Organic chemistry is the chemistry of carbon compounds. Organic compounds include hydrocarbons, sugars, alcohols, etc. The reason why there are so many carbon compounds is due to carbon's tetravalence (four valence electrons, and therefore four bonding sites). This tetravalence enables carbon to form long chains (which may or may not be branched), and rings (such as the benzene ring of six carbon atoms).

Hydrocarbons

Hydrocarbons are the simplest organic compounds, containing only carbon and hydrogen. All other organic compounds are considered derivative forms of hydrocarbons.

Hydrocarbons can be subdivided into two categories: aromatic hydrocarbons and aliphatic hydrocarbons. Aromatic hydrocarbons all contain a benzene ring or a similar structure. Aliphatic hydrocarbons do not contain a benzene ring.

Aliphatic hydrocarbons

Aliphatic hydrocarbons are divided into saturated and unsaturated hydrocarbons. In saturated hydrocarbons, there are only single bonds between the carbon atoms (all carbon atoms are bonded to the maximum number of hydrogen atoms). If a hydrocarbon is unsaturated, there may be double or triple bonds between carbon atoms.

Saturated hydrocarbons are further subdivided into alkanes and cycloalkanes; unsaturated hydrocarbons are classified as alkenes or alkynes.

Alkanes

Alkanes are saturated hydrocarbons with the general formula C_nH_{2n + 2}. Thus the simplest alkane is methane (CH₄).

Naming of Alkanes and Substituted Alkanes

1. Identify the longest CONTINUOUS chain of carbon atoms present. A prefix is used to indicate this number as follows:
   1. meth-
   2. eth-
   3. prop-
   4. but-
   5. pent-
   6. hex-
   7. hept-
   8. oct-
   9. non-
   10. dec-
2. Use the ending -ANE for all alkanes. Each functional group has its own suffix.
3. A substitution is an element or group that takes the place of a hydrogen off the carbon chain. Halogens are common substituents and are named by replacing the ending -ine with -o (for example, fluoro, chloro, etc.). An alkyl group is a branch that consists of carbon, hydrogen, and single bonds, and is given the suffix -yl. Attach the name of the alkyl group or other substitution as a prefix to the name of the parent carbon chain. The position of substituents on the longest continuous chain of carbon atoms is indicated by a number.
   
   e.g. 2-methylpropane

   

4. In numbering branched alkanes, you must assign a number to each carbon atom in the longest chain of carbon atoms present in the molecule. The numbering must start at whichever end is nearest a branch. In other words, your numbering system must result in the lowest possible numbers for the substituents on the longest chain of carbon atoms.
5. Arrange substituents alphabetically by name, regardless of their position or complexity. Numbers are separated from other numbers by commas, and from letters by dashes.
   e.g. 3-bromo-2-methylhexane
6. If the same alkyl group or substitution occurs more than once, indicate this by the use of the prefix di-, tri-, tetra-, etc., and indicate the positions of the alkyl groups or orther substitutions with the use of numbers. When there is more than one identical alkyl group substituted at the same carbon atom the number is repeated. When placing substituents in alphabetical order, the prefixes di-, tri-, etc. are ignored.
   
   e.g. 2,2-dimethylbutane
   
   e.g. 5-ethyl-2,2-dimethylheptane
   
   e.g. 5-ethyl-2,4-dimethylheptane
   
   
7. If the first side chain is the same distance from either end, choose the numbering scheme that is lowest at the point of difference.
8. If there are two chains of equal length, choose the one having the larger number of side chains.

Naming Cycloalkanes

Cycloalkanes are named using the same guidelines as for alkanes. For example, cyclopropane is so named because it contains three carbons in a ring. (Note: the hydrogens on the rings have been deliberately excluded to better show the ring structure.)

Alkenes and Alkynes

1. The IUPAC rules for naming alkenes and alkynes are adaptations of the rules for naming alkanes. The "parent chain" of an alkene is the longest continuous carbon chain that contains the carbon-carbon double bond (for an alkyne, the longest carbon chain containing the carbon-carbon triple bond). The name of an alkene parent carbon chain is given the suffix -ene and the appropriate prefix. The name of an alkyne parent carbon chain is given the suffix -yne and the appropriate prefix.
   
2. The position of the double (or triple) bond is indicated by the number of the first carbon in the double bond. The numbering begins from the end of the chain that is closest to the double or triple bond.
   
   e.g. 2-hexene
   
   
3. Some alkenes have two double bonds and are called dienes. Alkenes with three double bonds are called trienes, etc. The location of each double bond is indicated with the appropriate number.
   
   e.g. 2,4-octadiene
   
   

Isomers

Isomers are compounds with the same chemical formula but different arrangements of atoms. They have different arrangements of properties due to their different arrangements. The two major kinds of isomers are structural isomers and stereoisomers. Structural isomers differ in how the atoms are joined together, whereas stereoisomers are isomers in which the atoms are bonded together in the same order but differ in the precise arrangement of the atoms in space.

Ionization Isomers

Ionization isomers are isomers of a complex that differ in the anion that is coordinated to the metal atom. The following cobalt complexes provide an example:

[Co(NH₃)₅(SO₄)]Br (red compound)

[Co(NH₃)₅Br]SO₄ (violet compound)

These isomers differ in that either the sulphate or the bromide ion is attached to the cobalt atom. The red compound gives a precipitate of AgBr when mixed with silver nitrate solution, but no precipitate of BaSO₄ when mixed with barium chloride solution. This implies that the sulphate ion is strongly attached to the cobalt atom, whereas the bromide ion is not. The violet compound gives a precipitate of BaSO₄ when treated with barium chloride, but no precipitate of AgBr when treated with silver nitrate. This implies that the bromide ion is strongly attached to the cobalt atom, whereas the sulphate ion is not.

Hydrate Isomers

Hydrate isomers are isomers of a complex that differ in the placement of water molecules in the complex. An example is that of the three chromium complexes with composition CrCl₃ * 6H₂O.

[Cr(H₂O)₆]Cl₃ (violet compound)

[Cr(H₂O)₅Cl]Cl₂ * H₂O (light green compound)

[Cr(H₂O)₄Cl₂]Cl * 2H₂O (dark green compound)

In the violet complex, all the water molecules are coordinated to the chromium atom. In the others, one or two water molecules are not directly attached to the metal atom but occur elsewhere in the crystal lattice. The isomers can be differentiated by conductance measurements (which determine the number of ions per formula unit) and by the amount of AgCl precipitated by excess silver nitrate. (Cl^- bonded to Cr is not precipitated.) As well, the water molecules not directly coordinated to a Cr atom are easily lost. Therefore, the isomers behave differently when exposed to a dry atmosphere in contact with a dehydrating agent (such as concentrated sulfuric acid).

Coordination Isomers

Coordination isomers are isomers consisting of complex cations and complex anions that differ in the way the ligands are distributed between the metal atoms. (A ligand is a Lewis base that bonds to a metal ion to form a complex ion.) An example is:

[Cu(NH₃)₄][PtCl₄] and [Pt(NH₃)₄][CuCl₄]

In the first compound, the NH₃ ligands are associated with copper and the Cl^- ligands with platinum. In the second compound, the ligands are transposed. It is also possible for ligands to be distributed in different ways between two metal atoms of the same element. An example of this sort of coordination isomerism is:

[Pt(NH₃)₄][PtCl₄] and [Pt(NH₃)₃Cl][Pt(NH₃)Cl₃]

Linkage Isomers

Linkage isomers are isomers of a complex that differ in the atom of a ligand that is bonded to the metal atom. A ligand such as the nitrite ion, NO₂^-, can coordinate to a metal atom either with the electron pair on the nitrogen atom or with an electron pair on an oxygen atom. A complex with an O-bonded NO₂ ligand has the structure [Co(NH₃)₅(ONO)]Cl₂, where the nitrate ligand is written ONO to emphasize its O-bonding to cobalt. The compound is red and slowly changes to the yellow-brown isomer [Co(NH₃)₅(NO₂)]Cl₂, in which the nitrate group is N-bonded. Ligands such as NO₂^- that can bond through one atom or another are called ambidentate. Another ambidentate ligand is the thiocyanate ion, SCN^-, which can bond through the sulphur atom or the nitrogen atom.

Geometric Isomers

Rotation does not occur about a carbon-carbon double bond. This creates a form of isomer called geometric isomers. Geometric isomers in alkenes have the same molecular formula, and the same organization of atoms and bonds, but they differ in the direction of placement of the substituted groups at the double bond carbons. The two terms used to distinguish the two different directions are cis- (on the same side) and trans- (on opposite sides).

Cis-isomer of Pt(NH₃)₂Cl₂

Trans-isomer of Pt(NH₃)₂Cl₂

Derivatives of Hydrocarbons

Functional Groups

The distinctive properties of an organic molecule depend not only on the arrangement of its carbon skeleton, but also on the molecular components attached to that skeleton. Certain groups of atoms are frequently attached to carbon skeletons of organic molecules. These ensembles of atoms are known as functional groups because they are the regions of organic molecules most commonly involved in chemical reactions. The six functional groups most important in the chemistry of life are the hydroxyl, carbonyl (aldehydes, which occur at the end of a carbon chain, and ketones, which occur in the middle of a carbon chain), carboxyl, amino, sulfhydryl, and phosphate groups.

Hydroxyl and Carbonyl Groups

Hydroxyl groups (-OH) are attached at the end of alcohols, whereas carbonyl groups (-C=O) are attached to the carbon chains of aldehydes and ketones (depending on the carbonyl's placement in the carbon chain).

Carboxyl Groups

Carboxyl groups (-COOH) are attached at the end of organic acids (carboxylic acids).

Amino Groups

Amino groups (-NH₃⁺) are attached to amines.

Sulfhydryl Groups

Sulfhydryl groups (-SH) are attached to thiols.

Phosphate Groups

Phosphate groups (-PO₄^-2) are attached to organic phosphates.

Alcohols

Alcohols are common organic substances which undergo a variety of chemical reactions. The two simplest alcohols, methanol and ethanol, are very important commercially.

Methanol, CH₃OH, also known as wood alcohol, is toxic, leading to blindness and death if swallowed. Methanol can be used as a motor fuel, and it is the starting point for the manufacture of many other chemicals.

Ethanol, CH₃CH₂OH, is the alcohol found in alcoholic beverages. Ethanol is a depressant. When abused it causes loss of coordination and long term abuse damages the brain and liver. The fetus of a pregnant woman is particularly vulnerable. Ethanol can also be used as a motor fuel and is often mixed with gasoline to form "gasohol".

Nomenclature Rules for Alcohols

1. Select the longest chain of carbon atoms that contains the -OH functional group.
2. Number the chain so that the carbon with the -OH attached gets the lowest possible number.
3. The name of the compound is derived from the corresponding alkane by replacing the final -e with -ol.
4. Name any other groups in the usual way.

Types of Alcohols

Primary alcohols have one carbon atom bonded to the carbon atom that the -OH group is attached to (e.g. ethanol). Secondary alcohols have two carbon atoms bonded to the carbon atom that the -OH group is attached to (e.g. 2-propanol). Tertiary alcohols have three carbon atoms attached to the carbon atom that the -OH group is attached to (e.g. 2-methyl-2-propanol).

Oxidation Reactions of Alcohols

Primary alcohols oxidize to aldehydes (which may in turn oxidize to carboxylic acids). Secondary alcohols oxidize to ketones. Tertiary alcohols do not oxidize.

Oxidation of a Primary Alcohol

Oxidation of a Secondary Alcohol

Oxidation of a Tertiary Alcohol

Carbohydrates

Carbohydrates are derivatives of hydrocarbons. Carbohydrates are named based on the number of carbons in the chain. For example, a three-carbon sugar is called a triose, a five-carbon sugar is called a pentose, and a six-carbon sugar is called a hexose.

Monosaccharides

Monosaccharides are the monomers or building blocks of carbohydrates. They have the general formula C_nH_2nO_n. They are single carbohydrate units which join together by dehydration synthesis to form larger carbohydrate polymers. Monosaccharides include glucose, fructose, and galactose.

Disaccharides

Disaccharides are two monosaccharides joined together by dehydration synthesis. In dehydration synthesis, a molecule of water is lost. Disaccharides include sucrose (glucose + fructose), maltose (glucose + glucose), and lactose (glucose + galactose).

Polysaccharides

Polysaccharides are polymers of glucose. The structure and rigidity of the polymer depends on the rings forms of glucose (alpha or beta) that are present. As well, 1-4 (carbon 1 to carbon 4) linkages give linear structure and 1-6 (carbon 1 to carbon 6) linkages cause branched polymers.

Starch

Starch is composed of alpha 1-4 linked glucose monomers that make up very flexible linear chains. Starch is a plant glucose storage product. Plants store starch as granules within cellular structures called plastids, including chloroplasts. It may then be broken down by hydrolysis into the component glucose monomers when required by the plant. Most animals, including humans, also have enzymes that can digest starch. The enzyme in saliva that digests starch is salivary amylase.

Cellulose

Cellulose is composed of beta 1-4 linked glucose monomers. Since all of the glucose molecules are in the beta ring form, the three-dimensional structure of cellulose is very different from that of starch. Cellulose makes up the support structures of plants. In the cell walls of plants, many parallel cellulose structures, held together by hydrogen bonds between the hydroxyl groups of the glucose monomers, are arranged as units called microfibrils.

Glycogen

Glycogen is composed of alternating alpha 1-4 and 1-6 linked glucose molecules. Due to the 1-6 linkages, glycogen is a very branched polymer. It is the storage form of glucose in animals.

Chitin

Chitin is made up of alpha 1-4, beta 1-4, and beta 1-6 linked glucose molecules. It makes up insect exoskeletons and is also used in surgical thread that does not need to be removed.

Proteins

Proteins are essential for the proper functioning of our bodies. Approximately 50% of an human's dry weight is protein. Proteins are structural constituents of the cell membrane, collagen, elastin, and keratin. Most enzymes are proteins (although some are lipids). Proteins are necessary for movement (they make up the actin and myosin of muscles), transport, blood clotting (fibrinogen is a protein), immune system function (antibodies), food reserves (albumin and casein), and in the stabilizing of DNA. Proteins are made up of amino acids (which are composed of a side group which is bonded to a carbon backbone that is also bonded to an amino group (-NH₃) and a carbonyl group (COO^-).

Lipids

The compounds called lipids are grouped together because they share one important trait: They have little or no affinity for water. The hydrophobic behaviour of lipids is due to their molecular structure. Although lipids may have some polar bonds associated with oxygen, lipids consist mostly of hydrocarbon. Three important families of lipids are fats, phospholipids and steroids. Other families of lipids include waxes and certain pigments in plants and animals.

Fats

Fats are large molecules, but not polymers. Fats are made up of a glycerol backbone and three fatty acids. Glycerol is an alcohol with three carbons, each bearing a hydrozyl group. A fatty acid has a long carbon skeleton, usually 16 or 18 carbon atoms in length. At one end of the fatty acid is a "head" consisting of a carboxyl group (the functional group of organic acids). Attached to the carboxyl group is a long hydrocarbon "tail". Since C-H bonds are nonpolar, they cannot n=bond to the polar regions of water and thus are hydrophobic.

Phospholipids

Phospholipids are structurally related to fats, but only have two fatty acids instead of three. The third hydroxyl group of glycerol is attached to a phosphate group which carries a negative charge. Additional small molecules, usually charged or polar, can be linked to the phosphate group to form a variety of phospholipids. Phospholipids show "ambivalent" behaviour towards water: the phosphate heads, which are hydrophilic, have an affinity for water. The hydrophobic tails of phospholipids are excluded from water.

Steroids

Resources:

Campbell, Neil A., "Biology", 4th ed., The Benjamin/Cummings Publishing Company, Inc., Don Mills, Ontario, 1996

Ebbing, Darrell D., "General Chemistry", 5th ed., Houghton Mifflin Company, Toronto, 1996

Many thanks to my chemistry teacher Dr. Mustoe and my biology teacher Ms. O'Mahony.

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