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The substitution of a single hydrogen atom in a protein by fluorine yields a site-specific probe for sensitive detection by 19 F nuclear magnetic resonance (NMR) spectroscopy, where the absence of background signal from the protein facilitates the detection of minor conformational species. We developed genetic encoding systems for the site-selective incorporation of 4-fluorotryptophan, 5-fluorotryptophan, 6-fluorotryptophan, and 7-fluorotryptophan in response to an amber stop codon and used them to investigate conformational heterogeneity in a designed amino acid binding protein and in flaviviral NS2B-NS3 proteases. These proteases have been shown to present variable conformations in X-ray crystal structures, including flips of the indole side chains of tryptophan residues. The 19 F NMR spectra of different fluorotryptophan isomers installed at the conserved site of Trp83 indicate that the indole ring flip is common in flaviviral NS2B-NS3 proteases in the apo state and suppressed by an active-site inhibitor.

Fluorine NMR is a highly sensitive technique for delineating the conformational states of biomolecules and has shown great utility in drug screening and in understanding protein function. Current fluorinated protein tags leverage the intrinsic chemical shift sensitivity of the 19 F nucleus to detect subtle changes in protein conformation and topology. This chemical shift sensitivity can be amplified by embedding the fluorine or trifluoromethyl reporter within a pyridone. Due to their polarizability and rapid tautomerization, pyridones exhibit a greater range of electron delocalization and correspondingly greater 19 F NMR chemical shift dispersion. To assess the chemical shift sensitivity of these tautomeric probes to the local environment, 19 F NMR spectra of all possible monofluorinated and trifluoromethyl-tagged versions of 2-pyridone were recorded in methanol/water mixtures ranging from 100% methanol to 100% water. 4-Fluoro-2-pyridone and 6-(trifluoromethyl)-2-pyridone (6-TFP) displayed the greatest sensitivity of the monofluorinated and trifluoromethylated pyridones, exceeding that of known conventional CF 3 reporters. To evaluate the utility of tautomeric pyridone tags for 19 F NMR of biomolecules, the alpha subunit of the stimulatory G protein (G s α) and human serum albumin (HSA) were each labeled with a thiol-reactive derivative of 6-TFP and the spectra were recorded as a function of various adjuvants and drugs. The tautomeric tag outperformed the conventional tag, 2-bromo- N -(4-(trifluoromethyl)phenyl)acetamide through the improved resolution of several functional states.

In-cell NMR spectroscopy is a powerful approach to study protein structure and function in the native cellular environment. It provides precious insights into the folding, maturation, interactions, and ligand binding of important pharmacological targets directly in human cells. However, its widespread application is hampered by the fact that soluble globular proteins often interact with large cellular components, causing severe line broadening in conventional heteronuclear NMR experiments. 19 F NMR can overcome this issue, as fluorine atoms incorporated in proteins can be detected by simple background-free 1D NMR spectra. Here, we show that fluorinated amino acids can be easily incorporated in proteins expressed in human cells by employing a medium switch strategy. This straightforward approach allows the incorporation of different fluorinated amino acids in the protein of interest, reaching fluorination efficiencies up to 60%, as confirmed by mass spectrometry and X-ray crystallography. The versatility of the approach is shown by performing 19 F in-cell NMR on several proteins, including those that would otherwise be invisible by 1 H- 15 N in-cell NMR. We apply the approach to observe the interaction between an intracellular target, carbonic anhydrase 2, and its inhibitors, and to investigate how the formation of a complex between superoxide dismutase 1 and its chaperone CCS modulates the interaction of the chaperone subunit with the cellular environment.

Direct C Ar -F arylation is effective and sustainable for synthesis of polyfluorobiaryls with different degrees of fluorination, which are important motifs in medical and material chemistry. However, with no aid of transition metals, the engagement of C Ar -F bond activation has proved difficult. Herein, an unprecedented transition-metal-free strategy is reported for site-selective C Ar -F arylation of polyfluoroarenes with simple (het)arenes. By merging N , N -bis(2,6-diisopropylphenyl)perylene-3,4,9,10-bis(dicarboximide)-catalyzed electrophotocatalytic reduction and anodic nitroxyl radical oxidation in an electrophotocatalytic cell, various polyfluoroaromatics (2F-6F and 8F), especially inactive partially fluorinated aromatics, undergo sacrificial-reagents-free C-F bond arylation with high regioselectivity, and the yields are comparable to those for reported transition-metal catalysis. This atom- and step-economic protocol features a paired electrocatalysis with organic mediators in both cathodic and anodic processes. The broad substrate scope and good functional-group compatibility highlight the merits of this operationally simple strategy. Moreover, the easy gram-scale synthesis and late-stage functionalization collectively advocate for the practical value, which would promote the vigorous development of fluorine chemistry.

We report a trifluoromethylarene reductive coupling method that dramatically expands the scope of difluorobenzylic substructures accessible via C-F bond functionalization. Catalytic quantities of a Lewis base, combined with a disilane reagent in formamide solvent, promotes the replacement of a single trifluoromethyl fluorine atom with a silylated hemiaminal functional group. The reaction proceeds through a difluorobenzyl silane intermediate that can also be isolated. Together, these defluorinated products are shown to provide rapid access to over 20 unique difluoroalkylarene scaffolds.

Cobalt precatalysts for the meta -selective borylation of fluorinated arenes are described. Initial screening and stoichiometric reactivity studies culminated in the preparation of a cobalt alkyl precatalyst supported by the sterically protected terpyridine ( 5,5″-Me 2 Ar Tpy = 4'-(4- N,N' -dimethylaminophenyl)-5,5″-dimethyl-2,2':6',2″-terpyridine). Under the optimized conditions, borylation with this precatalyst afforded up to 16 turnovers and near-exclusive meta regioselectivity with a range of substituted fluoroarenes in cyclopentyl methyl ether solvent at room temperature. Deuterium kinetic isotope effects of 2.9(2) at 23 °C support a turnover-limiting and selectivity-determining C(sp 2 )-H activation step, and stoichiometric C-H activation experiments provided insights into the identity of the C-H activating intermediate in catalysis. Analysis of the relevant Co-C and C-H bond thermodynamics support that the thermodynamics of C-H activation favor ortho -to-fluorine selectivity, providing additional, indirect support for kinetic control of C-H activation as the origin of meta selectivity.

Amyloid imaging by positron emission tomography (PET) is an important method for diagnosing neurodegenerative disorders such as Alzheimer's disease. Many 11 C- and 18 F-labeled PET tracers show varying binding capacities, specificities, and affinities for their target proteins. The structural basis of these variations is poorly understood. Here we employ 19 F and 13 C solid-state NMR to investigate the binding sites of a PET ligand, flutemetamol, to the 40-residue Alzheimer's β-amyloid peptide (Aβ40). Analytical high-performance liquid chromatography and 19 F NMR spectra show that flutemetamol binds the current Aβ40 fibril polymorph with a stoichiometry of one ligand per four to five peptides. Half of the ligands are tightly bound while the other half are loosely bound. 13 C and 15 N chemical shifts indicate that this Aβ40 polymorph has an immobilized N-terminus, a non-β-sheet His14, and a non-β-sheet C-terminus. We measured the proximity of the ligand fluorine to peptide residues using 19 F- 13 C and 19 F- 1 H rotational-echo double-resonance (REDOR) experiments. The spectra show that three segments in the peptide, 12 VHH 14 , 18 VFF 20 , and 39 VV 40 , lie the closest to the ligand. REDOR-constrained docking simulations indicate that these three segments form multiple binding sites, and the ligand orientations and positions at these sites are similar across different Aβ polymorphs. Comparison of the flutemetamol-interacting residues in Aβ40 with the small-molecule binding sites in other amyloid proteins suggest that conjugated aromatic compounds preferentially bind β-sheet surface grooves lined by aromatic, polar, and charged residues. These motifs may explain the specificity of different PET tracers to different amyloid proteins.

Modern polymer science suffers from the curse of multidimensionality. The large chemical space imposed by including combinations of monomers into a statistical copolymer overwhelms polymer synthesis and characterization technology and limits the ability to systematically study structure-property relationships. To tackle this challenge in the context of 19 F magnetic resonance imaging (MRI) agents, we pursued a computer-guided materials discovery approach that combines synergistic innovations in automated flow synthesis and machine learning (ML) method development. A software-controlled, continuous polymer synthesis platform was developed to enable iterative experimental-computational cycles that resulted in the synthesis of 397 unique copolymer compositions within a six-variable compositional space. The nonintuitive design criteria identified by ML, which were accomplished by exploring <0.9% of the overall compositional space, lead to the identification of >10 copolymer compositions that outperformed state-of-the-art materials.

Due to the lack of genetically encoded probes for fluorine-19 nuclear magnetic resonance spectroscopy ( 19 F NMR), its utility for probing eukaryotic membrane protein dynamics is limited. Here we report an efficient method for the genetic incorporation of an unnatural amino acid (UAA), 3'-trifluoromenthyl-phenylalanine (mtfF), into cannabinoid receptor 1 (CB1) in the Baculovirus Expression System. The probe can be inserted at any environmentally sensitive site, while causing minimal structural perturbation to the target protein. Using 19 F NMR and X-ray crystallography methods, we discovered that the allosteric modulator Org27569 and agonists synergistically stabilize a previously unrecognized pre-active state. An allosteric modulation model is proposed to explain Org27569's distinct behavior. We demonstrate that our site-specific 19 F NMR labeling method is a powerful tool in decoding the mechanism of GPCR allosteric modulation. This new method should be broadly applicable for uncovering conformational states for many important eukaryotic membrane proteins.

Fluoroarenes are widely used in medicinal, agricultural, and materials chemistry, and yet their production remains a critical challenge in organic synthesis. Indeed, the nearly identical physical properties of these vital building blocks hinders their purification by traditional methods, such as flash chromatography or distillation. As a result, the Balz-Schiemann reaction is currently employed to prepare fluoroarenes instead of more atom-economical C-H fluorination reactions, which produce inseparable mixtures of regioisomers. Herein, we propose an alternative solution to this problem: the purification of mixtures of fluoroarenes using metal-organic frameworks (MOFs). Specifically, we demonstrate that controlling the interaction of fluoroarenes with adjacent coordinatively unsaturated Mg 2+ centers within a MOF enables the separation of fluoroarene mixtures with unparalleled selectivities. Liquid-phase multicomponent equilibrium adsorption data and breakthrough measurements coupled with van der Waals-corrected density functional theory calculations reveal that the materials Mg 2 (dobdc) (dobdc 4- = 2,5-dioxidobenzene-1,4-dicarboxylate) and Mg 2 ( m -dobdc) ( m -dobdc 4- = 2,4-dioxidobenzene-1,5-dicarboxylate) are capable of separating the difluorobenzene isomers from one another. Additionally, these frameworks facilitate the separations of fluoroanisoles, fluorotoluenes, and fluorochlorobenzenes. In addition to enabling currently unfeasible separations for the production of fluoroarenes, our results suggest that carefully controlling the interaction of isomers with not one but two strong binding sites within a MOF provides a general strategy for achieving challenging liquid-phase separations.

Galactose oxidase (GAO) contains a Cu(II)-ligand radical cofactor. The cofactor, which is autocatalytically generated through the oxidation of the copper, consists of a cysteine-tyrosine radical (Cys-Tyr • ) as a copper ligand. The formation of the cross-linked thioether bond is accompanied by a C-H bond scission on Tyr272 with few details known thus far. Here, we report the genetic incorporation of 3,5-dichlorotyrosine (Cl 2 -Tyr) and 3,5-difluorotyrosine (F 2 -Tyr) to replace Tyr272 in the GAO V previously optimized for expression through directed evolution. The proteins with an unnatural tyrosine residue are catalytically competent. We determined the high-resolution crystal structures of the GAO V , Cl 2 -Tyr272, and F 2 -Tyr272 incorporated variants at 1.48, 1.23, and 1.80 Å resolution, respectively. The structural data showed only one halogen remained in the cofactor, indicating that an oxidative carbon-chlorine/fluorine bond scission has occurred during the autocatalytic process of cofactor biogenesis. Using hydroxyurea as a radical scavenger, the spin-coupled hidden Cu(II) was observed by EPR spectroscopy. Thus, the structurally defined catalytic center with genetic unnatural tyrosine substitution is in the radical containing form as in the wild-type, i.e., Cu(II)-(Cl-Tyr • -Cys) or Cu(II)-(F-Tyr • -Cys). These findings illustrate a previously unobserved C-F/C-Cl bond cleavage in biology mediated by a mononuclear copper center.

SF 5 Phe, para -pentafluorosulfanyl phenylalanine, is an unnatural amino acid with extreme physicochemical properties, which is stable in physiological conditions. Here we present newly developed aminoacyl-tRNA synthetases that enable genetic encoding of SF 5 Phe for site-specific incorporation into proteins in high yields. Owing to the SF 5 moiety's dichotomy of strong polarity and high hydrophobicity, the unnatural amino acid forms specific and strong interactions in proteins. The potential of SF 5 Phe in protein research is illustrated by (i) increasing the binding affinity of a consensus pentapeptide motif toward the β subunit of Escherichia coli DNA polymerase III holoenzyme by mutation of a phenylalanine to a SF 5 Phe residue, (ii) site-specifically adhering β-cyclodextrin to the surface of ubiquitin, and (iii) selective detection of 19 F- 19 F nuclear Overhauser effects in the Escherichia coli peptidyl-prolyl cis / trans -isomerase B following mutation of two phenylalanine residues in the core of the protein to SF 5 Phe. With increasing use of the SF 5 moiety in pharmaceutical chemistry, this general method of functionalizing proteins with SF 5 groups opens unique opportunities for structural biology and in vivo studies.

Fluorinated RNA molecules, particularly 2'-F RNA, have found a wide range of applications in RNA therapeutics, RNA aptamers, and ribozymes and as 19 F NMR probes for elucidating RNA structure. Owing to the instability of 4'-F ribonucleosides, synthesis of 4'-F-modified RNA has long been a challenge. In this study, we developed a strategy for synthesizing a 4'-F-uridine ( 4'F U) phosphoramidite, and we used it to prepare 4'-F RNA successfully. In the context of an RNA strand, 4'F U, which existed in a North conformation, was reasonably stable and resembled unmodified uridine well. The 19 F NMR signal of 4'F U was sensitive to RNA secondary structure, with a chemical shift dispersion as large as 4 ppm (compared with <1 ppm for 2'F U), which makes it a valuable probe for discriminating single-stranded RNA and A-type, B-type, and mismatched duplexes. In addition, we demonstrated that because RNA-processing enzymes treated 4'F U the same as unmodified uridine, 4'F U could be used to monitor RNA structural dynamics and enzyme-mediated RNA processing. Taken together, our results indicate that 4'-F RNA represents a probe with wide utility for elucidation of RNA structure and function by means of 19 F NMR spectroscopy.

A direct and versatile copper-catalyzed trifluoromethylthiolation and trifluoromethylselenation of primary, secondary, and tertiary aliphatic C-H bonds was developed. The reaction provides direct access to molecules containing these emerging moieties in the presence of a wide range of common functional groups and in complex molecular environments.

The mechanism of C(sp 2 )-H borylation of fluorinated arenes with B 2 Pin 2 (Pin = pinacolato) catalyzed by bis(phosphino)pyridine ( iPr PNP) cobalt complexes was studied to understand the origins of the uniquely high ortho -to-fluorine regioselectivity observed in these reactions. Variable time normalization analysis (VTNA) of reaction time courses and deuterium kinetic isotope effect measurements established a kinetic regime wherein C(sp 2 )-H oxidative addition is fast and reversible. Monitoring the reaction by in situ NMR spectroscopy revealed the intermediacy of a cobalt(I)-aryl complex that was generated with the same high ortho -to-fluorine regioselectivity associated with the overall catalytic transformation. Deuterium labeling experiments and stoichiometric studies established C(sp 2 )-H oxidative addition of the fluorinated arene as the selectivity-determining step of the reaction. This step favors the formation of ortho -fluoroaryl cobalt intermediates due to the ortho fluorine effect, a phenomenon whereby ortho fluorine substituents stabilize transition metal-carbon bonds. Computational studies provided evidence that the cobalt-carbon bonds of the relevant intermediates in ( iPr PNP)Co-catalyzed borylation are strengthened with increasing ortho fluorine substitution. The atypical kinetic regime involving fast and reversible C(sp 2 )-H oxidative addition in combination with the thermodynamic preference for forming cobalt-aryl bonds adjacent to fluorinated sites are the origin of the high regioselectivity in the catalytic borylation reaction.

Fluorinated organic molecules are pervasive within the pharmaceutical and agrochemical industries due to the range of structural and physicochemical properties that fluorine imparts. Currently, the most abundant methods for the synthesis of the aryl-CF 2 functionality have relied on the deoxyfluorination of ketones and aldehydes using expensive and poorly atom economical reagents. Here, we report a general method for the synthesis of aryl-CF 2 R and aryl-CF 2 H compounds through activation of the corresponding trifluoromethyl arene precursors. This strategy is enabled by an endergonic electron transfer event that provides access to arene radical anions that lie outside of the catalyst reduction potential. Fragmentation of these reactive intermediates delivers difluorobenzylic radicals that can be intercepted by abundant alkene feedstocks or a hydrogen atom to provide a diverse array of difluoalkylaromatics.

Peptoids are peptidomimetics of interest in the fields of drug development and biomaterials. However, obtaining stable secondary structures is challenging, and designing these requires effective control of the peptoid tertiary amide cis/trans equilibrium. Herein, we report new fluorine-containing aromatic monomers that can control peptoid conformation. Specifically, we demonstrate that a fluoro-pyridine group can be used to circumvent the need for monomer chirality to control the cis/trans equilibrium. We also show that incorporation of a trifluoro-methyl group ( N CF 3 Rpe) rather than a methyl group ( NRpe) at the α-carbon of a monomer gives rise to a 5-fold increase in cis-isomer preference.

Elevated levels of reactive oxygen species and peroxidase expression are often associated with inflammation and inflammatory diseases. We developed two novel Co(II) complexes that can be used to detect oxidative activity associated with inflammation using 19 F magnetic resonance imaging (MRI). These agents display a large change in 19 F chemical shift upon oxidation from Co(II) to Co(III), facilitating selective visualization of both species using chemical shift selective pulse sequences. This large chemical shift change is attributed to a large magnetic anisotropy in the high spin Co(II) complexes. Importantly, the differing reactivity of the two agents allows for detection of either H 2 O 2 production and/or the activity of peroxidase enzymes, providing two useful platforms for 19 F MR hot spot imaging of oxidative events associated with biological inflammation.

We report the multifunctional nanocomposites (NCs) consisting of 19 F-moieties grafted Cu 7 S 4 -Au nanoparticles (NPs) for negligible background 19 F-magnetic resonance imaging ( 19 F-MRI) and computed tomography (CT) imaging guided photothermal therapy. The localized surface plasmon resonance (LSPR) absorption can be reasonably tuned to the in vivo transparent window (800-900 nm) by coupling Au (<10 nm, LSPR ∼530 nm) with Cu 7 S 4 (<15 nm, LSPR ∼1500 nm) into Cu 7 S 4 -Au heterodimers. The in vivo photothermal tests show that Cu 7 S 4 -Au show deeper light penetration with 808 nm irradiation, better photothermal efficacy, and less damage to normal tissues than Cu 7 S 4 with 1500 nm irradiation. Moreover, compared to traditional 1 H-MRI, the 19 F-MRI based on these NCs demonstrates much better sensitivity due to the negligible background. This work offers a promising strategy for multimodal imaging guided photothermal therapy of deep tissue with good efficacy.

The photocatalytic C-F functionalization of highly fluorinated arenes is a powerful method for accessing functionalized multifluorinated arenes. The decisive step in the determining regioselectivity in fluorine functionalization is fluoride fragmentation from the radical anion of the multifluorinated arene. To date, the availability of regioisomers has been dictated by the innate electronics of the fluorinated arene, limiting the synthetic utility of the chemistry. This study investigates the remarkable ability of a strategically located hydrogen bond to transcend the normal regioselectivity of the C-F functionalization event. A significant rate acceleration is additionally observed for hydrodefluorination of fluorines that can undergo intramolecular hydrogen bonds that form 5-8-membered cycles with moderately acidic N-H's. The hydrogen bond is expected to facilitate the fragmentation not only by bending the C-F bond of the radical anion out of planarity but also by increasing the exothermicity of the fluoride extrusion step through protonation of the naked fluoride. Finally, the synthetic utility of the method is demonstrated in an expedited synthesis of the trifluorinated α-phenyl acetic acid derivative required for the commercial synthesis of Januvia, an antidiabetic drug. This represents the first synthesis of a commercially important multifluorinated arene via a defluorination strategy and is significantly shorter than the current strategy.

A practical method for enantioselective synthesis of fluoroalkyl-substituted Z-homoallylic tertiary alcohols has been developed. Reactions may be performed with ketones containing a polylfluoro-, trifluoro-, difluoro-, and monofluoroalkyl group along with an aryl, a heteroaryl, an alkenyl, an alkynyl, or an alkyl substituent. Readily accessible unsaturated organoboron compounds serve as reagents. Transformations were performed with 0.5-2.5 mol % of a boron-based catalyst, generated in situ from a readily accessible valine-derived aminophenol and a Z- or an E-γ-substituted boronic acid pinacol ester. With a Z organoboron reagent, additions to trifluoromethyl and polyfluoroalkyl ketones proceeded in 80-98% yield, 97:3 to >98:2 α:γ selectivity, >95:5 Z:E selectivity, and 81:19 to >99:1 enantiomeric ratio. In notable contrast to reactions with unsubstituted allylboronic acid pinacol ester, additions to ketones with a mono- or a difluoromethyl group were highly enantioselective as well. Transformations were similarly efficient and α- and Z-selective when an E-allylboronate compound was used, but enantioselectivities were lower. In certain cases, the opposite enantiomer was favored (up to 4:96 er). With a racemic allylboronate reagent that contains an allylic stereogenic center, additions were exceptionally α-selective, affording products expected from γ-addition of a crotylboron compound, in up to 97% yield, 88:12 diastereomeric ratio, and 94:6 enantiomeric ratio. Utility is highlighted by gram-scale preparation of representative products through transformations that were performed without exclusion of air or moisture and through applications in stereoselective olefin metathesis where Z-alkene substrates are required. Mechanistic investigations aided by computational (DFT) studies and offer insight into different selectivity profiles.

Virus-like particles (VLPs) are stable protein cages derived from virus coats. They have been used extensively as biomolecular platforms, e.g., nanocarriers or vaccines, but a convenient in situ technique is lacking for tracking functional status. Here, we present a simple way to monitor disassembly of 19 F-labeled VLPs derived from bacteriophage Qβ by 19 F NMR. Analysis of resonances, under a range of conditions, allowed determination not only of the particle as fully assembled but also as disassembled, as well as detection of a degraded state upon digestion by cells. This in turn allowed mutational redesign of disassembly and testing in both bacterial and mammalian systems as a strategy for the creation of putative, targeted-VLP delivery systems.

The copper-catalyzed H-F insertion into α-diazocarbonyl compounds is described using potassium fluoride (KF) and hexafluoroisopropanol. Access to complex α-fluorocarbonyl derivatives is achieved under mild conditions, and the method is readily adapted to radiofluorination with [(18)F]KF. This late-stage strategy provides an attractive route to (18)F-labeled biomolecules.

Fluorinated tyrosines (FnY's, n = 2 and 3) have been site-specifically incorporated into E. coli class Ia ribonucleotide reductase (RNR) using the recently evolved M. jannaschii Y-tRNA synthetase/tRNA pair. Class Ia RNRs require four redox active Y's, a stable Y radical (Y·) in the β subunit (position 122 in E. coli), and three transiently oxidized Y's (356 in β and 731 and 730 in α) to initiate the radical-dependent nucleotide reduction process. FnY (3,5; 2,3; 2,3,5; and 2,3,6) incorporation in place of Y122-β and the X-ray structures of each resulting β with a diferric cluster are reported and compared with wt-β2 crystallized under the same conditions. The essential diferric-FnY· cofactor is self-assembled from apo FnY-β2, Fe(2+), and O2 to produce ∼1 Y·/β2 and ∼3 Fe(3+)/β2. The FnY· are stable and active in nucleotide reduction with activities that vary from 5% to 85% that of wt-β2. Each FnY·-β2 has been characterized by 9 and 130 GHz electron paramagnetic resonance and high-field electron nuclear double resonance spectroscopies. The hyperfine interactions associated with the (19)F nucleus provide unique signatures of each FnY· that are readily distinguishable from unlabeled Y·'s. The variability of the abiotic FnY pKa's (6.4 to 7.8) and reduction potentials (-30 to +130 mV relative to Y at pH 7.5) provide probes of enzymatic reactions proposed to involve Y·'s in catalysis and to investigate the importance and identity of hopping Y·'s within redox active proteins proposed to protect them from uncoupled radical chemistry.

The first 4-position-selective C-H perfluoroalkylation and perfluoroarylation of six-membered heteroaromatic compounds were achieved using nucleophilic perfluoroalkylation and perfluoroarylation reagents. The regioselectivity was controlled by electrophilically activating the heteroaromatic rings, while sterically hindering the 2-position, with a sterically bulky borane Lewis acid. The reaction proceeded in good yield, even in gram scale, and by a sequential reaction without isolating the intermediates. This reaction could be applied to late-stage trifluoromethylation of a bioactive compound.

Herein we report the intramolecular arene C-H and C-F bond oxygenation by tetranuclear iron complexes. Treatment of [LFe3(PhPz)3OFe][OTf]2 (1) or its fluorinated analog [LFe3(F2ArPz)3OFe][OTf]2 (5) with iodosobenzene results in the regioselective hydroxylation of a bridging pyrazolate ligand, converting a C-H or C-F bond into a C-O bond. The observed reactivity suggests the formation of terminal and reactive Fe-oxo intermediates. With the possibility of intramolecular electron transfer within clusters in 1 and 5, different reaction pathways (Fe(IV)-oxo vs Fe(III)-oxo) might be responsible for the observed arene hydroxylation.

The transcriptional antirepressor AppA is a blue light using flavin (BLUF) photoreceptor that releases the transcriptional repressor PpsR upon photoexcitation. Light activation of AppA involves changes in a hydrogen-bonding network that surrounds the flavin chromophore on the nanosecond time scale, while the dark state of AppA is then recovered in a light-independent reaction with a dramatically longer half-life of 15 min. Residue Y21, a component of the hydrogen-bonding network, is known to be essential for photoactivity. Here, we directly explore the effect of the Y21 pKa on dark state recovery by replacing Y21 with fluorotyrosine analogues that increase the acidity of Y21 by 3.5 pH units. Ultrafast transient infrared measurements confirm that the structure of AppA is unperturbed by fluorotyrosine substitution, and that there is a small (3-fold) change in the photokinetics of the forward reaction over the fluorotyrosine series. However, reduction of 3.5 pH units in the pKa of Y21 increases the rate of dark state recovery by 4000-fold with a Brønsted coefficient of ∼ 1, indicating that the Y21 proton is completely transferred in the transition state leading from light to dark adapted AppA. A large solvent isotope effect of ∼ 6-8 is also observed on the rate of dark state recovery. These data establish that the acidity of Y21 is a crucial factor for stabilizing the light activated form of the protein, and have been used to propose a model for dark state recovery that will ultimately prove useful for tuning the properties of BLUF photosensors for optogenetic applications.

Fluorinated boronic acid-appended benzyl bipyridinium salts, derived from 4,4'-, 3,4'-, and 3,3'-bipyridines, were synthesized and used to detect and differentiate diol-containing analytes at physiological conditions via (19)F NMR spectroscopy. An array of three water-soluble boronic acid receptors in combination with (19)F NMR spectroscopy discriminates nine diol-containing bioanalytes--catechol, dopamine, fructose, glucose, glucose-1-phosphate, glucose-6-phosphate, galactose, lactose, and sucrose--at low mM concentrations. Characteristic (19)F NMR fingerprints are interpreted as two-dimensional barcodes without the need of multivariate analysis techniques.

A new biaryl monophosphine ligand (AlPhos, L1) allows for the room-temperature Pd-catalyzed fluorination of a variety of activated (hetero)aryl triflates. Furthermore, aryl triflates and bromides that are prone to give mixtures of regioisomeric aryl fluorides with Pd-catalysis can now be converted to the desired aryl fluorides with high regioselectivity. Analysis of the solid-state structures of several Pd(II) complexes, as well as density functional theory (DFT) calculations, shed light on the origin of the enhanced reactivity observed with L1.

This article describes the design and synthesis of quinoxaline-based semiconducting polymer dots (Pdots) that exhibit near-infrared fluorescence, ultrahigh brightness, large Stokes shifts, and excellent cellular targeting capability. We also introduced fluorine atoms and long alkyl chains into polymer backbones and systematically investigated their effect on the fluorescence quantum yields of Pdots. These new series of quinoxaline-based Pdots have a fluorescence quantum yield as high as 47% with a Stokes shift larger than 150 nm. Single-particle analysis reveals that the average per-particle brightness of the Pdots is at least 6 times higher than that of the commercially available quantum dots. We further demonstrated the use of this new class of quinoxaline-based Pdots for effective and specific cellular and subcellular labeling without any noticeable nonspecific binding. Moreover, the cytotoxicity of Pdots were evaluated on HeLa cells and zebrafish embryos to demonstrate their great biocompatibility. By taking advantage of their extreme brightness and minimal cytotoxicity, we performed, for the first time, in vivo microangiography imaging on living zebrafish embryos using Pdots. These quinoxaline-based NIR-fluorescent Pdots are anticipated to find broad use in a variety of in vitro and in vivo biological research.

We report the synthesis of fluorinated anilines by palladium-catalyzed coupling of fluoroalkylamines with aryl bromides and aryl chlorides. The products of these reactions are valuable because anilines typically require the presence of an electron-withdrawing substituent on nitrogen to suppress aerobic or metabolic oxidation, and the fluoroalkyl groups have steric properties and polarity distinct from those of more common electron-withdrawing amide and sulfonamide units. The fluoroalkylaniline products are unstable under typical conditions for C-N coupling reactions (heat and strong base). However, the reactions conducted with the weaker base KOPh, which has rarely been used in cross-coupling to form C-N bonds, occurred in high yield in the presence of a catalyst derived from commercially available AdBippyPhos and [Pd(allyl)Cl]2. Under these conditions, the reactions occur with low catalyst loadings (<0.50 mol % for most substrates) and tolerate the presence of various functional groups that react with the strong bases that are typically used in Pd-catalyzed C-N cross-coupling reactions of aryl halides. The resting state of the catalyst is the phenoxide complex, (BippyPhosPd(Ar)OPh); due to the electron-withdrawing property of the fluoroalkyl substituent, the turnover-limiting step of the reaction is reductive elimination to form the C-N bond.

A quinoline-based ligand was shown to promote palladium-catalyzed β-C(sp(3))-H fluorination for the first time. A range of unnatural enantiopure fluorinated α-amino acids were obtained through sequential β-C(sp(3))-H arylation and subsequent stereoselective fluorination from readily available L-alanine.

The rapid detection and differentiation of chiral compounds is important to synthetic, medicinal, and biological chemistry. Palladium complexes with chiral pincer ligands are demonstrated to have utility in determining the chirality of various amines. The binding of enantiomeric amines induces distinct (19)F NMR shifts of the fluorine atoms appended on the ligand that defines a chiral environment around palladium. It is further demonstrated that this method has the ability to evaluate the enantiomeric composition and discriminate between enantiomers with chiral centers several carbons away from the binding site. The wide detection window provided by optimized chiral chemosensors allows the simultaneous identification of as many as 12 chiral amines. The extraordinary discriminating ability of this method is demonstrated by the resolution of chiral aliphatic amines that are difficult to separate using chiral chromatography.

A series of narrow-band gap conjugated molecules with specific fluorine substitution patterns has been synthesized in order to study the effect of fluorination on bulk thermal stability. As the number of fluorine substituents on the backbone increase, one finds more thermally robust bulk structures both under inert and ambient conditions as well as an increase in phase transition temperatures in the solid state. When integrated into field-effect transistor devices, the molecule with the highest degree of fluorination shows a hole mobility of 0.15 cm(2)/V·s and a device thermal stability of >300 °C. Generally, the enhancement in thermal robustness of bulk organization and device performance correlates with the level of C-H for C-F substitution. These findings are relevant for the design of molecular semiconductors that can be introduced into optoelectronic devices to be operated under a wide range of conditions.

Isotopic labeling has been used to determine that a portion of the desired product in the Pd-catalyzed fluorination of electron-rich, non-ortho-substituted aryl triflates results from direct C-F cross-coupling. In some cases, formation of a Pd-aryne intermediate is responsible for producing undesired regioisomers. The generation of the Pd-aryne intermediate occurs primarily via ortho-deprotonation of a L·Pd(Ar)OTf (L = biaryl monophosphine) species by CsF and thus competes directly with the transmetalation step of the catalytic cycle. Deuterium labeling studies were conducted with a variety of aryl triflates.

Improved methods for quickly identifying neutral organic compounds and differentiation of analytes with similar chemical structures are widely needed. We report a new approach to effectively "fingerprint" neutral organic molecules by using (19)F NMR and molecular containers. The encapsulation of analytes induces characteristic up- or downfield shifts of (19)F resonances that can be used as multidimensional parameters to fingerprint each analyte. The strategy can be achieved either with an array of fluorinated receptors or by incorporating multiple nonequivalent fluorine atoms in a single receptor. Spatial proximity of the analyte to the (19)F is important to induce the most pronounced NMR shifts and is crucial in the differentiation of analytes with similar structures. This new scheme allows for the precise and simultaneous identification of multiple analytes in a complex mixture.

We report the late-stage functionalization of multisubstituted pyridines and diazines at the position α to nitrogen. By this process, a series of functional groups and substituents bound to the ring through nitrogen, oxygen, sulfur, or carbon are installed. This functionalization is accomplished by a combination of fluorination and nucleophilic aromatic substitution of the installed fluoride. A diverse array of functionalities can be installed because of the mild reaction conditions revealed for nucleophilic aromatic substitutions (S(N)Ar) of the 2-fluoroheteroarenes. An evaluation of the rates for substitution versus the rates for competitive processes provides a framework for planning this functionalization sequence. This process is illustrated by the modification of a series of medicinally important compounds, as well as the increase in efficiency of synthesis of several existing pharmaceuticals.

The method of continuous variation in conjunction with (1)H and (19)F NMR spectroscopies was used to characterize lithium and sodium enolates solvated by N,N,N',N'-tetramethylethyldiamine (TMEDA) and tetrahydrofuran (THF). A strategy developed using lithium enolates was then applied to the more challenging sodium enolates. A number of sodium enolates solvated by TMEDA or THF afford exclusively tetramers. Evidence suggests that TMEDA chelates sodium on cubic tetramers.

Fluorinated tungsten calix[4]arene imido complexes were synthesized and used as receptors to detect and differentiate neutral organic compounds. It was found that the binding of specific neutral organic molecules to the tungsten centers induces an upfield shift of the fluorine atom appended on the arylimido group, the extent of which is highly dependent on electronic and steric properties. We demonstrate that the specific bonding and size-selectivity of calix[4]arene tungsten-imido complex combined with (19)F NMR spectroscopy is a powerful new method for the analysis of complex mixtures.

A practical, palladium-catalyzed synthesis of aryl fluorides from arylboronic acid derivatives is presented. The reaction is operationally simple and amenable to multigram-scale synthesis. Evaluation of the reaction mechanism suggests a single-electron-transfer pathway, involving a Pd(III) intermediate that has been isolated and characterized.

The assembly of misfolded proteins is a critical step in the pathogenesis of amyloid and prion diseases, although the molecular mechanisms underlying this phenomenon are not completely understood. Here, we use (19)F NMR spectroscopy to examine the thermodynamic driving forces surrounding formation of β-sheet-rich oligomers early in the misfolding and aggregation pathway of the mammalian prion protein. We show that initial assembly of a small octameric intermediate is entropically driven, while further assembly to putative prefibrillar aggregates is driven by a favorable change in enthalpy. Kinetic data suggest that formation of the β-octamer represents a rate-limiting step in the assembly of prion aggregates. A disease-related mutation (F198S) known to destabilize the native state of PrP was also found to stabilize the β-octamer, suggesting that it can influence susceptibility to prion disease through two distinct mechanisms. This study provides new insight into the misfolding pathway leading to critical oligomers of the prion protein and suggests a physical basis for increased assembly of the F198S mutant.

The chemical variety present in the organic electronics literature has motivated us to investigate potential nonbonding interactions often incorporated into conformational "locking" schemes. We examine a variety of potential interactions, including oxygen-sulfur, nitrogen-sulfur, and fluorine-sulfur, using accurate quantum-chemical wave function methods and noncovalent interaction (NCI) analysis on a selection of high-performing conjugated polymers and small molecules found in the literature. In addition, we evaluate a set of nonbonding interactions occurring between various heterocyclic and pendant atoms taken from a group of representative π-conjugated molecules. Together with our survey and set of interactions, it is determined that while many nonbonding interactions possess weak binding capabilities, nontraditional hydrogen-bonding interactions, oxygen-hydrogen (CH···O) and nitrogen-hydrogen (CH···N), are alone in inducing conformational control and enhanced planarity along a polymer or small molecule backbone at room temperature.

Electrocatalytic water oxidation occurs at fluoride-doped tin oxide (FTO) electrodes that have been surface-modified by addition of Co(II). On the basis of X-ray photoelectron spectroscopy and transmission electron microscopy measurements, the active surface site appears to be a single site or small-molecule assembly bound as Co(II), with no evidence for cobalt oxide film or cluster formation. On the basis of cyclic voltammetry measurements, surface-bound Co(II) undergoes a pH-dependent 1e(-)/1H(+) oxidation to Co(III), which is followed by pH-dependent catalytic water oxidation. O2 reduction at FTO occurs at -0.33 V vs NHE, allowing for in situ detection of oxygen as it is formed by water oxidation on the surface. Controlled-potential electrolysis at 1.61 V vs NHE at pH 7.2 resulted in sustained water oxidation catalysis at a current density of 0.16 mA/cm(2) with 29,000 turnovers per site over an electrolysis period of 2 h. The turnover frequency for oxygen production per Co site was 4 s(-1) at an overpotential of 800 mV at pH 7.2. Initial experiments with Co(II) on a mesoporous, high-surface-area nanoFTO electrode increased the current density by a factor of ~5.

Highly enantio- and diastereoenriched monofluorocyclopropanes were accessed via the Simmons-Smith fluorocyclopropanation of allylic alcohols using difluoroiodomethane and ethylzinc iodide as the substituted carbenoid precursors. The scrambling of halogens at the zinc carbenoid led to the formation of the fluorocyclopropanating agent (fluoroiodomethyl)zinc(II) fluoride. This strategy circumvented the ongoing limitation in Simmons-Smith fluorocyclopropanations relying on the use of the relatively inaccessible and expensive carbenoid precursor fluorodiiodomethane.

Molecules that bind selectively to a given protein and then undergo a rapid chemoselective reaction to form a covalent conjugate have utility in drug development. Herein a library of 1,3,4-oxadiazoles substituted at the 2 position with an aryl sulfonyl fluoride and at the 5 position with a substituted aryl known to have high affinity for the inner thyroxine binding subsite of transthyretin (TTR) was conceived of by structure-based design principles and was chemically synthesized. When bound in the thyroxine binding site, most of the aryl sulfonyl fluorides react rapidly and chemoselectively with the pKa-perturbed K15 residue, kinetically stabilizing TTR and thus preventing amyloid fibril formation, known to cause polyneuropathy. Conjugation t50s range from 1 to 4 min, ~1400 times faster than the hydrolysis reaction outside the thyroxine binding site. X-ray crystallography confirms the anticipated binding orientation and sheds light on the sulfonyl fluoride activation leading to the sulfonamide linkage to TTR. A few of the aryl sulfonyl fluorides efficiently form conjugates with TTR in plasma. Eleven of the TTR covalent kinetic stabilizers synthesized exhibit fluorescence upon conjugation and therefore could have imaging applications as a consequence of the environment sensitive fluorescence of the chromophore.

Human telomeric DNA quadruplexes can adopt different conformations in solution. We have found that arabinose, 2'F-arabinose, and ribose substitutions stabilize the propeller parallel G-quadruplex form over competing conformers, allowing NMR structural determination of this particularly significant nucleic acid structure. 2'F-arabinose substitution provides the greatest stabilization as a result of electrostatic (F-CH---O4') and pseudo-hydrogen-bond (F---H8) stabilizing interactions. In contrast, 2'F-rG substitution provokes a dramatic destabilization of the quadruplex structure due to unfavorable electrostatic repulsion between the phosphate and the 2'-F.

A formal regioselective cross-coupling of various pyridines with alkyl and aryl groups can be achieved by a BF3·OEt2-mediated addition of Grignard or organozinc reagents to pyridines bearing various substituents (chloro, bromo, cyano, vinyl, phenyl, carbethoxy, nitro, etc.) followed by an oxidative aromatization mediated by chloranil. Good regioselectivity and wide functional group tolerance make this method very versatile for the preparation of polyfunctional pyridines. No transition-metal catalyst is required in these coupling reactions.

Cocaine addiction is a long-lasting relapsing illness characterized by cycles of abuse, abstinence, and reinstatement, and antibody-based therapies could be a powerful therapeutic approach. Herein, we explored the possibility of using halogenated cocaine haptens to enhance the immunological properties of anti-cocaine vaccines. Three fluorine-containing cocaine haptens (GNF, GNCF and GN5F) and one chlorine-containing cocaine hapten (GNCl) were designed and synthesized, based upon the chemical scaffold of the only hapten that has reached clinical trials, succinyl norcocaine (SNC). Hapten GNF was found to retain potent cocaine affinity, and also elicit antibodies in a higher concentration than the parent structure SNC. Our data suggests that not only could strategic hapten fluorination be useful for improving upon the current cocaine vaccine undergoing clinical trials, but it may also be a valuable new approach, with application to any of the vaccines being developed for the treatment of drugs of abuse.

A visible-light-mediated hydrotrifluoromethylation of unactivated alkenes that uses the Umemoto reagent as the CF(3) source and MeOH as the reductant is disclosed. This effective transformation operates at room temperature in the presence of 5 mol % Ru(bpy)(3)Cl(2); the process is characterized by its operational simplicity and functional group tolerance.

Three structurally identical polymers, except for the number of fluorine substitutions (0, 1, or 2) on the repeat unit (BnDT-DTBT), are investigated in detail, to further understand the impact of these fluorine atoms on open circuit voltage (V(oc)), short circuit current (J(sc)), and fill factor (FF) of related solar cells. While the enhanced V(oc) can be ascribed to a lower HOMO level of the polymer by adding more fluorine substituents, the improvement in J(sc) and FF are likely due to suppressed charge recombination. While the reduced bimolecular recombination with raising fluorine concentration is confirmed by variable light intensity studies, a plausibly suppressed geminate recombination is implied by the significantly increased change of dipole moment between the ground and excited states (Δμ(ge)) for these polymers as the number of fluorine substituents increases. Moreover, the 2F polymer (PBnDT-DTffBT) exhibits significantly more scattering in the in-plane lamellar stacking and out-of-plane π-π stacking directions, observed with GIWAXS. This indicates that the addition of fluorine leads to a more face-on polymer crystallite orientation with respect to the substrate, which could contribute to the suppressed charge recombination. R-SoXS also reveals that PBnDT-DTffBT has larger and purer polymer/fullerene domains. The higher domain purity is correlated with an observed decrease in PCBM miscibility in polymer, which drops from 21% (PBnDT-DTBT) to 12% (PBnDT-DTffBT). The disclosed "fluorine" impact not only explains the efficiency increase from 4% of PBnDT-DTBT (0F) to 7% with PBnDT-DTffBT (2F) but also suggests fluorine substitution should be generally considered in the future design of new polymers.