# O Atoms (o + atom)

Distribution by Scientific Domains

Kinds of O Atoms

 carbonyl o atom carboxyl o atom hydroxyl o atom one o atom phenolate o atom

## Selected Abstracts

### The Variable Binding Modes of Phenylbis(pyrid-2-ylmethyl)phosphane and Bis(pyrid-2-ylmethyl) Phenylphosphonite with AgI and CuI

EUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 20 2009
Fernando Hung-Low
Abstract A series of new bridging phosphane and phosphonite structures forming three- and six-membered rings with the metal centers were synthesized and characterized. The resulting compounds of phenylbis(pyrid-2-ylmethyl)phosphane (1) with the silver(I) salts of trifluoroacetate (tfa,), tetrafluoroborate (BF4,), and trifluoromethanesulfonate (OTf,), and copper tetrakis(acetonitrile) hexafluorophosphate (PF6,) shows the flexibility of the ligand by displaying different coordination modes associated with the electronic and structural characteristics of the corresponding anion. Accordingly, ligand 1 in these complexes displays two different binding modes. With Agtfa and AgBF4 compounds 3 and 4 are obtained where the ligand chelates to two silver atoms that exhibit normalAg,Ag contacts in the range of 2.9 Å. When AgOTf or Cu(NCCH3)4PF6 are used, one molecule of 1 bridges the metal centers through a phosphorus atom while another is terminally bound. This induces short M,M distances of 2.6871 and 2.568 Å for 5 and 6, respectively. Similarly, the coordination behavior of the heterofunctional bis(pyrid-2-ylmethyl) phenylphosphonite ligand (2) is reported with Cu(NCCH3)4PF6 (7) and AgBF4 (8) to form two novel discrete molecules. In these complexes 2 coordinates through the P and N atoms, with the difference that in 7 the O atom of one of the carbinol arms is also bound to the Cu. Elemental analysis, variable-temperature multinuclear NMR spectroscopy, single-crystal X-ray diffraction, and low-temperature luminescence studies were carried out to fully characterize the compounds. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2009) [source]

### Dicopper(II) Complexes with the Enantiomers of a Bidentate Chiral Reduced Schiff Base: Inclusion of Chlorinated Solvents and Chiral Recognition of1,2-Dichloroethane Rotamers in the Crystal Lattice

EUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 14 2006
Vamsee Krishna Muppidi
Abstract Bisphenoxo-bridged dicopper(II) complexes [Cu2Ln2Cl2] {1 (n = 1) and 2 (n = 2)} with the N,O-donor reduced Schiff bases N -(2-hydroxybenzyl)-(R)-,-methylbenzylamine (HL1) and N -(2-hydroxybenzyl)-(S)-,-methylbenzylamine (HL2) have been synthesised and characterised. In both 1 and 2, the bidentate chiral ligands coordinate the metal centres through the secondary amine N atom and the bridging phenolate O atom. The chloride ion occupies the fourth coordination site and completes a slightly distorted square-planar NO2Cl environment around each copper(II) centre. Magnetic susceptibility measurements in the solid state suggest a strong antiferromagnetic interaction between the metal centres in both complexes. Both 1 and 2 readily form 1:1 host-guest compounds with chlorinated solvents such as CH2Cl2, CHCl3 and Cl(CH2)2Cl. All the host-guest compounds crystallise in noncentrosymmetric space groups. 1·CH2Cl2 and 2·CH2Cl2 crystallise in the P21 space group while 1·CHCl3, 2·CHCl3, 1·Cl(CH2)2Cl and 2·Cl(CH2)2Cl crystallise in the P212121 space group. In these inclusion crystals, the C,H···Cl interactions between the guest and the host molecules are primarily responsible for enclatheration of the chloroalkane molecules. In the case of CH2Cl2, one of its Cl atoms acts as the acceptor. On the other hand, for CHCl3 and Cl(CH2)2Cl, the metal coordinated Cl atom of the host complex acts as the acceptor. The structures of 1·(P)-Cl(CH2)2Cl and 2·(M)-Cl(CH2)2Cl provide rare examples for chiral recognition of the right handed (P) and the left handed (M) gauche forms of Cl(CH2)2Cl in molecular assemblies. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2006) [source]

### Calculated spectral properties of perylene orange, perylene red, and their complex with sodium azide

INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 13 2007
Anuar Aldongarov
Abstract Using the method of density functional theory in approximating B3LYP with the basis set 6-31G(d) the computations of structures of the following dyes 2,2,- N - N,-di(1,3-diisopropylbenzene)-diimide 3,4,9,10-perylenetethracarbon acid (Perylene Orange-PO) and 1,6,7,12-tethraphenyl ether 2,2,- N,N,-di(1,3-diisopropylbenzene)-diimide 3,4,9,10-perylenetethracarbon acid (Perylene Red-PR) were performed. It was revealed that PO and PR have nonplanar structures. On the basis of the predicted geometrical structures and molecular orbitals of S0 ground state their theoretical UV-vis spectra, which are in good agreement with experiment, were obtained by applying time-dependent DFT (TDDFT) method. In addition, the calculations of complex [PR , NaN3] and its UV-vis spectrum, which was compared with the observed electron spectrum of PR ethanol solution in the presence of NaN3 under the laser irradiation at 532 nm, were carried out. By using DFT method at B3LYP level the calculations of the assumed complex were made where the reaction coordinate was the distance between Na+ and carbonyl group O atom. It was suggested that [PR , NaN3] complex formation involves transition of PR to the triplet state which brings about formation of PR anion. New peak at 793 nm in UV-vis spectrum of this solution under the laser irradiation at 532 nm is supposed to be a PR anion band. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2007 [source]

### H-doped PbTiO3: Structure and electronic properties

INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 6 2007
Arvids Stashans
Abstract The geometry and electronic properties of the interstitial H atom in the tetragonal PbTiO3 crystal have been studied using an advanced quantum chemical computer code developed for the modeling of crystals. The inserted H atom was found to bind to one of the O atoms and to form the hydroxyl, OH group, with the inter-atomic distance equal to 0.93 Å and 1.00 Å for the hydroxyls containing O atom in the dimerized and nondimerized TiOTi chains, respectively. Atomic displacements in the vicinity of OH complex are calculated and analyzed in relation to the H-produced changes upon the atomic charges in defective region. The role of H impurity on the ferroelectric polarization in the tetragonal PbTiO3 is discussed in terms of the results obtained in our research and those presented in the other studies on this subject. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007 [source]

### First-principle calculations on CO oxidation catalyzed by a gold nanoparticle

JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 2 2010
Hsin-Tsung Chen

### Intermolecular H-bond in propan-2-ol and its solutions with acetonitrile

JOURNAL OF RAMAN SPECTROSCOPY, Issue 12 2007
F. H. Tukhvatullin
Abstract Formation of propan-2-ol,acetonitrile dimers is manifested in the Raman spectra as an appearance of a band of aggregates in the high-wavenumber side of the CN vibrational band of liquid acetonitrile (,2 cm,1). The intensity of the band of aggregates changes with a change in the concentration of the mixture (1,0.05 mole fraction). For propan-2-ol we carried out nonempirical calculations of a structure of isolated dimer aggregates. The formation of an intramolecular H-bond between the H and the O atom of the \newbox\osprulebox \newdimen\osprulewd \def\osprule#1#2{ \global\setbox\osprulebox=\hbox{#1} \osprulewd=\wd\osprulebox\advance\osprulewd by -8pt \raise0.5pc\hbox{\matrix{\hskip-1pt\lower6.5pt\hbox{\vrule height #2pt}\lower4.5pt\hbox to \osprulewd{\hrulefill}\lower6.5pt\hbox{\vrule height #2pt}\cr \noalign{\vskip-1pt} \hbox{#1}\cr}} } $\osprule{{\rm HCO}}{2.5} \hbox{H}$ group of length 2.045 Å is possible in the monomer molecule. The CH3 groups of alcohol are not equivalent. In the dimer formation, intramolecular H-bond in the \newbox\osprulebox \newdimen\osprulewd \def\osprule#1#2{ \global\setbox\osprulebox=\hbox{#1} \osprulewd=\wd\osprulebox\advance\osprulewd by -8pt \raise0.5pc\hbox{\matrix{\hskip-1pt\lower6.5pt\hbox{\vrule height #2pt}\lower4.5pt\hbox to \osprulewd{\hrulefill}\lower6.5pt\hbox{\vrule height #2pt}\cr \noalign{\vskip-1pt} \hbox{#1}\cr}} } $\osprule{{\rm HCO}}{2.5} \hbox{H}$ group is preserved. An intermolecular H-bond of length 2.045 Å and energy 15 kJ/mole is formed between the H atom of one molecule and the O atom of another molecule of the OH. The length and energy of the H-bond for the propan-2-ol,acetonitrile dimer formations calculate to 2.27 Å and 12.9 kJ/mole, respectively. The H-bond is formed by ,-electrons of nitrogen. The experimental data and the results of calculations are in good agreement. Copyright © 2007 John Wiley & Sons, Ltd. [source]

### Uniaxial stress study of the Cu,H complex in ZnO

PHYSICA STATUS SOLIDI (B) BASIC SOLID STATE PHYSICS, Issue 12 2006
E. V. Lavrov
The cover picture of the current issue refers to the article by Lavrov and Weber which was selected as Editor's Choice [1]. The picture shows a microscopic model of the Cu,H complex investigated in the paper. The complex consists of a substitutional Cu atom at the Zn site with an H atom located between nearby O and Cu in the basal plane of the ZnO lattice. The atoms are shown in different colors: yellow for copper, red for hydrogen, cyan for oxygen, and grey for zinc. Hydrogen forms a strong bond with the O atom which gives rise to a local vibrational mode at 3192 cm,1 investigated in the paper under uniaxial stress. The c -axis is parallel to the Cu,O bond pointing to the top of the figure. The authors work at the Institute of Applied Physics/Semiconductor Physics, TU Dresden, Germany. [source]

### The exchange interaction in (Ga,Cr)N doped with oxygen impurities

PHYSICA STATUS SOLIDI (C) - CURRENT TOPICS IN SOLID STATE PHYSICS, Issue 12 2006
Tatsuya Nakano
Abstract We have studied the effect of O impurities on exchange interactions between Cr spins in (Ga,Cr)N by means of first-principles calculations based on the density functional theory. Although the magnetic moment par Cr atom is enhanced, the magnitude of ferromagnetic exchange interaction between Cr spins is reduced by co-doping with O into (Ga,Cr)N. In particular, the reduction is remarkable when the doped O atom forms a Cr-O-Cr complex. On the other hand, the ferromagnetic exchange interaction is not reduced if the O atom is separated from Cr atoms in (Ga,Cr)N. Nitrogen vacancy (VN) also has similar effects to O impurities. The formation energy of the Cr-O-Cr complex is lower than that of Cr- VN -Cr, so that excessive O codoping could reduce the ferromagnetic interaction between Cr spins more seriously than the formation of N vacancies. (© 2006 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source]

### First principles simulations of F centers in cubic SrTiO3

PHYSICA STATUS SOLIDI (C) - CURRENT TOPICS IN SOLID STATE PHYSICS, Issue 1 2005
J. Carrasco
Abstract Atomic and electronic structure of regular and O-deficient SrTiO3 have been studied. Several types of first principles atomistic simulations: Hartree-Fock method, Density Functional Theory, and hybrid HF-DFT functionals, have been applied to periodic models that consider supercells of different sizes (ranging between 40 and 240 atoms). We confirm the ionic character of the Sr-O bonds and the high covalency of the Ti-O2 substructure. For the stoichiometric cubic crystal; the lattice constant and bulk modulus correctly reproduce the experimental data whereas the band gap is only properly obtained by the B3PW functional. The relaxed geometry around the F center shows a large expansion of the two nearest Ti ions. Moreover, the vacancy formation energy is extremely sensitive to the size and the shape of the supercell as well as the calculation method. The electronic density map indicates the redistribution of two electrons of the missing O atom between the vacancy and 3d atomic orbitals of the two nearest Ti ions, in contrast to the F centers in ionic oxides where the charge centroid does not change. (© 2005 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source]

### The OD interpretation of the crystal structure of kettnerite CaBiOFCO3

ACTA CRYSTALLOGRAPHICA SECTION A, Issue 6 2009
í Hybler
The mineral kettnerite, CaBi(OFCO3), is a rare example of an order,disorder (OD) structure with a quadratic net. The lattice parameters of the simplest possible 1O polytype are a = 5.3641,(1), b = 5.3641,(1), c = 13.5771,(2),Å, and the space group is Pbaa. There are three kinds of OD layers, identical to structure-building layers. Two of them are non-polar: the Bi,O and Ca,F at z = 0 and z = 1/2, respectively, with the layer-group symmetry C2/m2/m(4/a,b)21/m21/m. The third kind of OD layer of CO3 groups (located between the Bi,O and Ca,F layers) is polar, with alternating sense of polarity. The layer group is Pba(4)mm. Triangular CO3 groups are parallel to (110) or () planes with one O atom oriented towards the Bi,O layer and the remaining two O atoms oriented towards the Ca,F layer. The orientations of CO3 groups alternate along the [110] and [] directions. As a result, each group parallel to (110) is surrounded by four nearest neighbors parallel to () and vice versa. These positions can be interchanged by an (a + b)/2 shift or by ,/2 rotation; thus stacking of the layer onto adjacent ones is ambiguous. Instead of OD layers, the polytypes are generated by stacking of OD packets, comprising the whole CO3 layers and adjacent halves of the Bi,O and Ca,F layers. They are polar, with alternating sense of polarity; the layer group is Pba(4)mm. Stacking sequences are expressed by ball-and-stick models, with the aid of symbolic figures, and by sequences of orientational characters. There are two maximum-degree-of-order (MDO) polytypes, 1O (really found and described, see lattice parameters and space group above) and 2O, with doubled c parameter and space group Ibca (not yet found). The derivation of the MDO generating operations of both polytypes is presented in this paper. The stacking rule also allows another, non-MDO, polytype with doubled c, i.e. the 2Q polytype, space group P42bc (tetragonal, not yet found). Various kinds of domains can exist: (i) out-of-step domains shifted by (a + b)/2, (ii) twin domains rotated by ,/2 around local tetrads of odd or even packets, and (iii) upside-down domains in the polar 2Q polytype. Stacking sequences of 16 possible domains of the polytypes mentioned above are listed. Also 60 domains of four distinct six-packet polytypes are theoretically possible. [source]

### Chemistry of Ru(& 6 -1,3,5-cyclooctatriene)(,2 -dimethyl fumarate)2

THE CHEMICAL RECORD, Issue 3 2006
Take-Aki Mitsudo
Abstract The chemistry of a novel zerovalent Ru complex, Ru(,6 -cot)(,2 -dmfm)2 (1) (cot=1,3,5-cyclooctatriene; dmfm=dimethyl fumarate), is reviewed with a focus on its reactivity toward phosphines, amines, and H2O, as well as arenes and p -quinones. A variety of novel zerovalent Ru complexes were synthesized from Ru(,6 -cot)(,2 -dmfm)2 (1), and it was shown that the complexes preferably bear both electron-donating and -accepting ligands simultaneously to exhibit thermodynamic stability. The first isolable zerovalent Ru aqua complexes were successfully prepared, and in these complexes, the generation of a chiral center on the O atom of the coordinated H2O was disclosed. In addition, the characteristic catalytic activity of 1 in organic synthesis was considered by reviewing recently developed novel reactions: (i) dimerization of 2,5-norbornadiene to pentacyclo[6.6.0.02,6.03,13.010,14]tetradeca-4,11-diene (PCTD), (ii) intramolecular hydroamination of aminoalkynes to cyclic imines, (iii) formal [4+2] cycloaddition of alkynes with dmfm to trans -4-cyclohexene-1,2-dicarboxylates, and (iv) co-dimerization of dihydrofurans with ,,,-unsaturated esters to 2-alkylidenetetrahydrofurans. The products obtained here are expected to be used as novel functional organic monomers. © 2006 The Japan Chemical Journal Forum and Wiley Periodicals, Inc. Chem Rec 6: 107,116; 2006: Published online in Wiley InterScience (www.interscience.wiley.com) DOI 10.1002/tcr.20076 [source]

### Syntheses, spectroscopic study and X-ray crystallography of some new phosphoramidates and lanthanide(III) complexes of N -(4-nitrobenzoyl)- N,,N,,-bis(morpholino)phosphoric triamide

ACTA CRYSTALLOGRAPHICA SECTION B, Issue 4 2010
Khodayar Gholivand
New phosphoramidates with the formula RC(O)N(H)P(O)X2, R = 2-NO2,C6H4, 3-NO2,C6H4 and 4-NO2,C6H4, X = N(CH2CH3) (1),(3), NC4H8 (4),(6), and NC4H8O (7),(9) were synthesized and characterized by 1H, 13C, 31P NMR and IR spectroscopy, and elemental analysis. The reaction of (9) with hydrated lanthanide(III) nitrate leads to ten- or nine-coordinated complexes, (10),(13). The crystal structure has been determined for (3), (5), (9), (10) and (13). In contrast to all of the previously reported similar phosphoramidate compounds, the ,C(O),N(H),P(O) skeleton in the free ligand (9) shows a cisoid conformation, with the C=O and P=O double bonds adopting a nearly syn conformation. Quantum chemical calculations were applied for clarifying this exceptional conformational behavior. The monodentate neutral ligand (9) is coordinated to the metal ions via the phosphoryl O atom, adopting the usual anti conformation between the C=O and P=O groups. [source]

### Persistence of the stereochemical activity of the Bi3+ lone electron pair in Bi2Ga4O9 up to 50,GPa and crystal structure of the high-pressure phase

ACTA CRYSTALLOGRAPHICA SECTION B, Issue 3 2010
Alexandra Friedrich
The crystal structure of the high-pressure phase of bismuth gallium oxide, Bi2Ga4O9, was determined up to 30.5,(5),GPa from in situ single-crystal in-house and synchrotron X-ray diffraction. Structures were refined at ambient conditions and at pressures of 3.3,(2), 6.2,(3), 8.9,(1) and 14.9,(3),GPa for the low-pressure phase, and at 21.4,(5) and 30.5,(5),GPa for the high-pressure phase. The mode-Grüneisen parameters for the Raman modes of the low-pressure structure and the changes of the modes induced by the phase transition were obtained from Raman spectroscopic measurements. Complementary quantum-mechanical calculations based on density-functional theory were performed between 0 and 50,GPa. The phase transition is driven by a large spontaneous displacement of one O atom from a fully constrained position. The density-functional theory (DFT) model confirmed the persistence of the stereochemical activity of the lone electron pair up to at least 50,GPa in accordance with the crystal structure of the high-pressure phase. While the stereochemcial activity of the lone electron pair of Bi is reduced at increasing pressure, a symmetrization of the bismuth coordination was not observed in this pressure range. This shows an unexpected stability of the localization of the lone electron pair and of its stereochemical activity at high pressure. [source]

### Orientational disorder and phase transitions in crystals of (NH4)2NbOF5

ACTA CRYSTALLOGRAPHICA SECTION B, Issue 5 2008
Anatoly A. Udovenko
Ammonium oxopentafluoroniobate, (NH4)2NbOF5, was synthesized in a single-crystal form and the structures of its different phases were determined by X-ray diffraction at three temperatures: phase (I) at 297,K, phase (II) at 233,K and phase (III) at 198,K. The distorted [NbOF5]2, octahedra are of similar geometry in all three structures, with the central atom shifted towards the O atom. The structure of (I) is disordered, with three spatial orientations of the [NbOF5]2, octahedron related by a jump rotation around the pseudo-threefold local axis such that the disorder observed is of a dynamic nature. As the temperature decreases, the compound undergoes two phase transitions. The first is accompanied by full anionic ordering and partial ordering of the ammonium groups (phase II). The structure of (III) is completely ordered. The F and O atoms in the structures investigated were identified via the Nb,X (X = O and F) distances. The crystals of all three phases are twinned. [source]

### Electron density and energy density view on the atomic interactions in SrTiO3

ACTA CRYSTALLOGRAPHICA SECTION B, Issue 4 2002
Elizabeth A. Zhurova
The results of topological analysis of the electron density in an SrTiO3 crystal based on the experimental (at 145,K) and theoretical data are presented and discussed. The features of the electron density lead to the conclusion that the Ti,O interaction is of the partly polar covalent (or intermediate) type. Complicated atomic shapes defined by the zero-flux surfaces in the electron density are revealed. It is found that, in general, they are far from spherical and have very slight asphericity in the close-packed layers. The topological coordination numbers of Sr and Ti are the same as the geometrical numbers, whereas the topological coordination for the O atom (6) differs from the geometrical value (12). The latter results from the specific shape of the Ti-atom basin, which prevents bond-path formation between the O atoms. The analysis of the kinetic and potential energy densities derived from the electron density using the density functional theory formulae revealed the stabilizing crystal-forming role of the O atoms in SrTiO3. Structural homeomorphism between the experimental electron density and the potential and kinetic energy densities is observed. [source]

### Poly[aqua(,2 -benzene-1,4-dicarboxylato)(,2 -4,4,-bipyridine N,N,-dioxide)cadmium(II)], a threefold interpenetrating diamond net

ACTA CRYSTALLOGRAPHICA SECTION C, Issue 8 2010
Guohai Xu
In the title compound, [Cd(C8H4O4)(C10H8N2O2)(H2O)]n, (I), each CdII atom is seven-coordinated in a distorted monocapped trigonal prismatic coordination geometry, surrounded by four carboxylate O atoms from two different benzene-1,4-dicarboxylate (1,4-bdc) anions, two O atoms from two distinct 4,4,-bipyridine N,N,-dioxide (bpdo) ligands and one water O atom. The CdII atom and the water O atom are on a twofold rotation axis. The bpdo and 1,4-bdc ligands are on centers of inversion. Each crystallographically unique CdII center is bridged by the 1,4-bdc dianions and bpdo ligands to give a three-dimensional diamond framework containing large adamantanoid cages. Three identical such nets are interlocked with each other, thus directly leading to the formation of a threefold interpenetrated three-dimensional diamond architecture. To the best of our knowledge, (I) is the first example of a threefold interpenetrating diamond net based on both bpdo and carboxylate ligands. There are strong linear O,H...O hydrogen bonds between the water molecules and carboxylate O atoms within different diamond nets. Each diamond net is hydrogen bonded to its two neighbors through these hydrogen bonds, which further consolidates the threefold interpenetrating diamond framework. [source]

### 3-Nitrophenol,4,4,-bipyridyl N,N,-dioxide (2/1): a DFT study and CSD analysis of DPNO molecular complexes

ACTA CRYSTALLOGRAPHICA SECTION C, Issue 8 2010
Rodolfo Moreno-Fuquen
The title 2:1 complex of 3-nitrophenol (MNP) and 4,4,-bipyridyl N,N,-dioxide (DPNO), 2C6H5NO3·C10H8N2O2 or 2MNP·DPNO, crystallizes as a centrosymmetric three-component adduct with a dihedral angle of 59.40,(8)° between the planes of the benzene rings of MNP and DPNO (the DPNO moiety lies across a crystallographic inversion centre located at the mid-point of the C,C bond linking its aromatic rings). The complex owes its formation to O,H...O hydrogen bonds [O...O = 2.605,(3),Å]. Molecules are linked by intermolecular C,H...O and C,H...N interactions forming R21(6) and R22(10) rings, and R66(34) and R44(26) macro-rings, all of which are aligned along the [01] direction, and R22(10) and R21(7) rings aligned along the [010] direction. The combination of chains of rings along the [01] and [010] directions generates the three-dimensional structure. A total of 27 systems containing the DNPO molecule and forming molecular complexes of an organic nature were analysed and compared with the structural characteristics of the dioxide reported here. The N,O distance [1.325,(2),Å] depends not only on the interactions involving the O atom at the N,O group, but also on the structural ordering and additional three-dimensional interactions in the crystal structure. A density functional theory (DFT) optimized structure at the B3LYP/6-311G(d,p) level is compared with the molecular structure in the solid state. [source]

### Ethyl 3-[1-(5,5-dimethyl-2-oxo-1,3,2-dioxaphosphorin-2-yl)propan-2-ylidene]carbazate: a combined X-ray and density functional theory (DFT) study

ACTA CRYSTALLOGRAPHICA SECTION C, Issue 7 2010
Youssef Arfaoui
In the title compound, C11H21N2O5P, one of the two carbazate N atoms is involved in the C=N double bond and the H atom of the second N atom is engaged in an intramolecular hydrogen bond with an O atom from the dimethylphosphorin-2-yl group, which is in an uncommon cis position with respect to the carbamate group. The cohesion of the crystal structure is also reinforced by weak intermolecular hydrogen bonds. Density functional theory (DFT) calculations at the B3LYP/6-311++g(2d,2p) level revealed the lowest energy structure to have a Z configuration at the C=N bond, which is consistent with the configuration found in the X-ray crystal structure, as well as a less stable E counterpart which lies 2.0,kcal,mol,1 higher in potential energy. Correlations between the experimental and computational studies are discussed. [source]

### Different hydrogen-bonding modes in two closely related oximes

ACTA CRYSTALLOGRAPHICA SECTION C, Issue 6 2010
Grzegorz Dutkiewicz
Two closely related oximes, namely 1-chloroacetyl-3-ethyl-2,6-diphenylpiperidin-4-one oxime, C21H23ClN2O2, (I), and 1-chloroacetyl-2,6-diphenyl-3-(propan-2-yl)piperidin-4-one oxime, C22H25ClN2O2, (II), despite their identical sets of hydrogen-bond donors and acceptors, display basically different hydrogen-bonding patterns in their crystal structures. While the molecules of (I) are organized into typical centrosymmetric dimers, created by oxime,oxime O,H...N hydrogen bonds, in the structure of (II) there are infinite chains of molecules connected by O,H...O hydrogen bonds, in which the carbonyl O atom from the chloroacetyl group acts as the hydrogen-bond acceptor. Despite the differences in the hydrogen-bond schemes, the ,OH groups are always in typical anti positions (C,N,O,H torsion angles of ca 180°). The oxime group in (I) is disordered, with the hydroxy groups occupying two distinct positions and C,C,N,O torsion angles of approximately 0 and 180° for the two alternatives. This disorder, even though the site-occupancy factor of the less occupied position is as low as ca 0.06, is also observed at lower temperatures, which seems to favour the statistical and not the dynamic nature of this phenomenon. [source]

### Hydrogen-bonded supramolecular networks of N,N,-bis(4-pyridylmethyl)oxalamide and 4,4,-{[oxalylbis(azanediyl)]dimethylene}dipyridinium dinitrate

ACTA CRYSTALLOGRAPHICA SECTION C, Issue 5 2010
Gene-Hsiang Lee
The molecule of N,N,-bis(4-pyridylmethyl)oxalamide, C14H14N4O2, (I) or 4py-ox, has an inversion center in the middle of the oxalamide group. Adjacent molecules are then linked through intermolecular N,H...N and C,H...O hydrogen bonds, forming an extended supramolecular network. 4,4,-{[Oxalylbis(azanediyl)]dimethylene}dipyridinium dinitrate, C14H16N4O22+·2NO3,, (II), contains a diprotonated 4py-ox cation and two nitrate counter-anions. Each nitrate ion is hydrogen bonded to four 4py-ox cations via intermolecular N,H...O and C,H...O interactions. Adjacent 4py-ox cations are linked through weak C,H...O hydrogen bonding between an ,-pyridinium C atom and an oxalamide O atom, forming a two-dimensional extended supramolecular network. [source]

### Fully and partially fluorinated flavone derivatives

ACTA CRYSTALLOGRAPHICA SECTION C, Issue 5 2010
Akiko Hori
In the crystal structures of the fully and partially fluorinated flavone derivatives 5,6,7,8-tetrafluoro-2-(2,3,4,5,6-pentafluorophenyl)-4H -1-benzopyran-4-one, C15HF9O2, (I), and 5,6,7,8-tetrafluoro-2-phenyl-4H -1-benzopyran-4-one, C15H6F4O2, (II), the pentafluorophenyl group and the pyranone moiety in (I) are twisted due to repulsion of the F substituents, and a CO(,,)...,(,+) intermolecular interaction is observed between the carbonyl O atom and the pentafluorophenyl group. In (II), on the other hand, the phenyl group and the pyranone moiety are almost coplanar, and arene,perfluoroarene interactions are observed in the head-to-tail intermolecular columnar stacking between the phenyl group and the tetrafluorophenylene moiety. [source]

### Poly[[[aqua(2,2,-bipyridine-,2N,N,)manganese(II)]-,-croconato-,4O,O,:O,,,O,,,] monohydrate]: a one-dimensional coordination polymer connected by hydrophilic,hydrophilic and lipophilic,lipophilic interactions at 135,K

ACTA CRYSTALLOGRAPHICA SECTION C, Issue 4 2010
Hong-Feng Chen
In the title one-dimensional coordination polymer, {[Mn(C5O5)(C10H8N2)(H2O)]·H2O}n, each MnII ion is seven-coordinated by four O atoms from two croconate ligands, two N atoms from a 2,2,-bipyridine (2,2,-bipy) ligand and one O atom from an aqua ligand. The croconate ligand bridges the MnII ions in a bis-bidentate chelation mode, forming an extended [Mn(C5O5)]n chain running parallel to the [001] direction, with the lipophilic 2,2,-bipy ligands lying along one side and the hydrophilic water molecules along the opposite side. Coordinated water and solvent water molecules are arranged in the hydrophilic layer, which is characterized by O,H...O hydrogen bonds between croconate ligands. Meanwhile, 2,2,-bipy ligands from adjacent chains partially overlap and exhibit ,,, interactions to form a lipophilic layer. The hydrophilic and lipophilic layers are arranged alternately to build a layer structure. [source]

ACTA CRYSTALLOGRAPHICA SECTION C, Issue 4 2010
Sitang Yan
The title compound, {[Cd2(C9HNO8)(H2O)4]·H2O}n, consists of two crystallographically independent CdII cations, one tetrabasic pyridine-2,3,5,6-tetracarboxylate (pdtc) anion, four coordinated water molecules and one solvent water molecule. The CdII cations have distorted square-antiprismatic (one pyridine N, six carboxylate O and one water O atom) and octahedral (three carboxylate O and three water O atoms) coordination environments. Each pdtc ligand employs its pyridine and carboxylate groups to chelate and bridge seven CdII cations. The square-antiprismatic coordinated CdII cations are linked by pdtc ligands into a lamellar framework structure, while the octahedral coordinated CdII cations are bridged by the ,2 -carboxylate O atoms and the pdtc ligands into a chain network that further joins neighbouring lamellae into a three-dimensional porous network. The cavities are filled with solvent water molecules that are linked to the host through complex hydrogen bonding. [source]

### Hydrogen-bonding patterns in three substituted N -benzyl- N -(3- tert -butyl-1-phenyl-1H -pyrazol-5-yl)acetamides

ACTA CRYSTALLOGRAPHICA SECTION C, Issue 4 2010
Gerson López
The molecules of N -(3- tert -butyl-1-phenyl-1H -pyrazol-5-yl)-2-chloro- N -(4-methoxybenzyl)acetamide, C23H26ClN3O2, are linked into a chain of edge-fused centrosymmetric rings by a combination of one C,H...O hydrogen bond and one C,H...,(arene) hydrogen bond. In N -(3- tert -butyl-1-phenyl-1H -pyrazol-5-yl)-2-chloro- N -(4-chlorobenzyl)acetamide, C22H23Cl2N3O, a combination of one C,H...O hydrogen bond and two C,H...,(arene) hydrogen bonds, which utilize different aryl rings as the acceptors, link the molecules into sheets. The molecules of S -[N -(3- tert -butyl-1-phenyl-1H -pyrazol-5-yl)- N -(4-methylbenzyl)carbamoyl]methyl O -ethyl carbonodithioate, C26H31N3O2S2, are also linked into sheets, now by a combination of two C,H...O hydrogen bonds, both of which utilize the amide O atom as the acceptor, and two C,H...,(arene) hydrogen bonds, which utilize different aryl groups as the acceptors. [source]

### Ba2Gd2(Si4O13): a silicate with finite Si4O13 chains

ACTA CRYSTALLOGRAPHICA SECTION C, Issue 3 2010
Maria Wierzbicka-Wieczorek
The title compound, dibarium digadolinium(III) tetrasilicate, crystallized from a molybdate-based flux. It represents a new structure type and contains finite zigzag-shaped C2 -symmetric Si4O13 chains and Gd2O12 dimers built of edge-sharing GdO7 polyhedra. The [9+1]-coordinated Ba atoms are located in voids in the atomic arrangement. All atoms are in general positions except for one O atom, which lies on a twofold axis. The structure is compared with those of the few other known tetrasilicates. [source]

### Poly[[trans -diaquabis(,2 -biphenyl-2,2,-dicarboxylato)bis(,2 -4,4,-bipyridine)dicobalt(II)] biphenyl-2,2,-dicarboxylic acid disolvate]

ACTA CRYSTALLOGRAPHICA SECTION C, Issue 2 2010
Ge Zhan
In the title compound, {[Co2(C14H8O4)2(C10H8N2)2(H2O)2]·2C14H10O4}n, each CoII ion is six-coordinate in a slightly distorted octahedral geometry. Both CoII ions are located on twofold axes. One is surrounded by two O atoms from two biphenyl-2,2,-dicarboxylate (dpa) dianions, two N atoms from two 4,4,-bipyridine (bpy) ligands and two water molecules, while the second is surrounded by four O atoms from two dpa dianions and two N atoms from two bpy ligands. The coordinated dpa dianion functions as a ,3 -bridge between the two CoII ions. One carboxylate group of a dpa dianion bridges two adjacent CoII ions, and one O atom of the other carboxylate group also chelates to a CoII ion. The CoII ions are bridged by dpa dianions and bpy ligands to form a chiral sheet. There are several strong intermolecular hydrogen bonds between the H2dpa solvent molecule and the chiral sheet, which result in a sandwich structure. [source]

### Bis(,-benzene-1,2-dicarboxylato)bis{aqua[2-(2-chloro-6-fluorophenyl)-1H -imidazo[4,5- f][1,10]phenanthroline]cadmium(II)} and its zinc(II) analogue

ACTA CRYSTALLOGRAPHICA SECTION C, Issue 12 2009
Xiu-Yan Wang
In the isomorphous title compounds, [Cd2(C8H4O4)2(C19H10ClFN4)2(H2O)2] and [Zn2(C8H4O4)2(C19H10ClFN4)2(H2O)2], the CdII centre is seven-coordinated by two N atoms from one [2-(2-chloro-6-fluorophenyl)-1H -imidazo[4,5- f][1,10]phenanthroline (L) ligand, one water O atom and four carboxylate O atoms from two different benzene-1,2-dicarboxylate (1,2-bdc) ligands in a distorted pentagonal,bipyramidal coordination, while the ZnII centre is six-coordinated by two N atoms from one L ligand, one water O atom and three carboxylate O atoms from two different 1,2-bdc ligands in a distorted octahedral coordination. Each pair of adjacent metal centres is bridged by two 1,2-bdc ligands to form a dimeric structure. In the dimer, each L ligand coordinates one metal centre. The dimer is centrosymmetric, with a crystallographic inversion centre midway between the two metal centres. The aromatic interactions lead the dimers to form a two-dimensional supramolecular architecture. Finally, O,H...O and N,H...O hydrogen bonds reinforce the two-dimensional structures of the two compounds. [source]

### catena -Poly[[aqua(11-chloropyrido[2,,3,:2,3]pyrimidino[5,6- f][1,10]phenanthroline-,2N4,N5)cadmium(II)]-,-benzene-1,4-dicarboxylato-,3O1,O1,:O4]: an inclined interpenetrating (6,3) network

ACTA CRYSTALLOGRAPHICA SECTION C, Issue 12 2009
Zhi-Guo Kong
The asymmetric unit of the title compound, [Cd(C8H4O4)(C17H8ClN5)(H2O)]n, contains one CdII atom, two half benzene-1,4-dicarboxylate (1,4-bdc) anions, one 11-chloropyrido[2,,3,:2,3]pyrimidino[5,6- f][1,10]phenanthroline (L) ligand and one coordination water molecule. The 1,4-bdc ligands are on inversion centers at the centroids of the arene rings. The CdII atom is six-coordinated by two N atoms from one L ligand, three carboxylate O atoms from two different 1,4-bdc ligands and one water O atom in a distorted octahedral coordination sphere. Each CdII center is bridged by the 1,4-bdc dianions to give a one-dimensional chain. ,,, stacking interactions between L ligands of neighboring chains extend adjacent chains into a two-dimensional supramolecular (6,3) network. Neighboring (6,3) networks are interpenetrated in an unusual inclined mode, resulting in a three-dimensional framework. Additionally, the water,carboxylate O,H...O hydrogen bonds observed in the network consolidate the interpenetrating nets. [source]

### Two isomorphous crotonatolanthanide complexes: tetra-,-but-2-enoato-bis[diaqua(but-2-enoato)Ln],2,6-diaminopurine (1/2) (Ln = Dy and Ho)

ACTA CRYSTALLOGRAPHICA SECTION C, Issue 11 2009
Ana María Atria
The title isomorphous compounds, tetra-,-but-2-enoato-bis[diaqua(but-2-enoato)dysprosium(III)],2,6-diaminopurine (1/2), [Dy2(C4H5O2)6(H2O)4]·2C5H6N6, and tetra-,-but-2-enoato-bis[diaqua(but-2-enoato)holmium(III)],2,6-diaminopurine (1/2), [Ho2(C4H5O2)6(H2O)4]·2C5H6N6, consist of [Ln(crot)3(H2O)2]2 dimers (crot is crotonate or but-2-enoate; Ln is the lanthanide cation), built up around inversion centres and completed by 2,6-diaminopurine molecules. The lanthanide cation is coordinated by three chelating crotonate units and two water molecules. One of the chelating carboxylate groups acts also in a bridging mode sharing one O atom with both cations and the final result is a pair of DyO9 tricapped prismatic polyhedra linked to each other through a central (Dy,O)2 loop. A feature of the structures is the existence of a complex intermolecular interaction scheme involving two sets of tightly interlinked non-intersecting one-dimensional structures, one of them formed by the [Dy(crot)3(H2O)2]2 dimers (running along [100] and linked by O,H...O hydrogen bonds) and the second formed by 2,6-diaminopurine molecules (evolving along [010] linked by N,H...N hydrogen bonds). [source]

### Trans influence in a mer -octahedral triiodidolanthanide: triiodidotris(tetrahydrofuran-,O)ytterbium(III)

ACTA CRYSTALLOGRAPHICA SECTION C, Issue 11 2009
Thomas J. Emge
The structure of the six-coordinate title complex, [YbI3(C4H8O)3], is the first mer -octahedral form of an LnI3L3 lanthanide (Ln) compound with neutral L ligands, and is closely related to that of several of the seven-coordinate LnX3L4 series of compounds, where X = Cl, Br or I and L = tetrahydrofuran (THF), isopropanol, pyridine or water. A structural trans effect can be assigned to YbI3(THF)3, in contrast to the LnX3L4 compounds, where steric and crystal packing effects are significant. The Yb,I bond lengths are 2.9543,(4) and 2.9151,(6),Å for I trans and cis to I, respectively, and the Yb,O bond lengths are 2.299,(5) and 2.251,(3),Å for O trans and cis to I, respectively. The crystal packing allows for six contact distances as weak C,H...I interactions in the range 3.10,3.24,Å. The title molecule has a crystallographic twofold axis passing through a THF O atom, the trans I atom and the Yb atom. [source]