Orientation Of Aromatic Rings Research Articles

Synthetic and Structural Studies of 1-Halo-8-(alkylchalcogeno)naphthalene Derivatives

A series of eight 1-halo-8-(alkylchalcogeno)naphthalene derivatives (1-8; halogen=Br, I; alkylchalcogen=SEt, SPh, SePh, TePh) containing a halogen and a chalcogen atom occupying the peri positions have been prepared and fully characterised by using X-ray crystallography, multinuclear NMR spectroscopy, IR spectroscopy and MS. Naphthalene distortion due to non-covalent substituent interactions was studied as a function of the bulk of the interacting chalcogen atoms and the size and nature of the alkyl group attached to them. X-ray data for 1, 2, 4 and 5-8 were compared. Molecular structures were analysed in terms of naphthalene ring torsions, peri-atom displacement, splay angle magnitude, X...E interactions, aromatic ring orientations and quasi-linear X...E-C arrangements. A general increase in the X...E distance was observed for molecules that contain bulkier atoms at the peri positions. The I...S distance of 4 is comparable with the I...Te distance of 8, and is ascribed to a stronger lone pair-lone pair repulsion due to the presence of an axial S(naphthyl) ring conformation. Density functional theory (B3LYP) calculations performed on 5-8 revealed Wiberg bond index values of 0.05-0.08, which indicate minor interactions taking place between the non-bonded atoms in these compounds.

Synthesis and structural study of (8-phenylsulfanylnaphth-1-yl)diphenylphosphine metal complexes

A series of three platinum(II) halide complexes 2– 4 [Pt(X) 2{Nap(PPh 2)(SPh)}] (Nap = naphthalene-1,8-diyl; X = Cl, Br, I) and a ruthenium(II) p-cymene complex 5 [Ru( η 6-MeC 6H 4 i Pr)(Cl){Nap(PPh 2)(SPh)}] +Cl − of the sterically crowded peri-substituted naphthalene phosphine 1 have been prepared. The compounds were fully characterised by multinuclear NMR, IR and MS and X-ray data for 1– 5 are compared. Molecular structures are analysed by naphthalene ring torsions, peri-atom displacement, splay angle magnitude, P···S interactions, aromatic ring orientations and geometry around the metal centre. Platinum adopts a strictly square planar geometry which increases the distortion of the naphthalene skeleton in 2– 4. Conversely, the classical-piano stool conformation of 5 results in a pseudo-octahedral conformation around the ruthenium atom which influences the naphthalene geometry to a much lesser extent with distortion of a similar magnitude to the free ligand 1.

Self-assembly of 2,6-naphthalenedicarboxylic acid and 4,4′-biphenyldicarboxylic acid on highly oriented pyrolytic graphite and Au(1 1 1) surfaces

Self-assemblies of 2,6-naphthalenedicarboxylic acid (NDC) and 4,4′-biphenyldicarboxylic acid (BDC) molecules on the highly oriented pyrolytic graphite (HOPG) and reconstructed Au(1 1 1) surfaces has been, respectively, studied by using scanning tunneling microscopy (STM). The NDC molecules form an incommensurate structure, while BDC molecules form a commensurate structure on the HOPG surface. The aromatic rings take the same orientation with that of the underlying HOPG substrate to gain optimum adsorbate–substrate interactions. On the Au(1 1 1) surface, both molecules form incommensurate structures. The orientations of aromatic ring locate about 20° with respect to the gold rows, the 〈1 1 0〉 direction. On the HOPG surface, the whole carboxyl groups are invisible, while the carbon atoms of the carboxyl groups may appear bright on the gold surface.

The Gas Phase Anisole Dimer: A Combined High-Resolution Spectroscopy and Computational Study of a Stacked Molecular System

The gas phase structures of anisole dimer in the ground and first singlet electronic excited states have been characterized by a combined experimental and computational study. The dimer, formed in a molecular beam, has been studied by resonance-enhanced multiphoton ionization and high-resolution laser-induced fluorescence techniques. The assignment of the rotational fine structure of the S(1) <-- S(0) electronic transition origin has provided important structural information on the parallel orientation of aromatic rings of anisole moieties. By comparison with the DFT/TD-DFT computational results, it has been possible to infer the detailed equilibrium structure of the complex. The analysis of the equilibrium structure and interaction energy confirms that the anisole dimer is stabilized by dispersive interaction in the gas phase. This is, to the best of our knowledge, the first detailed work (reporting both theoretical and high-resolution experimental data) on an isolated cluster in the pi-stacking configuration.

Modelling of carbohydrate–aromatic interactions: ab initio energetics and force field performance

Aromatic amino acid residues are often present in carbohydrate-binding sites of proteins. These binding sites are characterized by a placement of a carbohydrate moiety in a stacking orientation to an aromatic ring. This arrangement is an example of CH/pi interactions. Ab initio interaction energies for 20 carbohydrate-aromatic complexes taken from 6 selected ultra-high resolution X-ray structures of glycosidases and carbohydrate-binding proteins were calculated. All interaction energies of a pyranose moiety with a side chain of an aromatic residue were calculated as attractive with interaction energy ranging from -2.8 to -12.3 kcal/mol as calculated at the MP2/6-311+G(d) level. Strong attractive interactions were observed for a wide range of orientations of carbohydrate and aromatic ring as present in selected X-ray structures. The most attractive interaction was associated with apparent combination of CH/pi interactions and classical H-bonds. The failure of Hartree-Fock method (interaction energies from +1.0 to -6.9 kcal/mol) can be explained by a dispersion nature of a majority of the studied complexes. We also present a comparison of interaction energies calculated at the MP2 level with those calculated using molecular mechanics force fields (OPLS, GROMOS, CSFF/CHARMM, CHEAT/CHARMM, Glycam/AMBER, MM2 and MM3). For a majority of force fields there was a strong correlation with MP2 values. RMSD between MP2 and force field values were 1.0 for CSFF/CHARMM, 1.2 for Glycam/AMBER, 1.2 for GROMOS, 1.3 for MM3, 1.4 for MM2, 1.5 for OPLS and to 2.3 for CHEAT/CHARMM (in kcal/mol). These results show that molecular mechanics approximates interaction energies very well and support an application of molecular mechanics methods in the area of glycochemistry and glycobiology.

Molecular Conformation and Packing of Peptide β Hairpins in the Solid State: Structures of Two Synthetic Octapeptides Containing 1‐Aminocycloalkane‐1‐Carboxylic Acid Residues at the i+2 Position of the β Turn

Peptide beta-hairpin formation is facilitated by centrally positioned D-Pro-Xxx segments. The synthetic peptides Boc-Leu-Phe-Val-D-Pro-Ac(6)c-Leu-Phe-Val-OMe (1) and Boc-Leu-Phe-Val-D-Pro-Ac(8)c-Leu-Phe-Val-OMe (2) were synthesized in order to explore the role of bulky 1-aminocycloalkane-1-carboxylic acid residues (Ac(n)c, where n is the number of carbon atoms in the ring), at the i+2 position of the nucleating beta turn in peptide beta hairpins. Peptides 1 and 2 crystallize in the monoclinic space group P2(1) with two molecules in the asymmetric unit. The crystal structures of 1 and 2 provide conformational parameters for four peptide hairpin molecules. In all cases, the central segments adopts a type II' beta-turn conformation, and three of the four possible cross-strand hydrogen bonds are observed. Fraying of the hairpins at the termini is accompanied by the observation of NHpi interaction between the Leu(1)NH group and Phe(7) aromatic group. Cross strand stabilizing interactions between the facing residues Phe(2) and Phe(7) are suggested by the observed orientation of aromatic rings. Anomalous far-UV CD spectra observed in solution suggest that close proximity of the Phe rings is maintained even in isolated molecules. In both peptides 1 and 2, the asymmetric unit consists of approximately orthogonal hairpins, precluding the formation of a planar beta-sheet arrangement in the solid state. Solvent molecules, one dioxane and one water in 1, three water molecules in 2, mediate peptide association. A comparison of molecular conformation and packing motifs in available beta-hairpin structures permits delineation of common features. The crystal structures of beta-hairpin peptides provide a means of visualizing different modes of beta-sheet packing, which may be relevant in developing models for aggregates of polypeptides implicated in disease situations.

Spectroscopic witness from reactants to product: FTIR studies on selective mono- N-methylation of aniline on Cu 1− xZn xFe 2O 4

An active N-methylation ferrospinel catalyst, Cu 1− x Zn x Fe 2O 4, is reported for the first time. A mechanistic approach to selective mono- N-methylation of aniline on Cu 1− x Zn x Fe 2O 4 is successfully explained by in situ temperature-dependent DRIFTS studies of reactants on the catalyst. Perpendicular orientation of aromatic rings of aniline, methyl group availability, an optimum metal–ion distribution on the catalyst surface, and a stable methyl group on Zn leads selectively to N-methylaniline (NMA) on Cu 0.5Zn 0.5Fe 2O 4. Desorption-limited kinetics is evident from NMA formation at low temperatures.

Computer simulation of long side-chain substituted poly(phenylene vinylene) polymers.

A molecular dynamics (MD) simulation was employed to investigate structure features and segment orientation of four poly (phenylene vinylene) (PPV) derivatives with long, flexible side chains at room temperature. In the simulations, the main chains of the polymers were found to be semirigid and exhibit a tendency to coil into ellipsoidal helices or form zigzag conformations of limited regularity. The simulations show that continuous quasi-coplanar segments along the backbone are in a range of approximately 2-4 repeat units. The ordered orientation and coupling distance of interchain aromatic rings can be correlated with optical properties of materials. A simplified quantum-mechanical method was developed to investigate optical properties based on MD trajectories. The method was tested to simulate the absorption spectra of four PPV derivatives. The absorption maxima of the calculated spectra are in reasonable agreement with experimental data. This work implies that long-range electron transfer along the backbones of these polymers may not occur, but may be mediated by interchain interactions.

Molecular modelling of the uniaxial deformation of amorphous polyethylene terephthalate

Deformation of polyethylene terephthalate, PET, was simulated using atomistic molecular dynamics using a Parrinello–Rahman constant-stress constant-temperature algorithm under periodic boundary conditions. The evolution in trans and gauche populations is in good agreement with experimental data reported in the literature: In the isotropic model, approximately 15% trans angles are found, and the trans population increases up to a value of 50% at a draw ratio λ of 3.2. There is a gradual increase in the orientation function of the aromatic cycles, 〈P 2( cos θ)〉 c , with λ, but the values are higher than those reported in the literature, due to the absence of relaxation in the simulation. Moreover, the orientation of trans segments was found to be high, while the orientation of gauche segments was non negligible. A good agreement was found with the rubber elasticity model up to a λ of 2.0, as was the case for previous polyvinyl phenol simulations. Simulated data fit well with the aggregate model in a broad range, for 1.0 λ 5.0, contrarily to the case of poly(vinyl phenol), where the aggregate model predicted much higher orientation values that those obtained via molecular modelling simulations. This difference is attributed to the different rigidities of the chain backbones. Simulations were found in good agreement with those performed by Zhou, Nicholson, Davies and Ward, using a different deformation simulation approach, both in terms of orientation of aromatic rings and of conformer evolution during deformation.

Molecular Modeling of Lignin β-O-4 Model Compounds. Comparative Study of the Computed and Experimental Conformational Properties for a Guaiacyl β-O-4 Dimer

SummaryThe conformational preferences of thethreoanderythrodiastereomeric forms of a guaiacyl β-O-4 dimer have been investigated by molecular modeling using the CHARMM force field. Many low energy conformations have been identified for each diastereomer, showing that β-O-4 dimers can adopt a large variety of shapes. A consistent structural model has emerged that indicates different conformational behavior for thethreoanderythroforms, corresponding to a preferential extended overall shape for thethreoform. All the low energy conformers are stabilized by intramolecular H-bonds. In particular, the highly directional H-bond between the α or γ hydroxyl hydrogen and the aromatic methoxy oxygen governs the B aromatic ring orientation. However, it has appeared that the conformational preferences are predominantly governed by local steric interactions rather than by differences in the H-bonding pattern. From the satisfactory agreement between computed data (geometries and the Boltzmann distribution of the low energy conformers) and the experimental data reported in the literature (X-ray crystal structures and3JHαHβNMR coupling constant), the CHARMM force field has been validated for the study of β-O-4 structures. Clearly, the molecular modeling calculations have led to an improved rationalization of the conformational data collected by experimental techniques.

Intramolecular S⋯S and S⋯O close contacts in 1,8-bis(phenylsulfanyl)naphthalene derivatives of different sulfur valence state: an X-ray study

Four peri-substituted naphthalene derivatives, 1,8-bis(phenylsulfanyl)naphthalene (1), 1,8-bis[(2-methoxycarbonylphenyl)sulfanyl]naphthalene (2), bis[(2-methoxycarbonyl-phenyl)-sulfinyl]naphthalene (3) and bis[(2-methoxycarbonylphenyl)sulfonyl]naphthalene (4) with different valence states of sulfur were prepared and their molecular structures determined by X-ray diffraction. Data were collected on CAD-4 diffractometers with monochromated MoKα and CuKα radiations. Naphthalene ring torsions, aromatic ring orientations, S⋯S and S⋯O close contacts were analyzed and the controlling factors established. In both halves of the molecules, the naphthyl and phenyl rings assume axial–equatorial positions in bis-sulfides 1 and 2, and twist-axial positions in bis-sulfoxide 3 and bis-sulfone 4. The S⋯S distance was found to be 3.01, 3.18; 3.01 and 3.53Å, for 1, 2, 3 and 4, respectively. The equatorial S-phenyl rings in 2 and the steric crowd in 4 are unfavorable factors for S⋯S contacts. As expected, S(II)⋯O and S(IV)⋯O close contacts are formed in the equatorial and axial S-phenyl rings of 2 and 3, respectively, with 2.72, 2.73 and 2.77, 2.83Å distances. Steric repulsion in bis-sulfone 4 is moderated by two C(ar)–S(VI)⋯O(sulfonyl) type close contacts (2.89 and 3.02Å), which join the two halves of the molecule.

Comparison of the π-conjugated ring orientations in polyaniline and polypyrrole

While both polyaniline and polypyrrole are similar conducting polymers, from angle-resolved photoemission, they exhibit key structural differences. A temperature dependent change in the orientation of the aromatic ring orientation is observed in polypyrrole doped with the perchlorate (ClO 4 −) counter ion. This structural change occurs at about 220–240 K and is associated with a change in carrier mobility and ring orientation, but is not associated with a significant change in metallicity. Polyaniline exhibits a change in aromatic ring orientation with films thickness, but not with temperature.

X-ray structure of a trimeric 5,5'-biaryl/erythro-beta-O-4-ether lignin model: evidence for through-space weak interactions.

The crystal structure of a trimeric lignin model 1 presenting the characteristic pattern of biphenyl (5,5') and aryl-alkyl-ether (beta-O-4) linkages has been determined. The crystal system is triclinic and the crystallographic unit cell consists of two monomeric molecules. These results are compared with crystal data from the literature of simple models of the 5,5' and beta-O-4 structure type. The availability of a terminal aldehyde function on the model affords some interesting intermolecular interactions by weak hydrogen bonding which controls the conformation of the molecule and the aromatic ring orientation in particular; an unexpected cisoïd conformation of the biaryl unit is observed based on the 64.4 degrees value found for the torsion angle between the two 5,5' aromatic rings.

Enhancement of bleomycin-induced micronucleus formation in V79 cells as a rapid and sensitive screen for non-covalent DNA-binding compounds

Non-covalent drug/DNA interactions are difficult to study and because of this, the significance of such interactions from a safety standpoint and their contribution to positive genetic toxicology test findings is poorly understood. It is shown in the present study that such interactions may be detected and quantified in Chinese hamster V79 cells by an adaptation of the bleomycin amplification assay. This assay measures the ability of a test compound to enhance the DNA damaging activity of the antibiotic bleomycin using micronucleus formation as an endpoint. Results are presented examining the bleomycin amplification activity of known intercalating agents, groove-binding agents and other structurally diverse classes of compounds for which intercalative status has not been reported. The assay reveals a strong and predictable SAR for amplification activity based on number and orientation of aromatic rings. Moreover, excellent correlations are observed between DNA binding (viscometric analyses) and DNA amplification in V79 cells for a series of seven experimental compounds. The assay is shown to be useful in understanding the genotoxicity of marketed antihistamines and to help explain genetic toxicology findings observed in a series of novel pharmaceutical entities. It is proposed that assessment of bleomycin amplification activity of novel compounds in early genotoxicity prescreening may provide important information upon which to base synthesis of compounds with minimal or no genotoxic liability.

Monte Carlo simulations of a liquid crystal copolymer in the solid state

The condensed phase of the alternating copolyester of p-hydroxybenzoic acid (HBA) and 2-hydroxy-6-naphthoic acid (HNA) is investigated by studying the room temperature packing arrangement of the copolymer chains. A molecular modeling methodology is employed with a Monte Carlo sampling of the configurational phase space. Realistic poly(HBA-alt-HNA) polymer chains are represented by an explicit atom representation of the HBA/HNA dimers. States are sampled from the NVT ensemble using a sampling scheme consisting of (1) valence and torsional variations, (2) rigid body rotations of the chain about the chain axis, and (3) rigid body translations of the chain. The effect of chain packing on the conformation of chains, as well as the relative intra- and intermolecular orientations of aromatic rings, is investigated. Correlation of chain positioning along the chain axis is dominated by aromatic rings maintaining a center-to-center plane of registry. These layers of aromatic units pack with a preference for edge-to-face orientations in a herringbone-type pattern and have an intermolecular ring angle between the pairs of aromatic rings in the unit cell that is ca. 68°. The aromatic rings, on average, are rotated 38° out from the b–c plane. The phenylene rings of these copolyesters are less restricted in their relative orientation in comparison to the naphthalene rings. Intramolecular orientational probability density distributions indicate a preference for staggering the successive aromatic rings along the chain, with a staggering angle of ca. 66°. © 1998 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys 36: 727–741, 1998

Suggested binding mechanism of the HIV-gp120 to its CD4 receptor

The molecular recognition and attachment of the CD4 molecule and the HIV envelope glycoprotein (gp120) might be described as a consecutive three-step molecular recognition process. 1. (a) Long range interaction: electrostatic pre-orientation, 2. (b) short range interaction: electronic attachment followed by a ‘Locking-in’ (via aromatic ring orientation) and 3. (c) internal interaction (induced fit): conformational readjustment of the protein molecules. On the basis of the preliminary investigations (X-ray structures of CD4 and biological studies of CD4 and gp120 point mutants) we described a computational model. This approach consists of empirical calculations as well as ab initio level of quantum chemistry. The conformational analysis of the wild type and mutant CD4 molecules was supported by molecular mechanics and dynamics (Amber force field). The latter analysis involves the application of a novel method, the Amino Acid Conformation Assignment of Proteins (ACAP) software, developed for the notation of secondary protein structures. According to the cardinal role of the electrostatic factors during this interaction, several ab initio investigations were performed for better understanding of the recognition process on submolecular level. Using the above mentioned computational model, we could interpret the basic behaviours and predict some additional features of CD4-gp120 interaction, in spite of the missing gp120 X-ray structure.

Sodium Channel Binding and Anticonvulsant Activities of Hydantoins Containing Conformationally Constrained 5-Phenyl Substituents

As a preliminary investigation of the importance of the aromatic ring orientation in interactions of 5-phenylhydantoins with the anticonvulsant site on the neuronal voltage-sensitive sodium channel, two isomeric hydantoins containing conformationally constrained phenyl rings and their monocyclic analogues were synthesized. One, a spiro-hydantoin (2) derived from α-tetralone, contains the plane of the phenyl ring in an orientation approximately perpendicular to that for the hydantoin ring. The other, a tricyclic hydantoin (4) derived from tetrahydroiso-quinoline, contains the plane of the phenyl ring in an orientation roughly coplanar with that for the hydantoin ring. These compounds were evaluated in sodium channel binding and whole animal (mice) anticonvulsant assays. In both assays, 4 was significantly more potent than 2, suggesting that the anticonvulsant receptor site on the voltage-sensitive sodium channel may require a specific aromatic ring orientation.

Configurational requirements of aromatic amino acid residues for the activity of PRP-hexapeptide

The three analogues with D-amino acid substituents at position 1 and 5 of PRP-hexapeptide were synthesized and tested for its biological activity to check the influence of the spacial orientation of aromatic rings on the immune response. One of the analogs (Tyr-Val-Pro-Leu-D-Phe-Pro) was found to have the immunoregulatory activity.

Thermal Aging of Bi-axially Orifnted Pet Films: Relation between Structural Changes and Dielectric Behavior

The structural changes in bi-stretched poly(ethylene-terephthalate) films induced by thermal aging have been studied by recording the variations of crystallinity, orientation of aromatic rings, and elongation at break. An attempt has been made to correlate the variations of the activation energy of the a relaxation process to the changes in physical properties. A simultaneous decrease of activation energy and of elongation at break has been observed on aged samples.

Sensitivity of electronic transitions to molecule-surface orientation: ELS of benzene and pyridene on Ir(111)

A 7 eV π ∗← π adsorbate induced electron loss is observed for pyridene on Ir (111), but only very weakly for benzene adsorption, implying aromatic ring orientation parallel to the surface for benzene and perpendicular to the surface (or at least at a substantial angle to it) for pyridene. Less prominent losses at lower energy (4–5 eV) are present in both systems and are interpreted as π ∗← d charge transfer excitations. The carbon KVV Auger spectrum of the two molecules is very similar, with a common broad asymmetric profile and evidence of participation of screening electrons from the metal.