Orientation Of Molecular Axis Research Articles

Orientational order of tetra n-hexylesters of perylene and tetrachloroperylene tetracarboxylic acids in low-molar-mass liquid crystal investigated using absorption and fluorescence methods

The orientational order parameters <P2> and <P4> of perylene-3,4,9,10-tetra-(n-hexylester) (PTHE) and 1,6,7,12-tetrachloroperylene-3,4,9,10-tetra-(n-hexylester) (4Cl-PTHE) dye molecules dissolved in low-molar-mass liquid crystal, 4-(trans-4-n-hexylylcyclohexyl)-isothiocyanobenzene, are calculated from the experimental values of polarised absorption and fluorescence anisotropies. The experimental data show that the substitution of chlorine atoms instead of hydrogen in the perylene core reduces the value of <P2> parameter. Moreover, the <P2> and <P4> values for molecules of the perylene derivatives, playing the role of the guest in the liquid crystal matrix, are much less than these values for molecules of the liquid crystal host. The extremely low negative values of <P4> for the perylene dyes are explained as the result of the preferable oblique orientation of the main molecular symmetry axis of the probe with respect to the direction of the macroscopic orientation of the liquid crystal host molecules.

The liquid structure of tetrachloroethene: Molecular dynamics simulations and reverse Monte Carlo modeling with interatomic potentials

The liquid structure of tetrachloroethene has been investigated on the basis of measured neutron and X-ray scattering structure factors, applying molecular dynamics simulations and reverse Monte Carlo (RMC) modeling with flexible molecules and interatomic potentials. As no complete all-atom force field parameter set could be found for this planar molecule, the closest matching all-atom Optimized Potentials for Liquid Simulations (OPLS-AA) intra-molecular parameter set was improved by equilibrium bond length and angle parameters coming from electron diffraction experiments [I. L. Karle and J. Karle, J. Chem. Phys. 20, 63 (1952)]. In addition, four different intra-molecular charge distribution sets were tried, so in total, eight different molecular dynamics simulations were performed. The best parameter set was selected by calculating the mean square difference between the calculated total structure factors and the corresponding experimental data. The best parameter set proved to be the one that uses the electron diffraction based intra-molecular parameters and the charges qC = 0.1 and qCl = -0.05. The structure was further successfully refined by applying RMC computer modeling with flexible molecules that were kept together by interatomic potentials. Correlation functions concerning the orientation of molecular axes and planes were also determined. They reveal that the molecules closest to each other exclusively prefer the parallel orientation of both the molecular axes and planes. Molecules forming the first maximum of the center-center distribution have a preference for <30° and >60° axis orientation and >60° molecular plane arrangement. A second coordination sphere at ∼11 Å and a very small third one at ∼16 Å can be found as well, without preference for any axis or plane orientation.

Absolute multiple ionization cross sections of water and carbon monoxide molecules induced by very high-q fast projectiles (q/v > 1)

Molecular properties, including the orientation of molecular axis, electron population numbers of atoms and ions in molecular ions and ionization energies at every ionization stage, are considered to generate a relatively simple model to calculate the absolute multiple ionization cross sections of molecules impacted by the very high-q fast projectiles (q/v>1). The multiple ionization probabilities are obtained under the framework of independent event model (IEVM). Calculation results are consistent with available experimental data. According to the picture of sequential release process, the high-order ionization of CO will be significantly influenced by molecular orientation, while the multiple ionization of H2O will be quite different and totally isotropic.

Orientation behaviour of the minor director of homeotropically oriented nematic elastomers in mechanical fields

We report the synthesis of a thin nematic elastomer film where the major director of the mesogenic moieties (i.e. the average orientation of the main molecular axes) is permanently oriented parallel to the film's normal. This allows us to directly observe the orientation of the minor director (average orientation of the minor molecular axes) using optical techniques. We find that the elastomer exhibits spontaneous biaxiality at room temperature and the minor director is oriented in large domains. When a mechanical field is applied perpendicular to the major director, the domains of the minor director reorient into the direction of strain above a characteristic threshold, forming a monodomain with 3D orientational long-range order. This reorientation process is accompanied by a change in the slope of the stress–strain curve and X-ray scattering experiments reveal that the reorientation of the major director only sets in after the reorientation of the minor director is complete.

Helical twisting in nemato-cholesteric systems based on cholesterol derivatives and photosensitive azoxy compounds

For cholesteric liquid crystal systems containing photosensitive nematic ZhK�440 and a mixture of cholesterol derivatives, changes in helical twisting induced by UV radiation were studied. The UVinduced shift of selective reflection maximum λ max was shown to depend upon concentration of the nematic compo� nent. For low concentrations of ZhK�440, λmax increases, which correlates with corresponding changes with increasing temperature. For higher concentrations, λmax decreases, regardless of the temperature behavior of the system. A theoretical description of the available experimental data is proposed on the basis of develop� ment of molecular models of helical twisting, including an assumed possibility of ordered orientation of short molecular axes of cisisomers formed as a result of UV irradiatio n, which is determined by the sense of the cholesteric helix already present in the system.

Electron-transfer in MeV p-N2 collisions: Kinetic-energy releases and effects of the molecular orientation

We have experimentally investigated electron transfer processes in collisions between 1.04 MeV protons stored in the electron-cooler ion-storage ring, CRYRING and molecular nitrogen in a supersonic gas jet. We report distributions of kinetic energies of molecular nitrogen ions in charge states 1-3 detected in coincidence with neutralized projectiles. Further, we investigate the influence of the relative orientation of the target molecular axis and the direction of the incoming projectile.

Theory of diffraction in disordered crystals formed by linear asymmetric molecules

Using the general principles of Krivoglaz’s theory of diffraction for irregular crystals as well as the expansion of scattering structure amplitudes in spherical harmonics, a kinematic theory of diffraction has been developed for crystals, which consist of asymmetric linear molecules characterized by a “head-tail” disorder. The random variables that determine the statistics of deviations of molecular centers of mass and orientations of molecular axes from their average values are supposed to be independent. Detailed analysis is carried out for the N2O and CO cryocrystals, the structure of which is described on average by space group symmetry Pa3. The final formulas for integrated intensities of Bragg lines allow reconstruction of all parameters, which characterize the statistics of deviations of the relevant geometric parameters from their crystal averages.

Influence of Thiol Self‐Assembled Monolayer Processing on Bottom‐Contact Thin‐Film Transistors Based on n‐Type Organic Semiconductors

AbstractThe performance of bottom‐contact thin‐film transistor (TFT) structures lags behind that of top‐contact structures owing to the far greater contact resistance. The major sources of the contact resistance in bottom‐contact TFTs are believed to reflect a combination of non‐optimal semiconductor growth morphology on the metallic contact surface and the limited available charge injection area versus top‐contact geometries. As a part of an effort to understand the sources of high charge injection barriers in n‐channel TFTs, the influence of thiol metal contact treatment on the molecular‐level structures of such interfaces is investigated using hexamethyldisilazane (HMDS)‐treated SiO2 gate dielectrics. The focus is on the self‐assembled monolayer (SAM) contact surface treatment methods for bottom‐contact TFTs based on two archetypical n‐type semiconductors, α,ω‐diperfluorohexylquarterthiophene (DFH‐4T) and N,N′bis(n‐octyl)‐dicyanoperylene‐3,4:9,10‐bis(dicarboximide) (PDI‐8CN2). TFT performance can be greatly enhanced, to the level of the top contact device performance in terms of mobility, on/off ratio, and contact resistance. To analyze the molecular‐level film structural changes arising from the contact surface treatment, surface morphologies are characterized by atomic force microscopy (AFM) and scanning tunneling microscopy (STM). The high‐resolution STM images show that the growth orientation of the semiconductor molecules at the gold/SAM/semiconductor interface preserves the molecular long axis orientation along the substrate normal. As a result, the film microstructure is well‐organized for charge transport in the interfacial region.

Effects of UV Radiation on Helical Twisting in Cholesteric Systems Containing Photosensitive Azoxy Nematics

For cholesteric liquid crystal systems containing photosensitive nematic ZhK-440 and a mixture of cholesterol derivatives, the changes in helical twisting induced by UV radiation are studied. The UV-induced shift of the selective reflection maximum λmax is shown to depend on the concentration of the nematic component. For low concentrations of ZhK-440, λmax increases, which correlates with the corresponding temperature-induced changes. For higher azoxy nematic concentrations, λmax decreases, regardless of the temperature behavior of the system. To explain the experimental data, a theoretical description is proposed on the basis of the development of molecular models of helical twisting. Good agreement was obtained between calculated and measured values of the UV-induced shift as a function of the azoxy nematic concentration, with two extrema and an inversion point. The extra twisting arises from the cholesteric mesophase-induced orientation of short molecular axes of cis-isomers formed as a result of irradiation.

Molecular Dynamics in Strong Laser Fields

One of the goals for strong field physics is imaging the dynamics of the quantum systems, and in case of molecules, there is strong interest in imaging of the electron rearrangement during chemical reactions. Strong field ionization of molecules has many attractive features that make this process a candidate tool for strong field imaging of transient states and chemical reactions. In this paper, we present analysis of ionization dependence on orientation of molecular axis with respect to polarization of the electric field of the laser. By considering several examples of molecules at their equilibrium internuclear distances and an example of the simplest chemical reaction, namely, the dissociation of diatomic molecule, we present how symmetries of the molecular orbitals influence the alignment-dependent ionization and how this dependence can be used to follow molecular dynamics using strong field multiphoton ionization.

Surfactant–DNA interactions at the liquid crystal–aqueous interface

The presence of single-stranded (ssDNA) vs. double-stranded (dsDNA) DNA at a surfactant-laden aqueous–nematic liquid crystal (LC) interface results in distinctly different orientations of the LC molecular axis; this is of practical interest as a method to detect DNA hybridization. Results presented here provide new insights into the molecular-level mechanisms of these phenomena. The adsorption of ssDNA to a cationic surfactant-laden aqueous–LC interface caused LC reorientation, leading to coexistence between homeotropic and planar (birefringent) oriented regions. Fluorescence microscopy revealed that ssDNA preferentially partitioned into the birefingent regions, presumably causing a decreased surface coverage of surfactant and the resultant planar LC orientation. Both electrostatic and hydrophobic effects were found to be critical to inducing LC reorientation. In particular, insufficient ssDNA adsorption occurred in the absence of a cationic surfactant (e.g. with no surfactant or with a non-ionic surfactant), demonstrating the importance of electrostatic interactions with the polyanionic ssDNA. Even in the presence of a cationic surfactant, however, polyanions without hydrophobic side-group moieties (poly[acrylic acid] and dsDNA) caused no LC reorientation, while polyanions with hydrophobic side groups (polystyrene sulfonate and ssDNA) initiated the desired LC reorientation. These observations are consistent with the fact that interfacial hybridization of adsorbed probe ssDNA to complementary target ssDNA caused a reorientation from planar back to homeotropic. We propose that ssDNA forms an electrostatic interfacial complex with cationic surfactant where the hydrophobic nucleobases associate directly with the LC phase, effectively competing with surfactant molecules for interfacial sites. Upon hybridization, the hydrophobic character of the ssDNA is lost and the nucleobases no longer associate directly with the LC phase, allowing the surfactant molecules to pack more closely at the interface.

Faradaic Phase Transition of Dibenzyl Viologen on an HOPG Electrode Surface Studied by In Situ Electrochemical STM and Electroreflectance Spectroscopy

Phase transitions of an adsorption layer of dibenzyl viologen (dBV) as a typical diaryl viologen on a basal plane of a highly oriented pyrolytic graphite (HOPG) electrode are described using voltammetry, in situ electrochemical scanning tunneling microscopy (EC-STM), and electroreflectance (ER) spectroscopy. A monolayer redox process at less negative potential than the bulk redox process was found to be the first-order faradaic phase transition between a gaslike adsorption layer of dication (dBV(2+)) and a 2D condensed monolayer of radical cation (dBV(•+)). Comparison of the results of cyclic voltammetry and potential step chronoamperometry was made with those of heptyl viologen (HV), which also undergoes a faradaic phase transition of the first order. It suggested that the contribution of intermolecular π-π interaction between benzyl groups of dBV to the phase transition is minor and apparently equivalent to interchain interaction between the heptyl chains of HV. In situ EC-STM images of the 2D condensed monolayer demonstrated stripe patterns of the rows of dBV(•+) molecules forming 3-fold rotationally symmetric domains. The results of the ER measurements also revealed that the orientation of the longitudinal molecular axis of the bipyridinium moiety of dBV(•+) molecules lying flat on the HOPG electrode surface, most likely with a side-on configuration.

Crystal growth of para-sexiphenyl on clean and oxygen reconstructed Cu(110) surfaces

The formation of crystalline para-sexiphenyl (6P) films on Cu(110) and Cu(110)-(2 × 1)O (Cu-O) has been studied by low energy electron diffraction, X-ray absorption spectroscopy and both in situ and ex situ X-ray diffraction methods to elucidate the transition from the initial monolayers to crystalline thin films. It is found that, for Cu-O, a single and, for Cu(110), a double wetting layer is formed which then acts as a template for the subsequent 3D crystal growth. For both substrates the orientation of the long molecular axes of the 6P molecules in the first layers is conserved for the molecules in the bulk crystals growing on them. The main difference between both systems is that on Cu-O the first monolayer assembles in a form close to that of a 6P bulk plane which can be easily continued by crystallites grown upon them, while on the Cu(110) surface the 6P mono- and bi-layers differ substantially from the bulk structure. The bi-layer forms a complex periodically striped phase. Thin 6P films grow with the 6P(203) crystal plane parallel to the Cu-O substrate surface. For this orientation, the 6P molecules are stacked in layers and the molecules demonstrate only one tilt of the mean molecular plane with respect to the sample surface. On clean Cu(110), a more complex 6P(629) plane is parallel to the substrate surface and this orientation is likely a consequence of the super-molecular long-range periodicity of the second molecular layer striped phase.

Photodetachment of a homo-nuclear diatomic molecular negative ion with arbitrary molecular axis orientation

The photodetachment of a homo-nuclear diatomic molecular negative ion with arbitrary molecular axis orientation has been studied using the two-centre model. An analytic formula is presented for the photodetached electron flux distribution at a given observation plane. This formula is universal, applicable to all homo-nuclear diatomic molecular negative ions. Taking as an example, we calculate the electron flux distribution and photodetachment cross section for different molecular axis orientations. The results show that the molecular axis orientation has a great influence on the photodetachment of the diatomic molecular negative ion. The oscillation of the electron flux distribution is largest for the molecular axis perpendicular to the laser light polarized along the z direction and is smallest for the parallel molecular axis orientation. Our studies suggest that we can control the photodetachment process of the molecular negative ion by changing the molecular axis orientation. Our research will be helpful for the theoretical and experimental study of the molecular photodetachment microscope.

Liquid crystalline and antinematic behavior of shape-persistent macrocycles from molecular-dynamics simulations

In this work we present a molecular-dynamics study of a coarse-grained (CG) model for a system of planar shape-persistent macrocycles (SPMs). SPMs are synthetic organic rigid macromolecules typically comprised of meta- and para-aromatics groups connected by acetylene and/or diacetylene units. In the CG model, each SPM is represented as a rigid hexagonal arrangement of 24 soft-repulsive spheres, resembling a large ring or hoop. The supramolecular arrangement of these macrocycles at high pressures is studied using N-P-T molecular-dynamics simulation both by expansion of an initial hexagonal lattice structure and also by compression of an isotropic phase. In both cases, systems under consideration exhibit an isotropic-smectic-A phase transition, which is detected by monitoring relevant order parameters and analyzing snapshots of equilibrium configurations. The smectic-A phase is unique; although the molecules form layers, the system presents antinematic order where the orientation of the molecular axes is perpendicular to the direction of the layers themselves. Due to their planar geometry, the SPM molecules would be expected to form columnar or nematic phases. On the contrary, these phases seem suppressed by a novel smectic-A phase, formed by the mutual interpenetration of the cycles. These results are a unique example of how molecular nonconvexity can, by itself, induce mesomorphism in anisotropic systems.

Molecular Axis Orientation in Charge Transfer Reactions Determined with a Reaction Microscope

Based on the reaction microscope at the institute of modern physics, the reaction mechanism in molecular ion-atom collisions is investigated experimentally. The features of this system is illustrated by a kinematically complete experiment performed for the collision process. Using the so-called list-mode data recording technique and the coincidence measurement, the momentum vector of each fragment from the molecular ion were recorded event by event. The orientation of the molecular axis for H2+ dissociation reactions could be determined for each event in the off-line analysis. The measured orientation of the molecular ion is believed the same as the one at the instance of collision under axial recoil approximation. The polar angle resolution of the molecular orientation of 8 was obtained.

Young-type interferences in double-electron capture

We have measured the dependence on the molecular orientation of the cross section for two-electron transfer from hydrogen molecules to fast (1.2 and 2.0 MeV kinetic energy) He2+ ions. A very strong angular dependence is found, where the maximum and minimum cross sections differ by more than a factor of three. Further the angular dependencies are markedly different for the two different projectile energies. The variations are explained as resulting from the interference of two waves describing projectiles neutralized in the proximity of either of the two target protons. The molecular axis orientation determines the phase difference of these two waves and thereby affects the cross section.

Reading molecular messages from high-order harmonic spectra at different orientation angles

We investigate the orientation dependence of high-order harmonic generation (HHG) from H(2) (+) with different internuclear distances irradiated by intense laser fields both numerically and analytically. The calculated molecular HHG spectra are found to be sensitive to the molecular axis orientation relative to incident laser field polarization and internuclear separation. In particular, our simulations demonstrate that at certain harmonic orders the envelopes of the HHG spectra taken at different orientation angles intersect. Moreover, the position of intersection is largely independent of the laser intensity while strongly dependent on the internuclear separation. This striking "intersection" phenomenon is identified as arising due to intramolecular two-center interference in the HHG and can be used to probe the molecular instantaneous structure.

Orientational correlations in high-pressure fluid oxygen and nitrogen

High-pressure x-ray diffraction measurements for supercritical fluid oxygen at 0.9, 1.2, 4.3, and 5.2 GPa and for supercritical fluid nitrogen at 2.5 GPa have been carried out at room temperature by using synchrotron x-ray diffraction. The structure factors have been interpreted by means of the reverse Monte Carlo method. Site-site and center-center radial distribution functions and relative orientations of molecular axes as a function of distance between molecular centers have been calculated from the particle configurations. At distances below the position of the first maximum of the center-center radial distribution function, the dominance of parallel and ``X-shaped'' alignments of neighboring molecules has been revealed. Superfluid ${\text{O}}_{2}$ was found to display considerably stronger orientational correlations than ${\text{N}}_{2}$. Structural differences between oxygen at 4.3 and 1.2 GPa can be explained by the different densities of these systems.

Molecular dynamics simulations and hyperspherical mode analysis of NO in Kr crystals with the use of ab initio potential energy surfaces for the Kr‐NO complex

AbstractThe dynamics of structural relaxation of NO doped Kr solids on electronic excitation of the NO molecule has been characterized by molecular dynamics simulations and by normal and hyperspherical mode analysis, with special emphasis on the effects of the anisotropy of the Kr–NO interaction which has been modeled by ab initio potential energy surfaces (PESs). The time evolution of the cage radius and the radial distribution function for the ground and excited states have been calculated for various orientations of the molecular axis with respect the Kr atom matrix with the NO molecule treated as a rigid rotor. The ab initio PESs, considered in previous work, seem to be too repulsive when compared with potentials fitted to spectroscopic data, and this is more evident for the first Ryberg state than for the ground state, where effects of potential anisotropy are less important. The first shell response shows a relative increase, up to ∼10%, of the excited state equilibrium radius with respect to that of the ground state, while experiments indicate that such an increase should be less than 5%. The kinetic energy power spectrum method, presented in a previous work, has been applied to the total kinetic energy T(t) and to two characteristic quantities of the hyperspherical mode analysis, the hyperradial energy Tρ(t) and the grand angular energy TΛ(t) for NO molecular axis orientations of 67° and 90°, respectively, which represent the cases of the largest and smallest lattice distortions in the radial distribution function (RDF) of the atoms in the matrix for the excited state. The band structures of the calculated frequency spectra reveal a blue shift with respect to the case of the isotropic potentials used previously, and this is connected to the different lattice equilibrium structures for 67° and 90° directions. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008