ORGANIC CHEMISTRY

Textbook:
Hart et al., Organic Chemistry: A short Course, 12th edition, 2007.

Chapter 1 Bonding and isomerism

1.1 electrons are arranged in atoms

Atoms contain a small, dense nucles surrounded by electrons. The nucleus is positively charged and
contains most of the mass of the atom. The nucleus consists of protons which are positively charged,
and neutrons, which are neutral.

The atomic number of an element is equal to the number of protons (and to the number of
electrons around the nucleus in a neutral atom.

Atomic weight is approximately equal to the sum of the number of protons and the number of
neutrons in the nucleus. Electrons are very light.

Electrons are concentrated in certains region of space around nucleus called orbitals. Each orbital
can contain a maximum of two electrons. The orbitals, which differ in shape, are designated by the
letters, s, p, d, and f.

Outer electrons, or valence electrons, are mainly involved in chemical bonding.

1.2 ionic and covalent bonding

Ionic bond (consider the “Electrogenativity”)

The atom that gives up electrons becomes positively charged, a cation.

The atom that receives electrons becomes negatively charged, an anion.

Sodium tend to give up (donate) electrons are said to be electropositive. Chlorine tends to accept
electron are said to be electronegative. The reason of the electron moving is because of high

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electronegativity of chlorine.

Question:
Consider magnesium (Mg) and Fluorine atom (F) could form MgF2

Covalent bonding (similar electronegativity)

Elements that are neither strongly electronegative nor strongly electropositive, or that have similar
electronegativities, tend to form covalent bonds by sharing electron pairs rather than completely
transferring electrons.

Two (or more) atoms joined by covalent bonds constitute a molecule.

The energy to break it apart into atoms, we called bond energy.

The distance between two nuclei is bond length.

1.3 Carbon and the covalent bond

With four valence electrons, carbon usually forms covalent bonds with other atoms by sharing
electrons. For examples, carbon combines with four hydrogen atoms by sharing four electron pairs.
It is known as methane.

1.4 carbon-carbon single bond

Carbon could share electrons with not only different elements but also carbon.
In ethane, each carbon is connected to the other carbon and to three hydrogen atoms or three chlorine
atoms.

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The C-C bond in ethane, like the H-H bond is a hydrogen molecule, is a purely covalent, with the
electrons being shared equally between the two identical carbon atoms.

Less heat is required to break the C-C bond in ethane than the H-H bond in a hydrogen molecule.
The C-C-bond in ethane is 1.54 Å. The H-H bond in H2 molecule is 0.74 Å. The C-H is about 1.09 Å,
close to the average of H-H bond and C-C bond.

1.5 Polar Covalent Bonds

Two identical atoms share electrons to form covalents. However, two different atoms share
electrons unequally to form polar covalent bond, such as H-Cl, C-Cl. H-O bonds.

Hydrogen Chloride is an example of polar covalent bond.

The shared electron pair is attracted more toward chloride, which therefore is slightly negative with
repect to the hydrogen. The bond polarization is indicated by an arrow whose head is hegative and
whose tail is marked with a plus sign. Alternatively, a partial charge, written as + or  (read delta
plus or delta minus)

Others polar covalent bonds are common is organic compounds.

1.6 Multiple covalent bonds

1.7 Valence

The valence of an element is simply the number of bonds that an atom of the element can form.
The number is normally equal to the number of electron needed to fill the valence shell.

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1.8 Isomerism and Writing Structural Formulas

For the molecular formula C2H6O, there are two very different chemical substances are known.
One is a liquid with the boilding point at 78 oC, the other is a gas at ordinary temperature (-23.6 oC)

Molecules that have the same kinds and numbers of atoms but different arrangements are called
isomers. Structural (or constitutional) isomers are the compounds that have the same molecular
formula but different structural formulas.

Consider a formula of C5H12

C5H12
continuous chain
H H H H H
C C C C C H C C C C C H pentane
H H H H H

a branched chain
H H H H
2-methylbutane
C C C C H C C C C H
H H H
C
H C H
H

H
H C H
C H H 2,2-dimethylpropane
C C C H C C C H
C H H
H C H
H

1.10 Abbreviated structural Formulas

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Ultimate abbreviation of structures is the use of lines to represent the carbon framework.

“C-C bond can be abbreviated to a line. C-H bond is omitted.”

The atoms other than H and C should be presented, such as S, O, N, F, Br…etc.

n-pentane isopentane neopentane

3 lines at this posint

this carbon has 1 hydrogen attached to it

2 lines at this point

2 hydrogens attached to it.

1 line at his point

3 hydrogens attached to it

Consider these formulas

1.11 Formal Charge

In some molecules may be charged, either positively or negatively. Because such charges usually

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affect chemical reactions. Therefore, it is very important to know how to tell the charge is located.

Consider the formula for hydronium ion, H3O+, the product of the reaction of a water molecule with
a proton.

Six of these eight electrons are used to from three O-H bonds, leaving one unshared electron pair on
the oxygen.

Entire hydronium ion carries a positive charge. Which atom bears the charge?

To determine formal charge, we consider each atom to “own” all of its unshared electrons plus only
half of its shared electrons

For H atom
Formal charge = 1 – ( 0 + 1 ) = 0

For O atom
Formal charge = 6 – (2 + 3) = 1  +1

1.12 Resonance

Sometimes, an electron pair is involved with more than two atoms. Molecules and ions in which this
occurs can not be adequately represented by a single electron-dot structure. Please consider the
structure of the carbonate ion, CO32-

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Single bonded oxygen has a formal charge of -1, double bonded oxygen is neutral.
When you wrote the electron-dot structure, there are in fact three exactly equivalent structures.

Physical measurement tell us that all three C-O bond length are identical: 1.31 Angstrom (Å)
This distance is between the normal C=O (1.20 Å) and C-O (1.41 Å). We usually say the real
carbonate ion has s structure that is resonance hydride of the three contributing resonance
structures.

Sometimes we represent a resonance hydride with one formula by writing a solid line for each full
bond and a dotted line for each partial bond. (the dots represent one third of a single bond)

1.13 Arrow Formalisn

Arrow system is very important in Chemistry and has specific meaning.

Curved arrows a pair of electron moving

Fishhook arrows single electron moving

Straight arrows point from reactants to products in chemical reaction equactions

Straight arrow with half-heads used in pairs to indicate that the reaction is reversible.

double-headed straight arrow between two structures indicates that they are resonance
structure

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1.14 Bonding: the sigma bond

Atomic orbitals. The s orbitals are spherical. The three orbitals are dumbbell shaped and mutually
perpendicular, oriented along the three cooridinate axes, x, y, and z.

When atomic orbitals overlap to form a molecular orbital, electron occupy this molecular orbital. A
bond is formed.

Two s orbitals form a sigma bond.

Sigma bonds may also be formed by the overlap of an s and a p orbital or of two p orbitals.

1.15 Carbon sp3 hybrid orbitals

In a carbon atom, the six electrons are arranged as shown below.

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The farther the electron is from the nucleus, the greater its potential energy, because it takes energy
to keep the electron (negatively charged) and the nucleus (positively charged) apart.

Like CH4 and CCl4, Carbon usually forms four single bonds, and often these bonds are all equivalent.
It would like to mix or combine the four atomic orbitals of valence shell (one s and three p orbitals)
to form four identical hydride orbitals, each containing ine valence electron. This model we call sp3
hydrid orbital, because each one has one part of s character and three part of p character.

Now, the carbon has four identical sp3 orbitals, the geometry is called tetrahedron. The angle
between any two of the four bonds is approximately 109.5o. The angle made by lines drawn from the
center the corners of a regular tetrahedron.

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1.6 Tetrahedral carbon; the bonding in methane

With a molecular model

In methane, there are four sp3-s C-H sigma bonds, each directed from the carbon atom to one of the
four corners of a regular tetrahedron.
1.17 classification according to molecular framework

Acyclic
Cyclic
Heterocyclic

1.18 Classification according to functional group

A list of main functional group

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 structure class of compound example

C NH2 primary amine CH2CH2NH2

functional group
containing nitrogen

C N nitrile CH3CN

O O
functional group primary amide
C NH2 H C NH2
containing oxygen
and nitrogen

functional group alkyl and aryl halide CH3I

X
containing halogen

thiol (mercaptan) CH3SH

C SH

functional group
containing sulfur
C S C thioether (sulfide) H3CH2C S CH2CH3

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Chapter 2 Alkanes and cycloalkanes; conformational and geometric isomerism

The main components of petroleum and natural gas, resource that now supply most of our fuel and
energy, are hydrocarbon.

2.1 The structure of alkanes

The simplest alkane is methane. It is a structure of tetrahedral.

Name and formulas of unbranched alkanes.

All alkanes fit the general molecular formula CnH2n+2, where n is the number of carbon atoms.
Unbranched alkane are claaed normal alkanes. Each member of this series differs from the next one
by a -CH2 group (called methylele group.

2.2 Nomenclature of organic compounds

Internationally recognized systems of nomenclature were devised by a commission of the

International Union of Pure and Applied Chemistry; they are known as the IUPAC
(pronounced ”eye-you-pack”.

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2.3 IUPAC rules for naming alkanes

1. The -ane ending is used for all saturated hydrocarbon. Other ending will be used for other
functional groups.
2. Alkanes without branches are named according to the number of carbon atoms.
3. For alkanes with branches, the root name is that of the longest continuous chain of carbon
atoms.

The longest continuous chain has five carbon atoms. The compound is therefore named as a
substituted pentane, even through there are seven carbon atoms.

4. Groups attached to the main chain are called substituents. Saturated substituents that contain
only carbon and hydrogen are called alkyl groups. An alkyl group is named by taking the name
of the alkane with the same number of carbon atoms and changing the -ane to -yl.

More in Section 2.4

5. The main chain is numbered in such a way that the first substitutents encountered along the
chain receives the lowest possible number. Then each substituent is then located by its name
and by the number of the carbon atom to which it is attached. When two or more identical groups
are attached to the main chain, prefixes such as di-,tri-, tetra- are used.

6. IF two or more different types of substituents are present, they are listed alphabetically, Except
that prefixes such as di- and tri- are not considered when alphabetizing.
7. IUPAC names for hydrocarbon are written as one word. Numbers are separated from each other
by commas (,) and are separated from letters by hyphens (-). There is no space between the last
named substituent and the name of parent alkane.

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To easily let you understand these rule, we take the following steps to find an IUPAC name

A. Loctae the longest continuous carbon chain. This gives the name of parent alkane.

pentane not butane

B. Number the longest chain beginning at the end of nearest the first branch point.

C. If there are two equally long continuous chains, select the one with the most branched.

D. If there is a branch equidistant from each end of the longest chain, begin numbering nearest to a
third branch.

E. If there is no third brench, begin numbering nearest the substituent whose name has aliphabetic
priority.

2.4 Alkyl and halogen substituents

Alkyl substituents are named by changing the -ane ending of alkanes to -yl. Thus the two-carbon
alkyl group is called the ethyl group, from ethane.

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Ethane ethyl
Propane propyl
isopropyl

Alkyl groups with up to four carbons are very common. The letter R is used as a general symbol for
an alkyl group. Therefore, R-H represents alkanes. R-Cl stands for an alkyl chloride.

Halogen substituents are named by changing the -ine ending of the elements to -o.

F Fluoro-
Cl Chloro-
Br Bromo-
I Iodo-

2.5 Use of the IUPAC rules

Examples

2.7 Physical properties

Alkanes are insoluble in water. That is because water molecules are polar, whereas alkanes are
nopolar. (all C-C and C-H bonds are nearly purely covalent.)

Alkanes have lower boiling points for a given molecular weight than most other organic compounds.
The electrons in a nonpolar molecule can become unevenly distributed within the molecule, causing
the molecule to have partially positive and partially negative end. The temporarily polarized
molecules causes its neighbor molecules polarized as well. Such interaction are called Van der
Waals attraction.

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The boiling points fo alkanes rise as the chain length increases and fall as the chains because
brenched and more nearly spherical in shape.

Despite the same molecular weight, the rod-shaped pentane molecules have more surface area
available for contact than the spherical 2,2-dimethylpropane. Therefore, van der Waals in the
rod-shaped molecules is stronger than the spherical molecules. The boiling point of rod-shaped
molecules is higher.

2.8 Conformation of alkanes.

A simple molecule has an infinite number of shapes as a consequence of rotating one single bond.
These arrangements are called conformations or conformers. Conformers are stereoisomers,
isomers in which the atoms are connected in the same order but are arranged differently in space.
Two possible conformers for ethane are staggered and eclipsed.
Ethane as example:

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Projections
Dash-wedge projection
Sawhorse projection
Newman projection

Conformers are just different forms of a single molecule that can be intervonverted by rotational
motions about single bonds.

2.9 Cycloalkane nomenclature and conformation

Cycloalkanes are saturated hydrocarbons.

cyclopropane cyclobutane cyclopetane

cyclohexane

CH3 CH3
CH3 CH2CH3

(1-ethyl-2-methylcyclopentane
1,2-dimethylcyclopentane
(not 1,5-di......) (not 2-ethyl-1-methyl....)

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The C-C-C bond angle of cyclopropane is only 60o, therefore it has a great ring strain. (Remember
sp3-carbon is 109.5o)

Six-membered rings are so common in nature. It it has two common conformations, boat and chair
conformation. (with molecular model)

In the chair conformatiom, the hydrogens in cyclohexane fall into two sets, called axial and
equatorial. Three axial hydrogens lie above and three li below the average plane of the carbon
atoms. The six equatorial hydrogens lie approximately in that plane.

Conformation of methylcyclohexane

Draw a chair conformation of -D-glucopyranose)

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2.10 Cis-Trans isomerization in cycloalkanes

Stereoisomers deals with molecules that have the same order of attachment of atoms, but different
arrangement of the atoms in space. Cis-trans isomers (sometimes called germetric isomers. Unlike
conformers, stereoisomers are unique compounds. They are not interconverted by rotation around
C-C bond.

2.11 Summary of isomerism

2.12 Reactions of alkanes

1) Oxidation and Combustion: alkanes as fuels

CH4+2O2  CO2+ 2H2O + heat (212.8kcal/mol)

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2.13 The free-radical chain reaction of halogenations

Halogenation of alkanes. Halogenation occurs via a free-radical chain of reactions.

Initiation step

Propagation step

Termination steps

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