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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.

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 .

The clinical utility of emulsions as delivery vehicles is hindered by a dependence on passive release. Stimuli-responsive emulsions overcome this limitation but rely on external triggers or are composed of nanoparticle-stabilized droplets that preclude sizes necessary for biomedical applications. Here, we employ cleavable poly(2-oxazoline) diblock copolymer surfactants to form perfluorocarbon (PFC) nanoemulsions that release cargo upon exposure to glutathione. These surfactants allow for the first example of redox-responsive nanoemulsions in cellulo. A noncovalent fluorous tagging strategy is leveraged to solubilize a GFP plasmid inside the PFC nanoemulsions, whereupon protein expression is achieved selectively when employing a stimuli-responsive surfactant. This work contributes a methodology for non-viral gene delivery and represents a general approach to nanoemulsions that respond to endogenous stimuli.

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.

A systematic study of arene-perfluoroarene interactions in solution is presented. Using a combination of NMR titration experiments, X-ray crystallography, and computational analysis, we analyze the effects of fluorination, substituents, ring size, and solvation on the arene-perfluoroarene interaction. We find that fluorination, extension of the π systems, and enhancement of solvent polarity greatly stabilize the stacking energy up to 3 orders of magnitude (Ka =

Optical imaging within the shortwave infrared (SWIR, 1000-2000 nm) region of the electromagnetic spectrum has enabled high-resolution and high-contrast imaging in mice, non-invasively. Polymethine dyes, with their narrow absorption spectra and high absorption coefficients, are optimal probes for fast and multiplexed SWIR imaging. Here, we expand upon the multiplexing capabilities in SWIR imaging by obtaining brighter polymethine dyes with varied excitation wavelengths spaced throughout the near-infrared (700-1000 nm) region. Building on the flavylium polymethine dye scaffold, we explored derivatives with functional group substitution at the 2-position, deemed chromenylium polymethine dyes. The reported dyes have reduced nonradiative rates and enhanced emissive properties, enabling non-invasive imaging in mice in a single color at 300 fps and in three colors at 100 fps. Combined with polymethine dyes containing a red-shifted julolidine flavylium heterocycle and indocyanine green, distinct channels with well-separated excitation wavelengths provide non-invasive video-rate in vivo imaging in four colors.

Perfluorocarbons, saturated carbon chains in which all the hydrogen atoms are replaced with fluorine, form a separate phase from both organic and aqueous solutions. Though perfluorinated compounds are not found in living systems, they can be used to modify biomolecules to confer orthogonal behavior within natural systems, such as improved stability, engineered assembly, and cell-permeability. Perfluorinated groups also provide handles for purification, mass spectrometry, and 19 F NMR studies in complex environments. Herein, we describe how the unique properties of perfluorocarbons have been employed to understand and manipulate biological systems.

High-resolution, multiplexed experiments are a staple in cellular imaging. Analogous experiments in animals are challenging, however, due to substantial scattering and autofluorescence in tissue at visible (350-700 nm) and near-infrared (700-1,000 nm) wavelengths. Here, we enable real-time, non-invasive multicolour imaging experiments in animals through the design of optical contrast agents for the shortwave infrared (SWIR, 1,000-2,000 nm) region and complementary advances in imaging technologies. We developed tunable, SWIR-emissive flavylium polymethine dyes and established relationships between structure and photophysical properties for this class of bright SWIR contrast agents. In parallel, we designed an imaging system with variable near-infrared/SWIR excitation and single-channel detection, facilitating video-rate multicolour SWIR imaging for optically guided surgery and imaging of awake and moving mice with multiplexed detection. Optimized dyes matched to 980 nm and 1,064 nm lasers, combined with the clinically approved indocyanine green, enabled real-time, three-colour imaging with high temporal and spatial resolutions.

Methods to red-shift fluorophores have garnered considerable interest due to the broad utility of low energy light. The incorporation of silicon into xanthene and coumarin scaffolds has resulted in an array of visible and near-infrared fluorophores. Here, we extend this approach to polymethine dyes, another popular fluorophore class, performing experimental and computational analyses. We found that when oxygen was replaced with SiMe2, bathochromic shifts of up to 121 nm and fluorophores with emission above 900 nm were achieved.

Fluorophores that are sensitive to their environment are useful tools for sensing chemical changes and probing biological systems. Here, we extend responsive fluorophores to the fluorous phase with the synthesis of a reduction-sensitive fluorous-soluble fluorogenic coumarin. We demonstrate that this fluorophore responds to various reducing agents, most notably glutathione, a key biological reductant. The fluorous solubility of this probe allows for its encapsulation into two different fluorous nanomaterials: perfluorocarbon nanoemulsions and fluorous core-shell micelles. The fluorogenic coumarin allows us to study how efficiently these vehicles protect the contents of their interior from the external environment. In the presence of glutathione, we observe different degrees of release for micelles and emulsions. This understanding will help guide future applications of fluorous nanomaterials as drug delivery vehicles.

Emulsions are dynamic materials that have been extensively employed within pharmaceutical, food and cosmetic industries. However, their use beyond conventional applications has been hindered by difficulties in surface functionalization, and an inability to selectively control physicochemical properties. Here, we employ custom poly(2-oxazoline) block copolymers to overcome these limitations. We demonstrate that poly(2-oxazoline) copolymers can effectively stabilize nanoscale droplets of hydrocarbon and perfluorocarbon in water. The controlled living polymerization of poly(2-oxazoline)s allows for the incorporation of chemical handles into the surfactants such that covalent modification of the emulsion surface can be performed. Through post-emulsion modification of these new surfactants, we are able to access nanoemulsions with modified surface chemistries, yet consistent sizes. By decoupling size and surface charge, we explore structure-activity relationships involving the cellular uptake of nanoemulsions in both macrophage and non-macrophage cell lines. We conclude that the cellular uptake and cytotoxicity of poly(2-oxazoline)-stabilized droplets can be systematically tuned via chemical modification of emulsion surfaces.

Bright fluorophores in the near-infrared and shortwave infrared (SWIR) regions of the electromagnetic spectrum are essential for optical imaging in vivo. In this work, we utilized a 7-dimethylamino flavylium heterocycle to construct a panel of novel red-shifted polymethine dyes, with emission wavelengths from 680 to 1045 nm. Photophysical characterization revealed that the 1- and 3-methine dyes display enhanced photostability and the 5- and 7-methine dyes exhibit exceptional brightness for their respective spectral regions. A micelle formulation of the 7-methine facilitated SWIR imaging in mice. This report presents the first polymethine dye designed and synthesized for SWIR in vivo imaging.

The 1,3-dipolar cycloaddition of cyclooctynes with azides, also called "copper-free click chemistry", is a bioorthogonal reaction with widespread applications in biological discovery. The kinetics of this reaction are of paramount importance for studies of dynamic processes, particularly in living subjects. Here we performed a systematic analysis of the effects of strain and electronics on the reactivity of cyclooctynes with azides through both experimental measurements and computational studies using a density functional theory (DFT) distortion/interaction transition state model. In particular, we focused on biarylazacyclooctynone (BARAC) because it reacts with azides faster than any other reported cyclooctyne and its modular synthesis facilitated rapid access to analogues. We found that substituents on BARAC's aryl rings can alter the calculated transition state interaction energy of the cycloaddition through electronic effects or the calculated distortion energy through steric effects. Experimental data confirmed that electronic perturbation of BARAC's aryl rings has a modest effect on reaction rate, whereas steric hindrance in the transition state can significantly retard the reaction. Drawing on these results, we analyzed the relationship between alkyne bond angles, which we determined using X-ray crystallography, and reactivity, quantified by experimental second-order rate constants, for a range of cyclooctynes. Our results suggest a correlation between decreased alkyne bond angle and increased cyclooctyne reactivity. Finally, we obtained structural and computational data that revealed the relationship between the conformation of BARAC's central lactam and compound reactivity. Collectively, these results indicate that the distortion/interaction model combined with bond angle analysis will enable predictions of cyclooctyne reactivity and the rational design of new reagents for copper-free click chemistry.

The development of fluorophores with photoemission beyond 1000 nm provides the opportunity to develop novel fluorescence microscopes sensitive to those wavelengths. Imaging at wavelengths beyond the visible spectrum enables imaging depths of hundreds of microns in intact tissue, making this attractive for volumetric imaging applications. Here, a novel shortwave‐infrared line‐scan confocal microscope is presented that is capable of deep imaging of biological specimens, as demonstrated by visualization of labeled glomeruli in a fixed uncleared kidney at depths beyond 400 µm. Imaging of brain vasculature labeled with the near‐infrared organic dye indocyanine green, the shortwave‐infrared organic dye Chrom7, and rare earth‐doped nanoparticles is also shown, thus encompassing the entire spectrum detectable by a typical shortwave‐infrared sensitive InGaAs detector. [ABSTRACT FROM AUTHOR]

The temperature-sensitive miscibility of hydrocarbon, silicone and fluorocarbon liquids is used to establish a one-step method of making three- and four-phase complex emulsions with highly controllable morphologies that can be alternated between encapsulated and Janus configurations by varying the balance of interfacial tensions. Complex emulsions made switchable Emulsions are of critical importance for research and for applications in the medical sciences, food industry and elsewhere. This paper describes a one-step method that exploits the temperature-sensitive miscibility of hydrocarbon, silicone and fluorocarbon liquids to make three- and four-phase complex emulsions with highly controllable morphologies. The geometry of the emulsions can be accurately tuned between encapsulated and Janus configurations by varying the balance of interfacial tensions controlled through mixtures of surfactant or by stimuli such as light or pH. The ability to reversibly 'present' and 'hide' specific liquid-liquid interfaces within the droplet and tune the droplet morphology offers interesting practical possibilities. Emulsification is a powerful, well-known technique for mixing and dispersing immiscible components within a continuous liquid phase. Consequently, emulsions are central components of medicine, food and performance materials. Complex emulsions, including Janus droplets (that is, droplets with faces of differing chemistries) and multiple emulsions, are of increasing importance.sup.1 in pharmaceuticals and medical diagnostics.sup.2, in the fabrication of microparticles and capsules.sup.3,4,5 for food.sup.6, in chemical separations.sup.7, in cosmetics.sup.8, and in dynamic optics.sup.9. Because complex emulsion properties and functions are related to the droplet geometry and composition, the development of rapid, simple fabrication approaches allowing precise control over the droplets' physical and chemical characteristics is critical. Significant advances in the fabrication of complex emulsions have been made using a number of procedures, ranging from large-scale, less precise techniques that give compositional heterogeneity using high-shear mixers and membranes.sup.10, to small-volume but more precise microfluidic methods.sup.11,12. However, such approaches have yet to create droplet morphologies that can be controllably altered after emulsification. Reconfigurable complex liquids potentially have great utility as dynamically tunable materials. Here we describe an approach to the one-step fabrication of three- and four-phase complex emulsions with highly controllable and reconfigurable morphologies. The fabrication makes use of the temperature-sensitive miscibility of hydrocarbon, silicone and fluorocarbon liquids, and is applied to both the microfluidic and the scalable batch production of complex droplets. We demonstrate that droplet geometries can be alternated between encapsulated and Janus configurations by varying the interfacial tensions using hydrocarbon and fluorinated surfactants including stimuli-responsive and cleavable surfactants. This yields a generalizable strategy for the fabrication of multiphase emulsions with controllably reconfigurable morphologies and the potential to create a wide range of responsive materials., Author(s): Lauren D. Zarzar [sup.1] , Vishnu Sresht [sup.2] , Ellen M. Sletten [sup.1] , Julia A. Kalow [sup.1] , Daniel Blankschtein [sup.2] , Timothy M. Swager [sup.1] Author Affiliations: [...]

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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]