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This review article centers around structured liquids and their underlying mechanisms. The focus is on the chemistry, applications, characterization, reconfigurability, and future prospects of this class of soft materials.
Abstract This dataset contains ligand conformations and docking scores for 1.4 billion molecules docked against 6 structural targets from SARS-CoV2, representing 5 unique proteins: MPro, NSP15, PLPro, RDRP, and the Spike protein. Docking was carried out using the AutoDock-GPU platform on the Summit supercomputer and Google Cloud. The docking procedure employed the Solis Wets search method to generate 20 independent ligand binding poses per compound. Each compound geometry was scored using the AutoDock free energy estimate, and rescored using RFScore v3 and DUD-E machine-learned rescoring models. Input protein structures are included, suitable for use by AutoDock-GPU and other docking programs. As the result of an exceptionally large docking campaign, this dataset represents a valuable resource for discovering trends across small molecule and protein binding sites, training AI models, and comparing to inhibitor compounds targeting SARS-CoV-2. The work also gives an example of how to organize and process data from ultra-large docking screens.
Polymers of intrinsic microporosity (PIMs) are a family of materials with potential to be effective and scalable solutions for challenging adsorbent and membrane applications. The broad range of repeat unit chemistry, microporous structural features, and polymer processing makes exploration of the expansive PIM design space inefficient via chemical and materials intuition alone. Computational techniques such as molecular simulations and machine learning can provide a leap in capabilities to address this polymer design challenge and will be central to the future development of PIMs. In this work, we highlight recent microporous material studies that arrived at key results by employing computational techniques and provide our perspective on the prospects for in silico design and development of PIMs.
Controlling the interfaces and interactions of colloidal nanoparticles (NPs) via tethered molecular moieties is crucial for NP applications in engineered nanomaterials, optics, catalysis, and nanomedicine. Despite a broad range of molecular types explored, there is a need for a flexible approach to rationally vary the chemistry and structure of these interfacial molecules for controlling NP stability in diverse environments, while maintaining a small size of the NP molecular shell. Here, we demonstrate that low-molecular-weight, bifunctional comb-shaped, and sequence-defined peptoids can effectively stabilize gold NPs (AuNPs). The generality of this robust functionalization strategy was also demonstrated by coating of silver, platinum, and iron oxide NPs with designed peptoids. Each peptoid (PE) is designed with varied arrangements of a multivalent AuNP-binding domain and a solvation domain consisting of oligo-ethylene glycol (EG) branches. Among designs, a peptoid (PE5) with a diblock structure is demonstrated to provide a superior nanocolloidal stability in diverse aqueous solutions while forming a compact shell (similar to 1.5 nm) on the AuNP surface. We demonstrate by experiments and molecular dynamics simulations that PE5-coated AuNPs (PE5/AuNPs) are stable in select organic solvents owing to the strong PE5 (amine)-Au binding and solubility of the oligo-EG motifs. At the vapor-aqueous interface, we show that PE5/AuNPs remain stable and can self-assemble into ordered 2D lattices. The NP films exhibit strong near-field plasmonic coupling when transferred to solid substrates.
Extreme conditions inside ice giants such as Uranus and Neptune can result in peculiar chemistry and structural transitions, e.g., the precipitation of diamonds or superionic water, as so far experimentally observed only for pure C$-$H and H 2 O systems, respectively. Here, we investigate a stoichiometric mixture of C and H 2 O by shock-compressing polyethylene terephthalate (PET) plastics and performing in situ x-ray probing. We observe diamond formation at pressures between 72 ± 7 and 125 ± 13 GPa at temperatures ranging from ~3500 to ~6000 K. Combining x-ray diffraction and small-angle x-ray scattering, we access the kinetics of this exotic reaction. The observed demixing of C and H 2 O suggests that diamond precipitation inside the ice giants is enhanced by oxygen, which can lead to isolated water and thus the formation of superionic structures relevant to the planets’ magnetic fields. Moreover, our measurements indicate a way of producing nanodiamonds by simple laser-driven shock compression of cheap PET plastics.
Abstract Recent studies have indicated that the C 4 perennial bioenergy crops switchgrass ( Panicum virgatum ) and big bluestem ( Andropogon gerardii ) accumulate significant amounts of soil carbon (C) owing to their extensive root systems. Soil C accumulation is likely driven by inter‐ and intraspecific variability in plant traits, but the mechanisms that underpin this variability remain unresolved. In this study we evaluated how inter‐ and intraspecific variation in root traits of cultivars from switchgrass (Cave‐in‐Rock, Kanlow, Southlow) and big bluestem (Bonanza, Southlow, Suther) affected the associations of soil C accumulation across soil fractions using stable isotope techniques. Our experimental field site was established in June 2008 at Fermilab in Batavia, IL. In 2018, soil cores were collected (30 cm depth) from all cultivars. We measured root biomass, root diameter, specific root length, bulk soil C, C associated with coarse particulate organic matter (CPOM) and fine particulate organic matter plus silt‐ and clay‐sized fractions, and characterized organic matter chemical class composition in soil using high‐resolution Fourier‐transform ion cyclotron resonance mass spectrometry. C 4 species were established on soils that supported C 3 grassland for 36 years before planting, which allowed us to use differences in the natural abundance of stable C isotopes to quantify C 4 plant‐derived C. We found that big bluestem had 36.9% higher C 4 plant‐derived C compared to switchgrass in the CPOM fraction in the 0–10 cm depth, while switchgrass had 60.7% higher C 4 plant‐derived C compared to big bluestem in the clay fraction in the 10–20 cm depth. Our findings suggest that the large root system in big bluestem helps increase POM‐C formation quickly, while switchgrass root structure and chemistry build a mineral‐bound clay C pool through time. Thus, both species and cultivar selection can help improve bioenergy management to maximize soil carbon gains and lower CO 2 emissions.
Abstract The lithium–palladium and lithium–palladium–hydrogen systems are investigated at high pressures at and above room temperature. Two novel lithium–palladium compounds are found below $${18.7}\,{\mathrm{GPa}}$$ 18.7 GPa . An ambient temperature phase is tentatively assigned as $$F{\bar{4}}3m\,\hbox {Li}_{17}\hbox {Pd}_{4}$$ F 4 ¯ 3 m Li 17 Pd 4 , with $$a = 17.661(1)$$ a = 17.661 ( 1 ) Å at 8.64 GPa, isostructural with $$\hbox {Li}_{17}\hbox {Sn}_{4}$$ Li 17 Sn 4 . The other phase occurs at high-temperature and is $$I{\bar{4}}3m\, \hbox {Li}_{11}\hbox {Pd}_{2}$$ I 4 ¯ 3 m Li 11 Pd 2 , $$a = 9.218(1)$$ a = 9.218 ( 1 ) Å at 3.88 GPa and 200 $$^\circ {\mathrm{C}}$$ ∘ C , similar to $$\hbox {Li}_{11}\hbox {Pt}_{2}$$ Li 11 Pt 2 , which is also known at high pressure. The presence of hydrogen in the system results in an $$I{\bar{4}}3m$$ I 4 ¯ 3 m structure with $$a = 8.856(1)$$ a = 8.856 ( 1 ) Å at 9.74 GPa. This persists up to $${13.3}\,\mathrm{GPa}$$ 13.3 GPa , the highest pressure studied. Below $${2}\,{\mathrm{GPa}}$$ 2 GPa an fcc phase with a large unit cell, $$a = 19.324(1)$$ a = 19.324 ( 1 ) Å at 0.39 GPa, is also observed in the presence of hydrogen. On heating the hydrogen containing system at 4 GPa the $$I{\bar{4}}3m$$ I 4 ¯ 3 m phases persists to the melting point of lithium. In both systems melting the lithium results in the loss of crystalline diffraction from palladium containing phases. This is attributed to dissolution of the palladium in the molten lithium, and on cooling the palladium remains dispersed.
We investigated the chemistry and structure of the solid electrolyte interphase (SEI) grown over a silicon anode as a function of the lithium salt concentration. In these experiments, in situ neutron reflectivity measurements were performed to measure the thickness and composition of the SEI formed from 1.0 and 5.5 M lithium bis(trifluoromethane)sulfonimide (LiTFSI) in standard ethylene carbonate:dimethyl carbonate electrolytes. These measurements reveal the formation of a 350+ Å thick SEI layer that is predominantly organic (∼80%) and dimensionally stable when using a 1.0 M salt solution. In contrast, increasing the salt concentration to 5.5 M resulted in an SEI that exhibited thickness changes from 100 to 375 Å and became up to 30% inorganic. In conclusion, these compositional and structural changes point to the role of salt speciation on the resulting passivation of silicon electrodes and indicate the need to form more organic-like passivation layers to promote the calendar life of silicon anodes.
Here, in this work, we explore the use of scanning electron diffraction (also known as 4D-STEM) coupled with electron atomic pair distribution function analysis (ePDF) to understand the local order (structure and chemistry) as a function of position in a complex multicomponent system, a hot rolled, Ni-encapsulated, Zr 65 Cu 17.5 Ni 10 Al 7.5 bulk metallic glass (BMG), with a spatial resolution of 3 nm. We show that it is possible to gain insight into the chemistry and chemical clustering/ordering tendency in different regions of the sample, including in the vicinity of nano-scale crystallites that are identified from virtual dark field images and in heavily deformed regions at the edge of the BMG. In addition to simpler analysis, unsupervised machine learning was used to extract partial PDFs from the material, modeled as a quasi-binary alloy, and map them in space. These maps allowed key insights not only into the local average composition, as validated by EELS, but also a unique insight into chemical short-range ordering tendencies in different regions of the sample during formation. The experiments are straightforward and rapid and, unlike spectroscopic measurements, don’t require energy filters on the instrument. We spatially map different quantities of interest (QoI’s), defined as scalars that can be computed directly from positions and widths of ePDF peaks or parameters refined from fits to the patterns. We developed a flexible and rapid data reduction and analysis software framework that allows experimenters to rapidly explore images of the sample on the basis of different QoI’s. The power and flexibility of this approach are explored and described in detail. Because of the fact that we are getting spatially resolved images of the nanoscale structure obtained from ePDFs we call this approach scanning nano-structure electron microscopy (SNEM), and we believe that it will be powerful and useful extension of current 4D-STEM methods.
Glycoside hydrolases (GH) are a large family of hydrolytic enzymes found in all domains of life. As such, they control a plethora of normal and pathogenic biological functions. Thus, understanding selective inhibition of GH enzymes at the atomic level can lead to the identification of new classes of therapeutics. In these studies, we identified a 4-α-glucoside of valienamine (8) as an inhibitor of Streptomyces coelicolor (Sco) GlgE1-V279S which belongs to the GH13 Carbohydrate Active EnZyme family. The results obtained from the dose–response experiments show that 8 at a concentration of 1000 µM reduced the enzyme activity of Sco GlgE1-V279S by 65%. The synthetic route to 8 and a closely related 4-α-glucoside of validamine (7) was achieved starting from readily available D-maltose. A key step in the synthesis was a chelation-controlled addition of vinylmagnesium bromide to a maltose-derived enone intermediate. X-ray structures of both 7 and 8 in complex with Sco GlgE1-V279S were solved to resolutions of 1.75 and 1.83 Å, respectively. Structural analysis revealed the valienamine derivative 8 binds the enzyme in an E 2 conformation for the cyclohexene fragment. Also, the cyclohexene fragment shows a new hydrogen-bonding contact from the pseudo-diaxial C(3)–OH to the catalytic nucleophile Asp 394 at the enzyme active site. Asp 394, in fact, forms a bidentate interaction with both the C(3)–OH and C(7)-OH of the inhibitor. In contrast, compound 7 disrupts the catalytic sidechain interaction network of Sco GlgE1-V279S via steric interactions resulting in a conformation change in Asp 394. These findings will have implications for the design other aminocarbasugar-based GH13-inhibitors and will be useful for identifying more potent and selective inhibitors.
Radical structures derived from TBP during nuclear waste separation explored by EPR spectroscopy.
Sodium titanate anodes synthesized via “chimie-douce” methods generally require a post-synthesis dehydration step. Their crystal structures are sensitive to the heating conditions such as temperature, resulting in distinct sodium storage performance. Herein, using in situ and ex situ high-temperature X-ray diffraction, we studied in detail the structural changes of Na 0.74 Ti 1.815 $\square$ 0.185 O 4 ·1.27H 2 O (NTO) under various heating conditions. Electrochemical characterization revealed that NTOs heated at lower temperatures with layered structures deliver larger capacities than those heated at high temperatures with tunnel structures. Heat treatment at moderate temperatures greatly improves the capacity retention of NTO, especially stabilizing the high voltage processes that are major contributors to the capacity fading, because of the modified crystal structure and surface chemistry. As a result, our findings suggest that post-synthesis heating is a simple and effective strategy to tailor the crystal structure, surface chemistry, and electrochemical properties of sodium titanate anodes.
Results of a numerical study are presented for hypersonic low-density flow about a 70-deg blunt cone using direct simulation Monte Carlo (DSMC) and Navier-Stokes calculations. Particular emphasis is given to the effects of chemistry on the near-wake structure and on the surface quantities and the comparison of the DSMC results with the Navier-Stokes calculations. The flow conditions simulated are those experienced by a space vehicle at an altitude of 85 km and a velocity of 7 km/s during Earth entry. A steady vortex forms in the near wake for these freestream conditions for both chemically reactive and nonreactive air gas models. The size (axial length) of the vortex for the reactive air calculations is 25% larger than that of the nonreactive air calculations. The forebody surface quantities are less sensitive to the chemistry than the base surface quantities. The presence of the afterbody has no effect on the forebody flow structure or the surface quantities. The comparisons of DSMC and Navier-Stokes calculations show good agreement for the wake structure and the forebody surface quantities.
Abstract Developing functionally complex carbon materials from small aromatic molecules requires an understanding of how the chemistry and structure of its constituent molecules evolve and crosslink, to achieve a tailorable set of functional properties. Here, molecular dynamics (MD) simulations are used to isolate the effect of methyl groups on condensation reactions during the oxidative process and evaluate the impact on elastic modulus by considering three monodisperse pyrene‐based systems with increasing methyl group fraction. A parameter to quantify the reaction progression is designed by computing the number of new covalent bonds formed. Utilizing the previously developed MD framework, it is found that increasing methylation leads to an almost doubling of bond formation, a larger fraction of the new bonds oriented in the direction of tensile stress, and a higher basal plane alignment of the precursor molecules along the direction of tensile stress, resulting in enhanced tensile modulus. Additionally, via experiments, it is demonstrated that precursors with a higher fraction of methyl groups result in a higher alignment of molecules. Moreover, increased methylation results in the lower spread of single molecule alignment which may lead to smaller variations in tensile modulus and more consistent properties in carbon materials derived from methyl‐rich precursors.
The role of nanoscale chemomechanical behavior in the macroscopic performance of functional materials is well recognized. For lithium-ion battery cathodes, tremendous effort has been devoted to the development of new chemistry and structure, yet fundamental understanding of the correlation between redox processes and mechanical properties of the novel materials lags behind. In the present study, we prepare large discrete single grains of Li-excess cation-disordered rocksalts (DRX) and investigate their chemomechanical behavior at the particle level, using nanoresolution X-ray and electron-based spectro-imaging and chemical mapping techniques. While irregular cracking upon lithium extraction leads to the eventual breakdown of the baseline DRX oxide (Li 1.2 Ti 0.4 Mn 0.4 O 2 ) particles at a high delithiation state, the fluorinated-DRX (Li 1.3 Ti 0.3 Mn 0.4 O 1.7 F 0.3 ) clearly displays aligned cracking along the <001> direction. The resulting periodicity in the cracking pattern enables the particles to retain their integrity and, consequently, improved electrochemical stability. Density functional theory (DFT) calculations showed that fluorination leads to increased concentration of Li+ on the (001) planes and preferential Li movements along the <001>-family directions, revealing the underlying mechanism for directional cracking. Overall, our study demonstrates the unique role of fluorine in modulating nanoscale chemomechanics, which in turn influences the evolution of charge and strain heterogeneity at the particle level. These insights provide important design guidelines in further improving DRX cathode materials.
Molecules containing short-lived, radioactive nuclei are uniquely positioned to enable a wide range of scientific discoveries in the areas of fundamental symmetries, astrophysics, nuclear structure, and chemistry. Recent advances in the ability to create, cool, and control complex molecules down to the quantum level, along with recent and upcoming advances in radioactive species production at several facilities around the world, create a compelling opportunity to coordinate and combine these efforts to bring precision measurement and control to molecules containing extreme nuclei. In this paper, we review the scientific case for studying radioactive molecules, discuss recent atomic, molecular, nuclear, astrophysical, and chemical advances which provide the foundation for their study, describe the facilities where these species are and will be produced, and provide an outlook for the future of this nascent field.
Topotactic reduction of perovskite oxides offers a powerful approach for discovering novel phenomena, such as superconducting infinite-layer nickelates and polar metallicity, and is commonly accompanied by the emergence of multiple valence states and/or complex crystal fields of transition metals. However, understanding the complex interplay between crystal chemistry, electronic structure, and physical properties at the spin- and orbital-resolved levels in these reduced systems remains elusive. Here, in this study, x-ray absorption spectroscopy, resonant inelastic x-ray scattering (RIXS), and density functional theory calculations are used to uncover topotactic metal-insulator transition and orbital-specific crystal field excitations in brownmillerite La 0.67 Ca 0.33 MnO 2.5 thin films. The Mn valence states are found to be Mn 2+ /Mn 3+ , along with their corresponding populations at octahedral and tetrahedral sites, which effectively weaken the Mn-O hybridization compared to the parent perovskite phase. As a result, La 0.67 Ca 0.33 MnO 2.5 films exhibit an antiferromagnetic insulating ground state. Moreover, by combining the RIXS measurements on selected single-valence manganites, specifically MnO, LaMnO 3 , and CaMnO 3 , with orbital- and spin-resolved density-of-states calculations, the study identifies the dd excitations of octahedrally and tetrahedrally coordinated Mn 2+ /Mn 3+ ions, directly linking the microscopic electronic structure to the macroscopic magnetic/electrical properties.
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