BIOLOGY
YEAR 3
QUARTER 1
2020
Essentials of Organic
Chemistry
SUMMARY OF THE COURSE ORGANIC CHEMISTRY
NWI-MOL101
ELISE REUVEKAMP
,Content
Lecture 1: Structure determines properties............................................................................................ 3
Lecture 2: Alkanes and Cycloalkanes: introduction to hydrocarbons ................................................... 10
Sp3 hybridization................................................................................................................................ 11
Sp2 hybridization................................................................................................................................ 11
sp hybridization ................................................................................................................................. 12
IUPAC nomenclature system ............................................................................................................. 15
Lecture 3: Conformations and cis-trans isomers................................................................................... 19
Lecture 4: Chirality ................................................................................................................................ 22
Lecture 5: Introduction to reaction mechanisms .................................................................................. 26
Functional groups .............................................................................................................................. 26
Substitution reactions and reactivity trends ..................................................................................... 28
Reaction mechanisms........................................................................................................................ 28
Stability of carbocations .................................................................................................................... 29
Scrambling ......................................................................................................................................... 30
Rearrangments .................................................................................................................................. 30
Methyl and primary halides .............................................................................................................. 30
Lecture 6: Nucleophilic substitution...................................................................................................... 31
Relative reactivity of halide leaving groups ...................................................................................... 32
Kinetics of SN2 mechanism ................................................................................................................ 32
Stereochemistry ................................................................................................................................ 33
Nucleophiles and nucleophilicity....................................................................................................... 34
Kinetics of SN1 mechanisms............................................................................................................... 34
Solvents ............................................................................................................................................. 35
Sulfonates in nucleophilic substitution ............................................................................................. 36
Lecture 7: Elimination reactions ............................................................................................................ 37
Alkene nomenclature ........................................................................................................................ 37
Structure of alkenes .......................................................................................................................... 37
Stereoisomerism ............................................................................................................................... 38
Alkene stability .................................................................................................................................. 39
Elimination reactions......................................................................................................................... 39
Dehydration and E1 and E2 mechanisms .......................................................................................... 41
Dehydrohalogenation........................................................................................................................ 42
E2 mechanism of dehydrohalogenation ........................................................................................... 43
E2 stereochemistry ............................................................................................................................ 43
E1 elimination mechanism in hydrohalogenation ............................................................................ 44
1
, Competing reactions ......................................................................................................................... 45
Lecture 8: Addition reactions ................................................................................................................ 46
Hydrogenation ................................................................................................................................... 46
Electrophilic addition of hydrogen halides........................................................................................ 48
Carbocation rearrangements ............................................................................................................ 49
Acid-catalysed hydration ................................................................................................................... 49
Epoxidation of alkenes ...................................................................................................................... 50
Lecture 9: Conjugation in alkadienes and allylic systems ..................................................................... 51
Allyl group.......................................................................................................................................... 51
SN1 and SN2 reactions of allylic halides.............................................................................................. 51
Allylic anions ...................................................................................................................................... 53
Alkadienes ......................................................................................................................................... 53
Hydrohalogenation of dienes ............................................................................................................ 54
Lecture 10: Arenes and aromaticity ...................................................................................................... 56
Benzene stability ............................................................................................................................... 56
Nomenclature and trivial names ....................................................................................................... 56
The benzyl group ............................................................................................................................... 57
Nucleophilic substitution in benzylic halides .................................................................................... 58
Lecture 11: Alcohols, diols and thiols .................................................................................................... 60
Reduction via hydrogenation ............................................................................................................ 60
Metal hydride reduction ................................................................................................................... 61
Reduction of carboxylic acids ............................................................................................................ 61
Functional group transformations .................................................................................................... 62
Synthesis of ethers ............................................................................................................................ 63
Oxidation of alcohols ......................................................................................................................... 64
Thiols ................................................................................................................................................. 65
2
, Essentials of organic chemistry
Lecture 1: Structure determines properties
Organic chemistry is the branch of chemistry that deals with carbon compounds rather than simple
salts as carbonates. It studies the structure, properties, composition, reactions etc.
In the periodic table, the elements are listed in order of increasing atomic number, the atomic
number is the number of protons in the nucleus of an atom.
Proton
Mass = 1.67 x 10-27 kg
Charge = +1.60 x 10-19 C
Electron
Mass = 9.11 x 10-31 kg
Charge = -1.60 x 10-19 C
Neutron
Mass = 1.67 x 10-27 kg
Charge = 0.00 C
Atomic orbitals
The term atomic orbital may also refer to the physical region or space where the electron can be
calculated to be present, as predicted by the particular mathematical form of the orbital. Orbitals are
described by specifying their size, shape and directional properties.
S atomic orbitals are spherically shaped and start with n=1 (1 electron). There is
a single orbital within each ns subshell. Within a particular shell, s orbitals are
lower in energy than other orbitals. As the number of electrons increase (n),
additional sign changes (nodes) appear in the shape of the orbital.
- The letter s is preceded by the principal quantum number (shell). An
electron in a 1s orbital is likely to be found closer to the nucleus, is lower
in energy and is more strongly held than an electron in a 2s orbital
- Two electrons may occupy the same orbital only when they have
opposite or paired spins.
P atomic orbitals are dumbbell shaped and start with n=2 (2 electrons). There
are 3 orbitals within each np subshell, which correspond to the three cartesian
directions. The np orbitals all have the same energy; according to Hund’s rule
electrons are left unpaired when filling until they must be paired. All p orbitals
contain a node at the nucleus.
- Each orbital is singly occupied before any one is doubly occupied (Hund’s rule)
- Valence electrons are the outermost electrons, the ones that are most likely to be involved in
chemical bonding and reactions. Because 4 orbitals are involved the maximum numbers of
electrons in the valence shell is 8 of any second row element
- Outermost electrons for second row elements are 2s and 2p electrons
3
YEAR 3
QUARTER 1
2020
Essentials of Organic
Chemistry
SUMMARY OF THE COURSE ORGANIC CHEMISTRY
NWI-MOL101
ELISE REUVEKAMP
,Content
Lecture 1: Structure determines properties............................................................................................ 3
Lecture 2: Alkanes and Cycloalkanes: introduction to hydrocarbons ................................................... 10
Sp3 hybridization................................................................................................................................ 11
Sp2 hybridization................................................................................................................................ 11
sp hybridization ................................................................................................................................. 12
IUPAC nomenclature system ............................................................................................................. 15
Lecture 3: Conformations and cis-trans isomers................................................................................... 19
Lecture 4: Chirality ................................................................................................................................ 22
Lecture 5: Introduction to reaction mechanisms .................................................................................. 26
Functional groups .............................................................................................................................. 26
Substitution reactions and reactivity trends ..................................................................................... 28
Reaction mechanisms........................................................................................................................ 28
Stability of carbocations .................................................................................................................... 29
Scrambling ......................................................................................................................................... 30
Rearrangments .................................................................................................................................. 30
Methyl and primary halides .............................................................................................................. 30
Lecture 6: Nucleophilic substitution...................................................................................................... 31
Relative reactivity of halide leaving groups ...................................................................................... 32
Kinetics of SN2 mechanism ................................................................................................................ 32
Stereochemistry ................................................................................................................................ 33
Nucleophiles and nucleophilicity....................................................................................................... 34
Kinetics of SN1 mechanisms............................................................................................................... 34
Solvents ............................................................................................................................................. 35
Sulfonates in nucleophilic substitution ............................................................................................. 36
Lecture 7: Elimination reactions ............................................................................................................ 37
Alkene nomenclature ........................................................................................................................ 37
Structure of alkenes .......................................................................................................................... 37
Stereoisomerism ............................................................................................................................... 38
Alkene stability .................................................................................................................................. 39
Elimination reactions......................................................................................................................... 39
Dehydration and E1 and E2 mechanisms .......................................................................................... 41
Dehydrohalogenation........................................................................................................................ 42
E2 mechanism of dehydrohalogenation ........................................................................................... 43
E2 stereochemistry ............................................................................................................................ 43
E1 elimination mechanism in hydrohalogenation ............................................................................ 44
1
, Competing reactions ......................................................................................................................... 45
Lecture 8: Addition reactions ................................................................................................................ 46
Hydrogenation ................................................................................................................................... 46
Electrophilic addition of hydrogen halides........................................................................................ 48
Carbocation rearrangements ............................................................................................................ 49
Acid-catalysed hydration ................................................................................................................... 49
Epoxidation of alkenes ...................................................................................................................... 50
Lecture 9: Conjugation in alkadienes and allylic systems ..................................................................... 51
Allyl group.......................................................................................................................................... 51
SN1 and SN2 reactions of allylic halides.............................................................................................. 51
Allylic anions ...................................................................................................................................... 53
Alkadienes ......................................................................................................................................... 53
Hydrohalogenation of dienes ............................................................................................................ 54
Lecture 10: Arenes and aromaticity ...................................................................................................... 56
Benzene stability ............................................................................................................................... 56
Nomenclature and trivial names ....................................................................................................... 56
The benzyl group ............................................................................................................................... 57
Nucleophilic substitution in benzylic halides .................................................................................... 58
Lecture 11: Alcohols, diols and thiols .................................................................................................... 60
Reduction via hydrogenation ............................................................................................................ 60
Metal hydride reduction ................................................................................................................... 61
Reduction of carboxylic acids ............................................................................................................ 61
Functional group transformations .................................................................................................... 62
Synthesis of ethers ............................................................................................................................ 63
Oxidation of alcohols ......................................................................................................................... 64
Thiols ................................................................................................................................................. 65
2
, Essentials of organic chemistry
Lecture 1: Structure determines properties
Organic chemistry is the branch of chemistry that deals with carbon compounds rather than simple
salts as carbonates. It studies the structure, properties, composition, reactions etc.
In the periodic table, the elements are listed in order of increasing atomic number, the atomic
number is the number of protons in the nucleus of an atom.
Proton
Mass = 1.67 x 10-27 kg
Charge = +1.60 x 10-19 C
Electron
Mass = 9.11 x 10-31 kg
Charge = -1.60 x 10-19 C
Neutron
Mass = 1.67 x 10-27 kg
Charge = 0.00 C
Atomic orbitals
The term atomic orbital may also refer to the physical region or space where the electron can be
calculated to be present, as predicted by the particular mathematical form of the orbital. Orbitals are
described by specifying their size, shape and directional properties.
S atomic orbitals are spherically shaped and start with n=1 (1 electron). There is
a single orbital within each ns subshell. Within a particular shell, s orbitals are
lower in energy than other orbitals. As the number of electrons increase (n),
additional sign changes (nodes) appear in the shape of the orbital.
- The letter s is preceded by the principal quantum number (shell). An
electron in a 1s orbital is likely to be found closer to the nucleus, is lower
in energy and is more strongly held than an electron in a 2s orbital
- Two electrons may occupy the same orbital only when they have
opposite or paired spins.
P atomic orbitals are dumbbell shaped and start with n=2 (2 electrons). There
are 3 orbitals within each np subshell, which correspond to the three cartesian
directions. The np orbitals all have the same energy; according to Hund’s rule
electrons are left unpaired when filling until they must be paired. All p orbitals
contain a node at the nucleus.
- Each orbital is singly occupied before any one is doubly occupied (Hund’s rule)
- Valence electrons are the outermost electrons, the ones that are most likely to be involved in
chemical bonding and reactions. Because 4 orbitals are involved the maximum numbers of
electrons in the valence shell is 8 of any second row element
- Outermost electrons for second row elements are 2s and 2p electrons
3
