Chains, conformations tagged

The ability to fluorescently tag individual DNA molecules and visualize their dynamics in these flows can considerably enhance the information we obtain from these flows. Numerous single molecule visualization experiments have already led to significant advancements in our understanding of polymer chain dynamics in viscous flows. In addition, these experiments have recently been combined with Brownian dynamics simulations, which simulate the motion of bead-rod chains in viscous flows and can quantitatively predict the chain conformation for given flow conditions. This powerful combination has allowed for the validation of detailed molecular scale physics, as well as the development of new physical insights. These conclusions are described in a recent review [10] we summarize a few of the salient conclusions here. 

When a flexible chain is attached to a fluorescent dye, the rotational diffusion of the dye is slowed down, but as the chain is extended, approaches an asymptotic limit, since the whole of the chain does not participate in the motion of the dye (6, 7). The extent to which the rotational diffusion of the dye is impeded is then a measure of the rigidity of the chain. If the middle of the chain is tagged with a fluorescent label, the rotational relaxation will reflect, in principle,both the local conformational transition and the rotation of the molecule as a whole. Withp. and p characterizing these two processes, the observed relaxation time will be (8)... 

Fig. 7. Illustration of a polymer chain (the tagged chain) confined in the fictitious tube of diameter d formed by the matrix. The contour line of the tube is called the primitive path having a random-walk conformation with a step length a=d. The four characteristic types of dynamic processes (dotted arrow lines) and their time constants Zs, Zg, Zr, and za defined in the frame of the Doi/Edwards tube/reptation model are indicated...

For molecular properties of the TAG polymorphs, local molecular structural information such as methyl-end group, olefinic conformation, and chain-chain interaction are unveiled by infrared (IR) spectroscopy, especially Fourier-transformed infrared spectroscopy (FT-IR) (23, 24). Compared with a pioneering work by Chapman (25), great progress has been achieved by using various FT-IR techniques, such as polarized transmission FT-IR, reflection absorption spectroscopy (RAS), and attenuated total reflection (ATR) (26-28). 

There are two types of molecular conformation of TAG molecules in the crystal (39) tuning fork and chair, as shown in Figure 6. In a tuning fork conformation, the two outer acyl chains (sn-1 and sn-3) point in one direction and the middle acyl chain (sn-2) in the opposite direction. In contrast, a chair conformation has the two neighboring acyl chains (sn-1 and sn-2) pointing in one direction and the third acyl chain (sn-3) in the opposite direction. In the (3 form of CCC, LLL, and PPP, asymmetric mning fork conformation was revealed. 

The asphericity of instantaneous conformations of chain molecules is also demonstrated by experiments with tagged polymers ... 

In this chapter, molecular factors affecting structural behavior of fat polymorphism are discussed in terms of internal influences of the TAG molecules. In particular, the influences of fatty acid compositions and their positions connected to glycerol carbons on the polymorphism of fat crystals are of primary concern. It has been known that the fats with simple and symmetric fatty acid compositions tend to exhibit typical oc, P, and P forms, whereas those with asymmetric mixed-acid moieties often make the P form more stable (1,9). In the mixed-acid TAG containing unsaturated fatty acid moieties, the number and conformation of the double bond, cis or trans, give rise to remarkable influences on the polymorphic structures (10-12). The TAG containing different saturated fatty acids with different chain-lengths also revealed quite diversified polymorphism (13-15). Therefore, it may be worthwhile now to discuss the molecular aspects of the polymorphism of fats. This consideration may also be a prerequisite for molecular design of structured fats, in combination with nutritional and metabolic properties. 

Figure 2 illustrates diversity in the fatty acid types and compositions of the TAG. The mono-acid and mixed-acid TAG are defined, respectively, on whether the fatty acid chains are of the same fatty acid molecules or not. Even for the monoacid TAG, the diversity maintains in chainlength and parity (odd or even numbers of carbon atoms) of the fatty acids, the number and position of the double bond and the conformation of the double bond, cis or trans, etc. As for the mixed-acid TAG, polymorphic diversity is superimposed over that of the mono-acid TAG in the form of sn (stereo-specific numbered) position. 

The molecular structure of PPM P 2 shown in Figures 5 and 6 is a good example to understand the effect of combined interactions of the methyl end stacking, the lateral chain packing, and the glycerol conformation on the structural stabilization of the TAG crystals. For the moment, it is rather difficult to assess how these interactions cooperate and which interaction plays the dominant role. It has been widely observed that the P form is stabilized when a TAG contains different kinds of fatty acid moieties which are connected to the glycerol carbons in an asymmetric manner, like PPM (9). 

Due to the sensitivity of electronic excitation transport to the separation and orientation of chromophores, techniques which monitor the rate of excitation transport among chromophores on polymer chains are direct probes of the ensemble average conformation (S). It is straightforward to understand qualitatively the relationship between excitation transport dynamics and the size of an isolated polymer coil which is randomly tagged in low concentration with chromophores. An ensemble of tagged coils in a polymer blend will have some ensemble averaged root-mean-squared radius of gyration,... 

However, it can be rationalized when we postulate a rather specific conformational behavior of An-tagged shell-forming chains, which is depicted in Fig. 16. 

In a series of simulation papers, we used MD for studying the conformational behavior of linear and branched PEs. In one study, we addressed the time-resolved fluorescence anisotropy decays from fluorescently tagged weak PE chains in aqueous media, which we had experimentally studied earlier (see Sect. 3.2). We wanted to investigate and explore the relationship between the conformational behavior of the PE and the experimentally observable fluorescence anisotropy decays. 

Also, fluorous-tagged oligosaccharides could form micelle-like structures and access different conformations depending on their concentration and the nature of the solvents. These properties could also be used to alter the reaction patterns of the carbohydrate moieties. Clearly, the strong electron-withdrawing properties and the solvent-dependent reaction kinetics of long perfluorinated chains have only begun to be fully exploited in the realm of carbohydrate chemistry. 

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