Molecular replacement normal modes

In the first part to follow, the equations of motion of a soft solid are written in the harmonic approximation. The matrices that describe the potential, and hence the structure, of the material are then considered in a general way, and their properties under a normal mode transformation are discussed. The same treatment is given to the dissipation terms. The long wavelength end of the spectral density is of interest, and here it seems that detailed matrix calculations can be replaced by simple scaling arguments. This shows how the inertial term, usually absent in molecular problems, is magnified to become important in the continuum limit. 

Siihre, K. and Sanejouand, Y. H. (2004a) On the potential of normaL-mode analysis for solving difficult molecular-replacement problems. Acta Crystallogr. D 60, 796-799. 

Finally, some strategies are described which are employed to interpret the infrared difference spectra at a molecular level. The first goal is the identification of bands caused by the protein and cofactors (chromophore, substrate, etc.). In the case of retinal proteins in which the retinal chromophore can be removed and replaced by an artificial one, the method of isotope labeling has provided detailed information. Not only does it help to identify the chromophore bands, but it also enables their assignment to specific normal modes from which structural information can be derived. Of course, a similar technique should be applicable to quinones... 

Because IR absorption spectra are generated by transitions between vibrational states of sample molecules and the frequency of normal modes vibration depends (in addition to the force constants associated with deformations of the molecule) of the masses of atoms, it is expected that the replacement of atoms in molecular structure sample with different isotopes of the respective atoms (isotopic marking of the molecule) to induce dramatic changes of the IR absorption spectrum of the sample. 

The AC usually has several characteristics. The molecules going over the barrier are in equilibrium with all the other reactant molecules, and the AC can be treated as a normal molecular species except that one of its vibrational modes is missing and must be replaced by translation along the reaction coordinate. Also, the rate of formation of product C through the AC is the... 

Although no clinical testing of 5-trifluoromethyl-2 -deoxyurldine, i ich is reported to be a more potent analog of lUDR, has been carried out, molecular level studies have shown similar modes of action as this moiety is incorporated into vaccinia virus DNA replacing thymidine, and the resulting virions differ in morphology from normal . 

When operating in this cold plasma mode, the dominant species in the background spectrum are NO", 02", and HjO, replacing the normally observed Ar species. The magnitude of the °Ar 0 molecular species at m/z 56 can also be reduced to levels suitable for the determination of Fe. For example, if the ion current at m/z 56 under normal operating conditions is about 10 Hz, it is typically reduced to about 20 Hz under cold plasma conditions. 

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