Delocalized Two-Exciton States in DNA Scaffolded Cyanine Dimers.

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The engineering and manipulation of delocalized molecular exciton states is a key component for artificial biomimetic light harvesting complexes as well as alternative circuitry platforms based on exciton propagation. Here we examine the consequences of strong electronic coupling in cyanine homodimers on DNA duplex scaffolds. The most closely spaced dyes, attached to positions directly across the double-helix from one another, exhibit pronounced Davydov splitting due to strong electronic coupling. We demonstrate that the DNA scaffold is sufficiently robust to support observation of the transition from the lowest energy (J-like) one-exciton state to the nonlocal two-exciton state, where each cyanine dye is in the excited state. This transition proceeds via sequential photon absorption and persists for the lifetime of the exciton, establishing this as a controlled method for creating two-exciton states. Our observations suggest that DNA-organized dye networks have potential as platforms for molecular logic gates and entangled photon emission based on delocalized two-exciton states.

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CitationsShowing 10 of 36 papers
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Quantum Computing with Exciton Qubits in Colloidal Semiconductor Nanocrystals
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The present work evaluates the feasibility of quantum computing with exciton qubits in coupled colloidal semiconductor nanocrystals (NCs). A strategy for manipulating two-qubit states of colloidal NC hetero-dimers is described. We show that a sequence of laser pulses with the same photon energy can bring excitonic states of a nanocrystal hetero-dimer into entanglement and perform arbitrary qubit rotations (quantum gates). Our simulations of a realistic two-particle assembly of CdSe/CdS core/shell NCs demonstrate that such two-qubit gate operations can be driven by optical parametric oscillators with a theoretical error of 0.1%. A strategy for upscaling two-qubit hetero-dimers to N-qubit exciton gates in semiconductor NC assemblies is discussed.

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Linker dependent symmetry breaking charge separation in 9,10-bis(phenylethynyl)anthracene dimers
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Fast symmetry breaking charge separation (SB-CS) rate and slow CS recombination rate were achieved simultaneously via tuning the molecular geometry.

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Organizing Charge Flow with DNA
  • Jan 1, 2023
  • David J F Walker + 2 more

Abstract The seminal recognition by Ned Seeman that DNA could be programmed via base-pairing to form higher order structures is well known. What may have been partially forgotten is one of Dr. Seeman’s strong motivations for forming precise and programmable nanostructures was to create nanoelectronic devices. This motivation is particularly apt given that modern electronic devices require precision positioning of conductive elements to modulate and control electronic properties, and that such positioning is inherently limited by the scaling of photoresist technologies: DNA may literally be one of the few ways to make devices smaller (Liddle and Gallatin in Nanoscale 3:2679–2688 [1]). As with many other insights regarding DNA at the nanoscale, Ned Seeman recognized the possibilities of DNA-templated electronic devices as early as 1987 (Robinson and Seeman in Protein Eng. 1:295–300 [2]). As of 2002, Braun’s group attempted to develop methods for lithography that involved metalating DNA (Keren et al. in Science 297:72–75 [3]). However, this instance involved linear, double-stranded DNA, in which portions were separated using RecA, and thus, the overall complexity of the lithography was limited. Since then, the extraordinary control afforded by DNA nanotechnology has provided equally interesting opportunities for creating complex electronic circuitry, either via turning DNA into an electronic device itself (Gates et al. in Crit. Rev. Anal. Chem. 44:354–370 [4]), or by having DNA organize other materials (Hu and Niemeyer in Adv. Mat. 31(26), [5]) that can be electronic devices (Dai et al. in Nano Lett. 20:5604–5615 [6]).

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  • 10.1021/jacs.5c00128
Control of Indodicarbocyanine Dimer Geometry Using Variable-Length Linkers to DNA Scaffolds.
  • Aug 1, 2025
  • Journal of the American Chemical Society
  • Adam A Meares + 15 more

In recent years, DNA scaffolds have been utilized to organize dye molecules into aggregates with tailored optical and photophysical properties. While dye separation can be controlled with nanometer-scale accuracy, controlling the relative dye orientation in an aggregate on DNA remains challenging. In this work, we investigate varying the length of the two-point linker between indodicarbocyanine (Cy5) dyes and the DNA template as a method to better control the resulting dimer geometry. To test this approach, we synthesize Cy5 with either 2-carbon or 4-carbon two-point linkers and compare their behavior to commercially available Cy5 with 3-carbon two-point linkers. Using experimental spectroscopy, theoretical modeling, and molecular dynamics simulations, we demonstrate that shortening the linker from 3-carbon to 2-carbon limits the π-π interactions between dyes, thereby promoting the formation of J-like Cy5 dimers. Conversely, increasing the linker length provides the dye more freedom of motion, allowing greater π-π interactions and yielding dimers with greater H-like character. Furthermore, shorter linkers can restrict dye accessible volume, which, under the driving force of π-π interactions, suppresses heterogeneity in dye packing for specific placements of Cy5 on double stranded DNA and DNA Holliday junction scaffolds. These results emphasize the importance of dye linker chemistry in determining important optical and photophysical properties of DNA-scaffolded dye aggregates. They also suggest that tuning the length of the dye linker is an effective strategy to overcome two challenges that currently limit DNA-scaffolded dye aggregates in photonics applications: gaining control of dye aggregate geometry and suppressing heterogeneity in dye packing.

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  • 10.1002/ange.202425422
Proximal Oblique‐Packing of Heptamethine Cyanines through Spiro‐Connection Boosts Triplet State Generation in Near‐Infrared
  • Jan 22, 2025
  • Angewandte Chemie
  • Xueli Wang + 9 more

Abstract Near‐infrared (NIR) triplet dyes are the cornerstones of cutting‐edge biomedical and material applications. The difficulty in rational development of triplet dyes increases exponentially as the absorption wavelength shifts deeper into the NIR range. Although classical H‐/J‐typed packing of NIR dyes has the potential to enhance intersystem crossing (ISC) compared with that in single‐chromophore dyes, the triplet state quantum yields remain limited in such strategy. Herein, proximal oblique‐packed (V‐shaped) heptamethine cyanines (SZ780) through spiro‐connection were achieved. Multi‐channel ultrafast ISC were direct observed in SZ780 and a record high ISC rate constant (up to ~1011 s−1) is registered among all the reported NIR triplet dyes. SZ780 exhibits a triplet state quantum yield of 18.9 % upon excitation at 750 nm, which is almost an order of magnitude higher than that of the monomer (IR780, 2.1 %) and nearly threefold increase compared to that of the H‐packed dimer (SC780) (6.7 %). Moreover, SZ780 efficiently generates singlet oxygen under 808 nm light irradiation, inducing cancer cell apoptosis in vivo. These findings demonstrate that constructing V‐aggregated dyes system by spiro‐connection offers a powerful approach for the design of high‐performance NIR triplet sensitizers.

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  • 10.1016/j.chempr.2020.12.020
Engineering couplings for exciton transport using synthetic DNA scaffolds
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Engineering couplings for exciton transport using synthetic DNA scaffolds

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  • Cite Count Icon 23
  • 10.1021/acs.jpclett.2c00017
Tuning between Quenching and Energy Transfer in DNA-Templated Heterodimer Aggregates.
  • Mar 23, 2022
  • The journal of physical chemistry letters
  • Azhad U Chowdhury + 18 more

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.

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  • 10.1002/ange.202208647
Cyanine Dye Coupling Mediates Self‐assembly of a pH Sensitive Peptide into Novel 3D Architectures
  • Oct 26, 2022
  • Angewandte Chemie
  • Rita Fernandes + 10 more

Abstract Synthetic multichromophore systems are of great importance in artificial light harvesting devices, organic optoelectronics, tumor imaging and therapy. Here, we introduce a promising strategy for the construction of self‐assembled peptide templated dye stacks based on coupling of a de novo designed pH sensitive peptide with a cyanine dye Cy5 at its N‐terminus. Microscopic techniques, in particular cryogenic TEM (cryo‐TEM) and cryo‐electron tomography technique (cryo‐ET), reveal two types of highly ordered three‐dimensional assembly structures on the micrometer scale. Unbranched compact layered rods are observed at pH 7.4 and two‐dimensional membrane‐like assemblies at pH 3.4, both species displaying spectral features of H‐aggregates. Molecular dynamics simulations reveal that the coupling of Cy5 moieties promotes the formation of both ultrastructures, whereas the protonation states of acidic and basic amino acid side chains dictates their ultimate three‐dimensional organization.

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  • Cite Count Icon 1
  • 10.1021/acs.jpclett.4c00065
Unveiling Multiquantum Excitonic Correlations in Push-Pull Polymer Semiconductors.
  • Mar 28, 2024
  • The Journal of Physical Chemistry Letters
  • Yulong Zheng + 4 more

Bound and unbound Frenkel-exciton pairs are essential transient precursors for a variety of photophysical and biochemical processes. In this work, we identify bound and unbound Frenkel-exciton complexes in an electron push-pull polymer semiconductor using coherent two-dimensional spectroscopy. We find that the dominant A0-1 peak of the absorption vibronic progression is accompanied by a subpeak, each dressed by distinct vibrational modes. By considering the Liouville pathways within a two-exciton model, the imbalanced cross-peaks in one-quantum rephasing and nonrephasing spectra can be accounted for by the presence of pure biexcitons. The two-quantum nonrephasing spectra provide direct evidence for unbound exciton pairs and biexcitons with dominantly attractive force. In addition, the spectral features of unbound exciton pairs show mixed absorptive and dispersive character, implying many-body interactions within the correlated Frenkel-exciton pairs. Our work offers novel perspectives on the Frenkel-exciton complexes in semiconductor polymers.

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Optical Properties of Vibronically Coupled Cy3 Dimers on DNA Scaffolds.
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  • The Journal of Physical Chemistry B

  • Research Article
  • 10.1021/jpv129i030_1965852
Issue Publication Information
  • Jul 31, 2025
  • The Journal of Physical Chemistry B

  • Research Article
  • 10.1021/jpv129i029_1963520
Issue Publication Information
  • Jul 24, 2025
  • The Journal of Physical Chemistry B

  • Research Article
  • 10.1021/jpv129i029_1963521
Issue Editorial Masthead
  • Jul 24, 2025
  • The Journal of Physical Chemistry B

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