Mean Molecular Plane Research Articles

Crystal structure of poly(p‐phenylene) prepared by organometallic technique

AbstractThe two‐dimensional crystal structure of poly(p‐phenylene) is investigated by linkedatom Rietveld analysis of the x‐ray diffraction powder profile. Two molecular chains are packed in a rectangular pgg unit cell (a = 0.779 nm; b = 0.551 nm) with a paracrystalline shift distortion along the chain axis. The molecular conformation is not rigidly planar; rotations between adjacent phenyl‐ring planes in a molecule alternate with an angle of about 20°. The setting angle between the mean molecular plane and the a axis is 55.5°.

Conformation of condensed polycyclic aromatic hydrocarbons Part III. The molecular and crystal structure of tribenzo [ a,h,rst] phenanthra [1,2,10- cde] pentaphene: a simple analysis of the in-plane distortions due to overcrowding

The crystal and molecular structure of tribenzo [ a,h,rst] phenanthra [1,2,10- cde] pentaphene was determined by X-ray diffraction with final agreement factor R=0.057 for 2842 reflections. The molecule is largely distorted from a planar structure owing to a steric repulsion between the overcrowded hydrogen atoms. The deviations of the atoms from the mean plane of the whole molecule range from −1.78 to 1.52 Å. The molecule has an approximate twofold axis perpendicular to the mean molecular plane and takes a saddle form. A simple analysis of the out-of-plane and in-plane distortions shows that the latter should not be neglected.

Crystal and molecular structure of bis(N-ethanol-2-oxy-1-naphthylideneaminato)copper(II)

The crystal structure of the title compound has been determined from single-crystal X-ray diffraction data. The compound crystallizes in the monoclinic space groupp21 witha=5.5406(4),b=17.0461(9),c=11.3762(6) A,β=93.99(1)°, andZ=2. The structure was solved by direct methods, and refined by full-matrix least squares toR=0.036 andR w =0.039 for 2134 intensities above 3σ(7). The ethanolic O atoms [O(3) and O(4)] are not involved in the Cu coordination. The two bidentate ligands are connected to copper(II) atoms by their phenolic O atoms and imino N atoms in the O-O and N-N trans positions. A tetrahedral distortion of the square coordination is observed. The ethanolic oxygen atoms are involved as donors in intramolecular hydrogen bonds O(4)-H-O(1) and as donors and acceptors in intermolecular O(3)-H-O(4) ones. The molecule is substituent-trans, as the ethanol groups are oriented towards the opposite sides of the mean molecular plane. The molecular structure is compared with the literature data.

The crystal structure of 1-methyltriphenylene

The crystal structure of 1-methyltriphenylene, C 19 H 14 , has been determined by application of direct methods to single-crystal X-ray diffractometric data, with refinement by least-squares to R = 0.087 over 987 independent reflections to give apparent estimated standard deviations of 0.01 Å in C – C bond lengths and 0.6° in C – C – C angles. In the methyl-substituted bay region, molecular overcrowding is relieved by a long beach bond C13 – C14 = 1.50(1) Å and a C14 – C1 – C19 bond angle of 126° to the methyl group, with the beach-arm bond angles C12 – C13 – C14 = 122° and C13 – C14 – C1 = 124° compared with about 121° in the unsubstituted bay regions. Substitution of the methyl group into nearly planar triphenylene also causes ring-carbon atoms in all three peripheral rings to deviate by as much as ± 0.3 Å from the mean molecular plane; the methyl-carbon atom is 0.8 Å below this plane. The ring-methyl C1 – C19 bond is long [1.53(1) Å]; and, in the unsubstituted rings, the peripheral bonds C6 – C7 and C10 – C11 at 1.35(1) Å and 1.36(1) Å, respectively, are slightly shorter than in triphenylene.

Intramolecular hydrogen bonding. IX. Theoretical geometries of substituted anthraquinones relevant to proton transfer studies

Equilibrium geometries have been determined at the STO-3G RHF level for the ground electronic states of 1,4-, 1,5-, and 1,8-dihydroxyanthraquinone (DHAQ) and 1-aminoanthraquinone. Calculated bond lengths agree well with the limited available experimental data. The structure around the intramolecular hydrogen bonds is very similar in all three dihydroxyanthraquinones, including 1,8-DHAQ where both hydrogen bonds are to the same oxygen atom. The form arising from double intramolecular proton transfer in 1,4-DHAQ (quinizarin) is 10.4 kcal/mol higher in energy. Even though the hydrogen bond in 1-aminoanthraquinone is weak by the usual spectroscopic criteria, it appears to play a major role in organizing the molecule's structure. The oxygen and nitrogen atoms of the NH…OC hydrogen bond are moved in opposite directions out of the mean molecular plane. This, along with rotation about the CN bond, brings the proton of the hydrogen bond close to the plane in which the carbonyl oxygen lone pair electrons are expected to lie.

Structural Aspects of the Enantioselectivity of Tartrates with α‐Amino‐alcohol Salts part. I. Crystal structures of eleven tartaric‐acid diesters

AbstractEnantioselective host‐guest complexes of α‐amino‐alcohol salts with chiral tartaric‐acid esters can not be crystallised up to now. To study structural aspects of their enantioselectivity, crystal structures of the components were determined. The structures of eleven diesters with myrtanol, borneol, menthol, neomenthol, and cis‐4‐(tert‐butyl)cyclohexanol in different configurations showed a remarkable rigidity of the tartaric‐acid conformation, partly because of intramolecular H‐bonding between OH and C=O groups. The conformation of the tartaric‐acid part in these diesters is the same as the one observed in optically active tartaric acid (torsion angle OCCOH ca. 0°), The binding site for guest molecules is a parallelogram formed by two hydroxy and two carbonyl O‐atoms, all lying on the same side of a mean molecular plane. There is one exception: the dimenthyl ester, which is the most enantioselective with a norephedrine guest, has one of the ester groups turned (torsion angle OCCOH ca. 180°), forming a triangle of O‐atoms and moving the bulky menthyl group to the vicinity of the binding site.

The crystal and molecular structure of 9,10-dimethylphenanthrene

The crystal structure of 9,10-dimethylphenanthrene, C16H14, at room temperature, has been determined by direct methods and refined by least-squares to R = 0.030 over 554 independent reflections measured by diffractometer from a single crystal. Two molecules crystallise in a monoclinic unit cell, a = 9.103(3) Å, b = 5.454(2) Å, c = 11.666(3) Å, β = 104.27(2)°, in space group P21. Carbon atoms of each ring are planar to within 0.01 Å and adjacent ring planes are inclined at 1°. Methyl carbons C(15) and C(16) lie respectively 0.06 and 0.04 Å above and below the mean molecular plane of carbon atoms; this plane also contains the non-methyl hydrogen atoms to within 0.1 Å. Carbon – carbon bond lengths are C(12) – C(13) = 1.444(3) Å at the bay and C(9) – C(10) = 1.356(4) Å at the substituted K region.

Structures of the E,Z (cis–trans) isomer of diacetamide and the 1:1 complex with acetamide at 123 K. Ab-initio molecular orbital calculations on the Z,Z (trans–trans), E,Z (cis–trans) and E,E (cis–cis) isomers of diacetamide

The crystal structure of the E,Z (cis-trans) isomer of diacetamide, N-acetylacetamide, C4HvNO 2, has been refined using X-ray diffractometer data at 123 K. The crystal data are P2l/n, Z=4, a=4.069 (1), b= 16.818 (5), c = 7.604 (2) A, fl = 94.10 (3) °. The final agreement factors are R(F) = 0-050, wR(F) = 0.041 and S= 1-40 with 1384 observed reflections. The structure is disordered with an 8.2% minor component in which the molecules are appoximately related to those in the major site by a 180 ° rotation about the N1-C2 bond followed by a 51 ° rotation in the mean molecular plane about an axis through the central N atom. The crystal structure of the 1:1 complex of (E,Z)-diacetamide with acetamide, C4HvNO2.C2HsNO, is monoclinic, P2~/m, Z=2, a=7.695(9), b=6.443(8), c=8.918(9)A, fl= 108.90 (9) ° at 123 K. The structure was solved by direct methods and refined to R(F) = 0.059, wR(F) = 0.049, S = 1.61 with 1275 observed reflections. Ab-initio molecular orbital calculations at the HF/3-21G level gave energies for the Z,Z (trans-trans) and E,E (cis-cis) isomers of diacetamide of 24.6 and 45.8kJmol -I respectively higher than that of the most stable E,Z isomer. The largest difference in calculated bond lengths between the isomers was 0-014 A between the C-N bonds in the E,Z and Z,Z isomers. The theoretical calculations indicate that the significant differences in the C-N and C=O bond lengths observed in the crystal structures of diacetamide and acetamide are due, in part, to the differences in intermolecular hydrogen bonding of the NH, NH 2 and C=O groups.

X-ray refinement of the crystal and molecular structure of 1,12-dimethylbenz[a]anthracene.

The molecular and crystal structure of 1,12-dimethylbenz[a]anthracene, one of the least carcinogenic of the benz[a]anthracenes, has been refined, from new X-ray diffractometric data collected at room temperature, to an R index 0.047 over 1217 independent reflections. Improved determination of molecular geometry shows that steric strain arising from the presence of two bay-methyl substituents causes even greater molecular distortion than in the highly carcinogenic 7,12-dimethylbenz[a]anthracene, with the benzo A ring inclined at about 29 degrees to the furthest C and D rings. Methyl carbon atoms are displaced 1.0 and 1.3 A on opposite sides of the mean molecular plane and the beach bond of the bay region is 1.480(4) A long, flanked by C-C-C angles of 124.3 and 125.0 degrees. The shortest carbon-carbon bond is C5-C6 = 1.327(5) A at the K region, with the next shortest C8-C9 = 1.346(6) A. Close intramolecular approaches of methyl hydrogens across the bay and to nearest aromatic hydrogens are 2.3-2.6 A.

Solid state phase transitions in linear transition metal polymers: M-M VS. M-L-M modification in bisglyoximato nickel(II)

Abstract The band structure of bisglyoximato nickel(II) 1 , has been studied by means of crystal orbital (CO) calculations based on the tight-binding approximation as a function of the angle between the stacking axis and the mean molecular plane of the bisglyoximato ligand. The M-M phase of 1 is characterized by an angle of 90° (Δα = 0°) between the one-dimensional (1D) axis and the π plane of the organic fragments. The molecular planes of the glyoximato polymer are inclined to the 1D axis by an angle that differs from 90° in the M-L-M phase where the shortest intercell contacts are found between the 3d center and ligand atoms. Computational framework for the investigation of this phase transition (M-M ⇹ M-L-M) is a semiempirical INDO CO model. The band gap of 1 is reduced with increasing slipping deformations Δα. The width of the valence band is not significantly modified by the solid state transformation while the conduction band is broadened. The nature of the “Ni 3d bands” is significantly influenced by the mutual orientation of the organic π layers. Correlations between Ni 3dσ and 3dδ states and interconversions between ligand and transition metal CO wave functions are predicted in the M-L-M phase for large deformations Δα. Pronounced intramolecular charge redistributions are predicted as a function of the slipping deformation in the 1D stack. The intercell interactions in the M-M phase are prevailingly determined by classical Coulomb potentials while a strong covalent metal-ligand coupling is encountered in the M-L-M modification of 1 .

Structure and packing arrangement of molecular compounds. X. 9,10-Diazaphenanthrene–2,3-dichloro-5,6-dicyano-1,4-benzoquinone (2:1)

Crystals of the title compound, 2C12HsN2. CsCl2N202, M r = 587.4, are monoclinic, space group P2t/a, with four units of the complex in a unit cell of dimensions: a = 13.022 (8), b = 11.521 (8), c = 18.386 (8) A, fl97.36 (4)°; V = 2735.7 A a, D c = 1.305 Mg m -3, p(Mo Ka) = 0.28 mm -~. The structure was solved from four-circle diffractometer data by direct methods and was refined to a conventional R- 0.045 and a weighted r w = 0.041 for 1738 observations. The structure consists of sheets of 'dimerized' donors (diazaphenanthrene) which alternate with relatively flat layers of the acceptor (dichlorodicyanobenzoquinone) molecules. Each acceptor is thus enclosed in a 'vise' formed by two nearly coplanar donors, the mean molecular planes of donors and acceptor being nearly perpendicular. The existence of a significant attractive donor-acceptor interaction is suggested by short contacts (2.85-2.92 A) between the N atoms of the donors and the quinoid ring of the acceptor. The charge-transfer interaction is probably of the n-n* type. A remarkable similarity of the packing arrangement of the diazaphenanthrene layers to that found in uncomplexed diazaphenanthrene has been observed. This, rather unique, packing arrangement is illustrated in detail.

The crystal and molecular structure of R-(–)-1,1′-binaphthyl: the conformational isomerism and a comparison of the chiral with the racemic packing mode

The molecular and crystal structure of R-(–)-1,1′-binaphthyl has been determined from single-crystal X-ray data and refined by least-squares methods to R 0.045. The tetragonal crystal has unit-cell dimensions, a= 7.212 6(9), c= 27.510(5)A, space group P41212, and Z= 4. The molecule has a transoid conformation in the active crystal with a dihedral angle of 103° between the mean molecular planes of the two naphthalene residues. The packing modes of the molecules in the active and in the more dense (9.4%) racemic crystal are compared in connection with the spontaneous optical resolution of 1,1′-binaphthyl by crystallisation at temperatures above 76°.

Rational synthesis of unidimensional mixed valence solids. Structural, spectral, and electrical studies of charge distribution and transport in partially oxidized nickel and palladium bisdiphenylglyoximates

A detailed study is presented of solid-state structure, oxidation state, and electron transport in Ni(dpg)/sub 2/I and Pg(dpg)/sub 2/I, dpg = diphenylglyoximato. The crystal structure of Ni(dpg)/sub 2/I has been studied by x-ray diffraction at 23 and -160/sup 0/C. The compound crystallizes in the tetragonal space group D/sub 4h//sup 8/-P4/ncc, with four formula units of Ni(dpg)/sub 2/I in a unit cell having dimensions at -160/sup 0/C of a = 19.774 (8), c = 6.446 (3) A. Full-matrix least-squares refinement of 31 variables gave a final value of the conventional R index (on F) of 0.093 for 353 reflections having F/sub 0//sup 2/ > 3 sigma(F/sub 0//sup 2/). The crystal structure consists of stacked Ni(dpg)/sub 2/ units (staggered by 90/sup 0/) and disordered chains of iodine atoms extending in the c direction. At -160/sup 0/C the Ni--Ni separation is 3.223 (2) A; other important distances are Ni--N = 1.868 (15), N--C = 1.33 (3), N--O = 1.34 (3) A. The Ni(dpg)/sub 2/ moiety is decidedly nonplanar (D/sub 2/ symmetry) with coordinated N atoms displaced 0.12 (2) A above or below the mean molecular plane. Analysis of diffuse x-ray scattering associated with the disordered iodine chains is consistent with I/sub 5//sup -/more » being the predominant species. This result is in agreement with resonance Raman spectroscopic studies on Ni(dpg)/sub 2/I and Pd(dpg)/sub 2/I as well as on model compounds. Fundamental polyiodide transitions in the M(dpg)/sub 2/I materials are observed(..nu../sub 0/ = 4880--6471 A)at 161 vs and 107 w cm/sup -1/; weak M(dpg)/sub 2/-centered scattering is also noted. Iodination brings about an increase in conductivity of > 10/sup 8/ (Ni) and > 10/sup 7/ (Pd), which is especially noteworthy since the only major change in crystal structure upon iodination is a ca. 0.27 A decrease in the M(dpg)/sub 2/ stacking distance. Variable-temperature studies show the Ni(dpg)/sub 2/I and Pd(dpg)/sub 2/I conductivities to be thermally activated.« less

A naphtho-tri- t-butyltrisdehydro[16]annulene

Synthesis of a naphtho-tri- t-butyltrisdehydro[16]annulene has been described. Suppression of paratropicity of the 16-membered ring was observed. Comparison of 1H NMR spectrum of the [16]annulene with that of naphtho-tri- t-butylbisdehydro[14]annulene suggests that the trans double bond adjacent to naphthalene in the [16]annulene is twisted out of the mean molecular plane.

Crystal and molecular structures of overcrowded halogenated compounds. VIII. Decachlorophenanthrene

Decachlorophenanthrene, C14Cl10, is orthorhombic, a= 5.065 (3), b= 17.946 (6), e= 18.554 (5)A, space group Pbcn, Z=4, molecular symmetry C2 (2). The structure was solved by MULTAN and refined to R = 0.119 (1976 reflexions measured with Mo K0c on a Stoe semi-automatic Weissenberg diffractometer). The molecule is highly distorted from planarity, C1(4) and CI(5) being 1-43/~, respectively, above and below the mean molecular plane; d[Cl(4)... C1(5)] = 3.099 (3) A. Because of the buttressing effect of the other CI atoms, the phenanthrene skeleton shows less splaying apart than, for example, in 1,10-dichloro3,8-dimethyl-4,7-phenanthroline [Herbstein, Kapon & Rabinovich, Israel J. Chem. (1972), 10, 537558]. The crystal structures of decachlorophenanthrene, in which both enantiomers occur, and of benzo[c]phenanthrene [Herbstein & Schmidt, J. Chem. Soc. (1954), pp. 3302-3314] in which only one enantiomer occurs, are related in the same way as the crystal structures of DLand L-alanine, and other such racemate-optically active pairs.

The Crystal and Molecular Structures of Overcrowded Halogenated Compounds VII. 1:10‐Dichloro‐3:8‐Dimethyl4:7‐Phenanthroline

Abstract1,10‐dichloro‐3,8‐dimethyl‐4,7‐phenanthroline crystallizes in the triclinic system with a = 7.651(3), b = 7.792(3), c = 12.301(3)Å, α = 108.48(6), β = 82.74(2), γ = 116.53(4)° space group magnified image, Dm = 1.479 g cm−3, Dc = 1.480(5) g cm−3 for two formula units per cell. The intensities of about 2000 reflections were measured by semi‐automatic Weissenberg diffractometer and supplemented by precession diffractometer measurements. The crystal structure was solved by the SEARCH method (Rabinovich and Schmidt, Nature, 211: 1391 (1968)) and refined by full‐matrix least squares methods, using anisotropic temperature factors for non‐hydrogen atoms. The final R‐factor was 0.067 and the “goodness of fit” 0.94. The molecule has an approximate two‐fold axis of symmetry and is appreciably distorted from planarity, the two chlorines being displaced by +1.12Å and −1.15Å from the mean molecular plane; the non‐bonded ClCl distance is 3.082(3)Å. Bond lengths are close to standard values but there are appreciable distortions in bond angles, torsion angles and fold angles. There is hexagonal close packing of stacks of molecules, with van der Waals binding between stacks. Anti‐parallelism of adjacent molecules in a stack suggests that dipole‐dipole forces are important in the intrastack binding. Comparison of the present molecular structure with that of 2,7‐dibromo‐4,5‐bis‐(2‐pyridyl)phenanthrene‐3,6‐diol (Smith and Barrett, Acta Crystallogr., B27: 419 (1971)) shows that the present molecule is the more highly overcrowded.

The crystal structure of the 1:1 complex of s-trinitrobenzene and s-triaminobenzene

The crystals of the 1 : 1 complex formed between s-trinitrobenzene and s-triaminobenzene are purpleblack needles and monoclinic, space group P2 ~/a with cell dimensions: a = 14.063, b = 15.079, c = 6982/~ fl= 103.5 ° and Z = 4 . The structure has been determined by a three-dimensional X-ray analysis using visually estimated Cu K~ data. Phases were found for 110 reflexions by the symbolic addition procedure and the subsequent refinement was carried out by block-diagonal least-squares with anisotropic temperature factors, to an R value of 0.082. The component molecules are stacked alternalely in infinite columns parallel to the c axis. The mean molecular planes are inclined at 69-3 : to the stacking axis. The average spacings between overlapping molecules are 3.24 and 3.29 A, respectively. Bond lengths and angles in the s-trinitrobenzene molecule are in reasonable agreement with the corresponding values for the same molecule in other s-trinitrobenzene complexes. For the s-triaminobenzene molecule the average values are found to be: C -C= 1.400, C N = 1.398 A, /_CCC= 1200 ~ and ACCN = 119-8 °. Nitrogen atoms of amino groups are slightly out of the plane of the benzene ring.

The absorption and circular dichroism spectra and the absolute configuration of (+)-1-fluoro-12-methylbenzo[c] phenanthrene

The circular dichroism and electronic absorption spectra of (+)-1-fluoro-12-methylbenzo[c]phenanthrene are reported. The results are compared with the theoretical rotational and dipole strengths of the lower-energy π → π * transitions in the optical isomers of the overcrowded, non-coplanar, benzo[c]phenanthrene molecule. The comparison indicates that (+)-1-fluoro-12-methylbenzo[c]phenanthrene has the stereochemical form of a segment of a right-handed helix (I), viewed in the direction perpendicular to the mean molecular plane.

The crystal and molecular structure of perylene

Crystals of perylene, C20H12, are monoclinic with four molecules in a unit cell of dimensionsa= 11.277,b= 10.826,c= 10.263Å, B = 100.55°, space groupP21/a The intensities of 1135 reflexions were measured with a scintillation counter and MoKa radiation, and the 436 strongest reflexions were used in the structure refinement. The gross features of the structure previously determined from two projections, have been confirmed by the new threedimensional data, the positional and thermal parameters of the carbon atoms have been refined by least-squares and differential syntheses, and the hydrogen atoms have been approximately located. There are small, but significant deviations from a completely planar arrangement ; this minor distortion of the molecule is the result of slight intermolecular steric effects, and does not appear to be associated with any possible overcrowding in the 1, 12 and 6, 7 positions. The mean bond distances agree fairly closely with the values predicted by valence-bond and molecular-orbital calculations; theperi-bond lengths are 1.471 + 0.006 Å. All the intermolecular separations correspond to normal van der Waals interactions; the perpendicular distance between mean molecular planes is 3.46 Å.

The crystal structure of benzene at — 3°C

A new X -ray analysis has confirmed that the space group is Pbca , with four molecules per unit cell, and a = 7⋅460, b = 9⋅666 and c = 7⋅034 Å. 284 structure factors have been measured from oscillation photographs using Cu Kα radiation. The structure suggested by Cox (1932) was refined by the Fourier transform method and by two-dimensional Fourier and difference syntheses. The co-ordinates derived from the projections were refined by three-dimensional differential syntheses in which isotropic thermal parameters were used and termination of series errors corrected by the backshift method. After five differential cycles, electron density and difference maps calculated in the mean molecular plane revealed appreciable angular oscillations of the molecules about their senary axes. The refinement was continued by means of three-dimensional differential syntheses with anisotropic thermal parameters for the carbon atoms, and difference syntheses computed in the plane of the molecule and adjacent parallel planes. The criterion finally used to determine the anisotropic parameters was the equality of the observed and calculated atomic peak curvatures, the scale factor being adjusted to give the corrected integrated number of electrons in the molecule. The r. m. s. amplitude of angular oscillation about the senary axis is approximately 7⋅9°. An important consequence of the molecular angular oscillation is that the mean C—C bond length is increased by 0⋅015 Å to 1⋅392 Å, the likely limits o f error being not less than 0⋅010 Å. The result agrees satisfactorily with other determinations o f the C—C distance in benzene, notably Langseth & Stoicheff’s value (1956) of 1⋅397 4 ± 0⋅001 Å from the Raman spectrum of the gas. The carbon ring is accurately planar, individual co-ordinates being only 0⋅0013 Å from the mean plane. The final value of the residual R was 9⋅9%. During the refinement, an attempt was made to derive an accurate difference synthesis from which conclusions about bonding electrons could be drawn. The experimental data did not prove sufficiently reliable, and only very tentative conclusions have been obtained. Detailed examination of the crystal structure has shown that the molecules pack together like sheets of six-toothed gear wheels. This allows an easy in-phase oscillation o f the molecules about their senary axes, and explains the large r. m. s. amplitudes observed. Occasional rotations of molecules in groups are probably responsible for the narrowing of the nuclear magnetic resonance line above 120°K.