Mean Molecular Plane Research Articles

Crystal growth of para-sexiphenyl on clean and oxygen reconstructed Cu(110) surfaces

The formation of crystalline para-sexiphenyl (6P) films on Cu(110) and Cu(110)-(2 × 1)O (Cu-O) has been studied by low energy electron diffraction, X-ray absorption spectroscopy and both in situ and ex situ X-ray diffraction methods to elucidate the transition from the initial monolayers to crystalline thin films. It is found that, for Cu-O, a single and, for Cu(110), a double wetting layer is formed which then acts as a template for the subsequent 3D crystal growth. For both substrates the orientation of the long molecular axes of the 6P molecules in the first layers is conserved for the molecules in the bulk crystals growing on them. The main difference between both systems is that on Cu-O the first monolayer assembles in a form close to that of a 6P bulk plane which can be easily continued by crystallites grown upon them, while on the Cu(110) surface the 6P mono- and bi-layers differ substantially from the bulk structure. The bi-layer forms a complex periodically striped phase. Thin 6P films grow with the 6P(203) crystal plane parallel to the Cu-O substrate surface. For this orientation, the 6P molecules are stacked in layers and the molecules demonstrate only one tilt of the mean molecular plane with respect to the sample surface. On clean Cu(110), a more complex 6P(629) plane is parallel to the substrate surface and this orientation is likely a consequence of the super-molecular long-range periodicity of the second molecular layer striped phase.

Experimental and theoretical investigations of magnetic properties for two low-dimensional spin systems based on bis(2-thioxo-1,3-dithiole-4,5-dithiolato)nickelate monoanion building blocks

Two complexes of [Ni(dmit) 2] − (dmit 2− = 2-thioxo-1,3-dithiole-4,5-dithiolate) with nonmagnetic Schiff base cations, 1-(4-bromobenzylideneamino)pyridinium (4-BrBz-1-APy +; 1) and 1-(3-nitrobenzylideneamino)pyridinium (3-NO 2Bz-1-APy +; 2), have been characterized structurally. Their striking structural feature is the deviation of the [Ni(dmit) 2] − anion from the square-planar environment around the Ni atom with 11.42° and 6.57° dihedral angles (between the mean molecular planes of two dmit 2− ligands) in 1 and 2, respectively. These twists arise from the molecular packing interactions between the superimposed anion and cation. In 1, the magnetic [Ni(dmit) 2] − anions are arranged into a wave-shaped regular spin chain, whose magnetism was well fitted by one-dimensional (1D) Heisenberg uniform linear antiferromagnetic chain with | J/ k B| = 66 K. In 2, 1D ladder-shape [Ni(dmit) 2] − chains are formed through lateral-to-lateral S ⋯ S contacts between the adjacent anions, which are further aligned into a two-dimensional (2D) anion layer via van der Waals forces. Complex 2 shows Curie–Weiss-type paramagnetic behavior with Curie constant C = 0.421 emu K mol −1 and Weiss constant θ = −1.279 K. The broken-symmetry DFT approach was utilized to evaluate the magnetic coupling nature for 1 and 2, the theoretical analyses performed at ubpw91/lanl2dz level and concerned the so-called “weak bonding” regime approaches qualitatively explained the magnetic behaviors of 1 and 2.

Crystal structure of a p-tert-butylcalix[8]arene – N-methyl-morpholine complex

Abstract p-tert-Butyl-calix[8]arene crystallizes with six molecules of N-methyl-morpholine in a triclinic lattice, space group P1 with a = 12.142(3) Å, b = 16.596(4) Å, c = 17.211(2) Å, α = 83.72(2)°, β = 80.66(2)°, γ = 69.55(2)°, Z = 1. The formation of hydrogen bonds with two molecules of N-methyl-morpholine, induces the calix[8]arene skeleton to adopt a chair-like conformation in which two 3/4-cone moieties are oriented above and below the mean molecular plane, respectively. The other four solvent molecules per unit cell simply fill the interstitial voids in a “like-tubular” solid state assembly built by p-tert-butylcalix[8]arene molecules piled along the a-axis direction.

Fourier-transform infrared spectroscopic studies of dithia tetraphenylporphine

We present here infrared absorption spectra of dithia tetraphenylporphine and its cation in the 450–1600 and 2900–3400 cm−1 regions. Most of the allowed IR bands are observed in pairs due to overallD 2h point group symmetry of the molecule. The observed bands have been assigned to the porphyrin skeleton and phenyl ring modes. Some weak bands, which are forbidden underD 2h , also appear in the spectra due to the distortion of the molecule from planarity-caused by the out-of-plane positioned N and S atoms. Increased intensity of some phenyl ring bands compared to free-base tetraphenylporphine is explained on the basis of rotation of phenyl rings towards the mean molecular plane. Contrary to the point group symmetry of cation of dithia tetraphenylporphine, certain bands are observed to be degenerate due to identical bonding arrangements in pyrrole rings of the cation

Isogentisin (1,3-dihydroxy-7-methoxyxanthone)

The crystal structure of isogentisin, C14H10O5, a natural product isolated from Gentiana lutea, has been determined. The phenolic ring system is essentially planar and the displacement of the methoxy substituent from the mean molecular plane is very small. The structure is stabilized by a one-dimensional chain of intermolecular hydrogen bonds.

Zn(II), Cd(II) and Hg(II) complexes with 2,2′-Biquinoline, syntheses and X-ray crystal structures of [Hg(bq)(SCN)2

Reaction of the ligand 2,2′-biquinoline (bq) with Zn(ClO4)2, CdCl2 and Hg(SCN)2 gives complexes [Zn(bq)2] (ClO4)2, [Cd(bq)2Cl2] and [Hg(bq)(SCN)2] which were characterized by elemental analyses and IR spectroscopy. The crystal structure of [Hg(bq)(SCN)2] was determined by X-ray crystallography. The complex comprises a monomeric Hg(SCN)2 unit with one 2,2′-biquinoline (bq) ligand coordinated to the Hg atom via the two quinolinic nitrogens, giving rise to a five-membered chelate ring in a distorted tetrahedral environment. A π–π stacking interaction exists between the parallel aromatic rings in adjacent chains, resulting in a planar species in which the mean molecular planes are close to parallel and separated by a distance of ∼3.5 Å, close to that of the planes in graphite.

Syntheses and Characterization of Zinc, Cadmium, and Mercury(II) Complexes with N‐(2‐pyridyl)carbonylaniline (L), X‐ray Crystal Structure of [Hg(L)(SCN)2

AbstractThe reaction of N‐(2‐pyridyl)carbonylaniline (L) with Zn(NO3)2, CdCl2, and Hg(SCN)2 gives the following complexes: [Zn(L)2](NO3)2, [Cd(L)2Cl2], and [Hg(L)(SCN)2]. The new complexes were characterized by elemental analyses and IR‐, 1H‐, 13C‐NMR spectroscopy. The crystal structure of the [Hg(L)(SCN)2] was determined by single crystal X‐ray analysis. The monomeric complex is built up of a Hg(SCN)2 unit with one N‐(2‐pyridyl)carbonylaniline (L) ligand coordinated to the Hg atom via the ring pyridinic nitrogen atom and the carbonyl oxygen atom forming a five‐membered chelate ring. The Hg atom has a distorted tetrahedral environment. There is π‐π stacking interaction between the parallel aromatic rings belonging to adjacent chain as planar species in which the mean molecular planes are close to parallel and separated by a distance of ∼ 3.5Å, close to that of the planes in graphite. The coordinated N‐(2‐pyridyl)carbonylaniline (L) molecule is involved in hydrogen bonding acting as hydrogen‐bond donors with S and N atoms from SCN— ligand as potential hydrogen‐bond acceptors. There is a shortest intermolecular contacts between the S and N atoms. The hydrogen bonding and shortest intermolecular contacts between the S and N atoms yields infinite chains parallel to the crystallographic vector c. Each molecule is bonded to two neighbors.

1,4,5,8-Tetramethoxyanthracene

The structure of the title compound, C18H18O4, consists of separate centrosymmetric planar mol­ecules arranged in columns parallel to the monoclinic unique axis. The normal to the mean molecular plane lies at 55.4° to the unique axis, giving adjacent columns with alternating stacking directions. The mean deviation of all non-H atoms from the least-squares molecular plane is 0.064 Å. Bond lengths in the aromatic rings range from 1.347 (2) to 1.440 (2) Å and the two unique Me—O bond distances are 1.418 (2) and 1.419 (2) Å.

Trans-1-Cyano-2-(2-methoxyphenyl)-1-nitroethylene

The title compound, C10H8N2O3, has been prepared by condensation of 2-methoxy­benz­aldehyde and nitro­aceto­nitrile in ethanol at room temperature. Its investigation has been undertaken as a part of search for new nonlinear optical compounds. The π-conjugated mol­ecule is almost planar. Molecules in the crystal are packed in stacks with antiparallel molecular orientation and slightly alternating distances between mean molecular planes.

Trans-1-Cyano-2-(2-methoxyphenyl)-1-nitroethylene.

The title compound, C(10)H(8)N(2)O(3), has been prepared by condensation of 2-methoxybenzaldehyde and nitroacetonitrile in ethanol at room temperature. Its investigation has been undertaken as a part of search for new nonlinear optical compounds. The pi-conjugated molecule is almost planar. Molecules in the crystal are packed in stacks with antiparallel molecular orientation and slightly alternating distances between mean molecular planes.

P-Sexiphenyl/metal interfaces studied by photoemission and metastable atom electron spectroscopy

Abstract p -Sexiphenyl(6P)/metal (Au, Mg) interfaces were studied by ultraviolet photoemission spectroscopy (UPS), X-ray photoemission spectroscopy (XPS), and metastable atom electron spectroscopy (MAES). The vacuum level shifts ( Δ ) at the interface were observed in both 6P/Au ( Δ =−0.8±0.1 eV) and 6P/Mg ( Δ =−0.4±0.1 eV) systems. The MAES spectra indicate that the 6P molecules are on the substrate with their mean molecular plane parallel to the substrate surface in both systems, and that the 6P film on Mg substrate has some disorder. Thickness dependence of UPS, MAES, and XPS spectra suggests no significant chemical interaction for 6P on Au, Mg as well as Au, Mg on 6P interfaces. In the system of Au on 6P/Au, the spectral feature of 6P in MAES spectra did not disappear even when the thickness of evaporated gold reached 20 nm, indicating a penetration of Au atoms (or the clusters) into the 6P film.

Molecular Crystal Structure of Acetylacetone at 210 and 110 K: Is the Crystal Disorder Static or Dynamic?

The molecular and crystal structure of acetylacetone (AA) was studied at 210 and 110 K in order to reveal the nature of the hydrogen bond and possible crystal disorder. The single crystal was grown by an in situ crystallization from the melt using an IR laser beam producing a molten zone in a Lindeman capillary. At both temperatures the crystals are orthorhombic (space group Pnma, Z = 4) with molecules having a crystallographic mirror plane perpendicular to the mean molecular plane. The intramolecular hydrogen bond is characterized by the O···O distances 2.541(2) and 2.547(1) A at 210 and 110 K, with the central hydrogen atom equally distributed over the two positions near the oxygens. So, the hydrogen bond in AA has two distinct potential minima that are in agreement with previous NMR data and recent quantum-chemical calculations. The bond lengths C−O and C−C in the cis-enol fragment have averaged values (1.291(1) and 1.402(1) A at 110 K) corresponding to the superposition of two enol isomers due to the ...

The Two Conformations of Hindered Photochromic 4a,4b-Dihydrophenanthrenes

We analyze conformational stereoisomerism in the sterically hindered 4a,4b-dihydrophenanthrenes of C2 symmetry. In these labile photointermediates, steric hindrance brought about by disubstitution at the 4 and 5 positions or by benzoannelation at the [c] and [g] bonds allows observation of two interconvertible intermediates denoted as L and S. In such molecules, theoretical analysis suggests two low-energy structures (C and T). These differ in the chirality of the polyene perimeter helix for one given configuration of the 4a,4b-ethane unit. C and T can be distinguished by the position of atom pair H4a, X4, or of the equivalent atom pair H4b, X5 with respect to the the mean molecular plane. In C, atoms H4a and X4 are on one side of the mean molecular plane, while in T atoms H4a and X4 are on opposite sides of this plane. The same holds for the atom pair H4b, X5. The C conformation is assigned to the primary photocyclization product (L modification) in which the intersubstituent distance X4−X5 is short and where the angular hydrogens are quasi-antiperiplanar. This is the regular conformation of the unhindered 4a,4b-dihydrophenanthrenes. The T conformation is assigned to the secondary conformers (S modification) formed spontaneously from the primary L product. Here the distances H4a−X5 and H4b−X4 are short, and in the case of severe steric hindrance (X = t-Bu) the angular hydrogens are anticlinal. The observed stability order (usually S > L at around room temperature, except in the 4,5-dimethyl, 4,5-di-tert-butyl, and 4,5-dichloro molecules) is the outcome of steric hindrance opposing skeletal deformations. X4−X5 steric interactions are dominant in the C forms while the H4a−X5 and H4b−X4 interactions (and corresponding interactions in the [c] and [g] dibenzoannelated systems) play a foremost role in the T forms. Computed strain energies for C and T reproduce the observed stability trends of L and S modifications. Differences in visible absorption band energies are traced to different extents of departure from planarity of the polyene perimeter. The L intermediates assigned to the more planar C structure are thus predicted to absorb at longer wavelengths. The low intensity of the visible band in the L modifications is attributed to symmetry-imposed cancelling-out of one-ethylene-bond transition moments. The present analysis explains also the simultaneous existence and the observed range of values of potential barriers separating the two modifications. The present analysis changes the previous structure assignment for the S and L modifications of the dibenzo system, leading to full agreement with the observed trend of the electronic spectra of the S and L modifications. Similar considerations applied to the 4a,4b-dimethyl system suggest that its labile low-temperature intermediate (λmax = 360 nm) could have a T-like conformation.

Topological Effects on Intramolecular Electron Transfer via Quantum Interference

The three isomers of diferrocenylbenzenes (ortho, 1o; meta, 1m; para, 1p) as well as 5-substituted derivatives of m-diferrocenylbenzene with R = NH2 (2), Cl (3), CH3 (4), CN (5), NO2 (6), and N(CH3)33+ (7) have been prepared. Crystal structures of 1o, 3, and 5 have been solved. In 3 and 5, the cyclopentadienyl rings are nearly parallel to the benzene mean planes with angles ranging from 9.99(5)° to 14.74(5)°. One ferrocene group is above and the other below the mean molecular plane. For 1o, there is an important twist between the benzene and cyclopentadiene rings (68.6(8)° and 32.5(8)°) for steric reasons. Controlled potential electrolysis yields the mixed-valence ferrocene/ferrocenium species in comproportionation equilibrium with homovalent species. Intervalence transitions have been observed and corrected from comproportionation. From the intervalence band parameters, metal−metal couplings (Vab) are calculated using Hush's equation. The values are much higher for 1o (0.025 eV) and 1p (0.043 eV) than fo...

9α-Fluoro-11β,17α,21-trihydroxy-1,4-pregnadiene-3,20-dione-21-acetate (9-fluoroprednisolone-21-acetate)

The synthetic steroid 9α-fluoro-11β,17α,21-trihydroxy-1,4-pregnadiene-3,20-dione-21-acetate (9-fluoroprednisolone-21-acetate), formula C23H29O6F, is related to substances which are potent inducers of hepatic microsomal enzymes and anti-inflammatory agents. The structure was determined at 294 K from counter-collected data by direct methods. Crystals are tetragonal, space groupP41212,a, b=9.214(2),c=49.452(39) A,V=4198(4), A,Dx=1.33μg/m3 forZ=8;R (onF) 0.063 for 915 independent intensities (I>2σ1). The structure shows H-bonding and packing of the mean molecular plane approximately perpendicular to the crystallographic 4-fold axis.

The Heterocyclic Diradical Benzo-1,2:4,5-bis(1,3,2-dithiazolyl). Electronic, Molecular and Solid State Structure

The preparation and purification of the heterocyclic diradical benzo-1,2:4,5-bis(1,3,2-dithiazolyl) (BBDTA) is described. Crystals of BBDTA, grown by fractional sublimation at 120-180 °C/10-3 Torr, are monoclinic, space group P21/c, with a ) 4.144(2), b ) 9.0344(13), and c ) 10.7424(16) A,‚ ) 91.11(3)°, and Z ) 2. The crystal structure consists of discrete, unassociated molecules of BBDTA. The molecules form slipped stacks along the x direction, with the mean molecular plane making an angle of 32.4° to the x axis. The interplanar separation between consecutive molecules along the stacking direction is 3.49 A. The ESR spectrum of BBDTA is solvent dependent, displaying signals attributable to partially associated materials ( not exchange coupled) and to free diradical (exchange coupled). Ab initio molecular orbital calculations suggest a small (ca. 0.5 kcal/mol) separation between the triplet and singlet diradical states. Cyclic voltammetry on BBDTA and the related benzo-1,3,2-dithiazolyl BDTA, coupled with gas phase photoelectron studies on BDTA, establish that both compounds are strong electron donors. Magnetic susceptibility measurements show that BBDTA is essentially diamagnetic up to room temperature; variable temperature single-crystal conductivity measurements provide a band gap of 0.22 eV. The transport properties are discussed in the light of extended Huckel band structure calculations, which suggest a highly three-dimensional electronic structure for bulk BBDTA in the solid state.

Synthesis and Diatropicity of trans-10b-Methyl-10c-undecyl- and trans-10b-Methyl-10c-pentadecyl-10b,10c-dihydropyrene. An Empirical Approach to a Semiquantitative Assessment of the Diamagnetic Ring Current in a [14]Annulene

trans-10b-Methyl-10c-undecyl- and trans-10b-methyl-10c-pentadecyl-10b,10c-dihydropyrene, 3b and 3c, were obtained from the valence isomerization of their corresponding [2.2]cyclophanedienes 28a and 28b. The long internal alkyl chain in each case was previously introduced via a Wittig reaction followed by reduction. The cyclophanedienes were synthesized from their corresponding dithia[3.3]cyclophanes via a Wittig rearrangement−Hofmann elimination sequence. Proton chemical shifts of H1‘ to H9‘ of the alkyl chains in 3b and 3c, respectively, are identical, suggesting that the C1‘−C9‘ section of the long alkyl chain in 3b or 3c has similar averaged conformational movement. Application of the Johnson−Bovey (J−B) model to 3b does not give a satisfactory correlation between the proton ring current shift and the out-of-plane distance. A direct empirical plot of the out-of-plane distance, D, against the proton ring current shifts, Δδ, however, gives a curve similar to that obtained from the J−B model of benzene. This curve in fact corresponds to a linear relationship between D and log |Δδ|. Calculated ring current shifts of several derivatives of 10b,10c-dihydropyrene based on the above empirical correlation agree well with the reported experimental values. Our model shows that the experimental detectable limit for the diatropicity of 10b,10c-dihydropyrene is about 14 Å from the mean molecular plane. A similar empirical treatment based on the carbon chemical shifts of the n-undecyl chain in 3b gives unsatisfactory results. Our model does not support the prediction that the magnitude of ring current effect on proton and carbon chemical shifts is essentially the same at the sample position in space relative to the mean plane of delocalization of an aromatic π-electron cloud.

The 7,7,8,8-Tetracyanoquinodimethane Salt of (C-meso-5,5,7,12,12,14-Hexamethyl-1,4,8,11-tetraazacyclotetradecane)nickel(II), [Ni(C-meso-Me6[14]aneN4)](TCNQ)2

The title compound, [Ni(C 16 H 36 N 4 )](C 12 H 4 N 4 ) 2 , consists of cationic (C-meso-5,5,7,12,12,14-hexamethyl-1,4,8,11-tetraazacyclotetradecane)nickel(II) entities and 7,7,8,8-tetracyanoquinodimethane anions. The Ni atom is surrounded by four N atoms from the tetraaza macrocycle in a square-planar arrangement. The average Ni-N distance is 1.953 (3) A. The TCNQ − radical anions are arranged so as to form discrete dimers with the usual twist-type π overlap which leads to a diamagnetic ground state. The intra- and interdimer separations between the mean molecular planes within a TCNQ column are 3.081 (5) and 5.113 (5) A, respectively

Complete assignment and additivity rule for 1H and 13C chemical shifts of non‐planar, nonacyclic aromatic hydrocarbons

AbstractComplete assignments of 1H and 13C NMR spectra were made for heptacyclic peropyrene and five isomers of dibenzoperopyrenes, using 2D correlation spectroscopic techniques of homonuclear HH‐COSY and NOESY and heteronuclear CH‐COSY and HMBC methods. New additivity rules of 1H and 13C chemical shift values were established for compounds having two types of benzene ring condensation. All 1H chemical shifts were satisfactorily interpreted by a very simple magnetic point dipole model. This model includes net contributions from each constituent benzene ring due to the ring current anisotropy and permits some ring planes to deviate from the mean molecular plane. The conjugated ring currents are consistent with the chemical shifts. Thus, the aromatic properties are normal even if the molecular skeleton is considerably deformed and becomes non‐planar.

Bimetallic Reactivity. Preparation and Characterization of Symmetrical Bimetallic Complexes of a Binucleating Macrocyclic Ligand, Cytim, Containing 6- and 4-Coordinate Sites

A binucleating macrocylic ligand, cytim, incorporating 6- and 4-coordinate sites has been prepared. The two metals arc bridged by phenolic oxygen ligands, and the 4-coordinate site is completed by a trimethylenediimine link. The 6-coordinate site carries two 2-methylenepyridyl arms and is completed by a trimethylenediamine chelate. This ligand was constructed in order to determine whether the trimethylenediamine chelate in the 6-coordinate site would produce symmetrical complexes where the pyridine ligands lie trans above and below the mean molecular plane