Crystallographic Threefold Axis Research Articles

Tri-p-tolylphosphine

In the title compound C21H21P, the P atom is situated on a crystallographic threefold rotatory-inversion axis, resulting in threefold rotation symmetry of the title compound. The dihedral angles between the symmetry-related benzene rings are 87.40 (18)°.

Structural Chemistry of Borazines

AbstractThe solid‐state structure of (HN=BF)3 has been redetermined. It is characterised by a stacking of the molecules, similar to hexagonal boron nitride. In contrast, (F3CH2N=BF)3 shows no intermolecular interactions between the planar borazine rings. In (Cl2BN=BCl)3, the Cl2B groups are almost perpendicularly oriented to the planar borazine ring and its B–Cl bonds are shorter than the Cl–B bonds to the ring boron atoms. Reactions of (Cl2BN=BCl)3 with Me3SiNMe2 allows a successive Cl/Me2N exchange. Depending on the molar ratio, the compounds [Cl(Me2N)BN=BCl]3, [(Me2N)2BN=BCl]3 and [(Me2N)2BN=BNMe2]3 are obtained. The latter two react with CH2Cl2 by B–N bond cleavage of one ring boron bonded Me2N group with formation of an N–H bond. These molecules not only possess a strongly distorted BN hexagon with short B–NH bonds but also a nonplanar borazine ring. The nonplanarity of the borazine ring is even more pronounced in [Me3SiN=BCl]3. A planar borazine ring is observed for (MeN=BBr)3. Its molecules are ordered into stacks by translation with borazine planes 4.2 Å apart from each other. Characteristic of the structure are close contacts between neighbouring bromine atoms. Due to the steric demand of pentafluorophenyl groups, the borazine ring of (F5C6N=BBr)3 forms no stacks because one of the three F5C6 rings stands almost perpendicular to the borazine plane while the other two are twisted by 70°. Aminolysis of (F5C6N=BBr)3 yields (F5C6N=BNH2)3 with NH2 groups that are coplanar with the borazine ring. The phenyl groups of (HN=BPh)3 are twisted by only 30–40° relative to the borazine ring. A threefold crystallographic axis stands perpendicular to the ring plane. The sixfold crystallographic axis of the unit cell generates a channel structure with an internal diameter of 4.5 Å. The two isomeric borazines, (iPrN=BMe)3 and (MeN=BiPr)3 are structurally rather similar although the first of these has longer B–N bonds due to the shorter N–C bonds. Moreover, the B–N–B and N–B–N bond angles are slightly different.(© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2008)

Tetra-kis(triphenyl-arsine)copper(I) hexa-fluoridophosphate.

In the crystal structure of the title compound, [Cu(C18H15As)4]PF6, the Cu atom is coordinated by four As atoms of triphenyl­arsine ligands in a tetra­hedral geometry. The complex cation is located on a crystallographic threefold axis. Both PF6 − anions are located on special positions of site symmetry . The Cu—As bond of the independent arsine ligand is shorter than the Cu—As bonds of the three symmetry-related arsine ligands.

Production, purification and preliminary X-ray crystallographic studies of adeno-associated virus serotype 7.

Crystals of baculovirus-expressed adeno-associated virus serotype 7 capsids diffract X-rays to approximately 3.0 A resolution. The crystals belong to the rhombohedral space group R3, with unit-cell parameters a = 252.4, c = 591.2 A in the hexagonal setting. The diffraction data were processed and reduced to an overall completeness of 79.0% and an R(merge) of 12.0%. There are three viral capsids in the unit cell. The icosahedral threefold axis is coincident with the crystallographic threefold axis, resulting in one third of a capsid (20 monomers) per crystallographic asymmetric unit. The orientation of the viral capsid has been determined by rotation-function searches and is positioned at (0, 0, 0) by packing considerations.

Structure of Staphylococcus aureus1,4-dihydroxy-2-naphthoyl-CoA synthase (MenB) in complex with acetoacetyl-CoA.

Vitamin K(2), or menaquinone, is an essential cofactor for many organisms and the enzymes involved in its biosynthesis are potential antimicrobial drug targets. One of these enzymes, 1,4-dihydroxy-2-naphthoyl-CoA synthase (MenB) from the pathogen Staphylococcus aureus, has been obtained in recombinant form and its quaternary structure has been analyzed in solution. Cubic crystals of the enzyme allowed a low-resolution structure (2.9 A) to be determined. The asymmetric unit consists of two subunits and a crystallographic threefold axis of symmetry generates a hexamer consistent with size-exclusion chromatography. Analytical ultracentrifugation indicates the presence of six states in solution, monomeric through to hexameric, with the dimer noted as being particularly stable. MenB displays the crotonase-family fold with distinct N- and C-terminal domains and a flexible segment of structure around the active site. The smaller C-terminal domain plays an important role in oligomerization and also in substrate binding. The presence of acetoacetyl-CoA in one of the two active sites present in the asymmetric unit indicates how part of the substrate binds and facilitates comparisons with the structure of Mycobacterium tuberculosis MenB.

Pinch points and Kasteleyn transitions in kagome ice

Complex disordered states—from liquids and glasses to exotic quantum matter—are ubiquitous in nature. Their key properties include finite entropy, power-law correlations and emergent organizing principles. In spin ice, spin correlations are determined by the ‘ice rules’ organizing principle that stabilizes a magnetic state with the same zero-point entropy as water ice. The entropy can be manipulated with great precision by an applied magnetic field: when directed along the three-fold crystallographic axis, the field produces a state of finite entropy, known as kagome ice. Here, we investigate the spin-ice material Ho2Ti2O7 by tilting the magnetic field slightly away from that axis. We thus realize a classic statistical system named after Kasteleyn, in which the entropy of a critical phase can be continuously tuned. Our neutron scattering experiments reveal how this process occurs at a microscopic level.

(Acetonitrile){hydridotris[3,5-bis(trifluoromethyl)-1-pyrazolyl]borato}copper(I)

The title compound, [Cu(C15H4BF18N6)(C2H3N)] or [HB(3,5-(CF3)2Pz)3]CuI(CH3CN), was synthesized from [CuI(CF3SO3)]2·C6H5CH3 and [HB(3,5-(CF3)2Pz)3]Na(H2O) in CH2Cl2/CH3CN. The CuI atom adopts a distorted tetra­hedral geometry and is coordinated by four N atoms, three N atoms from the tridentate tris­(pyrazol­yl)borate ligand [Cu—N = 2.0992 (12) A] and one N atom from acetonitrile [Cu—N = 1.888 (3) A]. The acetonitrile ligand is linear. The Cu atom, acetonitrile ligand, B and its attached H atom lie on a crystallographic threefold rotation axis.

Tris[2-(1H-imidazol-2-yl)phenolato-κ2N,O]chromium(III) methanol trisolvate

In the title complex, [Cr(C9H7N2O)3]·3CH4O, the Cr3+ ion is coordinated by three anionic 2-(1H-imidazol-2-yl)phenolate ligands. Each ligand provides one O atom and one N atom. The complex adopts octa­hedral geometry. The Cr3+ ion has site symmetry 3. A crystallographic threefold rotoinversion axis passes through the Cr atom.

Crystal Structure of d(gcGXGAgc) with X = G: a Mutation at X is Possible to Occur in a Base-Intercalated Duplex for Multiplex Formation

DNA fragments with the sequences d(gcGX[Y]n Agc) (n = 1, X = A, and Y = A, T, or G) form base-intercalated duplexes, which is a basic unit for formation of multiplexes such as octaplex and hexaplex. To examine the stability of multiplexes, a DNA with X = Y = G and n = 1 was crystallized under conditions different from those of the previously determined sequences, and its crystal structure has been determined. The two strands are coupled in an anti-parallel fashion to form a base-intercalated duplex, in which the first and second residues form Watson-Crick type G:C pairs and the third and sixth residues form a sheared G:A pairs at both ends of the duplex. The G4 and G5 bases are stacked alternatively on those of the counter strand to form a long G column of G3-G4-G5*-G5-G4*-G3*, the central four Gs being protruded. In addition, the three duplexes are associated to form a hexaplex around a mixture of calcium and sodium cations on the crystallographic threefold axis. These structural features are similar to those of the previous crystals, though slightly different in detail. The present study indicates that mutation at the 4th position is possible to occur in a base-intercalated duplex for multiplex formations, suggesting that DNA fragments with any sequence sandwiched between the two triplets gcG and Agc can form a multiplex.

Tetra-μ3-iodo-tetrakis[(tri-tert-butylphosphine)copper(I)

The title compound, [Cu4I4(C12H27P)4], recovered from an attempt to prepare triisopropyl­silylthiol­ato(tri-tert-butyl­phosphine)copper(I), is found to be tetra­meric with a distorted heterocubane structure, one of the body diagonals of the cube being a crystallographic threefold rotation axis.

Sodium tris(acetylacetonato-κ2O,O′)manganese(II)

In the title compound, Na[Mn(C5H7O2)3], the manganese(II) ions are each coordinated by six O atoms from three different acetylacetonate ligands in a trigonal prismatic geometry. The octahedrally coordinated Na cations are sandwiched between two adjacent [Mn(acac)3]− units (acac is acetyl­acetonate). The three crystallographically distinct Mn cations are each located on a crystallographic threefold rotation axis. Two Na cations are also located on special positions with site symmetry 3 and two further Na cations occupy special positions with site symmetry \overline 3.

Structure ofEscherichia coliglutamate decarboxylase (GADα) in complex with glutarate at 2.05 Å resolution

Glutamate decarboxylase (GAD) is a pyridoxal enzyme that catalyzes the conversion of L-glutamate into gamma-aminobutyric acid and carbon dioxide. The Escherichia coli enzyme exists as two isozymes, referred to as GADalpha and GADbeta. Crystals of the complex of the recombinant isozyme GADalpha with glutarate as a substrate analogue were grown in space group R3, with unit-cell parameters a = b = 117.1, c = 196.4 angstroms. The structure of the enzyme was solved by the molecular-replacement method and refined at 2.05 angstroms resolution to an R factor of 15.1% (R(free) = 19.9%). The asymmetric unit contains a dimer consisting of two subunits of the enzyme related by a noncrystallographic twofold axis which is perpendicular to and intersects a crystallographic threefold axis. The dimers are related by a crystallographic threefold axis to form a hexamer. The active site of each subunit is formed by residues of the large domains of both subunits of the dimer. The coenzyme pyridoxal phosphate (PLP) forms an aldimine bond with Lys276. The glutarate molecule bound in the active site of the enzyme adopts two conformations with equal occupancies. One of the two carboxy groups of the glutarate occupies the same position in both conformations and forms hydrogen bonds with the N atom of the main chain of Phe63 and the side chain of Thr62 of one subunit and the side chains of Asp86 and Asn83 of the adjacent subunit of the dimer. Apparently, it is in this position that the distal carboxy group of the substrate would be bound by the enzyme, thus providing recognition of glutamic acid by the enzyme.

Tris(trimethylsilyl)‐Substituted Heavy Group 14‐Element‐Centered Anions: Unsolvated Trimeric Germyllithium and Solvated Dimeric Silyl‐ and Stannyllithiums

AbstractTris(trimethylsilyl)‐substituted group 14‐element‐centered anion monomers [LiE(SiMe3)3·3THF] (E = Si, Ge, and Sn) can be distilled under reduced pressure to give dimeric silyllithium 4 and stannyllithium 6, and trimeric germyllithium 5 without pyrolysis products such as dilithiometallanes. The molecular structures of 4, 5, and 6 were unequivocally determined by X‐ray diffraction. Dimer 4 has a symmetrical bent four‐membered‐ring structure consisting of two anionic silicon atoms and two cationic lithium atoms with coordinated THF molecules. Dimer 6 has an unsymmetrical distorted four‐membered‐ring structure consisting of two anionic tin atoms, a bridged unsolvated lithium atom, and a bridged lithium atom solvated by a THF molecule. Interestingly, 6 aggregates to form dimers of dimers by an intermolecular CH3···Li interaction. Trimeric germyllithium 5 forms an equilateral triangular lithium cluster without solvation. Compound 5 has a crystallographic threefold axis with three anionic germanium atoms and three cationic lithium atoms lying in the same plane. The lithium atoms in 5 are stabilized by an intramolecular CH3···Li interaction. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2004)

Crystal structure determination of Ga3(H3O)H8(PO4)6 · 6 H2O from X-ray powder diffraction data

Abstract The crystal structure of the gallium hydrogen phosphate hydrate, Ga3(H3O)H8(PO4)6 · 6 H2O, has been determined from X-ray powder diffraction data. The structure is trigonal, space group P31c (No. 159), with unit cell dimensions a = 9.0227(1) Å, c = 16.6389(3) Å, V = 1173.08(3) Å3, Z = 2, and D x = 2.59 g/cm3. The structure was solved by direct methods using EXPO program and refined by FULLPROF package to R Bragg value of 8.6%. Positions of hydrogen atoms were not defined. There are three unique gallium atoms in the crystal structure, having octahedral oxygen coordination. GaO6 octahedra are linked together via the corners of PO4 tetrahedra to form a three-dimensional network with channels running along the c axis. There are two types of water molecules in the crystal, which essentially differ in their atomic environment. Oxonium cations, lying on crystallographic threefold axis, are surrounded by oxygen atoms of the phosphate groups and water molecules.

Different packing in three polymorphs of 2,4,6-trimethoxy-1,3,5-triazine.

2,4,6-trimethoxy-1,3,5-triazine was found to exhibit three different polymorphs. The alpha-polymorph undergoes reversible phase transformation to the beta-polymorph at 340 K with an enthalpy of 3.9 kJ mol(-1). The heat of fusion of the beta-polymorph at 404 K is 18.1 kJ mol(-1). The low-temperature phase (alpha-polymorph) crystallizes in the orthorhombic space group Pnma. The high-temperature phase (beta-polymorph) can be obtained from the melt and crystallizes in the monoclinic space group P2(1). The gamma-polymorph is obtained by crystallization from a 1:1 mixture of methanol and methylenechloride from hydrolyzed 2,4-dimethoxy-6-oxybenzophenone-1,3,5-triazine. The gamma-polymorph melts at 409 K with an enthalpy of 11.4 kJ mol(-1). The gamma-polymorph crystallizes in the trigonal space group R3c. The molecules occupy a crystallographic threefold axis. Molecules of 2,4,6-trimethoxy-1,3,5-triazine are planar in all three polymorphs. The major difference between the three polymorphs is the mode of packing of the molecules in the crystal.

Nanosized Au2Pd41(CO)27(PEt3)15 containing two geometrically unprecedented 13-coordinated Au-centered (mu 13-Au)Pd13 polyhedra connected by triangular face-sharing and three interpenetrating 12-coordinated Pd-centered (mu 12-Pd)Au2Pd10 icosahedra: geometrical change in centered polyhedra induced by Au/Pd electronegativity-mismatch.

The synthesis, isolation, and stereochemical characterization of Au(2)Pd(41)(CO)(27)(PEt(3))(15)(1) are described. This nanosized Au(2)Pd(41) cluster (maximum metal-core diameter, 1.04 nm) was originally obtained with Au(2)Pd(21)(CO)(20)(PEt(3))(10) as low-yield by-products together with Pd(145)(CO)(x)(PEt(3))(30)(x approximately 60) from the reaction of Pd(PEt(3))(2)Cl(2) and Au(PPh(3))Cl in DMF with NaOH under CO atmosphere. The subsequent preparation of Au(2)Pd(21)(CO)(20)(PEt(3))(10) in greatly improved yields (preceding article) thereby provided the starting material that led to the isolation of 1 in reasonable yields (54%) from an overnight refluxing of the preformed Au(2)Pd(21) cluster in THF under N(2). Both the composition (subsequently ascertained from elemental analysis) and molecular geometry of 1 were unequivocally established from a low-temperature CCD X-ray diffraction study, which revealed a cubic unit cell of P2(1)3 symmetry with four molecules of 1 and four co-crystallized triphenylphosphine oxide molecules each lying on a crystallographic three-fold axis. The entire Au(2)Pd(41) core of pseudo-C(3h) symmetry may be viewed as a central Au(2)Pd(29) fragment of pseudo-D(3h) symmetry composed of two heretofore geometrically unknown 13-coordinated Au-centered (mu(13)-Au)Pd(13) polyhedra that share a common internal Pd(i)(3) triangular face perpendicular to the C(3) principal axis and of three three-fold-related interpenetrating 12-coordinated Pd-centered (mu(12)-Pd)Au(2)Pd(10) icosahedra. A comparative analysis of this central Au(2)Pd(29) fragment in with an internal Au(i)(2)Pd(i)(3) trigonal bipyramid vs. the corresponding central Pd(29) fragment in the known homopalladium Pd(35)(CO)(23)(PMe(3))(15) (2) with an internal Pd(i)(5) trigonal bipyramid resulting from five interpenetrating 12-coordinated Pd-centered [(mu(12)-Pd)Pd(12)] icosahedra is particularly illuminating; it provides a striking illustration of the remarkable observed difference between Pd- vs. Au-centered polyhedra which is attributed to a large electronegativity-mismatch in radial bonding interactions that occurs upon replacement of the Pd-centered atom with a highly electronegative Au-centered atom. The entire Au(2)Pd(41) core-geometry is obtained by additional face-condensations of 12 tetracapping Pd(cap) atoms. This cluster is stabilized by 15 PEt(3) ligands and 27 doubly- and triply-bridging CO ligands. A close geometrical resemblance between the three three-fold-related Au(2)Pd(14) moities within the Au(2)Pd(41) core in 1 and the entire Au(2)Pd(14) core in the known [Au(2)Pd(14)(CO)(9)(PMe(3))(11)](2+) dication (3) is observed; resulting stereochemical implications are given.

6-(4-Fluorophenyl)-5,6-dihydrobenzimidazo[1,2-c]quinazoline

The title compound, C20H14FN3, contains one conventional N—H⋯N hydrogen bond which links the mol­ecules into spiral chains running parallel to the c axis; the conformation of this chain appears to be stabilized by an antiparallel C—H⋯F contact. The structure also contains non-localized solvent in isolated cavities which lie along the crystallographic threefold axis.

Crystal structure of the Escherichia coli YcdX protein reveals a trinuclear zinc active site.

Crystal structure of the Escherichia coli YcdX protein reveals a trinuclear zinc active site.

Tetramethyllead(IV) at 150 K

Tetra­methyl­lead, [Pb(CH3)4], crystallizes in the cubic space group Pa\overline 3, with the Pb atom and one C atom on a crystallographic threefold axis. The average Pb—C distance is 2.211 (11) Å. The crystal structure is isostructural with that of the Sn analogue, and adopts the SnI4-type structure.

Tris[2-(2-oxazolin-2-yl)phenolato]iron(III).

The title compound, tris[2-(4,5-dihydrooxazol-2-yl-kappa N)phenolato-kappa O]iron(III), [Fe(C(9)H(8)NO(2))(3)], is disordered over a non-crystallographic twofold rotation axis perpendicular to the crystallographic threefold rotation axis. The disorder can be a pure rotational disorder of an iron complex in the facial configuration, or the consequence of a mixture of facial and meridional configurations. In the latter case, at least 25% of the iron complexes must adopt the facial configuration in order to obtain the disorder ratio observed in the crystal.