DNA base-pair flipping with fluorescent perylenediimide pincers.

The synthesis, structure, and electronic spectra of a series of DNA hairpins possessing two perylenediimide (PDI) base pair surrogates are reported. The PDI chromophores are located in opposite strands of the hairpin base pair domain opposite abasic sites and are either adjacent to each other or separated by a variable number of AT or GC base pairs. Molecular modeling of the conjugate having adjacent PDI chromophores shows that they adopt a slipped, pi-stacked geometry with an angle of 40 degrees between the PDI long axes. The electronic absorption, fluorescence, and circular dichroism of this conjugate are consistent with a stacked PDI structure. Conjugates having one or two GC base pairs between the PDI chromophores display spectra that are consistent with isolated PDIs. Conjugates having 1-4 AT base pairs have more complex spectra, suggestive of an equilibrium between base paired and flipped structures having stacked PDIs. Heating of the conjugates possessing isolated PDI chromophores results in base pair flipping. The free energy for PDI stacking is greater than that for a single AT base pair and comparable to that for a single GC base pair or two AT base pairs.

Dynamics of ultrafast singlet and triplet charge transfer in anthraquinone-DNA conjugates.

The efficiency of singlet and triplet charge radical ion-pair formation and the dynamics of radical-pair charge recombination in DNA-anthraquinone conjugates have been investigated by means of femtosecond time-resolved transient absorption spectroscopy. Singlet charge separation is more efficient than intersystem crossing, resulting in inefficient formation of the long-lived triplet radical ion pair. Both singlet charge separation and charge recombination are faster when guanine rather than adenine is the neighboring purine base.

Single molecule conductance of bipyridyl ethynes: the role of surface binding modes.

We report on the experimental studies of single molecule conductance of 1,2-bi(pyridin-4-yl)ethyne (BPY-EY) and perfluoro-1,2-bi(pyridin-4-yl)ethyne (PFBPY-EY). The conductance measurements of the molecules bridging two Au electrodes have been carried out in toluene solutions using the scanning tunneling microscopy (STM) based break junction technique. Two conductance values of (2.2 ± 0.5) × 10(-4) and (5.0 ± 0.8) × 10(-5) G(0) have been found for BPY-EY but only one, (4.2 ± 0.5) × 10(-5) G(0), for PFBPY-EY. The disparity is attributed to steric differences between the molecules at the electrode.

Hydrophobic dimerization and thermal dissociation of perylenediimide-linked DNA hairpins.

The structure and properties of hairpin-forming bis(oligonucleotide) conjugates possessing perylenediimide (PDI) chromophores as hairpin linkers have been investigated using a combination of spectroscopic and computational methods. These conjugates exist predominantly as monomer hairpins at room temperature in the absence of added salt and as head-to-head hairpin dimers in the presence of >50 mM NaCl. The hairpin dimer structure is consistent with the results of small-angle X-ray scattering in aqueous solution and molecular dynamics simulation. The structure of the nonconjugated PDI dimer in water is investigated using potential of mean force calculations. The salt dependence is attributed to increased cation condensation in the hairpin dimer vs monomer. Upon heating at low salt concentrations, the hairpin dimer undergoes sequential dissociation to form the monomer hairpin followed by conversion to a random coil structure; whereas at high salt concentrations both dissociation processes occur over the same temperature range. The monomer and dimer hairpins have distinct spectroscopic properties both in the ground state and excited singlet state. The UV and CD spectra provide evidence for electronic interaction between PDI and the adjacent base pair. Low fluorescence quantum yields are observed for both the monomer and dimer. The transient absorption spectrum of the dimer undergoes time-dependent spectral changes attributed to a change in the PDI-PDI torsional angle from ca. 20 degrees in the Franck-Condon singlet state to ca. 0 degrees in the relaxed singlet state, a process which occurs within ca. 40 ps.

Excited state, charge transfer, and spin dynamics in DNA hairpin conjugates with perylenediimide hairpin linkers.

A series of short DNA hairpins (nG) using perylene-3,4:9,10-bis(dicarboximide) (PDI) as the hairpin linker was synthesized in which the distance between the PDI and a guanine-cytosine (G-C) base pair is systematically varied by changing the number (n - 1) of adenine-thymine (A-T) base pairs between them. Due to the relatively large hydrophobic surface of PDI, the nG hairpins dimerize in buffer solutions. The photophysics and photochemistry of these hairpins were investigated using femtosecond transient absorption and time-resolved electron paramagnetic resonance (TREPR) spectroscopy. Photoexcitation of the self-assembled PDI dimer within each nG hairpin results in subpicosecond formation of its lower exciton state ((1*)PDI(2)) followed by formation of an excimer-like state ((1*X)PDI(2)) with tau = 10-28 ps. Both of these states are lower in energy than (1*)PDI, so that neither can oxidize A, C, and T. Electron transfer from G to (1*)PDI(2) is faster than formation of (1*X)PDI(2) only for 1G. Electron transfer from G to (1*X)PDI(2) for 2G-8G, occurs by the superexchange mechanism and, thus, becomes exponentially less efficient as the G-PDI(2) distance increases. Nevertheless, TREPR studies show that photoexcitation of 2G and 4G produce spin-correlated radical ion pairs having electron spin polarization patterns indicating that a low yield of charge separation proceeds from (1*X)PDI(2) by the radical pair intersystem crossing (RP-ISC) mechanism to initially yield a singlet radical ion pair. The strong spin-polarization of the radical ion pairs makes it possible to observe them, even though their concentration is low. As expected, the hairpin lacking G (0G) and that having the longest G-PDI(2) distance (8G) display no TREPR radical ion pair signals. Hairpins 0G, 2G, 4G, and 8G all exhibit triplet EPR spectra at 85 K. Simulations of the spectra show that (3*)PDI is produced mainly by a spin-orbit-induced intersystem crossing mechanism, while the spectra of 2G and 4G have 5% and 21% contributions, respectively, from (3*)PDI produced by charge recombination of radical ion pairs that originate from RP-ISC. These low percentages of RP-ISC derived (3*)PDI result mainly from the low yield of radical ion pairs in 2G and 4G.

Charge-transfer and spin dynamics in DNA hairpin conjugates with perylenediimide as a base-pair surrogate.

A perylenediimide chromophore (P) was incorporated into DNA hairpins as a base-pair surrogate to prevent the self-aggregation of P that is typical when it is used as the hairpin linker. The photoinduced charge-transfer and spin dynamics of these hairpins were studied using femtosecond transient absorption spectroscopy and time-resolved EPR spectroscopy (TREPR). P is a photooxidant that is sufficiently powerful to quantitatively inject holes into adjacent adenine (A) and guanine (G) nucleobases. The charge-transfer dynamics observed following hole injection from P into the A-tract of the DNA hairpins is consistent with formation of a polaron involving an estimated 3-4 A bases. Trapping of the (A 3-4) (+*) polaron by a G base at the opposite end of the A-tract from P is competitive with charge recombination of the polaron and P (-*) only at short P-G distances. In a hairpin having 3 A-T base pairs between P and G ( 4G), the radical ion pair that results from trapping of the hole by G is spin-correlated and displays TREPR spectra at 295 and 85 K that are consistent with its formation from (1*)P by the radical-pair intersystem crossing mechanism. Charge recombination is spin-selective and produces (3*)P, which at 85 K exhibits a spin-polarized TREPR spectrum that is diagnostic of its origin from the spin-correlated radical ion pair. Interestingly, in a hairpin having no G bases ( 0G), TREPR spectra at 85 K revealed a spin-correlated radical pair with a dipolar interaction identical to that of 4G, implying that the A-base in the fourth A-T base pair away from the P chromophore serves as a hole trap. Our data suggest that hole injection and transport in these hairpins is completely dominated by polaron generation and movement to a trap site rather than by superexchange. On the other hand, the barrier for charge injection from G (+*) back onto the A-T base pairs is strongly activated, so charge recombination from G (or even A trap sites at 85 K) most likely proceeds by a superexchange mechanism.

Ortho effect in the Bergman cyclization: interception of p-benzyne intermediate by intramolecular hydrogen abstraction.

Intramolecular hydrogen atom (H-atom) abstraction from the o-OCH3 group effectively intercepts the p-benzyne intermediate in the Bergman cycloaromatization of 2,3-diethynyl-1-methoxybenzene (1) before this intermediate undergoes either retro-Bergman ring opening or external H-atom abstraction. This process leads to the formation of a new diradical and renders the cyclization step essentially irreversible. Chemical and kinetic consequences of this phenomenon were investigated through the combination of computational and experimental studies.

Ortho effect in the Bergman cyclization: comparison of experimental approaches and dissection of cycloaromatization kinetics.

Four different experimental sources of kinetic information were combined to study the effect of ortho substituents on the rate of Bergman cycloaromatization. All methods confirm that the cyclization barrier is highly sensitive to the nature of the ortho substituents. However, the measured activation energies strongly depend on the choice of experimental technique: even the relative trends provided by the different methods agree with each other only in the case of acceptor substituents. Both the onset peaks and the activation energies determined by differential scanning calorimetry (DSC; either in neat enediynes or in their solutions in 10.6 M 1,4-cyclohexadiene (1,4-CHD)) strongly overestimate the reactivity of 1,2-diethynylbenzene, suggesting that DSC cannot be taken as a reliable indicator of enediyne reactivity. This discrepancy is likely to stem from the presence of side reactions with low activation barriers, especially important when the reaction is conducted in neat enediyne. On the other hand, kinetic measurements based on monitoring the concentrations of enediyne reactants and naphthalene products provide reliable general trends that include the parent benzannelated enediyne. These measurements confirm that both ortho-NO2 and ortho-CHO substituents substantially decrease activation energies for the Bergman cyclization, supporting earlier computational predictions. A comparison of theory and experiment suggests that computations at the Moeller-Plesset second-order perturbation theory (MP2)/6-31G level provide an excellent alternative to DFT when an accurate description of the contribution of noncovalent interactions to the activation energy is needed. Activation energies derived from k(eff), the effective rate constant under the pseudo-first-order approximation, depend on the 1,4-CHD concentrations. The true rate constant, k(1), for the cyclization step and the ratio of constants for the retro-Bergman ring opening, k(-1), and the intermolecular H-atom abstraction, k2, were determined from the dependence of cycloaromatization kinetics of ortho- and para-NO2 substituted enediynes on the concentration of 1,4-CHD.

Triplet acetylenes as synthetic equivalents of 1,2-bicarbenes, part II: new supramolecular scaffolds from photochemical cycloaddition of diarylacetylenes to 1,4-cyclohexadienes.

1,5-Diaryl substituted homoquadricyclanes which are readily available through cascade photocycloaddition of diarylacetylenes to 1,4-cyclohexadienes are useful supramolecular scaffolds with an angle of about 60 degrees formed by the two aromatic rings defining a hydrophobic cavity. These structural features of pyridinyl homoquadricyclanes were applied to the design of composite organic/inorganic materials with topologies depending on the ratio of ligand to metal. The crystal structure of complex 1 (L1/AgNO(3) in a 1:1 ratio) shows an alternating ligand-metal polymer in which each of the silver ions in its linear coordination geometry is shared between two L1 molecules. A small change in the crystallization method yields a supramolecular rhomboid (complex 2, L1/AgNO(3) 3:2 ratio) which has two ligands that occupy opposite corners of the rhomboid and two silver atoms occupy the other two corners. Connection of the rhomboids units through a third molecule forms unique "beads on a string" polymeric chains. In complex 2, the silver ions adopt a distorted tetrahedral geometry with the nitrate anion occupying one of the vertices of the tetrahedron. The crystal packing of the chain of rhomboids generates cavities which are filled with disordered solvent molecules. Non-symmetrical homoquadricyclane L3 coordinates with silver only through the nitrogen of the pyridine ring but not through the nitrogen of the tetrafluoropyridine ring in which the electron density of the nitrogen lone-pair is very low. The substituents on the polycyclic moiety of the homoquadricyclane cause restricted rotation of the pyridine rings which suggests that the flexibility of such systems can be fine-tuned to create a family of supramolecular scaffolds of controlled rigidity.

Triplet acetylenes as synthetic equivalents of 1,2-bicarbenes: phantom n,pi state controls reactivity in triplet photocycloaddition.

Diaryl acetylenes, in which one of the aryl groups is either a pyridine or a pyrazine, undergo efficient triplet state photocycloaddition to 1,4-cyclohexadiene with formation of 1,5-diaryl substituted tetracyclo[3.3.0.0(2,8).0(4,6)]octanes (homoquadricyclanes). In the case of pyrazinyl acetylenes, the primary homoquadricyclane products undergo a secondary photochemical rearangement leading to diaryl substituted tricyclo[3.2.1.0(4,6)]oct-2-enes. Mechanistic and photophysical studies suggest that photocycloaddition proceeds through an electrophilic triplet excited state whereas the subsequent rearrangement to the tricyclooctenes proceeds through a singlet excited state. Chemical and quantum yields for the cycloaddition, in general, correlate with the electron acceptor character of aryl substituents but are attenuated by photophysical factors, such as the competition between the conversion of acetylene singlet excited state into the reactive triplet excited states (intersystem crossing: ISC) and/or to the radical-anion (photoelectron transfer from the diene to the excited acetylene: PET). Dramatically enhanced ISC between pi-pi S(1) state and "phantom" n,pi triplet excited state is likely to be important in directing reactivity to the triplet pathway. The role of PET can be minimized by the judicious choice of reaction conditions (solvent, concentration, etc.). From a practical perspective, such reactions are interesting because "capping" of the triple bond with the polycyclic framework orients the terminal aryl (4-pyridyl, 4-tetrafluoropyridyl, phenyl, etc.) groups in an almost perfect 60 degrees angle and renders such molecules promising supramolecular building blocks, especially in the design of metal coordination polymers.

Homoanomeric effects in six-membered heterocycles.

Structural and energetic consequences of homoanomeric n(X) --> beta-sigma(C-Y) interactions in saturated six-membered heterocycles where X = O, N, S, Se and Y = H, Cl were studied computationally using a combination of density functional theory (B3LYP) and Natural Bond Orbital (NBO) analysis. Unlike the classic anomeric effect where the interacting donor and acceptor orbitals are parallel and overlap sidewise in a pi-fashion, orbital interactions responsible for homoanomeric effects can follow different patterns imposed by the geometric restraints of the respective cyclic moieties. For the equatorial beta-C-Y bonds in oxa-, thia- and selena-cyclohexanes, only the homoanomeric n(X)(ax) --> sigma(C-Y)(eq) interaction (the Plough effect) with the axial lone pair of X is important, whereas the n(X)(eq) --> sigma(C-Y)(eq) interaction (the W-effect) is negligible. On the other hand, the W-effect is noticeably larger than the n(X)(ax) --> sigma(C-Y)(eq) interaction in azacyclohexanes. Hyperconjugation is a controlling factor which determines relative trends in the equatorial beta-C-H bonds in heterocycloxanes. In contrast, all homoanomeric interactions are weak for the respective axial bonds where relative lengths are determined by intramolecular electron transfer through exchange interactions and polarization-induced rehybridization. Although the homoanomeric effects are considerably weaker than the classic vicinal anomeric n(X)(ax)-->alpha-sigma(C-Y)(ax) interactions, their importance increases significantly when the acceptor ability of sigmaorbitals increases as a result of bond stretching and/or polarization. Depending on the number of electrons and the topology of interactions, homoconjugation interactions can be cooperative (enhance each other) or anticooperative (compete with each other). Such effects reflect symmetry of the wave function and can be considered as weak manifestations of sigma homoaromaticity or homoantiaromaticity.

Stereoelectronic effects and general trends in hyperconjugative acceptor ability of sigma bonds.

A systematic study of general trends in sigma acceptor properties of C-X bonds where X is a main group element from groups IVa-IIa is presented. The acceptor ability of the C-X sigma bonds in monosubstituted ethanes increases when going to the end of a period and down a group. Enhancement of acceptor ability of C-X sigma bonds as one moves from left to right in periods parallels the increase in electronegativity of X, whereas augmentation of acceptor ability in groups is opposite to the changes in electronegativity of X and in the C-X bond polarization, following instead the decrease in the energy of sigma(C)(-)(X) orbitals when one moves from the top to the bottom within a group. This simple picture of acceptor ability of sigma bonds being controlled by electronegativity in periods and by sigma orbital energy in groups is changed in monosubstituted ethenes where the role of electronegativity of the substituent X becomes more important due to increased overlap between sigma orbitals. The combination of several effects of similar magnitude influences acceptor ability of sigma bonds in monosubstituted ethenes in a complex way. As a result, the acceptor ability of sigma bonds can be significantly modified by substitution and is conformer dependent. Stereoelectronic effects displayed by C-X bonds with X from second and third periods are highly anisotropic. For example, C-chalcogen bonds are excellent sigma acceptors at the carbon end but poor sigma acceptors at the chalcogen end. This effect can be relied upon in the design of molecular diodes with sigma bridges with unidirectional electron conductivity. While the general trends revealed in this work should be useful for the qualitative understanding of stereoelectronic effects, one should bear in mind that the magnitude of hyperconjugative effects is extremely sensitive to small variations in structure and in substitution. This advocates for the increased role of theoretical methods in analysis of stereoelectronic effects.