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At least 649 records · Page 36

Predicting Hugoniot equation of state in erythritol with ab initio and reactive molecular dynamics

Erythritol has been proposed as an inert surrogate for developing theoretical and computational models to study aging in energetic materials. In this work, we present a comparison of mechanical and shock properties of erythritol computed using the ReaxFF reactive force field and from ab initio calculations employing density functional theory (DFT). We screened eight different ReaxFF parameterizations, of which the CHO parameters developed for hydrocarbon oxidation provide the most accurate predictions of mechanical properties and the crystal structure of erythritol. Further validation of the applicability of this ReaxFF parameterization for modeling erythritol is demonstrated by comparing predictions of the elastic constants, crystal structure, vibrational density of states, and Hugoniot curves against DFT calculations. The ReaxFF predictions are in close agreement with the DFT simulations for the elastic constants and shock Hugoniot when the crystal is loaded along its c axis but show as much as 30% disagreement in the elastic constants in the ab plane and 12% difference in shock pressures when shocked along the a or b crystal axes. Last, we compare thermomechanical properties predicted from classical molecular dynamics with those calculated using the quasi-harmonic approximation and show that quantum mechanical effects produce large discrepancies in the computed values of heat capacity and thermal expansion coefficients compared with classical assumptions. Combining classical molecular dynamics predictions of mechanical behavior with phonon-based calculations of thermal behaviors, we show that predicted shock-induced temperatures for pressures up to 6.5 GPa do not exceed the pressure-dependent melting point of erythritol.

Hu, Jing↗

Ground Based Program for the Physical Analysis of Macromolecular Crystal Growth

During the past year we have focused on application of in situ Atomic Force Microscopy (AFM) for studies of the growth mechanisms and kinetics of crystallization for different macromolecular systems. Mechanisms of macrostep formation and their decay, which are important in understanding of defect formation, were studied on the surfaces of thaumatin, catalase, canavalin and lysozyme crystals. Experiments revealed that step bunching on crystalline surfaces occurred either due to two- or three-dimensional nucleation on the terraces of vicinal slopes or as a result of uneven step generation by complex dislocation sources. No step bunching arising from interaction of individual steps in the course of the experiment was observed. The molecular structure of the growth steps for thaumatin and lipase crystals were deduced. It was further shown that growth step advance occurs by incorporation of single protein molecules. In singular directions growth steps move by one-dimensional nucleation on step edges followed by lateral growth. One-dimensional nuclei have different sizes, less then a single unit cell, varying for different directions of step movement. There is no roughness due to thermal fluctuations, and each protein molecule which incorporated into the step remained. Growth kinetics for catalase crystals was investigated over wide supersaturation ranges. Strong directional kinetic anisotropy in the tangential step growth rates in different directions was seen. The influence of impurities on growth kinetics and cessation of macromolecular crystals was studied. Thus, for catalase, in addition to pronounced impurity effects on the kinetics of crystallization, we were also able to directly observe adsorption of some impurities. At low supersaturation we repeatedly observed filaments which formed from impurity molecules sedimenting on the surfaces. Similar filaments were observed on the surfaces of thaumatin, canavalin and STMV crystals as well, but the frequency was low compared with catalase crystallization. Cessation of growth of xylanase and lysozyme crystals was also observed and appeared to be a consequence of the formation of dense impurity adsorption layers. Attachment: "An in situ AFM investigation of catalase crystallization", "Atomic force microscopy studies of living cells: visualization of motility, division, aggregation, transformation, and apoptosis", AFM studies on mechanisms of nucleation and growth of macromolecular crystals", and "In situ atomic force microscopy studies of surface morphology, growth kinetics, defect structure and dissolution in macromolecular crystallization".

Malkin, Alexander J.↗

Structural analyses of the PKA RIIβ holoenzyme containing the oncogenic DnaJB1-PKAc fusion protein reveal protomer asymmetry and fusion-induced allosteric perturbations in fibrolamellar hepatocellular carcinoma

When the J-domain of the heat shock protein DnaJB1 is fused to the catalytic (C) subunit of cAMP-dependent protein kinase (PKA), replacing exon 1, this fusion protein, J-C subunit (J-C), becomes the driver of fibrolamellar hepatocellular carcinoma (FL-HCC). Here, we use cryo-electron microscopy (cryo-EM) to characterize J-C bound to RIIβ, the major PKA regulatory (R) subunit in liver, thus reporting the first cryo-EM structure of any PKA holoenzyme. We report several differences in both structure and dynamics that could not be captured by the conventional crystallography approaches used to obtain prior structures. Most striking is the asymmetry caused by the absence of the second cyclic nucleotide binding (CNB) domain and the J-domain in one of the RIIβ:J-C protomers. Using molecular dynamics (MD) simulations, we discovered that this asymmetry is already present in the wild-type (WT) RIIβ 2 C 2 but had been masked in the previous crystal structure. This asymmetry may link to the intrinsic allosteric regulation of all PKA holoenzymes and could also explain why most disease mutations in PKA regulatory subunits are dominant negative. The cryo-EM structure, combined with small-angle X-ray scattering (SAXS), also allowed us to predict the general position of the Dimerization/Docking (D/D) domain, which is essential for localization and interacting with membrane-anchored A-Kinase-Anchoring Proteins (AKAPs). This position provides a multivalent mechanism for interaction of the RIIβ holoenzyme with membranes and would be perturbed in the oncogenic fusion protein. The J-domain also alters several biochemical properties of the RIIβ holoenzyme: It is easier to activate with cAMP, and the cooperativity is reduced. These results provide new insights into how the finely tuned allosteric PKA signaling network is disrupted by the oncogenic J-C subunit, ultimately leading to the development of FL-HCC.

59 BASIC BIOLOGICAL SCIENCES↗

DNA Crystals as a Template for Patterned Functional Materials

DNA nanotechnology offers a wide toolkit of molecular functionalities and scales, including intricate motifs less than 10 nm and periodic structures exceeding 100 µm. At larger scales, however, there are often significant tradeoffs for DNA structures, namely stability and mechanical strength. This work describes the design, synthesis, and characterization of a functionalized DNA crystal. Using a ligated DNA crystal grants significant freedom for various functional materials to be applied, in this case, semiconducting cadmium sulfide and palladium metal. Properties investigated in this study include stability, mechanical strength, and optoelectronic properties such as photoluminescence (PL) and electric conductivity. Significant changes are observed based on the functional material applied to DNA crystals. The Young's modulus of the crystal varies by about five orders of magnitude when functionalized with palladium. PL and semiconductive behaviors were observed when cadmium sulfide was attached. These crystals represent an expansion of the capabilities of DNA structures at these length scales, and additionally a platform for future studies exchanging the materials or altering the ligation scheme.

CdS↗

On the role of methyl groups in the molecular architectures of mesophase pitches

The role of methyl groups on the liquid–crystal structure of mesophase pitches was investigated by combining experimental characterizations and atomic-scale computational modeling, using three pitches synthesized from different precursors. Of the three pitches, C-9 alkyl benzene and naphthalene-based pitches have 13 and 7 methyl groups per average polyaromatic hydrocarbon, respectively. By contrast, mesophase produced from a coal-tar pitch has about one methyl group. The coal tar–based mesophase pitch is hydrogen deficient or more aromatic compared with C-9 alkyl benzene- and naphthalene-based pitches. Additionally, X-ray diffraction data showed that average coherent domain sizes of C-9 alkyl benzene (3.7 nm) and naphthalene-based (3.6 nm) pitches with more methyl groups are larger than that of coal tar–based mesophase (2.4 nm). Based on the identified features, the influence of the methyl group on the layering structures was investigated via molecular dynamics simulations. The results revealed that methyl groups are critical in mesophase layering in C-9 alkyl benzene- and naphthalene-based pitches, by reducing CH-π interaction. However, similar alignment could be achieved without the same degree of methyl substitutions for the coal tar-based pitch because of stronger π-π interaction than the other precursors. The insights from this study contribute to our understanding of the formation of conventional mesophase pitch and have implications for the processing of coal-derived materials. In conclusion, this knowledge is vital to produce valuable products like carbon fiber and graphite from pitches.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Ice Recrystallization Inhibition Activity of Soy Protein Hydrolysates

Identifying and developing ice recrystallization inhibitors from sustainable food proteins such as soy protein isolate (SPI) can lead to practical applications in both pharmaceutical and food industries. Here, the objective of this study was to investigate the ice recrystallization inhibition (IRI) activity of SPI hydrolysates, and this was achieved by using an IRI activity-guided fractionation approach and relating IRI activity to interfacial molecular activity measured by vibrational sum frequency generation (VSFG). In addition, the impact of molecular weight (MW) and enzyme specificity was analyzed using three different proteases (Alcalase, trypsin, and pancreatin) and varying hydrolysis times. Using preparative chromatography, hydrolysates from each enzyme treatment were fractionated into five different MW fractions (F1–F5), which were then characterized by high-performance liquid chromatography (HPLC). All SPI hydrolysates had IRI activity, resulting in a 57–29% ice crystal diameter reduction when compared to native SPI. The F1 fraction (of 4–14 kDa) was most effective among all tested hydrolysates, while the lower MW peptide fractions lacked activity. One sample (SPI-ALC 20-F1) had a 52% reduction of ice crystal size at a lower concentration of 2% compared to the typical 4% used. SFG showed a difference in H-bonding and hydrophobic interactions of the molecules on the water/air interface, which may be linked to IRI activity. This study demonstrates for the first time the ability of SPI hydrolysates to inhibit ice crystal growth and the potential application of SFG to study molecular interaction at the interface that may help illustrate the mechanism of action.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Low-energy magneto-optics of Tb 2 Ti 2 O 7 in a [111] magnetic field

The pyrochlore magnet Tb 2 Ti 2 O 7 shows a lack of magnetic order to low temperatures and is considered to be a quantum spin liquid candidate. Here we perform time-domain THz spectroscopy on high-quality Tb 2 Ti 2 O 7 crystals and study the low-energy excitations as a function of [111] magnetic field with high energy resolution. The low-energy crystal-field excitations change their energies anomalously under magnetic field. Despite several sharp field-dependent changes, we show that the material's spectrum can be described not by phase transitions but by field-dependent hybridization between the low-energy crystal-field levels. We highlight the strong coupling between spin and lattice degrees of freedom in Tb 2 Ti 2 O 7 as evidenced by the magnetic-field tunable crystal-field environment. Calculations based on single ion physics with field-induced symmetry reduction of the crystal-field environment can reproduce our data.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Potential Challenges in Near-Field Scanning Optical Microscopy for Space Applications

Near-field scanning optical microscopy (NSOM) also called scanning near-field optical microscopy (SNOM) is now well accepted as a powerful tool for sub-wavelength (nanoscale in the optical region) spatial resolution microscopy and a large number of related tasks. The importance lies in the fact of strategic advantages of standard microscopy but with significantly enhanced resolution. Since many modern optical diagnostic techniques have found useful applications in space, it is logical to consider the future role of NSOM in such situations. For example, protein crystal growth study under microgravity conditions is a valid candidate. If applied successfully, processes at molecular level can be studied during the growth. NSOM has already been demonstrated to be useful for the study of such crystals here on earth. The basic principle of NSOM can be illustrated. The illumination-collection mode is shown although several other possible approaches exist. In this, the sample is illuminated and the light from the sample is collected through the same tiny aperture opening. A tapered optical fiber is scanned near the sample surface. The tip is coated generally with a metal with a sub-wavelength aperture opening. The tip-sample distance is maintained constant while scanning. Thus, the optical signal available for collection is generally a function of the optical properties of the sample surface. Since the aperture is sub-wavelength in diameter and the tip is held very close (again in the sub-wavelength domain) to the surface, the lateral resolution in the sub-wavelength domain is obtained. Thus, the typical wavelength- order resolution of ordinary microscopy can be significantly enhanced while maintaining the strategic advantages (no need of sample in vacuum chamber, electron beams, etc). Commercial NSOM systems play a key role in the success and widespread acceptance of the tool. These commercial systems work fairly well in laboratory conditions on earth. However, they may not be deployed on a space mission as such with comparable outcome. In this communication we discuss several potential problems and some possible solutions.

Vikram, Chandra S.↗

Stress-Induced Structural Transformations in Au Nanocrystals

Nanocrystals can exist in multiply twinned structures like icosahedron or single crystalline structures like cuboctahedron. Transformations between these structures can proceed through diffusion or displacive motion. Experimental studies on nanocrystal structural transformations have focused on high-temperature diffusion-mediated processes. Limited experimental evidence of displacive motion exists. We report structural transformation of 6 nm Au nanocrystals under nonhydrostatic pressure of 7.7 GPa in a diamond anvil cell that is driven by displacive motion. X-ray diffraction and transmission electron microscopy were used to detect the structural transformation from multiply twinned to single crystalline. Single crystalline nanocrystals were recovered after unloading, then quickly reverted to the multiply twinned state after dispersion in toluene. Furthermore, the dynamics of recovery was captured using TEM which showed surface recrystallization and rapid twin boundary motion. Molecular dynamics simulations showed that twin boundaries are unstable due to defects nucleated from the interior of the nanocrystal.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

Helfrich-Hurault elastic instabilities driven by geometrical frustration

Here, the Helfrich-Hurault (HH) elastic instability is a well-known mechanism behind patterns that form as a result of strain upon liquid crystal systems with periodic ground states. In the HH model, layered structures undulate and buckle in response to local, geometric incompatibilities in order to maintain the preferred layer spacing. Classic HH systems include cholesteric liquid crystals under electromagnetic field distortions and smectic liquid crystals under mechanical strains, where both materials are confined between rigid substrates. However, richer phenomena are observed when undulation instabilities occur in the presence of deformable interfaces and variable boundary conditions. Understanding how the HH instability is affected by deformable surfaces is imperative for applying the instability to a broader range of materials. In this review, the HH mechanism is reexamined and special focus is given to how the boundary conditions influence the response of lamellar systems to geometrical frustration. Lamellar liquid crystals confined within a spherical shell geometry are used as the model system. Made possible by the relatively recent advances in microfluidics within the past 15 years, liquid crystal shells are composed entirely of fluid interfaces and have boundary conditions that can be dynamically controlled at will. Past and recent work that exemplifies how topological constraints, molecular anchoring conditions, and boundary curvature can trigger the HH mechanism in liquid crystals with periodic ground states is examined. The review ends by identifying similar phenomena across a wide variety of materials, both biological and synthetic. The fact that the HH mechanism is a generic and often overlooked response of periodic materials to geometrical frustration is highlighted.

42 ENGINEERING↗

pH-Driven Restructuring of Hydration Layers and Cation Adsorption at the Alumina–Water Interface

Oxide−water interfaces underpin ion separations, catalysis, and electrochemical energy technologies, where the electrical double layer (EDL) controls adsorption, transport, and reactivity. However, the molecular-scale links between pHdependent surface protonation, hydration-layer structure, and counterion adsorption remain poorly defined. Here, we combine in situ crystal truncation rod (CTR) and resonant anomalous X-ray reflectivity (RAXR) with streaming potential measurements and ab initio molecular dynamics (AIMD) simulations to resolve the chemical and structural evolution of the EDL at the single-crystal alumina (012)−water interface in 10 mM Rb + over pH 3−12. CTR measurements reveal two distinct adsorbed water layers at ∼2.2 and ∼3.5 Å above the surface. Each water layer shifts toward the substrate at transition pHs near 6.5 and 10.6, respectively, reflecting changes in primary hydration layer structure in response to the deprotonation of bridging and terminal aluminol groups. RAXR shows a 10-fold increase in Rb + coverage and a decrease in mean adsorption height from ∼3.5 to ∼2.7 Å with increasing pH, indicating enhanced counterion binding accompanied by Stern layer contraction. Streaming potential measurements demonstrate that the zeta potential, i.e., the potential at the hydrodynamic shear plane, is positive at pH 3 and becomes negative at pH ≥ 3.5. The negative charge magnitude increases with increasing pH, consistent with progressive surface deprotonation at higher pH. AIMD identifies inner- and outer-sphere Rb+ complexes whose adsorption heights and coordination geometries depend sensitively on the protonation state of surface oxygens, providing atomistic support for the experimentally inferred trends. These measurements establish two discrete, site-specific pH transitions in hydration-layer structure that track aluminol (de)protonation and quantitatively link them to a pH-driven contraction of the Stern layer (increasing Rb + coverage and decreasing adsorption height). This provides a direct structural basis for connecting surface acid−base chemistry to ion binding distances at an oxide−water interface.

Adsorption↗

Design and evaluation of novel analogs of 2-amino-4-boronobutanoic acid (ABBA) as inhibitors of human gamma-glutamyl transpeptidase

Inhibitors of gamma-glutamyl transpeptidase (GGT1, aka gamma-glutamyl transferase) are needed for the treatment of cancer, cardiovascular illness and other diseases. Compounds that inhibit GGT1 have been evaluated in the clinic, but no inhibitor has successfully demonstrated specific and systemic GGT1 inhibition. All have severe side effects. L-2-amino-4-boronobutanoic acid (l-ABBA), a glutamate analog, is the most potent GGT1 inhibitor in vitro. In this study, we have solved the crystal structure of human GGT1 (hGGT1) with ABBA bound in the active site. The structure was interrogated to identify interactions between the enzyme and the inhibitor. Based on these data, a series of novel ABBA analogs were designed and synthesized. Their inhibitory activity against the hydrolysis and transpeptidation activities of hGGT1 were determined. The lead compounds were crystalized with hGGT1 and the structures solved. The kinetic data and structures of the complexes provide new insights into the critical role of protein structure dynamics in developing compounds for inhibition of hGGT1.

60 APPLIED LIFE SCIENCES↗

Interface-enhanced conductivities in surfactant-mediated, solution-grown ionic crystalline complexes

Renewable energy is increasingly relying on optimized electrolytes and interfaces. In this work, Tween 20 and sodium chloride are selected as a model system to reveal the effects of surfactants on salt crystallization in the context of ionic conductivity and interface optimization. At a varied crystallization speed and mix ratio, it is demonstrated that the resultant solution-grown ionic crystalline complexes can achieve a highly tunable ion transport with a controllable crystalline interface. X-ray diffraction results rule out the possibility of polymorphism in the NaCl/Tween 20 systems, which further supports the importance of an optimized crystalline network for optimizing permittivity or ionic conductivity. Raman mapping and machine learning techniques are used to perform semantic segmentation on highly heterogeneous NaCl/Tween 20 complexes. Furthermore, FTIR measurements demonstrate that inter- and intra-molecular interactions play critical roles in the formation of these crystals. This work lays a foundation toward future optimization of such complex ion systems for a specific salt or crystallization modifier in energy storage or ion transport applications.

36 MATERIALS SCIENCE↗

Molecular mechanism of biased signaling at the kappa opioid receptor

The κ-opioid receptor (KOR) has emerged as an attractive drug target for pain management without addiction, and biased signaling through particular pathways of KOR may be key to maintaining this benefit while minimizing side-effect liabilities. As for most G protein-coupled receptors (GPCRs), however, the molecular mechanisms of ligand-specific signaling at KOR have remained unclear. To better understand the molecular determinants of KOR signaling bias, we apply structure determination, atomic-level molecular dynamics (MD) simulations, and functional assays. We determine a crystal structure of KOR bound to the G protein-biased agonist nalfurafine, the first approved KOR-targeting drug. We also identify an arrestin-biased KOR agonist, WMS-X600. Using MD simulations of KOR bound to nalfurafine, WMS-X600, and a balanced agonist U50,488, we identify three active-state receptor conformations, including one that appears to favor arrestin signaling over G protein signaling and another that appears to favor G protein signaling over arrestin signaling. These results, combined with mutagenesis validation, provide a molecular explanation of how agonists achieve biased signaling at KOR.

59 BASIC BIOLOGICAL SCIENCES↗

A Four‐Coordinate Pr 4+ Imidophosphorane Complex

Abstract The imidophosphorane ligand, [NP t Bu 3 ] − ( t Bu= tert ‐butyl), enables isolation of a pseudo‐tetrahedral, tetravalent praseodymium complex, [Pr 4+ (NP t Bu 3 ) 4 ] ( 1‐Pr ), which is characterized by a suite of physical characterization methods including single‐crystal X‐ray diffraction, electron paramagnetic resonance, and L 3 ‐edge X‐ray near‐edge spectroscopies. Variable‐temperature direct‐current magnetic susceptibility data, supported by multiconfigurational quantum chemical calculations, demonstrate that the electronic structure diverges from the isoelectronic Ce 3+ analogue, driven by increased crystal field. The four‐coordinate environment around Pr 4+ in 1‐Pr , which is unparalleled in reported extended solid systems, provides a unique opportunity to study the interplay between crystal field splitting and spin‐orbit coupling in a molecular tetravalent lanthanide within a pseudo‐tetrahedral coordination geometry.

Boggiano, Andrew C.↗

A Four‐Coordinate Pr 4+ Imidophosphorane Complex

Abstract The imidophosphorane ligand, [NP t Bu 3 ] − ( t Bu= tert ‐butyl), enables isolation of a pseudo‐tetrahedral, tetravalent praseodymium complex, [Pr 4+ (NP t Bu 3 ) 4 ] ( 1‐Pr ), which is characterized by a suite of physical characterization methods including single‐crystal X‐ray diffraction, electron paramagnetic resonance, and L 3 ‐edge X‐ray near‐edge spectroscopies. Variable‐temperature direct‐current magnetic susceptibility data, supported by multiconfigurational quantum chemical calculations, demonstrate that the electronic structure diverges from the isoelectronic Ce 3+ analogue, driven by increased crystal field. The four‐coordinate environment around Pr 4+ in 1‐Pr , which is unparalleled in reported extended solid systems, provides a unique opportunity to study the interplay between crystal field splitting and spin‐orbit coupling in a molecular tetravalent lanthanide within a pseudo‐tetrahedral coordination geometry.

Boggiano, Andrew C.↗

In Situ Scattering Studies of Superconducting Vacancy‐Ordered Monoclinic TiO Thin Films

Abstract The structural and transport properties of vacancy‐ordered monoclinic superconducting titanium oxide (TiO) thin films grown by molecular beam epitaxy are investigated. The evolution of the crystal structure during growth is monitored by in situ synchrotron X‐ray diffraction. Long‐range ordering of Ti and O vacancies in the disordered cubic phase stabilizes the vacancy‐ordered monoclinic TiO phase. The reduced structural disorder arising from vacancy‐ordering is correlated with a superconductor‐metal transition (SMT) in contrast to the superconductor‐insulator transition (SIT) observed in cubic TiO, orthorhombic Ti 2 O 3 , and the Magneli γ − Ti 3 O 5 and γ − Ti 4 O 7 phase. Magnetoresistance measurements for the SIT phases indicate superconducting fluctuations persisting in the normal phase. These results confirm the role of disorder related to Ti and O vacancies and structural inhomogeneity in determining the electronic properties of the normal state of titanium oxide‐based superconductors.

Baksi, Merve↗