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The Emergence of a New Radical-Cationic Amino Acid Dynamics:
The Proton Patches Model
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Where I’m Going With It All
• “Proton scissors”• “Proton patches”• Examples and results
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Methodology
• Lowest energy conformers of neutral amino acid
• Geometry in Gaussian• Charge = +1; Multiplicity = 2 (ionization)• Run CPMD simulation to test
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“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.,
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Amino Acids
• Arginine
• Asparigine
• Aspartic Acid
• Threonine
• Tryptophan
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Radical-Cationic Arginine (Arg+•)
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Arg+•
0
2
4
6
8
10
12
0 100 200 300 400 500 600 700 800
Time (fs)
C-C
Bon
d Le
ngth
(Ang
stro
ms)
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Arg+•
00.20.40.60.8
11.21.41.61.8
2
0 100 200 300 400 500 600 700 800
Time (fs)
N-H
Bon
d D
ista
nce
(Ang
stro
ms)
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Radical-Cationic Asparigine (Asn+•)
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Asn+•
00.20.40.60.8
11.21.41.61.8
22.2
0 100 200 300 400 500 600 700 800
Time (fs)
O-H
Bon
d Di
stan
ce (A
ngst
rom
s)
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Asn+•
0
1
2
3
4
5
6
7
0 100 200 300 400 500 600 700 800
Time (fs)
C-C
Bond
Dis
tanc
e (A
ngst
rom
s)
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Radical-Cationic Aspartic Acid (Asp+•)
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Asp+•
0
1
2
3
4
5
6
7
0 100 200 300 400 500
Time (fs)
C-C
Bon
d D
ista
nce
(Ang
stro
ms)
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Asp+•
0
1
2
3
4
5
6
0 100 200 300 400 500
Time (fs)
O-H
Bon
d Di
stan
ce
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Asp+•
00.2
0.40.60.8
11.21.4
1.61.8
0 100 200 300 400 500
Time (fs)
O-H
Bon
d D
ista
nce
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Asp+•
0
1
2
3
4
5
6
0 100 200 300 400 500
Time (fs)
O-H
Bon
d Di
stan
ce (A
ngst
rom
s)
~124 fs
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Radical-Cationic Threonine (Thr+•)
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Thr+•
0
2
4
6
8
10
12
0 100 200 300 400 500 600 700 800
Time (fs)
C-C
Bon
d Le
ngth
(Ang
stro
ms)
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Thr+• (Other conformer)
0
1
2
3
4
5
6
0 100 200 300 400 500 600
Time (fs)
C-C
Bon
d Le
ngth
(Ang
stro
ms)
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Thr+•
0
0.5
1
1.5
2
2.5
3
3.5
0 100 200 300 400 500 600
Time (fs)
O-H
Bon
d Di
stan
ce (A
ngst
rom
s)
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Radical-Cationic Tryptophan (Trp+•)
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Trp+•
00.5
11.5
22.5
33.5
44.5
0 100 200 300 400 500 600 700 800
Time (fs)
C-C
Bond
Len
gth
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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
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Future Work
• Di- and tripeptides (ThrGly, GlyThr, …)• Cu2+ complexes• Cys+• (problems)• GROMACS
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Acknowledgements
Nicole McNeilLiu YangJames GoodineDr. OrlovaCBUATCS
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Thr+•
00.20.40.60.8
11.21.41.61.8
2
0 100 200 300 400 500 600
Time (fs)
O-H
Bon
d Le
ngth
(Ang
stro
ms)