Absorption anisotropic

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... 

Attention must now be paid to the exponential factor, exp( 2nir (n iij)/A), in Equation 6.5, where (n it) is known as the complex refractive index of a substance. It can be seen that the effect of this factor upon the electromagnetic wave increases with the distance Irl that the light travels in that medium. In the general case of an anisotropic medium, n and are referred to as a specific set of axes, usually chosen to coincide with the optical axes of the medium. For example, the axes of maximum and minimum transmittance are selected for anisotropic absorption. The extinction f for an anisotropic medium is related to the extinction coefficient through Equation 6.9. 

The unique spectral absorption of the Rhodonines contains two visual band components, an isotropic absorption associated with the conjugated dipole molecular structure of the molecule, and a anisotropic absorption associated with an additional resonant slow-wave stmcture intimately associated with the triplet electrons of the oxygen atoms of the molecule. The unusual relaxation properties of these molecules are also associated with these triplet state electrons. The Rhodonines do not fluoresce or phosphoresce significantly while in a dilute liquid solution. 

Dipole molecular absorption- A medium energy-level change involving a change in the energy levels of a molecule characterized by anisotropic absorption in the visible or ultraviolet range. 

Second, the absorption characteristic of each Rhodonine chromophore is highly directional (15R). This anisotropic absorption is only observed for radiation applied perpendicular to the surface of the film, i.e., parallel to the axis of the Outer Segment. The peak absorption wavelength for resonant absorption by these chromophores is nominally either 342,437, 532 or 625 nm. The chromophore is not polarization sensitive for excitation along this axis. For radiation applied along other axes, such as transverse to the axis of the OS, only the intrinsic absorption characteristic due to conjugate absorption and shared by all retinoids of the Vitamin A Group will be observed. This intrinsic spectrum has a nominal spectral peak at 502 nm at 37C. 

A primary reason for the above disparities is the critically important structural organization of the chromophores when found in-vivo. These relationships make a major (several orders of magnitude) difference in the absorbance of the material and also lead to anisotropic absorption. These relationships have not been maintained by the chemists. A second reason relates particularly to the L-channel. The chromophore of that channel exhibits a more intimate relationship with the electronic portion of the photoreceptor neuron than do the S- and M-channel chromophores. As a result, the L-channel exhibits an effective absorption characteristic very different from that observed by the chemist. This characteristic also accounts for the loss of red response in the mesopic and scotopic regions. These relationships have not been emulated in the environment of the chemist. Failure to emulate these conditions leads to extraneous absorption spectra for the L-channel chromophore. A third reason is due to the frequent chemical reactions occurring in the chemists solutions that he may not be aware of. It has been rare in the past for the chemist to document the pH of the solutions he has measured. This is a particular problem as mentioned in a later section [Section 5.5.12], The chromophores of vision are members of the "indicator class of chemicals. Their spectral characteristics are intimately related to the pH of their environment. They are also complex organics. Their spectral characteristics are a function of the organic solvent used. They are also subject to chemical attack. This mechanism has been documented by Wald, et. al. and more recently by Ma, et. al. 

Wald, et. al97,98. performed a set of experiments during the 1940 s that purported to demonstrate the formation of rhodopsin from either retinene, (now known as retinal) or Vitamin A, and a native protein. While their work involved materials showing a peak absorption at 500 nm, this is the wavelength of peak isotropic absorption of a large number of dipolar retinoids. Such a peak is not exclusive to the chromophoies of vision. Neither is it relevant to the anisotropic absorption spectrum of the chromophores of vision. 

Although the physical thickness of the liquid crystal is only about 15 Angstrom, it is quantum-mechanically resonant at the wavelength of the incident photons due to its slow-wave electronic structure. The spatial profile of the anisotropic absorption spectrum is shown without dimensions. It is dependent on the absorption cross section of the liquid crystalline film. The array factor for this array cannot be determined easily using conventional antenna theory because of its sub-wavelength dimensions and other currently unknown parameters. 

Figure 5.5.4-1 Putative arrangement of a liquid crystalline chromophore on the surface of the opsin substrate. The individual molecules are arranged with their long axis nearly perpendicular to the surface of the substrate. The angle of tilt of the array is estimated. It is not documented in both directions and may differ slightly from a straight line drawn between the two auxochromes of the molecules. The pitch and dimensions of the substrate molecules are from Corliss and from Nilsson. The hydrogen bonds between the chromophores and the substrate are shown as dots. The anisotropic absorption profile of the chromophore is illustrative due to the many quantum-mechanical factors in determining it precisely.

For experiments where the radiation is applied parallel to the axis of the disk stack, entirely different results are obtained. This is the case of some of the later Baylor experiments and most noninvasive photo-micro-spectrometry studies. These studies, if performed so as to only illuminate one photoreceptor at a time, produce peak spectral absorptions that conform to the actual anisotropic absorption spectra of the chromophores of vision. These peaks are at 437, 532, 625 nm 2 nm at mammalian temperatures. 

As the molarity of the solution is increased, the Rhodonines will begin to coalesce into filaments and globules that show liquid crystalline characteristics. These individual structures will exhibit anisotropic absorption at their resonant wavelengths. However, from a global perspective, the overall absorption of the solution will still appear isotropic but with an added absorption peak. Their relaxation modes will remain the same as above. 

If the molarity is further increased, and the material is allowed to precipitate on a substrate, the liquid crystalline structure of the precipitate will exhibit a highly anisotropic absorption spectrum at the resonant wavelength of its chromophore as well as its normal isotropic molecular absorption spectrum. The relaxation characteristic will either remain unchanged or be impacted by the electronic characteristics of the substrate. 

The uncomplexed Rhodonines are found in two locations within the retina. They are found within the pigmented globules of the RPE and they are found deposited on the disks. When in the globules, it is likely that they are in a liquid crystalline state and probably sorted spectrally due to their separate stereo-graphic features. Each individual globule may show significant anisotropic absorption. Their means of relaxation while in this configuration is currently unknown. 

The data collected by Baylor and Hodgkin is shown in Figure 5.5.10-6154. It leaves little doubt concerning the three spectral peaks found in the absorption spectra of the turtle. It also leaves little doubt as the the broadness of these peaks as described by Fermi-Dirac statistics rather than Gaussian statistics. Notice that there is no absorption with a peak at 502 nm in this figure. They illuminated the photoreceptors end-on and measured the anisotropic absorption expected from this configuration. 

The anisotropic absorption of the disks of humans and other chordates... 

Spatial Profile of resonant (anisotropic) absorption by resonant liquid crystalline structure of chromophore... 

Molecular (but anisotropic) absorption, at 500 nm, reflecting the physical arrangement of the chromophores... 

Figure 5.5.11-1 Absorption characteristics of a complete disk showing the variation in absorption properties as a function of spatial angle and absorbing species. Top 3-D isometric view. Bottom 2-D projection, plane contains vertical axis perpendicular to disk surface. The shared quantum-mechanical structure of the liquid crystalline chromophore(s) creates a highly focused (anisotropic) absorption profile. This structure is in quantum-mechanical contact with the microtubules surrounding the disk. The retinoids within the opsin proteins are not in quantum-mechanical contact with each other or the microtubules.

These devices are based on the anisotropic absorption of light. Usually molecular crystals exhibit this property and tourmaline is the classical example for this. For practical purposes, however, micro crystals are oriented in polymer sheets. Polymers containing chromophors become after stretching dichroic polarizers. The devices produced in this manner are called polawids. They have found a broad application in many technologies. Their application in spectroscopy is limited to the near ultraviolet and to the visible and near infrared range of the spectrum. In vibrational spectroscopy polaroids are employed as analyzers only for Raman spectroscopy. 

An LCAO (linear combination of atomic orbitals) local-density functional approach was used to calculate the band structures of a series of polymer chain conformations unsubstituted polysilane in the all-trans conformation and in a 411 helical conformation, and all-trans poly(dimethylsilane). Calculated absorption spectra predict a highly anisotropic absorption for the all-trans conformation of polysilane, with the threshold absorption peak arising strictly from polarizations parallel to the chain axis. The absorption spectrum for the helical conformation is much more isotropic. Results for the dimethyl-substituted polysilane chain suggest that the states immediately surrounding the Fermi level retain their silicon-backbone a character upon alkyl-group substitution, although the band gap decreases by I eV because of contributions from alkyl substituent states both below the valence band and above the conduction band to the frontier states. 

This dominant feature is essentially the same for both the unsubstituted and dimethyl-substituted all-trans polysilane chains, and an equivalent feature is found when a smaller basis set is used for the dimethyl-, diethyl-, and dipropyl-substituted poly silanes. For the helical conformation, however, along with the larger band gap in this conformation (Figure 3c), a pronounced shift of the direct-gap absorption peak to higher energy is observed, with a trend toward a less anisotropic absorption. 

Absorption spectra of polysilanes anisotropic absorption for helical conformation, 549 bathochromic shifts, 549 effect of conformation on extinction coefficient, 547, 548/ low-energy feature for al -trans conformations, 547, 548/, 549 Acetylenes... 

Solvent reorientation and isomerization of trans-stilbene in alkane solutions has been studied by ps time scale anisotropic absorption and polarization239 Coupling of solute and solvent decreases as the size of the solvent molecules increases. The applicability of currently favoured models for the activated barrier crossing in the photoisomerization of stilbene is discussed, A method for measuring quantum yields in the photoisomerization of trans-stilbene gives high accuracy without use of a chemical actinometer . Evidence has been found for dynamic solvent effects on the photoisomerization of 4,4 -dimethoxystilbene in which the effects of temperature and hydrostatic pressure were made in n-alkane and n-alkyl alcohol. A ps laser time-resolved study fits frequency dependent solvent shifts but gives results inconsistent with the free volume model. Photophysical and theoretical studies of trans and 9-... 

Fig. 3. Nanostructured composite of p-nitroaniline (pNA, top left) and AIPO4-5. Top right Anisotropic absorption of the composite The crystals appear yellow only when the electric field vector E of the linearly polarized light oscillates in the direction of the transition dipole moment of the blue absorption of the pNA molecules. When E and these dipole moments are perpendicular to each other, no absorption occurs in the visible region, so that the pNA/AlPO -S crystals appear colourless. Center Experiment to measure the second harmonic generation (SHG) of the pNA/AIP04-5 composite. Bottom right The measured SHG effect is a function of cos q>, where q> is the rotation angle of the polarization rotator. This result is in agreement with the expectation if it is assumed that the pNA molecules are aligned in the channels and their dipoles all possess the same orientation. After the work of Caro, Marlow and co-workers [30-32],...

Fig. 6. Anisotropic absorption behaviour under the polarizing microscope of crystals of (a) [Co(cp)2]F-NON, (b) [Co(cp)2]F-AST and [Co(cp)2]F-DOH. The shading of the crystals indicates yellow colours of different...

Crystals of [Co(cpme)2]F-DOH have a similar shape to those of [Co(cp)2]F-DOH, but they are much smaller [25]. Anisotropic absorption is thus very difficult to observe. In fact, we were not able... 

The monolayer of dye A which has been reorganized on the gypsum crystal shows a strong anisotropy (absorptions band between 400 nm and 600 nm). The monolayer of dye B exhibits the expected anisotropic absorption between 300 nm and 400 nm. However, the anisotropy is somewhat smaller than in the original monolayer. This indicates that under the conditions of the experiments the reorganization of the dye B monolayer to a mirror... 

The questions set forth here are answered as follows Eirst, broad and anisotropic absorption bands where found to gradually increase from the near- to mid-infrared region of all-trans-p-carotenc single crystals. Second, the stretched-exponentiai and power-law recoveries of the photoinduced bleaching of the infrared absorption bands may correspond to the recombination of the solitonlike excitations in all-trans-P-carotene single crystals. 

Problems that may be encountered due to external birefringence effects in the anisotropic absorption method of Shank and Ippen have been discussed. In the event of these interferences being unavoidable, methods have been described to allow the rotational reorientation times of the dye molecules in fluid solution to be determined. ... 

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