CASSCF/AMBER

As shown by the calculations of bacteriorhodopsin (Section 2.3.2.1), ONIOM is an excellent tool for excited-state reactions in biology. The important rhodopsin system has been studied both by TD-B3LYP Amber [80] and CASSCF Amber [81]. Another example of the combination of CASSCF with Amber for the surrounding protein can be found for the yellow protein [82],... 

CASPT2//CASSCF/AMBER level of theory. J Am Chem Soc 125 6868-6869... 

Ferre, N., Olivucci, M., Probing the Rhodopsin Cavity with Reduced Retinal Models at the CASPT2/CASSCF/AMBER Level of Theory, J. Am. Chem. Soc. 2003, 125, 6868 6869. 

A step forward along the route to the correct modelling of the spectroscopy and photochemical reactivity of photoreactive proteins is represented by the implementation of a Quantum Mechanics/Molecular Mechanics (QM/MM) computational strategy based on a suitable QM part coupled with a protein force field such as AMBER [34] (or CHARMM [35]). Very recently a CASPT2//CASSCF/AMBER method for rhodopsin has been implemented in our laboratory [36,37] within the QM/MM hnk-atom scheme [38]. Special care has been taken in the parametrization of the protonated Schiff base linkage region that describes the dehcate border region between the MM (the protein)... 

The CASSCF/AMBER method allows for geometry optimization on the excited state. Thus, we can also predict the emission maxima. The results, schematically illustrated in Scheme 12.5, indicate that the protein/gas-phase similarity also holds for the emission suggesting that the protein matrix mimics the gas phase even for the relaxed excited state chromophore. 

We recently [36] provide evidence that our CASPT2//CASSCF/AMBER QM/MM strategy can be correctly applied to the investigation of the excited state of Rh with a computational error <5 kcal mol Thus, our simulation allows for a semiquantitative analysis of the factor determining the properties of the protein environment. Comparing the computed vertical excitation energy with the experimental values (see Scheme 12.6), we found that for Rh the absorption maximum is reproduced with only 3 kcal mol (476 nm vi. 498 nm) while for the solution the error is only 1 kcal mol (433 nm vj . 442 nm). These results confirm the quality of our approach and allow to reproduce the so-called opsin-shift (the 445 nm A ax observed for PSB 11 in methanol is red shifted to 498 nm in Rh) with a 2 kcal mol error. 

Fig. 12.11. CASPT2//CASSCF/AMBER energy profile for the Rh—> bathoRh photochemical reaction compared to the experimental values (in bold) (redrawn with permission from Ref. [50] 2004 by The National Academy of Sciences of the USA).

For the full protein model of the I state the calculated peaks for absorption and emission are 468 and 507 nm, respectively, compared with the experimental values of 495 and 508 nm (Brejc et al. 1997 Chattoraj et al. 1996) resulting in an error of less than 4kcal moP. A somewhat better agreement with experimental data is achieved by Altoe et al. (2007) using a similar computational protocol. The calculations were performed at the CASPT2//CASSCF/AMBER level for the chromophore with the same basis set. Prior the QM/MM excited state calculation the model was equilibrated by MD simulation. The authors calculated the absorption of504 nm for the I state (experimentally 495 nm). 

Top Observed A° values and excited state lifetimes associated with the initial steps of the photoisomerization of Rh. Bottom Schematic representation of the excited state isomerization motion of PSB11 dominated by an asynchronous crankshaft structure deformation (Frutos et al. 2007) and documented for a CASSCF/AMBER model of Rh... 

Strambi, A., Goto, P. B., Ferr6, N., Olivucci, M. (2007). Effects of water re-location and cavity trimming on the CASPT2//CASSCF/AMBER excitation energy of rhodopsin. Theoretical Chemistry Accounts, 118(1), 185-191. doi 10.1007/ s00214-007-0273-y. 

Vision involves cis-trans photoisomerization of a chromophore and many studies have been done using different models/ For example, a CASSCF/AMBER procedure has been used to study the nonadiabatic dynamics of retinal in rhodopsin proteins/ In another study, a simple model of a photosynthetic center was examined by Worth and Cederbaum. They proposed that the presence of conical intersections facilitated the long-range intermolecular photo-initiated electron transfer between the protein s porphyrin and a nearby quinone. Semiempirical methods and QM/MM methods have been developed by Martinez and coworkers " to study the cis-trans isomerization dynamics of the Green Fluorescent Protein chromophore in solution, which occurs through conical intersections.The chromophore in this protein consists of two rings connected with a double bond and has been studied in vacuo as well. ... 

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