Tools for Studying Macromolecules

The dynamic mechanical thermal analyzer (DMTA) is an important tool for studying the structure-property relationships in polymer nanocomposites. DMTA essentially probes the relaxations in polymers, thereby providing a method to understand the mechanical behavior and the molecular structure of these materials under various conditions of stress and temperature. The dynamics of polymer chain relaxation or molecular mobility of polymer main chains and side chains is one of the factors that determine the viscoelastic properties of polymeric macromolecules. The temperature dependence of molecular mobility is characterized by different transitions in which a certain mode of chain motion occurs. A reduction of the tan 8 peak height, a shift of the peak position to higher temperatures, an extra hump or peak in the tan 8 curve above the glass transition temperature (Tg), and a relatively high value of the storage modulus often are reported in support of the dispersion process of the layered silicate. 

As explained previously, flow birefringence is due to the optical anisotropy created by the orientation of the macromolecules within a stress field. It will thus be an interesting tool for studying orientation and stresses. 

As in the case of aqueous solutions of electrolytes, computer studies have shed much light on the behaviour of aqueous solutions of non-polar and apolar molecules. They can give information on solute-solvent and solvent-solvent interactions in such solutions. This is a powerful tool for studying hydrophobic phenomena and is limited only by the accuracy of the assumed model and the quantities relevant to this model which are fed into the computer simulations. Simulation is of particular importance in the solution chemistry of large macromolecules and polymers which are extremely difficult to study experimentally, especially in dilute solutions. They are likely to be a dominant feature of the future study of hydrophobic hydration. 

These and related phenomena can be explained in terms of the thermodynamic theory of macrocyclics distribution, formulated by Jacobson and Stockmayer9) and its kinetic extension 10). The Jacobson-Stockmayer theory, relating the distribution of cyclic oligomers to the conformational probability of ring closure, does not take into account kinetic limitations and has mostly been used as a convenient tool for studying the conformation of macromolecules in solution s). A number of papers appeared in which distribution of cyclic oligomers was studied with this aim and which ignored mechanistic and kinetic aspects of the cyclization processes. 

SDSL EPR as pioneered by W. L. Hubbel and co-workers has become a powerful tool for studying structure and dynamics of macromolecules, in particular biological macromolecules as proteins, which do not necessarily contain endogenous paramagnetic centers [1 ]. While SDSL EPR is applied to many biomacromolecules, this chapter provides a rather selective insight into the field of SDSL EPR of proteins and is organized as follows. 

In this chapter, intermolecular forces that are the basis of self-assembly are considered in Section 1.2. Section 1.3 outlines common features of structural ordering in soft materials. Section 1.4 deals similarly with general considerations concerning the dynamics of macromolecules and colloids. Section 1.5 focuses on phase transitions along with theories that describe them, and the associated definition of a suitable order parameter is introduced in Section 1.6. Scaling laws are defined in Section 1.7. Polydispersity in particle size is an important characteristic of soft materials and is described in Section 1.8. Section 1.9 details the primary experimental tools for studying soft matter and Section 1.10 summarizes the essential features of appropriate computer simulation methods. 

Thus to date very little which is new has been learned about the properties of macromolecules themselves from the spectra of Rayleigh scattered light. However there are a number of promising but difficult pathways ahead particularly in the use of scattered light as a tool for studying reaction kinetics possibly on even large molecules. For an introduction to work along these lines the reader is referred elsewhere (5 ). 

Pecora,R. U t Scattering Spectroscopy as a Tool for Studying Macro-molecular Dynamics and Chemkal Kinetics. In Ihotodianistry of macromolecules, ed R. F. Reinisdr p. 145. New York nenum Press 1970. 

Dielectric spectroscopy is a valuable tool for studying the conformational and dynamic properties of polar macromolecules. The conformational features can be determined by dielectric relaxation strength measurements, whereas the dielectric spectrum provides information on the dynamics of the macromolecules. Phenomenological and molecular theories of dielectric permittivity and dielectric relaxation of polymers have also been developed to elucidate the experimentally observed phenomena. As Adachi and Kotaka have stressed (see Further reading), experimental information depends on each monomer s dipole vector direction as related to the chain contour. A classification of polar polymers into three categories was introduced by Stockmayer type-A polymers, where the dipole is parallel to the chain contour (Fig. 12.4), type-B, where it is perpendicular to the chain contour, and type-C, where the dipoles are located on mobile side groups. For type-A chains, the global dipole moment of each chain is directly proportional to the chain s end-to-end vector R. 

All the macroscopic properties of polymers depend on a number of different factors prominent among them are the chemical structures as well as the arrangement of the macromolecules in a dense packing [1-6]. The relationships between the microscopic details and the macroscopic properties are the topics of interest here. In principle, computer simulation is a universal tool for deriving the macroscopic properties of materials from the microscopic input [7-14]. Starting from the chemical structure, quantum mechanical methods and spectroscopic information yield effective potentials that are used in Monte Carlo (MC) and molecular dynamics (MD) simulations in order to study the structure and dynamics of these materials on the relevant length scales and time scales, and to characterize the resulting thermal and mechanical proper-... 

The results summarized above were obtained by using fluorescence based assays employing phospholipid vesicles and fluorescent labeled lipopeptides. Recently, surface plasmon resonance (SPR) was developed as new a technique for the study of membrane association of lipidated peptides. Thus, artificial membranes on the surface of biosensors offered new tools for the study of lipopeptides. In SPR (surface plasmon resonance) systemsI713bl changes of the refractive index (RI) in the proximity of the sensor layer are monitored. In a commercial BIAcore system1341 the resonance signal is proportional to the mass of macromolecules bound to the membrane and allows analysis with a time resolution of seconds. Vesicles of defined size distribution were prepared from mixtures of lipids and biotinylated lipopeptides by extruder technique and fused with a alkane thiol surface of a hydrophobic SPR sensor. 

It is exceedingly difficult to determine the molecular structure of a synthetic macromolecule. X-ray diffraction—the ultimate structural tool for small-molecule studies—yields only limited information for most synthetic high polymers, and crucial data about bond lengths and bond angles are difficult to obtain.47 However, that same information can be obtained relatively easily from single crystal X-ray diffraction studies of cyclic trimers, tetramers, and short-chain linear phosphazene oligomers. The information obtained may then be used to help solve the structures of the high polymeric counterparts. 

Recently, there has been a marked development in the methodologies to observe and manipulate single biopolymers (Mehta et al., 1999 Arai et al., 1999 Cui and Bustamante, 2000 Liphardt et al., 2001). The key procedure in the successful manipulation of single biopolymers has been the tight attachment of the end of the polymer to a micrometer-sized object. To achieve a wider application of such single-molecular technology, it would be important to manipulate individual macromolecules and control their conformation without any structural modifications (Chiu and Zare, 1996 Brewer et al., 1999). Thus, the manipulation of the compact DNAs without the attachment to a micrometer-sized bead or to any other macroscopic objects is expected to be useful for micrometer-scale laboratory experiments. This manipulation will also be a powerful tool for lab-on-a-chip or lab-on-a-plate (Katsura et al., 1998 Yamasaki et al., 1998 Matsuzawa et al., 1999, 2000). It may of value to refer to a recent study in transporting a compact DNA into a cell-sized liposome (Nomura et al., 2001). 

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