Introduction to Organic Chemistry

1
Introduction to Organic Chemistry

• Yes!!
• I cant wait!!!
• I hear everyone fails this in college!!!

2
Intro - Organic Molecules

• Living things are composed of organic molecules,
  which means that they contain carbon
• carbon has four electrons in outer shell which
  can bond with other atoms
• carbon can be linked to other carbons or atoms
  such as hydrogen (H), oxygen (O) and nitrogen(N)
• long links of these carbons can form into chains
  or rings
• Some organic molecules ONLY contain linked
  carbons and hydrogen ----gthydrocarbons (ex
  methane)
• living organisms tend to be composed of very long
  and unreactive carbon chains (unlike methane,
  which is very reactive!)

3
Intro Functional Groups

• In organic chemistry, molecules with similar
  properties are grouped together
• These all have similar groups of atoms, and these
  groups of atoms are called functional groups
• Functional groups can provide physical and
  chemical properties such as polarity and acidity
  (ex carboxyl, -COOH, is a weak acid)
• Most reactions in living organisms involves the
  transfer of a functional group from one molecule
  to another
• The following is a list of common functional
  groups
• OH Hydroxyl
• CO Carbonyl
• COOH Carboxyl
• NH2 Amino
• SH Sulfhydryl
• PO4 Phosphate
• CH3 Methyl

YOU MUST MEMORIZE THIS LIST!!!
4
Intro Functional Groups
5
Intro Functional Groups
6
Intro - Macromolecules

• Construction of Macromolecules
• many macromolecules are polymers, which means
  that they are constructed of many linked
  identical or similar subunits
• How are macromolecules made? Remove an OH from
  one molecule, and an H from another molecule
• this requires energy
• it is called dehydration synthesis (do you see
  the water above?!)
• in living organisms, enzymes assist in these
  reactions
• Macromolecules are disassembled in the opposite
  way, by adding a water molecule (OH added to one,
  H to another subunit)
• this releases energy
• a reaction of this type is called a hydrolysis

7
Intro - Dehydration Synthesis
8
Hydrocarbons - Naming

• Compounds containing just carbons and hydrogens
  are the most basic compounds encountered in
  organic chemistry.
• hydrocarbons.
• can be divided into three groups
• those containing just single bonds
• those containing one or more double bonds
• those containing one or more triple bonds.
• Before discussing how to name these compounds, it
  is instructive to examine how they are
  represented by chemists.

9
Drawing Hydrocarbons

• Recall - carbon makes four bonds and had the
  tetrahedral geometry
• only two bonds can occupy a plane simultaneously.
  
• The other two bonds point in back or in front of
  the plane.
• In order to represent the tetrahedral geometry in
  two dimensions
• solid wedges are used to represent bonds pointing
  out of the plane of the drawing toward the viewer
• dashed wedges are used to represent bonds
  pointing out of the plane of the drawing away
  from the viewer
• Consider the following representation of the
  molecule methane
• Two dimensional representation of methane

10
Drawing Hydrocarbons

• it can be time-consuming to write out each atom
  and bond individually.
• hydrocarbons can be represented in a shorthand
  notation called a skeletal structure.
• only the bonds between carbon atoms are
  represented.
• Individual carbon and hydrogen atoms are not
  drawn
• bonds to hydrogen are not drawn.
• If the molecule contains just single bonds drawn
  in a "zig-zag" fashion.
• This is because in the tetrahedral geometry all
  bonds point as far away from each other as
  possible, and the structure is not linear.
• representations of the molecule propane
• Full structure of propane Skeletal structure of
  propane

11
Drawing Hydrocarbons

• Only the bonds between carbons have been drawn,
  and these have been drawn in a "zig-zag" manner.
• no evidence of hydrogens in a skeletal structure.
  
• in the absence of double or triple bonds, carbon
  makes four bonds total, the presence of hydrogens
  is implicit.
• Whenever an insufficient number of bonds to a
  carbon atom are specified in the structure, it is
  assumed that the rest of the bonds are made to
  hydrogens.
• For example
• if the carbon atom makes only one explicit bond,
  there are three hydrogens implicitly attached to
  it.
• If it makes two explicit bonds, there are two
  hydrogens implicitly attached, etc.
• Two lines are sufficient to represent three
  carbon atoms.
• It is the bonds only that are being drawn out
  it is understood that there are carbon atoms
  (with three hydrogens attached!) at the terminal
  ends of the structure.

12
Alkane nomenclature

• When hydrocarbons contain only single bonds, they
  are called alkanes.
• Alkanes are named using a prefix for the number
  of carbon atoms they contain, followed by the
  suffix -ane.
• Number root example Structure
• 1 meth- methane (see board)
• 2 eth- ethane
• 3 prop- propane
• 4 but- butane
• 5 pent- pentane
• 6 hex- hexane
• 7 hept- heptane
• 8 ox- oxane
• 9 non- nonane

13
Alkane nomenclature

• Alkane nomenclature is straightforward
• difficulties come if one of the hydrogen or
  carbon atoms on the molecule is replaced by
  another atom or group.
• When this takes place, the group which replaces
  the hydrogen or carbon is called a substituent.
• Let's consider the situation in which one of the
  hydrogen atoms on an alkane has been replaced by
  another alkane.
• Consider the following molecule, 3-methypentane

14
Alkane nomenclature

• Consider the following molecule, 3-methypentane
• Long chain of five carbon atoms at the top of the
  image.
• If this were all that composed the molecule, it
  would simply be called pentane.
• However, one of the hydrogens on the carbon third
  from the end has been replaced with an alkane,
  specifically methane.
• How are we to name this molecule?

15
Alkane nomenclature - Rules

• First, we identify the longest chain of carbon
  atoms. We name this alkane. It will serve as the
  root name for the molecule.
• In the example above, the root name is pentane.
• Next, we number the carbon atoms, starting at the
  end that gives the substituent the lowest number.
  
• In the example above, we can count from either
  end and arrive at 3 for the substituent.
• Next, we name the substituent as if it were an
  independent alkane. However, we replace suffix
  -ane with -yl. This name will serve as the
  prefix.
• In the example above, methane is the
  substituent, so we call it methyl.
• The compound is named "number-prefixrootname".
• In the example above, the name is
  3-methylpentane

16
Alkane nomenclature - Rules

• What happens if the alkane has more than one
  substituent?
• In this case, the rules above are followed, and
  the carbons on the longest chain are numbered to
  give the lowest number possible to one of the
  substituent.
• The substituents are then all named in the prefix
  (e.g. 2-ethyl,3-methyl).
• If more than one substituent is attached to the
  same carbon atom, the number of that carbon atom
  is repeated to indicate the number of
  substituents and the prefixes di- (2) or tri- (3)
  are used.
• If there are more than one substituent on
  different carbon atoms, the prefixes are ordered
  alphabetically (e.g. ethene before methane).
• The prefixes di- and tri- are ignored when
  considering alphabetical order. Consider the
  following compound

17
Alkane nomenclature

• The longest carbon chain has seven carbon atoms,
  so the root name is heptane.
• Numbering from the right gives the lowest number
  to the first substituent.
• There are two methyl substituents at the second
  carbon atom, so we use the prefix 2,2-dimethyl.
• There is another substituent on the fourth carbon
  atom, so we use the prefix ethyl.
• Ethyl comes before methyl alphabetically, so we
  name the compound 4-ethyl-2,2-dimethylheptane.

18
Alkene Nomenclature

• Alkenes are hydorcarbons containing one or more
  double bonds.
• Alkenes are named using the same general naming
  rules for alkanes, except that the suffix is now
  -ene. There are a few other small differences
• The main chain of carbon atoms must contain both
  carbons in the double bond.
• The main chain is numbered so that the double
  bond gets the smallest number.
• Before the root name, the number of the carbon
  atom at which the double bond starts (the smaller
  number) is written.
• If more than one double bond is present, the
  prefixes di-, tri-, tetra-, etc. are used before
  the -ene, and (strangely) the letter "a" is added
  after the prefix for the number of carbon atoms.

19
Alkyne Nomeclature

• Hydorcarbons containing one or more triple bonds
  are called Alkynes.
• Alkynes are named using the same general
  procedure used for alkenes, replacing the suffix
  with -yne.
• If a molecule contains both a double and a triple
  bond, the carbon chain is numbered so that the
  first multiple bond gets a lower number.
• If both bonds can be assigned the same number,
  the double bond takes precedence.
• The molecule is then named "n-ene-n-yne", with
  the double bond root name preceding the triple
  bond root name
• (e.g. 2-hepten-4-yne).

20
Functional Group Nomenclature

• Alkanes are extremely unreactive.
• Carbon-carbon and carbon-hydrogen bonds are among
  the most stable bonds in chemistry
• alkanes serve as a backbone or template on which
  unreactive carbon or hydrogen atoms can be
  replaced by substituents consisting of more
  reactive atoms or groups of atoms.
• A substitient consisting of an atom or group of
  atoms other than carbons and hydrogens is called
  a functional group.
• Functional groups are significant because they
  are the part of the molecule that undergoes
  reactions.
• One functional group may change into another one,
  or a functional group might react with a separate
  molecule to build up a larger structure.
• Functional groups are the essential "reacting
  units" in organic chemistry.

21
Functional Group Nomenclature

• We have already encountered two functional
  groups. The double bonds in alkenes and the
  triple bonds in alkynes are able to undergo
  reactions that the single bonds in alkanes
  cannot.
• There are several other significant functional
  groups, summarized in the table below. Note that
  in organic chemistry, the letter "R" represents
  any alkane, and the letter "X" represents any
  halogen.
• Functional group Structure
• Alkyl halide R-X
• Alcohol R-OH
• Ether R-O-R
• Amine NR3

22
Naming Alkyl Halides

• One of the simplest functional groups is the
  alkyl halide.
• In an alkyl halide, one of the hydrogen atoms in
  an alkane has been replaced by a halogen.
• What are halogens again?
• Alkyl halides are easy to name
• name of the alkane is preceded by the number of
  the carbon on which the halogen is substituted
  and the name of the halogen,
• modified so that -ine is replaced by -o (e.g.
  2-bromopropane).
• If a molecule also contains a multiple bond,
  numbers are assigned to give the lowest number to
  the first functional group. In the event of a
  tie, the lowest number goes to the multiple bond.

23
Naming Alcohols

• The alcohol is a very common functional group and
  a very easy one to name.
• The molecule is named as if it were an alkane (or
  alkene or alkyne)
• except that the suffix -ane is replaced by -ol
• and the number of the carbon atom on which the
  -OH group is located is placed before the name of
  the compound (e.g. 2-butanol).
• The alcohol functional group takes precedence
  over alkyl substituents, multiple bonds, and
  halides and always gets the lowest number.

24
Naming Ethers

• An ether is a molecule consisting of two alkyl
  groups connected to an oxygen atom.
• Ethers are named by considering one alkyl group
  (the shorter one) plus the oxygen atom to be a
  substituent and the other alkyl group (the longer
  one) to be an alkane.
• The alkyl group plus oxygen atom is called an
  "alkoxy" substituent and is named by replacing
  -ane suffix from the alkane with -oxy (e.g.
  methane becomes methoxy).
• The allkoxy substituent gets priority over alky
  and halide substituents, but not over alcohols,
  which will get the lower number.

25
Naming Amines

• An amine is a derivatives of the molecule
  ammonia, NH3, in which one or more of the
  hydrogens has been replaced by an alkyl
  substitutent (R group).
• Amines are named by treating the amino group as a
  substituent and giving it the name "amino" (e.g.
  2-aminobutane).
• If multiple hydrogens have been replaced by alkyl
  substituents, then these alkyl substituents are
  stated before the word "amino" (e.g.
  2-dimethylaminobutane).

26
Cycloalkanes

• The alkanes we have studied so far have been of
  two types linear and branched. There is a third
  type of alkane in which the molecule does not
  have ends but instead forms a ring.
• These molecules are called cycloalkanes
• Figure 1 Skeletal structure of cyclohexane, a
  cycloalkane

27
Cycloalkanes

• Stable cycloalkanes cannot be formed with carbon
  chains of just any length.
• Recall that in alkanes, carbon adopts the
  tetrahedral geometry in which the angles between
  bonds are 109.5.
• For some cylcoalkanes to form, the angle between
  bonds must deviate from this ideal angle, an
  effect known as angle strain.
• Additionally, some hydrogen atoms may come into
  cloeser proximity with each other than is
  desirable (become eclipsed), an effect called
  torsional strain.
• These destabilizing effects, angle strain and
  torsional strain are known together as ring
  strain.

28
Cycloalkanes

• The smaller cycloalkanes, cyclopropane and
  cyclobutane, have particularly high ring strains
  because their bond angles deviate substantially
  from 109.5 and their hydrogens eclipse each
  other.
• Cyclopentane is a more stable molecule with a
  small amount of ring strain, while cyclohexane is
  able to adopt th perfect geometry of a
  cycloalkane in which all angles are the ideal
  109.5 and no hydrogens are eclipsed it has no
  ring strain at all.
• Cycloalkanes larger than cyclohexane have ring
  strain and are not commonly encountered in
  organic chemistry.

29
Cyclohexane

• Most of the time, cyclohexane adopts the fully
  staggered, ideal angle chair conformation (Figure
  2).
• In the chair conformation, if any carbon-carbon
  bond were examined, it would be found to exist
  with its substituents in the staggered
  conformation and all bonds would be found to
  possess an angle of 109.5.

30
Methylcyclohexane

• Methylcyclohexane is cyclohexane in which one
  hydrogen atom is replaced with a methyl group
  substituent.
• Methylcyclohexane can adopt two basic chair
  conformations one in which the methyl group is
  axial, and one in which it is equatorial.
• Methylcyclohexane strongly prefers the equatorial
  conformation.
• In the axial conformation, the methly group comes
  in close proximity to the axial hydrogens, an
  energetically unfavorable effect known as a
  1,3-diaxial interaction
• Thus, the equatorial conformation is preferred
  for the methyl group. In most cases, if the
  cyclohexane ring contains a subsituent, the
  substituent will prefer the equatorial
  conformation.

31
OUCH!!!

• Stop please stop my head is hurting and I am
  pretty sure my brain is bleeding?
• Do we really have to know all of this for the
  test?
• Will I really have to know all of this for the
  future in organic chemistry?
• Can I quit now and just become a Kindergarten
  teacher?