Cytosine conical intersections

Figure 11-6. Structures of representative conical intersections Sj/Sq in the pyrimidine bases, uracil, thymine, and cytosine. Uracil structures (a,d) are taken from Ref. [147, 210]. Thymine structures (b,e) are taken from Ref. [152], Cytosine structures (c,f) are taken from Ref. [157]...

Figure 11-7. Minimum energy pathways on the Si surface of cytosine connecting the Si minimum to two Si/So conical intersections. The five singlet state energies at the MRCI level are shown. Energies are given in eV with respect to the ground state minimum energy, ciIJ represents conical intersection between states S/, Sj. (From Ref. [157])...

Figure 11-12. Sj pathways for cytosine and 5M2P from vertical excitations to the sofa and twist conical intersections. Cytosine paths are shown in blue, and 5M2P are shown in green. MRCI energies are given in eV. (From Ref. [144])...

Keywords Cytosine, Guanine, Watson-Crick Base-Pair, DNA Oligomers, Conical Intersection,... 

Eth)x is an analogue of the twisted conical intersection of ethylene, as proposed in the guanine-cytosine study [47], where the degenerate states are the ground... 

Figure 17-4. Energy profile for decay of singlet excited cytosine along ethylenic path (torsion of C5-C6 bond). (AE)X is the conical intersection analog for aminoethylene (adapted from Ref. [29]). Energies in eV distances in A...

In addition to the ethylenic type intersection, there are two further conical intersections with the ground state. These conical intersections were described in our first cytosine paper [27], and the (n0, tt )x intersection was found to be the lowest one... 

For cytosine, in common with other pyrimidine nucleobases, photostability is the result of an ethylenic-type conical intersection associated with torsion around a C = C double bond. This interpretation remains - but the barrier is reduced - when the solvent is included approximately. 

In the cytosine-guanine Watson-Crick base-pair, radiationless decay occurs instead via an intermolecular charge transfer state, and is triggered by proton transfer. The locally excited states that were studied in the isolated cytosine are rapidly displaced to higher energy along the proton transfer coordinate. Here the protein environment causes a part of the conical intersection seam to become accessible which cannot be reached in the gas phase. 

In all of these computations, there is a dense manifold of excited states present [83], Thus the computations are sensitive to dynamic electron correlation and the details of the reaction coordinates involved. In the cytosine-guanine base pair simulations, trajectory calculations proved to be necessary to determine the extent of the conical intersection that is actually accessible. Subsequent improvements in the level of theory used for the static calculation of single molecules will be possible, but these should be balanced against a more realistic treatment of vibrational kinetic energy and environmental effects (solvent/protein). 

Figure 2.3 Reaction profile for the excited-state decay of cytosine through a conical intersection. (Adapted from Ismail, N., Blancafort, L., Olivucci, M., Kohler, B. and Robb, M.A., J. Am. Chem. Soc., 124, 6818-6819, 2002. With permission.)...

Fig. 6 Basics of the theoretical model for charge transport based on conical intersections (Coins) and the excimer-Hke interaction between the donor and acceptor electronic states of a molecular system formed by 2 monomers (a), PESs of the donor and acceptor electronic states in the adenine-cytosine (AC) heterodimer and the cytosine-cytosine homodimer (b) and scheme of the Coin-based mechanism for charge transport in DNA (c).

Pig. 21. Conical intersections in the amino keto tautomer of cytosine. The values of the relevant structural parameters are given in A and degrees. Data from Ref. 103. 

It is also possible to find MECI for 2 -f 2 and 2 + 2 structures for this cycloaddition. Such structures He on the same seam (see F re 3.1) as the 2s + 2s structure just discussed. Thus the conditions of Eqns (3.6) and (3.7) hold, however, Q changes. (Q is the coulomb energy corresponding to the energy of the system if all the Ky were zero.) Thus the 2s + 2 and 2a 4" 2a conical intersections are much higher in energy. The same type of conical-intersection structure is also found for the ultrafast deactivation of an excited cytosine-guanine base pair in DNA. ... 

Kistler KA, Matsika S (2008) Three-state conical intersections in cytosine and pyrimidinone bases. J Chem Phys 128... 

Gonzdlez-Vdzquez, J., 8c Gonzalez, L. (2010). A time-dependent picture of the ultrafast deactivation of keto-cytosine including three-state conical intersections. A European Journal of Chemical Physics and Physical Chemistry, 11(17), 3617-3624. 

---