CHEM 1

ORGANIC CHEMISTRY
ORGANIC CHEMISTRY

● Is a branch of chemistry that studies the structures, properties or

composition of organic compounds, which contains carbon-carbon
covalent bond, or the carbon compounds.
● The study of organic chemistry is very important because 90% or
more that 30 million of chemical compound present contains
carbon.
● On the periodic table, elements with similar properties are group as
families. Carbon, for example, belonged to 4A elements.
ATOMIC STRUCTURE

Atom is the smallest unit of ordinary matter that forms a chemical element.
It is the basic unit of a chemical element. An atom is extremely small with a
diameter of 2´ 10-10 m = 200 pm.
● The atomic number (Z): number of protons in nucleus
● The mass number (A): number of protons plus neutrons
● All atoms of the same element have the same (Z) value
ISOTOPES

● atoms of the same element with different numbers of neutrons and thus
different A
ATOMIC MASS OF ISOTOPES
ATOMIC ORBITALS FOR ELECTRONS

● Orbitals is the space around the nucleus where there is high probability of
finding electrons.
ATOMIC ORBITALS FOR ELECTRONS

● Each orbital can be occupied by two electrons

● Four different kinds of orbitals for electrons based on those derived
for a hydrogen atom: denoted s, p, d, and f (sub-shells)
● Different shells contain different numbers and kinds of orbitals.
● s and p orbitals most important in organic and biological chemistry
● s orbitals: spherical, nucleus at center, and can only accommodate
2 electrons
● p orbitals: dumbbell-shaped, nucleus at middle, and can
accommodate 6 electrons (3 orbitals)
● d orbitals: elongated dumbbell-shaped, nucleus at center, and can
accommodate 10 electrons (5 orbitals).
ATOMIC ORBITALS FOR ELECTRONS
SUBSHELL
ELECTRON CONFIGURATION

Rules:
1. Lowest-energy orbitals fill first: 1s ® 2s ® 2p ® 3s ® 3p ® 4s ® 3d (Aufbau (“build-
up”) principle)
2. Electrons act as if they were spinning around an axis. Electron spin can have
only two orientations, up and down ¯. Only two electrons can occupy an
orbital, and they must be of opposite spin (Pauli exclusion principle) to have
unique wave equations
3. If two or more empty orbitals of equal energy are available, electrons occupy
each with spins parallel until all orbitals have one electron (Hund's rule).
ELECTRON CONFIGURATION
BONDING THEORY

1. Covalent Bond
● A covalent bond consists of the mutual sharing of one or more
pairs of electrons between two atoms.
● Organic compounds have covalent bonds from sharing electrons
(G. N. Lewis, 1916)
Lewis structures (electron dot) show valence electrons of an
atom as dots
● G.N Lewis
● Hydrogen has one dot, representing its 1s electron
● Carbon (1 s22s2 2p2) has four dots (2s2 2p2) due to 4 e- in
valence shell
● Kekulé structures (line-bond structures) have a line drawn between two atoms
indicating a 2 e- covalent bond.
● Valence electrons not used in bonding are called nonbonding electrons, or
lone-pair electrons
● Covalent bond forms when two atoms approach each other closely so
that a singly occupied orbital on one atom overlaps a singly occupied
orbital on the other atom.
● Two models to describe covalent bonding.
⮚ Valence bond theory
⮚ Molecular orbital theory
VALENCE BOND THEORY

● Electrons are paired in the overlapping orbitals and are attracted to nuclei of both
atoms
⮚ H–H bond results from the overlap of two singly occupied hydrogen 1s orbitals
⮚ H-H bond is cylindrically symmetrical, sigma (s) bond
● Distance between nuclei that leads to maximum stability. If too
close, they repel because both are positively charged. If too far
apart, bonding is weak.
sp3 Orbitals and the Structure of Methane
● Carbon has 4 valence electrons (2s2 2p2)
● In CH4, all C–H bonds are identical (tetrahedral)
● sp3 hybrid orbitals: The hybridization of methane molecules
occurs by mixing one orbital with three p orbitals. Each
orbital consists of one unpaired electron. The s and three p
orbitals of carbon overlap with the 1s orbitals of hydrogen to
form bonds. Thus methane is sp3 hybridized
sp³ Hybrid Orbitals and the Structure of
Ethane
●The simplest molecule with a carbon-
carbon bond is ethane, C2H6. In ethane
(CH3CH3), both carbons are sp3-hybridized,
meaning that both have four bonds with
tetrahedral geometry. An sp3 orbital of one
carbon atom overlaps end to end with an
sp3 orbital of the second carbon atom to
form a carbon-carbon σ bond
sp 2 Orbitals and the Structure of
Ethylene (C2H4)
● sp2 hybrid orbitals: 2s orbital
combines with two 2p orbitals, giving
3 orbitals (s + pp = sp2). This results
in a double bond (pi (π) bond)
● sp2 orbitals are in a plane with120°
angles
▪ Remaining p orbital is perpendicular
to the plane
sp Orbitals and the Structure of Acetylene
●Sharing of six electrons forms C ºC
●Two sp orbitals form s bonds with hydrogens
●C-C a triple bond sharing six electrons
●Carbon 2s orbital hybridizes with a single p
orbital giving two sp hybrids
●two p orbitals remain unchanged
●sp orbitals are linear, 180° apart on x-axis
●Two p orbitals are perpendicular on the y-
axis and the
●z-axis
MOLECULAR ORBITAL THEORY

● combines the tendency of atoms to fill their octets by sharing

electrons with their wavelike properties, assigning electrons to
a volume of space called an orbital.
MOLECULAR ORBITAL THEORY

● The difference between

atomic orbital and
molecular orbital is that
the atomic orbital refer to
the orbital of the atom,
while molecular orbital
shows the electron of the
entire molecule.
TYPES OF MO (FOR SIGMA BOND)

● Low Energy Bonding MO

(Constructive Interference)
● High Energy Antibonding
MO (Destructive
Interference)
TYPES OF MO (FOR SIGMA BOND)

For pi bond
● The p bonding MO is from
combining p orbital lobes
with the same algebraic sign
● The p antibonding MO is
from combining lobes with
opposite signs
● Only bonding MO is occupied
Polar Covalent Bond; Acid and Base
Polar Covalent Bond is the uneven sharing of electrons
● Bonding electrons attracted more strongly by one atom than by
the other
● Difference in EN of atoms < 2
Nonpolar Covalent Bonds: atoms with similar EN (0.0 ~0.4)
Ionic Bonds: Difference in EN > 2
Electronegativity is the measure of an
element strength. It is the ability of an
atom to attract electrons to itself.
● Lunis Pauling – the one who develop
the scale of electronegativity
● F is most electronegative (EN = 4.0),
Cs is least (EN = 0.7)
● Metals on left side of periodic table
attract electrons weakly, lower EN
● Halogens and other reactive
nonmetals on right side of periodic
table attract electrons strongly,
higher electronegativities
Electrostatic potential maps show calculated charge distributions. Colors indicate
electron-rich (red) and electron-poor (blue) regions.

Inductive effect: shifting of electrons in a bond in response to EN of nearby atoms

Since the electrons are not shared evenly, there is what we called as a Dipole
moment.
● Bonding electrons toward electronegative atom
● Electronegative atom acquires partial negative
charge, δ-
● Example HCL. Chlorine is more electronegative than
Hydrogen and so electrons are pulled towards it.
Therefore, chlorine δ- and hydrogen is δ+ (since
electrons are pulled away from it)

● μ - magnitude of charge Q at end of molecular dipole

times distance r between charges
● μ = Q × r, in debyes (D), 1 D = 3.336 × 10−30 coulomb
meter
● length of an average covalent bond), the dipole
moment would be 1.60 × 10−29 C⋅m, or 4.80 D.
Absence of a Dipole moment
● In symmetrical
molecules, the dipole
moments of each bond
has one in the opposite
direction
● The effects of the local
dipoles cancel each other
Formal Charges is the process
that allows us to identify which is
the best formal charge by a
compound.
● We compare the bonding of
the atom in the molecule to
the valence electron
structure
● If the atom has one more
electron in the molecule, it
is shown with a “-” charge
● If the atom has one less
electron, it is shown with a
“+” charge
● Neutral molecules with both
a “+” and a “-” are dipolar
RESONANCE
● Some molecules are have structures
that cannot be shown with a single
representation
● In these cases we draw structures
that contribute to the final
structure but which differ in the
position of the π bond(s) or lone
pair(s)
● Such a structure is delocalized and
to is represented by resonance
forms
● The resonance forms are connected
by a double-headed arrow
RESONANCE HYBRID

● A structure with resonance forms

does not alternate between the forms
● Instead, it is a hybrid of the two
resonance forms, so the structure is
called a resonance hybrid
● For example, benzene (C6H6) has two
resonance forms with alternating
double and single bonds
● In the resonance hybrid, the actual
structure, all its C-C bonds equivalent,
midway between double and single
Different Atom in Resonance form
● Sometimes resonance forms involve different atom types as well as locations
● The resulting resonance hybrid has properties associated with both types of
contributors
● The types may contribute unequally
● The “enolate” derived from acetone is a good illustration, with delocalization
between carbon and oxygen
ACIDS AND BASES

3 definitions:

1. Arrhenius definition
● Acid: donates an H+ is aqueous solution (H2O)
● Base: gives an OH-] is aqueous solution (H2O)
● Example: HCl vs NaOH
ACIDS AND BASES

2. Brønsted–Lowry definition
● A Brønsted acid is a substance that donates a hydrogen ion (H+)
● A Brønsted base is a substance that accepts the H+
o “proton” is a synonym for H+ - loss of an electron from H leaving the bare
nucleus—a proton

Acids are shown in red, bases in blue. Curved arrows go from bases to acids. When an
acid reacts, it forms conjugate base. When a base reacts, it forms conjugate acid.

Note: the trends of the acid is negative (+) or partially (δ+). For base, (-) and (δ-).
ACID/BASE STRENGTH
Acid disassociation constant [Ka] - The concentration of water as a solvent does not change
significantly when it is protonated. Ka value is directly proportional to the H+ value (high value
of Ka = strong acid).
● The “ability” of a Brønsted acid to donate a proton to is sometimes referred to as the
strength of the acid (imagine that it is throwing the proton – stronger acids throw it harder)
pKa = -log Ka
● A larger value of pKa indicates a stronger acid and is proportional to the energy difference
between products and reactants. But inversely proportional to the Ka value.
● The pKa of water is 15.74
ORGANIC ACID AND BASE
● Organic acid - Those that lose a proton from O–H, such as
methanol and acetic acid
● Those that lose a proton from C–H, usually from a carbon
atom next to a C=O double bond (O=C–C–H)
ORGANIC ACID AND BASE
● Organic Base- Have an atom with a lone pair of electrons that can
bond to H+
● Nitrogen-containing compounds derived from ammonia are the
most common organic bases
● Oxygen-containing compounds can react as bases when with a
strong acid or as acids with strong bases
NON COVALENT INTERACTION
Has 3 types:
● Dipole – Dipole Forces - Occur between polar molecules as a result of electrostatic
interactions among dipoles. Forces can be attractive or repulsive depending on
orientation of the molecules.

Example: δ- δ+ (attraction); δ- δ- (repulsion)

● Dispersion Forces - Occur between all neighboring molecules and arise because the
electron distribution within molecules that are constantly changing.
NON COVALENT INTERACTION
● Hydrogen Bond - Most important noncovalent interaction in biological
molecules. Forces are result of attractive interaction between a hydrogen
bonded to an electronegative atom and an unshared electron pair on another
O or N atom
MOLECULAR MODELS

● We often need to visualize the shape or connections of a molecule in three

dimensions
● Molecular models are three dimensional objects, on a human scale, that
represent the aspects of interest of the molecule’s structure (computer
models also are possible)
● Drawings on paper and screens are limited in what they can present to you
● Framework models (ball-and-stick) are essential for seeing the
relationships within and between molecules – you should own a set
● Space-filling models are better for examining the crowding within a
molecule
FUNCTIONAL GROUP

● A functional group is defined as an atom or group of atoms within a

molecule that has similar chemical properties whenever it appears in
various compounds. Even if other parts of the molecule are quite
different, certain functional groups tend to react in certain ways
● For example, the double bonds in simple and complex alkenes react
with bromine in the same way.
● The systematic study of the shapes molecules and properties from these
shapes is Stereochemistry.
● The letter R is used in molecular structures to represent the “Rest of the
molecule”. It consists of a group of carbon and hydrogen atoms of any
size. It is used as an abbreviation since a group of carbon and hydrogen
atoms does not affect the functionality of the compound. In some
molecules, you will see R, R’, or R’’ which indicates that the R groups in
the molecule can be different from one another. For example, R might be
–CH2CH3 while R’ is –CH2CH2CH2CH3
Carbon-Carbon Bond (single, multiple,
with rings)
● Hydrocarbon – Carbon carbon
bond
● Aromatic – Carbon bond with ring
Carbon single bond with
electronegative atom
● Alcohol & Ether
Carbon oxygen double bond
● Carbonyl compound
● Carboxylic acid and derivatives
Nitrogen atom as functional groups
● Amine and Amide
ALKANES AND ITS ISOMERS

● Alkanes are organic compounds that consist entirely of single-

bonded carbon and hydrogen atoms and lack any other
functional groups. Alkanes are often called saturated
hydrocarbons because they have the maximum possible
number of hydrogens per carbon. Alipathic compound.
Use a prefix to indicate the number of carbons in a chain.End in –ane.
 Compounds are given systematic names by a process that uses

1. Name the longest carbon chain (root + "ane")

2. Name the branches (root + "yl")
3. Number the long chain
4. List the substituents alphabetically
 Compounds are given systematic names by a process that uses

1. Name the longest carbon chain (root + "ane")

2. Name the branches (root + "yl")
3. Number the long chain
4. List the substituents alphabetically
Compounds are given systematic names by a process that uses
Compounds are given systematic names by a process that uses
Compounds are given systematic names by a process that uses
ISOMERS

● All of the alkanes containing 4 or more carbon atoms show structural

isomerism, meaning that there are two or more different structural formulas
that you can draw for each molecular formula. Isomers (from the Greek isos +
meros, meaning "made of the same parts") are molecules that have the same
molecular formula, but have a different arrangement of the atoms in space.
In condensed structural formulas the bonds to each carbon are omitted,
but each distinct structural unit (group) is written with subscript
numbers designating multiple substituents, including the hydrogens.
The most important sources for alkanes are oil and natural gas. Oil is a
mixture of liquid alkanes and other hydrocarbons. Higher alkanes (which
are solid) occur as residues from oil distillation ("tar"). One of the largest
natural deposits of solid alkanes is in an asphalt lake known as the Pitch
Lake in Trinidad and Tobago. Natural gas contains primarily methane
(70-90%) with some ethane, propane and butane; some gas sources
deliver up to 8% CO2.
 Cycloalkanes and Their Stereochemistry

● Cycloalkanes are cyclic hydrocarbons, meaning that the carbons of the molecule
are arranged in the form of a ring. Several biomolecules such as protein, lipids,
carbohydrates, and nucleic acid exist as cyclic molecules. All these compound are
called Alicyclic Compound.
● Cycloalkanes are cyclic alkanes. Have 2H fewer than the open chain. (C
n H 2n ) Are named by using the prefix cyclo- before the name of the
alkane chain with the same number of carbon atoms.
Example of cycloalkane:
 Naming of Cycloalkanes:

1) Find the parent: Count the number carbons in the chain and the
substituents. If the substituents are longer than the ring then the
parent’s name is the substituent. If the ring is longer then the ring is
the parent.
 Naming of Cycloalkanes:

2. ) Number the substituents, and write the name: Make sure that you follow the
ring so that the substituents have the lowest numbers. If two or more alkyl chains
can be the same number then number alphabetically. Treat halogens as alkyl chains
(F, Cl, Br, I).
Naming of Cycloalkanes:
Naming of Cycloalkanes:
 CIS-TRANS ISOMERISM

● Cycloalkanes are less flexible than open-chain alkanes. Also have much less
conformational freedom in cycloalkanes
● Cycloalkanes have two isomers: cis (“top” face)-/trans (“bottom” face) isomers.
● Isomerism is possible in substituted cycloalkanes.
● Ex. 1,2-dimethylcyclopropane isomer.
 STEREOISOMERS
● Unlike Constitutional Isomers which have the same molecular formula but
a different orientation. Stereoisomers have the same order of connection
but differ in spatial (or three dimensional) orientation.
Stability of Cycloalkane – Ring Strain
● Rings larger than 3 atoms are not flat.
● Strain is an increase in molecular potential energy due to electron
repulsion or a deviation from ideal geometry.
● Larger rings have many more possible conformations than smaller rings
and are more difficult to analyze
Types of Strain
● Angle Strain (Ring Strain) is the strain due to expansion or
compression of bond angles.
Example: cyclopropane and cyclohexane
● Torsional Strain is the strain due to eclipsing of bonds on
neighboring atoms.

When atoms are eclipsed then there is a

natural tendency to move away from each
other
● Steric Strain is the strain due to repulsive interactions when atoms
approach each other too closely.

Because rings don’t rotate freely in space like

linear chains then energy is higher when they are
on the same side. For example: Cyclopropane
 The Baeyer Strain Theory
● Baeyer (1885): since carbon prefers to have bond angles of approximately 109°,
ring sizes other than five and six may be too strained to exist
● Rings from 3 to 30 C’s do exist but are strained due to bond bending distortions
and steric interactions

Because we know that SP 3 carbons like to have

bond angles of 109 o when the angles are smaller
or larger than 109 o the energy increases. It does
not like bond angles. The greater the angle
difference the more it is ready to explode to
alleviate the strain.
 CONFORMATION OF CYCLOALKANES
Cyclopropane
● 3-membered ring must have planar structure. The most ring
strained alkane ring 60° instead of 109.5°
● Bonds are weaker and more reactive than any other cycloalkanes.
● All C-H bonds are eclipsed
 CONFORMATION OF CYCLOALKANES
Cyclobutane
● The most torsional strain alkane ring due to the increase number of
hydrogens.
● Because of the increased torsional strain, the total energy of
cyclopropane and cyclobutane are the same.
 CONFORMATION OF CYCLOALKANES
Cyclopentane
● Cyclopentane has no angle (ring) strain but has a lot of torsional
strain so it twists to a puckered non-planar configuration.
 CONFORMATION OF CYCLOALKANES
Hexane
● Cyclohexane is strain free which means that it is stable.
● Cyclohexane is widely used in nature. Adopt 2 three-dimensional
structures or conformations (Chair and Boat).