Organic Chemistry I

Dept. of Integrative Biotechnology, Konkuk Univ.

Spring Semester, 2025

Instructor: 여운석

Office: 생명과학관 320호

Text: Organic Chemistry, 7th edition, McMurry, Thomson

 1. Structure and Bonding

Organic Chemistry: Transformation of one structure to another

Reactions (Transformations): Bond breaking & making

Organic Chemistry is about nothing but Chemical Bonding

 What is Organic Chemistry?
• Organic chemistry is study of carbon compounds.
• Why is it so special?
- 90% of more than 30 million chemical compounds contain carbon.
- Examination of carbon in periodic chart answers some of these
questions.
- Carbon is group 4A element, it can share 4 valence electrons and
form 4 covalent bonds.

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 What is Organic Chemistry?
◼ Living things are made of organic chemicals
◼ Proteins, DNA, lipids, …
◼ Foods, medicines
◼ Examine structures below

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Why this chapter?
• Review ideas from general chemistry: atoms, bonds,
molecular geometry
Please do not worry about the backgrounds and details
of the chemical bonding theory.
We just need to catch what we really need to know.

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 1.1 Atomic Structure
◼ Structure of an atom
◼ Positively charged nucleus (very dense, protons and neutrons)
and small (10-15 m)
◼ Negatively charged electrons are in a cloud (10-10 m) around
nucleus

◼ Diameter is about 2  10-10 m (200 picometers (pm)) [the unit

angstrom (Å ) is 10-10 m = 100 pm]

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 Atomic Number and Atomic Mass
◼ The atomic number (Z) is the number of protons in the atom's nucleus

◼ The mass number (A) is the number of protons plus neutrons

◼ All the atoms of a given element have the same atomic number

◼ Isotopes are atoms of the same element that have different

numbers of neutrons and therefore different mass numbers

◼ The atomic mass (atomic weight) of an element is the weighted

average mass in atomic mass units (amu) of an element’s naturally
occurring isotopes

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 1.2 Atomic Structure: Orbitals
◼ Then, where are the electrons?

◼ Quantum mechanics: describes electron energies and locations by

a wave equation
◼ Wave function solution of wave equation
◼ Each wave function is an orbital, 

◼ A plot of 2 describes where electron most likely to be

◼ Electron cloud has no specific boundary so we show most probable

area

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 Shapes of Atomic Orbitals for
Electrons
◼ Four different kinds of orbitals for electrons based on those derived
for a hydrogen atom
◼ Denoted s, p, d, and f
◼ s and p orbitals most important in organic and biological chemistry
◼ s orbitals: spherical, nucleus at center
◼ p orbitals: dumbbell-shaped, nucleus at middle
◼ d orbitals: elongated dumbbell-shaped, nucleus at center

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 Orbitals and Shells part 1
◼ Orbitals are grouped in shells of increasing size and energy
◼ Different shells contain different numbers and kinds of orbitals
◼ Each orbital can be occupied by two electrons

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 Orbitals and Shells part 2
◼ First shell contains one s orbital, denoted 1s, holds only two electrons
◼ Second shell contains one s orbital (2s) and three p orbitals (2p),
eight electrons
◼ Third shell contains an s orbital (3s), three p orbitals (3p), and five d
orbitals (3d), 18 electrons

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 p-Orbitals
◼ In each shell there are three perpendicular p orbitals, px, py, and pz,
of equal energy

◼ Lobes of a p orbital are separated by region of zero electron density,

a node

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 1.3 Atomic Structure: Electron
Configurations
◼ How electrons occupy the orbitals?
◼ Ground-state electron configuration (lowest energy arrangement)
of an atom lists orbitals occupied by its electrons. Rules:
◼ 1. Lowest-energy orbitals fill first [1s → 2s → 2p → 3s → 3p → 4s
→ 3d (Aufbau (“build-up”) principle)]
◼ 2. Electrons act as if they were spinning around an axis. Electron
spin can have only two orientations, up  and down . Only two
electrons can occupy an orbital, and they must be of opposite
spin (Pauli exclusion principle) to have unique wave equations
◼ 3. If two or more empty orbitals of equal energy are available,
electrons occupy each with spins parallel until all orbitals have
one electron (Hund's rule).
◼ Valence Shell Electrons !!! (Octet Rule)
◼ Main-group elements tend to take on the electron configuration of
the nearest noble gas (Octet)
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 1.3 Atomic Structure: Electron
Configurations
◼ Problem 1.1
◼ Give the ground-state electron configuration
(a) Oxygen (b) Silicon (c) Sulfur

(a) 1s22s22p4
(b) 1s22s22p63s23p2
(c) 1s22s22p63s23p4

◼ Problem 1.2
◼ How many electrons does each of the following elements have in
its outermost electron shell?
(a) Magnesium[12] (b) Molybdenum[42] (c) Selenium[34]

(a) 2 (b) 2 (c) 6

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 1.4 Development of Chemical
Bonding Theory
◼ From atoms to molecules (Valence Bond Theory)

◼ Why do atoms bond together??

◼ Atoms form bonds because the compound that results is more
stable than the separate atoms

◼ Bond making: Energy (heat) flows out of the system

◼ Bond breaking: Energy (heat) must be put into the system

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◼ How do atoms bond together??
◼ Chemistry of main-group elements is governed by their tendency
to take on the electron configuration of the nearest noble gas
(Octet rule)

◼ Ionic bonds: Electron transfer between valence shells of alkali

metal (loss of s electron) and halogens (gain of p electron) [Na+Cl-]

◼ Elements closer to the middle of the periodic table?: Too much

energy for ionic (1s22s22p2) → Share instead of losing or gaining
electrons (covalent bond) [CH4]

◼ Organic compounds have covalent bonds from sharing electrons

(G. N. Lewis, 1916)
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◼ Carbon always has four bonds (Kekulé and Couper)

◼ Four bonds of carbon have specific spatial directions (van't Hoff and
Le Bel)
◼ Hydrogen atoms surround carbon as corners of a tetrahedron

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◼ Lewis structures (electron dot) show valence electrons of an atom
as dots
◼ Hydrogen has one dot, representing its 1s electron
◼ Carbon has four dots (2s2 2p2)

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◼ Kekule structures (line-bond structures) have a line drawn between
two atoms indicating a 2 electron covalent bond.

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◼ Stable molecule results at completed shell, octet (eight dots) for
main-group atoms (two for hydrogen)
◼ Atoms with one, two, or three valence electrons form one, two, or
three bonds.
◼ Atoms with four or more valence electrons form as many bonds as
they need electrons to fill the s and p levels of their valence shells to
reach a stable octet.
◼ C: 4 valence electrons (2s2 2p2), forming 4 bonds (CH4).
◼ N: 5 valence electrons (2s2 2p3) but forms only 3 bonds (NH3).
◼ O: 6 valence electrons (2s2 2p4) but forms 2 bonds (H2O)

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 Non-bonding electrons
◼ Valence electrons not used in bonding are called nonbonding
electrons, or lone-pair electrons
◼ Nitrogen atom in ammonia (NH3): Shares 6 valence electrons in 3
covalent bonds and remaining 2 valence electrons are
nonbonding lone pair

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 1.4 Development of Chemical
Bonding Theory
◼ Problem 1.3
◼ Draw a molecule of chloroform, CHCl3, using solid, wedged, and
dashed lines to show its tetrahedral geometry.

◼ Problem 1.4
◼ Convert the following representation of ethane, C2H6, into a
conventional drawing

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 1.4 Development of Chemical
Bonding Theory
◼ Problem 1.5
◼ What are likely formulas?
(a) GeCl? (b) AlH? (c) CH?Cl2 (d) SiF? (e) CH3NH?
Ge: 4th row, Group 4A, Al: 3rd row, Group 3A, Si: 3rd row, Group 4A

(a) GeCl4 (b) AlH3 (c) CH2Cl2 (d) SiF4 (e) CH3NH2

◼ Problem 1.6
◼ Write line-bond structures for the following substances, showing
all nonbonding electrons:
(a) CHCl3, Chloroform (b) H2S, hydrogen sulfide
(c) CH3NH2, Methylamine (d) CH3Li, methyllithium

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 1.5 The Nature of Chemical
Bonds: Valence Bond Theory
◼ Two models to describe covalent bonding.
◼Valence bond theory
◼ Molecular orbital theory
◼ Valence bond theory
◼ Easily visualized
◼ Covalent bond forms when two atoms approach each other
closely so that a singly occupied orbital on one atom overlaps a
singly occupied orbital on the other atom

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 1.5 The Nature of Chemical
Bonds: Valence Bond Theory
Valence Bond Theory:
◼ Electrons are paired in the overlapping orbitals and are attracted to
nuclei of both atoms
◼ H–H bond results from the overlap of two singly occupied
hydrogen 1s orbitals
◼ H-H bond is cylindrically symmetrical, sigma () bond

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 Bond Energy
◼ Reaction 2 H· → H2 releases 436 kJ/mol
◼ Product has 436 kJ/mol less energy than two atoms: H–H has bond
strength of 436 kJ/mol. (1 kJ = 0.2390 kcal; 1 kcal = 4.184 kJ)

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 Bond Length
◼ Distance between nuclei that leads to maximum stability
◼ If too close, they repel because both are positively charged
◼ If too far apart, bonding is weak

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 1.6 sp3 Orbitals and the Structure
of Methane
◼ Carbon has 4 valence electrons (2s2 2p2) to make 4 bonds
◼Two different kinds of C-H bonds?
◼ In CH4, all C–H bonds are identical (tetrahedral)… How??
◼ sp3 hybrid orbitals
◼ s orbital and three p orbitals combine to form four equivalent,
unsymmetrical, tetrahedral orbitals (sppp = sp3), Pauling (1931)
◼ (+)-p orbital adds to s-orbital, (-)-p orbital subtracts from s-orbital
◼ Unsymmetrical lobes: More effective overlap upon bonding

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 The Structure of Methane
◼ sp3 orbitals on C overlap with 1s orbitals on 4 H atoms to form four
identical C-H bonds
◼ Each C–H bond has a strength of 439 kJ/mol and length of 109 pm
◼ Bond angle: each H–C–H is 109.5°, the tetrahedral angle.

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 1.7 sp3 Orbitals and the Structure
of Ethane
◼ Two C’s bond to each other by  overlap of an sp3 orbital from each
◼ Three sp3 orbitals on each C overlap with H 1s orbitals to form six C–
H bonds
◼ C–H bond strength in ethane 421 (cf. C-H: 439 in methane) kJ/mol
◼ C–C bond is 154 (C-H, 109) pm long and strength is 377 kJ/mol
◼ All bond angles of ethane are tetrahedral

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1.8 sp2 Orbitals and the Structure
of Ethylene
◼ sp2 hybrid orbitals:
◼ 2s orbital combines with two 2p orbitals, giving 3 orbitals (spp =
sp2). One 2p orbital remains unchanged.
◼ sp2 orbitals are in a plane with120° angles
◼ Remaining p orbital is perpendicular to the plane

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 Bonds From sp2 Hybrid Orbitals
◼ Two sp2-hybridized orbitals overlap to form a  bond
◼ p orbitals overlap side-to-side to formation a pi () bond
◼ sp2–sp2  bond and 2p–2p  bond result in sharing four electrons and
formation of C-C double bond
◼ Electrons in the  bond are centered between nuclei
◼ Electrons in the  bond occupy regions are on either side of a line
between nuclei

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 Structure of Ethylene
◼ H atoms form  bonds with four sp2 orbitals
◼ H–C–H and H–C–C bond angles of about 120°
◼ C–C double bond in ethylene shorter and stronger than single bond in
ethane
◼ Ethylene C=C bond length 134 pm (C–C 154 pm)

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 1.9 sp Orbitals and the Structure of
Acetylene
◼ C-C a triple bond sharing six electrons
◼ Carbon 2s orbital hybridizes with a single p orbital giving two sp
hybrids
◼ two p orbitals remain unchanged
◼ sp orbitals are linear, 180° apart on x-axis
◼ Two p orbitals are perpendicular on the y-axis and the z-axis

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 Orbitals of Acetylene
◼ Two sp hybrid orbitals from each C form sp–sp  bond
◼ pz orbitals from each C form a pz–pz  bond by sideways overlap and
py orbitals overlap similarly

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 Bonding in Acetylene
◼ Sharing of six electrons forms C C

◼ Two sp orbitals form  bonds with hydrogens

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 1.10 Hybridization of N, O, P, S
◼ Nitrogen
◼ H–N–H bond angle in ammonia (NH3) 107.3°
◼ C-N-H bond angle is 110.3°
◼ N’s orbitals (sppp) hybridize to form four sp3 orbitals
◼ One sp3 orbital is occupied by two nonbonding electrons, and
three sp3 orbitals have one electron each, forming bonds to H and
CH3.

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 1.10 Hybridization of N, O, P, S
◼ Oxygen
◼ C–O–H bond angle in methanol (CH3OH) 108.5°(close to 109.5o)
◼ O’s orbitals (sppp) hybridize to form four sp3 orbitals
◼ Two sp3 orbital is occupied by four nonbonding electrons, and two
sp3 orbitals have one electron each, forming bonds to H and CH3.

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 1.10 Hybridization of N, O, P, S
◼ Phosphorous (Organophosphates)
◼ 3rd-row analog of N: Expanded outer-shell octets (5 covalent
bonds) are possible
◼ P–O–P bond angle in methyl phosphate (CH3OPO32-) 110-112°
(sp3-hybridization for P)

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 1.10 Hybridization of N, O, P, S
◼ Sulfur (Thiols, Sulfides)
◼ 3rd-row analog of O: Expanded outer-shell octets (4 covalent
bonds) are possible
◼ sp3-hybridization for S (96.5 – 99.1o), but significant deviation
from 109.5o

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 1.10 Hybridization of N, O, P, S
◼ Problem 1.14
◼ Nonbonding lone pairs? Geometry?
(a) Oxygen atom in dimethyl ether
(b) Nitrogen atom in trimethylamine
(c) Phosphorous atom in phosphine
(d) Sulfur atom in methionine

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 1.11 Molecular Orbital Theory
◼ A molecular orbital (MO): where electrons are most likely to be
found (specific energy and general shape) in a molecule
◼ LCAO-MO: Linear Combination of Atomic Orbitals
◼ Additive combination (bonding) MO is lower in energy (egg-shape)
◼ Subtractive combination (antibonding) MO is higher energy
(elongated dumbbell-shape)
◼ Only bonding MO is occupied
◼ Particularly useful for describing π bonds in multiple double bonds

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 1.12 Drawing Structures
◼ Drawing every bond in organic molecule can become tedious.
◼ Several shorthand methods have been developed to write structures.
◼ Condensed structures don’t have C-H or C-C single bonds shown.
They are understood.

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◼ Skeletal Structures (Even Simpler), 3 General Rules:
1) Carbon atoms aren’t
usually shown. Instead
a carbon atom is
assumed to be at each
intersection of two
lines (bonds) and at
the end of each line.
2) Hydrogen atoms
bonded to carbon
aren’t shown.
3) Atoms other than
carbon and hydrogen
are shown

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 1.12 Drawing Structures
◼ Problem 1.17
◼ Para-aminobenzoic acid (PABA) of sunscreen. Skeletal structure?

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 Summary
◼ Organic chemistry – chemistry of carbon compounds
◼ Atom: positively charged nucleus surrounded by negatively charged
electrons
◼ Electronic structure of an atom described by wave equation
◼ Electrons occupy orbitals around the nucleus.
◼ Different orbitals have different energy levels and different shapes
◼ s orbitals are spherical, p orbitals are dumbbell-shaped

◼ Covalent bonds - electron pair is shared between atoms

◼ Valence bond theory - electron sharing occurs by overlap of two
atomic orbitals
◼ Molecular orbital (MO) theory, - bonds result from combination of
atomic orbitals to give molecular orbitals, which belong to the entire
molecule

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 Summary (cont’d)
◼ Sigma () bonds - Circular cross-section and are formed by head-on
interaction
◼ Pi () bonds – “dumbbell” shape from sideways interaction of p
orbitals
◼ Carbon uses hybrid orbitals to form bonds in organic molecules.
◼ In single bonds with tetrahedral geometry, carbon has four sp3
hybrid orbitals
◼ In double bonds with planar geometry, carbon uses three
equivalent sp2 hybrid orbitals and one unhybridized p orbital
◼ Carbon uses two equivalent sp hybrid orbitals to form a triple
bond with linear geometry, with two unhybridized p orbitals
◼ Atoms such as nitrogen and oxygen hybridize to form strong, oriented
bonds
◼ The nitrogen atom in ammonia and the oxygen atom in water are
sp3-hybridized
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