Observed and predicted hydrogen bond motifs in crystal structures of hydantoins, dihydrouracils and uracils

A survey of crystal structures containing hydantoin, dihydrouracil and uracil derivatives in the Cambridge Structural Database revealed four main types of hydrogen bond motifs when derivatives with extra substituents able to interfere with the main motif are excluded. All these molecules contain two hydrogen bond donors and two hydrogen bond acceptors in the sequence of NH, C = O, NH, and C=O groups within a 5-membered ring (hydantoin) and two 6-membered rings (dihydrouracil and uracil). In all cases, both ring NH groups act as donors in the main hydrogen bond motif but there is an excess of hydrogen bond acceptors (two C=O able to accept twice each) and so two possibilities are found: (i) each carbonyl O atom may accept one hydrogen bond or (ii) one carbonyl O atom may accept two hydrogen bonds while the other does not participate in the hydrogen bonding. We observed different preferences in the type and symmetry of the motifs adopted by the different derivatives, and a good agreement is found between motifs observed experimentally and those predicted using computational methods. We identified certain molecular factors such as chirality, substituent size and the possibility of C-H⋯O interactions as important factors influencing the motif observation. © 2012 The Royal Society of Chemistry and the Centre National de la Recherche Scientifique.

2-(3-Hydroxy-propyl)isoindoline-1,3-dione:Competition among hydrogen-bond acceptors

The title compound, C11H11NO3, has two mol-ecules in the asymmetric unit, which differ in the orientation of their side-chain OH groups, allowing them to form inter-molecular O - H⋯O hydrogen bonds to different acceptors. In one case, the acceptor is the OH group of the other mol-ecule, and in the other case it is an imide O=C group. This is the first example in the N-substituted phthalimide series in which independent mol-ecules have different types of acceptor. Mol-ecular-orbital calculations place the greatest negative charge on the OH group. © 2008 International Union of Crystallography.

Experiments and analysis of combined diffraction and self diffraction effects in a nematic liquid crystal cell

The potential for nonlinear optical processes in nematic-liquid-crystal cells is great due to the large phase changes resulting from reorientation of the nematic-liquid-crystal director. Here the combination of diffraction and self-diffraction effects are studied simultaneously by the use of a pair of focused laser beams which are coincident on a homeotropically aligned liquid-crystal cell. The result is a complicated diffraction pattern in the far field. This is analyzed in terms of the continuum theory for liquid crystals, using a one-elastic-constant approximation to solve the reorientation profile. Very good comparison between theory and experiment is obtained. An interesting transient grating, existing due to the viscosity of the liquid-crystal material, is observed in theory and practice for large cell-tilt angles.

Observations of diffraction and self diffraction effects during two wave mixing in a nematic liquid crystal

We report observations of the diffraction pattern resulting when a nematic liquid crystal is illuminated with two equal power, high intensity beams of light from an Ar+ laser. The time evolution of the pattern is followed from the initial production of higher diffraction orders to a final striking display arising as a result of the self-diffraction of the two incident beams. The experimental results are described with good approximation by a model assuming a phase distribution at the output plane of the liquid crystal in the form of the sum of a gaussian and a sinusoid.

Experimental and theoretical studies on six-membered ring hydrogen bond systems in crystalline drug substances

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Observations of diffraction and self diffraction effects during two wave mixing in a nematic liquid crystal

We report observations of the diffraction pattern resulting when a nematic liquid crystal is illuminated with two equal power, high intensity beams of light from an Ar+ laser. The time evolution of the pattern is followed from the initial production of higher diffraction orders to a final striking display arising as a result of the self-diffraction of the two incident beams. The experimental results are described with good approximation by a model assuming a phase distribution at the output plane of the liquid crystal in the form of the sum of a gaussian and a sinusoid.

Experiments and analysis of combined diffraction and self diffraction effects in a nematic liquid crystal cell

The potential for nonlinear optical processes in nematic-liquid-crystal cells is great due to the large phase changes resulting from reorientation of the nematic-liquid-crystal director. Here the combination of diffraction and self-diffraction effects are studied simultaneously by the use of a pair of focused laser beams which are coincident on a homeotropically aligned liquid-crystal cell. The result is a complicated diffraction pattern in the far field. This is analyzed in terms of the continuum theory for liquid crystals, using a one-elastic-constant approximation to solve the reorientation profile. Very good comparison between theory and experiment is obtained. An interesting transient grating, existing due to the viscosity of the liquid-crystal material, is observed in theory and practice for large cell-tilt angles.

True liquid crystal templating of SBA-15 with reduced microporosity

Mesoporous silica SBA-15 was synthesised by the true liquid crystal templating method, yielding a material with reduced microporosity compared with that produced by the more conventional liquid crystal templating route. Further advancements allow the generation of metal nanoparticle-doped SBA-15 materials with well-defined metal particle sizes, which posses potential as catalytic systems. © 2013 Elsevier Inc. All rights reserved.

Dynamics of cholesteric liquid crystals in the presence of a random magnetic field:stochastic dynamics of cholesteric liquid crystal

Based on dynamic renormalization group techniques, this letter analyzes the effects of external stochastic perturbations on the dynamical properties of cholesteric liquid crystals, studied in presence of a random magnetic field. Our analysis quantifies the nature of the temperature dependence of the dynamics; the results also highlight a hitherto unexplored regime in cholesteric liquid crystal dynamics. We show that stochastic fluctuations drive the system to a second-ordered Kosterlitz-Thouless phase transition point, eventually leading to a Kardar-Parisi-Zhang (KPZ) universality class. The results go beyond quasi-first order mean-field theories, and provides the first theoretical understanding of a KPZ phase in distorted nematic liquid crystal dynamics.

Unique temperature dependence of selectively liquid-crystal-filled photonic crystal fibers

We demonstrate a unique temperature-dependent characteristic of the selectively liquid-crystal-filled photonic crystal fiber, which is realized by a selectively infiltrating liquid crystal into a single air hole located at the second ring near the core of the PCF. Three-resonance dips are observed in the transmission spectrum. Theoretical and experimental investigations reveal that the three-resonance dips all result from the coupling between the LP01 core mode and the rod modes, i.e., LP03 and LP51. Then, we find that the dip shift induced by temperature shows good agreements with the thermo-optic performance of the LC employed. Furthermore, the dips shift greatly with changes in temperature, providing a method to achieve temperature measurement in such a compact structure.

Dielectric and electro-optical properties of some cyanobiphenyl liquid-crystals

A variety of methods have been reviewed for obtaining parallel or perpendicular alignment in liquid-crystal cells. Some of these methods have been selected and developed and were used in polarised spectroscopy, dielectric and electro-optic studies. Also, novel dielectric and electro-optic cells were constructed for use over a range of temperature. Dielectric response of thin layers of E7 and E8 (eutectic mixture liquid-crystals) have been measured in the frequency range (12 Hz-100 kHz) and over a range of temperature (183-337K). Dielectric spectra were also obtained for supercooled E7 and E8 in the Hz and kHz range. When the measuring electric field was parallel to the nematic director, one loss peak (low-frequency relaxation process) was observed for E7 and for E8, that exhibits a Debye-type behaviour in the supercooled systems. When the measuring electric field was perpendicular to the nematic director, two resolved dielectric processes have been observed. The phase transitions, effective molecular polarisabilities, anisotropy of polarisabilities and order parameters of three liquid crystal homologs (5CB, 6CB, and 7CB), 60CB and three eutectic nematic mixtures E7, E8, and E607 were calculated using optical and density data measured at several temperatures. The order parameters calculated using the different methods of Vuks, Neugebauer, Saupe-Maier, and Palffy-Muhoray are nearly the same for the liquid crystals considered in the present study. Also, the interrelationship between density and refractive index and the molecular structure of these liquid crystals were established. Accurate dielectric and dipole results of a range of liquid-crystal forming molecules at several temperatures have reported. The role of the cyano-end group, biphenyl core, and flexible tail in molecular association, were investigated using the dielectric method for some molecules which have a structural relationship to the nematogens. Analysis of the dielectric data for solution of the liquid-crystals indicated a high molecular association, comparable to that observed in the nematic or isotropic phases. Electro-optic Kerr effect were investigated for some alkyl cyanobiphenyls, their nematic mixtures and the eutectic mixture liquid-crystals E7 and E8 in the isotropic phase and solution. The Kerr constant of these liquid crystals found to be very high at the nematic-isotropic transition temperatures as the molecules are expected to be highly ordered close to phase transition temperatures. Dynamic Kerr effect behaviour and transient molecular reorientation were also observed in thin layers of some alkyl cyanobiphenyls. Dichroic ratio R and order parameters of solutions containing some azo and anthraquinone dyes in the nematic solvent (E7 and E8), were investigated by the measurement of the intensity of the absorption bands in the visible region of parallel aligned samples. The effective factors on the dichroic ratio of the dyes dissolved in the nematic solvents were determined and discussed.

Dielectric relaxation of polysiloxanes and kerr effect of p-phenylene vinylene oligomers

The dielectric relaxation behaviour of a series of cyclic and linear poly(dimethylsiloxanes) with overline nn in the range 28 to 99 has been studied, as a function of temperature (142.0K-157.5K) and frequency (12-105Hz). Activation energies for the -relaxation process, Davidson-Cole empirical distribution factors, , and mean-square dipole moments per repeat unit, < 2> , have been calculated. Differences in values of H_act reflected restricted dipolar rotation for the cyclic structures, compared to the linear structures, over the range of molecular weights studied. The dielectric relaxation behaviour of a series of linear oligomers of methyl phenyl siloxane, with n in the range 4 to 10, a series of linear fractions of poly(methyl phenyl siloxane), with overline n_n in the range 31 to 1370, and a cyclic oligomer of mehyl phenyl siloxane, with n = 10, has been studied as a function of temperature (155.5K-264.0K) and frequency (12-105Hz). Activation energies for the -relaxation process, Davidson-Cole and Cole-Cole empirical distribution factors, and , respectively, and mean-square dipole moments per repeat unit have been calculated. The reduced flexibility of short methyl phenyl siloxane chains, compared to dimethyl siloxane chains, was apparent from a comparison of dipole moment ratios. The dilectric relaxation behaviour of poly(methyl hydrogen siloxane) and poly(n-hexyl methyl siloxane) has been studied as a function of temperature and frequency. A polysiloxane liquid crystal has been synthesised and its dielectric relaxation behaviour has been studied, as a function of temperature and frequency, in the liquid crystalline phase and below T_g. Poly(p-phenylene vinylene) and related oligomers have been synthesised and characterised by a variety of experimental techniques. The Kerr effect of two oligomeric fractions, in solution in PPG 2025, has been measured. The electrical conductivities of the undoped and I_2-doped polymer and oligomers have been measured.

Investigating polymer-peptide conjugates and electrospinning for the production of advanced materials

This thesis describes the production of advanced materials comprising a wide array of polymer-based building blocks. These materials include bio-hybrid polymer-peptide conjugates, based on phenylalanine and poly(ethylene oxide), and polymers with intrinsic microporosity (PIMs). Polymer-peptides conjugates were previously synthesised using click chemistry. Due to the inherent disadvantages of the reported synthesis, a new, simpler, inexpensive protocol was sought. Three synthetic methods based on amidation chemistry were investigated for both oligopeptide and polymerpeptide coupling. The resulting conjugates produced were then assessed by various analytical techniques, and the new synthesis was compared with the established protocol. An investigation was also carried out focussing on polymer-peptide coupling via ester chemistry, involving deprotection of the carboxyl terminus of the peptide. Polymer-peptide conjugates were also assessed for their propensity to self-assemble into thixotropic gels in an array of solvent mixtures. Determination of the rules governing this particular self-assembly (gelation) was required. Initial work suggested that at least four phenylalanine peptide units were necessary for self-assembly, due to favourable hydrogen bond interactions. Quantitative analysis was carried out using three analytical techniques (namely rheology, FTIR, and confocal microscopy) to probe the microstructure of the material and provided further information on the conditions for self-assembly. Several polymers were electrospun in order to produce nanofibres. These included novel materials such as PIMs and the aforementioned bio-hybrid conjugates. An investigation of the parameters governing successful fibre production was carried out for PIMs, polymer-peptide conjugates, and for nanoparticle cages coupled to a polymer scaffold. SEM analysis was carried out on all material produced during these electrospinning experiments.

Conformational Evaluation of Indol-3-yl-N-alkyl-glyoxalylamides and Indol-3-yl-N,N-dialkyl-glyoxalylamides

Restricted rotation in indol-3-yl-N-alkyl- and indol-3-yl-N,N-dialkyl-glyoxalylamides can in principle give the syn-periplanar and anti-periplanar rotamers. In asymmetrically disubstituted glyoxalylamides, steric effects lead to the occurrence of both rotamers, as observed by NMR spectroscopy. The predominant peak corresponds with the anti rotamer, in which the bulkier alkyl group is orientated trans to the amide carbonyl group. In monoalkylated glyoxalylamides, only one set of peaks is observed, consistent with the presence of only one rotamer. Crystal structures of 5-methoxyindole-3-yl-N-tert-butylglyoxalylamide, indole-3-yl-N-tert-butylglyoxalylamide, and indole-3-yl-N-isopropylglyoxalylamide reported here reveal a syn conformation held by an intramolecular N-HO hydrogen bond.

A comparative molecular similarity indices (CoMSIA) study of peptide binding to the HLA-A3 superfamily

Epitope identification is the basis of modern vaccine design. The present paper studied the supermotif of the HLA-A3 superfamily, using comparative molecular similarity indices analysis (CoMSIA). Four alleles with high phenotype frequencies were used: A*1101, A*0301, A*3101 and A*6801. Five physicochemical properties—steric bulk, electrostatic potential, local hydro-phobicity, hydrogen-bond donor and acceptor abilities—were considered and ‘all fields’ models were produced for each of the alleles. The models have a moderate level of predictivity and there is a good correlation between the data. A revised HLA-A3 supermotif was defined based on the comparison of favoured and disfavoured properties for each position of the MHC bound peptide. The present study demonstrated that CoMSIA is an effective tool for studying peptide–MHC interactions.