Organic and Biological Molecules

Unique Nature of Carbon Carbon has two properties that enable it to form such an extensive range of compounds: 1. Catenation – the ability to form chains of atoms. 2. The ability to form multiple bonds.

Catenation Carbon readily forms long chains of bonds with itself. This property is called catenation, and is fairly unique. It results for several reasons: 1. Carbon can make up to 4 bonds. 2. The carbon-carbon bond is generally as strong as bonds between carbon and other elements. 3. The catenated compounds are inert.

Catenation in Phosphorus white phosphorus black phosphorus red phosphorus

Elemental Phosphorus

Catenation in Sulfur

Catenation of Silicon Silicon can also make long chains within its compounds, but, since the silicon oxygen bond is much stronger than that between two silicon atoms, the chains typically contain –O-Si-O-Si- type links, rather than -Si-Si- bonds. Silicon also has empty low-lying d orbitals which make its compounds more reactive.

Typical Bond Energies 358 C−O

Catenation Since carbon can undergo extensive catenation and make as many as four bonds, the array of compounds is limitless. The simplest compounds, those with carbon and hydrogen, are used as the basic structure of all molecules.

Optical Isomerism

Optical Isomerism When a carbon atom is bonded to four different atoms or groups, optical isomers result. The isomers have differing spatial arrangements, with the two molecules being mirror images of each other. The mirror images are nonsuperimposable, like a left hand and a right hand.

Optical Isomerism

Optical Isomerism A molecule that exhibits optical isomerism is called chiral. Most biological molecules are chiral, often with one isomer performing important biological functions while the other may be biologically inactive. Although inorganic molecules can also be chiral, the chirality of organic molecules is of major biochemical importance.

Optical Isomerism Optical isomers are also called enantiomers. A pair of enantiomers are identical in many respects. They have the same melting point, density, polarity and solubility. The two differences are that they bend plane polarized light in opposite directions, and they behave differently in a chiral environment.

Chiral Environments Many biologically active sites are chiral. Examples might be the site of enzyme activity. Only one configuration of the chiral molecule fits properly into the reaction site, so only one enantiomer will be biologically active.

Chiral Environments

Hydrocarbons Hydrocarbons are compounds composed of carbon and hydrogen. If all of the carbon-carbon bonds are single bonds, the compound is saturated. Hydrocarbons containing double or triple bonds between carbon atoms are called unsaturated.

Saturated Hydrocarbons Saturated hydrocarbons are alkanes. Alkanes have the general formula CnH2n+2.

Saturated Hydrocarbons

Isomers Butane, C4H10, has two structural isomers. That is, they contain the same atoms, but a different arrangement of bonds.

Structural Isomers The two isomers of butane will have different properties. The n-butane, with four carbon atoms in a single chain, has a boiling point of -.5oC. Isobutane, with the branched chain, has a boiling point of -12oC.

Naming Organic Compounds Many compounds are known by their “common” names, such as acetic acid for CH3COOH. A system of organic nomenclature has been developed for naming compounds.

Nomenclature The butyl groups have three different structures. Tert-butyl contains a tertiary carbon atom- one that is bonded to three carbons. Sec-butyl contains a secondary carbon atom – one that is bonded to two carbons.

Reactions of Alkanes At room temperature, alkanes are relatively inert, especially when compared to unsaturated hydrocarbons. At elevated temperatures, alkanes undergo combustion (burn) with oxygen. 2 C4H10(g) + 13 O2(g)  8 CO2(g) + 10 H2O(g)

Reactions of Alkanes Alkanes burn cleanly to form carbon dioxide and water vapor. The reactions are exothermic, so alkanes make excellent fuels.

Reactions of Alkanes Alkanes undergo substitution reactions with the halogens in the presence of light. One or more hydrogen atom can be replaced with a halogen atom. The other product is gaseous HX. CH4 + Cl2  CH3Cl + HCl hν

Cyclic Alkanes The carbon atoms in hydrocarbons can form rings instead of chains. Cyclic alkanes have the general formula CnH2n. The smallest member of the series, cyclopropane, has a three-membered ring, and bond angles of 60o. However, each carbon atom is sp3 hybridized, with orbitals at 109.5o.

Cyclic Alkanes Three-membered rings are quite strained, and cyclopropane is very reactive. Cyclobutane is also quite strained, with four carbon atoms in a ring. The bond angles are 88o, and the molecule is fairly unstable.

Cyclic Alkanes Cyclopentane and cyclohexane both have bond angles very close to tetrahedral angles, and are quite stable as a result. Cyclohexane, C6H12, doesn’t lie flat, but “puckers” to attain the proper bond angles.

Cyclic Alkanes The cyclohexane molecule exists in two forms. The “chair” form has 4 carbon atoms in a plane, with one end “flipped up” and the other “flipped down.”

Cyclic Alkanes The “boat” form has 4 carbon atoms in a plane, with both ends “flipped up.” This arrangement is less stable, with repulsion between hydrogen atoms.

Alkenes and Alkynes Hydrocarbons containing at least one carbon-carbon double bond are called alkenes. Alkenes have the general formula CnH2n. The simplest alkene is ethylene, H2C=CH2.

Ethylene The double bond between the carbon atoms prevents rotation of one side of the molecule relative to the other.

Ethylene As a result, cis and trans isomers are possible. The isomers have different polarities, melting points and boiling points. cis trans

Alkynes Alkynes contain at least one carbon-carbon triple bond. Acetylene, H−C≡C−H, is the simplest alkyne.

Reactions of Alkenes and Alkynes In addition to combustion and substitution reactions, alkenes and alkynes can undergo addition reactions, in which atoms are added across the multiple bond. Hydrogenation: H2C=CH2 + H2  H3C−CH3 Bromination: H2C=CH2 + Br2  H2BrC−CH2Br catalyst

Aromatic Hydrocarbons There is a separate class of cyclic unsaturated hydrocarbons called aromatic hydrocarbons. These compounds have a planar ring structure and a delocalized π system. The extended pi bonding provides exceptional stability to these molecules. Unlike other hydrocarbons, they do not burn well or cleanly. During reactions, the extended pi system remains intact.

Aromatic Hydrocarbons Benzene C6H6

Aromatic Hydrocarbons Benzene C6H6

Aromatic Hydrocarbons Benzene, C6H6, is the simplest aromatic hydrocarbon. It undergoes substitution reactions rather than addition reactions. The aromatic ring behaves more like a saturated hydrocarbon than an unsaturated one. FeCl3 + Cl2  HCl + −Cl

Aromatic Hydrocarbons In similar reactions, NO2 or a methyl group (CH3) can be added to the benzene ring. All of these reactions require the use of catalysts. AlCl3 + CH3Cl  HCl + −CH3

Functional Groups Many organic molecules can be viewed as hydrocarbons that have an additional atom or group of atoms called a functional group. For example, hydrocarbons with an –O-H bonded to them are called alcohols. Alcohols tend to undergo similar reactions and have similar properties.

F U N C T I O A L G R O U P S

Alcohols All alcohols contain the hydroxyl group, -OH. This greatly changes the properties of the hydrocarbon to which it is attached. Hydrocarbons are non-polar, with low boiling points and poor solubility in polar solvents. The presence of an –OH group increases the polarity of the molecule, and provides a site for “hydrogen bonding” or protonic bridging.

Alcohols Alcohols have higher boiling points than expected (as does water) due to the presence of protonic bridging between molecules. Although hydrocarbons are insoluble in water, the presence of the hydroxyl group enables smaller alcohol molecules to fully dissolve in water.

Alcohols Methyl alcohol, or methanol, is also called wood alcohol. Its formula is CH3OH. Methanol is very toxic, and causes blindness and death of it is consumed. Methanol is used to make other compounds, notably acetic acid. It is also used as a motor fuel.

Alcohols C6H12O6  2 CH3CH2OH + 2 CO2 yeast Ethanol, CH3CH2OH, is consumed in beverages such as beer, wine and liquor. It is produced by the fermentation of sugars. C6H12O6  2 CH3CH2OH + 2 CO2 yeast

Aldehydes and Ketones Both aldehydes and ketones contain the carbonyl group: C=O In aldehydes, the carbon atom is attached to at least one hydrogen atom. In ketones, the carbon atom is attached to two other carbon atoms.

Aldehydes The simplest aldehyde is formaldehyde, CH2O. It has a pungent odor and is used as a preservative and disinfectant. Aromatic aldehydes have pleasant odors, and cause the aromas of vanilla, cinnamon and almonds.

Ketones The simplest ketone is acetone, (CH3)2CO. Acetone is used in nail polish remover. Other ketones are responsible for the smell of cloves, raspberries and spearmint.

Carboxylic Acids & Esters Carboxylic acids taste sour, and are found in vinegar (acetic acid), insect stings and bites (formic acid), and citrus fruits (citric acid). Esters are known for their pleasant aromas, such as the smell of apples, pineapples or bananas.