Author: Milan Vrabel
Publisher: Springer
ISBN: 3319296868
Category : Science
Languages : en
Pages : 157

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Book Description
The series Topics in Current Chemistry Collections presents critical reviews from the journal Topics in Current Chemistry organized in topical volumes. The scope of coverage is all areas of chemical science including the interfaces with related disciplines such as biology, medicine and materials science. The goal of each thematic volume is to give the non-specialist reader, whether in academia or industry, a comprehensive insight into an area where new research is emerging which is of interest to a larger scientific audience. Each review within the volume critically surveys one aspect of that topic and places it within the context of the volume as a whole. The most significant developments of the last 5 to 10 years are presented using selected examples to illustrate the principles discussed. The coverage is not intended to be an exhaustive summary of the field or include large quantities of data, but should rather be conceptual, concentrating on the methodological thinking that will allow the non-specialist reader to understand the information presented. Contributions also offer an outlook on potential future developments in the field.

Author: David Phillips
Publisher: Createspace Independent Publishing Platform
ISBN: 9781979607919
Category :
Languages : en
Pages : 300

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Book Description
Each review within the volume critically surveys one aspect of that topic and places it within the context of the volume as a whole. The most significant developments of the last 5 to 10 years are presented using selected examples to illustrate the principles discussed. The coverage is not intended to be an exhaustive summary of the field or include large quantities of data, but should rather be conceptual, concentrating on the methodological thinking that will allow the non-specialist reader to understand the information presented. Contributions also offer an outlook on potential future developments in the field.The scope of coverage is all areas of chemical science including the interfaces with related disciplines such as biology, medicine and materials science. The goal of each thematic volume is to give the non-specialist reader, whether in academia or industry, a comprehensive insight into an area where new research is emerging which is of interest to a larger scientific audience.

Author: Steven Alexander Lopez
Publisher:
ISBN:
Category :
Languages : en
Pages : 50

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Book Description
The 1,3-dipolar cycloaddition and Diels-Alder reaction have been applied countless times in synthetic organic chemistry, materials chemistry, and now chemical biology. The stereoselectivity and rapid kinetics have been harnessed to develop the field of bioorthogonal chemistry. In this thesis, the origins of the rapid kinetics and exo-facial selectivity of norbornene was explained and extended to a series of pyramidalized norbornenes and sesquinorbornenes. These were studied using DFT (Density Functional Theory) at the M06-2X/6-311G(d, p) level along with other computational models. The transition structures and activation barriers for these reactions were calculated. An analysis of the calculations revealed that distortion energy is greatly responsible for the observed stereoselectivity, and a simple relationship was derived between pyramidalization and activation barriers. We propose the term, distortion-accelerated, to describe why the reactions are fast, rather than strain-promoted, because the alkenes release most of their strain energy before the transition state. In a second portion of the thesis I applied the concept of distortion-acceleration to a recently discovered mutually orthogonal 1,3-dipolar cycloaddition and an inverse-demand Diels-Alder reaction. Mutually orthogonal reactions were used in the literature to selectively label two different cancer cells simultaneously. We explained this selectivity difference using modern computational methodology. DFT was used for this computational investigation at the M06-2X/6-311+G(d, p) level and the Polarizable Continuum Model (PCM) was used to correct for solvation effects. It was found that distortion energy, LUMO energies, and steric effects are responsible for the observed selectivity. General rules were developed to easily predict new mutually orthogonal pairs once their bioorthogonality is known.

Author: Ellen Sletten
Publisher:
ISBN:
Category :
Languages : en
Pages : 1408

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Book Description
Bioorthogonal is defined as not interfering or interacting with biology. Chemical reactions that are bioorthogonal have recently become valuable tools to visualize biomolecules in their native environments, particularly those that are not amenable to traditional genetic modification. The field of bioorthogonal chemistry is rather young, with the first published account of the term bioorthogonal in 2003, yet it is expanding at a rapid rate. The roots of this unique subset of chemistry are in classic protein modification and subsequent bioconjugation efforts to obtain uniformly and site-specifically functionalized proteins. These studies are highlighted in Chapter 1. Chapter 2 opens with a summary of the bioorthogonal chemical reporter strategy, a two-step approach where a bioorthogonal functional group is installed into a biomolecule of interest, most often using endogenous metabolic machinery, and detected through a secondary covalent reaction with an appropriately functionalized chemical partner. It is this chemical reporter strategy that empowers bioorthogonal chemistry and allows for a wide variety of biological species to be assayed. Chapter 2 proceeds to outline the discovery of the Staudinger ligation, the first chemical reaction developed for use in the bioorthogonal chemical reporter strategy. The Staudinger ligation employed the azide as the chemical reporter group and, since its debut in 2000, many laboratories have capitalized on the exquisite qualities of the azide (small, abiotic, kinetically stable) that make it a versatile chemical reporter group. The success of the azide prompted the development of other bioorthogonal chemistries for this functional group. One of these chemistries, Cu-free click chemistry, is the 1,3-dipolar cycloaddition between cyclooctynes and azides. The cycloaddition is promoted at physiological conditions by the 1̃8 kcal/mol of ring strain contained within cyclooctyne, and further modifications to the cyclooctyne reagents have lead to increased reactivity through augmentation of the ring strain or optimization of orbital overlap. When I began my graduate work, a difluorinated cyclooctyne (DIFO), which was 60-fold more reactive than other existing bioorthogonal chemistries, had just been synthesized and employed for labeling azides on live cells and within living mice. DIFO performed very well on cultured cells, but it was outperformed by the slower Staudinger ligation in the more complex environment of the mouse. We hypothesized that DIFO was too hydrophobic to be effective in mice and designed a more hydrophilic cyclooctyne reagent, a dimethoxyazacyclooctyne (DIMAC). DIMAC was synthesized in nine steps in a 10% overall yield (Chapter 3). As predicted, DIMAC displayed reaction kinetics similar to early generation cyclooctynes, but exhibited improved water-solubility. Consequently, DIMAC labeled cell-surface azides with comparable efficiencies to the early generation cyclooctynes but greater signal-to-noise ratios were achieved due to minimal background staining. Encouraged by these results, we assayed the ability for DIMAC to label azides in living mice and found that DIMAC was able to modify azides in vivo with moderate signal over background. However, the Staudinger ligation was still the superior bioorthogonal reaction for labeling azides in vivo. Our results collectively indicated that both hydrophilicity and reactivity are important qualities when optimizing the cyclooctynes for in vivo reaction with azides (Chapter 4). We were also interested in modifying DIMAC so that it would become fluorescent upon reaction with an azide. Previous work in the lab had established that fluorogenic reagents could be easily created if a functional group was cleaved from the molecule upon reaction with an azide. We envisioned a leaving group could be engineered into the azacyclooctyne scaffold by strategically positioning a labile functional group across the ring from a nitrogen atom. The cyclooctyne structure should be stable, as it is rigid and intramolecular reactions are not favorable. However, upon reaction with an azide, a significant amount of strain is liberated and the intramolecular reaction should readily occur. Efforts toward the synthesis of this modified DIMAC reagent are chronicled in Chapter 5. Chapter 6 is a very short account of our early work to use DIFO-based reagents for proteomics. The results contained in this chapter are preliminary and further endeavors towards this goal are underway by others within the group. Chapters 7, 8 and 9 are devoted to strategies to increase the second-order rate constant of Cu-free click chemistry. In Chapter 7, various routes toward a tetrafluorinated cyclooctyne are outlined, although none of them successfully yielded this putatively highly reactive cyclooctyne. Chapter 8 describes the synthesis of a difluorobenzocyclooctyne (DIFBO), which is more reactive than DIFO, but unstable due to its propensity to form trimer products. However, DIFBO can be kinetically stabilized by encapsulation in beta-cyclodextrin. Only beta-cyclodextrin and not the smaller (alpha) or larger (gamma) cyclodextrins were able to protect DIFBO. We did observe an intriguing result when complexation with the larger gamma-cyclodextrin was attempted. It appears as though two DIFBO molecules can fit inside the gamma-cyclodextrin and dimeric products, which were not apparent in the absence of gamma-cyclodextrin, were observed. We hypothesized that all oligomer products of DIFBO were derived from a common cyclobutadiene intermediate. While DIFBO was chemically interesting, it was not a useful reagent for labeling azides in biological settings. Thus, Chapter 9 is devoted to the modification of DIFBO, with the aim of identifying a reactive yet stable cyclooctyne. The data from Chapter 9 suggest we are rapidly approaching the reactivity/stability limit for cyclooctyne reagents. The results contained within Chapters 7-9 indicated that it was time to explore other bioorthogonal chemistries. When embarking on the development of a new bioorthogonal chemical reaction, we aimed to explore unrepresented reactivity space, such that the new reaction would be orthogonal to existing bioorthogonal chemistries. We became attracted to the highly strained hydrocarbon quadricyclane and performed a screen to find a suitable reactive partner for this potential chemical reporter group (Chapter 10). Through this analysis, we discovered that quadricyclane cleanly reacts with Ni bis(dithiolene) reagents and this transformation appeared to be a good prototype for a new bioorthogonal chemical reaction. After a thorough mechanistic investigation and many rounds of modification to the Ni bis(dithiolene) species, a nickel complex with suitable reaction kinetics, water-solubility, and stability was obtained (Chapter 11). Gratifyingly, this Ni bis(dithiolene) reagent selectively modified quadricyclane-labeled bovine serum albumin, even in the presence of cell lysate (Chapter 12). Other results in Chapter 12 highlight that this new bioorthogonal ligation reaction is indeed orthogonal to Cu-free click chemistry as well as oxime ligation chemistry. Additionally, quadricyclane-dependent labeling is observed on live cells, although further optimization is necessary. The final chapter of this dissertation outlines the current state of the field. There are now many methods to modify biomolecules including several new, although relatively untested, bioorthogonal chemistries. The rapid pace of this field makes it an exciting time to be pursuing bioorthogonal chemistry.

Author: W. Russ Algar
Publisher: John Wiley & Sons
ISBN: 3527683445
Category : Technology & Engineering
Languages : en
Pages : 430

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Book Description
This timely, one-stop reference is the first on an emerging and interdisciplinary topic. Covering both established and recently developed ligation chemistries, the book is divided into two didactic parts: a section that focuses on the details of bioorthogonal and chemoselective ligation reactions at the level of fundamental organic chemistry, and a section that focuses on applications, particularly in the areas of chemical biology, biomaterials, and bioanalysis, highlighting the capabilities and benefits of the ligation reactions. With chapters authored by outstanding scientists who range from trailblazers in the field to young and emerging leaders, this book on a highly interdisciplinary topic will be of great interest for biochemists, biologists, materials scientists, pharmaceutical chemists, organic chemists, and many others.

Author: Chelsea Gloria Gordon
Publisher:
ISBN:
Category :
Languages : en
Pages : 368

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Book Description
Bioorthogonal chemistries are reactions that are designed to proceed in living environments without perturbing endogenous biological functionalities. These reactions are valuable tools for labeling and studying biomolecules both in vitro and in vivo, often providing unique insights into dynamic, living processes. For a reaction to be considered bioorthogonal, it must proceed in aqueous solvents at physiological pH and temperature. The reaction must also be rapid and selective, generating a stable, covalent adduct that is not reactive towards biological functionalities. Finally, one of the reaction partners must be capable of installation onto the biomolecule of interest. A major motivator in the development of bioorthogonal chemistries is their potential utility in imaging and studying biomolecules in living animals. Chapter one chronicles advancements in the use of bioorthogonal reactions to tag biomolecules in multicellular organisms, focusing on the most prevalent reactions developed to date -- the Staudinger ligation, copper-click chemistry, copper-free click chemistry, and the tetrazine ligation. Examples are provided to highlight the importance of fast reaction kinetics as well as pharmacokinetics on the success of a ligation in vivo. Chapter one also provides commentary on unmet challenges in the field as well as an outlook on future advancements. The in vivo applications of bioorthogonal chemistry discussed in chapter one serve as motivation for the experimental work presented in chapter two. Here, we describe our efforts to understand the factors that contribute to the kinetic profile of the copper-free click reaction. Copper-free click chemistry is a bioorthogonal 1,3-dipolar cycloaddition between azides and strained cyclooctynes to form triazoles. The reaction has seen widespread use in selectively tagging biomolecules both in vitro and in vivo. These successes have prompted the development of cyclooctyne analogs with improved reactivity toward the azide. However, predicting a cyclooctyne's reactivity is challenging, requiring researchers to design and undertake lengthy syntheses of alkynes that may or may not prove successful bioorthogonal reagents. In chapter two, we discuss our work towards defining and predicting the effects of strain and electronics on the reactivity of a cyclooctyne reagent. Through synthesis of analogs of biarylazacyclooctynone (BARAC), the fastest cyclooctyne developed to date, and subsequent reactivity measurements, we gain new insights into the effects of cyclooctyne strain and electronics on reactivity. As well, through computational modeling of our BARAC analogs we conclude that the distortion/interaction model of 1,3-dipolar cycloaddition kinetics serves as a valuable predictor of cyclooctyne reactivity in the copper-free click reaction. Chapter three describes our motivation to develop new bioorthogonal ligations, highlighting the dearth of mutually orthogonal reactions capable of achieving multiplexed imaging. In addition, we discuss the need for bioorthogonal chemistries with new functional capabilities (i.e. polymerizations, reversible reactions, etc.). We then introduce the quadricyclane (QC) ligation, a new bioorthogonal reaction developed in the Bertozzi lab. The QC ligation is a formal [2s+2s+2p] reaction between QC and nickel bis(dithiolene). The reaction has been shown to fulfill many of the requirements of bioorthogonality, but no method of incorporating the QC functionality into a biomolecule of interest has been demonstrated. In chapter three, we discuss our use of the pyrrolysine synthetase/tRNACUA system for site-specific incorporation of a QC amino acid into a protein and subsequent tagging of this QC functionality with a nickel bis(dithiolene) reagent. In chapter four we discuss efforts to further develop the QC ligation, exploring new chemical transformations accessible through this unique reaction. Specifically, we analyze the photodissociation of the QC/nickel bis(dithiolene) adduct to form nickel bis(dithiolene) and norbornadiene, a transformation that has the potential to make the QC ligation a "click-unclick" reaction. In addition, we have begun to analyze possible secondary reaction partners for the norbornadiene product of the photodissociation. Chapter four chronicles our ongoing work to optimize these unique chemical transformations for reversible tagging of model proteins.

Author: Magdalene Heuser
Publisher: ISSN
ISBN:
Category : Autobiography
Languages : de
Pages : 448

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Book Description
Der vorliegende Tagungsband greift eine empfindliche Lücke der Autobiographieforschung auf, die bisher kaum oder unzureichend berücksichtigte Autobiographik von Frauen. Die Beiträge untersuchen mit unterschiedlichen methodischen Ansätzen und unter Einbeziehung neuen Quellenmaterials ausgewählte Autobiographien und autobiographisches Erzählen von Frauen des 17. bis 20. Jahrhunderts: Entwicklung und Wandel der dargestellten Lebenszusammenhänge, der Schreib- und Erzählmuster sowie der Veröffentlichungspraxis. Wie diese Studien zeigen, thematisiert und reflektiert die Autobiographik von Frauen die weiblich-männlichen Geschlechterverhältnisse zur allgemeinen Theorie und Geschichte der Autobiographik.

Author: Paolo Quadrelli
Publisher: Elsevier
ISBN: 0128152745
Category : Science
Languages : en
Pages : 352

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Book Description
Modern Applications of Cycloaddition Chemistry examines this area of organic chemistry, with special attention paid to cycloadditions in synthetic and mechanistic applications in modern organic chemistry. While many books dedicated to cycloaddition reactions deal with the synthesis of heterocycles, general applications, specific applications in natural product synthesis, and the use of a class of organic compounds, this work sheds new light on pericyclic reactions by demonstrating how these valuable tools elegantly solve synthetic and mechanistic problems. The work examines how pericyclic reactions have been extensively applied to different chemistry areas, such as chemical biology, biological processes, catalyzed cycloaddition reactions, and more. This work will be useful for organic chemists who deal with organic chemistry, medicinal chemistry, agrochemistry and material chemistry. Provides details on the synthesis of antiviral and anticancer compounds, marking the key role of unconventional catalyzed cycloaddition reactions for preparing new derivatives in a unique reaction pathway that is scalable in industrial processes Contains the most up-to-date review of the use of pericyclic reactions in drug delivery Includes the enzyme-catalyzed processes involving cycloaddition reactions for different targets, demonstrating that cycloaddition is more common in nature than expected Features new applications for cycloadditions in material chemistry and provides a general view of the most recent results in the area

Author: Yizhong Wang
Publisher:
ISBN:
Category :
Languages : en
Pages : 169

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Book Description
A mild, photoactivated 1,3-dipolar cycloaddition procedure based on photolysis of 2,5-disubstituted tetrazoles was successfully developed to serve as a new bioorthogonal reaction called photoclick chemistry. This procedure involved the in situ generation of the reactive nitrile imine dipoles using a hand-held UV lamp with wavelength at 302 nm, followed by spontaneous [3+2] cycloaddition with a broad range of 1,3-dipolarophiles with excellent solvent compatibility, functional group tolerance, regioselectivity, and yield. This reaction provided a convenient method for the synthesis of polysubstituted pyrazolines as well as a powerful tool for molecular manipulations such as protein modifications and peptide stapling. By screening a series of substituted diaryltetrazoles, a few long-wavelength (365 nm) photoactivatable diaryltetrazoles were also discovered. These tetrazoles showed excellent reactivity in the photoactivated 1,3-dipolar cycloaddition reactions toward electron-deficient and conjugated alkenes. The reaction rate of this [3+2] cycloaddition can be increased by systematically tuning the HOMO energies of the nitrile imines generated in the photolysis. A dipole HOMO-lifting effect was observed in the study. Finally, unnatural amino acids containing the tetrazole motif were synthesized.

Author: Wenjiao Song
Publisher:
ISBN:
Category :
Languages : en
Pages : 122

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Book Description
Bioorthogonal chemistry has emerged as a powerful tool in probing biomolecular structure and function in living systems. Combined with recent developments in introducing novel chemical reporters into biomolecules site-selectively in vivo, bioorthogonal chemistry offers an unprecedented opportunity to monitor and expand biomolecular function in living systems. The objective of this thesis work is to develop a tetrazole-based photoinducible bioorthogonal reaction and apply it to image protein in live cells. Chapter 2 describes a photoinducible 1, 3-dipolar cycloaddition that allows for fast and residue-specific modification of engineered proteins carrying a diphenyltetrazole group.^In a peptide tetrazole model study, the reaction was found to undergo a rapid photoinduced cycloreversion to generate a highly reactive nitrile imine dipolar (t1/2 = 5.1 sec) which spontaneously cyclizes with acrylamide with a second-order rate constant of 11.0 M-1s-1. When the diaryltetrazole was introduced into lysozyme, we found that labeling by acrylamide, coumarin methacrylamide, and palmityl methacrylamide occurred selectively at the tetrazole sites of the modified lysozyme after 1 min photoinduction at 302 nm. The resulting cycloaddition products, pyrazolines, showed strong fluorescence in the wavelength region of 487-538 nm. In addition, a robust lipidation of green fluorescent protein was achieved by introducing photoreactive diaryltetrazoles to the C-terminus of EGFP through chemical ligation followed by irradiating the tetrazole-containing EGFP in the presence of a lipid dipolarophile in vitro.^Taken together, this tetrazole-based photoinducible 1, 3-dipolar cycloaddition reaction represents a new and robust bioorthogonal reaction for selective protein modification in biological buffer. Chapter 3 describes the employment of the tetrazole-based, photoclick chemistry to selectively functionalize a genetically alkene-encoded protein inside E. coli cells. The reaction procedure was simple, straightforward, and nontoxic to E. coli cells. Additionally, fluorescent cycloadducts were formed, which enabled a facile monitoring of the reaction in vivo. The strategy to further optimize the tetrazole reactivity has also been put forth by systematically tuning the HOMO-lifting effect on nitrile imine dipoles. One of the optimized tetrazoles with the electron-donating methoxy substituent was found to label an alkene-encoded protein in less than 1 min inside E. coli cells.^Chapter 4 describes a simple alkene tag, homoallylglycine (HAG), that can be co-translationally incorporated into a recombinant protein as well as into endogenous newly synthesized proteins in mammalian cells with high efficiency. In conjunction with a photoinduced tetrazole-alkene cycloaddition reaction ("photoclick chemistry"), this alkene tag further served as a bioorthogonal chemical reporter both for selective protein functionalization in vitro and for spatiotemporally controlled imaging of the newly synthesized proteins in live mammalian cells.^Since the non-symmetrical spatial distribution of newly synthesized proteins in animal cells plays a central role in many cellular processes, this two-step metabolic alkene tagging-photo-controlled chemical functionalization approach may offer a potentially useful tool to study the role of the spatiotemporally regulated protein synthesis in mammalian cells. Chapter 5 describes a chemical lipidation model to study protein lipidations in live mammalian cells based on the bioorthogonal, photoinduced tetrazole-alkene cycloaddition reaction. The localization effect of photoinduced chemical lipidations on tetrazole conjugated EGFP both in organic solvent/PBS buffer mixture and in live HeLa cells have been demonstrated. This chemical strategy recapitulated some aspects of protein lipidation in vivo, e.g., the effect of lipid numbers on membrane association stability and the lipidation induced translocation into vesicles inside cells.