Table 7.
Gas-phase QM-none (e.g., QM at protein geometry) and QM/MM excitation energies (nm) for the absorbing state of bovine Rh in the absence (R1) and presence (R2) of Glu113 in the QM region and the effect retinal protonation (basis set: 6-31G*) along with QM and QM/MM spectral shifts with deprotonation of retinal (in parentheses) and with inclusion of Glu113 in the QM model (△)
| Protonation State | Method | QM region = R1 (without Glu113) | QM region = R2 (with Glu113) | △ = E(R2) - E(R1) |
|---|---|---|---|---|
| QM=TD-B3LYP | ||||
| PSBR (deprotonated Glu113) | QM-none | 560 (0) | 500 (0) | -60 |
| QM/MM | 503 (0) | 499 (0) | -4 | |
| SBR with protonated Glu113 | QM-none | 408 (152) | 423 (77) | 15 |
| QM/MM | 429 (74) | 435 (64) | 6 | |
| SBR with deprotonated Glu113 | QM-none | 396 (164) | 380 (120) | -16 |
| QM/MM | 380 (123) | 382 (117) | -2 | |
| QM=DDCI2+Q(12/12) | ||||
| PSBR (deprotonated Glu113) | QM-none | 527 (0) | 395 (0) | -133 |
| QM/MM | 435 (0) | 432 (0) | -2 | |
| SBR with protonated Glu113 | QM-none | 318 (209) | 309 (86) | -9 |
| QM/MM | 336 (99) | 337 (95) | 1 | |
| SBR with deprotonated Glu113 | QM-none | 313 (214) | 298 (97) | -15 |
| QM/MM | 309 (126) | 294 (138) | -15 |