TABLE I.
Summary of constraints for all simulations.
| Model-1 | |||
|---|---|---|---|
|
| |||
| Simulation set | Constrained groups | Force constant | K (Eq. (2)a |
| Set-1 | Donorb | 15570 pN/Åc | 469 cm−1 |
| Acceptora | 15570 pN/Å | 406 cm−1 | |
| Hydrogena | 15570 pN/Å | 1624 cm−1 | |
|
| |||
| Set-2 | Donora | 15570 pN/Å | 469 cm−1 |
| Acceptora | 15570 pN/Å | 406 cm−1 | |
| Hydrogena | 15570 pN/Å | 1624 cm−1 | |
| carboxylate group (COO− )d | 15570 pN/Å | 469 cm−1e | |
| Model-2 | |||
|---|---|---|---|
|
| |||
| Simulation set | Constrained groups | Force constant | K (Eq. (2)) |
| Set-1 | Donora | 15570 pN/Å | 469 cm−1 |
| Acceptora | 15570 pN/Å | 406 cm−1 | |
| Hydrogena | 15570 pN/Å | 1624 cm−1 | |
|
| |||
| Set-2 | Donora | 15570 pN/Å | 469 cm−1 |
| Acceptora | 15570 pN/Å | 406 cm−1 | |
| Hydrogena | 15570 pN/Å | 1624 cm−1 | |
| Ile839(COO− )b | 15570 pN/Å | 469 cm−1c | |
|
| |||
| Set-3 | Donora | 15570 pN/Å | 469 cm−1 |
| Acceptora | 15570 pN/Å | 406 cm−1 | |
| Hydrogena | 15570 pN/Å | 1624 cm−1 | |
| His499,His504,His690, Asn694, Ile839(COO− )b | 155690 pN/Åf | 1483 cm−1c | |
The force constant is provided in units of pN/Å and cm−1. The latter is obtained by utilizing the mass of the atom on which the constraint is applied.
The donor, the acceptor and transferring hydrogen are coupled to bath variables, that bias the dyanmics of these quantities towards achieving the transfer process. The force constants mentioned in these cases is related to η(Eq. (1)) and K (Eq. (2)).
The quantity 15570 pN/Å ≈ 224.10 kcal/mol.Å2
These groups are harmonically constrained to remain close to their original positions. The harmonic force constants are as noted. The goal is to probe the effect of the dynamics of these groups on the transfer process.
Computed assuming carbon mass.
The quantity155690 pN/Å ≈ 2240.82 kcal/mol.Å2. The stringent constraint probes the effect of active site flexibility. See text here and also in Section III C.