Tracking Hole Transport in DNA Hairpins Using a Phenylethynylguanine Nucleobase

Interaction of Photogenerated Spin Qubit Pairs with a Third Electron Spin in DNA Hairpins

The designing of tunable molecular systems that can host spin qubits is a promising strategy for advancing the development of quantum information science (QIS) applications. Photogenerated radical pairs are good spin qubit pair (SQP) candidates because they can be initialized in a pure quantum state that exhibits relatively long coherence times. DNA is a well-studied molecular system that allows for control of energetics and spatial specificity through careful design and thus serves as a tunable scaffold on which to control multispin interactions. Here, we examine a series of DNA hairpins that use naphthalenediimide (NDI) as the hairpin linker. Photoexcitation of the NDI leads to subnanosecond oxidation of guanine (G) within the duplex or a stilbenediether (Sd) end-cap to give NDI^•--G^•+ or NDI^•--Sd^•+ SQPs, respectively. A 2,2,6,6-tetramethylpiperdinyl-1-oxyl (TEMPO) stable radical is covalently attached to the hairpin at varying distances from the SQP spins. While TEMPO has a minimal effect on the SQP formation and decay dynamics, EPR spectroscopy indicates that there are significant spin-spin dipolar interactions between the SQP and TEMPO. We also demonstrate the ability to implement more complex spin manipulations of the NDI^•--Sd^•+-TEMPO system using pulse-EPR techniques, which is important for developing DNA hairpins for QIS applications.

Tuning molecular fluctuation to boost the conductance in DNA based molecular wires

Inherent molecular fluctuations are known to have a significant influence on the charge transport properties of biomolecules like DNA, PNA and proteins. In this work, we show ways to control these fluctuations and further demonstrate their use to enhance the conductance of two widely studied molecular wires, namely dsDNA (DNA) and G4 Quadruplex (G4-Quad). We quantify the molecular fluctuation in terms of the root mean square deviation (RMSD) of the molecule. In the case of DNA, we use temperature to control the fluctuations, while in the case of G4-Quad the fluctuations are tuned by the ions inside the pore. The electronic coupling between the bases of dsDNA and G4-Quad, which measures the conductance of these molecular wires, shows a non-monotonic behaviour with the increase in fluctuation. We find values of fluctuation which give rise to maximum electronic coupling and hence high conductivity for both the cases. In the case of DNA, these optimal fluctuations (∼2.5 Å) are achieved at a temperature of 210 K, which gives rise to an electronic coupling of 0.135 eV between the DNA bases. The optimal fluctuations in G4-Quad are achieved (∼7 Å) in a 4 base pair long system with 2 Na⁺ ions inside the pore, giving rise to an electronic coupling of 0.09 eV.

Nickel-Catalyzed Stereodivergent Synthesis of E- and Z-Alkenes by Hydrogenation of Alkynes

A convenient protocol for stereodivergent hydrogenation of alkynes to E- and Z-alkenes by using nickel catalysts was developed. Simple Ni(NO3 )2 ⋅6 H2 O as a catalyst precursor formed active nanoparticles, which were effective for the semihydrogenation of several alkynes with high selectivity for the Z-alkene (Z/E>99:1). Upon addition of specific multidentate ligands (triphos, tetraphos), the resulting molecular catalysts were highly selective for the E-alkene products (E/Z>99:1). Mechanistic studies revealed that the Z-alkene-selective catalyst was heterogeneous whereas the E-alkene-selective catalyst was homogeneous. In the latter case, the alkyne was first hydrogenated to a Z-alkene, which was subsequently isomerized to the E-alkene. This proposal was supported by density functional theory calculations. This synthetic methodology was shown to be generally applicable in >40 examples and scalable to multigram-scale experiments.

Directional and regioselective hole injection of spiropyran photoswitches intercalated into A/T-duplex DNA

The hole electron transfer of UV excited spiropyran intercalated in dsDNA is directional, asymmetric and regioselective, as shown by quantitative multiscale computations.

Tracking Photoinduced Charge Separation in DNA: from Start to Finish

The initial studies of the dynamics of photoinduced charge separation conducted in our laboratories 20 years ago found strongly distance-dependent rate constants over short distances but failed to detect intermediates in the transport of positive charge (holes). These observations were consistent with the single-step superexchange or tunneling mechanism that had been observed for numerous donor-bridge-acceptor systems at that time. Subsequent studies found weak distance dependence for hole transport over longer distances in DNA, characteristic of incoherent hopping of either localized or delocalized holes. The introduction of synthetic DNA capped hairpin constructs possessing hole donor and acceptor chromophores (or purine bases) at opposite ends of a base-pair domain made it possible to determine the time required for transit of charge from one chromophore to the other and, in some cases, to distinguish between the transit time and the much faster initial charge injection time. These studies eliminated conventional tunneling as a viable mechanism for charge transport in DNA except at very short donor-acceptor separations; however, they did not establish the presence or nature of intermediates in the charge separation process. Recent studies in our laboratories have succeeded in identifying key intermediates as well as untangling the dynamics and efficiency of the charge separation process from start to finish. The dynamics of the initial charge injection process is dependent upon both its free energy and the stacking of the hole donor chromophore and adjacent purine base. The transport of positive charge (holes) over multiple base pairs in duplex DNA occurs most efficiently via repeating adenine bases, known as A-tracts. The transit time across an A-tract is strongly dependent upon the free energy for hole injection, whereas the efficiency of charge separation depends on the competition between charge delocalization and charge recombination in the contact radical ion pair. The guanine cation radical has been detected both by femtosecond transient absorption and by stimulated Raman spectroscopies when the guanine is located near the chromophore employed for hole injection into an A-tract. Replacement of guanine by its derivative 8-phenylethynylguanine (EG), permits tracking of hole transport across longer poly(purine) sequences as a consequence of the stronger transient absorption and stimulated Raman scattering for EG^+• vs G^+•. We have recently obtained evidence based on femtosecond transient absorption spectroscopy for the formation of delocalized A-polarons in A-tracts possessing four or more A-T base pairs. Similar methods have been used to track hole transport across less-common DNA structures including diblock and triblock poly(purines), locked nucleic acids, three-way junctions, and G-quadruplexes. Similar methods are have been applied to the study of photoinduced electron transport in DNA.

Fluorescent excimers and exciplexes of the purine base derivative 8-phenylethynyl-guanine in DNA hairpins

The ground- and excited-state electronic interactions between the nucleobase analog 8-(4'-phenylethynyl)deoxyguanosine, EG, with natural nucleobases and 7-deazaguanine, as well as between adjacent EG base analogs, have been characterized using a combination of steady-state spectroscopy and time-resolved fluorescence, absorption, and stimulated Raman spectroscopies. The properties of the nucleoside EG-H2 are only weakly perturbed upon incorporation into synthetic DNA hairpins in which thymine, cytosine or adenine are the bases flanking EG. Incorporation of the nucleoside to be adjacent to guanine or deazaguanine results in the formation of short-lived (40-80 ps) exciplexes, the charge transfer character of which increases as the oxidation potential of the donor decreases. Hairpins possessing two or three adjacent EG base analogs display exciton-coupled circular dichroism in the ground state and form long-lived fluorescent excited states upon electronic excitation. Incorporation of EG into the helical scaffold of the DNA hairpins places it adjacent to its neighboring nucleobases or a second EG, thus providing the close proximity required for the formation of exciplex or excimer intermediates upon geometric relaxation of the short-lived EG excited state. The three time-resolved spectroscopic methods employed permit both the characterization of the several intermediates and the kinetics of their formation and decay.

X-ray Generated Recombination Exciplexes of Substituted Diphenylacetylenes with Tertiary Amines: A Versatile Experimental Vehicle for Targeted Creation of Deep-Blue Electroluminescent Systems

Customizable and technology-friendly functional materials are one of the mainstays of emerging organic electronics and optoelectronics. We show that recombination exciplexes of simple substituted diphenylacetylenes with tertiary amines can be a convenient source of tunable deep-blue emission with possible applications in organic electroluminescent systems. The optically inaccessible exciplexes were produced via recombination of radiation-generated radical ion pairs in alkane solution, which mimics charge transport and recombination in the active layer of practical organic light-emitting diodes in a simple solution-based experiment. Despite varying and rather poor intrinsic emission properties, diphenylacetylene and its prototypical methoxy (donor) or trifluoromethyl (acceptor) monosubstituted derivatives readily form recombination exciplexes with N,N-dimethylaniline and other tertiary amines that produce emission with maxima ranging from 385 to 435 nm. The position of emission band maximum linearly correlates with readily calculated gas-phase electron affinity of the corresponding diphenylacetylene, which can be used for fast computational prescreening of the candidate molecules, and various substituted diphenylacetylenes can be synthesized via relatively simple and universal cross-coupling reactions of Sonogashira and Castro. Together, the simple solution-based experiment, computationally cheap prescreening method, and universal synthetic strategy may open a very broad and chemically convenient class of compounds to obtain OLEDs and OLED-based multifunctional devices with tunable emission spectrum and high conversion efficiency that has yet not been seriously considered for these purposes.