New insights on the role of paired membrane structures in coronavirus replication

The replication of coronaviruses, as in other positive-strand RNA viruses, is closely tied to the formation of membrane-bound replicative organelles inside infected cells. The proteins responsible for rearranging cellular membranes to form the organelles are conserved not just among the Coronaviridae family members, but across the order Nidovirales. Taken together, these observations suggest that the coronavirus replicative organelle plays an important role in viral replication, perhaps facilitating the production or protection of viral RNA. However, the exact nature of this role, and the specific contexts under which it is important have not been fully elucidated. Here, we collect and interpret the recent experimental evidence about the role and importance of membrane-bound organelles in coronavirus replication.

Capacitive electrolyte-insulator-semiconductor structures functionalised with a polyelectrolyte/enzyme multilayer: New strategy for enhanced field-effect biosensing

A novel strategy for enhanced field-effect biosensing using capacitive electrolyte-insulator-semiconductor (EIS) structures functionalised with pH-responsive weak polyelectrolyte/enzyme or dendrimer/enzyme multilayers is presented. The feasibility of the proposed approach is exemplarily demonstrated by realising a penicillin biosensor based on a capacitive p-Si-SiO(2) EIS structure functionalised with a poly(allylamine hydrochloride) (PAH)/penicillinase and a poly(amidoamine) dendrimer/penicillinase multilayer. The developed sensors response to changes in both the local pH value near the gate surface and the charge of macromolecules induced via enzymatic reaction, resulting in a higher sensitivity. For comparison, an EIS penicillin biosensor with adsorptively immobilised penicillinase has been also studied. The highest penicillin sensitivity of 100 mV/dec has been observed for the EIS sensor functionalised with the PAH/penicillinase multilayer. The lower and upper detection limit was around 20 mu M and 10 mM, respectively. In addition, an incorporation of enzymes in a multilayer prepared by layer-by-layer technique provides a larger amount of immobilised enzymes per sensor area, reduces enzyme leaching effects and thus, enhances the biosensor lifetime (the loss of penicillin sensitivity after 2 months was 10-12%). (C) 2010 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim

Exploring new molecular species on the (1)[H, Se, F] singlet potential energy surface: Energetics, structures, IR spectra, and heats of formation

Structural, energetic, and vibrational properties of new molecular species, HSeF and HFSe, the associated transition state, and dissociation fragments are investigated using a state-of-the-art theoretical approach, CCSD(T)/CBS. HSeF is a normal covalently bonded molecule 38.98 kcal mol (1) more stable than the complex HF-Se, which shows an unusual structure with a central fluorine atom and a bond angle of 101.8 degrees.A barrier (Delta G(#)) of 49.01 kcal mol (1) separates the two species. Vibrational frequencies are also quite distinct. Heats of formation are evaluated for the diatomic fragments and HSeF. Final Delta(f)H values depend on the experimental accuracy of those of Se(g) and H(2)Se. (c) 2009 Elsevier B.V. All rights reserved.

Synthesis, Spectroscopic Studies and X-ray Crystal Structures of New Pyrazoline and Pyrazole Derivatives

The synthesis and characterization of some pyrazoline compounds of 1,3-diketones with hydrazine derivatives, namely, 1-(S-benzyldithiocarbazate)-3-methyl-5-phenyl-5-hydroxypyrazoline (1); 1-(2-thiophenecarboxylic)-3-methyl-5-phenyl-5-hydroxypyrazoline (2); 1-(2-thiophenecarboxylic)-3,5-dimethyl-5-hydroxypyrazoline (3); 1-(S-benzyldithiocarbazato)-3-methyl-5-phenylpyrazole (4); 1-(2-thiophenecarboxylic)-3-methyl-5-phenylpyrazole (5) and 1-(S-benzyldithiocarbazate)-3,5-dimethylpyrazole (6) are reported. Studies by IR, ((1)H, (13)C)-NMR spectroscopies and single crystal X-ray diffraction revealed that compounds (1)(,) (2) and (3) are formed as pyrazoline, whereas (4) and (5) are formed as pyrazole derivatives only under acidic conditions. Compound (1) crystallizes in orthorhombic P2(1)2(1)2(1), a = 6.38960(10) angstrom, b = 12.9176(3) angstrom, c = 21.2552(5) angstrom, (2) crystallizes in monoclinic, P2(1)/n, a = 11.3617(2) angstrom, b = 8.4988(2) angstrom, c = 92.8900(10)angstrom and beta = 92.8900(5)degrees, (3) crystallizes in monoclinic, C2/c, a = 15.9500(5) angstrom, b = 9.3766(3) angstrom, c = 16.6910(5)angstrom and beta = 113.825(2)degrees, (4) crystallizes in monoclinic, P2(1)/c, a = 15.228(4) angstrom, b = 5.5714(13) angstrom, c = 19.956(5)angstrom and beta = 91.575(7)degrees and (6) crystallizes in orthorhombic, P2(1)2(1)2(1), a = 5.3920(2) angstrom, b = 11.2074(5) angstrom, c = 21.885(1)angstrom . The (3) derivative represents the first pyrazoline compound prepared from 2,4-pentanedione and characterized crystallographically.

NiBr2 complexes with triphenylarsine oxide (Ph3AsO). Two new interesting structures

The synthesis and crystal structure of two complexes resulting from interaction between NiBr2 and triphenylarsine oxide (Ph3AsO) is described. Green and orange complexes can be obtained from the blue, probably tetrahedral complex [NiBr2(Ph3AsO)2], depending on the solvents used for recrystallization. NiBr2·4[(C6H5)3AsO]·8H2O (green): M = 1650.2, P21/c, a = 13.731(2), b = 16.267(3), c = 17.647(2) Å, β = 112.04(1)°, V = 3651.4 Å3, Z = 2, Dx = 1.501 g cm-3, CuKα, λ = 1.54184 Å, μ = 38.67 cm-1, R = 0.039, 3741 unique reflections, 3203 with I > 3σ(I). NiBr2·4[(C6H5)3AsO]·3|2(C6H5CH3)·H2O (orange): M = 1663.7, P1, a = 12.647(8), b = 13.953(5), c = 22.853(6) Å, α = 90.91(3), β = 96.70(4), γ = 111.16(4)°, V = 3727.4 Å3, Z = 2, Dx = 1.482 g cm-3, MoKα, λ = 0.71073 Å, μ = 30.48 cm-1, R = 0.087, 8600 unique reflections, 4293 with I > 3σ(I). In the green complex the Ni(II) ion is sited on a center of symmetry and is octahedrally coordinated to six water molecules, hydrogen bonded to the Ph3AsO molecules and to the bromide anions forming a second coordination sphere in a nearly octahedral arrangement. In the orange complex the cation is pentacoordinated with the four oxygen atoms of the Ph3AsO ligands forming the basis of a tetragonal pyramid and with one Br- anion in the apical position. The absorption spectrum of the orange complex is compared with the spectra of other Ni(II) square pyramidal complexes described in the literature. © 1984.

Ordovician klippen structures of the Sierra de Umango: New insights on Tectonic evolution of the Western Sierras Pampeanas, Argentina

The basement rock of the Pampean flat-slab (Sierras Pampeanas) in the Central Andes was uplifted and rotated in the Cenozoic era. The Western Sierras Pampeanas are characterised by meta-igneous rocks of Grenvillian Mesoproterozoic age and metasedimentary units metamorphosed in the Ordovician period. These rocks, known as the northern Cuyania composite terrane, were derived from Laurentia and accreted toward Western Gondwana during the Early Paleozoic. The Sierra de Umango is the westernmost range of the Western Sierras Pampeanas.This range is bounded by the Devonian sedimentary rocks of the Precordillera on the western side and Tertiary rocks from the Sierra de Maz and Sierra del Espinal on the eastern side and contains igneous and sedimentary rocks outcroppings from the Famatina System on the far eastern side. The Sierra de Umango evolved during a period of polyphase tectonic activity, including an Ordovician collisional event, a Devonian compressional deformation, Late Paleozoic and Mesozoic extensional faulting and sedimentation (Paganzo and Ischigualasto basins) and compressional deformation of the Andean foreland during the Cenozoic. A Nappe System and an important shear zone, La Puntilla-La Falda Shear Zone (PFSZ), characterise the Ordovician collisional event, which was related to the accretion of Cuyania Terrane to the proto-Andean margin of Gondwana. Three continuous deformational phases are recognised for this event: the D1 phase is distinguished by relics of 51 preserved as internal foliation within interkinematic staurolite por-phyroblasts and likely represents the progressive metamorphic stage; the D2 phase exhibits P-T conditions close to the metamorphic peak that were recorded in an 52 transposition or a mylonitic foliation and determine the main structure of Umango; and the D3 phase is described as a set of tight to recumbent folds with S3 axial plane foliation, often related to thrust faults, indicating the retrogressive metamorphic stage. The Nappe System shows a top-to-the S/SW sense direction of movement, and the PFSZ served as a right lateral ramp in the exhumation process. This structural pattern is indicative of an oblique collision, with the Cuyania Terrane subducting under the proto-Andean margin of Gondwana in the NE direction. This continental subduction and exhumation lasted at least 30 million years, nearly the entire Ordovician period, and produced metamorphic conditions of upper amphibolite-to-granulite facies in medium- to high-pressure regimes. At least two later events deformed the earlier structures: D4 and D5 deformational phases. The D4 deformational phase corresponds to upright folding, with wavelengths of approximately 10 km and a general N-S orientation. These folds modified the S2 surface in an approximately cylindrical manner and are associated with exposed, discrete shear zones in the Silurian Guandacolinos Granite. The cylindrical pattern and subhorizontal axis of the D4 folds indicates that the S2 surface was originally flat-lying. The D4 folds are responsible for preserving the basement unit Juchi Orthogneiss synformal klippen. This deformation corresponds to the Chanica Tectonic during the interval between the Devonian and Carboniferous periods. The D5 deformational phase comprehends cuspate-lobate shaped open plunging folds with E W high-angle axes (D5 folds) and sub-vertical spaced cleavage. The D5 folds and related spaced cleavage deformed the previous structures and could be associated with uplifting during the Andean Cycle. (C) 2012 Elsevier Ltd. All rights reserved.

Prediction of new crystal structures under extreme conditions

One of the most important challenges in chemistry and material science is the connection between the contents of a compound and its chemical and physical properties. In solids, these are greatly influenced by the crystal structure.rnrnThe prediction of hitherto unknown crystal structures with regard to external conditions like pressure and temperature is therefore one of the most important goals to achieve in theoretical chemistry. The stable structure of a compound is the global minimum of the potential energy surface, which is the high dimensional representation of the enthalpy of the investigated system with respect to its structural parameters. The fact that the complexity of the problem grows exponentially with the system size is the reason why it can only be solved via heuristic strategies.rnrnImprovements to the artificial bee colony method, where the local exploration of the potential energy surface is done by a high number of independent walkers, are developed and implemented. This results in an improved communication scheme between these walkers. This directs the search towards the most promising areas of the potential energy surface.rnrnThe minima hopping method uses short molecular dynamics simulations at elevated temperatures to direct the structure search from one local minimum of the potential energy surface to the next. A modification, where the local information around each minimum is extracted and used in an optimization of the search direction, is developed and implemented. Our method uses this local information to increase the probability of finding new, lower local minima. This leads to an enhanced performance in the global optimization algorithm.rnrnHydrogen is a highly relevant system, due to the possibility of finding a metallic phase and even superconductor with a high critical temperature. An application of a structure prediction method on SiH12 finds stable crystal structures in this material. Additionally, it becomes metallic at relatively low pressures.

Dynamic distance analysis : new geometric data structures and algorithms for the real-time calculation of tolerance violating regions in the digital mockup process

In vielen Industriezweigen, zum Beispiel in der Automobilindustrie, werden Digitale Versuchsmodelle (Digital MockUps) eingesetzt, um die Konstruktion und die Funktion eines Produkts am virtuellen Prototypen zu überprüfen. Ein Anwendungsfall ist dabei die Überprüfung von Sicherheitsabständen einzelner Bauteile, die sogenannte Abstandsanalyse. Ingenieure ermitteln dabei für bestimmte Bauteile, ob diese in ihrer Ruhelage sowie während einer Bewegung einen vorgegeben Sicherheitsabstand zu den umgebenden Bauteilen einhalten. Unterschreiten Bauteile den Sicherheitsabstand, so muss deren Form oder Lage verändert werden. Dazu ist es wichtig, die Bereiche der Bauteile, welche den Sicherhabstand verletzen, genau zu kennen. rnrnIn dieser Arbeit präsentieren wir eine Lösung zur Echtzeitberechnung aller den Sicherheitsabstand unterschreitenden Bereiche zwischen zwei geometrischen Objekten. Die Objekte sind dabei jeweils als Menge von Primitiven (z.B. Dreiecken) gegeben. Für jeden Zeitpunkt, in dem eine Transformation auf eines der Objekte angewendet wird, berechnen wir die Menge aller den Sicherheitsabstand unterschreitenden Primitive und bezeichnen diese als die Menge aller toleranzverletzenden Primitive. Wir präsentieren in dieser Arbeit eine ganzheitliche Lösung, welche sich in die folgenden drei großen Themengebiete unterteilen lässt.rnrnIm ersten Teil dieser Arbeit untersuchen wir Algorithmen, die für zwei Dreiecke überprüfen, ob diese toleranzverletzend sind. Hierfür präsentieren wir verschiedene Ansätze für Dreiecks-Dreiecks Toleranztests und zeigen, dass spezielle Toleranztests deutlich performanter sind als bisher verwendete Abstandsberechnungen. Im Fokus unserer Arbeit steht dabei die Entwicklung eines neuartigen Toleranztests, welcher im Dualraum arbeitet. In all unseren Benchmarks zur Berechnung aller toleranzverletzenden Primitive beweist sich unser Ansatz im dualen Raum immer als der Performanteste.rnrnDer zweite Teil dieser Arbeit befasst sich mit Datenstrukturen und Algorithmen zur Echtzeitberechnung aller toleranzverletzenden Primitive zwischen zwei geometrischen Objekten. Wir entwickeln eine kombinierte Datenstruktur, die sich aus einer flachen hierarchischen Datenstruktur und mehreren Uniform Grids zusammensetzt. Um effiziente Laufzeiten zu gewährleisten ist es vor allem wichtig, den geforderten Sicherheitsabstand sinnvoll im Design der Datenstrukturen und der Anfragealgorithmen zu beachten. Wir präsentieren hierzu Lösungen, die die Menge der zu testenden Paare von Primitiven schnell bestimmen. Darüber hinaus entwickeln wir Strategien, wie Primitive als toleranzverletzend erkannt werden können, ohne einen aufwändigen Primitiv-Primitiv Toleranztest zu berechnen. In unseren Benchmarks zeigen wir, dass wir mit unseren Lösungen in der Lage sind, in Echtzeit alle toleranzverletzenden Primitive zwischen zwei komplexen geometrischen Objekten, bestehend aus jeweils vielen hunderttausend Primitiven, zu berechnen. rnrnIm dritten Teil präsentieren wir eine neuartige, speicheroptimierte Datenstruktur zur Verwaltung der Zellinhalte der zuvor verwendeten Uniform Grids. Wir bezeichnen diese Datenstruktur als Shrubs. Bisherige Ansätze zur Speicheroptimierung von Uniform Grids beziehen sich vor allem auf Hashing Methoden. Diese reduzieren aber nicht den Speicherverbrauch der Zellinhalte. In unserem Anwendungsfall haben benachbarte Zellen oft ähnliche Inhalte. Unser Ansatz ist in der Lage, den Speicherbedarf der Zellinhalte eines Uniform Grids, basierend auf den redundanten Zellinhalten, verlustlos auf ein fünftel der bisherigen Größe zu komprimieren und zur Laufzeit zu dekomprimieren.rnrnAbschießend zeigen wir, wie unsere Lösung zur Berechnung aller toleranzverletzenden Primitive Anwendung in der Praxis finden kann. Neben der reinen Abstandsanalyse zeigen wir Anwendungen für verschiedene Problemstellungen der Pfadplanung.

Epothilones as lead structures for the synthesis-based discovery of new chemotypes for microtubule stabilization

Epothilones are macrocyclic bacterial natural products with potent microtubule-stabilizing and antiproliferative activity. They have served as successful lead structures for the development of several clinical candidates for anticancer therapy. However, the structural diversity of this group of clinical compounds is rather limited, as their structures show little divergence from the original natural product leads. Our own research has explored the question of whether epothilones can serve as a basis for the development of new structural scaffolds, or chemotypes, for microtubule stabilization that might serve as a basis for the discovery of new generations of anticancer drugs. We have elaborated a series of epothilone-derived macrolactones whose overall structural features significantly deviate from those of the natural epothilone scaffold and thus define new structural families of microtubule-stabilizing agents. Key elements of our hypermodification strategy are the change of the natural epoxide geometry from cis to trans, the incorporation of a conformationally constrained side chain, the removal of the C3-hydroxyl group, and the replacement of C12 with nitrogen. So far, this approach has yielded analogs 30 and 40 that are the most advanced, the most rigorously modified, structures, both of which are potent antiproliferative agents with low nanomolar activity against several human cancer cell lines in vitro. The synthesis was achieved through a macrolactone-based strategy or a high-yielding RCM reaction. The 12-aza-epothilone ("azathilone" 40) may be considered a "non-natural" natural product that still retains most of the overall structural characteristics of a true natural product but is structurally unique, because it lies outside of the general scope of Nature's biosynthetic machinery for polyketide synthesis. Like natural epothilones, both 30 and 40 promote tubulin polymerization in vitro and at the cellular level induce cell cycle arrest in mitosis. These facts indicate that cancer cell growth inhibition by these compounds is based on the same mechanistic underpinnings as those for natural epothilones. Interestingly, the 9,10-dehydro analog of 40 is significantly less active than the saturated parent compound, which is contrary to observations for natural epothilones B or D. This may point to differences in the bioactive conformations of N-acyl-12-aza-epothilones like 40 and natural epothilones. In light of their distinct structural features, combined with an epothilone-like (and taxol-like) in vitro biological profile, 30 and 40 can be considered as representative examples of new chemotypes for microtubule stabilization. As such, they may offer the same potential for pharmacological differentiation from the original epothilone leads as various newly discovered microtubule-stabilizing natural products with macrolactone structures, such as laulimalide, peloruside, or dictyostatin.

New copper(II) complexes with isoconazole: Synthesis, structures and biological properties

There is an increasing demand for novel metal-based complexes with biologically relevant molecules in technology and medicine. Three new Cu(II) coordination compounds with antifungal agent isoconazole (L), namely mononuclear complexes CuCl2(L)(2) (1), and Cu(O2CMe)(2)(L)(2)center dot 2H(2)O (2) and coordination polymer Cu(pht)(L)(2)(n) (3) (where H(2)pht - o-phthalic acid) were synthesized and characterized by IR spectroscopy, thermogravimetric analysis and X-ray crystallography. X-ray analysis showed that in all complexes, the isoconazole is coordinated to Cu(II) centres by a N atom of the imidazole fragment. In complex I, the square-planar environment of Cu(II) atoms is completed by two N atoms of isoconazole and two chloride ligands, whereas the Cu(II) atoms are coordinated by two N atoms from two isoconazole ligands and two O atoms from the different carboxylate residues: acetate in 2 and phthalate in 3. The formation of an infinite chain through the bridging phthalate ligand is observed in 3. The biosynthetic ability of micromycetes Aspergillus niger CNMN FD 10 in the presence of the prepared complexes 1-3 as well as the antifungal drug isoconazole were studied. Complexes 2 and 3 accelerate the biosynthesis of enzymes (beta-glucosidase, xylanase and endoglucanase) by this fungus. Moreover, a simplified and improved method for the preparation of isoconazole nitrate was developed.

Syntheses, characterization and crystal structures of a new functionalised TTF derivative and its Ni(II) complex

The new ligand 4,5-bis (2-pyridylmethylsulfanyl)-4',5'-bis(cyanoethylthio)tetrathiafulvalene (BPM-BCET-TTF) and its nickel(II) complex have been prepared and crystallographically characterized. The Ni(II) complex shows octahedral geometry around the metal ion with the coordination site occupied by the pyridyl nitrogen atoms, the thioether sulfur atoms of the ligand and cis coordination of the halide ions.