Structure of 2,4-Difluorophenylboronic acid
CAS No.: 144025-03-6
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Fluorination Modulates Solid‐State Reactivity and Guest Confinement in Organoboronic Ester Adducts
Shaw, Alaric ; Bondarenko, Ivan ; Bhaniramka, Vanshika ; West, Munroe Alexandra ; Gilbert, Peter F ; Loya, Jesus Daniel , et al.
Abstract: Fluorination of organoboronic ester adducts via B ← N coordination enables the formation of photoactive solids capable of [2 + 2]-photodimerization, or confinement of a hydrocarbon guest (i.e., benzene). Specifically, self-assembly of organoboronic acids with varying levels and patterns of fluorination with catechol and 4-stilbazole resulted in T-shaped B ← N adducts, that organize into either photoactive dimeric assemblies (2,4- and 3,5-difluorophenlboronic acids) or photostable architectures that encapsulate benzene (2,4,6-trifluorophenylboronic and 2,3,5,6-tetrafluorophenylboronic acids). Combined crystallographic analysis, molecular modeling, and Hirshfeld surface analysis revealed the formation of photoactive adducts with up to two fluorine atoms to be driven by enhanced face-to-face [π…π] stacking aided by [C-H…π] contacts, while [C-H…F], [C-H…O], and [C-H…π] contacts in adducts with higher fluorination level sustained the inclusion of benzene molecules in the lattice. These findings support fluorination of organoboron systems as an effective strategy for property engineering in molecular materials.
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Keywords: [2+2]-photocycloaddition ; boron ; crystal engineering ; self-assembly ; supramolecular chemistry
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| CAS No. : | 144025-03-6 |
| Formula : | C6H5BF2O2 |
| M.W : | 157.91 |
| SMILES Code : | C1=C(F)C=CC(=C1F)B(O)O |
| MDL No. : | MFCD01318998 |
| InChI Key : | QQLRSCZSKQTFGY-UHFFFAOYSA-N |
| Pubchem ID : | 2734334 |
| GHS Pictogram: |
|
| Signal Word: | Warning |
| Hazard Statements: | H315-H319-H335 |
| Precautionary Statements: | P261-P305+P351+P338 |
| Num. heavy atoms | 11 |
| Num. arom. heavy atoms | 6 |
| Fraction Csp3 | 0.0 |
| Num. rotatable bonds | 1 |
| Num. H-bond acceptors | 4.0 |
| Num. H-bond donors | 2.0 |
| Molar Refractivity | 36.18 |
| TPSA ? Topological Polar Surface Area: Calculated from |
40.46 Ų |
| Log Po/w (iLOGP)? iLOGP: in-house physics-based method implemented from |
0.0 |
| Log Po/w (XLOGP3)? XLOGP3: Atomistic and knowledge-based method calculated by |
1.03 |
| Log Po/w (WLOGP)? WLOGP: Atomistic method implemented from |
0.48 |
| Log Po/w (MLOGP)? MLOGP: Topological method implemented from |
1.15 |
| Log Po/w (SILICOS-IT)? SILICOS-IT: Hybrid fragmental/topological method calculated by |
0.13 |
| Consensus Log Po/w? Consensus Log Po/w: Average of all five predictions |
0.56 |
| Log S (ESOL):? ESOL: Topological method implemented from |
-1.81 |
| Solubility | 2.47 mg/ml ; 0.0156 mol/l |
| Class? Solubility class: Log S scale |
Very soluble |
| Log S (Ali)? Ali: Topological method implemented from |
-1.47 |
| Solubility | 5.35 mg/ml ; 0.0339 mol/l |
| Class? Solubility class: Log S scale |
Very soluble |
| Log S (SILICOS-IT)? SILICOS-IT: Fragmental method calculated by |
-1.83 |
| Solubility | 2.31 mg/ml ; 0.0147 mol/l |
| Class? Solubility class: Log S scale |
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) |
No |
| CYP2C19 inhibitor? Cytochrome P450 2C19 inhibitor: SVM model built on 9272 molecules (training set) |
No |
| CYP2C9 inhibitor? Cytochrome P450 2C9 inhibitor: SVM model built on 5940 molecules (training set) |
No |
| 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 |
-6.53 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 |
1.0 |
| 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) |
2.16 |
* 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 |
|---|---|---|
| 52% | With sodium hydroxide;(1,1'-bis(diphenylphosphino)ferrocene)palladium(II) dichloride; In tetrahydrofuran; water; at 60℃; for 12h; | A stirred solution of <strong>[1006-33-3]2-bromo-5-fluoroacetophenone</strong> (11.72 g, 54 MMOL) and 2, 4-DIFLUOROPHENYLBORONIC acid (8.53 g, 54 MMOL) in tetrahydrofuran (600 mL) was treated under nitrogen with [1, 1APOS;-BIS (DIPHENYLPHOSPHINO) ferrocene] DICHLOROPALLADIUM (II) complex with DICHLOROMETHANE (2.20 g, 2.69 mmol, 5 molepercent) and a 5 N sodium hydroxide solution (21.6 mL, 108 MMOL). The reaction was heated at 60 °C for twelve hours, cooled to room temperature, and the solvent removed in vacuo. The residue was dissolved in diethyl ether, filtered through a short column of silica gel, and the solvent EVAPORATED IN VACUO to a crude brown oil (11.72 g). The crude oil was purified by preparative liquid chromatography on a BIOTAGE 40 Mi column of pre-packed silica gel (90 g), ELUTING with a gradient of between 3percent and 10percent methyl tert-butyl ether in hexane at a flow rate of 50 mL/min to afford, after evaporation of the solvent, the title compound as a purified, colorless oil (7.11 g, 28.4 mmol, 52percent); HRMS [ (+ESI), M/Z] : 251.06705 [M+H] +. Calcd for C14HGF3O : 251.06783 ; IR (FILM), VMAX : 2918,1695, 1604,1481, 1424,1267, 1186,1139, 1100,962, 850,814 CM-1 ; 1H NMR (400 MHz, DMSO-D6) B : 2.44 (s, 3H), 7.16 (tdd, J = 8. 5,2. 5,0. 9 Hz, 1 H), 7.28 (ddd, J = 10. 5,9. 4,2. 6 Hz, 1 H), 7.37-7. 45 (m, 2H), 7.50 (td, J = 8. 5,2. 7 Hz, 1 H), 7.75 (dd, J = 9. 4,2. 7 Hz, 1 H) ; Anal. calcd for C14HGF3O : C, 67.20 ; H, 3.63 ; N, 0.00. Found: C, 67.37 ; H, 3.46 ; N, 0.00. |
| Yield | Reaction Conditions | Operation in experiment |
|---|---|---|
| 39% | With sodium carbonate;bis-triphenylphosphine-palladium(II) chloride; In water; acetonitrile; for 0.166667h;Microwave irradiation; | Next, a synthesis method of a ligand of the present invention, 2-(2,4-difuluorophenyl)-3,5-dimethylpyrazine is described. 2.14 g of<strong>[38557-72-1]2-chloro-3,5-dimethylpyrazine</strong> which was obtained as the intermediate described above, 2.37 g of 2,4-difluorophenyl boronic acid, 1.59 g of sodium carbonate, 0.069 g of bis(triphenylphosphine)palladium(II)dichloride (abbreviation : Pd(PPh3)2Cl2), 15 mL of water, and 15 mL of acetonitrile were put in an eggplant flask equipped with a reflux pipe, and the inside thereof was substituted by argon. This reaction container was subjected to irradiation with microwave (2.45 GHz, 100W) for 10 minutes to be heated. Then, water was added to this solution, and extraction using dichloromethane was conducted to separate an organic layer. The organic layer obtained was washed with water and dried with magnesium sulfate. After the drying, the solution was filtrated. A solvent of this solution was distilled off, and then the residue obtained by the distillation was purified by silica gel column chromatography which uses dichloromethane as a developing solvent; thereby obtaining an objective pyrazine derivative, HdmF2ppr (white powder, yield of 39 %). A synthetic scheme of Step 1 is shown by the following (a-2). |
| Yield | Reaction Conditions | Operation in experiment |
|---|---|---|
| 71% | With sodium carbonate;tetrakis(triphenylphosphine) palladium(0); In water; toluene; at 20 - 100℃; | (3) Tert-butyl 4-[4-(2,4-difluorophenyl)pyrimidin-2-yl]piperazine-1-carboxylate To a mixture of <strong>[479691-42-4]tert-butyl 4-(4-chloropyrimidin-2-yl)piperazine-1-carboxylate</strong> (1.0 g, 3.35 mmol), 2,4-difluorophenylboric acid (793 mg, 5.02 mmol), 2N aqueous sodium carbonate solution (13.4 ml) and toluene (33 ml) was added tetrakistriphenylphosphine palladium (464 mg, 0.402 mmol) at room temperature under nitrogen atmosphere, and the mixture was stirred at 100 C. overnight. The reaction was poured into water and extracted with ethyl acetate. The extract was washed with water, dried over anhydrous magnesium sulfate, and the solvent was distilled off under reduced pressure. The residue was purified by silica gel column chromatography (ethyl acetate:hexane=1:1) to obtain the title compound (894 mg, 71%) as an oily material. 1H NMR (CDCl3) delta: 1.50 (9H, s), 3.46-3.58 (4H, m), 3.85-3.93 (4H, m), 6.83-7.08 (3H, m), 8.08-8.22 (1H, m), 8.39 (1H, d, J=5.3 Hz). |
| 71% | With tetrakis(triphenylphosphine) palladium(0); sodium carbonate; In toluene; at 100℃;Inert atmosphere; | General procedure: A mixture of tert-butyl 4-(2-chloropyrimidin-4-yl)piperazine-1-carboxylate (1.80g, 6.02mmol), (2,4-difluorophenyl)boronic acid (1.43g, 9.04mmol), 1M aq Na2CO3 (24 mL, 48.2 mmol), tetrakis(triphenylphosphine)palladium (0) (835mg, 0.723mmol), and toluene (60mL) was stirred at 100C overnight under N2 atmosphere. The mixture was diluted with water, and extracted with EtOAc. The organic layer was washed with water, dried over anhydrous MgSO4, and concentrated in vacuo. The residue was purified by silica gel column chromatography (hexane-EtOAc) to give 8 (907mg, 40%) as a colorless viscous oil. |
| Yield | Reaction Conditions | Operation in experiment |
|---|---|---|
| 3 g (80%) | With potassium carbonate;Pd(PPh3)4; In 1,2-dimethoxyethane; dichloromethane; water; | (2) Synthesis of 2-(2,4-difluorophenyl)-5-dimethylamino-pyridine <strong>[39856-56-9]2-bromo-5-dimethylaminopyridine</strong> (3.2 g, 16 mmol), 2,4-difluorophenylboronic acid (4.8 g, 30 mmol), K2CO3 (13 g, 94 mmol) and Pd(PPh3)4 (400 mg, 0.35 mmol) in a degassed mixture of DME/H2O (60/50 ml) were refluxed 24 hours under nitrogen. After being cooled to room temperature, the organic layer was separated and the aqueous phase extracted with EtOAc (100 ml). The combined organic fractions were washed with brine, dried over MgSO4 and evaporated to dryness. The crude compound was purified by column chromatography (SiO2, CH2Cl2 then CH2Cl2/MeOH: 97/3). The resulting brown solid was dissolved in CH2Cl2 and decolorized with charcoal. Filtration and evaporation of the solvent afford 3 g (80%) of the desired compound as a slightly yellow crystalline solid. 1H-NMR (CDCl3, 298K, 200 MHz, delta ppm) delta 3.03 (s, 6H), 6.9-7.1 (m, 3H), 7.60 (dd, J=2.5*9 Hz, 1H), 7.95 (m, 1H), 8.24 (d, J=2.5 Hz, 1H). |
| Yield | Reaction Conditions | Operation in experiment |
|---|---|---|
| 312 mg | With tetrakis(triphenylphosphine) palladium(0); sodium carbonate; In 1,2-dimethoxyethane; ethanol; water; at 100℃; for 18h;Inert atmosphere; | General procedure: In an argon gas atmosphere, tetrakis(triphenylphosphine)palladium (83 mg) and a 2 M aqueous sodium carbonate solution (2.2 mL) were added to a mixture of <strong>[63927-22-0]8-bromoisoquinoline</strong> (300 mg), 2,4-difluorophenylboronic acid (342 mg), 1,2-dimethoxyethane (10 mL), and ethanol (1 mL), followed by stirring for 18 hours at an oil temperature of 100° C. The reaction liquid was cooled to room temperature, and then water and ethyl acetate were added thereto to perform liquid separation. The organic layer was washed with saturated brine and then dried, followed by concentration under reduced pressure. The residue was purified by silica gel column chromatography (hexane/ethyl acetate), thereby obtaining 8-(2,4-difluorophenyl)isoquinoline (312 mg). |
| Yield | Reaction Conditions | Operation in experiment |
|---|---|---|
| 89% | With (1,1'-bis(diphenylphosphino)ferrocene)palladium(II) dichloride; potassium dihydrogenphosphate; In toluene; at 140℃; for 0.5h;Inert atmosphere; Microwave irradiation; | Step 1 (0579) Compound iii-51 (300mg, 1.22mmol), (2,4-difluorophenyl)boronic acid (290mg, 1.84mmol), PdCl2 (dppf) (90mg, 0.12mmol) and potassium phosphate (780mg, 3.67mmol) were dissolved into toluene (12mL) under nitrogen atmosphere under microwave irradiation, and the mixture was stirred at 140C for 30 minutes. After the reaction mixture was filtrated by Celite, the solvent was removed in vacuo. The obtained residue was purified by silica gel column chromatography (hexane-ethyl acetate) to give Compound iii-52 (304mg, 89%). 1H-NMR (CDCl3) delta: 8.09-8.05 (m, 2H), 7.72 (d, J = 1.5 Hz, 1H), 7.46-7.40 (m, 1H), 7.00-6.91 (m, 2H), 4.82 (d, J = 5.8 Hz, 2H), 3.94 (s, 3H), 1.83 (t, J = 5.9 Hz, 1H). |

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