1. The Emergence of a New Radical-Cationic
Amino Acid Dynamics:
The Proton Patches Model

2. Where I’m Going With It All
• “Proton scissors”
• “Proton patches”
• Examples and results

3. Methodology
• Lowest energy conformers of neutral
amino acid
• Geometry in Gaussian
• Charge = +1; Multiplicity = 2 (ionization)
• Run CPMD simulation to test

4. “Proton Scissors”
12 AWFULLY
COMPLICATED
STEPS
This fragmentation of C-N bond to give
oxazolone cation and neutral fragment
occurs at 31.3 kcal/mol. This size barrier is
common with protonated species (between
30 and 40 kcal/mol). The fragmentation of
any C-N or C-C bond in GGG is always
preceded by proton transfer.
Fragments
+
+
Rodriquez, C.F.,

5. Amino Acids
• Arginine
• Asparigine
• Aspartic Acid
• Threonine
• Tryptophan

6. Radical-Cationic Arginine (Arg+•
)

7. Arg+•
0
2
4
6
8
10
12
0 100 200 300 400 500 600 700 800
Time (fs)
C-CBondLength(Angstroms)

8. Arg+•
0
0.2
0.4
0.6
0.8
1
1.2
1.4
1.6
1.8
2
0 100 200 300 400 500 600 700 800
Time (fs)
N-HBondDistance(Angstroms)

9. Radical-Cationic Asparigine (Asn+•
)

10. Asn+•
0
0.2
0.4
0.6
0.8
1
1.2
1.4
1.6
1.8
2
2.2
0 100 200 300 400 500 600 700 800
Time (fs)
O-HBondDistance(Angstroms)

11. Asn+•
0
1
2
3
4
5
6
7
0 100 200 300 400 500 600 700 800
Time (fs)
C-CBondDistance(Angstroms)

12. Radical-Cationic Aspartic Acid
(Asp+•
)

13. Asp+•
0
1
2
3
4
5
6
7
0 100 200 300 400 500
Time (fs)
C-CBondDistance(Angstroms)

14. Asp+•
0
1
2
3
4
5
6
0 100 200 300 400 500
Time (fs)
O-HBondDistance

15. Asp+•
0
0.2
0.4
0.6
0.8
1
1.2
1.4
1.6
1.8
0 100 200 300 400 500
Time (fs)
O-HBondDistance

16. Asp+•
0
1
2
3
4
5
6
0 100 200 300 400 500
Time (fs)
O-HBondDistance(Angstroms)
~124 fs

17. Radical-Cationic Threonine (Thr+•
)

18. Thr+•
0
2
4
6
8
10
12
0 100 200 300 400 500 600 700 800
Time (fs)
C-CBondLength(Angstroms)

19. Thr+•
(Other conformer)
0
1
2
3
4
5
6
0 100 200 300 400 500 600
Time (fs)
C-CBondLength(Angstroms)

20. Thr+•
0
0.5
1
1.5
2
2.5
3
3.5
0 100 200 300 400 500 600
Time (fs)
O-HBondDistance(Angstroms)

21. Radical-Cationic Tryptophan (Trp+•
)

22. Trp+•
0
0.5
1
1.5
2
2.5
3
3.5
4
4.5
0 100 200 300 400 500 600 700 800
Time (fs)
C-CBondLength

23. Summary
• Radical-cationic amino acids do not obey the
“proton scissors” motif (Proton transfer before C-
C bond cleavage); we see variety
• Arg+•
, Asp+•
, and Thr+•
(conformer 2) show C-C
bond cleavage before proton transfer
• Asn+•
shows C-C bond cleavage and proton
transfer occurring almost simultaneously
• Thr+•
, Trp+•
show C-C bond cleavage without any
proton transfer
• Explanation for lack of IE potentials of amino
acids

24. Future Work
• Di- and tripeptides (ThrGly, GlyThr, …)
• Cu2+
complexes
• Cys+•
(problems)
• GROMACS

25. Acknowledgements
Nicole McNeil
Liu Yang
James Goodine
Dr. Orlova
CBU
ATCS

26. Thr+•
0
0.2
0.4
0.6
0.8
1
1.2
1.4
1.6
1.8
2
0 100 200 300 400 500 600
Time (fs)
O-HBondLength(Angstroms)