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Nanocrystalline materials: recent advances in crystallographic characterization techniques

This feature article reviews the control and understanding of nanoparticle shape from their crystallography and growth. Particular emphasis is placed on systems relevant for plasmonics and catalysis.




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X-ray techniques for innovation in industry

Are synchrotrons needed for innovation in industry? What can scientists at large-scale facilities offer for R&D in industry? Is the comfort of life profiting from research?


























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Characterization of the Pseudomonas aeruginosa T6SS PldB immunity proteins PA5086, PA5087 and PA5088 explains a novel stockpiling mechanism

The bacterial type VI secretion system (T6SS) secretes many toxic effectors to gain advantage in interbacterial competition and for eukaryotic host infection. The cognate immunity proteins of these effectors protect bacteria from their own effectors. PldB is a T6SS trans-kingdom effector in Pseudomonas aeruginosa that can infect both prokaryotic and eukaryotic cells. Three proteins, PA5086, PA5087 and PA5088, are employed to suppress the toxicity of PldB-family proteins. The structures of PA5087 and PA5088 have previously been reported, but the identification of further distinctions between these immunity proteins is needed. Here, the crystal structure of PA5086 is reported at 1.90 Å resolution. A structural comparison of the three PldB immunity proteins showed vast divergences in their electrostatic potential surfaces. This interesting phenomenon provides an explanation of the stockpiling mechanism of T6SS immunity proteins.




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Structure-based screening of binding affinities via small-angle X-ray scattering

Protein–protein and protein–ligand interactions often involve conformational changes or structural rearrangements that can be quantified by solution small-angle X-ray scattering (SAXS). These scattering intensity measurements reveal structural details of the bound complex, the number of species involved and, additionally, the strength of interactions if carried out as a titration. Although a core part of structural biology workflows, SAXS-based titrations are not commonly used in drug discovery contexts. This is because prior knowledge of expected sample requirements, throughput and prediction accuracy is needed to develop reliable ligand screens. This study presents the use of the histidine-binding protein (26 kDa) and other periplasmic binding proteins to benchmark ligand screen performance. Sample concentrations and exposure times were varied across multiple screening trials at four beamlines to investigate the accuracy and precision of affinity prediction. The volatility ratio between titrated scattering curves and a common apo reference is found to most reliably capture the extent of structural and population changes. This obviates the need to explicitly model scattering intensities of bound complexes, which can be strongly ligand-dependent. Where the dissociation constant is within 102 of the protein concentration and the total exposure times exceed 20 s, the titration protocol presented at 0.5 mg ml−1 yields affinities comparable to isothermal titration calorimetry measurements. Estimated throughput ranges between 20 and 100 ligand titrations per day at current synchrotron beamlines, with the limiting step imposed by sample handling and cleaning procedures.




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Chirality in Biological Nanospaces: Reactions in Active Sites. By Nilashis Nandi. Pp. 209. CRC Press, 2011. Price £79.99. ISBN 9781439840023.




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Visualization Bench for the screening of crystallization assays and the automation of in situ experiments




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The crystal structure of the heme d1 biosynthesis-associated small c-type cytochrome NirC reveals mixed oligomeric states in crystallo

The crystal structure of the c-type cytochrome NirC from Pseudomonas aeruginosa has been determined and reveals the simultaneous presence of monomers and 3D domain-swapped dimers in the same asymmetric unit.




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Structure of P46, an immunodominant surface protein from Mycoplasma hyopneumoniae: interaction with a monoclonal antibody

Structures of the immunodominant protein P46 from M. hyopneumoniae has been determined by X-ray crystallography and it is shown that P46 can bind a diversity of oligosaccharides, particularly xylose, which exhibits a very high affinity for this protein. Structures of a monoclonal antibody, both alone and in complex with P46, that was raised against M. hyopnemoniae cells and specifically recognizes P46 are also reported.




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Structure of ClpC1-NTD in complex with the anti-TB natural product ecumicin reveals unique binding interactions

Comparison of the structures of ClpC1-Ecumicin and ClpC1-Rufomycin reveals unique interaction relevant to the mode of action.




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Structural basis of carbohydrate binding in domain C of a type I pullulanase from Paenibacillus barengoltzii




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6-Amino-2-iminiumyl-4-oxo-1,2,3,4-tetra­hydro­pyrimidin-5-aminium sulfate monohydrate

The title compound, C4H9N5O2+·SO42−·H2O, is the monohydrate of the commercially available compound `C4H7N5O·H2SO4·xH2O'. It is obtained by reprecipitation of C4H7N5O·H2SO4·xH2O from dilute sodium hydroxide solution with dilute sulfuric acid. The crystal structure of anhydrous 2,4,5-tri­amino-1,6-di­hydro­pyrimidin-6-one sulfate is known, although called by the authors 5-amminium-6-amino-isocytosinium sulfate [Bieri et al. (1993). Private communication (refcode HACDEU). CCDC, Cambridge, England]. In the structure, the sulfate group is deprotonated, whereas one of the amino groups is protonated (R2C—NH3+) and one is rearranged to a protonated imine group (R2C=NH2+). This arrangement is very similar to the known crystal structure of the anhydrate. Several tautomeric forms of the investigated mol­ecule are possible, which leads to questionable proton attributions. The measured data allowed the location of all hydrogen atoms from the residual electron density. In the crystal, ions and water mol­ecules are linked into a three-dimensional network by N—H⋯O and O—H⋯O hydrogen bonds.




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Dodecan-1-aminium sulfate trihydrate

The asymmetric unit of the title salt, 2C12H28N+·SO42−·3H2O, contains two n-do­decyl­ammonium cations, one sulfate anion and three water mol­ecules. In the crystal, N—H⋯O hydrogen bonds link the cations and anions into layers parallel to (100). These layers are further connected through O—H⋯O hydrogen-bonding inter­actions involving the sulfate ions and the isolated water mol­ecules. The three-dimensional structure can also be considered as the superposition of thin inorganic layers of SO42− anions and thick layers of alkyl­ammonium cations perpendicular to the c axis.




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n-Decyl­tri­methyl­ammonium bromide

The title compound, C13H30N+·Br− (systematic name: N,N,N-trimethyl-1-deca­naminium bromide), forms crystals having a bilayer structure, comprised of layers of tri­methyl­ammonium cations and bromide anions separated by the inter-digitated n-decyl groups of the cation; close ammonium-methyl-C—H⋯Br contacts connect the ions. The n-decyl chain adopts a slightly distorted all-trans conformation. The n-decyl chain exhibits positional disorder with all atoms at half occupancy. The sample was a racemic twin.




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trans-Bis(dimethyl sulfoxide-κO)bis­(3-nitro­benzo­hydroxamato-κ2O,O')zinc(II)

Single crystals of the title complex, [Zn(C7H5N2O4)2(C2H6OS)2] or [Zn(NBZH)2(DMSO)2], were isolated from a dimethyl sulfoxide (DMSO) solution containing [Zn(NBZH)2]·2H2O (NBZH = 3-nitro­benzo­hydroxamate anion). The asymmetric unit comprises of one O,O'-chelating NBZH anion, one O-bound DMSO ligand and one zinc(II) cation localized on an inversion centre. The three-dimensional crystal packing includes N—H⋯O and C—H⋯O hydrogen bonding, as well as O⋯H and H⋯H contacts identified by Hirshfeld isosurface analysis.




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(2,2-Bi­pyridine-κ2N,N')chlorido­[η6-1-methyl-4-(propan-2-yl)benzene]­ruthenium(II) tetra­phenyl­borate

The title complex, [RuCl(C10H14)(C10H8N2)](C24H20B), has monoclinic (P21) symmetry at 100 K. It was prepared by the reaction of the di­chlor­ido[1-methyl-4-(propan-2-yl)benzene]­ruthenium(II) dimer with 2,2'-bi­pyridine, followed by the addition of ammonium tetra­phenyl­borate. The 1-methyl-4-(propan-2-yl)benzene group, the 2,2'-bi­pyridine unit and a chloride ion coordinate the ruthenium(II) atom, with the 1-methyl-4-(propan-2-yl)benzene ring and bi­pyridine moieties trans to each other. In the crystal, the complex cations are linked by C—H⋯Cl hydrogen bonds, forming chains parallel to [010]. These chains are linked by a number of C—H⋯π inter­actions, involving the phenyl rings of the tetra­phenyl­borate anion and a pyridine ring of the bpy ligand, resulting in the formation of layers parallel to (10overline{1}).




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6-Nitro-1,10-phenanthrolin-5-amine

In the title compound, C12H8N4O2, the dihedral angle between the phenanthroline ring system and the nitro group is 23.75 (14)°. The mol­ecule features intra­molecular N—H⋯O and C—H⋯O hydrogen bonds. In the crystal, N—H⋯(N,N), C—H⋯N and C—H⋯O hydrogen bonds link the mol­ecules into [100] chains.




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(Pyridine-2,6-di­carboxyl­ato-κ3O,N,O')(2,2':6',2''- terpyridine-κ3N,N',N'')nickel(II) di­methyl­formamide monosolvate monohydrate

In the title complex, [Ni(C7H3NO4)(C15H11N3)]·C3H7NO·H2O, the NiII ion is six-coordinated within an octa­hedral geometry defined by three N atoms of the 2,2':6',2''-terpyridine ligand, and two O atoms and the N atom of the pyridine-2,6-di­carboxyl­ate di-anion. In the crystal, the complex mol­ecules are stacked in columns parallel to the a axis being connected by π–π stacking [closest inter-centroid separation between pyridyl rings = 3.669 (3) Å]. The connections between columns and solvent mol­ecules to sustain a three-dimensional architecture are of the type water-O—H⋯O(carbon­yl) and pyridyl-, methyl-C—H⋯O(carbon­yl).




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S-Di­ethyl­amino-S-(3-methyl­benzoyl­imino)-S,S-di­phenyl­sulfonium tetra­fluoro­borate

The title salt, C24H27N2OS+·BF4−, was prepared by an alkyl­ation at the amino N atom attached to the sulfur atom of the corresponding sulfodi­imide. The configuration around the sulfur atom is a slightly distorted tetra­hedral geometry with two S—N bonds and two S—C bonds. The lengths of the S—N(di­ethyl­amine) and S=N(m-methyl­benzoyl­imine) bonds are 1.619 (2) and 1.551 (2) Å, respectively. The two N—S—N—C(eth­yl) and the N—S—N—C(m-methyl­benzoyl­imine) torsion angles are −85.43 (3), 58.94 (17) and 62.03 (16)°, respectively. The dihedral angle between the two phenyl rings is 84.03 (14)°. In the crystal, C—H⋯F hydrogen bonds link the cation and anion, forming a three-dimensional network.




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Bis(μ2-4-nitro­phenolato)bis­(4-nitro­phenolato)di-μ3-oxido-octaphenyltetra­tin chloro­form sesquisolvate [+ solvate]: a tetra­nuclear stannoxane

The title tetra­nuclear stannoxane, [Sn4(C6H5)8(C6H4NO3)4O2]·1.5CHCl3·solvent, crystallized with two independent complex mol­ecules, A and B, in the asymmetric unit together with 1.5 mol­ecules of chloro­form. There is also a region of disordered electron density, which was corrected for using the SQUEEZE routine [Spek (2015). Acta Cryst. C71, 9–18]. The oxo-tin core of each complex is in a planar `ladder' arrangement and each Sn atom is fivefold SnO3C2 coordinated, with one tin centre having an almost perfect square-pyramidal coordination geometry, while the other three Sn centres have distorted shapes. In the crystal, the complex mol­ecules are arranged in layers, composed of A or B complexes, lying parallel to the bc plane. The complex mol­ecules are linked by a number of C—H⋯O hydrogen bonds within the layers and between the layers, forming a supra­molecular three-dimensional structure.




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6-Nitro-1,3-benzoxazole-2(3H)-thione

In the title compound, C7H4N2O3S, the dihedral angle between the fused ring system (r.m.s. deviation = 0.008 Å) and the nitro group at the 6-position is 7.3 (2)°. In the crystal, bifurcated N—H⋯(O,O) hydrogen bonds link the mol­ecules into [010] chains. The chains are cross-linked by π–π stacking inter­actions to form (001) sheets.




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Crystal structure of a salt with a protonated sugar cation and a cobalt(II) complex anion: (GlcN–H, K)[Co(NCS)4]·2H2O

The title compound, d-(+)-glucosa­mmonium potassium tetra­thio­cyanato­cobaltate(II) dihydrate, K(C6H14NO5)[Co(NCS)4]·2H2O or (GlcNH)(K)[Co(NCS)4]·2H2O, has been obtained as a side product of an incomplete salt metathesis reaction of d-(+)-glucosa­mine hydro­chloride (GlcN·HCl) and K2[Co(NCS)4]. The asymmetric unit contains a d-(+)-glucos­ammonium cation, a potassium cation, a tetra­iso­thio­cyanato­cobalt(II) complex anion and two water mol­ecules. The water mol­ecules coordinate to the potassium cation, which is further coordinated via three short K+⋯SCN− contacts involving three [Co(NCS)4]2− complex anions and via three O atoms of two d-(+)-glucosa­mmonium cations, leading to an overall eightfold coordination around the potassium cation. Hydrogen-bonding inter­actions between the building blocks consolidate the three-dimensional arrangement.




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[SP-4-2]-(Aceto­nitrile-κN)chlorido­[2-(4,6-di­phenyl­pyridin-2-yl)phenyl-κ2C1,N]platinum(II)

The synthesis and crystal structure of the title PtII complex, [Pt(C23H16N)Cl(CH3CN)], based on the C,N-chelating 2,4,6-tri­phenyl­pyridine as the primary ligand, is described. The central PtII atom is in a distorted square-planar coordination environment. In the crystal, mol­ecules are arranged via a metallophilic inter­action between platinum atoms with a Pt⋯Pt contact of 7.052 (2) Å. In addition, a π–π inter­action occurs.




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N,N,N-Trimethyl-1-[4-(pyridin-2-yl)phen­yl]meth­anaminium hexa­fluorido­phosphate

In the cation of the title mol­ecular salt, C15H19N2+·PF6−, the dihedral angle between the benzene and pyridine rings is 38.21 (10)°. In the crystal, weak C—H⋯F inter­actions arising from methyl and methyl­ene groups adjacent to the quaternary N atom generate (001) sheets.




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Bis(quinolinium) tetra­bromido­manganate(II)

The title compound, (C9H8N)2[MnBr4], consists of two quinolinium cations and a [MnBr4]2− anion. The manganese(II) atom, which lies on a twofold rotation axis, is coordinated by four bromide ligands and exhibits a tetra­hedral coordination geometry. The [MnBr4]2− anion and the quinolinium cations are linked by N—H⋯Br hydrogen bonds. π–π stacking inter­actions are observed between the quinolinium cations.




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3-Bromo­pyridine-2-carbo­nitrile

The title compound, C6H3BrN2, also known as 3-bromo­picolino­nitrile, was synthesized by cyanation of 2,3-di­bromo­pyridine. In the solid state, short inter­molecular Br⋯N contacts are observed. Additionally, the crystal packing is consolidated by π–π stacking inter­actions with centroid–centroid distances of 3.7893 (9) Å.




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4-Amino-5-{[cyclo­hex­yl(meth­yl)amino]­meth­yl}iso­phthalo­nitrile

The title compound, C16H20N4, was synthesized by cyanation of brom­hexine. The compound crystallizes with two unique mol­ecules in the asymmetric unit. The substituted aniline and cyclo­hexane rings are inclined to one another by 37.26 (6)° in one mol­ecule and by 22.84 (7)° in the other. In the crystal packing, intra- and inter­molecular N—H⋯N hydrogen bonds and an inter­molecular C—H⋯N contact were observed.




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Decacarbon­yl(μ-ethyl­idenimino-1κN:2κC)-μ-hydrido-triangulo-triosmium(3 Os–Os)

The title complex, [Os3(C2H4N)H(CO)10] or [Os3(CO)10(μ-H)(μ-HN=C—CH3-1κN:2κC)], was synthesized in 41.6% yield by reactions between Os3(CO)11(CH3CN) and 2,4,6-tri­methyl­hexa­hydro-1,3,5-triazine. The central osmium triangle has two OsI atoms bridged by a hydride ligand and a μ-HN= C—CH3-1κN:2κC triazine fragment. Three CO ligands complete the coordination sphere around each OsI atom, while the remaining Os0 atom has four CO ligands. Each Os atom exhibits a pseudo-octa­hedral coordination environment, discounting the bridging Os—Os bond.




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2,4-Di­chloro-6-[(2-hy­droxy-5-methyl­anilino)methyl­idene]cyclo­hexa-2,4-dienone

The title compound, C14H11Cl2NO2, has been prepared by the condensation of 3,5-di­chloro­salicyl­aldehyde and 2-amino-4-methyl­phenol. The asymmetric unit consists of two independent mol­ecules, both of which are almost planar; the dihedral angle between the two benzene rings is 10.61 (8)° for one mol­ecule and 2.46 (8)° for the other. There is an intra­molecular N—H⋯O hydrogen bond that generates S(6) ring motifs in each mol­ecule. In the crystal, the two independent mol­ecules are linked by O—H⋯O and C—H⋯Cl hydrogen bonds, forming a pseudo-inversion dimer. A π–π inter­action, with a centroid–centroid distance of 3.6065 (12) Å, is also observed.