› › Design And Synthesis Of Donor Acceptor Donor Xanthene Based Near Infrared I And Shortwave Infrared Swir Dyes For Biological Imaging

Design and Synthesis of Donor-acceptor-donor Xanthene-based Near Infrared I and Shortwave Infrared (SWIR) Dyes for Biological Imaging

Author : Chathuranga Rathnamalala

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File Size : 28,65 MB

Release : 2023

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Small molecule organic dyes with absorption and emission in the near infrared region (NIR) attracted much attention for various applications such as dye sensitized solar cells, fluorescent guided surgery, stimuli responsive bioimaging and photodynamic therapy. Dyes with high absorption and emission in the NIR region are beneficial for stimuli responsive bioimaging due to the deeper penetration of NIR light, less cell damage, high resolution, and low background autofluorescence from biomolecules. Of the many small molecule dyes, xanthene-based dyes exhibit outstanding photophysical properties and good stimuli response for use in bioimaging applications. However, absorption and emission of the xanthene dyes lie in the visible region, which limit their applications in cellular imaging. Many of the NIR dyes have very poor fluorescence; consequently, an alternative approach to fluorescent imaging is photoacoustic imaging that uses sound waves to generate pictures of deep tissues. In this dissertation, we discuss the utility of xanthene based NIR dyes as photoacoustic imaging contrast agents for multiplex imaging and deep tissue nitric oxide sensing in the drug-induced liver injury. Chapter I discuss the fundamentals of fluorescence and photoacoustic imaging, background of the xanthene dyes and other fluorescent dyes, and the design strategies to develop NIR xanthene-based dyes. Chapter II is based on our approach to the design and synthesis of NIR xanthene-based dyes by C-H bond functionalization, with the first example being Rhodindolizine, which absorb and emits in NIR II or short-wave infrared (SWIR) region. In chapter III, we describe the design and synthesis of thienylpiperidine xanthene-based NIR and shortwave-infrared (SWIR) dyes for the photoacoustic imaging. One dye in particular (XanthCR-880) boasts a strong PA signal at 880 nm with good biological compatibility and photostability, yields multiplexed imaging with an aza-BODIPY reference dye, and is detected at a depth of 4 cm. In chapter IV, we report a series of SWIR dyes based on a dibenzazepine donor conjugated to thiophene (SCR-1, SCR-4), thienothiophene (SCR-2, SCR-5), and bithiophene (SCR-3, SCR-6). We leverage the fact that SCR-1 undergoes a bathochromic shift when aggregated to develop a ratiometric nanoparticle for nitric oxide (NO) (rNP-NO). rNP-NO was used to successfully perform in vivo studies to visualize pathological levels of nitric oxide in a drug-induced liver injury model via deep tissue SWIR photoacoustic (PA) imaging. Chapter V describes another series of xanthene-based dyes with a thiophene þ̀± spacer and several different donors. UV-Vis absorption studies were performed after converting the dyes to the opened form with trifluoracetic acid. These novel XanthCR-TD dyes exhibit absorption maxima in NIR I region from 700 - 900 nm.



Design and Synthesis of Novel Donor-acceptor-donor Xanthene-based Dyes from Heteronuclear Ring Systems for Chemical, Electrochemical, and Biological Sensory Materials

Author : Ishanka Nirmani Rajapaksha

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File Size : 45,3 MB

Release : 2022

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Conventional xanthene dyes (eg: fluorescein and rhodamine) have their absorptions and emissions in the visible region, which limits their use in cellular imaging. Absorptions and emissions at longer wavelengths allow for low background cellular autofluorescence, deep tissue penetration, and minimum cell damage. Chapter I discusses the background of fluorescent dyes and the importance of near-infrared (NIR) emissive dyes for biological applications. Chapter II is based on the design and synthesis of new xanthene-based NIR I dyes using simple and short synthetic routes. This study used pyrrole and indole as donor molecules and combined them to the xanthene core by the Suzuki cross-coupling reaction to prepare the new dyes. After the treatment with trifluoroacetic acid, these new dyes transformed from their non-fluorescent to fluorescent forms and exhibited excellent red shifts in their maximum absorption and emission wavelengths. The novel pyrrole-based xanthene dye was used to investigate the efficacy of the dye as a probe for fluoride ions. We were able to modify this dye with a silyl ester receptor and develop a probe as a colorimetric turn-off fluoride ion sensor. In chapter III, we describe the synthesis of different NIR emissive xanthene dyes using the donor-acceptor-donor concept. New xanthene-based dyes were designed with five-membered heterocycles and fused heteronuclear molecules. Additionally, xanthene-based dyes containing an alkyne spacer were synthesized using the D-pi-A model to extend the pi-conjugation through the alkyne spacer. All of the dyes exhibited absorption and emission maxima in the visible to NIR I region, between 500-850 nm. In chapter IV, we discussed the synthesis of xanthene-based electrochromic materials. These compounds used xanthene as the chromophore and ferrocene as the electrophore units. Novel rhodamine-based symmetric and unsymmetric dyes were synthesized by attaching the ferrocene unit through the lactam ring. The compounds were then investigated as an electrochromic probe using UV-Vis, cyclic voltammetry, and spectroelectrochemical analysis.



Design of Novel Dyes Towards the Near-infrared

Author : Aurore Loudet

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Page : pages

File Size : 45,64 MB

Release : 2010

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A series of seven functionalized near-infrared aza-BODIPY dyes have been synthesized and their spectroscopic properties measured. Their fluorescence emissions could be tuned by altering the electronic substituents on the aryl-groups. A through-bond energy transfer cassette featuring two fluorescein units as donor, and an aza-BODIPY dye as acceptor, was then synthesized and its preliminary spectroscopic properties examined. This cassette exhibited absorption and fluorescence characteristics that were highly dependent on the pH and the solvent polarity. Furthermore, no energy transfer was observed upon excitation of the donor. Novel near-infrared aza-BODIPY were also synthesized via a one-pot, two step reaction. Upon demethylation and intermolecular cyclization onto the B-atom, a ~ 100 nm red-shift of both the absorption and fluorescence emission maxima could be observed. Through-bond energy transfer cassettes based on squaraines have also been synthesized and their spectroscopic properties studied. These cassettes exhibited fast and efficient energy transfer from the donor to the acceptor. In depth experiments have also been realized to correlate the rate of energy transfer and structure on 3 different sets of through-bond energy transfer cassettes. No correlations could be made between the rate of the energy transfer and the nature of the acceptor, and the distance between the donor and acceptor. Finally, the use of DPP (diketo-pyrrolopyrolle) pigment as a potential donor for through-bond energy transfer cassettes was investigated. Three water-soluble DPPs dyes were prepared and studied. They all displayed weak fluorescence in water.









The Design and Synthesis of Infrared Flourescent Colorants

Author : A. Zweig

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Page : 56 pages

File Size : 21,93 MB

Release : 1974

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A full spectral examination revealed that the total fluorescence emission from Direct Blue 108, a commercial dioxazine dye with moderate near infrared fluorescence, is much greater than that from Basic Blue 3, the strongest near infrared fluorescer uncovered in a Natick investigation of commercial dyes. Molecular orbital calculations performed on twenty-one related dioxazine structures indicate that a ring system with two perylene moieties fused to the dioxazine system, should fluoresce near 750 nm when dyed on nylon. These calculations, coupled with literature reports of high fluorescence yield for perylene derivatives, incidate that this ring system is likely to fulfill the Natick Laboratories' requirements. Ongoing efforts to synthesize nylon dyes containing the desired ring system are discussed. A total of 16 new compounds prepared during the course of this effort are described and characterized. A reliable method of preparing the essential intermediate, 3-aminoperylene, (3-AMP) from commercially available starting materials in good yields was developed.



Transparency in Biology

Author : Kohei Soga

Publisher : Springer Nature

Page : 263 pages

File Size : 29,85 MB

Release : 2020-12-21

Category : Science

ISBN : 9811596271

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This book explains transparency in biology with emphasis on bending and absorption, which together are the essence of transparency. The reader is provided with an understanding of why the interior of the body can be made to appear transparent through the application of elementary physics. Based on the principle of transparency, emerging imaging techniques using near-infrared light to view the body transparently are explained with examples such as cancer detection and temperature imaging of deep tissues. This book is useful to many researchers, including biologists, physicists, chemists, materials scientists, and device engineers as well as developers—all who seek a deep understanding of transparency in bioimaging.



Design and Syntheses of Dyes for Biological Applications

Author : Cliferson Thivierge

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Page : pages

File Size : 25,24 MB

Release : 2012

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The challenges in modern biological imaging applications are two-fold: (i) to develop better methods of imaging, and (ii) develop dyes that are suitable for these methods. This dissertation deals with the design and synthesis of dyes mainly by modification of known dyes to make them suitable for modern biological applications. Towards this aim, novel ways of derivatizing BODIPY dyes are explored. One method involves extending the conjugation via phenyl acetylene units, pushing fluorescence wavelengths near 600 nm. A different approach deals with C-H functionalization of BODIPY in which the fluors are functionalized with acrylate units, extending their fluorescence to the red. The BODIPY dyes developed are then incorporated in through-bond energy transfer cassettes. We examine the factors affecting energy transfer efficiencies by synthesizing analogs of the cassettes and also studying the electrochemical behavior of the donor and acceptor parts. The concept of through-bond energy transfer is incorporated into conjugated polymers by random incorporation of BODIPY dyes into polyfluorenes. The ideal ratio of fluorene to BODIPY parts was found to be 4:1. The BODIPY doping agents result in dispersed emissions when excited the polyfluorene polymers. Concurrently, the polyfluorene backbone acts as an energy harvester for the BODIPY dyes, in effect increasing their molar absorptivities. Finally the use of BODIPY dyes as photodynamic therapeutic agents was examined. We found that BODIPY dyes are efficient at producing reactive oxygen species when halogens are attached directly on the BODIPY core. Furthermore, the mechanism of cell death by using such agents was elucidated. Attachment of the most promising agent to polyglutamic acid is done to promote the EPR effect. Lastly we develop a potentially new type of PDT agent that absorbs strongly above 800 nm, permitting its use in deep tissue PDT.



Novel Near Infrared Fluorescent Dyes

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Page : 0 pages

File Size : 36,21 MB

Release : 2001

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The overall objective of this program is to produce new fluorophores suitable for biosensor signal transduction with excitation wavelengths greater than 665 nm and having electrophilic functionalities for covalent attachment to proteins and nucleic acids. The Phase I effort demonstrated the synthesis of representative fluorophores and characterized their fluorescence emission spectra. The main approach was to synthesize novel styryl dyes with features that result in long wavelength absorbance and emission spectra. The results obtained in the Phase I provide a rationale to achieve specific bathochromic shifts This approach will be implemented in the Phase II effort to develop a series of dyes. To date we have a) demonstrated the feasibility of the proposed synthetic approaches to design long-wavelength styryl dyes, b) have prepared a series of dyes with long wavelength absorption, high quantum yield and large extinction coefficients, c) prepared derivatives of styryl dyes with succinimydyl ester groups, and d) demonstrated the feasibility of using these derivatives for covalent labeling of biological macromolecules.