Acid-switched Eu(III) coordination inside reverse aggregates: Insights into a synergistic liquid-liquid extraction system
Abstract not provided
Ellis, Ross J.↗
SEARCH · Engineering Papers
Results for “structural complexity”
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Li 4 Ru 2 OCl 10 ·10H 2 O: crystal structure, magnetic properties and bonding interactions in ruthenium-oxo complexes
The results of the structural determination, magnetic characterization, and theoretical calculations of a new ruthenium-oxo complex, Li 4 [Ru 2 OCl 10 ]·10H 2 O, are presented. Single crystals were grown using solvent methods and the crystal structure was characterized by single crystal X-ray diffraction. Li 4 [Ru 2 OCl 10 ]·10H 2 O crystallizes into a low-symmetry triclinic structure ($P\bar1$) due to the much smaller Li + cation compared to K + cation in the tetragonal complex K 4 [Ru 2 OCl 10 ]·H 2 O. The X-ray photoelectron spectra confirm only the single valent Ru 4+ in Li 4 [Ru 2 OCl 10 ]·10H 2 O even though two distinct Ru sites exist in the crystal structure. Magnetic measurements reveal the diamagnetic property of Li 4 [Ru 2 OCl 10 ]·10H 2 O with unpaired electrons existing on Ru 4+ . Furthermore, the molecular orbital analysis matches well with the observed UV and magnetic measurements.
36 MATERIALS SCIENCE↗
Integrated experimental studies of pore structure and fluid uptake in the Bossier Shale in eastern Texas, USA
Within the Haynesville-Bossier Shale complex, the Bossier Shale has not been extensively studied by either industry and academia, despite it being an unconventional gas reservoir and a potential caprock for carbon storage in the underlaying Haynesville Shale. The lack of knowledge of the complex pore structures and fluid-rock interactions hinders the effective extraction of gas and the characterization of fluid reservoirs and sealing capacity. Integrated experimental studies of pore structure and fluid-rock interactions were conducted in seven Bossier Shale core samples collected in eastern Texas. Petrographic, geochemical, and petrophysical properties such as mineral composition, organic richness, thermal maturity, porosity, pore/pore throat diameter distribution, water-accessible pores, liquid water imbibition, and water vapor adsorption were characterized using complementary approaches of thin-section petrography, scanning electron microscopy, X-ray diffraction, total organic matter, pyrolysis, mercury intrusion porosimetry, nuclear magnetic resonance, (Ultra-) small angle X-rays scattering as well as small angle neutron scattering with deuterated liquids and contrast variation. Further, the results show that the thermally mature Bossier Shales are composed of mixed argillaceous mudstone, mixed mudstone, and mixed carbonate mudstone. The shale contains both organic and inorganic pores, with porosities of 3.24-9.37 %, pore-to-throat ratios of 1.65 to 19.4, and water-accessible pores accounting for 28.7-72.6 % of total pores. Approaches of liquid water imbibition and water vapor adsorption, with and without direct contact of water with shale samples, indicate that liquid water first enters the nano-sized pores under high capillary pressures, and water vapor adsorption is mainly controlled by both clay minerals and pores with diameters less than 10 nm. These findings contribute to a better understanding of pore structures and water-shale interactions and their controlling factors in the Bossier Shale.
58 GEOSCIENCES↗
Syntheses, crystal structures, and characterization of three 1D, 2D and 3D complexes based on mixed multidentate N- and O-donor ligands
Three new 1D to 3D complexes, namely, ([Ni(btec)(Himb){sub 2}(H{sub 2}O){sub 2}]·6H{sub 2}O){sub n} (1), ([Cd(btec){sub 0.5}(imb)(H{sub 2}O)]·1.5H{sub 2}O){sub n} (2), and ([Zn(btec){sub 0.5}(imb)]·H{sub 2}O){sub n} (3) (H{sub 4}btec=1,2,4,5-benzenetetracarboxylic acid, imb=2-(1H-imidazol-1-methyl)-1H-benzimidazole) have been synthesized by adjusting the central metal ions. Single-crystal X-ray diffraction analyses reveal that complex 1 possesses a 1D chain structure which is further extended into the 3D supramolecular architecture via hydrogen bonds. Complex 2 features a 2D network with Schla¨fli symbol (5{sup 3}·6{sup 2}·7)(5{sup 2}·6{sup 4}). Complex 3 presents a 3D framework with a point symbol of (4·6{sup 4}·8)(4{sup 2}·6{sup 2}·8{sup 2}). Moreover, their IR spectra, PXRD patterns, thermogravimetric curves, and luminescent emissions were studied at room temperature. - Graphical abstract: Three new 1D to 3D complexes with different structural and topological motifs have been obtained by modifying the central metal ions. Additionally, their IR, TG analyses and fluorescent properties are also investigated. - Highlights: • Three complexes based on mixed multidentate N- and O-donor ligands. • The complexes are characterized by IR, luminescence and TGA techniques. • Benzenetetracarboxylates display different coordination modes in complexes 1–3. • Changing the metal ions can result in complexes with completely different structures.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Molecular association model of PPARα and its new specific and efficient ligand, pemafibrate: Structural basis for SPPARMα
Highlights: • Computationally constructed the structure of hPPARα in a complex with pemafibrate. • Structural basis for potent effects of pemafibrate predicted by in silico FMO method. • Computational results were confirmed by in vitro luciferase assay analysis. • Unlike fibrates, pemafibrate binds efficiently that makes it as a novel SPPARMα. Peroxisome proliferator-activated receptor-α (PPARα) is a ligand-activated transcription factor involved in the regulation of lipid homeostasis and improves hypertriglyceridemia. Pemafibrate is a novel selective PPARα modulator (SPPARMα) that activates PPARα transcriptional activity. Here, we computationally constructed the structure of the human PPARα in a complex with pemafibrate, along with that of hPPARα complexed with the classical fenofibrate, and studied their interactions quantitatively by using the first-principles calculations-based fragment molecular orbital (FMO) method. Comprehensive structural and protein-ligand binding elucidation along with the in vitro luciferase analysis let us to identify pemafibrate as a novel SPPARMα. Unlike known fibrate ligands, which bind only with the arm I of the Y-shaped ligand binding pocket, the Y-shaped pemafibrate binds to the entire cavity region. This lock and key nature causes enhanced induced fit in pemafibrate-ligated PPARα. Importantly, this selective modulator allosterically changes PPARα conformation to form a brand-new interface, which in turn binds to PPARα co-activator, PGC-1α, resulting in the full activation of PPARα. The structural basis for the potent effects of pemafibrate on PPARα transcriptional activity predicted by the in silico FMO methods was confirmed by in vitro luciferase assay for mutants. The unique binding mode of pemafibrate reveals a new pattern of nuclear receptor ligand recognition and suggests a novel basis for ligand design, offering cues for improving the binding affinity and selectivity of ligand for better clinical consequences. The findings explain the high affinity and efficacy of pemafibrate, which is expected to be in the clinical use soon.
60 APPLIED LIFE SCIENCES↗
Structures of FOX-4 Cephamycinase in Complex with Transition-State Analog Inhibitors
Boronic acid transition-state analog inhibitors (BATSIs) are partners with β-lactam antibiotics for the treatment of complex bacterial infections. Herein, microbiological, biochemical, and structural findings on four BATSIs with the FOX-4 cephamycinase, a class C β-lactamase that rapidly hydrolyzes cefoxitin, are revealed. FOX-4 is an extended-spectrum class C cephalosporinase that demonstrates conformational flexibility when complexed with certain ligands. Like other β-lactamases of this class, studies on FOX-4 reveal important insights into structure–activity relationships. We show that SM23, a BATSI, shows both remarkable flexibility and affinity, binding similarly to other β-lactamases, yet retaining an IC 50 value < 0.1 μM. Our analyses open up new opportunities for the design of novel transition-state analogs of class C enzymes.
59 BASIC BIOLOGICAL SCIENCES↗
Structure of a tripartite protein complex that targets toxins to the type VII secretion system
Type VII secretion systems are membrane-embedded nanomachines used by Gram-positive bacteria to export effector proteins from the cytoplasm to the extracellular environment. Many of these effectors are polymorphic toxins comprised of an N-terminal Leu-x-Gly (LXG) domain of unknown function and a C-terminal toxin domain that inhibits the growth of bacterial competitors. In recent work, it was shown that LXG effectors require two cognate Lap proteins for T7SS-dependent export. Here, we present the 2.6 Å structure of the LXG domain of the TelA toxin from the opportunistic pathogen Streptococcus intermedius in complex with both of its cognate Lap targeting factors. The structure reveals an elongated α-helical bundle within which each Lap protein makes extensive hydrophobic contacts with either end of the LXG domain. Remarkably, despite low overall sequence identity, we identify striking structural similarity between our LXG complex and PE–PPE heterodimers exported by the distantly related ESX type VII secretion systems of Mycobacteria implying a conserved mechanism of effector export among diverse Gram-positive bacteria. Overall, our findings demonstrate that LXG domains, in conjunction with their cognate Lap targeting factors, represent a tripartite secretion signal for a widespread family of T7SS toxins.
59 BASIC BIOLOGICAL SCIENCES↗
Skeletides: A Modular, Simplified Physical Model of Protein Secondary Structure
Three-dimensional (3D) models are essential for visualization and conceptual understanding of complex architectures such as protein structure. Although there is a plethora of software platforms that allow digital depictions of protein structure at an atomic level in silico, physical models are needed to convey an intuitive understanding of biomolecular architecture. However, it is a challenge to represent all the relevant features of proteins in a single physical model due to their sheer structural complexity. Here, we describe a modular protein model that focuses only on representation of the secondary structure—the underlying structural skeleton. The simplified model consists of amino acid units, which can be linked together to reproduce the two most fundamental structural features of protein secondary structure: the relative positions of the amino acid alpha carbon atoms, and the intra-main chain hydrogen bonding pattern. We use 3D printing and magnets to create a set of three modular amino acid building blocks, which when linked together into a chain, can faithfully represent alpha helices, beta sheets, and turns. These simple to make models can be used to quickly assemble the alpha carbon trace of an entire protein domain, which conveys a tactile experience of the complexity of protein skeletal architecture. These models highlight the modularity of protein structure: where a single structural unit, the amino acid, can be linked together to form a larger, regular secondary structure. These models also have a propensity to spontaneously organize into alpha helices and beta sheets, as demonstrated by their ability to autonomously assemble when placed in a circulating water tank. These models provide a missing educational tool to expand knowledge of protein structure, foster deeper insight into protein folding, and inspire greater interest in biomacromolecular architecture.
36 MATERIALS SCIENCE↗
Structures of EccB 1 and EccD 1 from the core complex of the mycobacterial ESX-1 type VII secretion system
Abstract not provided
Wagner, Jonathan M.↗
Systematic approach for simultaneously correcting the band-gap and p - d separation errors of common cation III-V or II-VI binaries in density functional theory calculations within a local density approximation
We propose a systematic approach that can empirically correct three major errors typically found in a density functional theory (DFT) calculation within the local density approximation (LDA) simultaneously for a set of common cation binary semiconductors, such as III-V compounds, (Ga or In)X with X = N,P,As,Sb, and II-VI compounds, (Zn or Cd)X, with X = O,S,Se,Te. By correcting (1) the binary band gaps at high-symmetry points , L, X, (2) the separation of p-and d-orbital-derived valence bands, and (3) conduction band effective masses to experimental values and doing so simultaneously for common cation binaries, the resulting DFT-LDA-based quasi-first-principles method can be used to predict the electronic structure of complex materials involving multiple binaries with comparable accuracy but much less computational cost than a GW level theory. This approach provides an efficient way to evaluate the electronic structures and other material properties of complex systems, much needed for material discovery and design.
Wang, Jianwei↗
The DDB1–DCAF1–Vpr–UNG2 crystal structure reveals how HIV-1 Vpr steers human UNG2 toward destruction
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Wu, Ying↗
Quantum transport model for zigzag molybdenum disulfide nanoribbon structures : A full quantum framework
Mainly based on non-equilibrium Green’s function technique in combination with the three-band model, a full atomistic-scale and full quantum method for solving quantum transport problems of a zigzag-edge molybdenum disulfide nanoribbon (zMoSNR) structure is proposed here. For transport calculations, the relational expressions of a zMoSNR crystalline solid and its whole device structure are derived in detail and in its integrity. By adopting the complex-band structure method, the boundary treatment of this open boundary system within the non-equilibrium Green’s function framework is so straightforward and quite sophisticated. The transmission function, conductance, and density of states of zMoSNR devices are calculated using the proposed method. The important findings in zMoSNR devices such as conductance quantization, van Hove singularities in the density of states, and contact interaction on channel are presented and explored in detail.
77 NANOSCIENCE AND NANOTECHNOLOGY↗
Toward Molecular Engineering of Polymer Glasses
Glass formation has been central to fabrication technologies since the dawn of civilization. Glasses not only encompass window panes, the insulation in our homes, the optical fibers supplying our cable TV, and vessels for eating and drinking, but they also include a vast array of ‘‘plastic’’ polymeric materials. Glasses find applications in high technology (e.g., producing microelectronic materials, etc., amorphous semiconductors), and recent advances have created ‘‘plastic metallic glasses’’ that are promising for fabricating everyday structural materials. Many commercially relevant systems, such as microemulsions and colloidal suspensions, have complex molecular structures and thus solidify by glass formation. Despite the importance of understanding the fundamental nature of glass formation for the synthesis of new materials, a predictive molecular theory has been lacking. Much of our understanding of glass formation derives from the analysis of experimental data, a process that has uncovered a number of interesting universal behaviors, namely, relations between properties that are independent of molecular details. However, these empirically derived relations and their limitations remain to be understood on the basis of theories, and, more importantly, there is strong need for theories of the explicit variation with molecular system to enable the rational design and tailoring of new materials. We have recently developed the generalized entropy theory, the only analytic, theory that enables describing the dependence of the properties of glass-formation on monomer molecular structures. These properties include the two central quantities of glass formation, the glass transition temperature and the glass fragility parameter, material dependent properties that govern how a material may be processed (e.g., by extrusion, ink jet, molding, etc.) Our recent works, which are further described below, extend the studies of glass formation in polymer systems to test the theory by directly comparing between the predictions of our generalized entropy theory with experiment and with simulations and to expand the vistas of the theory to describe a wider range of important systems (e.g. glass formation in binary blends and systems with specific interactions) and phenomena that are describable by the generalized entropy theory. In addition, we have addressed longstanding fundamental problems associated with the validity of the Adam-Gibbs theory, one of the underpinnings of the general entropy theory. Theoretical advances to enable describing the properties of glass-formation over a wider class of important polymeric systems, included semi-flexible systems, the more general situation of specific interactions, and more. Our recent work removes the simplest approximation uses the simplest model in which the interaction is approximated by a single, monomer average. Thus, the theory has been extended to allow some variations of the energy parameters between the atoms within the monomers. The theory has also been extended to include all the contributions from chain semi-flexibility. Both projects are extremely difficult, but the payback is that the process of solving the problems developed strong theoretical skills in Dr. Xu, who has recently begun a postdoc position at ORNL. The theory has also been extended to describe glass formation in partially miscible blends, with good general agreement with experiment. Again, the development of the theory presented an extremely difficult problem, but the payback is the development of a theory for a very important class of systems. Another project provides an extremely simple approximation for certain properties of glass formation in polymer melts and should make the theory more accessible to everyone.
36 MATERIALS SCIENCE↗
Ultrastructure of Critical-Gel-like Polyzwitterion–Polyoxometalate Complex Coacervates: Effects of Temperature, Salt Concentration, and Shear
The structure of unconventional complex coacervates, such as polymer-nonpolymer complex coacervates, remains less investigated than that of the conventional coacervates formed between oppositely charged polyelectrolytes with symmetric charge species. Yet, their microscopic structural organization is important to further elucidate the mechanism of liquid-liquid-phase separation processes upon complexation. In this work, we characterize the microstructural organization of complex coacervates formed between inorganic polyoxometalate (POM) and polyzwitterion by small-angle X-ray scattering (SAXS) with in situ temperature and shear control. Furthermore, despite the apparent transparent and homogeneous morphology of dense coacervates as observed by optical microscopy, our previous results (Macromolecules 2018, 51, 22, 9405-9411) suggest that dense polyzwitterion-POM coacervates exhibit critical-gel-like networks containing both complex-poor region (mesh pore) and complex-rich region (connective network). SAXS results as reported in this work support that the complex-rich region is actually in the form of loosely packed POM aggregates linked by polyzwitterion, designated as complex particles. The structure of aggregating complex particles is further examined against varied composition and salt concentrations, temperature, and shear, thanks to the high X-ray scattering contrast of POMs from that of other components in the coacervates. The complex particles in the dense coacervates appear to grow with more tightly packed POM aggregates with increasing POM-to-polyzwitterion concentration ratio, in contrast to more loosely packed POM aggregates with decreasing salt concentration. Conversely, increasing temperature could result in smaller complex particles containing more loosely packed POM aggregates, consistent with temperature-dependent viscoelasticity of dense coacervates. Furthermore, such POM-based hybrid dense coacervates exhibit intriguing strain-hardening behavior, resulting from shear-enhanced POM packing inside the complex particles. Distinct from the shear-thinning behavior of most conventional crosslinked polymeric networks, the strain-hardening property combined with thermal- and salt-responsive characteristics of polyzwitterion-POM coacervates could broaden the applications of hybrid organic-inorganic macroion coacervates as smart functional materials working under extreme environmental conditions.
36 MATERIALS SCIENCE↗
Studies of Structure and Dynamics of Light Harvesting Complex 1 of R. Sphaeroides by Solid State NMR
Studies of the structure and dynamics of a light harvesting complex from photosynthetic bacteria are described. Using Nuclear Magnetic Resonance methods, we explored the idea that optical properties are modulated via a conformational switch in the BChl chromophores, in a way that provides benefits for the efficiency of energy conversion.
14 SOLAR ENERGY↗
Synthesis, crystal structures, and dye removal properties of a series of discrete and polymeric copper, zinc, cobalt, and cadmium complexes containing bis-pyridyl-bis-amine ligands
Two bis-pyridyl-bis-amine ligands, trans-1,2-bis(m-picolyamino)cyclohexane (rac-m-picchxn) and trans-1,2-bis(p-picolyamino)cyclohexane (rac-p-picchxn), derived from trans-1,2-diaminocyclohexane (rac-chxn), were assembled with CuCl{sub 2}, ZnCl{sub 2}, ZnBr{sub 2}, Co(NO{sub 3}){sub 2}, and CdCl{sub 2} through reactants slow diffusion to afford corresponding metal complexes. Complexes [Cu(R,R-m-picchxn)Cl{sub 2}] (1) and [Zn(rac-m-picchxn)Br{sub 2}] (3) are mononuclear coordination structures, complex [Zn{sub 2}(rac-m-picchxn)Cl{sub 4}]{sub n} (2) adopts a one-dimensional (1D) helical chain, complex {[Co(R,R-p-picchxn)(NO_3)_2]·THF·2/3H_2O}{sub n} (4) has a two-dimensional (2D) kgm layer structure, complex [Cd(rac-p-picchxn)Cl{sub 2}]{sub n} (5) suits a 1D double-stranded zigzag chain structure, and compound [Cu(rac-chxn){sub 2}][CuCl{sub 3}] (6) is a Cu(I)-Cu(II) mixed-valence ionic product generated from the hydrolysis of rac-p-picchxn associated with the reduction of Cu(II) ion. The two bis-pyridyl-bis-amine ligands possess a chelating-bridging mode in forming infinite network and a chelating-only mode in forming discrete complexes. These metal–organic architectures show the influence of metal ion combining with organic ligand and anion on the structure variation. Noteworthy, chain polymers 2 and 5 could be utilized in the removal of methyl orange (MO), acid orange 7 (AO7), and malachite green (MG) from water through adsorptive processes. The adsorption dynamics of MO and AO7 on 2 and MG on both 2 and 5 obeyed a pseudo-second-order kinetics while that of MO and AO7 on 5 followed a pseudo-first-order kinetics.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Structure determination of the HgcAB complex using metagenome sequence data: insights into microbial mercury methylation
Bacteria and archaea possessing the hgcAB gene pair methylate inorganic mercury (Hg) to form highly toxic methylmercury. HgcA consists of a corrinoid binding domain and a transmembrane domain, and HgcB is a dicluster ferredoxin. However, their detailed structure and function have not been thoroughly characterized. We modeled the HgcAB complex by combining metagenome sequence data mining, coevolution analysis, and Rosetta structure calculations. In addition, we overexpressed HgcA and HgcB in Escherichia coli, confirmed spectroscopically that they bind cobalamin and [4Fe-4S] clusters, respectively, and incorporated these cofactors into the structural model. Surprisingly, the two domains of HgcA do not interact with each other, but HgcB forms extensive contacts with both domains. The model suggests that conserved cysteines in HgcB are involved in shuttling HgII, methylmercury, or both. These findings refine our understanding of the mechanism of Hg methylation and expand the known repertoire of corrinoid methyltransferases in nature.
59 BASIC BIOLOGICAL SCIENCES↗