Alignment of molecules

A range of physicochemical properties such as partial atomic charges [9] or measures of the polarizabihty [10] can be calculated, for example with the program package PETRA [11]. The topological autocorrelation vector is invariant with respect to translation, rotation, and the conformer of the molecule considered. An alignment of molecules is not necessary for the calculation of their autocorrelation vectors. 

C and T Lengauer 2000. Computational Methods for the Structural Alignment of Molecules. nal of Computer-Aided Molecular Design 14 215-232. 

While cooling the melt to solidify in a processing operation, alignment of molecules controlling the crystallinity and overall morphology depends on the molecular structural parameters of PEs. 

The angular momentum conservation equation couples the viscous and the elastic effects. The angular profiles of the director and the effective viscosity data are computed for one set of material parameters based on published data in literature. The velocity profiles are also attained from the same dataset. The results show that the alignment of molecules has a strong influence on the lubrication properties. 

Lemmen, C. and Lengauer, T. Computational methods for the structural alignment of molecules. 

Klebe, G. Structural alignment of molecules.3D QSAR in Drug Design. ESCOM Science Publishers, Leiden, Netherlands, 1993, 173-199. 

Parretti, M.F., Kroemer, R.T., Rothmann, ).H., and Richards, W.G. Alignment of molecules by the M onte C arlo optimization of molecular similarity indices./. Comput. Chem. 

Lemmen, C. and Lengauer, T. (2000) Computational methods for the structural alignment of molecules../. Comput.-Aided Mol. Design 14, 215-232. 

As a consequence of this almost perfect alignment of molecule structures, such polyamides are able to orientate in solution and to form liquid crystalline phases (see Sect. 1.3.4). Out of these solutions one obtains fibers of poly(p-phenylene terephthalamide) (PPTA) having 5-10-fold higher values for stiffness and strength as the all-mefa linked polymers. In addition, PPTA crystallizes, whereupon the fibers achieve an extraordinary temperature resistance in a nitrogen atmosphere they decompose at temperatures above 550 °C without melting. 

The local direction of alignment of molecules in liquid crystals is described by a unit vector 7j, called the director, which gives the direction of the preferred axis at each point... 

F. Rosca-Pruna and M. J. J. Vrakking. Revival structures in picosecond laser-induced alignment of molecules. I. Experimental results. J. Chem. Phys., 116(15) 6567-6578 (2002). 

Crystals. In Section III.D, we noted that the photobehavior of molecules on the surface and in the interior of crystals need not be the same. In addition the arrangement and excited state energy of molecules at defect sites are often not the same as in the bulk of the crystal. Indeed, there are a number of examples wherein the stereochemistry of photoproducts cannot be predicted on the basis of the molecular alignment of molecules in the bulk of a crystal [214],... 

Alignment method does the program require pre-alignment of molecules On what basis are the molecules aligned together ... 

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. 

Sinha, M.P., Caldwell, C.D. and Zare, R.N. (1974). Alignment of molecules in gaseous transport Alkali dimers in supersonic nozzle beams, J. Chem. Phys., 61, 491-503. 

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