Aligned substructures

Polar molecules like II2O show apparent polymerization to an extent quite impossible in the gas phase at low pressures. The dipole field interaction, which is of the order of 1 ev., results in an artificial multilayer physical adsorption at pressures and temperatures where ordinarily only a minute fraction of the first layer would exist. Since multilayer adsorption is quite liquid-like, the high degree of polymerization can be explained. It is interesting to note that at low fields individual peaks show some substructure, which could be due to alignment differences at the time of ionization or could correspond to ionization from different layers within the adsorbate. It is hoped to study physical adsorption near the condensation point at low pressure with nonpolar rare gas atoms to see if layer structure can be elucidated in this way. 

Macroscopically, elastin appears to be an amorphous mass. Ultrastruc-tural electron microscopy studies reveal that elastin has a fibrillar substructure comprised of parallel-aligned 5nm thick filaments that appear to have a twisted ropelike structure (Gotte et al., 1974 Pasquali-Ronchetti et al, 1998). A variety of techniques have been used to resolve these filaments, including negative staining electron microscopy of sonicated fragments of purified elastic fibers (Serafini-Fracassini et al., 1976), freeze... 

Fig. 8. Generation of the form of the helical diffraction pattern. (A) shows that a continuous helical wire can be considered as a convolution of one turn of the helix and a set of points (actually three-dimensional delta-functions) aligned along the helix axis and separated axially by the pitch P. (B) shows that a discontinuous helix (i.e., a helical array of subunits) can be thought of as a product of the continuous helix in (A) and a set of horizontal density planes spaced h apart, where h is the subunit axial translation as in Fig. 7. This discontinuous set of points can then be convoluted with an atom (or a more complicated motif) to give a helical polymer. (C)-(F) represent helical objects and their computed diffraction patterns. (C) is half a turn of a helical wire. Its transform is a cross of intensity (high intensity is shown as white). (D) A full turn gives a similar cross with some substructure. A continuous helical wire has the transform of a complete helical turn, multiplied by the transform of the array of points in the middle of (A), namely, a set of planes of intensity a distance n/P apart (see Fig. 7). This means that in the transform in (E) the helix cross in (D) is only seen on the intensity planes, which are n/P apart. (F) shows the effect of making the helix in (E) discontinuous. The broken helix cross in (E) is now convoluted with the transform of the set of planes in (B), which are h apart. This transform is a set of points along the meridian of the diffraction pattern and separated by m/h. The resulting transform in (F) is therefore a series of helix crosses as in (E) but placed with their centers at the positions m/h from the pattern center. (Transforms calculated using MusLabel or FIELIX.)...

For drawing similar molecules in a similar way, the Feature Tree comparisons are useful as they detect similarity beyond mere substructure identity and they also provide a mapping that can be viewed as alignments of molecule fragment pairs. 

The method is based on three fundamental phases. The first phase consists in the generation of low-energy conformations for each molecule and in the choice of one conformer as the one most likely to be bioactive all selected conformers are aligned, along with the identified pharmacophore or a substructure common to all molecules in the data set. A molecule pose is a conformation of the molecule in a particular alignment. 

Comparative molecular field analysis (CoMFA) [24] is a popular 3D-QSAR technique that uses PLS as the data analysis method. In CoMFA, compounds are aligned to a common substructure, and the magnitudes of the steric and... 

Unlike the common grid-based QSAR techniques, FRAU expresses features of molecules having different size and substructures since they do not require alignment of molecules. 

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