Mass Spec Flashcards
What are the essentials of Mass Spectrometry?
- Molecules converted into ions
- Ions isolated in a vacuum to prevent ion-molecule interactions
- Ions separated based on their mass/charge ratios (m/z)
Is electron ionisation (EI) at atmospheric pressure or under vacuum?
Vacuum
Is electrospray ionisation (ESI) at atmospheric pressure or under vacuum?
Atmospheric pressure
Is Matrix assisted laser desorption ionisation (MALDI) under atmospheric pressure or vacuum?
Atmospheric pressure
Define Electron Ionisation (EI)
Gas phase molecules are converted to ions by bombardment with a beam of electrons of energy (16-70 eV)
What are the 2 steps of Electron Ionisation (EI)?
1) An electron passing close to the molecule extracts an electron and the molecule is converted to a cation with an unpaired electron (+.)
2) The molecule gains addition energy from the electron beam
What is an OE ion?
an odd-electron ion
What is the base peak?
The peak that is scaled to 100%
How do you locate the Molecular Ion (M+.) peak in Electron Ionsation?
It is the highest m/z value ignoring isotope peaks (small bits that have e.g. 13C)
What need to happen for ionisation to occur in Electron Ionisation (EI)?
When the energy supplied equals the ionisation energy (5-16 eV)
What happens for the Molecular ion (M+.) to form in Electron Ionisation (EI)?
When ionising energy populates many vibrational states
What causes fragmentation?
During ionisation transfer of energy in excess of the enthalpy of the highest vibrational state leads to bond rupture producing fragment ions.
What is the relationship between high and low eV values in Electron Ionisation (EI)?
Low values (16 eV) typically favours the molecular ion where as higher values (70 eV) favours fragment ions.
What is the adduct ion?
The protonated or sodiated molecule
What is the molecular ion?
The ionised molecule
What is the difference between OE and EE?
OE - has lone electron (Odd electron)
EE -has no lone electrons (Even Electron)
What are the ‘soft’ ionisation techniques?
ESI
MALDI
CI
APCI
What are the benefits of ‘soft’ ionisation?
Produces ions from molecules not suitable for Electron Ionisation (EI) (involatile/unstable)
Can analyse molecules with weak bonds
Can analyse involatile moelcules
What is the downfall of ‘soft’ ionisation?
Little fragmentaion or prominent adduct ions so little information about structue
What does CI stand for?
Chemical ionisation
What does APCI stand for?
Atmospheric pressure chemical ionisation
How does Chemical Ionisation work?
Employs a reagent gas (CH4, NH3, 2-Methylpropane)
Reagent gas is ionised within the chemical ionisation source
Creates an ionising agent e.g. CH5
This reacts with analyte molecule
How can Chemical Ionisation (CI) help when Electron Ionisation is indistinct?
It allows confirmation of the mass as it does not produce fragments
What is the requirement for proton transfer to occur?
If the Proton Affinity (PA) of the analyte is higher than the Proton Affinity (PA) of the reagent gas
What effect does increasing energy transfer during ionisation have on the spectra in Chemical Ionisation?
Increases fragmentation and decreases relative intensity of the molecular adduct ion
What are the steps of Atmospheric Pressure Chemical Ionisation (APCI)?
Analyte introduced into the source in solution at atmospheric pressure
Warm N2 gas converts solvent to mist
Heater vaporises the solvent and analyte
Corona discharge needle held at a potential of 5kV emits electrons, ionising N2 gas
Reagent ions (from secondary reactions) transfer proton to analytes with higher Proton Affinity
What is the ionising species in APCI?
Hydronium ion H3O
What is the reaction forming the hydronium ion in APCI?
H2O+. + H2O —> H3O+ + .OH
Where will the majority of the protonations in a molecule occur?
At atom with the highest proton affinity
Define isotopologue
A molecule that differs only in the isotopic composition of one or more of their atoms (diff in mass)
(Isotopic homologue)
What is the nominal mass?
Value calculated from the combination most abundant isotope of each element in the compound (lowest mass isotopologue) rounded DOWN to the nearest integer
How do you find the resolution?
R = (m/z) / (change in m/z)
What is unit mass resolution?
The ability to distinguish ions separated by 1 m/z
How can you distinguish between 2 identical formulae?
Find the exact mass (high resolution)
What is Mass Defect?
The difference between the nominal mass and the monoisotopic (exact) mass of an atom, molecule or ion
What is an isobar?
Atomic or molecular species with the same nominal mass bit a different exact mass
What are the possible isotopic combinations of Cl2 and what is their ratio?
IN THIS ORDER:
35Cl 35Cl , 35Cl 37Cl, 37Cl 37Cl
9:6:1
What are the isotopes of Bromine?
79 and 81
If the natural abundance of 13C is 1.1% what would the probability of a C13 in a molecule of butane?
4.4%
(1.1% x no. of C atoms)
What is the probability of 2 C13 atoms in a small molecule?
trick question, it is negligible in small molecules
What is the error range for ion intensity?
+10% and -10%
Where can you find isotope abundances and what must you do to use them?
In the data book and you must re scale them so that the most abundant is 100%
What is the equation for degrees of unsaturation?
du (r+db) = x- 0.5y + 0.5z +1
du = Degrees of unsaturation
r = rings
db = double bonds
x = tetravalent atoms
y = monovalent atoms
z = trivalent atoms
What is the Nitrogen rule?
Most organic compounds contain only: C H O N S P Si or Hal
and with the exception of N, even mass elements have even valence, odd mass elements have odd valence and combine to give even mass compounds, the Molecular Ion peak will be even
However Nitrogen has an even mass but odd valence
Compounds with odd numbers of Nitrogen give odd molecular ion peaks
Compounds with even numbers of Nitrogen give even molecular ion peaks
What is the order of priority of ionisation?
Non bonding orbital > pi orbital > sigma orbital
- lowest ionisation energy preferred
What is stevensons rule?
When cleavage of a single bond generates more than one ion and radical pair
*the fragment with higher ionisation energy retains the unpaired electron, the ion is generated from the other fragment**
What is the alkane ion series?
When part of a molecule has a long hydrocarbon chain, a series of even electron ions differing by 14 units can be seen
What is the exception to the alkane ion series?
Aromatics
What is the order of priority of ion abundance for cation stability?
tertiary > secondary > primary
What effect does electron sharing have on ion abundance?
the more stable, the more abundant
What kind of ions lose neutral loses?
Even electron ions,
Odd electron ions lose both neutral and radicals
What trend makes charge migration more favourable (R+ ion forms) (alkyl)? and what is the order of the trend?
electronegativity
Halogen > O,S,»_space; N, C
Do ethers prefer inductive cleavage or alpha cleavage?
Inductive but oxygen supports both
What does alpha cleavage favour?
loss of largest alkyl radical
What does inductive cleavage favour?
Formation of the most stable cation
What forms a distonic radical?
sigma cleavage of one bond in a ring structure
What routes can cyclohexene rings fragment with (retro diels alder reaction)
Alpha and Inductive Cleavage (one may be favoured depending on stability of charge)
What is a rearrangment with displacement?
Formation of a bond between the radical site and a distant atom leads to cyclisation with displacement of a radical, which gives charge retention
What factors can compromise interpretation of mass spectra?
Multiple bond migration during fragmentation
Too simple (soft)
Too complex (multiple fragments)
Co- elution
How can we locate double bonds in a structure?
Isotope method - Reduce double Bonds with D2 (wilkinsons catalyst) -2D on double bond - 3D on single bonds
Chemical labelling method - React double bond with I2 (iodide)/dimethyl disulphide to form 1,2 dithiane
ionisation forms radical cation on Sulphur
- only good for 1 double bond
What do Q1 Q2 and Q3 do in tandem spectrometry?
Q1 + Q3 - perform mass analysis
Q2 - collison cell - acts as ion guide
What can cause an odd mass other than Nitrogen?
A very large molecule (over 1000 m/z)
Where to find steps of interpretation?
Last page in handout lol
