dynamic light scattering data and transmission electron microscopy confirm the particle size distribution. UV–vis measurements are performed, and the Beer–Lambert relationship is used to determine the concentration of the generated ink. The inks generated at two different repetition rates are compared: 200 kHz and 1 MHz. X-Ray diffraction analysis of the aerosol jet printed thin film post-thermal sintering confirms the grain size and phase purity of the printed thin films. This work demonstrates the effectiveness of the LASiS technique in producing printable nanoparticle inks with little-to-no postprocessing.

36 MATERIALS SCIENCE↗

Exceptional Alignment in a Donor–Acceptor Conjugated Polymer via a Previously Unobserved Liquid Crystal Mesophase

Abstract Orienting polymer semiconductors is desirable to optimize device characteristics, provide insight into microstructure, and magnify subtle phase behavior. Here, a combination of uniaxial strain and subsequent heating of the donor–acceptor (DA) polymer PBnDT‐FTAZ is discovered to lead to exceptional optical dichroic ratios of up to 38 (and close to 50 near the polymer's absorption edge). This alignment is achieved due to the existence of a previously undetected thermotropic liquid crystal (LC) mesophase. The LC transition, not discernable through calorimetry, is uncovered through a combination of in situ UV–vis spectroscopy, X‐ray scattering, and dynamic mechanical analysis (DMA). Comparing PBnDT‐FTAZ to the non‐fluorinated PBnDT‐HTAZ and the homo polymer PBnDT, all of which show similar thermal transitions, reveals that exceptional alignment is only found in PBnDT‐FTAZ. This is attributed to the PBnDT‐FTAZ film having two distinct liquid crystal populations, and the polymer templating to a highly aligned, high‐clearing temperature population when heated. The DMA thermal relaxation behavior observed here is also seen in other DA conjugated polymers suggesting that such thermotropic LC mesophases may be common in these materials. These findings demonstrate a polymer semiconductor with remarkable alignment and uncover phase behavior with broad implications for process‐structure‐property relationships in polymer semiconductors.

36 MATERIALS SCIENCE↗

Porous Polymers as Universal Reversal Agents for Heparin Anticoagulants through an Inclusion–Sequestration Mechanism

Heparins are widely used anticoagulants for surgical procedures and extracorporeal therapies. However, all of them have bleeding risks. Protamine sulfate, the only clinically approved antidote for unfractionated heparin (UFH), has adverse effects. Moreover, protamine can only partially neutralize low-molecular-weight heparins (LMWHs) and is not effective for fondaparinux. In this report an inclusion–sequestration strategy for efficient neutralization of heparin anticoagulants by cationic porous supramolecular organic frameworks (SOFs) and porous organic polymers (POPs) is reported. Isothermal titration calorimetric and fluorescence experiments show strong binding affinities of these porous polymers toward heparins, whereas dynamic light scattering and zeta potential analysis confirm that the heparin sequences are adsorbed into the interior of the porous hosts. Activated partial thromboplastin time, anti-FXa, and thromboelastography assays indicate that their neutralization efficacies are higher than or as high as that of protamine for UFH and generally superior to protamine for LMWHs and fondaparinux, which is further confirmed by tail-transection model in mice and ex vivo aPTT or anti-FXa analysis in rats. Acute toxicity evaluations reveal that one of the SOFs displays outstanding biocompatibility. This work suggests that porous polymers can supply safe and rapid reversal of clinically used heparins, as protamine surrogates, providing an improved approach for their neutralization.

36 MATERIALS SCIENCE↗

Genetic Fusion of Thermoresponsive Polypeptides with UCST‐type Behavior Mediates 1D Assembly of Coiled‐Coil Bundlemers

Abstract Thermoresponsive resilin‐like polypeptides (RLPs) of various lengths were genetically fused to two different computationally designed coiled coil‐forming peptides with distinct thermal stability, to develop new strategies to assemble coiled coil peptides via temperature‐triggered phase separation of the RLP units. Their successful production in bacterial expression hosts was verified via gel electrophoresis, mass spectrometry, and amino acid analysis. Circular dichroism (CD) spectroscopy, ultraviolet‐visible (UV/Vis) turbidimetry, and dynamic light scattering (DLS) measurements confirmed the stability of the coiled coils and showed that the thermosensitive phase behavior of the RLPs was preserved in the genetically fused hybrid polypeptides. Cryogenic‐transmission electron microscopy and coarse‐grained modeling revealed that functionalizing the coiled coils with thermoresponsive RLPs leads to their thermally triggered noncovalent assembly into nanofibrillar assemblies.

Patkar, Sai S.↗

Genetic Fusion of Thermoresponsive Polypeptides with UCST–type Behavior Mediates 1D Assembly of Coiled–Coil Bundlemers

Thermoresponsive resilin-like polypeptides (RLPs) of various lengths were genetically fused to two different computationally designed coiled coil-forming peptides with distinct thermal stability, to develop new strategies to assemble coiled coil peptides via temperature-triggered phase separation of the RLP units. Furthermore, their successful production in bacterial expression hosts was verified via gel electrophoresis, mass spectrometry, and amino acid analysis. Circular dichroism (CD) spectroscopy, ultraviolet-visible (UV/Vis) turbidimetry, and dynamic light scattering (DLS) measurements confirmed the stability of the coiled coils and showed that the thermosensitive phase behavior of the RLPs was preserved in the genetically fused hybrid polypeptides. Cryogenic-transmission electron microscopy and coarse-grained modeling revealed that functionalizing the coiled coils with thermoresponsive RLPs leads to their thermally triggered noncovalent assembly into nanofibrillar assemblies.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A Woven Supramolecular Metal‐Organic Framework Comprising a Ruthenium Bis(terpyridine) Complex and Cucurbit[8]uril: Enhanced Catalytic Activity toward Alcohol Oxidation

Abstract The self‐assembly of a diamondoid woven supramolecular metal–organic framework wSMOF‐1 has been achieved from intertwined [Ru(tpy) 2 ] 2+ (tpy=2,2′,6′,2′′‐terpyridine) complex M1 and cucurbit[8]uril (CB[8]) in water, where the intermolecular dimers formed by the appended aromatic arms of M1 are encapsulated in CB[8]. wSMOF‐1 exhibits ordered pore periodicity in both water and the solid state, as confirmed by a combination of 1 H NMR spectroscopy, UV‐vis absorption, isothermal titration calorimetry, dynamic light scattering, small angle X‐ray scattering and selected area electron diffraction experiments. The woven framework has a pore aperture of 2.1 nm, which allows for the free access of both secondary and primary alcohols and tert ‐butyl hydroperoxide (TBHP). Compared with the control molecule [Ru(tpy) 2 ]Cl 2 , the [Ru(tpy) 2 ] 2+ unit of wSMOF‐1 exhibits a remarkably higher heterogeneous catalysis activity for the oxidation of alcohols by TBHP in n ‐hexane. For the oxidation of 1‐phenylethan‐1‐ol, the yield of acetophenone was increased from 10 % to 95 %.

Zhang, Yun‐Chang↗

27 Al NMR diffusometry of Al 13 Keggin nanoclusters

Although nanometer-sized aluminum hydroxide clusters (i.e., ϵ-Al 13 , [Al 13 O 4 (OH) 24 (H 2 O) 12 ] 7+ ) command a central role in aluminum ion speciation and transformations between minerals, measurement of their translational diffusion is often limited to indirect methods. Here, in this work, 27 Al pulsed field gradient stimulated echo nuclear magnetic resonance (PFGSTE NMR) spectroscopy has been applied to the AlO 4 core of the ϵ-Al 13 cluster with complementary theoretical simulations of the diffusion coefficient and corresponding hydrodynamic radii from a boundary element-based calculation. The tetrahedral AlO 4 center of the ϵ-Al 13 cluster is symmetric and exhibits only weak quadrupolar coupling, which results in favorable T 1 and T 2 27 Al NMR relaxation coefficients for 27 Al PFGSTE NMR studies. Stokes–Einstein relationship was used to relate the 27 Al diffusion coefficient of the ϵ-Al 13 cluster to the hydrodynamic radius for comparison with theoretical simulations, dynamic light scattering from literature, and previously published 1 H PFGSTE NMR studies of chelated Keggin clusters. This first-of-its-kind observation proves that 27 Al PFGSTE NMR diffusometry can probe symmetric Al environments in polynuclear clusters of greater molecular weight than previously considered.

27Al↗