Electric-field-induced molecular alignment of side-chain liquid-crystalline polyacetylenes containing biphenyl mesogens

Electric-field-induced molecular alignments of side-chain liquid-crystalline polyacetylenes [-{HC=C[(CH2)(m)OCO-biph-OC7H15]}-, where biph is 4,4'-biphenylyl and m is 3 (PA3EO7) or 9 (PA9EO7)] were studied with X-ray diffraction and polarized optical microscopy. An orientation as high as 0.84 was obtained for PA9EO7. Furthermore, the molecular orientation of]PA9EO7 was achieved within a temperature range between the isotropic-to-smectic A transition temperature and 115 degreesC, and this suggested that the orientational packing was affected by the thermal fluctuation of the isotropic liquid and the mobility of the mesogenic moieties. The maximum achievable orientation for PA9EO7 was much greater than that for PA3EO7. This was the first time that the electric-field-induced molecular orientation of a side-chain liquid-crystalline polymer with a stiff backbone was studied.

Molecular alignment relaxation in polymer optical fibers for sensing applications

A systematic study of annealing behavior of drawn PMMA fibers was performed. Annealing dynamics were investigated under different environmental conditions by fiber longitudinal shrinkage monitoring. The shrinkage process was found to follow a stretched exponential decay function revealing the heterogeneous nature of the underlying molecular dynamics. The complex dependence of the fiber shrinkage on initial degree of molecular alignment in the fiber, annealing time and temperature was investigated and interpreted. Moreover, humidity was shown to have a profound effect on the annealing process, which was not recognized previously. Annealing was also shown to have considerable effect on the fiber mechanical properties associated with the relaxation of molecular alignment in the fiber. The consequences of fiber annealing for the climatic stability of certain polymer optical fiber-based sensors are discussed, emphasizing the importance of fiber controlled pre-annealing with respect to the foreseeable operating conditions.

Quantum interference in laser-induced nonsequential double ionization in diatomic molecules: Role of alignment and orbital symmetry

We address the influence of the orbital symmetry and the molecular alignment with respect to the laser-field polarization on laser-induced nonsequential double ionization of diatomic molecules, in the length and velocity gauges. We work within the strong-field approximation and assume that the second electron is dislodged by electron-impact ionization, and also consider the classical limit of this model. We show that the electron-momentum distributions exhibit interference maxima and minima due to electron emission at spatially separated centers. The interference patterns survive integration over the transverse momenta for a small range of alignment angles, and are sharpest for parallel-aligned molecules. Due to the contributions of the transverse-momentum components, these patterns become less defined as the alignment angle increases, until they disappear for perpendicular alignment. This behavior influences the shapes and the peaks of the electron-momentum distributions.

Electrostatic-field-induced chain alignment of liquid crystalline copolyether TPP thin films

A liquid crystalline (LC) copolyether has been synthesized from 1-(4-hydroxy-4'-biphenyl)-2-(4-hydroxyphenyl)propane with 1,7-dibromoheptane and 1,11-dibromoundecane with a 50/50 (both in %) equal composition of the 7- and 11-methylene monomers [coTPP-7/11(5/5)]. A mono-domain with a homeotropic alignment can be induced by a thin film surface in the LC phase. When an electrostatic field is applied to the surface-induced mono-domains parallel to the thin film surface normal, the molecular alignment undergoes a change from the homeotropic to uniaxial homogeneous arrangement. However, when the field is applied to a direction perpendicular to the thin film surface normal. the molecular alignment is about 10 degrees -tilt with respect to the homeotropic alignment toward the a*-axis. This is because the permanent dipole moment of the copolyether is not right vertical to the molecular direction. The calculation of molecular dipoles indicates that the permanent dipole moment of this copolyether is about 70 degrees away from the molecular axis, which leads to a negative dielectric anisotropy. It is speculated that the 10 degrees- rather than 20 degrees -tilt is due to a balance between the alignment induced by the electrostatic field and the surface. In the electrostatic field, molecules are subjected to a torque tau, which is determined by the permanent dipole moment P and the electrostatic field E: tau = P x E. The molecular realignment in both parallel and perpendicular directions to the thin film surface normal is determined by satisfying the condition of tau = P x E = 0. (C) 2001 Elsevier Science Ltd. All rights reserved.

Estructura computacional i aplicacions de la semblança molecular quàntica

La tesis tracta diferents aspectes relacionats amb el càlcul de la semblança quàntica, així com la seva aplicació en la racionalització i predicció de l'activitat de fàrmacs. Es poden destacar dos progressos importants en el desenvolupament de noves metodologies que faciliten el càlcul de les mesures de semblança quàntica. En primer lloc, la descripció de les molècules mitjançant les funciones densitat aproximades PASA (Promolecular Atomic Shell Approximation) ha permès descriure amb suficient precisió la densitat electrònica dels sistemes moleculars analitzats, reduint substancialment el temps de càlcul de les mesures de semblança. En segon lloc, el desenvolupament de tècniques de superposició molecular específiques de les mesures de semblança quàntica ha permès resoldre el problema de l'alineament en l'espai dels compostos comparats. El perfeccionament d'aquests nous procediments i algoritmes matemàtics associats a les mesures de semblança molecular quàntica, ha estat essencial per poder progressar en diferents disciplines de la química computacional, sobretot les relacionades amb les anàlisis quantitatives entre les estructures moleculars i les seves activitats biològiques, conegudes amb les sigles angleses QSAR (Quantitative Structure-Activity Relationships). Precisament en l'àrea de les relacions estructura-activitat s'han presentat dues aproximacions fonamentades en la semblança molecular quàntica que s'originen a partir de dues representacions diferents de les molècules. La primera descripció considera la densitat electrònica global de les molècules i és important, entre altres, la disposició dels objectes comparats en l'espai i la seva conformació tridimensional. El resultat és una matriu de semblança amb les mesures de semblança de tots els parells de compostos que formen el conjunt estudiat. La segona descripció es fonamenta en la partició de la densitat global de les molècules en fragments. S'utilitzen mesures d'autosemblança per analitzar els requeriments bàsics d'una determinada activitat des del punt de vista de la semblança quàntica. El procés permet la detecció de les regions moleculars que són responsables d'una alta resposta biològica. Això permet obtenir un patró amb les regions actives que és d'evident interès per als propòsits del disseny de fàrmacs. En definitiva, s'ha comprovat que mitjançant la simulació i manipulació informàtica de les molècules en tres dimensions es pot obtenir una informació essencial en l'estudi de la interacció entre els fàrmacs i els seus receptors macromoleculars.

Dynamic nature of proteins - interpretation of residual dipolar couplings

Protein conformations and dynamics can be studied by nuclear magnetic resonance spectroscopy using dilute liquid crystalline samples. This work clarifies the interpretation of residual dipolar coupling data yielded by the experiments. It was discovered that unfolded proteins without any additional structure beyond that of a mere polypeptide chain exhibit residual dipolar couplings. Also, it was found that molecular dynamics induce fluctuations in the molecular alignment and doing so affect residual dipolar couplings. The finding clarified the origins of low order parameter values observed earlier. The work required the development of new analytical and computational methods for the prediction of intrinsic residual dipolar coupling profiles for unfolded proteins. The presented characteristic chain model is able to reproduce the general trend of experimental residual dipolar couplings for denatured proteins. The details of experimental residual dipolar coupling profiles are beyond the analytical model, but improvements are proposed to achieve greater accuracy. A computational method for rapid prediction of unfolded protein residual dipolar couplings was also developed. Protein dynamics were shown to modulate the effective molecular alignment in a dilute liquid crystalline medium. The effects were investigated from experimental and molecular dynamics generated conformational ensembles of folded proteins. It was noted that dynamics induced alignment is significant especially for the interpretation of molecular dynamics in small, globular proteins. A method of correction was presented. Residual dipolar couplings offer an attractive possibility for the direct observation of protein conformational preferences and dynamics. The presented models and methods of analysis provide significant advances in the interpretation of residual dipolar coupling data from proteins.

Laser intensity dependence of high-order harmonic generation from aligned CO2 molecules

We investigate experimentally the high-order harmonic generation from aligned CO2 molecules and demonstrate that the modulation inversion of the harmonic yield with respect to molecular alignment can be altered dramatically by fine-tuning the intensity of the driving laser pulse for harmonic generation. The results can be modeled by employing the strong field approximation including a ground state depletion factor. The laser intensity is thus proved to be a parameter that can control the high-harmonic emission from aligned molecules.

Ionization suppression of diatomic molecules in strong laser fields

The ionization rate of molecules in intense laser fields may be much lower than that of atoms with similar binding energy. This phenomenon is termed the ionization suppression of molecules and is caused by the molecular inner structure. In this paper, we perform a comprehensive study of the ionization suppression of homonuclear diatomic molecules in intense laser fields of linear and circular polarizations. We find that for linear polarization the total ionization rate and the ionization suppression depend greatly on the molecular alignment, and that for circular polarization the ionization suppression of molecules in the antibonding (bonding) shells disappears (appears) for laser intensities around 10(15) W/cm(2). We also find that the molecular photoelectron energy spectra are greatly changed by the interference effect, even though the total ionization rate of molecules remains almost the same as that of their companion atoms.

Photoelectron angular distributions of molecules in bichromatic laser fields of circular polarization

Photoelectron angular distributions (PADs) from above-threshold ionization of O-2 and N-2 molecules irradiated by a bichromatic laser field of circular polarization are Studied. The bichromatic laser field is specially modulated such that it can be used to mimic a sequence of one-cycle laser pulses. The PADs are greatly affected by the molecular alignment, the symmetry of the initial electronic distribution, and the carrier-envelope phase of the laser pulses. Generally, the PADs do not show any symmetry, and become symmetric about an axis only when the symmetric axis of laser field coincides with the symmetric axis of molecules. This study shows that the few-cycle laser pulses call be used to steer the photoelectrons and perform the selective ionization of molecules. (C) 2008 Elsevier B.V. All rights reserved.

The crystal structure and drawing induced polymorphism in poly(aryl ether ketone)s .3. Crystallization during hot-drawing of poly(ether ether ketone ketone)

The evolution of crystallinity and polymorphism during hot-drawing of amorphous poly(ether ether ketone ketone) (PEEKK) as a function of strain rate, draw ratio, and temperature was investigated. In modification I, the competition of chain extension and molecular alignment is responsible for the strain rate and temperature dependence. Modification II crystallization is basically controlled by chain extension during stretching. The former can be transformed into the latter via relaxation during stretching or annealing at elevated temperature.

Role of Halogen Bonds in Thyroid Hormone Receptor Selectivity: Pharmacophore-Based 3D-QSSR Studies

Most physiological effects of thyroid hormones are mediated by the two thyroid hormone receptor subtypes, TR alpha and TR beta. Several pharmacological effects mediated by TR beta might be beneficial in important medical conditions such as obesity, hypercholesterolemia and diabetes, and selective TR beta activation may elicit these effects while maintaining an acceptable safety profile, To understand the molecular determinants of affinity and subtype selectivity of TR ligands, we have successfully employed a ligand- and structure-guided pharmacophore-based approach to obtain the molecular alignment of a large series of thyromimetics. Statistically reliable three-dimensional quantitative structure-activity relationship (3D-QSAR) and three-dimensional quantitative structure-selectivity relationship (3D-QSSR) models were obtained using the comparative molecular field analysis (CoMFA) method, and the visual analyses of the contour maps drew attention to a number of possible opportunities for the development of analogs with improved affinity and selectivity. Furthermore, the 3D-QSSR analysis allowed the identification of a novel and previously unmentioned halogen bond, bringing new insights to the mechanism of activity and selectivity of thyromimetics.

Fragment-guided approach to incorporating structural information into a CoMFA study: BACE-1 as an example

Alzheimer`s disease is an ultimately fatal neurodegenerative disease, and BACE-1 has become an attractive validated target for its therapy, with more than a hundred crystal structures deposited in the PDB. In the present study, we present a new methodology that integrates ligand-based methods with structural information derived from the receptor. 128 BACE-1 inhibitors recently disclosed by GlaxoSmithKline R&D were selected specifically because the crystal structures of 9 of these compounds complexed to BACE-1, as well as five closely related analogs, have been made available. A new fragment-guided approach was designed to incorporate this wealth of structural information into a CoMFA study, and the methodology was systematically compared to other popular approaches, such as docking, for generating a molecular alignment. The influence of the partial charges calculation method was also analyzed. Several consistent and predictive models are reported, including one with r (2) = 0.88, q (2) = 0.69 and r (pred) (2) = 0.72. The models obtained with the new methodology performed consistently better than those obtained by other methodologies, particularly in terms of external predictive power. The visual analyses of the contour maps in the context of the enzyme drew attention to a number of possible opportunities for the development of analogs with improved potency. These results suggest that 3D-QSAR studies may benefit from the additional structural information added by the presented methodology.