Rotational diffusion effects on absorbance measurements: limitations to the magic-angle approach.

Optical absorbance changes are commonly used to characterize intermediates which appear in the bleaching sequence of rhodopsin and in the photocycle of bacteriorhodopsin. Absorbance changes can be caused by an intermediate's rotational diffusion, and when this occurs it can distort absorbance changes due to the structural evolution of intermediates. Linear polarization of an optical probe source at 54.7 degrees (the magic angle) relative to the polarization direction of a linearly polarized actinic source has often been used to eliminate signals due to rotational diffusion. We used Jones calculus to investigate the validity of the magic-angle strategy. Taylor expansion of the result in powers of the absorbances of the bleached ground state and of the intermediates leads to a relatively simple expression which can be used to determine whether rotational contributions are likely under various experimental conditions. This expression shows that in first order no dichroism-dependent term appears in the absorbance measured at magic angle. In second order, however, linear dichroism contributes to signals. For the sequence of rhodopsin intermediates: rhodopsin hv----bathorhodopsin in equilibrium BSI----lumirhodopsin, where BSI is a recently discovered blue-shifted intermediate, we determined the magnitude of the dichroism signals to be, on average, less than 2% of the true absorbance change due to the intermediates themselves (and hence undetectable). Freedom from dichroism artifacts in this case results from the fact that the transition dipoles of these intermediates are similar to that of rhodopsin. Larger and certainly detectable dichroism signals are predicted to occur, even at the magic angle, for later intermediates which have transition dipole moments which differ significantly from that of rhodopsin.(ABSTRACT TRUNCATED AT 250 WORDS)     

Imaging of tautomerism in a single molecule

Fluorescence imaging is used to visualize directly the transfer of two inner hydrogen atoms in single porphycene molecules. This reaction leads to a chemically equivalent but differently oriented structure and hence results in a rotation of the transition dipole moments. By probing single immobilized molecules with an azimuthally polarized laser beam in the focal spot of a confocal microscope we observe ring-like emission patterns, possible only for a chromophore with two nearly orthogonal transition dipole moments. Numerical simulations of the observed emission patterns yield a value of 72 degrees for the angle between the S0-S1 transition moments in the two tautomeric forms.     

黑皂膜中染料分子的共振Raman光谱及其分子取向

本文研究了BSF中染料BY和MO分子的取向问题, 建立了三点式数据采集方法,测得各种入射角θ下BSF中BY和MO分子的-N=N-对称伸缩振动谱带的Raman偏振比R~1和R~2, 分别用单轴唯一角取向模型和取向分布模型, 讨论偏振比R~1和R~2与入射角θ的关系。单轴唯一角取向模型处理上述偏振数据的结果表明, BY以较大的倾角(约80°)斜躺在BSF的膜壁上; 凝胶相的BSF中, MO取向角约为70°, 随温度升高,BSF转变为液晶相对, MO的取向角减小到65°。用取向分布模型处理, 得到染料分子的取向分布图象, BY和MO在BSF中均以90°取向几率为最大, 但其它各方向亦有一定的取向几率, BSF的相变导致MO分子的取向分布图象由较为集中型转变为更加弥散型。     

On the origin of high optical director tilt in a partially fluorinated orthoconic antiferroelectric liquid crystal mixture

We have investigated the orthoconic antiferroelectric liquid crystal mixture W107 by means of optical, X-ray and calorimetry measurements in order to assess the origin of the unusally high tilt angle between the optic axis and the smectic layer normal in this material. The optical birefringence increases strongly below the transition to the tilted phases, showing that the onset of tilt is coupled with a considerable increase in orientational order. The layer spacing in the smectic A* (SmA*) phase is notably smaller than the extended length of the molecules constituting the mixture, and the shrinkage in smectic C* (SmC*) and smectic C_a* (SmC_a*) is much less than the optical tilt angle would predict. These observations indicate that the tilting transition in W107 to a large extent follows the asymmetric de Vries diffuse cone model. The molecules are on average considerably tilted with respect to the layer normal already in the SmA* phase but the tilting directions are there randomly distributed, giving the phase its uniaxial characteristics. At the transition to the SmC* phase, the distribution is biased such that the molecular tilt already present in SmA* now gives a contribution to the macroscopic tilt angle. In addition, there is a certain increase of the average tilt angle, leading to a slightly smaller layer thickness in the tilted phases. Analysis of the wide angle scattering data show that the molecular tilt in SmC_a* is about 20° larger than in SmA*. The large optical tilt (45°) in the SmC_a* phase thus results from a combination of an increased average molecule tilt and a biasing of tilt direction fluctuations.     

On the origin of high optical director tilt in a partially fluorinated orthoconic antiferroelectric liquid crystal mixture

We have investigated the orthoconic antiferroelectric liquid crystal mixture W107 by means of optical, X-ray and calorimetry measurements in order to assess the origin of the unusally high tilt angle between the optic axis and the smectic layer normal in this material. The optical birefringence increases strongly below the transition to the tilted phases, showing that the onset of tilt is coupled with a considerable increase in orientational order. The layer spacing in the smectic A* (SmA*) phase is notably smaller than the extended length of the molecules constituting the mixture, and the shrinkage in smectic C* (SmC*) and smectic C_a* (SmC_a*) is much less than the optical tilt angle would predict. These observations indicate that the tilting transition in W107 to a large extent follows the asymmetric de Vries diffuse cone model. The molecules are on average considerably tilted with respect to the layer normal already in the SmA* phase but the tilting directions are there randomly distributed, giving the phase its uniaxial characteristics. At the transition to the SmC* phase, the distribution is biased such that the molecular tilt already present in SmA* now gives a contribution to the macroscopic tilt angle. In addition, there is a certain increase of the average tilt angle, leading to a slightly smaller layer thickness in the tilted phases. Analysis of the wide angle scattering data show that the molecular tilt in SmC_a* is about 20° larger than in SmA*. The large optical tilt (45°) in the SmC_a* phase thus results from a combination of an increased average molecule tilt and a biasing of tilt direction fluctuations.     

Vapor phase self-assembly of electrooptic thin films via triple hydrogen bonds

The donor-acceptor pi-electron chromophore 5-{4-[2-(4,6-diamino-[1,3,5]triazin-2-yl)-vinyl]-benzylidene}-pyrimidine-2,4,6-trione (DTPT) was designed and synthesized. Triple H-bonding interactions between neighboring molecules direct self-assembled chromophore alignment in a head-to-tail orientation using a straightforward vapor phase deposition process. Angle-dependent SHG interference patterns and the quadratic dependence of the 532 nm light output intensity on the thickness of the DTPT films for glass substrates coated on both sides demonstrate high, reproducible film quality and uniformity. XRD also demonstrates long-range order in the film and yields a molecular tilt angle in good agreement with polarized SHG data, clearly showing that out-of-plane ordering of chromophore molecules has been achieved.     

Reflective thermal lens detection device

A reflective thermal lens detection device was developed for realizing a portable and sensitive detector for a microsystem. An aluminum mirror was formed on the main plate of a microchip, and a reflected probe beam was detected with a single pick-up unit. The background signal due to light absorption of the aluminum mirror was 60 times reduced when the microchannel and the mirror were separated with an interval of 600 microm. The tilt angle of the microchip significantly affected the precision of the measurement. Then a quadrant photodiode was used to detect the center of gravity of the reflected probe beam to regulate the tilt angle within +/-0.05 degrees , and this value was enough to achieve 1% CV (coefficient of variance) precision in the measurements. The limit of detection (LOD) was 60 nM for xylene cyanol solution, and the absorbance was 9.4 x 10(-6) AU. About 40 times higher sensitivity was obtained in comparison with a spectrophotometer.     

Structural and optical properties of DNA layers covalently attached to diamond surfaces

Label-free detection of DNA molecules on chemically vapor-deposited diamond surfaces is achieved with spectroscopic ellipsometry in the infrared and vacuum ultraviolet range. This nondestructive method has the potential to yield information on the average orientation of single as well as double-stranded DNA molecules, without restricting the strand length to the persistence length. The orientational analysis based on electronic excitations in combination with information from layer thicknesses provides a deeper understanding of biological layers on diamond. The pi-pi* transition dipole moments, corresponding to a transition at 4.74 eV, originate from the individual bases. They are in a plane perpendicular to the DNA backbone with an associated n-pi* transition at 4.47 eV. For 8-36 bases of single- and double-stranded DNA covalently attached to ultra-nanocrystalline diamond, the ratio between in- and out-of-plane components in the best fit simulations to the ellipsometric spectra yields an average tilt angle of the DNA backbone with respect to the surface plane ranging from 45 degrees to 52 degrees . We comment on the physical meaning of the calculated tilt angles. Additional information is gathered from atomic force microscopy, fluorescence imaging, and wetting experiments. The results reported here are of value in understanding and optimizing the performance of the electronic readout of a diamond-based label-free DNA hybridization sensor.     

Molecular arrangement in a chiral smectic liquid crystal cell studied by polarized infrared spectroscopy

The structure of the chiral smectic C phase (SmC*) of the mesogen MHP10CBC in a homogeneously aligned thin cell, that exhibits V-shaped-like switching in a certain frequency range, was studied using polarized Fourier-transform infrared spectroscopy and optical microscopy. The molecular orientational distributions were analysed quantitatively in terms of dichroic parameters of the absorbance profiles, by taking into account the orientational properties of the transition moments for several phenyl and carbonyl bands. The polar angles of the transition moments, with respect to the molecular long axis and their azimuthal orientational parameters used in calculations, were determined from the infrared dichroic data for helical and electrically unwound structures in a thicker cell of this material. For a sufficiently thin cell in the SmC* phase at zero electric field, the results on the azimuthal orientational distribution of the director over a ferroelectric liquid crystal cone, with respect to the substrate normal, are in agreement with the model of a partly twisted SmC* structure. The voltage-dependent dichroic parameters in relation to the direction and the degree of the preferable orientation of the molecules in a sample are compared for the SmC* and the SmC* A phases.     

A critical theoretical study on the two-photon absorption properties of some selective triaryl borane-1-naphthylphenyl amine based charge transfer molecules

In the present work, we have studied the two-photon absorption (TPA) properties of some selective molecules containing triarylborane and 1-naphthylphenylamine as the acceptor and donor moiety, respectively. The calculations are performed by using the state-of-the-art linear and quadratic response theory in the framework of the time dependent density functional theoretical method. The TPA parameters are calculated with CAMB3LYP functional and the cc-pVDZ basis set. The one-photon results indicate that both the electronic transitions (S(0)-S(1) and S(0)-S(2)) are associated with the charge transfer interaction between the donor and acceptor moieties along with the reorganization of the π-electron density. All these chromophores are found to have very strong two-photon active modes. In order to find out the origin of large TP transition probability of these molecules, we have performed two-state model (TSM) and sum-over-states (SOS) calculations. We have found that the TSM failed to reproduce the correct trend of the TP transition probability of the molecules obtained from the response theory, while SOS is quite successful in doing so. The whole study indicates that the transition moments between the excited states play a pivotal role in controlling the TP transition probabilities of these molecules. The role of solvent in the TP transition probability of these molecules has meticulously been scrutinized within the polarized continuum model (PCM). Further more, we have benchmarked our theoretical findings by calculating the TPA cross-section of a boron and nitrogen containing a charge transfer molecule for which the experimental result is available and we found that our theoretical result is in good agreement with the experimental one which definitely demonstrates the potential of all these light-emitting diode molecules as TP active materials too.     

ORIENTATION OF CHLOROPHYLLS IN LIQUID CRYSTALS

Abstract— Chlorophyll derivatives can be oriented in a liquid crystal matrix. The temperature and angular dependence of the absorption spectra are studied with polarized light. From these results we can deduce the orientation of the molecules of dye in the liquid crystal. The deconvolution of the Soret band also allows us to assign to the different components their related transition moments.     

Molecular arrangement in a chiral smectic liquid crystal cell studied by polarized infrared spectroscopy

The structure of the chiral smectic C phase (SmC * ) of the mesogen MHP10CBC in a homogeneously aligned thin cell, that exhibits V-shaped-like switching in a certain frequency range, was studied using polarized Fourier-transform infrared spectroscopy and optical microscopy. The molecular orientational distributions were analysed quantitatively in terms of dichroic parameters of the absorbance profiles, by taking into account the orientational properties of the transition moments for several phenyl and carbonyl bands. The polar angles of the transition moments, with respect to the molecular long axis and their azimuthal orientational parameters used in calculations, were determined from the infrared dichroic data for helical and electrically unwound structures in a thicker cell of this material. For a sufficiently thin cell in the SmC * phase at zero electric field, the results on the azimuthal orientational distribution of the director over a ferroelectric liquid crystal cone, with respect to the substrate normal, are in agreement with the model of a partly twisted SmC * structure. The voltage-dependent dichroic parameters in relation to the direction and the degree of the preferable orientation of the molecules in a sample are compared for the SmC * and the SmC * A phases.     

Banana-shaped liquid crystals with two oligosiloxane end-groups: field-induced switching of supramolecular chirality

The first bent core mesogen carrying branched oligosiloxane units at both ends was synthesized and investigated with polarized light microscopy, DSC, X-ray diffraction of well aligned samples, and electrooptical methods. Two different antiferroelectric switching liquid crystalline phases were found. Both can be regarded as modulated smectic phases in which the molecules have extremely large tilt angles. In both mesophases, the field-induced switching takes place by rotation around the molecular long axes. This field-induced reorientation switches the layer chirality. The transition between the two mesophases is associated with a change of the tilt direction from synclinic to anticlinic. The synclinic high-temperature phase is an obliquelike ribbon phase whereas the anticlinic low-temperature phase represents a sinusoidal undulated layer structure (SmCAPA). It is proposed that the phase transition from the ribbon phase to the undulated layer structure is mainly driven by the change of the interlayer correlation.     

Isosbestic-like point in the polarized reflectance spectra of monoclinic crystals--A quantitative approach

If two overlapping bands originate from transition moments that are perpendicular and lie along the principal axes of the infinity frequency dielectric tensor, an isosbestic-like point (ILP) appears in the overlaid polarized IR reflectance spectra of single crystals. These conditions can also be met in principle in case of the reflectance from the ac-plane of a monoclinic crystal despite of the crystal's low symmetry. In order to determine the transition moment directions, diagonalization of the infinity frequency dielectric tensor should be performed. It is shown that a critical magnitude for the appearance of ILP is the angle of incidence. An increase of this angle leads to a transformation of the ILP to an isosbestic-like region, which eventually vanishes at higher incidence angles. Polarized reflectance spectra of gypsum (CaSO4.2H2O), recorded from the ac crystal face, were used to verify the theoretical results.     

Oriented structure of octadecyl acridine orange intercalated in the monolayer and Langmuir–Blodgett film of octadecyl adenine‐thymine base pairs

The oriented structure of acridine orange (AO) in both monolayer and Langmuir–Blodgett (LB) film has been studied by optical waveguide (OWG) spectroscopy using polarized incident light. Mixed monolayer and LB films, consisting of octadecyl acridine orange (C₁₈‐AO) incorporated in stacked base pairs of octadecyl adenine (C₁₈‐Ade) and octadecyl thymine (C₁₈‐Thy), were prepared on a quartz waveguide. Absorption of transverse electric field (TE) polarized light was about twice that of transverse magnetic field (TM) polarized light. Both OWG spectra have λ_max at 500 nm, which is characteristic of monomeric AO molecules. This result strongly suggests that C₁₈‐AO molecules were dispersed uniformly in the mixed monolayer and were excited more effectively by the TE polarized light. Since the absorption moment of AO molecules is related to their long axis, it is proposed that C₁₈‐AO molecules are incorporated in C₁₈‐Ade/C₁₈‐Thy pairs with the long axis parallel to the layer surface. The absorbance at 500 nm was proportional to the number of layers on the waveguide. The dichroic ratio of the absorbance at 500 nm for TE polarized light to that for TM polarized light was constant regardless of the number of layers. The C₁₈‐AO molecules were uniformly incorporated in each layer with the long axis relatively parallel to the layer surface. Copyright © 2004 John Wiley & Sons, Ltd.     

Light diffraction studies on director arrangement in the polymer‐pinned striped pattern obtained via the electric field‐induced Fréedericksz transition of nematics

We have observed an anomalous pattern forming phenomenon in which a striped pattern in a nematic liquid crystal appeared after removing an electric field following a Fréedericksz transition, and this pattern was preserved even in the equilibrium state in zero‐electric field. The nematic director arrangement in the striped pattern was investigated by light diffraction measurements. The stripes are proposed to consist of a periodic distortion of the nematic directors, specifically, tilted directors with the same absolute value of tilt angle but of opposite sign are alternately arrayed. The proposed model of the stripes is in good accord with the experimental results of light diffraction dependence on polarizing direction and light incidence angle.     

Oriented ensembles in ultrafast electron diffraction.

Electron scattering expressions are presented which are applicable to very general conditions of implementation of anisotropic ultrafast electron diffraction (UED) experiments on the femto- and picosecond time scale. "Magic angle" methods for extracting from the experimental diffraction patterns both the isotropic scalar contribution (population dynamics) and the angular (orientation-dependent) contribution are described. To achieve this result, the molecular scattering intensity is given as an expansion in terms of the moments of the transition-dipole distribution created by the linearly polarized excitation laser pulse. The isotropic component (n=0 moment) depends only on population and scalar internuclear separations, and the higher moments reflect bond angles and evolve in time due to rotational motion of the molecules. This clear analytical separation facilitates assessment of the role of experimental variables in determining the influence of anisotropic orientational distributions of the molecular ensembles on the measured diffraction patterns. Practical procedures to separate the isotropic and anisotropic components of experimental data are evaluated and demonstrated with application to reactions. The influence of vectorial properties (bond angles and rotational dynamics) on the anisotropic component adds a new dimension to UED, arising through the imposition of spatial order on otherwise randomly oriented ensembles.     

Photoinduced anchoring transitions in a nematic doped with azo dyes

Recently, we reported on a light-induced anchoring transition of an azobenzene nematic from planar to homeotropic alignment. In the proposed model of the transition, the changes in shape of the liquid crystal molecules and of their net dipole moment, due to the photoisomerization, were considered to play a vital role in the occurrence of the transition. In order to assess the validity of this model, a study of the anchoring behaviour of nematic guest-host liquid crystal mixtures containing two photochromic dyes, 3,3'- and 4,4'-substituted azobenzenes, was carried out. The dyes have very similar molecular structures to that of the azobenzene nematic previously studied, and their molecules, having a linear shape in the trans-form, maintained this shape after photoisomerization in the case of the 3,3'-azo dye, and changed it to bent in the case of the 4,4'-azo dye. The dyes possessed similar net dipole moments that increased substantially after photoisomerization, resulting in a preferential adsorption of their cis-isomers on the solid substrate. However, only the mixture containing the 4,4'-azo dye exhibited an anchoring transition from planar to homeotropic alignment upon illumination with unpolarized UV light, a behaviour in excellent agreement with the prediction of the model for the light-induced anchoring transition. An anchoring transition from random planar to uniform planar alignment was found to take place in the mixtures when linearly polarized UV light was used, requiring, however, a different exposure time for the two dyes.     

Frenkel‐exciton decomposition analysis of circular dichroism and circularly polarized luminescence for multichromophoric systems

Recently, a method to calculate the absorption and circular dichroism (CD) spectra based on the exciton coupling has been developed. In this work, the method was utilized for the decomposition of the CD and circularly polarized luminescence (CPL) spectra of a multichromophoric system into chromophore contributions for recently developed through‐space conjugated oligomers. The method which has been implemented using rotatory strength in the velocity form and therefore it is gauge‐invariant, enables us to evaluate the contribution from each chromophoric unit and locally excited state to the CD and CPL spectra of the total system. The excitonic calculations suitably reproduce the full calculations of the system, as well as the experimental results. We demonstrate that the interactions between electric transition dipole moments of adjacent chromophoric units are crucial in the CD and CPL spectra of the multichromophoric systems, while the interactions between electric and magnetic transition dipole moments are not negligible. © 2018 Wiley Periodicals, Inc.     

Extracting maximum information from polarized surface vibrational spectra: application to etched, H-terminated Si(110) surfaces

A general method to maximize the information extracted from polarized surface absorption spectra is developed and applied to the study of etched Si(110) surfaces. In essence, this technique transforms spectra from the experimental reference frame, which is defined by the direction of the surface electric field during irradiation by s- and p-polarized light, into a more appropriate Cartesian reference frame defined by the surface normal and the plane of incidence. If the Cartesian reference frame is aligned with high symmetry directions of the system, significant spectral simplification can result. This analysis relies on the well-known boundary conditions on interfacial electric fields and is independent of any adsorbate screening or the effective dielectric constant of the adsorbate layer. The validity of this analysis is demonstrated on the spectra of NH4F-etched, H-terminated Si(110). The transition dipole moments of the symmetric and antisymmetric Si[Single Bond]H stretch modes associated with flat terraces are polarized along the [110] and [001] directions, respectively. Two additional modes with transition dipoles polarized along the [001] and [110] directions are assigned to defect species associated with microfaceting and other surface roughness. Data taken in two different experimental geometries are shown to be in excellent quantitative agreement, confirming the validity of the technique. Additionally, the measured adsorbate layer dielectric constant is in good agreement with previously reported values for hydrogen-terminated silicon surfaces.