Local Molecular Alignment

It is known from experience that only chiral molecules have the ability to rotate the plane of polarization. This observation suggests that molecular chirality is a manifestation of residual orbital angular momentum, and vice versa. When an achiral molecule is placed in a magnetic field the molecular magnetic vectors are aligned in the diection of the field and not along the local molecular symmetry directions. The molecule therefore acquires a... 

The negative Ni is the result of the coupling of molecular tumbling under flow and the local molecular-orientation distribution. At low shear rates, the director tumbles with the flow and Ni will be positive. At intermediate shear rates, nonlinear viscoelastic effects are important. The director tumbling competes with the steady director alignment along... 

In a molecule such as ethane H C-CH, each carbon atom has four sp hybrids. Between the two carbon nuclei, there is a localized molecular orbital built up from two hybrids, one for each carbon atom, and pointing at one another. The alignment of the hybrid axes gives the most stable system. Indeed the orbital overlap is maximum and therefore the interaction between atomic orbitals is the strongest The corresponding energy is the highest in absolute... 

The definitions of the dielectric tensor components in the local molecular frame, and main alignment structures sandwiched SmC materials in thin films. For testing the dielectric constant, small electric fields, not enough to cause any reorientation, are applied across the plates. 

Altschul S F, W Gish, W Miller, E W Myers and D J Lipman 1990. Basic Local Alignment Search Tool. Journal of Molecular Biology 215 403-410. 

Oiengo C A and W R Taylor 1993. A Local Alignment Method for Protein Structure Motifs. ]ourr Molecular Biology 233 488-497. 

The Surflex-Sim method operates significantly differently [104]. Each of the molecules is surrounded by a set of observer points that characterizes the local character of the surface and potential interactions. Two similar molecules will have a common subset of comparable observer points. A optimal alignment occurs when the differences in pharmacophore character and molecular surface inferred from the observer points are minimized between two molecules. To speed up the algorithm, large molecules can be fragmented into parts which are then compared, and then tested for consistency. This feature also makes the method capable of identifying alignments when one molecule is much smaller than the other. 

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