Table 1.
Parameters for undoped PPy and doped PPyCl
| Undoped Polypyrrole | |||
|---|---|---|---|
| Atom Type | Charge (e−) | σ (Å) | ε(kcal/mol) |
| NA opls_542 | −0.386 | 3.250 | 0.170 |
| CW opls_543 | 0.107 | 3.550 | 0.070 |
| CS opls_544 | −0.215 | 3.550 | 0.070 |
| H opls_545 | 0.320 | 0.000 | 0.000 |
| HA opls_547 | 0.141 | 2.420 | 0.030 |
| Bonds | bo(Å) | kb (kcal/mol/Å2) |
|---|---|---|
| NA-H | 0.9937 | 434 |
| NA-CW | 1.3657 | 427 |
| CW-CW | 1.4567 | 469 |
| CW-CS | 1.3644 | 546 |
| CS-CS | 1.4223 | 469 |
| CS-HA | 1.0715 | 367 |
| CW-HA | 1.0698 | 367 |
| Angles | θ0(degrees) | kθ(kcal/mol/rad2) |
|---|---|---|
| H-NA-CW | 124.42 | 35 |
| NA-CW-CW | 121.34 | 70 |
| NA-CW-CS | 107.49 | 70 |
| NA-CW-HA | 121.04 | 35 |
| CW-NA-CW | 110.12 | 70 |
| CW-CW-CS | 131.17 | 70 |
| CW-CS-CS | 107.44 | 70 |
| CW-CS-HA | 125.93 | 35 |
| CS-CW-HA | 130.85 | 35 |
| CS-CS-HA | 126.54 | 35 |
| N-C-C-N Torsion Parameter* | (kcal/mol) | ||
|---|---|---|---|
| Ryckaert-Bellemans function | Fourier series | ||
| C0 | 2.797 | V0 | 0.000 |
| C1 | −0.718 | V1 | 1.093 |
| C2 | −4.557 | V2 | 2.307 |
| C3 | 0.228 | V3 | −0.114 |
| C4 | 2.250 | V4 | −0.563 |
| Doped Polypyrrole | |||
|---|---|---|---|
| Atom Type | Charge (e−) | σ (Å) | ε(kcal/mol) |
| NA opls_542 | −0.486 | 3.250 | 0.170 |
| CW opls_543 | 0.269 | 3.550 | 0.070 |
| CS opls_544 | −0.195 | 3.550 | 0.070 |
| H opls_545 | 0.363 | 0.000 | 0.000 |
| HA opls_547 | 0.154 | 2.420 | 0.030 |
| Cl-opls_401 | −0.999 | 4.417 | 0.118 |
| Bonds | bo(Å) | kb(kcal/mol/Å2) |
|---|---|---|
| NA-H | 1.0280 | 434 |
| NA-CW | 1.3526 | 427 |
| CW-CW | 1.4127 | 469 |
| CW-CS | 1.4197 | 546 |
| CS-CS | 1.3660 | 469 |
| CS-HA | 1.0700 | 367 |
| CW-HA | 1.0698 | 367 |
| Angles | θ0(degrees) | kθ (kcal/mol/rad2) |
|---|---|---|
| H-NA-CW | 124.86 | 35 |
| NA-CW-CW | 124.09 | 70 |
| NA-CW-CS | 107.38 | 70 |
| NA-CW-HA | 121.04 | 35 |
| CW-NA-CW | 110.28 | 70 |
| CW-CW-CS | 128.54 | 70 |
| CW-CS-CS | 107.49 | 70 |
| CW-CS-HA | 125.82 | 35 |
| CS-CW-HA | 130.85 | 35 |
| CS-CS-HA | 126.68 | 35 |
| N-C-C-N Torsion Parameter* | (kcal/mol) | ||
|---|---|---|---|
| Ryckaert-Bellemans function | Fourier series | ||
| C0 | 5.042 | V0 | 0.000 |
| C1 | 2.466 | V1 | −1.233 |
| C2 | 15.57 | V2 | 5.042 |
| C3 | −2.466 | V3 | 1.233 |
| C4 | −20.612 | V4 | 5.153 |
*
Ryckaert-Bellemans (R-B) function is used in Gromacs [23] and Fourier series is used in TINKER [22].
All values are shown in units of kcal/mol. The R-B parameters listed use the Gromacs convention where 0° is the trans configuration (i.e., the “polymer convention”). The Fourier series parameters listed use the Tinker convention where 0° is the cis configuration.