Chapter 2: Structure and Properties of

Organic Molecules

Atomic Orbitals (2.1-2.5)

– Wave functions that represent the probability of finding electrons in a specific region of space

s, p, d, f orbitals

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– In organic chemistry, need to concentrate only on s and p orbitals

p orbitals have a nodal plane

– Area of space where the probability of finding electrons is almost zero

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ÚMolecular orbitals (2.2)are produced when atomic orbitals (either native or hybridized) of different atoms interact

q Produces bonding and anti-bonding orbitals

* antibonding molecular orbital

Molecular Orbitals for H2

35bonding molecular orbital

relativeenergy

s atomicorbital ofhydrogen

s atomicorbital ofhydrogen

Ú In the case of p orbitals, the overlap can take place in two different forms

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Single Bonds (2.3)All single bonds are sigma bonds and all double or triple bonds contain only one sigma bond

ÚSigma bonds can be formed from

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ÚSigma bonds can be formed from atomic orbitals, hybridized or native or a combination

Ú2 other types of bonds in organic molecules:

ÚPi (ππππ) bond

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ÚHydrogen-bond (H-bond)

Ú ππππ-bond: cannot exists if a σσσσ-bond is not already present

ÚResult from the overlap of p orbitals of two atoms. The ππππ-bond is always perpendicular to the sigma bond connecting the nuclei.

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ÚOccur in sp2 and sp hybridized atoms (double/triple bonds)

ÚDouble bond 4 electrons in the bonding region between the nuclei

* first pair forms the sigma bond* second pair forms the pi bond

Normal combination for a double

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Normal combination for a double bond such as the one found in ethylene

Example: Ethene or ethylene

C C

H

H

H

H

ÚTriple Bond 6 electrons in the bonding region between the nuclei

* first pair forms the sigma bond* second/third pairs form the pi bondsNormal combination for a triple bond such as

the one found in acetylene

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the one found in acetylene

Hybridization and Molecular shapes (2.4)

ÚMolecular shapes are related to hybridization of central atom

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sp3: only single bonds; 109.5o angle (methane)

sp2: double bond; 120o angle (ethylene)sp: triple bond; 180o angle (acetylene)

ÚAtomic orbitals can combine to generate new orbitals:* Hybridization: combination of atomic orbitals of

the same atom producing new orbitals of lower energy

* sp, sp2 and sp3 These orbitals explain the geometry of molecules

Shape of sp Hybrid Orbitals

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in phase

out-of-phase one s orbital combines with 3 p orbitalsto form 4 new sp3 hybrid orbitals

sp sp3

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ÚOnly 3 general shapes are normally found in organic molecules:

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Rotation of Single Bond vs Rigidity of Double Bond (2.7)

ÚConsider ethane: CH3-CH3

Each carbon is sp3

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Many structures of ethane are possible. They differ only by the position of one methyl group in relation to the other one:

ÚCONFORMATIONS:Structures that differ only by rotation along a single bondEx: ethane Both forms exist, and all other

structures in between. In facta real ethane molecule rotatesthrough all the conformations,

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through all the conformations, but the staggered conformationis favoured.

ÚConsider ethylene: CH2=CH2

Ethylene is quite rigid and rotation along the C=C is not allowed.

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Ú In ethylene, rotation does not affect the sigma bond, but the pi overlap is broken

ÚRULE: Rotation is allowed along single bonds, but double/triple bonds are rigid and cannot be twisted

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ÚBecause of this rigidity, compounds with different substituent arrangements on a double bond are different:

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Úthese 2 compounds are different and have different chemical/physical properties. They are called:

Isomers

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Compounds having the same molecular formula, but different structures

Structural Isomers (2.8)

Also known as “constitutional isomers, they differ only by their bonding sequence

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Example 2: C5H12 pentane has3 structural isomers

CH3CH2CH2CH2CH3 CH3CHCH2CH3 CH3CCH3

CH3

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3 2 2 2 3

pentane

3 2 3

CH3isopentane

CH3CCH3CH3

neopentane

ÚProblem:How many structural isomers with a molecular formula C6H14 can you draw?

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ÚStereoisomerism (2.8)compounds that differ by the 3D arrangements of atoms (or groups) in space. They are called:

Stereoisomers

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ÚProblem: what is the relationship between A/B, A/C and B/C?

H3C

H

CH3

H

H3C

H

H

CH3

H

H

CH3

CH3

A B C

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Problem: Draw all the possible isomers of formula C5H10 and identify the structural and stereoisomers.

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Polarity of molecules (2.9)

Bond polarity can range from:

Non-polar covalent (C-C)

Polar covalent (C-O)

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Polar covalent (C-O)

Ionic (NH4+ -Cl)

The polarity of bonds is related to electronegativity of atoms

ÚElectronegativity of some important elements (for more examples see Figure 1-7)

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Example:

Bond polarity is the most important topic

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Bond polarity is the most important topic to remember in order to understand organic chemistry

The dipole momentthe dipole moment of a bond is the measure of its polarity Ǻ (in Debye: D)

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ÚFor example:

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The molecular dipole moment is the dipole moment of the molecule taken as a whole. It is a good indicator of the

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overall polarity of molecules.

Its value is the vector sum of individual bond dipole moments

Examples:

H

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O

Hformaldehyde

2.3D

O C O

carbon dioxide

0 D

ÚBecause of bond dipole, partial positive and negative charges are induced within a neutral molecule. These induced charges will be important in reactivity as well as in interactions that exist between molecules.

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H Cl H OH

H NHH

Intermolecular Forces (2-10)

3 major kinds of attractive forces cause molecules to associate into solids or liquids:

Údipole-dipole forces (polar molecules)

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ÚLondon forces (affect all molecules)

ÚHydrogen bonds (for molecules with NH or OH groups)

ÚDipole-dipole forces:

attractive intermolecular forces resulting from the attraction of the positive and negative ends of polar molecules

The greater the forces, the higher will be the boiling point of a given compound

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the boiling point of a given compound

O

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cyclopentaneno dipole momentbp: 49oC

tetrahydrofurandipole moment existsbp: 65oC

ÚLondon dispersion forces:In non-polar molecules (alkanes), this is the principal attractive force

They arise from temporary dipolemoments created by the proximity of other molecules

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molecules

ÚResult: molecules with larger surface area will have a higher boiling/melting point

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Hydrogen bondingNot a true bond, but a very strong form of dipole-dipole attraction. An H atom can participate in H-bonding if it is bonded to O or N (-OH, -NH)

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ÚHydrogen bonds form between the hydrogen and the lone pair of the heteroatom from another molecule

Ú result: the stronger the H-bond, the higher the boiling/melting point– alcohols (OH) have higher boiling points

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– alcohols (OH) have higher boiling points than amines (NH) of similar molecular weights, because the OH bond is more strongly polarized than NH

OH NH2

Ethanolbp= 78oC

Propyl aminebp= 49oC

Nomenclature(will be covered as we introduce new functional groups

ÚTypes of Functional Groups

The following slides are to help you

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The following slides are to help you recognize organic compounds

See Inside Front Cover of Book

Ú3 general classes of organic compounds:

A) Hydrocarbons (contains only C, H)B) Compounds containing “O”C) Compounds containing “N”

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C) Compounds containing “N”

ÚHydrocarbons: compounds composed only of carbon and hydrogen. They include:– alkanes (saturated hydrocarbons)– alkenes (double bond)– alkynes (triple bond)

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– alkynes (triple bond)– Aromatics (double and single bonds

in conjugation)

ÚAlkanes:General formula CnH2n + 2

Names: ends with the suffix “anes”

First part of the names refer to the

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First part of the names refer to the number of carbon atoms.All other compounds are named based on the corresponding alkanes

#C Name Formula1 methane CH4

2 ethane C2H6

3 propane C3H8

4 butane C4H10

5 pentane C5H12

6 hexane C6H14

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6 hexane C6H14

7 heptane C7H16

8 octane C8H18

9 nonane C9H20

10 decane C10H22

Ú If the alkane molecule forms a ring, it is a “cycloalkane” and is formula is: CnH2n

(same as an alkene)

pentane heptane

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Ú If a molecule contains a non alkane part, the non alkane portion is referred to as:

Functional group

ÚThe alkane portion is then referred to as the Alkyl group

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pentanol

OH

alkyl

functionalgroup

ÚAlkyl group: the alkane portion of a molecule minus one H atom which was removed to allow bonding to the functional group

ÚNames of Alkyl groups: derived from the alkane

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alkane[alkane name - ane] + yl = alkyl

ÚWhen the structure of the alkyl group is of no concern, it is often replaced by “R’ as a generalization

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ÚAlkenes: hydrocarbons with a C=CGeneral formula CnH2n (same as cycloalkanes)The C=C is the most reactive part of an alkene: it is the functional group

Names: [alkane – ane] + ene =alkene

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ethane ethene cyclohexanecyclohexene

Ú Alkene may have stereochemistry and can be labeled as cis or trans.

Ú In small rings (4-8 carbon atoms) containing a

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Ú In small rings (4-8 carbon atoms) containing a double bond, the term “cis” is omitted since the double bond is always in that geometry.

Ú In alkenes where there is more than one possibility for the position of the double bond, the location of the C=C must be specified

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ÚAlkynesHydrocarbons with a C-C triple bondThe triple bond is the functional group

Names: [alkane – ane] + yne = alkyne

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ÚAromatic Hydrocarbons:Aromatic hydrocarbons are derived from “benzene”Benzene is a 6-carbon cyclic structure containing 3 double bonds. Each double bond is separated from the next one by a single bond…a conjugated system where

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single bond…a conjugated system where the electron are delocalized

ÚNames: alkyl group first + benzene

ÚThe symbol Ar represents aryl groups the

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ÚThe symbol Ar represents aryl groups the same way R represented alkyl groups

Compounds Containing “O”– Alcohols– Ethers– Aldehydes and Ketones– Carboxylic Acids– Carboxylic Acid Derivatives

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– Carboxylic Acid Derivatives

ÚAlcohols: compounds containing the “OH” group, the hydroxyl group

ÚNames: [alkane – e] + ol = alkanolPosition of the “OH” group must be specified

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Ú Ethers: made of 2 alkyl groups bonded to the same “O”

Ú Names: [alkyl + alkyl] + ether or [dialkyl] + ether

If alkyl groups are different, use

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If alkyl groups are different, use alphabetical order.

Ú Aldehydes and Ketones

For both of these compounds, the functional group is the carbonyl group: C=O

Ú Ketones: 2 alkyl groups attached to C=O

Ú Aldehydes: 1 alkyl group and one H attached to C=O

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C=O

Ketones: [alkane – e] + one = alkanone C=O position must be specified

Aldehydes: [alkane – e] + al = alkanal OR[alkane – e] + aldehyde = alkanaldehydenot necessary to specify the position of

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not necessary to specify the position of C=O (always #1 unless with an acid derivative)

O

propanone(acetone)

O

2-pentanoneH

O

ethanal(acetaldehyde))

H

O

butanal

Ú Carboxylic acids: molecules containing the “carboxyl group”

OH

O

COOH CO2H

carboxyl group

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Ú Names: [alkane – e] + oic acid = alkanoic acid

Ú Carboxylic acid derivativesAll acid derivatives contain the carbonyl group bonded to an heteroatom (Cl, O, N).

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ÚCompounds Containing “N”

– Amines– Amides– Nitriles

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ÚAmines: alkylated derivatives of ammonia (NH3)

ÚAmines are basic. They are classified based on the number of alkyl groups attached to “N”.

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NH2R NHR NR N+RR R

R

R

RR

primaryamine

secondaryamine

tertiaryamine

quaternaryammoniumsalt

ÚNames: [alkyl + alkyl] + amine OR(di) or (tri) + amine

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Study Problems:Ú 2-35

What is the relationship between the following pairs of compounds (same, structural or stereoisomers).

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Ú 2-41Which compound in each of the following pair has the higher boiling point? Why?

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Ú 2-42Circle and name the functional groups in the following compounds.

O

OH CHO

Cl

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Ú 2-37Predict whether the following compounds have a dipole moment or not. Use an arrow to show the direction of the dipole when present.

O

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