The AmpC campaign used the structure in PDB 1L2S, while the D4 campaign used PDB 5WIU. In each, 45 matching spheres were calculated around and including the ligand atoms—a 26 μM thiophene carboxylate for AmpC and nemonapride for D4 structures were prepared and AMBER united atom charges assigned14 (link). The magnitude of the partial atomic charges for five residues in AmpC were increased without changing the net residue charge56 . For both targets, the low protein dielectric was extended into the binding site using pseudo-atom positions representing possible ligand docking sites, the radius was 1.0 Å and 2.0 Å for D4 and AmpC respectively14 (link),54 ,60 . For the D4 dopamine receptor, the desolvation volume of the site was also increased by similar atom positions, using a radius of 0.3 Å. This improved ligand charge-balance in benchmarking calculations, reducing the number of high-ranking dications. Energy grids representing the AMBER van der Waals potential61 , Poisson-Boltzmann electrostatic potentials using QNIFFT62 ,63 , and ligand desolvation from the occluded volume of the target for different ligand orientations54 were calculated. Using DOCK3.7.264 , over 99 million and over 138 million library molecules were docked against AmpC and the D4 dopamine receptor, respectively. Each library molecule was sampled in about 4054 and 3300 orientations and, on average, 280 and 479 conformations for AmpC and D4, respectively, and were rigid-body minimized with a simplex minimizer. The throughput averaged 1 second per library compound.
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Thiophene
Thiophene
Thiophene is a heterocyclic aromatic compound consisting of a five-membered ring with one sulfur atom.
It is an important building block in organic chemistry, with wide applications in the development of pharmaceuticals, agrochemicals, and functional materials.
Thiophene and its derivatives exhibit diverse biological activities, including antimicrobial, anti-inflammatory, and anticancer properties.
Researchers studying thiophene compounds can leverrage the power of PubCompare.ai to optimize their research workflows, identifying the most effective protocols from literature, pre-prints, and patents using AI-driven comparisions to enhance reproducibility and accuaracy.
It is an important building block in organic chemistry, with wide applications in the development of pharmaceuticals, agrochemicals, and functional materials.
Thiophene and its derivatives exhibit diverse biological activities, including antimicrobial, anti-inflammatory, and anticancer properties.
Researchers studying thiophene compounds can leverrage the power of PubCompare.ai to optimize their research workflows, identifying the most effective protocols from literature, pre-prints, and patents using AI-driven comparisions to enhance reproducibility and accuaracy.
Most cited protocols related to «Thiophene»
Amber
Binding Sites
cDNA Library
Diet, Protein-Restricted
Dopamine Receptor
Electrostatics
Human Body
Ligands
Mental Orientation
Muscle Rigidity
nemonapride
Radius
Thiophene
Acids
Anabolism
Carboxylic Acids
Iodination
pentamer formyl thiophene acetic acid
Sodium
Sodium Chloride
Sodium Hydroxide
Thiophene
R-ketamine hydrochloride and S-ketamine hydrochloride were prepared by recrystallization of RS-ketamine (Ketalar, ketamine hydrochloride, Daiichi Sankyo Pharmaceutical, Tokyo, Japan) and d -(−)-tartaric acid (or l - (+)-tartaric acid), as described previously.34 The purity of these stereoisomers was determined by a high-performance liquid chromatography (CHIRALPAK IA, column size: 250 × 4.6 mm, mobile phase: n-hexane/dichloromethane/diethylamine (75/25/0.1), Daicel, Tokyo, Japan). NBQX, 2,3-dioxo-6-nitro-1,2,3,4-tetrahydrobenzo[f]quinoxaline-7-sulfonamide (catalog number: 0373, Tocris Bioscience, Bristol, UK, 10 mg kg−1) was dissolved in saline. ANA-12, N2-(2-{[(2-oxoazepan-3-yl) amino]carbonyl}phenyl)benzo[b]thiophene-2-carboxamide (catalog number: BTB06525SC, Maybridge, Trevillett Tintagel, Cornwall, UK, 0.5 mg kg−1) was prepared in vehicle of 1% dimethylsulfoxide in phosphate-buffered saline. The dose of ketamine, NBQX and ANA-12 was selected as reported previously.34 , 35 , 36 (link), 37 (link), 38 (link), 39 (link), 40 (link) Other reagents were purchased commercially.
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2,3-dioxo-6-nitro-7-sulfamoylbenzo(f)quinoxaline
diethylamine
High-Performance Liquid Chromatographies
Ketalar
Ketamine
Ketamine Hydrochloride
Methylene Chloride
n-hexane
Pharmaceutical Preparations
Phosphates
Quinoxalines
Saline Solution
Stereoisomers
Sulfonamides
Sulfoxide, Dimethyl
tartaric acid
Thiophene
The AmpC campaign used the structure in PDB 1L2S, while the D4 campaign used PDB 5WIU. In each, 45 matching spheres were calculated around and including the ligand atoms—a 26 μM thiophene carboxylate for AmpC and nemonapride for D4 structures were prepared and AMBER united atom charges assigned14 (link). The magnitude of the partial atomic charges for five residues in AmpC were increased without changing the net residue charge56 . For both targets, the low protein dielectric was extended into the binding site using pseudo-atom positions representing possible ligand docking sites, the radius was 1.0 Å and 2.0 Å for D4 and AmpC respectively14 (link),54 ,60 . For the D4 dopamine receptor, the desolvation volume of the site was also increased by similar atom positions, using a radius of 0.3 Å. This improved ligand charge-balance in benchmarking calculations, reducing the number of high-ranking dications. Energy grids representing the AMBER van der Waals potential61 , Poisson-Boltzmann electrostatic potentials using QNIFFT62 ,63 , and ligand desolvation from the occluded volume of the target for different ligand orientations54 were calculated. Using DOCK3.7.264 , over 99 million and over 138 million library molecules were docked against AmpC and the D4 dopamine receptor, respectively. Each library molecule was sampled in about 4054 and 3300 orientations and, on average, 280 and 479 conformations for AmpC and D4, respectively, and were rigid-body minimized with a simplex minimizer. The throughput averaged 1 second per library compound.
Amber
Binding Sites
cDNA Library
Diet, Protein-Restricted
Dopamine Receptor
Electrostatics
Human Body
Ligands
Mental Orientation
Muscle Rigidity
nemonapride
Radius
Thiophene
On the day of injection, fresh solutions were prepared by dissolving compounds in sterile endotoxin-free isotonic saline. Lipopolysaccharide (LPS, 0.5mg/kg; L-4130, serotype 0111:B4, Sigma-Aldrich) was administered intraperitoneally (i.p.). 7,8-Dihydroxyflavone (7,8-DHF; Catalog number: D1916) and 5,7-dihydroxyflavone (5,7-DHF: Catalog number: C1652) were purchased from Tokyo Chemical Industry (Supplementary Figure 1 ). 7,8-DHF (1, 3, or 10mg/kg, i.p.) and 5,7-DHF (10mg/kg, i.p.) were prepared in a vehicle of 17% dimethylsulfoxide in phosphate-buffered saline (Ren et al., 2013 (link)
2014 (link)). ANA-12, N2-(2-{[(2-oxoazepan-3-yl) amino]carbonyl}phenyl)benzo[b]thiophene-2-carboxamide (0.5mg/kg, i.p., Catalog number: BTB06525SC, Maybridge;Supplementary Figure 1 ), was dissolved in 1% dimethylsulfoxide in physiological saline. Paroxetine (as the hydrochloride salt, at 10mg/kg, i.p.) and venlafaxine (as the hydrochloride salt, at 10mg/kg, i.p.; Wako Pure Chemical Ltd.) were dissolved in physiological saline. Rapamycin (0.2 nmol/L in 2 µL, Calbiochem-Novabiochem) was administered intracerebroventricularly (i.c.v.), after the mice were anesthetized with pentobarbital (5mg/kg). The dose of rapamycin was selected as previously reported (Li et al., 2010 (link)
2011 (link)). The doses of 7,8-DHF and ANA-12 were also selected as previously reported (Ren et al., 2013 (link)
2014 (link); Cazorla et al., 2011 (link)).
2014 (link)). ANA-12, N2-(2-{[(2-oxoazepan-3-yl) amino]carbonyl}phenyl)benzo[b]thiophene-2-carboxamide (0.5mg/kg, i.p., Catalog number: BTB06525SC, Maybridge;
2011 (link)). The doses of 7,8-DHF and ANA-12 were also selected as previously reported (Ren et al., 2013 (link)
2014 (link); Cazorla et al., 2011 (link)).
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Endotoxins
Mice, House
Paroxetine
Pentobarbital
Phosphates
physiology
Saline Solution
Sirolimus
Sodium Chloride
Sterility, Reproductive
Sulfoxide, Dimethyl
Thiophene
Venlafaxine
Most recents protocols related to «Thiophene»
Example 15
Step 1:
Compound 1 (100 mg, 0.62 mmol), tert-butyl 2-amino-4-(thiophen-2-yl)phenylcarbamate (151 mg, 0.52 mmol), HOAt (141 mg, 1.04 mmol), EDCI (200 mg, 1.04 mmol), and Et3N (0.2 mL) were combined in THE (5 mL), and the reaction was stirred at rt overnight. After completed, the mixture was concentrated and the crude was carried over for next step (300 mg, crude).
Step 2:
The crude Compound 2 (300 mg, crude) and TFA (3 mL) were combined in DCM (6 mL). The reaction was stirred at rt for 2 h. The mixture was purified by Prep-HPLC (base method). White solid was afforded to obtain compound 018 (130 mg, 43%, 2 steps). LCMS: m/z=334.8 (M+H)+. 1H NMR (400 MHz, DMSO) δ 9.77 (s, 1H), 8.39 (d, J=33.4 Hz, 2H), 7.90 (d, J=7.6 Hz, 1H), 7.71 (s, 1H), 7.51 (s, 1H), 7.39-7.21 (m, 3H), 7.07 (dd, J=13.2, 9.0 Hz, 1H), 6.83 (d, J=8.2 Hz, 1H).
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1H NMR
Anabolism
High-Performance Liquid Chromatographies
Lincomycin
Sulfoxide, Dimethyl
TERT protein, human
Thiophene
Example 12
Step 1:
Compound 1 (177 g, 1 mmol), iodomethane (426 mg, 3 mmol), and NaH (60%, 160 mg, 4 mmol) were combined in THE (5 mL). The reaction mixture was stirred at 60° C. for 3 h. The mixture was concentrated to get a residue The crude residue was dissolved in Py (5 mL). tert-Butyl 2-amino-4-(thiophen-2-yl)phenylcarbamate (290 mg, 1 mmol) and EDCI (382 mg, 2 mmol) were added and the reaction was stirred at rt overnight. The mixture was concentrated to get a residue, which was purified by silica gel to get compound 2 (246 mg, 50%, 2 steps) as yellow solid.
Step 2:
Compound 2 (246 mg, 0.5 mmol) and TFA (1 mL) were combined in DCM (2 mL), and the reaction was stirred at rt overnight. The mixture was concentrated to get compound 014 (156 mg, 80%) as yellow solid. LCMS: m/z=492 (M+H)+. 1H NMR (400 MHz, DMSO) δ 9.88 (s, 1H), 8.02 (d, J=8.0 Hz, 2H), 7.53 (s, 1H), 7.42 (t, J=7.5 Hz, 2H), 7.34 (d, J=3.4 Hz, 1H), 7.17 (d, J=8.2 Hz, 1H), 7.09 (d, J=4.3 Hz, 1H), 6.99 (d, J=8.3 Hz, 1H), 3.21 (s, 3H), 1.34 (s, 6H).
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1H NMR
Anabolism
Lincomycin
methyl iodide
Silica Gel
Sulfoxide, Dimethyl
TERT protein, human
Thiophene
Example 7
Step 1:
Compound 1 (830 mg, 5 mmol) and cyclopropanecarboxylic acid (430 mg, 5 mmol) were combined in 4M HCl (20 mL). The reaction was refluxed overnight. After completed, the mixture was concentrated and purified by Prep-HPLC. White solid was afforded as Compound 2 (312 mg, 31%).
Step 2:
Compound 2 (100 mg, 0.50 mmol), tert-butyl 2-amino-4-(thiophen-2-yl)phenylcarbamate (144 mg, 0.50 mmol), and EDCI (288 mg, 1.50 mmol) were combined in Py (5 mL). The reaction was stirred at rt overnight. After completed, the mixture was concentrated and purified by column chromatography (DCM/MeOH=10/1). Compound 3 was isolated as a colorless oil (54 mg, 23%).
Step 3:
Compound 3 (54 mg, 0.11 mmol) was dissolved in DCM (2 ml). Then TFA (1 ml) was added. The mixture was stirred at rt for 2 h. The crude material was concentrated and washed with Et2O. Compound 009 was isolated as a white solid (30 mg, TFA salt). LCMS: m/z=375.0 (M+H)+. 1H NMR (400 MHz, DMSO) δ 9.96 (s, 1H), 8.26 (s, 1H), 8.07 (d, J=8.0 Hz, 1H), 7.76 (d, J=8.5 Hz, 1H), 7.50 (s, 1H), 7.35 (dd, J=8.5, 2.5 Hz, 2H), 7.28 (d, J=3.0 Hz, 1H), 7.07 (t, J=3.5 Hz, 1H), 6.88 (s, 1H), 2.42 (t, J=3.0 Hz, 1H), 1.37 (dd, J=2.5 Hz, 4H).
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1H NMR
Anabolism
Chromatography
cyclopropanecarboxylic acid
High-Performance Liquid Chromatographies
Lincomycin
Salts
Sulfoxide, Dimethyl
TERT protein, human
Thiophene
Example 22
Synthesis of 155-A.
A mixture of potassium (bromomethyl)trifluoroborate (1.00 g, 4.98 mmol) and pyrrolidine (371 mg, 5.23 mmol) in THF (10 mL) was stirred at 80° C. for 4 h. The solvent was removed in vacuo. The residue was dissolved in acetone and the solution filtered to remove KCl. The filtrate was concentrated in vacuo, dissolved in a minimal amount of hot acetone (10 mL), and precipitated by the dropwise addition of Et2O (5 mL). Additional Et2O (150 mL) was added to facilitate filtering to give 155-A (750 mg, 98%) as a white solid.
Synthesis of 155-B.
A mixture of 155-A (750 mg, 4.90 mmol), SM-A (500 mg, 4.67 mmol), Cs2CO3 (4.56 g, 14.0 mmol), Pd(OAc)2 (52 mg, 0.23 mmol) and XPhos (224 mg, 0.47 mmol) in THF/H2O (20 mL/2 mL) was stirred 80° C. for 12 h under Ar. The mixture was cooled to room temperature and diluted with H2O (50 mL). The mixture was extracted with EtOAc (20 mL×3). The combined organics washed with brine (20 mL×3), dried over anhydrous Na2SO4 and then concentrated in vacuo. The residue was purified by column chromatography on silica gel (PE:EtOAc=8:1˜3:1) to give 155-B (700 mg, 47%) as a yellow solid.
Synthesis of 155-C.
To a solution of 155-B (350 mg, 1.15 mmol) in DCM (8 mL) was added TFA (4 mL) and stirred at room temperature for 1 h. when LCMS showed the reaction was finished. The solvent was removed in vacuo to give 155-C as a crude product and used to next step directly.
Synthesis of 155-D.
A mixture of 143-C (200 mg, 0.42 mmol) and 155-C (crude product from last step) in acetonitrile (5 mL) was stirred at 50° C. for 30 min. Then Na2CO3 (356 mg, 3.36 mmol) was added into above mixture and stirred at 50° C. for 3 h. After the reaction was completed according to LCMS, the mixture was cooled to room temperature. The Na2CO3 was removed by filtered. The filtrate was concentrated in vacuo. The residue was purified by column chromatography on silica gel (DCM:MeOH=100:1˜50:1) to give 155-D (180 mg, 93%) as a yellow solid.
Synthesis of 155.
A mixture of 155-D (180 mg, 0.39 mmol) and Pd/C (180 mg) in MeOH (5 mL) was stirred at room temperature for 1 h under H2 atmosphere. Pd/C was removed by filtration through the Celite. The filtrate was concentrated and the residue was purified by Pre-TLC (DCM:MeOH=8:1) to give 155 (125 mg, 74%) as a yellow solid
Compound 144 was synthesized in a similar manner using thiophen-2-ylboronic acid variant of 155. Compound 144. 80 mg, 60%, a yellow solid.
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Acetone
acetonitrile
Acids
Anabolism
AR-12 compound
Atmosphere
brine
Celite
Chromatography
Filtration
Lincomycin
Potassium
pyrrolidine
Silica Gel
Solvents
Thiophene
Example 9
Step 1:
Compound 3 (231 mg, 1 mmol), amine tert-butyl 2-amino-4-(thiophen-2 yl)phenylcarbamate (290 mg, 1 mmol), and EDCI (382 mg, 2 mmol) were combined in Py (5 mL). The reaction was stirred at rt overnight. The mixture was concentrated to get a residue, which was purified by silica gel to get compound 4 (302 mg, 60%) as yellow solid.
Step 2:
Compound 4 (252 mg, 0.5 mmol) and TFA (1 mL) were combined in DCM (2 mL). The reaction was stirred at rt for 1 h. The mixture was concentrated to get a compound 011 (161, 80%) as yellow solid. LCMS: m/z=404 (M+H)+. 1H NMR (400 MHz, DMSO) δ 9.66 (s, 1H), 8.00 (m, 1H), 7.93 (s, 1H), 7.46 (s, 1H), 7.36 (m, 1H), 7.31 (m, 1H), 7.30 (m 2H), 7.06 (m, 1H), 6.81 (m, 1H), 5.14 (s, 2H). 3.68 (m, 2H), 3.62 (m, 2H), 1.17 (m, 1H), 0.48 (m, 2H), 0.36 (m, 2H)
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1H NMR
Amines
Anabolism
Lincomycin
Silica Gel
Sulfoxide, Dimethyl
TERT protein, human
Thiophene
Top products related to «Thiophene»
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Thiophene is a heterocyclic aromatic organic compound. It is a colorless, volatile liquid with a characteristic odor. Thiophene is commonly used as a building block in the synthesis of various organic compounds and materials.
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Methanol is a clear, colorless, and flammable liquid that is widely used in various industrial and laboratory applications. It serves as a solvent, fuel, and chemical intermediate. Methanol has a simple chemical formula of CH3OH and a boiling point of 64.7°C. It is a versatile compound that is widely used in the production of other chemicals, as well as in the fuel industry.
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DMSO is a versatile organic solvent commonly used in laboratory settings. It has a high boiling point, low viscosity, and the ability to dissolve a wide range of polar and non-polar compounds. DMSO's core function is as a solvent, allowing for the effective dissolution and handling of various chemical substances during research and experimentation.
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Acetonitrile is a colorless, volatile, flammable liquid. It is a commonly used solvent in various analytical and chemical applications, including liquid chromatography, gas chromatography, and other laboratory procedures. Acetonitrile is known for its high polarity and ability to dissolve a wide range of organic compounds.
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Ethanol is a clear, colorless liquid chemical compound commonly used in laboratory settings. It is a key component in various scientific applications, serving as a solvent, disinfectant, and fuel source. Ethanol has a molecular formula of C2H6O and a range of industrial and research uses.
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N,N-dimethylformamide is a clear, colorless liquid organic compound with the chemical formula (CH3)2NC(O)H. It is a common laboratory solvent used in various chemical reactions and processes.
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Chloroform is a colorless, volatile liquid with a characteristic sweet odor. It is a commonly used solvent in a variety of laboratory applications, including extraction, purification, and sample preparation processes. Chloroform has a high density and is immiscible with water, making it a useful solvent for a range of organic compounds.
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N-bromosuccinimide is a chemical compound used as a laboratory reagent. It is a source of electrophilic bromine and is commonly utilized in organic synthesis reactions, such as bromination and substitution reactions.
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Toluene is a colorless, flammable liquid with a distinctive aromatic odor. It is a common organic solvent used in various industrial and laboratory applications. Toluene has a chemical formula of C6H5CH3 and is derived from the distillation of petroleum.
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Ferrocene is an organometallic compound with the formula Fe(C5H5)2. It consists of two cyclopentadienyl rings bound to an iron center. Ferrocene is a versatile compound used in various applications, including organic synthesis, electrochemistry, and material science.
More about "Thiophene"
Thiophene, a crucial heterocyclic aromatic compound, is a versatile and widely used building block in organic chemistry.
With its five-membered ring structure featuring a sulfur atom, thiophene and its derivatives exhibit a diverse range of biological activities, including antimicrobial, anti-inflammatory, and anticancer properties.
Researchers studying this important class of compounds can leverage the power of PubCompare.ai to optimize their research workflows.
By utilizing PubCompare.ai, researchers can identify the most effective protocols and methods from a vast array of literature, pre-prints, and patents.
Through AI-driven comparisons, they can enhance the reproducibility and accuracy of their thiophene studies, ensuring that their work is built upon the most robust and reliable protocols.
Beyond thiophene, researchers may also explore related solvents and reagents, such as methanol, DMSO, acetonitrile, ethanol, N,N-dimethylformamide, chloroform, N-bromosuccinimide, toluene, and ferrocene, which are commonly used in thiophene-based reactions and applications.
By leveraging the insights and capabilities of PubCompare.ai, researchers can optimize their entire workflow, from experimental design to data analysis, and deliver more impactful results in their thiophene-focused studies.
Remember, with the power of PubCompare.ai at your fingertips, you can navigate the vast landscape of thiophene research with confidence, avoiding human-like tpyos and ensuring that your work stands out for its reproducibility and accuracy.
With its five-membered ring structure featuring a sulfur atom, thiophene and its derivatives exhibit a diverse range of biological activities, including antimicrobial, anti-inflammatory, and anticancer properties.
Researchers studying this important class of compounds can leverage the power of PubCompare.ai to optimize their research workflows.
By utilizing PubCompare.ai, researchers can identify the most effective protocols and methods from a vast array of literature, pre-prints, and patents.
Through AI-driven comparisons, they can enhance the reproducibility and accuracy of their thiophene studies, ensuring that their work is built upon the most robust and reliable protocols.
Beyond thiophene, researchers may also explore related solvents and reagents, such as methanol, DMSO, acetonitrile, ethanol, N,N-dimethylformamide, chloroform, N-bromosuccinimide, toluene, and ferrocene, which are commonly used in thiophene-based reactions and applications.
By leveraging the insights and capabilities of PubCompare.ai, researchers can optimize their entire workflow, from experimental design to data analysis, and deliver more impactful results in their thiophene-focused studies.
Remember, with the power of PubCompare.ai at your fingertips, you can navigate the vast landscape of thiophene research with confidence, avoiding human-like tpyos and ensuring that your work stands out for its reproducibility and accuracy.