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.

Organic and Organic and Biological Biological MoleculesMolecules

Unique Nature of CarbonUnique Nature of Carbon

Carbon has two properties that Carbon has two properties that enable it to form such an extensive enable it to form such an extensive range of compounds:range of compounds:

1. Catenation – the ability to 1. Catenation – the ability to form chains of form chains of atoms. atoms.

2. The ability to form multiple 2. The ability to form multiple bonds.bonds.

CatenationCatenation

Carbon readily forms long chains of Carbon readily forms long chains of bonds with itself. This property is called bonds with itself. This property is called catenationcatenation, and is fairly unique. It results for , and is fairly unique. It results for several reasons:several reasons:

1. Carbon can make up to 4 bonds.1. Carbon can make up to 4 bonds.

2. The carbon-carbon bond is generally as 2. The carbon-carbon bond is generally as

strong as bonds between carbon and strong as bonds between carbon and otherother

elements.elements.

3. The catenated compounds are inert.3. The catenated compounds are inert.

Catenation in Catenation in PhosphorusPhosphorus

white

phosphorus

black

phosphorus

red

phosphorus

Elemental PhosphorusElemental Phosphorus

Catenation in SulfurCatenation in Sulfur

Catenation of SiliconCatenation of Silicon

Silicon can also make long chains Silicon can also make long chains within its compounds, but, since the within its compounds, but, since the silicon oxygen bond is much stronger silicon oxygen bond is much stronger than that between two silicon atoms, than that between two silicon atoms, the chains typically contain –O-Si-O-Si- the chains typically contain –O-Si-O-Si- type links, rather than -Si-Si- bonds.type links, rather than -Si-Si- bonds.

Silicon also has empty low-lying Silicon also has empty low-lying dd orbitals which make its compounds orbitals which make its compounds more reactive.more reactive.

Typical Bond EnergiesTypical Bond Energies

C−O 358

CatenationCatenation

Since carbon can undergo Since carbon can undergo extensive catenation and make as extensive catenation and make as many as four bonds, the array of many as four bonds, the array of compounds is limitless.compounds is limitless.

The simplest compounds, those The simplest compounds, those with carbon and hydrogen, are used with carbon and hydrogen, are used as the basic structure of all as the basic structure of all molecules.molecules.

HydrocarbonsHydrocarbons

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

Saturated HydrocarbonsSaturated Hydrocarbons

Saturated Saturated hydrocarbons hydrocarbons are are alkanesalkanes. . Alkanes have Alkanes have the general the general formula Cformula CnnHH2n+22n+2..

Saturated HydrocarbonsSaturated Hydrocarbons

IsomersIsomers

Butane, Butane, CC44HH1010, has two , has two structure structure isomersisomers. That . That is, they contain is, they contain the same atoms, the same atoms, but a different but a different arrangement of arrangement of bonds.bonds.

Structural IsomersStructural Isomers

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

Naming Organic Naming Organic CompoundsCompounds

Many compounds are known by Many compounds are known by their “common” names, such as their “common” names, such as acetic acid for CHacetic acid for CH33COOH. A system COOH. A system of organic nomenclature has been of organic nomenclature has been developed for naming compounds.developed for naming compounds.

NomenclatureNomenclature

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

Reactions of AlkanesReactions of Alkanes

At room temperature, alkanes are At room temperature, alkanes are relatively inert, especially when relatively inert, especially when compared to unsaturated hydrocarbons.compared to unsaturated hydrocarbons.

At elevated temperatures, alkanes At elevated temperatures, alkanes undergo combustion (burn) with undergo combustion (burn) with oxygen.oxygen.

2 C2 C44HH1010((gg) + 13 O) + 13 O22((gg) ) 8 CO 8 CO22((gg) + 10 ) + 10 HH22O(O(gg) )

Reactions of AlkanesReactions of Alkanes

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

Reactions of AlkanesReactions of Alkanes

Alkanes undergo Alkanes undergo substitution substitution reactionsreactions with the halogens in the with the halogens in the presence of light. One or more presence of light. One or more hydrogen atom can be replaced hydrogen atom can be replaced with a halogen atom. The other with a halogen atom. The other product is gaseous HX.product is gaseous HX.

CHCH44 + Cl + Cl22 CH CH33Cl + HClCl + HCl

hν

Cyclic AlkanesCyclic Alkanes

The carbon atoms in The carbon atoms in hydrocarbons can form rings instead hydrocarbons can form rings instead of chains. Cyclic alkanes have the of chains. Cyclic alkanes have the general formula Cgeneral formula CnnHH2n2n. .

The smallest member of the The smallest member of the series, cyclopropane, has a three-series, cyclopropane, has a three-membered ring, and bond angles of membered ring, and bond angles of 6060oo. However, each carbon atom is . However, each carbon atom is spsp33 hybridized, with orbitals at 109.5 hybridized, with orbitals at 109.5oo..

Cyclic AlkanesCyclic AlkanesThree-membered Three-membered

rings are quite rings are quite strained, and strained, and cyclopropane is very cyclopropane is very reactive.reactive.

Cyclobutane is also Cyclobutane is also quite strained, with quite strained, with four carbon atoms in a four carbon atoms in a ring. The bond angles ring. The bond angles are 88are 88oo, and the , and the molecule is fairly molecule is fairly unstable. unstable.

Cyclic AlkanesCyclic Alkanes

Cyclopentane and cyclohexane Cyclopentane and cyclohexane both have bond angles very close both have bond angles very close to tetrahedral angles, and are to tetrahedral angles, and are quite stable as a result.quite stable as a result.

Cyclohexane, CCyclohexane, C66HH1212, doesn’t lie , doesn’t lie flat, but “puckers” to attain the flat, but “puckers” to attain the proper bond angles.proper bond angles.

Cyclic AlkanesCyclic Alkanes

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

Cyclic AlkanesCyclic Alkanes

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

Alkenes and AlkynesAlkenes and Alkynes

Hydrocarbons containing at Hydrocarbons containing at least one carbon-carbon double bond least one carbon-carbon double bond are called are called alkenesalkenes. Alkenes have the . Alkenes have the general formula Cgeneral formula CnnHH2n2n. .

The simplest alkene is ethylene, The simplest alkene is ethylene, HH22C=CHC=CH22..

EthyleneEthylene

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

EthyleneEthylene

As a result, As a result, ciscis and and transtrans isomers isomers are possible. The are possible. The isomers have isomers have different different polarities, melting polarities, melting points and boiling points and boiling points.points.

cis

trans

AlkynesAlkynes

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

Reactions of Alkenes and Reactions of Alkenes and AlkynesAlkynes

In addition to combustion and In addition to combustion and substitution reactions, alkenes and substitution reactions, alkenes and alkynes can undergo alkynes can undergo addition reactionsaddition reactions, , in which atoms are added across the in which atoms are added across the multiple bond.multiple bond.

Hydrogenation:Hydrogenation:

HH22C=CHC=CH22 + H + H22 H H33C−CHC−CH33

Bromination:Bromination:

HH22C=CHC=CH2 2 + Br+ Br22 H H22BrC−CHBrC−CH22BrBr

catalyst

Aromatic HydrocarbonsAromatic Hydrocarbons

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

Aromatic HydrocarbonsAromatic Hydrocarbons

Benzene, CBenzene, C66HH66, is the simplest , is the simplest aromatic hydrocarbon. It undergoes aromatic hydrocarbon. It undergoes substitution reactions rather than addition substitution reactions rather than addition reactions. The aromatic ring behaves reactions. The aromatic ring behaves more like a saturated hydrocarbon than an more like a saturated hydrocarbon than an unsaturated one.unsaturated one.

+ Cl2 HCl +

FeCl3

−Cl

Aromatic HydrocarbonsAromatic Hydrocarbons

In similar reactions, NOIn similar reactions, NO22 or a methyl or a methyl group (CHgroup (CH33) can be added to the ) can be added to the benzene ring. All of these reactions benzene ring. All of these reactions require the use of catalysts.require the use of catalysts.

+ CH3Cl HCl +

AlCl3

−CH3

Functional GroupsFunctional Groups

Many organic molecules can be Many organic molecules can be viewed as hydrocarbons that have an viewed as hydrocarbons that have an additional atom or group of atoms additional atom or group of atoms called a called a functional groupfunctional group..

For example, hydrocarbons with For example, hydrocarbons with an –O-H bonded to them are called an –O-H bonded to them are called alcoholsalcohols. Alcohols tend to undergo . Alcohols tend to undergo similar reactions and have similar similar reactions and have similar properties.properties.

FUNCTIONAL

GROUPS

AlcoholsAlcohols

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

AlcoholsAlcohols

Alcohols have higher boiling Alcohols have higher boiling points than expected (as does water) points than expected (as does water) due to the presence of protonic due to the presence of protonic bridging between molecules.bridging between molecules.

Although hydrocarbons are Although hydrocarbons are insoluble in water, the presence of insoluble in water, the presence of the hydroxyl group enables smaller the hydroxyl group enables smaller alcohol molecules to fully dissolve in alcohol molecules to fully dissolve in water.water.

AlcoholsAlcohols

Methyl alcohol, or methanol, is Methyl alcohol, or methanol, is also called wood alcohol. Its formula also called wood alcohol. Its formula is CHis CH33OH. Methanol is very toxic, OH. Methanol is very toxic, and causes blindness and death of it and causes blindness and death of it is consumed.is consumed.

Methanol is used to make other Methanol is used to make other compounds, notably acetic acid. It is compounds, notably acetic acid. It is also used as a motor fuel.also used as a motor fuel.

AlcoholsAlcohols

Ethanol, Ethanol, CHCH33CHCH22OH, is OH, is consumed in beverages consumed in beverages such as beer, wine and such as beer, wine and liquor. It is produced liquor. It is produced by the fermentation of by the fermentation of sugars.sugars.

CC66HH1212OO6 6 2 CH 2 CH33CHCH22OH OH + 2 CO+ 2 CO22

yeast

Aldehydes and KetonesAldehydes and Ketones

Both aldehydes and ketones Both aldehydes and ketones contain the contain the carbonyl groupcarbonyl group: :

C=OC=O

In aldehydes, the carbon atom is In aldehydes, the carbon atom is attached to at least one hydrogen attached to at least one hydrogen atom. In ketones, the carbon atom is atom. In ketones, the carbon atom is attached to two other carbon atoms.attached to two other carbon atoms.