1. PROTON TRANSFER IN NEUTRAL PEPTIDES EXAMINED BY CONFORMATIONAL SPECIFIC IR/UV SPECTROSCOPY
Sander Jaeqx 67th International Symposium on Molecular Spectroscopy

2. Motivation Protein (large peptide)
Active site: Part of the protein that binds to the substrate and where the chemical reactions takes place
Structure of the active site is important for the function of a protein
Buried deep in peptide  difficult to study
Protein
(large peptide)

3. Motivation
Glu
Proton
Transfer
Arg
Active site mimics to study intrinsic properties of chemical reaction mediated by active site in the gas phase
Amino acids in the active site often exhibit proton transfer
Therefore, the mimic also needs to exhibit this proton transfer, however this is not trivial in the gas phase

4. Can proton transfer occur in the gas phase ???
Motivation
Can proton transfer occur in the gas phase ???

5. Outline Experimental set-up / computational methods
Proton transfer in Z-Arg-OH
Proton transfer in Z-Glu-Alan-Arg-NHMe (n=0,1,3)
Conclusions

6. Experimental Gas-phase measurements Laser desorption
Intrinsic properties
Laser desorption
Create gas phase molecules
Supersonic expansion in a molecular beam (Ar)
Cool the translational and vibrational temperature of the molecules
desorption laser
1064 nm
molecular beam (Ar)
sample
skimmer

7. IR-UV spectroscopy Fix laser on electronic transition in REMPI
 Constant ion signal belonging to a single conformation
IR pulse precedes the UV
If resonant with vibrational level depletion of ground state
 dip in ion signal
Conformation specific IR absorption spectrum
Ion signal
IR wavelength

8. Techniques - IR spectroscopy
IR spectroscopy gives an direct view on the hydrogen bond network present:
Amide I  C=O stretch
Amide II NH bend
Experimental IR absorption spectra compared with theoretical spectra

9. Computational approach: Conformational search
Simulated annealing
Max T: 1300 K
Simulation time: 10 – 20 ns
# structures: 500 – 1000
~50 structures optimized on B3LYP/6-31G** level
~25 structures optimized and frequency calculation on B3LYP/6-311+G** level

10. Proton transfer in Z-Arg-OH ?
Arginine most basic amino acid
Proton tranfer possible from C-terminus to guanidine side chain of arginine forming a zwitterion
Neutral
Zwitterion
Z-cap
Proton
Transfer

11. Proton transfer in Z-Arg-OH ?
Gas phase structure arginine still under debate;
Canonical form ( Carboxylic acid C=O stretch + 2 x NH bend )
Tautomeric form ( Carboxylic acid C=O stretch + 1 x NH bend )
Zwitterionic form ( 2 x NH bend )
Canonical
Tautomeric
Zwitterionic

12. Proton transfer in Z-Arg-OH ?
Z-Arg-OH has two dominant gas-phase conformations:
Conformation A : 2x NH bend + Carboxylic acid C=O stretch  Canonical structure
Conformation B : 1 x NH bend + Carboxylic acid C=O stretch  Tautomeric structure
There is no proton transfer in Z-Arg-OH

13. Z-Arg-OH: no proton transfer
Tautomeric form
Conformation A
Conformation B
Canonical form

14. Proton transfer in Z-Glu-Alan-Arg-NHMe (n = 0,1,3)
Proton transfer from carboxylic acid group (Glu) to guanidine group (Arg)
Z-cap
Glu
Ala
Arg
NHMe

15. Z-Glu-Arg-NHMe: Side chain interactionsB
Arg
Glu C D
Backbone
Arg
Arg
Glu
Glu

16. Z-Glu-Arg-NHMe: Side chain interactions
 MATCH!!
 No Match
 No Match
 No Match

17. Structural assignement Z-Glu-Arg-NHMe

18. Assigned structures for
Z-Glu-Alan-Arg-NHMe
Assigned structures for
Z-Glu-Ala-Arg-NHMe
Z-Glu-Ala3-Arg-NHMe

19. Type of interactions Two types of interactions:
Conventional hydrogen bonding
Electrostatic interactions
Dispersion interaction
Induced dipole – induced dipole interactions
Major disadvantage DFT: Dispersion interactions are not included
 New dispersion corrected functionals are being developed: DFT-D

20. B3LYP deficiencies Dispersion No dispersion
DFT-D better than DFT for Structure optimization and energy calculations
Includes more interactions
DFT (B3LYP) does better frequency calculations in Amide I and Amide II region
However, it has difficulties in fingerprint region when dispersion interactions are present
Ik zou zeggen: both Amide I& II well
However when dispersion interactions are present: DFT-D better as soon in Fingerprint region
Spectrum arg disp/no disp met DFT en DFT -D
Dispersion
No dispersion

21. Conclusions Two tautomers observed in gas-phase
Proton transfer does not occur in Z-Arg-OH
Z-Glu-Alan-Arg-NHMe (n=0,1 and 3) all show proton transfer
All exhibit an electrostatic interaction + dispersion interaction

22. MOLDYN Group FELIX Group Jos Oomens Anouk Rijs Joost Bakker
Vivike Lapoutre
FELIX Group
Lex van der Meer
Britta Redlich
Giel Berden
Cor Tito
Rene van Buuren
Wybe Roodhuyzen
Joop Stakenborg
Michel Riet
Josipa Grzetic
Denis Kiawi
Juehan Gao

23. Dispersion corrected DFT (DFT-D)
Structure optimization and energy calculations with DFT-D are of better quality compared with DFT
Includes more interactions
Z-Arg-OH Conformation A: With dispersion interaction
DFT
DFT-D

24. Dispersion corrected DFT (DFT-D)
Structure optimization and energy calculations with DFT-D are of better quality compared with DFT
Includes more interactions
Z-Arg-OH Conformation B: Without dispersion interaction
DFT
DFT-D

25. Intermolecular interactions
Two types of interactions:
Conventional hydrogen bonding
Electrostatic interactions
Dispersion interaction
Induced dipole – induced dipole interactions
Major disadvantage DFT: Dispersion interactions are not included
 New dispersion corrected functionals are being developed: DFT-D