Atom-based superimposition

Every nab molecule includes a frame, or handle that can be used to position two molecules in a generalization of superimposition. Traditionally,when a molecule is superimposed on a reference molecule, the user first forms a correspon-dance between a set of atoms in the first molecule and another set of atoms in the reference molecule. The superimposition algorithm then determines the transformation that will minimize the rmsd between corresponding atoms. Because superimposition is based on actual atom positions, it requires that the two molecules have a common substructure, and it can only place one molecule on top of another and not at an arbitrary point in space. 

Among the -> hyperstructure-based QSAR techniques, the MTD method is based on the approximate atom-per-atom superimposition of the n molecules of a -> data set in order to build a - hypermolecule (i.e. 3D - hyperstructure) hydrogen atoms, small differences in atomic positions, bond lengths and bond angles are neglected. The S vertices of the hypermolecule correspond to the positions of the data set molecule atoms [Simon et al, 1973 Simon and Szabadai, 1973 Simon et al., 1984]. 

Structure alignment The superimposition or fitting of the 3-D structures of molecules can be based on electron density, atom positions, molecular electrostatic fields, or secondary structures. This is a crucial step for 3D-QSAR and x-ray structure elucidation. 

Example The NICI mass spectrum of tetraiodoethene, I2C=CI2, has been obtained using isobutane reagent gas (Fig. 7.12). The negative molecular ion, NT, at m/z 531.6 has a relative intensity of just 0.15%, while the product of nucleophilic addition, [M+I]", tn/z 658.5, yields the base peak [77], Losses of T and I2 from M"" are also observed. The series of peaks at m/z 126.9, 253.8, and 380.7 corresponds to traces of iodine present as impurity of tetraiodoethene. The iodine is also ionized by both electron capture (EC, next paragraph) and iodide addition. The spectrum nicely exemplifies the superimposition of mass spectra of two components of a mixture. It is not always simple to tell the corresponding peaks apart accurate mass measurements or tandem mass spectrometry may be required. It is worth noting the mass defect introduced by the iodine and the C isotopic peak of merely 2% due to only two carbon atoms present. 

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