Organic Chemistry!

•  History!
–  1770 Bergman: organic chemistry is the chemistry of compounds from living organisms!
–  1816 Chevreul: convert one organic substance into another!

NaOH H3O+
Fat (Animal) Glycerin + Soap Fatty Acids
H2O

–  1828 Wöhler: convert inorganic substance into organic substance!

O
! NH4 OCN
Δ H2N NH2
•  Organic Chemistry: study of carbon compounds, their reactivity and function!
–  Many organic compounds are part of living systems including proteins, DNA….. Organic chemistry is important for
understanding and studying biochemistry, medicinal chemistry, and pharmaceutical sciences!

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 Atoms and Atomic Orbitals!
•  Atoms: diameter ~2x10-10 m!
–  Nucleus: diameter ~10-14-10-15 m positively charged containing neutrons (neutral) and protons
(positively charged)!
–  Electrons: negatively charged! ! 1H! 2D! 3T!
–  Atomic number (Z): number of protons in nucleus! Z! 1! 1! 1!
–  Mass number (A): number of protons and neutrons in nucleus! A! 1! 2! 3!
–  Isotopes: atoms with the same atomic number but different mass number!
–  Wave equation: mathematic expression of a specific electron in an atom based on quantum
mechanics!
–  Wave function (ψ, also called orbital): solution to the wave equation!
•  Square of wave function (ψ2) describes the volume of space an electron occupies!
Energy!
•  Atomic Orbitals!
–  Electron shells: different layers of orbitals in an atom!
–  s orbital: spherical symmetry ! !! 2p
•  can make sigma bonds! 2nd shell!
–  p orbital: two lobes (dumbbell shape)! 2s
•  Along x, y, z axes!
•  can make sigma and pi bonds!
1st shell! 1s
•  Node: site of no electron density (nodal plane)!

z z z
y y y
x x x
s!
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 Electron Configuration!
•  Ground state electron configuration: lowest energy arrangement of electrons in atomic orbitals!
•  Aufbau Principle: building order!
–  Fill from low energy orbital to high energy orbital! Carbon!
–  1s 2s 2p 3s 3p 4s 3d!
•  Pauli exclusion principle! valence! 2p
–  Only 2 electrons per orbital! (outer)!
–  2 electrons must be opposite in spin! shell!
•  Hund’s rule! 2s
–  Fill degenerate (same energy) orbitals across!
–  Don’t pair electrons until necessary! core!
(inner)! 1s
shell!
Hydrogen! !H !1 !1s!
!

Carbon ! !C !6 !1s 2s 2p !
!

Nitrogen ! !N !7 !1s 2s 2p!

!

Oxygen ! !O !8 !1s 2s 2p!

!

Fluorine ! !F !9 !1s 2s 2p!

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Problem !Page!
1, 2ac! !6!
 Chemical Bonding Theory!
•  History:!
–  1858 Kekulé and Couper independently: carbon is tetravalent!
CH4 methane!
–  Erlenmeyer: carbon≡carbon triple bond for acetylene! going into! H
–  Brown: carbon=carbon double bond for ethylene! within the plane!
the page!
of the page!
–  1865 Kekulé: rings and cyclic compounds! C
H
–  1874 van’t Hoff and LeBel: tetrahedral geometry!
H H
–  1916 Lewis: covalent bonds are shared electron bonds!
•  Valence shell: the most outer shell with electrons! coming out of the page!
•  Octet rule: filled valence shell electron configuration is most stable (typically 8)!
•  Lone pairs (non-bonding electrons): valence electrons not used for bonding!
–  Frequently omitted in drawing structures!
•  Hydrogen: 1s1, 1 bond!

!
•  Carbon: 2s22p2, 4 bonds !

•  Nitrogen: 2s22p3, 3 bonds, 1 lone pair!

N
H
H H
•  Oxygen: 2s22p4, 2 bonds, 2 lone pairs!
O
H H
•  Halogens: F, Cl, Br, I, ns2np5, 1 bond, 3 lone pairs! Problem !Page!
3 ! !9!
4-7 ! !10!
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 Valence Bond Molecular Orbital
Theory! Theory!
•  Covalent bonds form when two atoms •  MO: mathematical combination of atomic
approach each other closely and the singly orbitals form molecular orbitals that describe
occupied atomic orbitals overlap! covalent bond formation!
–  Region of space in a molecule where electrons
•  σ bond: bonds formed by head-on overlap are most likely to be found!
of two atomic orbitals along the inter-atomic –  LCAO-MO: linear combination atomic orbitals
axis (bond axis) with cylindrical symmetry! molecular orbitals!
–  Number of atomic orbitals = the number of
bond strength!
molecular orbitals!
2H H2 + 104 kcal/mol –  Bonding molecular orbitals: occupy inter-
436 kJ/mol! atomic space!
–  Antibonding molecular orbitals: no density in
inter-atomic space!

H2
Energy! H H
σ* antibonding orbital!

H H

1s! 1s!
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H H σ bonding orbital!
 Bonding in CH4!
•  Carbon needs to form four bonds!
•  Ground state carbon only has 2 unpaired electrons to share (can make 2 bonds)!
•  1931 Pauling: hybridization: mathematical combination of atomic orbitals!
–  Energy is used to redistribute the electrons into the hybrid orbitals!
–  Combine one s and three p to get four sp3 hybrid orbitals!

Energy!

2p hybridization
sp3
tetrahedral geometry! 25% s!
2s 75% p!
H
109.5°!
C
H
H H
1.09 Å!
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 C-H Bond in CH4 and C2H6!
•  σ bond: cylindrical symmetry along the inter-atomic axis (bond axis)!
H H 101 kcal/mol!
C2H6 ethane! H
421 kJ/mol!
C C

H H
1.54 Å! H
90 kcal/mol!
377 kJ/mol!

C H C C
Energy!
σ*! σ*!

C! sp3! 1s!
H! C! sp3! C!
sp3!

σ
σ

C H C C
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Problem !Page!
8,9 ! !14!
 H H
π Bonding in H2C=CH2! C C 111 kcal/mol!
•  Ethylene: all atoms are coplanar! 464 kJ/mol!
–  Carbons linked by double bond sharing 4 electrons!
–  sp2 hybridized carbons: 120° bond angle, trigonal planar! 1.34 Å!
H H
•  π bond: side to side overlap of p orbitals! 174 kcal/mol!
–  nodal planes! 728 kJ/mol!
–  σ bond stronger than π bond!

C C
C C Energy!
π*!
σ*!
C! p! p!
C!
C! C!
sp2! sp2!
π

σ
C C
C C
Problem !Page!
10-12 ! !16!
37,38 ! !27d!
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 Hybridization and Geometry!
•  VSEPR : valence shell electron pair repulsion!
–  Due to electron repulsion, bonding electrons and lone pair electrons are positioned as far apart as
possible.!
•  sp3: tetrahedral, 109.5°! methanol! methylamine! water! methane thiol!
25% s!
75% p!

•  sp2: trigonal planar, 120°!

33% s!
67% p!

•  sp: linear, 180°! acetylene! acetonitrile!

50% s!
50% p! H C C H H3C C N
Problem !Page!
1.20 Å! allene! 13 ! !18!
133 kcal/mol! 231 kcal/mol! 14 ! !20!
558 kJ/mol! 965 kJ/mol! H 26 ! !27b!
C C C H 35,36 ! !27d!

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10

!27g!

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 H2O!
•  Lone pairs need to be considered in determining geometry and hybridization!
–  Lone pairs more diffuse!

Energy!
Oxygen!

2p hybridization
sp3

2s

H! 1s! H! 1s!

O! 2p! sp3!
O!

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 Drawing Organic Structures!
•  Skeletal Structures!
–  Carbons are not usually labeled, and are assumed to be at the intersection of two lines
and at the end of each line!
–  Hydrogens bonded to the carbons are not usually shown!
–  Atoms other than carbon and hydrogen are shown!
•  Best: skeletal with all heteroatom lone pairs to show octet!

Lewis! Kekulé! Condensed!

Skeletal! Best!
Problem !Page!
15-17 ! !24!
18 ! !27a!
21,27 ! !27b!
30 ! !27c!
33 ! !27d!
42 ! !27e!
43 ! !27f!
49 ! !27g!
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