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Chemistry 1102Charlie BondMCS Rm 4.16/4.27Charles.Bond@uwa.edu.au

What is Organic Chemistry?Organic Reactions I IIAlkanes Conformational Analysis I IIStereochemistry I II IIIAlkyl Halides I IIAlcohols and Ether I II

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Representing Organic Molecules

Palytoxin from the anenome Palythoa toxica

Isolated 0.15 mg/kgof Anenome

Lethal to humansat 4 µ g

Palytoxin

How do we draw an organic molecule in the best way?

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Representing Organic Molecules

In general, organic compounds consist of two components:

When drawing molecules, think about laying out the hydrocarbon backbone in an extended manner, and then decorate with functional groups

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Representing Organic Molecules

Take linoleic acid:

Molecular formula C18

H32

O2

Structural FormulaCH

3CH

2CH

2CH

2CH

2CH=CHCH

2CH=CHCH

2CH

2CH

2CH

2CH

2CH

2CH

2CO

2H

Is this realistic? This kind of represenation is found in older books as it was easier to print, but can we represent linoleic acid better?

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Representing Organic Molecules

The experimentally-determined 3D structure of linoleic acid looks like this:

So a better representation is something like this.

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Representing Organic Molecules

Finally, do we really need to see all of those C's and H's?

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Representing Organic MoleculesSummary: Guidelines for drawing molecules

1. Draw chains of atoms as zig-zagsArrange the molecule with the longest chain running horizontallyUse angles of ~120°

2. Miss out Hydrogen atoms if attached to carbon unless absolutely necessary*Leave out C-H bonds too

3. Miss out the capital C for Carbon atoms atoms unless necessary*

*sometimes a particular C or H may be important in a functionalgroup or may be part of a reaction mechanism.These are not rules, but guidelines to helpyou communicate chemistry better

It's not always easy, though:O

O

O

O

ON

H

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NOTE: Shorthand

Sometimes drawings of structures are simplified by using shorthand for bulky groups. Don't ignore them if you see them.For example AcOH, is ethanoic acid, not Actinium Hydroxide

Start simple: Draw butanol Draw butanoic acid Draw phenol

Chemical Bonds

Three basic types of bonds: Ionic

Electrostatic attraction between ions

Covalent Sharing of electrons

Metallic Metal atoms bonded to several other

atoms

Figure 7.1

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Electronegativity

Electronegativity: The ability of an atom to attract electrons to itself when part of a compound (or bound). Linus Pauling 1954 Noble

Prize, Chemical Bonding

http://lpi.oregonstate.edu/lpbio/lpbio2.html

Definiton: How tightly an atom holds electrons it shares with another atom

Electronegativity has no scale, Fluorine is the highest at 4.0 and rest of theelements are relative to this number

One way to classify bonds is through the Pauling method of electronegativity

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Electronegativity

Increases up the group, because of the decreasing distances of theouter shell electrons from the nucleus

Increases to the right because of the increasing positive charge of the nucleus

Elements which have low electronegativites are considered electropositve

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ElectronegativityAdditional classification

Examples

KCl (Potassium Chloride) 0.8 vs 3.0; difference is 2.2, thus Ionic

C-N single bond 2.5 vs 3.0; difference 0.5 thus Polar Covalent

H-Cl single bond 2.1 vs 3.0; difference 0.9, thus Polar Covalent

Can you think of an example of a Nonpolar Covalent bond?

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Electronegativity

Non-Polar covalent bond: An electron pair is sharing a region of space between the two nuclei. This electron pair has narrow limits between each nuclei

Ionic Bond: Electron transfer and each of the atoms have formed a distinctive ion and those ions are attracted to one another

Polar covalent bond: An electron pair is sharing a region of space between the two nuclei, however unequally. It is

attracted more to one nucleus than the other

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Covalent Bonding and Lewis Dot Structures

Example: H2O

O HH 2 x Mutual Sharing of Electrons

In this case two single bonds

Lewis Dot Representation

Note: Shape of Molecule and two lone pair of electrons

OH H

Example: CH4 - Methane

CH

H

H

HNote: No lone pairs of electrons 2-D representation

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Important Rules for More difficult examples: NF3

Covalent Bonding and Lewis Dot Structures

Step 1. Decide on the sequence of Atoms. Example NF3, place the atom with

the lower group number in centre. (usually lower elecronegativity)

N

F

F F

Step 2. Determine the total number of valence electrons available. Example NF3 = [1 x N (5e-)] + [3 x F (7e-)] = 5 + 21 = 26 valence electrons

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Covalent Bonding and Lewis Dot Structures

Important Rules for More difficult examples: NF3

Step 3. Draw a single bond from each surrounding atom to the centre atom

N

F

F F

Subtract 2 e-’s for each single bond from the total number of valence electrons available, to find the number of electrons remaining[26e- - (3 x 2e-) = 20 electrons]

Step 4. Distribute the remaining electrons in pairs so that each atom obtains eight electrons (Place lone pairs on the surrounding more electronegative atoms first)

N

F

F F

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** Carry on only for when the central Atom has not enough electrons!

Covalent Bonding and Lewis Dot Structures

C

O

O O

-2

C

O

O O

-2

If Needed: Step 5. Central atom has not got 8 electrons!!!! We alter one of the more electronegative lone pairs to a bonding pair to give each atom an octet. In the case of Carbonate….

to

What is the Lewis dot structure for ethene C2H4?

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Covalent Bonding and Lewis Dot Structures

What about molecular oxygen?O2

O OHas 12 valence electrons, however whenthese are arranged with a single bondeach oxygen only has 7 electrons

O O

Thus, the single lone electron is pairedto form another bond

O O“Oxygen Bar”

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Covalent Bonding and Lewis Dot Structures

What about the Cyanide ion CN-

Has 9 valence electrons in total plus one for the charge

C N-

(10) Subtract two for the bond, 8 electrons left

C N Carbon has not enough electrons

C N Carbon has not enough electrons

C N Correct both have eight electrons, but thecharge is in brackets. Where is the formalcharge?

NaCN

Used in goldExtraction,

Suicide tabletsWWII

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Polyatomic Ions and Formal Charge

C NThe cyanide ion is a polyatomic ion and the overall chargeIs – 1. However for the reactivity and structural aspectsIt is important to determine which of the atoms bears the charge

The charge on the atom in a polyatomic ion is the formal charge

Formal charge = Number of valence electrons – All unsharedelectrons

+One half ofall sharedelectrons

( )

For Nitrogen = 5 – (2 + 6/2) = 0

For Carbon = 4 – (2 + 6/2) = -1

C NFormal charges are written as or and are written next to the atom+ -+ -

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Q. Determine the formal charge on the blue atoms in the following species:

Formal Charge

OH

C

CH3

H3C H

NO

O

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Organic ReactionsUnderstanding structure is just a part of organic chemistry.

Understanding reactions and predicting reactivity is very important.

1. Why don’t molecules generally react with one another?

2. Why do molecules sometimes react with each other?

3. In chemical reactions, electrons move from full orbitals to empty orbitals.

4. How do we represent the movement of electrons in reactions (mechanisms)?

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Molecular CollisionsAs well as vibrating, molecules move with respect to another.

Collisions with each other, with solvent molecules and the walls of the container are very frequent.

Most collisions do not result in chemical change (a reaction)

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To write mechanisms for organic chemistry, we show the flow of electrons

from electron-rich species to electron-poor species with curly arrows.

Placement of the curly arrow is important!

It originates at the electron pair and terminates

at the electron-poor atom

Example: - bond making

Write reaction mechanism between hydroxide ion and proton:

Reaction Mechanisms

a curly arrow represents the movement of two electrons

O H O H

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Example:Example: bond breakingbond breaking

Reaction MechanismsReaction Mechanisms

C Cl C Cl

carbone lost oneelectron and becomes positively charged

chlorine had gained oneelectron and becamesnegatively charged

curly arrow is directed from single bond to electronegativeatom

Lone pairs:Lone pairs: nonbonding electrons can also be used in bond-making process.nonbonding electrons can also be used in bond-making process.

Write the reaction between water and a proton:Write the reaction between water and a proton:

H

an oxoniumcation

H

O

HH O H

H

C loses one C loses one electron and electron and becomes positively becomes positively chargedcharged

Cl gains an electron Cl gains an electron and becomes and becomes negatively chargednegatively charged

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Reaction Mechanisms

CARBON

- has valency of four

- carbon can also bond to just three other atoms by donating a pair of

electrons to one of the atoms originally bonded (breaking the bond)

C

tetravalent carbon

C X C

CARBOCATIONcarbone lost one

electron and becomes positively charged

curly arrow is directed from single bond to electronegativeatom

X

HC H C

CARBOANION

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NITROGEN

- has valency of three

- has three bonding electrons and a lone pair

- however it can also bond to four atoms by donating its lone pair, in

which case it will than carry a positive charge.

Write reaction between ammonia and proton:

H N

H

H H H N

H

H

H

trivalent nitrogen an ammoniumcation

What shape is ammonia?

What shape is an ammonium ion?

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OXYGEN- has two bonding electrons and two lone pairs- it can bond to two other atoms and it is usually divalent

- it can also bond to one atom in a negatively charged form, or to three atoms in positively charged form.

O

divalent oxygenH

an oxide anion

HO O

H

O O

H

an oxonium cation

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BOND POLARITY

- because different atomic nuclei have a particular ability to attract electrons

bonds between unlike atoms may not be shared equally. This leads to

charge imbalance, with one of the atoms taking more than its share of

electrons.

- an atom that is more electronegative than carbon will polarize the bond,

this is indicated by putting partial charge δ + and δ - above the atoms. It

can also be represented by putting an arrowhead on the bond in the

direction of electron excess.

H3C Brδ+ δ−

bromine is more electronegative than carbon

H3C Br

δ+ δ−C O

δ+ δ−C N

polarity in C-O and C-N bonds

δ+ δ−C O