Structure Determination From Molecule to Materials by Mass Spectrometry

B S KITAWAT Research Scholar School of Chemical Sciences Date: April 01,2011

Basic principles Accurate method: Determining molecular mass & elemental composition In this tech : Molecules are bombarded with a beam of energetic e-

The molecules are ionized & broken up into fragments, some of which are +ve The masses of the fragments & their relative abundance reveal information about the structure of

How do achieve this? Persuade the molecule to enter the vapor phase (can be difficult) Produce ions from the molecules that enter the gas phase Separate the ions according to their mass-to-charge ratios (m/z) Measure and record these ions

Electron Impact
H H-C:H + H
H H-C H H

H H-C H + 2e H Radical cation

H H-C + + H Radical Cation H
Molecular ion base peak

CH4

Bond-breaking

H . + + H H-C H

fragments 1

m/z

15 16

Only cations are carried to detector

Typical LC-MS

The Mass Spectrometer

Mass Spectrometer

Ionization Methods
Electron ionization (EI)=50-70eV beam, volatile solvent, low MW compounds analyzed Chemical ionization (CI)= Ionized gas like CH4& NH3 Desorption ionization tech.(SIMS,FAB & MALDI) for high MW up to 20,000 Da SIMS= Sec. ion mass spe. (1-10keV, Ar+ & Cs+ beam) FAB= Fast Atom bombardment (Ar, Xe beam) MALDI=Matrix assisted laser desorption ionization (Used nitrogen laser emits at 337nm) Electrospray Ionization (ESI)= Sample contain sol. sprayed into heated chamber, high MW biomolecules like lysozyme 14,306 Da can analyzed

Mass Analyzer: Ions are separated according to m/z

Magnetic Sector Mass Analyzers Double Focusing Mass Analyzers Quadrupole Mass Analyzers Time of Flight (TOF) Mass Analyzers

How we get a mass peak ?

In EI-MS, a molecule is bombarded by high-energy e- in the ionization chamber The collision between sample molecules & the e- initially results in the sample molecule losing one e- to form a radical cation The molecule also absorbs a considerable amount of extra energy during its collision with the incident e-

 This extra energy places the molecular ion in a highly excited vibrational state The vibrationally excited molecular ion may be unstable, & it may lose some of its extra energy by breaking apart into fragments If the lifetime of the molecular ion is >105 sec, a peak corresponding to the molecular ion will appear in the mass spectrum

Structural Analysis & Fragmentation Patterns Stevensons Rule: States that the most probable fragmentation is the one that leaves the positive charge on the fragment with the lowest ionization energy

Figure: Mass spectra expected for various combinations of bromine & chlorine

Initial Ionization Event: The e- most likely to be ejected

during the ionization event are the ones that are in the highest potential energy molecular orbitals, that is, the e- held least tightly by the molecule

Example: It is much easier to eject an e- from a orbital in comparison to a orbital

Retro Diels-Alder Cleavage

Unsaturated six-membered rings can undergo a retro Diels Alder fragmentation to produce the radical cation of a diene & a neutral alkene

McLafferty Rearrangement
A H- atom on a carbon 3 atom away from the radical cation of an alkene, arene, carbonyl, or imine (a so-called -hydrogen) is transferred to the charge site via a sixmembered T.S., with concurrent cleavage of the bond between the & positions This forms a new radical cation & an alkene with a bond between what were the original and carbons

Other Cleavage Types Alkanes

Cleavage of the C1-C2 bond results in the loss of a methyl radical & the formation of the propyl carbocation (m/z = 43). Cleavage of the C2/C3 bond results in the loss of a ethyl radical and the formation of the ethyl carbocation (m/z = 29)

Alkenes
trans-2-hexene, MW = 84 Methyllyl cation, m/z = 55 Ethyl radical, m/z = 29

29

Alkynes
1-pentyne, MW = 68 Loss of ethyl radical(m/z =29) to form propargylic cation(m/z =53), m/z = 39 due to loss of [C2H5]+

Aromatic Hydrocarbons
Benzene Toluene

m- Xylene

Cumene

Aldehydes
Mass Spectrum of Valeraldehyde m/z = 86.13 Loss of 1H m/z = 85 Due to CHO+ m/z = 29 Propyl cation m/z = 43 due to Beta cleavage m/z =57, [CH3CH2CH2CH2]+

Ketones
2- butanone (MW =72) CH3CH2CO+ m/z = 57 CH3CO+ m/z = 43

Alcohols

CH2OH+ m/z = 31 Loss of OH+ m/z = 70 CH3CH2CH+ m/z = 42

Nitrogen rule (Amides)

If a compound contains an even number of N atoms (or no N atoms), its molecular ion will appear at an even mass number If, an odd number of N atoms, then its molecular ion will appear at an odd mass value In the case of benzamide the molecular ion appears at m/z 121, indicating an odd number of N atoms in the structure
[CONH2]+ m/z = 44 [C6H5]+ m/z = 77 Loss of NH2 gives m/z = 105