TABLE 3.
Vertical S0 → S1 Excitation Energies (in nm) Calculated Using B3LYP at Gas Phase (Labeled none) and at Different ONIOM (ME or EE) Levels for the Wild-Type Rh and Some of its Mutants along with the Shifts in Excitation Energies (in nm, in Parentheses) with Respect to the Wild-Type Rh
| retinal protonation | B3LYP-none//B3LYP-ME | B3LYP-ME//B3LYP-ME | B3LYP-EE//B3LYP-ME | B3LYP-none//B3LYP-EE | B3LYP-EE//B3LYP-EE | experiment | |
|---|---|---|---|---|---|---|---|
| WT | PSBR | 535 (0) | 504 (0) | 505 (0) | 560 (0) | 503 (0) | 500 (0)1-3 |
| WT | SBR | 400 (−135)a | 399 (−105) | 412 (−93) | 408 (−152) | 429 (−74) | |
| 399 (−136)b | 366 (−138) | 382 (−123) | 396 (−164) | 380 (−123) | |||
| E122Q | PSBR | 533 (−2)c | 503 (−1) | 497 (−8) | 566 (6) | 492 (−11) | 480 (−20)33-35 |
| 544 (9)d | 509 (5) | 512 (7) | 566 (6) | 514 (11) | |||
| E122Q | SBR | 402 (−133)a,c | 395 (−109) | 406 (−99) | 408 (−152) | 418 (−85) | |
| 399 (−136)b,c | 362 (−142) | 382 (−123) | 397 (−163) | 379 (−124) | |||
| E113Q | PSBR | 536 (1)e | 521 (17) | 526 (21) | 536 (−24) | 530 (27) | 496 (−4)32,34,66 |
| E113Q | SBR | 398 (−137)e | 390 (−114) | 397 (−108) | 398 (−162) | 409 (−94) | 384 (−116)32,34,66 |
| 399 (−136)f | 396 (−108) | 408 (−97) | 407 (−153) | 425 (−78) | |||
| 391 (−144)g | 389 (−115) | 397 (−108) | 395 (−165) | 422 (−81) | |||
| E113D | PSBR | 533 (−2) | 504 (0) | 505 (0) | 557 (−3) | 499 (−4) | 510 (10)67 |
| G90D | PSBR | 544 (9)h | 493 (−11) | 490 (−15) | 587 (27) | 475 (−28) | 483 (−17)68 |
| 544 (9)i | 501 (−3) | 503 (−2) | 574 (14) | 502 (−1) | |||
| A292S | PSBR | 542 (7)j | 500 (−4) | 503 (−2) | 571 (11) | 501 (−2) | 491 (−9)68 |
| 537 (2)k | 496 (−8) | 499 (−6) | 567 (7) | 500 (−3) | |||
| 542 (7)l | 502 (−2) | 504 (−1) | 570 (10) | 507 (4) | |||
| A269T | PSBR | 542 (7)m | 502 (−2) | 504 (−1) | 568 (8) | 506 (3) | 514 (14)70 |
| 543 (8)n | 499 (−5) | 502 (−3) | 571 (11) | 506 (3) | |||
| 547 (12)o | 500 (−4) | 504 (−1) | 574 (14) | 503 (0) | |||
| 542 (7)p | 500 (−4) | 502 (−3) | 568 (8) | 498 (−5) | |||
| D83N | PSBR | 534 (−1) | 501 (−3) | 503 (−2) | 570 (10) | 502 (−1) | 495 (−5)33 |
| W265Y | PSBR | 536 (1) | 495 (−9) | 503 (−2) | 574 (14) | 497 (−6) | 485 (−15)69 |
| H211C | PSBR | 543 (8) | 499 (−5) | 501 (−4) | 573 (13) | 501 (−2) | 495 (−5)71 |
| E181Q | PSBR | 541 (6)q | 499 (−5) | 501 (−4) | 571 (11) | 499 (−4) | 502 (2)72 |
| 543 (8)r | 500 (−4) | 502 (−3) | 570 (10) | 500 (−3) |
The computational results in the row were obtained with
Protonated Glu113.
Deprotonated Glu113.
Q112 whose NH2 moiety is oriented toward one of the methyl groups attached to C1 atom of the chromophore.
Q112 whose O=C-NH2 plane is rotated by ca. 90° compared with that in footnote c.
Q113 whose side chain NH2 and carbonyl O moieties are oriented toward its backbone carbonyl O and Schiff-base nitrogen, respectively.
Q113 whose side chain NH2 moiety is oriented to form a H-bond with Schiff-base nitrogen.
Q113 whose side chain NH2 and carbonyl O moieties are oriented toward Gly90 and Schiff-base nitrogen, respectively.
Deprotonated Asp90.
Protonated Asp90.
Side chain -OH unit of S292 that forms a H-bond with carbonyl O of Met288.
Side chain -OH unit of S292 that forms a H-bond with a water molecule.
Side chain -OH unit of S292 that is oriented toward -OH unit of Ser186, a higher energy conformer.
Side chain methyl moiety of T269 that is oriented toward Leu266 side chain and side chain -OH unit that is oriented toward its backbone carbonyl O and becomes closer to a methyl group attached to C1 atom of the chromophore (ca. 2.6 Å).
Side chain methyl moiety of T269 that is oriented toward C1 (one of methyl groups attached to it) and C2 atoms of the chromophore and side chain -OH unit as in footnote m.
Side chain methyl moiety of T269 as in footnote n and side chain -OH unit that forms a H-bond with Leu266.
Side chain methyl moiety of T269 as in footnote n and side chain -OH unit that forms a H-bond with Trp265.
OE2 atom of E181 that is replaced with NH2 moiety.
OE1 atom of E181 that is replaced with NH2 moiety.