First-Principles Simulations of the Initial Phase of Self-Aggregation of a Cyanine Dye: Structure and Optical Spectra

Solution-based Supramolecular Hierarchical Assembly of Frenkel Excitonic Nanotubes Driven by Gold Nanoparticle Formation and Temperature

Translating nature's successful design principle of solution-based supramolecular self-assembling to broad applications─ranging from renewable energy and information technology to nanomedicine─requires a fundamental understanding of supramolecular hierarchical assembly. Though the forces behind self-assembly (e.g., hydrophobicity) are known, the specific mechanism by which monomers form the hierarchical assembly still remains an open question. A crucial step toward formulating a complete mechanism is understanding not only how the monomer's specific molecular structure but also how manifold environmental conditions impact the self-assembling process. Here, we elucidate the complex correlation between the environmental self-assembling conditions and the resulting structural properties by utilizing a well-characterized model system: well-defined supramolecular Frenkel excitonic nanotubes (NTs), self-assembled from cyanine dye molecules in aqueous solution, which further self-assemble into bundled nanotubes (b-NTs). The NTs and b-NTs inhabit distinct spectroscopic signatures, which allows the use of steady-state absorption spectroscopy to monitor the transition from NTs to b-NTs directly. Specifically, we investigate the impact of temperature (ranging from 23 °C, 55 °C, 70 °C, 85 °C, up to 100 °C) during in situ formation of gold nanoparticles to determine their role in the formation of b-NTs. The considered time regime for the self-assembling process ranges from 1 min to 8 days. With our work, we contribute to a basic understanding of how environmental conditions impact solution-based hierarchical supramolecular self-assembly in both the thermodynamic and the kinetic regime.

Manifestation of the anisotropic properties of the molecular J-aggregate shell in the optical spectra of plexcitonic nanoparticles

The theoretical studies of light absorption and scattering spectra of the plexcitonic two-layer triangular nanoprisms and three-layer nanospheres are reported. The optical properties of such metal-organic core-shell and core-double-shell nanostructures were previously explained within the framework of pure isotropic models for describing their outer excitonic shell. In this work, we show that the anisotropy of the excitonic shell permittivity can drastically affect the optical spectra of such hybrid nanostructures. This fact is confirmed by directly comparing our theory with some available experimental data, which cannot be treated using conventional isotropic shell models. We have analyzed the influence of the shell anisotropy on the optical spectra and proposed a type of hybrid nanostructure that seems the most convenient for experimental observation of the effects associated with the anisotropy of the excitonic shell. A strong dependence of the anisotropic properties of the J-aggregate shell on the material of the intermediate spacer layer is demonstrated. This allows proposing a new way to effectively control the optical properties of metal-organic nanostructures by selecting the spacer material. Our results extend the understanding of physical effects in optics of plexcitonic nanostructures to more complex systems with the anisotropic and multi-excitonic properties of their molecular aggregate shell.

Atomistic simulation studies of ionic cyanine dyes: self-assembly and aggregate formation in aqueous solution

Cyanine dyes are known to form large-scale aggregates of various morphologies via spontaneous self-assembly in aqueous solution, akin to chromonic liquid crystals. Atomistic molecular dynamics simulations have been performed on four cyanine dyes: pseudoisocyanine chloride (PIC), pinacyanol chloride (PCYN), 5,5',6,6'-tetrachloro-1,1',3,3'-tetraethylbenzimidazolylcarbocyanine chloride (TTBC) and 1,1'-disulfopropyl-3,3'-diethyl-5,5',6,6'-tetrachloro-benzimidazolylcarbocyanine sodium salt (BIC). Simulations employed an optimised general AMBER force field and demonstrate the organisation of the dyes into stacked structures at dilute concentrations. The thermodynamics of self-assembly was studied by calculating potentials of mean force for n-mers (n = 2, 3 or 4), from which the free energies of association are determined. We report binding free energies in the range of 8 to 15k_BT for dimerisation, concordant with typical values for ionic chromonics (7 to 14k_BT), and examine the enthalpic and entropic contributions to the aggregation process. The self-assembly of these dyes yields two distinct classes of structures. We observe the formation of H-aggregate stacks for PCYN, with further complexity in these assemblies for PIC; where the aggregates contain shift and Y junction defects. TTBC and BIC associate into a J-aggregate sheet structure of unimolecular thickness, and is composed of a brickwork arrangement between molecules. These sheet structures are characteristic of the smectic chromonic mesophase, and such assemblies provide a route to the emergence of nanoscale tubular architectures.

Revealing the evolving mixture of molecular aggregates during organic film formation using simulations of in situ absorbance

In this work, we introduce a method for modeling the evolving absorbance spectrum of an organic molecule, pseudoisocyanine (PIC), measured during the process of molecular aggregation. Despite being historically considered a J-aggregate, we find that the absorbance spectrum of PIC cannot be adequately modeled using solely J-aggregates either during molecular aggregation or in the final dry film. The collection of absorbance spectra during solution-casting is particularly difficult since a distribution of aggregates with various sizes and structures can coexist. Here, spectra measured during film formation are fit to a weighted sum of simulated spectra of two aggregate species, revealing the combinations of Coulombic coupling values, Huang-Rhys parameters, and aggregate sizes that provide good fits to measured spectra. The peak intensity ratios and relative peak positions are highly sensitive to the aggregate structure, and fitting only these features enables the rapid comparison of aggregate combinations. We find that the spectra of PIC aggregates cannot be modeled using the Huang-Rhys factor of the PIC monomer, as is typically assumed, leading us to consider models that utilize independent Huang-Rhys factors for each aggregate species. This method of fitting only the key spectral features allows an experimental spectrum to be modeled within 1 h-2 h when using a single Huang-Rhys factor, making the simulation of a series of in situ measurements during aggregation computationally feasible.

Solid-State Effects on the Optical Excitation of Push-Pull Molecular J-Aggregates by First-Principles Simulations

J-aggregates are a class of low-dimensional molecular crystals which display enhanced interaction with light. These systems show interesting optical properties as an intense and narrow red-shifted absorption peak (J-band) with respect to the spectrum of the corresponding monomer. The need to theoretically investigate optical excitations in J-aggregates is twofold: a thorough first-principles description is still missing and a renewed interest is rising recently in understanding the nature of the J-band, in particular regarding the collective mechanisms involved in its formation. In this work, we investigate the electronic and optical properties of a J-aggregate molecular crystal made of ordered arrangements of organic push-pull chromophores. By using a time-dependent density functional theory approach, we assess the role of the molecular packing in the enhancement and red shift of the J-band along with the effects of confinement in the optical absorption, when moving from bulk to low-dimensional crystal structures. We simulate the optical absorption of different configurations (i.e., monomer, dimers, a polymer chain, and a monolayer sheet) extracted from the bulk crystal. By analyzing the induced charge density associated with the J-band, we conclude that it is a longitudinal excitation, delocalized along parallel linear chains and that its overall red shift results from competing coupling mechanisms, some giving red shift and others giving blue shift, which derive from both coupling between transition densities and renormalization of the single-particle energy levels.

In Situ Measurement of Exciton Dynamics During Thin-Film Formation Using Single-Shot Transient Absorption

The exciton dynamics of pseudoisocyanine (PIC) is reported during the formation of a thin film dropcast from solution. Tilted pump pulses are used to spatially encode a pump-probe time delay, enabling the collection of a transient in a single shot. We demonstrate that a spatially encoded delay can be used to accurately measure exciton dynamics in thin-film samples, with a signal-to-noise ratio above 20 attained in 2 s. We report in situ linear absorption, fluorescence, and transient absorption measurements during the molecular aggregation of PIC. These measurements reveal a highly fluorescent intermediate stage during thin-film formation that we ascribe to J-aggregates, in contrast to the final, less fluorescent, dry thin film that exhibits photophysics indicative of disordered J-aggregates. The ability to measure exciton dynamics in situ during materials formation will provide a deeper understanding of how functional materials properties evolve, and will enable direct feedback for rational materials design.

Molecular model of J-aggregated pseudoisocyanine fibers

Aggregated cyanines form ordered supramolecular structures with the potential to transport energy efficiently over long distances, a hallmark of photosynthetic light-harvesting complexes. In concentrated aqueous solution, pseudoisocyanine (PIC) spontaneously forms fibers with a chiral J-band red-shifted 1600 cm^-1 from the monomeric 0-0 transition. A cryogenic transmission electron microscopy analysis of these fibers show an average fiber width of 2.89 nm, although the molecular-level structure of the aggregate is currently unknown. To determine a molecular model for these PIC fibers, the calculated spectra and dynamics using a Frenkel exciton model are compared to experiment. A chiral aggregate model in which the PIC monomers are neither parallel nor orthogonal to the long axis of the fiber is shown to replicate the experimental spectra most closely. This model can be physically realized by the sequential binding of PIC dimers and monomers to the ends of the fiber. These insights into the molecular aggregation model for aqueous PIC can also be applied to other similar cyanine-based supramolecular complexes with the potential for long-range energy transport, a key building block for the rational design of novel excitonic systems.

Tubular J-aggregates of a new thiacarbocyanine Cy5 dye for the far-red spectral region – a spectroscopic and cryo-transmission electron microscopy study

A new phenol-substituted Cy5 dye forms tubular J-aggregates that are active in the far-red spectral region.

Structure-Guided Design and Synthesis of a Mitochondria-Targeting Near-Infrared Fluorophore with Multimodal Therapeutic Activities

An urgent challenge for imaging-guided disease-targeted multimodal therapy is to develop the appropriate multifunctional agents to meet the requirements for potential applications. Here, a rigid cyclohexenyl substitution in the middle of a polymethine linker and two asymmetrical amphipathic N-alkyl side chains to indocyanine green (ICG) (the only FDA-approved NIR contrast agent) are introduced, and a new analog, IR-DBI, is developed with simultaneous cancer-cell mitochondrial targeting, NIR imaging, and chemo-/PDT/PTT/multimodal therapeutic activities. The asymmetrical and amphipathic structural modification renders IR-DBI a close binding to albumin protein site II to form a drug-protein complex and primarily facilitates its preferential accumulation at tumor sites via the enhanced permeability and retention (EPR) effect. The released IR-DBI dye is further actively taken up by cancer cells through organic-anion-transporting polypeptide transporters, and the lipophilic cationic property leads to its selective accumulation in the mitochondria of cancer cells. Finally, based on the high albumin-binding affinity, IR-DBI is modified into human serum albumin (HSA) via self-assembly to produce a nanosized complex, which exhibits significant improvement in the cancer targeting and multimodal cancer treatment with better biocompatibility. This finding may present a practicable strategy to develop small-molecule-based cancer theranostic agents for simultaneous cancer diagnostics and therapeutics.