Monomer based representation

Polymeric substances are represented on the TSCA Inventory in one of two ways. Depending on the type of polymer, a monomer-based representation or a structnral repeating nnit (SRU) representation is nsed. In either case, EPA generally reqnires that the naming of chemical snbstances be done with as mnch specificity as possible, based on knowledge of the chemical strnctnre. 

Most polymers are listed by their monomers and other starting materials, which the EPA calls monomer-based representation. The EPA succinctly summarized this method in the Toxic Substances Control Act Inventory Representation for Polymeric Substances in section II A ... 

Monomer-based representation is appropriate when the polymer does not have a definite structural diagram and either (i) has only one monomer with an unknown degree of polymerization, or (ii) has more than one type of monomer in no particular pattern. It is also appropriate for homopolymers with more than ten monomers even if the substance has a definite structural diagram, and this is the sole exception to requirement that polymers have a distribution of molecular weights. ... 

In Sgroups, repeating units are enclosed in square brackets and a subscript n is placed to the right of the closing bracket. The subscript blk indicates a block copolymer and mon a monomer in a source-based representation. Superscripts indicate the orientation of the repeating units (hh = head-to-head, ht = head-to-tail, eu = either unknown) in a structure-based description. Crossing bonds (bonds... 

Expressions such as —(—O—CH2—) — and (H2N—(CH2)6—NH2 HO2C— (0112)4—C02H)x depict actual structures, not molecular formulae. Although expressions such as (CH20)n and (C6Hi6N2 C6Hio04)a are used by CAS to represent the molecular formulae of poly(oxymethylene) and nylon-6,6 respectively, these expressions are, per se, neither structure-based nor source-based representations of these two polymers. There is a link, however, between the full structural representation and its molecular formula. The subscript n is used consistently for both an SRU and its molecular formula similarly, the subscript x is used consistently for both a homopolymer (copolymer) structure expressed in terms of monomer(s) and its corresponding molecular formula. 

Source-based Method. For source-based representations, CAS structures homopol5aners by an expression such as (A)x, where A is a monomer. A typical CAS source-based homopol5aner representation is shown as Figure 5. 

CAS makes no distinction among ordered, segmented, and imordered block pol5uners. For source-based representation, block polymers are distinguished from random pol5uners by indexing as copolymers at the monomer names. The term block is cited in a special modification after all other structin-al information (2). 

In such strategies, two comonomers are intentionally defined as 0 and 1 bits. The monomer T is a thymine nucleotide, which is used to start the sequence and facilitates the pol rmer characterization, (b) Extended-ASCII encoded text that was implemented in the primary structure of a polymer using the monomer-based digital code, (c) Schematic representation of the primary structure of the corresponding sequence-coded polymer and its characterization by negative mode electrospray mass spectrometry (ESI-MS). 

A number of special methods for handling synthetic polymers have been developed. These can generally be divided into those that are based on representations of the monomer precursor(s), and those based on the structural repeating units (SRUs) of the polymer itself. The former obviously requires little extension to the system for small molecules, except the inclusion of some indication that the representation is of a polymer of... the structure shown. There are some similarities in the requirements for SRU-based representations and those for handling Markush structures, especially where copolymers are concerned. 

B) Cartoon representation of the parallel superpleated /J-structure proposed for the N-terminal 70 residues of Ure2p in the fibril. This view down the fibril axis shows the stacking of N-termini with a twist of 3°. For reference, the calculated twist based on fibril pitch ranges from 0.7° to 3.4° from one monomer to the next (Kajava et al., 2004). 

In Figure 16.15 we show a schematic representation of the duplex formed from d(GAATTC). Bases from one monomer pair with those from a second to form the duplex. G forms base-pairs with C, and A with T through hydrogen bonding. These base-pairs are referred to as Watson-Crick base-pairs, and they make up the rungs of the ladder associated with the familiar double helix of DNA. 

Figure 16.15 A schematic representation of a duplex formed from the self-complementary monomer, d(GAATTC), that illustrates base-pairing and nearest-neighbor stacking interactions.

As indicated in Chapter 1, the constitution of a given molecule, monomer, or ion is the foundation on which the entire concept of chemical nomenclature has been based. With this in mind, there is a convenient representation of such moieties using a connectivity matrix. As an example, compare the antiquated perspective of the benzene molecule as 1,3,5-cyclohexatriene (Table 1) with the chemically more accurate matrix (Table 2) that has (3 bonds between adjacent carbon atoms. Table 3 is an abbreviation of Table 2 using the C designation. 

Figure 3 The structural levels of proteins, exemplified by human insulin in the T6 form. (A) Primary structure residues 15-18 of human insulin B-chain, shown as sticks. (B) Secondary structure residues 8-20 of the B-chain form an a-helix, here depicted as a superposition of sticks, and a cartoon-representation. (C) Tertiary structure insulin A- and B-chains fold up to a monomer, which is assumed to be the active form, binding to the insulin receptor. Insulin can exist in different oligomeric forms, depending on formulation and protein concentration. (D) The Zn -stabilized hexamer form is shown. 2 Zn ions are bound per insulin hexamer (only one Zn2" "-ion is visible in this view). The hexamer is a trimer of dimmers. Figure based on pdb-file IMSO, produced in Pymol. Source Bente Vestergaard, Biostructural Research, Faculty of Pharmaceutical Sciences, University of Copenhagen.

In synthetic polymers, the interpretation is necessarily more difficult The form of Equation 4 and Equation 5 requires that the kinetics of formation and decay of complexes are modelled adequately by rate-constants and that they take place in a homogeneous medium. If, as in synthetic polymers, the population of excimer trap sites, may occur through energy migration or rotational diffusion, a rate-constant may not be an adequate representation of the process, some time-dependent parameter being required (see below.) Heterogeneity may also play an important role. Thus in earlier work the fluorescence decay of excimer-forming polymers was modelled adequately by a scheme based upon simple excimer kinetics to which had been added terms to account for the occurrence in co-polymers of monomer sites which, by their isolation, could not form excimers (4-10). For polymers which contain isotactic and syndiotactic sequences, or rather, are made up of meso and racemic triads (14), the kinetics may be similarly a superimposition of simple schemes appropriate for the different sequences. 

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