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Photoexcitation of anthraquinones (AQ) in association with DNA results in DNA damage mainly at guanine residues, with products from thymine oxidation also observed. Studies of adenine oxidation will be aided by systems with an increased driving force for charge transfer, achieved by adding electron-withdrawing groups to the AQ ring. Attaching AQ derivatives to adenine via a bridge with two carbon atoms should enable the intended regiocontrol within the DNA duplex structure. Herein we report the synthesis of conjugates between AQ and adenine in which the AQ moieties have been modified with a formyl, a trifluoroacetyl, and two methyl ester groups. These have been synthesized by palladium coupling of tert-butyldiphenylsilyl 5'-protected 8-ethynyl-2'-deoxyadenosine with the corresponding bromoanthraquinone intermediates. Bromo intermediates bearing formyl or trifluoroacetyl were prepared by monolithiation of 2,6-dibromoanthraquinone, a step that required protection of the anthraquinone carbonyls. A bromo intermediate bearing two methyl ester groups was obtained from 1,2,4-trimethylbenzene by Friedel-Crafts acylation with 4-bromobenzoyl chloride followed by oxidation to the tricarboxylic acid, cyclization to form the anthraquinone ring, and finally esterification. Hydrogenation of the ethynyl linker gave the ethanyl linker. Cyclic voltammetry showed that the conjugate with the two ester groups and ethynyl linker was the most easily reduced of the derivatives synthesized. These derivatives, with reduction potentials favorable for electron transfer, can be used in studies of adenine oxidation in DNA.

The goal of this work is to produce high yields of long-lived AQ(*-)/dA(*+) charge transfer (CT) excited states (or photoproducts). This goal fits within a larger context of trying generally to produce high yields of long-lived CT excited states within DNA nucleoside conjugates that can be incorporated into DNA duplexes. Depending upon the energetics of the anthraquinonyl (AQ) (3)(pi,pi) state as well as the reduction potentials of the subunits in particular anthraquinonyl-adenine conjugates, CT quenching of the AQ (3)(pi,pi*) state may or may not occur in polar organic solvents. In MeOH, bis(3',5'-O-acetyl)-N(6)-(anthraquinone-2-carbonyl)-2'-deoxyadenosine (AQCOdA) behaves as intended and forms a (3)(AQ(*-)/dA(*+)) CT state with a lifetime of 3 ns. However, in nonpolar THF the AQ(*-)/dA(*+) CT states of AQCOdA are too high in energy to be formed, and in DMSO a (1)(AQ(*-)/dA(*+)) CT state is formed but lives only 6 ps. Although the lowest energy excited state for AQCOdA in MeOH is a (3)(AQ(*-)/dA(*+)) CT state, for N(6)-(anthraquinone-2-methylenyl)-2'-deoxyadenosine (AQMedA) in the same solvent it is a (3)(pi,pi*) state. Changing the linking carbonyl in AQCOdA to methylene in AQMedA makes the anthraquinonyl subunit harder to reduce by 166 mV. This raises the energy of the (3)(AQ(*-)/dA(*+)) CT state above that of the (3)(pi,pi*) in AQMedA. The conclusion is that anthraquinonyl-dA conjugates will not have lowest energy AQ(*-)/dA(*+) CT states in polar organic solvents unless the anthraquinonyl subunit is also substituted with an electron-withdrawing group that raises the AQ-subunit's reduction potential above that of AQ. A key finding in this work is that the lifetime of the (3)(AQ(*-)/dA(*+)) CT excited state (ca. 3 ns) is ca. 500-times longer than that of the corresponding (1)(AQ(*-)/dA(*+)) CT excited state (ca. 6 ps).'

In this work we present calculated absorption and emission spectra in acetonitrile (MeCN) solution of N-acetyl-1-aminopyrene (PAAc, a spectroscopic model compound) and N-(1-pyrenyl)-1-methyluracil-5-carboxamide (PAU(Me), a computational model for 5-(N-carboxyl-1-aminopyrenyl)-2'-deoxyuridine (PAdU)). The computational method used--the discrete reaction field approach (DRF)--combines a quantum mechanical (QM) description of the solute (here DFT and INDOs/CIS, i.e., the INDO parametrization for spectroscopy) with a classical, molecular mechanics (MM) description of the solvent molecules. The latter are modeled with point charges representing the permanent charge distribution and polarizabilities to account for many-body interactions among the solute and other solvent molecules. Molecular dynamics is used to sample the degrees of freedom of the solution around several solute conformations each in two electronic excited states. This leads to a large number of solute/solvent configurations from which 800 are selected for each excited state and collected into a single ensemble by means of proper Boltzmann averaging. DRF INDOs/CIS applied to the selected solute/solvent configurations give simulated absorption and emission band spectra--each based on 15,200 calculated transitions--that compare well with experimental results. For example, the much broader absorption and emission bands in PAdU compared with PAAc are reproduced, and the simulated emission spectra of PAU(Me) agree well with broad (380-550 nm) charge transfer (CT) emission seen for PAdU in MeCN. The observed multiexponential fluorescence decay profiles for PAdU in different polar solvents are interpreted in terms of solute/solvent conformational heterogeneity here generated in the MD simulations for PAU(Me) in MeCN. Additionally, the simulations demonstrate the mixing of the forbidden Py*+/dU*- CT states with allowed pyrenyl 1(pi,pi*) states.

Femtosecond, picosecond, and nanosecond transient absorbance (TA) and picosecond emission kinetics results are presented for three 5-(1-pyrenyl)-2'-deoxyuridine nucleosides each with a different two-atom linker joining pyrenyl C-1 to uracil C-5. The linkers are respectively -NHCO-, -(CH(2))(2)-, and -C[triple bond]C- for PAdU, PEdU, and PYdU. For all three nucleoside conjugates, most conformers undergo intramolecular charge transfer (CT) from their pyrenyl (1)(pi,pi) excited states to form Py(*+)/dU(*-) CT products in ultrashort times:

Studies of six 5-(pyren-1-yl-ethynyl)-2'-deoxyuridine (U(PY))-substituted DNA duplexes in this work test and support the conclusions reported by Gaballah et al. (J. Phys. Chem. B 2005, 109, 5927-5934) based on investigations of 5-(2-pyren-1-yl-ethylenyl)-2'-deoxyuridine (U(PE))-substituted DNA hairpins. As expected because of the rigid ethynyl linker in U(PY) (compared to the flexible ethylenyl linker in U(PE)), U(PY)-substituted duplexes do not show enhanced charge transfer (CT) emission quantum yields for duplexes with 5-fluorodeoxyuridine (U(F)) electron traps near U(PY) compared to duplexes without traps. Furthermore, the average CT lifetime and emission quantum yield of U(PY)-substituted duplexes is independent of the U(F) trap location. These new results strongly suggest that the excess electron in the PY*+/dU*- CT state of U(PY) is restrained from hopping to nearby U(F) traps due to attraction to PY*+.

In this work nine DNA hairpins (HPs) are studied at room temperature to observe their pyrene(*+)/dU(*-) CT excited-state dynamics following photoexcitation at 355 nm with a 25 ps laser pulse. The HPs are 18-24 bases long, have a central tetra-T loop, and have a single U(PE) (5-(2-pyren-1-yl-ethylenyl)-2'-deoxyuridine) substitution in the central region of their stems. Three of the HPs are also substituted with 5-XdU traps, where X = Br or F, to learn about the effects of these traps on CT excited-state lifetimes and emission quantum yields in U(PE) substituted HPs. The combination of lengthened average CT lifetime and enhanced CT emission quantum yield in HPs with excess electron traps compared to HPs lacking traps strongly suggests that excess electrons are injected into the DNA stem at pyrimidine sites external to U(PE) as well via charge separation within U(PE) itself. Furthermore, the increased CT emission quantum yield in HPs with traps compared to HPs without traps implies that externally injected electrons can migrate to uracil in U(PE) (i.e., Py(*+)dU) and thus indirectly form the emissive Py(*+)dU(*-) CT state of U(PE).

The challenge in working with anthraquinone-2'-deoxyadenosine (AQ-dA) conjugates is that they are insoluble in water and only sparingly soluble in most organic solvents. However, water-soluble AQ-dA conjugates with short linkers are required for study of their electrochemical and intramolecular electron transfer properties in this solvent prior to their use in laser kinetics investigations of photoinduced hole (cation) transport in DNA. This article first describes the synthesis of a water-soluble, ethynyl-linked AQ-dA conjugate, 8-[(anthraquinone-2-yl)ethynyl]-2'-deoxyadenosine 3'-benzyl hydrogen phosphate, based on initial formation of a 5'-O-(4,4'-dimethoxytrityl) (5'-O-DMTr) intermediate. Because intended H2 over Pd/C reduction of the ethynyl linker in 5'-O-DMTr-protected 2'-deoxyadenosines cleaves the DMTr protecting group and precipitates multiple side products, this work also describes the synthesis of an ethylenyl-linked AQ-dA conjugate, 8-[2-(anthraquinone-2-yl)ethyl]-2'-deoxyadenosine 3'-benzyl hydrogen phosphate, starting with a 5'-O-tert-butyldiphenylsilyl protecting group.

The desire to produce reversible electron traps for direct, room temperature studies of excess electron transport in DNA duplexes and hairpins motivated our efforts first to link pyridines to 2'-deoxyuridine (pyridinyl-dU) and then to convert these new conjugates into pyridiniumyl-dU nucleosides. Base sensitivity studies presented here rule out general use of bipyridinediiumyl compounds, but show that pyridiniumyl compounds are suitable for use under the strand cleavage and base deprotection procedures required for automated solid-phase oligonucleotide synthesis. This paper presents the synthesis of four 5'-O-DMT-protected 5-(N-methylpyridiniumyl)-dU conjugates using either ethynyl or ethylenyl linkers to join the pyridiniumyl and dU subunits.

The synthesis of 2,2'-bipyridinyl-2'-deoxyuridine metal-chelator nucleosides (Bipy-dU) with either ethynyl or ethylenyl linkers was now been accomplished. These new nucleosides will permit the construction of a number of corresponding metallo-DNA conjugates where many types of metals can be complexed to the 2,2'-bipyridinyl chelator group and the resulting metallo-dU conjugates incorporated into DNA oligonucleotides. Additionally this paper also reports the synthesis of a di-N-alkylated bipyridinediiumyl-2'-deoxyuridine nucleoside (Bipy(2+)-dU) with an ethylenyl linker. The Bipy(2+)-dU nucleoside was found to decompose under basic conditions precluding its use in standard automated DNA-synthesis by the phosphoramidite method. No such restrictions apply to the two Bipy-dU nucleosides reported here for use as metal chelators.

Described are picosecond and nanosecond time-resolved optical (TRO) spectral and nanosecond time-resolved infrared (TRIR) spectral studies of intermediates generated when the rhodium(I) complexes trans-RhCl(CO)L2 (L = PPh3 (I), P(p-tolyl)3 (II), or PMe3 (III)) are subjected to photoexcitation. Each of these species, which are precursors in the photocatalytic activation of hydrocarbons, undergoes CO labilization to form an intermediate concluded to be the solvated complex RhCl(Sol)L2 (A(i)). The picosecond studies demonstrate that an initial transient is formed promptly (<30 ps), which decays to A(i) with lifetimes ranging from 40 to 560 ps depending upon L and the medium. This is proposed on the basis of ab initio calculations to be a metal-to-ligand charge transfer (MLCT) excited state. Second-order rate constants (kCO) for reaction of the A(i) with CO were determined, and these depend on the nature of L and the solvent, the slowest rate being for A(I) in tetrahydrofuran (kCO = 7.1 x 10(6) M(-1) x s(-1)), the fastest being for A(III) in dichloromethane (1.3 x 10(9) M(-1) x s(-1)). Each A(i) also undergoes competitive unimolecular reaction with solvent to form long-lived transients with TRIR properties suggesting these to be Rh(III) products of oxidative addition. Although this was mostly suppressed by the presence of higher concentrations of CO (which trapped A(i) to re-form the starting complexes in each case), both TRO and TRIR experiments indicate that a fraction of the oxidative addition could not be quenched. Thus, the short-lived MLCT state or a vibrationally hot species formed during the decay of this excited state appears to participate directly in C-H activation.

Syntheses of two analogs of deoxyuridine with N,N-dialkylaniline chromophores are reported. 5-[3-(N-methylphenylamino)propanoyl]-2'-deoxyuridine (1) and 5-[2-(4-N,N-dimethylaminophenyl)ethyl)]-2'-deoxyuridine (2) are prepared by palladium-mediated coupling. Preparation of 2 was facilitated by in situ transient O4-trimethylsilyl protection during alkynylation which suppressed secondary cyclization of the coupling adduct.

Comparison of picosecond kinetic and spectroscopic data for Zn octaethylporphine and Fe(III)Cl octaethylporphine with that for Zn-Fe(III)Cl, a cofacial diporphyrin composed of a Zn porphyrin covalently bound to an Fe(III)Cl porphyrin with two chains of five atoms each, supports the assignment of a light-driven electron transfer (k > 10(11)s(-1)) within Zn-Fe(III)Cl to form [Zn(+).-Fe(II)]Cl. The kinetics (k approximately 10(10)s(-1)) and thermodynamics of the reverse electron transfer are compared to those of a similar electron transfer in bacterial photosynthesis, the reduction of an oxidized bacteriochlorophyll dimer, (BChl)(2) (+)., by Fe(II) cytochrome c.

A transient absorption spectrum has been measured in Rhodopseudomonas spheroides R26 reaction centers. Its salient features indicate that both the bacteriopheophytin and bacteriochlorophyll chromophores play a role in the excited state. Decay of this state yields a rise time for oxidation of the reaction center complex of about 150 picoseconds.