Alignment Analyzer

Another drawback of 3D molecular descriptors worth consideration is that they are sensitive to the position and orientation of the molecular structures in space. Tropsha and Cho have demonstrated that the results of conventional CoMEA are sensitive to the overall orientation of superimposed molecules. They show that for a given alignment analyzed in different orientations, the single (f value obtained from standard CoMEA will most likely fall within the region of the highest frequency of q. Therefore, they propose cross-validated guided region selection for CoMEA... 

The deviation from planarity that is present in a structure such as 1 raises the question of how severely a conjugated system can be distorted from the ideal coplanar alignment of p orbitals and still retain aromaticity. This problem has been analyzed by determining the degree of rehybridization necessary to maximize p orbital overlap in 1. It is found that rehybridization to incorporate fractional amounts of s character can improve orbital alignment substantially. Orbitals with about 6% s character are suggested to be involved... 

Pulsed deuteron NMR is described, which has recently been developed to become a powerftd tool for studying molectdar order and dynamics in solid polymers. In drawn fibres the complete orientational distribution function for the polymer chains can be determined from the analysis of deuteron NMR line shapes. By analyzing the line shapes of 2H absorption spectra and spectra obtained via solid echo and spin alignment, respectively, both type and timescale of rotational motions can be determined over an extraordinary wide range of characteristic frequencies, approximately 10 MHz to 1 Hz. In addition, motional heterogeneities can be detected and the resulting distribution of correlation times can directly be determined. 

We have analyzed the run-to-run reproducibility of the two-dimensional capillary electrophoresis system. The relative standard deviation in both MECC and CSE dimensions is better than 2% for the 50 most intense components in a set of five runs, and a simple gel alignment algorithm provides a twofold improvement in precision. 

Nakano, T., Kaibara, K., Tabata, Y., Nagata, N., Enomoto, S., Marukawa, E. and Umakoshi, Y. (2002) Unique alignment and texture of biological apatite crystallites in typical calcified tissues analyzed by microbeam X-ray diffractometer system. Bone, 31, 479-487. 

The crystal lattices of a series of ternary alkali metal-silver acetylenediide [M Ag(C=C)] (M1 = Li 161, Na, K 162, Rb, Cs 163) have been analyzed by Ruschewitz and co-workers using X-ray powder diffraction.209 Neutron powder diffraction experiments have also been performed on 161-163 for obtaining precise bond lengths. It has been found that for 161 and 162, the [Ag(C C)] chains were packed parallel to each other, whereas for 163, they were aligned in layers that were rotated by 90° with respect to each other (see Figure 51). 

Martin observed an extremely facile thermal decomposition of bisperester 53, which gave 54 (Scheme 7).74 The decomposition proceeds via a transition state 55, with the simultaneous participation of the cr (0 O)—np(S)—a (0-0) type.74 The transition state can be draw by the 5c 6e interaction. Alvalez discussed the structure and the stability of Br42, together with neutral Br4.lla The dianion could be analyzed by the 4c 6e model, if the four atoms align linearly with suitable distances. Farnham investigated the fluorine-bridged linear C-I- -F- I C interaction based on 5c-6e.llb... 

Cl).80 The linear alignments of E2A2 could be analyzed by the 4c-6e model, based on the results shown in Table 4. 

The linear bond in 12 Br4 is analyzed by the 6c 8e model. Linear Br-Se-Br 3c-4e bonds in 1 Br2 interact mutually to give 12 Br4, which contains the linear alignment of the six Se2Br4 atoms. The linear bond in 12 Br6 is analyzed... 

Fig. 4. Multiple sequence alignment of six distinct SH2 domain sequences. The SH2 domain notifiers are given on the left, the bottom line represents the consensus sequence as analyzed from the alignment. Highly conserved sequence positions are marked with capital letters. The sequential position of the major secondary structure elements (helices and sheets) are indicated by boxes...

Freely suspended films provide a perfect homeotropic alignment of smectic LCs since the layers always orient parallel to the LC/air interface.33 The director structure in such films can then be determined by analyzing the optical properties of plane-polarized light reflected from the surface of the films at a slightly oblique angle.34 The technique gains additional power when electrodes are added to the setup, allowing observation of the behavior of the films in the presence of an electric field parallel to the plane of the film.35... 

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