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“Classification, Nomenclature, Isomerism of Bioorganic Compounds

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ODESSA NATIONAL MEDICAL UNIVERSITY Department of Clinical Chemistry and Laboratory Diagnostics Bioorganic chemistry Information block for first-year students of medical and dental faculties (Second semester) “Classification, nomenclature, isomerism of bioorganic compounds. The nature of chemical bonds” Control questions: 1. Classification of organic compounds. 2. Nomenclature system of organic chemistry (trivial system, common system, international substituent nomenclature system IUPAC) 3. Type of isomerism of organic compounds: a) Structural isomerism (chain isomerism, isomerisme of functional group position, isomerism between classes of organic compounds, dynamic tautomerism). b) Spatial isomerism. Configuration and conformation conception. Geometrical or cis-trans isomerism. Optical isomerism. 1 Theoretical matter of the topic Organic compounds are classified according to the following features: • a structure of molecular framework (sometimes called a molecular skeleton); • the presence of functional groups in a molecule. 1.1. Classification According to the Molecular Framework Organic compounds are subdivided into the following groups. Acyclic compounds. They have unbranched or branched carbon chain, but no rings. In the examples below, the first two represent compounds with unbranched carbon chain, whereas the third one is a compound with a branched chain: Carbocyclic compounds. They contain a ring (or rings) of carbon atoms only. The ring may contain multiple bonds and may have side carbon chains. Heterocyclic compounds. They contain a cyclic skeleton having at least one heteroatom, an atom that is not carbon. The most common heteroatoms are nitrogen, oxygen, or sulfur. More than one heteroatom may be present and these atoms may be identical or different. The structures of some natural heterocyclic compounds are presented below: 2 1.2. Classification According to Functional Groups Hydrocarbons are parent compounds in organic chemistry, which, according to their name, consist of only carbon and hydrogen atoms. Most organic molecules involve functional groups, i. e. an atom or a group of atoms of non-hydrocarbon origin that determine chemical properties of a compound. Indeed, chemical changes occur in most reactions at the functional group whereas the molecular framework remains unchanged. Thus, the knowledge of properties of the functional groups will greatly help in the study of organic chemistry. Organic compounds are divided into classes depending on the functional groups present. Some of the main functional groups and classes are listed in Table 1. Table 1. Some of the functional groups and the corresponding classes of organic compounds * The symbol R is usually used for any hydrocarbon radical, the symbol Ar - for an aromatic radical only. ** Multiple bonds in unsaturated compounds are sometimes related to the functional groups. *** Only primary ones are shown. 3 Molecules with one functional group belong to monofunctional compounds. Polyfunctional compounds contain several identical functional groups, for example, chloroform and glycerol. Molecules with different functional groups are considered as heterofunctional compounds, they may be related to several classes. For example, lactic acid is both an alcohol and a carboxylic acid. Similarly, taurine belongs both to amines and sulfonic acids. Classification characteristics form a foundation of the systematic chemical nomenclature of organic compounds. NOMENCLATURE At the earliest stage of organic chemistry, each new compound was usually named on the basis of its source (caffeine – from coffee-beans, urea – from urine) or its evident properties (glycerol and glucose – from the Greek glykys, sweet). Such names are known as trivial or common names. Trade names are widely used in pharmacy and medicine indicating some pharmaceutical effect (anesthesin, sarcolysin). Trivial and trade names are very convenient because of their brevity, but they give no information about the structure of a compound and cannot be systematized. Some trivial names went out of use with time; others have shown their viability and are used now in the systematic nomenclature. Systematic nomenclature is an arrangement of terms that describes complete structure of organic molecules. The first systematic nomenclature appeared as far back as 1892 (Geneva Rules). It was then perfected by a commission of the International Union of Pure and Applied Chemistry (IUPAC) and is known now as the IUPAC rules or the IUPAC nomenclature. 4 1.3. General Principles of the IUPAC Nomenclature To minimize confusion the following terms are used in the present rules. Parent name: a part of the name used for the formation of a particular name according to the appointed rules. For example, the name ethanol is derived from ethane. The parent name may be both systematic. Characteristic group: this term is practically equal to the term functional group, for example, the amino group -NH2, the carbonyl group >C=O, the oxo group =O, the carboxyl group -COOH. Principal (senior) group: the characteristic group chosen for expression as a suffix in a particular name. This group has no other advantages over remainder groups. Substituent: any atom or group replacing hydrogen of a parent compound. Radical: a part of a molecule that remains after removal of one or more hydrogen atoms from it. For example, the radicals, such as methyl, CH3-, and methylene, -CH2-, are derived from methane, CH4. Locant: a numeral or a letter showing a position of a substituent or a multiple bond in a parent structure. Multiplying affix: syllables di-, tri-, tetra-, etc., which are used to indicate a set of identical substituents or multiple bonds. Nomenclature Systems. There are eight basic nomenclature systems from which the most versatile and common therefore is the substitutive nomenclature. The next in prevalence is the radicofunctional nomenclature. These two nomenclatures, especially the former, will be considered in greater detail. Substitutive nomenclature. The particular name of a polyfunctional compound represents a complex word that consists of a root (parent name), a suffix (principal group), and prefixes (other substituents). Fig.1 demonstrates this approach. 5 Figure 1. The scheme for constructing the IUPAC substitutive name. The symbol × represents multiplying affix(es). There are two types of characteristic groups. One type is designated in a name only as prefixes. Nitro group, halogens, and some other groups belong to this type; they are listed in the lower part of Table 2. Most of characteristic groups (the upper part of Table 2, beyond the coloured line) may be cited either as suffixes or as prefixes. But only one kind of group (principal group) is to be cited as a suffix. Within these groups, a conventional order of priority has been established (Table 2). It means the principal group is that which characterizes the class occurring as high as possible in Table 2. All other characteristic groups are then cited as prefixes. Multiplying affixes and locants are added as necessary. Radicofunctional nomenclature. The principles of the radicofunctional nomenclature are identical with those of the substitutive nomenclature except that suffixes are never used. Instead of the principal group being named as a suffix, the class name of a compound is expressed as one word and the remainder of the molecule as another. Provided that the characteristic group is univalent (for example, an OH group of alcohols or a halogen atom of halogen derivatives) the remainder of the molecule attached to that group is expressed in its radical form as another word, which precedes the class name. When the class name refers to a characteristic group that is bivalent (for example, the fragment -Oof ethers), the two radicals attached to it are each named as separate words in alphabetic order. Table 2. Suffixes and prefixes used for some important groups in the substitutive nomenclature IUPAC (in order of decreasing priority) 6 * Coloured carbon atoms are included in the name of parent structure and not in the suffix or prefix. ** Should be added in front of the name. *** Phenols have usually common names. **** Used only with the name of radical R, e. g. ROalkoxy- or RSalkylthio-. This type of nomenclature is the most convenient one for such classes as ethers, sulfides, amines, and halogen compounds, especially for the compounds with simple radicals. 1.4. General Principles of Forming a Systematic Name The formation of a name for a chemical compound usually involves the following steps in the order given below. Step 1. From the nature of the compound determine the most pertinent type of nomenclature (substitutive, radicofunctional, or else). 7 Step 2. Determine the kind of characteristic group for use as the principal group, if any. It is this group that stipulates then the choice of a parent structure and its numbering. Step 3. Determine the parent structure (principal chain or parent ring system2). When in an acyclic compound there is a choice for principal chain, the following criteria are applied successively, in the order listed, until a decision is reached: a) the maximum number of substituents of the highest priority from Table 2.2; b) the maximum number of double and triple bonds considered together; c) the maximum length of the chain; d) the maximum number of substituents cited as prefixes. Step 4. Name the parent structure and the principal group(s). Step 5. Determine and name prefixes. Step 6. Complete the numbering. The starting point and direction of
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