Nomenclature and Coding

Several polycyclic conjugated hydrocarbons (Clar 1964) of chemical interest (in addition to the carbon cluster C q) are described above in this chapter. In the next chapter, some aspects of the difficult task of classification of chemical graphs are explained. These classifi— cations/explanations account for aU the conjugated hydrocarbons in Sections 1.3—1.7, and also for the carbon cluster (Sect. 1.8). 

CLASSIFICATIONS OF POLYGONAL SYSTEMS, AND SOME ASPECTS OF KEKULE STRUCTURES 

The below diagram shows an example for each of the operations (a) and (b). The deleted objects are indicated by a white dot and dotted lines. 

The below scheme of classification applies to benzenoids and coronoids, and to the single coronoids in particular. It is consistent with the classifications adopted previously, which are detailed in Vol. I and elsewhere (Gutman and Cyvin 1989 Brunvoll, Cyvin SJ and Cyvin 1991a). 

The Kekulean and non-Kekulean systems are those which possess Kekule structures K 0) oi do not possess Kekule structures K = 0), respectively. In an essentially disconnected system there are fixed bonds, viz. edges which correspond to double and/or single bonds in the same positions of all Kekule structures. Kekulean systems without fixed bonds are called normal Obvious- and concealed non—Kekulean systems have A 0 and A = 0, respectively, where A is the color excess, viz. the absolute magnitude of the difference between the numbers of peaks and valleys (1-3.2.4). Finally, the catacondensed (unbranched or branched) and the pericondensed systems have n- = 0 and n- 0, respectively, where n- designates the number of internal vertices (I-3.3.1). 

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Gottlieb O R, Kaplan MAC 1986 Replacement-nodal-subtractive nomenclature and codes of chemical compounds. J Chem Inf Comp Sci 26 1-3... 

Association (ABMA), recommendations for boiler-water limits, 23 221t American Chemical Society Committee on Nomenclature and Notation, 17 385 American Chemistry Council (ACC) 14 204 codes of management practices, 21 580 Process Safety Code, 21 831 Responsible Care initiatives, 25 337 American Conference of Governmental Industrial Hygienists (ACGIH),... 

We close this section with one more note on careful nomenclature. A code renders a model into a set of instructions that can be understood by a digital computer. Thus, if one applies a particular model, let us say the molecular mechanics model called MM3 (which will be described in the next chapter) to a particular problem, say the energy of chair cyclohexane, the results should be completely independent of which code one employs to carry out the calculation. If two pieces of software (let s call them MyProg and YourProg) differ by more than the numerical noise that can arise because of different round-off conventions with different computer chips (or having set different tolerances for what constitutes a converged calculation) then one (or both ) of those pieces of software is incorrect. In colloquial tenns, there is a bug in the incorrect code(s). 

The representation is unambiguous since it corresponds to one and only one substance, but it is not unique because alternative numberings of the connection table would result in different representations for the same chemical substance (the connection table representation is discussed in more detail below). In addition to being categorized according to their uniqueness and ambiguity, chemical substance representations commonly used within computer-based systems can be further classified as systematic nomenclature, fragment codes, linear notations, connection tables, and coordinate representations. 

Table 11.2 Nomenclature and structure of the principal amino acids. The common name, the three-letter code and the single-letter code are given...

I erminology and nomenclature serve science and technology in a variety of ways, of which the most obvious are the communication and recording of information. Equally important is the use of scientific and technical terms as building blocks for constructing indexes, classification systems, and codes for mechanical searching. 

Each container or grouping of containers should be identified with standard nomenclature and a distinctive code for each lot in each shipment received, which should be used in recording the disposition of each lot Each lot should be appropriately labelled and identified as to its status (i.e., quarantined, approved or rejected). This may be done manually or the status may be controlled by appropriate and validated computer systems. 

Rubbery materials, and compositions based upon them, are commonly referred to by a number of letters which refer to the monomers on which the polymer is based. The standard recommended practice (D1418-72A) issued by the American Society for Testing Materials (ASTM) is the most widely used for the nomenclature of elastomers (rubbers) and lattices. This practice recommends that the elastomers be grouped and coded into a number of classes according to-the chemical composition of the polymer chain. Of the various types, the R and M classes are the most commercially important. 

Section 1. The first part of Section 1 identifies the substance by name, formula, and various numbers and codes. Most organic compounds have more than one name. In this case, the systematic (or International Union of Pure and Applied Chemistry [lUPAC]) name is methanol, and the other names are common names or are from an older system of nomenclature. The Chemical Abstract Service Number (CAS No.) is often used to identify a substance, and it may be used to access extensive information about a substance found in many computer databases or in the library. 

Notation coded description of chemical substances, which does not use the common tools of chemical structure drawings and nomenclature and which is mainly used for the conversion in electronic form,... 

Membrane proteins (I) (peptides a, b, c in Hoober s nomenclature L-protein, or peptides Va, Vb are synthesized by cytoplasmic 80 S ribosomes (II) and coded for by nuclear DNA (III). The transcription process can be inhibited by actinomycin D, but not by rifampicin. The translation process can occur in the dark and is inhibited by cycloheximide (II). The proteins are transferred to the chloroplast and become incorporated into chloroplast membrane (IV), which as such, are photosynthetically inactive. Activation proteins " synthesized in the chloroplast (V), coded for by chlorplast—as well as nuclear DNA—and translated on 70 S ribosomes inhibited by chloramphenicol are added to the inactive membrane which becomes photosynthetically functional (VI). The activation proteins include components which are essential for the activity of the photosystem II and I reaction centers and can be made and inserted into the growing membrane in absence of concomitant chlorophyll synthesis or protein synthesis in the cytoplasm, provided that the inactive membranes containing the cytoplasmic proteins are already formed. ... 

For chemical documentation purposes, each molecular graph should have a unique name or code which should allow indexing and retrieval. This necessity has been partly fulfilled by the traditional chemical nomenclature and by the development of linear notation systems. Both approaches are in use and are able to discriminate among isomeric structures, but rely heavily on conventions. Chemical names may be indexed alphabetically within a set of isomeric systems, which in turn may be ordered according to the molecular formula this fact makes chemistry the best-documented natural science. Linear notation... 

Abbreviations for amino acids and their derivatives follow the revised recommendation of the lUPAC-IUB Committee on Biochemical Nomenclature, entitled Nomenclature and Symbohsm for Amino Acids and Peptides (recommendations of 1983). Nomenclature of branched polypeptides is used in accordance with the recommended nomenclature of graft polymers (lUPAC-lUB recommendations, 1984). For the sake of brevity codes of branched polypeptides were constracted by us using the one-letter symbols of amino acids (Table 1). The abbreviations used in this paper are the following. AK, poly[Lys-(DL-Ala )] AXK, poly[Lys-(DL-Ala -Xi)] XAK, poly[Lys(Xi-DL-Ala )] X = Ser (SAK), Om (OAK), Glu (EAK), or Ac-Glu (Ac-EAK). All amino acids are of L-configuration unless otherwise stated. DPH, l,6-diphenyl-l,3,5-hexatriene ANS, sodium anilino naphthalene sulfonate DPPC, dipalmitoyl phosphatidyl choline PG, phosphatidyl glycerol Z, benzyloxycarbonyl Pep, pentachlorophenol P, polarisation. 

Enzymes are classified in terms of the reactions which they catalyse and were formerly named by adding the suffix ase to the substrate or to the process of the reaction. In order to clarify the confusing nomenclature a system has been developed by the International Union of Biochemistry and the International Union of Pure and Applied Chemistry (see Enzyme Nomenclature , Elsevier, 1973). The enzymes are classified into divisions based on the type of reaction catalysed and the particular substrate. The suffix ase is retained and recommended trivial names and systematic names for classification are usually given when quoting a particular enzyme. Any one particular enzyme has a specific code number based upon the new classification. 

The major significance of chemical nomenclature or notation systems is that they denote compounds in order to reproduce and transfer them from one coding to another, according to the intended application. As each coding may not include all the pieces of information in the other coding, or may have interpre table coding rules, the transformation is not always unambiguous and unique. 

While the trivial and trade nomenclature in most cases has accidental character, the lUPAC Commission has worked out a series of rules [4] which allow the great majority of structures to be represented uniformly, though there still exists some ambiguity within this nomenclature. Thus, many structures can have more than one name. It is important that the rules of some dialects of the lUPAC systematic nomenclature are transformed into a program code. Thus, programs for generating the names from chemical structures, and vice versa (structures from names) have been created [5] (see Chapter II, Section 2 in the Handbook). 

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