The largest database of trusted experimental protocols
> Chemicals & Drugs > Inorganic Chemical > Hydroxyl Radical

Hydroxyl Radical

Hydroxyl radicals are highly reactive oxygen species that play a crucial role in various chemical and biological processes.
These free radicals are formed through the homolytic cleavage of the oxygen-hydrogen bond in water molecules and can react with a wide range of organic and inorganic compounds.
Hydroxyl radicals are key intermediates in oxidation reactions and have been studied extensively in fields such as environmental chemistry, atmospheric science, and biomedicine.
Researchers investigating hydroxyl radical-mediated processes can leverage the power of PubCompare.ai, an AI-driven platform that helps optimize research by identifying the most reliable protocols from literature, preprints, and patents.
With detailed comparisons, scientists can pinpoit the best methods and products to enhance reproducibility and accuracy in their hydroxyl radical studies, experience the future of research optimization today.

Most cited protocols related to «Hydroxyl Radical»

Protocol full text hidden due to copyright restrictions

Open the protocol to access the free full text link

Publication 2009
acryloyl chloride Anabolism Ethyl Ether Hydroxyl Radical Molar poly(ethylene glycol)diacrylate Toluene triethylamine
To maximize transferability of the parameters, multidimensional structure scans were employed to generate conformational diversity. For smaller side chains, grid scans in dihedral space were used to generate side chain variety, including both α and β backbone conformations for each side chain rotamer. Grid scans were generated for Val in one dimension, as it only has χ1, at an interval of 10°. Grids were generated for Asp, Asn, Cys, Phe, His (δ-, ɛ-, and doubly-protonated), Ile, Leu, Ser, Thr, and Trp in two dimensions, as they have χ1 and χ2, at intervals of 20°, yielding 324 structures per amino acid.
We were unable to exhaustively explore side chain conformational space side chains with more than two rotatable bonds. Tyrosine has 3 rotatable χ bonds, but dihedral space is reduced as 180° rotation of either the phenol (χ2) or of the hydroxyl produce the same effect when accounting for symmetry of the ring. We therefore fully scanned each tyrosine dihedral when the other two were at a stable rotamer defined as any instance of that value in the rotamer library for this amino acid, rounded to the nearest 10° and limiting χ2 to (−90°, 90°] to account for symmetry. Stable rotamers for the hydroxyl, not in the rotamer library, were inferred from the QM energy profiles discussed above. Stable rotamers were 180° or ±60° for χ1, ±30° or 90° for χ2, and 0° or 180° for the hydroxyl. Conformations were generated using a full scan for each dihedral (at 20° increments), repeated for every combination of stable rotamer values for the other two dihedrals. As protonated aspartate has nearly the same dihedrals as Tyr (χ1, χ2 and hydroxyl), it was scanned in the same manner, but without χ2 restriction because aspartate does not have the same symmetry properties.
Cysteine presents a special case, as it can form disulfide bonds that bridge two amino acids. In addition to developing parameters for reduced Cys (no disulfide), a pair of Cys dipeptides with a disulfide bond was employed to scan the S-S energy profile. However, a disulfide between CysA and CysB has a total of five dihedrals: χ1A, χ2A, χSS, χ2B, and χ1B. As full sampling across five dihedrals is clearly intractable, conformation space was reduced by applying the same χ1 / χ2 values to both dipeptides. Using this symmetry, a two-dimensional scan was performed for all χ1 / χ2 combinations using 20° spacing; this scan was repeated with χSS restrained to 180°, ±60°, or ±90° (five 2D scans). Separately, the χSS profile was scanned with 20° spacing using χ1 of 180° or ±60° and χ2 of 180° or ±60° (nine 1D scans total). As with the other amino acids, the entire procedure was repeated with the backbone in α and β conformations; here, both dipeptides adopted the same backbone conformation.
The remaining side chains, Arg+, Gln, Glu (protonated), Glu,Lys+, and Met, have at least three side chain dihedrals (Table S1). Rather than performing a grid search, MD simulations were used to generate diverse conformations of these side chains. Each dipeptide was simulated twice, with α or β backbone restraints, for 100 ns each. To overcome kinetic traps, these simulations were performed at 500 K and the dielectric was set to 4r. Next, a diverse subset was generated by mapping each conformation to a multidimensional grid spaced 10° in each χ. The five lowest energy conformations at each grid point were saved. From each simulation grid, five hundred structures were randomly selected (comparable to the number generated by the grid procedure described above for Tyr). Because the longer, more flexible side chains of these amino acids can adopt conformations with strong interactions between backbone and side chain, conformations where we suspected the in vacuo MM description may produce fitting artifacts were excluded, using electrostatic and distance cutoffs defined in the Supporting Information.
Publication 2015
Amino Acids Aspartate Dipeptides Disulfides DNA Library Electrostatics Hydroxyl Radical Kinetics Phenol Radionuclide Imaging Tyrosine Vertebral Column
We genetically engineered S. cerevisiae to contain a cysteine at position 47 in histone H4. Cells grown to mid-log phase were harvested, permeabilized and labeled with N(1,10 phenanthroline- 5-yl) iodoacetamide. The label covalently bound to the cysteine and allowed for copper chelation. Copper chloride, mercaptoproprionic acid and hydrogen peroxide were added sequentially creating hydroxyl radicals that cleaved the nucleosomal DNA at sites flanking the center. After the mapping reaction, the genomic DNA was purified from the cells and ran on an agarose gel. The shortest molecular weight DNA fragment (~150-200bp) was purified and prepared for highthroughput parallel sequencing.
Publication 2012
Acids Cells Chlorides Copper Cysteine Genome Histone H4 Hydroxyl Radical Iodoacetamide Nucleosomes Peroxide, Hydrogen Phenanthrolines Sepharose
We genetically engineered S. cerevisiae to contain a cysteine at position 47 in histone H4. Cells grown to mid-log phase were harvested, permeabilized and labeled with N(1,10 phenanthroline- 5-yl) iodoacetamide. The label covalently bound to the cysteine and allowed for copper chelation. Copper chloride, mercaptoproprionic acid and hydrogen peroxide were added sequentially creating hydroxyl radicals that cleaved the nucleosomal DNA at sites flanking the center. After the mapping reaction, the genomic DNA was purified from the cells and ran on an agarose gel. The shortest molecular weight DNA fragment (~150-200bp) was purified and prepared for highthroughput parallel sequencing.
Publication 2012
Acids Cells Chlorides Copper Cysteine Genome Histone H4 Hydroxyl Radical Iodoacetamide Nucleosomes Peroxide, Hydrogen Phenanthrolines Sepharose
Full length HIV-1 genomic RNA was gently purified from NL4-3 virions (Genbank AF324493). The RNA was equilibrated in a native buffer [50 mM Hepes (pH 8.0), 200 mM potassium acetate (pH 8.0), 3 mM MgCl2] at 37 °C for 15 min and treated with 1M710 (link). Sites of 2′-hydroxyl modification were identified over read lengths spanning several hundred nucleotides using 31 primer extension reactions resolved by fluorescence-detected capillary electrophoresis6 (link),11 (link). Pairing probabilities were determined using RNA-Decoder13 (link) and secondary structure models were developed by incorporating SHAPE reactivities as a pseudo-free energy change term, in conjunction with nearest-neighbor parameters, in an accurate thermodynamics-based prediction algorithm22 (link),23 (link).
Publication 2009
Buffers Capillaries Fluorescence Genome HEPES HIV-1 Hydroxyl Radical Magnesium Chloride Nucleotides Oligonucleotide Primers Potassium Acetate Virion

Most recents protocols related to «Hydroxyl Radical»

Example 4

Octadecanoate Functionalized Core (IMS 018 H)

To a round bottom flask was added one or more of the following “core” compounds: tripentaerythritol (“H”) made from the above cores. These were dissolved in tetrahydrofuran. 1.1 molar equivalents (per —OH of the hydroxyl terminated cores or dendrimers) of Octadecanoic Acid were added to the solution of cores. To these reagents were added 1.2 molar equivalents (per —OH of the hydroxyl terminated cores or dendrimers) of dicyclohexylcarbodiimide and 0.1 molar equivalents (per —OH of hydroxyl-terminated core or of dendrimer) of 4-dimethylaminopyridine (DMAP).

The reaction mixture was stirred vigorously for approximately 12 hours at standard temperature and pressure. The reaction was monitored by MALDI-TOF MS to determine completion of the reaction for each of the cores present in the reaction. After complete esterification is observed by MALDI-TOF MS, the flask contents were transferred to a separatory funnel, diluted with dichloromethane, extracted twice with 1M aqueous NaHSO4 (sodium bisulfate) and extracted twice with 1M aqueous NaHCO3 (sodium bicarbonate). The organic layer was reduced in vacuo to concentrate the sample. A MALDI-TOF MS spectra of the purified product confirmed the purity of the mixture of esterified products and is shown in FIG. 11.

FIG. 11 shows MALDI-TOF MS data for IMS 018 H, the product of octadecanoic acid functionalization of core H (IMS018H).

Full text: Click here
Patent 2024
4-dimethylaminopyridine Bicarbonate, Sodium Chromatography Dendrimers Dicyclohexylcarbodiimide Esterification Hydroxyl Radical Methylene Chloride Molar Pressure sodium bisulfate Spectrometry Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization Stearates stearic acid tetrahydrofuran
Not available on PMC !

Example 125

[Figure (not displayed)]

Methyl 4-((5-(benzyloxy)-2-methoxyphenyl)(ethyl)amino)butanoate (184). 5-(Benzyloxy)-N-ethyl-2-methoxyaniline (146) (0.681 g, 2.65 mmol), DIEA (0.92 mL, 5.3 mmol), and methyl 4-iodobutyrate (0.72 mL, 5.3 mmol) in DMF (5 mL) were stirred at 70° C. for 5 days. The reaction mixture was cooled to rt, diluted with EtOAc (60 mL), washed with water (4×50 mL), brine (75 mL), dried over Na2SO4 and evaporated. The residue was purified by chromatography on a silica gel column (2.5×30 cm bed, packed with CHCl3), eluant: 5% MeOH in CHCl3 to get compound 184 (0.72 g, 76%) as a dark amber oil.

Methyl 4-(ethyl(5-hydroxy-2-methoxyphenyl)amino)butanoate (186). Ester 184 (0.72 g, 2.0 mmol) was stirred under reflux with 6 mL of water and 6 mL of conc HCl for 1.5 hrs and then evaporated to dryness to give acid 185 as a brown gum. The crude acid was dissolved in 50 mL of methanol containing 1 drop (cat.) of methanesulfonic acid ant the solution was kept for 2 hrs at rt. After that the mixture was concentrated in vacuum and the residue was mixed with 20 mL of saturated NaHCO3. The product was extracted with EtOAc (3×40 mL). The extract was washed with brine (40 mL), dried over Na2SO4 and evaporated. The residue was purified by chromatography on a silica gel column (2.5×30 cm bed, packed with CHCl3), eluant: 5% MeOH in CHCl3 to get compound 186 (0.444 g, 83%) as a brown oil.

N-(6-(dimethylamino)-9-(4-(ethyl(4-methoxy-4-oxobutyl)amino)-2-hydroxy-5-methoxyphenyl)-3H-xanthen-3-ylidene)-N-methylmethanaminium chloride (187). To a stirred suspension of tetramethylrhodamine ketone 101 (0.234 g, 0.830 mmol) in 10 mL of dry chloroform was added oxalyl chloride (72 μL, 0.82 mmol) upon cooling to 0-5° C. The resulting red solution was stirred for 0.5 h at 5° C., and the solution of compound 186 (0.222 g, 0.831 mmol) in dry chloroform (5 mL) was introduced. The reaction was allowed to heat to rt, stirred for 72 h, diluted with CHCl3 (100 mL and washed with sat. NaHCO3 solution (2×30 mL) The organic layer was extracted with 5% HCl (3×25 mL). The combined acid extract was washed with CHCl3 (2×15 mL; discarded), saturated with sodium acetate and extracted with CHCl3 (5×30 mL). The extract was washed with brine (50 mL), dried over Na2SO4 and evaporated. The crude product was purified by chromatography on silica gel column (2×50 cm bed, packed with CHCl3/MeOH/AcOH/H2O (100:20:5:1)), eluant: CHCl3/MeOH/AcOH/H2O (100:20:5:1) to give the product 187 (0.138 g, 29%) as a purple solid.

4-((4-(6-(dimethylamino)-3-(dimethyliminio)-3H-xanthen-9-yl)-5-hydroxy-2-methoxyphenyl)(ethyl)amino)butanoate (188). Methyl ester 187 (0.136 g, 0.240 mmol) was dissolved in 5 mL of 1M KOH (5 mmol). The reaction mixture was kept at rt for 1.5 hrs and the acetic acid (1 mL) was added. The mixture was extracted with CHCl3 (4×30 mL), and combined extract was washed with brine (20 mL), filtered through the paper filter and. The crude product was purified by chromatography on silica gel column (2×50 cm bed, packed with MeCN/H2O (4:1)), eluant: MeCN/H2O/AcOH/(4:1:1) to give the product 188 (0.069 g, 98%) as a purple solid.

N-(6-(dimethylamino)-9-(4-((4-(2,5-dioxopyrrolidin-1-yloxy)-4-oxobutyl)(ethyl)amino)-2-hydroxy-5-methoxyphenyl)-3H-xanthen-3-ylidene)-N-methylmethanaminium chloride (189). To a solution of the acid 188 (69 mg, 0.12 mmol) in DMF (2 mL) and DIEA (58 μL, 0.33 mmol) was added N-hydroxysuccinimide trifluoroacetate (70 mg, 0.33 mmol). The reaction mixture was stirred for 30 min, diluted with chloroform (100 mL) and washed with water (5×50 mL), brine (50 mL), filtered through paper and concentrated in vacuum. The crude product was purified by precipitation from CHCl3 solution (5 mL) with ether (20 mL) to give compound 189 (55 mg, 67%) as a purple powder.

Full text: Click here
Patent 2024
Acetic Acid Acids Amber Anabolism Bicarbonate, Sodium brine Chlorides Chloroform Chromatography Esters Ethyl Ether Hydroxyl Radical Ketones methanesulfonic acid Methanol N,N-diisopropylethylamine N-hydroxysuccinimide oxalyl chloride Powder Silica Gel Sodium Acetate tetramethylrhodamine Trifluoroacetate Vacuum
Not available on PMC !

Example 8

Cyclohexene (1a) and polar organic solvent (as mentioned in Table 1) in (1:2 to 1:10 weight ratio with respect to the substrate) was taken in to a 60 ml vessel. Further, the hybrid photocatalyst was added and the resulting mixture was saturated with CO2 by purging at 1 atm pressure. The reaction vessel was sealed and irradiated with 20 W LED light (Model No. HP-FL-20 W-F, Hope LED Opto-Electric CO., Ltd) for 24 h. The conversion of the olefin and selectivity of the α,β-unsaturated hydroxyl or carbonyl compound as determined by GC-FID and GC-MS is mentioned in the Table 1 (entry 8-13).

Full text: Click here
Patent 2024
Alkenes Blood Vessel cyclohexene Electricity Gas Chromatography-Mass Spectrometry Genetic Selection Hybrids Hydroxyl Radical Light Pressure Solvents
Not available on PMC !

Example 3

Cyclohexene (1a) and polar organic solvent, preferably acetonitrile in (1:2 to 1:10 weight ratio with respect to the substrate) was taken in to a 60 ml vessel. Further, the bare graphene oxide as photocatalyst (1 to 10 mol % of the substrate) was added and the resulting mixture was saturated with CO2 by purging at 1 atm pressure. The reaction vessel was sealed and irradiated with 20 W LED light (Model No. HP-FL-20 W-F, Hope LED Opto-Electric CO., Ltd) for 24 h. The intensity of the LED light at the reaction flask was measured to be 86 W/m2 by intensity meter. The conversion of the olefin was examined by GC-FID based on the unreacted substrate. The selectivity of the α,β-unsaturated hydroxyl or carbonyl compounds was determined by GC-MS. The conversion of olefin and the selectivity towards the corresponding α,β-unsaturated hydroxyl and ketone is given in the Table 1, entry 3.

Full text: Click here
Patent 2024
acetonitrile Alkenes Blood Vessel cyclohexene cyclohexene oxide Electricity Gas Chromatography-Mass Spectrometry Genetic Selection Graphene graphene oxide Hydroxyl Radical Ketones Light Pressure Solvents

Example 6

White solid, 5.2 g, two-step yield is 70.3%. 1H NMR (400 MHz, CD3OD) δ 5.08 (t, J=6.8 Hz, 1H, H-24), 4.39 (d, J=6.2 Hz, 1H, H-1′), 3.82 (s, 1H), 3.71 (dd, J=10.6, 6.6 Hz, 1H), 3.64 (dd, J=10.8, 6.4 Hz, 1H), 3.46-3.42 (m, 3H), 3.35 (d, J=9.4 Hz, 1H), 3.14 (dd, J=10.7, 4.5 Hz, 1H), 2.52-2.40 (m, 2H), 2.11 (dd, J=12.7, 2.3 Hz, 1H), 1.66 (s, 4H), 1.62 (s, 3H), 1.27 (s, 3H), 1.11 (s, 3H), 0.98 (s, 3H), 0.97 (s, 3H), 0.80 (s, 3H), 0.74 (s, 3H); 13C NMR (150 MHz, CD3OD) δ 215.6, 131.9, 126.0, 98.8, 82.4, 79.3, 76.1, 75.6, 73.1, 70.1, 62.1, 57.5, 57.2, 57.1, 56.4, 43.0, 41.9, 40.7, 40.6, 40.0, 39.9, 38.8, 35.6, 33.0, 28.6, 27.9, 25.9, 24.9, 24.7, 22.9, 19.5, 17.8, 17.1, 16.7, 16.3, 16.0.

MALDI-HRMS calcd for C36H60NaO8 [M+Na]+643.4180, found 643.4190.

Full text: Click here
Patent 2024
1H NMR Carbon-13 Magnetic Resonance Spectroscopy dammarane Hydroxyl Radical Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization

Top products related to «Hydroxyl Radical»

Sourced in United States, Germany, United Kingdom, China, Italy, Sao Tome and Principe, France, Macao, India, Canada, Switzerland, Japan, Australia, Spain, Poland, Belgium, Brazil, Czechia, Portugal, Austria, Denmark, Israel, Sweden, Ireland, Hungary, Mexico, Netherlands, Singapore, Indonesia, Slovakia, Cameroon, Norway, Thailand, Chile, Finland, Malaysia, Latvia, New Zealand, Hong Kong, Pakistan, Uruguay, Bangladesh
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.
Sourced in United States, China, United Kingdom, Germany, Australia, Japan, Canada, Italy, France, Switzerland, New Zealand, Brazil, Belgium, India, Spain, Israel, Austria, Poland, Ireland, Sweden, Macao, Netherlands, Denmark, Cameroon, Singapore, Portugal, Argentina, Holy See (Vatican City State), Morocco, Uruguay, Mexico, Thailand, Sao Tome and Principe, Hungary, Panama, Hong Kong, Norway, United Arab Emirates, Czechia, Russian Federation, Chile, Moldova, Republic of, Gabon, Palestine, State of, Saudi Arabia, Senegal
Fetal Bovine Serum (FBS) is a cell culture supplement derived from the blood of bovine fetuses. FBS provides a source of proteins, growth factors, and other components that support the growth and maintenance of various cell types in in vitro cell culture applications.
Sourced in United States, Germany, Italy, India, China, Spain, Poland, France, United Kingdom, Australia, Brazil, Singapore, Switzerland, Hungary, Mexico, Japan, Denmark, Sao Tome and Principe, Chile, Malaysia, Argentina, Belgium, Cameroon, Canada, Ireland, Portugal, Israel, Romania, Czechia, Macao, Indonesia
DPPH is a chemical compound used as a free radical scavenger in various analytical techniques. It is commonly used to assess the antioxidant activity of substances. The core function of DPPH is to serve as a stable free radical that can be reduced, resulting in a color change that can be measured spectrophotometrically.
Sourced in United States, Germany, United Kingdom, Italy, France, Spain, Australia, Poland, Denmark, Japan, Ireland
H2DCFDA is a fluorescent probe used for the detection of reactive oxygen species (ROS) in biological samples. It is a non-fluorescent compound that becomes highly fluorescent upon oxidation by ROS. This property makes it useful for monitoring oxidative stress in cells.
Sourced in United States, Germany, Italy, Spain, France, India, China, Poland, Australia, United Kingdom, Sao Tome and Principe, Brazil, Chile, Ireland, Canada, Singapore, Switzerland, Malaysia, Portugal, Mexico, Hungary, New Zealand, Belgium, Czechia, Macao, Hong Kong, Sweden, Argentina, Cameroon, Japan, Slovakia, Serbia
Gallic acid is a naturally occurring organic compound that can be used as a laboratory reagent. It is a white to light tan crystalline solid with the chemical formula C6H2(OH)3COOH. Gallic acid is commonly used in various analytical and research applications.
Sourced in Germany, United States, India, United Kingdom, Italy, China, Spain, France, Australia, Canada, Poland, Switzerland, Singapore, Belgium, Sao Tome and Principe, Ireland, Sweden, Brazil, Israel, Mexico, Macao, Chile, Japan, Hungary, Malaysia, Denmark, Portugal, Indonesia, Netherlands, Czechia, Finland, Austria, Romania, Pakistan, Cameroon, Egypt, Greece, Bulgaria, Norway, Colombia, New Zealand, Lithuania
Sodium hydroxide is a chemical compound with the formula NaOH. It is a white, odorless, crystalline solid that is highly soluble in water and is a strong base. It is commonly used in various laboratory applications as a reagent.
Sourced in Germany, United States, Italy, India, United Kingdom, China, France, Poland, Spain, Switzerland, Australia, Canada, Sao Tome and Principe, Brazil, Ireland, Japan, Belgium, Portugal, Singapore, Macao, Malaysia, Czechia, Mexico, Indonesia, Chile, Denmark, Sweden, Bulgaria, Netherlands, Finland, Hungary, Austria, Israel, Norway, Egypt, Argentina, Greece, Kenya, Thailand, Pakistan
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.
Sourced in United States, Germany, United Kingdom, China, Italy, Japan, France, Sao Tome and Principe, Canada, Macao, Spain, Switzerland, Australia, India, Israel, Belgium, Poland, Sweden, Denmark, Ireland, Hungary, Netherlands, Czechia, Brazil, Austria, Singapore, Portugal, Panama, Chile, Senegal, Morocco, Slovenia, New Zealand, Finland, Thailand, Uruguay, Argentina, Saudi Arabia, Romania, Greece, Mexico
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.
Sourced in United States, Germany
Butylated hydroxyl toluene is a chemical compound used as a food preservative and antioxidant. It functions as a stabilizer in various products by preventing oxidation and retarding the development of rancidity, color changes, and flavor deterioration.
Sourced in Germany, United States, United Kingdom, Italy, India, France, China, Australia, Spain, Canada, Switzerland, Japan, Brazil, Poland, Sao Tome and Principe, Singapore, Chile, Malaysia, Belgium, Macao, Mexico, Ireland, Sweden, Indonesia, Pakistan, Romania, Czechia, Denmark, Hungary, Egypt, Israel, Portugal, Taiwan, Province of China, Austria, Thailand
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.

More about "Hydroxyl Radical"