Transition structures envelope-shaped

Sigmatropic rearrangements, like the [2,3]-Wittig rearrangement 6.83 and its sulfur and aza analogues, are drawn for the general case in Fig. 6.13, where X=0, S, SR+, or NR2+. An envelope-shaped transition structure is almost always involved, because this allows the smooth development of head-on overlap... 

The absorption spectrum of phenylalanine is shown in Fig. 1. The low intensity absorption peak centered slightly below 2600 A corresponds to a forbidden x it transition. Vibrational fine structure is quite evident in this region. Aside from increased blurring of the fine structure which is to be expected on passing into successively more polar media, change of solvent effects little change in the general size, shape, and location of the absorption envelope. 

If two or more transitions overlap, the quantitative interpretation of the MCD spectrum becomes much more difficult and computational curve fitting that requires simple band shapes is needed. Often, the vibrational structure of the MCD spectrum, which will in general be different from the one in the absorption spectrum, will be so pronounced that this assumption is not fulfilled. Although uncommon, there are some cases known where some sections of the vibrational envelope associated with a single electronic transition are positive and some negative. Thus, the appearance of both positive and negative MCD peaks in a spectral region does not necessarily mean that... 

We note that such a transition from a circular to a quadratic envelope of the crystals has also been reproduced by computer simulations [13,14]. There, this transition is due to the reduction of the growth front nucleation probability. Wliile the disk-like pattern consists of multiple crystals, the square-shaped pattern represents a single crystal. We thus assume that, for the given film thickness, we observed a transition from a poly crystalline structure to a single crystal within the temperature interval from 45 to 50°C. 

In order to visualize how dendritic crystals grow and how a square-shape envelope is formed from such dendritic structures, we have superposed two images from the same crystal taken at an interval of 95 sec (see Fig. 11.8). As we want to focus on single crystals only, we have chosen a rather thin film of about 40 nm in order to avoid growth front nucleation (GFN) [13,14j. GFN depends on the number of molecules present. Thus, in such thin films the transition from poly-crystals to single crystals can occur at lower temperatures than in the 108 nm thick 111 ins discussed above. 

Thermal titration circular dichroism spectroscopy continued the results obtained by fluorescence spectroscopy. Only subtle changes were observed in the shape of the spectral envelope, and a monotonic decrease in helix content was observed (Figure 6B). Deconvolution of the spectra reveal that the protein is about 30% helix in the range of 2-40 C, but even at 90 C, the peptide retains nearly 50% of its initial helix character. Apparently, pre-pro-GnRH does not pass through a transition state as a function of temperature. Rather the protein appears to flex, resulting in minor and subtle (and probably localized) changes in secondary structure. 

The structure of the upper ferriin envelope is shown in Figure 5C by a 3D perspective display technique [27]. In this representation the shape of the core region of each spiral resembles that of a chemical tornado . One finds that inside the core (diameter, 0.7 mm) a transition takes place from the rotation center - a singular site (diameter < 30 /xm) at which the concentration of the catalyst remains quasi-stationary - to the surrounding area, where waves attain their full amplitude between maximum oxidation and partial reduction of the catalyst. For the given initial chemical composition the location of this singular site remains remarkably stable in time [36]. In Figure 5D the location of this rotation center is marked for an individual spiral. 

A molecule has three principal moments of inertia for rotation about its three principal axes. If at least one of these moments is very small, the IR spectrum in the gas phase shows a great deal of fine structure on both sides of its vibrational bands. The 950 cm band in this spectrum is a good example. If the moments of inertia are a little larger or the instrumental resolution is a little poorer, only the envelope of this fine structure is seen. One then observes an apparent doublet (at 3120 and 3078 cm ) or triplet (e.g., the bands centered at 2990, 1890, and 1443 cm ). If the moments of inertia are still larger, even this detail is lost, and one observes the usual bell-shaped curve, as in liquids. For both doublets and triplets, the center frequency is the pure vibrational transition and is the wavenumber that should be used in assignments. From the fine structure observed in this spectrum, one knows immediately that the sample is a very light molecule and therefore a small one. Even propane and benzene are too large. 

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