ALBERT

Beschreibung: The self-assembly reaction of (+)-dibenzoyltartaric acid (D-H2DBTA) with 2,2′-bipyridine (bpy) and Mn(CH3CO2)2·4H2O yielded a new coordination polymer, namely, catena-poly[[[diaqua(2,2′-bipyridine-κ2 N,N′)manganese(II)]-μ-2,3-bis(benzoyloxy)butanedioato-κ2 O 2:O 3] dihydrate], {[Mn(C18H12O8)(C10H8N2)(H2O)2]·2H2O} n or {[Mn(DBTA)(bpy)(H2O)2]·2H2O} n , (I). Complex (I) has been characterized by elemental analysis, IR spectroscopy, thermogravimetric analysis (TGA) and single-crystal and powder X-ray diffraction. It crystallizes in the orthorhombic space group P212121. In the complex, the Mn2+ cation displays a distorted octahedral {MnO4N2} geometry, formed from two carboxylate O atoms of two DBTA2− ligands, two cis-oriented N atoms from one chelating 2,2′-bipyridine ligand and two trans-oriented O atoms from coordinated water molecules. The polymer displays a 1D chain with an Mn...Mn distance of 9.428 (1) Å. Due to the presence of flexible polycarboxylate and rigid bipyridyl ligands in the molecular structure, a high thermal stability of the complex is attained. The magnetic properties of (I) were analyzed based on the mononuclear Mn2+ model due to the long intramolecular Mn...Mn distance. The zero field splitting (ZFS) contribution in the high-spin Mn2+ cation is almost negligible and there are weak antiferromagnetic couplings between 1D chains [zJ′ = −0.062 (5) cm−1], corresponding to an intermolecular Mn...Mn distance of 7.860 (2) Å.

Beschreibung: As part of our ongoing investigation on the chemical and biological properties of piperazinium salts, we synthesized three novel compounds: 1-ethylpiperazinium 3,5-dinitrobenzoate (I), 1-methylpiperazinium 3,5-dinitrobenzoate (II) and 1-methylpiperazinium 4-iodobenzoate (III). The crystal structures of these compounds are built up of organic layers formed by the strong connection between the molecules by hydrogen bonds of type N—H...O. These layers are linked through N—H...O hydrogen bonds and C—H...O interactions or C—I...N halogen bonding, leading to the formation of a three-dimensional network.

Beschreibung: The title CoIII complex, bis[bis(2-hydroxy-3-methoxybenzaldehyde thiosemicarbazonato)cobalt(III)] dithionate–dimethylformamide–methanol (1/4/3), [Co(C9H10N3O2S)2]2(S2O6)·4C3H7NO·3CH3OH, with monodeprotonated 2-hydroxy-3-methoxybenzaldehyde thiosemicarbazone as ligands crystallizes in the space group Poverline{1}. The asymmetric unit consists of two mononuclear [CoL 2]+ cations, one dithionate anion (S2O6)2− as counter-anion and seven solvate molecules (four dimethylmethanamide and three methanol). Each CoIII ion has a moderately distorted octahedral S2N2O2 geometry. In the crystal, the components are linked by numerous N—H...O and O—H...O contacts.

Beschreibung: The initiation of infection of host tissues by Staphylococcus aureus requires a family of staphylococcal adhesive proteins containing serine–aspartate repeat (SDR) domains, such as ClfA. The O-linked glycosylation of the long-chain SDR domain mediated by SdgB and SdgA is a key virulence factor that protects the adhesive SDR proteins against host proteolytic attack in order to promote successful tissue colonization, and has also been implicated in staphylococcal agglutination, which leads to sepsis and an immunodominant epitope for a strong antibody response. Despite the biological significance of these two glycosyltransferases involved in pathogenicity and avoidance of the host innate immune response, their structures and the molecular basis of their activity have not been investigated. This study reports the crystal structures of SdgB and SdgA from S. aureus as well as multiple structures of SdgB in complex with its substrates (for example UDP, N-acetylglucosamine or SDR peptides), products (glycosylated SDR peptides) or phosphate ions. Together with biophysical and biochemical analyses, this structural work uncovered the novel mechanism by which SdgB and SdgA carry out the glycosyl-transfer process to the long SDR region in SDR proteins. SdgB undergoes dynamic changes in its structure such as a transition from an open to a closed conformation upon ligand binding and takes diverse forms, both as a homodimer and as a heterodimer with SdgA. Overall, these findings not only elucidate the putative role of the three domains of SdgB in recognizing donor and acceptor substrates, but also provide new mechanistic insights into glycosylation of the SDR domain, which can serve as a starting point for the development of antibacterial drugs against staphylococcal infections.

Beschreibung: Thyroglobulin is a homodimeric glycoprotein that is essential for the generation of thyroid hormones in vertebrates. Upon secretion into the lumen of follicles in the thyroid gland, tyrosine residues within the protein become iodinated to produce monoiodotyrosine (MIT) and diiodotyrosine (DIT). A subset of evolutionarily conserved pairs of DIT (and MIT) residues can then engage in oxidative coupling reactions that yield either thyroxine (T4; produced from coupling of a DIT `acceptor' with a DIT `donor') or triiodothyronine (T3; produced from coupling of a DIT acceptor with an MIT donor). Although multiple iodotyrosine residues have been identified as potential donors and acceptors, the specificity and structural context of the pairings (i.e. which donor is paired with which acceptor) have remained unclear. Here, single-particle cryogenic electron microscopy (cryoEM) was used to generate a high-resolution reconstruction of bovine thyroglobulin (2.3 Å resolution in the core region and 2.6 Å overall), allowing the structural characterization of two post-reaction acceptor–donor pairs as well as tyrosine residues modified as MIT and DIT. A substantial spatial separation between donor Tyr149 and acceptor Tyr24 was observed, suggesting that for thyroxine synthesis significant peptide motion is required for coupling at the evolutionarily conserved thyroglobulin amino-terminus.

Beschreibung: Membrane proteins (MPs) play vital roles in the function of cells and are also major drug targets. Structural information on proteins is vital for understanding their mechanism of function and is critical for the development of drugs. However, obtaining high-resolution structures of membrane proteins, in particular, under native conditions is still a great challenge. In such cases, the low-resolution methods small-angle X-ray and neutron scattering (SAXS and SANS) might provide valuable structural information. However, in some cases small-angle scattering (SAS) provides ambiguous ab initio structural information if complementary measurements are not performed and/or a priori information on the protein is not taken into account. Understanding the nature of the limitations may help to overcome these problems. One of the main problems of SAS data analysis of solubilized membrane proteins is the contribution of the detergent belt surrounding the MP. Here, a comprehensive analysis of how the detergent belt contributes to the SAS data of a membrane-protein complex of sensory rhodopsin II with its cognate transducer from Natronomonas pharaonis (NpSRII–NpHtrII) was performed. The influence of the polydispersity of NpSRII–NpHtrII oligomerization is the second problem that is addressed here. It is shown that inhomogeneity in the scattering length density of the detergent belt surrounding a membrane part of the complex and oligomerization polydispersity significantly impacts on SAXS and SANS profiles, and therefore on 3D ab initio structures. It is described how both problems can be taken into account to improve the quality of SAS data treatment. Since SAS data for MPs are usually obtained from solubilized proteins, and their detergent belt and, to a certain extent, oligomerization polydispersity are sufficiently common phenomena, the approaches proposed in this work might be used in SAS studies of different MPs.

Beschreibung: A new two-dimensional (2D) coordination polymer, namely, poly[[diaqua-[μ4-2,2′-[terephthaloylbis(azanediyl)]diacetato]calcium(II)] monohydrate], {[Ca(C12H10N2O6)(H2O)2]·H2O} n , (I), has been synthesized by the reaction of CaCl2 with 2,2′-[terephthaloylbis(azanediyl)]diacetic acid (H2 L). The title compound was structurally characterized by single-crystal X-ray diffraction analysis, elemental analysis and IR spectroscopy. In the crystal structure of (I), each CaII cation binds to six carboxylate groups from four symmetry-related L 2− dianions. The hexadentate L 2− ligand links four symmetry-related calcium cations into a 2D layer-like structure, which can be simplified as a uninodal SP 2-periodic (3,6)III net with the point symbol (43·63). In the lattice, all layers pack in parallel arrays through weak interlayer hydrogen bonding and π–π interactions. The thermal stability and photoluminescence properties of (I) have been investigated. Thermogravimetric analysis reveals the different thermal stabilities of the two coordinated water molecules due to their different hydrogen-bonding interactions. The title coordination polymer exhibits an excitation-wavelength-dependent fluorescence in the solid state.

Beschreibung: Four new solvates of the anti-HIV compound etravirine [systematic name: 4-({6-amino-5-bromo-2-[(4-cyanophenyl)amino]pyrimidin-4-yl}oxy)-3,5-dimethylbenzonitrile, C20H15BrN6O] with dimethyl sulfoxide (C2H6OS, two distinct monosolvates), 1,4-dioxane (C4H8O2, the 0.75-solvate) and N,N-dimethylacetamide (C4H9NO, the monosolvate), which exhibit conversion to the same anhydrous etravirine phase upon desolvation, and a stable etravirinium oxalate salt {6-amino-5-bromo-4-(4-cyano-2,6-dimethylphenoxy)-2-[(4-cyanophenyl)amino]pyrimidin-1-ium hemioxalate, C20H16BrN6O+·0.5C2O4 2−} were obtained. The crystal structures were solved by single-crystal X-ray diffraction and analyzed by powder X-ray diffraction, and the intermolecular interactions were explored by Hirshfeld surface analysis. Lattice energies were evaluated using the atom–atom force field Coulomb–London–Pauli (AA CLP) approximation, which distributes the total energy as four separate contributions: Coulombic, polarization, dispersion and repulsion. The formation of the solvates and the oxalate salt was further characterized by thermal analysis and IR spectroscopy.

Beschreibung: A dinuclear nickel complex with (S)-limonene based aminooxime ligand has been isolated and its crystal structure determined. The resolved structure of dichloridobis{(2S,5R)-2-methyl-5-(prop-1-en-2-yl)-2-[(pyridin-2-yl)methylamino]cyclohexan-1-one oxime}dinickel(II), [Ni2Cl2(C16H23ClN3O)2], at 100 K has monoclinic (P21) symmetry. The two NiII ions in the dinuclear complex are each coordinated in a distorted octahedral environment by three nitrogen atoms, a terminal chloride and two μ bridging chlorides. Each oxime ligand is coordinated to nickel(II) by the three nitrogen atoms, leading to two five-membered chelate rings, each displaying an envelope conformation. In the crystal, numerous intermolecular and intramolecular hydrogen bonds lead to the formation of a three-dimensional network structure.

Beschreibung: The title four-coordinate mononuclear complex, [Hg(C3H5OS2)2(C6H16N2)] or [Hg(C3H5OS2)2(tmeda)] (tmeda: N,N,N′,N′-tetramethylethane-1,2-diamine), has a distorted tetrahedral geometry. The HgII ion is coordinated to two N atoms of the N,N,N′,N′-tetramethylethylenediamine ligand and two S atoms from two ethylxanthate xanthate ligands. In the crystal, molecules are linked by weak C—H...S hydrogen bonds, forming a two-dimensional supramolecular architecture in the ab plane. The most important contributions for the crystal packing are from H...H (59.3%), S...H (27.4%) and O...H (7.5%) interactions.

Beschreibung: The title compound, C16H17NO, is a Schiff base that exists in the enol–imine tautomeric form and adopts a Z configuration. The molecule is non-planar, with the twisted rings making a dihedral angle of 39.92 (4)°. The intramolecular O—H...N hydrogen bond forms an S(6) ring motif. In the crystal, molecules are linked by C—H...π interactions and very weak π-π stacking interactions also help to consolidate the crystal packing. A Hirshfeld surface analysis was performed to investigate the contributions of different intermolecular contacts within the supramolecular structure. The major contributions are from H...H (65%), C...H (19.2%) and O...H (6.6%) interactions.

Beschreibung: In the fused ring system of the title compound, C24H27BrO5, the mean plane and maximum deviations of the central pyran ring are 0.0384 (2) and 0.0733 (2) Å, respectively. The cyclohexenone rings both adopt envelope conformations with the tetra-substituted C atoms as flap atoms, whereas the central pyran ring adopts a flattened boat conformation. The central pyran and phenyl substituent rings are almost perpendicular to each other, making a dihedral angle of 89.71 (2)°. In the crystal, pairs of molecules are linked via O—H...O hydrogen bonds, forming inversion dimers with an R 2 2(20) ring motif. A Hirshfeld surface analysis indicates that the most important contributions to the crystal packing are from H...H (50.6%), O...H/H...O (22.9%) and C...H/H...C (11.1%) contacts. Quantum chemical calculations for the frontier molecular orbitals were undertaken to determine the chemical reactivity of the title compound.

Beschreibung: Azotobacter vinelandii is a model diazotroph and is the source of most nitrogenase material for structural and biochemical work. Azotobacter can grow in above-atmospheric levels of oxygen, despite the sensitivity of nitrogenase activity to oxygen. Azotobacter has many iron–sulfur proteins in its genome, which were identified as far back as the 1960s and probably play roles in the complex redox chemistry that Azotobacter must maintain when fixing nitrogen. Here, the 2.1 Å resolution crystal structure of the [2Fe–2S] protein I (Shethna protein I) from A. vinelandii is presented, revealing a homodimer with the [2Fe–2S] cluster coordinated by the surrounding conserved cysteine residues. It is similar to the structure of the thioredoxin-like [2Fe–2S] protein from Aquifex aeolicus, including the positions of the [2Fe–2S] clusters and conserved cysteine residues. The structure of Shethna protein I will provide information for understanding its function in relation to nitrogen fixation and its evolutionary relationships to other ferredoxins.

Beschreibung: Single crystals of the high-temperature form I of [Co(NCS)2(DMAP)2] (DMAP = 4-dimethylaminopyridine, C7H10N2) were obtained accidentally by the reaction of Co(NCS)2 with DMAP at slightly elevated temperatures under kinetic control. This modification crystallizes in the monoclinic space group P21/m and is isotypic with the corresponding Zn compound. The asymmetric unit consists of one crystallographically independent Co cation and two crystallographically independent thiocyanate anions that are located on a crystallographic mirror plane and one DMAP ligand (general position). In its crystal structure the discrete complexes are linked by C—H...S hydrogen bonds into a three-dimensional network. For comparison, the crystal structure of the known low-temperature form II, which is already thermodynamically stable at room temperature, was redetermined at the same temperature. In this polymorph the complexes are connected by C—H...S and C—H...N hydrogen bonds into a three-dimensional network. At 100 K the density of the high-temperature form I (ρ = 1.462 g cm−3) is lower than that of the low-temperature form II (ρ = 1.457 g cm−3), which is in contrast to the values determined by XRPD at room temperature. Therefore, these two forms represent an exception to the Kitaigorodskii density rule, for which extensive intermolecular hydrogen bonding in form II might be responsible.

Beschreibung: A hydrogen sulfate salt, C15H18NSe+·HSO4 −·H2O or [BnSeCH2CH(Ph)NH3 +](HSO4 −), of a chiral selenated amine (R)-2-(benzylselanyl)-1-phenylethanamine (BnSeCH2CH(Ph)NH2) has been synthesized and characterized by elemental analysis,1H and 13C{1H} NMR, FT–IR analysis, and single-crystal X-ray diffraction studies. The title salt crystallizes in the monohydrate form in the non-centrosymmetric monoclinic P21 space group. The cation is somewhat W shaped with the dihedral angle between the two aromatic rings being 60.9 (4)°. The carbon atom attached to the amine nitrogen atom is chiral and in the R configuration, and, the –C—C– bond of the –CH2—CH– fragment has a staggered conformation. In the crystal structure, two HSO4 − anions and two water molecules form an R 4 4(12) tetrameric type of assembly comprised of alternating HSO4 − anions and water molecules via discrete D(2) O—H...O hydrogen bonds. This tetrameric assembly aggregates along the b-axis direction as an infinite one-dimensional tape. Adjacent tapes are interconnected via discrete D(2) N—H...O hydrogen bonds between the three amino hydrogen atoms of the cation sandwiched between the two tapes and the three HSO4 − anions of the nearest asymmetric units, resulting in a complex two-dimensional sheet along the ab plane. The pendant arrangement of the cations is stabilized by C—H...π interactions between adjacent cations running as chains down the [010] axis. Secondary Se...O [3.1474 (4) Å] interactions are also observed in the crystal structure. A Hirshfeld surface analysis, including d norm, shape-index and fingerprint plots of the cation, anion and solvent molecule, was carried out to confirm the presence of various interactions in the crystal structure.

Beschreibung: In the cation of the title salt, C30H28NO2 +·CF3O3S−, the four tetrahydrofuran rings adopt envelope conformations. In the crystal, pairs of cations are linked by dimeric C—H...O hydrogen bonds, forming two R 2 2(6) ring motifs parallel to the (001) plane. The cations and anions are connected by further C—H...O hydrogen bonds, forming a three-dimensional network structure. Hirshfeld surface analysis indicates that the most important contributions to the crystal packing are from H...H (47.6%), C...H/H...C (20.6%), O...H/H...O (18.0%) and F...H/H...F (9.9%) interactions.

Beschreibung: The title compound, C17H7F8N3O, was obtained via the reaction of 1-azido-2,3,4,5,6-pentafluorobenzene with 4,4,4-trifluoro-1-(p-tolyl)butane-1,3-dione using triethylamine as a base catalyst and solvent. The dihedral angles between the pentafluorophenyl (A), triazole (B) and p-tolyl (C) rings are A/B = 62.3 (2), B/C = 43.9 (3) and A/C = 19.1 (3)°. In the crystal, the molecules are linked by C—H...F and C—H...O hydrogen bonds as well as by aromatic π–π stacking interactions into a three-dimensional network. To further analyse the intermolecular interactions, a Hirshfeld surface analysis was performed.

Beschreibung: According to Löwenstein's rule, Al–O–Al bridges are forbidden in the aluminosilicate framework of zeolites. A graph-theoretical interpretation of the rule, based on the concept of independent sets, was proposed earlier. It was shown that one can apply the vector method to the associated periodic net and define a maximal Al/(Al+Si) ratio for any aluminosilicate framework following the rule; this ratio was called the independence ratio of the net. According to this method, the determination of the independence ratio of a periodic net requires finding a subgroup of the translation group of the net for which the quotient graph and a fundamental transversal have the same independence ratio. This article and a companion paper deal with practical issues regarding the calculation of the independence ratio of mainly 2-periodic nets and the determination of site distributions realizing this ratio. The first paper describes a calculation technique based on propositional calculus and introduces a multivariate polynomial, called the independence polynomial. This polynomial can be calculated in an automatic way and provides the list of all maximal independent sets of the graph, hence also the value of its independence ratio. Some properties of this polynomial are discussed; the independence polynomials of some simple graphs, such as short paths or cycles, are determined as examples of calculation techniques. The method is also applied to the determination of the independence ratio of the 2-periodic net dhc.

Beschreibung: To decompose a wide-angle X-ray diffraction (WAXD) curve of a semi-crystalline polymer into crystalline peaks and amorphous halos, a theoretical best-fitted curve, i.e. a mathematical model, is constructed. In fitting the theoretical curve to the experimental one, various functions can be used to quantify and minimize the deviations between the curves. The analyses and calculations performed in this work have proved that the quality of the model, its parameters and consequently the information on the structure of the investigated polymer are considerably dependent on the shape of an objective function. It is shown that the best models are obtained employing the least-squares method in which the sum of squared absolute errors is minimized. On the other hand, the methods in which the objective functions are based on the relative errors do not give a good fit and should not be used. The comparison and evaluation were performed using WAXD curves of seven polymers: isotactic polypropylene, polyvinylidene fluoride, cellulose I, cellulose II, polyethylene, polyethylene terephthalate and polyamide 6. The methods were compared and evaluated using statistical tests and measures of the quality of fitting.

Beschreibung: The section of the Bilbao Crystallographic Server (https://www.cryst.ehu.es/) dedicated to subperiodic groups contains crystallographic and Brillouin-zone databases for the layer groups. The crystallographic databases include the generators/general positions (GENPOS), Wyckoff positions (WYCKPOS) and maximal subgroups (MAXSUB). The Brillouin-zone database (LKVEC) offers k-vector tables and Brillouin-zone figures of all 80 layer groups which form the background of the classification of their irreducible representations. The symmetry properties of the wavevectors are described applying the so-called reciprocal-space-group approach and this classification scheme is compared with that of Litvin & Wike [(1991), Character Tables and Compatibility Relations of the Eighty Layer Groups and Seventeen Plane Groups. New York: Plenum Press]. The specification of independent parameter ranges of k vectors in the representation domains of the Brillouin zones provides a solution to the problems of uniqueness and completeness of layer-group representations. The Brillouin-zone figures and k-vector tables are described in detail and illustrated by several examples.

Beschreibung: The crystal structure of the title solvated coordination compound, [Co(NCS)2(C6H12N4)2(H2O)2]·2C6H12N4·2C2H3N, consists of discrete complexes in which the Co2+ cations (site symmetry overline{1}) are sixfold coordinated by two N-bonded thiocyanate anions, two water molecules and two hexamethylenetetramine (HMT) molecules to generate distorted trans-CoN4O2 octahedra. The discrete complexes are each connected by two HMT solvate molecules into chains via strong O—H...N hydrogen bonds. These chains are further linked by additional O—H...N and C—H...N and C—H...S hydrogen bonds into a three-dimensional network. Within this network, channels are formed that propagate along the c-axis direction and in which additional acetonitrile solvent molecules are embedded, which are hydrogen bonded to the network. The CN stretching vibration of the thiocyanate ion occurs at 2062 cm−1, which is in agreement with the presence of N-bonded anionic ligands. XRPD investigations prove the formation of the title compound as the major phase accompanied by a small amount of a second unknown phase.

Beschreibung: The molecular orbitals (MOs) of diformohydrazide have been determined from the electron density measured by X-ray diffraction. The experimental and refinement procedures are explained in detail and the validity of the obtained MOs is assessed from the crystallographic point of view. The X-ray structure factors were measured at 100 K by a four-circle diffractometer avoiding multiple diffraction, the effect of which on the structure factors is comparable to two-centre structure factors. There remained no significant peaks on the residual density map and the R factors reduced significantly. Among the 788 MO coefficients, 731 converged, of which 694 were statistically significant. The C—H and N—H bond distances are 1.032 (2) and 1.033 (3) Å, respectively. The electron densities of theoretical and experimental MOs and the differences between them are illustrated. The overall features of the electron density obtained by X-ray molecular orbital (XMO) analysis are in good agreement with the canonical orbitals calculated by the restricted Hartree Fock (RHF) method. The bonding-electron distribution around the middle of each bond is well represented and the relative phase relationships of the π orbitals are reflected clearly in the electron densities on the plane perpendicular to the molecular plane. However, differences are noticeable around the O atom on the molecular plane. The orbital energies obtained by XMO analysis are about 0.3 a.u. higher than the corresponding canonical orbitals, except for MO10 to MO14 which are about 0.7 a.u. higher. These exceptions are attributed to the N—H...O′′ intermolecular hydrogen bond, which is neglected in the MO models of the present study. The hydrogen bond is supported by significant electron densities at the saddle points between the H(N) and O′′ atoms in MO7, 8, 14 and 17, and by that of O′′-p extended over H(N) in MO21 and 22, while no peaks were found in MO10, 11, 13 and 15. The electron density of each MO clearly exhibits its role in the molecule. Consequently, the MOs obtained by XMO analysis give a fundamental quantum mechanical insight into the real properties of molecules.

Beschreibung: The novel hemilabile ferrocenylbisphosphane 1,1′-bis(bis{2-[(dimethylamino)methyl]phenyl}phosphanyl)ferrocene, [Fe{C5H4P(C6H4CH2NMe2-o)2}2] (1), was synthesized by reacting bis(dichlorophosphanyl)ferrocene, [Fe{C5H4(PCl2)}2] with LiC6H4CH2NMe2-o. Treatment of 1 with gray selenium and anhydrous ZnCl2 yielded, respectively, the bisselenide (ferrocene-1,1′-diyl)bis(bis{2-[(dimethylamino)methyl]phenyl}phosphine selenide), [Fe(C23H28N2PSe)2] (2), and the dizinc complex [μ-1,1′-bis(bis{2-[(dimethylamino)methyl]phenyl}phosphanyl)ferrocene-κ2 N,P:κ2 N′,P′]bis[dichloridozinc(II)] dichloromethane monosolvate, [FeZn2Cl4(C23H28N2P)2]·CH2Cl2 (3), and both have been structurally characterized. Both compounds crystallized with the asymmetric unit containing half a molecule and with the Fe atom on an inversion centre. A Hirshfeld surface analysis indicated that the most significant contributions to the crystal packing of 2 are from H...H (76.7%), C...H/H...C (13.2%) and Se...H/H...Se (7.1%) contacts, while those for 3 are from H...H (62.3%), Cl...H/H...Cl (24.4%) and C...H/H...C (10.9%) contacts.

Beschreibung: The study of various forms of pharmaceutical substances with specific physicochemical properties suitable for putting them on the market is one of the elements of research in the pharmaceutical industry. A large proportion of active pharmaceutical ingredients (APIs) occur in the salt form. The use of an acidic coformer with a given structure and a suitable pK a value towards purine alkaloids containing a basic imidazole N atom can lead to salt formation. In this work, 2,6-dihydroxybenzoic acid (26DHBA) was used for cocrystallization of theobromine (TBR) and caffeine (CAF). Two novel salts, namely, theobrominium 2,6-dihydroxybenzoate, C7H9N4O2 +·C7H5O4 − (I), and caffeinium 2,6-dihydroxybenzoate, C8H11N4O2 +·C7H5O4 − (II), were synthesized. Both salts were obtained independently by slow evaporation from solution, by neat grinding and also by microwave-assisted slurry cocrystallization. Powder X-ray diffraction measurements proved the formation of the new substances. Single-crystal X-ray diffraction studies confirmed proton transfer between the given alkaloid and 26DHBA, and the formation of N—H...O hydrogen bonds in both I and II. Unlike the caffeine cations in II, the theobromine cations in I are paired by noncovalent N—H...O=C interactions and a cyclic array is observed. As expected, the two hydroxy groups in the 26DHBA anion in both salts are involved in two intramolecular O—H...O hydrogen bonds. C—H...O and π–π interactions further stabilize the crystal structures of both compounds. Steady-state UV–Vis spectroscopy showed changes in the water solubility of xanthines after ionizable complex formation. The obtained salts I and II were also characterized by theoretical calculations, Fourier-transform IR spectroscopy (FT–IR), thermogravimetric analysis (TGA), differential scanning calorimetry (DSC) and elemental analysis.

Beschreibung: Glutamine synthetase (GS) is a decameric enzyme that plays a key role in nitrogen metabolism. Acetylation of the N-terminal degron (N-degron) of GS is essential for ubiquitylation and subsequent GS degradation. The full-length GS structure showed that the N-degron is buried inside the GS decamer and is inaccessible to the acetyltransferase. The structure of N-degron-truncated GS reported here reveals that the N-degron is not essential for GS decamer formation. It is also shown that the N-degron can be exposed to a solvent region through a series of conformational adjustments upon ligand binding. In summary, this study elucidated the dynamic movement of the N-degron and the possible effect of glutamine in enhancing the acetylation process.

Beschreibung: The title compound, [Cu2(C7H4NO4)4(C3H7NO)2]·(C3H7NO)2, is a binuclear copper(II) complex located on an inversion center midway between the two copper(II) cations. The asymmetric unit consists of one CuII cation, two 3-nitrobenzoato ligands, and two dimethylformamide (DMF) molecules, one of which coordinates to the CuII cation and one is a solvate molecule. The carboxylate groups of the ligands bridge two CuII cations with a Cu—Cu distance of 2.6554 (6) Å, completing a distorted octahedral O5Cu coordination environment. The dihedral angles between the carboxylate and the aromatic ring planes of the two independent ligands are different from one another, viz. 5.2 (3) and 23.9 (3)°. The three-dimensional structure is consolidated by weak C—H...O interactions and stabilized by π–π stacking interactions between the aromatic rings. The complex and the free ligand were further characterized by Fourier-transform infrared spectroscopy (FT–IR), and the energies of the frontier molecular orbitals of the complex were determined by DFT calculations at the B3LYP/def2-TZVP level of theory.

Beschreibung: In the title compound, C14H7Cl4FN2, the dihedral angle between the 4-fluorophenyl ring and the 2,4-dichlorophenyl ring is 46.03 (19)°. In the crystal, the molecules are linked by C—H...N interactions along the a-axis direction, forming a C(6) chain. The molecules are further connected by C—Cl...π interactions and face-to-face π–π stacking interactions, forming ribbons along the a-axis direction. Hirshfeld surface analysis indicates that the greatest contributions to the crystal packing are from Cl...H/H...Cl (35.1%), H...H (10.6%), C...C (9.7%), Cl...Cl (9.4%) and C...H/H...C (9.2%) interactions.

Beschreibung: The capability to obtain essential nutrients in hostile environments is a critical skill for pathogens. Under zinc-deficient conditions, Pseudomonas aeruginosa expresses a pool of metal homeostasis control systems that is complex compared with other Gram-negative bacteria and has only been partially characterized. Here, the structure and zinc-binding properties of the protein PA4063, the first component of the PA4063–PA4066 operon, are described. PA4063 has no homologs in other organisms and is characterized by the presence of two histidine-rich sequences. ITC titration detected two zinc-binding sites with micromolar affinity. Crystallographic characterization, performed both with and without zinc, revealed an α/β-sandwich structure that can be classified as a noncanonical ferredoxin-like fold since it differs in size and topology. The histidine-rich stretches located at the N-terminus and between β3 and β4 are disordered in the apo structure, but a few residues become structured in the presence of zinc, contributing to coordination in one of the two sites. The ability to bind two zinc ions at relatively low affinity, the absence of catalytic cavities and the presence of two histidine-rich loops are properties and structural features which suggest that PA4063 might play a role as a periplasmic zinc chaperone or as a concentration sensor useful for optimizing the response of the pathogen to zinc deficiency.

Beschreibung: Data reduction and correction steps and processed data reproducibility in the emerging single-crystal total-scattering-based technique of three-dimensional differential atomic pair distribution function (3D-ΔPDF) analysis are explored. All steps from sample measurement to data processing are outlined using a crystal of CuIr2S4 as an example, studied in a setup equipped with a high-energy X-ray beam and a flat-panel area detector. Computational overhead as pertains to data sampling and the associated data-processing steps is also discussed. Various aspects of the final 3D-ΔPDF reproducibility are explicitly tested by varying the data-processing order and included steps, and by carrying out a crystal-to-crystal data comparison. Situations in which the 3D-ΔPDF is robust are identified, and caution against a few particular cases which can lead to inconsistent 3D-ΔPDFs is noted. Although not all the approaches applied herein will be valid across all systems, and a more in-depth analysis of some of the effects of the data-processing steps may still needed, the methods collected herein represent the start of a more systematic discussion about data processing and corrections in this field.

Beschreibung: The concepts of `wavevector star channel' and `wavevector star channel group' are newly defined, which allow the effective study of phase transitions considering directly the translational symmetry breaking in crystals. A method is suggested by which the wavevector star channels can be found using the image of the representation of the translational group. According to this method, the wavevector star channels are found for the 80 Lifschitz stars in the reciprocal lattice. The wavevector star channel group is defined as the set of symmetry elements of the parent phase which leave the star channel invariant, and the wavevector star channel groups with one, two, three and four arms are calculated. It is shown that the complicated symmetry changes in the pyroelectric crystal Pb1−x Ca x TiO3 (PCT) can be described using the new five-component reducible order parameter transformed according to the representation of the wavevector star channel group, rather than the nine-component one based on the theory of the full irreducible representation of the space group.

Beschreibung: β-Mannanase (EC 3.2.1.78) is an enzyme that cleaves within the backbone of mannan-based polysaccharides at β-1,4-linked D-mannose residues, resulting in the formation of mannooligosaccharides (MOS), which are potential prebiotics. The GH26 β-mannanase KMAN from Klebsiella oxytoca KUB-CW2-3 shares 49–72% amino-acid sequence similarity with β-mannanases from other sources. The crystal structure of KMAN at a resolution of 2.57 Å revealed an open cleft-shaped active site. The enzyme structure is based on a (β/α)8-barrel architecture, which is a typical characteristic of clan A glycoside hydrolase enzymes. The putative catalytic residues Glu183 and Glu282 are located on the loop connected to β-strand 4 and at the end of β-strand 7, respectively. KMAN digests linear MOS with a degree of polymerization (DP) of between 4 and 6, with high catalytic efficiency (k cat/K m) towards DP6 (2571.26 min−1 mM −1). The predominant end products from the hydrolysis of locust bean gum, konjac glucomannan and linear MOS are mannobiose and mannotriose. It was observed that KMAN requires at least four binding sites for the binding of substrate molecules and hydrolysis. Molecular docking of mannotriose and galactosyl-mannotetraose to KMAN confirmed its mode of action, which prefers linear substrates to branched substrates.

Beschreibung: In crystallography, the phase problem can often be addressed by the careful preparation of molecular-replacement search models. This has led to the development of pipelines such as MrBUMP that can automatically identify homologous proteins from an input sequence and edit them to focus on the areas that are most conserved. Many of these approaches can be applied directly to cryo-EM to help discover, prepare and correctly place models (here called cryo-EM search models) into electrostatic potential maps. This can significantly reduce the amount of manual model building that is required for structure determination. Here, MrBUMP is repurposed to fit automatically obtained PDB-derived chains and domains into cryo-EM maps. MrBUMP was successfully able to identify and place cryo-EM search models across a range of resolutions. Methods such as map segmentation are also explored as potential routes to improved performance. Map segmentation was also found to improve the effectiveness of the pipeline for higher resolution (

Beschreibung: The predictive power of simulation has become embedded in the infrastructure of modern economies. Computer-aided design is ubiquitous throughout industry. In aeronautical engineering, built infrastructure and materials manufacturing, simulations are routinely used to compute the performance of potential designs before construction. The ability to predict the behaviour of products is a driver of innovation by reducing the cost barrier to new designs, but also because radically novel ideas can be piloted with relatively little risk. Accurate weather forecasting is essential to guide domestic and military flight paths, and therefore the underpinning simulations are critical enough to have implications for national security. However, in the pharmaceutical and biotechnological industries, the application of computer simulations remains limited by the capabilities of the technology with respect to the complexity of molecular biology and human physiology. Over the last 30 years, molecular-modelling tools have gradually gained a degree of acceptance in the pharmaceutical industry. Drug discovery has begun to benefit from physics-based simulations. While such simulations have great potential for improved molecular design, much scepticism remains about their value. The motivations for such reservations in industry and areas where simulations show promise for efficiency gains in preclinical research are discussed. In this, the first of two complementary papers, the scientific and technical progress that needs to be made to improve the predictive power of biomolecular simulations, and how this might be achieved, is firstly discussed (Part 1). In Part 2, the status of computer simulations in pharma is contrasted with aerodynamics modelling and weather forecasting, and comments are made on the cultural changes needed for equivalent computational technologies to become integrated into life-science industries.

Beschreibung: The structures of the six hydrogen-bonded 1:1 compounds of 4-methylquinoline (C10H9N) with chloro- and nitro-substituted benzoic acids (C7H4ClNO4), namely, 4-methylquinolinium 2-chloro-4-nitrobenzoate, C10H10N+·C7H3ClNO4 −, (I), 4-methylquinoline–2-chloro-5-nitrobenzoic acid (1/1), C10H9N·C7H4ClNO4, (II), 4-methylquinolinium 2-chloro-6-nitrobenzoate, C10H9.63N0.63+·C7H3.37ClNO4 0.63−, (III), 4-methylquinolinium 3-chloro-2-nitrobenzoate, C10H9.54N0.54+·C7H3.46ClNO4 0.54−, (IV), 4-methylquinolinium 4-chloro-2-nitrobenzoate, C10H10N+·C7H3ClNO4 −, (V), and 4-methylquinolinium 5-chloro-2-nitrobenzoate, C10H10N+·C7H3ClNO4 −, have been determined at 185–190 K. In each compound, the acid and base molecules are linked by a short hydrogen bond between a carboxy (or carboxylate) O atom and an N atom of the base. The O...N distances are 2.5652 (14), 2.556 (3), 2.5485 (13), 2.5364 (13), 2.5568 (13) and 2.5252 (11) Å, respectively, for compounds (I)–(VI). In the hydrogen-bonded acid–base units of (III) and (IV), the H atoms are each disordered over two positions with O site:N site occupancies of 0.37 (3):0.63 (3) and 0.46 (3):0.54 (4), respectively, for (III) and (IV). The H atoms in the hydrogen-bonded units of (I), (V) and (VI) are located at the N-atom site, while the H atom in (II) is located at the O-atom site. In all the crystals of (I)–(VI), π–π stacking interactions between the quinoline ring systems and C—H...O hydrogen bonds are observed. Similar layer structures are constructed in (IV)–(VI) through these interactions together with π–π interactions between the benzene rings of the adjacent acid molecules. A short Cl...Cl contact and an N—O...π interaction are present in (I), while a C—H...Cl hydrogen bond and a π–π interaction between the benzene ring of the acid molecule and the quinoline ring system in (II), and a C—H...π interaction in (III) are observed. Hirshfeld surfaces for the title compounds mapped over d norm and shape index were generated to visualize the weak intermolecular interactions.

Beschreibung: A novel three-dimensional (3D) CdII coordination polymer, namely, poly[[μ2-4,4′-bis(2-methylimidazol-1-yl)-[1,1′-biphenyl]](μ2-5-methylisophthalato)cadmium(II)], [Cd(C9H6O4)(C20H18N4)] n or [Cd(MIP)(4,4′-BMIBP)] n , (I), was synthesized by the hydrothermal method using 5-methylisophthalic acid (H2MIP), 4,4′-bis(2-methylimidazol-1-yl)-[1,1′-biphenyl] (4,4′-BMIBP) and Cd(NO3)2·6H2O, and characterized by single-crystal X-ray diffraction, elemental analysis, IR spectroscopy and thermogravimetric analysis. Compound (I) exhibits a novel fivefold interpenetrating 3D diamondoid framework. Additionally, it shows fluorescence emission in the solid state and promising photocatalytic activities for the degradation of methylene blue (MB) in water at room temperature.