Conformational energies of aromatic polyamides

PCILO conformational calculations have been made on several model compounds of aromatic polyamides. The calculated structures can be compared with the X-Ray crystallographic analyses and related to the physical properties of these polymers. Poly-p-phenylene terephthalamide appears as a more flexible polymer than poly-p-benzamide.     

Conformational energies of cyclenes

An universal function for non-bonded interactions, which takes into account the relative orientation of the bonds is considered in calculating the conformational energies of cycloalkenes and cycloalkadienes. A comparison is made with previous results obtained by using usual 6-exp functions for non-bonded interactions.     

Conformational energies and hydrogen bonding in dichloroethanol

The conformational energy differences have been measured for 2,2-dichloroethanol in the neat liquid and in DMSO and H2O via Raman spectroscopy. In contrast to earlier results on 2-chloroethanol, ΔH was not markedly effected by dilution in these hydrogen bonding solvents. Spectra in the OH valence region were utilized to determine the energy difference between intra- and intermolecularly hydrogen bonded species. The result indicated stronger intramolecular hydrogen bond formation in dichloroethanol than in the monohalogenated alcohol.     

Dipoles-dipole association of mesogenic molecules in solution

The dielectric polarization has been used to study dipolar association of 4-n-pentyl-4'-cyanobiphenyl in benzene solution. The results have been interpreted with the assumption of a monomer-dimer equilibrium. To explain the relatively high effective dipole moment of the dimers, a new structure has been proposed for them.     

Conformational analysis. Part 16 Conformational free energies in substituted piperidines and piperidinium salts

Summary The conformational free energies (-G^o) of a number of 4-substituted piperidines and piperidinium salts have been determined by the J-value method. For the 4-substituted piperidines (R=Me, Phenyl, CO₂Et, Br, OH, F) the relative conformer energies are almost identical to those of the analogous cyclohexanes.The methyl and phenyl compounds showed no change in the couplings on protonation, implying no change in the conformer energies. In constrast, in the remaining compounds with polar 4-substituents an almost constant stabilisation of the axial conformer of ca. 0.7–0.8 kcal mol^-1 was observed on protonation. In three cases (R=F, OH and Br) the conformational preferences is reversed on protonation and the axial form is favoured.The conformer energies of both the free bases and the piperidinium salts can be quantitatively predicted by molecular mechanics calculations using the COSMIC force-field, in which the electrostatic interactions are calculated by a simple Coulombic model with the partial atomic charges in the molecules given by the CHARGE2 routine, and an effective dielectric constant of five. The precise agreement obtained demonstrates conclusively that the electrostatic interactions between the substituents and the protonated nitrogen are the cause of the conformational changes on protonation, and that these can be modelled successfully using existing force-fields.For Part 15, see Ref. 1.     

Conformational preference of polyglycine in solution to elongated structure

Do polypeptide chains ever behave like a random coil? In this report we demonstrate that glycine, the residue with the fewest backbone restrictions, exhibits a strong preference for an extended conformation in solution when polymerized in short segments of polyglycine. A model peptide system comprised of two unique tripeptide units, between which 1 to 18 glycine residues are inserted, is characterized by NMR and by small-angle X-ray scattering (SAXS). The residual dipolar coupling (RDC) values of the two tripeptide units are insensitive to changes in number of intervening glycines, suggesting that extension of the linker does not alter the average angular relationship between the tripeptides. Polyglycine segments longer than nine residues form insoluble aggregates. SAXS measurements using synchrotron radiation provide direct evidence that polyglycine peptides adopt elongated conformations. In particular, the construct with a linker with six glycines showed a scattering profile indicative of a monomeric state with a radius of gyration and the maximum dimension of 9.1 A and approximately 34 A, respectively. The ensemble averaged global structure of this 12-mer peptide can best be approximated by a cylinder with a radius of 4 A and a length of approximately 33 A, making it intermediate in extension between a beta strand and an alpha helix.     

Photoluminescence of polysiloxane containing mesogenic 4-cyanobiphenyl in solution

Photoluminescent characteristics of polysiloxane containing pendant mesogenic 4-cyanobiphenyl (CB) and its monomeric analogues were studied in THF solution. An excimer formation was observed, and the increase in CB content in polysiloxane induced the increase in the fluorescence intensity from the excimers. The fluorescence decays were analyzed by triexponential function. A high CB content induced small decay rates, indicating the decrease of nonradiational decay. Such suppression of the nonradiation decay in higher CB content was explained by a strong mesogenic interaction between CB groups in solution. © 1996 John Wiley & Sons, Inc.     

Conformational analysis—CIX : Applications of molecular mechanics to the structures and energies of alkynes

An earlier described force-field has been extended to include alkynes. The structures and heats of formation of simple alkynes were calculated to approximately within experimental error for those for which data are available, and predictions are made for others. Rotational barriers and conformational equilibria were also adequately dealt with. Some macrocyclic alkynes were also examined.     

Conformational free energies of 1,2-dichloroethane in nanoconfined methanol

Monte Carlo simulations have been used to construct free energy surfaces of 1,2-dichloroethane dissolved in methanol confined in hydrophobic spherical cavities of varying size (10-15 A) and solution density (0.6-0.79 g/cm3). The free energy surfaces are functions of two variables: the (center-of-mass) distance from the cavity wall of 1,2-dichloroethane and the Cl-C-C-Cl dihedral angle. Umbrella sampling and the weighted histogram analysis method were used to obtain accurate results for the free energy in these two degrees of freedom. Our results indicate that the conformational equilibrium and the barrier to internal rotation of the 1,2-dichloroethane depend on the position in the cavity. The results are discussed in the context of the solvent density, orientational distributions, and packing effects.     

Electrooptical properties of mesogenic chain molecules in solution and in nematic state

Electrooptical characteristics of mesogenic chain molecules in solution and in mesophase can be described in terms of intra- and intermolecular orientational orders. The value and sign of electric birefringence δn in a solution of kinetically rigid chain molecules are determined by the combination of two factors: intramolecular orientational order which depends on the dipolar and anisotropic architecture of the molecule and intermolecular orientational order caused by the action of the external electric field E. The value and sign of the dielectric anisotropy δε of the polymer nematic phase are also determined by the combination of intra- and intermolecular orders. However, in this case the latter is not maintained by the external field but by the nematic potential of the mesophase. Therefore, comparative investigations of electrooptical properties of polymers in solutions and in nematic melts make it possible to obtain information about the intra- and intermolecular orientational orders of the molecules under investigation in these two states. These investigations were carried out using the method of electric birefringence in solutions and the method of orientational deformations of nematic textures in an electric field. The objects being investigated were nematogenic dimers and trimers. Experimental data obtained for these compounds showed the presence of intramolecular order in their molecules, which is manifested in the odd-even oscillations of the value and sign of Kerr constant K≈δn/E² in solution and δε in the nematic phase when the number of C-C bonds in the methylene spacers of these molecules is varied. This effect is particularly dramatic in the mesophase where it is enhanced by intermolecular nematic potential.     

Conformational analysis of oligosaccharides in solution

A complete understanding of the role of carbohydrates in biological systems is to a large extent dependent on the information available about the equilibrium mixture and about the preferred conformation of the carbohydrate molecules in solution. The conformational analysis offers a tool which can determine all possible conformations which influence the solution behavior of carbohydrates. This paper attempts to survey the progress in the theoretical conformational analysis of saccharides in solution. The conformational analysis will be discussed in detail both with respect to the strategy for the investigation of conformational properties but also with regard to the quality of the method used for calculations of the energy of the isolated molecule and free energy of solvation. Finally, examples will be given to illustrate how the methods of conformational analysis can be used to estimate the solution behavior of cyclic model compounds of carbohydrates 2-methoxytetrahydropyran, monosaccharide D -glucopyranose, and two disaccharides; β-maltose and β-cellobiose.     

Study of kinetics of thermal degradation and to determine the activation energies of polyamides based on s-triazine

A series of ten polyamides was prepared by the high-temperature polycondensation of 4,6-bis(N-(4-(benzoylchloride)amino))-2-(N-phenyl- piperazin-1-yl)-1,3,5-triazine with different aromatic and aliphatic diamines. The synthesized polyamides were analyzed by physico-chemical properties such as solubility, density, viscosity etc. The structure of prepared polyamides was evaluated by ¹H NMR and FTIR spectrum. Thermogravimetric analysis used to study the kinetics of thermal degradation of some synthesized polyamides. Broido, Horowitz & Metzger, Coats Redfern and Chan et al. models were applied to respective thermograms to determine the activation energy (E_a). Activation energy data shows that the polyamides obtained from aromatic diamine has greater stability than the polyamides obtained from aliphatic amine.     

Conformational changes in proteins at interfaces: From solution to the interface,and back

After adsorption, polymer molecules, including proteins, undergo conformational relaxation. It involves a certain degree of spreading of the polymer molecule over the sorbent surface. Adsorption kinetics experiments reveal that the characteristic time of spreading is much longer for globular proteins than for highly flexible polymers. Based on differential scanning calorimetry it is concluded that the degree of spreading of protein molecules decreases with increasing rate of covering the surface with the protein. It is furthermore inferred that the relaxation does not proceed gradually but rather in steps. According to circular dichroism spectra the relaxed protein molecules still contain a large fraction of ordered structure. As a rule, protein molecules that, by homomolecular exchange, are released from the surface re-adopt their original structure; however, an exception to this rule is reported.     

Conformational properties of structurally rigid polyamides. I. Conformation of polyamides and model diamides derived from optically active cyclic 1,2-dicarboxylic acids

The conformational equilibria of piperidine diamides derived from five cyclic 1,2-dicarboxylic acids (I–V) have been investigated by dipole moment measurements and a priori conformational energy estimates. Since these diamides represent the building blocks of the polyamides derived from the above cyclic diacids and piperazine or trans-2,5-dimethylpiperazine, the results obtained in the study of the models have been used to investigate the conformation of the polymers. The overall evidence suggests that cyclopentane, cyclohexane, and bicyclooctane piperazine polymers behave as rigid rods in which the structural units possess approximately the same conformational preference exhibited by the respective model diamides.     

Conformational equilibria of ethanolamine and its hydrochloride in solution

The conformational preferences of ethanolamine and its hydrochloride in solution were estimated by comparing experimental NMR vicinal proton-proton coupling constants to semiemprical coupling constants for each staggered rotamer, derived by the Haasnoot-Altona method. Strong gauche preferences are observed for both ethanolamine and its hydrochloride over a wide range of solvent polarities. Concentration was not observed to significantly affect the position of the conformer equilibria.     

Conformational properties of glucosyl-thioglucosides and their S-oxides in solution

A stereochemical study of a series of alkyl glucosyl-β-(1→6)-thioglucosides and their S-oxides by means of nuclear magnetic resonance and circular dichroism revealed that the populations around the thioglucosidic bond (ring I) as well as those of the interglycosidic linkage ω depend on the aglycone, the solvent and, in the S-oxides, on the absolute configuration of the sulfur atom. The results for the thio-disaccharides showed the strong influence of the solvent polarity on the conformational preferences of the interglycosidic bond. In polar solvents, the magnitudes of the rotamer populations, P_gg and P_gt, remained practically constant through the series, while in non-polar solvents a clear predominance of gt conformation was observed as well as the influence of the aglycone on the conformational equilibrium. The results for both (S_S)- and (R_S)-alkyl thiogentiobiosyl S-oxide series showed a clear predominance of the gt rotamer, P_gt always having a higher magnitude in the latter series than in the former. Both series exhibited linear correlations between interglycosidic P_gg and P_gt and Taft’s steric parameter (E_S) for the alkyl group attached to the sulfinyl group, especially in non-polar solvents. The stereochemical study around the C1–S bond established that the flexibility around this linkage depends on aglycone size, solvent polarity, and the absolute configuration of the sulfur, derivatives of the S_S series showing higher flexibility in both polar and non-polar media. The conformational properties of these compounds in solution are explained in terms of stereoelectronic, steric, and solvent effects.     

Local measures of intermolecular free energies in solution

Proton spin-lattice relaxation rate changes induced by freely diffusing oxygen in aqueous and mixed solvents are reported for representative amino acids and glucose. The local oxygen concentration at each spectrally resolved proton was deduced from the paramagnetic contribution to the relaxation rate. The measured relaxation increment is compared to that of the force-free diffusion relaxation model, and the differences are related to a free energy for the oxygen association with different portions of the solute molecules. The free energy differences are small, on the order of -800 to -2000 J/mol, but are uniformly negative for all proton positions measured on the amino acids in water and reflect the energetic benefit of weak association of hydrophobic cosolutes. For glucose, CH proton positions report negative free energies for oxygen association, the magnitude of which depends on the solvent; however, the hydroxyl positions report positive free energy differences relative to the force-free diffusion model, which is consistent with partial occupancy in the OH region by a solvent hydrogen bond.     

Vertical ionization energies of halogen anions in solution

Based on the constrained equilibrium state theory, the nonequilibrium solvation energy is derived in the framework of the continuum model. The formula for spectral shift and vertical ionization energy are deduced for a single sphere cavity with the point charge assumption. The new model is adopted to investigate the vertical ionization for halogen atomic and molecular anions X^? (X = Cl, Br, I, Cl₂, Br₂, I₂) in aqueous solution. According to the calculation using the CCSD-t/aug-cc-pVQZ method in vacuum, our final estimated vertical ionization energies in solution are very close to the experimental observations, while the traditional nonequilibrium solvation theory overestimates these vertical ionization energies.     

A convenient method for the synthesis of DNA-recognizing polyamides in solution

A convenient method for the synthesis of polyamides containing N-methylpyrrole (Py) and N-methylimidazole (Im) in solution has been developed. Most of the building blocks have been prepared by a haloform reaction in a simple way that column chromatography can be avoided. By use of the DCC/HOBT coupling reaction, the building blocks prepared have been effectively connected to construct a variety of subchains and polyamides without employing amino protection and deprotection. By use of the present method, an eight-ring polyamide, PyPyPyPygammaPyImImPybetaDp (gamma is gamma-aminobutyric acid, beta is beta-alanine, Dp is N, N-dimethylpropyldiamine), has been synthesized by the coupling of two four-ring subchains in one step.     

Synthesis of aromatic polyamides having pyridine moiety and their lyotropic properties in solution

Fully aromatic polyamide containing pyridine moieties (PPy) were successfully synthesized either by interfacial or solution polycondensation to prepare polyamide with inherent viscosity as high as 4. Solution properties of PPy in sulfuric acid were investigated in terms of solution viscosity and lyotropic behavior. The polyamide had a better solubility in sulfuric acid than in poly(p-phenylene terephthalamide) (PT) and the PPy solution in sulfuric acid exhibited an optically anisotropic property in a wider range of concentrations at relatively low temperatures in comparison with the PT solution. Viscosities of the PPy solution and the film cast from the PPy solution indicated a phenomenon characteristic of a highly oriented rigid polymer molecule caused by a lyotropic behavior.