A three-state model for the photophysics of adenine

An ab initio theoretical study at the CASPT2 level is reported on minimum energy reaction paths, state minima, transition states, reaction barriers, and conical intersections on the potential energy hypersurfaces of two tautomers of adenine: 9H- and 7H-adenine. The obtained results led to a complete interpretation of the photophysics of adenine and derivatives, both under jet-cooled conditions and in solution, within a three-state model. The ultrafast subpicosecond fluorescence decay measured in adenine is attributed to the low-lying conical intersection (gs/pipi* La)(CI), reached from the initially populated 1(pipi* La) state along a path which is found to be barrierless only in 9H-adenine, while for the 7H tautomer the presence of an intermediate plateau corresponding to an NH2-twisted conformation may explain the absence of ultrafast decay in 7-substituted compounds. A secondary picosecond decay is assigned to a path involving switches towards two other states, 1(pipi* Lb) and 1(npi*), ultimately leading to another conical intersection with the ground state, (gs/npi*), with a perpendicular disposition of the amino group. The topology of the hypersurfaces and the state properties explain the absence of secondary decay in 9-substituted adenines in water in terms of the higher position of the 1(npi*) state and also that the 1(pipi* Lb) state of 7H-adenine is responsible for the observed fluorescence in water. A detailed discussion comparing recent experimental and theoretical findings is given. As for other nucleobases, the predominant role of a pipi*-type state in the ultrafast deactivation of adenine is confirmed.     

A three-state model for the polymorphism in linear tricobalt compounds

The remarkable polymorphism exhibited by the linear tricobalt compounds, Co3(mu3-dpa)4Cl2 and Co3(mu3-dpa)4Br2, can be explained using a model involving three distinct electronic states. At high temperatures, symmetric and unsymmetric forms arise from the population of doublet (2A) and quartet (4B) states, respectively, the latter containing a localized high-spin Co(II) center. In the unsymmetric form, a reduction in temperature leads to a spin-crossover to a second quite distinct doublet state, 2B, where, uniquely, the d(x2-y2) character on the localized Co(II) center is distributed between the occupied and vacant manifolds. The variable population of the Co d(x2-y2) orbital gives rise to the continuous change in Co-Co and Co-N bond lengths as the temperature is decreased.     

Nuclear dynamics for a three-state Jahn-Teller model system

We report wavepacket dynamics on a model system with a three-state conical intersection. Quantum wavepacket dynamics using the multiconfigurational time-dependent Hartree method have been carried out for the T ? (e + t(2)) Jahn-Teller problem, using a Jahn-Teller vibronic model Hamiltonian. The effects of the magnitude of the coupling parameters and of the initial position of the wavepacket on the dynamics around the three-state conical intersection have been considered. It was found that the effect of the coupling strength is not dramatic for the population transfer in most cases, but the details of the dynamics and the involvement of the different modes are affected by it.     

A three-state effective Hamiltonian for symmetric cationic diarylmethanes

We analyze the low-energy electronic structure of a series of symmetric cationic diarylmethanes, which are bridge-substituted derivatives of Michler's Hydrol Blue. We use a four-electron, three-orbital complete active space self-consistent field and multi-state multi-reference perturbation theory model to calculate a three-state diabatic effective Hamiltonian for each dye in the series. We exploit an isolobal analogy between the active spaces of the self-consistent field solutions for each dye to represent the electronic structure in a set of analogous diabatic states. The diabatic states can be identified with the bonding structures in classical resonance-theoretic models of cyanine dyes. We identify diabatic states with opposing charge and bond-order localization, analogous to the classical resonance structures, and a third state with charge on the bridge. While the left- and right-charged structures are similar for all dyes, the structure of the bridge-charged diabatic state, and the Hamiltonian matrix elements connected to it, change significantly across the series. The change is correlated with an inversion of the sign of the charge carrier on the bridge, which changes from an electron pair to a hole as the series is traversed.     

Ab initio studies on the photophysics of guanine tautomers: out-of-plane deformation and NH dissociation pathways to conical intersections

The radiationless decay mechanisms of the S1 excited states of the 7H-keto-amino, 7H-enol-amino, and 7H-keto-imino tautomers of guanine have been investigated with the CASPT2//CASSCF method. Out-of-plane deformation of the six-membered ring or the imino group as well as dissociation of NH bonds have been considered as photochemical pathways leading to conical intersections with the electronic ground state. It has been found that all three tautomers can reach S0-S1 conical intersections by out-of-plane deformation. However, only in the 7H-keto-amino tautomer the reaction path leading to the conical intersection is barrierless. This tautomer also has the lowest energy barrier for hydrogen detachment via the (1)pi sigma* state, whose potential energy surface intersects that of the (1)pi pi* state as well as that of the ground state. The other tautomers of guanine exhibit substantial energy barriers on their S1 potential energy surfaces with respect to both reaction mechanisms. These findings suggest that the 7H-keto-amino tautomer exhibits the shortest excited-state lifetime of the three tautomers due to particularly fast nonradiative deactivation processes through S0-S1 conical intersections. The computational results explain the remarkable observation that the energetically most stable 7H-keto-amino tautomer is missing in the resonant two-photon ionization spectrum of guanine in a supersonic jet. The results also explain that the energetically less stable 7H-enol-amino and 7H-keto-imino tautomers have longer excited-state lifetimes and are thus detectable by resonant two-photon ionization.     

A theoretical insight into the photophysics of psoralen

Psoralen photophysics has been studied on quantum chemistry grounds using the multiconfigurational second-order perturbation method CASPT2. Absorption and emission spectra of the system have been rationalized by computing the energies and properties of the low-lying singlet and triplet excited states. The S1 pipi* state has been determined to be responsible of the lowest absorption and fluorescence bands and to initially carry the population in the photophysical processes related to the phototherapeutic properties of psoralen derivatives. The low-lying T1 pipi* state is, on the other hand, protagonist of the phosphorescence, and its prevalent role in the reactivity of psoralen is suggested to be related to the elongation of the pyrone ring C3-C4 bond, where the spin density is distributed on both carbon atoms. Analysis of energy gaps and spin-orbit coupling elements indicates that the efficient photophysical process leading to the population of the lowest triplet state does not take place at the Franck-Condon region but along the S1 relaxation path.     

Statistical mechanical treatment of protein conformation. II. A three-state model for specific-sequence copolymers of amino acids.

A one-dimensional three-state Ising model [involving alpha-helical (alpha), extended (epsilon), and coil (or other) (c) states] for specific-sequence copolymers of amino acids ahs been formulated in order to treat the conformational states of proteins. This model involves four parameters (wh,iota, vh, iota, v episilon, iota, and uc, iota), and requires a 4 X 4 matrix for generating statistical weights. Some problems in applying this model to a specific-sequence copolymer of amino acids are discussed. A nearest-neighbor approximation for treating this three-state model is also formulated; it requires a 3 X 3 matrix, in which the same four parameters appear, but (as with the 4 X 4 matrix treatment) only three parameters (wh, uh, and v epsilon) are required if relative statistical weights are used. The relationship between the present three-state model (3 X 3 matrix treatment) and models of the helix--coil transition is discussed. Then, the three-state model (3 X 3 matrix treatment) is incorporated into an earlier (Tanaka--Scheraga) model of the helix-coil transition, in which asymmetric nucleation of helical sequences is taken into account. A method for calculating molecular averages and conformational-sequence probabilities, P(iota/eta/(rho)), i.e., the probability of finding a sequence of eta residues in a specific conformational state (rho), starting at the iotath position of the chain, is described. Two alternative methods for calculating P(iota/eta/(rho)), that can be applied to a model involving any number of states, are proposed and presented; one is the direct matrix-multiplication method, and the other uses a first-order a priori probability and a conditional probability. In this paper, these calculations are performed with the nearest-neighbor model, and without the feature of asymmetric nucleation. Finally, it is indicated how the three-state model and the methods for computing P(iota/eta/(rho)) can be applied to predict protein conformation.     

Excited-state potential energy surface for the photophysics of adenine

The decay paths on the singlet excited-state surface of 9H-adenine and the associated energy barriers have been calculated at the CAS-PT2//CASSCF level. There are three fundamental paths for the photophysics: two paths for the (1)L(b) state which are virtually barrierless at the present level of theory and correspond to formation of the (n,pi) intermediate and direct decay to the ground state and a third path for ground-state decay of the (n,pi) state with an activation barrier of approximately 0.1 eV. The (1)L(a) state, which has the largest oscillator strength, either decays directly to the ground state or contributes indirectly to the excited-state lifetime by populating the two other states. The results are used to interpret the photophysics in terms of an excited-state plateau for the (1)L(b) state that corresponds to the short-lived excited-state component (approximately 0.1 ps) and a well (i.e., a proper minimum) for the (n,pi) state that gives rise to the long component (1 ps or more). The direct decay to the ground state of the (1)L(b) state is probably the decay channel invoked to explain the experimental wavelength dependence of the relative amplitudes of the two components. In addition to that, the excited-state component in the nanosecond range detected in the time-resolved photoelectron spectrum is proposed to be a triplet (pi,pi) state formed after intersystem crossing from the singlet (n,pi) state.     

Extended Born-Oppenheimer equation for a three-state system

We present explicit forms of nonadiabatic coupling (NAC) elements of nuclear Schrodinger equation (SE) for a coupled three-state electronic manifold in terms of mixing angles of real electronic basis functions. If the adiabatic-diabatic transformation (ADT) angles are the mixing angles of electronic bases, ADT matrix transforms away the NAC terms and brings diabatic form of SE. ADT and NAC matrices are shown to satisfy a curl condition with nonzero divergence. We have demonstrated that the formulation of extended Born-Oppenheimer (EBO) equation from any three-state BO system is possible only when there exists a coordinate-independent ratio of the gradients for each pair of mixing angles. On the contrary, since such relations among the mixing angles lead to zero curl, we explore its validity analytically around conical intersection(s) and support numerically considering two nuclear-coordinate-dependent three surface BO models. Numerical calculations are performed by using newly derived diabatic and EBO equations and expected transition probabilities are obtained.     

A three-state surface-confined molecular switch with multiple channel outputs

A self-assembled monolayer of a tetrathiafulvalene derivative on indium tin oxide is shown to operate as a ternary redox switch in which the magnetic and optical outputs are employed to provide a readout of the state. This surface-confined molecular switch exhibits excellent reversibility and stability and is thus promising for the development of molecular electronics.     

A three-state mechanism for DNA hairpin folding characterized by multiparameter fluorescence fluctuation spectroscopy

The folding of a dye-quencher labeled DNA hairpin molecule was investigated using fluorescence autocorrelation and cross-correlation spectroscopy (FCS) and photon counting histogram analysis (PCH). The autocorrelation and cross-correlation measurements revealed the flow and diffusion times of the DNA molecules through two spatially offset detection volumes, the relaxation time of the folding reaction, and the total concentration of DNA molecules participating in the reaction. The PCH measurements revealed the equilibrium distribution of DNA molecules in folded and unfolded conformations and the specific brightnesses of the fluorophore in each conformational state. These measurements were carried out over a range of NaCl concentrations, from those that favored the open form of the DNA hairpin to those that favored the closed form. DNA melting curves obtained from each sample were also analyzed for comparison. It was found that the reactant concentrations were depleted as the reaction progressed and that the equilibrium distributions measured by FCS and PCH deviated from those obtained from the melting curve analyses. These observations suggest a three-state mechanism for the DNA hairpin folding reaction that involves a stable intermediate form of the DNA hairpin. The reaction being probed by FCS and PCH is suggested to be a rapid equilibrium between open and intermediate conformations. Formation of the fully closed DNA hairpin is suggested to occur on a much longer time scale than the FCS and PCH measurement time. The closed form of the hairpin thus serves as a sink into which the reactants are depleted as the reaction progresses.     

Photoprotection and the photophysics of acylated anthocyanins

The proposed role of anthocyanins in protecting plants against excess solar radiation is consistent with the occurrence of ultrafast (5-25?ps) excited-state proton transfer as the major de-excitation pathway of these molecules. However, because natural anthocyanins absorb mainly in the visible region of the spectra, with only a narrow absorption band in the UV-B region, this highly efficient deactivation mechanism would essentially only protect the plant from visible light. On the other hand, ground-state charge-transfer complexes of anthocyanins with naturally occurring electron-donor co-pigments, such as hydroxylated flavones, flavonoids, and hydroxycinnamic or benzoic acids, do exhibit high UV-B absorptivities that complement that of the anthocyanins. In this work, we report a comparative study of the photophysics of the naturally occurring anthocyanin cyanin, intermolecular cyanin-coumaric acid complexes, and an acylated anthocyanin, that is, cyanin with a pendant coumaric ester co-pigment. Both inter- and intramolecular anthocyanin-co-pigment complexes are shown to have ultrafast energy dissipation pathways comparable to those of model flavylium cation-co-pigment complexes. However, from the standpoint of photoprotection, the results indicate that the covalent attachment of co-pigment molecules to the anthocyanin represents a much more efficient strategy by providing the plant with significant UV-B absorption capacity and at the same time coupling this absorption to efficient energy dissipation pathways (ultrafast internal conversion of the complexed form and fast energy transfer from the excited co-pigment to the anthocyanin followed by adiabatic proton transfer) that avoid net photochemical damage.     

The photophysics and photobiology of the eye

The eye consists of three major segments: the cornea, lens and retina. The main function of the anterior ocular tissue, the cornea and the lens is to transmit and focus light on the retina without distortion. They also filter out UV light (less than 400 nm) and prevent it from reaching the retina. Much of the light reaching the retina is used for sight. However, light can have numerous other effects on the constituents of the eye, both beneficial and deleterious. This article reviews the interaction of light with the eye, various protective mechanisms, the possible role of light in aging and disease states and the role of light in biological processes other than sight such as mood, hormonal secretions and the cyclic growth and phagocytosis of the rods and cones.     

Photochemistry and photophysics of thienocarbazoles

Two methylated thienocarbazoles and two of their synthetic nitro-precursors have been examined by absorption, luminescence, laser flash photolysis and photoacoustic techniques. Their spectroscopic and photophysical characterization involves fluorescence spectra, fluorescence quantum yields and lifetimes, and phosphorescence spectra and phosphorescence lifetimes for all the compounds. Triplet-singlet difference absorption spectra, triplet molar absorption coefficients, triplet lifetimes, intersystem crossing S1 --> T1 and singlet molecular oxygen yields were obtained for the thienocarbazoles. In the case of the thienocarbazoles it was found that the lowest-lying singlet and triplet excited states, S1 and T1, are of pi,pi* origin, whereas for their precursors S1 is n,pi*, and T1 is pi,pi*. In both thienocarbazoles it appears that the thianaphthene ring dictates the S1 --> T1 yield, albeit there is less predominance of that ring in the triplet state of the linear thienocarbazole, which leads to a decrease in the observed phiT value.     

Compartmental analysis in photophysics: fluorescence decay kinetics and identifiability analysis of a model for successive complexation

The triple-exponential fluorescence delta-response function is derived for the photophysical model of successive complexation between ligand and analyte. Initially, a complex with 1:1 stoichiometry between ligand and analyte is formed. Further binding leads to a complex with two analyte molecules per ligand molecule. We show that this model is uniquely identifiable. This means that all deactivation and exchange rate constants in the excited state and all spectral parameters associated with photoexcitation and fluorescence emission can be uniquely determined. The issues of controllability and observability are discussed for this photophysical system. The conditions, under which a non-controllable or non-observable system is obtained, are described.     

Ultrafast photophysics of the isolated indole molecule

The relaxation dynamics of the isolated indole molecule has been tracked by femtosecond time-resolved ionization. The excitation region explored (283-243 nm) covers three excited states: the two ππ* L(b) and L(a) states, and the dark πσ* state with dissociative character. In the low energy region (λ > 273 nm) the transients collected reflect the absorption of the long living L(b) state. The L(a) state is met 1000-1500 cm(-1) above the L(b) origin, giving rise to an ultrafast lifetime of 40 fs caused by the internal conversion to the lower L(b) minimum through a conical intersection. An additional ~400 fs component, found at excitation wavelengths shorter than 263 nm, is ascribed to dynamics along the πσ* state, which is likely populated through coupling to the photoexcited L(a) state. The study provides a general view of the indole photophysics, which is driven by the interplay between these three excited surfaces and the ground state.     

Effect of hexafluorobenzene on the photophysics of pyrene

Absorption and fluorescence spectroscopy studies reveal the formation of a weak complex between pyrene and C(6)F(6) even in very dilute systems. The complex affects the photophysics of pyrene and reveals a combination of static and dynamic-quenching phenomena in both polar and nonpolar solvents. The results are supported by computational studies that shed light on the structure of the complex and the interactions involved and suggest that ground and excited-state interactions are of comparable magnitude; the association is believed to be driven by quadrupolar interactions. Understanding these interactions in solution is important for applications that aim at controlling the regio- or stereoselectivity of organic reactions.