Module A Module A

Foundations for studying Foundations for studying

Organic chemistry Organic chemistry
Based on Bruice’s Organic Chemistry: Chapters 1-2 Based on Bruice’s Organic Chemistry: Chapters 1-2

Learning Outcomes: At the end of this module, you will learn: Learning Outcomes: At the end of this module, you will learn:
1. Why should we study carbon-based chemistry? 1. Why should we study carbon-based chemistry?
2. What kinds of chemical bonds are found in organic molecules? 2. What kinds of chemical bonds are found in organic molecules?
3. How does chemical structure affect molecular properties? 3. How does chemical structure affect molecular properties?
4. What acid-base properties are important in organic chemistry? 4. What acid-base properties are important in organic chemistry?
5. How to draw organic molecules professionally? 5. How to draw organic molecules professionally?

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Organic Compounds Organic Chemistry

 Organic compounds are those based on carbon  Organic compounds are
 Why separate out carbon-containing compounds out of the molecules of life
all of the other 100+ elements as a special category?  Organic chemistry
studies the structures
Carbon is relatively abundant and reactions of organic
compounds
Carbon is a the most
abundant biogenic element

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 Carbon vs. other elements
Carbon vs. other elements

DOUBLE BOND

TRIPLE BOND

Relatively stable Very unstable

 Carbon forms a higher number of bonds  Carbon has a unique ability to form multiple bonds (with
than many other elements itself and with other elements)
 https://www.airspacemag.com/daily-planet/silicon-based-life-staple-science-fiction-may-not-be-
5
likely-after-all-180975083/ 6

Carbon vs. other elements Module A

Foundations for studying

Organic chemistry
Based on Bruice’s Organic Chemistry: Chapters 1-2

Learning Outcomes: At the end of this module, you will learn:

1. Why should we study carbon-based chemistry?
2. What kinds of chemical bonds are found in organic molecules?
 Elements to the left of carbon give up electrons 3. How does chemical structure affect molecular properties?
Ionic bonds
 Elements to the right of carbon accept electrons 4. What acid-base properties are important in organic chemistry?
 Carbon shares electrons Covalent bonds 5. How to draw organic molecules professionally?

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 Review

Structures of Organic Compounds Hybridization of Carbon-Valence Bond Theory

 sp hybrid orbitals: linear

 Carbon atoms in organic compounds form Ethyne

bonds with themselves (C-C single bonds and
multiple bonds) to build the framework of an
organic molecule
 Carbon hybridizes to form various kinds of
bonds

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Review Review

Hybridization of Carbon-Valence Bond Theory Hybridization of Carbon-Valence Bond Theory

 sp2 hybrid orbitals: planar at 120° angles  sp3 orbitals: each H-C-H=109.5°, the tetrahedral angle
 Has three-dimensional structure
Ethylene or Ethene

Methane

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 The sp3-tetrahedral carbon
Importance of Bonding
 The tetrahedral carbon has two sets of adjacent bonds
on two perpendicular bisecting planes:  Bonds connect atoms to make molecules
 The nature of the bond tells us about the reactivity or
= 90 ° chemistry of the molecule
 To understand chemistry and chemical reactions, you
must be able to recognize what molecules and which
structures are reactive, and which parts are not

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Review

 Bonds and  Bonds

 Bonds and  Bonds
 C-C  bonds and C-H bonds are generally unreactive
and provide a stable molecular framework for organic  The bond is weaker than the  bond , because the -
compounds bond overlap above and below the atoms, is less
effective than -bond overlap

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 Review

 Bonds and  Bonds Bond Strength: Multiple Bonds

  bonds are less stable: these bonds will tend to  Multiple bonds involve more overlap and sharing of electrons
undergo reactions in organic chemistry
 Multiple bonds results in an overall shorter and stronger
bonding between the two atoms
 A double bond is shorter and stronger than a single bond because
there are two bonds

 You will see this when we discuss the very first organic
reaction in Chapter 5
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Review
Bond Strength: Multiple Bonds Bond Strength:  Bonds
  Bonds that involve more electron density will be stronger
 More s character (greater electron density) in the bonding
orbital leads to stronger bonds

Compare C-C, C-H bonds:

 With multiple bonds, more bonds mean more overlap and Compare C-H bonds:
an overall shorter and stronger connection between the
two atoms, ie. it requires more energy to completely break
the bond 19 20
 Bonding with Heteroatoms Bonding with Heteroatoms
 Other than carbon and hydrogen, additional  Bonding with heteroatoms having different
elements are also featured in organic molecules: electronegativity lead to polar covalent bonds and
polar multiple bonds
 We call them heteroatoms
 These bonds are more reactive than C-C, C-H bonds
 Some heteroatoms are biogenic
 The resultant molecules can have dipole moments
elements

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Module A
The Shapes of Molecules
Foundations for studying  If we are able to see molecules with a very powerful
Organic chemistry microscope, we will find that they are constantly
moving—by rotating, vibrating, twisting, stretching…
Based on Bruice’s Organic Chemistry: Chapters 1-2  But if we take a snapshot at any moment in time, most of
them will be found in their relatively more stable form—
Learning Outcomes: At the end of this module, you will learn: that is going to be that molecule’s characteristic shape—
1. Why should we study carbon-based chemistry? even though the molecules are actually moving and
2. What kinds of chemical bonds are found in organic molecules? changing all the time
3. How does chemical structure affect molecular properties?
4. What acid-base properties are important in organic chemistry?
5. How to draw organic molecules professionally?

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 The Shapes of Molecules Stereochemistry
 The systematic study of the shapes of molecules, and
 Why a molecule adopts a certain shape result from the properties of these shapes is called stereochemistry
balance of many forces  The field of stereochemistry is central to organic chemistry
 Why is water an angular molecule, and not linear?  The shape of the molecule affects its physical and chemical
properties
 Eg. Stereochemistry helps us understand why these isomers
have such different properties, even though they have the
same composition and molecular weight

C5 hydrocarbons
&need the
Boiling point= 36 C Boiling point= 9.5 C models
Melting point= -129 C Melting point= -17 C

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Physical Properties of Compounds Physical Properties of Compounds

 The physical properties of any compound are due to the  Boiling point: temperature at which a compound
characteristics of the individual molecules (bonding, changes phase from liquid to gas
 The greater the intermolecular attractive forces, the higher
size, elemental composition, shape), and as a result, the the boiling point
intermolecular forces that can exist between them  Melting point: temperature at which a compound
changes phase from solid to liquid
 The greater the intermolecular attractive forces and
symmetry in the molecule (related to packing in the solid
form), the higher the melting point
Intermolecular attractive forces:
 Van der Waals  Solubility: whether a compound can dissolve
 Dipole-dipole interactions (become solvated) by a different compound (solvent)
 Hydrogen bonding
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 Van der Waals Forces Van der Waals Forces
BOILING POINTS OF ALKANES C5 hydrocarbons
• Methane (1C) – 167.7 °C n-pentane neopentane
• Ethane (2C) –88.6 °C
• Propane (3C) –42.1 °C Boiling point= 36 C Boiling point= 9.5 C
• Butane (4C) –0.5 °C Greater surface area, more VDW forces
 Alkanes are non-polar molecules having • Pentane (5C) 36.1 °C Melting point= -129 C Melting point= -17 C
only C and H: the only intermolecular More symmetrical, more crystalline
attractive force is van der Waals forces: • Hexane (6C) 68.7 °C
induced dipole-dipole interactions, and they • Heptane (7C) 98.4 °C
are weak interactions  In addition to the strength of the intermolecular forces, melting points also
• Octane (8C) 125.7 °C depend on how well molecules pack together to form a crystal lattice
 The greater the surface area of the alkane,
 Symmetrical molecules pack together more tightly and have higher melting
the higher the bp &convert to a chart points
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Dipole–Dipole Interactions Dipole–Dipole Interactions

 Organic compounds with heteroatoms with elements of different
electronegativity form polar covalent bonds: eg. Alkyl halides, ethers
 These compounds can have permanent dipoles, and therefore
Van der Waals only Van der Waals + dipole–dipole
stronger intermolecular attractions called dipole-dipole interactions
Comparing the Boiling Points of Alkanes and Alkyl Fluorides

Dipole–dipole interactions
are stronger than van der
+ + Waals forces.
 

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 Hydrogen Bonding Interactions Hydrogen Bonding Interactions
 A special type of dipole-dipole interaction is hydrogen bonds 2-methylbutan-1-amine sec-butylmethylamine Diethylmethylamine
 Hydrogen bonds are stronger than other dipole–dipole interactions
Hydrogen bond acceptor
+ 

Hydrogen bond donor

Stronger Hydrogen bonds Weaker Hydrogen bonds No Hydrogen bonds

 “Hydrogen bond donor” is the molecule giving the H for the bond
CH4 –167.7 °C H 2O 100 °C
 “Hydrogen bond acceptor” is molecule that accepts H
C-H no hydrogen bonds O-H hydrogen bonds 33 34

Hydrogen Bonding Interactions Solubility

 Hydrogen bonding can also occur  Solubility results from interactions between different
intramolecularly (within the same molecules— solute and solvent
molecule)  “Like dissolves like”, really means that Similar intermolecular forces are
 Hydrogen bonding interactions result in stabilizing
a linear protein molecule to fold into a  Nonpolar solutes dissolve in nonpolar solvents (eg. hydrocarbons)
secondary structure called an alpha-  Polar molecules dissolve in polar solvents (eg. alcohols)
helix
 The hydrogen bonding is between the
amine protons (H-bond donor) and the
carbonyl oxygen (H-bond acceptor)

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 Solubility Solubility in Water
 But particularly important are solubility in/interactions with
water, due to our biology:  When the qualities of the polar bond predominate, the overall
 “Hydrophilicity”: attraction to and solubility in water molecule is polar and more hydrophilic and soluble in water
 “Hydrophobic” molecules are repelled by water  When the hydrocarbon (nonpolar) part of the molecule predominates,
the overall molecule becomes hydrophobic

Solvation of a polar
compound by water

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A Cell Membrane “Like Dissolves Like”

 The structure of the cell membrane is also a consequence of Solubility is an Important Factor in Drug Action
solubility, hydrophilicity and hydrophobicity
 Crossing the blood–brain barrier requires a fat-soluble (hydrophobic)
drug
Hydrophilic Hydrophobic  THC and barbiturates have a hydrocarbon tail to facilitate crossing the
barrier
CH3 O

OH HN NH
H
O O
H
O

Tetrahydrocannabinol or THC Pentobarbital

(Marihuana active component) (Barbiturate)
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Compounds with Similar Shapes and Properties Organic Chemistry
Often Have Similar Physiological Activities Bonding

Stereochemistry
Shape— dipole moment, size, topology

Properties
chemistry, solubility, melting point, acidity, conductance

 Drugs bind to the same receptors by van der Waals interactions,

Function
dipole-dipole interactions, and hydrogen bonding
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biological reactions, drug properties, electronic properties 42

Module A Hydrogen Bonding

Foundations for studying
Organic chemistry
Based on Bruice’s Organic Chemistry: Chapters 1-2

Learning Outcomes: At the end of this module, you will learn:

1. Why should we study carbon-based chemistry?
2. What kinds of chemical bonds are found in organic molecules?  Among the same molecules, hydrogen bonding makes an
3. How does chemical structure affect molecular properties? intermolecular network
4. What acid-base properties are important in organic chemistry?  Between different molecules, a hydrogen bond in the extreme is
5. How to draw organic molecules professionally? when the proton is transferred: there is bond cleavage and new
species formed: this becomes an acid-base reaction
43 44
 Acids and Bases Conjugate Bases and Acids
 When an acid loses a proton, its conjugate base is formed
 When a base gains a proton, its conjugate acid is formed
a base
an acid

bond breaks

an acid
a base
new bond

 Brønsted Acid = proton/H+ donor

 Brønsted Base = proton/H+ acceptor
 Organic compounds can be acids or bases conjugate base
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Acids and Bases Acid Strength

, pKa= -log Ka

 Strong acids donate protons readily, are highly ionized, therefore

they have large Ka, and small pKa
Hydrochloric acid
Trichloroacetic acid

 Compounds can have the roles of acids or bases in different reactions Chloroacetic acid
&show gradation Acetic acid
 Whether a compound reacts as acid or base depends on the other
reactant, which will determine where the equilibrium lies Water

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 The Position of the Equilibrium Stability of the Conjugate Base
 The equilibrium always favors the formation of the more
The stronger the acid,
stable product the weaker (and more stable) its conjugate base.
 The equilibrium favors the formation of the weaker (less
reactive, more stable) acid B H B: + H

Eg. H Cl Cl + H

? Therefore Stable
Strong acid conjugate base
?
 To determine the acidity of a compound, we should
evaluate the stability of its conjugate base
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Lewis Acids and Bases Module A

Foundations for studying

 Lewis acid: an electron pair acceptor Organic chemistry
 Lewis base: an electron pair donor
Based on Bruice’s Organic Chemistry: Chapters 1-2

Learning Outcomes: At the end of this module, you will learn:

1. Why should we study carbon-based chemistry?
All Brønsted acids are Lewis acids 2. What kinds of chemical bonds are found in organic molecules?
All Brønsted bases are Lewis bases 3. How does chemical structure affect molecular properties?
4. What acid-base properties are important in organic chemistry?
5. How to draw organic molecules professionally?

51 52
 Talking about Molecules Molecular Models
 To visualize the shape or connections of a molecule in three
 To discuss chemistry, we need to talk about dimensions and from different perspectives, molecular models or
computer models are helpful
molecules and their reactions
 We cannot see molecules but a tool that helps
chemists visualize molecules, particular their 3-D &simulation
structures, are by using molecular models

Framework Space-filling Computer

simulation

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How do we draw molecules?

Talking about Molecules
 Kekulé structures—draw all atoms and all bonds
 Another way chemists envision and talk about
molecules with each other is by using drawings

 Tedious for larger and larger molecules!

 It is going to slow you down
 Be professional and do not draw molecules this way!

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 Condensed Structures Skeletal Structures
 The focus is on the bonds/skeleton
 The focus is on the atoms  Only the bonds are shown, as lines
 Atoms and groups around each carbon are gathered and
 Carbon atoms not written out
shown with number subscripts
 Assumed to be at each intersection of two lines (bonds) and at end of each line
 Bonds are either not shown or minimized  Hydrogens on carbon atoms also not shown – it is assumed that hydrogens
 Substituents on carbon are shown hanging off the carbon will fill the rest of the tetravalency of the carbon
or in brackets  Atoms other than C and H are shown

Kekule structure Kekule structure

C
C C
C C

57 58

Skeletal Structures Skeletal structures

 Carbon chain is shown ‘zig-zag’ because the alkane is  Hydrogens bonded to carbons are not shown – assume that
also not straight-- being made up of sp3-hybridized whatever number of hydrogens to fulfill the valence will be there
carbon atoms  All atoms other than C and H are shown
H
O O
H3C CH CH2 CH2 CH2 CH2 CH2 CH CH C O H
Queen honeybee pheromone

**Many students make mistakes counting the

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carbons, even on the final exam!** 60
Tetrahedral Carbons in Skeletal Structures Tetrahedral Carbons in Skeletal Structures
 Recall: To show all four bonds in this 3-dimensional  Always represent tetrahedral carbon atom bonds using
structure in 2-dimensions (ie. on paper): two “V’s”:
 The tetrahedral carbon has two sets of adjacent bonds on  One “V” made of two planar bonds
two perpendicular bisecting planes  The other “V” has one bond going into the page, one bond
coming out of the page:

= 90 °

IN BOND

X
OUT BOND

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Tetrahedral Carbons in Skeletal Structures

Practice!
 Hydrogens bonded to carbons are not shown – assumed to be there  Practice viewing, interpreting and drawing skeletal structures
 Even though the textbook will use a combination of condensed
structures and skeletal structures, you should use skeletal
structures in your work, problem sets, tests, quizzes, exams… as
much as possible
 If you use chemistry software, all the structures will be skeletal
structures

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 outro
Module A

Foundations for studying

Organic chemistry
Based on Bruice’s Organic Chemistry: Chapters 1-2
Check that you have achieved these learning outcomes, and can give
examples to explain and answer each of these questions:
1. Why should we study carbon-based chemistry?
2. What kinds of chemical bonds are found in organic molecules?
3. How does chemical structure affect molecular properties?
4. What acid-base properties are important in organic chemistry?
5. How to draw organic molecules professionally?

65