Molecular nomenclature

Of the wide range of organo-metallic complexes likely to exist in natural waters only a small number have been structurally identified. Two examples of identified complexes found in sea water are cobalt(II)-containing cyanocobalamine or vitamin B,2 (Carlucci, 1970) and magnesium in chlorophyll a (Riley and Chester, 1971). Although a great deal is known about the properties of the unidentified complexes, it is not possible to classify them according to the systematic molecular nomenclature used in classical chemistry (lUPAC, 1973 Cahn, 1974). This undoubtedly has contributed... 

The nomenclature of FA reflects the long history of their smdy and description. Most FA were originally described under trivial names prior to the adoption of the international molecular nomenclature rules in 1892 (Table 3.1). Even after adopting the International Union of Pure and Applied Chemistry (lUPAC) system for nomenclature (lUPAC-IUB, 1977), the habit of assigning trivial names to FA continues. The basis of the systematic nomenclature system is an extension of that accepted for hydrocarbon (alkane/alkene) naming. Hence, the descriptive name is based on the number of carbon atoms contained in the molecule, with the suffix -e replaced with -oic acid. However, in most instances, FA are referred to by their formula notations. As is the case with systematic and trivial names, there exists an lUPAC accepted formula notation nomenclature and several earher versions (Table 3.2). Each system... 

Harper, Charles A., Ed. (2000) Modern Plastics Handbook, New York, McGraw-Hill International Union of Pure and Applied Chemistry, Macromolecular Division, Conunission on Macro-molecular Nomenclature (1991) Compendium of Macromolecular Nomenclature, Oxford, Blackwell Scientific... 

Metanomski, W. V. (ed.) (1991) Compendium of Macro-molecular Nomenclature. Blackwell Scientific, Oxford. 

The definition proposed by the lUPAC Commission on the molecular nomenclature [24] made things clearer in the late 1970s - early 1980s of the last century Oligomer is a substance consisting of molecules formed by atoms of one or several types or atomic groups (constitutional imits). 

When atoms, molecules, or molecular fragments adsorb onto a single-crystal surface, they often arrange themselves into an ordered pattern. Generally, the size of the adsorbate-induced two-dimensional surface unit cell is larger than that of the clean surface. The same nomenclature is used to describe the surface unit cell of an adsorbate system as is used to describe a reconstructed surface, i.e. the synmietry is given with respect to the bulk tenninated (unreconstructed) two-dimensional surface unit cell. 

The systematic lUPAC nomenclature of compounds tries to characterize compounds by a unique name. The names are quite often not as compact as the trivial names, which are short and simple to memorize. In fact, the lUPAC name can be quite long and cumbersome. This is one reason why trivial names are still heavily used today. The basic aim of the lUPAC nomenclature is to describe particular parts of the structure (fi agments) in a systematic manner, with special expressions from a vocabulary of terms. Therefore, the systematic nomenclature can be, and is, used in database systems such as the Chemical Abstracts Service (see Section 5.4) as index for chemical structures. However, this notation does not directly allow the extraction of additional information about the molecule, such as bond orders or molecular weight. 

In 1986, David Weininger created the SMILES Simplified Molecular Input Line Entry System) notation at the US Environmental Research Laboratory, USEPA, Duluth, MN, for chemical data processing. The chemical structure information is highly compressed and simplified in this notation. The flexible, easy to learn language describes chemical structures as a line notation [20, 21]. The SMILES language has found widespread distribution as a universal chemical nomenclature... 

The simplest molecular orbital method to use, and the one involving the most drastic approximations and assumptions, is the Huckel method. One str ength of the Huckel method is that it provides a semiquantitative theoretical treatment of ground-state energies, bond orders, electron densities, and free valences that appeals to the pictorial sense of molecular structure and reactive affinity that most chemists use in their everyday work. Although one rarely sees Huckel calculations in the resear ch literature anymore, they introduce the reader to many of the concepts and much of the nomenclature used in more rigorous molecular orbital calculations. 

At one time thiols were named mercaptans Thus CH3CH2SH was called ethyl mercaptan according to this system This nomenclature was abandoned beginning with the 1965 revision of the lUPAC rules but is still sometimes encountered When one encounters a thiol for the first time especially a low molecular weight thiol its most obvious property is its foul odor Ethanethiol is added to natural gas so that leaks can be detected without special equipment—your nose is so sensitive that it can detect less than one part of ethanethiol m 10 000 000 000 parts of arr The odor of thiols weakens... 

In the days of alchemy and the phlogiston theory, no system of nomenclature that would be considered logical ia the 1990s was possible. Names were not based on composition, but on historical association, eg, Glauber s salt for sodium sulfate decahydrate and Epsom salt for magnesium sulfate physical characteristics, eg, spirit of wiae for ethanol, oil of vitriol for sulfuric acid, butter of antimony for antimony trichloride, Hver of sulfur for potassium sulfide, and cream of tartar for potassium hydrogen tartrate or physiological behavior, eg, caustic soda for sodium hydroxide. Some of these common or trivial names persist, especially ia the nonchemical Hterature. Such names were a necessity at the time they were iatroduced because the concept of molecular stmcture had not been developed, and even elemental composition was incomplete or iadeterminate for many substances. 

This system of nomenclature has withstood the impact of later experimental discoveries and theoretical developments that have since the time of Guyton de Morveau and Lavoisier greatiy altered the character of chemical thought, eg, atomic theory (Dalton, 1802), the hydrogen theory of acids (Davy, 1809), the duahstic theory (Berzehus, 1811), polybasic acids (Liebig, 1834), Periodic Table (Mendeleev and Meyer, 1869), electrolytic dissociation theory (Arrhenius, 1887), and electronic theory and modem knowledge of molecular stmcture. 

International Union of Biochemistry and Molecular Biology, Biochemical Nomenclature and Related Documents, 2nd ed., Pordand Press, London, 1992. 

The general formula for boric acid esters is B(OR)2. The lower molecular weight esters such as methyl, ethyl, and phenyl are most commonly referred to as methyl borate [121 -43-7] ethyl borate [130-46-9J, and phenyl borate [1095-03-0] respectively. Some of the most common boric acid esters used in industrial appHcations are Hsted in Table 1. The nomenclature in the boric acid ester series can be confusing. The lUPAC committee on boron chemistry has suggested using trialkoxy- and triaryloxyboranes (5) for compounds usually referred to as boric acid esters, trialkyl (or aryl) borates, trialkyl (or aryl) orthoborates, alkyl (or aryl) borates, alkyl (or aryl) orthoborates, and in the older Hterature as boron alkoxides and aryloxides. CycHc boric acid esters, which are trimeric derivatives of metaboric acid (HBO2), are known as boroxines (1). 

Hsynthesis from, 3, 767 Indenobenzazepines pharmacological properties, 7, 546 Indenone oxide, 2,3-diphenyl-photochromic compound, 1, 385 In deno[ 1,2-c][ 1,2,4]triazines synthesis, 3, 434 Indicated hydrogen nomenclature, 1, 33 Indigo, I, 317, 318-319, 4, 370 Baeyer synthesis, 1, 319 colour and constitution, 1, 344-345 molecular structure, 4, 162 photochromic compound, 1, 386 synthesis, 4, 247 Indigoid dyes... 

Pedersen prepared a series of macrocyclic polyethers, cyclic compounds containing four or more oxygens in a ring of 12 or more atoms. He called these compounds crown ethers, because their molecular- models resemble crowns. Systematic nomenclature of crown ethers is somewhat cumbersome, and so Pedersen devised a shorthand description whereby the word crown is preceded by the total number of atoms in the ring and is followed by the number of oxygen atoms. 

Protonation of the anion [SN2] by acetic acid in diethyl ether produces the thermally unstable sulfur diimide S(NH)2. Like all sulfur diimides, the parent compound S(NH)2 can exist as three isomers (Scheme 5.5). Ab initio molecular orbital calculations indicate that the (cis,cis) configuration is somewhat more stable than the (cis,trans) isomer, while the (trans,trans) isomer is expected to possess considerably higher energy. The alternative syn,anti or E,Z nomenclatures may also be used to describe these isomers. The structures of organic derivatives S(NR)2 (R = alkyl, aryl) are discussed in Section 10.4.2. 

International Union of Biochemistry and Molecular Biology Nomenclature Committee, 1992. Enzyme Nomenclature. New York Academic Press. A reference volume and glossary on die official classification and nomenclature of enzymes. 

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