Bence B. Botlik’s research while affiliated with University of Oxford and other places

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Publications (10)


Oxidative amination by nitrogen atom insertion into carbon-carbon double bonds
  • Article

March 2025

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37 Reads

Science

Yannick Brägger

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Nima Nasiri

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The synthesis of nitrogen-containing molecules through carbon–nitrogen (C–N) bond formation is critical for the discovery and preparation of medicines, agrochemicals, and materials. Here, we report the direct insertion of a nitrogen atom into unactivated carbon-carbon double bonds to access aza-allenium intermediates, which can be converted either into nitriles or amidine products, depending on the initial alkene substitution pattern. This operationally simple and highly functionally compatible reaction works on a wide range of unactivated alkenes. PIFA, a commercially available and inexpensive hypervalent iodine reagent, is key to this reactivity. Our mechanistic proposal is supported by chemical trapping experiments, which concomitantly demonstrate the utility of our method to access valuable N -heterocycles. Additionally, our method can be used as a general strategy for synthesizing amides and amines, as well as ¹⁵ N-labeled molecules.


Enantioconvergent approaches for nucleophilic substitution
a, Nucleophilic substitution via SN1, SN2, SN2X, transition metal-catalysed and photoredox mechanisms. b, HBPTC for the desymmetrization of meso-onium-type electrophiles with alkali metal fluoride salts (MF). c, S-HBPTC (this work): enantioconvergent nucleophilic substitution of benzylic bromides and α-haloketones with KF and two phase-transfer catalysts (a chiral HBD and an achiral onium salt). hv, visible light; cat*, chiral catalyst; DKR, dynamic kinetic resolution; TMS, trimethylsilyl; Nu, nucleophile; LG, leaving group.
Reaction optimization
a, Optimization of enantioselective fluorination under S-HBPTC. Conditions: rac-1a (0.05 mmol) at 25 mM concentration. ¹⁹F NMR yields are reported. Enantiomeric ratios were determined using high-performance liquid chromatography with a chiral stationary phase. b, Spectroscopic study of the phase transfer of MF salts by bis-urea catalyst (S)-3a. 1,2-DFB, 1,2-difluorobenzene; DCE, dichloroethane; MBTE, methyl tert-butyl ester; THF, tetrahydrofuran.
Reaction scope
a, Scope of benzylic fluorides. b, Scope of α-fluoroketones. The yields of the isolated products are reported. aPerformed at 15 °C. bPerformed at 40 °C. c98% recovery of (S)-3h. dIn 1,4-difluorobenzene for 96 h. ePerfomed at 25 °C.
Mechanistic investigations
a, Spectroscopic evidence for the formation of [UPF] species. b, SKIE studies, predicted values and pseudo first-order kinetic plots. [RBr]0, initial concentration of bromide substrate; [RBr]t, concentration of bromide at time (t). c, Investigation into the enantiomeric excess of 1a and 2a via ex situ time course monitoring. d, Diastereomeric transition state structures (computed using: M06-2X-D3ZERO/def2-TZVPP (C, H) ma-def2-TZVPP). e, Proposed catalytic cycle. CLIP-HSQC, clean in-phase heteronuclear single quantum coherence; DFT, density functional theory; TS, transition state; tm, mixing time delay.
Enantioconvergent nucleophilic substitution via synergistic phase-transfer catalysis
  • Article
  • Full-text available

February 2025

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82 Reads

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2 Citations

Catalytic enantioconvergent nucleophilic substitution reactions of alkyl halides are highly valuable transformations, but they are notoriously difficult to implement. Specifically, nucleophilic fluorination is a renowned challenge, especially when inexpensive alkali metal fluorides are used as fluorinating reagents due to their low solubility, high hygroscopicity and Brønsted basicity. Here we report a solution by developing the concept of synergistic hydrogen bonding phase-transfer catalysis. Key to our strategy is the combination of a chiral bis-urea hydrogen bond donor (HBD) and an onium salt—two phase-transfer catalysts essential for the solubilization of potassium fluoride—as a well-characterized ternary HBD–onium fluoride complex. Mechanistic investigations indicate that this chiral ternary complex is capable of enantiodiscrimination of racemic benzylic bromides and α-bromoketones, and upon fluoride delivery affords fluorinated products in high yields and enantioselectivities. This work provides a foundation for enantioconvergent fluorination chemistry enabled through the combination of a HBD catalyst with a co-catalyst specifically curated to meet the requirement of the electrophile.

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Carbon-to-nitrogen atom swap enables direct access to benzimidazoles from drug-like indoles

October 2024

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43 Reads

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1 Citation

The ability to selectively edit organic molecules at the atomic level has the potential to streamline lead discovery and optimization in the pharmaceutical and agrochemical industry. While numerous atom insertion and deletion reactions have recently been reported, examples of single atom swaps remain scarce due to the challenge of orchestrating the selective cleavage and formation of multiple chemical bonds around the same atom. We herein report a method for the carbon-to-nitrogen atom swap in N-alkyl indoles, allowing for the direct conversion of indoles to the corresponding benzimidazoles. The reaction leverages the innate reactivity of the indole scaffold to engage in an initial oxidative cleavage step, followed by oxidative amination, Hofmann-type rearrangement and cyclization. This complex sequence of steps is mediated by the simple combination of commercially available PIDA and ammonium carbamate as nitrogen atom source. The reaction tolerates a wide range of functional groups which is demonstrated by the interconversion of 15 drug-like molecules implying its immediate applicability across a wide range of discovery programs. Furthermore, it shows how leveraging the innate reactivity of a common heterocycle can unlock otherwise challenging skeletal editing reactions.


Context of this work.
Proof of concept.
Substrate scope of the reaction. Yields are isolated yields, unless stated otherwise. [a] Determined by ¹H NMR using mesitylene as internal standard. [b] Pentane used as solvent in the first step instead of THF, and pentane:methanol=1 : 1 mixture as solvent in the second step. [c] 2.5 equiv. of Et3N and 2.2 equiv. TBSOTf used in the first step. [d] Traditional Beckmann conditions. 1) NH2OH 2) PPA[46] [e] Modified Beckmann conditions. NH2OH, thiamine hydrochloride.[47] For details, see Supporting Information.
Applications of the developed methodology for ¹⁵N‐labelling, and product derivatisation. Conditions for the derivatisation of pyridone 2 c: (i) 2‐iodopyridine (2 equiv.), CuI (10 mol %), K2CO3 (1.2 equiv.), DMF, 150 °C, 24 h (ii) POCl3 (neat), 100 °C, 16 h (iii) (4‐fluorophenyl)boronic acid (1.2 equiv.), Pd(OAc)2 (2.5 mol %), PPh3 (10 mol %), K2CO3 (2.7 equiv.), DME/H2O, 90 °C, 18 h (iv) Pd/C, HCOONH4 (2 equiv.), MeOH, 55 °C, 16 h.
Control experiments and working hypothesis for the plausible mechanism of the reaction. [a] Determined by ¹H NMR using mesitylene as internal standard. For details, see Supporting Information.
Streamlining the Synthesis of Pyridones through Oxidative Amination of Cyclopentenones

August 2024

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54 Reads

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9 Citations

Herein we report the development of an oxidative amination process for the streamlined synthesis of pyridones from cyclopentenones. Cyclopentenone building blocks can undergo in situ silyl enol ether formation, followed by the introduction of a nitrogen atom into the carbon skeleton with successive aromatisation to yield pyridones. The reaction sequence is operationally simple, rapid, and carried out in one pot. The reaction proceeds under mild conditions, exhibits broad functional group tolerance, complete regioselectivity, and is well scalable. The developed method provides facile access to the synthesis of ¹⁵N‐labelled targets, industrially relevant pyridone products and their derivatives in a fast and efficient way.



Streamlining the Synthesis of Pyridones through Oxidative Amination of Cyclopentenones

June 2024

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13 Reads

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2 Citations

Angewandte Chemie

Herein we report the development of an oxidative amination process for the streamlined synthesis of pyridones from cyclopentenones. Cyclopentenone building blocks can undergo in situ silyl enol ether formation, followed by the introduction of a nitrogen atom into the carbon skeleton with successive aromatisation to yield pyridones. The reaction sequence is operationally simple, rapid, and carried out in one pot. The reaction proceeds under mild conditions, exhibits broad functional group tolerance, complete regioselectivity, and is well scalable. The developed method provides facile access to the synthesis of 15N‐labelled targets, industrially relevant pyridone products and their derivatives in a fast and efficient way.


Oxidative amination of unactivated alkenes via nitrogen atom insertion into carbon-carbon double bonds

May 2024

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55 Reads

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1 Citation

The synthesis of nitrogen-containing molecules through C–N bond formation is critical for the discovery and preparation of medicines, agrochemicals and materials. Traditional synthetic methods using alkenes as ubiquitous substrates leverage the reactivity of the C(sp2)–C(sp2) π bond for C–N bond formation. In contrast, methods that can form C–N bonds through complete cleavage of the double bond are scarce, despite the considerable synthetic potential of such a strategy. Here, we report the direct insertion of a nitrogen atom into unactivated carbon-carbon double bonds to access aza-allenium intermediates which can be converted either into nitriles or amidine products, depending on the initial alkene substitution pattern. This operationally simple and highly functional group tolerant reaction works on a wide range of unactivated alkenes. Our mechanistic proposal is supported by chemical trapping experiments, which concomitantly demonstrate the utility of our method to access valuable N-heterocycles. Overall, this study demonstrates the possibility to access reactive nitrogen-containing intermediates (i.e. aza-alleniums), which have ample potential for downstream diversification, from unactivated alkenes, opening new avenues for the discovery and preparation of important products.



Context of this work
Substrate scope. For the scXRD structures, the ellipsoids are shown at 50% probability and hydrogen atoms are omitted for clarity.a 1H-NMR yield of 0.05-mmol scale crude reaction mixture using 1,1,2,2-tetrachloroethane as the internal standard.b Isolated yield of a 1.00-mmol scale reaction, conditions: indene (1.0 mmol), PIDA (2.5 mmol), ammonium carbamate (4.0 mmol), methanol (0.07 M), 0 °C for 20 min, then rt for 10 min
Isotopically labelled structures. aIsolated yields
Selected optimisation data for the nitrogen atom insertion into indenes a
Nitrogen atom insertion into indenes to access isoquinolines

February 2023

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184 Reads

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75 Citations

We report a convenient protocol for a nitrogen atom insertion into indenes to afford isoquinolines. The reaction uses a combination of commercially available phenyliodine(iii) diacetate (PIDA) and ammonium carbamate as the nitrogen source to furnish a wide range of isoquinolines. Various substitution patterns and commonly used functional groups are well tolerated. The operational simplicity renders this protocol broadly applicable and has been successfully extended towards the direct interconversion of cyclopentadienes into the corresponding pyridines. Furthermore, this strategy enables the facile synthesis of 15N labelled isoquinolines, using 15NH4Cl as a commercial 15N source.


Scheme 1. Context of this work.
Scheme 3. Isotopically labeled structures. [a] Isolated yields.
Nitrogen atom insertion into indenes to access isoquinolines

December 2022

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121 Reads

We report a convenient protocol for a nitrogen atom insertion into indenes to afford isoquinolines. The reaction uses a combination of commercially available (diacetoxy¬iodo)benzene (PIDA) and ammonium carbamate to furnish a wide range of isoquinolines. Various substitution patterns and commonly used functional groups are well tolerated and the operational simplicity renders this protocol broadly applicable. Furthermore, this strategy enables the facile synthesis of 15N labeled isoquinolines, using 15NH4Cl as a commercial 15N source.

Citations (5)


... 135 Removal, addition, or exchange of a single atom in a molecule is oen achieved by modifying the synthesis of the compound from an early point in the route or by a totally different route. However, recent advantages in direct atom deletion, insertion, and exchange [136][137][138][139][140][141][142][143][144][145][146][147][148][149][150][151][152][153] can in some cases remove the need for new retrosynthetic analysis and provide new diverse compounds more efficiently. Additionally, subtle changes to the overall molecular shape and not just single atoms can have a large impact on the function and properties of compounds. ...

Reference:

Unifying principles for the design and evaluation of natural product-inspired compound collections
Carbon-to-nitrogen atom swap enables direct access to benzimidazoles from drug-like indoles
  • Citing Preprint
  • October 2024

... Their strategy enabled as well to incorporate 15 N-labels in various synthetic targets. 109 Another significant class of compounds that have been explored for nitrogen insertion reactions is cyclic olefins, particularly indenes 69, which can be transformed into isoquinolines 70-a crucial scaffold in various pharmaceuticals. 77 Early studies by Fields, Frincke, and McLean demonstrated this transformation through oxidative cleavage (ozonolysis) of the indene backbone using ozone (O3) or osmium tetroxide (OsO4) in the presence of ammonia or ammonium salts as the nitrogen source (Scheme 9A). ...

Streamlining the Synthesis of Pyridones through Oxidative Amination of Cyclopentenones

... 69 In this study, DFT calculations were conducted to reveal that the TEMPO-catalyzed C�C bond cleavage proceeded through a key 1,5-hydrogen atom transfer (HAT) process (Scheme 22, B to C). Very recently, the Morandi group discovered the oxidative amination of unactivated alkenes by using hypervalent iodine nitrene. 70 ...

Oxidative amination of unactivated alkenes via nitrogen atom insertion into carbon-carbon double bonds
  • Citing Preprint
  • May 2024

... [20] Therefore, a key focus in contemporary synthetic organic chemistry is the development of novel, efficient, green, and versatile methodologies for constructing these moieties from readily available starting materials under mild reaction conditions. [21][22][23][24][25] In this respect, one of the most attractive synthetic approaches is the use of ionic liquids as a catalyst or a solvent. ...

Direct Access to Quinazolines and Pyrimidines from Unprotected Indoles and Pyrroles through Nitrogen Atom Insertion
  • Citing Article
  • November 2023

Organic Letters

... The Morandi group advanced this area by applying their iodonitrene 67-based approach for nitrogen insertion in indenes 69, leading to isoquinolines 70 synthesis via an aziridination-fragmentation-aromatization pathway (Scheme 9B). 113 However, their protocol required strong oxidizing agents (hypervalent iodine), further constraining its substrate scope. 113 In 2024, Alcarazo and colleagues introduced a novel electrophilic nitrogen source, N-(sulfonio)sulfilimine 71 acting as sulfonitrene 72 precursors under rhodium catalysis. ...

Nitrogen atom insertion into indenes to access isoquinolines