Structure superposition dependent

Fig. 1. Superposition of three crystal structures of cAMP-dependent protein kinase that show the protein in a closed conformation (straight line), in an intermediate conformation (dashed line), and in an open conformation (broken line). The structures were superimposed on the large lobe. In three locations, arrows identify corresponding amino acid positions in the small lobe.

Figure 6.13 shows the Mossbauer spectra of ferritin [51], which is an iron-storage protein consisting of an iron-rich core with a diameter around 8 nm with a structure similar to that of ferrihydrite and which is surrounded by a shell of organic material. At 4.2 K essentially all particles contribute to a magnetically split component, but at higher temperatures the spectra show the typical superposition of a doublet and a sextet with a temperature dependent area ratio. At 70 K the sextet has disappeared since all particles have fast superparamagnetic relaxation at this temperature. 

Because the time scale of the Raman scattering event ( 3.3 x 10-14s for a vibration with wavenumber shift 1000 cm-1 excited in the visible) is much shorter than that of the fastest conformational fluctuations in biomolecules, the ROA spectrum is a superposition of snapshot spectra from all the distinct chiral conformers present in the sample. Together with the dependence of ROA on chirality, this leads to an enhanced sensitivity to the dynamic aspects of biomolecular structure. The two-group model provides a qualitative explanation since it predicts ROA intensities that depend on absolute chirality in the form of a sin x dependence... 

In what I broadly regard as structure (essentially quantum theory), the equation that epitomizes the transition from classical mechanics to quantum mechanics, is the de Broglie relation, k = hip, for it summarizes the central concept of duality. Stemming from duality is the aspect of reality that distinguishes quantum mechanics from classical mechanics, namely superposition y = y/A + y/R with its implication of the roles of constructive and destructive interference. Then of course, there is the means of calculating wavefixnctions, the Schrodinger equation. For simplicity I will write down its time-independent form, Hip = Eip, but it is just as important for a physical chemist to be familiar with its time-dependent form and its ramifications for spectroscopy and reaction. 

In the absence of electron donor-acceptor interactions, the London dispersive energy is the dominant contributor to the overall attractions of many molecules to their surroundings. Hence, understanding this type of intermolecular interaction and its dependency on chemical structure allows us to establish a baseline for chemical attractions. If molecules exhibit stronger attractions than expected from these interactions, then this implies the importance of other intermolecular forces. To see the superposition of these additional interactions and their effect on various partitioning phenomena below, we have to examine the role of dispersive forces in more detail,... 

J.-C. Lorquet The energy resolution of Prof. Schlag s spectra is indeed impressive. But would there be an advantage in recording the spectra at a low resolution, just good enough to resolve the vibrational structure, in order to get a better appreciation of the intensity pattern Could then that pattern be interpreted as a superposition of several progressions Also, can one rationalize any observed dependence of the intensities on experimental parameters of the ion source ... 

T. P. Softley There is little doubt that in most ZEKE experiments using nanosecond lasers the Rydberg level structure is so dense that a coherent superposition of levels is populated initially, and the correct description of the dynamics should be a time-dependent one. It is possible that some control over the dynamics could be achieved using some of the methods described earlier in the conference, for example, simultaneous excitation through three-photon and one-photon transitions, using third-harmonic generation. 

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