Lesson 1: Review of Basic Organic Chemistry Principles

ORGANIC CHEMISTRY
➔ Is the study of compounds of carbon
◆ Organic compounds are carbon centric, made up of C covalently
◆ H, O, N, S, P, F, Cl, Br, I, and Halogens (Hetero atoms) join with Carbon.
◆ Cyanides, carbonate, carbides - inorganic compounds with Carbon

WHY DO WE STUDY ORGANIC CHEMISTRY

HISTORICAL
● It was believed that a “vital force” in living organisms was necessary to produce an organic
compound
○ Jöns Jacob Berzelius - vital force/ vitalism/ vitalist theory
○ Past used urine (for urea) as mordant - to increase the affinity of stains. (for dyes)
○ In 1828, Friedrich Wöhler showed that it was possible to produce the organic substance
urea from inorganic compounds; disapproved of vital force theory. ammonium cyanate +
silver chloride = urea.

THE SHEER NUMBER OF ORGANIC COMPOUNDS

● Chemists have discovered or made over 10 million organic compounds and an estimated 100,000
new ones are discovered or made each year
● Approximately 85% of all known compounds are organic

THE LINK TO BIOCHEMISTRY

● Carbohydrates, lipids, proteins, enzymes, nucleic acids, hormones, vitamins, and almost all other
chemicals in living systems are organic compounds

A COMPARISON OF ORGANIC AND INORGANIC

ORGANIC INORGANIC

Bonding is almost entirely covalent Most have ionic bonds

Many are gasses, liquids, or solids with low Most are solids with high melting points
melting points (less than 360℃)

Most are insoluble in water Many are soluble in water

Most are soluble in organic solvents such as Almost all are insoluble in organic solvents
diethyl ether, toluene, and dichloromethane
 Aqueous solutions do not conduct electricity Aqueous solutions form ions that conduct
electricity

Almost all burn and decompose Very few burn

Reactions are usually slow Reactions are often very fast

STRUCTURE OF ORGANIC COMPOUNDS

➔ Carbon has 4 valence electrons and forms 4 covalent bonds
◆ Able to bond with one another to form long chains and rings
◆ Only element that can form immense
❖ MOLECULAR FORMULA - shows an actual number of atoms of each element in a molecule.
Identity and number of atoms comprising each molecule. Numbers, but not what’s bonded to
what. Not very informative.
❖ STRUCTURAL FORMULA - shows the atoms present in a molecule and the bonds that connect
them. Atom-to-atom connectivity. Has additional info which is the bonds. Is used more often
➢ Expanded structural formula - (Kekule or line bond structure) shows 2 electron covalent
bond as a line drawn between atoms
➢ Condensed structural formula - shows symbols of atoms which are listed in order as they
appear in the molecule’s structure with bond dashes (C-H or C-C) omitted
❖ SKELETAL STRUCTURE - (line angle structure) shows the carbon skeleton in the structure,
with H atoms omitted and line ends & vertices represent C. Atoms other than C and H are still
shown

EMPIRICAL FORMULA - divide the subscript by the highest number; a simpler form of molecular
formula

LED polymer - light-emitting diodes

Caramelize - Maillard reaction, a reaction between the sugar and the protein in the cream

Chiral Carbon - has 4 different substituents; attached to four different types of atoms or groups of atoms.

CARBON COMPOUNDS IN DIFFERENT BONDING FORMS

1. ALIPHATIC COMPOUNDS - continuous or branched chain of C atoms
2. CYCLIC or AROMATIC COMPOUNDS - C atoms in ring shape
3. HETEROCYCLIC COMPOUNDS - with elements (N, halogens, P, S) other than C in the ring.

CARBON-CARBON BONDS - especially strong covalent bonds.

➢ Carbon can form single, double, and triple bonds
● Carbon - unique in its ability to catenate (can form chains of atoms )
○ Forms long chains and rings of molecules composed of C-C bonds
 ● Bond dissociation energy - (kJ mol^-1)
○ C-C - 348
○ N-N - 163
○ O-O - 157

STRUCTURAL FORMULA SHOWING STEREOCHEMISTRY

➢ How atoms are arranged in 3D shape
1) A dashed line indicates that the bond is extending behind the plane of the drawing surface
2) A bold-wedged line indicates that the bond is protruding out from the plane of the drawing
surface
3) A solid line indicates that the bond exists in the plane of the drawing surface
4) A wavy line indicates that the stereochemistry of the bond is unknown
5) A dotted line indicates that the bond is not full, it is only a partial bond as in a hydrogen bond or a
partially formed or broken bond in a transition state. Also as Mrigank Pawagi notes in the
comments, the dotted line can be used along with the solid line to denote bonds that have partial
double bond character due to resonance.
6) An arrow indicates a dative bond, in which both electrons in the bond originate from one atom
(not common)

STRUCTURAL FORMULA
➢ Shows the exact way in which the atoms are connected to each other
➢ Used more often than molecular formula

ISOMERS - same molecular formula but different arrangement of atoms. Ex: glucose and galactose

FUNCTIONAL GROUPS
➔ It is an atom or group of atoms within a molecule that shows a characteristic set of predictable
physical and chemical properties.

WHY ARE FUNCTIONAL GROUPS IMPORTANT

● Serve as sites of predictable chemical reactions
○ Alcohol - will readily convert to gas because of its functional group
● To a large measure, they determine the chemical and physical properties of a molecule
● Serve as units to classify organic compounds into families
● Serve as a basis for naming organic compounds

AMINO ACIDS - has N’

STRUCTURES OF SOME FUNCTIONAL GROUPS

NAME STRUCTURE NAME ENDING EXAMPLE

ALKENE Double bond -ene Ethene

ALKYNE Triple bond -yne Ethyne

ARENE Aromatic ring none Benzene

HALIDE X = F, Cl, Br, I none Chloromethane

ALCOHOL OH -ol Methanol

ETHER O ether Dimethyl ether

MONOPHOSPHATE OPO₃^2- phosphate Methyl phosphate

DIPHOSPHATE OP₂O₆^3- diphosphate Methyl diphosphate

AMINE NH₂ -amine Methylamine

IMINE (Schiff base) N(double bond)H none Acetone imine

NITRILE Triple bond N -nitrile Ethanenitrile

THIOL SH -thiol Methanethiol

SULFIDE S sulfide Dimethyl sulfide

DISULFIDE SS disulfide Dimethyl disulfide

SULFOXIDE O- S+ sulfoxide Dimethyl sulfoxide

ALDEHYDE O(double bond)CH -al Ethanal

KETONE O(double bond)C -one Propanone

CARBOXYLIC ACID O(double bond)COH -oic acid Ethanoic acid

ESTER O(double bond)COCH₃ -oate Methyl ethanoate

THIOESTER O(double bond)CSCH₃ -thioate Methyl ethanethioate

AMIDE O(double bond)CNH₂ -amide ethanamide

ACID CHLORIDE O(double bond)CCl -oyl chloride Ethanoyl chloride

CARBOXYLIC ACID O(double bond) COC -oic anhydride Ethanoic anhydride

ANHYDRIDE (double bond)O
Review of Pertinent Organic Chemistry Principles

DIFFERENCE OF ORGANIC AND INORGANIC

ORGANIC COMPOUNDS INORGANIC COMPOUNDS

Organic compounds always contain carbon as
their main element. It can mostly be obtained
SOURCE
from living organisms like animals and plants.
Some examples would be proteins and lipids.
Most organic compounds are colorless. It can
appear as a solid, liquid, or gas. Since it has a
stable bond, it is difficult to react, making
chemical reactions slow. There is also a low and
PHYSICAL
weak interaction among organic compounds,
AND
making them easy to break, hence having a low
CHEMICAL
boiling and melting point. They do not dissolve
PROPERTIES
easily in water because organic compounds are
polar and water is polar; a non-polar organic
solvent is needed for them to dissolve. Because
they mostly contain carbon, they are flammable.
Organic compounds have a covalent bond. It is ionic bonds. Ionic bonds are bonds
CHEMICAL because they are composed of nonmetal atoms. between metal and nonmetal atoms.
BONDS Organic compounds not having ions also makes These ions make inorganic compounds
them non-electrolytes.
Organic compounds have a more complex
structure since it contains carbon which has four
valence electrons, making it more frequent for
COMPLEXITY
other bonds to form because each carbon atom
OF
can link with four other atoms. Covalent bonds
STRUCTURE
also involve sharing of electrons, creating more
bonds. With more bonds comes a larger and
more complex structure.
Inorganic compounds mostly do not
contain carbon. It can be obtained from
the earth's crust like minerals. Some
examples would be table salt and
water.
Most inorganic compounds are
colorful because they are in group b,
and their natural properties are
colorful. They mainly appear as solids.
Because they do not have a stable
bond, there is a rapid chemical
reaction. And because of this strong
reaction, they have high boiling and
melting points. They are not
flammable, for not all inorganic
compounds come from carbon.
Because they have ionic bonds, they
are generally soluble in water.
Inorganic compounds mostly have
electrolytes, meaning they can conduct
electricity.
Inorganic compounds have a less
complex structure because they
usually have no carbon. In addition,
ionic compounds only give electrons
resulting in a smaller and simpler
structure.

SOME TERMS
❖ ORGANIC COMPOUNDS - are molecules that contain carbon atoms that are covalently bonded
to hydrogen atoms (C-H bonds). Various organic compounds are formed from chains of covalently-
 linked carbon atoms with hydrogen atoms attached to the chain. This depicts that all organic
compounds share the similar trait of having both the presence of carbon and hydrogen atoms.
❖ VITAL FORCE - Vital force or also known as Spiritual force is a hypothetical force in which
organic living compounds are not formed from any inorganic compounds but rather with a “vital
force”. It is also considered the causative factor in the evolution and development of living
organisms.
❖ COVALENT BONDING - It is a bond that forms when two nonmetal atoms share a pair of
electrons. Covalent bonds are also considered “strong”, requiring a lot of energy to break them.
Substances with covalent bonds often form molecules that have low melting and boiling points.
❖ VALENCE ELECTRONS - an electron in an outer shell of an atom that can participate in forming
chemical bonds with other atoms. For instance, in a single covalent bond, both atoms in the bond
contribute one valence electron to form a shared pair. The presence of this helps determine the
element’s chemical properties and whether it may bond with other elements.
❖ HYDROCARBONS - This refers to an organic chemical compound composed exclusively of
hydrogen and carbon atoms. Hydrocarbons are also naturally-occurring or exist naturally without
the interference of any human or artificial aid. They are described as highly combustible and
produce carbon dioxide, water, and heat when burned.
❖ FUNCTIONAL GROUPS - are groups of atoms in a compound that is responsible for determining
the chemical behavior of the class compound in which the group occurs. This includes the hydroxyl
group in alcohols.
❖ ACYCLIC or OPEN-CHAIN COMPOUNDS - Acyclic or open-chain compounds are those in
which carbon atoms don’t form any ring. They have a linear pattern, hence the name open-chain.
Straight-chain and branched-chain compounds can both be used to comprehend open-chain
molecules. In contrast to branched-chain compounds, which have one or more side chains
connected to their atoms, straight-chain compounds have no side chains.
❖ CYCLIC or CLOSE CHAINED - Cyclic compounds are organic compounds with a closed or cyclic
carbon atom chain. Sometimes also called "ring compounds" because a sealed ring is formed due
to the connection of one or more atoms. However, it is not necessary for these compounds' rings to
all be the same size.
❖ ORGANIC CHEMISTRY - is defined as the study of the structure, properties, compositions,
reactions, and preparation of carbon-containing compounds. This definition includes chemicals
extracted from living things, but also man-made polymers, like lastics.