[Year 2] PL Flashcards
What is the use of mass spectrometry?
To find the relative molecular mass (Mr) of a compound.
What is on the x-axis of a mass spectroscopy graph?
m/z
mass to charge ratio
(if the charge is +1 then m/z is the mass of the fragment.)
What does the last significant peak of a mass spectrometry show?
The molecular ion peak, M+.
the same as the relative molecular mass of the molecule
What are the smaller peaks towards the very end of a mass spectrometry known as?
M+1 peak, as a result of the isotope C-13.
could also be M+2, if it has a stable isotope of Cl-37, instead of 35.
What is fragmentation?
When molecules break up when they are bombarded with high energy electrons.
Which fragments are able to be detected?
Charged fragments.
(the radical cannot be detec
What does the number of major peaks in a mass spectra show?
The number of charged fragments.
What can fragment patterns in mass spectrometry show?
To identify molecules with the same constiuent atoms (same Mr).
This is because the fragment masses will be different.
How might you identify a molecules after a mass spectrometry?
Compare against the library of known spectra.
Why might a fragment not show up?
- If the fragment is uncharged (a radical).
- If fragments are not stable.
How might you find out about a fragment that may no show up on a mass spectrometry chart?
Find the difference between peaks.
What ration between peaks might you see if chlorine is involved in your mass spectrometry?
3:1
M+ : M+2
Cl-35 : Cl-37
What is the use of high res mass spectrometry
To identify different molecules with the same molecular mass rounder to the nearest whole number.
What is the use of NMR spectroscopy?
Used to determine the structure of a molecule.
What are the two types of NMR?
¹³C NMR
(High res) ¹H NMR
What must be true about an isotpoe for NMR to work?
An odd number of nucleons.
and thus a nuclear spin, creating a weak mag field.
What is the difference between the two NMRs?
¹³C NMR: tells us information on how carbon atoms are arranged (number of carbon environments).
(High res) ¹H NMR: tells us information on how hydrogen atoms are arranged (number of hydrogen environments) .
Why does a CH₂ environment in pentane have a different peak from another CH₂?
The central CH₂ is shielded more than the outer middle CH₂ environments.
What chemical is used as a reference when doing NMR?
TMS (Tetramethylsilane)
What is the chemical shift when doing NMR?
The difference between the TMS peak and the peaks produced by a substance.
Symbol: δ
What does a δ=0 in NMR mean?
This is the TMS peak.
How can we predict functional groups based on δ? What are the limitations
- Look at datasheet.
- Some overlap.
What does the number above a ¹H NMR tell us?
The ratio of the area under the peaks.
- the relative number of hydrogens in each environment.
What does the splitting pattern tell us in ¹H NMR
The number of H atoms on the adjacent carbon + 1
n+1 rule
What do the following mean:
- a singlet peak?
- a doublet peak?
- a triplet peak?
- a quartet peak?
- a singlet peak = 0 hydrogens on a neighbouring carbon.
- a doublet peak = 1 hydrogens on a neighbouring carbon.
- a triplet peak = 2 hydrogens on a neighbouring carbon.
- a quartet peak = 3 hydrogens on a neighbouring carbon.
What are optical isomers?
- A form of stereoisomer
- They have the same structural formula but a different arrangement of atoms in space.
- They are non-superimposable and have chiral carbons.
How can you show a centre is chiral?
- Identify the chiral centre
- Draw both enantiomers as a mirror image of each other.
How do we detect optical isomers?
Plane polarised light.
- optical isomers will rotate plane polarised light
- one enantiomer will rotate it clockwise whilst the other will rotate it anticlockwise
What is the same about aldehydes and ketones?
They both have a C=O (carbonyl) group.
How do aldehydes and ketones differ?
- Aldehydes have their carbonyl group on the end.
- Hetones have their carbonyl group on the inner carbon.
How do you name aldehydes?
- al
e. g. propanal, ethanal
How do you name ketones?
- x-one
e. g. propanone, pentan-2-one
What is a phenol?
A benzene ring with a hydroxyl group attached to it.
How do you number phenols?
Carbon with -OH is always carbon 1.
What are diols?
Molecules with two alcohol groups attached to them.
What are acid anhydrides?
- Molecules made from two carboxylic acids.
- Have then general formula R-COOCOR’
How are acid anhydrides named?
- Carboxylic acid name
- take of ‘acid’
- add anhydride.
- if the carboxylic acid chains are different then name in alphabetical order.
(e.g. ethanoic anhydride, ethanoic propanoic anhydride)
List all of the functional groups that you need to know.
20 of them
Acid anhydrides Acyl chlorides Alcohols (and Diols) Aldehydes Alkane Alkene Alkyne Amides Amines Arenes (also known as phenyls) Azo Carboxylic acids (and dicarboxylic acids) Diazonium salts Esters Ethers Haloalkanes Ketones Nitrile Phenols Sulfonic acids
What do these functional groups look like…
Acid anhydrides Acyl chlorides Alcohols (and Diols) Aldehydes Alkane Alkene Alkyne Amides Amines Arenes (also known as phenyls) Azo Carboxylic acids (and dicarboxylic acids) Diazonium salts Esters Ethers Ketones Nitrile Phenols
(draw on paper)
Acid anhydrides: R-COOCOR’
Acyl chlorides: R-COCl
Alcohols (and Diols): R-OH
Aldehydes: R-COH
Alkane: C-C
Alkene: C=C
Alkyne: C≡C
Amides: R-CONH₂
Amines: R-NH₂ / R-NHR’
Arenes (also known as phenyls): a benzene ring
Azo: R-N=N-R’
Carboxylic acids (and dicarboxylic acids): R-COOH
Diazonium salts: R-N⁺≡N X⁻
Esters: R-COO-R’
Ethers: R-O-R’
Ketones: R-COR’
Nitrile: R-C≡N
Phenols: Benzene-OH
How do you name the following functional groups…
Acid anhydrides Acyl chlorides Alcohols (and Diols) Aldehydes Alkane Alkene Amides Amines Arenes (also known as phenyls) Carboxylic acids (and dicarboxylic acids) Esters Ethers Haloalkanes Ketones
Acid anhydrides: -oic anhydride
Acyl chlorides: -oyl chloride
Alcohols (and Diols): hydorxy- / -ol (dihydroxy- / -diol)
Aldehydes: -al
Alkane: -ane
Alkene: -ene
Amides: -amide
Amines: amino- / -amine
Arenes (also known as phenyls): phenyl- / -benzene
Carboxylic acids (and dicarboxylic acids): carboxy- / -oic acid
Esters: alkyl-…-oate
Ethers: -oxy-
Haloalkanes: floro- / chloro- / bromo- / iodo-
Ketones: -one
How can you test for amines?
Why does this work?
Turn red litmus paper blue
- as they are bases.
React with acyl chloride to get white misty fumes
- as acidic HCl is produced.
Why do amines act as bases?
They have a lone pair of elections that allows them to accept a proton.
and bases are proton acceptors.
How do amines bond with protons?
Through dative covalent bonds from the amine to the proton.
[R-NH₂→H]⁺
What is the difference between primary and secondary amides?
Primary amides have the amide group on the end…
R-CONH₂
Whilst secondary amides have the amide group in the molecule…
R-CONHR’
How are secondary amides named?
Prefix: N-alkyl-…-amide
where ‘alkyl’ is the group attached to the nitrogen.#
(e.g. N-methylpropanamide)
How are primary amides hydrolysed?
- by acids to produce carboxylic acids and an ammonium salt
- by dilute alkalis to produce a salt of the carboxylic acids and ammonium gas
(as in acidic conditions H is added and in alkali conditions, H is lost).
How are secondary amides hydrolysed?
- by acids to produce carboxylic acids and a salt of the primary amine.
- by dilute alkalis to produce a salt of the carboxylic acids and an amine.
Why are carboxylic acids weak acids?
They dissociate partially to form a H⁺ ion and a carboxylate ion.
(in a reversible reaction the equilibria lies to the left as it dissociates poorly)
What do carboxylic acids react with?
Metals:
- Reacts with metals to give a salt and hydrogen gas.
Bases:
- Reacts with sodium hydroxide to give a salt and water
Carbonates:
- Reacts with sodium carbonate to give a salt, water, and carbon dioxide
What happens when carboxylic acids/acid anhydride/acyl chloride reacts with alcohols?
Esterification
- esters are made
What are the conditions and products for esterification?
With carboxylic acids and alcohols:
- Sulfuric acid catalyst.
- products = ester +water
With acid anhydride:
- no catalyst
- product = ester + carboxylic acid.
How are esters named?
alcohols group first
carboxylic acids last
as…
alky- …-oate
e.g. ethyl ethanoate
Numbering:
1 is C=O carbon and O-C carbon
count going outwards from the ester.
e.g. ethyl 2-methylpropanoate
How do we hydrolyse esters?
and conditions
Acid hydrolysis:
- using sulfric/hydrochloric acids under reflux
- producing a carboxylic acid and alcohol.
Base hydrolysis:
- using sodium hydroxide under reflux
- producing a carboxylate ion and alcohol.
What type of reaction is the esterification involving acyl chlorides and alcohols?
A nucleophilic substitution.
What type of reaction is the production of secondary amides from a primary amine involving acyl chlorides?
A nucleophilic substitution.
What are the different types of polymerisation reactions?
Addition polymers:
- between alkene monomers
Condensation polymers:
- between diamines and dicarboxylic acids (polyamides) OR diols and carboxylic acids (polyesters)
- water is a byproduct.
How are nylons named?
First number is number of carbons in diamine.
Second number is number of carbons in dicarboxylic acid.
(e.g. Nylon 6,6)
If there is one number (e.g. Nylon 6) then the monomer has an amine AND carbocyclic acid on each end.
Nuber is number of carbons
What happens when you hydrolise a condensation polymer?
You get the original monomers.
Why are addition polymers unreactive?
As they have no polar links to aid in reaction.
What are the components of an amino acid?
- an amino group (-NH₂).
- a carboxyl group (-COOH).
- an organic sidechain (R group) (apart from glycine).
What does amphoteric mean?
The molecule has acidic and basic properties.
What is a zwitterion?
A molecule with both positive and negative ions.
What happens if an amino acid is at a pH lower than the isoelectric point?
It will accept H⁺.
What happens if an amino acid is at a pH higher than the isoelectric point?
It will lose H⁺.
What happens if an amino acid is at a pH at its isoelectric point?
It will exist as a zwitterion.
How can you separate mixtures of and identify amino acids?
TLC
How do you carry out TLC?
- Select a suitable mobile phase (a solvent that can dissolve the mixture)
- Draw a pencil line on stationary phase (silica or alumina)
- Place stationary phase in the mobile phase in a beaker, so the pencil line is above the solvent level.
- Add a lid to prevent evaporation.
- Leave until the solvent front has reached near the top of the plate and mark it.
- Allow the stationary phase to dry.
- If components of the mixture are colourless, you can use an iodine/ninhydrin solution OR a fluorescent dye(and UV).
- you should see separate spots which you can calculate an Rf value for.
- the Rf value can then be compared to a data book.
What is the primary structure of a protein?
- individual sequence of amino acids.
- a polypeptide chain.
What is the secondary structure of a protein?
- Hydrogen bonds between polypeptides that form α-helices and β-pleated sheets.
What is the tertiary structure of a protein?
- Long protein chain coils further with more H-bonds.
- also has disulfide bonds, id-id bonds and ionic bonds.
What is an id-id bond?
Instantaneous dipole-induced dipole.
What components make up DNA/RNA?
- a phosphate
- a sugar
- a base
How are nucleotides joined?
In a condensation reaction.
How are two strands of DNA joined?
Hydrogen bonds
3 between C and G
2 between A and T
Can only be like this because of the lone pairs on the NH and O
How do drugs work?
The pharmacophore of the drug binds to a complementary binding site of the cell receptors on a target cell.
What criteria do pharmacophores need to meet?
- right shape and size.
- right orientation (E/Z isomer).
- able to form temperate bonds such as (ionic interactions, H-bonds and dipole-dipole interactions.)
What happens to an enzyme at low or high pHs or temperatures?
- Hydrogen bonds, disulfide bridges and id-id interactions will break.
- This will alter the tertiary structure of the enzyme.
- Changing the shape of the active site
- Leading to a slower rate of reaction.
(at low temperatures there is also less kinetic energy)
Describe the graph of rate against substrate concentration for an enzyme catalysed reaction
- Initially first order with respect to the substrate contraction.
- Then plateaus and becomes zero order with respect to substrate concentration
- as all the active sites of the enzymes are full.
