Synthesis and characterization of thermally stable second-order nonlinear optical side-chain polyimides containing thiazole and benzothiazole push-pull chromophores

Push-pull nonlinear optical (NLO) chromophores containing thiazole and benzothiazole acceptors were synthesized and characterized. Using these chromophores a series of second-order NLO polyimides were Successfully prepared from 4,4'-(hexafluoroisopropylidene) diphthalic anhydride (6FDA), pyromellitic dianhydride (PMDA) and 3,3'4,4'-benzophenone tetracarboxylic dianhydride (BTDA) by a standard condensation polymerization technique. These polyimides exhibit high glass transition temperatures ranging from 160 to 188 degrees C. UV-vis spectrum of polyimide exhibited a slight blue shift and decreases in absorption due to birefringence. From the order parameters, it was found that chromophores were aligned effectively. Using in situ poling and temperature ramping technique, the optical temperatures for corona poling were obtained. It was found that the optimal temperatures of polyimides approach their glass transition temperatures. These polyimides demonstrate relatively large d(33) values range between 35.15 and 45.20 pm/V at 532 nm. (C) 2008 Elsevier B.V. All rights reserved.

The effect of the molecular weight on the electro-optic properties of methacrylate-based side-chain liquid crystal polymers

A series of methacrylate-based side-chain liquid crystal polymers has been prepared with a range of molecular weights. For the high molecular weight polymers a smectic phase is observed with a very narrow nematic range; however, for low molecular weight polymers only the nematic phase is observed. A marked reduction in the glass transition temperature, TSN and TNI is observed with a reduction in the molecular weight. The orientational order parameters for these polymers in the liquid crystal phase have been determined using infra-red dichroism. It is found that the higher the molecular weight of the polymer, the greater is the threshold voltage of the electro-optic response and the lower the order parameter. The increase in the threshold voltage with increasing molecular weight may be related to the intrinsic curvature elasticity and hence to the coupling between the mesogenic units and the polymer backbone.

The effect of the spacer length on the nature of coupling in side chain liquid crystals polymers and elastomers

Side chain liquid crystal polymers and elastomers exhibit a rich phase behaviour which arises from the antagonistic influences of the entropically disordered polymer chain configuration and the long range orientational ordering of the mesogenic units. This competition arises since the natural macroscopic phase separation is inhibited by the inherent chemical connectivity of the system. At the heart of this connectivity is the spacer link and we consider here its influence on the phase behaviour. In particular we consider a series of elastomers in which the number of alkyl units in the spacer is systematically varied from 2 to 6. The lengthening of the coupling spacer is accompanied by an alternation of the sign of coupling between the polymer chain and the mesogenic unit. These results demonstrate the dominating influence of the so-called hinge effect in determining the phase behaviour. In addition to the alternation of the sign there is some decrease in the magnitude of the coupling with increasing spacer length.

Coupling between mesogenic units and polymer backbone in side-chain liquid crystal polymers and elastomers

The levels of alignment of the mesogenic units and of the polymer backbone trajectory for polyacrylate based nematic side-chain liquid crystal polymers and elastomers were evaluated by using wide angle X-ray and small angle neutron scattering procedures. The X-ray scattering measurements show that substantial levels of preferred orientation of the mesogenic units may be introduced through magnetic fields for uncrosslinked polymers and through mechanical extension for liquid crystal elastomers. Small angle neutron scattering measurements show that for highly aligned samples an anisotropic polymer backbone trajectory is observed in which the envelope is slightly extended by ∼ 10% in the direction parallel to the axis of alignment of the mesogenic units. The sense of this coupling differs from that recorded for other uncrosslinked side-chain liquid crystal polymers. Possible mechanisms to account for this anisotropy and its relationship to the properties of liquid crystal elastomers are discussed. The observed deformation behaviour of the liquid crystal elastomer is non-affine and this appears to confirm the dominating influence of the liquid crystal order of the side chains on the mechanical properties of these novel networks.

Side-chain liquid crystalline elastomers: the relationship between the orientational ordering of the polymer backbone and the length of the coupling chain

The influence of cross-linking on the phase behaviour of a series of side-chain liquid crystalline elastomers has been studied. For samples cross-linked in the temperature range corresponding to the nematic phase, the phase transition was shifted compared to that observed when an identical sample was cross-linked in the isotropic phase. This shift represented a stabilisation of the nematic phase in the former case, in line with theoretical expectations. By utilising a novel, slow cross-linking method, which allows the polymer backbone to take up an equilibrium conformation prior to network formation, it proved possible to monitor the shifts in phase transition temperature as a function of the length of the methylene chain coupling the mesogenic units to the polymer backbone. The results obtained are related to the backbone anisotropy and indicate that the level of orientational order of the polymer in the nematic phase backbone increases with a reduction in the length of the coupling chain.

Cinnamate ester containing liquid crystalline side chain polymers

The synthesis of methacrylate esters of 4-cyanophenyl-(4-(ω-hydroxyalkyloxy)) cinnamates, with spacer lengths of 2 and 6 methylene units and the synthesis of the corresponding acrylate ester with a spacer of 2 methylene units are described. The methacrylate monomers were polymerized by free radical polymerization, both as homopolymers and as copolymers with the analogous benzoate monomer of spacer length 6. The acrylate ester could not be polymerized successfully under the same reaction conditions. Polymers were characterized by NMR spectroscopy, gel permeation chromatography, differential scanning calorimetry, and thermo-optic observations. Of the monomers prepared, only the cinnamate with a hexamethylene spacer shows a mesophase, seen on supercooling of the melt. All of the polymers prepared were liquid crystalline, with smectic behavior predominating in the polymethacrylates with the longer spacer group. A narrow nematic region is seen just below the clearing temperature with a range of 3–9°C, nematic character is increased in the copolymer series with the degree of incorporation of the cinnamate monomer with the spacer group of length 2.

Approaches to the synthesis of novel photoactive side chain liquid crystalline polymers containing analogues of the cinnamate ester group

A series of chain liquid crystalline copolymers of 4-cyanophenyl 4′-(6-methacryloyloxyhexyloxy)benzoate and 2-methacryloyloxyethyl β-(1-naphthyl)-propenoate were prepared by free radical polymerization. The corresponding polyacrylates could not be prepared in the same way and an alternative method was used for their preparation involving the synthesis of copolymers of the mesogenic monomer and 2-hydroxyethyl acrylate followed by treatment of the resulting polymers with β-(1-naphthyl)propenoyl chloride. The materials are of interest as photoactive liquid crystalline polymers. The effect of introducing a bulky nonmesogenic group into a liquid crystalline copolymer generally lowers the clearing temperature and raises Tg but also gives rise to contrasting phase behaviour in these two series of polymers. Polymethacrylates which show mesomorphism have sharp transitions and continue to exhibit a highly ordered smectic phase over the bulk of their liquid crystal range. Polyacrylates, on the other hand, exhibit a weakening and broadening-out of their thermal transitions consistent with a lowering of order. These results emphasize the effect of the polymer backbone on phase behaviour.

Synthesis and phase behaviour of a homologous series of polymethacrylate-based side-chain liquid crystal polymers

The homologous series of side chain liquid crystal polymers, the poly[x-(4-methoxyazobenzene- 40-oxy)alkyl methacrylate]s, has been prepared in which the length of the flexible alkyl spacer has been varied from 3 to 11 methylene units. All the polymers exhibit liquid crystalline behaviour. The propyl and butyl members show exclusively nematic behaviour. The pentyl, hexyl, octyl and decyl members show a nematic and a smectic A phase while the heptyl, nonyl and undecyl homologues exhibit only a smectic A phase. The smectic A phase has been studied using X-ray diffraction and assigned as a smectic A1 phase in which the side chains are fully overlapped and the backbones are confined to lie between the smectic layers. For the nonyl member an incommensurate smectic phase is observed. The dependence of the transition temperatures on the length of the flexible spacer is understood in terms of the average shapes of the side chains.

Amino acid pairing preferences in parallel beta-sheets in proteins

Statistical approaches have been applied to examine amino acid pairing preferences within parallel beta-sheets. The main chain hydrogen bonding pattern in parallel beta-sheets means that, for each residue pair, only one of the residues is involved in main chain hydrogen bonding with the strand containing the partner residue. We call this the hydrogen bonded (HB) residue and the partner residue the non-hydrogen bonded (nHB) residue, and differentiate between the favorability of a pair and that of its reverse pair, e.g. Asn(HB)-Thr(nHB)versus Thr(HB)-Asn(nHB). Significantly (p < or = 0.000001) favoured pairings were rationalised using stereochemical arguments. For instance, Asn(HB)-Thr(nHB) and Arg(HB)-Thr(nHB) were favoured pairs, where the residues adopted favoured chi1 rotamer positions that allowed side-chain interactions to occur. In contrast, Thr(HB)-Asn(nHB) and Thr(HB)-Arg(nHB) were not significantly favoured, and could only form side-chain interactions if the residues involved adopted less favourable chi1 conformations. The favourability of hydrophobic pairs e.g. Ile(HB)-Ile(nHB), Val(HB)-Val(nHB) and Leu(HB)-Ile(nHB) was explained by the residues adopting their most preferred chi1 and chi2 conformations, which enabled them to form nested arrangements. Cysteine-cysteine pairs are significantly favoured, although these do not form intrasheet disulphide bridges. Interactions between positively and negatively charged residues were asymmetrically preferred: those with the negatively charged residue at the HB position were more favoured. This trend was accounted for by the presence of general electrostatic interactions, which, based on analysis of distances between charged atoms, were likely to be stronger when the negatively charged residue is the HB partner. The Arg(HB)-Asp(nHB) interaction was an exception to this trend and its favorability was rationalised by the formation of specific side-chain interactions. This research provides rules that could be applied to protein structure prediction, comparative modelling and protein engineering and design. The methods used to analyse the pairing preferences are automated and detailed results are available (http://www.rubic.rdg.ac.uk/betapairprefsparallel/).

Amino acid pairing preferences in parallel beta-sheets in proteins

Statistical approaches have been applied to examine amino acid pairing preferences within parallel beta-sheets. The main chain hydrogen bonding pattern in parallel beta-sheets means that, for each residue pair, only one of the residues is involved in main chain hydrogen bonding with the strand containing the partner residue. We call this the hydrogen bonded (HB) residue and the partner residue the non-hydrogen bonded (nHB) residue, and differentiate between the favourability of a pair and that of its reverse pair, e.g. Asn(HB)-Thr(nHB) versus Thr(HB)-Asn(nHB). Significantly (p <= 0.000001) favoured pairings were rationalised using stereochemical arguments. For instance, Asn(HB)-Thr(nHB) and Arg(HB)-Thr(nHB) were favoured pairs, where the residues adopted favoured chi(1) rotamer positions that allowed side-chain interactions to occur. In contrast, Thr(HB)-Asn(nHB) and Thr(HB)-Arg(nHB) were not significantly favoured, and could only form side-chain interactions if the residues involved adopted less favourable chi(1) conformations. The favourability of hydrophobic pairs e.g. Ile(HB)-Ile(nHB), Val(HB)-Val(nHB) and Leu(HB)-Ile(nHB) was explained by the residues adopting their most preferred chi(1) and chi(2) conformations, which enabled them to form nested arrangements. Cysteine-cysteine pairs are significantly favoured, although these do not form intrasheet disulphide bridges. Interactions between positively and negatively charged residues were asymmetrically preferred: those with the negatively charged residue at the HB position were more favoured. This trend was accounted for by the presence of general electrostatic interactions, which, based on analysis of distances between charged atoms, were likely to be stronger when the negatively charged residue is the HB partner. The Arg(HB)-Asp(nHB) interaction was an exception to this trend and its favourability was rationalised by the formation of specific side-chain interactions. This research provides rules that could be applied to protein structure prediction, comparative modelling and protein engineering and design. The methods used to analyse the pairing preferences are automated and detailed results are available (http:// www.rubic.rdg.ac.uk/betapairprefsparallel/). (c) 2005 Elsevier Ltd. All rights reserved.

X-ray crystallographic study of DNA duplex cross-linking: simultaneous binding to two d(CGTACG)(2) molecules by a bis(9-aminoacridine-4-carboxamide) derivative

Acridine-4-carboxamides form a class of known DNA mono-intercalating agents that exhibit cytotoxic activity against tumour cell lines due to their ability to inhibit topoisomerases. Previous studies of bis-acridine derivatives have yielded equivocal results regarding the minimum length of linker necessary between the two acridine chromophores to allow bis-intercalation of duplex DNA. We report here the 1.7 angstrom resolution X-ray crystal structure of a six-carbon-linked bis(acridine-4-carboxamide) ligand bound to d(CGTACG)(2) molecules by non-covalent duplex cross-linking. The asymmetric unit consists of one DNA duplex containing an intercalated acridine-4-carboxamide chromophore at each of the two CG steps. The other half of each ligand is bound to another DNA molecule in a symmetry-related manner, with the alkyl linker threading through the minor grooves. The two crystallographically independent ligand molecules adopt distinct side chain interactions, forming hydrogen bonds to either O6 or N7 on the major groove face of guanine, in contrast to the semi-disordered state of mono-intercalators bound to the same DNA molecule. The complex described here provides the first structural evidence for the non-covalent cross-linking of DNA by a small molecule ligand and suggests a possible explanation for the inconsistent behaviour of six-carbon linked bis-acridines in previous assays of DNA bis-intercalation.

Modeling the tetraphenylalanine-PEG hybrid amphiphile: from DFT calculations on the peptide to molecular dynamics simulations on the conjugate

The conformational properties of the hybrid amphiphile formed by the conjugation of a hydrophobic peptide with four phenylalanine (Phe) residues and hydrophilic poly(ethylene glycol), have been investigated using quantum mechanical calculations and atomistic molecular dynamics simulations. The intrinsic conformational preferences of the peptide were examined using the building-up search procedure combined with B3LYP/ 6-31G(d) geometry optimizations, which led to the identification of 78, 78, and 92 minimum energy structures for the peptides containing one, two, and four Phe residues. These peptides tend to adopt regular organizations involving turn-like motifs that define ribbon or helicallike arrangements. Furthermore, calculations indicate that backbone ... side chain interactions involving the N-H of the amide groups and the pi clouds of the aromatic rings play a crucial role in Phe-containing peptides. On the other hand,MD simulations on the complete amphiphile in aqueous solution showed that the polymer fragment rapidly unfolds maximizing the contacts with the polar solvent, even though the hydrophobic peptide reduce the number of waters of hydration with respect to an individual polymer chain of equivalent molecular weight. In spite of the small effect of the peptide in the hydrodynamic properties of the polymer, we conclude that the two counterparts of the amphiphile tend to organize as independent modules.

Nanozipper formation in the solid state from a self-assembling tripeptide with a single tryptophan residue

The self-assembly of a terminally protected tripeptide Boc-gamma-Abu(1)-Ala(2)-Trp(3)-OMe (gamma-Abu = gamma-aminobutyric acid) I results in the formation of a nanostructured supramolecular zipper through various non-covalent interactions in the crystal in which the indole side-chain of the Trp(3) residue plays a key role via N-H...pi interactions. (c) 2006 Published by Elsevier Ltd.

Guanine specific binding at a DNA junction formed by d[CG(5-BrU)ACG]2 with a topoisomerase poison in the presence of Co2+Ions†,‡

The structure of the duplex d[CG(5-BrU)ACG]2 bound to 9-bromophenazine-4-carboxamide has been solved through MAD phasing at 2.0 Å resolution. It shows an unexpected and previously unreported intercalation cavity stabilized by the drug and novel binding modes of Co2+ ions at certain guanine N7 sites. For the intercalation cavity the terminal cytosine is rotated to pair with the guanine of a symmetry-related duplex to create a pseudo-Holliday junction geometry, with two such cavities linked through the minor groove interactions of the N2/N3 guanine sites at an angle of 40°, creating a quadruplex-like structure. The mode of binding of the drug is shown to be disordered, with the major conformations showing the side chain bound to the N7 position of adjacent guanines. The other end of the duplex exhibits a terminal base fraying in the presence of Co2+ ions linking symmetry-related guanines, causing the helices to intertwine through the minor groove. The stabilization of the structure by the intercalating drug shows that this class of compound may bind to DNA junctions as well as duplex DNA or to strand-nicked DNA (‘hemi-intercalated'), as in the cleavable complex. This suggests a structural basis for the dual poisoning of topoisomerase I and II enzymes by this family of drugs.

Electro-optical properties of liquid crystal copolymers and their relationship to structural order

A range of side chain liquid crystal copolymers have been prepared using mesogenic and non-mesogenic units. It is found that high levels of the non-mesogenic moieties may be introduced without completely disrupting the organization of the liquid crystal phase. Incorporation of this comonomer causes a marked reduction in the glass transition temperature (Tg), presumably as a result of enhanced backbone mobility and a corresponding lowering of the nematic transition temperature, thereby restricting the temperature range for stability of the liquid crystal phase. The effect of the interactions between the various components of these side-chain polymers on their electro-optic responses is described. Infrared (i.r.) dichroism measurements have been made to determine the order parameters of the liquid crystalline side-chain polymers. By identifying a certain band (CN stretching) in the i.r. absorption spectrum, the order parameter of the mesogenic groups can be obtained. The temperature and composition dependence of the observed order parameter are related to the liquid crystal phase transitions and to the electro-optic response. It is found that the introduction of the non-mesogenic units into the polymer chain lowers the threshold voltage of the electro-optic response over and above that due to the reduction in the order parameter. The dynamic electro-optic responses are dominated by the temperature-dependent viscosity and evidence is presented for relaxation processes involving the polymer backbone which are on a time scale greater than that for the mesogenic side-chain units.