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You access the old version of our website. Please point your browser to our new home page. Protonation of the aromatic amino group at different pH values calculated with Quantum 3.2.
The blue curve represents the calculated charged on the side chain amino group as a function of the pH value. The dashed (magenta) line is the best fit with an S-shape curve, yielding pKr=4.5. The experimental value pKr=4.7 is reported in [1]. The details of the calculation are attached below.
[1] Jankowski A. et al. (1988) Two new fluorophore pairs, tyrosine-4’-aminophenylalanine and tyrosine-4’0dimethylaminophenylalanine, in the determination of molecular dimensions in peptides. Biophysical Chemistry, 31:147-153.
Supplementary material:
QUANTUM used a number of different molecular ions state (see the table below) to calculate the net charge on the side chain amino group. Depending on the pH value, different ions have various relative concentrations, as presented on the graph:
The results
of the calculation are summarized in the Table 2.
Table 1: molecular ion states participating in
pKr calculation
|
H11m0 |
NH2-R-C(NH2)(COO-) |
|
H12m0 |
NH2-R-C(NH2)(COOH) |
|
H12m1 |
NH2-R-C(NH3+)(COO-) |
|
H12m2 |
NH3+-R-C(NH2)(COO-) |
|
H13m0 |
NH2-R-C(NH3+)(COOH) |
|
H13m1 |
NH3+-R-C(NH3+)(COO-) |
|
H13m2 |
NH3+-R-C(NH2)(COOH) |
|
H14m0 |
NH3+-R-C(NH3+)(COOH) |
Table 2: The concentrations (calculated) of
different molecular ions states (see Table 1) as a function of pH.
|
pH |
H11m0 |
h12m0 |
h12m1 |
h12m2 |
h13m0 |
h13m1 |
h13m2 |
h14m0 |
|
|
Charge of the arom. Amino gr. |
0 |
0 |
0 |
1 |
0 |
1 |
1 |
1 |
Total charge |
|
0 |
1.10E-17 |
1.56E-12 |
1.29E-11 |
6.38E-12 |
0.000243 |
0.000134 |
5.60E-07 |
0.999623 |
1.00E+00 |
|
1 |
1.09E-14 |
1.56E-10 |
1.29E-09 |
6.35E-10 |
0.002422 |
0.001331 |
5.58E-06 |
0.996242 |
9.98E-01 |
|
2 |
1.06E-11 |
1.51E-08 |
1.24E-07 |
6.15E-08 |
0.023423 |
0.012877 |
5.40E-05 |
0.963646 |
9.77E-01 |
|
3 |
7.98E-09 |
1.13E-06 |
9.37E-06 |
4.63E-06 |
0.176481 |
0.097026 |
0.000407 |
0.726071 |
8.24E-01 |
|
4 |
2.30E-06 |
3.27E-05 |
0.00027 |
0.000134 |
0.509071 |
0.279878 |
0.001173 |
0.209439 |
4.91E-01 |
|
5 |
0.00028211 |
0.000401 |
0.003313 |
0.001638 |
0.624121 |
0.34313 |
0.001438 |
0.025677 |
3.72E-01 |
|
6 |
0.0267914 |
0.00381 |
0.031461 |
0.015555 |
0.592714 |
0.325863 |
0.001366 |
0.002439 |
3.45E-01 |
|
7 |
0.652241 |
0.009276 |
0.076593 |
0.037869 |
0.144297 |
0.079332 |
0.000333 |
5.94E-05 |
1.18E-01 |
|
8 |
0.978086 |
0.001391 |
0.011486 |
0.005679 |
0.002164 |
0.00119 |
4.99E-06 |
8.90E-08 |
6.87E-03 |
|
9 |
0.998072 |
0.000142 |
0.001172 |
0.000579 |
2.21E-05 |
1.21E-05 |
5.09E-08 |
9.08E-11 |
5.92E-04 |
|
10 |
0.99981 |
1.42E-05 |
0.000117 |
5.80E-05 |
2.21E-07 |
1.22E-07 |
5.10E-10 |
9.10E-14 |
5.82E-05 |
|
11 |
0.999981 |
1.42E-06 |
1.17E-05 |
5.81E-06 |
2.21E-09 |
1.22E-09 |
5.10E-12 |
9.10E-17 |
5.81E-06 |
|
12 |
0.999998 |
1.42E-07 |
1.17E-06 |
5.81E-07 |
2.21E-11 |
1.22E-11 |
5.10E-14 |
9.10E-20 |
5.81E-07 |
|
13 |
1 |
1.42E-08 |
1.17E-07 |
5.81E-08 |
2.21E-13 |
1.22E-13 |
5.10E-16 |
9.10E-23 |
5.81E-08 |
|
14 |
1 |
1.42E-09 |
1.17E-08 |
5.81E-09 |
2.21E-15 |
1.22E-15 |
5.10E-18 |
9.10E-26 |
5.81E-09 |