Probing DNA Structural Heterogeneity by Identifying Conformational Subensembles of a Bicovalently Bound Cyanine Dye

DNA is a re-configurable, biological information-storage unit, and much remains to be learned about its heterogeneous structural dynamics. For example, while it is known that molecular dyes templated onto DNA exhibit increased photostability, the mechanism by which the structural dynamics of DNA affect the dye photophysics remains unknown. Here, we use femtosecond, two-dimensional electronic spectroscopy measurements of a cyanine dye, Cy5, to probe local conformations in samples of single-stranded DNA (ssDNA–Cy5), double-stranded DNA (dsDNA–Cy5), and Holliday junction DNA (HJ–DNA–Cy5). A line shape analysis of the 2D spectra reveals a strong excitation–emission correlation present in only the dsDNA–Cy5 complex, which is a signature of inhomogeneous broadening. Molecular dynamics simulations support the conclusion that this inhomogeneous broadening arises from a nearly degenerate conformer found only in the dsDNA–Cy5 complex. These insights will support future studies on DNA’s structural heterogeneity

Tuning Between Quenching and Energy Transfer in DNA-Templated Heterodimer Aggregates

Molecular excitons, which propagate spatially via electronic energy transfer, are central to numerous applications including light harvesting, organic optoelectronics, and nanoscale computing; they may also benefit applications such as photothermal therapy and photoacoustic imaging through the local generation of heat via rapid excited-state quenching. Here we show how to tune between energy transfer and quenching for heterodimers of the same pair of cyanine dyes by altering their spatial configuration on a DNA template. We assemble “transverse” and “adjacent” heterodimers of Cy5 and Cy5.5 using DNA Holliday junctions. We find that the transverse heterodimers exhibit optical properties consistent with excitonically interacting dyes and fluorescence quenching, while the adjacent heterodimers exhibit optical properties consistent with nonexcitonically interacting dyes and disproportionately large Cy5.5 emission, suggestive of energy transfer between dyes. We use transient absorption spectroscopy to show that quenching in the transverse heterodimer occurs via rapid nonradiative decay to the ground state (∼31 ps) and that in the adjacent heterodimer rapid energy transfer from Cy5 to Cy5.5 (∼420 fs) is followed by Cy5.5 excited-state relaxation (∼700 ps). Accessing such drastically different photophysics, which may be tuned on demand for different target applications, highlights the utility of DNA as a template for dye aggregation

Oblique Packing and Tunable Excitonic Coupling in DNA-Templated Squaraine Rotaxane Dimer Aggregates

When molecules are aggregated such that their excited states form delocalized excitons, their spatial arrangement, or packing, can be coarsely controlled by templating and finely controlled by chemical substitution; however, challenges remain in controlling their packing on intermediate length scales. Here, we use an approach based on mechanically interlocked molecules to promote an elusive oblique packing arrangement in a series of three squaraine rotaxane dimers. We template the squaraine rotaxane dimers using DNA and observe two excitonically split bands of near-equal intensity in their absorption spectra – a distinct signature of oblique packing, validated by theoretical modeling of the experimental results. Additional fine control of packing is demonstrated by fluorinating the macrocycle of the rotaxane, which promotes denser packing and stronger excitonic interactions

Tunable Electronic Structure via DNA-Templated Heteroaggregates of Two Distinct Cyanine Dyes

Molecular excitons are useful for applications in light harvesting, organic optoelectronics, and nanoscale computing. Electronic energy transfer (EET) is a process central to the function of devices based on molecular excitons. Achieving EET with a high quantum efficiency is a common obstacle to excitonic devices, often owing to the lack of donor and acceptor molecules that exhibit favorable spectral overlap. EET quantum efficiencies may be substantially improved through the use of heteroaggregates─aggregates of chemically distinct dyes─rather than individual dyes as energy relay units. However, controlling the assembly of heteroaggregates remains a significant challenge. Here, we use DNA Holliday junctions to assemble homo- and heterotetramer aggregates of the prototypical cyanine dyes Cy5 and Cy5.5. In addition to permitting control over the number of dyes within an aggregate, DNA-templated assembly confers control over aggregate composition, i.e., the ratio of constituent Cy5 and Cy5.5 dyes. By varying the ratio of Cy5 and Cy5.5, we show that the most intense absorption feature of the resulting tetramer can be shifted in energy over a range of almost 200 meV (1600 cm–1). All tetramers pack in the form of H-aggregates and exhibit quenched emission and drastically reduced excited-state lifetimes compared to the monomeric dyes. We apply a purely electronic exciton theory model to describe the observed progression of the absorption spectra. This model agrees with both the measured data and a more sophisticated vibronic model of the absorption and circular dichroism spectra, indicating that Cy5 and Cy5.5 heteroaggregates are largely described by molecular exciton theory. Finally, we extend the purely electronic exciton model to describe an idealized J-aggregate based on Förster resonance energy transfer (FRET) and discuss the potential advantages of such a device over traditional FRET relays

Hydrogen-Bond Driven Chemical Separations: Elucidating the Inter-facial Steps of Self-Assembly in Solvent Extraction

Chemical separations, particularly liquid extractions, are pervasive in academic and industrial laboratories, yet a mechanistic understanding of the events governing their function are obscured by interfacial phenomena that are notoriously difficult to measure. In this work, we investigate the fundamental steps of ligand self-assembly as driven by changes in the interfacial H-bonding network using vibrational sum frequency generation. Our results show how the bulk pH modulates the interfacial structure of extractants at the buried oil/aqueous interface via the formation of unique H-bonding networks that order and bridge ligands to produce self-assembled aggregates. These extended H-bonded structures are key to the subsequent extraction of Co2+ from the aqueous phase in promoting micelle formation and subsequent ejection of said micelle into the oil phase. The combination of static and time resolved measurements reveals the mechanisms underlying complexities of liquid extractions at high [Co2+]:[DEHPA] ratios by showing an evolution of interfacially assembled structures that are readily tuned on a chemical basis by altering the compositions of the aqueous phase. The results of this work point to new mechanistic principles to design separations through the manipulation of surface charge, electrostatic screening, and the associated H-bonding networks that arise at the interface to facilitate organization and subsequent extractio

Exciton Coupling Model for the Emergence of Second Harmonic Generation from Assemblies of Centrosymmetric Molecules

A simple model is presented for interpreting the presence of substantial second harmonic generation (SHG) activity from assemblies of centrosymmetric molecular building blocks. Using butadiene as a computationally tractable centrosymmetric model system, time-dependent Hartree–Fock calculations of the nonlinear polarizability of butadiene dimer were well-described through exciton coupling arguments based on the electronic structure of the monomer and the relative orientation between the monomers within the dimer. Experimental studies of the centrosymmetric molecule 2,6-di-<i>tert</i>-butylanthraquinone suggest the formation of a combination of SHG-active and SHG-inactive crystal forms. The structure for the centrosymmetric form is known, serving as a negative control for the model, while the presence of an additional SHG-active metastable form is consistent with predictions of the model for alternative molecular packing configurations

Exciton Coupling Model for the Emergence of Second Harmonic Generation from Assemblies of Centrosymmetric Molecules

A simple model is presented for interpreting the presence of substantial second harmonic generation (SHG) activity from assemblies of centrosymmetric molecular building blocks. Using butadiene as a computationally tractable centrosymmetric model system, time-dependent Hartree–Fock calculations of the nonlinear polarizability of butadiene dimer were well-described through exciton coupling arguments based on the electronic structure of the monomer and the relative orientation between the monomers within the dimer. Experimental studies of the centrosymmetric molecule 2,6-di-<i>tert</i>-butylanthraquinone suggest the formation of a combination of SHG-active and SHG-inactive crystal forms. The structure for the centrosymmetric form is known, serving as a negative control for the model, while the presence of an additional SHG-active metastable form is consistent with predictions of the model for alternative molecular packing configurations

Interfacial Acidity on Oxide Surfaces: A Scaling Paradigm and the Role of the Hydrogen Bond

A fundamental understanding of acidity at an interface, as mediated by structure and molecule-surface interactions, is essential to elucidate the mechanisms of a range of chemical transformations. While the strength­­­­ of an acid in the gas and solution phases is conceptually well understood, how acid-base chemistry works at an interface is notoriously more complicated. Using density functional theory and nonlinear vibrational spectroscopy, we have developed a method to determine the interfacial Brønsted-Lowry acidity of aliphatic alcohols adsorbed on the {100} surface of the model perovskite, strontium titanate. Here we show that, while shorter and less branched alkanols are less acidic as a gas and more acidic in solution, shorter alcohols are less acidic whereas less substituted alkanols are more acidic at the gas-surface interface. Hydrogen bonding plays a critical role in defining acidity, whereas structure-acidity relationships are dominated by van der Waals interactions between the alcohol and the surface. </p

Insight into the Mechanisms Driving the Self-Assembly of Functional Interfaces: Moving from Lipids to Charged Amphiphilic Oligomers

Polymer-stabilized liquid-liquid interfaces are an important and growing class of bioinspired materials that combine the structural and functional capabilities of advanced synthetic materials with naturally evolved biophysical systems. These platforms have the potential to serve as selective membranes for chemical separations, molecular sequencers, and to even mimic neuromorphic computing elements. Despite the diversity in function, basic insight into the assembly of well-defined amphiphilic polymers to form functional structures remains elusive, which hinders the continued development of these technologies. In this work we provide new mechanistic insight into the assembly of an amphiphilic polymer-stabilized oil/aqueous interface, in which the headgroups consist of positively charged methylimidazolium ionic liquids, and the tails are short, monodisperse oligodimethylsiloxanes covalently attached to the headgroups. We demonstrate using vibrational sum frequency generation spectroscopy and pendant drop tensiometery that the composition of the bulk aqueous phase, particularly the ionic strength, dictates the kinetics and structures of the amphiphiles in the organic phase as they decorate the interface. These results show that H-bonding and electrostatic interactions taking place in the aqueous phase bias the grafted oligomer conformations that are adopted in the neighboring oil phase. The kinetics of self-assembly were ionic strength dependent and found to be surprisingly slow, being composed of distinct regimes where molecules adsorb and reorient on relatively fast time scales, but where conformational sampling and frustrated packing takes place over longer timescales. These results set the stage for understanding related chemical phenomena of bioinspired materials in diverse technological and fundamental scientific fields and provide a solid physical foundation on which to design new functional interfaces