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Block Course Mass Spectrometry

Course No. 21 235

Target Group

The mass spectrometry tutorial addresses MSc and PhD students with an interest in the dark side of analytical chemistry. Others are welcome, if places are available. Since we intend to demonstrate the instruments available at the institute, the number of places is limited to 24. If less than 15 students register for the course, we may combine two courses and switch to a yearly basis. So, if possible, do not plan for the course in your last master semester.


Dates of Next Course

The course comprises ca. 32 hours as a block course. It is offered after the semester end in order to avoid collisions with other courses. Please find a detailed schedule in pdf format here.

Time: Monday, Mar 14th, 2011 to Monday, Mar 21st, 2011, 10:00 am (s.t.) - 11:30 am, 12:45 pm - 2:15 pm, and 2:45 pm - 4:15 pm.

Location: Chemistry Lecture Hall, Institute for Chemistry, Takustr. 3

The course will be announced. Please register as detailed in the announcement. For this course, you can get 3 LP which you can use for a the "Wahlbereich" contingent either in Organic Chemistry or Analytical Chemistry. As a requirement, you need to pass an oral exam with Prof. Dr. Christoph Schalley and/or Dr. Andreas Springer.


Course Materials, Literature, Excercises

Most of the presentations are electronically available and can be downloaded below. Just click on the headlines in the table of contents below (the login/password will be provided in the course).

Besides the literature references provided in the table of contents, two books are highly recommended. They are densely packed with information. Parallel to Jürgen Gross's book, an interesting collection of excercises is available online at http://www.ms-textbook.com/

Recommended MS Books

  • Jürgen Gross, Mass Spectrometry - A Textbook, 2nd ed., Springer-Verlag, Heidelberg 2011
  • Edmont de Hoffmann, Vincent Stroobant, Mass Spectrometry - Principles and Applications, Wiley, Chichester 2001
  • Manfred Hesse, Herbert Meier, Bernd Zeeh, Spektroskopische Methoden in der organischen Chemie, Thieme, Stuttgart 2002

You will find our excercises for download below as pdf files. They are chosen to reflect a couple of different types of chemistry which you may find in the research groups at the FU Berlin (e.g. dendrimers - Haag, peptides - Koksch, rotaxanes - Schalley, EI of small molecules - Reißig etc.). These excercises likely require some time and effort. We have therefore reserved some time in the schedule between the course and the discussion of the excercises. You benefit most, if you first try to solve the excercises on your own.

For calculation isotope patterns and exact masses, please refer to the internet-based calculators:

Gas-Phase thermochemical data (formation enthalpies, ionisation energies, proton affinities etc.) are available from the freely accessible NIST database (National Institute of Standards and Technology, Washington).


Topics to be Discussed

With this course we hope to provide the basis for a general understanding of the arsenal of mass spectrometric methods and the chemistry in the gas phase. Since gas phase chemistry is quite different from chemistry in solution, we will discuss some of the fundamental differences in order to broaden the view on chemistry. At the end you should be able to decide on your own, which method to apply to what chemical problem. You should have an idea of the scope and limitations of a mass spectrometric approach to structural questions and issues of reactivity. We also provide some insight into the technical/practical side by demonstrating the instruments available at the FU Berlin.

1. Intro

a) Basics: Why Mass Spectrometry?

b) Historical Remarks

c) Information Content of a Mass Spectrum: More than just the Molecular Mass?

d) General Scheme of a Mass Spectrometer

e) Vacuum Technology

f) Terms and Units


2. Ionization Methods (German version)

a) MS Classics: Electron Ionization (EI)

b) Closed-Shell Quasi-Molecular Ions: Chemical Ionization (CI)

c) On the Way to Softness I: Fast-Atom-Bombardment (FAB)

d) On the Way to Softness II: Matrix-Assisted Laser Desorption/Ionization (MALDI)

e) Finally There: Electrospray Ionization


3. Fragmentations in the EI Ion Source (Lehmann script)

a) Open- and Closed-Shell Ions

b) Preferred Decomposition Reactions of Cation Radicals

c) Thermal Decomposition in the Inlet System

d) Ion/Dipole Complexes

e) Distonic Ions


4. Analyzers and Detectors (German version)

a) Sector-Field Instruments

b) Linear Quadrupols and Quadrupole Ion Traps

c) Time-of-Flight Instruments

d) Fourier-Transform-Ion-Cyclotron-Resonance Mass Spectrometers


5. Ion Energetics in High Vacuum

a) Vertical and Adiabatic Ionization, Franck-Condon Principle

b) Stable - Metastable - Unstable

c) Quasi-Equilibrium Theory (QET)

d) The Temperature Dilemma: Non-Boltzmann Distribution of Inner Energies

e) How Non-Covalent Bonds Change Upon Transition into the Gas Phase

f) Environmental Effects: Absolute Acidity - Gas-Phase Proton Affinities

g) Environmental Effects: Nucleophilic Substitutions in the Gas Phase


6. Isotopes and Isotope Effects (German version)

a) Isotope Patterns and Elemental Composition

b) Kinetic Isotope Effects


7. Hyphenated Methods (German version)

a) Basics of Chromatography (German version)

b) GC-MS Coupling

c) LC-MS Coupling


8. Tandem Mass Spectrometry and Gas-Phase Chemistry

a) Mass Selection (updated: German version)

b) Metastable Ions and Collisional Activation: Rearrangements and Direct Bond Cleavages

c) Bimolecular Reactions: Examination of Reaction Mechanisms

Literature: R. Wesendrup, D. Schröder, H. Schwarz, Angew. Chem. 1994, 106, 1232; Angew. Chem. Int. Ed. 1994, 33, 1174

d) MS for the Analysis of Dendritic Effects

e) Peptide Sequencing (German version)

f) Radiative Processes: IRMPD and BIRD

g) Thermochemical Data: Ways out ot the Temperature Dilemma

Literature: a) P.B. Armentrout, Top. Curr. Chem. 2003, 225, 233; b) W. D. Price, P. D. Schnier, R. A. Jokusch, E. F. Strittmatter, E. R. Williams, J. Am. Chem. Soc. 1996, 118, 10640. c) P. D. Schnier, J. S. Klassen, E. F. Strittmatter, E. R. Williams, J. Am. Chem. Soc. 1998, 120, 9605.

h) The Best-Fit Model of Alkali-Crownether Binding

Literature: P.B. Armentrout, Int. J. Mass Spectrom. 1999, 193 , 227


9. Demonstration of Instruments (à 2 Stunden)

a) EI and Sector-Field Instrument

b) ESI-FTICR, Tandem-MS

c) GC-MS and LC-MS


10. Case Studies

a) Peptide Sequencing: ECD and IRMPD

b) Chirality: Magic Number Clusters: The Serine Octamer

c) Thermochemistry: Is Watson-Crick Base Pairing Conserved in the Gas Phase?

d) Structure Analysis: Pyrogallarene Hexamers - Are they Capsules?

e) Reactivity in Solution: Seeing Self-Sorting At Work

f) Reactivity in the Gas Phase: Crown Ether Spacewalk


11. Excercises

a) Interpretation of EI Mass Spectra

b) Peptide Sequencing with MS and MS/MS

c) Structure Analysis of Interlocked Molecules

d) Metal Complexes: Multiply Charged Ions

e) Dendritic Molecules: Defects and Ionization Artifacts