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10 Introduction to Organic Chemistry
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 CC and CH, 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 CH3-CH2-OH is polar because the CO bond is qu ite polar and
the OH bond is even more polar than the CH 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 CCl4 is non-polar because of
the symmetrical tetrahedral geometry of four polar CCl bonds.
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10 Introduction to Organic Chemistry

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.

COOH

C

R

H 2 N H

COOH

C

R

H NH 2

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:

  1. Onium cations
  2. Carboxylic acids, sulfonic acids
  3. Acid anhydrides
  4. Esters
  5. Acid halogenides
  6. Amides
  7. Nitriles
    1. Aldehydes
    2. Ketones
    3. Alcohols, phenols, thiols
    4. Hydroperoxides
    5. Amines
    6. Ethers, sulfides
    7. Peroxides, disulfides

O

OH

NH 2

H 2 N

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:

  1. Find basic structure, the main chain has the highest number of characteristic groups and multiple bonds.
  2. Determine, which of the characteristic groups will be expressed by the suffix as the main one.
  3. Name the basic structure.
  4. Name the main group by the suffix.
  5. Determine other substituents and to name them by prefixes.
  6. Determine locants, so that the main group has the lowest locant.
  7. Set individual parts, prefixes are arranged in the alphabetical order. Prefixes and suffixes for some characteristic groups are presented in the following table. Type of compound Group Prefix Suffix Onium cation Carboxylic acids Sulfonic acids Salts of carboxylic acids Esters Amides Nitriles Aldehydes Ketones Alcoholes, phenoles Thiols Amines Ethers Sulfides b Halogenderivates b Nitroderivates b
  • a
  • COOH
  • SO 3 H
  • COO-
  • COOR
  • CONH 2
  • C N
  • CH=O >C=O
  • OH
  • SH
  • NH 2
  • OR
  • SR
  • F, - Cl, - Br, - I
  • NO 2

carboxy- sulfo-

R-oxycarbonyl- carbamoyl- cyano- formyl- oxo- hydroxy- sulfanyl- amino- R-oxy- R-sulfanyl- fluoro-, chloro-, bromo-, iodo- nitro-

  • onium
  • oic / - carboxylic acid
  • sulfonic acid
  • (o)ate, - carboxylate R-(o)ate, R-carboxylate
  • (carbox)amide
  • (carbo)nitrile
  • al, - carbaldehyde
  • one
  • ol
  • thiol
  • amine
  • ether

a E.g. RNH 3

  • (^) alkylammonium, ROH 2
  • (^) alkyloxonium, R 3 S
  • (^) trialkylsulfonium. b (^) Exclusively as prefixes. Example: basic structure: hexane suffix group: - COOH ( - oic acid ) prefix groups: - NH 2 ( amino ), multiple prefix: di locants: 2, complete set = systematic name: 2,6-diaminohexanoic acid (lysine)
  1. Elimination (dehydrogenation) yields alkenes during the thermal or catalytic cleavage of petrole- um, e.g.: CH 3 - CH 3 H 2 + CH 2 =CH 2. Cycloalkanes have monocyclic or polycyclic structures. The five- and six-membered rings are com- mon because of little or no strain due to deformations of bond angles. Cyclopentane has a nearly pla- nar ring of five carbon atoms. Cyclohexane forms two most stable chair conformations which are interconvertible by rotation of the carbon-carbon bonds through a less stable boat conformation_._ Unsaturated hydrocarbons Alkenes and cycloalkenes contain one carbon-carbon double bond, two double bonds are present in alkadienes and there are also alkatrienes, tetraenes and even polyenes. When two or more double bonds are present in a molecule, properties depend on their relative positions. Isolated double bonds are separated by two or more single bonds; they do not influence each other. Very important compounds are those with conjugated bonds which alternate with single bonds (double bonds are separated by a single bond). The most common is isoprene (2-methylbuta-1,3-diene), a building unit of many naturally occurring compounds (isoprenoids, terpenes). Nomenclature. The simplest alkene of the homologous series is ethene, CH 2 =CH 2 (trivial name eth- ylene is quite common), followed by propene (commonly propylene), and the four isomeric butenes: but- 1 - ene, cis - but- 2 - ene, trans - but- 2 - ene (geometric isomers), and 2 - methylpropene. The chain is numbered from the end nearest to the multiple bond and its position is indicated by a lower-numbered carbon of that bond. In branched unsaturated hydrocarbons, the parent structure is the longest chain that includes most of the multiple bonds and the position of the multiple bond is designated by a num- ber which takes preference (lower number) over that for alkyl substituents, E.g. 2 - ethyl- 3 - methylbut- 1 - ene, notice that the main chain has four carbons, not five: Monovalent groups are generally alkenyls. For instance, vinyl from ethene H 2 C=CH- (ethenyl, as it would be logical, is not allowed), 1-propenyl (prop- 1 - en- 1 - yl) CH 3 – CH=CH-, and 2 - propenyl (prop- 2 - chair conformation boat conformation real structure of cyclohexane (simplified formulas without H atoms)

H 3 C CH

CH 3

C

CH 2

C H 2 CH 3 2 - ethyl-^3 - methylbut-^1 - ene

C C
H
H CH 3
C
H
C
H
H

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.

  1. Addition reactions are the most common reactions with unsaturated compounds. The - bond of the multiple bond is broken, the reactant attached and the saturated product results, examples are given in the table: If an asymmetrical reagent (HBr, H 2 O) is added to an asymmetrical alkene, the hydrogen in the rea- gent goes to the carbon atom with a greater number of hydrogen atoms (Markovnikov's rule). Alkenes can undergo addition polymerization. Low-molecular unsaturated monomers join each other to produce high-molecular polymers as natural or synthetic rubber, neoprene, polyethylene, teflon, polystyrene, polyvinyl chloride (PVC), polymethacrylate, etc. However, not all polymers are adducts, another class of polymers is produced by condensation reactions as polyamides, polyesters, polyethers, not speaking of natural biopolymers (polysaccharides, proteins, and nucleic acids).
  2. Oxidation of alkenes may convert them to dihydroxycompounds, called glycols (alkanediols), or may lead to breaking the double bond and forming two carbonyl compounds. Alkynes possess one or more triple bonds. Their reactivity is similar but somewhat lower than that of alkenes. The simplest compound is gaseous ethyne , H-C C-H, common name acetylene. It can be prepared from calcium carbide CaC 2 and water and exhibits a slightly acidic character. It might be assumed that vinylalcohol, H 2 C=CH-OH, is the product of ethyne hydration. However, acetaldehyde is the product because of a rearrangement of unstable enol to its more stable carbonyl form, keto-enol tautomerism (H 2 C=CH-OH ⇄ CH 3 - CH=O). Aromatic hydrocarbons form a distinct group of hydrocarbons which comprise one or more benzene rings. In benzene, C 6 H 6 , all six carbons of the cycle as well as six hydrogen atoms lie in the same plane and all bond angels are 120° (hybridization sp^2 ). Six - electrons of the unhybridized carbon p - orbitals are delocalized within the molecular orbital spread over the ring which makes the ring very stable. In spite of the occasional Reaction Reagent Product Hydrogenation Chlorination Hydration H 2 Cl 2 H 2 O alkane dichloroalkane alcohol

C C

H

H H

H

H 2 O H 2

H 3 C C H 2 OH^ H 3 C^ C^ H 3

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.

  1. Addition reactions do not occur readily.
  2. Substitutions are the major type of reaction of the aromatic ring, hydrogen atom(s) can be replaced with a halogen atom (halogenation), with a nitro group - NO 2 (nitration), or an acidic - SO 3 H group (sulfonation). Any substituent attached to the ring polarizes the ring directing so other substituents which may react to certain positions on the ring.
  3. The benzene ring resists to oxidation. Oxidation of side chains, if present, takes place as well as oxidation of some of the fused rings in polycyclic aromatic hydrocarbons. Polycyclic aromatic hydrocarbons (PAH) have more fused benzene rings. The most common of them are naphthalene (two rings), anthracene (three rings condensed linearly), and its isomer phenan- threne (three rings condensed forming an angle). Some of them are carcinogenic. They are found in coal tar, soot or tobacco smoke, they can be formed also by overheating unsaturated fatty acids in fats during barbecuing and frying. 1 2 naphthalene anthracene^ phenanthrene