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C (sp3)-heteroatom bond formation by iron-catalyzed soft couplings
Semenya, Julius ; Yang, Yuanjie ; Lee, Hye Joon , et al. Commun. Chem.,2025,8,73.
Abstract: Carbon-heteroatom bonds are of great importance due to their prevalence in pharmaceuticals, agrochemicals, materials, and natural products. Despite the effective use of metal-catalyzed crosscoupling reactions between sp2-hybridized organohalides and soft heteroatomic nucleophiles for carbon-heteroatom bond formation, the use of sp3-hybridized organohalides remain limited and the coupling with thiols remains elusive. Here, we report the coupling of sp3-hybridized benzyl or tertiary halides with soft thiol nucleophiles catalyzed by iron and extend the utility to alcohol and amine nucleophiles. The reaction is broad in substrate scope for both coupling partners and applicable in the construction of congested tri- and tetrasubstituted carbon centers as well as β-quaternary heteroatomic products. The synthetic utility is further emphasized by gram-scale synthesis and rapid herbicide library synthesis. Overall, we provide an efficient method to prepare pharmaceutically and materially relevant carbon-heteroatom bonds by expanding iron-catalyzed cross-coupling reactions to the coupling of sp3-hybridized organohalides with soft nucleophiles.
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Purchased from AmBeed: 76041-72-0 ; 2564-83-2 ; 73018-10-7 ; 63295-48-7 ; 1564-64-3 ; 65130-46-3 ; 15687-27-1 ; 91-60-1 ; 59163-91-6 ; 15570-12-4 ; 56673-34-8 ; 7217-59-6 ; 696-63-9
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CAS No. : | 91-60-1 |
Formula : | C10H8S |
M.W : | 160.24 |
MDL No. : | MFCD00004086 |
InChI Key : | RFCQDOVPMUSZMN-UHFFFAOYSA-N |
Pubchem ID : | 7058 |
GHS Pictogram: |
![]() ![]() |
Signal Word: | Danger |
Hazard Statements: | H301-H314 |
Precautionary Statements: | P501-P270-P264-P280-P303+P361+P353-P301+P330+P331-P363-P301+P310+P330-P304+P340+P310-P305+P351+P338+P310-P405 |
Class: | 8(6.1) |
UN#: | 2923 |
Packing Group: | Ⅲ |
Num. heavy atoms | 11 |
Num. arom. heavy atoms | 10 |
Fraction Csp3 | 0.0 |
Num. rotatable bonds | 0 |
Num. H-bond acceptors | 0.0 |
Num. H-bond donors | 0.0 |
Molar Refractivity | 51.2 |
TPSA ? Topological Polar Surface Area: Calculated from |
38.8 ?2 |
Log Po/w (iLOGP)? iLOGP: in-house physics-based method implemented from |
2.13 |
Log Po/w (XLOGP3)? XLOGP3: Atomistic and knowledge-based method calculated by |
3.11 |
Log Po/w (WLOGP)? WLOGP: Atomistic method implemented from |
3.13 |
Log Po/w (MLOGP)? MLOGP: Topological method implemented from |
3.61 |
Log Po/w (SILICOS-IT)? SILICOS-IT: Hybrid fragmental/topological method calculated by |
3.3 |
Consensus Log Po/w? Consensus Log Po/w: Average of all five predictions |
3.06 |
Log S (ESOL):? ESOL: Topological method implemented from |
-3.47 |
Solubility | 0.0549 mg/ml ; 0.000342 mol/l |
Class? Solubility class: Log S scale |
Soluble |
Log S (Ali)? Ali: Topological method implemented from |
-3.59 |
Solubility | 0.0409 mg/ml ; 0.000255 mol/l |
Class? Solubility class: Log S scale |
Soluble |
Log S (SILICOS-IT)? SILICOS-IT: Fragmental method calculated by |
-4.17 |
Solubility | 0.0108 mg/ml ; 0.0000675 mol/l |
Class? Solubility class: Log S scale |
Moderately soluble |
GI absorption? Gatrointestinal absorption: according to the white of the BOILED-Egg |
High |
BBB permeant? BBB permeation: according to the yolk of the BOILED-Egg |
Yes |
P-gp substrate? P-glycoprotein substrate: SVM model built on 1033 molecules (training set) |
No |
CYP1A2 inhibitor? Cytochrome P450 1A2 inhibitor: SVM model built on 9145 molecules (training set) |
Yes |
CYP2C19 inhibitor? Cytochrome P450 2C19 inhibitor: SVM model built on 9272 molecules (training set) |
Yes |
CYP2C9 inhibitor? Cytochrome P450 2C9 inhibitor: SVM model built on 5940 molecules (training set) |
Yes |
CYP2D6 inhibitor? Cytochrome P450 2D6 inhibitor: SVM model built on 3664 molecules (training set) |
No |
CYP3A4 inhibitor? Cytochrome P450 3A4 inhibitor: SVM model built on 7518 molecules (training set) |
No |
Log Kp (skin permeation)? Skin permeation: QSPR model implemented from |
-5.07 cm/s |
Lipinski? Lipinski (Pfizer) filter: implemented from |
0.0 |
Ghose? Ghose filter: implemented from |
None |
Veber? Veber (GSK) filter: implemented from |
0.0 |
Egan? Egan (Pharmacia) filter: implemented from |
0.0 |
Muegge? Muegge (Bayer) filter: implemented from |
2.0 |
Bioavailability Score? Abbott Bioavailability Score: Probability of F > 10% in rat |
0.55 |
PAINS? Pan Assay Interference Structures: implemented from |
0.0 alert |
Brenk? Structural Alert: implemented from |
1.0 alert: heavy_metal |
Leadlikeness? Leadlikeness: implemented from |
No; 1 violation:MW<1.0 |
Synthetic accessibility? Synthetic accessibility score: from 1 (very easy) to 10 (very difficult) |
1.0 |
* All experimental methods are cited from the reference, please refer to the original source for details. We do not guarantee the accuracy of the content in the reference.
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
40% | In 2,4-dichlorophenoxyacetic acid dimethylamine; mineral oil; | The 4-hydroxy-4-[3-(naphth-2-ylthio)-5-trifluoromethylphenyl]tetrahydropyran used as a starting material was obtained as follows: Sodium hydride (60% w/w dispersion in mineral oil; 0.5 g) was added portionwise to a mixture of 2-naphthalenethiol (1.42 g) and DMA (30 ml) and the mixture was stirred at ambient temperature for 1 hour. A solution of <strong>[130723-13-6]1-bromo-3-fluoro-5-trifluoromethylbenzene</strong> (2.43 g) in DMA (10 ml) was added and the mixture was stirred at ambient temperature for 16 hours. The mixture was partitioned between ethyl acetate and water. The organic layer was washed with brine (50 ml), dried (MgSO4) and evaporated. The residue was purified by column chromatography using hexane as eluent. There was thus obtained 3-bromo-5-trifluoromethylphenyl 2-naphthyl sulphide (1.37 g, 40%), as an oil. A solution of the product so obtained in THF (10 ml) was cooled to -60 C. and n-butyl-lithium (1.6M in hexane; 2.3 ml) was added dropwise. |
40% | In 2,4-dichlorophenoxyacetic acid dimethylamine; mineral oil; | The 4-hydroxy-4-[3-(naphth-2-ylthio)-5-trifluoromethylphenyl]tetrahydropyran used as a starting material was obtained as follows:- Sodium hydride (60% w/w dispersion in mineral oil; 0.5 g) was added portionwise to a mixture of 2-naphthalenethiol (1.42 g) and DMA (30 ml) and the mixture was stirred at ambient temperature for 1 hour. A solution of <strong>[130723-13-6]1-bromo-3-fluoro-5-trifluoromethylbenzene</strong> (2.43 g) in DMA (10 ml) was added and the mixture was stirred at ambient temperature for 16 hours. The mixture was partitioned between ethyl acetate and water. The organic layer was washed with brine (50 ml), dried (MgSO4) and evaporated. The residue was purified by column chromatography using hexane as eluent. There was thus obtained 3-bromo-5-trifluoromethylphenyl 2-naphthyl sulphide (1.37 g, 40%), as an oil. A solution of the product so obtained in THF (10 ml) was cooled to -60C and n-butyl-lithium (1.6 M in hexane; 2.3 ml) was added dropwise. |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
21% | With sodium hydride; In N,N-dimethyl-formamide; at 0 - 80℃; under 760.051 Torr; for 14.16h; | Example 1 1; Synthesis of (5)-2-hydroxy-4-(naphthalen-2-ylsulfonyl)-7V-((i?)-6-(piperidin- 1 -ylmethyl)- l,2,3,4-tetrahydronaphthalen-l-yl)butanamide; Step A: Synthesis of (iotaS)-2-hydroxy-4-(naphthalen-2-ylthio)butanoic acid; A solution of (5)-(-)-alpha-hydroxy-gamma-butyrolactone (505 mg, 4.947 mmol) and naphthalene-2-thiol (872 mg, 5.4 mmol) in DMF (20 mL) was cooled to 0 C under nitrogen, and treated with sodium hydride, 60% dispersion in mineral oil (416 mg, 10 mmol). After 10 minutes, the reaction was heated to 80 C for 14 h, cooled to 23 C, diluted with EtOAc (100 EPO <DP n="96"/>mL) and washed with 10% hydrochloric acid solution (50 mL) and brine (50 mL). The organic layer was dried over MgSOphi concentrated in vacuo and purified using silica gel chromatography (eluant: 2 - 5 - 10% methanol/dichloromethane), affording the title compound (274 mg, 21%) as a yellow solid. MS: 261.1 (M-H). |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
With tris-(dibenzylideneacetone)dipalladium(0); 4,5-bis(diphenylphos4,5-bis(diphenylphosphino)-9,9-dimethylxanthenephino)-9,9-dimethylxanthene; sodium t-butanolate; In toluene; at 105℃; for 24h;Inert atmosphere; | [00879] Xantphos (154 mg, 10%) was added to a mixture of <strong>[18791-99-6]4-bromothiophene-2-carbonitrile</strong> (0.5 g, 2.66 mmol), NaO'Bu (306 mg, 3.18 mmol), naphthalene-2-thiol (51 1 mg, 3.19 mmol), Pd2dba3 (244 mg, 10%) and toluene (13.3 mL). The mixture was thoroughly degassed with argon and stirred at 105 C for 24 h. After cooling to rt, the mixture was filtered through celite and washed with EtOAc (50 mL). The organic phase was washed with 1 :1 H20/brine (80 mL), dried over MgSC , filtered and the solvent was removed under reduced pressure. The crude was purified by chromatography (EtOAc/cyclohexane 0?5%) to afford the intermediate 4-(naphthalen-2-ylthio)thiophene-2- carbonitrile. This was dissolved in DCM (17.7 mL) and m-CPBA (70-75%; 1 .90 g, -7.98 mmol) was added portionwise. The mixture was allowed to stir at rt for 2 h. EtOAc (40 mL) was added and the organic phase was washed with sat NaHC03 (3 chi 40 mL), dried over MgS04, filtered and the solvent was removed under reduced pressure. The crude was purified by chromatography (EtOAc/cyclohexane 0?70%) to afford 4-(naphthalen-2-ylsulfonyl)thiophene-2-carbonitrile as a white solid (509 mg, 64%). |