Structural Building Blocks Research Articles

Opportunities for Lipid-Based Probes in the Field of Immunology.

Lipids perform a wide range of functions inside the cell, ranging from structural building block of membranes and energy storage to cell signaling. The mode of action of many signaling lipids has remained elusive due to their low abundance, high lipophilicity, and inherent instability. Various chemical biology approaches, such as photoaffinity or activity-based protein profiling methods, have been employed to shed light on the biological role of lipids and the lipid-protein interaction profile. In this review, we will summarize the recent developments in the field of chemical probes to study lipid biology, especially in immunology, and indicate potential avenues for future research.

Synthesis of cationic molybdenum-cobalt heterometallic clusters protected against hydrolysis by macrocyclic triazacyclononane complexes.

Four kinds of cobalt-polyoxomolybdenum clusters were synthesized by a combination of polyoxomolybdates and a Co-tacn (tacn = 1,4,7-triazacyclononane) complex. The heterometallic polynuclear clusters were obtained by the reaction of Na2MoO4 and [Co(tacn)(H2O)3](CF3SO3)3·H2O in water. The peripherals of polyoxomolybdates are capped by thermodynamically stable [Co(tacn)]3+ protecting groups to prevent further hydrolysis and condensation reactions. Intra-molecular hydrogen bonds between N-H groups on tacn and oxygen atoms on the molybdate core contribute to the stability of the complexes in water. Under the optimized synthetic conditions, the molar ratios of Na2MoO4 and [Co(tacn)(H2O)3](CF3SO3)3·H2O were adjusted to 1 : 0.3, 1 : 0.9, or 1 : 1.5, producing [{Co(tacn)}2Mo3O12]·2NaCF3SO3·7H2O (1), [{Co(tacn)}4H2Mo7O27](CF3SO3)2·13H2O (2), and [{Co(tacn)}4H3Mo4O17](CF3SO3)5·6H2O (3), respectively. As one of the most important factors, the adjustments of the pH values by changing the molar ratio enabled us to isolate these clusters. The presence of pyridine produces a neutral complex, [Co2(tacn)2(pyridine)Mo5O18]·4.5H2O (4) containing a lacunary Lindqvist-type polyoxomolybdate. The synthesis of complexes 2-4 is also possible starting from cluster 1, implying that 1 is a precursor for the formation of 2-4 in aqueous solution. Complexes 2-4 have a common structural building block, [{Co(tacn)}2Mo3O13], in each of the cluster units. The 1H NMR spectra of 2 and 3 in aqueous solution show multiple splitting patterns of methylene signals on tacn ligands according to the chemical environments indicated by the crystallographic structure. The 59Co NMR spectrum of cluster 3 in CH3NO2 has two signals from two different Co units with a 3 : 1 integration ratio ensuring the structural integrity in solution. The broadening of one of the signals for the 59Co NMR spectrum of cluster 3 in water as a protic solvent reveals the presence of the deprotonation equilibrium of the acidic protons on the cluster framework in water.

Conformational and structural stability of the single molecule and hydrogen bonded clusters of para aminobenzoic acid in the gas and solution phases

The structures of α- and β-para aminobenzoic acid are deconstructed into their hydrogen bonding molecular structural building blocks, where they are analysed usingab initioquantum mechanical calculations of their conformation and cluster stability in solution.

MooreCube: A Scalable and Flexible Architecture for Cloud Computing Data Centers on Multi-port Servers

Networks provide the infrastructure of cloud computing data centers. Servers in data centers grow to respond to the growing user demands. Data center scalability and flexibility in the use of multi-port servers is a challenging issue. Heretofore, no method has been considered for scalability and flexibility issues. This paper proposes a new architecture called MooreCube that can increase network scalability and decrease network diameter as well as increase flexibility. MooreCube is a scalable and flexible architecture that each multi-port server directly connected to other servers via bi-directional links, without using any switch. Furthermore, MooreCube is a recursively defined architecture that uses Moore graph as Building Block (BB) structure and uses the hierarchical structure to meet high scalability. The paper proposes a multipath routing to increase fault tolerance and decrease links burden. MooreCube architecture compared with other switchless architectures that use reserved ports to increase scalability. The simulation results show MooreCube increase scalability and flexibility along with decrease the diameter of the network.

Efficient Detection of Communities in Biological Bipartite Networks.

Methods to efficiently uncover and extract community structures are required in a number of biological applications where networked data and their interactions can be modeled as graphs, and observing tightly-knit groups of vertices ("communities") can offer insights into the structural and functional building blocks of the underlying network. Classical applications of community detection have largely focused on unipartite networks - i.e., graphs built out of a single type of objects. However, due to increased availability of biological data from various sources, there is now an increasing need for handling heterogeneous networks which are built out of multiple types of objects. In this paper, we address the problem of identifying communities from biological bipartite networks - i.e., networks where interactions are observed between two different types of objects (e.g., genes and diseases, drugs and protein complexes, plants and pollinators, and hosts and pathogens). Toward detecting communities in such bipartite networks, we make the following contributions: i) (metric) we propose a variant of bipartite modularity; ii) (algorithms) we present an efficient algorithm called biLouvain that implements a set of heuristics toward fast and precise community detection in bipartite networks (https://github.com/paolapesantez/biLouvain); and iii) (experiments) we present a thorough experimental evaluation of our algorithm including comparison to other state-of-the-art methods to identify communities in bipartite networks. Experimental results show that our biLouvain algorithm identifies communities that have a comparable or better quality (as measured by bipartite modularity) than existing methods, while significantly reducing the time-to-solution between one and four orders of magnitude.

Oxidation Of Phosphatidylethanolamines As Ferroptotic Signals: Control By Lipoxygenases

Phospholipids were essential for life from the very early stages of it emerence. With the appearance of molecular oxygen and multicellularity - polyunsaturated lipids played two important roles: 1) as structural building blocks of membranes, and 2) as communication signals. Among many different mechanisms, oxygenation of polyunsaturated lipids played an essential role in coordinating numerous metabolic reactions and pathways. This paramount role of oxygenated polyunsaturated lipids in regulation is also associated with a risk of their involvement in aberrant injury reactions due to lipid peroxidation and the production of secondary reactive lipid electrophiles. Discoordination of these oxygenation reactions leads to ferroptosis, a non-apoptotic, iron dependent form of regulated cell death. We will present new data identifying hydroperoxy-phosphatidylethanolamines generated by 15-lipoxygenases (15LO). We found that 15LO oxygenate free polyunsaturated fatty acids (PUFA) but can change their substrate specificity to generate hydroperoxy-PUFA phosphatidyl-ethanolamines (PUFAPEs) which - under conditions of GPX4 deficiency - trigger ferroptosis. We sought a common pro-ferroptotic regulator for 15LO using oxidative phospholipidomics, confocal-based immunolocalization techniques, redox biochemistry and computational biology. We discovered that PEBP1, a scaffold protein inhibitor of protein kinase cascades, complexes with two 15LO isoforms, 15LO1 and 15LO2, and changes their substrate competence to generate pro-ferroptotic hydroperoxy-PUFA-PE.

Polyarylester nanofiltration membrane prepared from monomers of vanillic alcohol and trimesoyl chloride

Abstract Ammonium lignosulfonate (AL), a cheap lignin derivative with abundant phenolic building block structures, was first used as the monomer to synthesize a thin film composite nanofiltration (NF) membrane via interfacial polymerization with trimesoyl chloride (TMC) on the cross-linked poly(ether imide) substrate. The AL-TMC NF membranes show superior organic solvent resistance, the optimal NF-2AL membrane has a permeance of 0.97 L m−2 h−1 MPa−1 and a 98% rejection for Brilliant Blue R-250 (BB, 825 g mol−1) in DMSO. To enhance the permeance further, we adopted vanillic alcohol (VA), which possesses a molecular structure similar to the subunit of AL, to synthesize a VA-TMC NF membrane. Combining with characterizations of ATR-FTIR, 13C NMR, XPS, SEM and AFM, etc., it is illustrated that the VA-TMC NF membrane is composed of polyarylester and exhibits high DMSO permeance about 21 L m−2 h−1 MPa−1, the comparable BB rejection of 89% and a rejection of 81% for clindamycin phosphate. These results suggest a promising route to select potential monomers to synthesize desirable nanofiltration membrane with superior antisolvent property and separation performance.

Die Europium(II)-Oxidhalogenide Eu2OBr2 und Eu2OI2

Abstract The syntheses and crystal structures of the two isotypic europium(II) oxide halides Eu2OBr2 and Eu2OI2 are reported. They crystallize orthorhombically in the space group Ibam (Z=4; Eu2OBr2: a=709.86(5), b=1200.34(9), c=628.71(4) pm; Eu2OI2: a=739.78(5), b=1295.13(9), c=644.82(4) pm). The unit cell parameters presented here, and thus the interatomic distances of Eu2OI2, are significantly smaller than the ones reported in the literature, which is explained by the substitution of europium with larger barium cations due to the synthesis route described in the early study. Central building blocks of both crystal structures are trans-edge-connected [OEu4]6+ tetrahedra forming straight ∞ 1 { [ OEu 4/2 e ] 2 + } $_\infty ^1\{ {[{\text{OEu}}_{{\text{4/2}}}^{\text{e}}]^{2 + }}\} $ chains running parallel to the [001] direction. Bundled like a hexagonal rod packing, their interaction is achieved by Br− or I− anions for charge compensation.

Maximal Rashba-like spin splitting via kinetic-energy-coupled inversion-symmetry breaking.

Engineering and enhancing the breaking of inversion symmetry in solids-that is, allowing electrons to differentiate between 'up' and 'down'-is a key goal in condensed-matter physics and materials science because it can be used to stabilize states that are of fundamental interest and also have potential practical applications. Examples include improved ferroelectrics for memory devices and materials that host Majorana zero modes for quantum computing. Although inversion symmetry is naturally broken in several crystalline environments, such as at surfaces and interfaces, maximizing the influence of this effect on the electronic states of interest remains a challenge. Here we present a mechanism for realizing a much larger coupling of inversion-symmetry breaking to itinerant surface electrons than is typically achieved. The key element is a pronounced asymmetry of surface hopping energies-that is, a kinetic-energy-coupled inversion-symmetry breaking, the energy scale of which is a substantial fraction of the bandwidth. Using spin- and angle-resolved photoemission spectroscopy, we demonstrate that such a strong inversion-symmetry breaking, when combined with spin-orbit interactions, can mediate Rashba-like spin splittings that are much larger than would typically be expected. The energy scale of the inversion-symmetry breaking that we achieve is so large that the spin splitting in the CoO2- and RhO2-derived surface states of delafossite oxides becomes controlled by the full atomic spin-orbit coupling of the 3d and 4d transition metals, resulting in some of the largest known Rashba-like spin splittings. The core structural building blocks that facilitate the bandwidth-scaled inversion-symmetry breaking are common to numerous materials. Our findings therefore provide opportunities for creating spin-textured states and suggest routes to interfacial control of inversion-symmetry breaking in designer heterostructures of oxides and other material classes.

Self‐Assembly of DNA Nanostructures Using Three‐Way Junctions on Small Circular DNAs

AbstractMolecular self‐assembly using DNA as a structural building block has proven to be an efficient route to the construction of nanoscale objects and arrays. Using the pre‐circularised DNA as the core strand of DNA motifs provides new components for the assembly of one‐, two‐, and three‐dimensional (1D, 2D, 3D) nanostructures. We report here honeycomb‐like and grid‐like framework nanostructures constructed from 3‐arm triangle and 4‐arm square tiles with pivotal three‐way junctions on small circular oligonucleotides of 32‐nt and 42‐nt, respectively. However the flexible three‐way junction, the crowded spatial environment of the small circular DNA motifs, and the lack of rigidity in the double helix connection may reduce the possibility to grow large single crystalline DNA lattices.

A crawling robot driven by multi-stable origami

Using origami folding to construct and actuate mechanisms and machines offers attractive opportunities from small, scalable, and cheap robots to deployable adaptive structures. This paper presents the design of a bio-inspired origami crawling robot constructed by folding sheets of paper. The origami building block structure is based on the Kresling crease pattern (CP), a chiral tower with a polygonal base, which expands and contracts through coupled longitudinal and rotational motion similar to a screw. We design the origami to have multi-stable structural equilibria which can be tuned by changing the folding CP. Kinematic analysis of these structures based on rigid-plates and hinges at fold lines precludes the shape transformation associated with the bistability of the physical models. To capture the kinematics of the bi-stable origami, the panels’ deformation behavior is modeled utilizing principles of virtual folds. Virtual folds approximate material bending by hinged, rigid panels, which facilitates the development of a kinematic solution via rigid-plate rotation analysis. As such, the kinetics and stability of folded structures are investigated by assigning suitable torsional spring constants to the fold lines. The results presented demonstrate the effect of fold-pattern geometries on the snapping behavior of the bi-stable origami structure based on the Kresling pattern. The crawling robot is presented as a case study for the use of this origami structure to mimic crawling locomotion. The robot is comprised of two origami towers nested inside a paper bellow, and connected by 3D printed end plates. DC motors are used to actuate the expansion and contraction of the internal origami structures to achieve forward locomotion and steering. Beyond locomotion, this simple design can find applications in manipulators, booms, and active structures.

Characterization of conformational deformation-coupled interaction between immunoglobulin G1 Fc glycoprotein and a low-affinity Fcγ receptor by deuteration-assisted small-angle neutron scattering

A recently developed integrative approach combining varied types of experimental data has been successfully applied to three-dimensional modelling of larger biomacromolecular complexes. Deuteration-assisted small-angle neutron scattering (SANS) plays a unique role in this approach by making it possible to observe selected components in the complex. It enables integrative modelling of biomolecular complexes based on building-block structures typically provided by X-ray crystallography. In this integrative approach, it is important to be aware of the flexible properties of the individual building blocks. Here we examine the ability of SANS to detect a subtle conformational change of a multidomain protein using the Fc portion of human immunoglobulin G (IgG) interacting with a soluble form of the low-affinity Fcγ receptor IIIb (sFcγRIIIb) as a model system. The IgG-Fc glycoprotein was subjected to SANS in the absence and presence of 75%-deuterated sFcγRIIIb, which was matched out in D2O solution. This inverse contrast-matching technique enabled selective observation of SANS from IgG-Fc, thereby detecting its subtle structural deformation induced by the receptor binding. The SANS data were successfully interpreted by considering previously reported crystallographic data and an equilibrium between free and sFcγRIIIb-bound forms. Our SANS data thus demonstrate the applicability of SANS in the integrative approach dealing with biomacromolecular complexes composed of weakly associated building blocks with conformational plasticity.

Spray-drying-assisted reassembly of uniform and large micro-sized MIL-101 microparticles with controllable morphologies for benzene adsorption

Significant research has been focused on the synthesis of metal-organic frameworks (MOFs) with controllable compositions and structures, while much fewer works have been devoted to the construction of large micro-sized MOFs with uniform sizes and morphologies, which could be beneficial for practical applications. In this paper, a unique microfluidic jet spray drying technology has been adopted to reassemble nano-sized MIL-101 building blocks into hierarchical microparticles with uniform and large particle sizes. Specifically, suspension precursors of nano-sized MIL-101 building blocks are atomized into uniform droplets and then converted to microparticles on a one-to-one basis through a fast and scalable spray drying process. The particle size and morphology can be controlled by adjusting the solid concentration of the suspension and the drying temperature. The particle formation process with evolution of different morphologies are discussed. The resultant uniform MIL-101 microparticles possess hierarchical porosities and maintain the intrinsic crystal structure, microporosity and thermal stability of the nano-sized building blocks. They demonstrate a high efficiency toward benzene adsorption from n-octane solutions with high adsorption rates and very high adsorption capacities under batch conditions. Moreover, the large particle size and hierarchical structure make them applicable as filler of a fixed bed for dynamic flow separation of benzene from n-octane solutions with promising performance. The microfluidic jet spray drying technology can also be extended for the reassembly of other uniform MOF microparticles.

3D hierarchical Co3O4: Controlled preparation of coral-/urchin-like structures and application in photo-catalytic degradation

Three-dimensional (3D) hierarchical architectures built from spherical assembly of nanowires/nanorods have found applications in a wide range of fields. However, although some literatures have reported their successful preparation, up to now, it is difficult to adjust the size of the building blocks of the 3D structures, which indeed largely affects the performance of the materials. In this work, by adopting metal ions and PVP modified carbon spheres as templates, we demonstrate a seed-mediated growing strategy to control Co3O4 shapes to be 3D urchin-like hierarchical structures constructed from 40 nm-diameter nano-wires, or 3D coral-like ones assembled from thicker 100 nm-diameter nano-rods. XRD patterns show both structured Co3O4 are cubic phase, and N2 sorption demonstrates they own both mesopores and macropores. Besides, the obtained materials display good photocatalytic performance and reusability to degrade Congo Red dye.

Toward Covalent Organic Frameworks Bearing Three Different Kinds of Pores: The Strategy for Construction and COF-to-COF Transformation via Heterogeneous Linker Exchange.

Covalent organic frameworks (COFs) are an emerging class of crystalline porous organic materials which are fabricated via reticular chemistry. Their topologic structures can be precisely predicted on the basis of the structures of building blocks. However, constructing COFs with complicated structures has remained a great challenge, due to the limited strategies that can access to the structural complexity of COFs. In this work, we have developed a new approach to produce COFs bearing three different kinds of pores. The design is fulfilled by the combination of vertex-truncation with multiple-linking-site strategy. On the basis of this design, a "V"-shaped building block carrying two aldehyde groups on the end of each branch has been synthesized. Condensation of it with 1,4-diaminobenzene or benzidine leads to the formation of two triple-pore COFs, TP-COF-DAB and TP-COF-BZ, respectively. The topological structures of the triple-pore COFs have been confirmed by PXRD studies, synchrotron small-angle X-ray scattering (SAXS) experiments, theoretical simulations, and pore size distribution analyses. Furthermore, for the first time, an in situ COF-to-COF transformation has also been achieved by heating TP-COF-BZ with 1,4-diaminobenzene under solvothermal condition, which leads to the formation of TP-COF-DAB via in situ replacing the benzidine linkers in TP-COF-BZ with 1,4-diaminobenzene linkers.

Optical Reflectivity of Spin-Coated Multilayered ZnO and Al:ZnO Thin Films

Zinc oxide (ZnO) and its doped counterparts such as Al:ZnO are extensively investigated as indium-free alternatives for oxide electronics including solar cells, light emitting diodes and also display technologies. For the latter application, thin film transistor (TFT) devices are the building-block structures. High fidelity TFTs require conductive channel materials, with good field effect mobility for majority carriers and tunable optical transparency. Controlling growth, doping, crystallization, and thickness of thin films of these materials is required in order to improve and control physical properties, primarily electronic conductivity and optical transparency. With the advent of flexible electronics and curved TFT-based display panels, low cost, solution-processed methods are important and provide scalable coating methods on a range of substrates. This work demonstrates the changes to the morphology, crystalline structure, optical reflectivity and electrical conductance of solution-processed ZnO thin films by the inclusion of an aluminium dopant during spin-coating. The is work also determines the compositional chemical state of the Al:ZnO structures compared to ZnO using X-ray photoelectron spectroscopy in conjunction with detailed X-ray diffraction and transmission electron microscopy examination of the film morphology. We also demonstrate a method of determining the optical thickness of multilayer thin films using simple, non-destructive angle-resolved reflectance measurements. Using optical interference, the optical thickness of the multi-layered deposited ZnO and Al:ZnO can be determined and show good agreement with the thicknesses measured by transmission electron microscopy of electron transparent lamellar cross-sections. We also show the visible and near-infra red (VIS-NIR) light spectroscopy of ZnO and Al:ZnO multi-layered thin film structures grown on oxidized silicon substrates also define the growth conditions and processing to provide tunable antireflection coatings of ZnO and AZO.

One-pot synthesis of 1,5,3-oxathiazepanes via the three-component condensation of primary amines, formaldehyde and 2-mercaptoethanol

The three-component condensation reaction of primary amines, formaldehyde and 2-mercaptoethanol using salts of transition and rare earth metals as catalysts was developed to obtain a new 7-membered heterocyclic structural building block, 1,5,3-oxathiazepanes, in good to excellent yields. The structure of the heterocyclic fragment was confirmed by NMR spectroscopy.

Characterization of a pyrolysis liquid from a German brown coal by use of negative and positive ion mode electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry and collision-induced dissociation

A pyrolysis oil produced by slow pyrolysis from a German brown coal was analysed using a combination of three mass spectrometric methods. Various compounds of the pyrolysis liquid sample were ionized by electrospray ionization, both in positive (ESI(+)) and negative (ESI(−)) ion mode, and analysed by Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS). ESI(−)-FT-ICR-MS analyses mainly exhibit oxygen- as well as sulfur-/oxygen-containing compounds in the pyrolysis oil. In contrast, ESI(+)-FT-ICR-MS analyses were dominated by nitrogen- and nitrogen-/oxygen-containing species. Structural suggestions were possible by plotting the carbon number (nC) vs. the double bond equivalent (DBE). The assigned structures were further examined by applying ESI(−)-FT-ICR-MS with collision-induced dissociation mass spectrometry (CID-MS). The degradation of the pyrolysis oil constituents into their structural building blocks was monitored by varying the collision energy and its influence on the peak number and the median m/z. According to our results, dealkylation and decomposition processes of multiaromatic systems dominated during the CID event. Possible structural building blocks of pyrolysis oil S500 were found to be polycyclic aromatic ketones and quinones, partially bound to thiophenic structures. It was shown that the developed combination of ESI(+)- and ESI(−)-FT-ICR-MS with ESI(−)-CID-FT-ICR-MS gives the possibility to examine a complex sample, such as a pyrolysis liquid, by investigating its basic chemical backbone.

A comparative study of new linear and hyperbranched polyurethanes built up from a synthesized isocyanate-terminated polyester/urethane

In the present study, the effects of architecture and structural building blocks of the polyurethane chains on their properties were studied. New linear and hyperbranched polyurethanes (LPU and HPU) were prepared via A2 + B2 and A2 + B3 methodologies, respectively. Polyethylene glycol (PEG-1000) and castor oil (CO) were used as bi- and trifunctional monomers (B2 and B3), respectively. However, A2 monomers were synthesized by the reaction between ethylene glycol (EG) with terephthaloyl chloride (TPC) and reacting the product with excess toluene diisocyanate (TDI) to produce isocyanate-terminated PU (NCO-PU). NCO-PU was reacted with PEG to synthesize LPU; however, its reaction with CO synthesized HPU. NCO-PU, LPU and HPU were characterized by FTIR, H-NMR, GPC, TEM, TGA, DSC and XRD. The prepared PUs were applied as coatings and their physical, chemical and mechanical properties were investigated. The results showed that the degree of branching of HPU was 79%. No phase separation was observed in NCO-PU as indicated by its DSC curve. However, two phases are detected in HPU and LPU that represent to the hard and soft segments. NCO-PU displayed the highest crystallinity index (CrI = 89.26%). However, the high degree of branching in HPU led to lower CrI than LPU. The lack of entanglements in HPU led to its slightly lower solution viscosity than LPU. TEM images showed spherical PU nano-particles. The surface of HPU coating showed the highest gloss which is due to its low degree of crystallinity. HPU and LPU exhibited excellent chemical resistivity.

The topology of inter-industry relations from the Portuguese national accounts

In last years, the Portuguese economy has gone through a severe adjustment process, affecting almost all industrial sectors, the building blocks of economic structures. Research on economic structural changes has made use of input/output tables to define networks of industrial relations. Here, these networks are induced from output tables of the Portuguese national accounting system, being each inter-industry relation defined by the output made by any two industries for the products that they both produce. The topological analysis of these networks allows to uncover a particular structure that comes out during the Portuguese adjustment program. The evolution of the industrial networks shows an important structural change in 2011–2014, confirming the usefulness of inducting similarity networks from output tables and the consequent promising power of the graph formulation for the analysis of inter-industry relations.