3D-Orientation

Figure Cl.5.14. Fluorescence images of tliree different single molecules observed under the imaging conditions of figure Cl.5.13. The observed dipole emission patterns (left column) are indicative of the 3D orientation of each molecule. The right-hand column shows the calculated fit to each observed intensity pattern. Molecules 1, 2 and 3 are found to have polar angles of (0,( ))=(4.5°,-24.6°), (-5.3°,51.6°) and (85.4°,-3.9°), respectively. Reprinted with pennission from Bartko and Dickson [148]. Copyright 1999 American Chemical Society.

Four polarized ATR spectra can be recorded to characterize the three-dimensional (3D) orientation of a sample, p- and s-polarized spectra are recorded with the sample clamped with its Z- and X-axes sequentially aligned perpendicular to the incidence plane (that is, parallel to the s-polarized electric field). The absorbance measured in these different configurations is related to the anisotropic absorption indices of the sample, kj, as... 

The Oriented Substituent Pharmacophore PRopErtY Space (OSPPREYS) approach, introduced by Martin and Hoeffel [6], is in software terms an extension of CCG s MOE package, written using SVL. The 3D oriented substituent pharmacophores are aimed towards better representation of diversity and similarity in combinatorial libraries in the 3D pharmacophore space. Combinatorial library design often operates only on substituents rather than on the final products as the complications related to the conformational coverage in the 3D space and the scaffold dependency limit the product-based approaches to smaller libraries. The 3D oriented substituent pharmacophores add two more points and the corresponding distances to each substituent pharmacophore which represent the relationship of the substituents in the product with only little additional information. The fingerprints permit the creation of property space by multidimensional scaling (MDS) and, since scaffold independent, can be stored separately and applied to different libraries [6],... 

The 3D orientation distributions of structural features within damage zones are important for modelling of fluid flow as the non-parallel members of the arrays induce an intersection network which will control the connectivity of barriers. It is insufficient to characterise the average fault orientations or to identify average fault trends or families. A more detailed statistical analysis of fault orientations is needed in order to evaluate the 3D distribution of flow paths and barriers. An analysis of fault dips from North Sea wells (-20 km of total core studied) yields an average dip of 59°. However the standard deviations of these data sets, which will control the density and pattern of intersections, is typically between 15° and 26°. Fig. 15 illustrates one example which com... 

The backscattering intensity of the horizontally oriented particle is much stronger than that of its 3D oriented counterparts. This is due to the stronger likelihood for retroreflection for this illumination condition and... 

In our work, the tip of a catheter is equipped with an IPMC artificial muscle as a stirrer. A schematic of an attached IPMC stirrer to the tip of a catheter is depicted in Fig. 2.4. Bi-directional bending of the catheter, along with the manual twisting motion of the wire, enables 3D orientation control of the active catheter. Successful actuation is achieved in a fluidic environment as shown in Fig. 2.5. The tip of the actuator is easily bent about 90°, which is sufficient to maneuver through the endovascular branches. 

Very recently, (Bafna et al., 2003) developed a technique to determine the three-dimensional (3D) orientation of various hierarchical organic and inorganic structures in a PLS nanocomposite. They studied the effect of comjjatibilizer concentration on the orientation of various structures in PLS nanocomposites using 2D SAXS and 2D WAXD in three sample / camera orientations. 

It should be noted that the equivalence of the DLM electronic structure problem to that of an Ising-like system is purely a consequence of the symmetry of the paramagnetic state, and is not the result of om imposing any restriction on the moment directions. Indeed, in the formalism for the paramagnetic spin susceptibility, which we outline now, we maintain and consider the full 3D orientational freedom of the moments. 

In Figure 12.9, Osewe (2014) showed the effects of ID, 2D, and 3D orientations of zeolitic channels and cavities on the half-life of malathion degradation in waste waters [16]. 

The effect of shear on the orientation of polymer-clay nanocomposites has been examined by a number of groups (Somani et al. 2000, 2001 Fong et al. 2002 Jimenez et al. 1997), and in some cases, the three-dimensional (3D) orientation of the polymer and clay has been determined (Kojima et al. 1994 Bafiia et al. 2003 Varlot et al. 2001). 

Using somewhat more sophisticated, the so-called radial and azimuthal, modes of polarization enabled the observation of tautomerism in single molecules of porphycenes [23, 24] (Figure 3.5) and porphyrins [25]. These techniques also allowed obtaining the 3D orientation patterns for single molecules of porphycenes embedded in a polymer film [24]. 

O. Yaroshchuk, T. Bidna, M. Dumont, and J. Lindau, Photoinduced 3D orientational order in hquid crystalhne azopolymers studied by the method of attenuated total reflechon. Molecular Crystals and Liquid Crystals 409, 229 (2204). 

O. Yaroshchuk, M. Dumont, Yu. Zakrevskyy, T. Bidna, and J. Lindau, Molecular structure of azopolymers and photoinduced 3D orientational order. 1. Azobenzene polyesters. Journal of Physical Chemistry B 108, 4647 (2004). 

Hie frill 3D orientation of single molecules can be obtained by other techniques that can determine the absorption or emission transition dipole moment. Annular illumination is a technique that can determine the orientation of the absorption dipole moment, while the 3D orientation of the emission dipole moment can be revealed using defocused wide-field imaging, ° introducing aberrations or by direcdy recording the emission pattern in the objective s back focal plane. In... 

These techniques are all based on the fact that single fluorophores do not emit light equally in all direaions, but they emit light with a sine-squared distribution relative to the transition dipole orientation, as mentioned before. As such, an anisotropic distribution is obtained resulting in a fluorescence pattern of which the appearance strongly depends on the 3D orientation of the transition dipole moment. Normally, this fluorescence pattern is not seen, since most objectives are corrected and all molecules appear as relatively sharp spots. However, by introducing aberrations, the anisotropic distribution can be observed. 

Aberrations can be introduced by passing the light through a water layer before it reaches the sample. With this technique, molecules of which the transition dipole moment is oriented along the optical axis appear to be out of focus, while molecules oriented in the sample plane are observed to be in focus. The full 3D orientation can be determined by periodically rotating the laser polarization. The rotation of DilCig (l,T-dioctadecyl-3,3,3, 3 -tetramethylindocarbocyanine perchlorate) in PMMA has been observed using this technique. The timescale of the rotational diffusion was found to be several hundreds of milliseconds. 

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