Chromophore modeling

M. Garavelli, T. Vreven, P. Celani, F. Bernardi, M. A. Robb, and M. Olivucci,/. Am. Chem. Soc., 120, 1285 (1998). Photoisomerization Path for a Realistic Retinal Chromophore Model The Nonatetraeniminium Cation. 

Neocarcinostatin chromophore model Intramol. HR of an alkenyl bromide [175]... 

Fig. 2 Schematic representation of the Si /Sq conical intersection seam along the torsion coordinate of the central bond of the minimal retinal chromophore model pentadieniminium cation (reprinted with permission from [20])...

Durbeej B, Borg OA, Eriksson LA (2004) Phytochromobdin C15-Z, syn —> C s E, anti isomerization concerted or stepwise Phys Chem Chem Phys 6 5066-5073 Altoe P, Chment T, De Fusco GC, Stenta M, Bottom A, Serrano-Andres L, Merchan M, Orlandi G, GaraveUi M (2009) Deciphering intrinsic deactivation/isomerization routes in a phytochrome chromophore model. 1 Phys Chem B 113 15067-15073... 

Migani, A., Rohh, M. A., Olivucci, M., Relationship between Photoisomerization Path and Intersection Space in a Retinal Chromophore Model, J. Am. Chem. Soc. 2003,125,2804 2808. 

PJ Wright and J Abbot. Kinetic Models for Peroxide Bleaching under Alkaline Conditions. Part 1. One and Two Chromophore Models. J. Wood Chem. Technol. 11 349-371, 1991. 

The explicit form of the interaction Hamiltonian // ,(() consists of a series of multipolar terms, but for most purposes the electric-dipole (El) approximation is sufficient. Although the results are calculated within this approximation for each molecular center detailed analysis of the coupling provides results equivalent to the inclusion of higher-order multipole terms for the pair. The same assumption underlies the well-known coupled-chromophore model of optical rotation (Kuhn 1930 Boys 1934 Kirkwood 1937). The Hamiltonian for the system may thus be written as... 

Model compounds of the chromophore do not fluoresce in solution. This is presumably due to the lack of constraints imposed by the protein environment. The excited state of the model compounds can freely rotate around their cp and z dihedral angles, which allows NAC to occur, resulting in fluorescence quenching. Fluorescence can, however, be obtained by lowering the temperature to 77K, this presumably freezes the solution and imposes steric barriers to rotation. Similar behavior is observed when the protein is denatured - the fluorescence yield decreases by at least three orders of magnitude [42]. Furthermore, chromophore model compounds that are non- or minorly substituted emit minimal fluorescence, while sterically bulky substituents modify the equilibrium between radiative and nonradiative deexcitation pathways, making the sterically hindered compounds more fluorescent [43]. 

A volume analysis of the t and cp 90° OBFs and HTs in a GFP chromophore model compound, revealed that the t-OBF displaces a larger volume than both the HT and the cp-OBF. However, the HT and cp-OBF processes displace the same vol-... 

Interestingly ab initio calculations on a chromophore model compound have shown that a correlated torsion about a double bond and its adjacent single bond exists in both the gas and solution phases, implying that a HT may occur even in the absence of volume-conserving requirements [49]. 

Hansen AE, Ballhausen CJ (1965) Electronic structure of copper acetate monohydrate based on a coupled chromophore model. Trans Far Soc 61 631... 

Figure 12. A representation of the coupled chromophore model. The orbitals designated (a) represent the frontier four-otbitals of one monomer chlorophyll unit, those labeled (b), the orbitals of the second monomer unit. Upon mixing, symmetry determines combinations of the monomer orbitals, yielding those of the dimer, labeled with (d).

Cembran A, Bemardi F, Olivucci M, Garavelli M (2004) Counterion controlled photoisomerization of retinal chromophore models a computational investigation. J Am Chem Soc 126 16018... 

Migani A, Robb M, Olivucci M. Relationship between photoisomerization path and intersection space in a retinal chromophore model. J Am Chem Soc. 2003 25 2804-2808. 

Gozem S, Melaccio F, Lindh R, Krylov AI, Granovsky AA, Angeli C, Olivucci M (2013) Mapping the excited state potential energy surface of a retinal chromophore model with multireference and equation-of-motion coupled-cluster method. J Chem Theor Comput 9 4495 506... 

Schapiro, I., Weingart, O., Buss, V. (2009). Bicycle-pedal isomerization in a rhodopsin chromophore model. Journal of the American Chemical Society, 131(1), 16. doi 10.1021/ Ja805586z. 

Vreven, T., Bernard , R, Garavelli, M., Olivucci, M., Robb, M. A., 8c Schlegel, H. B. (1997). Ab initio photoisomerization dynamics of a simple retinal chromophore model. Journal of the American Chemical Society, 119(51), 12687-12688. 

Weingart, O., Schapiro, I., 8c Buss, V. (2007). Photochemistry of visual pigment chromophore models by ab initio molecular dynamics. The Journal of Physical Chemistry B, 111(14), 3782-3788. 

Case Studies of Isolated Chromophores Photoisomerization in a Rhodopsin Chromophore Model... 

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