Interaction with overall rotation

The main difficulty in theoretical predictions of the PRE effects is caused by the description of electron spin relaxation. The transient ZFS interaction is usually considered as present in every complex with S> 1 and its modulation is assumed to provide the dominant mechanism for the electron spin relaxation. The commonly used pseudorotation model 27,85,86), described earlier, has two advantages it captures the essential physics of electron spin relaxation (i.e., the fact that relaxation can be caused by motions faster than the overall rotation of the paramagnetic complex, provided that these motions displace the principal axis of the ZFS), and it leads to relatively straightforward mathematical formulation. The assumption that the... 

With the seven-helix bundle construct in hand, we turned our attention to incorporation of the three extracellular (EC) loops. The cytoplasmic loops were disregarded because they would not be involved in molecular recognition between the receptor and the SFLLRN ligand. Extracellular loop 3, the smallest of the three EC loops, was added first via the loop-search routine in the Biopolymer mode of Sybyl. The loop backbone choices found in the Brookhaven PDB were examined in 3-D and selected on the basis of their fit to the overall protein structure. After the side chains were added to EC3, some of them had to be rotated to avoid unfavorable steric interactions with other parts of the protein. Then, the entire protein was energy minimized. Extracellular loop 1 was then added, followed by EC2, and each time the loop selection was made after analyzing the protein in 3-D. Side chains of amino... 

As discussed in the introduction to this chapter the final rotation of the photofragment reflects three sources overall rotation of the parent molecule, which is preserved in the electronic excitation process, internal bending or torsional motion in the electronic ground state, and final state interaction. The latter two sources have been analyzed in Sections 10.1-10.4. The influence of overall rotation will be discussed in this section. Its relative contribution increases gradually with the magnitude of the total angular momentum J and therefore it increases with the temperature of the molecular sample. As we will demonstrate below, the conversion of overall rotation of the parent molecule in the electronic ground state into... 

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