New polyamides with main-chain cyanine chromophores

Polyamides containing main-chain cyanine chromophores are synthesized, and their molecular, nonlinear optical, and mechanical properties are studied. It is shown that the Kerr electro-optical effect in polymer solutions is determined by the rigidity of polymer chains and that the nonlinear optical properties are dependent only on the chromophore content.     

Electrospray ionization mass spectrometric analysis of noncovalent complexes between DNA and polyamides containing N-methylpyrrole and N-methylimidazole

Electrospray ionization mass spectrometry was utilized to investigate the noncovalent complexes between novel polyamides and DNA containing the TCCT sequence. We analyzed the noncovalent binding of the polyamides with the DNA and assessed their relative affinities and stoichiometry. The results confirm that hairpin polyamides have higher binding affinities than three-ring polyamides. The hairpin polyamide (PyPyPyPygammaPyImImPybetaDp) has the highest affinity, and the beta-linked polyamide (PyPyPybetaImImImbetaDp) shows a dominant 1:2 binding stoichiometry. Two groups of competition experiments were undertaken to compare the binding affinities of the duplex DNA with different polyamides directly. The affinity scale thus obtained for the group-1 polyamides is PyPyPyPygammaPyImImPybetaDp > PyPyPybetaImImImbetaDp approximately PyPyPygammaImImImbetaDp > PyPyPybetaDp > PyImImbetaDp approximately ImImPybetaDp, and the order for the group-2 polyamides is PyPyPygammaImImImbetaDp > PyPyPygammaImImImbetaOEt > PyPyPygammaImImImbetaCOOH.     

Influence of a terminal formamido group on the sequence recognition of DNA by polyamides

Pyrrole (Py)-imidazole (Im)-containing polyamides bind in the minor groove of DNA and can recognize specific sequences through a stacked antiparallel dimer. It has been proposed that there are two different low energy ways to form the stacked dimer and that these are sensitive to the presence of a terminal formamido group: (i) a fully overlapped stacking mode in which the N-terminal heterocycles of the dimer stack on the amide groups between the two heterocycles at the C-terminal and (ii) a staggered stacking mode in which the N-terminal heterocycles are shifted by approximately one unit in the C-terminal direction (Structure 1997, 5, 1033-1046). Two different DNA sequences will be recognized by the same polyamide stacked in these two different modes. Despite the importance of polyamides as sequence specific DNA recognition agents, these stacking possibilities have not been systematically explored. As part of a program to develop agents that can recognize mismatched base pairs in DNA, a set of four polyamide trimers with and without terminal formamido groups was synthesized, and their interactions with predicted DNA recognition sequences in the two different stacking modes were evaluated. Experimental difficulties in monitoring DNA complex formation with polyamides were overcome by using surface plasmon resonance (SPR) detection of the binding to immobilized DNA hairpin duplexes. Both equilibrium and kinetic results from SPR show that a terminal formamido group has a pronounced effect on the affinity, sequence specificity, and rates of DNA-dimer complex formation. The formamido polyamides bind preferentially in the staggered stacking mode, while the unsubstituted analogues bind in the overlapped mode. Affinities for cognate DNA sequences increase by a factor of around 100 when a terminal formamido is added to a polyamide, and the preferred sequences recognized are also different. Both the association and the dissociation rates are slower for the formamido derivatives, but the effect is larger for the dissociation kinetics. The formamido group thus strongly affects the interaction of polyamides with DNA and changes the preferred DNA sequences that are recognized by a specific polyamide stacked dimer.     

Synthesis and characterization of tough polycyclic polyamides containing 4,9-Diamantyl moieties in the main chain

A series of new polyamides were synthesized by direct polycondensation of the 4,9-diamantane dicarboxylic acid ( I ) with various aromatic diamines in N-methyl-2-pyrrolidone (NMP) containing lithium chloride. The polyamides had inherent viscosities of 0.56–1.85 dL/g. Dynamic mechanical analysis revealed the polymers IIIa–IIId to have main melting transitions at 403, 431, 423, and 452°C, respectively. Moreover, these polymers were quite stable at high temperatures and maintained good mechanical properties (G′ = ca. 10⁸ Pa) up to temperatures close to the main transition well above 400°C. Although the polyamides contained rigid 4,9-diamantyl moieties in the main chain, the tensile properties of the polyamides showed toughness. Elongations of polyamides IIIa and IIIb reached 38.3 and 31.7%, respectively, before breaking. A glass transition was not observed. However, polyamide IIIc shows a melting transition with a sharp endothermic peak at 423°C by DSC measurement. Additionally, the introduction of 4,9-diamantyl units into the polyamide backbone resulted in polyamides with high thermal stability and good mechanical properties. © 1996 John Wiley & Sons, Inc.     

Sequence‐Specific DNA Recognition by Cyclic Pyrrole–Imidazole Cysteine‐Derived Polyamide Dimers

Pyrrole–imidazole (PI) polyamides bind to the minor groove of the DNA duplex in a sequence‐specific manner and thus have the potential to regulate gene expression. To date, various types of PI polyamides have been designed as sequence‐specific DNA binding ligands. One of these, cysteine cyclic PI polyamides containing two β‐alanine molecules, were designed to recognize a 7 bp DNA sequence with high binding affinity. In this study, an efficient cyclization reaction between a cysteine and a chloroacetyl residue was used for dimerization in the synthesis of a unit that recognizes symmetrical DNA sequences. To evaluate specific DNA binding properties, dimeric PI polyamide binding was measured by using a surface plasmon resonance (SPR) method. Extending this molecular design, we synthesized a large dimeric PI polyamide that can recognize a 14 bp region in duplex DNA.     

Structural and Kinetic Profiling of Allosteric Modulation of Duplex DNA Induced by DNA-Binding Polyamide Analogues

A combined structural and quantitative biophysical profile of the DNA binding affinity, kinetics and sequence-selectivity of hairpin polyamide analogues is described. DNA duplexes containing either target polyamide binding sites or mismatch sequences are immobilized on a microelectrode surface. Quantitation of the DNA binding profile of polyamides containing N-terminal 1-alkylimidazole (Im) units exhibit picomolar binding affinities for their target sequences, whereas 5-alkylthiazole (Nt) units are an order of magnitude lower (low nanomolar). Comparative NMR structural analyses of the polyamide series shows that the steric bulk distal to the DNA-binding face of the hairpin iPr-Nt polyamide plays an influential role in the allosteric modulation of the overall DNA duplex structure. This combined kinetic and structural study provides a foundation to develop next-generation hairpin designs where the DNA-binding profile of polyamides is reconciled with their physicochemical properties.     

Conformational energies of para-aromatic and aryl-aliphatic polyamides: Relation to mesogenic character in solution

PCILO conformational calculations have been carried out on several model compounds of aromatic polyamide oxamides and polyamide hydrazides. The comparison of the entropy of the equilibrium conformations allows a classification of the various constitutive units into “rigid” segments, and “flexible” ones having respectively low or high entropies. From the results, it is possible to predict the mesogenic nature of solutions of a large number of aromatic polyamides, polyamide hydrazides, and polyamide oxamides.     

Thermal Oxidative Stability of Heat-Stabilised Polyamide 66 by Differential Scanning Calorimetry

The thermal stability of heat-stabilised polyamide 66 in an oxidative environment is evaluated by DSC. The oxidative stability of the polyamide decreases as a result of repeated injection moulding. The results also indicate that the presence of glass fibres in the polyamide has a negative influence on the oxidative stability. Both isothermal and dynamic DSC measurements seem to be useful tools for assessing the stability of polyamides and there is a relationship between data determined using both procedures. This revised version was published online in July 2006 with corrections to the Cover Date.     

Organic sol-gel materials for second-order nonlinear optics based on melamines

A series of all organic nonlinear optical (NLO) sol-gel materials based on melamines and an azobenzene dye (Disperse Orange 3; DO3) have been investigated. Different contents of DO3 were covalently bonded with the melamine-based organic network via condensation of amino and methylol groups. The optically clear samples exhibited second-order optical nonlinearity (second-harmonic coefficient d₃₃) = 35.4 and 11.5 pm/V at 1064 and 1542 nm, respectively) after poling and curing at 220°C for 1 h. Thermal behavior of these organic NLO sol-gel systems was studied by temperature-dependent dielectric relaxation. The results indicate that the incorporation of rigid NLO-active chromophore into the melamine-based matrix leads to high rigidity and dense packing of the organic network. Subsequently, higher glass transition temperatures were obtained for the organic NLO sol-gel material with higher DO3 content. The influence of composition on the temporal stability at 100°C was also investigated. Temporal stability at 100°C was studied as a function of system composition. © 1999 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 37: 2503–2510, 1999     

Mapping Polyamide–DNA Interactions in Human Cells Reveals a New Design Strategy for Effective Targeting of Genomic Sites

Targeting the genome with sequence‐specific synthetic molecules is a major goal at the interface of chemistry, biology, and personalized medicine. Pyrrole/imidazole‐based polyamides can be rationally designed to target specific DNA sequences with exquisite precision in vitro; yet, the biological outcomes are often difficult to interpret using current models of binding energetics. To directly identify the binding sites of polyamides across the genome, we designed, synthesized, and tested polyamide derivatives that enabled covalent crosslinking and localization of polyamide–DNA interaction sites in live human cells. Bioinformatic analysis of the data reveals that clustered binding sites, spanning a broad range of affinities, best predict occupancy in cells. In contrast to the prevailing paradigm of targeting single high‐affinity sites, our results point to a new design principle to deploy polyamides and perhaps other synthetic molecules to effectively target desired genomic sites in vivo.     

Investigation of non-covalent complexes of HIV-1 promoter DNA and polyamides containing N-methylpyrrole by electrospray ionization mass spectrometry

Eight novel polyamides containing N-methylpyrrole were designed to target the sequence (5'-CTGCATATAAGCAG-3'/5'-CTGCTTATATGCAG-3') of the TATA box element of the HIV-1 promoter DNA. The non-covalent complexes of the promoter DNA and the polyamides were investigated by electrospray ionization (ESI) mass spectrometry, which provided strong evidence for the binding of the novel polyamides to the sequence of the TATA box element. It also revealed that polyamide 2 (PyPyPyPybetaDp), a potent binder of HIV-1 promoter DNA and a lead molecule for the design of new anti-HIV-1 drugs, had the highest binding affinity with the TATA box element DNA among these polyamides by examining the stoichiometry and the selectivity.     

Discrimination of A/T sequences in the minor groove of DNA within a cyclic polyamide motif

Eight-ring cyclic polyamides containing pyrrole (Py), imidazole (Im), and hydroxypyrrole (Hp) aromatic amino acids recognize predetermined six base pair sites in the minor groove of DNA. Two four-ring polyamide subunits linked by (R)-2,4-diaminobutyric acid [(R)H2Ngamma] residue form hairpin polyamide structures with enhanced DNA binding properties. In hairpin polyamides, substitution of Hp/Py for Py/Py pairs enhances selectivity for T. A base pairs but compromises binding affinity for specific sequences. In an effort to enhance the binding properties of polyamides containing Hp/Py pairings, four eight ring cyclic polyamides were synthesized and analyzed on a DNA restriction fragment containing three 6-bp sites 5'-tAGNNCTt-3', where NN = AA, TA, or AT. Quantitative footprint titration experiments demonstrate that contiguous placement of Hp/Py pairs in cyclo-(gamma-ImPyPyPy-(R)H2Ngamma-ImHpHpPy-) (1) provides a 20-fold increase in affinity for the 5'-tAGAACTt-3' site (Ka = 7.5 x 10(7)M(-1)) relative to ImPyPyPy-(R)H2Ngamma-ImHpHpPy-C3-OH (2). A cyclic polyamide of sequence composition cyclo-(gamma-ImHpPyPy-(R)H2Ngamma-ImHpPyPy-) (3) binds a 5'-tAGTACTt-3' site with an equilibrium association constant KA= 3.2 x 10(9)M(-1), representing a fivefold increase relative to the hairpin analogue ImHpPyPy-(R)H2Ngamma-ImHpPyPy-C3-OH (4). Arrangement of Hp/Py pairs in a 3'-stagger regulates specificity of cyclo-(gamma-ImPyHpPy-(R)H2Ngamma-ImPyHpPy-) (5) for the 5'-tAGATCTt-3' site (Ka = 7.5 x 10(7)M(-1)) threefold increase in affinity relative to the hairpin analogue ImPyHpPy-(R)H2Ngamma-ImPyHpPy-C3-OH (6), respectively. This study identifies cyclic polyamides as a viable motif for restoring recognition properties of polyamides containing Hp/Py pairs.     

Evaluation of binding selectivity of a polyamide probe to single base-pair different dna in A·T-rich region by electrospray ionization mass spectrometry

In this study, electrospray ionization mass spectrometry (ESI-MS) was used for the evaluation of the binding selectivity of a polyamide probe to single-base pair different DNA in an A.T-rich region. In this procedure, DeltaIr(dsn) was introduced as a parameter to compare the binding affinities of the polyamides with the duplex DNA. The results show that ESI-MS is a very useful tool for analysis of binding selectivity of a polyamide probe to single-base pair different DNA.     

Crystalline copolyamides of β-(4-aminophenyl)-propionic acid and caprolactam

Methyl β-(4-aminophenyl)propionate was prepared and converted to a crystalline polyamide. The copolymerization of β-(4-aminophenyl)propionic acid or its methyl esters with caprolactam resulted in polyamides having wide ranges of crystallinity and thermal stability, depending on the chemical composition. Copolymers with 10, 50, 85, 90, and 95 mole-% of caproamide sequences were shown by x-ray and differential scanning calorimetry to be semicrystalline. The composition and thermal stability of the polyamides were studied by infrared spectroscopy and thermogravimetric analysis, respectively.     

New indole-based chromophore-containing main-chain polyurethanes: architectural modification of isolation group, enhanced nonlinear optical property, and improved optical transparency

Three indole-based nonlinear optical (NLO) chromophores with changeable isolation groups were successfully introduced into the polymer backbone to yield a series of main-chain polyurethanes. Thanks to the main-chain structure and the advantages of the indole-based chromophores, all of the polymers show excellent transparency, good processability, thermal stability, and relatively good NLO effects. The obtained experimental results indicated that the polymer backbone, in addition to the linked isolation moieties, could act as isolation spacers in some special cases. The tested NLO results demonstrated that the isolation groups with apparent site-isolation effect might not benefit the macroscopic NLO effect of the resultant polymers.     

Fragrance release from the surface of branched poly (amide)s

Enzymes are powerful tools in organic synthesis that are able to catalyse a wide variety of selective chemical transformations under mild and environmentally friendly conditions. Enzymes such as the lipases have also found applications in the synthesis and degradation of polymeric materials. However, the use of these natural catalysts in the synthesis and the post-synthetic modification of dendrimers and hyperbranched molecules is an application of chemistry yet to be explored extensively. In this study the use of two hydrolytic enzymes, a lipase from Candida cylindracea and a cutinase from Fusarium solani pisii, were investigated in the selective cleavage of ester groups situated on the peripheral layer of two families of branched polyamides. These branched polyamides were conjugated to simple fragrances citronellol and L-menthol via ester linkages. Hydrolysis of the ester linkage between the fragrances and the branched polyamide support was carried out in aqueous buffered systems at slightly basic pH values under the optimum operative conditions for the enzymes used. These preliminary qualitative investigations revealed that partial cleavage of the ester functionalities from the branched polyamide support had occurred. However, the ability of the enzymes to interact with the substrates decreased considerably as the branching density, the rigidity of the structure and the bulkiness of the polyamide-fragrance conjugates increased.     

Effect of N-methyl substitution on the thermal decomposition processes in aliphatic–aromatic polyamides

The thermal decomposition processes of two polyamides, derived from succinic acid and two aromatic diamines, were studied by direct pyrolysis mass spectrometry. Fast atom bombardment (FAB) mass spectrometry has been also used in order to provide additional information for the elucidation of the thermal degradation mechanism of the polymers investigated. FAB mass spectra, obtained by introducing in the FAB ion source the solid residues from polymer pyrolysis performed in thermogravimetric experiments, allowed the detection of diagnostic compounds up to about 1600 amu. Our results indicate that the thermal stability of the N-methyl-substituted polyamide is higher than that of the unsubstituted polyamide. The difference in the thermal degradation mechanism accounts for the difference in the thermal stability of the two polyamides. In fact, the unsubstituted polyamide decomposes via an intramolecular exchange and a concomitant N? H hydrogen transfer process with formation of compounds with amine and/or succinimide end groups. Instead, the N-methyl-substituted polyamide decomposes via an α C? H hydrogen transfer process from the methyl group to the nitrogen atom with formation of compounds with amine and/or 2,5-piperidinedione end groups.     

High-transition-temperature polyamides based on 2(2-aminophenyl)1,1-dimethylethylamine

Novel polyamides have been prepared from the 2(4-aminophenyl) 1,1-dimethylethylamine (APDEA) and various diacyl compounds. Unique properties have been found in these polyamides in that they possess a high glass-transition temperature (Tg), yet have an exceptionally high Tg/Tm ratio. Structure—property relationships in these interesting polyamide and copolyamide systems are investigated. Unsubstituted polyamides and those with saturated rings were synthesized to demonstrate the important role played by the methyl substitution and the rigid ring in affecting the Tg and Tm. It seems reasonable to conclude that the gem-dimethyl substituents and the stiff phenyl group or the interaction of these two groups with each other and with other adjacent segments in this particular molecular architecture contribute to this desirable transition-temperature performance.     

Polyamide-bound metal complex catalysts: Synthesis,characterization and catalytic properties

A series of polyamides having different numbers of methylene groups in their repeating units have been synthesized by interfacial polycondensation of terephthaloyl chloride with piperazine and aliphatic diamines H₂N(CH₂)_nNH₂ (n = 2, 6, 10). These materials, which have high thermal stability, were used for immobilization of rhodium and platinum complexes. Chloroplatinic acid and the compounds PtCl₂(CH₃CN)₂ and [RhCl(CO)₂]₂ were used as precursors of the supported catalysts. Low molecular weight analogues of the polyamides were prepared for a study of the coordination mode between the metal ion and the polymer by IR spectroscopy. The results suggest that the carbonyl oxygen of the polyamide is the site of coordination to both rhodium and platinum. The bound catalysts exhibited high activity in hydrosilylation of hexene-1. The activities of the rhodium complexes were found to be dependent on the structure of the polyamide support, decreasing with increasing distance between the amide groups, and closely paralled the changes in the degree of crystallinity of the polymers. Repeated use of the polymers bearing rhodium complexes showed that the bond between the metal and polyamide is fairly stable.     

Synthesis and characterization of optically active polyamides derived from carbohydrate-based monomers

The synthesis of three new stereoregular AB-type polyamides based on D -ribono-1,4-lactone, L -arabinose, and D -xylose has been carried out by the active ester polycondensation method. These polyamides were characterized by elemental analysis, IR and NMR spectroscopies, and powder X-ray diffraction. They displayed optical activity and had a pronounced affinity to water, although they were not soluble in this solvent. The polyamide obtained from D -ribono-1,4-lactone was highly crystalline and yielded films with spherulitic texture. © 1997 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 35: 3645–3653, 1997