Systematic Investigation of Lipophilicity Modulation by Aliphatic Fluorination Motifs

I2-mediated convenient ring-opening of simple gem-difluorocyclopropanes

We previously reported an efficient method for the ring-opening 1,3-difunctionalization of gem-difluorinated cyclopropanes (F2CPs) using KBr in the presence of ceric ammonium nitrate or potassium persulfate, resulting in the formation of 3-bromo-2,2-difluoropropanes with a bromine atom or a hydroxy group at the 1 position by the highly regioselective cyclopropane bond cleavage. In spite of the usefulness of this process, the concern of the use of these irritant oxidants and the insufficient reactivity of Br incorporated at the 1 position allowed us to modify this system to find out that the environmentally friendly as well as easy-to-handle reagent, an iodine molecule, works quite efficiently, enabling the successful introduction of not only a hydroxy group but also alkoxy, sulfenyl, and aryl groups at the 1 position of products.

Impact of Fluorine Pattern on Lipophilicity and Acid-Base Properties of 2-(Thiofluoroalkyl)pyridines: Insights from Experiments and Statistical Modeling

Lipophilicity and acid-base properties are two key aspects of the optimization of a compound in drug discovery. Using 19F NMR, we experimentally determined the log D7.4 of a wide array of 2-thiofluoroalkyl (SRF) and 2-sulfonyl fluoroalkyl (SO2RF) substituted pyridines and the pKa values of their protonated counterparts. Statistical modeling based on constitutional and DFT descriptors provided further insights into the structure-property relationship, explaining the experimental observations and predicting log D7.4 values. Our results highlight the influence of fluorination topology in SRF fragments and demonstrate the dual effect of fluorine on molecular polarity, increasing the hydrophobic surface and the polarity of the sulfur moiety. By analyzing methyl- and ethyl-derived fragments, we found a gradient in log D7.4 values influenced by the oxidation state of the sulfur atom and fluorination pattern. Our findings emphasize the context-dependent impact of fluorination and offer insights to better understand the impact of thiofluoroalkyl chains on these physicochemical properties.

Physicochemical and Biological Evaluation of gem-Difluorinated Saturated Oxygen Heterocycles as Bioisosteres for Drug Discovery

A comprehensive study on the physicochemical properties of gem-fluorinated O-heterocyclic substituents is reported. Systematic additive effects of introducing O- and gem-CF2 group introduction on acidic properties (pKa) of the corresponding carboxylic acids/protonated primary amines were demonstrated. The impact of the O/CF2 moieties on lipophilicity (LogP) was found to be complex; significant mutual influence of the corresponding polar moieties governed the compound's overall properties in this case. Biological evaluation of MAPK kinase inhibitors incorporating the title substituents demonstrated their utility as promising fragments for bioisosteric replacements in drug discovery campaigns.

Inverse conjugate additions of acrylic amides and esters with F/Cl/O/N-nucleophiles and CF3+ reagents

The conjugate additions of nucleophiles to conjugate acceptors are among the most powerful hetero-carbon bond formation reactions. The conjugate addition normally occurs via a β-nucleophilic addition, resulting in the formation of a stabilized α-carbanion intermediate that can be subsequently quenched by electrophiles or protons. Nevertheless, the inverse conjugate addition involving an α-specific nucleophilic addition remains less explored because of the electronic mismatch. In this research, we disclosed an α-specific nucleophilic addition of the nucleophiles including Py·HF, TBACl, HOR, H2O, H218O, RCO2H, and pyrazole to conjugate acceptors concurrent with a trifluoromethylation. This umpolung and inversely regioselective conjugate addition, enabled by a visible light-induced redox photocatalysis, occurred via an unusual α-nucleophilic addition other than the normal β-nucleophilic addition to efficiently generate diverse α-functionalized CF3-containing amides/esters. The broad substrate scope, excellent functional-group tolerance, and versatile late-stage derivatizations as well as the biologically and functionally important CF3-containing products demonstrated the potential applications of this protocol in materials, agrochemicals, and pharmaceutical chemistry.

Synthesis and Evaluation of 68Ga- and 177Lu-Labeled [diF-Pro14]Bombesin(6-14) Analogs for Detection and Radioligand Therapy of Gastrin-Releasing Peptide Receptor-Expressing Cancer

Background/Objectives: Overexpressed in various solid tumors, the gastrin-releasing peptide receptor (GRPR) is a promising target for cancer diagnosis and therapy. However, the high pancreas uptake of the current clinically evaluated GRPR-targeted radiopharmaceuticals limits their applications. In this study, we replaced the Pro14 residue in our previously reported GRPR-targeted LW02056 and ProBOMB5 with 4,4-difluoroproline (diF-Pro) to obtain an agonist LW02060 (DOTA-Pip-[D-Phe6,Tle10,NMe-His12,diF-Pro14]Bombesin(6-14)) and an antagonist LW02080 (DOTA-Pip-[D-Phe6,NMe-Gly11,Leu13(ψ)diF-Pro14]Bombesin(6-14)), respectively. Methods/Results: The binding affinities (Ki) of Ga-LW02060, Ga-LW02080, Lu-LW02060, and Lu-LW02080 were measured by in vitro competition binding assays using PC-3 cells and were found to be 5.57 ± 2.47, 21.7 ± 6.69, 8.00 ± 2.61, and 32.1 ± 8.14 nM, respectively. The 68Ga- and 177Lu-labeled ligands were obtained in 36-75% decay-corrected radiochemical yields with >95% radiochemical purity. PET imaging, SPECT imaging, and ex vivo biodistribution studies were conducted in PC-3 tumor-bearing mice. Both [68Ga]Ga-LW02060 and [68Ga]Ga-LW02080 enabled clear tumor visualization in PET images at 1 h post-injection (pi). Tumor uptake values of [68Ga]Ga-LW02060 and [68Ga]Ga-LW02080 at 1 h pi were 16.8 ± 2.70 and 7.36 ± 1.33 %ID/g, respectively, while their pancreas uptake values were 3.12 ± 0.89 and 0.38 ± 0.04 %ID/g, respectively. Compared to [177Lu]Lu-LW02080, [177Lu]Lu-LW02060 showed higher tumor uptake at all time points (1, 4, 24, 72, and 120 h pi). However, fast tumor clearance was observed for both [177Lu]Lu-LW02060 and [177Lu]Lu-LW02080. Conclusions: Our data demonstrate that [68Ga]Ga-LW02060 is promising for clinical translation for the detection of GRPR-expressing tumor lesions. However, further optimizations are needed for [177Lu]Lu-LW02060 and [177Lu]Lu-LW02080 to prolong tumor retention for therapeutic applications.

Design, synthesis and investigation of biological activity and mechanism of fluoroaryl-substituted derivatives at the FL118 position 7

Addition of fluorine atoms into chemical compounds is a validated strategy to enhance their physical, chemical and biological properties. In this study, FL118, a novel camptothecin-related small molecule known for its unique mechanism of action and superior antitumor efficacy, was utilized as a foundational drug platform. By replacing the hydrogen atom at position 7 of FL118 with a fluoroaryl group, a diverse array of FL118 derivatives were synthesized. Our investigations revealed that the majority of these newly synthesized compounds exhibited improved cytotoxicity compared to FL118, with some demonstrating enhanced in vivo antitumor efficacy. Among these derivatives, compound 7h stood out and was subjected to detailed analysis. Compound 7h demonstrated a remarkable ability to inhibit colorectal cancer (CRC) cell colony formation and cell migration, while also promoting reactive oxygen species (ROS) production and CRC cell apoptosis. Notably, our studies unveiled that the presence of DDX5 could modulate Topoisomerase I (Top1) activity, a process effectively reversed by a low concentration of 7h, but not SN38. Moreover, only 7h was able to decrease DDX5 expression, SN38 was not. Molecular docking studies further supported the binding of 7h to DDX5. Interestingly, although both 7h and SN38 exhibited similar inhibitory effects on Top1 activity, only 7h, and not SN38, could inhibit DDX5. These findings not only pave the way for deeper mechanistic explorations of FL118 and its derivatives in cancer research but also position the identified compound 7h as a promising candidate for further development.

Quantifying the ability of the CF2H group as a hydrogen bond donor

The CF2H group can act as a hydrogen bond donor, serving as a potential surrogate for OH or SH groups but with a weaker hydrogen bond donation ability. Here, we describe a series of CF2H group-containing moieties that facilitate hydrogen bond interactions. We survey hydrogen bond donation ability using several established methods, including 1H NMR-based hydrogen bond acidity determination, UV-vis spectroscopy titration with Reichardt's dye, and 1H NMR titration using tri-n-butylphosphine oxide as a hydrogen bond acceptor. Our experiments reveal that the direct attachment of the CF2H group to cationic aromatic systems significantly enhances its hydrogen bond donation ability, a result consistent with theoretical calculations. We anticipate that this chemistry will be valuable for designing functional molecules for chemical biology and medicinal chemistry applications.

CF2H-synthon enables asymmetric radical difluoroalkylation for synthesis of chiral difluoromethylated amines

The difluoromethyl group is a crucial fluorinated moiety with distinctive biological properties, and the synthesis of chiral CF₂H-containing analogs has been recognized as a powerful strategy in drug design. To date, the most established method for accessing enantioenriched difluoromethyl compounds involves the enantioselective functionalization of nucleophilic and electrophilic CF₂H synthons. However, this approach is limited by lower reactivity and reduced enantioselectivity. Leveraging the unique fluorine effect, we design and synthesize a radical CF₂H synthon by incorporating isoindolinone into alkyl halides for asymmetric radical transformation. Here, we report an efficient strategy for the asymmetric construction of carbon stereocenters featuring a difluoromethyl group via nickel-catalyzed Negishi cross-coupling. This approach demonstrates mild reaction conditions and excellent enantioselectivity. Given that optically pure difluoromethylated amines and isoindolinones are key structural motifs in bioactive compounds, this strategy offers a practical solution for the efficient synthesis of CF₂H-containing chiral drug-like molecules.

FON: An Innovative Fluorinated Group via Hydroetherification-Type Reactivity

An efficient strategy for preparing the novel O-difluoroalkylhydroxylamine fluorinated functional group, coined FON, is reported. This analogue of medicinally important β-phenethyl ether scaffolds in uniting gem-difluoro and N-O moieties is synthesized in one step via chemo- and regioselectivity metal-free hydroetherification-type additions. As shown, this unique mode of reactivity is realized for a diverse substrate scope and applied to gram-scale synthesis and site-selective deuterium incorporation. Lastly, a mechanistic understanding with implications in Brønsted acid catalysis is offered.

Discovery of N-Trifluoromethylated Noscapines as Novel and Potent Agents for the Treatment of Glioblastoma

The search for new and effective chemotherapeutic agents for the treatment of glioblastoma (GBM) represents an unmet need in drug discovery. Herein, a class of novel N-trifluoromethylated noscapines has been disclosed. Among them, 9'-bromo-N-trifluoromethyl noscapine 15c displayed superior in vitro anti-GBM potency. Unexpectedly, in contrast with the general N-trifluoromethyl amines, these compounds exhibited good hydrolytic stability and further investigation of this distinct stability revealed a novel strategy for the structure modification of tetrahydroisoquinoline alkaloids, where N-methyl could be bioisosterically replaced with trifluoromethyl. Furthermore, 15c showed excellent BBB permeability and good in vivo anti-GBM activity and could efficiently suppress the migration of GBM cells, while no apparent toxicity was observed, thus representing an attractive lead for further drug discovery. Further mechanistic studies revealed that 15c exhibited an ability to induce G2/M-phase arrest in GBM cells associated with the disruption of tubulin polymerization, which is consistent with the mechanism of action of noscapine.

Exploring fluorinated heptose phosphate analogues as inhibitors of HldA and HldE, key enzymes in the biosynthesis of lipopolysaccharide

The growing threat of bacterial resistance to antibiotics has led to the rise of anti-virulence strategies as a promising approach. These strategies aim to disarm bacterial pathogens and improve their clearance by the host immune system. Lipopolysaccharide, a key virulence factor in Gram-negative bacteria, has been identified as a potential target for anti-virulence agents. In this study, we focus on inhibiting HldA and HldE, bacterial enzymes from the heptose biosynthesis pathway, which plays a key role in lipopolysaccharide biosynthesis. We present the synthesis of two fluorinated non-hydrolysable heptose phosphate analogues. Additionally, the inhibitory activity of a family of eight heptose phosphate analogues against HldA and HldE was assessed. This evaluation revealed inhibitors with affinities in the low μM range, with the most potent compound showing inhibition constant values of 15.4 μM for HldA and 16.9 μM for HldE. The requirement for a phosphate group at the C-7 position was deemed essential for inhibitory activity, while the presence of a hydroxy anomeric group was found to be beneficial, a phenomenon rationalized through computational modeling. Additionally, the introduction of a single fluorine atom α to the phosphonate moiety conferred a slight advantage for inhibition. These findings suggest that mimicking the structure of d-glycero-β-d-manno-heptose 1,7-bisphosphate, the product of the phosphorylation step in heptose biosynthesis, could be a promising strategy to disrupt this biosynthetic pathway. In terms of the in vivo effects, these heptose phosphate analogues neither demonstrated significant LPS-disrupting effects nor exhibited growth inhibitory activity on their own. Additionally, they did not alter the susceptibility of bacteria to hydrophobic antibiotics. The highly charged nature of these molecules may hinder their ability to penetrate the bacterial cell wall. To overcome this limitation, alternative strategies such as incorporating protecting groups that facilitate their entry and can subsequently be cleaved within the bacterial cytoplasm could be explored.

Metallaphotocatalytic triple couplings for modular synthesis of elaborate N-trifluoroalkyl anilines

The integration of trifluoromethyl groups and three-dimensional quaternary carbon moieties into organic molecules has emerged as a prominent strategy in medicinal chemistry to augment drug efficacy. Although trifluoromethyl (hetero)aromatic amines and derivatives are prevalent frameworks in pharmaceuticals, the development of trifluoromethyl-embedded, intricately structured alkyl amine scaffolds for medicinal research remains a significant challenge. Herein, we present a metallaphotoredox multicomponent amination strategy employing 3,3,3-trifluoropropene, nitroarenes, tertiary alkylamines, and carboxylic acids. This synthetic pathway offers notable advantages, including the accessibility and cost-effectiveness of starting materials, high levels of chemo- and regioselectivity, and modularity. Furthermore, this approach enables the synthesis of a broad spectrum of aniline compounds featuring both trifluoromethyl group and distal quaternary carbon motifs along the aliphatic chains. The accelerated access to such elaborate N-trifluoroalkyl anilines likely involves three sequential radical-mediated coupling events, providing insightful implications for the retrosynthesis of potential compounds in organic synthesis and drug discovery.

18F-Difluoromethyl(ene) Motifs via Oxidative Fluorodecarboxylation with [18F]Fluoride

Herein, we report that α-fluorocarboxylic acids undergo manganese-mediated oxidative 18F-fluorodecarboxylation with [18F]fluoride affording biologically relevant 18F-difluoromethyl(ene)-containing molecules. This no-carrier added process provides a solution to a known challenge in radiochemistry and expands the radiochemical space available for positron emission tomography (PET) ligand discovery. Scalability on a fully automated radiosynthetic platform is exemplified with the production of [18F]4,4-difluoropiperidine that, we demonstrate, is amenable to postlabeling functionalization including N-heteroarylation and amide as well as sulfonamide bond formation.

2,2-Difluoroethylation of Heteroatom Nucleophiles via a Hypervalent Iodine Strategy

The 2,2-difluoroethyl group is an important lipophilic hydrogen bond donor in medicinal chemistry, but its incorporation into small molecules is often challenging. Herein, we demonstrate electrophilic 2,2-difluoroethylation of thiol, amine and alcohol nucleophiles with a hypervalent iodine reagent, (2,2-difluoro-ethyl)(aryl)iodonium triflate, via a proposed ligand coupling mechanism. This transformation offers a complementary strategy to existing 2,2-difluoroethylation methods and allows access to a wide range of 2,2-difluoroethylated nucleophiles, including the drugs Captopril, Normorphine and Mefloquine.

Visible light-induced Mallory reaction of tertiary benzanilides via iminium intermediates

The Mallory reaction, which involves the photocyclization of stilbenes/diarylethenes and their analogues into polycyclic aromatics, is of significant synthetic importance. However, its application to tertiary benzanilides has not been explored to date. Besides, most of the reported Mallory reactions require ultraviolet irradiation. In this study, we show the first Mallory reaction of tertiary benzanilides promoted by visible light via iminium intermediates formed in situ from tertiary benzanilide, Tf2O (triflic anhydride) and pyridine. UV/vis absorption spectroscopy combined with density functional theory (DFT) calculations revealed that the formation of the iminium intermediate decreased the HOMO-LUMO energy gap, thereby enhancing visible light absorption. This study provides a rapid and practical approach for the preparation of the phenanthridinone skeleton and provides a new idea for the design of new visible light photoswitches.

Searching for "Greener" Bioequivalents of CF3 to Lower its Environmental Impact

Considering the broad use of the trifluoromethyl functional group (-CF3) in medicinal chemistry and taking into account the recent concerns on the negative environmental effects of CF3 containing compounds, we are searching for "greener" alternatives. Thus, different chemical groups (i. e. iodide, fluoride, cyclopropyl, isopropyl, cyclobutyl, 3-oxetyl, 2-oxetyl, methylsulfide, pentafluorosulfide, methylsulfonyl and sulfonamide) have been considered as potential bioequivalents of -CF3 aiming to use them in compounds with therapeutic interest instead of the polyfluoride functionality. Different structural (molecular surface and volume) and physicochemical (electronic and lipophilic) aspects of the bioequivalent functionalities proposed have been theoretically calculated and compared to those of -CF3. Additionally, the corresponding phenyl derivatives carrying these functionalities have been purchased or prepared and their experimental lipophilicity (i. e. LogP) measured using shake-flask experiments and UV-vis spectroscopy.

Addressing the Opioids Lipophilicity Challenge via a Straightforward and Simultaneous 1H NMR-Based logP/D Determination, Both Separately and in Mixtures

A systematic study of trends in the lipophilicity of prominent representatives of the opioid family, including natural, semisynthetic, synthetic, and endogenous neuropeptide opioids, is described. This was enabled by a straightforward 1H NMR-based logP/D determination method developed for compounds holding at least one aromatic hydrogen atom. Moreover, the new method enables a direct simultaneous logD determination of opioid mixtures, overcoming the high sensitivity of this family to the measurement conditions, which is critical when a determination of the exact ΔlogD values of matched pairs is required. Interpretation of the experimental ΔlogD7.4 values of selected matched pairs, focusing inter alia on the 3-OMe and 14-OMe motifs in morphinan opioids, is suggested with the aid of DFT calculations and may be useful for the discovery of new opioid therapeutics.

Modular synthesis of cyclic β-difluoroamines

Fluorine-containing saturated nitrogen heterocycles are very attractive structures in medicinal and biological chemistry because fluorine can be used to tune conformation as well as key properties such as basicity and bioavailability. At present cyclic fluorinated amines are accessed using hazardous reagents such as DAST or by lengthy synthesis routes. Here we report a modular two-step synthesis of cyclic β-fluoroalkyl amines using a photoredox-catalysed cyclisation/hydrogen atom transfer reaction of bromodifluoroethylamines.

Benzylic C(sp3)-H fluorination

The selective fluorination of C(sp3)-H bonds is an attractive target, particularly for pharmaceutical and agrochemical applications. Consequently, over recent years much attention has been focused on C(sp3)-H fluorination, and several methods that are selective for benzylic C-H bonds have been reported. These protocols operate via several distinct mechanistic pathways and involve a variety of fluorine sources with distinct reactivity profiles. This review aims to give context to these transformations and strategies, highlighting the different tactics to achieve fluorination of benzylic C-H bonds.

The 18F-Difluoromethyl Group: Challenges, Impact and Outlook

The difluoromethyl functionality has proven useful in drug discovery, as it can modulate the properties of bioactive molecules. For PET imaging, this structural motif has been largely underexploited in (pre)clinical radiotracers due to a lack of user-friendly radiosynthetic routes. This Minireview provides an overview of the challenges facing radiochemists and summarises the efforts made to date to access 18F-difluoromethyl-containing radiotracers. Two distinct approaches have prevailed, the first of which relies on 18F-fluorination. A second approach consists of a 18F-difluoromethylation process, which uses 18F-labelled reagents capable of releasing key reactive intermediates such as the [18F]CF2H radical or [18F]difluorocarbene. Finally, we provide an outlook for future directions in the radiosynthesis of [18F]CF2H compounds and their application in tracer radiosynthesis.

Enantioselective Construction of C-SCF3 Stereocenters via Nickel Catalyzed Asymmetric Negishi Coupling Reaction

The construction of the SCF3-containing 1,1-diaryl tertiary carbon stereocenters with high enantioselectivities is reported via a nickel-catalyzed asymmetric C-C coupling strategy. This method demonstrates simple operations, mild conditions and excellent functional group tolerance, with newly designed SCF3-containing synthon, which can be easily obtained from commercially available benzyl bromide and trifluoromethylthio anion in a two-step manner. Further substrate exploration indicated that the reaction system could be extended to diverse perfluoroalkyl sulfide (SC2F5, SC3F7, SC4F9, SCF2CO2Et)-substituted 1,1-diaryl compounds with excellent enantioselectivities. The synthetic utility of this transformation was further demonstrated by convenient derivatization to optical SCF3-containing analogues of bioactive compounds without an apparent decrease in enantioselectivity.

Catalytic Asymmetric Difluoroalkylation Using In Situ Generated Difluoroenol Species as the Privileged Synthon

A robust and practical difluoroalkylation synthon, α,α-difluoroenol species, which generated in situ from trifluoromethyl diazo compounds and water in the presence of dirhodium complex, is disclosed. As compared to the presynthesized difluoroenoxysilane and in situ formed difluoroenolate under basic conditions, this difluoroenol intermediate displayed versatile reactivity, resulting in dramatically improved enantioselectivity under mild conditions. As demonstrated in catalytic asymmetric aldol reaction and Mannich reactions with ketones or imines in the presence of chiral organocatalysts, quinine-derived urea, and chiral phosphoric acid (CPA), respectively, this relay catalysis strategy provides an effective platform for applying asymmetric fluorination chemistry. Moreover, this method features a novel 1,2-difunctionalization process via installation of a carbonyl motif and an alkyl group on two vicinal carbons, which is a complementary protocol to the metal carbene gem-difunctionalization reaction.

Conformational Analysis Explores the Role of Electrostatic Nonclassical CF···HC Hydrogen Bonding Interactions in Selectively Halogenated Cyclohexanes

The conformational equilibria of selectively halogenated cyclohexanes are explored both experimentally (VT-NMR) for 1,1,4,-trifluorocyclohexane 7 and by computational analysis (M06-2X/aug-cc-pVTZ level), with the latter approach extending to a wider range of more highly fluorinated cyclohexanes. Perhaps unexpectedly, 7ax is preferred over the 7eq conformation by ΔG = 1.06 kcal mol-1, contradicting the accepted norm for substituents on cyclohexanes. The axial preference is stronger again in 1,1,3,3,4,5,5,-heptafluorocyclohexane 9 (ΔG = 2.73 kcal mol-1) as the CF2 groups further polarize the isolated CH2 hydrogens. Theoretical decomposition of electrostatic and hyperconjugative effects by natural bond orbital analysis indicated that nonclassical hydrogen bonding (NCHB) between the C-4 fluorine and the diaxial hydrogens at C-2 and C-6 in cyclohexane 7 and 9 largely accounts for the observed bias. The study extended to changing fluorine (F) for chlorine (Cl) and bromine (Br) at the pseudoanomeric position in the cyclohexanes. Although these halogens do not become involved in NCHBs, they polarize the geminal -CHX- hydrogen at the pseudoanomeric position to a greater extent than fluorine, and consequent electrostatic interactions influence conformer stabilities.

The Role of Small Molecules Containing Fluorine Atoms in Medicine and Imaging Applications

The fluorine atom possesses many intrinsic properties that can be beneficial when incorporated into small molecules. These properties include the atom's size, electronegativity, and ability to block metabolic oxidation sites. Substituents that feature fluorine and fluorine-containing groups are currently prevalent in drugs that lower cholesterol, relieve asthma, and treat anxiety disorders, as well as improve the chemical properties of various medications and imaging agents. The dye scaffolds (fluorescein/rhodamine, coumarin, BODIPY, carbocyanine, and squaraine dyes) reported will address the incorporation of the fluorine atom in the scaffold and the contribution it provides to its application as an imaging agent. It is also important to recognize radiolabeled fluorine atoms used for PET imaging in the early detection of diseases. This review will discuss the many benefits of incorporating fluorine atoms into small molecules and give examples of fluorinated molecules used in the pharmaceutical industry and imaging techniques.

Aza-Heterocyclic Building Blocks with In-Ring CF2 -Fragment

Modern organic chemistry is a titan supporting and reinforcing pharmaceutical, agricultural, food and material science products. Over the past decades, the organic compounds market has been evolving to meet all the research demands. In this regard, medicinal chemistry is especially dependent on available chemical space as subtle tuning of the molecule structure is required to create a drug with relevant physicochemical properties and a remarkable activity profile. The recent rapid evolution of synthetic methodology to deploy fluorine has brought fluorinated compounds to the spotlight of MedChem community. And now unique properties of fluorine still keep fascinating more and more as its justified installation into a molecular framework has a beneficial impact on membrane permeability, lipophilicity, metabolic stability, pharmacokinetic properties, conformation, pKa , etc. The backward influence of medicinal chemistry on organic synthesis has also changed the landscape of the latter towards new fluorinated topologies as well. Such complex relationships create a flexible and ever-changing ecosystem. Given that MedChem investigations strongly lean on the ability to reach suitable building blocks and the existence of reliable synthetic methods in this review we collected advances in the chemistry of respectful, but still enigmatic gem-difluorinated aza-heterocyclic building blocks.

Controllable Fluorocarbon Chain Elongation: TMSCF2Br-Enabled Trifluorovinylation and Pentafluorocyclopropylation of Aldehydes

Controllable fluorocarbon chain elongation (CFCE) is a promising yet underdeveloped strategy for the well-defined synthesis of structurally novel polyfluorinated compounds. Herein, the direct and efficient trifluorovinylation and pentafluorocyclopropylation of aldehydes are described by using TMSCF2Br (TMS = trimethylsilyl) as the sole fluorocarbon source, accomplishing the goals of CFCE from C1 to C2 and from C1 to C3, respectively. The key to the success of these CFCE processes lies in the unique and diversified chemical reactivity of TMSCF2Br, which can serve as two different precursors, namely, a TMSCF2 radical precursor and a difluorocarbene precursor. Various functional groups are amenable to this new synthetic protocol, providing streamlined access to a broad range of alcohols containing trifluorovinyl or pentafluorocyclopropyl moieties from abundantly available aldehydes. The potential utility of these methods is further demonstrated by the gram-scale synthesis, derivatization, and measurement of log P values of the products.

Applications of Bioisosteres in the Design of Biologically Active Compounds

The design of bioisosteres represents a creative and productive approach to improve a molecule, including by enhancing potency, addressing pharmacokinetic challenges, reducing off-target liabilities, and productively modulating physicochemical properties. Bioisosterism is a principle exploited in the design of bioactive compounds of interest to both medicinal and agricultural chemists, and in this review, we provide a synopsis of applications where this kind of molecular editing has proved to be advantageous in molecule optimization. The examples selected for discussion focus on bioisosteres of carboxylic acids, applications of fluorine and fluorinated motifs in compound design, some applications of the sulfoximine functionality, the design of bioisosteres of drug-H2O complexes, and the design of bioisosteres of the phenyl ring.

N-(2-Tetrafluoro(trifluoromethyl)-λ6-sulfanyl(CF3SF4)-ethyl) Amines: The Influence of the CF3SF4 Group on Lipophilicity and pKa

A practical synthetic path for the preparation of trans-CF3SF4-substituted amines has been described. Primary and secondary amines bearing a variety of different functional groups including amino acids, cyclic amines, and nucleosides were prepared. The desired amines were synthesized under mild conditions. The influence of the CF3SF4-group on the pKa and log D of a standard amine was established. The unusual conformation of the trans-CF3SF4-substituted tosylate has been verified via its crystal structure.

Species-specific lipophilicities of fluorinated diketones in complex equilibria systems and their potential as multifaceted reversible covalent warheads

Combined molecular, physicochemical and chemical properties of electrophilic warheads can be applied to create covalent drugs with diverse facets. Here we study these properties in fluorinated diketones (FDKs) and their multicomponent equilibrium systems in the presence of protic nucleophiles, revealing the potential of the CF2(CO)2 group to act as a multifaceted warhead for reversible covalent drugs. The equilibria compositions of various FDKs in water/octanol contain up to nine species. A simultaneous direct species-specific 19F-NMR-based log P determination of these complex equilibria systems was achieved and revealed in some cases lipophilic to hydrophilic shifts, indicating possible adaptation to different environments. This was also demonstrated in 19F-MAS-NMR-based water-membrane partitioning measurements. An interpretation of the results is suggested by the aid of a DFT study and 19F-DOSY-NMR spectroscopy. In dilute solutions, a model FDK reacted with protected cysteine to form two hemi-thioketal regioisomers, indicating possible flexible regio-reactivity of CF2(CO)2 warheads toward cysteine residues.

Mono- and Difluorinated Saturated Heterocyclic Amines for Drug Discovery: Systematic Study of Their Physicochemical Properties

A comprehensive study of physicochemical properties (pKa , LogP, and intrinsic microsomal clearance) within the series of mono- and difluorinated azetidine, pyrrolidine, and piperidine derivatives was performed. While the number of fluorine atoms and their distance to the protonation center were the major factors defining the compound's basicity, both pKa and LogP values were affected considerably by the conformational preferences of the corresponding derivatives. For example, features of "Janus face" (facially polarized) cyclic compounds (i. e., unusually high hydrophilicity) were identified for cis-3,5-difluoropiperidine, preferring a diaxial conformation. Intrinsic microsomal clearance measurements demonstrated high metabolic stability of the compounds studied (with a single exception of the 3,3-difluoroazetidine derivative). According to pKa - LogP plots, the title compounds provide a valuable extension of the fluorine-containing (e. g., fluoroalkyl-substituted) saturated heterocyclic amine series as building blocks for rational optimization studies in early drug discovery.

Structure-property relationships of fluorinated carboxylic acid bioisosteres

Fluorinated alcohols and phenols are potentially useful as bioisosteres of the carboxylic acid functional group. To enable a direct comparison of the properties of fluorinated carboxylic acid surrogates with those of other commonly used, non-fluorinated bioisosteres, we conducted a structure-property relationship (SPR) study based on matched molecular pair (MMP) analyses. A series of representative examples have been characterized by experimentally determining physicochemical properties, such as acidity (pKa), lipophilicity (logD7.4), and permeability (PAMPA). The results presented can help estimate the relative changes in physicochemical properties that may be attainable by replacing the carboxylic acid functional group with fluorine containing surrogate structures.

Placing CF2 in the Center: Major Physicochemical Changes Upon a Minor Structural Alteration in Gem-Difunctional Compounds

Fluorine atoms play an important role in all branches of chemistry and accordingly, it is very important to study their unique and varied effects systematically, in particular, the structure-physicochemical properties relationship. The present study describes exceptional physicochemical effects resulting from a H/F exchange at the methylene bridge of gem-difunctional compounds. The Δlog P_(CF2-CH2) values, that is, the change in lipophilicity, observed for the CH₂ /CF₂ replacement in various α,α-phenoxy- and thiophenoxy-esters/amides, diketones, benzodioxoles and more, fall in the range of 0.6-1.4 units, which for most cases, is far above the values expected for such a replacement. Moreover, for compounds holding more than one such gem-difunctional moiety, the effect is nearly additive, so one can switch from a hydrophilic compound to a lipophilic one in a limited number of H/F exchanges. DFT studies of some of these systems revealed that polarity, conformational preference as well as charge distributions are strongly affected by such hydrogen to fluorine atom substitution. The pronounced effects described, are a result of the interplay between changes in polarity, H-bond basicity and molecular volume, which were obtained with a very low 'cost' in terms of molecular weight or steric effects and may have a great potential for implementation in various fields of chemical sciences.

Electronically Ambivalent Hydrodefluorination of Aryl‐CF3 groups enabled by Electrochemical Deep‐Reduction on a Ni Cathode

We report a general procedure for the direct mono- and di-hydrodefluorination of ArCF3 compounds. Exploiting the tunability of electrochemistry and the selectivity enabled by a Ni cathode, the deep reduction garners high selectivity with good to excellent yields up to gram scale. The late-stage peripheral editing of CF3 feedstocks to construct fluoromethyl moieties will aid the rapid diversification of lead-compounds and compound libraries.

Catalytic and Chemodivergent Synthesis of 1-Substituted 9H-Pyrrolo[1,2-a]indoles via Annulation of β-CF3 Enones with 3-Substituted Indoles

Chemodivergent reactions are more advantageous in organic synthesis that yield diversely functionalized scaffolds from common starting materials. Herein, we report an efficient metal-free chemodivergent protocol for the synthesis of 1-substituted 9H-pyrrolo[1,2-a]indole derivatives in the presence of catalytic amounts of Lewis acid/Brønsted acid conditions using 3-substituted indoles and β-trifluoromethyl-α,β-unsaturated ketones. Fine-tuning of the catalyst and solvent system in the reaction conditions deliver the trifluoromethyl, trifluoroethylcarboxylate, or carboxylic acid substituents on the C1-position of 9H-pyrrolo[1,2-a]indole derivatives in situ. It is postulated that the solvent and LA/BA catalyst interaction was found to be crucial for the catalytic C-F activation in these transformations.

KHMDS/Triglyme Cryptate as an Alternative to Phosphazene Base in Stereodivergent Pentafluoroethylation of N-Sulfinylimines Using HFC-125

A protocol for the stereodivergent pentafluoroethylation of N-sulfinylimines using HFC-125 with KHMDS/triglyme has been developed. Both diastereomers of the pentafluoroethylated amines can be selectively synthesized based on the presence or absence of triglyme. This additive-controlled protocol allows the KHMDS/triglyme cryptate to be a straightforward and cheap alternative to previously reported base-controlled stereodivergent trifluoromethylation using potassium hexamethyldisilazide (KHMDS) versus P₄-^tBu.

Diastereo- and enantioselective synthesis of compounds with a trifluoromethyl- and fluoro-substituted carbon centre

Molecules that contain one or more fluorine atoms are crucial to drug discovery. There are protocols available for the selective synthesis of different organofluorine compounds, including those with a fluoro-substituted or a trifluoromethyl-substituted stereogenic carbon centre. However, approaches for synthesizing compounds with a trifluoromethyl- and fluoro-substituent stereogenic carbon centre are far less common. This potentially impactful set of molecules thus remains severely underdeveloped. Here we introduce a catalytic regio-, diastereo- and enantioselective strategy for the preparation of homoallylic alcohols bearing a stereogenic carbon centre bound to a trifluoromethyl group and a fluorine atom. The process, which involves a polyfluoroallyl boronate and is catalysed by an in situ-formed organozinc complex, can be used for diastereodivergent preparation of tetrafluoro-monosaccharides, including ribose core analogues of the antiviral drug sofosbuvir (Sovaldi). Unexpected reactivity/selectivity profiles, probably originating from the trifluoromethyl- and fluoro-substituted carbon site, are discovered, foreshadowing other unique chemistries that remain unknown.

N-Trifluoropropylation of Azoles through N-Vinylation and Sequential Hydrogenation

Installing a fluoroalkyl group onto the nitrogen atom of azoles represents a potential strategy for lead optimization in medicinal chemistry. Herein, we describe a method for the N-trifluoropropylation of azoles. This process is accomplished using a combination of regioselective N-vinylation and sequential hydrogenation. The two-step sequence is applicable to a diverse set of azoles and tolerates a wide range of functionalities. In addition, we showcase its practicability and utility through the gram-scale synthesis and the late-stage modification of a complex molecule.

Asymmetric construction of allylicstereogenic carbon center featuring atrifluoromethyl group via enantioselective reductive fluoroalkylation

Emerging as a powerful tool for lead optimization in pharmaceutical research and development, to develop the facile, general protocols that allows the incorporation of fluorine-containing motif in drug candidates has accumulated enormous research interest in recent years. Among these important motifs, the incorporation of strategic motif CF₃ on aliphatic chain especially with the concomitant construction of trifluoromethylated alkanes bearing a CF₃-substituted stereogenic carbon, is of paramount importance. Herein, we disclose an asymmetric nickel-catalyzed reductive trifluoroalkylation of alkenyl halides for enantioselective syntheses of diverse α-trifluoromethylated allylic alkanes, offering a general protocol to access the trifluoromethyl analogue to chiral α-methylated allylic alkanes, one of the most prevalent key components among natural products and pharmaceuticals. Utilities of the method including the application of the asymmetric trifluoroalkylation on multiple biologically active complex molecules, derivatization of transformable alkenyl functionality were demonstrated, providing a facile method in the diversity-oriented syntheses of CF₃-containing chiral drugs and bioactive-molecules.

A General and Efficient Solution to Monofluoroalkylation: Divergent Synthesis of Aliphatic Monofluorides with Modular Synthetic Scaffolds

Monofluoroalkanes are important in many pharmaceuticals, agrochemicals and functional materials. However, the lack of easily available and transformable monofluoroalkylating reagents that facilitate a broad array of transformations has hampered the application of monofluoroalkylation. Herein, we report a general and efficient method of preparing diverse aliphatic monofluorides with monofluoroalkyl triflate as the synthetic scaffold. Using both nickel-catalyzed hydromonofluoroalkylation of unactivated alkenes and copper-catalyzed C-C bond formation, the general diversification of the monofluoroalkylating scaffold has been exhibited. The broad utility of this monofluoroalkylating reagent is shown by concise conversion into various conventional fluoroalkylating reagents and construction of monofluoro-alkoxy, -alkylamino motifs with commercially available heteroatom-based coupling partners.

Turning the Other Cheek: Influence of the cis-Tetrafluorocyclohexyl Motif on Physicochemical and Metabolic Properties

The targeted introduction of substituents in order to tailor a molecule’s pharmacologic, physicochemical, and metabolic properties has long been of interest to medicinal chemists. The all-cis tetrafluorocyclohexyl motif—dubbed Janus face, due to its electrostatically polarized cyclohexyl ring—represents one such example where chemists might incorporate a metabolically stable, polar, lipocompatible motif. To better understand its potential utility, we have synthesized three series of matched molecular pairs (MMPs) where each MMP differs only in the cyclohexane unit, i.e., with a tetrafluorocyclohexyl or a standard cyclohexyl motif. With the introduction of the facially polarized all-cis tetrafluorocyclohexyl ring, the resulting compounds have significantly modified physicochemical properties (e.g., kinetic solubility, lipophilicity and permeability) and metabolic stabilities. These results further speak to the promise of this substituent as a tactic to improve the drug-like properties of molecules.

Octanol-Water Partition Coefficients of Fluorinated Drug Molecules with Continuum Solvation Models

In this work, we have examined the efficiency of continuum solvation models, used with density functional theory methods, in calculating octanol-water partition coefficients (logP) of 56 fluorine containing drug molecules. The solvation model based on density model computed logP values that are in good agreement with the benchmark values. The conductor-like polarizable continuum models computed results have issues in predicting correct trend, often with reversal of sign from benchmark. The choice of basis set does not show significant effect, and the selection of atomic radii affects geometry convergence during calculations.

Mechanochemical Conversion of Aromatic Amines to Aryl Trifluoromethyl Ethers

Increased interest in the trifluoromethoxy group in organic synthesis and medicinal chemistry has induced a demand for new, selective, general, and faster methods applicable to natural products and highly functionalized compounds at a later stage of hit-to-lead campaigns. Applying pyrylium tetrafluoroborate, we have developed a mechanochemical protocol to selectively substitute the aromatic amino group with the OCF₃ functionality. The scope of our method includes 31 examples of ring-substituted anilines, including amides and sulfonamides. Expected S_NAr products were obtained in excellent yields. The presented concise method opens a pathway to new chemical spaces for the pharmaceutical industry.

The N,N,O-Trisubstituted Hydroxylamine Isostere and Its Influence on Lipophilicity and Related Parameters

The influence of substitution of an N,N,O-trisubstituted hydroxylamine (-NR-OR'-) unit for a hydrocarbon (-CHR-CH2-), ether (-CHR-OR'-), or amine (-NR-CHR'-) moiety on lipophilicity and other ADME parameters is described. A matched molecular pair analysis was conducted across five series of compounds, which showed that the replacement of carbon-carbon bonds by N,N,O-trisubstituted hydroxylamines typically leads to a reduction in logP comparable to that achieved with a tertiary amine group. In contrast, the weakly basic N,N,O-trisubstituted hydroxylamines have greater logD 7.4 values than tertiary amines. It is also demonstrated that the N,N,O-trisubstituted hydroxylamine moiety can improve metabolic stability and reduce human plasma protein binding relative to the corresponding hydrocarbon and ether units. Coupled with recent synthetic methods for hydroxylamine assembly by N-O bond formation, these results provide support for the re-evaluation of the N,N,O-trisubstituted hydroxylamine moiety in small-molecule optimization schemes in medicinal chemistry.

Enantioselective Synthesis of Secondary β-Trifluoromethyl Alcohols via Catalytic Asymmetric Reductive Trifluoroalkylation and Diastereoselective Reduction

Fluorinated motifs are frequently encountered in drugs and agrochemicals. Incorporating fluorine-containing motifs in drug candidates for lead optimization in pharmaceutical research and development has emerged as a powerful tool. The construction of molecules that feature a trifluoromethyl (CF₃-) group on a stereogenic carbon has accumulated broad research efforts. Unlike its well-explored, biologically active methyl counterpart, asymmetric construction of β-trifluoromethylated alcohols bearing adjacent stereocenters still remains elusive. Through retrosynthetic analysis, we posited that followed by sequential reduction of carbonyl, the initial construction of chiral α-trifluoromethylated ketones could render the desired product in a facile, one-pot fashion. Herein, we developed the first example of nickel-catalyzed asymmtric reductive cross-coupling trifluoroalkylation of acyl chlorides for enantioselective synthesis of diverse α-trifluoromethylated ketones. The one-pot reduction of these α-trifluoromethylated ketones furnished corresponding alcohols bearing β-CF₃-substituted stereogenic carbons with excellent diastereoselectivity and complete enantioselective retention. High yields/enantioselectivity, mild conditions, and good functional group compatibility are shown in the system. Utilities of the method are also illustrated by applying asymmetric, late-stage trifluoroalkylation of biologically active complex molecules, revealing tremendous potential for development of CF₃-containing chiral drugs.

Effect of gem-Difluorination on the Key Physicochemical Properties Relevant to Medicinal Chemistry: The Case of Functionalized Cycloalkanes

Physico-chemical properties important to drug discovery (pK_a , LogP, and aqueous solubility), as well as metabolic stability, were studied for a series of functionalized gem-difluorinated cycloalkanes and compared to those of non-fluorinated and acyclic counterparts to evaluate the impact of the fluorination. It was found that the influence of the CF₂ moiety on the acidity/basicity of the corresponding carboxylic acids and amines was defined by inductive the effect of the fluorine atoms and was nearly the same for acyclic and cyclic aliphatic compounds. Lipophilicity and aqueous solubility followed more complex trends and were affected by the position of the fluorine atoms, ring size, and even the nature of the functional group present; also, significant differences were found for the acyclic and cyclic series. Also, gem-difluorination either did not affect or slightly improved the metabolic stability of the corresponding model derivatives. The presented results can be used as a guide for rational drug design employing fluorine and establish the first chapter in a catalog of the key in vitro properties of fluorinated cycloalkanes.

Fluorinated Sulfinates as Source of Alkyl Radicals in the Photo-Enantiocontrolled β-Functionalization of Enals

The generation of sulfonyl radicals has long been known as a flexible strategy in a wide range of different sulfonylative transformations. Meanwhile their use in alkylation processes has been somehow limited due to their inherent difficulty in evolving to less-stable radicals after sulfur dioxide extrusion. Herein we report a convenient strategy that involves gem-difluorinated sulfinates as an "upgrading-mask", allowing these precursors to decompose into their corresponding alkyl radicals. The electron-donor character of sulfinates in the formation of an electron donor-acceptor (EDA) complex with transient iminium ions is displayed, achieving the first example of a stereocontrolled light-driven insertion of gem-difluoro derivatives into unsaturated aldehydes. This methodology is compatible with flow conditions, maintaining identical levels of enantiocontrol.