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Singlet fluorescence lifetimes of adenosine, cytidine, guanosine, and thymidine, determined by femtosecond pump-probe spectroscopy (Pecourt, J.-M. L.; Peon, J.; Kohler, B. J. Am. Chem. Soc. 2000, 122, 9348. Pecourt, J.-M. L.; Peon, J.; Kohler, B. J. Am. Chem. Soc. 2001, 123, 10370), show that the excited states produced by 263 nm light in these nucleosides decay in the subpicosecond range (290-720 fs). Ultrafast radiationless decay to the ground state greatly reduces the probability of photochemical damage. In this work we present a theoretical study of isolated cytosine, the chromophore of cytidine. The experimental lifetime of 720 fs indicates that there must be an ultrafast decay channel for this species. We have documented the possible decay channels and approximate energetics, using a valence-bond derived analysis to rationalize the structural details of the paths. The mechanism favored by our calculations and the experimental data involves (1) a two-mode decay coordinate composed of initial bond length inversion followed by internal vibrational energy redistribution (IVR) to populate a carbon pyramidalization mode, (2) a state switch between the pi,pi* and nO,pi* (excitation from oxygen lone pair) excited states, and (3) decay to the ground state through a conical intersention. A second decay path through the nN,pi* state (excitation from the nitrogen lone pair), with a higher barrier, involves out-of-plane bending of the amino substituent.

The minimum energy path for photoisomerization of the minimal retinal protonated Shiff base model tZt-penta-3,5-dieniminium cation (cis-C5H6NH2 +) is computed using MC−SCF and multireference Møller−Plesset methods. The results show that, upon excitation to the spectroscopic state, this molecule undergoes a barrierless relaxation toward a configuration where the excited and ground states are conically intersecting. The intersection point has a ∼80° twisted central double bond which provides a route for fully efficient nonadiabatic cis → trans isomerization. This mechanism suggests that cis-C5H6NH2 + provides a suitable “ab initio” model for rationalizing the observed “ultrafast” (sub-picosecond) isomerization dynamics of the retinal chromophore in rhodopsin. The detailed analysis of the computed reaction coordinate provides information on the changes in molecular structure and charge distribution along the isomerization path. It is shown that the initial excited state motion is dominated by stretching modes which result in an elongation of the central double bond of the molecule associated with the change in bond order in the excited state. Thus, the actual cis → trans isomerization motion is induced only after the bond stretching has been completed. It is also demonstrated that, along the excited state isomerization coordinate, the positive charge is progressively transferred from the -CHCHNH2 to the CH2CHCH- molecular fragment. Thus, at the intersection point, the charge is completely localized on the CH2CHCH- fragment. This result suggests that strategically placed counterions can greatly affect the rate, specificity, and quantum yield of the photoisomerization.

In this paper we use ab initio multiconfigurational second-order perturbation theory to establish the intrinsic photoisomerization path model of retinal chromophores. This is accomplished by computing the ground state (S0) and the first two singlet excited-state (S1, S2) energies along the rigorously determined photoisomerization coordinate of the rhodopsin chromophore model 4-cis-␥-methylnona-2,4,6,8-tetraeniminium cation and the bacteriorhodopsin chromophore model all-trans-hepta-2,4,6-trieniminium cation in isolated conditions. The computed S2 and S1 energy profiles do not show any avoided crossing feature along the S1 reaction path and maintain an energy gap >20 kcal⅐mol ؊1 . In addition, the analysis of the charge distribution shows that there is no qualitative change in the S2 and S1 electronic structure along the path. Thus, the S1 state maintains a prevalent ionic (hole-pair) character whereas the S2 state maintains a covalent (dot-dot) character. These results, together with the analysis of the S1 reaction coordinate, support a two-state, two-mode model of the photoisomerization that constitutes a substantial revision of the previously proposed models.T he photoisomerization of the retinal chromophore triggers the conformational changes underlying the activity of rhodopsin proteins (1). In rhodopsin itself (the human retina visual pigment) the retinal molecule is embedded in a cavity where it is covalently bound to a lysine residue via a protonated Schiff base (PSB) linkage. The absorption of a photon of light causes the isomerization (see equation below) of the 11-cis isomer of the retinal PSB (PSB11) to its all-trans isomer (PSBT).Similarly in the bacterial proton-pump bacteriorhodopsin, the photoexcitation causes the isomerization of the PSBT to its 13-cis isomer (PSB13). The photoisomerization of PSB11 and PSBT in the protein environment are among the fastest chemical reactions observed so far. Thus, the photoexcitation of PSB11 in rhodopsin yields a fluorescent transient with a lifetime of ca. 150 fs (2). After this state is left, ground-state PSBT is formed within 200 fs (3). Similarly, irradiation of PSBT in bacteriorhodopsin leads to formation of a 200-fs (4-7) transient and production of the PSB13 within 500 fs. In contrast, the photochemistry of free PSB11 in solution (8) is more than 1 order of magnitude slower: in methanol, PSB11 has a ca. 3-ps fluorescence lifetime and PSBT is formed in 10 ps (9). Similar lifetimes have been reported for PSBT (10-12) and PSB13 (10) in solution.The decrease in excited-state lifetime and the increase in reaction rate of chromophores bound within the protein with respect to the corresponding free forms in solution is a central problem of photobiology. The first step in the quest for a solution to this problem is the detailed understanding of the chromophore photoisomerization path. Recently, Anfinrud and coworkers (13,14) have summarized the experimental evidence in support of a three-electronic state (S 0 , S 1 , and S 2 ) model-the three-state model-of the p...

Atomistic QM/MM simulations have been carried out on the complete photocycle of Photoactive Yellow Protein, a bacterial photoreceptor, in which blue light triggers isomerization of a covalently bound chromophore. The "chemical role" of the protein cavity in the control of the photoisomerization step has been elucidated. Isomerization is facilitated due to preferential electrostatic stabilization of the chromophore's excited state by the guanidium group of Arg52, located just above the negatively charged chromophore ring. In vacuo isomerization does not occur. Isomerization of the double bond is enhanced relative to isomerization of a single bond due to the steric interactions between the phenyl ring of the chromophore and the side chains of Arg52 and Phe62. In the isomerized configuration (ground-state cis), a proton transfer from Glu46 to the chromophore is far more probable than in the initial configuration (ground-state trans). It is this proton transfer that initiates the conformational changes within the protein, which are believed to lead to signaling.

An MC-SCF/4-31G characterization of the possible photochemical pathways of S, and S2 benzene is documented. A complete mechanistic scheme is presented through the characterization of minima and transition states on S0, Sb and S2.The full characterization of Born-Oppenheimer violation regions, where the products of the diabatic processes relax to lower electronic states, is also performed. On the S0 surface the reversion of Dewar benzene to benzene is shown to occur via a concerted path along a symmetric coordinate where the bridgehead Dewar benzene bond and the pair of "quinoid" double bonds are being synchronously broken. No evidence for an asymmetric path could be found. The ground-state potential energy surface along the reaction path between benzene and benzvalene has a flat diradicaloid region corresponding to prefulvene.However, prefulvene itself is a transition state. The S, reaction path from benzene toward prefulvene contains an excited-state minimum with D6h symmetry and a transition state between this minimum and a prefulvene diradicaloid located on the ground-state surface. The Bom-Oppenheimer violation region has been fully characterized by optimizing the conical intersection that occurs between the transition state on S, and the prefulvene biradicaloid region on S0. The existence of a low-energy diradicaloid minimum on S2 with an immediately adjacent S3/S2 conical intersection at only slightly higher energy has been demonstrated. This suggests that the radiationless decay from S2 is almost completely efficient in contrast to the commonly held view. The different photochemistry of S2 is shown to arise from the fact that the S0/St decay that occurs subsequent to passage through the S,/S2 conical intersection occurs at a geometry on the S0/S, crossing surface where there is a C]-C4 bond similar in length to the bridgehead bond of the S0 transition state between Dewar benzene and benzene. Thus there exists a ground-state reaction path to Dewar benzene from a high-energy region of the S0/S| crossing surface.

In electron donor/acceptor species such as 4-(dimethylamino)benzonitrile (DMABN), the excitation to the S(2) state is followed by internal conversion to the locally excited (LE) state. Dual fluorescence then becomes possible from both the LE and the twisted intramolecular charge-transfer (TICT) states. A detailed mechanism for the ICT of DMABN and 4-aminobenzonitrile (ABN) is presented in this work. The two emitting S(1) species are adiabatically linked along the amino torsion reaction coordinate. However, the S(2)/S(1) CT-LE radiationless decay occurs via an extended conical intersection "seam" that runs almost parallel to this torsional coordinate. At the lowest energy point on this conical intersection seam, the amino group is untwisted; however, the seam is accessible for a large range of torsional angles. Thus, the S(1) LE-TICT equilibration and dual fluorescence will be controlled by (a) the S(1) torsional reaction path and (b) the position along the amino group twist coordinate where the S(2)/S(1) CT-LE radiationless decay occurs. For DMABN, population of LE and TICT can occur because the two species have similar stabilities. However, in ABN, the equilibrium lies in favor of LE, as a TICT state was found at much higher energy with a low reaction barrier toward LE. This explains why dual fluorescence cannot be observed in ABN. The S(1)-->S(0) deactivation channel accessible from the LE state was also studied.