Molecular absorption spectra

The reciprocal of the FRET-unperturbed donor lifetime, td, is given by the sum of all rate constants for deactivation. These parameters have been extensively discussed in earlier chapters. We note in passing that the constants with extreme values in Eq. (12.1) disappear if one expresses the absorption (excitation) spectrum of the acceptor in terms of the molecular absorption cross-section, o (2) = 1017ln[10] Njy x e (2)(nnr/moleculc). 

The basic instrumentation used for spectrometric measurements has already been described in the previous chapter (p. 277). Methods of excitation, monochromators and detectors used in atomic emission and absorption techniques are included in Table 8.1. Sources of radiation physically separated from the sample are required for atomic absorption, atomic fluorescence and X-ray fluorescence spectrometry (cf. molecular absorption spectrometry), whereas in flame photometry, arc/spark and plasma emission techniques, the sample is excited directly by thermal means. Diffraction gratings or prism monochromators are used for dispersion in all the techniques including X-ray fluorescence where a single crystal of appropriate lattice dimensions acts as a grating. Atomic fluorescence spectra are sufficiently simple to allow the use of an interference filter in many instances. Photomultiplier detectors are used in every technique except X-ray fluorescence where proportional counting or scintillation devices are employed. Photographic recording of a complete spectrum facilitates qualitative analysis by optical emission spectrometry, but is now rarely used. 

The basic instrumentation used for spectrometric measurements has already been described in Chapter 7 (p. 277). The natures of sources, monochromators, detectors, and sample cells required for molecular absorption techniques are summarized in Table 9.1. The principal difference between instrumentation for atomic emission and molecular absorption spectrometry is in the need for a separate source of radiation for the latter. In the infrared, visible and ultraviolet regions, white sources are used, i.e. the energy or frequency range of the source covers most or all of the relevant portion of the spectrum. In contrast, nuclear magnetic resonance spectrometers employ a narrow waveband radio-frequency transmitter, a tuned detector and no monochromator. 

When electromagnetic radiation passes through transparent matter, some of it is absorbed. Strong absorption will occur if there is a close match between the frequency of the radiation and the energy of one of the possible electronic or molecular absorption processes characteristic of the medium. A plot of absorbance (A) against wavelength (X) or frequency (v) for a particular material is termed an absorption spectrum. The complexity of the absorption spectrum depends on whether atomic (simple, with a few sharp absorption bands) or molecular (complex, with many broad bands) processes are responsible. 

What is an absorption spectrum What is the difference between a molecular absorption spectrum and an atomic absorption spectrum and why does this difference exist ... 

Why is a molecular absorption spectrum called a molecular fingerprint ... 

Imagine an experiment in which the molecular absorption spectrum of a particular chemical species is needed. Which instrument is preferred—a single-beam or double-beam instrument Why ... 

Measure the molecular absorption spectrum in the visible region (400 to 700 nm) of each of the standards. Also measure the molecular absorption spectrum of the heptane layer in the separatory funnel (the extract). You can fill the cuvette conveniently by using a dropper to draw the solution (top layer) out of the separatory funnel. Obtain the maximum absorbance for each and create the standard curve. Determine the concentration of iodine in the extract. 

An absorption spectrum is the plot of absorbance vs. wavelength—the unique pattern of absorption useful for qualitative analysis. A molecular absorption spectrum is of the continuous variety, while an atomic absorption spectrum is a line spectrum. Only specific wavelengths get absorbed by atoms because only specific energy transitions are possible (no vibrational transitions—only electronic). Both vibrational and electronic are possible with molecules, and thus all wavelengths get absorbed to some degree. 

It is slow and tedious for an experiment in which a molecular absorption spectrum is measured. It is slow and tedious because the wavelengths are manually scanned in small increments, and each time the wavelength is changed, the calibration step with the blank needs to be performed due to the variability of light intensity from the light source at the different wavelengths. 

Do not have to continually replace sample with blank when obtaining a molecular absorption spectrum 2) errors due to fight source and detector fluctuations are minimized and 3) accurate rapid scanning of wavelengths is possible. 

Molecular absorption spectroscopy deals with measurement of the ultraviolet-visible spectrum of electromagnetic radiation transmitted or reflected by a sample as a function of the wavelength. Ordinarily, the intensity of the energy transmitted is compared to that transmitted by some other system that serves as a standard. 

The IR spectrum of thieno[2,3-6]thiophene (1) was first reported by Godart in 1937 in work devoted to the UV and IR spectral analysis of thiophene, thienothiophene 1, and benzo[6]thiophene. Comparison of spectral features in the 4000-11,000 cm" region of thiophene and benzene, thieno[2,3-6]thiophene (1) and naphthalene, and benzo[6]-thiophene, benzene, and naphthalene demonstrated, in Godart s opinion, the similarity of IR spectra (in this region) of thiophene, thienothiophene 1, and benzo[6]thiophene, on the one hand, and benzene, thienothiophene 1, and naphth ene, on the other hand. The molecular absorption coefficients of benzene and thiophene, as well as of naphthalene and thienothiophene 1, were also similar. 

In the absorption spectra of nanoparticles of CdSe and other semiconductors, not only can the shift in wavelength be observed, but there are also bands corresponding to absorption to discrete energy levels in the conduction band. For example, 11.5 nm diameter particles of CdSe have an absorption spectrum that shows an almost featureless edge, but particles of diameter 1.2 nm show features resembling molecular absorption bands shifted about 200 nm to shorter wavelengths, as depicted in Figure 11.8. 

FIGURE 11.8 The absorption spectrum of 11.5 nm diameter particles of CdSe has an almost featureless edge, but particles of diameter 1.2 nm show features resembling molecular absorption bands shifted about 200 nm to shorter wavelengths. 

Molecular absorption of visible or ultraviolet light usually excites electrons into higher energy states. Chemicals used as dyes absorb only a portion of the visible spectrum, and thus appear colored. Many of these dyes also generate spontaneous emission... 

The probability profile on the right is indicative of the absorption characteristic of each individual chromophore. Note the use of the symbols c and a to indicate the half amplitude points of this profile. Note also that the difference in two exponential profiles remains an exponential profile, albeit with modified parameters. These parameters, and the nominal center energy, represent the conjugated-dipole-molecular absorption band of the Rhodonines. This spectrum is frequently reported in the literature for the chromophores of vision. It is usually attributed to the putative rhodopsin. However, the presence of opsin is not required. Only a conventional concentration of Rhodonine is required to record this isotropic spectrum since it is the only feature in the visual range of the spectrum for these materials. 

Figure 5.5.9-2 The energy band structures of the Rhodonines in the liquid crystalline state with the relevant profiles and the associated difference in energy profile that describes the molecular absorption spectrum of the molecules when in the liquid crystalline state. See text.

As discussed above, there are three pertinent situations with respect to the absorption spectrum of the retinoids in the visual range. For most of the retinoids, there is no significant visible spectrum absorption. The dominant mode of molecular absorption is due to bulk excitation and this absorption is most prominent in the ultraviolet. The relevant visual band absorption cross section is zero. 

Figure 5.5.9-3 Caricature of the individual S-, M- L-spectral components of functional importance in long wavelength trichromatic vision combined with the spectrum related to dipole-molecular absorption (solid line). The vertical scale is linear and normalized. The width of the three chromatic spectra are shown at one fourth of their functional width as reported for the human eye. The dipole-molecular spectrum is shown at normal width. See text.

Note as the discussion proceeds, the near total independence of the functional absorption spectra of the Rhodonines, based on their resonant absorption cross section, from the nature of the ionone ring and whether the chromogen was Vitamin Al, A2 or A3. While the dipole-molecular absorption of the Rhodonines in the visual spectrum may reflect a small change relative to the parent chromogen, the enhancement related to resonant-molecular absorption does not. 

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. 

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