Organic Chemistry Fundamentals

Key Takeaways
IUPAC nomenclature
Bonding: σ, π, single, double, and triple bonds
Hybridization
Molecular shapes

Basic Nomenclature

Carbon Chain Prefixes and Alkane names

Number of carbons Preflix Alkane Name
atoms in a row
1 meth- CH4 methane

2 eth- CH3CH3 ethane

3 prop- CH3CH2CH3 propane

4 but- CH3CH2CH2CH3 butane

5 pent- CH3(CH2)3CH3 pentane

6 hex- CH3(CH2)4CH3 hexane

7 hept- CH3(CH2)5CH3 heptane

8 oct- CH3(CH2)6CH3 octane

9 non- CH3(CH2)7CH3 nonane

10 dec- CH3(CH2)8CH3 decane

Nomenclature for Substituents

Substituent Name Substituent Name
-CH3 methyl -CH2CH2CH2CH3 butyl (or n-butyl)
-CH2CH3 ethyl
sec-butyl
-CH2CH2CH3 propyl

isopropyl tert-butyl (or t-butyl)

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The International Union of Pure and Applied Chemistry (IUPAC) has designated five
steps for naming chemical compounds:
1. Find the longest carbon chain in the compound that contains the highest-priority
functional group. This is called the parent chain.

2. Number the chain in such a way that the highest-priority functional group receives the
lowest possible number.

Correct Incorrect

3. Name the substituents with a prefix.

Multiple substituents of a single type receive another prefix denoting how many are
present (di–2, tri–3, tetra–4, and so on).

Number of carbons Prefix

atoms in a row
1 meth-
2 eth-
3 prop-
4 but-
5 pent-
6 hex-
7 hept-
8 oct-

4. Assign a number to each of the substituents depending on the carbon to which it is

bonded.
5. Complete the name by alphabetizing the substituents and separating numbers from
each other by commas and from words by hyphens.
The only prefix which is used when putting the substituents in alphabetical order is
iso, as in isopropyl or isobutyl.

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Common Functional Groups

Functional Group Prefix Suffix

Carboxylic acid carboxy- -oic acid
Anhydride alkanoyloxycarbonyl- anhydride
Ester alkoxycarbonyl- -oate
Amide carbamoyl- or amido- -amide
Aldehyde oxo- -al
Ketone oxo- or keto- -one
Alcohol hydroxy- -ol
Alkene* alkenyl- -ene
Alkyne* alkynyl- -yne
Alkane alkyl- -ane

Alkanes

Alkanes have the general formula CnH(2n + 2) and are named according to the number of
carbons present followed by the suffix -ane.

Butane C4H10

Q1. The correct name for the compound given below is:

A. 2,3 dimethylpentane
B. 3,4 dimethylpentane
C. 3-methyl, 4-ethyl butane
D. 1-ethyl, 2-methyl butane

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Alkenes

Alkenes contain at least a double bond and have the general formula (CnH2n).

Alkenes are named by substituting -ene for the suffix and numbering the double bond by
its lower-numbered carbon.

Ethene C2H4

Q2. Which of the following formulas represents an alkene?

A. CH3CH2CH3
B. CH3CH3
C. CH3CH2CHCH2
D. CHCH

Alkynes

Alkynes contain a triple bonds and have the general formula (CnH2n-2).

Alkynes are named by substituting -yne for the suffix and numbering the triple bond by its
lower-numbered carbon.

Acetylene C2H2

Q3. What is the IUPAC name of the following compound?

A. 2,6-diethyl-3-nonyne
B. 2,5-diethyl-3-nonyne
C. 3,7-dimethyl-5-nonyne
D. 3,7-dimethyl-4-nonyne

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Benzene

Benzene have the general formula (C6H6) and is composed of six carbon atoms joined in
a planar ring with one hydrogen atom attached to each.

Alcohol

Alcohols have the general formula (CnH2n+1OH) and contain a hydroxyl (–OH) group,
which substitutes for one or more of the hydrogens in the hydrocarbon chain.

Q4. What is the IUPAC name for (CH3)3CCH(OH)CH2CH(CH3)2?

A. 2,5,5-trimethyl-3-hexanol
B. 1,1,4,4-pentamethylbutanol
C. 1,1-dimethylisopentanol
D. 2,5-dimethyl-4-hexanol

Aldehyde

Aldehydes and ketones contain a carbonyl group – a carbon double-bonded to an

oxygen (C=O).

Ketone

Ketones have the carbonyl group on a nonterminal carbon and are named with the suffix
-one and share the prefix oxo- if a higher-priority group is present.

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Carboxylic acids

Carboxylic acids have the general formula (CnH2n+1COOH) are the highest-priority
functional group.

Esters

Esters are carboxylic acid derivatives where –OH is replaced with –OR, an alkoxy
group.
Esters use the suffix -oate or the prefix alkoxycarbonyl-.

Amides

Amides replace the hydroxyl group of a carboxylic acid with an amino group that may or
may not be substituted.

Anhydries

Anhydrides are formed from two carboxylic acids by dehydration.

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Bonding

Sigma bonds (σ) forms when the bonding pair of electrons are localized to the space
directly between the two bonding atoms.
Pi bonds (π) are created by overlapping p orbitals. Double and triple bonds are made by
adding π bonds to a σ bond.
A single bond must be a sigma (σ) bond, which is the first type of covalent bond form.
Double bonds contain one σ bond and one pi (π) bond.
Triple bonds contain one σ bond and two π bonds.

Q5. Relative to σ bonds, π bonds exhibit which of the following characteristics?

I. Higher energy orbitals

II. Increased stability
III. Greater strength

A. I only
B. I and II only
C. II and III only
D. I, II and III

Hybridization

Atomic orbitals of a lone carbon atom:

Atomic orbitals of a carbon atom with 4 σ bonds:

Orbitals overlap to form bonds:

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 sp3 hybridization involves one 2s orbital and three 2p orbitals mixing to form four sp3
hybridized orbitals.
➢ sp3-hybridized orbitals have 25% s character and 75% p character.

sp2 hybridization involves one 2s orbital and two 2p orbitals mixing to form three sp3
hybridized orbitals. There is one unhybridized 2p orbital remaining.
➢ sp2-hybridized orbitals have 33% s character and 67% p character.

sp hybridization involves one 2s orbital and one 2p orbitals mixing to form two sp3
hybridized orbitals. There are two unhybridized 2p orbitals remaining.
➢ sp-hybridized orbitals have 50% s character and 50% p character.

Q6. In the Wittig reaction, a phosphorus ylide reacts with a ketone to yield an alkene.
What is the hybridization of carbon 2 in the ketone, the betaine, and the alkene,
respectively?

A. sp3, sp2, sp3

B. sp2, sp2, sp3
C. sp2, sp3, sp2
D. sp3, sp4, sp3

Q7. How much s character is in the hybridized orbital on either nitrogen atom in
diatomic nitrogen (N2)?

A. 33%
B. 50%
C. 66.6%
D. 100%

Hybridization and Molecular Shape

Hybridization Bond angles Shape Examples

sp 180° Linear Ethyne C2H2
sp2 120° Trigonal planar Formaldehyde CH2O
sp3 109.5° Tetrahedral, trigonal Methane CH4, ammonia
pyramidal, or bent NH3, water H2O
sp3d 90°, 120° Trigonal-bipyramidal, see- Phosphorus
saw, t-shaped or linear pentachloride PCl5
sp3d2 90°, 90° Octahedral, square Sulfur hexafluoride SF6
pyramidal, or square planar

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 Passage

Osteoporosis is a common bone disorder in the elderly that leads to the progressive loss of
bone mass and the subsequent weakening of bones. It increases the risk for a variety of
fractures which can lead to disability, chronic pain, or kyphosis-a hunched posture
associated with collapse of the thoracic vertebrae.

Bisphosphonates are a class of drugs commonly prescribed to slow the rate of bone loss.
They resemble pyrophosphate which is present throughout the body and has a strong affinity
for calcium. Unlike pyrophosphate, the phosphate moieties in bisphosphonate drugs are
bridged with bonds to carbon. These carbon phosphate bonds are stronger and not liable to
undergo chemical decomposition in the body.

General structure of bisphosphonates Pyrophosphate

Figure 1 Structures of bisphosphonate drugs and pyrophosphate

The mechanism by which bisphosphonates slow bone loss is not completely understood. It
is believed that the drug is first integrated into the bone structure. When osteoclasts dissolve
the bone during bone resorption, the drug is released and inhibits their ability to further
dissolve bone. The R1 and R2 groups have a substantial effect on the pharmacological
properties of these drugs. Below, in Table 1, is a list of various bisphosphonates and their R1
and R2 groups.

Agent R1 group R2 group

Etidronate — OH — CH3

Clodronate — Cl — Cl

— CH2—CH2—
Pamidronate — OH
NH2

Tiludronate —H

Zoledronate — OH

Table 1 Selected bisphosphonates

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Q8. Hydrolysis of pyrophosphate occurs naturally in the body and produces inorganic
phosphate (shown below).

What is the hybridization of phosphorous in inorganic phosphate and the geometry of

this molecule?

A. sp3, square planar

B. sp3, tetrahedral
C. sp3d, tetrahedral
D. sp3d2, see-saw

Q9. Which bond angle best describes the carbon-sulfur-carbon bond in tiludronate?

A. 90°
B. 109.5°
C. 120°
D. 180°