II.

OR G ANIC CHEMISTRY TIMELINE

Let's examine som e hallmark m om ents that have been influential in the development of the organic
chemistry discipline.

1828: Friedrich Wohler proved the 'vital for ce' theory wrong by synthetically pr oducing urea. He
reacted silver cyanate (AgOCN) and am m onium chloride (NH 4 Cl), expecting to get am m onium
cyanate (NH 4 OCN). What he expected is described by the following equation .

AgOCN + NH 4 Cl → A gCl + NH 4 OCN

Instead, he found the pr oduct to be ur ea (NH 2 CONH 2 ), a well-known organic m aterial readily
isolated from urine. This result led to a series of experim ents in which a wide variety of organic
compounds wer e m ade from inorganic starting m aterials. The vital force theory gradually went away
as chemists learned that they could make m any organic com pounds in the labor atory.

1865: Friedrich Aug ust Kek ule von Strad onitz discov ered the benzene ring structure. A n important
breakthrough was discovering the organic structure of the benzene ring. Typically, double bonds ar e
shorter than single bonds, yet due to benzene's unique circular shape with double bonds placed at
every other bond, all of the bonds are of equal length. This unique structure of benzene was difficult
for scientists to figure out.Then in 1865 Friedrich A ugu st Kekule von Stradonitz, often sim ply referred to
as Kekule, figured it out. Kekule explains he discovered this structure after days of studying benzene
and trying to determine how and why it reacts in the way that it does. One night he had a dr eam of
snakes twisting toget her until they form ed a circle. He woke up from this dream and realized that
benzene was circular. From there he was able to figure out the structur e of benzene, which led to
further discov eries about how organic com pounds react.

1874: Jacobus va n 't Hoff a nd Josep h-Achille Le B el dev eloped an organic m olecule m odeling
system.

Jacobus van 't Hoff and J oseph-A chille Le B el dev eloped a system to indicate what way these atoms
were coming off of the carbon, called a 3D stereochemical represe ntation. A solid line indicates the
atom coming up from the carbon, while a dashed line indicates that it is going backwards. They also
discover ed that carbon is tetrahedral. In other words, carbon can have four atoms coming off of it.
The valence shell electron pair repulsion (V SEPR) theory is a m od el used to predict 3-D m olecular
geom etry based on the numb er of valence shell electron bond pairs a mong the atom s in a m olecule
or ion. This model assum es that electron pairs will arrange themselv es to minimi ze repulsion effects
from one another.

Carbon is unique am ong the other elem ents in that its atoms can form stable covalent bonds with
each other and with at oms of other elem ents in a m ultitude of variations. The resulting m olecules can
contain from one to millions of carbon atoms.

Versatility and uniq ueness of Carb on

1. Atoms of carbon can unite with one anot her by sharing one or m or e pairs of electron to
from chains, both branched and unbranched, or ring m olecules.
2. Carbon atoms hav e four valence electrons so it always forms four covalent bonds.
3. Organic m olecules ex hibit isom erism. Even the sam e number and kind of at oms ar e
present, different organic compounds can be form ed if the arrangem ent of these at oms
is changed,

Today organic chemistry is the study of the chemistry of the carbon com pounds, and inorganic
chemistry is the study of the chemistry of all other elem ents. It may s eem strange that we divide
chemistry int o two branches —one that considers compounds of only one elem ent and one that
covers the 100-plus rem aining elements. Howev er, this division seems m ore reasonable when we
consider that of tens of millions of com pounds that have been characterized, the overwhelming
m ajority are carbon compounds.

Classification of Orga nic Comp ounds

There are m any ways to classify organic com pounds. One of them is bas ed on how they ar e
synthesized.

Exa mple:

Natural vs. Sy nthetic Org anic Comp ounds

A natural orga nic com pound (or simply natural compound ) - one that is produced naturally, such as
by plants or anim als. Natural com pounds are organic compounds that can be obtained from natural
sour ces. They m ay be produced artificially but the pr ocess of doing so will m ake them rather
expensive. Exam ples of natural com pounds are sugars, enzym es, hor m ones, lipids, antigens, fatty
acids, neurotrans mitters, nucleic acids, proteins, peptides, amino acids, vitamins, lectins, som e
alkaloids and terpenoids, etc.

A sy nthetic organic comp ound (or synthetic comp ound) - Organic com pounds ar e m ajor
components of living systems, but chemists can m ake many of them in the laboratory (prepar ed by
chemical manipulations (chemical reactions) from substances that have no direct connection with
living systems. Chemically speaking , a pure sam ple of an organic com pound such as Vitamin C
prepar ed in a laborat ory is chemically identical to a pure sample of Vitamin C isolated from a natur al
sour ce s uch as an orange or other citrus fruit. Many polym ers ( e.g., plastics, rubbers) are als o
produced synt hetically.

I.2. Atom Structure

To-Do Date: Jan 12 at 7:30a m

Matter is anything that occupies space and has m ass. Matter consists of ATO MS (building blocks of
m atter) m ade up of pr otons, neutrons and electrons.

The m asses of the neutron and prot on are very nearly

equal: 1 amu each. The m ass of the electron is 1/1840
of this.

Atomic number (Z) = num ber of electrons = number of

protons

Mass number (A) = atomic num ber (Z) + num ber of

neutrons

EXAMPL E:

The atom is mainly em pty space because its diam eter is m any thousand times greater than the
diam eter of the nucleus.

An ISOTOPE of an elem ent is an at om which has the sam e at omic number (Z) as other atoms of the
element, but a different m ass num ber (A).

Each of two or m ore forms of the sam e elem ent that contain equal numbers of prot ons but different
numbers of neutrons in their nuclei, and hence differ in relative atomic mass but not in chemical
properties; in particular, a radioactive for m of an elem ent.

"Som e elem ents have only one stable isot ope"

All the differ ent types of

Atoms ar e referred t o as nuclides; that is, a list of the nuclides would include all the isot opes of all the
elements.

The Mod ern Periodic Table

The periodic table has u ndergone extensive changes in the tim e since it was originally developed by
Mendeleev and Mos eley. Many new elem ents have been discover ed, while others have been
artificially synt hesized. Each fits properly int o a group of elem ents with similar properties. The periodic
table is an arrangem ent of the elem ents in order of their atomic numbers, so that elem ents with
similar properties appear in the same v ertical colum n or gr oup.

The figure below s hows the m ost comm only used form of the periodic table. Each square shows the
chemical sym bol of the elem ent along with its nam e. Notice that several of the symbols seem to be
unrelated to the nam e of the elem ent: FeFe for iron, PbPb for lead, etc. Most of thes e are the
elements that have been known since ancient tim es and have symbols based on their Latin nam es.
The atomic num ber of each elem ent is written above the symbol.

I.3. Chemical B onding and Lewis Structure/F orm ula

I. CHEMICAL BO NDING

Chemical B onding refers to the for mation of a chemical bond between two or m ore atoms,
m olecules, or ions to give rise to a chemical com pound. Thes e chemical bonds ar e what keep the
atoms together in the resulting com pound.

Covalent Bond

The cov alent, or shar ed electro n pair, m odel of chemical bonding was first suggested by G.N.
Lewis in 1926. In covalent bonding, atoms attain a filled valence shell by sharing electrons. This type
of bonding is seen with atoms of the sam e closer electronegativities.

Octet Rule

• Atoms transfer or share e- in such a way to attain a filled valence shell of electrons (the
electronic configuration of noble gases such as He, Ne, or Ar).

*Exception to the rule:

Hydr ogen com pletes its valence electrons with one m ore e - to attain the electronic
configuration of helium (Duet Rule).
Take a look at the following elements and look at the no. of electrons they need and how m any
bonds they'll form to complete their valence e-.

Table 1. Application of the octet and duet rule.

II. LEWIS STR UCTUR E/FO R MUL A

Lewis structur e give connectivity of the location of all bonding and non -bonding electrons, as
well as for mal charges. Howev er, It does not give inform ation about the 3 -dim entional orientation in
space.

General rule:

1. Take the sum of valence e- for all at oms.

2. Arrange at oms in the proper orientation.

• Hydrogen atoms are terminal atoms.

• Carbon atoms are generally central at oms.

3. Distribute e- by playing bonds between at oms (1 bond is equal to 2 e -).

4. Use rem aining e- to satisfy the duet rule for H and the oct et rule for the 2 n d row elements.
5. If all valence e- are used and an atom does not have an octet, form m ultiple bonds where
possible.

How to predict the type of b ond betw een two atoms ?

The electronegativity values ar e us ed to predict the type of bond bet ween two atoms.
Electronegativity is the tendency of an atom to attract electrons.

Table 2: The differ ences in electronegativity of two at oms and the corresponding type of bond.
Difference in Electronegativity Betw een B onded
Type of Bond
Atoms

0.4 or less Nonpolar covalent

0.5 to 1.8 Polar Covalent

1.9 and greater Ionic

*Polar m olecules (consist of atoms bonded polar cov alently) are dipoles. It m eans that a polar
m olecule has a positive end and a negative end.

*Nonp olar m olecules (consist of atoms bonded nonpolar covalently) are whose charge distribution is
spherically sym m etric when av eraged over time.

Three m ain fact ors that control the polarity of covalently bonded m olecules i.e.,

1. Electronegativity- the tendency of a n atom to attract a shared pair of electrons from a covalent
bond

2. Dipole m om ents (μ) - a vector qua ntity, repres ents both the ma gnitud e (m easured in Deb ye, D) as
well as the direction of a p olar bond or m olecule

3. Arrangem ent of atoms in the m olecule/ m olecular shape

How the p olarity of a m olecule affects its solubility in water?

Like dissolves like. A ccording to this general rule, polar m olecules dissolve in polar solvents such as
water (H2O) while non-polar m olecules dissolve in non-polar organic solv ents such as CCl 4 .

I.4. Ways of Drawing Struct ures Organic Molecules based on F orm ulas

Empirical Form ula ex presses the sim plest whole num ber ratio of atoms in a com pound.
Molecular F orm ula shows the actual num ber of at oms in each elem ent in a compound.

Exa mples:

I. Cond ens ed Structures

Condensed structur es are shorthand way of drawing m olecules when som e or all the covalent
bonds ar e left out. They ar e drawn in a way that gives inform ation about how the at oms are bonded
together.

Guidelines:

1. Atoms ar e us ually drawn next to the atoms to which they are bonded.
2. Parent hes es are used ar ound similar groups bonded to the sam e atom.
3. Lone pairs on heter oat oms (atoms other than car bon) are usually omitted.
4. Form al charges are shown on the at om t o which they belong.

From Lewis struct ure to condensed structure:

*Start at the left side of the m olecules and rem ember that the carbon atoms must have 4 bonds.

- A car bon bonded to 3H’s becom es CH 3 .

- A car bon bonded to 2H’s becom es CH 2 .

- A car bon bonded to 1 H becom es CH.

Consider the m olecules in Lewis structur e below:

II. Sk eletal (B ond-Like) Structures ar e simplified way of

drawing m ore com plex m olecules especially those
containing rings.

a. Wat ch and Learn on how to draw skeletal structure

on bond line notation for organic m olecules using the
link below:

You can also use the thes e Guidelines:

1. Assum e there is a carbon at the junction of any 2 lines or at the end of any line.
2. Assum e there ar e enough hydrogens around each C to m ake it tetravalent (having 4
bonds).
3. Draw in all heter oat oms (at oms other than C) and the hydrogens directly bonded to them.
4. C at om in a straight chain are drawn in as a zig -zag.
5. Lone pairs are often left out and ar e understood.
6. Always include form al changes (if there are).
1.5. Functional Groups

Functional group is a structural unit m ade up of either heteroatoms or Π-bonds (pi-bond). A specific
combination of atoms that has a unique set of chemical properties.

Heter oatoms: an atom other than carbon or hydrogen com m on het eroatoms are N, O, S, P,
and halogens

Π-bonds: the m ost com m on Π-bond occur in C-C and C -O double bonds and, C-C and C-N
triple bonds.

Functional groups are im portant for 3 reasons:

1. They are the units by which we divide the organic com pounds int o classes.
2. Serve as a basis for naming organic com pounds .
3. Char act erizes the chemical (sites of chemical reaction) and physical pr operties
of the m olecule

How do heter oat oms and Π-bonds confer reactivity on a m olecule?

o Heteroatoms have lone pairs and cr eat e e- deficient or e- rich sites on a

m olecule.
o Π-bond bonds on the other hand could easily be br oken in chemical reaction.
C-C double bonds create e- rich sites in a m olecule.

The exam ple below shows that Π bond is: 1.) e-rich and readily react to electrophilic atom, 2.)
weak bond or easily broken.
Figure 1. Som e F unctional gr oups and their major clas s