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Foundations for Studying

Organic chemistry
Bruices Organic Chemistry: Chapters 1, 2

Learning Outcomes
1. Review and understand electronic structure and
bonding in molecules, particularly compounds
important to organic chemistry (General Chemistry)
2. Review the factors which affect acid-base properties,
bond strengths.

IMPORTANT concepts! (e.g. Basicity vs. Nucleophilicity)


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Background
General Chemistry (CHEM1042):
Atomic and electronic structure
Ionic and covalent bonds, dipole moments
Lewis and Kekule structures
Atomic orbitals, hybridization and molecular
geometry (VSEPR theory)
How single, double, triple bonds are
formed
... Reviewed in Bruice Chapter 1
2

Background
General Chemistry (CHEM1042):
Atomic and electronic structure
1. Underlying foundation for all chemical reactions;
2. Electronic structure is the basis for atom
bonding and therefore determines all chemical
reactivities;

Background
H and He

total orbitals: 1 + 3 + 5 = 9

total orbitals: 1 + 3 = 4
total orbitals: 1 + 3 + 5 + 7 = 16

Larger shells with more orbitals can accommodate more electrons.


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Background
H and He

Most of this class involves this shell


Carbon: 1s2 2s2 2p2

Background
Aufbau principle: An electron goes into the
atomic orbital with the lowest energy. (Why:
The closer of the electrons to the postitive
nucleus, the lower its energy is.)

The first shell is closest to the nucleus.


The closer the atomic orbital is to the
nucleus, the lower its energy.
Within a shell, s < p < d

Background
Aufbau principle: An electron goes into the
atomic orbital with the lowest energy. (The
closer of the electrons to the nucleus, the
lower the is its energy)
Pauli exclusion principle: No more than two
electrons can be in an atomic orbital and the
two electrons must be of opposite spin.
(Determined by quantum physics)

Background

Background
Aufbau principle: An electron goes into the
atomic orbital with the lowest energy. (The
closer of the electrons to the nucleus, the
lower the is its energy)
Pauli exclusion principle: No more than two
electrons can be in an atomic orbital and the
two electrons must be of opposite spin.
Hunds rule: An electron goes into an empty
degenerate orbital rather than pairing up. (This
minimizes electron repulsion)
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Things are actually more complicated


Remembering the
Diagonal Rule of filling
electrons into orbitals?
e.g.: after 3p, next is 4s,
which has lower energy
than 3d

Mostly we do not need to


go beyond the 3p orbital

Following the n + l rule


n: principal quantum number (electron shell number)
l: azimuthal quantum number (s = 0, p = 1, d = 2, f = 3, ......)
The addition of these two numbers determines orbital energy.
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Background
After orbitals are filled, now we need to look at valence
electrons (the ones in the outermost shell).
IMPORTANT: Electrons in inner shells do not participate
in bonding, only outer shell valence electrons do.
valence electrons

1s

2s 2px 2py 2pz

do not involve in reactions

So for carbon, we care the 4 valence electrons only;


For N: 5; for O: 6; for F: 7.
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Background
Octet rule:
A chemical rule of thumb that reflects observation
that atoms of main-group elements tend to combine
in such a way that each atom has eight electrons in
its valence shell, giving it the same electronic
configuration as a noble gas.
The rule is especially applicable to carbon, nitrogen,
oxygen, and the halogens, but also to metals such as
sodium or magnesium.

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Background
Octet rule:
Explanation for Li+, Na+, F-, Cl-, Br-, I-, H+. H-.
Less than 8 electrons
Br, I

want more electrons, F, Cl,

More than 8 electrons


Na+

tend to give electrons, Li,

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Background
Octet rule:
Explanation for Li+, Na+, F-, Cl-, Br-, I-, H+. H-.
1s22s22p5

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Background
Octet rule:
Explanation for electron-sharing in covalent
bond to fulfill the rule.
Explanation for different bonds formed by
H, Cl, O, N, and C.
needs to form bonds
(share electrons) to
achieve 8 electrons

O=C=O

Noble gases: Neon (Ne), 1s2 2s2 2p6; already 8 electrons, very stable
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Background
Physical basis of EN:
smaller, more compact atoms

valence
electrons are in
different shells;

valence electrons are further


away from the nucleus

valence electrons are in the same shell;


more and more protons in nucleus.

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Background
Electronegativity (EN)

no sharing

equal sharing

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Background

Bond polarity is important in chemical reactions.

ionic
too separated

equal sharing
too stable

sharing but uneven


sweet point for
chemical reactions!

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Background

Polar covalent bonds have dipole moments due to uneven


distribution of electrons.
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Background
General Chemistry (CHEM1042):
Atomic and electronic structure
Ionic and covalent bonds, dipole moments
Lewis and Kekule structures
Atomic orbitals, hybridization and molecular
geometry (VSEPR theory)
How single, double, triple bonds are
formed
... Reviewed in Bruice Chapter 1
20

Lets start by looking at the word: organic


Organic compounds: from living organisms (with a vital
force, associated with life forms)
Inorganic compounds: from minerals (without a vital
force)

1828, Friedrich Wohler, first time, creating vital compound


from non-vital material.
Could be considered as the start of organic synthesis
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Organic Compounds
Organic compounds are those based on carbon
Why separate out carbon-containing compounds out of
all of the other 100+ elements as a special category?
Carbon is relatively abundant

why carbon is so special?

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Carbon vs. other elements

Carbon forms greater number of bonds than many


other elements
Enables versatility and complexity
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Carbon vs. other elements


EN of C: in the middle

Atoms to the left of carbon give up electrons.


Tendency to be cationic (positively charged, low EN)

Atoms to the right of carbon accept electrons.


Tendency to be anionic (negative charged, high EN)

Carbon vs. other elements


EN of C: in the middle

Carbon shares electrons, so it can form stable bonds


with other atoms!
However, carbon forms a variety of bonds that can be
broken and formed under different conditions with
different atoms to form new bonds, which makes
carbon also versatile.

Carbon vs. other elements


1s2 2s2 2p2

1s2 2s22p6 3s23p2

DOUBLE BOND

TRIPLE BOND

Relatively stable Very unstable

Si: orbitals are further away from the nucleus,


therefore less control of electrons, bonds are
easier to be broken.

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Carbon vs. other elements


Then what about phosphorus, which can form five
bonds
phosphorus
atom

1s22s22p63s23p33d0

Third shell orbital, less EN;


Bonding involves using high energy d orbitals;
Less stable than carbon bonds
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Carbon vs. other elements


Then what about phosphorus, which can for five
bonds

However, phosphorus is indeed important in


biomolecules such as DNA and RNAs, and is
relatively stable in physiological environment;
It is not bad but is not as good as carbon.
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Carbon vs. other elements

1s22s22p6

Carbon forms greater number of bonds than many


other elements;
And the bonds formed by C are stable
And C has medium EN which can form polar bonds
(bonds are stable but can be broken/reformed)

Organic Compound Structure

EN: 2.1

C-C bond is not polar, equal sharing,


stable;

C-H bond has little polarity, nearly


equal sharing, also stable

EN: 2.5

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Organic Compound Structure


Other than carbon and hydrogen,
additional elements are also featured in
organic molecules:
We call them heteroatoms
Structural diversity;
Chemical reactivity

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