This document discusses computing infrared spectra of protonated peptides and fragments to compare with experimental data for identification. It summarizes previous work using tandem mass spectrometry and ion traps to obtain experimental IR spectra of peptides, as well as computational methods using PM6 and DFT to calculate IR spectra for comparison. Specific examples are provided of calculating spectra for phenylalanine and dialanine and comparing to experimental data.
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Dissertation Presentation
1. Computing the IR spectra of
protonated peptides and their
fragments
Thomas Rook
2. Aim
Compute accurate infrared
spectra of protonated peptides
and their fragments.
This spectra can then be compared with experimental data
to help identify conformers
3. Introduction
1. H. Steen and M. Mann, Nat. Rev. Mol. Cell Biol., 2004, 5, 699–711.
H. Steen et al1
Proteomics
Identify proteins from peptides
A lot of protonation sites are available
All structures determined by inspection
Everything calculated at PM6 and then B3LYP/6-31++G*
4. Initial structure
Molecule is excited
Numerous conformers available
A lot of protonation sites are available
Mobile proton theory2
All structures determined by inspection
Everything calculated at PM6 and then B3LYP/6-31++G*
Possible protonation sites of di-alanine as stated by the mobile
proton theory (Drawn in Gaussian 093)
2; B. Palzs and S. Suhal, Mass Spectrom. Rev., 2005, 24, 508–548. 3; M. Frisch, G. Trucks and H. Schlegel, Gaussian Inc, 2009.
5. Theory level and basis set
PM6
Semi empirical
Fast structure optimization
B3LYP/6-31++G*
Hybrid DFT technique
Split valence,
IR data
Geometry optimization produces Hessian
Need mass weighted hessian
This produces frequencies
4; M. Orio, D. a Pantazis and F. Neese, Photosynth. Res., 2009, 102, 443–53.
6. Rizzo et al
Tandem MS/MS with an ion trap
Ions drawn through and separated by first MS
Ions trap cooled to 6k+
2nd MS separates ions created/parent ions
In the ion trap
Molecules excited from the ground state
Ions sampled by IR (10Hz) and UV(20Hz) radiation 100ns apart
IR causes excititaion = UV Depletion
The apparatus used by Rizzo et. al5
5; J. Stearns, S. Mercier, C. Seaiby, M. Guidi, O. V. Boyarkin and T. Rizzo, J. Am. Chem. Soc., 2007, 129, 11814–11820.
7. Phenylalanine Lowest Energy Conformer
Rizzo et. al5 experimental
(black) and computational (red)
spectra.
5; J. Stearns, S. Mercier, C. Seaiby, M. Guidi, O. V. Boyarkin and T. Rizzo, J. Am. Chem. Soc., 2007, 129, 11814–11820.
8. Centre Laser Infrarouge d'Orsay (CLIO)
Next 2 experiments performed at this facility
FT-ICR
Fourier Transform Ion Cyclotron Resonance
Proceeded by both Hexapole and Quadrople
IRMPD
Infrared multiphoton dissociation
Tuneable free electron laser (FEL)
9. B. Lucas et al
Examination of the possible conformers of
protonated dialanine
Numerous likely conformers
Including unlikely cis conformer
0.0000
50.0000
100.0000
150.0000
200.0000
250.0000
300.0000
350.0000
400.0000
827 888 949 1010 1071 1133 1192 1253 1314 1375 1436 1498 1558 1619 1680 1741
6; B. Lucas, G. Grégoire and J. Lemaire, Phys. Chem. Chem. Phys., 2004, 6, 2659–2663.
Spectra from Lucas et. al6
10. Wysocki et al
Analysis of Proline containing b2+ ions
Glycine, Alanine, Valine, Isoleucine, Histidine
Form two types of ring
5 membered Oxazalone
6 membered Diketopiperazine
GP+Oxa1 GP+DKP3
GP+DKP3
GP+Oxa1
7; A. Gucinski, J. Chamot-Rooke, V. Steinmetz, A. Somogyi and V. Wysocki, J. Phys. Chem., 2013, 117, 1291–1298.
11. Conclusions
IR Data can be reliably produced from computational techniques
This data is comparable to experimental data.