CHEMISTRY OF THE COVALENTCOMPOUNDS OF CARBON

H B N O Si P S F Cl Br I

H C N O F

P S Cl

Br

I

Si

Organic Chemistry Organic Chemistry

COMBINED WITH A FEW OTHER COMMON ELEMENTS:

B

Millions of things Millions of things contain organic contain organic

molecules….molecules….

UNIQUE PROPERTIES OF CARBONUNIQUE PROPERTIES OF CARBON

Carbon is TETRAVALENT - whichmeans it bonds four times….

Carbon is one of the few elements that can form chainswith itself…

C-C-C-C-C-C-C-C-C

Carbon can also form BRANCHED NETWORKS and RINGS

C

CCC

CC

CC C C C

C C C

C C

Most organic Most organic molecules have no molecules have no

charge….charge….

Most organic molecules contain C-C and C-H bonds which are non-polar…water, which has slight charge, is polar

Because of this, most organic molecules do not dissolve in water – For example, oil and water do not mix!

Most organic molecules are gases or quickly evaporating liquids at room temperature because they have no charge – they have weak physical bonds (London Dispersion bonds)

Organic molecules will not have charge unless they contain a bond with polarity

Those that do have slightly charged bonds – like C-O or O-H bonds (as in alcohols) dissolve well in water!

Water - has slight charge…is a liquid

Methane – has no charge…is a gas

NO ATTRACTION

Methanol – Has slight charge – is a liquid and dissolves well in water

ATTRACTION!

Water - has slight charge…is a liquid

Hydrocarbons – contain hydrogen and carbon bonds

Aliphatic hydrocarbons – chains of carbons and hydrogens

Aromatic hydrocarbons – contain benzenec

Alkanes – all single bonds

Alkenes – has some double bonds

Alkynes has some triple bonds

saturated unsaturated

Functional groups – altered hydrocarbons

-Ether-Ester-Aldehyde-Ketone-Carboxylic acid-alcohol

Aliphatic HydrocarbonsAliphatic Hydrocarbons

• Hydrocarbons are compounds composed Hydrocarbons are compounds composed of carbon and hydrogen in chainsof carbon and hydrogen in chains

• Aliphatic – meaning chains of carbons – Aliphatic – meaning chains of carbons – either straight or branched chainseither straight or branched chains

Aliphatic HydrocarbonsAliphatic Hydrocarbons

• Unsaturated:Unsaturated: contains carbon-contains carbon-carbon double or carbon double or triple bonds.triple bonds.

C C C

H H

H

H

H

H

• Saturated:Saturated: contains contains all all carbon-carbon carbon-carbon single bonds.single bonds.

C C

H

H

H

H

H

H

Common Hydrocarbon TypesCommon Hydrocarbon Types

C CC C

C

H

H

H

H

HH

H H

H

H

H

HC C

C

C

C

H

H

H

H

H

H

H

H

H H

H

H

C C

H

CH

C

H

H

H

HH

H

C C CH H

H

H

C C C C

H

H

H

C

H

H

H

H

H

H C C C C

H

H H

H

H

H H

ALKANESALKANESCCnnHH2n+22n+2

ALKENESALKENESCCnnHH2n2n

ALKYNESALKYNESCCnnHH2n-22n-2

onlyonlysinglesinglebondsbonds

at leastat leastoneonedoubledoublebondbond

at leastat leastoneonetripletriplebondbond

Structural Formulas – show the Structural Formulas – show the structure of the atomsstructure of the atoms

CondensedStructuralFormulas

CH3CH2CH2CH2CH3

somebondsshown

Unbranched(“linear”) Alkane

Branched Alkane

CHCH CH3CH3CH2

CH3CH3

CH3CHCH2CHCH3

CH3 CH3

CH2CH2 CH3CH3CH2

Molecular Formula – Tells me nothing about Structure – just how manyof each element there are!

C7H16C5H12

CH3CH(CH3)CH2CH(CH3)CH3

StructuralFormulas

C C CH H

H

H

H C C C C

H

H H

H

H

H H

CH3CH2CH=CH2

CH3CH2-CH=CH2

H-C C-CH3

HC CCH3

CH CCH3

or

Condensed NotationCondensed Notation

Alkene

Alkyne

CH3 CH

CH3

CH

CH2

CH2 CH3

CH3

CH3CH(CH3)CH(CH2CH3)CH2CH3

EVEN COMPLICATED BRANCHED STRUCTURESEVEN COMPLICATED BRANCHED STRUCTURESCAN BE WRITTEN ON A SINGLE LINECAN BE WRITTEN ON A SINGLE LINE

Condensed NotationCondensed Notation

for this reason manyhandbooks usecondensed notation

note use of parentheses -these atoms are attached to the Carbon atom that they follow

BranchedAlkane

C C CH3H CH3 C C CH2CH3

CH3CH2CH2CH2CH3 CH3 C CH3

CH3

CH3

C C CH3CH3

H

H

CH3CH2CH CH2

Skeleton NotationSkeleton Notation

Cyclic MoleculesCyclic Molecules

• For some molecules, the carbon For some molecules, the carbon chain may close on itself to form a chain may close on itself to form a ring.ring.

• These types of substances are called These types of substances are called cyclic molecules.cyclic molecules.

• These do not follow the general These do not follow the general formulas for alkanes, alkenes, and formulas for alkanes, alkenes, and alkynes (Calkynes (CnnHH2n+22n+2, C, CnnHH2n2n, and C, and CnnHH2n-22n-2))

Examples of Cyclic Examples of Cyclic MoleculesMolecules

C C

C

CH2 CH2

CH2

H H

H

HH

H

C

C C

C CH2

CH2 CH2

CH2

H

H

H

H

H H

HH

C C

C

C

C

CH2 CH2

CH2

CH2

CH2

H H

H

H

H

H

HH

HH

Cyclopropane C3H6

Cyclobutane C4H8

Cyclopentane C5H10

Testosterone

How to name compounds…How to name compounds…

Prefixes for organic are different than traditional naming…

Endings: -ane = single bonds – ene = double bonds – yne = triple bonds

Groups are named according to the number of carbon chains in the group….

The group has the ending –yl if it is a carbon group – the group has the ending –o if it is a halogen

-CH3 methyl group -CH2CH3 ethyl group

C

-Cl chloro group

Longest chain….? Six carbons….

Bond types….? All single bonds….

Hex….

-ane….

Attached groups…? -CH3 = methyl

Number from what side…?

The right….

Why…?The group is attached to carbon 3, and not carbon 4

3-methyl hexane

• Nomenclature for other types of hydrocarbons…Nomenclature for other types of hydrocarbons…

1, 1 dimethyl cyclobutane

•Longest chain…?

•Did you include the entire double bond…?

•Start numbering from what end…?

•Is the double bond or attached groups more important…?

•How many groups are attached…?

•What are they?

•Remember to report the groups alphabetically….!

•Longest chain…?

•Did you include the entire double bond…?

•Start numbering from what end…?

•Is the double bond or attached groups more important…?

•How many groups are attached…?

•What are they?

•Remember to report the groups alphabetically….!

5-chloro 7-methyl - 3 – nonene

CHC CCH2 CH2

CH2CH2CH2CH3CH3

C CH3

Name this sucker….! 4-butyl 2-methyl 1, 5 heptene-yne

• Important things to remember…Important things to remember…

• Double and triple bonds are Double and triple bonds are most most important when counting the longest important when counting the longest chainchain

• Always include Always include bothboth the double and triple bond in the longest chain – even the double and triple bond in the longest chain – even if it isn’t the most number of carbons!if it isn’t the most number of carbons!

• Start counting from the end closest to the double or triple bond – Start counting from the end closest to the double or triple bond – whichever has the lowest numberwhichever has the lowest number

• If there is a tie, and only then, do double bonds take priority over triple If there is a tie, and only then, do double bonds take priority over triple bondsbonds

• If there isn’t a double or triple bond, find the longest continuous chain of If there isn’t a double or triple bond, find the longest continuous chain of carbons, and start counting from the end closest to an attached group – carbons, and start counting from the end closest to an attached group –

• It doesn’t matter what the group is – all groups have the same importance It doesn’t matter what the group is – all groups have the same importance – CH– CH33, -CH, -CH22-CH-CH33, -Cl, etc., -Cl, etc.

• If there is a tie, start counting from the end that has the If there is a tie, start counting from the end that has the mostmost groups on groups on the lowest numberthe lowest number

Which end do you number from? Cl

CH3CCH2CH2CCH3

CH3

CH3

Cl

CH3CCH2CH2CCH3

CH3

CH3

• Great websites for tutorials….Great websites for tutorials….

http://www.chem.ucalgary.ca/courses/351/orgnom/index.html

http://www.cem.msu.edu/~reusch/VirtualText/nomen1.htm

http://en.wikipedia.org/wiki/IUPAC_nomenclature_of_organic_chemistry

http://chemistry.boisestate.edu/people/richardbanks/organic/nomenclature/organicnomenclature1.htm

http://www.chembio.uoguelph.ca/educmat/chm19104/nomenclature/quizes.html

http://www.quia.com/jg/65803.html

http://eppe.tripod.com/orgtable.htm

http://www.cem.msu.edu/~reusch/VirtualText/Questions/Nomencl/nomencl.htm

http://www.chemguide.co.uk/atoms/bonding/vdw.html

Boiling points of various hydrocarbons…

Why do they increase…?

•Boiling point as we halogenate, or add a halogen to a hydrocarbon, goes….

•Up! Why????

•Methane = -1620C

•Fluoromethane = -78.20C

•Difluoromethane = -51.60C

•Trifluoromethane = -50C

•Tetrafluoromethane = -1280C

•Why would we want to halogenate a hydrocarbon…?

•Does it matter what halogen you add…?

1.The compressor compresses cool Freon gas1.The compressor compresses cool Freon gas, causing it to become , causing it to become hot, hot, high-pressure Freon gashigh-pressure Freon gas (red in the diagram above). (red in the diagram above).

2.This hot gas runs through a set of coils so it can dissipate its heat, and it 2.This hot gas runs through a set of coils so it can dissipate its heat, and it condenses into a condenses into a liquidliquid..

3.The Freon liquid runs through an expansion valve, and in the process it 3.The Freon liquid runs through an expansion valve, and in the process it evaporates to become evaporates to become cold, low-pressure Freon gascold, low-pressure Freon gas (light blue in the (light blue in the diagram above).diagram above).

4.This cold gas runs through a set of coils that allow the gas to absorb heat 4.This cold gas runs through a set of coils that allow the gas to absorb heat and cool down the air inside the building.and cool down the air inside the building.

Halogenated hydrocarbons are used as refrigerants…

CH3

CH2CH2 CH3CH3CH2 CH2 CH2

Structural Isomers…

Molecules that have the same molecular formula, meaning same numbers of carbons and hydrogens, but different structures…

CH2CH2CH3CH3

CH2 CH2 CH2 CH2

Isomers of octane…..there are 18 different arrangements!

Octane

2-methyl heptane

Are these both octane though?

CH3

CH2CH2 CH3CH3CH2 CH2 CH2

Structural Isomers…

The problem is that some chemists generically refer to both of the following compounds as octane, since they both contain 8 carbons and 18 hydrogens…

CH2CH2CH3CH3

CH2 CH2 CH2 CH2

Octane

2-methyl heptane

The official naming system, the IUPAC naming system, does not call both of these molecules octane though!

Look at these two molecules - both of these molecules are generically referred to as structural isomers of hexane, because they both have 6 carbons and 14 hydrogens (C6H14). They don’t have the same IUPAC name at all – they are totally different molecules, with totally different properties!

CH3-CH2 - CH2-CH2-CH2-CH3CH3-CH2 - CH2-CH2-CH2-CH3

CH3

CH3-CH2 - CH-CH2-CH3

CH3

CH3-CH2 - CH-CH2-CH3

•Molecules that have the same molecular formula, but differ in how groups attached to the double bond are oriented

•Must have a double bond, and different groups on both the left and right sides!

Geometric Isomers

Cis means same side…

Trans means opposite side…

•This doesn’t happen with a single bond…

•The atoms are free to rotate around the single bond, to form both molecules….

•With a double bond, the atoms are locked into place by the p orbitals bonding in the double bond!

Geometric Isomers

Both are the same molecule!

1,2 dichloroethane

2 different molecules:

trans – 1,2 dichloroethene

cis – 1,2 dichloroethene

Geometric Isomers

Which are isomers, and which are the same molecule…?

H HCH3

C C

H H CH3

C C

H

HH HCH3

C C

H H CH3

C C

H

H

Same molecule..

CH2CH3H

H

CH3

C C

H

CH3

C C

HCH2CH3

CH2CH3H

H

CH3

C C

H

CH3

C C

HCH2CH3

Isomers!

To have geometric isomers:

1.You must have a double bond in the molecule2.You must have two different groups on the left hand side of the bond, and two different groups on the right hand side of the double bond. The left side groups do not have to be the same as the right side groups!

CH3

CH3

H

H CH3

C C

H

CH3

C C

HCH3

CH3

H

H CH3

C C

H

CH3

C C

H

Isomers!

H

H

CH3H

CH3

CH3

C C

CH3

C C

H

H

H

CH3H

CH3

CH3

C C

CH3

C C

H

Same molecule..

Stereoisomers

•Molecules that have the same molecular formula, have the same sequence of bonded atoms, but differ in their 3-d orientation!

•Stereoisomers can be non-superimposable mirror images!

•We call the carbons that they are attached to chiral, or asymmetric!

•This means they are non-symmetrical!

•Our hands are chiral!

- In nature, only one stereoisomer of biological molecules is usually present (example – amino - In nature, only one stereoisomer of biological molecules is usually present (example – amino acids)acids)- In medicine, different stereoiomers of a compound may have substantially different biological - In medicine, different stereoiomers of a compound may have substantially different biological effects.effects.- For example, for certain cancer drugs, such as cisplatin and leucovorin, only one of the two - For example, for certain cancer drugs, such as cisplatin and leucovorin, only one of the two stereoisomers are effective in combating cancer – the other stereoisomer is either ineffective or stereoisomers are effective in combating cancer – the other stereoisomer is either ineffective or poisonous!poisonous!- Robutissin contains D-methorphan – a powerful cough suppressant – the stereoisomer of this - Robutissin contains D-methorphan – a powerful cough suppressant – the stereoisomer of this molecule, L-methorphan, is an illegal opiate that has totally different effects in the body!molecule, L-methorphan, is an illegal opiate that has totally different effects in the body!- How do they separate stereoisomers, if their only difference is the fact that they are mirror - How do they separate stereoisomers, if their only difference is the fact that they are mirror images? Chemically, they look nearly identical!images? Chemically, they look nearly identical!

The two stereoisomers of the amino acid alanine…

D-methorphan D-methorphan L-methorphan L-methorphan

Benzene….Benzene….

•Any compound containing benzene is called an aromatic or arene compound…

•Any compound containing straight or branched chains of carbons is called aliphatic… Notice the resonance in the

benzene ring…

Common benzene compoundsCommon benzene compounds

toluene phenol anisole aniline xylene

cresol styrene benzoic acid salicylic acid

Benzene rings with two Benzene rings with two attached groups use a attached groups use a special naming system…special naming system…They use the ortho, meta, They use the ortho, meta, and para system…and para system…Ortho (o) means one Ortho (o) means one apart…apart…Meta (m) means two Meta (m) means two apart…apart…Para (p) means three Para (p) means three apart…apart…This only applies to This only applies to benzene rings with TWO benzene rings with TWO groups…groups…

Cl

CH3

p-bromo phenol

o-chloro toluene

Names…?Names…?

CH2CH3

CH3

Clm-ethyl anisole

2-chloro 3-ethyl toluene

1,4 dibromo aniline NH2

Br

Br

NH2

Br

Br

Benzene can also be called Benzene can also be called phenylphenyl when you when you want to treat it as an attached want to treat it as an attached

group….either name is acceptable!group….either name is acceptable!

3-ethyl-2-phenyl pentane 2-chloro-2-phenyl heptane

1,3,5 tri-nitro 1,3,5 tri-nitro toluene…toluene…

TNT!TNT!

CH3

NO2NO2

NO2

Dichloro-Diphenyl-Trichloroethane

DDT…

http://www.chem.ucalgary.ca/courses/351/orgnom/functional/func.htmlhttp://www.chem.ucalgary.ca/courses/351/orgnom/functional/func.html

CR

O

OR

CR

O

R

CR

O

OH

R O R

OHR

Functional Group Name Ending

•Alcohol -ol

•Aldehyde -al

•Ketone - one

•Ether - oxy (small) normal chain (large)

•Carboxylic Acid - oic acid

•Ester -yl -oate

CR

O

HCR

O

H

OH

CH3CHCH2CH3

CH2CH2CH2CH3C

O

H

CH2CHCH3C

O

alcohol…

Carboxylic acid…

aldehyde…

ketone…

2-butanol

1-pentanal

1-phenyl 1-butanone

CH3CH2CH2 C

O

HCH3CH2CH2 C

O

H

Aldehyde… 1-butanal

C

O

OHCH3CH2 C

O

OHCH3CH2 1-propanoic acid

Cl

CH2CHCH3C

O

CH3CH2

CH2CH2CH3C

O

CH3CH2

C

O

OHCH3CH2CH2

CH2CH3

O

CH3CHCH3

Carboxylic acid…

ketone…

ester…

ether…

ketone…

1-butanoic acid

3-hexanone

Ethyl butanoate

2-ethoxy propane

5-chloro 3-hexanone

OCH3CH2CH2 C

O

CH2CH3OCH3CH2CH2 C

O

CH2CH3

CH3C

O

OHCH3C

O

OH

H C

O

OHH C

O

OH

Ethanoic acid

Acetic acid (nickname!)

Methanoic acid

Formic Acid (nickname!)

H C

O

HH C

O

H

Methanal

Formaldehyde (nickname!)

Example Structures of complex organic molecules…

nicotine cholesterol

caffeine mescaline

CH3O

CH3O

OCH3

NH2N

N

N

N

O

O

CH3

CH3

CH3

HON

N

CH3H

Meth amphetamine

Think nomenclature is hard…?Think nomenclature is hard…?ZITHROMAX (azithromycin tablets and azithromycin for oral suspension) contain the active ingredient azithromycin, an azalide, a subclass of macrolide antibiotics, for oral administration. Azithromycin has the chemical name (2R,3S,4R,5R,8R, 10R,11R,12S,13S,14R)-13-[(2,6-dideoxy-3-C-methyl-3-O-methyl-α-L-ribo-hexopyranosyl) oxy]-2-ethyl-3,4,10-trihydroxy-3,5,6,8,10,12,14-heptamethyl-11-[[3,4,6-trideoxy-3- (dimethylamino)-β-D-xylo-hexopyranosyl]oxy]-1-oxa-6-azacyclopentadecan-15-one. Azithromycin is derived from erythromycin; however, it differs chemically from erythromycin in that a methyl-substituted nitrogen atom is incorporated into the lactone ring. Its molecular formula is C38H72N2O12, and its molecular weight is 749.00.