Vibrational relaxation and hydrogen bond dynamics in methanol-d dissolved in CCl 4 have been measured with ultrafast infrared pump-probe spectroscopy. We excited the subensemble of methanol-d molecules both accepting and donating hydrogen bonds at ∼2500 cm -1 . Following vibrational relaxation with a ∼500 fs lifetime, the signal does not decay to zero. Rather, the signal increases to a second maximum at ∼4 ps. The decay from the second maximum occurs on two time scales. We propose a model in which hydrogen bond dissociation, following vibrational relaxation, decreases the concentration of methanol-d molecules that accept and donate hydrogen bonds and produce the observed long-lived bleach of the absorption signal. Using a set of coupled kinetic equations, the time constants for hydrogen bond dissociation and reformation have been determined. Hydrogen bond breaking occurs with ∼200 fs and ∼2 ps time constants. We attribute the fast rate to a direct breaking mechanism wherein the excited hydroxyl stretch decays into modes that directly lead to the hydrogen bond dissociation. The slower rate of breaking is attributed to an indirect mechanism wherein the dissociation of hydrogen bonds follows vibrational energy flow from the initially excited molecule to other components of the same oligomer. The final stage of relaxation, after the second maximum, involves reformation of transiently broken hydrogen bonds. The bonds that break directly recover with ∼7 ps and .10 ns time constants, while the bonds that break indirectly recover with ∼20 ps and .10 ns time constants. Experiments conducted on ethanol-d solutions in CCl 4 demonstrate that the same vibrational relaxation and hydrogen bond dynamic events occur with very similar amplitudes and rate constants. Measurements of the rates of spectral diffusion and polarization anisotropy decay via vibrational excitation transfer and orientational relaxation verify that the initial fast decay of the signal is dominated by vibrational relaxation.

Coherent exciton delocalization in dye aggregate systems gives rise to a variety of intriguing optical phenomena, including J- and H-aggregate behavior and Davydov splitting. Systems that exhibit coherent exciton delocalization at room temperature are of interest for the development of artificial light-harvesting devices, colorimetric detection schemes, and quantum computers. Here, we report on a simple dye system templated by DNA that exhibits tunable optical properties. At low salt and DNA concentrations, a DNA duplex with two internally functionalized Cy5 dyes (i.e., dimer) persists and displays predominantly J-aggregate behavior. Increasing the salt and/or DNA concentrations was found to promote coupling between two of the DNA duplexes via branch migration, thus forming a four-armed junction (i.e., tetramer) with H-aggregate behavior. This H-tetramer aggregate exhibits a surprisingly large Davydov splitting in its absorbance spectrum that produces a visible color change of the solution from cyan to violet and gives clear evidence of coherent exciton delocalization.

Exciton delocalization in dye aggregate systems is a phenomenon that is revealed by spectral features, such as Davydov splitting, J- and H-aggregate behavior, and fluorescence suppression. Using DNA as an architectural template to assemble dye aggregates enables specific control of the aggregate size and dye type, proximal and precise positioning of the dyes within the aggregates, and a method for constructing large, modular two- and three-dimensional arrays. Here, we report on dye aggregates, organized via an immobile Holliday junction DNA template, that exhibit large Davydov splitting of the absorbance spectrum (125 nm, 397.5 meV), J- and H-aggregate behavior, and near-complete suppression of the fluorescence emission (∼97.6% suppression). Because of the unique optical properties of the aggregates, we have demonstrated that our dye aggregate system is a viable candidate as a sensitive absorbance and fluorescence optical reporter. DNA-templated aggregates exhibiting exciton delocalization may find application in optical detection and imaging, light-harvesting, photovoltaics, optical information processing, and quantum computing.

Molecular excitons are used in a variety of applications including light harvesting, optoelectronics, and nanoscale computing. Controlled aggregation via covalent attachment of dyes to DNA templates is a promising aggregate assembly technique that enables the design of extended dye networks. However, there are few studies of exciton dynamics in DNA-templated dye aggregates. We report time-resolved excited-state dynamics measurements of two cyanine-based dye aggregates, a J-like dimer and an H-like tetramer, formed through DNA-templating of covalently attached dyes. Time-resolved fluorescence and transient absorption indicate that nonradiative decay, in the form of internal conversion, dominates the aggregate ground state recovery dynamics, with singlet exciton lifetimes on the order of tens of picoseconds for the aggregates versus nanoseconds for the monomer. These results highlight the importance of circumventing nonradiative decay pathways in the future design of DNA-templated dye aggregates.

DNA-templated molecular (dye) aggregates are a novel class of materials that have garnered attention in a broad range of areas including light harvesting, sensing, and computing. Using DNA to template dye aggregation is attractive due to the relative ease with which DNA nanostructures can be assembled in solution, the diverse array of nanostructures that can be assembled, and the ability to precisely position dyes to within a few Angstroms of one another. These factors, combined with the programmability of DNA, raise the prospect of designer materials custom tailored for specific applications. Although considerable progress has been made in characterizing the optical properties and associated electronic structures of these materials, less is known about their excited-state dynamics. For example, little is known about how the excited-state lifetime, a parameter essential to many applications, is influenced by structural factors, such as the number of dyes within the aggregate and their spatial arrangement. In this work, we use a combination of transient absorption spectroscopy and global target analysis to measure excited-state lifetimes in a series of DNA-templated cyanine dye aggregates. Specifically, we investigate six distinct dimer, trimer, and tetramer aggregates—based on the ubiquitous cyanine dye Cy5—templated using both duplex and Holliday junction DNA nanostructures. We find that these DNA-templated Cy5 aggregates all exhibit significantly reduced excited-state lifetimes, some by more than 2 orders of magnitude, and observe considerable variation among the lifetimes. We attribute the reduced excited-state lifetimes to enhanced nonradiative decay and proceed to discuss various structural factors, including exciton delocalization, dye separation, and DNA heterogeneity, that may contribute to the observed reduction and variability of excited-state lifetimes. Guided by insights from structural modeling, we find that the reduced lifetimes and enhanced nonradiative decay are most strongly correlated with the distance between the dyes. These results inform potential tradeoffs between dye separation, excitonic coupling strength, and excited-state lifetime that motivate deeper mechanistic understanding, potentially via further dye and dye template design.

A promising application of DNA self-assembly is the fabrication of chromophore-based excitonic devices. DNA brick assembly is a compelling method for creating programmable nanobreadboards on which chromophores may be rapidly and easily repositioned to prototype new excitonic devices, optimize device operation, and induce reversible switching. Using DNA nanobreadboards, we have demonstrated each of these functions through the construction and operation of two different excitonic AND logic gates. The modularity and high chromophore density achievable via this brick-based approach provide a viable path toward developing information processing and storage systems.

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Vibrational relaxation of methanol-d ͑MeOD͒ in carbon tetrachloride has been investigated via ultrafast infrared pump-probe experiments. Exciting at 2690 cm Ϫ1 , only the free O-D ͑where the D is not H-bonded͒ stretching mode is initially populated. For MeOD mole fractions р0.025, a 2.15 ps single exponential decay is observed. At mole fractions у0.0375, the signal decays ͑2.15 ps decay time͒ below zero ͑increased absorption͒ and then recovers on time scales of 22 ps and ӷ300 ps. The increased absorption indicates the formation of additional free ODs caused by the breaking of H-bonds that are not directly coupled to the initially excited vibration. The two-time scale recovery of this signal arises from geminate and nongeminate recombination. The data are fit with a set of kinetic equations that accurately reproduce the data. The results suggest that vibrational relaxation of the initially excited free OD stretch into intramolecular modes of the methanol leads to H-bond breaking. This contrasts studies that suggest direct relaxation of a vibrationally excited OH stretch into an H-bond stretch is responsible for H-bond breaking.