Dimesogenic compounds consisting of a cholesteryl moiety and an aromatic mesogen interconnected through a central pentamethylene spacer

New non-symmetric dimesogens consisting of a cholesteryl moiety and an aromatic mesogenic unit interconnected through a pentamethylene spacer have been prepared. The aromatic units consist of two phenyl rings linked by carboxy, oxycarbonyl, ethylene, ethynylene, azo or Schiff's base groups. The mesomorphic and transitional properties have been investigated by using optical microscopy, differential scanning calorimetry, helical pitch measurements, and electric field and miscibility studies. The structures of the mesophases have been studied using X-ray diffraction. Several kinds of smectic packings are observed depending on the nature of the linking group and an attempt to understand the origin of the different phase structures at a molecular level is made.     

UV Raman markers for structural analysis of aromatic side chains in proteins

UV Raman spectroscopy is a powerful tool for investigating the structures and interactions of the aromatic side chains of Phe, Tyr, Trp, and His in proteins. This is because Raman bands of aromatic ring vibrations are selectively enhanced with UV excitation, and intensities and wavenumbers of Raman bands sensitively reflect structures and interactions. Interpretation of protein Raman spectra is greatly assisted by using empirical correlations between spectra and structure. Many Raman bands of aromatic side chains have been proposed to be useful as markers of structures and interactions on the basis of empirical correlations. This article reviews the usefulness and limitations of the Raman markers for protonation/deprotonation, conformation, metal coordination, environmental polarity, hydrogen bonding, hydrophobic interaction, and cation-π interaction of the aromatic side chains. The utility of Raman markers is demonstrated through an application to the structural analysis of a membrane-bound proton channel protein.     

Substituent effects on aromatic stacking interactions

Synthetic supramolecular zipper complexes have been used to quantify substituent effects on the free energies of aromatic stacking interactions. The conformational properties of the complexes have been characterised using NMR spectroscopy in CDCl(3), and by comparison with the solid state structures of model compounds. The structural similarity of the complexes makes it possible to apply the double mutant cycle method to evaluate the magnitudes of 24 different aromatic stacking interactions. The major trends in the interaction energy can be rationalised using a simple model based on electrostatic interactions between the pi-faces of the two aromatic rings. However, electrostatic interactions between the substituents of one ring and the pi-face of the other make an additional contribution, due to the slight offset in the stacking geometry. This property makes aromatic stacking interactions particularly sensitive to changes in orientation as well as the nature and location of substituents.     

Aromatic-aromatic interactions in proteins: beyond the dimer

Aromatic residues are key widespread elements of protein structures and have been shown to be important for structure stability, folding, protein-protein recognition, and ligand binding. The interactions of pairs of aromatic residues (aromatic dimers) have been extensively studied in protein structures. Isolated aromatic molecules tend to form higher order clusters, like trimers, tetramers, and pentamers, that adopt particular well-defined structures. Taking this into account, we have surveyed protein structures deposited in the Protein Data Bank in order to find clusters of aromatic residues in proteins larger than dimers and characterized them. Our results show that larger clusters are found in one of every two unique proteins crystallized so far, that the clusters are built adopting the same trimer motifs found for benzene clusters in vacuum, and that they are clearly nonlocal brining primary structure distant sites together. We extensively analyze the trimers and tetramers conformations and found two main cluster types: a symmetric cluster and an extended ladder. Finally, using calmodulin as a test case, we show aromatic clsuters possible role in folding and protein-protein interactions. All together, our study highlights the relevance of aromatic clusters beyond the dimer in protein function, stability, and ligand recognition.     

On the importance of carbohydrate-aromatic interactions for the molecular recognition of oligosaccharides by proteins: NMR studies of the structure and binding affinity of AcAMP2-like peptides with non-natural naphthyl and fluoroaromatic residues

The specific interaction of a variety of modified hevein domains to chitooligosaccharides has been studied by NMR spectroscopy in order to assess the importance of aromatic-carbohydrate interactions for the molecular recognition of neutral sugars. These mutant AcAMP2-like peptides, which have 4-fluoro-phenylalanine, tryptophan, or 2-naphthylalanine at the key interacting positions, have been prepared by solid-phase synthesis. Their three-dimensional structures, when bound to the chitin-derived trisaccharide, have been deduced by NMR spectroscopy. By using DYANA and restrained molecular dynamics simulations with the AMBER 5.0 force field, the three-dimensional structures of the protein-sugar complexes have been obtained. The thermodynamic analysis of the interactions that occur upon complex formation have also been carried out. Regarding binding affinity, the obtained data have permitted the deduction that the larger the aromatic group, the higher the association constant and the binding enthalpy. In all cases, entropy opposes binding. In contrast, deactivation of the aromatic rings by attaching fluorine atoms decreases the binding affinity, with a concomitant decrease in enthalpy. The role of the chemical nature of the aromatic ring for establishing sugar contacts has been thus evaluated.     

Doubly charged ion mass spectra. 2—aromatic hydrocarbons

Doubly charged ion mass spectra for 15 aromatic hydrocarbons have been obtained using a Nier-Johnson geometry, Hitachi RMU-7L mass spectrometer operating at 1.6 kV accelerating voltage. The doubly charged ion spectra have features that are characteristic of the individual compounds. Unsaturated aromatic molecules show intense molecular ions in contrast to saturated, substituted or heteroatom compounds which undergo extensive fragmentation. Ionization energies for forming doubly charged molecular ions and appearance energies for the prominent doubly charged fragment ions have been measured. Calculations of the SCF energies and structures of various doubly charged ions have been carried out. Measured and calculated ionization/appearance energies are in reasonable accord and lend support to the suggested ion structures.     

Skeletal rearrangements on chemical ionization of dibenzyl ether and derivatives

Protonated molecular ions of dibenzyl ether, formed by chemical ionization using hydrogen and isobutane as reagent gases, undergo skeletal rearrangements to lose water and formaldehyde, both in the ion source and the flight path. The rearrangements have been elucidated by deuterium labelling and chemical substitution. The water lost contains the reagent proton and an aromatic hydrogen atom, and the aromatic hydrogen atoms have been shown to be mobile prior to the reaction. It is proposed that the skeletal rearrangement for water loss is initiated by protonation on the ether oxygen atom, followed by benzyl migration. The formaldehyde lost contains benzylic hydrogen atoms exclusively, and it is proposed that the skeletal rearrangement is preceded by hydrogen rearrangement of an oxygen protonated molecular ion to a ring protonated molecular ion. Daughter ion structures are supported by comparisons of their collision induced dissociation spectra with those of isomeric ions prepared by alternative routes.     

Synthesis and Molecular Recognition of Novel Cleft-type Receptors

A novel type of molecular cleft has been designed and synthesized from estrogen and approprite spacer groups such as xylylene or pyridine dimethylene. These receptor compounds 1a-d and 2a-d have been characterized by Mass spectra,¹H-NMR spectra,IR spectra and elemental analyses. The structures of the receptors are shown in scheme 1. Their molecular recognition properties for the aromatic amine and aromatic amino acids have been investigated by UV-visble spectrophotometric titration. The titration data were analyzed by using the Benesi-Hildebrand equation^[1].     

Structures of carbohydrate-boronic acid complexes determined by NMR and molecular modelling in aqueous alkaline media

The structures of thermodynamically stable aromatic boronic acid : cyclic carbohydrate chelates in aqueous alkaline media have been studied using 1H NMR spectroscopy and molecular modelling. It is found that interacting saccharides must necessarily possess a synperiplanar diol functionality for complexation to occur. While this is possible for furanose structures which tend to have a puckered planar geometry, for pyranose forms it is postulated that bis-complexation occurs with twist conformers of the pyranose ring, providing the ring has the requisite 1,2 : 3,4 polyol stereochemistry; specifically axial,equatorial : equatorial,axial or equatorial,axial : axial,equatorial orientations. In this respect it is possible to be predictive with regard to individual carbohydrate boronic acid interactions and to give reasonably comprehensive structural assignments to complexed components. In this paper twenty four polyhydroxy compounds have been screened using 1H NMR to monitor complexation along with computational techniques on a model system to substantiate proposed structures. It has been found that all of these materials interact with aromatic mono boronic acids as expected and structures for the resulting chelates are proposed.     

High-performance liquid chromatographic method for screening disorders of aromatic acid metabolism using a multi-detection system

This paper describes the use of a high-performance liquid chromatograph equipped with an ultraviolet multi-detection system for the analysis of aromatic acids to help establish a high-risk screening system for disorders of organic acid metabolism. The peak height ratios of about seventy metabolically important aromatic acids have been compiled using the multi-detection system. It may be possible to identify aromatic acids by comparing retention time and peak height ratios. The method was very effective for the diagnosis of disorders of aromatic acid metabolism.     

NMR analysis of aromatic interactions in designed peptide beta-hairpins

Designed octapeptide beta-hairpins containing a central (D)Pro-Gly segment have been used as a scaffold to place the aromatic residues Tyr and Trp at various positions on the antiparallel beta-strands. Using a set of five peptide hairpins, aromatic interactions have been probed across antiparallel beta-sheets, in the non-hydrogen bonding position (Ac-L-Y-V-(D)P-G-L-Y/W-V-OMe: peptides 1 and 2), diagonally across the strands (Boc-Y/W-L-V-(D)P-G-W-L-V-OMe: peptides 3 and 6), and along the strands at positions i and i + 2 (Boc-L-L-V-(D)P-G-Y-L-W-OMe: peptide 4). Two peptides served as controls (Boc-L-L-V-(D)P-G-Y-W-V-OMe: peptide 5; Boc-L-Y-V-(D)P-G-L-L-V-OMe: peptide 7) for aromatic interactions. All studies have been carried out using solution NMR methods in CDCl(3) + 10% DMSO-d(6) and have been additionally examined in CD(3)OH for peptides 1 and 2. Inter-ring proton-proton nuclear Overhauser effects (NOEs) and upfield shifted aromatic proton resonances have provided firm evidence for specific aromatic interactions. Calculated NMR structures for peptides 1 and 2, containing aromatic pairs at facing non-hydrogen bonded positions, revealed that T-shaped arrangements of the interacting pairs of rings are favored, with ring current effects leading to extremely upfield chemical shifts and temperature dependences for specific aromatic protons. Anomalous far-UV CD spectra appeared to be a characteristic feature in peptides where the two aromatic residues are spatially proximal. The observation of the close approach of aromatic rings in organic solvents suggests that interactions of an electrostatic nature may be favored. This situation may be compared to the case of aqueous solutions, where clustering of aromatic residues is driven by solvophobic (hydrophobic) forces.     

Chiral ordering and conformational dynamics for a class of oligo-phenylene-ethynylenes on Au(111)

Adsorption structures formed from a class of planar organic molecules on the Au(111) surface under ultrahigh vacuum conditions have been characterized using scanning tunneling microscopy (STM). The molecules have different geometries, linear, bent, or three-spoke, but all consist of a conjugated aromatic backbone formed from three or four benzene rings connected by ethynylene spokes and functionalized at all ends with an aldehyde, a hydroxyl, and a bulky tert-butyl group. Upon adsorption, the molecules adopt different surface conformations some of which are chiral. For the majority of the observed adsorption structures, chirality is expressed also in the molecular tiling pattern, and the two levels of chirality display a high degree of correlation. The formation and chiral ordering of the self-assembled structures are shown to result from dynamic interchanges between a diffusing lattice gas and the nucleated islands, as well as from a chiral switching process in which molecules alter their conformation by an intramolecular rotation around a molecular spoke, enabling them to accommodate to the tiling pattern of the surrounding molecular structures. The kinetics of the conformational switching is investigated from time-resolved, variable temperature STM, showing the process to involve an activation energy of approximately 0.3 eV depending on the local molecular environment. The molecule-molecule interactions appear primarily to be of van der Waals character, despite the investigated compounds having functional moieties capable of forming intermolecular hydrogen bonds.     

Effect of skin layer surface structures on the flux behaviour of RO membranes

The relationship between the surface structures of skin layers of crosslinked aromatic polyamide composite reverse osmosis (RO) membranes and their RO performances have been studied using two surface analytical techniques: SEM and AFM. As a result, it was found that RO membranes whose skin layer surface structures were rough produced high fluxes, and an approximately linear relationship existed between this surface roughness and RO membrane flux. Accordingly, skin layer surface unevenness of crosslinked aromatic polyamide composite RO membranes is regarded as an enlargement of the effective RO membrane area.     

Development of carbohydrate-based scaffolds for restricted presentation of recognition groups. Extension to divalent ligands and implications for the structure of dimerized receptors

The solution structure of glycosyl amides has been studied by using NMR. A strong preference is displayed by tertiary aromatic glycosyl amides for E-anti structures in contrast with secondary aromatic glycosyl amides where Z-anti structures predominate. The structural diversity displayed by these classes of molecules would seem to be important as the directional properties of the aromatic ring, or groups attached to the aromatic ring, would be determined by choosing to have either a secondary or tertiary amide at the anomeric center and could be considered when designing bioactive molecules with carbohydrate scaffolds. The structural analysis was also carried out for related divalent secondary and tertiary glycosyl amides and these compounds display preferences similar to that of the monovalent compounds. The constrained divalent compounds have potential for promoting formation of clusters that will have restricted structure and thus have potential for novel studies of mechanisms of action of multivalent ligands. Possible applications of such compounds would be as scaffolds for the design and synthesis of ligands that will facilitate protein-protein or other receptor-receptor interactions. The affinity of restricted divalent (or higher order) ligands, designed to bind to proteins that recognize carbohydrates which would facilitate clustering and concomitantly promote protein-protein interactions, may be significantly higher than monovalent counterparts or multivalent ligands without these properties. This may be useful as a new approach in the development of therapeutics based on carbohydrates.     

Thermogravimetry of dihydroxyviolanthrone esters

Dihydroxyviolanthrone esters of straight chain alkanoic acids contain a thermally stable aromatic system connected by an ester linkage to an aliphatic hydrocarbon moiety. These esters provide excellent models for studying the different pyrolysis behavior of aliphatic and aromatic structures. Using dynamic and isothermal thermogravimetry, the effect of atmosphere on volatilization, the variation of stability with chain length of the alkanoic acid, and the volatilization kinetics have been studied.     

UV-vis, IR and 1H NMR spectroscopic studies of some mono- and bis-azo-compounds based on 2,7-dihydroxynaphthalene and aniline derivatives

The absorption spectra of mono- and bis-azo-derivatives obtained by coupling the diazonium salts of aromatic amines and 2,7-dihydroxynaphthalene have been studied in six organic solvents. The different absorption bands have been assigned and the effect of solvents on the charge transfer band is also discussed. The diagnostic IR spectral bands and 1H NMR signals are assigned and discussed in relation to molecular structure. Also, semi-empirical molecular orbital calculations using the atom superposition and electron delocalization molecular orbital (ASED-MO) theory have been performed to investigate the molecular and electronic structures of these compounds. According to these calculations, an intramolecular hydrogen bonding is essential for stabilization of such molecules.     

Observation of amide anions in solution by electrospray ionization mass spectrometry

Negative quasimolecular ions of aromatic carboxylic acid amides have been observed unexpectedly under electrospray ionization conditions. Hypothetically, deprotonation of either carboxamide or carboximidic acid tautomers can produce anions with equivalent resonance structures, the stability of which is affected by conjugated aromatic substituents. In this study, a series of meta and para substituted benzamides were analyzed using electrospray ionization mass spectrometry in aqueous methanolic solutions. The degree of ionization was found to be pH dependent and was enhanced by electron-withdrawing substituents and suppressed by electron-donating groups. The observed effect on apparent acidity can be accounted for by resonance stabilization.     

Interaction of aromatic units of amino acids with guanidinium cation: The interplay of π···π, XH···π, and M+···π contacts

Complexes formed by guanidinium cation and a pair of aromatic molecules among benzene, phenol, or indole have been computationally studied to determine the characteristics of the cation···π interaction in ternary systems modeling amino acid side chains. Guanidinium coordinates to the aromatic units preferentially in the following order: indole, phenol, and benzene. Complexes containing two different aromatic units show an intermediate behavior between that observed for complexes with only one kind of aromatic unit. Most stable structures correspond to doubly‐T shaped arrangements with the two aromatic units coordinating guanidinium by its NH₂ groups. Other structures with only one aromatic unit coordinated to guanidinium, such as T‐shaped or parallel‐stacked ones, are less favorable but still showing significant stabilization. In indole and phenol complexes, the formation of hydrogen bonds between the aromatic molecules introduces extra stabilization in T‐shaped structures. Three body effects are small and repulsive in doubly T‐shaped minima. Only when hydrogen bonds involving the aromatic molecules are formed in T‐shaped structures a cooperative effect can be observed. In most complexes the interaction is controlled by electrostatics, with induction and dispersion also contributing significantly depending on the nature and orientation of the aromatic species forming the complex. Although the stability in these systems is mainly controlled by the intensity of the interaction between guanidinium and the aromatic molecules coordinated to it, interactions between aromatic molecules can modulate the characteristics of the complex, especially when hydrogen bonds are formed. © 2014 Wiley Periodicals, Inc.     

Interaction of anions with perfluoro aromatic compounds

The complexes formed by a variety of anions with perfluoro derivatives of benzene, naphthalene, pyridine, thiophene, and furan have been calculated using DFT (B3LYP/6-31++G**) and MP2 (MP2/6-31++G** and MP2/6-311++G**) ab initio methods. The minimum structures show the anion interacting with the pi-cloud of the aromatic compounds. The interaction energies obtained range between -8 and -19 kcal mol(-1). The results obtained at the MP2/6-31++G** and MP2/6-311++G** levels are similar. However, the B3LYP/6-31++G** results provide longer interaction distances and smaller interaction energies than do the MP2 results. The interaction energies have been partitioned using an electrostatic, polarization, and van der Waals scheme. The AIM analysis of the electron density shows a variety of topologies depending on the aromatic system considered.     

Self‐Assembly of a Tripod Aromatic Rod into Stacked Planar Networks

Threefold symmetric rigid‐core molecules with an internally grafted poly(ethylene oxide) (PEO) chain were synthesized, and their self‐assembled structures were characterized using differential scanning calorimetry, TEM, and 1D and 2D X‐ray scatterings in the solid state. The tripod compounds based on short PEO chains (n=8, 13, 17, 21), self‐assemble into 2D channel‐like network structures, whereas the compound with the longest PEO chain (n=34) forms a lamellar liquid crystalline phase. The interiors of the channel structures are filled with flexible PEO chains along the double‐walled aromatic circumference. In these channel‐like networks, three aromatic rods connected in the meta‐position to each other are superimposed in parallel to other adjacent molecules to form the double‐walled aromatic frameworks stacked perpendicular to the resulting channels. These are novel examples of supramolecular channel‐like structures developed using amphiphilic diblock molecules based on a threefold symmetric rigid scaffold.