ale Amarinder Singh seeks Centre's permission to allow liquor sale in Punjab By www.newkerala.com Published On :: Wed, 22 Apr 2020 13:18:01 +0530 Full Article
ale Coronavirus | What turned Koyambedu, Chennai’s popular wholesale complex market, into a COVID-19 hotspot? By www.thehindu.com Published On :: Sun, 10 May 2020 01:09:09 +0530 Why has Koyambedu been so badly affected in all stages of the pandemic response? Full Article Tamil Nadu
ale Drangsale des 30jhr. Krieges im Chiemgau Von Mitterwieser By daten.digitale-sammlungen.de Published On :: Wed, 06 May 2020 13:12:02 +0100 Autor: Mitterwieser, Alois Erschienen 1918 BSB-Signatur Bavar. 4392 u URN: urn:nbn:de:bvb:12-bsb00131415-2 URL: http://daten.digitale-sammlungen.de/~db/0013/bsb00131415/images/ Full Article
ale Alert train driver averts accident near Pune, saves 20 migrants’ lives By timesofindia.indiatimes.com Published On :: Sun, 10 May 2020 04:59:00 IST An alert loco driver of a goods train saved the lives of at least 20 migrant workers by applying the emergency brakes and halting the train just 100 metres away from them near Pune on Friday evening. The migrants were walking on the tracks between the Uruli and Loni stations. The incident happened barely 14 hrs after 16 migrants were killed on Aurangabad tracks. Full Article
ale Rashtriya Chemicals & Fertilisers records 35 per cent hike in sale of ‘Suphala’ fertilisers By www.thehindubusinessline.com Published On :: Sun, 10 May 2020 10:24:24 +0530 A PIB press statement said that Rashtriya Chemicals & Fertilisers Ltd (RCF) has registered a hike of 35.47 per cent in the sale of fertilisers und Full Article Companies
ale COVID-19 testing capacity scaled to 95k per day: Govt By www.rediff.com Published On :: Sat, 09 May 2020 21:43:08 +0530 A total of 15,25,631 tests have been conducted so far across 332 government and 121 private laboratories. Full Article
ale If the lockdown is not lifted, there may be defiance on a larger scale than at present By indianexpress.com Published On :: Sat, 09 May 2020 19:00:16 +0000 Full Article Columns Opinion
ale EXAFS and XANES analysis of oxides at the nanoscale By journals.iucr.org Published On :: This work presents a discussion of the possibilities offered by X-ray absorption spectroscopy (XAS) to study the local structure of nanomaterials. The current state of the art for the interpretation of extended X-ray absorption fine structure (EXAFS), including an advanced approach based on the use of classical molecular dynamics, is described and exemplified in the case of NiO nanoparticles. In addition, the limits and possibilities of X-ray absorption near-edge spectroscopy (XANES) in determining several effects associated with the nanocrystalline nature of materials are also discussed in connection with the development of ZnO-based dilute magnetic semiconductors and iron oxide nanoparticles. Full Article text
ale Decision day looms over Ellesmere Port shale gas plan - Cheshire Live By www.cheshire-live.co.uk Published On :: Fri, 24 Jan 2020 08:00:00 GMT Decision day looms over Ellesmere Port shale gas plan Cheshire Live Full Article
ale Compasses at Greenwich Are About to Do Something Not Observed in Over 300 Years - ScienceAlert By www.sciencealert.com Published On :: Mon, 02 Sep 2019 07:00:00 GMT Compasses at Greenwich Are About to Do Something Not Observed in Over 300 Years ScienceAlert Full Article
ale Fracking: UK shale gas reserves 'significantly lower than previous estimates' - Energy Live News - Energy Made Easy By www.energylivenews.com Published On :: Wed, 21 Aug 2019 07:00:00 GMT Fracking: UK shale gas reserves 'significantly lower than previous estimates' Energy Live News - Energy Made Easy Full Article
ale Bond-valence analyses of the crystal structures of FeMo/V cofactors in FeMo/V proteins By journals.iucr.org Published On :: The bond-valence method was performed on 51 crystal data sets from nitrogenase proteins, indicating the presence of molybdenum(III) in FeMo cofactors and vanadium(III) with more reduced iron complements in FeV cofactors. Full Article text
ale (E)-1-(2-Hydroxy-6-methoxyphenyl)-3-(2-methoxynaphthalen-1-yl)prop-2-en-1-one By scripts.iucr.org Published On :: 2019-09-27 In the title compound, C21H18O4, the dihedral angle between the naphthelene ring system (r.m.s. deviation = 0.014 Å) and the benzene ring is 9.68 (1)°. The C atom of the methoxy group of the naphthalene ring system is almost coplanar with the ring [C—O—C—C = −2.0 (3)°], whereas the C atom of the methoxy group of the phenol ring is slightly twisted [C—O—C—C = 6.2 (3)°]. An intramolecular O—H⋯O hydrogen bond generates an S(6) ring motif. Full Article text
ale 1,4-Bis(4-methoxyphenyl)naphthalene By scripts.iucr.org Published On :: 2020-02-21 The title naphthalene derivative, C24H20O2, features 4-methyoxy-substituted benzene rings in the 1 and 4 positions of the naphthalene ring system. There are two crystallographically independent molecules (A and B) in asymmetric unit. The independent molecules have very similar conformations in which the naphthalene ring systems are only slightly bent, exhibiting dihedral angles between the constituent benzene rings of 3.76 (15) and 3.39 (15)° for A and B, respectively. The pendent 4-methyoxybenzene rings are splayed out of the plane through the naphthalene ring system to which they are connected [range of dihedral angles = 59.63 (13) to 67.09 (13)°]. In the crystal, the molecular packing is consolidated by intermolecular C—H⋯π interactions, leading to supramolecular chains along the b axis. The chains assemble without directional interactions between them. Full Article text
ale [(1R*,3S*,4S*)-3-(2-Hydroxybenzoyl)-1,2,3,4-tetrahydro-1,4-epoxynaphthalen-1-yl]methyl 4-nitrobenzoate By scripts.iucr.org Published On :: 2020-02-28 The relative stereo- and regiochemistry of the racemic title compound, C25H19NO7, were established from the crystal structure. The fused benzene ring forms dihedral angles of 77.3 (1) and 60.3 (1)° with the hydroxy-substituted benzene ring and the nitro-substituted benzene ring, respectively. The dihedral angle between the hydroxy-substituted benzene ring and the nitro-substituted benzene ring is 76.4 (1)°. An intramolecular O—H⋯O hydrogen bond closes an S(6) ring. In the crystal, weak C—H⋯O hydrogen bonds connect the molecules, forming layers parallel to (100). Within these layers, there are weak π–π stacking interactions with a ring centroid–ring centroid distance of 3.555 (1) Å. Full Article text
ale N-[2-(Trifluoromethyl)phenyl]maleamic acid: crystal structure and Hirshfeld surface analysis By scripts.iucr.org Published On :: 2019-05-10 The title molecule, C11H8F3NO3, adopts a cis configuration across the –C=C– double bond in the side chain and the dihedral angle between the phenyl ring and side chain is 47.35 (1)°. The –COOH group adopts a syn conformation (O=C—O—H = 0°), unlike the anti conformation observed in related maleamic acids. In the crystal, inversion dimers linked by pairs of O—H⋯O hydrogen bonds are connected via N—H⋯O hydrogen bonds and C—H⋯O interactions into (100) sheets, which are cross-linked by another C—H⋯O interaction to result in a three-dimensional network. The Hirshfeld surface fingerprint plots show that the highest contribution to surface contacts arises from O⋯H/H⋯O contacts (26.5%) followed by H⋯F/F⋯H (23.4%) and H⋯H (17.3%). Full Article text
ale Crystal structure of N,N'-bis[3-(methylsulfanyl)propyl]-1,8:4,5-naphthalenetetracarboxylic diimide By scripts.iucr.org Published On :: 2019-05-31 The title compound, C22H22N2O4S2, was synthesized by the reaction of 1,4,5,8-naphthalenetetracarboxylic dianhydride with 3-(methylsulfanyl)propylamine. The whole molecule is generated by an inversion operation of the asymmetric unit. This molecule has an anti form with the terminal methylthiopropyl groups above and below the aromatic diimide plane, where four intramolecular C—H⋯O and C—H⋯S hydrogen bonds are present and the O⋯H⋯S angle is 100.8°. DFT calculations revealed slight differences between the solid state and gas phase structures. In the crystal, C—H⋯O and C—H⋯S hydrogen bonds link the molecules into chains along the [2overline20] direction. adjacent chains are interconnected by π–π interactions, forming a two-dimensional network parallel to the (001) plane. Each two-dimensional layer is further packed in an ABAB sequence along the c-axis direction. Hirshfeld surface analysis shows that van der Waals interactions make important contributions to the intermolecular contacts. The most important contacts found in the Hirshfeld surface analysis are H⋯H (44.2%), H⋯O/O⋯H (18.2%), H⋯C/C⋯H (14.4%), and H⋯S/S⋯H (10.2%). Full Article text
ale Synthesis, detailed geometric analysis and bond-valence method evaluation of the strength of π-arene bonding of two isotypic cationic prehnitene tin(II) complexes: [{1,2,3,4-(CH3)4C6H2}2Sn2Cl2][MCl4]2 (M = Al and Ga) By scripts.iucr.org Published On :: 2019-06-25 From solutions of prehnitene and the ternary halides (SnCl)[MCl4] (M = Al, Ga) in chlorobenzene, the new cationic SnII–π-arene complexes catena-poly[[chloridoaluminate(III)]-tri-μ-chlorido-4':1κ2Cl,1:2κ4Cl-[(η6-1,2,3,4-tetramethylbenzene)tin(II)]-di-μ-chlorido-2:3κ4Cl-[(η6-1,2,3,4-tetramethylbenzene)tin(II)]-di-μ-chlorido-3:4κ4Cl-[chloridoaluminate(III)]-μ-chlorido-4:1'κ2Cl], [Al2Sn2Cl10(C10H14)2]n, (1) and catena-poly[[chloridogallate(III)]-tri-μ-chlorido-4':1κ2Cl,1:2κ4Cl-[(η6-1,2,3,4-tetramethylbenzene)tin(II)]-di-μ-chlorido-2:3κ4Cl-[(η6-1,2,3,4-tetramethylbenzene)tin(II)]-di-μ-chlorido-3:4κ4Cl-[chloridogallate(III)]-μ-chlorido-4:1'κ2Cl], [Ga2Sn2Cl10(C10H14)2]n, (2), were isolated. In these first main-group metal–prehnitene complexes, the distorted η6 arene π-bonding to the tin atoms of the Sn2Cl22+ moieties in the centre of [{1,2,3,4-(CH3)4C6H2}2Sn2Cl2][MCl4]2 repeating units (site symmetry overline{1}) is characterized by: (i) a significant ring slippage of ca 0.4 Å indicated by the dispersion of Sn—C distances [1: 2.881 (2)–3.216 (2) Å; 2: 2.891 (3)–3.214 (3) Å]; (ii) the non-methyl-substituted arene C atoms positioned closest to the SnII central atom; (iii) a pronounced tilt of the plane of the arene ligand against the plane of the central (Sn2Cl2)2+ four-membered ring species [1: 15.59 (11)°, 2: 15.69 (9)°]; (iv) metal–arene bonding of medium strength as illustrated by application of the bond-valence method in an indirect manner, defining the π-arene bonding interaction of the SnII central atoms as s(SnII—arene) = 2 − Σs(SnII—Cl), that gives s(SnII—arene) = 0.37 and 0.38 valence units for the aluminate and the gallate, respectively, indicating that comparatively strong main-group metal–arene bonding is present and in line with the expectation that [AlCl4]− is the slightly weaker coordinating anion as compared to [GaCl4]−. Full Article text
ale 5-Methyl-1,3-phenylene bis[5-(dimethylamino)naphthalene-1-sulfonate]: crystal structure and DFT calculations By scripts.iucr.org Published On :: 2019-06-28 The title compound, C31H30N2S2O6, possesses crystallographically imposed twofold symmetry with the two C atoms of the central benzene ring and the C atom of its methyl substituent lying on the twofold rotation axis. The two dansyl groups are twisted away from the plane of methylphenyl bridging unit in opposite directions. The three-dimensional arrangement in the crystal is mainly stabilized by weak hydrogen bonds between the sulfonyl oxygen atoms and the hydrogen atoms from the N-methyl groups. Stacking of the dansyl group is not observed. From the DFT calculations, the HOMO–LUMO energy gap was found to be 2.99 eV and indicates n→π* and π→π* transitions within the molecule. Full Article text
ale Crystal structure of 4,4'-bis(4-bromophenyl)-1,1',3,3'-tetrathiafulvalene By scripts.iucr.org Published On :: 2019-07-16 The molecule of the title compound, C18H10Br2S4, has a C-shape, with Cs molecular symmetry. The dihedral angle between the planes of the dithiol and phenyl rings is 8.35 (9)°. In the crystal, molecules form helical chains along [001], the shortest interactions being π⋯S contacts within the helices. The intermolecular interactions were investigated by Hirshfeld surface analysis. Density functional theory (DFT) was used to calculate HOMO–LUMO energy levels of the title compound and its trans isomer. Full Article text
ale Crystal structure of a binuclear mixed-valence ytterbium complex containing a 2-anthracene-substituted phenoxide ligand By scripts.iucr.org Published On :: 2019-08-23 Reaction of 2-(anthracen-9-yl)phenol (HOPhAn, 1) with divalent Yb[N(SiMe3)2]2·2THF in THF–toluene mixtures affords the mixed-valence YbII–YbIII dimer {[2-(anthracen-9-yl)phenolato-κO]bis(tetrahydrofuran)ytterbium(III)}-tris[μ-2-(anthracen-9-yl)phenolato]-κ4O:O;κO:1,2-η,κO-{[2-(anthracen-9-yl)phenolato-κO]ytterbium(II)} toluene trisolvate, [Yb2(C20H13O)5(C4H8O)2]·3C7H7 or [YbIII(THF)2(OPhAn)](μ-OPhAn)3[YbII(OPhAn)]·3C7H7 (2), as the major product. It crystallized as a toluene trisolvate. The Yb—O bond lengths in the crystal structure of this dimer clearly identify the YbII and YbIII centres. Interestingly, the formally four-coordinate YbII centre shows a close contact with one anthracene C—C bond of a bridging OPhAn ligand, bringing the formal coordination number to five. Full Article text
ale Crystal structure and Hirshfeld surface analysis of 2-hydroxy-7-methoxy-1,8-bis(2,4,6-trichlorobenzoyl)naphthalene By scripts.iucr.org Published On :: 2019-09-10 In the title compound, C25H12Cl6O4, the two carbonyl groups are oriented in a same direction with respect to the naphthalene ring system and are situated roughly parallel to each other, while the two 2,4,6-trichlorobenzene rings are orientated in opposite directions with respect to the naphthalene ring system: the carbonyl C—(C=O)—C planes subtend dihedral angles of 45.54 (15) and 30.02 (15)° to the naphthalene ring system are. The dihedral angles formed by the carbonyl groups and the benzene rings show larger differences, the C=O vectors being inclined to the benzene rings by 46.39 (16) and 79.78 (16)°. An intramolecular O—H⋯O=C hydrogen bond forms an S(6) ring motif. In the crystal, no effective intermolecular hydrogen bonds are found; instead, O⋯Cl and C⋯Cl close contacts are observed along the 21 helical-axis direction. The Hirshfeld surface analysis reveals several weak interactions, the major contributor being Cl⋯H/H⋯Cl contacts. Full Article text
ale The crystal structures and Hirshfeld surface analysis of 6-(naphthalen-1-yl)-6a-nitro-6,6a,6b,7,9,11a-hexahydrospiro[chromeno[3',4':3,4]pyrrolo[1,2-c]thiazole-11,11'-indeno[1,2-b]quinoxaline] and 6'-(naphthalen-1-yl)-6a By scripts.iucr.org Published On :: 2019-09-27 The title compounds, 6-(naphthalen-1-yl)-6a-nitro-6,6a,6 b,7,9,11a-hexahydrospiro[chromeno[3',4':3,4]pyrrolo[1,2-c]thiazole-11,11'-indeno[1,2-b]quinoxaline], C37H26N4O3S, (I), and 6'-(naphthalen-1-yl)-6a'-nitro-6',6a',6b',7',8',9',10',12a'-octahydro-2H-spiro[acenaphthylene-1,12'-chromeno[3,4-a]indolizin]-2-one, C36H28N2O4, (II), are new spiro derivatives, in which both the pyrrolidine rings adopt twisted conformations. In (I), the five-membered thiazole ring adopts an envelope conformation, while the eight-membered pyrrolidine-thiazole ring adopts a boat conformation. An intramolecular C—H⋯N hydrogen bond occurs, involving a C atom of the pyran ring and an N atom of the pyrazine ring. In (II), the six-membered piperidine ring adopts a chair conformation. An intramolecular C—H⋯O hydrogen bond occurs, involving a C atom of the pyrrolidine ring and the keto O atom. For both compounds, the crystal structure is stabilized by intermolecular C—H⋯O hydrogen bonds. In (I), the C—H⋯O hydrogen bonds link adjacent molecules, forming R22(16) loops propagating along the b-axis direction, while in (II) they form zigzag chains along the b-axis direction. In both compounds, C—H⋯π interactions help to consolidate the structure, but no significant π–π interactions with centroid–centroid distances of less than 4 Å are observed. Full Article text
ale Crystal structure of a two-dimensional coordination polymer of formula [Zn(NDC)(DEF)] (H2NDC is naphthalene-2,6-dicarboxylic acid and DEF is N,N-diethylformamide) By scripts.iucr.org Published On :: 2019-10-29 A zinc metal–organic framework, namely poly[bis(N,N-diethylformamide)(μ4-naphthalene-2,6-dicarboxylato)(μ2-naphthalene-2,6-dicarboxylato)dizinc(II)], [Zn(C12H6O4)(C15H11NO)]n, built from windmill-type secondary building units and forming zigzag shaped two-dimensional stacked layers, has been solvothermally synthesized from naphthalene-2,6-dicarboxylic acid and zinc(II) acetate as the metal source in N,N-diethylformamide containing small amounts of formic acid. Full Article text
ale checkCIF validation ALERTS: what they mean and how to respond By scripts.iucr.org Published On :: 2020-01-01 Authors of a paper that includes a new crystal-structure determination are expected to not only report the structural results of interest and their interpretation, but are also expected to archive in computer-readable CIF format the experimental data on which the crystal-structure analysis is based. Additionally, an IUCr/checkCIF validation report will be required for the review of a submitted paper. Such a validation report, automatically created from the deposited CIF file, lists as ALERTS not only potential errors or unusual findings, but also suggestions for improvement along with interesting information on the structure at hand. Major ALERTS for issues are expected to have been acted on already before the submission for publication or discussed in the associated paper and/or commented on in the CIF file. In addition, referees, readers and users of the data should be able to make their own judgment and interpretation of the underlying experimental data or perform their own calculations with the archived data. All the above is consistent with the FAIR (findable, accessible, interoperable, and reusable) initiative [Helliwell (2019). Struct. Dyn. 6, 05430]. Validation can also be helpful for less experienced authors in pointing to and avoiding of crystal-structure determination and interpretation pitfalls. The IUCr web-based checkCIF server provides such a validation report, based on data uploaded in CIF format. Alternatively, a locally installable checkCIF version is available to be used iteratively during the structure-determination process. ALERTS come mostly as short single-line messages. There is also a short explanation of the ALERTS available through the IUCr web server or with the locally installed PLATON/checkCIF version. This paper provides additional background information on the checkCIF procedure and additional details for a number of ALERTS along with options for how to act on them. Full Article text
ale Crystal structure, characterization and Hirshfeld analysis of bis{(E)-1-[(2,4,6-tribromophenyl)diazenyl]naphthalen-2-olato}copper(II) dimethyl sulfoxide monosolvate By scripts.iucr.org Published On :: 2020-02-18 In the title compound, [Cu(C16H8Br3N2O)2]·C2H6OS, the CuII atom is tetracoordinated in a square-planar coordination, being surrounded by two N atoms and two O atoms from two N,O-bidentate (E)-1-[(2,4,6-tribromophenyl)diazenyl]naphthalen-2-olate ligands. The two N atoms and two O atoms around the metal center are trans to each other, with an O—Cu—O bond angle of 177.90 (16)° and a N—Cu—N bond angle of 177.8 (2)°. The average distances between the CuII atom and the coordinated O and N atoms are 1.892 (4) and 1.976 (4) Å, respectively. In the crystal, complexes are linked by C—H⋯O hydrogen bonds and by π–π interactions involving adjacent naphthalene ring systems [centroid–centroid distance = 3.679 (4) Å]. The disordered DMSO molecules interact weakly with the complex molecules, being positioned in the voids left by the packing arrangement of the square-planar complexes. The DMSO solvent molecule is disordered over two positions with occupancies of 0.70 and 0.30. Full Article text
ale Ligand pathways in neuroglobin revealed by low-temperature photodissociation and docking experiments By scripts.iucr.org Published On :: 2019-07-10 A combined biophysical approach was applied to map gas-docking sites within murine neuroglobin (Ngb), revealing snapshots of events that might govern activity and dynamics in this unique hexacoordinate globin, which is most likely to be involved in gas-sensing in the central nervous system and for which a precise mechanism of action remains to be elucidated. The application of UV–visible microspectroscopy in crystallo, solution X-ray absorption near-edge spectroscopy and X-ray diffraction experiments at 15–40 K provided the structural characterization of an Ngb photolytic intermediate by cryo-trapping and allowed direct observation of the relocation of carbon monoxide within the distal heme pocket after photodissociation. Moreover, X-ray diffraction at 100 K under a high pressure of dioxygen, a physiological ligand of Ngb, unravelled the existence of a storage site for O2 in Ngb which coincides with Xe-III, a previously described docking site for xenon or krypton. Notably, no other secondary sites were observed under our experimental conditions. Full Article text
ale LAT1 (SLC7A5) and CD98hc (SLC3A2) complex dynamics revealed by single-particle cryo-EM By scripts.iucr.org Published On :: 2019-06-28 Solute carriers are a large class of transporters that play key roles in normal and disease physiology. Among the solute carriers, heteromeric amino-acid transporters (HATs) are unique in their quaternary structure. LAT1–CD98hc, a HAT, transports essential amino acids and drugs across the blood–brain barrier and into cancer cells. It is therefore an important target both biologically and therapeutically. During the course of this work, cryo-EM structures of LAT1–CD98hc in the inward-facing conformation and in either the substrate-bound or apo states were reported to 3.3–3.5 Å resolution [Yan et al. (2019), Nature (London), 568, 127–130]. Here, these structures are analyzed together with our lower resolution cryo-EM structure, and multibody 3D auto-refinement against single-particle cryo-EM data was used to characterize the dynamics of the interaction of CD98hc and LAT1. It is shown that the CD98hc ectodomain and the LAT1 extracellular surface share no substantial interface. This allows the CD98hc ectodomain to have a high degree of movement within the extracellular space. The functional implications of these aspects are discussed together with the structure determination. Full Article text
ale Supercell refinement: a cautionary tale By scripts.iucr.org Published On :: 2019-08-28 Theoretically, crystals with supercells exist at a unique crossroads where they can be considered as either a large unit cell with closely spaced reflections in reciprocal space or a higher dimensional superspace with a modulation that is commensurate with the supercell. In the latter case, the structure would be defined as an average structure with functions representing a modulation to determine the atomic location in 3D space. Here, a model protein structure and simulated diffraction data were used to investigate the possibility of solving a real incommensurately modulated protein crystal using a supercell approximation. In this way, the answer was known and the refinement method could be tested. Firstly, an average structure was solved by using the `main' reflections, which represent the subset of the reflections that belong to the subcell and in general are more intense than the `satellite' reflections. The average structure was then expanded to create a supercell and refined using all of the reflections. Surprisingly, the refined solution did not match the expected solution, even though the statistics were excellent. Interestingly, the corresponding superspace group had multiple 3D daughter supercell space groups as possibilities, and it was one of the alternate daughter space groups that the refinement locked in on. The lessons learned here will be applied to a real incommensurately modulated profilin–actin crystal that has the same superspace group. Full Article text
ale ALEPH: a network-oriented approach for the generation of fragment-based libraries and for structure interpretation By scripts.iucr.org Published On :: 2020-02-26 The analysis of large structural databases reveals general features and relationships among proteins, providing useful insight. A different approach is required to characterize ubiquitous secondary-structure elements, where flexibility is essential in order to capture small local differences. The ALEPH software is optimized for the analysis and the extraction of small protein folds by relying on their geometry rather than on their sequence. The annotation of the structural variability of a given fold provides valuable information for fragment-based molecular-replacement methods, in which testing alternative model hypotheses can succeed in solving difficult structures when no homology models are available or are successful. ARCIMBOLDO_BORGES combines the use of composite secondary-structure elements as a search model with density modification and tracing to reveal the rest of the structure when both steps are successful. This phasing method relies on general fold libraries describing variations around a given pattern of β-sheets and helices extracted using ALEPH. The program introduces characteristic vectors defined from the main-chain atoms as a way to describe the geometrical properties of the structure. ALEPH encodes structural properties in a graph network, the exploration of which allows secondary-structure annotation, decomposition of a structure into small compact folds, generation of libraries of models representing a variation of a given fold and finally superposition of these folds onto a target structure. These functions are available through a graphical interface designed to interactively show the results of structure manipulation, annotation, fold decomposition, clustering and library generation. ALEPH can produce pictures of the graphs, structures and folds for publication purposes. Full Article text
ale Crystallography at the nanoscale: planar defects in ZnO nanospikes By scripts.iucr.org Published On :: 2019-08-29 The examination of anisotropic nanostructures, such as wires, platelets or spikes, inside a transmission electron microscope is normally performed only in plan view. However, intrinsic defects such as growth twin interfaces could occasionally be concealed from direct observation for geometric reasons, leading to superposition. This article presents the shadow-focused ion-beam technique to prepare multiple electron-beam-transparent cross-section specimens of ZnO nanospikes, via a procedure which could be readily extended to other anisotropic structures. In contrast with plan-view data of the same nanospikes, here the viewing direction allows the examination of defects without superposition. By this method, the coexistence of two twin configurations inside the wurtzite-type structure is observed, namely [2 {overline 1} {overline 1} 0]^{ m W}/(0 1 {overline 1} 1) and [2 {overline 1} {overline 1} 0]^{ m W}/(0 1 {overline 1} 3), which were not identified during the plan-view observations owing to superposition of the domains. The defect arrangement could be the result of coalescence twinning of crystalline nuclei formed on the partially molten Zn substrate during the flame-transport synthesis. Three-dimensional defect models of the twin interface structures have been derived and are correlated with the plan-view investigations by simulation. Full Article text
ale Small-angle neutron scattering (SANS) and spin-echo SANS measurements reveal the logarithmic fractal structure of the large-scale chromatin organization in HeLa nuclei By journals.iucr.org Published On :: This paper reports on the two-scale fractal structure of chromatin organization in the nucleus of the HeLa cell. Full Article text
ale Crystal structures of two furazidin polymorphs revealed by a joint effort of crystal structure prediction and NMR crystallography By scripts.iucr.org Published On :: 2020-04-16 This work presents the crystal structure determination of two elusive polymorphs of furazidin, an antibacterial agent, employing a combination of crystal structure prediction (CSP) calculations and an NMR crystallography approach. Two previously uncharacterized neat crystal forms, one of which has two symmetry-independent molecules (form I), whereas the other one is a Z' = 1 polymorph (form II), crystallize in P21/c and P1 space groups, respectively, and both are built by different conformers, displaying different intermolecular interactions. It is demonstrated that the usage of either CSP or NMR crystallography alone is insufficient to successfully elucidate the above-mentioned crystal structures, especially in the case of the Z' = 2 polymorph. In addition, cases of serendipitous agreement in terms of 1H or 13C NMR data obtained for the CSP-generated crystal structures different from the ones observed in the laboratory (false-positive matches) are analyzed and described. While for the majority of analyzed crystal structures the obtained agreement with the NMR experiment is indicative of some structural features in common with the experimental structure, the mentioned serendipity observed in exceptional cases points to the necessity of caution when using an NMR crystallography approach in crystal structure determination. Full Article text
ale Structure of the dihydrolipoamide succinyltransferase catalytic domain from Escherichia coli in a novel crystal form: a tale of a common protein crystallization contaminant By scripts.iucr.org Published On :: 2019-08-29 The crystallization of amidase, the ultimate enzyme in the Trp-dependent auxin-biosynthesis pathway, from Arabidopsis thaliana was attempted using protein samples with at least 95% purity. Cube-shaped crystals that were assumed to be amidase crystals that belonged to space group I4 (unit-cell parameters a = b = 128.6, c = 249.7 Å) were obtained and diffracted to 3.0 Å resolution. Molecular replacement using structures from the PDB containing the amidase signature fold as search models was unsuccessful in yielding a convincing solution. Using the Sequence-Independent Molecular replacement Based on Available Databases (SIMBAD) program, it was discovered that the structure corresponded to dihydrolipoamide succinyltransferase from Escherichia coli (PDB entry 1c4t), which is considered to be a common crystallization contaminant protein. The structure was refined to an Rwork of 23.0% and an Rfree of 27.2% at 3.0 Å resolution. The structure was compared with others of the same protein deposited in the PDB. This is the first report of the structure of dihydrolipoamide succinyltransferase isolated without an expression tag and in this novel crystal form. Full Article text
ale Females are giants in newly discovered species of golden orb weaver spider By insider.si.edu Published On :: Wed, 21 Oct 2009 13:36:23 +0000 Native to Africa and Madagascar, females of the species have a body length of 1.5 inches and a leg span of 4 to 5 inches. Males are tiny in comparison. The post Females are giants in newly discovered species of golden orb weaver spider appeared first on Smithsonian Insider. Full Article Research News Science & Nature endangered species National Museum of Natural History new species spiders
ale Clouded leopard cubs born at National Zoo’s Front Royal campus on Valentine’s Day By insider.si.edu Published On :: Thu, 18 Feb 2010 20:48:06 +0000 Staff had been on a pregnancy watch focused on the 3 1/2-year-old clouded leopard Jao Chu (JOW-chew) for four days. Jao Chu gave birth to the first cub at 6:04 p.m. and the second cub at 6:20 p.m. The post Clouded leopard cubs born at National Zoo’s Front Royal campus on Valentine’s Day appeared first on Smithsonian Insider. Full Article Animals Science & Nature animal births biodiversity conservation conservation biology endangered species extinction Smithsonian's National Zoo
ale Females shut down male-male sperm competition in leafcutter ants By insider.si.edu Published On :: Thu, 18 Mar 2010 18:25:30 +0000 “Two things appear to be going on here,” explains Jacobus Boomsma, professor at the University of Copenhagen and Research Associate at STRI. “Right after mating there is competition between sperm from different males. Sperm is expendable. Later, sperm becomes very precious to the female who will continue to use it for many years to fertilize her own eggs, producing the millions of workers it takes to maintain her colony.” The post Females shut down male-male sperm competition in leafcutter ants appeared first on Smithsonian Insider. Full Article Animals Research News Science & Nature bees conservation biology insects Tropical Research Institute
ale Ancient gray whales may have been homebodies By insider.si.edu Published On :: Tue, 02 Nov 2010 06:05:25 +0000 A new study suggests that the annual long-distance migration of gray whales may be a relatively recent phenomenon, and that only a few thousand years ago, these marine mammals stayed much closer to home. The post Ancient gray whales may have been homebodies appeared first on Smithsonian Insider. Full Article Animals Marine Science Research News Science & Nature biodiversity climate change conservation conservation biology endangered species mammals National Museum of Natural History whales
ale Tiger numbers could triple if large-scale landscapes are protected By insider.si.edu Published On :: Wed, 26 Jan 2011 16:07:05 +0000 The tiger reserves of Asia could support more than 10,000 wild tigers – three times the current number – if they are managed as large-scale […] The post Tiger numbers could triple if large-scale landscapes are protected appeared first on Smithsonian Insider. Full Article Animals Research News Science & Nature conservation conservation biology endangered species mammals Smithsonian's National Zoo
ale Whale sharks featured in award-winning documentary following the work of Tropical Research Institute’s Héctor Guzman By insider.si.edu Published On :: Thu, 17 Feb 2011 19:10:06 +0000 The awarded film features STRI marine biologist Héctor M. Guzman diving with a group of five whale sharks while traveling in the Tropical Eastern Pacific. In the video, Guzmán tags a radiotransmitter to one of the sharks in order to follow its voyages. The post Whale sharks featured in award-winning documentary following the work of Tropical Research Institute’s Héctor Guzman appeared first on Smithsonian Insider. Full Article Animals Marine Science Research News Science & Nature conservation conservation biology endangered species Tropical Research Institute
ale Ancient bond between humans and dogs revealed in isotopic signatures of their bones By insider.si.edu Published On :: Thu, 10 Mar 2011 19:48:03 +0000 In recent research on Santa Rosa Island off the coast of Southern California, isotope readings of carbon and nitrogen found in the bones of Chumash Indians and domestic dogs excavated from archaeological sites show that both humans and dogs have nearly identical signatures of stable isotopes. The post Ancient bond between humans and dogs revealed in isotopic signatures of their bones appeared first on Smithsonian Insider. Full Article Anthropology Dinosaurs & Fossils Research News Science & Nature mammals National Museum of Natural History prehistoric
ale Hormone tests show Mei Xiang, the National Zoo’s female giant panda, may be pregnant By insider.si.edu Published On :: Wed, 18 May 2011 17:03:05 +0000 Scientists at the Smithsonian’s National Zoo detected a secondary rise in urinary progesterone levels in the Zoo’s female giant panda Mei Xiang (may-SHONG). This hormone rise indicates that it should be 40 to 50 days before Mei Xiang either gives birth to a cub or comes to the end of a pseudopregnancy, or false pregnancy, which is common in giant pandas. The post Hormone tests show Mei Xiang, the National Zoo’s female giant panda, may be pregnant appeared first on Smithsonian Insider. Full Article Animals Research News Science & Nature captive breeding giant panda
ale Stranding records are faithful reflection of live whale and dolphin populations, new study reveals By insider.si.edu Published On :: Tue, 24 May 2011 12:15:50 +0000 By compiling and comparing long-term data from stranding records and visual sighting records, both taken from nearly every ocean basin in the world, Pyenson verified that stranding records “faithfully reflect the number of species and the relative abundance” found in live surveys. The post Stranding records are faithful reflection of live whale and dolphin populations, new study reveals appeared first on Smithsonian Insider. Full Article Animals Marine Science Research News Science & Nature conservation conservation biology Ecuador endangered species mammals National Museum of Natural History osteology South America whales
ale Scientists discover the largest assembly of whale sharks ever recorded By insider.si.edu Published On :: Thu, 26 May 2011 02:32:37 +0000 This new research, which involved both surface and aerial surveys, has revealed an enormous aggregation of whale sharks—the largest ever reported—with up to 420 individuals off the coast of the Yucatán Peninsula in Mexico. The post Scientists discover the largest assembly of whale sharks ever recorded appeared first on Smithsonian Insider. Full Article Animals Marine Science Research News Science & Nature conservation conservation biology National Museum of Natural History Tropical Research Institute whales
ale Damai, a two-and-a-half-year-old female Sumatran tiger, makes her debut at the National Zoo By insider.si.edu Published On :: Thu, 02 Jun 2011 12:09:05 +0000 The National Zoo’s great cat program recently expanded with the arrival of two-and-a-half-year-old female Sumatran tiger, Damai, who is now out of quarantine and spending time outside in her exhibit where visitors can see her. The post Damai, a two-and-a-half-year-old female Sumatran tiger, makes her debut at the National Zoo appeared first on Smithsonian Insider. Full Article Animals Science & Nature captive breeding conservation conservation biology endangered species mammals new acquisitions Smithsonian's National Zoo veterinary medicine
ale Fossil skull of an extinct toothed whale excavated from Panamanian sediments By insider.si.edu Published On :: Fri, 24 Jun 2011 12:47:13 +0000 A scientist from the Smithsonian Tropical Research Institute uses a pick to dislodge the fossil skull of an extinct toothed whale from sediments on the […] The post Fossil skull of an extinct toothed whale excavated from Panamanian sediments appeared first on Smithsonian Insider. Full Article Dinosaurs & Fossils Marine Science Research News Science & Nature Spotlight Caribbean collections fossils geology National Museum of Natural History prehistoric Tropical Research Institute
ale Dictionary captures traditional ice knowledge of the Inupiaq people of Wales, Alaska By insider.si.edu Published On :: Fri, 01 Jul 2011 12:52:42 +0000 To prevent the loss of Inupiaq words for ice and the knowledge that it embodies, Igor Krupnik, ethnologist at the Arctic Studies Center of the National Museum of Natural History, and Wales native Winton Weyapuk Jr., recently compiled an illustrated dictionary of some 120 Kingikmiut words used in Wales to describe different types of ice. The post Dictionary captures traditional ice knowledge of the Inupiaq people of Wales, Alaska appeared first on Smithsonian Insider. Full Article Anthropology Research News Science & Nature climate change National Museum of Natural History
ale Varied diet has allowed gray whales to survive millions of years, study reveals By insider.si.edu Published On :: Thu, 07 Jul 2011 05:46:03 +0000 Gray whales survived many cycles of global cooling and warming over the past few million years, likely by exploiting a more varied diet than they do today, according to a new study by University of California, Berkeley, and Smithsonian Institution paleontologists. The post Varied diet has allowed gray whales to survive millions of years, study reveals appeared first on Smithsonian Insider. Full Article Animals Dinosaurs & Fossils Marine Science Research News Science & Nature climate change endangered species extinction mammals National Museum of Natural History prehistoric whales
ale Females can place limits on evolution of attractive features in males, research shows By insider.si.edu Published On :: Fri, 05 Aug 2011 15:13:46 +0000 In a new paper appearing this week in Science, a group of biologists have shown that females themselves can also limit the evolution of increased elaboration. The post Females can place limits on evolution of attractive features in males, research shows appeared first on Smithsonian Insider. Full Article Animals Research News Science & Nature evolution frogs mammals Tropical Research Institute
ale Swift satellite alerts astronomers to cosmic accident in constellation Draco By insider.si.edu Published On :: Wed, 24 Aug 2011 18:03:04 +0000 Two studies appearing in the Aug. 25 issue of the journal Nature provide new insights into a cosmic accident that has been streaming X-rays toward Earth since late March. NASA's Swift satellite first alerted astronomers to intense and unusual high-energy flares from the new source in the constellation Draco. The post Swift satellite alerts astronomers to cosmic accident in constellation Draco appeared first on Smithsonian Insider. Full Article Science & Nature Space astronomy astrophysics Center for Astrophysics | Harvard & Smithsonian Smithsonian Astrophysical Observatory