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Structure Determination From

Molecule to Materials by MassSpectrometry

B S KITAWATResearch Scholar

School of Chemical Sciences

Date: April 01,2011

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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

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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

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H-C:H

H

H

+ e H-C

H

H

H + 2e CH4

Radical cation

H-C

H

H

HH-C

H

H+ + H

Bond-breaking CationRadical

Only cations are carried to detector

Electron Impact

H-C

H

H

H++

1 15 16

Molecular ion

fragments

base peak

m/z

.

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Typical LC-MS

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The Mass Spectrometer

Mass Spectrometer

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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

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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 aradical cation

The molecule also absorbs a considerable amount of extra

energy during its collision with the incident e-

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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

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tructura na ys s ragmentat on atternsStevensons 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 expectedfor various

combinations

of bromine &

chlorine

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

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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

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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 six-membered 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

Oth Cl T

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Other Cleavage Types

Alkanes

Cleavage of the C1-C2

bond results in the lossof 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 theformation of the ethyl

carbocation (m/z = 29)

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Alkenestrans-2-hexene, MW = 84

Methyllyl cation, m/z = 55Ethyl radical, m/z = 29

29

Alk

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Alkynes1-pentyne, MW = 68

Loss of ethyl radical(m/z =29) to form propargyliccation(m/z =53), m/z = 39 due to loss of [C2H5]

+

A i H d b

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Aromatic Hydrocarbons

Benzene

Toluene

m- Xylene Cumene

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Aldehydes

Mass Spectrum ofValeraldehyde 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, [CH3CH

2CH

2CH

2]+

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Ketones

2- butanone (MW=72)

CH3CH2CO+ m/z = 57

CH3CO+ m/z = 43

Al h l

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Alcohols

CH2OH+ m/z = 31

Loss of OH+ m/z = 70

CH3CH2CH+ m/z = 42

Nit l (A id )

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Nitrogen rule (Amides) If a compound contains an even number ofN atoms (or no

N atoms), its molecular ion will appear at an even mass

number If, an odd number ofN atoms, then its molecular ion will

appear at an odd mass value

In the case of benzamide the molecular ion appears at m/z121, indicating an odd number ofN atoms in the structure

[CONH2]+ m/z = 44

[C6H5]+

m/z = 77Loss of NH2 gives m/z =

105

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