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Ultrafast Radiationless Decay Mechanisms Through Conical Intersections in Cytosine. a New Semi-Planar Conical Intersection

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Ultrafast Radiationless Decay Mechanisms Through Conical Intersections in Cytosine. a New Semi-Planar Conical Intersection Indian Journal of Chemistry Vol. 53A, February 2014, pp. 143-151 Ultrafast radiationless decay mechanisms through conical intersections in cytosine. A new semi-planar conical intersection Saadullah G Aziza, Walid I Hassanb, Shaaban K Alroubya, c, Abdulrahman Alyoubia & Rifaat Hilala, b, * aChemistry Department, Faculty of Science, King Abdulaziz University, Jeddah, SA bChemistry Department, Faculty of Science Cairo University, Giza, Egypt cChemistry Department, Faculty of Science Beni-Suief University, Beni-Suief, Egypt Email: [email protected] Received 26 November 2013; revised and accepted 27 January 2014 Geometry, energetics and dipole moment of all possible conformers of cytosine in the ground state are calculated using density functional theory B3LYP method and the 6-311++G(3df,3pd) basis set. The most stable conformer is keto-amino conformer. The amino group hydrogen atoms are slightly out of plane by about 6.3° and 9.9° each. Ultrafast radiationless decay mechanism has been theoretically investigated using Complete Active Space Multiconfiguration SCF calculations. Effective pathways of ultrafast radiationless transitions from the optically allowed π π* state to the ground state S0 of cytosine are explored. The nπ*, nσ*, and the ππ* states have been taken into account as states involved in the radiationless process. Optimized geometry and conical intersections have been searched in the full dimensional space for the vibrational degrees of freedom. Three competing direct decay mechanisms through three possible conical intersections have been found to exist. The first pathway is through the bending of molecule in a sofa-like structure leading to conical intersection with ground state at 4.23 eV. The second pathway occurs through a twisted structure that has hydrogen twisted and the cytosine ring slightly deformed leading to conical intersection at 4.08 eV. The third mechanism takes place via semi-planar conical intersection with main deformations inside the cytosine ring and C=O bond that have 3.97 eV at the intersection with ground state. The three mechanisms contribute to the stability of cytosine. The g-vector and h-vector for semi-planar conical intersection are calculated and discussed along with their geometrical parameters. Keywords: Theoretical chemistry, Density functional calculations, Ultrafast radiationless decay, Cytosine, Conical intersection, Ultrastability The ability of DNA and RNA to absorb ultraviolet Broad-band transient absorption spectroscopy rule out light without significant reaction or fluorescence is a the involvement of excited state proton transfer property that is vital for life.1,2 The excited state mechanism for cytosine which is the dominated lifetime of cytosine has been measured to be in the mechanism for cytosine-guanine pair in the gas picoseconds time scale at values from 0.72 to 3.2 ps.3-6 phase.30 Gas-phase ultrafast excited state dynamics of It has been proposed that the DNA/RNA cytosine using femto second pump-probe nucleobases, when excited by UV light, rapidly funnel photoionization spectroscopy reveals that the cytosine their excited-state population to the ground state enol tautomer exhibits a significantly longer excited through conical intersections between the first excited state lifetime than its keto and imino counterparts. 1,7-27 singlet state, S1, and the ground state surface, S0. The initially excited states of the cytosine keto and Thus, the excited population cannot, in general, imino tautomers decay with sub-picoseconds remain excited long enough to fluoresce or to be dynamics for excitation wavelengths shorter than reactive in an intermolecular collision. Instead, the 300 nm, whereas that of the cytosine enol tautomer excess energy is rapidly dissipated as vibrational decays with time constants ranging from 3 – 45 ps energy (heat) to the surroundings. for excitation between 260 and 285 nm.31 The Two possible decay mechanisms from S to S have 1 0 picoseconds fragment decay times in cytosine can be been proposed28 through two conical intersections, the linked to passage over a barrier to reach one of the so-called “sofa” and “twist”. Ab initio electronic conical intersections.32 structure calculations and ultrafast laser pulses probed with strong field near infrared pulses reveal that the Car Parrinello MD method in combination with deactivation proceeds through at least two pathways.29 CASPT2 calculations show that the keto N1H form is 144 INDIAN J CHEM, SEC A, FEBRUARY 2014 the most stable one, and the calculated spectra of this of electrons and U(,)r R represents the electrostatic tautomer show good agreement with experimental interactions among electrons and nuclei. 33 measurements. Excited state dynamics of cytosine The adiabatic potential energy surfaces near the using AIMS method reveal multiple intrinsic pathways intersection point can be obtained by solving Eq. (3), * involving conical intersection between nπ with S0 and * * H ()()()R − EHR R ππ with S0. Their calculations showed that nπ with αα aβ = 0 … (3) S0 pathway has two possible conical intersections, and H βα ()()()R HEββ RR− in the dominant one the population transfer was similar to the sofa-form conical intersection which takes as Eq. (4). * almost half of the trajectories while for S0 and ππ 1 pathway there was one conical intersection similar Ea or b ()()()RRR=HHαα + ββ 2{ to the twist-form conical intersection.34 2 The present study aims to contribute to the 2 ± HHαα (R )−ββ (R ) + 4 |Hαβ (R ) | . understanding of the ultrafast radiationless decay of cytosine. We have investigate the global and local … (4) optimized geometry of cytosine in the ground state. The a-b conical intersection is determined by the The ultrafast relaxation mechanisms of cytosine condition that the energy difference between the two through conical intersections are investigated adiabatic electronic states is equal to zero, that is Eq. (5). theoretically at a high level of theory. The present 2 2 study report a new conical intersection that has a HHαα (R )−ββ (R ) + 4 |Hαβ (R ) |= 0 … (5) smaller deformation in geometry relative to the already reported conical intersections. This may led to The difference between the two diagonal matrix better understanding for the deactivation pathway elements can be expanded to the first order of internal mechanisms of cytosine in the gas phase. coordinates {Q} around a position R = R* that locates close to the intersection position R = Rc as Eq. (6). Theoretical H (RR)()− H Brief description of conical intersection αα ββ Let us consider a case in which two electronic ∂ 21 ≈HHαα(R *) − ββ (R *) +∑ HH αα()()RR − ββ Qi states (a and b) intersect at a position Rc. ∂Q R= R* i i Adiabatic electronic wave functions Ψa(r,R) and =HHαα(R *) − ββ ( R *) + g ⋅ Q Ψb(r,R) in which r and R represent electronic and nuclear coordinates respectively, are expanded in … (6) terms of diabatic electronic wave functions ψα(r,R) Here, the g-vector represents the difference in the and ψβ(r,R) as Eq. (1), gradient of the diabatic potential energy between the ΘΘ()()R R two electronic states at position R = R*: Eq. (7). cos− sin Ψ (,)r R ψ (,)r R a 2 2 α g ≡[ ψ (,)r R | ∇H (r ,R ) | ψ (,)r R = α α ΘΘ()()R R ψ (,)r R Ψb (,)r R sin cos β −ψ (,)r R | ∇H (r , R ) | ψ (,)r R ] 2 2 β β R= R* … (1) … (7) where Θ()R can be expressed in terms of the The internal coordinates {Q} involved in the matrix elements, Haa(R), Hbb(R) and g-vector, {Qt}, are referred to as tuning or accepting modes.35 The off-diagonal matrix element is expanded Hαβ ()(,)(,)(,)R(= ψ α r RH r Rψ β r R ) of the r in the similar way described above as Eq. (8). electronic Hamiltonian at R, H(r, R). ∂ 2H (R ) αβ HHαβ (RRR)≈αβ ( *) + ∑ Hαβ () Qi tanΘ (R ) = … (2) ∂Q RR= * i i Hαα()()RR− H ββ The electronic Hamiltonian is given by =Hαβ (R *) + h ⋅ Q . H(,)(,)r R=TUr + r R , where Tr is the kinetic energy … (8) AZIZ et al.: ULTRAFAST RADIATIONLESS DECAY OF CYTOSINE BY CONICAL INTERSECTIONS 145 Here, the h - vector is defined as 6-311++G(3df,3pd) basis set using Beek’s three- parameter-hybrid (B3LYP) DFT method.36–38 The h ≡ ψ (,)|r R∇H (,)| r Rψ (,) r R α β RR= * B3LYP method provides energetic typically better than Hartree–Fock method39 and can reproduce better … (9) geometrical parameters comparable to the experimental 40 The internal coordinates involved in the h-vector, values. All geometry optimizations, and vibrational {Q }, are called coupling or promoting modes.35 frequency calculations were carried out using the c Gaussian 09 software package.41 No symmetry When we find the conical intersection R* = Rc, Eqs. (6) and (8) with Eqs. (7) and (9) are evaluated at constrains were applied during the geometry optimization. Solvent effect was estimated using the R = Rc as SCI-PCM model where the SCRF calculation uses a HHαα ()()R−ββ R ≈ g ⋅ Q … (10) cavity determined self-consistently from an isodensity surface. The formalism is based on the conductor and screening model as implemented in G09 program. H αβ ()R≈ h ⋅ Q … (11) Conical intersection We now define d as the energy difference between Complete Active Space Multi-configuration SCF 42-47 the two electronic states, a and b, near Rc. Then, (CASSCF) level of theory with the 6-31G basis from Eq.(11) we obtain Eq. (12) set were used to calculate the energies of electronic states and to optimize the geometrical structures of 2 2 2 HH(R )− (R ) + 4H (R ) = d the conical intersections between two states. The αα ββ αβ … (12) CASSCF active space for cytosine include four Computational details occupied molecular orbitals (two π and two lone Ground state geometry optimization pairs) and five unoccupied molecular orbitals (three The molecular geometry of all possible tautomeric π* and two σ*).
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