Polymer representation

Usually, MD methods are applied to polymer systems in order to obtain short-time properties corresponding to problems where the influence of solvent molecules has to be explicitly included. Then the models are usually atomic representations of both chain and solvent molecules. Realistic potentials for non-bonded interactions between non-bonded atoms should be incorporated. Appropriate methods can be employed to maintain constraints corresponding to fixed bond lengths, bond angles and restricted torsional barriers in the molecules [117]. For atomic models, the simulation time steps are typically of the order of femtoseconds (10 s). However, some simulations have been performed with idealized polymer representations [118], such as Bead and Spring or Bead and Rod models whose units interact through parametric attractive-repulsive potentials. 

While considerable progress has been made in the area of small molecule informatics over the past several decades, any effort in the field of polymers has been timid at best and there is considerable scope for development. The main reason for the virtual non-existence of polymer informatics is the complex nature of polymers. This review will therefore start with an examination of the particular informatics challenges posed by polymers, in particular in the area of polymer representation and will also discuss some of the peculiarities of polymer information ( the science of information ). It will look at information systems for polymers ( engineering of information systems ) and a final section will review attempts to develop structure-property relationships for polymers ( practice of information processing ). The modeling of polymers either on the molecular - or meso-level - is outside the scope of this review. 

PML can also represent polymers at different levels of certainty where the structure is known, it can be encoded and where this information is not available, a polymer can be codified in terms of other concepts, such as the monomers it was prepared from. Furthermore, PML provides essentially a coarse-grained representation larger structural fragments can be mapped back to fully atomistic fragments, if desired. PML, therefore, allows data to be associated with a polymer representation at the atom, molecular fragment, molecule and molecule ensemble level, and. 

Liu and Zhong introduced a number of QSPR models based on molecular connectivity indices [151, 152], In a first iteration, the researchers developed polymer-dependent correlations descriptors were calculated for a set of solvents and models were developed per polymer type [151], Polymer classes under consideration were polystyrene, polyethylene, poly-1-butene, poly-l-pentene, poly(4-methyl-l-pentene), polydimethylsiloxane, and polyisobutylene. As the authors fail to provide any validation for their models, it is difficult to asses their predictive power. In a subsequent iteration and general expansion of this study, mixed and therefore more general models based on the calculated connectivity indices of both solvent and polymers were developed. While it is unclear from the paper which polymer representation was used for the calculation of the connectivity indices, the best regression model (eight parameter model) yields only acceptable predictive power (R = 0.77, = 0.77, s = 34.47 for the training set, R = 0.75... 

A discussion of mass-subtraction in field theory can be found in standard textbooks [AiniM, ZJ80]. The equivalent argument directly in the polymer representation has been presented in [CloSOa]. The problems associated with mass-subtraction for d < 4 from a field theoretic point of view are discussed in [SD89]. For a polymer system in d = 3 a discussion has been presented iu [Clo82]. (See also [CJ90] Sect. 12,3,2.)... 

Additives that do not chemically react to become part of the polymer are disregarded for purposes of the two percent rule, and do not have to be named as part of the polymer. Examples of these additives include colorants and UV adsorbers, among others. Similarly, emulsifiers and plasticizers do not become part of the polymer s chemical composition and are not part of the polymer s description. Catalysts are not consumed in reactions and therefore do not have to be part of the polymer representation. 

However, before 1989 manufacturers were not consistently reporting all free radical initiators that were charged to the reaction vessel because it was unclear whether they were intended to become part of the final polymer. The EPA clarified its position on representation of free radical initiators in the June 28,1989 Federal Register and said that all free radical initiators charged at greater than two percent by weight of the starting reactants must be listed as part of the polymer representation, unless the manufacturer could prove... 

Polymer representation (A = terminal moiety, B = structural unit). 

Source-based polymer representation (also called product-by-process representation) the polymer is represented in terms of the names and structures (where known) of the substance(s) from which the polymer was formed. For example, polyethylene is represented by the expression (CH2=CH2)j , because the structure of the monomer, ethylene, from which it is made is CH2=CH2. 

Source-based polymer representation preceded structure-based representation because polymers were made before they were structurally characterized. The... 

For source-based polymer representation, the expression used is (A B-.. where A, B, etc, represent the atom-by-atom or group-by-group rep-resentation(s) of polymerizable substance(s) used to prepare the polymer and the subscript x indicates that A, B, etc, are repeated an indefinite number of times. Thus, nylon-6,6 can be expressed as (H2N-(CH2)6-NH2H02C-(CH2)4-C02H). ... 

For structure-based polymer representation the advantages and disadvantages are as follows. 

Any polymer representation used for identification must be predictable, ie, easily arrived at by a searcher applying a set of rational and invariable rules. Without knowledge of rules for determining the order of an atom-by-atom representation of an SRU, a searcher seeking information on poly(ethylene terephtha-late) (PET), for example, would theoretically have to search for all seven structures shown in Figure 2. 

Lately it was offered to consider polymers amorphous state stmcture as a natural nanocomposite [6]. Within the frameworks of cluster model of polymers amorphous state stmcture it is supposed, that the indicated structure consists of local order domains (clusters), immersed in loosely packed matrix, in which the entire polymer free volume is concentrated [7, 8]. In its turn, clusters consist of several coUinear densely packed statistical segments of different macromolecules, that is, they are an amorphous analog of crystallites with stretched chains. It has been shown [9] that clusters are nanoworld objects (tme nanoparticles-nano clirsters) and in case of polymers representation as natural nanocomposites they play nanofiller role and loosely packed matrix-nanocomposite matrix role. It is significant that the nanoclusters dimensional effect is identical to the indicated effect for particulate filler in polymer nano composites sizes decrease of both nano clusters [10] and disperse particles [11] resrdts to sharp enhancement of nanocomposite reinforcement degree... 

The lUPAC Commission on Nomenclature in Orguiic Chemistry prefers these symbols to the one-letter ones (N-3), designed for polymer representation. The three-letter symbols sho d be uskl whenever chemical changes involving nucleosides or nucleotides are being discussed. 

Structure-based polymer representation the polymer is represented in terms of the structure of its constitutional or structural repeating unit (see Structure Databases). Two common expressions are in use constitutional repeating unit (CRU) - preferred by lUPAC - and structural repeating unit (SRU) - preferred by Chemical Abstracts Service (CAS) (see Chemical Abstracts Service Information System)-, the two are virtually synonymous, and SRU will be used in this article. For example, polyethylene can be represented by the SRU -(-CH2-)rt- (the largest fragment that can be written without repetition) or by the SRU -(-CH2-CH2-)n (obtained by opening the double bond in ethylene). ... 

Source-based polymer representation preceded structure-based representation because polymers were made before they were structurally characterized. The introduction of structure-based representation, however, did not render source-based representation obsolete, and currently the two complementary systems coexist. Source-based representation continues to exist for several reasons ... 

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