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Chemistry 102 Week 2 lecture. Starting chapter 14 Organic and Biochemistry for the Allied Health Fields Dr Mark Deming. Organic Chemistry Part II. Compounds with O and N and sometimes S and P. Next few chapters compounds with OXYGEN.

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chemistry 102 week 2 lecture
Chemistry 102Week 2 lecture
  • Starting chapter 14
  • Organic and Biochemistry for the Allied Health Fields
  • Dr Mark Deming
organic chemistry part ii
Organic Chemistry Part II
  • Compounds with O and N and sometimes S and P
next few chapters compounds with oxygen
Next few chapterscompounds with OXYGEN

Alcohols Ethers

Aldehydes Ketones

Carboxylic acids Esters


CH 14


Connections to O

CH 17

More oxidized


CH 18

CH 19


chapter 14 oxygen single bonded only
Chapter 14(oxygen single bonded only)
  • Alcohols COH
  • Phenols ArOH (Ar=aromatic or benzene ring)
  • Ethers COC
  • Thiols CSH (and CSSC)
Alcohol: has OH attached to aliphatic carbon
  • Hydroxy group --OH functional group
  • Phenol -OH attached to benzene
  • Ether - has an oxygen between carbons
naming of alcohols iupac
Naming of AlcoholsIUPAC

1. Name the longest chain to which a hydroxy group ( -OH) is attached and end in -ol

2. Number the longest chain to give the lowest number to the carbon with the hydroxy

3. Put location of hydroxy in front of root name

4. Locate and name any side groups in prefix


Naming Alcohols

Step 1: Name the longest chain to which the –OH group is attached. Use the alkane name of the chain, drop the –e ending, and replace it with –ol.

Step 2: Number the longest chain to give the lowest number to the carbon with the –OH.

Step 3: Locate the –OH position.





6 5 4 3 2 1









Naming Alcohols, cont.

Step 4: Locate and name any other groups attached to the longest chain.

Step 5: Combine the name and location of other groups, the location of the –OH, and the longest chain into the final name.



6 5 4 3 2 1


  • Problem: write the IUPAC name for each alcohol.
  • Solution:
common names for alcohols
Common Names for Alcohols
  • The alkyl group name is followed by the word alcohol
  • CH3OH methyl alcohol (IUPAC: methanol)
  • CH3CH2OH ethyl alcohol
  • CH3CHCH3 isopropyl alcohol OH
vitamin b2 riboflavin
VITAMIN B2 - Riboflavin

Stimulates health andgrowth of hair, nails, skin cells. Helps eyes bybringing oxygen tobody tissues. Can help eliminatedandruff. May aid in preventing hair loss.

Alcohol, poly functional, highly conjugated 14 atoms (16 atoms)

riboflavin vitamin b2
Riboflavin, Vitamin B2

Highly conjugated 14 atoms (16 atoms)

14+ carbons conjugated becomes colorful

This compound is a pale yellow solid named after latin flavis (yellow)

Riboflavin is a water-soluble vitamin that was named from the Latin word flavius (yellow) to denote the deep color of crystals formed from the pure vitamin and the deep yellow color it gives to urine. Biochemically, riboflavin is metabolized to form the flavin coenzymes: flavin adenine dinucleotide (FAD) and flavin mononucleotide (FMN). The functional moiety in both coenzymes is riboflavin's isoalloxazine ring system, which serves as a two-electron acceptor in enzymatic biochemical reductions. Enzymes that use a flavin cofactor are termed "flavoproteins" and have been extensively studied. Clinically, riboflavin promotes normal growth, helps with the breakdown of fat, and assists in the synthesis of steroids, red blood cells, and glycogen. Symptoms associated with riboflavin deficiency are inflammation of the tongue, light sensitivity, itching, dizziness, insomnia, and slow learning. In one open clinical study, high-dose riboflavin showed significant effectiveness as a migraine treatment. Common sources of riboflavin are almonds, yeast, cheese, eggs, chicken, beef, kidney, liver, and wheat germ. 
  • Recommended Dietary Allowances: Men = 1.7 mg; Women = 1.3 mg; Pregnant
aliphatic alcohols
Aliphatic Alcohols
  • They come in three types:

primary, secondary, tertiary

  • This is based on how they react in reactions but does not affect naming
  • Primary (1°): only 1 carbon attached to carbon with OH
    • KEY: end of a chain, has 2 H’s on carbon attached
  • Secondary (2°): two carbons attached to carbon with OH
    • KEY: middle of chain, has 1 H on carbon attached
  • Tertiary (3°): three carbons attached to carbon with OH
    • KEY: middle of chain and NO H’s on carbon attached but it has an extra carbon attached to it.
can you find all the types of oh s
Can You find all the types of OH’s?

(primary, secondary, tertiary, aromatic)

1-aromatic 2-primary 3-aromatic 4-tertiary 5-secondary 6-primary 7-secondary

8-secondary 9-primary 10-aromatic 11-primary 12-tertiary 13-tertiary 14-secondary

Caution: these molecules were made up and may not be biologically relevant

polar and hydrogen bonding
Polar and Hydrogen Bonding
  • We will focus today on the concept of
    • Polarity
    • Hydrogen bonding
intermolecular forces between molecules
Intermolecular Forces (between molecules)

Ionicmust be an ionic compound (made of full charges)starts with metal or ammonium (acid-base salts)

Super H-bondingH-bonding + polar + partially ionizescarboxylic acid COOH


from a O-H > N-H to a lone pair on O: > N:Amide (with H) > alcohol (OH) > amine (NH)


net polar moleculeester > amide (no H) > aldehyde > ketone > ether

London Dispersion Forces (LDF)Non polar molecule (all molecules) aromatic > -ynes > -enes > -anes (only C,H)

Same force higher mass  higher mp, higher bp, lower vapor pressure

Same approx. mass higher force  higher mp, higher bp, lower vapor pressure

= Energy of Attraction (additive)

Energy of Disruption

High TEMP(higher velocity)



Acid -CO2H

Low Mass (MW) High Vibration High Velocity Starts with at given temp.(same force)High Mass (MW) Low Vibration Low Velocity

Has OH or NH


Increase Energy of Attraction

Increase Energy of Disruption


Has O or N


Low TEMP(lower velocity)

  • Polarity happens when an atom has an unequal pull on electrons
  • H C N O P S Cl
  • 2.1 2.4 3.0 3.5 2.1 2.4 3.0
  • The bigger the number below (electronegativity, EN) the more pull and if difference in EN is 0.4 or less then nonpolar
polarity cont
Polarity cont.
  • Example C O charge separation



physical properties
Physical Properties
  • Alcohols are polar molecules
    • The C-O and O-H bonds are both polar covalent.
imf i nter m olecular f orces alcohols and ether
IMF (Intermolecular Forces)alcohols and ether

All molecules have LDF

Polar if has O or N

H-bonding if O-H or N-H to O or N

Alcohols have LDF and are polar and can both give and receive an H-bond

Ethers are polar but can only receive an H-bond





hydrogen bond
Hydrogen Bond
  • A special connection between molecules
  • One molecule must give an H-bond and one molecule must take an H-bond
  • To give an H-bond the molecule must have an O-H or an N-H bond (NOT C-H)
  • To take an H-bond the molecule must have and O or N with three or less connections (at least one lone pair)

Alcohol to Water bonding










Polar + H-bondingHydrophilic

Alkane likeNon PolarHydrophobic

Important: Expected to knowRule of thumb: Each OH can make soluble 3 carbons


more soluble

Solubility of alcohols in water

Soluble-one layer

insoluble-two layers

less soluble

Four carbons is at the edge of visual solubility

not soluble

Remember that solubility means dissolve in (or mix with) another chemical

Fig. 13-2, p.419

physical properties of pure alcohols
Physical Properties of pure alcohols
  • In the liquid state, alcohols associate to each other by hydrogen bonding.

Note: C3 and C2O are about the same weight, both have 3 big atoms near each other in the table.

Difference must be type of IMF.





physical properties1
Physical Properties
  • bp increases as MW increases.
  • Solubility in water decreases as MW increases.
acidity of alcohols
Acidity of Alcohols
  • Alcohols have about the same pKa values as water; aqueous solutions of alcohols have the same pH as that of pure water.
  • Alcohols and phenols both contain an OH group.
    • Phenols are weak acids and react with NaOH and other strong bases to form water-soluble salts.
    • Alcohols are not acids and do not react in this manner.
reactions of alcohols
REACTIONS of Alcohols

In this chapter you are responsible for:

  • Elimination Reactions
    • To form alkenes (a type of reduction)
    • To form ethers (neutral )
  • Oxidation Reactions
    • Of primary and secondary alcohols
    • Tertiary and aromatic unreactive to oxidation

Note: other alcohol reactions we will see in future chaptersChapter 16- aldehydes and ketones react with alcohols to form acetals and ketalsChapter 17- carboxylic acids react with alcohols to become esters

reactions of alcohols1
Reactions of Alcohols

CO2 + H2O



excess O2

 Combustion 

C + H2O

or CO + H2O

limited O2

Dehydration([H], Reduction)

( losing H20 )



[O]=oxidizing agent







If primary (1º)

If secondary (2º)

If tertiary (3º)



No Reaction

Carboxylic Acid


reactions of alcohols2
Reactions of Alcohols

Dehydration of alcohols to give ethers

Dehydration of alcohols to give alkenes

[H]- Reduction

High concentration

Low concentration

Oxidation of Primary (1º) alcohol

Oxidation of secondary (2º) alcohol

Oxidation of Tertiary (3º) alcohol


alcohol reactions elimination
Alcohol Reactions- Elimination

Elimination Reaction -remove a molecule

  • Dehydration to form a double bond:

Elimination of H2O to form double bond

  • Dehydration to form an ether

Elimination of H2O to from 2 alcohols form an ether


Elimination Reactions of Alcohol (cont)

Elimination Reaction of an Alcohol

to form alkenes

The removal of water (dehydration) from an alcohol is an elimination reaction and produces an alkene.

Strong Acid Catalyst

The alcohol is usually in low concentrations to avoid ether formation


Elimination Reactions of Alcohol (cont)

Dehydration to form Ethers.

Under slightly different conditions, a dehydration reaction can occur between two alcohol molecules to produce an ether.

The alcohol is usually in high concentration and lower temperature to avoid alkene formation

reactions of alcohols oxidation
Reactions of Alcohols- Oxidation
  • Official Definitions: (chem 102 does not use)
      • Oxidation is really the losing of electrons at an atom by formal electron counting
      • Reduction is the gaining of the electrons at an atom
  • Practical Usage in this class: At a CARBON




Reactions of Alcohols- Oxidation

Remember that Oxidation:

Is the gain of oxygens or the loss of hydrogens at a carbon.

Usually done with a chemical that will itself get reduced called an oxidizing agent: and we will abbreviate it with [O]

reactions of alcohols oxidation1
Reactions of Alcohols- Oxidation
  • Oxidation of Aliphatic Alcohols
    • Primary alcohols  aldehyde  carboxylic acid.
    • Secondary alcohols  ketone.
    • Tertiary alcohols  no reaction.
  • Oxidation of Aromatic Alcohols
    • No reaction- not easily oxidized
alcohol reactions cont primary alcohol oxidation secondary alcohol oxidation

Note: most strong oxidizing agents will make the reaction go all the way to the carboxylic acid

Alcohol Reactions, cont.

Primary alcohol oxidation

Secondary alcohol oxidation


Potassium ChromateK2Cr2O4

(The oxidizing agent)


These are the reactants

Fig. 13-7a, p.423


Ethanol is oxidized to acetic acid

Chromate is reduced (green-grey)

When mixed the products are in the second tube

Fig. 13-7b, p.423

important alcohols
Important Alcohols
  • Methanol
    • Ethanol
    • Isopropyl alcohol
    • Glycerol
  • Aromatic alcohols
    • Phenol, BHA, BHT

Important Alcohols (cont.)

• Methanol (wood alcohol) CH3OH.

• Production:

• Useful as a solvent and industrial starting material.

• Highly toxic, causes blindness and/or death.


Important Alcohols (cont.)


Ethanol (ethyl alcohol, grain alcohol, drinking alcohol)

Useful as a solvent, industrial starting material, fuel (gasohol), and found in alcoholic beverages. Moderately toxic.

NON RENEWABLEFrom etheylene

RENEWABLEfermentation of carbohydrates (corn) by yeast (biological)


Important Alcohols (cont.)

2-propanol (isopropyl alcohol) is the main component of rubbing alcohol.

1,2,3-propanetriol (glycerol, glycerin) is used as a food moistening agent (nontoxic) and for its soothing qualities (soaps).

antifreezes 1 2 ethanediol ethylene glycol 1 2 propanediol propylene glycol

Important Alcohols (cont.)

Don’t need to know for test

Antifreezes1,2-ethanediol (ethylene glycol).

1,2-propanediol (propylene glycol).


Important Alcohols (cont.)

Phenols and their uses:

In a dilute solution, phenol is a disinfectant.

Phenol derivatives used as disinfectants



Phenol derivatives used as antioxidants in food

BHT (butylated hydroxy toluene)

BHA (butylated hydroxy anisole)

Phenol is a medical antiseptic first used by Joseph Lister in 1867. Lister showed that the occurrence of postoperative infection dramatically decreased when phenol was used to cleanse the operating room and the patient’s skin.
  • The medical use of phenol is now restricted because it can cause burns and is toxic. Only solutions with <1.5% phenol or lozenges with <50 mg of phenol are now allowed in nonprescription drugs. Many mouthwashes and throat lozenges contain alkyl-substituted phenols such as thymol as active ingredients for pain relief.
  • Alkyl-phenols such as the cresols are common as disinfectantsin hospitals. Antiseptics safely kill microorganisms on living tissue, disinfectants should only be used on inanimate objects.

Ethers –Official Naming

OXYto smallest group

Ethers There is NO ending name

Naming ethers – the –O-R group is called an alkoxy group. The –yl ending of the smaller R group is replaced by –oxy.

The smallest group attached to O is named as an alkoxy side group with the O


The Common naming of simple ethers is in some places preferred and are widely used.

Common Names of Ethers. – Name each group attached to the O as a side group and attach “ether” as a separate word to the end.

Ethers –Common Names

cyclic ethers heterocyclic rings contain atoms other than carbon in the ring
Cyclic Ethers

Heterocyclic rings contain atoms other than carbon in the ring.



Properties of Ethers

Properties of Ethers

Much less polar than alcohols.

More soluble in water than alkanes, but less soluble than alcohols.

Low boiling and melting points because of the inability to hydrogen bond between molecules.

hydrogen bonding of dimethyl ether a with water and b no hydrogen bonding in the pure state
Hydrogen bonding of dimethyl ether: (a) with water and (b) no hydrogen bonding in the pure state:
Ether Reactions

Like alkanes, ethers are inert and do not react with most reagents.

Also like alkanes, they are highly flammable.



Thiols: the –SH (sulfhydryl, mercaptan) group

Most distinguishing characteristic is their strong and offensive odor.

Ethanethiol – added to natural gas.

1-propanethiol – odor in garlic and onions.

Trans-2-butene-1-thiol – odor associated with skunks.

sulfur reactions
Sulfur Reactions

[O] (oxidation) -- (lose H’s as water)


2 RSH

Disulfide linkage


Found in proteins, enzymes and hair to retain specific shape

[H] (Reduction)

M= Hg2+ or Pb2+

Hg2+ or Pb2+

Accumulates over lifetime

Dimethyl mercury is nonpolar and will reside in fatty tissues and lymphatic system and cell walls. It is slowly released doing damage. Children affected more!

Metal Sulfides


Distorts shape of proteins, enzymes making them inactive. Retained in hair

Thiol Reactions

Oxidation forms disulfide (-S-S-) linkages which are important structural features of some proteins.


Thiol Reactions, cont.

Reacts with heavy metals (Pb2+, Hg2+) to form insoluble compounds, with adverse biological results. This is why lead and mercury are always in the news as pollutants.

Why is this so bad?

six chemical connectors in biology
Six Chemical Connectors in Biology
  • These will connect (bond) Biological units together and are energetically easy to undo.


  • Disulfide Linkage
  • Glycosidic Linkage (acetal, ketal linkage)
  • Ester Linkage (universal connector)
  • Amide Linkage
  • Phosphate Ester Linkage
  • Amino Glycosidic Linkage (DNA, ATP)variation of #2

Ch 17

Ch 19

Ch 19

Ch 17

Implied from Ch 16 and Ch 15

Note: We can make these connections in a test tube but biologically there is an enzyme to make and break each connector above.

3 binders used in biological systems
3 Binders used in Biological systems

These hold pieces or parts together but not bonded, Easier to break

  • Salt bridges amines (+) to acids (-)
  • H-bonding
    • OH to O strong ( starches, alpha helix, beta sheet)
    • OH to N medium
    • NH to O medium (DNA)
    • NH to N weak (DNA)
  • Nonpolar to Nonpolar (many times also used to exclude water)
    • Long straight chains (lots of overlap) waxes, cell memb.
    • Aromatic ring stacking

Ch 16,18


Ch 12

Ch 13


Polyfunctional Compounds

Compounds with two or more functional groups. Functional groups determine chemical properties of compounds.


more examples of finding functional groups in polyfunctional compounds
More examples of finding functional groups in polyfunctional compounds
  • Are found in the handout titled “Finding Function Groups Practice”
  • It covers groups from Chapters 11-19