Molecular alignments

Utilization of the second-order nonlinearity of a material requires that the nonlinear molecules or side-groups be arranged in a non-centro-symmetric configuration. In the previous section it was pointed out that the more commonly used polymer deposition techniques resulted in an isotropic, amorphous film, and would thus show no second-order nonlinear properties. However, controlled deposition and/or subsequent processing can be employed to create a degree of molecular alignment. 

Generally the poling field is applied in one of two ways, referred to as two-electrode poling or corona poling (Fig. 4.25). As the names indicate, either two electrodes are placed on the film (and a field applied) or a base electrode is used with a corona needle probe (or array of probes). For a detailed discussion of poling see Chapter 5. 

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Seideman T 1995 Rotational excitation and molecular alignment in intense laser fields J. Chem. Phys. 103 7887-96... 

Althorpe S C and Seideman T 1999 Molecular alignment from femtosecond time-resolved photoelectron angular distributions nonperturbative calculations on NO J. Chem. Phys. 110 147... 

The melt index (MI) or melt flow index (MFT) is an inverse measure of viscosity. High MI implies low viscosity and low MI means high viscosity. Plastics are shear thinning, which means that their resistance to flow decreases as the shear rate increases. This is due to molecular alignments in the direction of flow and disentanglements. 

Eisert, F., Gurka, M., Legant, A., Buck, M. and Grunze, M. (2000) Detection of molecular alignment in confined films. Science, 287, 468-470. 

A. Pelzer, S. Ramakrishna, and T. Seideman, Optimal control of molecular alignment in dissipative media, J. Chem. Phys. in press. 

Nucleation can occur either homogeneously or heterogeneously. Homogeneous nucleation occurs when random molecular motion in the molten state results in the alignment of a sufficient number of chain segments to form a stable ordered phase, known as a nucleus. The minimum number of unit cells required to form a stable nucleus decreases as the temperature falls. Thus, the rate of nucleation increases as the temperature of the polymer decreases. The rate of homogeneous nucleation also increases as molecular orientation in the molten polymer increases. This is because the entropy difference between the molten and crystalline states diminishes as molecular alignment in the molten state increases. 

The antibody array that was self-assembled on the protein A array was also visualized in molecular alignment by AFM. The antibody array was in contact with a pH 7.0, 10 mM phosphate buffer. The AFM measurement was conducted at a controlled force of molecular size of the antibody was estimated as 7 nm in diameter. 

S.A. Lee, Y. Yoshida, M. Fukuyama, and S. Hotta, Phenyl-capped oligothiophenes novel light-emitting materials with different molecular alignments in thin films, Synth. Met., 106 39-43, 1999. 

S. Hotta, Y. Ichino, Y. Yoshida, and M. Yoshida, Spectroscopic features of thin films of thiophene/ phenylene co-oligomers with vertical molecular alignment, J. Phys. Chem. B, 104 10316-10320, 2000. 

It is therefore highly desirable to establish an algorithm that allows to consistently perform molecular alignment before concluding any degree of similarity between molecules. Generally speaking, two approaches are used routinely. 

This chapter has dealt with introducing the main concepts within a theory called MQS. It has discussed the different steps to be taken to evaluate and quantify a degree of similarity between molecules in some molecular set but also fragments in molecules. QSM provides a scheme that relieves the arbitrariness of molecular similarity by using the electron density function as the sole descriptor, in agreement with the Hohenberg-Kohn theorems. It also addressed the different pitfalls that are present, for example the dependence on proper molecular alignment. 

Provided that an optically active molecular aggregate is photochemically perturbed to change the state of molecular alignment, the effect of a chiral environment on an achiral chromophore incorporated in the molecular aggregate will be also altered. It has been known that polypeptides bearing photochromic side groups change their optically active properties as a result of photochromic reaction(10-12). This phenomenon is likely to be related to non-linear photoresponsiveness. 

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