Insights into the Crystal Chemistry of the Serandite–Schizolite–Pectolite Series

ABSTRACT The compositional series {Na} [[M1+M2](Ca2XMn2–2X)Si3O8(OH)] includes the minerals serandite (X = 0), schizolite (X = 0.5), and pectolite (X = 1). Six crystals are structurally and chemically characterized in detail (four from Ilímaussaq, Greenland; two from Mont Saint-Hilaire, Québec, Canada): one serandite, one pectolite, and four schizolite crystals. Those originating from Greenland show up to 0.05 apfu LREE3+ (La + Ce + Pr + Nd + Eu + Gd). For each, all H atoms were located, and final R1 factors were below 4.4% (<R1> = 2.35%). The results are compared with previously published crystal structure data from an additional 16 samples, originating from worldwide (mostly) igneous environments. Across the series, for all investigated samples, Ca and Mn order preferentially at the octahedral M1 and M2 sites, respectively, following the exchange M2Ca + M1Mn ↔ M1Ca + M2Mn. Site-occupancies closely adhere to a two-site distribution coefficient, calculated here to be K = 20.0(5), for ideal mixing where activity coefficients approach unity. For the above order-disorder exchange, ΔHex is calculated to be –1.77 kcal. With knowledge of K, site assignment and species determination may be accurately made solely with compositional data, where 0 ≤ ΣCa < 0.55 apfu, serandite; 0.55 ≤ ΣCa < 1.45 apfu, schizolite; and 1.45 ≤ ΣCa ≤ 2 apfu, pectolite, with the dominant-constituent rule mandating M1Ca < M1Mn (M2Ca < M2Mn), serandite; M1Ca > M1Mn (M2Ca < M2Mn), schizolite; and M1Ca > M1Mn (M2Ca > M2Mn), pectolite. Polyhedral distortion and structural strain at the M1 and M2 sites, calculated using the equations of Robinson et al. (1971) and solutions to Kirchhoff network equations, respectively, show a predictable, cooperative variation across the entire compositional series; however, prominent discontinuities in distortion and strain behavior are observed for the schizolite composition.

Molecular structure from models to mastery - a study of human insulin-degrading enzyme in the undergraduate biochemistry laboratory

Using crystal structure data, site directed mutagenesis, and real-time kinetic assays, students designed, expressed, and purified engineered mutants of human insulin-degrading enzyme (IDE) to explore structural requirements for enzyme function. Students demonstrated mastery of critical concepts in enzymology including principles of experimental design, implications of enzyme structure-function relationships for molecular evolution, experimental methods for analysis of macromolecular interactions, and computational approaches to scientific inquiry. This investigation was conducted as part of the second-semester undergraduate biochemistry laboratory at Sacred Heart University

Synthesis and Characterization of Nickel(II) Complexes of Nitrogen based Ligands of Type N,N,N′,N′-tetrakis(2-Pyridylmethyl)alkanediamine

Hexadentate ligand of the type N,N,N′,N′-tetrakis(2-pyridylmethyl)alkanediamine (where alkane is butane (L1), hexane (L2) and octane (L3) reacted with Ni(ClO4)2·6H2O (stoichiometry 1:1) in alcoholic solutions yielding mononuclear complexes of the type [Ni(L)](ClO4)2·xH2O. The ligand L1 reacted with Ni(ClO4)2·6H2O in ethanol medium to give a violet powder of [Ni(L1)](ClO4)2·3H2O. The other mononuclear nickel(II) complexes using L2 and L3 were synthesized in methanol solution to give violet powders of [Ni(L2)](ClO4)2·2H2O and [Ni(L3)](ClO4)2·2H2O, respectively. All the three complexes were characterized by IR and elemental analysis. The X-ray crystallographic results for the purple crystals of [Ni(L1)](ClO4)2·3H2O shows the octahedral geometry on the Ni(II) ions together with the tetrahedral perchlorate anions separated from the [Ni(L1)]2+ cation. The crystal structure data show monoclinic space group P 21/c; a = 17.1748(10), b = 9.8273(6), c = 17.8146(10) Å; α = 90º, β = 95.0200(10)º, γ = 90º; V = 2995.2(3) Å3 , Z = 4.

Hydroflux syntheses and crystal structures of hydrogarnets Ba3[RE(OH)6]2 (RE = Sc, Y, Ho–Lu)

Colorless crystals of the barium rare earth hydrogarnets Ba3[RE(OH)6]2 (RE = Sc, Y, Ho–Lu) were synthesized under hydroflux conditions with KOH at about T = 200 °C starting from the respective RE2O3 and Ba (NO3)2. Single-crystal X-ray diffraction analysis on these distorted rhombic dodecahedra revealed the cubic space group Ia$‾{3}$d (no. 230). The crystal structures of the hydrogarnets Ba3[RE(OH)6]2 are discussed and compared with those of other hydrogarnets. The occurrence of additional reflections, which do not fulfill the reflection conditions of Ia$‾{3}$d, is analyzed and described by Renninger or λ/2 effects. A correlation is established between the space group adopted by a hydrogarnet and characteristic interatomic distances. In addition, single-crystal structure data of the strontium indium hydrogarnet Sr3[In(OH)6]2 are provided.

Mechanism of NanR gene repression and allosteric induction of bacterial sialic acid metabolism

Bacteria respond to environmental changes by inducing transcription of some genes and repressing others. Sialic acids, which coat human cell surfaces, are a nutrient source for pathogenic and commensal bacteria. The Escherichia coli GntR-type transcriptional repressor, NanR, regulates sialic acid metabolism, but the mechanism is unclear. Here, we demonstrate that three NanR dimers bind a (GGTATA)3-repeat operator cooperatively and with high affinity. Truncation of an N-terminal extension abolishes cooperative binding. The effector, N-acetylneuraminate, binds NanR and attenuates DNA binding. Crystal structure data show that N-acetylneuraminate binding to NanR causes a domain rearrangement that locks the protein in a conformation that prevents DNA binding. Single-particle cryo-electron microscopy structures of NanR bound to DNA reveal the DNA binding domain is reorganized to engage DNA, while the three dimers assemble in close proximity across the (GGTATA)3-repeat operator allowing protein-protein interactions to form via the N-terminal extensions. Our data provides a molecular basis for the regulation of bacterial sialic acid metabolism.

Same or different – that is the question: identification of crystal forms from crystal structure data

An analysis of the CSD with structural comparison tools shows that differentiating between polymorphism and redeterminations is not always straight forward and requires of complementary tools at the hands of an expert practitioner.