organic chemistry Flashcards
when do molecular orbitals form?
when atomic orbitals combine
2 types of molecular orbital (paired)
bonding and antibonding
max number of electrons in a molecular orbital
two
which electrons are placed in the bonding/antibonding orbital?
bonding - electrons that spend most of their time between the two nuclei
antibonding - electrons that spend most of their time outside the nuclei
what is a sigma bond?
one where two molecular orbitals overlap end-on
what is a pi bond?
one where two molecular orbitals overlap side-on
bonding in alkanes
sp3 hybridised, sigma bonds
bonding in alkenes
sp2 hybridised, sigma and pi bonds
bonding in alkynes
sp hybridised, sigma and pi bonds
why are organic compounds coloured?
If the electrons in the HOMO are given exactly the right amount of energy they can jump to the LUMO. The energy of light needed for this transition is absorbed and the complimentary colour is observed.
- don’t talk about d orbitals for organic compounds.
what is conjuagtion?
sections of alternating single and double bonds, which make it more likely a compound will be coloured.
relationship between conjugation and energy gap
the more atoms in a conjugated system, the smaller the gap between the HOMO and the LUMO
what is the name of the part of a molecule responsible for its colour?
the chromophore (conjugated part)
two kinds of stereoisomerism?
optical and geometric
what is stereoisomerism?
atoms have the same chemical formula and are bonded together in the same way, but the arrangement of atoms in the space is different (non-superimposable)
geometric isomers
- found where atoms do not have free rotation around a bond
- cyclic or unsaturated molecules
trans vs cis isomers
- trans isomers have higher mp/bp than cis ones as thry can pack together more tightly and therefore have stronger intermolecular bonds
- cis isomers will undergo dehydration regularly, trans ones wont as their functional groups are further apart
optical isomers
- found when looking at non-superimposable mirror images of molecules
- will occur when a central carbon atom is chiral (has four different groups attached)
isomers of chiral molecules
known as optical isomers or enantiomers
how are enantiomers different from each other?
they rotate polarised light in opposite directions
what is a racemic mixture?
when two entaniomers are present in equal amounts
why is chirality important in biological systems?
proteins are made from only one amino acid enantiomer
two types of fission
homolytic and heterolytic
homolytic fission
- occurs when each atom retains one electron from the sigma covalent bond and the bond breaks evenly
- results in the formation of two neutral radicals
- normally occurs when non-polar covalent bonds are broken
heterolytic fission
- occurs when one atom retains both electrons from the sigma covalent bond and the bond breaks unevenly
- results in the formation of two oppositely charged ions
- normally occurs when polar covalent bonds are broken
what is an electrophile?
a species attracted to atoms with a full or partial negative charge, they are electron deficient so can accept an electron pair to form a covalent bond
which types of molecules take part in electrophilic addition?
- alkenes (to form alkanes, mono/dihaloalkanes and alcohols)
Markovnikov’s rule?
when a hydrogen halide or water is added to an unsymmetrical alkene, the hydrogen atom attaches to the carbon atoms with the most hydrogen atoms
reactions alkanes can undergo
- reforming to form benzene
- cracking to form alkenes
- radical substitution to form haloalkanes
what is a reforming reaction?
changing the structure of the molecule
what is a cracking reaction?
splitting a molecule into a smaller molecule
reactions haloalkanes can undergo
- elimination to form alkenes
- nucleophilic substitution to form alcohols, ethers and nitriles
what is an elimination reaction?
- when several atoms are removed from a molecule and are not replaced
- requires a strong base
what is a nucleophile?
- species which are attracted to atoms with a full or partial positive charge
- they’re electron rich and so can donate an electron to form a covalent bond
what is nucleophilic substitution?
swapping a part of a molecule for something else, in this case the “something else” is a nucleophile
reactions involving nucleophilic substitution
- monohaloalkanes becoming ethers: alkali metals are added to form an alkoxide ion, which acts as a nucleophile
- monohaloalkanes becoming nitriles: requires ethanolic cyanide, the CN- acts as a nucleophile
reactions nitriles can undergo
- reduction to form amines
- hydrolysis to form carboxylic acids
lithium aluminium hydride
- strong reducing agent
- can reduce carboxylic acids, aldehydes and ketones back into alcohols
properties of primary amines
higher mp/bp than secondary and tertiary as they have a greater degree of hydrogen bonding
nitriles to carboxylic acids
use a dilute acid to hydrolyse the nitrile
what is a carbocation?
carbon atoms which have a positive charge, usually caused by the breaking of a double bond.
- carbocation intermediates are highly unstable species which react with nucleophiles
5 needed reaction mechanisms
water + alkene = alcohol
hydrogen halide + alkene = monohalo alkane
halogen + alkene = dihaloalkane
Sn1 for monohaloalkanes
Sn2 for monohaloalkanes
what type of molecules undergo nucleophilic substitution?
haloalkanes - because the halogen is a good leaving group
- can be either Sn1 or Sn2
Sn1 reactions
- one species in rate determining step
- minimum of two steps overall
- trigonal planar shaped carbocation intermediate
- racemic mixture formed because the nucleophile can attack the carbon from either side
- favoured by large alkyl groups
Sn2 reactions
- two species in rate determining step
- occurs in a single step via a single, five-centred, trigonal bipyramidal transition state
- preferred over Sn1 for smaller groups
ways carboxylic acids can be prepared
- oxidising primary alcohols
- oxidising aldehydes
- hydrolysing nitriles, esters or amides
reactions carboxylic acids can undergo
- formation of salts by reactions with metals or bases
- condensation reactions with alcohols to form esters, in the presence of concentrated sulphuric or phosphoric acid
- reactions with amines to form alkyl ammonium salts which form amides when heated
- reduction with LiAlH to form primary alcohols
what can alcohols be prepared from?
- haloalkanes by substitution
- alkenes by acid-catalysed hydration
- aldehydes and ketones by reduction using a reducing agent (e.g LiAlH)
reactions alcohols undergo
- dehydration to form alkenes
- oxidation of primary alcohols to form aldehydes, then carboxylic acids
- oxidation of secondary alcohols to form ketones
- formation of alcoholic alkoxides by reaction with some reaction mechanisms (Na, K), which can then be reacted with monohaloalkanes to form ethers
- formation of ester by reaction with carboxylic acid
- formation of ester by reaction with acid chlorides
why are acid chlorides preferred to carboxylic acids to react with alcohols to form esters
- faster
- no catalyst required
what are drugs?
substances that alter the biochemical processes in the body
where are drugs that have beneficial effects used?
in medicines
what do medicines generally contain?
the drug + other ingredients such as fillers to add bulk, or sweeteners to improve the taste
how do drugs usually work?
by binding to specific protein molecules which can either be found on the surface of cells (receptors) or can be specific enzyme molecules within a cell
what do agonists do?
mimic the natural compound and bind to the receptor molecules to produce a similar response to the natural active compound
what do antagonists do?
prevent the natural compound from binding tot he receptor, blocking the natural response from occuring
what are drugs that act on enzymes called and how do they work?
inhibitors
- bind to the active site of the enzyme and block the reaction which is normally catalysed there
what kinds of interactions are involved in the binding of drugs to receptors/active sites?
- ionic bonds
- van der waals forces
how can the structural fragment involved in the drug action be identified?
by comparing the structures of drugs that have similar effects on the body
