Topic 3 - Organic Chemistry Flashcards
What is a heteroatom?
An atom other than carbon or hydrogen that is found in an organic molecule.
Definition of the functional group?
The part of the molecule that is functional. Usually, the part containing the heteroatom. Chemical reactivity of molecules is associated with functional groups.
Definition of resonance?
When more than one arrangement of double bonds needs to be drawn in order to show electronic distribution; we say that the molecule exists as a resonance hybrid.
Requirements of an aromatic molecule?
To be aromatic a compound must be planar and cyclic and have (4n+2) delocalised pi electrons, where n is an integer.
4n+2 –> known as Huckles law –> number of delocalised electrons must fit.
Hence, according to Huckles law, you can have 2 (n=0), 6 (n=1), 10 (n=2), etc…. Pi electrons.
Definition of tautomer?
Tautomer is an example of a specific kind of isomer.
Structured isomers that differ only in the position of a hydrogen and a double bond.
Tautomerisation is the transformation of one tautomer to the other.
Keto-enol tautomerisation and imine-enamine tautomerisation are very important for biological systems.
Example of resonance?
Resonance example –> Carboxylate (COO-)
What are the two main types of tautomers?
- Keto-enol tautomerisation
Keto <—–> Enol
(aldehyde) (Double/alcohol)
Basically, hydrogen and double bond swap position.
- imine - enamine tautomerisation
imine <—–> enamine
Note tautomerisation becomes more favourable under specific acid/base conditions.
Definition of nucleophile?
A nucleophile is an electronegative functional group which has an electron pair that can be used to form a covalent bond.
- Attracted to positive charged
Example –> H2O
Definition of Electrophile?
An electrophile is an electron deficient group which can accept a pair of electrons to form a covalent bond; must possess an empty orbital.
- Attracted to the negative charge
Example –> carbon of carbonyl
Definition of polarized bond?
This is when the electrons are not shared evenly between two joined atoms.
The bond has a dipole moment.
Definition of polarizability?
Its a measure of the ease of change of electron distribution –> Basically how easy it is to cause a dipole moment.
Example:
Small atom –> less shielding –> harder to cause dipole moment as electrons are held close to the nucleus.
Big atom –> more shielding –> easier to cause dipole moment as electrons are further away from the nucleus.
Definition of electronegativity?
A measure of how strong the atom attracts electrons in a bond.
Definition of a leaving group?
The part of the molecule which takes bonding electrons when a bond is broken during a biochemical reaction.
What is hybridisation? What are the three main types?
Hybridisation refers to the mixing of atomic orbitals to make molecular orbitals. The shape/orientation of these new hybrid orbitals are optimised for bond formation.
- Sp3
- Sp2
- Sp
What are the rules for determining hybridisation?
- Carbon atoms and heteroatoms are always Sp3 hybridized if all the bonding is single.
- Carbon to carbon double bonds are always Sp2
- Partial double bonds are always Sp2 –> Pi orbitals are used to form delocalised system
- Triple bonds are Sp hybridised –> very rare in biological systems.
Explain the shape and main facts of Sp3 hybridisation.
- 1 S and 3 P orbitals combine to form 4 hybrid orbitals of identical shape/energy –> tetrahedral arrangement.
- Hybrid orbitals can undergo head-on overlap with other orbitals to form sigma bonds.
- If there are fewer than 4 bonds –> there must be a lone pair.
- Lone pair distorts tetrahedron –> can act as base or nucleophile –> also involved in H-bonding.
Explain the shape and main facts of Sp2 hybridisation.
- Combining of 1 S and 2 P orbitals to form Sp2 hybrid orbital –> this leaves one P orbital.
- All three hybrid orbitals are identical energy and shape —> trigonal planar arrangement.
- All hybrid orbitals lie in the same plane whereas P orbital is perpendicular to the plane.
What are the important oxygen based function groups?
Oxygen-based function groups include:
- Hydroxyl
- Alkoxyl (ether)
- Carbonyl (Aldehyde/ketone/carboxylic acid/esters)
What are the important nitrogen based functional groups?
Nitrogen-based functional groups
- Amino - NH2
- Amide - C(O)NH2
- Imine - C=N-R
Describe hybridisation and important properties of carbonyl (ketone + aldehyde)?
Carbonyl (ketone + aldehyde)
- Sp2 –> everything in the same plane except P orbital
- The difference in electronegativity creates a dipole.
- This makes carbon an important electrophile -> as it is positively charged.
- Important note –> Carbonyl molecules almost always have a hydrogen on the alpha carbon (carbon next to functional group). Hydrogen on alpha carbon is easily lost –> acidic –> this is also favourable as the structure becomes stabilised by resonance.
Describe hybridisation and important properties ester?
Ester
- Sp2 –> due to resonance formed
- Usually thioester is preferred in biological systems –> more reactive
- In resonance form the oxygen (not carbonyl oxygen) doesn’t pull electrons away from carbon –> instead it pushes electrons towards it to make it less reactive –> makes the ester less reactive than carbonyl.
Describe hybridisation and important properties of amide?
Amide
- Can form resonance –> Sp2
- In resonance form, the lone pair is not available –> not basic or nucleophilic.
- Resonance thus decreases reactivity/electrophilicity of carbon.
Draw and explain the mechanism for the SN1 mechanism?
- Leaving group leaves –> takes electrons –> forms carbocation intermediate
- The carbocation is Sp2 –> P orbital is empty –> Nucleophile attacks from above and below the plane.
- Nucleophile bonds –> gives electrons –> forms positive charge –> Forms product which is Sp3 –> racemic mixture but in biological systems only one –> enzymes control.
Draw and explain the mechanism for the SN2 mechanism.
- Nucleophile attack from the opposite side of leaving the group –> same time C – X starts breaking (X = leaving the group).
- Transition state formed –> partial bond –> Sp2 during transition.
- Leaving group leaves –> product is Sp3 but with reverse stereochemistry.
Draw and explain the mechanism for the E1 mechanism.
- Exactly the same step as the first step in SN1 –> leaving group leaves and takes electrons –> hybridization to Sp2
- Base steals H from alpha carbon and the electron from the hydrogen is used to form a double bond (enters P orbital).
Draw and explain the mechanism for the E2 mechanism.
Very similar to E1 but everything happens at the same time.
Explain and draw what happens in an addition reaction.
Reverse of elimination
- electrons in double bond attack electrophile
- Creates carbocation intermediate
- Nucleophile binds to positive carbocation.
Draw and explain the nucleophilic addition reaction of water to a double bond.
- Electron cloud is nucleophilic and it is disrupted when bond with H+ is formed.
Normally H+ binds to any carbon but enzymes control the bonding in bio systems.
- Water (nucleophile) bonds to carbocation with lone pair.
- Oxygen in water becomes positively charged as it uses one electron to form a double bond. Hydrogen gives an electron to oxygen (neutral again) when base bonds to Hydrogen.
- This forms an alcohol.
Draw the nucleophilic addition to a carbonyl double bond.
Note carbonyl can be replaced by imine.
- Nucleophile attacks electrophilic carbon.
- To allow nucleophile to bond –> oxygen from carbonyl take electron from double bond –> becomes negatively charged –> rehybridisation to Sp3
- Intermediate form – Negative oxygen gets protonated while positive Oxygen (nucleophile added) gets deprotonated by a base.
- The product formed –> Hemiacetal —> One hydroxyl and one ether.
The process is used to make sugar cyclic.
Explain and draw the aldol reaction?
A specific type of nucleophilic addition –> Natures favourite way of building bigger molecules.
Involves two carbonyl compounds –> One acts as nucleophile other as an electrophile.
- The first step is the removal of hydrogen from alpha carbon with the help of a base (not shown)
- Negative carbon acts as a nucleophile and attacks electrophilic carbon on another carbonyl molecule.
- Forces oxygen on electrophilic carbon to take the electron –> negatively charged.
- O- accepts the electron –> product β hydroxyaldehyde.
Note –> Aldol reaction is reversible (exactly the reverse) –> aided by the presence of enzymes.
Draw and explain the nucleophilic substitution of a thioester.
Different to normal Sp3 nucleophilic substitution.
Sp2 - substitution.
- Nucleophile attacks electrophilic carbon –> Oxygen on carbonyl becomes negatively charged –> Note mistake in the diagram –> double bond is no longer present in the intermediate
- Oxygen reforms double bond –> push of leaving the group.
- Positively charged nucleophile (H2O) forms carboxylate ion as the H+ is lost.
Basically in this reaction…
Thioester is broken down to carboxylate and thiol.
Explain and draw the Claissen condensation reaction.
A specific type of substitution reaction.
Consists of one Nucleophile and One electrophile.
- Base removes a proton from alpha carbon –> Hydrogen leaves electron to form C=C which results in C–O- formation.
- Carbon double bond acts as a nucleophile and attacks the electrophilic carbon on the other molecule.
- Electron fro C–O- moves back to form double bond –> pushes off leaving group
Product –> β keto thioether.
