1. BIO-ORGANIC
CHEMISTRY
Lesson 1
OBJECTIVES:
INTRODUCTION
At the end of the lesson students are expected to:
1. Recognize the works of scientists in the development of
organic chemistry as a science.
2. Understand the general importance of organic chemical
compounds.
3. Explain some general differences between inorganic and
organic compounds.
4. Determine the type of bonds present in organic
compounds.
5. Identify the different functional groups present in organic
compounds.
6. Differentiate isomers of organic compounds.
ust-nursing

2. BIO-ORGANIC
CHEMISTRY BEGINNINGS OF ORGANIC CHEMISTRY
Lesson 1
The name organic chemistry came from the word organism.
INTRODUCTION
Vitalism in the foundations of chemistry
In the history of chemistry, vitalism played a pivotal role, giving
rise to the basic distinction between organic and inorganic
substances, following Aristotle's distinction between the
mineral kingdom and the animal and vegetative kingdoms.
The basic premise of these vitalist notions was that organic
materials differed from inorganic materials in possessing a
"vital force", accordingly, vitalist theory predicted that organic
materials could not be synthesized from inorganic
components.
ust-nursing

3. BIO-ORGANIC
CHEMISTRY ORGANIC CHEMISTRY is the study of the
Lesson 1 compounds of carbon.
INTRODUCTION
The only distinguishing characteristic of organic
compound is that all contain the element
CARBON.
http://www.angelo.edu/faculty/kboudrea/index_2353/Notes_Chapter_01.pdf
ust-nursing

4. BIO-ORGANIC
CHEMISTRY
Lesson 1
Why is carbon special?
“The uniqueness of
INTRODUCTION
carbon among elements
is that its atoms can
bond to each other
http://www.webelements.com/webelements/elements/text/C/key.html
successively many
times”.
Polyethylene molecule, a plastic polymer
DNA molecule- blue print of life
ust-nursing

5. BIO-ORGANIC
CHEMISTRY
Lesson 1
Why is carbon special?
As a group 4A element,
INTRODUCTION
carbon atoms can share
four valence electrons and
form four strong covalent
bonds.
http://www.webelements.com/webelements/elements/text/C/key.html
Molecular model of Aspirin (ASA), a Structure of tetrahedral bonded
pain reliever amorphous carbon.
ust-nursing

6. BIO-ORGANIC
CHEMISTRY
Lesson 1
INTRODUCTION Why is carbon special?
Carbon atoms can form
very stable bonds to many
other elements such as H,
F, Cl, I, O, N, S and P.
http://www.webelements.com/webelements/elements/text/C/key.html
With numerous ways of bonding and
complexity, carbon atoms can form a multitude
of different compounds. More than 16,000,000
are known compared to inorganic compounds
which are about 600,000.
ust-nursing

7. BIO-ORGANIC
CHEMISTRY
Lesson 1
Why is carbon special?
Complex organic
INTRODUCTION
compounds produce
biologically functional
molecules such as
proteins, DNA, RNA,
carbohydrates, enzymes,
http://www.webelements.com/webelements/elements/text/C/key.html
lipids and ATP.
This image depicts the HIV Viral capsid
entering a T Cell and the HIV virus
These complex
releasing its viral capsid into the host T-
cells cytoplasm.
compounds are present
in foods, medicine, fuels
and industrial products.
ust-nursing

8. BIO-ORGANIC
CHEMISTRY
Lesson 1
INTRODUCTION Organic vs Inorganic Compounds
Can you classify the following as organic or inorganic?
a. NaOH b. CH3OH c. C6H6 d. Mg(NO3)2
ust-nursing

9. BIO-ORGANIC
CHEMISTRY
Lesson 1
INTRODUCTION
ust-nursing

10. BIO-ORGANIC
CHEMISTRY Atomic Structure
Lesson 1
A schematic view of an atom. The dense POSITIVELY
charged nucleus contains most of the atom’s mass and is
INTRODUCTION
surrounded by NEGATIVELY charged electrons.
Nucleus (Protons + Neutrons)
Volume around nucleus occupied
by orbiting electrons
• Nucleus consists of protons (positively charged)
and neutrons (electrically neutral).
•The nucleus contains essentially all the mass of
the atom ~ 10-14 to 10-15.
•Electrons have negligible mass and orbit the
nucleus at a distance ~ 10-10 m.
•The diameter of a typical atom is about 2 x 10-10 m
or 200 picometer.
ust-nursing

11. BIO-ORGANIC
CHEMISTRY
Lesson 1
Atomic Structure
All the atoms of a given element
INTRODUCTION
have the same atomic number--- 1
for H, 6 for C, 17 for Cl. The
average mass in atomic mass
units (amu) of many atoms of an
element is called the element’s
atomic weight --- 1.008 amu for H,
12.011 amu for C and so on..
Atomic Number (Z)
gives the number of protons or
electrons in an atom.
Mass Number (A)
gives the number of protons plus
neutrons in an atom.
ust-nursing

12. BIO-ORGANIC
CHEMISTRY
Lesson 1 Electronic Configuration
The lowest-energy arrangement or ground-state electron
INTRODUCTION
configuration of an atom is a description of the orbitals that the
atom’s electrons occupy.
One can predict the arrangement of electrons in an atom by the
following ways…
RULE 1
The orbitals of lowest energy are filled
first, according to the order 1s 2s
2p 3s 3p 4s 3d…
(as shown at the left figure)
ust-nursing

13. BIO-ORGANIC
CHEMISTRY
Electronic Configuration
Lesson 1
INTRODUCTION
http://images.encarta.msn.com/xrefmedia/aencmed/targets/illus/ilt/1e67a7af.gif
RULE 2
Only two electrons can occupy an orbital, and they must be of
opposite spin.
RULE 3
If two or more empty orbitals of equal energy are available, one
electron occupies each with the spins parallel until all orbitals are
half-full.
ust-nursing http://www.physchem.co.za/Atomic/Electron%20Configuration.htm

14. BIO-ORGANIC
CHEMISTRY
Atomic Orbitals
Lesson 1
WHAT ARE ATOMIC ORBITALS AND WHAT ARE MOLECULAR ORBITALS?
INTRODUCTION
The space occupied by electrons is described by the term
orbital. If the electrons are associated with the atom of a free
element, they are said to be atomic orbitals. Once bonds
have been formed, the atomic elements become part of
molecules, and the electronic positions are described by
molecular orbitals.
WHAT IS AN S-ORBITAL?
It is a spherically symmetrical orbital at a discreet distance
from the nucleus. This corresponds to the first quantum level.
Illustration of an s-orbital.
ust-nursing

15. BIO-ORGANIC
CHEMISTRY
Atomic Orbitals
Lesson 1
WHAT IS A P-ORBITAL?
INTRODUCTION
Beginning in the second row, there is a second energy level
fro elements. First, there is a 2s orbital, but there is also a 2p
level composed of three identical p-orbital. A p-orbital is
“dumbbell” shaped with electron density on the other side of
the nucleus.
ust-nursing
Illustration of p-orbitals.

16. BIO-ORGANIC
CHEMISTRY
BONDING IN ORGANIC COMPOUNDS
Lesson 1
A carbon atom does not form ions easily, since it has four
INTRODUCTION
valence electrons (1s2 2s2 2p2). It satisfies the octet rule in
compounds by sharing electrons.
These are the orbitals that exist on atomic carbon (not connected to
anything)
ust-nursing

17. BIO-ORGANIC
CHEMISTRY
BONDING IN ORGANIC COMPOUNDS
Lesson 1
Hybridization: sp3 Orbitals
INTRODUCTION
•When carbon atoms form bonds with each other, the resulting
bonds are described by hybrid orbitals, which are formed my
mixing (hybridizing) the carbon’s atomic orbitals. (Linus Pauling,
1931)
•When carbon atoms bond to 4 other atoms, the 2s and all three
2p orbitals in the valence shell combine to produce four sp3
orbitals.
ust-nursing

18. BIO-ORGANIC
CHEMISTRY
BONDING IN ORGANIC COMPOUNDS
Lesson 1
•All four sp3 orbitals are at the same energy level, with
INTRODUCTION
one electron in each hybrid orbital.
ust-nursing

19. BIO-ORGANIC
CHEMISTRY
BONDING IN ORGANIC COMPOUNDS
Lesson 1
•To minimize electron-electron repulsion, the sp3 orbitals
INTRODUCTION
are arranged in the shape of a tetrahedron around a
central carbon atom with bond angles of 109.5o.
ust-nursing

20. BIO-ORGANIC
CHEMISTRY
BONDING IN ORGANIC COMPOUNDS
Lesson 1
Hybridization: The Structure of METHANE
INTRODUCTION
ust-nursing

21. BIO-ORGANIC
CHEMISTRY
BONDING IN ORGANIC COMPOUNDS
Lesson 1
Hybridization: sp2 Orbitals
INTRODUCTION
When 2s orbital combines with two of the three available 2p
orbitals, this results to the formation of an sp2 hybrid with one
unhybridized orbital (leftover p orbital).
ust-nursing

22. BIO-ORGANIC
CHEMISTRY
BONDING IN ORGANIC COMPOUNDS
Lesson 1
Hybridization: sp2 Orbitals
INTRODUCTION
The sp2 orbitals are arranged in a trigonal planar shape
around the central carbon atom, with bond angles of 120o.
The unhybridized p orbital is perpendicular to this plane.
ust-nursing

23. BIO-ORGANIC
CHEMISTRY
BONDING IN ORGANIC COMPOUNDS
Lesson 1
Hybridization: Structure of Ethylene
INTRODUCTION
When two sp2 hybridized carbons are next to each other, two kinds of
overlap are formed:
-End-on-end overlap of the sp2 orbitals to make a σ -bond (sigma
bond)
-Side-to-side overlap of the unhybridized p orbitals to make a π -bond
(pi bond).
ust-nursing

24. BIO-ORGANIC
CHEMISTRY
BONDING IN ORGANIC COMPOUNDS
Lesson 1
Hybridization: Structure of Ethylene
INTRODUCTION
Free rotation is not possible along a pi-bond.
ust-nursing

25. BIO-ORGANIC
CHEMISTRY
BONDING IN ORGANIC COMPOUNDS
Lesson 1
Hybridization: Structure of Ethylene
INTRODUCTION
120o
Bonding in ethylene – It assumes a planar
configuration with a bond angle of 120O.
ust-nursing

26. BIO-ORGANIC
CHEMISTRY
BONDING IN ORGANIC COMPOUNDS
Lesson 1
Hybridization: Structure of Ethylene
INTRODUCTION
The planar structure of ethylene
ust-nursing

27. BIO-ORGANIC
CHEMISTRY
BONDING IN ORGANIC COMPOUNDS
Lesson 1
Hybridization: sp Orbitals
INTRODUCTION
Instead of combining two or three 2p orbitals, the carbon 2s orbital
hybridizes with only a single 2p orbital. Two sp hybrid orbitals result,
and two p orbitals remain unchanged.
ust-nursing

28. BIO-ORGANIC
CHEMISTRY
BONDING IN ORGANIC COMPOUNDS
Lesson 1
Hybridization: sp Orbitals
INTRODUCTION
The two sp orbitals are linear, or 180o apart on the x-axis and
the remaining two p orbitals are perpendicular on the y-axis and the
z-axis.
ust-nursing

29. BIO-ORGANIC
CHEMISTRY
Hybridization: sp Orbitals
Lesson 1
INTRODUCTION
Representation of the formation of an sp-hybrid carbon atom.
ust-nursing

30. BIO-ORGANIC
CHEMISTRY
BONDING IN ORGANIC COMPOUNDS
Lesson 1
Hybridization: Structure of Acetylene
INTRODUCTION
When two sp-hybridized carbon atoms approach each other, sp
hybrid orbitals from each overlap head-on to form a strong sp-sp
σ−bond. The remaining two unhybridized p-orbitals overlap similarly
thus forming two π- bonds.
ust-nursing

31. BIO-ORGANIC
CHEMISTRY
BONDING IN ORGANIC COMPOUNDS
Lesson 1
Hybridization: Structure of Acetylene
INTRODUCTION
The remaining two sp-hybrid orbitals forms a σ-bond with
hydrogens to complete the structure of acetylene – a linear
molecule.
ust-nursing

32. BIO-ORGANIC
CHEMISTRY COVALENT BONDING
Lesson 1
DEFINE A COVALENT BOND
INTRODUCTION
A covalent bond is usually composed of two electrons that
are shared between two atoms.
This type of bond occurs when the atom cannot easily gain or lose
electrons (there is very little electronegativity difference)
ust-nursing

33. BIO-ORGANIC
CHEMISTRY COVALENT BONDING
Lesson 1
WHAT IS VALENCE?
INTRODUCTION
Valence is usually defined as the number of bonds an atom
can form to satisfy the octet rule and remain electrically
neutral. This is not to be confused with valence electrons,
which are the number or electrons in the outermost shell.
WHAT IS POLARIZED COVALENT BOND?
When a bond is formed between two
atoms that are not identical, the
electrons do not have to be equally
shared. If one atom is more
electronegative, it will pull a greater
share of electrons from the bond.
Which of the following are polar covalent bonds? For the
polarized bond, identify the negative and the positive
poles? ANSWERS
a) C-O b) C-C c) O-H d) C-N e) C-Li f) O-O http://www.olysun.com/Chem_139/Bond.html
ust-nursing

34. BIO-ORGANIC
CHEMISTRY DIPOLE-DIPOLE INTERACTIONS
Lesson 1
WHAT IS VAN DER WAAL’S ATTRACTION?
When there are no polarizing atoms in the molecules, the
INTRODUCTION
only attraction between molecules results from the electrons
of one molecule being attracted to the positive nuclei of
atoms in another molecule.
WHAT IS DIPOLE-DIPOLE
INTERACTION?
This is an intermolecular
electrostatic interaction.
ust-nursing http://stezlab1.unl.edu/reu1999/dputn226/ChemHelp/RET_Web_Pages/im_forces/Intmole_Forces.htm

35. BIO-ORGANIC
CHEMISTRY HYDROGEN BONDS
Lesson 1
WHY IS THE ATTRACTION BETWEEN TWO GROUPS
BEARING AN O-H GROUP STRONGER THAN BETWEEN
INTRODUCTION
TWO GROUPS BEARING A C=O GROUP?
When hydrogen forms a polar covalent bond with heteroatoms, the
hydrogen takes the δ+ charge of the dipole. Since the classical
Bronsted acid is H+, a polarized hydrogen in O-H can be considered
somewhat acidic since it has positive character. The increased
acidity and bond polarity leads to stronger interaction with a
negative heteroatom when brought into close proximity to a positive
polarized hydrogen. Resulting to a significantly stronger than normal
dipole-dipole interaction known as HYDROGEN BOND.
www.sp.uconn.edu/~terry/images/mols/atomfig5.html
Figure showing the formation of H-Bonds in water molecules.
ust-nursing