Nomenclature complexes

As noted above, amorphous earbon films ean be produeed from earbon-eontaining gas phases (physieal vapour deposition, PVD). They ean also be produced from hydroearbon-eontaining gases (ehemical vapour deposition, CVD). Both PVD and CVD proeesses ean be thermally-aetivated or ean be plasma- and/or eleetrie field-assisted proeesses (e.g., mierowave assisted CVD and ion beam deposition). As a eonsequence a wide range of processes have been developed to form amorphous carbon films and a correspondingly complex nomenclature has evolved [70, 71]. 

A normal male karyotype is labeled 46,XY (46 chromosomes, including one X and one Y). Similarly, a normal female karyotype is labeled 46,XX. A complex nomenclature has been devised to describe deviations from these karyotypes. This nomenclature is given in Table II-3-1. 

Table 3. pKa Values for Various Acid-Base Equilibria of Aquaplatinum Complexes (nomenclature according to Scheme 1, Y = Cl or H20)... 

When forced to be explicit, chemists use a set of very specific kind terms corresponding to very specific chemical kinds. The results of chemists being forced to be explicit can be found in the extremely precise and often very complex nomenclature established by the International Union of Pure and Applied Chemistry. In this nomenclature, even the different phases of water, a concept which I have not discussed, are given their own designations like water (I), water (VI), etc. The vast majority of chemists and the chemical literature, however, refers to substances in a more straightforward manner—using terms like water, or ethanol, or tetrahydrafuran, which are clear in context. 

The scope of the above definition is difficult to comprehend without illustrative examples, a few of which comprise the major contents of this chapter. A few general definitions will lay the groundwork for the more complex nomenclature issues. 

Fig 5. In vitro phosphorylation pattern of the chlorophyll- protein complexes and their constituent polypeptides of B6 and y-1 thylakoids. Phosphorylation was carried out in the light as in Fig. 4, and the chlort hyl-proteins were resolved by nondenaturing PAGE in presence of Deriphat (9), (horizontal strips,ID, 6% acrylamide) the resolved complexes were run in the second dimension using denaturing SDS-PAGE (14% acrylamide, 2D). Note the difference between the y-1 and B6 phosphorylation pattern appearing in the 2D panel (white circles) chlorophyll- protein complexes nomenclature, as in (9). 

The interrelation among homovalent and ambivalent reactions on the five-atom pericycles (equations 3 and 4) was described and given a similar but more complex nomenclature reflecting their lower symmetry. Homovalent pericycles include the amine oxide eliminations in Scheme 1 and the sulfoxide-sulfenate rearrangement in Scheme 2, with the shells in boldface as in Figure 1. For the ambivalent reactions of equation (4) the ambivalent atom X is often not carbon, as seen in Scheme 3 for a metal reduction of vicinal dihalides (which may not be pericyclic) Scheme 3 has an unchanging shell of only one bond. The cycloaddition of sulfur dioxide to dienes in Scheme 4 is another with a three-bond shell. Numerous examples were quoted, again many not confirmed as pericyclic. ... 

Complex linear polyamines are best designated by replacement nomenclature. These trivial names are retained aniline, benzidene, phenetidine, toluidine, and xylidine. 

Organic ring systems are named by replacement nomenclature. Three- to ten-membered mono-cyclic ring systems containing uncharged boron atoms may be named by the specialist nomenclature for heterocyclic systems. Organic derivatives are named as outlined for substitutive nomenclature. The complexity of boron nomenclature precludes additional details the text by Rigaudy and Klesney should be consulted. 

Although the lUPAC has recommended the names tetrahydroborate, tetrahydroaluminate, etc, this nomenclature is not yet ia general use. Borohydrides. The alkaU metal borohydrides are the most important complex hydrides. They are ionic, white, crystalline, high melting soHds that are sensitive to moisture but not to oxygen. Group 13 (IIIA) and transition-metal borohydrides, on the other hand, are covalendy bonded and are either Hquids or sublimable soHds. The alkaline-earth borohydrides are iatermediate between these two extremes, and display some covalent character. 

Fig. 2. Classification/nomenclature of host—guest type inclusion compounds, definitions and relations (/) coordinative interaction, (2) lattice barrier interaction, (J) monomolecular shielding interaction (I) coordination-type inclusion compound (inclusion complex), (II) lattice-type inclusion compound (multimolecular/extramolecular inclusion compound, clathrate), (III) cavitate-type inclusion compound (monomolecular/intramolecular inclusion...

This was a great advance, as complex hydrocarbons of various kinds could be clearly named if their stmctures were known. The Geneva system, modified and expanded by subsequent Commissions, is used systematically in the fourth and fifth editions of Be /stem s Handbuch der Organischen Chemie (1), and as the basis of lUPAC nomenclature. In 1992 a commemorative symposium on the centennial anniversary of the Geneva Conference was held in Geneva (45). 

Recommendations on additional aspects of macromolecular nomenclature such as that of regular double-strand (ladder and spiro) and irregular single-strand organic polymers continue to be pubHshed in I ure and Applied Chemistty (100,101). Recommendations on naming nonlinear polymers and polymer assembHes (networks, blends, complexes, etc) are expected to be issued in the near future. 

Symmetrical diaLkyl peroxides are commonly named as such, eg, dimethyl peroxide. For unsymmetrical diaLkyl peroxides, the two radicals usually are hsted ia alphabetical order, eg, ethyl methyl peroxide. For organomineral peroxides or complex stmctures, ie, where R and R are difficult to name as radicals, the peroxide is named as an aLkyldioxy derivative, although alkylperoxy is stUl used by many authors. CycHc peroxides are normally named as heterocychc compounds, eg, 1,2-dioxane, or by substitutive oxa nomenclature, eg, 1,2-dioxacyclohexane however, when the two oxygens form a bridge between two carbon atoms of a ring, the terms epidioxy or epiperoxy are frequendy used. The resulting polycycHc stmcture has been called an endoperoxide, epiperoxide, or transaimular peroxide. 

Table 1 Hsts a number of chelating agents, grouped according to recognized stmctural classes. Because systematic nomenclature of chelating agents is frequently cumbersome, chelants are commonly referred to by common names and abbreviations. For the macrocyclic complexing agents, special systems of abbreviated nomenclature have been devised and are widely used. Some of the donor atoms involved ia chelation and the many forms ia which they can occur have been reviewed (5).

A system based partly on historical names, partly on the substrate, and partly on the type of reaction catalyzed is far from satisfactory. In 1956, the International Union of Biochemistry set up a Commission on Enzymes to consider the classification and nomenclature of enzymes. The Commission presented a report in 1961 whose recommendations for naming and classifying enzymes were subsequently adopted (12). Enzymes are classified on the basis of the reactions they catalyze. Despite its apparent complexities, the system is precise and very descriptive, accommodating existing enzymes and serving as a systematic basis for the naming of new enzymes. AH enzymes are placed in one of the six principal classes. 

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