Pseudo-merohedral Twinning Research Articles

(2E)-3-(6-Methoxynaphthalen-2-yl)-1-[4-(methylsulfanyl)phenyl]prop-2-en-1-one

The asymmetric unit of the title compound, C21H18O2S, consists of two crystallographically independent mol­ecules (A and B). The mol­ecules exist in a trans conformation with respect to the central C=C bond. The naphthalene ring system makes dihedral angles of 51.62 (12) (mol­ecule A) and 52.69 (12)° (mol­ecule B) with the benzene ring. In mol­ecule A, the prop-2-en-1-one group forms dihedral angles of 22.84 (15) and 29.02 (12)° with the adjacent naphthalene ring system and benzene ring, respectively, whereas the corresponding angles are 30.04 (12) and 23.33 (12)° in mol­ecule B. In the crystal, mol­ecules are linked by inter­molecular C—H⋯O hydrogen bonds into head-to-tail chains along the a axis. The crystal packing also features C—H⋯π inter­actions. The crystal studied was a pseudo-merohedral twin with twin law (100 0-10 00-1) and a refined component ratio of 0.6103 (16):0.3897 (16).

Dichloridobis(pyridine-2-thiolato-κ2N,S)tin(IV): a new polymorph

The title compound, [SnCl2(C5H4NS)2], is the product of reaction of 2,2′-dipyridyl disulfide with tin tetra­chloride. The SnIV atom adopts a distorted octa­hedral geometry, with the two bidentate pyridine-2-thiol­ate ligands forming two planar four-membered chelate rings. The two Sn—Cl, two Sn—N and two Sn—S bonds are in cis, cis and trans configurations, respectively. The crystal grown from acetonitrile represents a new monoclinic polymorph in space group C2/c with the mol­ecule having twofold rotational symmetry, the SnIV atom lying on the twofold axis. The mol­ecular structure of the monoclinic polymorph is very close to that of the triclinic polymorph studied previously in space group P-1, the mol­ecule occupying a general position [Masaki & Matsunami (1976 ▶). Bull. Chem. Soc. Jpn, 49, 3274–3279; Masaki et al. (1978 ▶). Bull. Chem. Soc. Jpn, 51, 3298–3301]. Apparently, the formation of the two polymorphs is determined by the different systems of inter­molecular inter­actions. In the crystal of the monoclinic polymorph, mol­ecules are bound into ribbons along the c axis by C—H⋯Cl hydrogen bonds, whereas in the crystal of the triclinic polymorph, mol­ecules form chains along the a axis by attractive S⋯S inter­actions. The crystal studied was a pseudo-merohedral twin; the refined BASF value is 0.221 (1).

1-(5-Bromo-4-phenyl-1,3-thiazol-2-yl)pyrrolidin-2-one

The asymmetric unit of the title compound, C13H11BrN2OS, consists of two crystallographically independent mol­ecules (A and B). In each mol­ecule, the pyrrolidine ring adopts an envelope conformation with a methyl­ene C atom as the flap atom. In mol­ecule A, the central thia­zole ring makes a dihedral angle of 36.69 (11)° with the adjacent phenyl ring, whereas the corresponding angle is 36.85 (12)° in mol­ecule B. The pyrrolidine ring is slightly twisted from the thia­zole ring, with C—N—C—N torsion angles of 4.8 (3) and 3.0 (4)° in mol­ecules A and B, respectively. In the crystal, C—H⋯π and π–π [centroid-to-centroid distance = 3.7539 (14) Å] inter­actions are observed. The crystal studied was a pseudo-merohedral twin with twin law (-100 0-10 101) and a refined component ratio of 0.7188 (5):0.2812 (5).

From structure topology to chemical composition. XII. Titanium silicates: the crystal chemistry of rinkite, Na2Ca4REETi(Si2O7)2OF3

AbstractRinkite, ideallyNa2Ca4REETi(Si2O7)2OF3, is a common mineral in alkaline and peralkaline rocks. The crystal structures of five rinkite crystals from three alkaline massifs: Ilimaussaq, Greenland; Khibiny, Kola Peninsula, Russia and Mont Saint-Hilaire, Canada, have been refined as two components related by the TWIN matrix (–1 0 0, 0 –1 0, 1 0 1)(Mo-αaradiation). The crystals,a =7.4132-7.4414,b =5.6595-5.6816,c =18.8181-18.9431 Å, β = 101.353-101.424(2)°,V=776.1-786.7 Å3, space groupP21lc, Z =2,Dcalc= 3.376—3.502 g cm–3, were analysed using an electron microprobe subsequent to collection of the X-ray intensity data. Transmission electron microscopy confirmed the presence of pseudomerohedral twinning in rinkite crystals. The crystal structure of rinkite is a framework of TS (titanium silicate) blocks. The TS block consists of HOH sheets (H-heteropolyhedral, O-octahedral). The TS block in rinkite exhibits linkage and stereochemistry typical for Group I (Ti = 1 a.p.f.u.) of Ti disilicate minerals: two H sheets connect to the O sheet such that two (Si2O7) groups link to thetransedges of a Na polyhedron of the O sheet. The crystal chemistry of rinkite and nacareniobsite-(Ce) is discussed.

The Solid‐State Structures of Dimethylzinc and Diethylzinc

The synthesis of dimethylzinc (Me2Zn) and diethylzinc (Et2Zn) by Frankland in the mid-nineteenth century marks a cornerstone in the history of chemistry.1 Not only were they among the first organometallic compounds, but studies on their chemical reactions and vapor densities led to the first clear exposition of valency theory.2 Since then both compounds have found widespread applications: They are important reagents in organic synthesis,3 for example in the enantioselective alkylation of carbonyls4 and imines5 and in cyclopropanation reactions.6 Their high vapor pressures have led to extensive uses in metalorganic chemical vapor deposition (MOCVD) for the preparation of wide band gap II–VI semiconducting films (e.g. ZnS, ZnSe, ZnTe),7 ZnO nanostructures, and as p-dopant precursors for III–V semiconductors (e.g. GaAs, InP, AlxGa1−xAs), which have numerous electronic and photonic applications.8

Synthesis and characterization of Cu(II) complexes of pyrazine-2,3-dicarboxylicacid

Four copper(II) coordination polymers, {[Cu(pz(COO) 2)(H 2O)] 4·HBr} n ( 1), {[Cu(pz(COO) 2)(NH 3) 2]·H 2O} n ( 2), {[Cu 3H 2(pz(COO) 2) 4(H 2O) 3]·2H 2O} n ( 3) and {[Cu 2(pz(COO) 2) 2(NH 3) 2(H 2O) 3][Cu(pz(COO) 2)(NH 3)(H 2O) 2][Cu(pz(COO) 2)(NH 3)(H 2O)]·2H 2O} n ( 4) were synthesized using pyrazine-2,3-dicarboxylic acid, CuBr 2, 2-(2-aminoethylamino)ethanol/triethanol amine/ammonia in a methanol:water (1:1) solution, and the mixed ligand complexes were characterized by spectroscopic methods, thermal and elemental analysis, and magnetic susceptibility. Complexes 2 and 4 were also characterized by means of single crystal X-ray crystallography. The characterizations show that the complexes have polynuclear molecular structures, except for complex 2, and all of the complex structures form polymeric chains. Complex 4 has a pseudo-merohedral twin structure.

Statistically disordered short hydrogen bonds in (pipzH2)(cdoH)2and a comparison with (pipzH2)(cdo)·H2O (pipz is piperazine and cdoH2is chelidonic acid)

Two related proton-transfer compounds, namely piperazine-1,4-diium 4-oxo-4H-pyran-2,6-dicarboxylate monohydrate, C(4)H(12)N(2)(2+)·C(7)H(2)O(6)(2-)·H(2)O or (pipzH(2))(cdo)·H(2)O, (I), and piperazine-1,4-diium bis(6-carboxy-4-oxo-4H-pyran-2-carboxylate), C(4)H(12)N(2)(2+)·2C(7)H(3)O(6)(-) or (pipzH(2))(cdoH)(2), (II), were obtained by the reaction of 4-oxo-4H-pyran-2,6-dicarboxylic acid (chelidonic acid, cdoH(2)) and piperazine (pipz). In (I), both carboxyl H atoms of chelidonic acid have been transferred to piperazine to form the piperazine-1,4-diium ion. The structure is a monohydrate. All potential N-H donors are involved in N-H···O hydrogen bonds. The water molecule spans two anions via the 4-oxo group of the pyranose ring and a carboxylate O atom. The hydrogen-bonding motif is essentially two-dimensional. The structure is a pseudomerohedral twin. In the asymmetric unit of (II), the anion consists of monodeprotonated chelidonic acid, while the piperazine-1,4-diium cation is located on an inversion centre. The single carboxyl H atom is disordered in two respects. Firstly, the disordered H atom is shared equally by both carboxylic acid groups. Secondly, the H atom is statistically disordered between two positions on either side of a centre of symmetry and is engaged in a very short hydrogen-bonding interaction; the relevant O···O distances are 2.4549 (11) and 2.4395 (11) Å, and the O-H···O angles are 177 (6) and 177 (5)°, respectively. Further hydrogen bonding of the type N-H···O places the (pipzH(2))(2+) cations in pockets formed by the chains of (cdoH)(-) anions. In contrast with (I), the (pipzH(2))(2+) cations form hydrogen-bonding arrays that are perpendicular to the anions, yielding a three-dimensional hydrogen-bonding motif. The structures of both (I) and (II) also feature π-π stacking interactions between aromatic rings.

2-(4-Chlorophenyl)-4-[1-(4-chlorophenyl)-3-methyl-1H-pyrazol-5-yl]-5-methyl-1H-pyrazol-3(2H)-one

The title compound, C20H16Cl2N4O, has two mol­ecules in the asymmetric unit. The two five-membered rings form a dihedral angle of 54.2 (3)° in one mol­ecule and 56.8 (3)° in the other independent mol­ecule. The amino group of the dihydro­pyrazolone unit of one mol­ecule acts as a hydrogen-bond donor to the carbonyl group of the dihydro­pyrazolone system of the other mol­ecule. The resulting N—H⋯O hydrogen bonds generate a chain running along the c axis. The crystal selected was a pseudo-merohedral twin with a 44.9 (3)% twin component.

Pseudo-Merohedral Twinning in the Structure of the Hydrated 1:1 Proton-Transfer Compound of 5-Sulfosalicylic Acid with 4-Aminopyridine

The structure of the pseudo-merohedrally twinned crystal of the 1:1 proton-transfer compound of 5-sulfosalicylic acid (3-carboxy-4-hydroxybenzenesulfonic acid) with 4-aminopyridine: 4-aminopyridinium 3-carboxy-4-hydroxybenzenesulfonate sesquihydrate has been determined at 180 K and the hydrogen-bonding pattern is described. Crystals of the compound are monoclinic with space group P21/c, with unit cell dimensions a = 35.2589(8), b = 7.1948(1), c = 24.5851(5) A, β = 110.373(2)°, and Z = 16. The monoclinic asymmetric unit comprises four cation–anion pairs and six water molecules of solvation with only the pyridinium cations having pseudo-symmetry as a result of inter-cation aromatic ring π–π stacking effects. Extensive hydrogen bonding gives a three-dimensional framework structure. The structure determination of the three-dimensional hydrogen-bonded structure of the 1:1 proton-transfer hydrate salt of 5-sulfosalicylic acid (3-carboxy-4-hydroxybenzenesulfonic acid) with 4-aminopyridine has revealed pseudo-merohedral twinning with four cations, four anions and six water molecules of solvation in the asymmetric unit.

Pseudomerohedral twinning, pseudosymmetry and complex hydrogen-bonded sheets in 2-methoxy-4-(pyrrolo[1,2-a]quinoxalin-4-yl)phenol

The title compound, C(18)H(14)N(2)O(2), crystallizes as a nonmerohedral twin, but the structure can be satisfactorily refined as a merohedral twin, in which a monoclinic unit cell with a cell angle beta close to 90 degrees emulates a metrically orthorhombic cell. The two molecules in the asymmetric unit are very similar in structure and they are related by an approximate pseudo-screw axis. The molecules are linked into complex sheets by a combination of two O-H...N hydrogen bonds and four C-H...O hydrogen bonds.

Structure of the Escherichia coli RNA polymerase alpha subunit C-terminal domain.

The alpha subunit C-terminal domain (alphaCTD) of RNA polymerase (RNAP) is a key element in transcription activation in Escherichia coli, possessing determinants responsible for the interaction of RNAP with DNA and with transcription factors. Here, the crystal structure of E. coli alphaCTD (alpha subunit residues 245-329) determined to 2.0 A resolution is reported. Crystals were obtained after reductive methylation of the recombinantly expressed domain. The crystals belonged to space group P2(1) and possessed both pseudo-translational symmetry and pseudo-merohedral twinning. The refined coordinate model (R factor = 0.193, R(free) = 0.236) has improved geometry compared with prior lower resolution determinations of the alphaCTD structure [Jeon et al. (1995), Science, 270, 1495-1497; Benoff et al. (2002), Science, 297, 1562-1566]. An extensive dimerization interface formed primarily by N- and C-terminal residues is also observed. The new coordinates will facilitate the improved modeling of alphaCTD-containing multi-component complexes visualized at lower resolution using X-ray crystallography and electron-microscopy reconstruction.

Pseudo-merohedral twinning and noncrystallographic symmetry in orthorhombic crystals of SIVmac239 Nef core domain bound to different-length TCRzeta fragments.

HIV/SIV Nef mediates many cellular processes through interactions with various cytoplasmic and membrane-associated host proteins, including the signalling zeta subunit of the T-cell receptor (TCRzeta). Here, the crystallization strategy, methods and refinement procedures used to solve the structures of the core domain of the SIVmac239 isolate of Nef (Nef(core)) in complex with two different TCRzeta fragments are described. The structure of SIVmac239 Nef(core) bound to the longer TCRzeta polypeptide (Leu51-Asp93) was determined to 3.7 A resolution (R(work) = 28.7%) in the tetragonal space group P4(3)2(1)2. The structure of SIVmac239 Nef(core) in complex with the shorter TCRzeta polypeptide (Ala63-Arg80) was determined to 2.05 A resolution (R(work) = 17.0%), but only after the detection of nearly perfect pseudo-merohedral crystal twinning and proper assignment of the orthorhombic space group P2(1)2(1)2(1). The reduction in crystal space-group symmetry induced by the truncated TCRzeta polypeptide appears to be caused by the rearrangement of crystal-contact hydrogen-bonding networks and the substitution of crystallographic symmetry operations by similar noncrystallographic symmetry (NCS) operations. The combination of NCS rotations that were nearly parallel to the twin operation (k, h, -l) and a and b unit-cell parameters that were nearly identical predisposed the P2(1)2(1)2(1) crystal form to pseudo-merohedral twinning.

Two crystal modifications of (Pro-Pro-Gly)4-Hyp-Hyp-Gly-(Pro-Pro-Gly)4reveal the puckering preference of Hyp(X) in the Hyp(X):Hyp(Y) and Hyp(X):Pro(Y) stacking pairs in collagen helices

Two crystal modifications of a collagen model peptide, (Pro-Pro-Gly)(4)-Hyp-Hyp-Gly-(Pro-Pro-Gly)(4) [where Hyp is (4R,2S)-L-hydroxyproline], showed very similar unit-cell parameters and belonged to the same space group P2(1). Both crystals exhibited pseudo-merohedral twinning. The main difference was in their molecular-packing arrangements. One modification showed pseudo-hexagonal packing, while the other showed pseudo-tetragonal packing. Despite their different packing arrangements, no significant differences were observed in the hydration states of these modifications. The peptide in the pseudo-tetragonal crystal showed a cyclic fluctuation of helical twists with a period of 20 A, while that in the pseudo-hexagonal crystal did not. In these modifications, the puckering conformations of four of the 12 Hyp residues at the X position of the Hyp(X)-Hyp(Y)-Gly sequence were in the opposite conformations to the previous hypothesis that Hyp(X) residues involved in Hyp(X):Hyp(Y) and Hyp(X):Pro(Y) stacking pairs prefer up-puckering and down-puckering conformations, respectively. Detailed investigation of the molecular interactions between Hyp(X) and adjacent molecules revealed that these opposite conformations appeared because the puckering conformation, which follows the hypothesis, is subject to steric hindrance from the adjacent molecule.

An efficient approach to characterize pseudo-merohedral twins by precession electron diffraction: Application to the LaGaO 3 perovskite

Pseudo-merohedral twins are frequently observed in crystals displaying pseudo-symmetry. In these crystals, many [ u v w] zone axis electron diffraction patterns are very close and can only be distinguished from intensity considerations. On conventional diffraction patterns (selected-area electron diffraction or microdiffraction), a strong dynamical behaviour averages the diffracted intensities so that only the positions of the reflections on a pattern can be considered. On precession electron diffraction patterns, the diffracted beams display an integrated intensity and a “few-beam” or “systematic row” behaviour prevails which strongly reduces the dynamical interactions. Therefore the diffracted intensity can be taken into account. A procedure based on observation of the weak extra-reflections connected with the pseudo-symmetry is given to identify without ambiguity any zone axis. It is successfully applied to the identification and characterization of {1 2 1} reflection twins present in the LaGaO 3 perovskite.

A 3,5-dinitrobenzoyl derivative of a stereoisomer of glycerol menthonide

The title compound, [(2S,5R,6S,9R)-6-isopropyl-9-methyl-1,4-dioxaspiro­[4.5]dec-2-yl]methyl 3,5-dinitro­benzoate, C20H26N2O8, was synthesized as part of a study of three-carbon stereochemical systems. The crystallographic assignment of the absolute stereochemistry is consistent with having started with (−)-menthone, the acetal carbon is R and the secondary alcohol is S. This brings the dinitro­benzoate into approximately the same plane as the menthyl ring and anti to the isopropyl group. Close inter­molecular C=O⋯NO2 contacts between neighboring mol­ecules [2.8341 (16) Å] contribute to the packing arrangement. The structure was refined as a pseudo-merohedral twin (monoclinic space group P21 emulating the ortho­rhom­bic space group C2221). Application of the twin law 100, 00, 0 gave a 2:1 ratio of twin moieties [refined BASF value = 0.3790 (7)].

Pseudo-merohedral twinning in monoclinic crystals of wild-type human brain neuroglobin

The purification, crystallization and successful structure determination by molecular replacement of wild-type human brain neuroglobin at 1.8 A resolution is reported. The apparent space group was orthorhombic C222(1), but the real space group was monoclinic P2(1), which resulted from twinning. Indeed, the unit-cell parameters, a = 31.2, b = 139.1, c = 31.2 A, beta = 102 degrees , display a fortuitously close to c and twinning by the operator l, -k, h occurs. Twinning was not evident from the initial analysis of intensity distribution, but pseudo-merohedral twinning was revealed by the Padilla and Yeates test based on local intensity differences. A twinning fraction of 0.5 was determined in SHELXL, indicating a perfect hemihedrally twinned crystal. To date, this type of twinning has been reported in more than ten structures, which makes it quite a common case in proteins.

Imperfect pseudo-merohedral twinning in crystals of fungal fatty acid synthase

The recent high-resolution structures of fungal fatty acid synthase (FAS) have provided new insights into the principles of fatty acid biosynthesis by large multifunctional enzymes. The crystallographic phase problem for the 2.6 MDa fungal FAS was initially solved to 5 A resolution using two crystal forms from Thermomyces lanuginosus. Monoclinic crystals in space group P2(1) were obtained from orthorhombic crystals in space group P2(1)2(1)2(1) by dehydration. Here, it is shown how this space-group transition induced imperfect pseudo-merohedral twinning in the monoclinic crystal, giving rise to a Moiré pattern-like interference of the two twin-related reciprocal lattices. The strategy for processing the twinned diffraction images and obtaining a quantitative analysis is presented. The twinning is also related to the packing of the molecules in the two crystal forms, which was derived from self-rotation function analysis and molecular-replacement solutions using a low-resolution electron microscopy map as a search model.

Pseudo-symmetry and twinning in crystals of homologous antibody Fv fragments

A difference of seven conservative amino-acid substitutions between two single-chain antibodies (scFvs) specific for chlamydial lipopolysaccharide does not significantly affect their molecular structures or packing contacts, but dramatically affects their crystallization. The structure of the variable domain (Fv) of SAG173-04 was solved to 1.86 A resolution and an R(cryst) of 18.9% in space group P2(1)2(1)2(1). Crystals of the homologous SAG506-01 diffracted to 1.95 A resolution and appeared at first to have Patterson symmetry I4/m or P4/mmm; however, no solution could be found in space groups belonging to the former and refinement in the only solution corresponding to the latter (in space group P4(3)2(1)2) stalled at R(free) = 30.0%. Detailed examination of the diffraction data revealed that the crystal was likely to be twinned and that the correct space group was P2(1)2(1)2(1). Both translational pseudo-symmetry and pseudo-merohedral twinning were observed in one crystal of SAG506-01 and pseudo-merohedral twinning was observed for a second crystal. The final R factor for SAG506-01 after refinement in P2(1)2(1)2(1) was 20.5%.

Crystallization and Preliminary Crystallographic Analysis of Laminarinase from Rhodothermus marinus: A Case of Pseudomerohedral Twinning

Thermophilic endo-1,3(4)-beta glucanase (laminarinase) from Rhodothermus marinus was crystallized by the hanging-drop vapor diffusion method. The needle-like crystals belong to space group P2(1) and contain two protein molecules in the asymmetric unit with a solvent content of 51.75 %. Diffraction data were collected to a resolution of 1.95A and resulted in a dataset with an overall R(merge) of 10.4% and a completeness of 97.8%. Analysis of the structure factors revealed pseudomerohedral twinning of the crystals with a twin fraction of approximately 42%.

Die molekularen Cluster [Bi10Au2](EBi3X9)2 (E = As, Bi; X = Cl, Br) – Synthese, Kristallstrukturen, Drillingsbildung und chemische Bindung

AbstractThe Molecular Clusters [Bi10Au2](EBi3X9)2 (E = As, Bi; X = Cl, Br) – Synthesis, Crystal Structures, Twinning and Chemical BondingCooling stochiometric mixtures of molten Bi, BiX3, (X = Cl, Br), E (E = As, Bi), and Au yields black crystals of the low‐valent, molecular compounds [Bi10Au2](EBi3X9)2. The molecules consist of an icosahedral [Bi10Au2]6+ cluster enclosed by two (EBi3X9)3− hemi‐spheres connected via Au–E bonds. The discrepancy of the symmetries of the heteroicosahedron (D5d) and the caps (C3v) gives rise to pseudomerohedral twinning. As a consequence of the superposition of three monoclinic unit cells (space group P21/c; e.g. a = 1059.02(5) pm, b = 1528.60(5) pm, c = 1463.55(6) pm, β = 93.69(1)° for E = Bi, X = Br), the diffraction patterns of the crystals simulate trigonal R‐centered cells with lattice parameters of a ≈ 3000 pm and c ≈ 1700 pm. The constitution of the molecules can be rationalized in terms of an uncommon combination of known and new structural motives: The Wade cluster [Bi10]4+ is capped by two Au+ atoms forming the hetero‐icosahedron [Bi10Au2]6+. In the anionic caps (E0BiII3X9)3−, the BiII atoms are in square planar coordination of four halogenide anions and are furthermore bonded to the E atom on the central axis of the molecule. Since the interaction between E and Au can be classified as a donor‐acceptor bond, the [AuI(E0R3)]2− fragment with R = BiIIX2/1X2/2 is a complex analog to cations [AuI(E0R3)]+ with E = P, As, Sb and R = alkyl or aryl.