On the relationships between molecular conformations and intermolecular contacts toward crystal self-assembly of mono-, di-, tri-, and tetra-oxygenated xanthone derivatives

Oxygenated xanthones have been extensively investigated over the years, but there are few reports concerning their crystal structure. Our chemical investigations of Brazilian plants resulted in the isolation of four natural products named 1-hydroxyxanthone (I), 1-hydroxy-7-methoxyxanthone (II), 1,5-dihydroxy-3-methoxyxanthone (III), and 1,7-dihydroxy-3,8-dimethoxyxanthone (IV). The structures of these compounds were established on the basis of single crystal X-ray diffraction. The xanthone nucleus conformation is essentially planar with the substituents adopting the orientations less sterically hindered. In addition, classical intermolecular hydrogen bonds (O-H center dot center dot center dot O) present in III and IV give rise to infinite ribbons. However, the xanthone I does not present any intermolecular hydrogen bonds, meanwhile the xanthone II presents only a non-classical one (C-H center dot center dot center dot O). The crystal packing of all xanthone structures is also stabilized by pi-pi interactions. The fingerprint plots, derived from the Hirshfeld surfaces, exhibited significant features of each crystal structures.

Crystal structure of Schistosoma purine nucleoside phosphorylase complexed with a novel monocyclic inhibitor

A novel inhibitor of Schistosoma PNP was identified using an ""in silico"" approach allied to enzyme inhibition assays. The compound has a monocyclic structure which has not been previously described for PNP inhibitors The crystallographic structure of the complex was determined and used to elucidate the binding mode within the active site Furthermore, the predicted pose was very similar to that determined crystallographically, validating the methodology The compound Sm_VS1, despite its low molecular weight, possesses an IC(50) of 1 3 mu M, surprisingly low when compared with purine analogues This is presumably due to the formation of eight hydrogen bonds with key residues in the active site E203, N245 and T244. The results of this study highlight the importance of the use of multiple conformations for the target during virtual screening. Indeed the Sm_VS1 compound was only identified after flipping the N245 side chain It is expected that the structure will be of use in the development of new highly active non-purine based compounds against the Sclustosoma enzyme. (c) 2010 Elsevier B V. All rights reserved

Pt(II) and Ag(I) complexes with acesulfame: Crystal structure and a study of their antitumoral, antimicrobial and antiviral activities

Two new complexes of platinum(II) and silver(I) with acesulfame were synthesized. Acesulfame is in the anionic form acesulfamate (ace). The structures of both complexes were determined by X-ray crystallography. For K(2)[PtCl(2)(ace)(2)] the platinum atom is coordinated to two Cl(-) and two N-acesulfamate atoms forming a trans-square planar geometry. Each K(+) ion interacts with two oxygen atoms of the S(=O)(2) group of each acesulfamate. For the polymeric complex [Ag(ace)](n) the water molecule bridges between two crystallographic equivalent Agl atoms which are related each other by a twofold symmetry axis. Two Agl atoms, related to each other by a symmetry centre, make bond contact with two equivalent oxygen atoms. These bonds give rise to infinite chains along the unit cell diagonal in the ac plane. The in vitro cytotoxic analyses for the platinum complex using HeLa (human cervix cancer) cells show its low activity when compared to the vehicle-treated cells. The Ag(I) complex submitted to in vitro antimycobacterial tests, using the Microplate Alamar Blue (MABA) method, showed a good activity against Mycobacterium tuberculosis, responsible for tuberculosis, with a minimal inhibitory concentration (MIC) value of 11.6 mu M. The Ag(I) complex also presented a promising activity against Gram negative (Escherichia colt and Pseudomonas aeruginosa) and Gram positive (Enterococcus faecalis) microorganisms. The complex K(2)[PtCl(2)(ace)(2)] was also evaluated for antiviral properties against dengue virus type 2 (New Guinea C strain) in Vero cells and showed a good inhibition of dengue virus type 2 (New Guinea G strain) replication at 200 mu M, when compared to vehicle-treated cells. (C) 2010 Elsevier Inc. All rights reserved.

Synthesis, Infrared Spectroscopy and Crystal Structure Determination of a New Decavanadate

Synthesis, infrared spectroscopy and crystal structure of a new potassium decavanadate decahydrate, K(6)[V(10)O(28)] 10H(2)O, has been reported The infrared spectrum is dominated by decavanadate polyanion and water bands The X-ray crystallography analysis found the compound crystallizes in a triclinic system with the parameters a = 10 5334 (4) angstrom, b = 10 6600 (4) angstrom, c = 17 7351 (5) angstrom, alpha = 76 940 (2)degrees, beta = 75 836 (2)degrees, gamma = 64 776 (2)degrees, V = 1,729 86 (11) A(3), Z = 2, space group P (1) over bar The polyanion consists of ten [VO(6)] octahedra sharing edges, in which the V-O distances are in good agreement with those reported for other decavanadates The crystal structure is stabilized by potassium cations and water molecules forming a complex pattern of hydrogen bonding and short contact ionic interactions

Structural requirement for PPAR gamma binding revealed by a meta analysis of holo-crystal structures

PPAR gamma is a ligand regulated transcriptional factor that modulates the transcription of several genes involved in fat and sugar metabolism. Due to its easy bacterial expression and crystallization, several crystal structures of holo-PPAR gamma have been reported and deposited in the Protein Data Bank. Here, we investigated the three-dimensional electrostatic properties of 55 PPAR gamma ligands and used this information for clustering them through principal component analysis. We found out that, according to their electrostatic potential, these ligands can be separated in three groups, with different binding features. We also observed that non-selective and selective ligands show different 3D electrostatic properties and are separated in different clusters. The relevance of this analysis for the development of new binders is discussed. (C) 2010 Elsevier Masson SAS. All rights reserved.

Crystal structure and statistical coupling analysis of highly glycosylated peroxidase from royal palm tree (Roystonea regia)

Royal palm tree peroxidase (RPTP) is a very stable enzyme in regards to acidity, temperature, H(2)O(2), and organic solvents. Thus, RPTP is a promising candidate for developing H(2)O(2)-sensitive biosensors for diverse applications in industry and analytical chemistry. RPTP belongs to the family of class III secretory plant peroxidases, which include horseradish peroxidase isozyme C, soybean and peanut peroxidases. Here we report the X-ray structure of native RPTP isolated from royal palm tree (Roystonea regia) refined to a resolution of 1.85 angstrom. RPTP has the same overall folding pattern of the plant peroxidase superfamily, and it contains one heme group and two calcium-binding sites in similar locations. The three-dimensional structure of RPTP was solved for a hydroperoxide complex state, and it revealed a bound 2-(N-morpholino) ethanesulfonic acid molecule (MES) positioned at a putative substrate-binding secondary site. Nine N-glycosylation sites are clearly defined in the RPTP electron-density maps, revealing for the first time conformations of the glycan chains of this highly glycosylated enzyme. Furthermore, statistical coupling analysis (SCA) of the plant peroxidase superfamily was performed. This sequence-based method identified a set of evolutionarily conserved sites that mapped to regions surrounding the heme prosthetic group. The SCA matrix also predicted a set of energetically coupled residues that are involved in the maintenance of the structural folding of plant peroxidases. The combination of crystallographic data and SCA analysis provides information about the key structural elements that could contribute to explaining the unique stability of RPTP. (C) 2009 Elsevier Inc. All rights reserved.

Crystal structure of a soluble decoy receptor IL-22BP bound to interleukin-22

Interleukin-22 (IL-22) plays an important role in the regulation of immune and inflammatory responses in mammals. The IL-22 binding protein (IL-22BP), a soluble receptor that specifically binds IL-22, prevents the IL-22/interleukin-22 receptor 1 (IL-22R1)/interleukin-10 receptor 2 (IL-10R2) complex assembly and blocks IL-22 biological activity. Here we present the crystal structure of the IL-22/IL-22BP complex at 2.75 angstrom resolution. The structure reveals IL-22BP residues critical for IL-22 binding, which were confirmed by site-directed mutagenesis and functional studies. Comparison of IL-22/IL-22BP and IL-22/IL-22R1 crystal structures shows that both receptors display an overlapping IL-22 binding surface, which is consistent with the inhibitory role played by IL-22 binding protein.

Synthesis, characterization, and single crystal X-ray structure of the 1-furoyl-3-cyclohexylthiourea cadmium chloride complex, Cd[C4H3OC(O)NHC(S)NHC6H11]4Cl2

Cadmium chloride complex of 1-furoyl-3-cyclohexylthiourea (CyTu) was prepared and characterized by elemental analysis, IR, and Raman spectroscopy. The structure of the complex was determined by single crystal X-ray methods (space group Bbab, a = 20.918(1), b = 23.532(1), c = 23.571(1) angstrom, = = , Z = 8). Each cadmium has distorted octahedral geometry, coordinated by two chlorides and the thiocarbonyl sulfurs from four CyTu molecules. All the spectroscopic data are consistent with coordination of CyTu by sulfur to cadmium.

Statistical coupling analysis of aspartic proteinases based on crystal structures of the Trichoderma reesei enzyme and its complex with pepstatin A

The crystal structures of an aspartic proteinase from Trichoderma reesei (TrAsP) and of its complex with a competitive inhibitor, pepstatin A, were solved and refined to crystallographic R-factors of 17.9% (R(free)=21.2%) at 1.70 angstrom resolution and 15.81% (R(free) = 19.2%) at 1.85 angstrom resolution, respectively. The three-dimensional structure of TrAsP is similar to structures of other members of the pepsin-like family of aspartic proteinases. Each molecule is folded in a predominantly beta-sheet bilobal structure with the N-terminal and C-terminal domains of about the same size. Structural comparison of the native structure and the TrAsP-pepstatin complex reveals that the enzyme undergoes an induced-fit, rigid-body movement upon inhibitor binding, with the N-terminal and C-terminal lobes tightly enclosing the inhibitor. Upon recognition and binding of pepstatin A, amino acid residues of the enzyme active site form a number of short hydrogen bonds to the inhibitor that may play an important role in the mechanism of catalysis and inhibition. The structures of TrAsP were used as a template for performing statistical coupling analysis of the aspartic protease family. This approach permitted, for the first time, the identification of a network of structurally linked residues putatively mediating conformational changes relevant to the function of this family of enzymes. Statistical coupling analysis reveals coevolved continuous clusters of amino acid residues that extend from the active site into the hydrophobic cores of each of the two domains and include amino acid residues from the flap regions, highlighting the importance of these parts of the protein for its enzymatic activity. (C) 2008 Elsevier Ltd. All rights reserved.

Rankamaite from the Urubu pegmatite, Itinga, Minas Gerais, Brazil: Crystal chemistry and Rietveld refinement

A new occurrence of rankamaite is here described at the Urubu pegmatite, Itinga municipality, Minas Gerais, Brazil. The mineral forms cream-white botryoidal aggregates of acicular to fibrous crystals, intimately associated with simpsonite, thoreaulite, cassiterite, quartz, elbaite, albite, and muscovite. The average of six chemical analyses obtained by electron microprobe is (range in parentheses, wt%): Na(2)O 2.08 (1.95-2.13), K(2)O 2.61 (2.52-2.74), Al(2)O(3) 1.96 (1.89-2.00), Fe(2)O(3) 0.01 (0.00-0.03), TiO(2) 0.02 (0.00-0.06), Ta(2)O(5) 81.04 (79.12-85.18), Nb(2)O(5) 9.49 (8.58-9.86), total 97.21 (95.95-101.50). The chemical formula derived from this analysis is (Na(1.55)K(1.28))(Sigma 2.83)(Ta(8.45)Nb(1.64)Al(0.89)Fe(0.01)(3+)Ti(0.01))(Sigma 11.00)[O(25.02)(OH)(5.98)](Sigma 31.00). Rankamaite is an orthorhombic ""tungsten bronze"" (OTB), crystallizing in the space group Cmmm. Its unit-cell parameters refined from X-ray diffraction powder data are: a = 17.224(3), b = 17.687(3), c = 3.9361(7) angstrom, V = 1199.1(3) angstrom(3), Z = 2. Rietveld refinement of the powder data was undertaken using the structure of LaTa(5)O(14) as a starting model for the rankamaite structure. The structural formula obtained with the Rietveld analyses is: (Na(2.21)K(1.26))Sigma(3.37)(Ta(9.12)NB(1.30) Al(0.59))(Sigma 11.00)[O(26.29)(OH)(4.71)](Sigma 31.00). The tantalum atoms are coordinated by six and seven oxygen atoms in the form of distorted TaO(6) octahedra and TaO(2) pentagonal bipyramids, respectively. Every pentagonal bipyramid shares edges with four octahedra, thus forming Ta(5)O(14) units. The potassium atom is in an 11-fold coordination, whereas one sodium atom is in a 10-fold and the other is in a 12-fold coordination. Raman and infrared spectroscopy were used to investigate the room-temperature spectra of rankamaite.

Major- and trace-element composition of olivine, perovskite, clinopyroxene, Cr-Fe-Ti oxides, phlogopite and host kamafugites and kimberlites, Alto Paranaiba, Brazil

An integrated whole-rock petrographic and geochemical study has been carried out on kamafugites and kimberlites of the Late Cretaceous Alto Paranaiba igneous province, in Brazil, and their main minerals, olivine, clinopyroxene, perovskite, phlogopite, spinels and ilmenite. Perovskite is by far the dominant repository for light lanthanides, Nb, Ta, Th and U, and occasionally other elements, reaching concentrations up to 3.4 x 10(4) chondrite values for light lanthanides and 105 chondrite for Th. A very strong fractionation between light and heavy lanthanides (chondrite-normalized La/Yb from similar to 175 to similar to 2000) is also observed. This is likely the first comprehensive dataset on natural perovskite. Clinopyroxene has variable trace-element contents. likely due to the different position of this phase in the crystallization sequence; Sc reaches values as high as 200 ppm whereas the lanthanides show very variable enrichment in light over heavy REE, and commonly show a negative Eu anomaly. The olivine, phlogopite (and tetra-ferriphlogopite), Cr-Ti oxide and ilmenite are substantially barren minerals for lanthanides and most other trace elements, with the exception of Ba, Cs and Rb in mica, and V, Nb and Ta in ilmenite. Estimated mineral/whole-rock partition coefficients for lanthanides in perovskite are similar to previous determinations, though much higher than those calculated in experiments with synthetic compositions, testifying once more to the complex behavior of these elements in a natural environment. The enormous potential for exploitation of lanthanides, Th, U and high-field-strength elements in the Brazilian kamafugites, kimberlites and related rocks is clearly shown.

Crystal structure of the (Mg,Fe)[UO2(P,As)O-4](2) center dot 10H(2)O solid solution - A novel mineral variety of saleeite

The crystal structure of a novel variety {[(Mg0.81Fe0.19)(H2O)(6)](H2O)(4)}{(UO2)[(P0.67As0.33)O-4]}(2) of the mineral saleeite is determined using X-ray diffraction (Bruker Smart diffractometer, lambda MoK alpha, graphite monochromator, 2 theta(max) = 56.62 degrees, R = 0.0321 for 2317 reflections, T = 100 K). The main crystal data are as follows: a = 6.952(6) angstrom, b = 19.865(5) , angstrom, c = 6.969(2) angstrom, beta = 90.806(4)degrees, space group P12(l)/n1, Z = 2, and P-calcd = 3.34 g/cm(3). It is shown that the structure is formed by alternating (along the [010] direction) anionic layers, which are composed of uranium bipyramids and T(P,As) tetrahedra, and cation layers consisting of M(Mg, Fe) octahedra and water molecules, which are joined through a system of asymmetric hydrogen bonds. The hydrogen atoms are located, the scheme of hydrogen bonds is established, and their geometric characteristics are calculated.

Menezesite, the first natural heteropolyniobate, from Cajati, Sao Paulo, Brazil: Description and crystal structure

Menezesite, ideally Ba2MgZr4(BaNb12O42)center dot 12H(2)O, occurs as a vug mineral in the contact zone between dolomite carbonatite and ""jacupirangite"" (=a pyroxenite) at the Jacupiranga mine, in Cajati county, Sao Paulo state, Brazil, associated with dolomite, calcite, magnetite, clinohumite, phlogopite, ancylite-(Ce), strontianite, pyrite, and tochilinite. This is also the type locality for quintinite-2H. The mineral forms rhombododecahedra up to I mm, isolated or in aggregates. Menezesite is transparent and displays a vitreous luster; it is reddish brown with a white streak. It is non-fluorescent. Mohs hardness is about 4. Calculated density derived from the empirical formula is 4.181 g/cm(3). It is isotropic, 1.93(1) (white light); n(calc) = 2.034. Menezesite exhibits weak anomalous birefringence. The empirical formula is (Ba1.47K0.53Ca0.3,Ce0.17Nd0.10Na0.06La0.02)(Sigma 2.66)(Mg0.94Mn0.23Fe0.23Al0.03)(Sigma 1.43)(Zr2.75Ti0.96Th0.29)(Sigma 4.00)[(Ba0.72Th0.26U0.02)(Sigma 1.00)(Nb9.23Ti2.29Ta0.36Si0.12)Sigma O-12.00(42)]center dot 12H(2)O. The mineral is cubic, space group 10 (204), a = 13.017(1) angstrom, V = 2206(1) angstrom(3), Z = 2. Menezesite is isostructural with the synthetic compound Mg-7[MgW12O42](OH)(4)center dot 8H(2)O. The mineral was named in honor of Luiz Alberto Dias Menezes Filho (born 1950), mining engineer, mineral collector and merchant. Both the description and the name were approved by the CNMMN-IMA (Nomenclature Proposal 2005-023). Menezesite is the first natural heteropolyniobate. Heteropolyanions have been employed in a range of applications that include virus-binding inorganic drugs (including the AIDs virus), homogeneous and heterogeneous catalysts, electro-optic and electrochromic materials, metal and protein binding, and as building blocks for nanostructuring of materials.

Alkaline magmatism in the Amambay area, NE Paraguay: The Cerro Sarambi complex

The Early Cretaceous alkaline magmatism in the northeastern region of Paraguay (Amambay Province) is represented by stocks, plugs, dikes, and dike swarms emplaced into Carboniferous to Triassic-Jurassic sediments and Precambrian rocks. This magmatism is tectonically related to the Ponta Pora Arch, a NE-trending structural feature, and has the Cerro Sarambi and Cerro Chiriguelo carbonatite complexes as its most significant expressions. Other alkaline occurrences found in the area are the Cerro Guazu and the small bodies of Cerro Apua, Arroyo Gasory, Cerro Jhu, Cerro Tayay, and Cerro Teyu. The alkaline rocks comprise ultramafic-mafic, syenitic, and carbonatitic petrographic associations in addition to lithologies of variable composition and texture occurring as dikes; fenites are described in both carbonatite complexes. Alkali feldspar and clinopyroxene, ranging from diopside to aegirine, are the most abundant minerals, with feldspathoids (nepheline, analcime), biotite, and subordinate Ti-rich garnet; minor constituents are Fe-Ti oxides and cancrinite as the main alteration product from nepheline. Chemically, the Amambay silicate rocks are potassic to highly potassic and have miaskitic affinity, with the non-cumulate intrusive types concentrated mainly in the saturated to undersaturated areas in silica syenitic fields. Fine-grained rocks are also of syenitic affiliation or represent more mafic varieties. The carbonatitic rocks consist dominantly of calciocarbonatites. Variation diagrams plotting major and trace elements vs. SiO(2) concentration for the Cerro Sarambi rocks show positive correlations for Al(2)O(3), K(2)O, and Rb, and negative ones for TiO(2), MgO, Fe(2)O(3), CaO, P(2)O(5), and Sr, indicating that fractional crystallization played an important role in the formation of the complex. Incompatible elements normalized to primitive mantle display positive spikes for Rb, La, Pb, Sr, and Sm, and negative for Nb-Ta, P, and Ti, as these negative anomalies are considerably more pronounced in the carbonatites. Chondrite-normalized REE patterns point to the high concentration of these elements and to the strong LRE/HRE fractionation. The Amambay rocks are highly enriched in radiogenic Sr and have T(DM) model ages that vary from 1.6 to 1.1 Ga. suggesting a mantle source enriched in incompatible elements by metasomatic events in Paleo-Mesoproterozoic times. Data are consistent with the derivation of the Cerro Sarambi rocks from a parental magma of lamprophyric (minette) composition and suggest an origin by liquid immiscibility processes for the carbonatites. (C) 2011 Elsevier Ltd. All rights reserved.

THE CRYSTAL STRUCTURE OF A MICROLITE-GROUP MINERAL WITH A FORMULA NEAR NaCaTa(2)O(6)F FROM THE MORRO REDONDO MINE, CORONEL MURTA, MINAS GERAIS, BRAZIL

We present electron-microprobe and single-crystal X-ray-diffraction data for a microlite-group mineral with a formula near NaCaTa(2)O(6)F from the Morro Redondo mine, Coronel Murta, Minas Gerais, Brazil. On the basis of these data, the formula is A(Na(0.88)Ca(0.88)Pb(0.02)square(0.22))(Sigma 2.00) (B)(Ta(1.70)Nb(0.14)Si(0.12)As(0.04))(Sigma 2.00) (X)[(O(5.75)(OH)(0.25)](Sigma 6.00) (Y)(F(0.73)square(0.27))(Sigma 1.00). According to the new nomenclature for the pyrochlore-supergroup minerals, it is intermediate between fluornatromicrolite and "" fluorcalciomicrolite"". The crystal structure, F (d3) over barm, a = 10.4396(12) angstrom, has been refined to an R(1) value of 0.0258 (wR(2) = 0.0715) for 107 reflections (MoK alpha radiation). There is a scarcity of crystal-chemical data for pyrochlore-supergroup minerals in the literature. A compilation of these data is presented here.