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Organic chemistry comprises the chemistry of carbon compounds. Carbon atoms exhibit a unique property called catenation, which means that they can form covalent bonds with other carbon atoms. There exist a variety of carbon chains of different lengths (simple, branched, cyclic), to which hydro- gen atoms are nearly always bonded (hydrocarbons); besides carbon and hydrogen, the compounds in human body include atoms of oxygen, nitrogen, sulfur, phosphorus, and a few others. Carbon com- pounds can be classified according to the carbon skeleton or the groups attached to it. According to the carbon skeleton, there are three main classes: Acyclic compounds: aliphatic, open chain structures either straight-chain or branched, both saturated and unsaturated (i.e. having double or triple bonds), e.g. ethane, ethanol, butyric acid. Carbocyclic compounds: closed rings of carbon atoms that may have branches attached to them and may contain multiple bonds, they are divided into two subgroups - alicyclic, and aromatic compounds (i.e., those with a ring stabilized by the fully conjugated system of double bonds) e.g. cyclohexane, benzene, naphthalene. Heterocyclic compounds: at least one atom in the ring is a heteroatom, an atom that is not carbon, e.g. pyridine, pyrimidine, pyrrole. Classification according to the functional groups: hydrocarbons, halogen derivatives, compounds with oxygen group (alcohols, phenols, aldehydes, ketones, carboxylic acid), sulfur (thiols, sulfides), nitro- gen (e.g. amines, amides, nitro compounds), and various combinations. Common properties of organic compounds Most of the bonds in organic compounds are covalent. Consequently, organic compounds are mostly typical covalent compounds exhibiting various degrees of polarity; only some of them are ionic (salts of organic acids and bases). The polarity of a covalent bond depends on the difference in electro- negativities of the two bonded atoms. Typical non-polar bonds are C–C and C–H, hydrocarbons do not exhibit any substantial dipole moment. With the increasing difference in electronegativities of bonded atoms, the polarity of a bond increases and the atoms acquire partial electric charges ( +, - ). For example, the molecule of ethanol CH 3 - CH 2 - OH is polar because the C–O bond is quite polar and the O–H bond is even more polar than the C–H bonds. Note that a polar bond is a prerequisite for the polarity of a molecule , but not all molecules with polar bonds must necessarily be polar. Dipole moments of individual bonds are vectors. When more polar bonds are present in a molecule, the resulting dipole moment of the molecule depends on the spatial arrangement of polar bonds. In some symmetrical molecules, internal cancelling of partial dipoles results in an overall absence of polarity. For example, tetrachloromethane CCl 4 is non-polar because of the symmetrical tetrahedral geometry of four polar C–Cl bonds.
Reactivity of organic compounds depends on bond energy as well as on bond polarity and other given conditions. Covalent bonds can be split in a symmetrical homolytic cleavage ; the result is a free radi- cal, which has a single (unpaired) electron to offer for bonding: X-Y ·X + ·Y. Another type of bond splitting is an asymmetrical heterolytic cleavage ; one of the products is the nucleophile having an unshared electron pair to offer for bonding, the second is the electrophile able to form a new bond by accepting a pair of electrons: X-Y X-^ + Y+. Reactions in organic chemistry are commonly divided according to the reaction mechanism and the resulting change of the substance (condensation, hydrolysis etc.). According to mechanism we recog- nise four basic types of reactions: addition, elimination, substitution, and rearrangement. During addition the multiple bonds are removed, the hybrid state of C is changed (sp^2 sp^3 ). E.g. CH 2 =CH 2 + Cl 2 CH 2 Cl-CH 2 Cl (chlorination of ethene to 1,2-dichloroethane). In elimination the multiple bond is formed and hybrid state of carbon is changed (sp^3 sp^2 ), e.g. elimination of water from ethanol gives ethene: CH 3 CH 2 OH CH 2 =CH 2 + H 2 O. In substitution the hybridization state is not changed. The H atom in the molecule is substituted by another atom (group), e.g. chlorination of methane gives chloromethane: CH 4 + Cl 2 CH 3 Cl + HCl. In molecular rearrangement atoms and groups migrate within one molecule; carbon chain is altered, the number of atoms is the same (e.g. glucose fructose). Condensation is the linkage of two molecules with elimination of a small molecule. E.g. the reaction of carboxylic acid with alcohol produces ester and water: R-COOH + R'-OH R-COOR' + H 2 O. Hydrolysis is the reaction of a substrate with water. Two smaller product molecules are formed from one molecule of substrate. The subjects of hydrolysis are esters, amides, proteins, lipids, polysaccha- rides, polynucleotides etc. Hydrolysis usually needs the catalytic amount of acid, base or enzyme. E.g. hydrolysis of an ester gives acid and alcohol: R-COOR' + H 2 O R-COOH + R'-OH. Redox reactions in organic chemistry are connected with the change of oxidation number of carbon, which gets in organic compounds values from – IV to III. Redox transformations of a substrate can principally occur in the six ways (see the table): Oxidation Reduction Loss of electron(s) Loss of 2 H atoms (dehydrogenation) Gain of oxygen (oxygenation) Gain of electron(s) Accepting 2 H atoms (hydrogenation) Loss of oxygen (deoxygenation) Very often, in biochemical processes, oxidations proceed by dehydrogenation. Two H atoms are eliminated from a substrate to form a double bond in the product.
Optical isomerism, chirality Any carbon atom with four different groups (or atoms) attached to it is called the stereogenic carbon atom (chiral centre). These dissimilar substituents can be arranged in two different ways to provide two distinct configurations which are non-superimposable on mirror images of each other. Such iso- mers are called enantiomers or optical antipodes. In most properties they behave identically, both exhibit optical activity (one of them is levorotatory, the other dextrorotatory). The example given is L- and D-amino acid. Conformers (rotamers) are the different arrangements (conformations) of a particular compound which result from free rotation about the carbon-carbon single bonds without breaking any bond. The energy barrier to rotation is, however, mostly small enough to allow free rotation in saturated com- pounds. Although different conformers cannot be isolated, the rotational arrangement of groups has an influence on chemical reactivity. Conformations in which large groups are as far apart as possible are generally the most stable ones. Nomenclature of Organic Compounds There are many common names of organic compounds which do not contain any structural infor- mation. These names were usually based on source material (citric acid, formic acid, lactate, caffeine, urea). Semisystematic names express certain chemical features, e.g. acetone is a ketone, cholesterol is a steroid alcohol. The complete structural information is contained in systematic names , which are based on the principles of IUPAC (International Union of Pure and Applied Chemistry). A part of the structure in molecule is taken as the basic structure , whereas the other parts are substit- uents, which replace some of hydrogen atoms of basic structure. The basic structure can be acyclic, cyclic or heterocyclic; only H atoms are bound to the atoms of the chain. Substituents are atoms or groups (e.g. - OH, - NH 2 , - COOH, methyl). Unsaturation of structure is expressed by the suffix - ene for a double bond, and - yne for a triple bond instead of – ane (for saturated skeleton). The presence of substituents in the basic structure is expressed by one suffix, one or more prefixes and locants. Suffix is a part of name, which expresses the present substituent with the highest priority, which determines the character of the compound. The hierarchy of the types of compounds for the application of the suffix is shown in the table below:
The other substituents (with lower priorities) are denoted by prefixes. The presence of a higher num- ber of the same substituents in the basic structure is expressed by multiple prefixes di- , tri - , tetra - etc. Locant is the number (1, 2, 3 …) or the symbol of an element (e.g. N- , O- ), which describes the posi- tion of the substituent(s) in the basic structure. Locants are placed just in front of the part of the name, to which they are directly related, for example: 1,2-dichloroethane, propane- 2 - ol, but- 2 - ene, cyclohex- 2 - ene- 1 - ol, N - methylbenzamide. To determine the name of an organic compound from the structural formula we follow several general steps:
carboxy- sulfo-
R-oxycarbonyl- carbamoyl- cyano- formyl- oxo- hydroxy- sulfanyl- amino- R-oxy- R-sulfanyl- fluoro-, chloro-, bromo-, iodo- nitro-
a E.g. RNH 3
isopren
en- 1 - yl), and CH 2 =CH–CH 2 - (allyl) from propene. Notice that the lower number is ascribed to the carbon with the free valence. The reactions of alkenes are typical for any compound that includes an isolated double bond.
ethanol ethene ethane
Reactions of aromatic hydrocarbons. Reactions of the side-chains attached to benzene rings are similar to the reactions of other hydrocarbons. Aromatic hydrocarbons do not react as other unsaturat- ed hydrocarbons due to the stable molecular - orbital.