Pseudo-merohedral Twinning Research Articles

Multiscale structure of LaAlO3 from single-crystal X-ray diffraction.

A domain-resolved synchrotron single-crystal X-ray diffraction study of a LaAlO3 pseudo-merohedral twin crystal was successfully carried out in combination with powder diffraction data from the same sample. Multiscale structure information ranging from micro- to nano- to atomic scale was determined from one single crystal. There is almost no change of domain ratios at temperatures of less than 400 K indicating no movement of the domain wall. The changes in domain ratio indicating domain-wall movement were observed in the temperature range of 450 to 700 K, which is consistent with the result of the previous mechanical measurement. It is also found that the ratio of four twin components becomes equal (25%), just below phase transition temperature. These findings are important for domain engineering and theoretical studies related to LaAlO3. The temperature dependence of domain ratio was preserved in the heating and cooling cycle except for the first heating process to 840 K. Therefore, the domain structure after heating to 840 K is intrinsic to the crystal. Accurate structure parameters were determined through unit-cell parameter calibration and domain-resolved structure analysis. The method for calibration of unit-cell parameters from twin crystal data was derived and used to solve the inconsistent unit-cell parameters between single crystal and powder data in the present and previous studies.

Structural basis of regioselective tryptophan dibromination by the single-component flavin-dependent halogenase AetF.

The flavin-dependent halogenase (FDH) AetF successively brominates tryptophan at C5 and C7 to generate 5,7-dibromotryptophan. In contrast to the well studied two-component tryptophan halogenases, AetF is a single-component flavoprotein monooxygenase. Here, crystal structures of AetF alone and in complex with various substrates are presented, representing the first experimental structures of a single-component FDH. Rotational pseudosymmetry and pseudomerohedral twinning complicated the phasing of one structure. AetF is structurally related to flavin-dependent monooxygenases. It contains two dinucleotide-binding domains for binding the ADP moiety with unusual sequences that deviate from the consensus sequences GXGXXG and GXGXXA. A large domain tightly binds the cofactor flavin adenine dinucleotide (FAD), while the small domain responsible for binding the nicotinamide adenine dinucleotide (NADP) is unoccupied. About half of the protein forms additional structural elements containing the tryptophan binding site. FAD and tryptophan are about 16 Å apart. A tunnel between them presumably allows diffusion of the active halogenating agent hypohalous acid from FAD to the substrate. Tryptophan and 5-bromotryptophan bind to the same site but with a different binding pose. A flip of the indole moiety identically positions C5 of tryptophan and C7 of 5-bromotryptophan next to the tunnel and to catalytic residues, providing a simple explanation for the regioselectivity of the two successive halogenations. AetF can also bind 7-bromotryptophan in the same orientation as tryptophan. This opens the way for the biocatalytic production of differentially dihalogenated tryptophan derivatives. The structural conservation of a catalytic lysine suggests a way to identify novel single-component FDHs.

Cation ordering, twinning, and pseudo-symmetry in silicate garnet: The study of a birefringent garnet with orthorhombic structure

AbstractThe crystal structure of a birefringent garnet (~Adr53Grs47) that occurs as a late-stage rim on andradite from Stanley Butte, Graham County, Arizona is analyzed and refined using single-crystal XRD. The structure has an orthorhombic I 2/a 1 2/d (unconventional setting for Fddd) space group symmetry, with unit-cell parameters of a = b = 11.966(3) Å, c = 11.964(3) Å, α = β = 90°, γ = 90.29(2)°, V = 1713.0(7) Å3, Z = 8. The orthorhombic garnet displays very high birefringence (δ ~0.021) produced by the strong Fe-Al ordering in the octahedral sites, with Fe occupancies of 0.804 and 0.221 in Y1 and Y2 sites, respectively. Diffraction peaks (such as 101 and 103) violating the Ia3d symmetry of cubic garnet are obvious even in powder XRD pattern. The homogenization temperatures of the fluid inclusions suggest that the low-crystallization temperature is responsible for the ordered orthorhombic structure. The strong ordering state of the structure and the sharp boundaries in the chemical zoning in the crystal (between ~Adr53Grs47 and ~Adr100) indicate the orthorhombic intermediate grandite garnet is a thermodynamically stable phase at low temperature, separated by wide miscibility gaps from the pure end-members (grossular and andradite) with cubic structures. Most of the previously reported triclinic garnet structures are likely artifacts produced by pseudo-merohedral twinning of less-ordered orthorhombic structure, as indicated by the characteristic pairing pattern of different Y-sites with the same occupancies.

Contributions to the stereochemistry of zirconium oxysalts\u2014part IV: syntheses and crystal structures of Zr2(OH)2(XO4)3\xb74H2O (X\u2009=\u2009S, Se), Zr(SO4)2\xb74H2O, and Zr(SeO3)2

Zr2(OH)2(XO4)3·4H2O (X = S, Se), Zr(SO4)2·4H2O, and Zr(SeO3)2 were synthesized at low-hydrothermal conditions from mixtures of Zr2O2(CO3)(OH)2, the respective acids, and minor amounts of water. While Zr2(OH)2(XO4)3·4H2O (X = S, Se) and Zr(SO4)2·4H2O form crystals up to several tenths of a mm, Zr(SeO3)2 was mainly obtained as microcrystalline powder, single crystals rarely exceeded 10 μm in size. Samples were investigated by single-crystal X-ray techniques and in the case of Zr(SeO3)2 also by X-ray powder diffraction. The compounds Zr2(OH)2(XO4)3·4H2O (X = S, Se) crystallize in the Ce2(OH)2(SO4)3·4H2O structure type (C2/c, Z = 4, a = 13.034(2) / 13.308(3), b = 6.500(1) / 6.683(2), c = 15.056(3) / 15.383(4) Å, β = 96.27(1) / 96.81(1)°, V = 1267.9(4) / 1358.5(6) Å3 for X = S / Se, respectively). Tetragonal aniprisms Zr[8]O8 are edge-connected to dimers that share corners with XO4 tetrahedra forming a three-dimensional network. Zr(SO4)2·4H2O (Fddd, Z = 8, a = 5.498(1), b = 11.618(3), c = 25.893(6) Å, V = 1653.9(6) Å3) is isotypic with the respective selenate compound. Occasionally, pseudomerohedral twinning is observed, simulating a larger monoclinic C-centered unit cell. Again, tetragonal antiprisms Zr[8]O8 are formed; however, they are corner-linked with SO4 tetrahedra to Zr(SO4)2 layers interconnected solely by hydrogen bonds. Zr(SeO3)2 crystallizes in P21/c, Z = 2; a = 4.9724(3), b = 8.5992(5), c = 6.9447(3) Å, β = 110.128(3)°, V = 278.81(3) Å3 (unit cell from powder data) and belongs to the β-Sn(SeO3)2 structure type established further for Ti(SeO3)2 and Pb(SeO3)2. Isolated ZrO6 octahedra share corners with the selenite groups forming a three-dimensional network.Graphical abstract

The structure of a pentachromium(II) extended metal atom chain at 3 K: Cotton's conjecture proven.

We provide definitive experimental proof that the archetypal string-like compound [Cr5(tpda)4(NCS)2] has alternating long and short Cr-Cr separations in the solid state, as conjectured by F. A. Cotton, rather than essentially equally spaced Cr atoms, as initially claimed (H2tpda = N2,N6-di(pyridin-2-yl)pyridine-2,6-diamine). Single-crystal X-ray data collected from 292 to 3 K revealed that the misinterpretation is caused by pseudo-merohedral twinning and that bond length alternation is enhanced at low temperature.

Structure of the E. coli agmatinase, SPEB.

Agmatine amidinohydrolase, or agmatinase, catalyzes the conversion of agmatine to putrescine and urea. This enzyme is found broadly across kingdoms of life and plays a critical role in polyamine biosynthesis and the regulation of agmatine concentrations. Here we describe the high-resolution X-ray crystal structure of the E. coli agmatinase, SPEB. The data showed a relatively high degree of pseudomerohedral twinning, was ultimately indexed in the P31 space group and led to a final model with eighteen chains, corresponding to three full hexamers in the asymmetric unit. There was a solvent content of 38.5% and refined R/Rfree values of 0.166/0.216. The protein has the conserved fold characteristic of the agmatine ureohydrolase family and displayed a high degree of structural similarity among individual protomers. Two distinct peaks of electron density were observed in the active site of most of the eighteen chains of SPEB. As the activity of this protein is known to be dependent upon manganese and the fold is similar to other dinuclear metallohydrolases, these peaks were modeled as manganese ions. The orientation of the conserved active site residues, in particular those amino acids that participate in binding the metal ions and a pair of acidic residues (D153 and E274 in SPEB) that play a role in catalysis, are similar to other agmatinase and arginase enzymes and is consistent with a hydrolytic mechanism that proceeds via a metal-activated hydroxide ion.

Polymorphs of VO(PO3)2: synthesis and crystal structure refinement revisited

Abstract The monoclinic α-polymorph of (VIVO)(PO3)2 is obtained reproducibly by reaction of V2O5 and H3PO4 (85%) (Au crucible, 380 °C, 4 d). Its crystal structure was refined from X-ray single-crystal data [C2/c, Z = 4, a = 15.1038(7) Å, b = 4.193(2) Å, c = 9.573(9) Å, β = 126.45(3), R 1 = 0.052, wR 2 = 0.189 for 976 unique reflections with F o > 4σ(F o ), 48 variables]. A single-phase powder of the β-polymorph is obtained by the reaction of V2O5, H3PO4 (85%) and oxalic acid, evaporating the mixture, and subsequent annealing (porcelain crucible, 800 °C in air, 2 d). Single crystals of β-(VIVO)(PO3)2 were grown in a sealed silica ampoule with chlorine as mineralizer. The crystal structure of the orthorhombic (pseudo-tetragonal) β-polymorph was refined from X-ray single-crystal data [pseudo-merohedral twin, Fdd2, Z = 8, a = 15.536(2) Å, b = 15.586(2) Å, c = 4.2611(5) Å, R 1 = 0.032, wR 2 = 0.068 for 1072 unique reflections with F o > 4σ(F o ), 50 variables]. Earlier reports on a tetragonal polymorph with unusual geometric structure of the [(V≡O)O5] polyhedron are corrected.

Halobismuth(III) salts with substituted aminopyridinium cations.

The crystal structures of six halobismuth(III) salts of variously substituted aminopyridinium cations display discrete mononuclear [BiCl6]3- and dinuclear [Bi2X10]4- anions (X = Cl or Br), and polymeric cis-double-halo-bridged [BinX4n]n- anionic chains (X = Br or I). Bis(2-amino-3-ammoniopyridinium) hexachloridobismuth(III) chloride monohydrate, (C5H9N3)2[BiCl6]Cl·H2O, (1), contains discrete mononuclear [BiCl6]3- and chloride anions. Tetrakis(2-amino-3-methylpyridinium) di-μ-chlorido-bis[tetrachloridobismuth(III)], (C6H9N2)4[Bi2Cl10], (2), tetrakis(2-amino-3-methylpyridinium) di-μ-bromido-bis[tetrabromidobismuth(III)], (C6H9N2)4[Bi2Br10], (3), and bis(4-amino-3-ammoniopyridinium) di-μ-chlorido-bis[tetrachloridobismuth(III)] dihydrate, (C5H9N3)2[Bi2Cl10]·2H2O, (4), incorporate discrete [Bi2X10]4- anions (X = Cl or Br), while catena-poly[2,6-diaminopyridinium [[cis-diiodidobismuth(III)]-di-μ-iodido]], {(C5H8N3)[BiI4]}n, (5), and catena-poly[2,6-diaminopyridinium [[cis-dibromidobismuth(III)]-di-μ-bromido]], {(C5H7N2)[BiBr4]}n, (6), include [BinX4n]n- anionic chains (X = Br or I). Structures (2) and (3) are isostructural, while that of (5) is a pseudomerohedral twin. There is no discernible correlation between the type of anionic species obtained and the cation or halide ligand used. The BiIII centres always have a slightly distorted octahedral geometry and there is a correlation between the Bi-X bond lengths and the number of classic N-H...X hydrogen bonds that the X ligand accepts, with a greater number of interactions corresponding with slightly longer Bi-X distances. The supramolecular networks formed by classic N-H...X hydrogen bonds include ladders, bilayers and three-dimensional frameworks.

Phase transition and structures of the twinned low-temperature phases of (Et4N)[ReS4

The title compound, tetraethylammonium tetrathiorhenate, [(C2H5)4N][ReS4], has, at room temperature, a disordered structure in the space group P63mc (Z= 2, α-phase). A phase transition to the monoclinic space group P21 (Z= 2, γ-phase) at 285 K leads to a pseudo-merohedral twin. The high deviation from the hexagonal metric causes split reflections. However, the different orientations could not be separated, but were integrated using a large integration box. Rapid cooling to 110-170 K produces a metastable β-phase (P63, Z= 18) in addition to the γ-phase. All crystals of the β-phase are contaminated with the γ-phase. Additionally, the crystals of the β-phase are merohedrally twinned. In contrast to the α-phase, the β- and γ-phases do not show disorder.

Bis{4-[(2-hy-droxy-5-meth-oxy-3-nitro-benzyl-idene)amino]-phen-yl} ether.

The mol-ecule of the title compound, C28H22N4O9, exhibits crystallographically imposed twofold rotational symmetry, with a dihedral angle of 66.0 (2)° between the planes of the two central benzene rings bounded to the central oxygen atom. The dihedral angle between the planes of the central benzene ring and the terminal phenol ring is 4.9 (2)°. Each half of the mol-ecule exhibits an imine E configuration. An intra-molecular O-H⋯N hydrogen bond is present. In the crystal, the mol-ecules are linked into layers parallel to the ab plane via C-H⋯O hydrogen bonds. The crystal studied was refined as a two-component pseudomerohedral twin.

A commensurately modulated crystal structure and the physical properties of a novel polymorph of the caesium manganese phosphate CsMnPO4.

A novel modification of the CsMnPO4 β-phase was achieved by hydrothermal synthesis at 553 K. The compound crystallizes in the monoclinic system with the basic unit-cell parameters a = 11.0699 (4), b = 11.0819 (6), c = 9.1106 (3) Å, γ = 119.480 (5)o; the modulation vectors are q1 = 0.4a* and q2 = 0.4b*. The structure was determined based on single-crystal X-ray diffraction data obtained from a pseudo-merohedral twin using a superspace approach in the (3 + 2)D symmetry group P11a(a1,b1,0)0(a2,b2,0)0 and refined to R = 0.083 for 10 266 reflections with I > 3σ(I). It is considered as a low-temperature polymorph of CsMnPO4 with the same UUUDDD-type layer topology built by MnO4 and PO4 tetrahedra, and stacked in a framework in the same manner as β-tridymite. Large open channels parallel to the [110] and [001] directions incorporate Cs atoms. All Cs atoms are distributed along the asuper = 55.35 (1) and bsuper = 55.41 (1) axes of the large unit cell with pseudo periods of asuper/5 and bsuper/5 which are broken mainly by the positions of oxygen atoms (orientation of Mn- and P-centered tetrahedra). The β-phase is discussed as a member of the morphotropic series of manganese phosphates with large cations of AMnPO4, where A = Cs, Rb, K and Ag. The title compound is an antiferromagnet with the Neel temperature TN = 4.5 K.

Twinned α p-Aminobenzoic Acid at 106 K

The α crystalline form of p-aminobenzoic acid is monoclinic and prone to twinning by pseudo-merohedry (a ≈ c). A structure was reported by Lai and Marsh (1967) on an almost untwinned specimen where (a-c)/σ is 36. In revisiting this structure, a sample showing twinning was obtained from the metabolites of a Streptomyces strain collected from the soil at the ancient Roman city of Pollentia on the Balearic island of Mallorca. A 106(2) K determination shows pseudo-merohedral twinning, with a = 18.5452(6), b = 3.73406(15), c = 18.5484(7) A, β = 93.790(3)°, V = 1281.65(8) A3, and (a−c)/σ 5. The refinement included twin contributions [major domain 0.7435(15)] and produced a higher resolution structure determination. The cell contains two neutral molecules per asymmetric unit. Both form complementary carboxylic acid dimers across inversions centers of P21/n. Nitrogens are pyramidal and donate Hydrogen-bonds through one amine hydrogen; a stronger two-center N–H⋯O in one case, and a weaker three-center N–H⋯(O, O’) in the other. The molecular structure shows a pronounced quinoid distortion, and a comparison is drawn with the previous studies, an ordered β monoclinic phase, and with other structural studies. The α monoclinic phase of p-aminobenzoic acid crystallizes commonly as pseudo-merohedral twins, and a specimen studied at 106 K had a ≈ c within 5 esd’s, allowing an improved refinement and a more accurate molecular model.

Crystal structures of the [IrIII{C(C4H6O2)(dppm)-κ3 P,C,O}(dppm)H](CF3O3S)2 and [IrIII{C(C4H6O2)(dppm)-κ2 P,C}(CO)(dppm)H](CF3O3S)2 phosphorus ylide complexes, generated by a Wittig-type carbon-carbon coupling reaction of a carbodiphospho-rane PCP ligand system.

The reaction of [IrIII{C(dppm)2-κ3 P,C,P'}ClH(NH3C2)]Cl with ethyl diazo-acetate, a well known C=C coupling reagent, leads to the formation of a C=C unit, accompanied by N2 abstraction, reorganization of a dppm subunit and, considered as a whole, to the transformation of the PCP pincer carbodi-phospho-rane system to a phospho-rus ylide ligand. After removal of the halogenides, the iridium center is stabilized by the carbonyl O atom through the formation of a five-membered chelate ring. A PCO pincer ligand system is thereby generated, which coordinates the iridium(III) atom threefold in a facial manner. The phospho-rus electron-donor atoms and the ylide carbon atom of the resulting [IrIII{C(C4H6O2)(dppm)-κ3 P,C,O}(dppm)H](CF3O3S)2 complex, also termed as [bis-(di-phenyl-phosphan-yl)methane]({[(di-phenyl-phosphan-yl)meth-yl]di-phenyl-phosphanyl-idene}(eth-oxy-oxoethanyl-idene)methanyl-idene-κ3 P,C,O)hydridoiridium(III) bis-(tri-fluoro-methane-sulfonate), are in plane and the hydrido ligand and the carbonyl O atom are located trans to each other, perpendicular to the meridional plane. The addition of carbon monoxide causes a replacement of the carbonyl O atom of the acetate subunit by a carbonyl ligand, thereby creating [bis-(di-phenyl-phosphan-yl)methane]-carbon-yl({[(di-phenyl-phosphan-yl)meth-yl]di-phenyl-phosphanyl-idene}(eth-oxy-oxoethanyl-idene)methanyl-idene-κ2 P,C}hydridoiridium(III) bis-(tri-fluoro-methane-sulfonate)-di-chloro-methane-ethyl acetate (6/2/3) or, more simply, [IrIII{C(C4H6O2)(dppm)-κ2 P,C}(CO)(dppm)H](CF3O3S)2·0.33CH2Cl2·0.5C4H8O2. One tri-fluoro-meth-ane-sulfonate counter-ion of 3 shows positional disorder in a 2:1 ratio. Complex 4 shows pseudo-merohedral twinning (matrix: 0 0 0 0 1 0 1). The di-chloro-methane solvent is disordered over two orientations with occupation factors of 0.5 and 0.166.

Crystal structures of methyl 3,5-di-bromo-4-cyano-benzoate and methyl 3,5-di-bromo-4-iso-cyano-benzoate.

The title crystals, C9H5Br2NO2, are the first reported 2,6-dihalophenyl cyanide-isocyanide pair that have neither three- nor two-dimensional isomorphism. Both crystals contain contacts between the carbonyl O atom and a Br atom. In the crystal of the cyanide, R22(10) inversion dimers form based on C≡N⋯Br contacts, a common packing feature in this series of crystals. In the isocyanide, the corresponding N≡C⋯Br contacts are not observed. Instead, the iso-cyano C atom forms contacts with the meth-oxy C atom. RNC was refined as a two-component pseudo-merohedral twin.

Crystal structures and supra-molecular features of 9,9-dimethyl-3,7-di-aza-bicyclo-[3.3.1]nonane-2,4,6,8-tetra-one, 3,7-di-aza-spiro-[bi-cyclo-[3.3.1]nonane-9,1'-cyclo-penta-ne]-2,4,6,8-tetra-one and 9-methyl-9-phenyl-3,7-di-aza-bicyclo-[3.3.1]nonane-2,4,6,8-tetra-one di-methyl-formamide monosolvate.

Compounds (I), C9H10N2O4, (II), C11H12N2O4, and (III), C14H12N2O4·C3H7NO represent 9,9-disubstituted-3,7-di-aza-bicyclo-[3.3.1]nonane-2,4,6,8-tetra-one deriv-atives with very similar mol-ecular geometries for the bicyclic framework: the dihedral angle between the planes of the imide groups is 74.87 (6), 73.86 (3) and 74.83 (6)° in (I)-(III), respectively. The dimethyl derivative (I) is positioned on a crystallographic twofold axis and its overall geometry deviates only slightly from idealized C2v symmetry. The spiro-cyclo-pentane derivative (II) and the phen-yl/methyl analog (III) retain only inter-nal Cs symmetry, which in the case of (II) coincides with crystallographic mirror symmetry. The cyclo-pentane moiety in (II) adopts an envelope conformation, with the spiro C atom deviating from the mean plane of the rest of the ring by 0.548 (2) Å. In compound (III), an N-H⋯O hydrogen bond is formed with the di-methyl-formamide solvent mol-ecule. In the crystal, both (I) and (II) form similar zigzag hydrogen-bonded ribbons through double inter-molecular N-H⋯O hydrogen bonds. However, whereas in (I) the ribbons are formed by two trans-arranged O=C-N-H amide fragments, the amide fragments are cis-positioned in (II). The formation of ribbons in (III) is apparently disrupted by participation of one of its N-H groups in hydrogen bonding with the solvent mol-ecule. As a result, the mol-ecules of (III) form zigzag chains rather than the ribbons through inter-molecular N-H⋯O hydrogen bonds. The crystal of (I) was a pseudo-merohedral twin.

A V16-type Polyoxovanadate Structure with Intricate Electronic Distribution: Insights from Magnetochemistry

The black-green solid (NEt4)5[V16O38(Br)]·2H2O (1) was synthesized by the pH-controlled reaction of a mixed-valence precursor (NH4)8[H9VIV12VV7O50]·11H2O with Et4NBr in water under aerobic conditions. Compound 1 crystallizes as pseudomerohedral three-domain twins with pronounced pseudosymmetry and very large voids accommodating the majority of the countercations and solvent water molecules. The central structural motif of 1 is represented by a spherical, mixed-valence, host–guest vanadium-oxo cluster [VIV/V16O38(Br)]q with q = 5–, 4–, or 6–, exhibiting dominant antiferromagnetic and weaker ferromagnetic exchange interactions. The intriguing valence-state and dependent magnetic behavior of this compound have been unraveled by weighted model Hamiltonian calculations combined with diffraction, quantum mechanical, spectroscopic, and spectrometric techniques. It appears that 1 features a hitherto not identified and initially not evident VIV/VV average ratio of 8:8 which corresponds to an average charge q = 5– ...

Crystal structure, Raman spectroscopy and crystal chemistry of K7Ca9[Si2O7]4F, a new potassium-calcium silicate-fluoride

In the course of a series of KF-flux synthesis experiments aiming at the preparation of new compounds in the ternary system K 2 O–CaO–SiO 2 , of interest to e.g . the glass and fertiliser industries and to recycling of ashes of biomass combustion, a novel potassium-calcium silicate-fluoride was obtained whose composition was determined as K 7 Ca 9 [Si 2 O 7 ] 4 F using electron-microprobe analysis. Polycrystalline material of the same compound could be also prepared by solid-state reactions. Applying direct methods it was possible to solve the crystal structure of this compound from single-crystal diffraction data. Structure solution was complicated due to complex pseudo-merohedral twinning. K 7 Ca 9 [Si 2 O 7 ] 4 F crystallises in the monoclinic space group P 2 1 / m , with a = 5.6122(2) A, b = 13.8143(5) A, c = 9.8016(4) A, β = 90.255(4)°, V = 759.90(5) A 3 , Z = 1. Additional characterisation has been performed by Raman spectroscopy. The compound belongs to the group of sorosilicates and is built up from Si 2 O 7 groups. Potassium and calcium cations are distributed among five crystallographically independent cation positions, which are coordinated in form of distorted octahedra, trigonal prisms or more irregular polyhedra. By sharing common faces, octahedra and trigonal prisms form infinite columns running parallel to [010]. These columns are connected to the Si 2 O 7 groups through common corners. Additional fluorine positions are located in voids between the Si 2 O 7 groups and the columns. A detailed comparison with structurally related compounds is given, including a group-theoretical discussion of the symmetry relationships.

Monoclinic-to-orthorhombic phase transition of the hexamethylenetetramine-2-methylbenzoic acid (1/2) cocrystal with temperature-dependent dynamic molecular disorder.

As a function of temperature, the hexamethylenetetramine-2-methylbenzoic acid (1/2) cocrystal, C6H12N4·2C8H8O2, undergoes a reversible structural phase transition. The orthorhombic high-temperature phase in the space group Pccn has been studied in the temperature range between 165 and 300 K. At 164 K, a t2 phase transition to the monoclinic subgroup P21/c space group occurs; the resulting twinned low-temperature phase was investigated in the temperature range between 164 and 100 K. The domains in the pseudomerohedral twin are related by a twofold rotation corresponding to the matrix (100/0-10/00-1. Systematic absence violations represent a sensitive criterium for the decision about the correct space-group assignment at each temperature. The fractional volume contributions of the minor twin domain in the low-temperature phase increases in the order 0.259 (2) → 0.318 (2) → 0.336 (2) → 0.341 (3) as the temperature increases in the order 150 → 160 → 163 → 164 K. The transformation occurs between the nonpolar point group mmm and the nonpolar point group 2/m, and corresponds to a ferroelastic transition or to a t2 structural phase transition. The asymmetric unit of the low-temperature phase consists of two hexamethylenetetramine molecules and four molecules of 2-methylbenzoic acid; it is smaller by a factor of 2 in the high-temperature phase and contains two half molecules of hexamethylenetetramine, which sit across twofold axes, and two molecules of the organic acid. In both phases, the hexamethylenetetramine residue and two benzoic acid molecules form a three-molecule aggregate; the low-temperature phase contains two of these aggregates in general positions, whereas they are situated on a crystallographic twofold axis in the high-temperature phase. In both phases, one of these three-molecule aggregates is disordered. For this disordered unit, the ratio between the major and minor conformer increases upon cooling from 0.567 (7):0.433 (7) at 170 K via 0.674 (6):0.326 (6) and 0.808 (5):0.192 (5) at 160 K to 0.803 (6):0.197 (6) and 0.900 (4):0.100 (4) at 150 K, indicating temperature-dependent dynamic molecular disorder. Even upon further cooling to 100 K, the disorder is retained in principle, albeit with very low site occupancies for the minor conformer.

Synthesis and crystal structure of [2,7,12-trimethyl-3,7,11,17-tetra-aza-bicyclo-[11.3.1]hepta-deca-1(17),13,15-triene-κ(4) N]copper(II) bis-(perchlorate).

The title copper(II) complex of a pyridine-containing macrocycle (PyMAC), [Cu(C16H28N4)](ClO4)2, has been prepared. The crystal structure reveals the Cu(II) atom to be octahedrally coordinated by a tetradentate aminopyridine macrocyclic ligand surrounding the metal cation in a square-planar geometry. Two weakly bound perchlorate counter-ions occupy the axial sites above and below the macrocyclic plane. The crystal studied was refined as a two-component pseudo-merohedral twin; the refined fractional contribution of the minor component is 38.77 (8).

Grappling with anisotropic data, pseudo-merohedral twinning and pseudo-translational noncrystallographic symmetry: a case study involving pyruvate kinase.

Pyruvate kinase is a key regulatory enzyme involved in the glycolytic pathway. The crystal structure of Escherichia coli type I pyruvate kinase was first solved in 1995 at 2.5 Å resolution. However, the space group was ambiguous, being either primitive orthorhombic (P2(1)2(1)2(1)) or C-centred orthorhombic (C222(1)). Here, the structure determination and refinement of E. coli type I pyruvate kinase to 2.28 Å resolution are presented. Using the same crystallization conditions as reported previously, the enzyme was found to crystallize in space group P2(1). Determination of the space group was complicated owing to anisotropic data, pseudo-translational noncrystallographic symmetry and the pseudo-merohedrally twinned nature of the crystal, which was found to have very close to 50% twinning, leading to apparent orthorhombic symmetry and absences that were not inconsistent with P2(1)2(1)2(1). The unit cell contained two tetramers in the asymmetric unit (3720 residues) and, when compared with the orthorhombic structure, virtually all of the residues could be easily modelled into the density. Averaging of reflections into the lower symmetry space group with twinning provided tidier electron density that allowed ∼30 missing residues of the lid domain to be modelled for the first time. Moreover, residues in a flexible loop could be modelled and sulfate molecules are found in the allosteric binding domain, identifying the pocket that binds the allosteric activator fructose 1,6-bisphosphate in this isozyme for the first time. Lastly, we note the pedagogical benefits of difficult structures to emerging crystallographers.