Applications of Porphyrinoid Macrocycles in Molecular Sensing and f-Element Coordination
Conclusion/ future work: UV-Vis supports metal complexation; Optimize crystal growth; Solid state EXAFS experiment.
36 MATERIALS SCIENCE↗
SEARCH · Engineering Papers
Results for “Molecular crystals”
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Comparing the performance of density functionals in describing the adsorption of atoms and small molecules on Ni(111)
Reaction networks calculated using density functional theory (DFT) play a crucial role in understanding and predicting heterogeneous catalyst performance. However, results obtained using different density functionals can vary significantly. Accordingly, it is important to assess the accuracy of available functionals in capturing adsorption energetics derived from single-crystal adsorption microcalorimetry experiments. Here, we evaluate how different density functionals describe the molecular and dissociative adsorption of CH 3 I, the adsorption of CH 3 , I, and H, and the dissociative adsorption of CH 4 on Ni(111). First, we identify energetically-preferred adsorbed states for each adsorbate at three surface coverages and calculate the corresponding enthalpies of adsorption at 160 K. Then, we compare the results to experimental measurements published in the literature. For each adsorption process we find at least one functional that is quantitatively accurate within experimental error, but no functional is accurate (within experimental error) for all adsorption processes studied. Even when assuming an additional DFT error of ±20 kJ/mol on top of the experimental error, only the PBE-D3 and RPBE-D3 functionals are accurate for all considered adsorption systems. Overall, these results indicate that quantitative agreement between density functional theory calculations and experimental measurements is both system- and functional-dependent. Importantly, single-crystal adsorption microcalorimetry experiments will continue to play an important role for benchmarking density functionals.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Uranium Doped Gallium Nitride Epitaxial Thin Films
Gallium nitride (GaN) is near ubiquitous in modern day technologies, forming the backbone of solid-state lighting and high-power electronics. Engineering the physical properties of GaN has been investigated to some degree by the incorporation or doping of most of the elements of the periodic table, but the actinides remain unexplored. Molecular beam epitaxy is used to demonstrate uranium doping of GaN single crystals. High structural quality of the host matrix is maintained despite partial elemental segregation of the uranium dopant into 1D structures at the levels presented here. Electronic transport measurements reveal relatively high conductivity, which persists down to cryogenic temperature and is characterized by the formation of narrow gaps in the electronic band structures very close to the Fermi level. Photoluminescence measurements reveal that the U-doped GaN exhibits optical behavior similar to that of the GaN substrate. The addition of actinide materials to a non-centrosymmetric, optically active, radiation-hard, and electronically tunable host matrix opens a world of possibilities for investigating and leveraging elements with high electron correlations in the pursuit of novel devices.
36 - MATERIALS SCIENCE↗
Small‐Molecule Mixed Ionic‐Electronic Conductors for Efficient N‐Type Electrochemical Transistors: Structure‐Function Correlations
Abstract The fundamental challenge in electron‐transporting organic mixed ionic‐electronic conductors (OMIECs) is simultaneous optimization of electron and ion transport. Beginning from Y6‐type/U‐shaped non‐fullerene solar cell acceptors, we systematically synthesize and characterize molecular structures that address the aforementioned challenge, progressively introducing increasing numbers of oligoethyleneglycol (OEG; g) sidechains from 1 g to 3 g, affording OMIECs 1gY, 2gY, and 3gY, respectively. The crystal structure of 1gY preserves key structural features of the Y n series: a U‐shaped/planar core, close π–π molecular stacking, and interlocked acceptor groups. Versus inactive Y6 and Y11, all of the new glycolated compounds exhibit mixed ion‐electron transport in both conventional organic electrochemical transistor (cOECT) and vertical OECT (vOECT) architectures. Notably, 3gY with the highest OEG density achieves a high transconductance of 16.5 mS, an on/off current ratio of ~10 6 , and a turn‐on/off response time of 94.7/5.7 ms in vOECTs. Systematic optoelectronic, electrochemical, architectural, and crystallographic analysis explains the superior 3gY‐based OECT performance in terms of denser n gY OEG content, increased crystallite dimensions with decreased long‐range crystalline order, and enhanced film hydrophilicity which facilitates ion transport and efficient redox processes. Finally, we demonstrate an efficient small‐molecule‐based complementary inverter using 3gY vOECTs, showcasing the bioelectronic applicability of these new small‐molecule OMIECs.
Cho, Yongjoon↗
Small‐Molecule Mixed Ionic‐Electronic Conductors for Efficient N‐Type Electrochemical Transistors: Structure‐Function Correlations
Abstract The fundamental challenge in electron‐transporting organic mixed ionic‐electronic conductors (OMIECs) is simultaneous optimization of electron and ion transport. Beginning from Y6‐type/U‐shaped non‐fullerene solar cell acceptors, we systematically synthesize and characterize molecular structures that address the aforementioned challenge, progressively introducing increasing numbers of oligoethyleneglycol (OEG; g) sidechains from 1 g to 3 g, affording OMIECs 1gY, 2gY, and 3gY, respectively. The crystal structure of 1gY preserves key structural features of the Y n series: a U‐shaped/planar core, close π–π molecular stacking, and interlocked acceptor groups. Versus inactive Y6 and Y11, all of the new glycolated compounds exhibit mixed ion‐electron transport in both conventional organic electrochemical transistor (cOECT) and vertical OECT (vOECT) architectures. Notably, 3gY with the highest OEG density achieves a high transconductance of 16.5 mS, an on/off current ratio of ~10 6 , and a turn‐on/off response time of 94.7/5.7 ms in vOECTs. Systematic optoelectronic, electrochemical, architectural, and crystallographic analysis explains the superior 3gY‐based OECT performance in terms of denser n gY OEG content, increased crystallite dimensions with decreased long‐range crystalline order, and enhanced film hydrophilicity which facilitates ion transport and efficient redox processes. Finally, we demonstrate an efficient small‐molecule‐based complementary inverter using 3gY vOECTs, showcasing the bioelectronic applicability of these new small‐molecule OMIECs.
Cho, Yongjoon↗
High yield production of ultrathin fibroid semiconducting nanowire of Ta 2 Pd 3 Se 8
Immediately after the demonstration of the high-quality electronic properties in various two dimensional (2D) van der Waals (vdW) crystals fabricated with mechanical exfoliation, many methods have been reported to explore and control large scale fabrications. Comparing with recent advancements in fabricating 2D atomic layered crystals, large scale production of one dimensional (1D) nanowires with thickness approaching molecular or atomic level still remains stagnant. Here, we demonstrate the high yield production of a 1D vdW material, semiconducting Ta 2 Pd 3 Se 8 nanowires, by means of liquid-phase exfoliation. The thinnest nanowire we have readily achieved is around 1 nm, corresponding to a bundle of one or two molecular ribbons. Transmission electron microscopy (TEM) and transport measurements reveal the as-fabricated Ta 2 Pd 3 Se 8 nanowires exhibit unexpected high crystallinity and chemical stability. Our low-frequency Raman spectroscopy reveals clear evidence of the existing of weak inter-ribbon bindings. The fabricated nanowire transistors exhibit high switching performance and promising applications for photodetectors.
1D semiconductor↗
Structure of VanS from vancomycin-resistant enterococci: A sensor kinase with weak ATP binding
The VanRS two-component system regulates the resistance phenotype of vancomycin-resistant enterococci. VanS is a sensor histidine kinase that responds to the presence of vancomycin by autophosphorylating and subsequently transferring the phosphoryl group to the response regulator, VanR. The phosphotransfer activates VanR as a transcription factor, which initiates the expression of resistance genes. Structural information about VanS proteins has remained elusive, hindering the molecular-level understanding of their function. Here, we present X-ray crystal structures for the catalytic and ATP-binding (CA) domains of two VanS proteins, derived from vancomycin-resistant enterococci types A and C. Both proteins adopt the canonical Bergerat fold that has been observed for CA domains of other prokaryotic histidine kinases. We attempted to determine structures for the nucleotide-bound forms of both proteins; however, despite repeated efforts, these forms could not be crystallized, prompting us to measure the proteins' binding affinities for ATP. Unexpectedly, both CA domains displayed low affinities for the nucleotide, with K D values in the low millimolar range. Since these K D values are comparable to intracellular ATP concentrations, this weak substrate binding could reflect a way of regulating expression of the resistance phenotype.
59 BASIC BIOLOGICAL SCIENCES↗
Structure of the divergent human astrovirus MLB capsid spike
Despite their worldwide prevalence and association with human disease, the molecular bases of human astrovirus (HAstV) infection and evolution remain poorly characterized. Here, we report the structure of the capsid protein spike of the divergent HAstV MLB clade (HAstV MLB). While the structure shares a similar folding topology with that of classical-clade HAstV spikes, it is otherwise strikingly different. We find no evidence of a conserved receptor-binding site between the MLB and classical HAstV spikes, suggesting that MLB and classical HAstVs utilize different receptors for host-cell attachment. We provide evidence for this hypothesis using a novel HAstV infection competition assay. Comparisons of the HAstV MLB spike structure with structures predicted from its sequence reveal poor matches, but template-based predictions were surprisingly accurate relative to machine-learning-based predictions. Our data provide a foundation for understanding the mechanisms of infection by diverse HAstVs and can support structure determination in similarly unstudied systems.
59 BASIC BIOLOGICAL SCIENCES↗
Mesoscale Frank–Kasper Crystal Structures from Dendron Assembly by Controlling Core Apex Interactions
Single-component polymeric materials open up a great potential for self-assembly into mesoscale complex crystal structures that are known as Frank-Kasper (FK) phases. Predicting the packing structures of the soft-matter spheres, however, remains a challenge even when the molecular design is precisely known. Here, we investigate the role of the molecules' enthalpic interaction in determining the low-symmetry crystal structures. To this end, we synthesize architecturally asymmetric dendrons by varying their apex functionalities and examine the packing structures of the second-generation (G2) dendritic wedges. Our work shows that weakening the hydrogen bonding of the dendron apex makes the particles softer and smaller, and leads to the formation of various FK structures at lower temperatures, including the new observation of a FK C14 phase in the cone-shaped dendron systems. As a consequence of the free energy balance between the particle's interfacial tension and the chain's stretching, various packing structures are mainly tuned by designing the hydrogen bonding interaction.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Multidisciplinary studies with mutated HIV-1 capsid proteins reveal structural mechanisms of lattice stabilization
Abstract HIV-1 capsid (CA) stability is important for viral replication. E45A and P38A mutations enhance and reduce core stability, thus impairing infectivity. Second-site mutations R132T and T216I rescue infectivity. Capsid lattice stability was studied by solving seven crystal structures (in native background), including P38A, P38A/T216I, E45A, E45A/R132T CA, using molecular dynamics simulations of lattices, cryo-electron microscopy of assemblies, time-resolved imaging of uncoating, biophysical and biochemical characterization of assembly and stability. We report pronounced and subtle, short- and long-range rearrangements: (1) A38 destabilized hexamers by loosening interactions between flanking CA protomers in P38A but not P38A/T216I structures. (2) Two E45A structures showed unexpected stabilizing CA NTD -CA NTD inter-hexamer interactions, variable R18-ring pore sizes, and flipped N-terminal β-hairpin. (3) Altered conformations of E45A a α9-helices compared to WT, E45A/R132T, WT PF74 , WT Nup153 , and WT CPSF6 decreased PF74, CPSF6, and Nup153 binding, and was reversed in E45A/R132T. (4) An environmentally sensitive electrostatic repulsion between E45 and D51 affected lattice stability, flexibility, ion and water permeabilities, electrostatics, and recognition of host factors.
60 APPLIED LIFE SCIENCES↗
Diffusion growth mechanism of penta-twinned Ag nanocrystals from decahedral seeds
Crystals with penta-twinned structures can be produced from diverse fcc metals, but the mechanisms that control the final product shapes are still not well understood. By using the theory of absorbing Markov chains to account for the growth of penta-twinned decahedral seeds via atom deposition and surface diffusion, we predicted the formation of various types of products: decahedra, nanorods, and nanowires. We showed that the type of product depends on the morphology of the seed and that small differences between various seed morphologies can lead to significantly different products. For the case of uncapped decahedra seeds, we compared predictions from our model to nanowire morphologies obtained in two different experiments and obtained favorable agreement. Finally, possible extensions of our model are indicated.
36 MATERIALS SCIENCE↗
Epitaxial (Al x Ga 1-x-y In y ) 2 O 3 Alloys Lattice Matched to Monoclinic Ga 2 O 3 Substrates
We have epitaxially stabilized a series of monoclinic (Al x Ga 1-x-y In y ) 2 O 3 alloys by careful choice of molecular beam epitaxy growth conditions, which balance alloy growth with suboxide desorption. The films are pseudomorphic to (010) β-Ga 2 O 3 substrates at thicknesses up to 150 nm with compositions ranging from (Al 0.01 Ga 0.83 In 0.16 ) 2 O 3 to (Al 0.24 Ga 0.75 In 0.03 ) 2 O 3 . The absorption edge shifts from approximately 4.62-5.14 eV with coincidently increasing Al and decreasing In mole fractions. J-V measurements reveal an increase in resistivity over four orders of magnitude with a maximum value of 4.2 x 10 5 Ω-cm for (Al 0.17 Ga 0.76 In 0.07 ) 2 O 3 , which has nearly identical lattice parameters (both in-plane and out-of-plane) to the underlying β-Ga 2 O 3 . Scanning transmission electron microscopy of this sample reveals a mostly uniform and single crystalline film, though we identify areas of non-uniform In incorporation and some γ-phase inclusions. This work demonstrates the feasibility of thick layers lattice-matched to β-Ga 2 O 3 with increased bandgap compared to phase-separation limited (Al,Ga) 2 O 3 . These alloys can enable higher bandgap epitaxial dielectrics and high sheet charge density transistors by increasing the conduction band offset with respect to β-Ga 2 O 3 .
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Design rules for liquid crystalline electrolytes for enabling dendrite-free lithium metal batteries
Significance Lithium metal anodes offer a promising approach to improve the energy density of batteries to enable electrification of transportation. Dendrite suppression plagues the safety and cycle life of lithium metal anodes. In this work, we perform a comprehensive analysis of the use of liquid crystalline electrolytes in lithium metal anodes. We report theoretical demonstration of spontaneous stabilization of metal-electrode position using a liquid crystalline electrolyte due to the energy that arises when the molecules of the liquid crystal reorient. Building on this, we develop a comprehensive set of molecular-level design rules that will pave the way toward the realization of this new class of electrolytes for practical lithium metal batteries.
Ahmad, Zeeshan↗
Rational design, synthesis, and evaluation of uncharged, “smart” bis-oxime antidotes of organophosphate-inhibited human acetylcholinesterase
Organophosphate (OP) intoxications from nerve agent and OP pesticide exposures are managed with pyridinium aldoxime–based therapies whose success rates are currently limited. The pyridinium cation hampers uptake of OPs into the central nervous system (CNS). Furthermore, it frequently binds to aromatic residues of OP-inhibited acetylcholinesterase (AChE) in orientations that are nonproductive for AChE reactivation, and the structural diversity of OPs impedes efficient reactivation. Improvements of OP antidotes need to include much better access of AChE reactivators to the CNS and optimized orientation of the antidotes' nucleophile within the AChE active-center gorge. On the basis of X-ray structures of a CNS-penetrating reactivator, monoxime RS194B, reversibly bound to native and venomous agent X (VX)–inhibited human AChE, here we created seven uncharged acetamido bis-oximes as candidate antidotes. Both oxime groups in these bis-oximes were attached to the same central, saturated heterocyclic core. Diverse protonation of the heterocyclic amines and oxime groups of the bis-oximes resulted in equilibration among up to 16 distinct ionization forms, including uncharged forms capable of diffusing into the CNS and multiple zwitterionic forms optimal for reactivation reactions. Conformationally diverse zwitterions that could act as structural antidote variants significantly improved in vitro reactivation of diverse OP-human AChE conjugates. Oxime group reorientation of one of the bis-oximes, forcing it to point into the active center for reactivation, was confirmed by X-ray structural analysis. Finally, our findings provide detailed structure-activity properties of several CNS-directed, uncharged aliphatic bis-oximes holding promise for use as protonation-dependent, conformationally adaptive, “smart” accelerated antidotes against OP toxicity.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Regioselectivity mechanism of the Thunbergia alata Δ 6 -16:0-acyl carrier protein desaturase
Plant plastidial acyl–acyl carrier protein (ACP) desaturases are a soluble class of diiron-containing enzymes that are distinct from the diiron-containing integral membrane desaturases found in plants and other organisms. The archetype of this class is the stearoyl-ACP desaturase which converts stearoyl-ACP into oleoyl (18:1Δ 9 cis )-ACP. Several variants expressing distinct regioselectivity have been described including a Δ 6 -16:0-ACP desaturase from black-eyed Susan vine ( Thunbergia alata ). We solved a crystal structure of the T. alata desaturase at 2.05 Å resolution. Using molecular dynamics (MD) simulations, we identified a low-energy complex between 16:0-ACP and the desaturase that would position C6 and C7 of the acyl chain adjacent to the diiron active site. The model complex was used to identify mutant variants that could convert the T. alata Δ 6 desaturase to Δ 9 regioselectivity. Additional modeling between ACP and the mutant variants confirmed the predicted regioselectivity. Furthermore, to validate the in-silico predictions, we synthesized two variants of the T. alata desaturase and analyzed their reaction products using gas chromatography-coupled mass spectrometry. Assay results confirmed that mutants designed to convert T. alata Δ 6 to Δ 9 selectivity exhibited the predicted changes. In complementary experiments, variants of the castor desaturase designed to convert Δ 9 to Δ 6 selectivity lost some of their Δ9 desaturation ability and gained the ability to desaturate at the Δ 6 position. The computational workflow for revealing the mechanistic understanding of regioselectivity presented herein lays a foundation for designing acyl-ACP desaturases with novel selectivities to increase the diversity of monoenes available for bioproduct applications.
59 BASIC BIOLOGICAL SCIENCES↗
Switching charge states in quasi-2D molecular conductors
Abstract 2D molecular entities build next-generation electronic devices, where abundant elements of organic molecules are attractive due to the modern synthetic and stimuli control through chemical, conformational, and electronic modifications in electronics. Despite its promising potential, the insufficient control over charge states and electronic stabilities must be overcome in molecular electronic devices. Here, we show the reversible switching of modulated charge states in an exfoliatable 2D-layered molecular conductor based on bis(ethylenedithio)tetrathiafulvalene molecular dimers. The multiple stimuli application of cooling rate, current, voltage, and laser irradiation in a concurrent manner facilitates the controllable manipulation of charge crystal, glass, liquid, and metal phases. The four orders of magnitude switching of electric resistance are triggered by stimuli-responsive charge distribution among molecular dimers. The tunable charge transport in 2D molecular conductors reveals the kinetic process of charge configurations under stimuli, promising to add electric functions in molecular circuitry.
Huang, Yulong (ORCID:0000000296160134)↗
Positive spin Hall magnetoresistance in single-crystalline Pt/CoO(001) bilayers
Here, the spin Hall magnetoresistance (SMR) effect in single-crystalline Pt/CoO(001) bilayers has been systematically investigated. X-ray magnetic linear dichroism measurements prove that CoO antiferromagnetic (AFM) spins can be switched into the direction orthogonal to the applied field. We find the SMR signal is comprised of two components related to either the switching of CoO AFM Néel order or the applied strong field effect. Both SMR components show a “positive” angular dependence with $R_{∥} > R_{⊥}$, while $R_{∥} (R_{⊥})$ is defined as the resistance with the applied in-plane field parallel (perpendicular) to the current. The observed positive SMR is mainly attributed to the uncompensated spins at the Pt/CoO interface, instead of the CoO AFM spins. Our study may attract a great deal of interest to understand the complicated SMR effect in AFM spintronics materials.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Nonisentropic Release of a Shocked Solid
Here, we introduce molecular dynamics simulations of shock and release in micron-scale tantalum crystals that exhibit postbreakout temperatures far exceeding those expected under the standard assumption of isentropic release. We illustrate via an energy-budget analysis that this is due to plastic-work heating from material strength that largely counters thermoelastic cooling. The simulations are corroborated by experiments where the release temperatures of laser-shocked tantalum foils are deduced from their thermal strains via in situ x-ray diffraction and are found to be close to those behind the shock.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗