Herringbone Arrangement Research Articles

A new polymorph of benzene-1,2-diamine: isomorphism with 2-aminophenol and two-dimensional isostructurality of polymorphs

A new crystalline form of benzene-1,2-diamine, C(6)H(8)N(2), crystallizing in the space group Pbca, has been identified during screening for cocrystals. The crystals are constructed from molecular bilayers parallel to (001) that have the polar amino groups directed to the inside and the aromatic groups, showing a herringbone arrangement, directed to the outside. The known monoclinic form and the new orthorhombic polymorph exhibit two-dimensional isostructurality as the crystals consist of nearly identical bilayers. In the monoclinic form, neighbouring bilayers are generated by a unit translation along the a axis, whereas in the orthorhombic form they are generated by a c-glide. Moreover, the new form of benzene-1,2-diamine is essentially isomorphous with the only known form of 2-aminophenol.

Structure and infrared absorption of the first layer C2H2 on the NaCl(100) single-crystal surface

The adsorbate structure of the first layer acetylene on the NaCl(100) single-crystal surface is investigated using polarization infrared spectroscopy in combination with low-energy electron diffraction (LEED) experiments, and potential calculations on the basis of pair potentials. In agreement with a previous study, a triplet of infrared absorptions in the region of the asymmetric stretch vibration of C(2)H(2) was observed and assigned to an adsorbate phase with (3 square root 2 x square root 2)R45 degrees translational symmetry determined in the LEED experiment. The polarization dependence of the infrared spectra is consistent with a parallel orientation of the molecules with respect to the surface. The number of molecules per unit cell is four to six as determined by photometric considerations. Total energy minimizations support a new structure model which contains five inequivalent molecules per unit cell in a herringbone arrangement. The application of a vibrational exciton approach demonstrates that this new structure model can reproduce the triplet spectrum observed in the infrared experiments.

2-(Naphthalen-2-yl)azulene.

In the title compound, C20H14, a naphthalene ring system is linked at the 2-position to the 2-C atom of the five-membered ring of an azulene unit. The compound crystallizes with two reasonably similar mol­ecules in the asymmetric unit. Neither mol­ecule is perfectly planar: the r.m.s. deviations from the best fit planes through all non-H atoms are 0.092 and 0.091 Å for the two mol­ecules. The dihedral angle between the mol­ecular planes is 49.60 (4)°. The naphthalene and azulene ring systems are inclined at dihedral angles of 6.54 (12) and 5.68 (12)° in the two mol­ecules. The crystal structure exhibits two sets of parallel layers, a typical edge-to-face herringbone packing arrangement. The structure is stabilized by an extensive series of weak C—H⋯π inter­actions.

Influence of intramolecular polar bonds on interface energetics in perfluoro-pentacene on Ag(111)

We investigated the structural and electronic properties of vacuum sublimed perfluoro-pentacene (PFP) thin films on Ag(111) substrates using x-ray standing waves (XSW), x-ray diffraction (XRD) and ultraviolet photoelectron spectroscopy (UPS). XSW results reveal a flat adsorption geometry of the monolayer PFP/Ag(111) with a relatively large bonding distance of $3.16\text{ }\text{\AA{}}$ for both, the carbon and fluorine atoms. Multilayers PFP/Ag(111) adopt a herringbone structure with the molecular long axis parallel to the substrate and a vertical lattice spacing of $3.06\text{ }\text{\AA{}}$ as evidenced by XRD. The strong intramolecular polar bond character of the fluorine-carbon bonds in PFP leads to an orientation dependent ionization energy (IE) that is experimentally observed by UPS for the monolayer-multilayer transition: The inclined molecular plane orientation in the multilayer herringbone arrangement leads to an increase of the PFP IE by $>0.4\text{ }\text{eV}$ compared to the flat lying monolayer.

Unique three-dimensional (3D) molecular array in dimethyl-DNTT crystals: a new approach to 3D organic semiconductors

Two isomeric dimethyl derivatives of dinaphtho[2,3-b:2′,3′-f]thieno[3,2-b]thiophene (2,9- and 3,10-DMDNTT) were synthesized and characterized. Their crystal structures were classified as unique three-dimensional (3D) herringbone arrangements. Of them, 3,10-DMDNTT preserves the same packing structure in the thin-film phase, and the film acted as a superior semiconductor channel in field-effect transistors with mobility up to 0.8 cm2 V−1 S−1.

(E)-4,4′-Bis(1,3-benzoxazol-2-yl)stilbene at 150 and 375 K

The title compound, a chromophore of formula C(28)H(18)N(2)O(2), crystallizes with the molecule lying on an inversion centre to give one-half of a crystallographically independent molecule in the asymmetric unit. The molecule is almost planar, with slight deviation of the benzene rings from the mean molecular plane. The structure is characterized by a herringbone packing arrangement arising from C-H...pi and pi-pi intermolecular interactions. The benzoxazole group is disordered between two orientations, with occupancy factors of 0.669 (10) and 0.331 (10) at 150 K [0.712 (7) and 0.288 (7) at 375 K].

(1R,2R)-1,2-Diphenyl-1,2-bis(1H-tetrazol-1-yl)ethane

The title compound, C16H14N8, is a new chiral ligand designed for applications in supra­molecular chemistry and Fe2+ spin-crossover complexes. The crystal structure shows a herring-bone arrangement of the mol­ecules, which are mutually linked via inter­molecular C—H⋯N inter­actions mainly donated by the alkyl and tetra­zole H atoms.

2-(1,3-Benzothiazol-2-ylsulfanyl)-1-phenylethanone

In the mol­ecule of the title compound, C15H11NOS2, the 1,3-benzothia­zole ring is oriented at a dihedral angle of 6.61 (6)° with respect to the phenyl ring. In the crystal structure, inter­molecular C—H⋯O inter­actions link the mol­ecules in a herring-bone arrangement along the b axis and π–π contacts between the thia­zole and phenyl rings [centroid–centroid distance = 3.851 (1) Å] may further stabilize the structure.

2-Chloro-1-(3-fluorobenzyloxy)-4-nitrobenzene

In the title compound, C13H9ClFNO3, the benzene rings are oriented at a dihedral angle of 41.23 (5)°. In the crystal structure, inter­molecular C—H⋯O inter­actions link the mol­ecules in a herring-bone arrangement along the b axis and weak π–π contacts between the benzene rings [centroid–centroid distance = 3.881 (1) Å] may further stabilize the structure.

Mesophase Semiconductors: The Alignment Control and Self-Assembling Nature for Transistor Applications

A new mesophase semiconductor, 2,2′-dioctyl-5,5′-dithienylnaphthalene (8TNAT8) was studied on the mesophase structure by the combination of dilatometry and XRD measurements. It was found that the mesophase has 3-D lattice of triclinic with a layered structure and the molecules align in a way of a herringbone arrangement. This layered structure has a similarity to that of the crystal phase, of which XRD patterns was obtained for a thin film transistor with a top-contact/botto-gate geometry showing a fast transistor mobility (0.14 cm2 V−1 s−1) at room temperature (a crystalline phase). Though the polydomain structures is formed in thin films of the transistor, the molecules are likely to totally align in a way that the molecular long axis is orthogonal to the substrate surface with a small tilt angle and this alignment of molecules is just fitting as a connector between the source and drain electrodes. This implies that mesomorphic properties could be a good character for the uniform alignment of molecules even for the crystalline phase as well as the relatively larger domain formation.

Vanadium (IV) benzenedicarboxylate: A novel adsorbent for selective separations

The crystal structure of VOBDC (BDC = 1,4-benzenedicarboxylate) has a 1-dimensional channel system with apertures of ∼8 Å, and shows remarkable flexibility upon adsorption/desorption of various guest molecules in the channels. VOBDC can selectively and rapidly adsorb organic molecules containing sulfur on exposure to a 5% CH4/He stream with different contents of thiophene or dimethyl sulfide at ambient temperature. Selective uptake of thiophene from liquid octane with thiophene concentrations from 2000 ppmw down to 100 ppmw is also observed. X-ray crystallographic data show that the adsorbed thiophene molecules adopt a herringbone packing arrangement within the channels of VOBDC while adsorbed dimethyl sulfide molecules are disordered among several positions in the channels with the sulfur atoms pointing toward the channel walls. The observed adsorptive capacities for thiophene and dimethyl sulfide are 155 mg and 208 mg sulfur per gram of VOBDC, respectively, consistent with the crystal structure data.

Conjugated Thiophene-Containing Oligoacenes Through Photocyclization: Bent Acenedithiophenes and a Thiahelicene

The preparation of bent anthradithiophenes (BADTs) using an oxidative photocyclization-based synthetic strategy is reported. The optical properties of the new compounds were characterized by UV-vis and fluorescence spectroscopies, and the redox properties were probed by cyclic voltammetry. Structural studies using single crystal X-ray crystallography show that the unsubstituted BADT adopts a slipped cofacial stacking arrangement in the solid state with pi-pi interactions along the intermolecular stacking axis. The dialkylated derivatives adopt similar packing motifs with varying degrees of slipping along their long and short molecular axes while the diphenyl derivative packs into an edge-to-face herringbone arrangement. Powder diffraction data show that in thin films prepared by vacuum evaporation, molecules of the unsubstituted BADT are oriented nearly perpendicular to the substrate surface whereas the dialkylated derivatives adopt either multiple phases or new polymorphs. A thiahelicene prepared from the oxidative photocyclization of two isomers of 2,5-dithienyl-1,4-distyrylbenzene is described and the crystal structure reported.

Room-temperature molecular-resolution characterization of self-assembled organic monolayers on epitaxial graphene

Graphene, a two-dimensional sheet of carbon atoms, is a promising material for next-generation technology because of its advantageous electronic properties, such as extremely high carrier mobilities. However, chemical functionalization schemes are needed to integrate graphene with the diverse range of materials required for device applications. In this paper, we report self-assembled monolayers of the molecular semiconductor perylene-3,4,9,10-tetracarboxylic dianhydride (PTCDA) formed on epitaxial graphene grown on the SiC(0001) surface. The molecules possess long-range order with a herringbone arrangement, as shown by ultra-high vacuum scanning tunnelling microscopy at room temperature. The molecular ordering is unperturbed by defects in the epitaxial graphene or atomic steps in the underlying SiC surface. Scanning tunnelling spectra of the PTCDA monolayer show distinct features that are not observed on pristine graphene. The demonstration of robust, uniform organic functionalization of epitaxial graphene presents opportunities for graphene-based molecular electronics and sensors.

Molecular design of photoactive acenes for organic photovoltaics

Absorption spectra of n-acenes (n from 2 to 6, for naphthalene, anthracene, tetracene, pentacene, and hexacene, respectively) have been calculated using a newly developed code based on time-dependent density-functional theory. Our calculations show that absorption spectra and charge carrier mobility of acenes not only depend on the molecular identity but also on the molecular packing. By designing the interaction between metal substrates and the first layer of acene molecules, they can be packed in a face-to-face fashion instead of the conventional herringbone (face-to-edge) arrangement. Acenes in the cofacial packing would increase the pi-orbital overlap and thus enhance the charge mobility by maximizing electronic coupling between adjacent molecules. Absorption spectra of cofacially packed acenes have a better overlap with the solar spectrum, which allows harvesting more of the solar energy from red photons.

Polymorphs, enantiomorphs, chirality and helicity in [Rh{N,O}(η4-cod)] complexes with {N,O} = salicylaldiminato Schiff base or aminocarboxylato ligands

The dimeric complex acetato(eta4-cycloocta-1,5-diene)rhodium(I), [Rh(O2CMe)(eta4-cod)]2 (cod = cycloocta-1,5-diene) reacts with N,O-chelating Schiff-base ligands or with N-phenylglycine to afford the diminato- or aminocarboxylato(4-cycloocta-1,5-diene)rhodium(I) complexes [{Rh(eta4-cod)}2(salen)] (1), [{Rh(eta4-cod)}2(salophen)] (2), [Rh((S)-N-phenylglycinato)(eta4-cod)] (3S), [Rh(rac-N-phenylglycinato)(eta4-cod)] (3rac), [Rh((R)-N-(4-methoxphenyl)ethyl-2-oxo-1-naphthaldiminato)(eta4-cod)] (4) and [Rh(N-(o-tolyl)-2-oxo-1-naphthaldiminato)(eta4-cod)] (5) [salen2- = N,N-ethylene-bis(salicylaldiminato), salophen2- = N,N-(1,2-phenylene)-bis(salicylaldiminato)]. The complexes are characterized by IR-, UV/Vis-, 1H/13C-NMR- and mass-spectroscopy. Complexes 1, 2, 4 and 5 contain six-membered metallaaromatic Rh-(N-CCC-O)-chelate rings which accept C-H...pi contacts. The crystal structure of 2 presents a polymorph (dimorph) (2a) to a previously reported structure (2b, CSD refcode SCLIRB10). Polymorphic forms 2a and 2b are traced to a different interlocking of adjacent dinuclear molecules with their corrugated van der Waals surface. The achiral N-phenylglycine ligand gives a chiral N-phenylglycinato complex [Rh(O2C-CH2-NHPh)(eta4-cod)] (3) with the nitrogen atom becoming the stereogenic center upon metal coordination. Complex 3 can crystallize as the enantiomorph 3S in the tetragonal, chiral space group P41 in a spontaneous resolution of the racemic mixture into homo-chiral helix-enantiomers due to inter-molecular N-H...O hydrogen bonding which connects only molecules of the same (S-) configuration into (right-handed or P-) 41-helical chains. Variation of the crystallization conditions gives 3 as a racemic polymorphic 3rac. R- and S-complexes 3 assemble in the polymorph 3rac in parallel chains along the 21-axes through N-HO hydrogen bonding. Again, only molecules of the same configuration are combined into a chain, albeit neighboring chains have complexes of opposite configuration. The chiral enantiomeric naphthaldiminato complex 4 displays a herring-bone arrangement. Achiral compound 5 crystallizes in the non-centrosymmetric polar space group Cc where all molecules show the same orientation.

(E)-1-(1,3-Benzodioxol-5-yl)-3-(3-bromophenyl)prop-2-en-1-one

In the title compound, C16H11BrO3, the mol­ecules adopt an E configuration with respect to the C=C double bond of the propenone unit. The 13 non-H atoms of the benzodioxole and propenone units are approximately coplanar (r.m.s. deviation = 0.027 Å) and the bromo­benzene ring plane forms a dihedral angle of 10.8 (1)° to this plane. The structure is layered, with the mol­ecules forming a herring-bone arrangement within each layer.

2,3-Diethoxy-9,10-anthraquinone

Anthraquinone derivatives form an important class of dyes and are also known for their medicinal properties. Recently, 2,3-disubstituted anthraquinones have been shown unexpectedly to jellify various organic solvents. No information on the packing mode of these derivatives was known. Here, the first X-ray structure of a 2,3-disubstituted anthraquinone is reported, namely 2,3-diethoxy-9,10-anthraquinone, C(18)H(16)O(4). The merit of this study lies in the observation of significant differences between the packing in 9,10-anthraquinone, which displays a herring-bone arrangement, and that in the title 2,3-diethoxy derivative, in which the molecules lie on parallel crystallographic morror planes separated by a distance of 3.4081 (1) A, reminiscent of the graphite layer architecture.

6,7-Dimethoxy-1,4-anthraquinone

The mol­ecule of the title compound, C16H12O4, is almost planar; the two meth­oxy groups are slightly out of the plane of the anthraquinone ring system, with C—C—O—C torsion angles of −6.25 (19) and −10.22 (19)°. In the crystal structure, the mol­ecules adopt a herringbone arrangement and form face-to-face slipped anti­parallel π–π stacking inter­actions along the b axis, with an inter­planar distance of 3.278 (2) Å.

(Z)-3-Anilino-1,3-diphenylprop-2-en-1-one

In the title compound, C21H17NO, the phenyl ring directly linked to the carbonyl group is oriented at an angle of 7.3 (2)° with respect to the aniline ring, and at an angle of 55.6 (2)° with respect to the other phenyl ring. There is an intra­molecular hydrogen bond involving the NH group and the carbonyl O atom. The crystal structure is stabilized by weak C—H⋯π inter­actions, which link the mol­ecules into a herringbone arrangement.

Crystal Packing Motifs of Oligothiophenes End-Capped with N-Containing Aryls

Oligothiophenes (OThs) end-capped with 3-quinolyl or pyridyl with nitrogen atom at meta-, ortho- or para-position were synthesized. The single-crystal structures of the resulting molecules, i.e., o-PyTh4, m-PyTh4, p-PyTh4, QuTh2, and QuTh3, were successfully determined by single-crystal X-ray analysis. Pyridyl end-capped OThs, o-PyTh4, m-PyTh4, and p-PyTh4, adopt the different herringbone packing arrangement in crystals depending on the position of the nitrogen atom because of the presence of weak C−H···N hydrogen bonds. The p-PyTh4 molecules are linked each other along the long axis of the molecules to form the extended chains by C−H···N dimer synthon. For m-PyTh4, the C−H···N interactions two-dimensionally extend through C−H···N trimer synthon. The weak hydrogen-bonding network is much more complex in o-PyTh4 crystals because o-PyTh4 has two crystallographically independent molecules. Two-dimensional (2D) hydrogen-bonding networks arranging along the direction of diagonals in the ab plane are formed by the C−H···N trimer synthon. The crystal packing motifs of 3-quinolyl end-capped OThs are distinctly different from pyridyl end-capped ones. The QuTh2 molecules form a 2D face to face π−π slip stacking driven by the interaction of donor and acceptor segments between the neighboring molecules. For QuTh3, the weak C−H···N hydrogen bonds between the two molecules in the same layer and the CH/π weak interactions together force the molecules to form a sandwich-herringbone crystal packing motif. These results provide a new protocol to control molecular packing arrangement of conjugated oligomers.