Silicon-RosIndolizine fluorophores with shortwave infrared absorption and emission profiles enable in vivo fluorescence imaging.

In vivo fluorescence imaging in the shortwave infrared (SWIR, 1,000-1,700 nm) and extended SWIR (ESWIR, 1,700-2,700 nm) regions has tremendous potential for diagnostic imaging. Although image contrast has been shown to improve as longer wavelengths are accessed, the design and synthesis of organic fluorophores that emit in these regions is challenging. Here we synthesize a series of silicon-RosIndolizine (SiRos) fluorophores that exhibit peak emission wavelengths from 1,300-1,700 nm and emission onsets of 1,800-2,200 nm. We characterize the fluorophores photophysically (both steady-state and time-resolved), electrochemically and computationally using time-dependent density functional theory. Using two of the fluorophores (SiRos1300 and SiRos1550), we formulate nanoemulsions and use them for general systemic circulatory SWIR fluorescence imaging of the cardiovascular system in mice. These studies resulted in high-resolution SWIR images with well-defined vasculature visible throughout the entire circulatory system. This SiRos scaffold establishes design principles for generating long-wavelength emitting SWIR and ESWIR fluorophores.

Near-atomic-resolution structure of J-aggregated helical light-harvesting nanotubes.

Cryo-electron microscopy has delivered a resolution revolution for biological self-assemblies, yet only a handful of structures have been solved for synthetic supramolecular materials. Particularly for chromophore supramolecular aggregates, high-resolution structures are necessary for understanding and modulating the long-range excitonic coupling. Here, we present a 3.3 Å structure of prototypical biomimetic light-harvesting nanotubes derived from an amphiphilic cyanine dye (C8S3-Cl). Helical 3D reconstruction directly visualizes the chromophore packing that controls the excitonic properties. Our structure clearly shows a brick layer arrangement, revising the previously hypothesized herringbone arrangement. Furthermore, we identify a new non-biological supramolecular motif-interlocking sulfonates-that may be responsible for the slip-stacked packing and J-aggregate nature of the light-harvesting nanotubes. This work shows how independently obtained native-state structures complement photophysical measurements and will enable accurate understanding of (excitonic) structure-function properties, informing materials design for light-harvesting chromophore aggregates.

In situ quantification of osmotic pressure within living embryonic tissues.

Mechanics is known to play a fundamental role in many cellular and developmental processes. Beyond active forces and material properties, osmotic pressure is believed to control essential cell and tissue characteristics. However, it remains very challenging to perform in situ and in vivo measurements of osmotic pressure. Here we introduce double emulsion droplet sensors that enable local measurements of osmotic pressure intra- and extra-cellularly within 3D multicellular systems, including living tissues. After generating and calibrating the sensors, we measure the osmotic pressure in blastomeres of early zebrafish embryos as well as in the interstitial fluid between the cells of the blastula by monitoring the size of droplets previously inserted in the embryo. Our results show a balance between intracellular and interstitial osmotic pressures, with values of approximately 0.7 MPa, but a large pressure imbalance between the inside and outside of the embryo. The ability to measure osmotic pressure in 3D multicellular systems, including developing embryos and organoids, will help improve our understanding of its role in fundamental biological processes.

Synthesis of Fluorous Ferrofluids and Effects of the Nanoparticle Coatings on Field- and Temperature-Dependent Magnetizations.

Ferrofluids have been extensively employed in industrial, environmental, and biomedical areas. Among them, fluorous ferrofluids are of particular interest because of the biorthogonal nature of perfluorocarbons (PFCs). However, the noninteracting nature of PFCs as well as challenges in functionalization of nanoparticle surfaces with fluorous ligands has limited their applications, especially in biomedicine. In particular, commercially available fluorous ferrofluids are stabilized using ionic surfactants with charged groups that physically interact with a wide range of charged biological molecules. In this paper, we developed a unique two-phase ligand attachment strategy to render stable fluorous ferrofluids using nonionic surfactants. The superparamagnetic Fe3O4 or MnFe2O4 core of the magnetic nanoparticles, the magnetic component of the ferrofluid, was coated with a silica shell containing abundant surface hydroxyl groups, thereby enabling the installation of fluorous ligands through stable covalent, neutral, siloxane bonds. We explored chemistry-material relationships between different ligands and PFC solvents and found that low-molecular-weight ligands can assist with the installation of high-molecular-weight ligands (4000-8000 g/mol), allowing us to systematically control the size and thickness of ligand functionalization on the nanoparticle surface. By zero-field-cooled magnetization measurements, we studied how the ligands affect magnetic dipole orientation forces and observed a curve flattening that is only associated with the ferrofluids. This work provided insight into ferrofluids' dependence on interparticle interactions and contributed a methodology to synthesize fluorous ferrofluids with nonionic surfactants that exhibit both magnetic and chemical stability. We believe that the doped MnFe2O4 fluorous ferrofluid has the highest combination of stability and magnetization reported to date.

A Fluorescent Unnatural Mannosamine Derivative with Enhanced Emission Upon Complexation with Cucurbit[7]uril.

Metabolic incorporation of unnatural functionality on glycans has allowed chemical biologists to observe and affect cellular processes. Recent work has resulted in glycan-fluorophore structures that allow for direct visualization of glycan-mediated processes, shining light on their role in living systems. This work describes the serendipitous discovery of a small chemical reporter-fluorophore. Investigations into the mechanism of fluorescence arising from (trimethylsilyl)methylglycine appended on mannosamine suggest rigidity and restriction of lone pair geometry contribute to the fluorescent behaviour. In fact, in situ cyclization and encapsulation in cucurbit[7]uril enhance fluorescence to levels that can be observed in live cells. While the reported unnatural mannosamine does not traverse the sialic acid biosynthetic pathway, this discovery may lead to small, "turn-on" chemical reporters for incorporation in living systems.

Shortwave infrared fluorescence imaging of peripheral organs in awake and freely moving mice.

Extracting biological information from awake and unrestrained mice is imperative to in vivo basic and pre-clinical research. Accordingly, imaging methods which preclude invasiveness, anesthesia, and/or physical restraint enable more physiologically relevant biological data extraction by eliminating these extrinsic confounders. In this article, we discuss the recent development of shortwave infrared (SWIR) fluorescent imaging to visualize peripheral organs in freely-behaving mice, as well as propose potential applications of this imaging modality in the neurosciences.

Shortwave infrared (SWIR) fluorescence imaging of peripheral organs in awake and freely moving mice.

Extracting biological information from awake and unrestrained mice is imperative to in vivo basic and pre-clinical research. Accordingly, imaging methods which preclude invasiveness, anesthesia, and/or physical restraint enable more physiologically relevant biological data extraction by eliminating these extrinsic confounders. In this article we discuss the recent development of shortwave infrared (SWIR) fluorescent imaging to visualize peripheral organs in freely-behaving mice, as well as propose potential applications of this imaging modality in the neurosciences.

Exploring the design of superradiant J-aggregates from amphiphilic monomer units.

Excitonic chromophore aggregates have wide-ranging applicability in fields such as imaging and energy harvesting; however their rational design requires adapting principles of self-assembly to the requirements of excited state coupling. Using the well-studied amphiphilic cyanine dye C8S3 as a template-known to assemble into tubular excitonic aggregates-we synthesize several redshifted variants and study their self-assembly and photophysics. The new pentamethine dyes retain their tubular self-assembly and demonstrate nearly identical bathochromic shifts and lineshapes well into near-infrared wavelengths. However, detailed photophysical analysis finds that the new aggregates show a significant decline in superradiance. Additionally, cryo-TEM reveals that these aggregates readily form short bundles of nanotubes that have nearly half the radii of their trimethine comparators. We employ computational screening to gain intuition on how the structural components of these new aggregates affect their excitonic states, finding that the narrower tubes are able to assemble into a larger number of arrangements, resulting in more disordered aggregates (i.e. less superradiant) with highly similar degrees of redshift.

Spectrally Selective Time-Resolved Emission through Fourier-Filtering (STEF).

We demonstrate a method for separating and resolving the dynamics of multiple emitters without the use of conventional filters. By directing the photon emission through a fixed path-length imbalanced Mach-Zehnder interferometer, we interferometrically cancel (or enhance) certain spectral signatures corresponding to one emissive species. Our approach, Spectrally selective Time-resolved Emission through Fourier-filtering (STEF), leverages the detection and subtraction of both outputs of a tuned Mach-Zehnder interferometer, which can be combined with time-correlated single photon counting (TCSPC) or confocal imaging to demix multiple emitter signatures. We develop a procedure to calibrate out imperfections in Mach-Zehnder interferometry schemes. Additionally, we demonstrate the range and utility of STEF by performing the following procedures with one measurement: (1) filtering out laser scatter from a sample, (2) separating and measuring a fluorescence lifetime from a binary chromophore mixture with overlapped emission spectra, (3) confocally imaging and separately resolving the standard fluorescent stains in bovine pulmonary endothelial cells and nearly overlapping fluorescent stains on RAW 264.7 cells. This form of spectral balancing can allow for robust and tunable signal sorting.

Shortwave Infrared Fluorofluorophores for Multicolor In Vivo Imaging.

Developing chemical tools to detect and influence biological processes is a cornerstone of chemical biology. Here we combine two tools which rely on orthogonality- perfluorocarbons and multiplexed shortwave infrared (SWIR) fluorescence imaging- to visualize nanoemulsions in real time in living mice. Drawing inspiration from fluorous and SWIR fluorophore development, we prepared two SWIR-emissive, fluorous-soluble chromenylium polymethine dyes. These are the most red-shifted fluorous fluorophores- "fluorofluorophores"-to date. After characterizing the dyes, their utility was demonstrated by tracking perfluorocarbon nanoemulsion biodistribution in vivo. Using an excitation-multiplexed approach to image two variables simultaneously, we gained insight into the importance of size and surfactant identity on biodistribution.

Water-soluble chromenylium dyes for shortwave infrared imaging in mice.

In vivo imaging using shortwave infrared light (SWIR, 1000-2000 nm) benefits from deeper penetration and higher resolution compared to using visible and near-infrared wavelengths. However, the development of biocompatible SWIR contrast agents remains challenging. Despite recent advancements, small molecule SWIR fluorophores are often hindered by their significant hydrophobicity. We report a platform for generating a panel of soluble and functional dyes for SWIR imaging by late-stage functionalization of a versatile fluorophore intermediate, affording water-soluble dyes with bright SWIR fluorescence in serum. Specifically, a tetra-sulfonate derivative enables clear video-rate imaging of vasculature with only 0.05 nmol dye, and a tetra-ammonium dye shows strong cellular retention for tracking of tumor growth. Additionally, incorporation of phosphonate functionality enables imaging of bone in awake mice. This modular design provides insights for facile derivatization of existing SWIR fluorophores to introduce both solubility and bioactivity towards in vivo bioimaging.

Macromolecular Crowding as an Intracellular Stimulus for Responsive Nanomaterials.

Stimuli-responsive materials are exploited in biological, materials, and sensing applications. We introduce a new endogenous stimulus, biomacromolecule crowding, which we achieve by leveraging changes in thermoresponsive properties of polymers upon high concentrations of crowding agents. We prepare poly(2-oxazoline) amphiphiles that exhibit lower critical solution temperatures (LCST) in serum above physiological temperature. These amphiphiles stabilize oil-in-water nanoemulsions at temperatures below the LCST but are ineffective surfactants above the LCST, resulting in emulsion fusion. We find that the transformations observed upon heating nanoemulsions above their surfactant's LCST can instead be induced at physiological temperatures through the addition of polymers and protein, rendering thermoresponsive materials "crowding responsive." We demonstrate that the cytosol is a stimulus for nanoemulsions, with droplet fusion occurring upon injection into cells of living zebrafish embryos. This report sets the stage for classes of thermoresponsive materials to respond to macromolecule concentration rather than temperature changes.

Extending optical chemical tools and technologies to mice by shifting to the shortwave infrared region.

Fluorescence imaging is an indispensable method for studying biological processes non-invasively in cells and transparent organisms. Extension into the shortwave infrared (SWIR, 1000-2000 nm) region of the electromagnetic spectrum has allowed for imaging in mammals with unprecedented depth and resolution for optical imaging. In this review, we summarize recent advances in imaging technologies, dye scaffold modifications, and incorporation of these dyes into probes for SWIR imaging in mice. Finally, we offer an outlook on the future of SWIR detection in the field of chemical biology.

Spatiotemporal Control of Biology: Synthetic Photochemistry Toolbox with Far-Red and Near-Infrared Light.

The complex network of naturally occurring biological pathways motivates the development of new synthetic molecules to perturb and/or detect these processes for fundamental research and clinical applications. In this context, photochemical tools have emerged as an approach to control the activity of drug or probe molecules at high temporal and spatial resolutions. Traditional photochemical tools, particularly photolabile protecting groups (photocages) and photoswitches, rely on high-energy UV light that is only applicable to cells or transparent model animals. More recently, such designs have evolved into the visible and near-infrared regions with deeper tissue penetration, enabling photocontrol to study biology in tissue and model animal contexts. This Review highlights recent developments in synthetic far-red and near-infrared photocages and photoswitches and their current and potential applications at the interface of chemistry and biology.

Counterion Pairing Effects on a Flavylium Heptamethine Dye.

Polymethine fluorophores have facilitated the advance of biological and material sciences, due to their advantageous photophysical properties. However, the need to maintain a monomeric state can severely limit the utility and processability of dyes. High concentrations of fluorophore can lead to aggregation and negate the beneficial photophysical properties of monomers. Another concern is "crossing the cyanine limit" in which delocalization within the polymethine scaffold is broken, producing the presence of an asymmetric state diminishing its photophysical behavior. Herein, we attempt to overcome these limitations by exploring anion exchange on a cationic flavylium heptamethine scaffold. By increasing the size and hydrophobicity of the anion, we can effectively tune the degree of ion pairing within the polymethine dye. Interestingly, we found that the effect of ion pairing on photophysical properties was subtle for the flavylium heptamethine scaffold in comparison to the more commonly used indolenine cyanine dye. Utilizing larger weakly coordinating anions enabled solubility of the flavylium heptamethine fluorophore in nonpolar solvents, which could otherwise not be achieved. Even with more subtle effects than classic cyanine dyes, anion exchange on flavylium polymethine dyes holds potential for further manipulation of the properties of these low energy dyes.

Establishing design principles for emissive organic SWIR chromophores from energy gap laws.

Rational design of bright near and shortwave infrared (NIR: 700-1000 SWIR: 1000- 2000 nm) emitters remains an open question with applications spanning imaging and photonics. Combining experiment and theory, we derive an energy gap quantum yield master equation (EQME), describing the fundamental limits in SWIR quantum yields (ϕ F ) for organic chromophores. Evaluating the photophysics of 21 polymethine NIR/SWIR chromophores to parameterize the EQME, we explain the precipitous decline of ϕ F past 900 nm through decreasing radiative rates and increasing nonradiative losses via high frequency vibrations relating to the energy gap. Using the EQME we develop an energy gap independent ϕ F NIR/SWIR chromophore comparison metric. We show electron donating character on polymethine heterocycles results in relative increases in radiative efficiency obscured by a simultaneous redshift. Finally, the EQME yields rational chromophore design insights shown by how deuteration (backed by our experimental results) or molecular aggregation increases SWIR ϕ F .

Cell-surface Labeling via Bioorthogonal Host-Guest Chemistry.

The widespread adoption of the bioorthogonal chemical reporter strategy revolutionized chemical biology. However, its translation to living mammals has been challenging, due to the size/stability properties of the chemical reporter group and/or the reaction kinetics of the labeling step. While developing new bioorthogonal reactions has been the traditional approach to optimizing the bioorthogonal chemical reporter strategy, here we present a different avenue, leveraging intermolecular interactions, to create bioorthogonal host-guest pairs. This approach, deemed "bioorthogonal complexation, does not rely on activated functional groups or second-order rate constants. We utilize the cucurbit[7]uril (CB[7]) scaffold to showcase bioorthogonal complexation and determine that medium-affinity (Ka ≈ 108-109 M-1) guests efficiently label cell surfaces and outperform the strain-promoted azide-alkyne cycloaddition. Finally, we implement bioorthogonal complexation in the chemical reporter strategy through the metabolic incorporation of ortho-carborane into cell-surface glycans and detection with a CB[7]-fluorescein conjugate.

Perfluorocarbon Nanoemulsions Create a Beneficial O2 Microenvironment in N2-fixing Biological | Inorganic Hybrid.

Powered by renewable electricity, biological | inorganic hybrids employ water-splitting electrocatalysis and generate H2 as reducing equivalents for microbial catalysis. The approach integrates the beauty of biocatalysis with the energy efficiency of inorganic materials for sustainable chemical production. Yet a successful integration requires delicate control of the hybrid's extracellular chemical environment. Such an argument is evident in the exemplary case of O2 because biocatalysis has a stringent requirement of O2 but the electrocatalysis may inadvertently perturb the oxidative pressure of biological moieties. Here we report the addition of perfluorocarbon (PFC) nanoemulsions promote a biocompatible O2 microenvironment in a O2-sensitive N2-fixing biological | inorganic hybrid. Langmuir-type nonspecific binding between bacteria and nanoemulsions facilitates O2 transport in bacterial microenvironment and leads to a 250% increase in efficiency for organic fertilizers within 120 hours. Controlling the biological microenvironment with nanomaterials heralds a general approach accommodating the compatibility in biological | inorganic hybrids.

Perfluorocarbon nanomaterials for photodynamic therapy.

Photodynamic therapy (PDT) is a treatment modality in which a photosensitizer is irradiated with light, producing reactive oxygen species, often via energy transfer with oxygen. As it is common for tumors to be hypoxic, methods to deliver photosensitizer and oxygen are desirable. One such approach is the use of perfluorocarbons, molecules in which all C-H bonds are replaced with C-F bonds, to co-deliver oxygen because of the high solubility of gases in perfluorocarbons. This review highlights the benefits and limitations of several fluorinated nanomaterial architectures for use in PDT.