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

The Emergence of a New Radical-Cationic Amino Acid Dynamics:

The Proton Patches Model

Where I’m Going With It All

• “Proton scissors”• “Proton patches”• Examples and results

Methodology

• Lowest energy conformers of neutral amino acid

• Geometry in Gaussian• Charge = +1; Multiplicity = 2 (ionization)• Run CPMD simulation to test

“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.,

Amino Acids

• Arginine

• Asparigine

• Aspartic Acid

• Threonine

• Tryptophan

Radical-Cationic Arginine (Arg+•)

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)

Arg+•

00.20.40.60.8

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2

0 100 200 300 400 500 600 700 800

Time (fs)

N-H

Bon

d D

ista

nce

(Ang

stro

ms)

Radical-Cationic Asparigine (Asn+•)

Asn+•

00.20.40.60.8

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22.2

0 100 200 300 400 500 600 700 800

Time (fs)

O-H

Bon

d Di

stan

ce (A

ngst

rom

s)

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)

Radical-Cationic Aspartic Acid (Asp+•)

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)

Asp+•

0

1

2

3

4

5

6

0 100 200 300 400 500

Time (fs)

O-H

Bon

d Di

stan

ce

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

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

Radical-Cationic Threonine (Thr+•)

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)

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)

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)

Radical-Cationic Tryptophan (Trp+•)

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

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

Future Work

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

Acknowledgements

Nicole McNeilLiu YangJames GoodineDr. OrlovaCBUATCS

Thr+•

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2

0 100 200 300 400 500 600

Time (fs)

O-H

Bon

d Le

ngth

(Ang

stro

ms)