Chemistry 121(01) Winter 2009
Introduction to Organic Chemistry and Biochemistry
Instructor Dr. Upali Siriwardane (Ph.D. Ohio State)
E-mail: upali@chem.latech.edu
Office: 311 Carson Taylor Hall ; Phone: 318-257-4941;
Office Hours: MTW 9:00 am - 11:00 am;
TR 9::00 - !0:00 am & 1:00-2:00 pm.
December 19, Test 1 (Chapters 12-14)
January 2 Test 1 (Chapters 15-16)
February 6 (Chapters 17-19)
February 27, (Chapters 20-22)
March 2, 2009, Make Up Exam:
Bring Scantron Sheet 882-E
Chemistry 121, Winter 2008, LA Tech
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Introduction to Organic and biochemistry
Chapter 1-12
Chemistry 121, Winter 2008, LA Tech
1-2
Introduction to organic & Biochemistry
Test 1
12. Saturated Hydrocarbons
13. Unsaturated Hydrocarbons
14. Alcohols, Phenols, and Ethers
Test 3
18. Carbohydrates
19. Lipids
20. Proteins
Test 2
15. Aldehydes and Ketones
16. Carboxylic Acids, Esters, and
Other Acid Derivatives
17. Amines and Amides
Test 4
21. Enzymes and Vitamins
22. Nucleic Acids
23. Biochemical Energy Production
Self Study
24. Carbohydrate Metabolism
25. Lipid Metabolism
26. Protein Metabolism
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Introduction to organic & Biochemistry
12.1 Organic and Inorganic Compounds
12.2 Bonding Characteristics of the Carbon Atom
12.3 Hydrocarbons and Hydrocarbon Derivatives
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Organic and Inorganic compounds
Ionic Compounds: Have cations and anions are also called salts made of
metlas and non-metals
Covalent Compounds: Consists of neutral molecules connected by
covalent bonds to non metallic elements.
Organic Compounds :
have carbon atoms sharing electrons in covalent bonds. Carbon atoms
form chains, and many atoms can be joined by covalent bonds.
Inorganic Compounds:
Consist of ions produced by loss or gain of electrons between a metal
and non metal.
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Covalent or Ionic
Identify covalent and ionic compounds:
H2O, NaCl, C2H5OH, CH3COOH, Na2CO3, CH3OK, KOH
Covalent :
Ionic:
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Organic or Inorganic
Identify organic and inorganic compounds:
H2O, NaCl, C2H5OH, CH3COOH, Na2CO3, C3H8, KOH
Organic :
Inorganic:
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Introduction
Organic chemistry is the study of the compounds
of carbon with H, N, O and S.
Biochemistry is the study of the chemical
processes in living organisms. It deals with the
structure and function of cellular components.
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More details.. Organic vs. Inorganic
Organic compounds are produced by living things.
Inorganic compounds are produced by non-living
naturalprocesses or by human intervention in the
laboratory.
This was the most common definition of "organic" until Wohler's 1828
synthesis of urea (an organic compound) from ammonium cyanate (a
salt, and therefore? Organic/inorganic). But we no longer use this
definition, for the simple reason that many compounds that everyone
agrees are organic -- including "natural products" which are routinely
made by living things -- have been synthesized by humans.
Organic compounds contain carbon.
Inorganic compounds don't.
Organic compounds contain carbon-hydrogen bonds.
Inorganic compounds don't.
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Bonding Characteristics of the Carbon Atom
C is a small atom
• it forms four bonds consisting of single, double,
and triple carbon to carbon bonds or other atoms
• Shows tetrahedral (all 4 - ), trigonal planar (2 - & 1
=) and linear ( 1 - & 1  )
• it forms strong bonds with C, H, O, N, and some
metals
• form stable covalent bonds to other carbon
atoms – catenation: Long carbon chains can be
produced.
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s and p hybrids
Four sp3 hybrids
Three sp2 hybrids
Two sp hybrids
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Hybrid Atomic Orbitals
Hybridization is the mixing up of two or more
atomic orbitals
There are three types of hybrid atomic orbitals for
carbon
sp3 (one s orbital + three p orbitals give four sp3
orbitals)
sp2 (one s orbital + two p orbitals give three sp2
orbitals)
sp (one s orbital + one p orbital give two sp orbitals)
Chemistry 121, Winter 2008, LA Tech
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 and  bonds in single and multiple bonds
single bond - one shared pair of electrons between
two atoms; a  bond
double bond - two shared pairs of electrons
between two atoms; one s bond and one  bond
triple bond - three shared pairs of electrons
between two atoms; one s bond and two p bonds
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 and  bonds
Overlap of hybrid orbitals can form two types
of bonds, depending on the geometry of the
overlap
 bonds are formed by “direct” overlap
s1 s1
p1
p1
s1
p1
 bonds are formed by “parallel” overlap of
unhybrid p prbitlas
Chemistry 121, Winter 2008, LA Tech
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Predicting hybridization of atoms in a Lewis
structure
Count sigma bonds and unshared electrons around
the atom
If the total number of pairs:
2 sp hybridization
3 sp2 hybridization
4 sp3 hybridization
Chemistry 121, Winter 2008, LA Tech
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Counting  and  bonds in Lewis structure
Hybridization
sp
3
sp
2
Types of
Bonds to Carbon
fou r s igma bond s
Example
HH
H-C-C-H
HH
H
three sigma bonds
and on e pi bond
Chemistry 121, Winter 2008, LA Tech
tw o sigma b on ds
and tw o p i bonds
Ethan e
H
C
H
sp
N ame
H-C
Ethylene
C
H
C-H Acetylene
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Draw Lewis structure of molecules
CHCl3
C2H4
C3H8O
CH3CH2CH2OH
CH3CH2OCH3
CH3CO2H
CH3CHO
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Resonance
For many molecules and ions with double
bonds, two or more Lewis structure could be
written
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Curved arrow Electron pushing
Curved arrow: a symbol used to show the
redistribution of valence electrons
In using curved arrows, there are only two
allowed types of electron redistribution:
• from a bond to an adjacent atom
• from an atom to an adjacent bond
Electron pushing by the use of curved arrows is
also used in explaining reaction mechanisms
Chemistry 121, Winter 2008, LA Tech
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Drawing Curved Arrows
To show the movement of electrons in breaking and forming
bonds. The tail of the arrow is started at the site of electron
density (negative character such as a pi bond or lone pair of
electrons) and proceeds to the arrowhead which is drawn to
the site of electron deficiency (positive character).
NEGATIVE TO POSITIVE!
Arrows can be drawn from:
tail
1) lone pair
bond
2) bond
lone pair
3) bond
bond
Chemistry 121, Winter 2008, LA Tech
head
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Bond Properties
Bond strength:
strongest
C C > C
C
weakest
> C C
Bond length:
longest
C
C > C
Chemistry 121, Winter 2008, LA Tech
shortest
C
> C
C
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Formula
Molecular formula
• kind and number of each type of atoms
Structural formula
• each atom and bond in a molecule
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Condensed formula
Condensed formula
•
Shorthand way of writing a formula.
•
Lists all atoms in order and tells how they are
bound together.
• Example.
Propane C3H8
CH3CH2CH3
This is a convenient format for describing a
molecule using text.
Chemistry 121, Winter 2008, LA Tech
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Structural Formula of hydrocarbons
One simple class of compound is the alkane which
has only C, H and single bonds.
methane
ethane
propane
CH4
CH3CH3
CH3CH2CH3
H
H
C
H
H
Chemistry 121, Winter 2008, LA Tech
H
H
H
C
C
H
H
H
H
H
H
H
C
C
C
H
H
H
butane
H
CH3CH2CH2CH3
H
H
H
H
H
C
C
C
C
H
H
H
H
H
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Line Formula of hydrocarbons
One simple class of compound is the alkane which
has only C, H and single bonds.
methane
ethane
propane
CH4
CH3CH3
CH3CH2CH3
Chemistry 121, Winter 2008, LA Tech
butane
CH3CH2CH2CH3
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Line formula
Similar to structural formula.
Each line represents a bond.
Carbons are assumed to be present at the end
of each line segment.
Hydrogen is not shown when bound to carbon.
OH
H2
C
H2
C
H2C
H2
C
CH 2
C
H2
C
H2
Chemistry 121, Winter 2008, LA Tech
H2C
H2
C
H2C
C
H2
N
C
H2
H2
C
O
H
H2
C
H2C
H2
C
N
C
H2
H
C
H2
H
H2C
H2
C
H2C
C
H2
C
H2
H2
C
CH 3
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Models
Three dimensional representations
Ball and Stick
Space Filling
Both are models of propane.
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Base names of organic compounds
Prefix
MethEthPropButPentHexHeptOctNonDec-
Carbons
1
2
3
4
5
6
7
8
9
10
Chemistry 121, Winter 2008, LA Tech
I see much
memorization in
your future!
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Functional Groups in Organic Compounds
Functional group: an atom or group of atoms within a
molecule that shows a characteristic set of physical and
chemical properties
Functional group
• divide organic compounds into classes
• the sites of characteristic chemical reactions
• the basis for naming organic compounds
Chemistry 121, Winter 2008, LA Tech
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Common Functional Groups
Alcohol(carbon, hydrogen and
oxygen)
CH3-CH2-OH
Thiol (thioalcohol) thio means
sulfur
CH3-CH2-SH
Amine
CH3-CH2-NH2
Ether
CH3-CH2-O-CH2-CH3
H H
H- C-C- O- H
H H
An alcohol
(Ethanol)
CH3 N H
H
(a 1° amine)
Chemistry 121, Winter 2008, LA Tech
CH3 N H
CH3 N CH3
CH3
(a 2° amin e)
CH3
(a 3° amine)
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Common Functional Groups (continued)
Carbonyl group
or unit
Aldehyde
ketones
O
Carboxylic acids
CH3 -C-O-H
or
CH3 COOH
or
CH3 CO2 H
Acetic acid
Chemistry 121, Winter 2008, LA Tech
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Classification of organic compounds
Class
Chemistry 121, Winter 2008, LA Tech
Functional group
Example
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IUPAC - a general system: Examples
prop-en-e = propene
CH3 CH=CH 2
eth-an-ol = ethanol
CH3 CH2 OH
O
but-an-one = butanone
O
but-an-al = butanal
H
O
pent-an-oic acid = pentanoic acid
cyclohex-an-ol = cyclohexanol
OH
OH
eth-yn-e = ethyne
eth-an-amine = ethanamine
HC
CH
CH3 CH2 NH 2
cyclo-pent-en-e
Chemistry 121, Winter 2008, LA Tech
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The IUPAC system: Naming Organic Compounds
As a general system of nomenclature
prefix-infix-suffix
• prefix tells the number of carbon atoms in the parent
• infix tells the nature of the carbon-carbon bonds
• suffix tells the class of compound
Infix
-an-en-yn-
Nature of Carbon-Carbon
Bonds in the Parent Chain
Suffix
Class
-e
hydrocarbon
all single bonds
-ol
one or more double bonds
one or more triple bonds
-al
-amine
-one
-oic acid
alcohol
aldehyde
amine
ketone
carboxylic acid
Chemistry 121, Winter 2008, LA Tech
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Hydrocarbons
Composed of only carbon and hydrogen; in petroleum
and coal
Saturated - hydrocarbons with all
C-C single bonds
Unsaturated - hydrocarbons with at
least one C-C double bond or triple bonds
Chemistry 121, Winter 2008, LA Tech
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Classification of Hydrocarbons
Hydrocarb on s
Satu rated
Class
Alkan es
(Ch apter 3)
Carb on - Only carboncarbon
carb on single
bond ing
bonds
HH
Example
H-C-C-H
HH
N ame
Ethan e
Chemistry 121, Winter 2008, LA Tech
Un saturated
Alk enes
(Ch apters 4-5)
Alkynes
(Chap ter 4)
Arenes
(Ch apter 9)
One or more
carb on -carbon
doub le bonds
H
H
C C
H
H
Ethylene
On e or more
carb on -carbon
triple b on ds
On e or more
ben zenelike
rin gs
H-C C-H
Acetylene
Benzen e
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Examples of Alkanes, Alkenes, Alkynes and Arenes:
H
H H
H C C H
H H
H
H
H
C C
H
H
H C C H
H
C
C
C
C
C
C
H
H
H
ethane
C2H6
ethene
C2H4
CnH2n+2
saturated
alkane
CnH2n
CnH2n-2
CnHn
unsaturated unsaturated Aromatic
alkene
alkyne
Arene
Chemistry 121, Winter 2008, LA Tech
ethyne
C2H2
benzene
C6H6
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Biochemical Principles
Structures of Monomers and Polymers found in
living systems
• Carbohydrates (glucose, starch, cellulose)
• Proteins (amino acids, proteins)
• Nucleic acids (Nucleotides-A,T,G,C and RNA & DNA)
Functions of Biological molecules
• Enzymes and Vitamins
• Nucleic Acids and hereditary
Biochemical Energy Production
• Carbohydrate Metabolism
• Lipid Metabolism
• Protein Metabolism
Chemistry 121, Winter 2008, LA Tech
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