Organic and Biological Molecules

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Organic and Biological Molecules
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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.

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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.

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Catenation in Phosphorus
white phosphorus
black phosphorus
red phosphorus
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Elemental Phosphorus
6
Catenation in Sulfur
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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.

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Typical Bond Energies
358
C-O
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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.

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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.

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Saturated Hydrocarbons

• Saturated hydrocarbons are alkanes. Alkanes
  have the general formula CnH2n2.

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Saturated Hydrocarbons
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Isomers

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

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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.

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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.

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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.

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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)

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Reactions of Alkanes

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

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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

h?
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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.

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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.

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Cyclic Alkanes

• Cyclopentane and cyclohexane both have bond
  angles very close to tetrahedral angles, and are
  quite stable as a result.
• Cyclohexane, C6H12, doesnt lie flat, but
  puckers to attain the proper bond angles.

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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.

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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.

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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, H2CCH2.

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Ethylene

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

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Ethylene

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

cis
trans
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Alkynes

• Alkynes contain at least one carbon-carbon
  triple bond. Acetylene, H-CC-H, is the simplest
  alkyne.

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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
• H2CCH2 H2 ? H3C-CH3
• Bromination
• H2CCH2 Br2 ? H2BrC-CH2Br

catalyst
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Aromatic Hydrocarbons

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

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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
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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
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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.

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

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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.

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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.

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Alcohols

• 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
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Aldehydes and Ketones

• Both aldehydes and ketones contain the carbonyl
  group
• CO
• 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.