Copyright by Nuria Romero & Ona Illa INTRODUCTION TO MS

STRUCTURAL DETERMINATION
Elucidation of the structure of chemical compounds
naturally occuring chemical compound
STRUCTURE ???
reactants product

Elemental Analysis
UV-vis Electronic Absorption Spectroscopy (UV-vis)
light-matter
Infrared Absorption Spectroscopy (IR) interaction
Nuclear Magnetic Resonance Spectroscopy (NMR) (Espectroscòpia)

Mass Spectrometry (MS)

Electron Paramagnetic Resonance Spectroscopy (EPR)
X-ray Diffraction (XRD)
….
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Copyright by Nuria Romero & Ona Illa INTRODUCTION TO MS

STRUCTURAL DETERMINATION

Part I. Introduction to MS (aprox. 2 weeks)

Part II. Review of UV-vis, IR and NMR spectroscopies

(aprox. 1.5 weeks)

Part III. Application of MS, UV-vis, IR and NMR to the

elucidation of chemical structures

a) Organic compounds

b) Inorganic compounds

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Copyright by Nuria Romero & Ona Illa INTRODUCTION TO MS

BASIC CONCEPTS

fragmentation
rearrangement
ionization other reactions
(m/z=105)

ion detection (m/z=120) (m/z=77)

RELATIVE INTENSITY

m/z
3

Copyright by Nuria Romero & Ona Illa INTRODUCTION TO MS

THE EXPERIMENTAL METHOD

Block diagram of a mass spectrometer

sample

gas-phase ions m/z

inlet neutral
ionizer (accelerated) mass separation
molecules detection
analyzer

vacuum system

High vacuum ~ 10-6 – 10-8 Torr

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Copyright by Nuria Romero & Ona Illa INTRODUCTION TO MS

THE EXPERIMENTAL METHOD

Block diagram of a mass spectrometer

sample

gas-phase ions m/z

neutral
ionizer (accelerated) mass separation
inlet molecules analyzer
detection

vacuum system

High vacuum ~ 10-6 – 10-8 Torr

Copyright by Nuria Romero & Ona Illa INTRODUCTION TO MS

THE EXPERIMENTAL METHOD: IONIZERS

Electron ionization (EI): typically, 70 eV EI

Hot W or Re

cathode anode

EI: gas-phase molecules

generates cations (ABC + e- → ABC.+ + 2 e-)
leads to extensive fragmentation (E of an average bond (3 eV);
ABC.+ → AB+ + C. ; …) 6
Copyright by Nuria Romero & Ona Illa INTRODUCTION TO MS

THE EXPERIMENTAL METHOD: IONIZERS

Chemical Ionization (CI):

Soft Ionization Technique

Useful technique when no molecular ion is observed in EI mass spectrum

Involves ionization of a gas molecule (usually CH4) by an electron beam. The resulting
ions end up ionizing the analyte (typically by protonation processes).

Ionizing gas usually present at concentrations 103-104 times the analyte molecules

CH4 produces ions from analyte molecule by H+ or H- transfer

Other gases used are NH3, iso-butane (methylpropane)

Produces [M+H]+ ions called quasimolecular ions (diff from M.+)

Copyright by Nuria Romero & Ona Illa INTRODUCTION TO MS

THE EXPERIMENTAL METHOD: IONIZERS Chemical Ionization

A) EI of reagent gas to form ions:

B) Reaction of reagent gas ions to form adducts:

Copyright by Nuria Romero & Ona Illa INTRODUCTION TO MS

THE EXPERIMENTAL METHOD: IONIZERS Chemical Ionization

C) Reaction of reagent gas ions with analyte molecules:

Proton transfer [M+1]+

QUASIMOLECULAR ION

Also [M+29]+
(C2H5+)

Hydride transfer [M-1]+

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Copyright by Nuria Romero & Ona Illa INTRODUCTION TO MS

THE EXPERIMENTAL METHOD: IONIZERS EI vs CI

NO2

M.+

EI

[M+1 ]+

CI

Chemically produced ion : not great excess of E, so less fragmentation 10

Copyright by Nuria Romero & Ona Illa INTRODUCTION TO MS

THE EXPERIMENTAL METHOD: IONIZERS Other soft ionization techniques

FAB MALDI ESI
Fast Atom Bombardment Matrix Assisted Laser Electrospray
Xe or Ar atoms Desorption Ionization
glycerol fast particle
analyte@matrix beam
matrix
ions analyte
ions

glycerol
nicotinic acid
urea
Direct ionization from the Direct ionization from the
condensed phase condensed phase
(desorption+ionization) Direct ionization from the (desorption+ionization)

Minor structural fragmentation condensed phase Minor structural fragmentation

(desorption+ionization) but multiple ionization
Major peaks: [M+H]+, [M+Na]+ Minor structural fragmentation Major peaks: [M+],[M+H]+, [M+Na]+ plus
For MW up to 10000 Da multiply charged species
Major peaks: [M+],[M+H]+, [M+Na]+

For MW up to 200000 Da For MW up to 100000 Da 11

Copyright by Nuria Romero & Ona Illa INTRODUCTION TO MS

THE EXPERIMENTAL METHOD: ANALYZERS

After ions are formed in the source region they are accelerated into the mass analyzer by
an electric field.

The mass analyzer separates these ions according to their m/z value.

Selection of a mass analyzer depends on: resolution, mass range, scan rate and detection
limits required

Resolution in MS:

https://www.youtube.com/watch?v=qUhi98o1qUU

Low Resolution (LRMS) High Resolution (HRMS)

R < 2000 R > 2000

Unit Mass Exact Mass

4 decimals
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Copyright by Nuria Romero & Ona Illa INTRODUCTION TO MS

RESOLUTION IN MASS SPECTROMETRY- EXERCISE

Consider the following sets of molecules with very close molecular mass (MM):

Set 1
CH3COCH3 MM= 58.08
CH3COOH MM = 60.05

Set 2
CO MM = 27.994915
N2 MM = 28.006148

Set 3
C18H36N2 MM = 280.28785
C18H36CO MM = 280.27662

1) Calculate the minimum resolution needed (R) for observing separate peaks in each case (please
use the doublet method and consider that the valley has 10% intensity of the peak maxima).

2) Which case do you think would require a lower resolution mass spectrometer? And which does a
higher one?

3) Compare the mass difference between set 2 and 3 and the required resolution. Which conclusion
can you extract? 13