13781-53-8|2-(Thiophen-3-yl)acetonitrile| Ambeed

Structure of 13781-53-8

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Quality Control of [ 13781-53-8 ] Purity: 98% SDS Specification

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Product Details of [ 13781-53-8 ]

CAS No. :	13781-53-8
Formula :	C₆H₅NS
M.W :	123.18
SMILES Code :	N#CCC1=CSC=C1
MDL No. :	MFCD00005471
InChI Key :	GWZCLMWEJWPFFA-UHFFFAOYSA-N
Pubchem ID :	83730

Safety of [ 13781-53-8 ]

GHS Pictogram:
Signal Word:	Warning
Hazard Statements:	H302+H312+H332-H315-H319-H335
Precautionary Statements:	P261-P280-P305+P351+P338

Computational Chemistry of [ 13781-53-8 ] Show Less

Physicochemical Properties

Num. heavy atoms	8
Num. arom. heavy atoms	5
Fraction Csp3	0.17
Num. rotatable bonds	1
Num. H-bond acceptors	1.0
Num. H-bond donors	0.0
Molar Refractivity	33.84
TPSA ? Topological Polar Surface Area: Calculated from Ertl P. et al. 2000 J. Med. Chem.	52.03 Å²

Lipophilicity

Log P_o/w (iLOGP)? iLOGP: in-house physics-based method implemented from Daina A et al. 2014 J. Chem. Inf. Model.	1.49
Log P_o/w (XLOGP3)? XLOGP3: Atomistic and knowledge-based method calculated by XLOGP program, version 3.2.2, courtesy of CCBG, Shanghai Institute of Organic Chemistry	1.26
Log P_o/w (WLOGP)? WLOGP: Atomistic method implemented from Wildman SA and Crippen GM. 1999 J. Chem. Inf. Model.	1.81
Log P_o/w (MLOGP)? MLOGP: Topological method implemented from Moriguchi I. et al. 1992 Chem. Pharm. Bull. Moriguchi I. et al. 1994 Chem. Pharm. Bull. Lipinski PA. et al. 2001 Adv. Drug. Deliv. Rev.	0.75
Log P_o/w (SILICOS-IT)? SILICOS-IT: Hybrid fragmental/topological method calculated by FILTER-IT program, version 1.0.2, courtesy of SILICOS-IT, http://www.silicos-it.com	2.8
Consensus Log P_o/w? Consensus Log P_o/w: Average of all five predictions	1.62

Water Solubility

Log S (ESOL):? ESOL: Topological method implemented from Delaney JS. 2004 J. Chem. Inf. Model.	-1.79
Solubility	1.98 mg/ml ; 0.0161 mol/l
Class? Solubility class: Log S scale Insoluble < -10 < Poorly < -6 < Moderately < -4 < Soluble < -2 Very < 0 < Highly	Very soluble
Log S (Ali)? Ali: Topological method implemented from Ali J. et al. 2012 J. Chem. Inf. Model.	-1.95
Solubility	1.38 mg/ml ; 0.0112 mol/l
Class? Solubility class: Log S scale Insoluble < -10 < Poorly < -6 < Moderately < -4 < Soluble < -2 Very < 0 < Highly	Very soluble
Log S (SILICOS-IT)? SILICOS-IT: Fragmental method calculated by FILTER-IT program, version 1.0.2, courtesy of SILICOS-IT, http://www.silicos-it.com	-2.11
Solubility	0.952 mg/ml ; 0.00773 mol/l
Class? Solubility class: Log S scale Insoluble < -10 < Poorly < -6 < Moderately < -4 < Soluble < -2 Very < 0 < Highly	Soluble

Pharmacokinetics

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) and tested on 415 molecules (test set) 10-fold CV: ACC=0.72 / AUC=0.77 External: ACC=0.88 / AUC=0.94	No
CYP1A2 inhibitor? Cytochrome P450 1A2 inhibitor: SVM model built on 9145 molecules (training set) and tested on 3000 molecules (test set) 10-fold CV: ACC=0.83 / AUC=0.90 External: ACC=0.84 / AUC=0.91	No
CYP2C19 inhibitor? Cytochrome P450 2C19 inhibitor: SVM model built on 9272 molecules (training set) and tested on 3000 molecules (test set) 10-fold CV: ACC=0.80 / AUC=0.86 External: ACC=0.80 / AUC=0.87	No
CYP2C9 inhibitor? Cytochrome P450 2C9 inhibitor: SVM model built on 5940 molecules (training set) and tested on 2075 molecules (test set) 10-fold CV: ACC=0.78 / AUC=0.85 External: ACC=0.71 / AUC=0.81	No
CYP2D6 inhibitor? Cytochrome P450 2D6 inhibitor: SVM model built on 3664 molecules (training set) and tested on 1068 molecules (test set) 10-fold CV: ACC=0.79 / AUC=0.85 External: ACC=0.81 / AUC=0.87	No
CYP3A4 inhibitor? Cytochrome P450 3A4 inhibitor: SVM model built on 7518 molecules (training set) and tested on 2579 molecules (test set) 10-fold CV: ACC=0.77 / AUC=0.85 External: ACC=0.78 / AUC=0.86	No
Log Kp (skin permeation)? Skin permeation: QSPR model implemented from Potts RO and Guy RH. 1992 Pharm. Res.	-6.16 cm/s

Druglikeness

Lipinski? Lipinski (Pfizer) filter: implemented from Lipinski CA. et al. 2001 Adv. Drug Deliv. Rev. MW ≤ 500 MLOGP ≤ 4.15 N or O ≤ 10 NH or OH ≤ 5	0.0
Ghose? Ghose filter: implemented from Ghose AK. et al. 1999 J. Comb. Chem. 160 ≤ MW ≤ 480 -0.4 ≤ WLOGP ≤ 5.6 40 ≤ MR ≤ 130 20 ≤ atoms ≤ 70	None
Veber? Veber (GSK) filter: implemented from Veber DF. et al. 2002 J. Med. Chem. Rotatable bonds ≤ 10 TPSA ≤ 140	0.0
Egan? Egan (Pharmacia) filter: implemented from Egan WJ. et al. 2000 J. Med. Chem. WLOGP ≤ 5.88 TPSA ≤ 131.6	0.0
Muegge? Muegge (Bayer) filter: implemented from Muegge I. et al. 2001 J. Med. Chem. 200 ≤ MW ≤ 600 -2 ≤ XLOGP ≤ 5 TPSA ≤ 150 Num. rings ≤ 7 Num. carbon > 4 Num. heteroatoms > 1 Num. rotatable bonds ≤ 15 H-bond acc. ≤ 10 H-bond don. ≤ 5	1.0
Bioavailability Score? Abbott Bioavailability Score: Probability of F > 10% in rat implemented from Martin YC. 2005 J. Med. Chem.	0.55

Medicinal Chemistry

PAINS? Pan Assay Interference Structures: implemented from Baell JB. & Holloway GA. 2010 J. Med. Chem.	0.0 alert
Brenk? Structural Alert: implemented from Brenk R. et al. 2008 ChemMedChem	0.0 alert: heavy_metal
Leadlikeness? Leadlikeness: implemented from Teague SJ. 1999 Angew. Chem. Int. Ed. 250 ≤ MW ≤ 350 XLOGP ≤ 3.5 Num. rotatable bonds ≤ 7	No; 1 violation:MW<1.0
Synthetic accessibility? Synthetic accessibility score: from 1 (very easy) to 10 (very difficult) based on 1024 fragmental contributions (FP2) modulated by size and complexity penaties, trained on 12'782'590 molecules and tested on 40 external molecules (r² = 0.94)	1.96

Application In Synthesis of [ 13781-53-8 ]

* 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.

Downstream synthetic route of [ 13781-53-8 ]

[ 13781-53-8 ] Synthesis Path-Downstream 1~54

1
[ 13781-53-8 ]
[ 59311-67-0 ]

Yield	Reaction Conditions	Operation in experiment
67%	With indium(III) chloride; sodium tetrahydroborate; In tetrahydrofuran; at 25℃; for 16h;Inert atmosphere;	This compound was synthesized according to a procedure described in literature.5 An oven-dried round-bottom flask (25 mL) cooled under argon was fitted with a rubber septum and charged with a stir bar, anhydrous InCl3 (0.681 g, 3.079 mmol), anhydrous THF (10 mL), and NaBH4 (0.341 g, 9.014 mmol). The reaction was stirred at 25 C for 1h, followed by the dropwise addition of 3-thiopheneacetonitrile (0.340 mL, 2.981 mmol), and the mixture was stirred at 25 C for 16 h. The solution was quenched with 10 mL of 2.8 M hydrochloric acid, and the solution was refluxed for 2 h to dissolve remaining metal salts. The reaction mixture was cooled to 25C, 5 mL of methanol were added, and the mixture was again refluxed for 2 h. The reaction mixture was then cooled to 25C and filtered, and the methyl borate/methanol was removed from the filtrate by evaporation. The remaining acidic solution was extracted with DCM (3 10 mL), and the organic layers were discarded. The acidic aqueous layer was then basified with NaOH pellets to pH ≈ 11 and again extracted with DCM (3 10 mL). The combined organic layers were dried on a WA filter filtered, and evaporated under vacuum to afford 2-(3-thienyl)ethanamine 7. Yellowish oil; 0.250 g, yield: 67%. 1H NMR (300 MHz, CDCl3): δ = 7.20-7.30 (m, 1H; ArH), 7.00 (m, 1H; ArH), 6.95 (m, 1H; ArH), 2.96 (t, 2H; J = 6.6 Hz, CH2), 2.78 (t, 2H; J = 6.6 Hz, CH2), 1.45 ppm (bs, 2H; NH2). The 1H NMR spectrum was according to literature.
	With hydrogenchloride;aluminium chloride; In diethyl ether; water;	(a) Thiophene-3-ethylamine A solution of anhydrous aluminium chloride (26.6 g) in diethylether (100 ml) was added to a stirred suspension of lithium aluminium hydride (7.6 g) in ether (100 ml) under nitrogen atmosphere at room temperature. To the stirred mixture was added thiophene-3-acetonitrile (24.6 g) in ether dropwise over 30 minutes, the exothermic reaction causing the mixture to reflux. After 1 hour water (8 ml) was added cautiously (exothermic) followed by 5M aqueous HCl (400 ml). The aqueous layer was separated and basified to pH~11 with 50% aqueous NaOH (160 ml). The aqueous solution was extracted with dichloromethane (2*200 ml) and the extracts dried over magnesium sulphate, filtered and evaporated to a pale yellow liquid. Distillation gave thiophene-3-ethylamine as a colourless liquid, b.p. 78-79 at 6 mmHg.
	With hydrogenchloride;aluminium chloride; In diethyl ether; water;	(a) Thiophene-3-ethylamine A solution of anhydrous aluminium chloride (26.6 g) in diethylether (100 ml) was added to a stirred suspension of lithium aluminium hydride (7.6 g) in ether (100 ml) under nitrogen atmosphere at room temperature. To the stirred mixture was added thiophene-3-acetonitrile (24.6 g) in ether dropwise over 30 minutes, the exothermic reaction causing the mixture to reflux. After 1 hour water (8 ml) was added cautiously (exothermic) followed by 5M aqueous hydrochloric acid (400 ml). The aqueous layer was separate and basified to pH ~11 with 50% aqueous sodium hydroxide (160 ml). The aqueous solution was extracted with dichloromethane (2*200 ml) and the extracts dried over magnesium sulphate, filtered and evaporated to a pale yellow liquid (25.0 g). Distillation gave thiophene-3-ethylamine as a colourless liquid, b.p. 78-79 at 6 mmHg.

		Thiophen-3-yl-acetonitrile (5.0 g, 40.6 mmol) was dissolved in 50 mL THF. BH3-THF (61 mL, 1M in THF) was added slowly. The reaction was heated to 60 C. overnight then quenched carefully with 4% aqueous HCl until no effervescence was observed. The crude reaction mixture was then partitioned between EtOAc and water (300 mL each). The aqueous layer was acidified with 30% NaOH to pH 12 and the product was extracted into DCM/EtOH (4:1, 3×). The organic extracts were dried over MgSO4 and concentrated to give 2.9 g of the subtitle compound as an oil.
	With dimethylsulfide borane complex; In tetrahydrofuran; at 70℃; for 15h;	To a solution of 2-<strong>[13781-53-8](thiophen-3-yl)acetonitrile</strong> (3.02 g, 24.3 mmol) in THF (48 mL), borane-methyl sulfide complex (3.5 mL, 35.4 mmol)was added dropwise and then stirred for 15 h at 70.After completion, the mixture was cooled to room temperature, and diluted with MeOH. HCl solutionin MeOH was added and stirred at room temperature. The mixture was concentrated in vacuum andwashed with Et2O to yield 5a.MS: 128.1[M+H]+.

References: [1]Journal of Organic Chemistry,2012,vol. 77,p. 221 - 228.
[2]Journal of Organic Chemistry,2021,vol. 86,p. 6207 - 6227.
[3]Tetrahedron Letters,2013,vol. 54,p. 6087 - 6089.
[4]MedChemComm,2015,vol. 6,p. 1679 - 1686.
[5]Journal of the American Chemical Society,1954,vol. 76,p. 4466.
[6]Journal of Medicinal Chemistry,1991,vol. 34,p. 2624 - 2633.
[7]Patent: US4904653,1990,A .
[8]Patent: US5028602,1991,A .
[9]Patent: US2006/3990,2006,A1 .Location in patent: Page/Page column 12; 24.
[10]Bioorganic and Medicinal Chemistry Letters,2018,vol. 28,p. 3004 - 3008.

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[ 13781-53-8 ]
[ 873-32-5 ]
[ 127667-28-1 ]

References: [1]Journal of Organic Chemistry,1990,vol. 55,p. 4817 - 4821.
[2]Chemistry - An Asian Journal,2020,vol. 15,p. 106 - 111.

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[ 13781-53-8 ]
[ 110-62-3 ]
[ 73812-05-2 ]