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Imidazoles

Imidazoles are a class of five-membered heterocyclic organic compounds containing two nitrogen atoms at positions 1 and 3 within the ring.
They are widely used in medicinal chemistry and have diverse biological activities, including antifungal, anti-inflammatory, and anticancer properties.
Imidazoles are also important intermediates in the synthesis of various pharmaceuticals and agrochemicals.
Researchers can streamline their imidazole research using PubCompare.ai, an AI-powered platform that helps locate the best protocols and products, explore literature, preprints, and patents, and optimize experiments through intelligent comparisons to improve reproducibility.
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Most cited protocols related to «Imidazoles»

Input PDB files can contain numerous errors and format inconsistencies, such as missing heavy atoms, suboptimal residue conformations and non-standard atom names. H++ attempts to make automatic, albeit conservative corrections for many of these problems when possible. Otherwise the errors are identified for possible manual correction. For example, the N and O atoms in the amide groups of ASN and GLN, and the N and C atoms in the imidazole ring of HIS cannot be easily distinguished from electron density maps. Thus, the assignment of these atoms in the PDB file may be (optionally) ‘flipped’ using the reduce algorithm that is based on an analysis of van der Waals contacts and H-bonding (26 (link)). An example of errors that are identified for manual correction are missing residues in the middle of protein chains. Input PDB files may also contain HETATM entries for solvent and ligand molecules; H++ removes these entries. Solvent molecules are removed by default because they are treated implicitly by the continuum solvent methodology used. Non-protein ligands are removed by default, but an option is now available to manually include many ligands and specific buried water molecules for processing, as described on the H++ site. Inclusion of buried waters has been shown to improve the accuracy of computed pK of nearby groups (27 (link)). For peptide, protein, DNA and RNA ligands, current AMBER force field parameters are used to add H atoms and assign atomic partial charges. For other organic ligands, H++ uses OpenBabel (28 ) to add H atoms, and atomic partial charges are assigned using the antechamber module from AmberTools (29 (link)) and the generalized AMBER force field (GAFF) parameter set. PDB structures may also contain residues with partial occupancy representing multiple possible conformations. Without manual intervention from the user, H++ selects the ‘A’ conformation and ignores all others.
An input PQR file, on the other hand, is assumed to have already been validated (e.g. in order to compute the atomic charges and radii included in the PQR file). Therefore, most error and consistency checks are bypassed for input PQR files. In addition, H++ requires AMBER compatible atom and residue names in the input PQR file.
Publication 2012
Amber Amides Electrons Imidazoles Ligands Microtubule-Associated Proteins Peptides Proteins Radius Solvents

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Publication 2007
Ampicillin Buffers Cells Cloning Vectors DNA, Complementary enhanced green fluorescent protein Imidazoles Medical Devices Polymerase Chain Reaction Proteins Sepharose Tromethamine
To simplify this study, all characterized AFEX pretreatment-derived biomass decomposition products were divided into five groups (Table 4): 1) nitrogenous compounds, 2) furans, 3) aliphatic acids, 4) aromatic compounds, and 5) carbohydrates.

Plant cell wall-derived decomposition products and water-soluble extractives present in AFEX-CS hydrolysate (ACH)

CategoryCompoundConcentration (mg/L)
Nitrogenous compoundsFeruloyl amide1065
p-Coumaroyl amide886
Acetamide5674
2-Methylpyrazine10
2,5-Dimethylpyrazine1
2,6-Dimethylpyrazine4
2,4-Dimethyl-1 H-imidazole24
4-Methyl-1 H-imidazole95
Furan5-Hydroxymethyl furfural145
Aliphatic acidsMalonic acid33
Lactic acid181
cis-Aconitic acid111
Succinic acid60
Fumaric acid30
trans-Aconitic acid329
Levulinic acid2.5
Itaconic acid8.2
Acetic acid1958
Formic acid517
Aromatic compoundsVanillic acid15
Syringic acid15
Benzoic acid59
p-Coumaric acid345
Ferulic acid137
Cinnamic acid14
Caffeic acid2
Vanillin20
Syringaldehyde29.5
4-Hydroxybenzaldehyde24
4-Hydroxyacetophenone3.4
CarbohydratesGlucose60 g/L
Xylose26 g/L
Arabinose5 g/L
Gluco-oligomers12 g/L
Xylo-oligomers18 g/L

The concentration of nitrogenous compounds and furan were calculated from the content of the analyte in dry pretreated biomass [15 (link)] based on 18% solids loading (w/v) assuming 100% solubilization into the liquid phase.

The effect of these five groups of compounds on xylose fermentation was tested individually and in combination (five groups in combination) in order to investigate their synergistic inhibitory effect. The fermentations were conducted in SM supplemented with 60 g/L glucose and 26 g/L xylose. The decomposition products in each group and their concentrations are given in Table 2, and matched their absolute abundance as found in 6% glucan loading-based ACHs. To make stock solutions of decomposition products, all compounds were dissolved in water according to the categories of aliphatic acids, aromatic acids, aromatic aldehyde/ketones, furans, imidazoles, and pyrazines at 50-fold higher concentrations and the stock solutions were sterile filtered prior to their addition into the SM. Ferulic acid, p-coumaric acid, amides, and carbohydrates were directly added to the fermentation media at the desired concentrations (Table 2) due to their lower solubility in water. Fermentations of SM without any decomposition products (blank) and ACHs were used as negative and positive controls, respectively. The ACH was adjusted to pH 5.5 before inoculum addition.
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Publication 2015
Ache Acids Aconitum Aldehydes Aliphatic Acids Amides Carbohydrates Cell Wall Compounds, Nitrogen Fermentation ferulic acid furan Furans Glucans Glucose Imidazoles Ketones Methyl-gag Psychological Inhibition Pyrazines Sterility, Reproductive trans-3-(4'-hydroxyphenyl)-2-propenoic acid Xylose
pETDUET-1 DNA (Cat. 71146-3) vector was obtained from Novagen (Merck Biosciences Division, Darmstadt, Germany). The full-length, 1647 bp long, wildtype Human TLK1B gene was obtained through a custom gene synthesis service from GeneScript Biotech Corporation, Nanjing, China. High-Fidelity (HF®) Restriction Endonucleases (BamHI, EcoRI, MfeI and XhoI), CutSmart® Buffer, T4 DNA Ligase and T4 DNA Ligase Reaction Buffer for the cloning procedures were purchased from New England Biolabs (Ipswich, MA, USA). Plasmid DNA Purification Kit and QIAquick® Gel Extraction Kit were purchased from Qiagen (Hilden, Germany). Escherichia coli DH5α (Cat. 18265-017) competent cells were purchased from Invitrogen Corporation (Carlsbad, CA, USA) and Rosetta Gami 2 (DE3) pLysS (Cat. 71352) competent cells were purchased from Novagen (Merck Biosciences Division, Darmstadt, Germany). Ampicillin, Chloramphenicol, Isopropyl-β-D-1-thiogalactopyranoside (IPTG), Luria-Bertani (LB) broth, Luria-Bertani (LB) agar, Trizma® (Tris base), Sodium Chloride (NaCl), Glycerol, Triton-X l00, Tween-20, Imidazole, Tris (2-Carboxyethyl) Phosphine Hydrochloride (TCEP), Acrylamide, N,N′-Methylenebisacrylamide, Tetramethylethylenediamine (TEMED), Magnesium chloride, Ammonium Per Sulphate (APS), Sodium Dodecyl Sulphate (SDS), β-Mercaptoethanol (BME), Bromophenol Blue, Coomassie Brilliant Blue R-250, Non-Fat Milk, Ponceau S, Bovine Serum Albumin (BSA) and Nuclease-Free water were purchased from Sigma-Aldrich (Darmstadt, Germany). Complete EDTA-Free Protease Inhibitor tablets (Cat. 04693132001) were obtained from Roche (Basel, Switzerland). Nuvia Immobilized Metal Affinity Chromatography (IMAC) Resin charged with Ni2+, Econo-Column® Chromatography Columns and Clarity ECL Western Blotting Substrate were purchased from Bio-Rad Laboratories (Hercules, CA, USA). HiLoad 16/600 Superdex 75 pg gel filtration chromatography column was purchased from GE Healthcare (Chicago, Illinois, USA). Amicon Ultra concentrator with a 10 kDa cut-off filter was obtained from Merck Millipore (Darmstadt, Germany). Immun-Blot PVDF Western Blotting Membrane was purchased from Bio-Rad Laboratories (Hercules, CA, USA). His-Tag (D3I10) XP® Rabbit Monoclonal Antibody (Cat. 12698) and Anti-Rabbit IgG HRP-linked Secondary Antibody (Cat. 7074) were obtained from Cell Signaling Technology (MA, USA). ADP-Glo Kinase Assay Kit was purchased from Promega Corporation (Madison, WI, USA). Recombinant ASF1a substrate (Cat. PRO-682) for the kinase assay was purchased from ProSpec Technogene Ltd., Ness-Ziona, Israel.
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Publication 2018
2-Mercaptoethanol Acrylamide Agar Ampicillin Anabolism Antibodies, Anti-Idiotypic ATP Synthetase Complexes Biological Assay Bromphenol Blue Buffers Cells Chloramphenicol Chromatography Chromatography, Affinity Cloning Vectors Coomassie brilliant blue R Deoxyribonuclease EcoRI DNA Restriction Enzymes Edetic Acid Escherichia coli Gel Chromatography Glycerin IGG-horseradish peroxidase Imidazoles Isopropyl Thiogalactoside Magnesium Chloride Metals Milk, Cow's Monoclonal Antibodies N,N'-methylenebisacrylamide NES protein, human phosphine Phosphotransferases Plasmids polyvinylidene fluoride ponceau S Promega Prospec Protease Inhibitors Rabbits Resins, Plant Serum Albumin, Bovine Service, Genetic Sodium Chloride Sulfate, Ammonium Sulfate, Sodium Dodecyl T4 DNA Ligase tetramethylethylenediamine Tissue, Membrane tris(2-carboxyethyl)phosphine Trizma Tromethamine Tween 20 Western Blot
A SMILES [25 ] represents a molecule as a sequence of characters corresponding to atoms as well as special characters denoting opening and closure of rings and branches. The SMILES is, in most cases, tokenized based on a single character, except for atom types which comprise two characters such as “Cl” and “Br” and special environments denoted by square brackets (e.g [nH]), where they are considered as one token. This method of tokenization resulted in 86 tokens present in the training data. Figure 3 exemplifies how a chemical structure is translated to both the SMILES and one-hot encoded representations.

Three representations of 4-(chloromethyl)-1H-imidazole. Depiction of a one-hot representation derived from the SMILES of a molecule. Here a reduced vocabulary is shown, while in practice a much larger vocabulary that covers all tokens present in the training data is used

There are many different ways to represent a single molecule using SMILES. Algorithms that always represent a certain molecule with the same SMILES are referred to as canonicalization algorithms [26 (link)]. However, different implementations of the algorithms can still produce different SMILES.
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Publication 2017
Character Imidazoles

Most recents protocols related to «Imidazoles»

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Example 45

2-(4-(6-amino-2-((4-cyano-2-fluorobenzyl)oxy)pyrimidin-4-yl)-2,5-difluorobenzyl)-1-(2-methoxyethyl)-1H-benzo[d]imidazole-6-carboxylic acid was prepared in a manner as described in Procedure 10. 1H NMR (400 MHz, DMSO-d6) δ 8.25 (s, 1H), 7.92 (d, J=10.0 Hz, 1H), 7.87-7.78 (m, 2H), 7.74 (s, 2H), 7.62 (d, J=8.5 Hz, 1H), 7.38 (dd, J=11.7, 6.0 Hz, 1H), 7.26 (s, 2H), 6.71 (d, J=1.4 Hz, 1H), 5.50 (s, 2H), 4.61 (t, J=5.1 Hz, 2H), 4.47 (s, 2H), 3.68 (t, J=5.1 Hz, 2H), 3.20 (s, 3H).

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Patent 2024
1H NMR Carboxylic Acids Imidazoles Sulfoxide, Dimethyl

Example 66

[Figure (not displayed)]

To a solution of 7,8-dichloro-N-(morpholin-2-ylmethyl)-4-(1H-pyrazol-4-yl)quinolin-2-amine (20 mg, 0.053 mmol) in THF (1 mL) was added triethylamine (0.074 mL, 0.53 mmol) and acetyl chloride (0.0057 mL, 0.08 mmol) at 0° C. After 1 h at rt, the reaction was quenched by MeOH (0.1 mL). After evaporation, the crude was purified directly by column chromatography on silica gel to give 1-(2-(((7,8-dichloro-4-(1H-pyrazol-4-yl)quinolin-2-yl)amino)methyl)morpholino)ethan-1-one as a solid (7 mg) (MS: [M+1]+ 420.0).

The following compounds are prepared essentially by the same method described above to prepare I-221.

MS
I-#Starting MaterialStructure[M + 1]+
I-400[Figure (not displayed)]
[Figure (not displayed)]
478.1
I-222[Figure (not displayed)]
[Figure (not displayed)]
436.1

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Patent 2024
8-methylquinoline acetyl chloride Amines Anabolism Chromatography Imidazoles Morpholinos pyrazole Silica Gel triethylamine

Example 85

[Figure (not displayed)]

To a mixture of (S)-1-(7,8-dichloro-4-(1H-imidazol-1-yl)quinolin-2-yl)pyrrolidine-2-carboxamide (100 mg, 0.27 mmol) and DCE (2 mL) was added (COCl)2(35 uL, 0.4 mmol) at r.t. The mixture was stirred at 70° C. overnight and then TMSN3 (1 mL) was added. The solution was stirred at 80° C. for 2 days. After cooling down to r.t., the crude was purified directly by a column chromatography on silica gel to give the titled product as a solid (MS: [M+1]+ 417.1).

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Patent 2024
Anabolism Chromatography Imidazoles pyrrolidine Silica Gel

Example 72

1-((3R,4S)-4-((tert-butoxycarbonyl)amino)tetrahydrofuran-3-yl)-2-(4-(6-((4-cyano-2-fluorobenzyl)oxy)pyridin-2-yl)-2,5-difluorobenzyl)-1H-benzo[d]imidazole-6-carboxylic acid (as a racemic mixture of enantiomers) was prepared in a manner as described in Procedure 22. 1H NMR (400 MHz, DMSO-d6) δ 8.44 (s, 1H), 7.94-7.86 (m, 2H), 7.81-7.70 (m, 4H), 7.54 (dd, J=11.0, 7.7 Hz, 2H), 7.30 (dd, J=11.2, 6.4 Hz, 1H), 7.09 (s, 1H), 7.00 (d, J=8.3 Hz, 1H), 5.62 (s, 2H), 5.40 (s, 1H), 4.63-4.43 (m, 4H), 4.30 (d, J=17.0 Hz, 1H), 4.20 (dd, J=10.9, 7.0 Hz, 1H), 4.08-3.89 (m, 3H), 1.12 (s, 9H).

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Patent 2024
1H NMR Carboxylic Acids Imidazoles Sulfoxide, Dimethyl TERT protein, human tetrahydrofuran

Example 33

[Figure (not displayed)]

Step 1: 1-(7,8-Dichloro-4-(1H-imidazol-1-yl)quinolin-2-yl)piperidin-3-ol was the same as that for compound I-353 (MS: [M+1]+ 263).

Step 2: (S)-1-(7,8-dichloro-4-(1H-imidazol-1-yl)quinolin-2-yl)piperidin-3-yl sulfamate. To a vial were added 1-(7,8-dichloro-4-(1H-imidazol-1-yl)quinolin-2-yl)piperidin-3-ol (20 mg, 0.0551 mmol), DMF (0.3 mL) and TEA (50 μl, 0.364 mmol). A stock solution of sulfamoyl chloride in DMF (38 mg/100 μl, 0.33 mmol) was added. The resulting reaction mixture was stirred at 100° C. for 6 hrs and cooled to room temperature followed by adding 4 mL of water. The mixture was centrifuged and the residue was purified by PTLC (30% MeOH/DCM) to afford the desired product as white solid (1 mg) (MS: [M+1]+ 442).

The following compounds are prepared essentially by the same methods as for I-223.

MS
I-#Starting MaterialStructure[M + 1]+
I-118[Figure (not displayed)]
[Figure (not displayed)]
[Figure (not displayed)]
456
I-96[Figure (not displayed)]
[Figure (not displayed)]
[Figure (not displayed)]
458

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Patent 2024
Anabolism Chlorides Imidazoles sulfamate

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Imidazole is a heterocyclic organic compound with the chemical formula C3H4N2. It is a five-membered aromatic ring containing two nitrogen atoms. Imidazole serves as a core functional group in various chemical and biological applications.
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NaCl is a chemical compound commonly known as sodium chloride. It is a white, crystalline solid that is widely used in various industries, including pharmaceutical and laboratory settings. NaCl's core function is to serve as a basic, inorganic salt that can be used for a variety of applications in the lab environment.
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Imidazole is a chemical compound used in various laboratory applications. It is a heterocyclic aromatic organic compound consisting of a five-membered ring with two nitrogen atoms. Imidazole serves as a key functional group in many biomolecules and is commonly used as a buffer, ligand, and building block in organic synthesis.
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Ni-NTA agarose is a solid-phase affinity chromatography resin designed for the purification of recombinant proteins containing a histidine-tag. It consists of nickel-nitrilotriacetic acid (Ni-NTA) coupled to agarose beads, which selectively bind to the histidine-tagged proteins.
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IPTG (Isopropyl β-D-1-thiogalactopyranoside) is a synthetic chemical compound commonly used in molecular biology and genetic engineering laboratories. It is a molecular mimic of allolactose, a natural inducer of the lac operon in Escherichia coli. IPTG is used to induce the expression of genes that are under the control of the lac promoter, allowing for the production of specific proteins in bacterial cultures.
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Dithiothreitol (DTT) is a reducing agent commonly used in biochemical and molecular biology applications. It is a small, water-soluble compound that helps maintain reducing conditions and prevent oxidation of sulfhydryl groups in proteins and other biomolecules.
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MgCl2 is a chemical compound used in various laboratory applications. It is a white, crystalline solid that is highly soluble in water. MgCl2 is commonly used as a source of magnesium ions in chemical reactions and analyses.
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Bovine serum albumin (BSA) is a common laboratory reagent derived from bovine blood plasma. It is a protein that serves as a stabilizer and blocking agent in various biochemical and immunological applications. BSA is widely used to maintain the activity and solubility of enzymes, proteins, and other biomolecules in experimental settings.
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Ni-NTA resin is a nickel-nitrilotriacetic acid (Ni-NTA) affinity chromatography medium used for the purification of recombinant proteins containing a histidine-tag (His-tag) sequence. The resin binds to the His-tag and allows the target protein to be isolated from complex mixtures.
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EDTA is a chemical compound commonly used as a laboratory reagent. Its primary function is as a chelating agent, capable of binding to metal ions and forming stable complexes. EDTA is widely used in various analytical and experimental procedures to control the availability of metal ions in solutions.

More about "Imidazoles"

Imidazoles are a versatile class of five-membered heterocyclic organic compounds that contain two nitrogen atoms at positions 1 and 3 within the ring.
These nitrogen-rich heterocycles have garnered significant attention in the fields of medicinal chemistry and pharmaceutical development due to their diverse biological activities, including antifungal, anti-inflammatory, and anticancer properties.
Imidazole-based compounds are also important intermediates in the synthesis of various pharmaceuticals and agrochemicals, making them indispensable in the chemical industry.
Researchers can streamline their imidazole-related investigations by utilizing AI-powered platforms like PubCompare.ai, which helps locate the best protocols and products, explore relevant literature, preprints, and patents, and optimize experiments through intelligent comparisons to improve reproducibility.
Beyond their pharmaceutical applications, imidazoles have found use in a variety of other areas, such as in the synthesis of dyes, pigments, and corrosion inhibitors.
The versatility of this heterocyclic moiety is further exemplified by its presence in the structure of histidine, an essential amino acid that plays crucial roles in protein structure and function.
Researchers exploring imidazole-based compounds may also encounter related chemical entities, such as sodium chloride (NaCl), Ni-NTA agarose, isopropyl β-D-1-thiogalactopyranoside (IPTG), dithiothreitol (DTT), magnesium chloride (MgCl2), bovine serum albumin (BSA), Ni-NTA resin, and ethylenediaminetetraacetic acid (EDTA), which are commonly used in various experimental procedures and purification techniques.
By leveraging the insights and tools provided by platforms like PubCompare.ai, scientists can streamline their imidazole research, optimize their experiments, and ultimately accelerate the development of novel imidazole-based therapeutics and other applications.