Synthesis, characterization, and single crystal X-ray structures of [CoIII(acacen)(thioacetamide)2]ClO4 and [CoIII((BA)2en)(thioacetamide)2]PF6 — Solvatochromic properties of [CoIII(acacen)(thioacetamide)2]ClO4

The trans-[CoIII(acacen)(ta)2]ClO4 (1) and trans-[CoIII((BA)2en)(ta)2]PF6 (2) complexes, where H2acacen = bis(acetylacetone)ethylenediimine, H2(BA)2en = bis(benzoylacetone)ethylenediimine, and ta = thioacetamide, have been synthesized by a solid-state method, and characterized by elemental analyses, IR, UV–vis, and 1H NMR spectroscopy. The crystal and molecular structures of 1 and 2 were determined by X-ray crystallography. Both compounds crystallize in the monoclinic space group P2/n. The ClO4 and PF6 ions are both disordered, ClO4 on a twofold axis in 1 and PF6 on an inversion center in 2. Also bridging N-CH2-CH2-N is disordered in both compounds. The octahedral coordination of Co(III) is slightly distorted in both cases. The thioacetamide ligands are S-bonded and occupy the axial position. The IR, UV–vis, and 1H NMR spectra of the two complexes and their solvatochromic properties are also discussed. The longest wavelength absorption that appears at 517 nm for 1 and at 528 nm for 2 in chloroform is solvent dependent, and is assigned as a metal-mediated ligand-to-ligand charge transfer (LLCT).Key words: solid-state synthesis, thioactamide, Co(III) (Schiff base), crystal structure, solvatochromism, metal-mediated LLCT.

Second-degree twinning and dynamic disorder in the crystal structure of deca-dodecasil 3R

The structure of deca-dodecasil 3R (DD-3R), Si120O240, a very well suited material for the synthesis of inorganic/organic composites structured on a nanometer level, has been investigated in detail. So far, a highly complicated twinning has hampered its structure description at a desirable level of accuracy. This twinning has now been resolved and a new structure determination is presented. Structure refinement in the R\bar 3 space group revealed a large, unusually shaped atomic displacement ellipsoid for oxygen-bridging units (tetrahedra), bridging Si-O bonds shorter than expected and the linear Si-O-Si' bond angle dictated by special positions at a threefold axis. A structure model based on a statistically disordered bridging O atom improved the accuracy of the Si-O bonds of interest, but provided unacceptable O-O contacts. To solve this dilemma, ab initio NVT molecular dynamics calculations were performed to study the possible configurations. Wavelet analysis of the time variations of selected Si-O distances pointed to a synchronous shift of the whole building units (tetrahedra). Low-frequency features of the calculated phonon density of states agree well with the published INS (inelastic neutron scattering) spectra of several silica polymorphs, indicating that the nature of the disorder in DD-3R is dynamic rather than static.

Three isomeric forms of hydroxyphenyl-2-oxazoline: 2-(2-hydroxyphenyl)-2-oxazoline, 2-(3-hydroxyphenyl)-2-oxazoline and 2-(4-hydroxyphenyl)-2-oxazoline

Crystal structures are reported for three isomeric compounds, namely 2-(2-hydroxyphenyl)-2-oxazoline, (I), 2-(3-hydroxyphenyl)-2-oxazoline, (II), and 2-(4-hydroxyphenyl)-2-oxazoline, (III), all C9H9NO2 [systematic names: 2-(4,5-dihydro-1,3-oxazol-2-yl)phenol, (I), 3-(4,5-dihydro-1,3-oxazol-2-yl)phenol, (II), and 4-(4,5-dihydro-1,3-oxazol-2-yl)phenol, (III)]. In these compounds, the deviation from coplanarity of the oxazoline and benzene rings is dependent on the position of the hydroxy group on the benzene ring. The coplanar arrangement in (I) is stabilized by a strong intramolecular O-H...N hydrogen bond. Surprisingly, the 2-oxazoline ring in molecule B of (II) adopts a 3T4 (C2TC3) conformation, while the 2-oxazoline ring in molecule A, as well as that in (I) and (III), is nearly planar, as expected. Tetramers of molecules of (II) are formed and they are bound together via weak C-H...N hydrogen bonds. In (III), strong intermolecular O-H...N hydrogen bonds and weak intramolecular C-H...O hydrogen bonds lead to the formation of an infinite chain of molecules perpendicular to the b direction. This paper also reports a theoretical investigation of hydrogen bonds, based on density functional theory (DFT) employing periodic boundary conditions.

Synthesis and structure determination of some nonanomerically C-C-linked serine glycoconjugates structurally related to mannojirimycin

The Bucherer-Bergs reaction of methyl 2,3-O-isopropylidene-alpha-d-lyxo-hexofuranosid-5-ulose gave (4'S)-4'-carbamoyl-4'-[methyl (4R)-2,3-O-isopropylidene-beta-l-erythrofuranosid-4-C-yl]-oxazolidin-2'-one instead of expected hydantoins. A mixture of hydantoins--(5'R)-triphenylmethoxymethyl-5'-[methyl (4R)-2,3-O-isopropylidene-beta-l-erythrofuranosid-4-C-yl]-imidazolidin-2',4'-dione and (5'S)-triphenylmethoxymethyl-5'-[methyl (4R)-2,3-O-isopropylidene-beta-l-erythrofuranosid-4-C-yl]-imidazolidin-2',4'-dione was obtained from the 5-ulose having protected primary OH group at C-6. The 4'-S configuration of 2 as well as 5'-S configuration of (5'S)-hydroxymethyl-5'-[methyl (4R)-2,3-O-isopropylidene-beta-l-erythrofuranosid-4-C-yl]-imidazolidin-2',4'-dione (9) was confirmed by X-ray crystallography. Corresponding alpha-amino acid--methyl (5S)-5-amino-5-C-carboxy-5-deoxy-alpha-d-lyxo-hexofuranoside (alternative name: 2-[methyl (4R)-beta-l-erythrofuranosid-4-C-yl]-l-serine) (11) was obtained from the hydantoin 9 by acid hydrolysis of the isopropylidene and trityl groups followed by basic hydrolysis of the hydantoin ring. Analogous derivatives with 5-R configuration, formed in a minority, were also isolated and characterised.

threo-2-(2,6-Dimethoxyphenoxy)-1-(4-hydroxy-3,5-dimethoxyphenyl)propane-1,3-diol: a conformational study

In the crystal structure of the title compound, C19H24O8, the molecules adopt a conformation in which the bulky 2,6-dimethoxyphenoxy and 4-hydroxy-3,5-dimethoxyphenyl groups are almost as far apart as possible. The C(aryl)...C(aryl) distance is 4.8766 (19) A, which is close to the calculated maximum value (4.92 A). The C(aryl)-C-C-O(aryloxy) torsion angle is 173.76 (11) degrees and the C(benzylic)-C-O-C(aryl) torsion angle is 149.09 (11) degrees. The conformation is compared with those of related lignin model compounds. The hydrogen-bonding pattern is discussed in terms of graph-set theory.

21-Deoxycortisone (17α-hydroxy-4-pregnene-3,11,20-trione)

The title compound, C21H28O4, a synthetic glucocorticoid, crystallizes with a single molecule in the asymmetric unit. Ring A is almost in a half-chair conformation, rings B and C are almost in chair conformations, and ring D is between a twist and a 13beta-envelope conformation. The A/B ring junction is quasi-trans, whereas the B/C and C/D ring junctions both approach trans characteristics. The molecule as a whole is slightly convex towards the beta side, with an angle of 9.60 (2) degrees between the C10-C19 and C13-C18 vectors. Molecular-packing and hydrogen-bonding (both intra- and intermolecular) interactions play a major role in the structural association of the compound.

Pseudo-merohedrally twinned tetrakis(1H-imidazole-κN3)bis(N-nitrocyanamidato-κN)copper(II)

Crystals of the title complex, [Cu(CN3O2)2(C3H4N2)4], the structure of which has been determined by single-crystal X-ray diffraction at 304 K, appear to be pseudo-merohedrally twinned. Transformation to a monoclinic C-centred cell was necessary in order to derive the twin law. Twin refinement in a triclinic unit cell significantly reduced the R value. The asymmetric unit of the triclinic cell consists of one molecule in a general position and two half entities with the Cu atom on a centre of inversion. The coordination of the Cu atom is quasi-octahedral, with four imidazole N-atom donors in the equatorial plane and two cyano N atoms from the N-nitrocyanamidate anion in axial positions. Owing to symmetry in the centrosymmetric molecules, the trans imidazole ligands are parallel, while those in the non-centrosymmetric molecule make angles of 22.8 (2) and 77.9 (2) degrees .

Structure of the azurin mutant Phe114Ala from Pseudomonas aeruginosa at 2.6 A resolution

The crystal structure of azurin mutant Phe114Ala from Pseudomonas aeruginosa has been solved by molecular replacement. The final crystallographic R value is 0.185 for 9832 reflections to a resolution of 2.6 A. The root-mean-square deviation for main-chain atom positions is 0.020 A between the four independent monomers in the asymmetric unit. The mutant Ala114 crystallized from PEG 4000 in a new crystal form and the crystals are monoclinic, P2(1), a= 51.0, b = 83.6, c= 66.4 A and beta = 110.5 degrees. The four molecules in the asymmetric unit are packed as a dimer of dimers and are related by an approximate twofold axis. The dimer packing and the dimer contact region are very similar to that of the Alcaligenes denitrificans azurin dimer. The mutation was performed at residue Phe114, which exhibits a pi-electron overlap with the copper ligand His117, to investigate its suggested role in the electron self-exchange reaction. Removal of steric constrains from the phenylalanine side chain created a somewhat different geometry around the copper site with an increased mobility of His117 resulting in an enlarged Cu-N length which may be responsible for the slight differences obtained in the spectral properties of the mutant versus the wild-type protein.

Synthesis and molecular structure of methyl 4-O-methyl-alpha-D-glucopyranuronate

A method for the preparation of methyl 4-O-methyl-α-D-glucopyranuronate and its single crystal X-ray structure determination are reported. The molecule adopts an almost ideal ⁴C₁ (^OC₃) conformation.

Pseudo-merohedrally twinned praseodymium hexacyanoferrate(III) tetrahydrate

Crystals of the title compound, diaquahexa-mu-cyano-ferrate(III)praseodymium(III) dihydrate, Pr[Fe(CN)(6)].4H(2)O or [PrFe(CN)(6)(H(2)O)(2)].2H(2)O, are twinned with three components. The Pr atom is coordinated by eight atoms, viz. six N and two symmetry-related water O atoms. The Pr polyhedron (Pr has site symmetry m2m, Wyckoff position 4c) is linked to an FeC(6) octahedron (Fe located on a site with imposed 2/m symmetry, Wyckoff position 4b) through N atoms, forming an infinite array. The second (symmetry independent) water molecule lies on a mirror plane, is not included in coordination and is weakly hydrogen bonded to N atoms.

Characterisation and X-ray crystallography of products from the Bucherer-Bergs reaction of methyl 2,3-O-isopropylidene-alpha-D-lyxo-pentodialdo-1,4-furanoside

Methyl 2,3-O-isopropylidene-alpha-D-mannofuranosidurononitrile [alternative name: methyl (5R)-5-C-cyano-2,3-O-isopropylidene-alpha-D-lyxofuranoside] (2), methyl 2,3-O-isopropylidene-alpha-D-mannofuranosiduronamide [methyl (5S)-5-C-carbamoyl-2,3-O-isopropylidene-alpha-D-lyxofuranoside; methyl (5S)-2,3-O-isopropylidene-alpha-D-lyxo-hexofuranosiduronamide] (3), methyl 2,3-O-isopropylidene-alpha-D-mannofuranosiduronic acid [methyl (5S)-2,3-O-isopropylidene-alpha-D-lyxo-hexofuranosiduronic acid] (4), methyl 5-deoxy-2,3-O-isopropylidene-5-ureido-beta-L-gulofuranosiduronamide [methyl (5R)-5-deoxy-2,3-O-isopropylidene-5-ureido-alpha-D-lyxo-hexofuranosiduronamide (5), and (4S,5S,6R)-5,6-dihydro-6-hydroxy-4,5-isopropylidenedioxy-4H-pyrido[2,1-e]imidazolidine-2',4'-dione [IUPAC name: (3aS,4R,8aS)-4-hydroxy-2,2-dimethyl-3a,8a-dihydro-4H-1,3-dioxa-4a,6-diaza-s-indacene-5,7-dione] (6), instead of the expected hydantoin derivative, were obtained from the Bucherer-Bergs reaction of methyl 2,3-O-isopropylidene-alpha-D-lyxo-pentodialdo-1,4-furanoside (1). The structure of 6 was deduced from NMR and mass spectral data and confirmed by X-ray crystallography. The configuration at C-5 in 2-5 was confirmed by establishing the 5S configuration of 3 by X-ray crystallography. Conformations of the six- and five-membered rings in 3 and 6 are also discussed.

Dirubidium aquapentachlorochromate(III) and dicaesium aquapentachlorochromate(III)

The structures of the two novel title compounds, Rb(2)[CrCl(5)(H(2)O)], (I), and Cs(2)[CrCl(5)(H(2)O)], (II), have been determined by single-crystal X-ray diffraction. Compounds (I) and (II) crystallize with Pnma and Cmcm symmetry, respectively. In (I), the Cr, three Cl and water O atom lie on a mirror plane; in (II), the Cs, Cr, O and one of the Cl atoms are at sites with m2m symmetry. The chromate anions are in a pseudo-cubic environment of eight Rb(+) cations in (I) and in a pseudo-octahedral environment of six Cs(+) cations in (II). The structural arrangement correlates with the r(anion)/r(cation) radius ratio.

Preparation and Crystal Structure of (1S, 5S, 7S, 8R)-8-Hydroxy-7-phenyl-2,6-dioxabicyclo[3.3.0]octan-3-one

The absolute configuration at two newly formed stereogenic centres (5S, 7S) during the key steps of the total synthesis of naturally occuring goniothalesdiol was established by single-crystal X-ray diffraction analysis relative to stereocentres (1S, 8R) of the title compound (alternatively named 3,6-anhydro-2-deoxy-6-phenyl-l-ido-1,4-hexonolactone, C₁₂H₁₂O₄). The conformation of both 5-membered lactone and furanose fused rings is also discussed.

Some non-anomerically C-C-linked carbohydrate amino acids related to leucine-synthesis and structure determination

(5'R)-5'-Isobutyl-5'-[methyl (4R)-2,3-O-isopropylidene-beta-L-erythrofuranosid-4-C-yl]-imidazolidin-2',4'-dione was synthesised starting from methyl 2,3-O-isopropylidene-alpha-D-lyxo-pentodialdo-1,4-furanoside via methyl 6-deoxy-6-isopropyl-2,3-O-isopropylidene-alpha-D-lyxo-hexofuranosid-5-ulose applying the Bucherer-Bergs reaction. Its 5'-R configuration was confirmed by X-ray crystallography. Corresponding alpha-amino acid-methyl (5R)-5-amino-5-C-carboxy-5,6-dideoxy-6-isopropyl-alpha-D-lyxo-hexofuranoside (alternative name: 2-[methyl (4R)-beta-L-erythrofuranosid-4-C-yl]-D-leucine) was obtained from the above hydantoin by acid hydrolysis of the isopropylidene group followed by basic hydrolysis of the hydantoin ring. Analogous derivatives with 5S configuration, formed in a minority, were also isolated and characterised.