Function Of Molecular Orientation Research Articles

Classification of mobile- and immobile-molecule timescales for the Stokes–Einstein and Stokes–Einstein–Debye relations in supercooled water

Molecular dynamics simulations have been performed on TIP4P/2005 supercooled water to investigate the molecular diffusion and shear viscosity at various timescales and assess the Stokes–Einstein (SE) and Stokes–Einstein–Debye (SED) relations. For this purpose, we calculated various time correlation functions, such as the mean-squared displacement, stress relaxation function, density correlation function, hydrogen-bond correlation function, rotational correlation function of molecular orientation, non-Gaussian parameter, and four-point correlation function. Our study of the SE and SED relations indicates that the transport coefficients and timescales obtained using these time correlation functions may be classified into two distinct classes: those governed by either mobile or immobile molecules, due to dynamical heterogeneity. In particular, we show that the stress relaxation time, hydrogen-bond lifetime, and large-angle rotational relaxation time are coupled with translational diffusion, and are characterized by mobile molecules. In contrast, the structural -relaxation time, small-angle rotational relaxation time, and characteristic timescales of four-point correlation functions are decoupled with translational diffusion, and are governed by immobile molecules. This decoupling results in a violation of the SE relation. These results indicate that the identification of timescales that appropriately characterize transport coefficients, such as translational diffusion constant and shear viscosity, provides a deep insight into the violation of the SE and SED relations in glass-forming liquids.

Impact of molecular quadrupole moments on the energy levels at organic heterojunctions

The functionality of organic semiconductor devices crucially depends on molecular energies, namely the ionisation energy and the electron affinity. Ionisation energy and electron affinity values of thin films are, however, sensitive to film morphology and composition, making their prediction challenging. In a combined experimental and simulation study on zinc-phthalocyanine and its fluorinated derivatives, we show that changes in ionisation energy as a function of molecular orientation in neat films or mixing ratio in blends are proportional to the molecular quadrupole component along the π-π-stacking direction. We apply these findings to organic solar cells and demonstrate how the electrostatic interactions can be tuned to optimise the energy of the charge-transfer state at the donor−acceptor interface and the dissociation barrier for free charge carrier generation. The confirmation of the correlation between interfacial energies and quadrupole moments for other materials indicates its relevance for small molecules and polymers.

High-order Harmonic Field Retrieval in Ethylene

The XUV field emitted by impulsively aligned ethylene molecules during high-order harmonic generation is retrieved as a function of molecular orientation. The results can be ascribed to multielectron contributions to the harmonic emission.

Sub-laser-cycle control of coupled electron–nuclear dynamics at a conical intersection

Nonadiabatic processes play a fundamental role in the understanding of photochemical processes in excited polyatomic molecules. A particularly important example is that of radiationless electronic relaxation at conical intersections (CIs). We discuss new opportunities for controlling coupled electron–nuclear dynamics at CIs, offered by the advent of nearly single-cycle, phase-stable, mid-infrared laser pulses. To illustrate the control mechanism, a two-dimensional model of the NO2 molecule is considered. The key idea of the control scheme is to match the time scale of the laser field oscillations to the characteristic time scale of the wave packet transit through the CI. The instantaneous laser field changes the shape and position of the CI as the wave packet passes through. As the CI moves in the laser field, it ‘slices’ through the wave packet, sculpting it in the coordinate and momentum space in a way that is sensitive to the carrier-envelope phase of the control pulse. We find that the electronic coherence imparted on the sub-laser-cycle time scale manifests during much longer nuclear dynamics that follow on the many tens of femtosecond time scale. Control efficiency as a function of molecular orientation is analyzed, showing that modest alignment is sufficient for showing the described effects.

Physical approaches for fabrication of organized nanostructure of resilin-mimetic elastic protein rec1-resilin

Protein adsorption on surfaces is a fundamental step in many applications. While various methods such as lithography, self assembly using nanoparticles, layer-by-layer attachment, etc. have been employed, here we report fabrication of controlled nanostructure of a new resilin-mimetic elastic protein rec1-resilin using physical approaches. We investigate the assembly, morphology and tunability of the nanostructure of adsorbed rec1-resilin architectures by atomic force microscopy (AFM) and scanning thermal microscopy (SThm) demonstrating that the protein conformation and structure during assembly can be controlled by tuning the physical conditions at the surface. Our findings show distinct morphology and height of monomolecular rec1-resilin film, dependent on substrate surface energy. We also show that these heights, a function of molecular orientation, can be maintained on swelling and drying.

Toward a Simple Molecular Understanding of Sum Frequency Generation at Air−Water Interfaces

Second-order vibrational spectroscopies successfully isolate signals from interfaces, but they report on intermolecular structure in a complicated and indirect way. Here, we adapt a perspective on vibrational response developed for bulk spectroscopies to explore the microscopic fluctuations to which sum frequency generation (SFG), a popular surface-specific measurement, is most sensitive. We focus exclusively on inhomogeneous broadening of spectral susceptibilities for OH stretching of HOD as a dilute solute in D(2)O. Exploiting a simple connection between vibrational frequency shifts and an electric field variable, we identify several functions of molecular orientation whose averages govern SFG. The frequency dependence of these quantities is well captured by a pair of averages, involving alignment of OH and OD bonds with the surface normal at corresponding values of the electric field. The approximate form we obtain for SFG susceptibility highlights a dramatic sensitivity to the way a simulated liquid slab is partitioned for calculating second-order response.

Formula omitted]-band ESR studies of structural anisotropy in P3HT and P3HT/PCBM blend polymer solid films: Paramagnetic defects after continuous wave Xe-lamp photolysis

K -band electron spin resonance (ESR) technique was employed to study films of regioregular poly(3-hexylthiophene) (P3HT) and P3HT/PCBM ([6,6]-phenyl- C 61-butyric acid methyl ester) blends to estimate their structural macroscopic anisotropy. As for nematic liquids (or liquid crystals) our consideration was based on the approach that the free energy of self-organised polymer molecules of P3HT is a function of molecular orientation and therefore chains in polymer films exhibit some degree of orientational order. The lamellar molecular orientation of the films was confirmed by angular-dependent ESR spectroscopy of polarons, which were considered as a localised paramagnetic centre with an unpaired carbon π -electron of the thiophene ring. The additional ESR signal initiated by the UV/visible CW Xe-lamp illumination of the films at air atmosphere was attributed to the negative polaron (trapped photo-electron) on the polymer chain, as well as to the radical due to chain degradation.

High‐Resolution Measurement of the Anisotropy of Charge Transport in Single Crystals

High-resolution measurement of anisotropic electrical properties allows the probing of transport in organic materials as an explicit function of molecular orientation and proximity. A new device architecture facilitates the efficient measurement of these properties; 15° angular resolution is demonstrated for the rubrene single crystal.

NLOPredict: Visualization and data analysis software for nonlinear optics

A data analysis and visualization program was developed to assist in the interpretation of second-order nonlinear optical (NLO) processes, including vibrational sum-frequency generation and electronically resonant second harmonic generation. A novel diagrammatic approach allows concise visual representations of the resonant NLO molecular response. By mapping the predicted NLO response as a function of molecular orientation, molecular modeling results can be combined with experimental measurements for orientational analysis. A method is developed and implemented to predict the nonlinear optical properties of the amide backbones in complete proteins with known structures. NLOPredict is available for most computer operating systems from http://sda.iu.edu/nlopredict/.

Birefringent characterization of necking phenomenon along cold‐drawn polypropylene fibers. I. Offline drawing

AbstractAn automated two‐beam interference Pluta microscope was used to measure the optical anisotropy or birefringence of polymer fibers. A sample of polypropylene (PP) fibers was used and cold‐drawn to low draw ratios. The neck shoulder “necking” was micro‐detected at draw ratio 1.3 and characterized using the measured thickness and birefringence along the drawn PP fiber. Birefringence profiles at different regions along deformed PP fiber were determined to confirm the effect of necking on these fibers. The influence of this phenomenon on the molecular orientation function of PP fibers was presented. The strong dependence of the birefringence on the thickness was formulated analytically at the necked zone of the drawn PP fiber. © 2007 Wiley Periodicals, Inc. J Appl Polym Sci 2007

Three-dimensional time-profile analysis of high-order harmonic generation in molecules: Nuclear interferences inH2+

We describe a numerical method used previously [Phys. Rev. A 70, 011404(R) (2004)] for solving the three-dimensional time-dependent Schr\"odinger equation for ${\mathrm{H}}_{2}^{+}$ (with fixed nuclei) in interaction with an intense, arbitrary oriented laser pulse. In this approach, we use the prolate spheroidal coordinate system, and expand the time-dependent wave function in a complex basis of Laguerre polynomials and Legendre functions. Our results indicate that ionization, excitation, and harmonic generation are strongly influenced by the orientation of the molecular axis with respect to the laser polarization axis. We evaluate the contribution of each nucleus to harmonic generation, as this permits a quantitative and nonambiguous assessment of interference effects as a function of molecular orientation. A time-profile analysis, using a Gabor transform of the harmonic spectrum around certain harmonics, shows that every half-cycle high-order harmonics are emitted by each nucleus when the electron wave packet returns for a recollision with the molecular core, thus confirming the strong field recollision model in molecules. In general, each nucleus emits both odd and even harmonics, but even harmonics are destroyed by interferences between contributions of each nucleus. These interferences are shown to be maximum at certain harmonic orders as a function of molecular orientation. A comparison of acceleration and dipole formulations of the harmonic emission process is made in order to assess the use of high-order harmonic generation for electron wave-function imaging.

Interaction of translational and rotational modes of a molecular impurity in two-dimensional atomic crystals

The interaction between the translational and rotational degrees of freedom of a diatomic homonu-clear molecule that executes a motion at the site of a two-dimensional close-packed atomic matrix located on a close-packed atomic substrate (a molecular substitutional impurity in the crystal field of the two-dimensional lattice of a solidified rare gas) is investigated theoretically. The relationships describing the effective dynamic properties of an impurity rotator in the presence of translational excitations of its center of inertia are derived in the framework of consistent procedures on the basis of the Lagrangian (the functional-integral method) and Hamiltonian (the canonical-transformation method) formalisms. The inclusion of the translational-rotational interaction leads to a radical change in the inertial properties of the molecule. This manifests itself in a change in the form of the operator for the rotational kinetic energy as compared to the corresponding expression for a free rotator. The inertia tensor components for the molecule become functions of molecular orientation, and the molecule, in terms of rotational motion, transforms into a “parametric rotator” whose effective kinetic energy is represented as a generalized quadratic form of the angular momentum (or the angular velocity) components with a symmetry corresponding to the symmetry of the external crystal field. The translational-rotational interaction also results in the renormalization of the parameters of the crystal potential without a change in its initial form.

The spectral dispersion curves of highly oriented fibres

Spectral dispersion curves of the refractive indices and birefringence of highly oriented fibres [poly(ethylene 2,6-naphthalene-dicarboxylate) (1000 denier/248 filaments, PEN-Q50M4; PEN), poly(ethylene terephthalate) (PET), Seun yarn (meta-aramid fibres, Teijin Japan; CONEX) and Technora T-240 (1000 denier/667 filaments aramid fibres, Teijin Japan; TECHNORA)] have investigated using the automatic variable-wavelength interferometric (VAWI) technique. This technique is especially recommended for measuring the refractive indices of highly oriented fibres. The polarizabilities per unit volume are calculated for these fibres and the molecular orientation function of PEN and PET are determined. Microinterferograms are given for illustration.

WAXS studies of global molecular orientation induced in nematic liquid crystals by simple shear flow

Global molecular orientation function coefficients for the nematic liquid crystal 4-cyano 4'-nn -pentylbiphenyl (5CB) in shear flow are presented, being extracted from 2-dimensional Wide-Angle X-ray Scattering data. A linear increase in orientation parameter P2 is observed with a logarithmic increase in shear rate. It is proposed that this arises from an increased number of LC directors aligning to the shear axis. Upon cessation of shear flow, the anisotropy is seen to relax away completely, over a time scale which is inversely proportional to the previously applied shear rate.

Non-linear responses of the hard-spheroid fluid under shear flow

We examine a simple non-equilibrium molecular dynamics (NEMD) technique for studying hard-spheroid fluids under shear flow. The method involves applying a thermostat which uses an analytical formula for the streaming angular velocity as a function of molecular orientation. Preliminary results indicate that this method is a significant improvement over the usual assumption of constant streaming angular velocity. We compare with the more sophisticated, and complicated, rotationally unbiased thermostat proposed by Travis et al.

Absolute electron impact ionization cross sections for , where X = H, F, Cl, Br, and I

Measurements of electron impact ionization cross sections have been made for methane and the series methyl fluoride to methyl iodide. The results for methane and methyl fluoride to methyl bromide have been compared with ionization efficiency curves calculated using Deutsch - Märk (DM) and binary-encounter-Bethe (BEB) methods, and also with the results of an ab initio model which gives the maximum cross section as a function of molecular orientation. In addition, the ab initio and DM methods have been used to calculate the steric ratios for the electron impact ionization of methyl chloride which have been compared with experimental measurements made previously.

A Direct Determination of the Direction for the Transition Dipole Moment by the Polarized Laser Photolysis of the Oriented CH3I Beam

A beam-intensity-depletion (BID) method to determine the direction of the transition dipole moment in the molecular frame was demonstrated in the polarized laser photolysis of the oriented CH3I beam. The depletion of the primary beam intensity of oriented CH3I via the photodissociation with linearly polarized laser light was measured as a function of molecular orientation and the polarization angle of the polarized laser light. The (X−A) transition of CH3I in the |111〉 rotational state was probed with linearly polarized laser light at 248 nm. The orientational dependence of the BID indicates that this transition is predominantly (96 ± 4%) a parallel-type transition at this wavelength. This result is in good agreement with the previous result deduced by the angular distribution of the photofragment, showing the usefulness of this direct method.

Molecular Dynamics Simulation of Macromolecular Interactions in Solution: Poly(.gamma.-benzyl glutamate) in Dimethylformamide and Tetrahydrofuran

We carry out molecular dynamics simulations of the interaction between pairs of short segments of poly(γ-benzyl glutamate) in dimethylformamide and in tetrahydrofuran as a function of molecular orientation and separation in the range between ∼1 and ∼3 nm. We find that the solvation shell structure induced by poly(γ-benzyl glutamate) in the surrounding solvent plays a significant role for the molecular interaction in solution. In particular, as in the case of macroscopic solid-liquid-solid interfaces, we show that the intersegment force shows a pronounced oscillatory behavior depending on the commensurability of the intersegment separation with the solvation shell structure. We also find a pronounced dependence of the force on the molecular orientation as well as on the type of solvent

Molecular orientation in plastic optical fibres

Molecular orientation in polystyrene fibres has been studied using polarized Fourier transform infrared spectroscopy. Polymerization of the monomers was carefully controlled to work with the same molecular weight and heterogeneity index. During drawing, the velocity of the fibres was maintained constant and the temperature was varied from 166 to 200 degrees C. Samples were cut from the different fibres. Two polarized spectra, with electric vectors parallel and perpendicular to the drawing direction, were recorded. The molecular orientation function was calculated from the area of the 1028 cm-1 peaks, which corresponds to the nu 18a in-plane CH bending normal mode of the aromatic ring. Results indicate that the molecular orientation depends strongly upon the drawing conditions. Annealing the fibre at a temperature slightly higher than the glass transition temperature allows one to recover most of the isotropic properties.

Scattering of molecular hydrogen at fixed orientation

Ionization of one-electron heavy ion projectiles in collisions with molecular hydrogen is usually treated as collisions with two free hydrogen atoms. An approach is proposed here to solve this six-body problem within the framework of Born theory taking full consideration of the molecular properties of H 2, such as wave function and orientation of molecular axis. For C 5+ collisions on H 2, the obtained cross sections as a function of molecular orientation show interference patterns typical of two-center scattering. Orientation-averaged total cross sections for H 2 are found to be essentially the same as for 2H, in agreement with recent experiment.