Science topics: Organic Synthesis
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Organic Synthesis - Science topic

Procedures and advances in the organic synthesis of organic compounds
Questions related to Organic Synthesis
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Hi guys,
I'm dealing with the synthesis of 1,1,2,2-tetrakis(4-aminophenyl)ethene follows the method in the reported paper. In which they used tin powder and concentrated HCl as reagents.
But I only obtained very low yield of desired product, the crude NMR shows the conversion was only 26%. I wonder if there is a procedure to activate Tin powder before using it in reaction?
Please check the attached for the original paper.
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Dear Van-Sieu Luc, I have performed many McMurry Reactions however we used actvated Zn dust to reduce TiCl4 to Ti(0). Prior to reaction, we have purified commercial Zn dust as follows: Zn dust was quickly washed with distilled water containing few drops of conc. HCl (0.5-1% HCl can be used/ I think it's in Vogel's Practical Organic Chemistry book) to remove the oxide coatings in any. Then thoroughly washed with distilled water to make acid free and finally with acetone and dried under vaccum. It can be stored. This Zn dust can be used for reduction of TiCl4 to Ti (0) in anhydrous dimethoxymethane solvent under reflux under inert atmosphere for 4-5 hours. We used 0.025 gm atom of Zinc for reduction of 0.0126 moles of TiCl4 and this insitu generated Ti(0) was used for McMurry coupling of 0.003 mole of beta chloro-alpha,beta-unsaturated aldehydes. Yields varied in between 50-92 %. You are welcome to go through the paper "STEREOSELECTIVE SYNTHESIS OF 1,6-DICHLORO-1,3,5-HEXATRIENE DERIVATIVES BY MCMURRY COUPLING
OF beta-CHLOROACRYLALDEHYDE DERIVATIVES" Susmita Gupta, Gandhi K. Kar and Jayanta K. Ray, SYNTHETIC COMMUNICATIONS, 30( 13), 2393-2399 (2000).
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Working with these two reducing agent since a long time just wanted to know the advantage of one over another.
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Dear Siddhant Singh, in order to get an answer compare their 'standard reduction potential'. Please have a look at the following video. My Regards
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I have been trying to reduce the chemical above and have run into issues. When the product is formed, it is not volatile enough to boil out.
These methods below I have tried:
- Sn/MeOH + HCl
- SnCl2/EtOH
- Zn/AcOH
I am under the impression I can do a steam distillation, but the bp of the product is 238 degC. If anyone has any literature or advice on this, it would be greatly appreciated.
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Aniketh, This is not true. Chlorine is strongly accepted to the benzene ring.
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I recently purchased 3 bottles of dimethyl acetylenedicarboxylate from Sigma-Aldrich and decided to check the purity of the product using TLC. I found out that the chromatogram actually showed 2 spots, Rf 0.1 and 0.8. I believe the bottom spot is due to the decomposed product since it's the minor compound of the mixture. Any idea what this could be?
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I have the same problem as you
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I am doing the synthesis of tert-butyl 6-(3-hydroxy-propyl-methy-lamino)quinoline-4-carboxylate, using Cesium carbonate, BINAP, and Pd2(dba)3 and N-methyl-1,3-propanolamine in Toulene.
TLC using different solvents and ratios didn't work out even using column chromatography, so does anyone know how to purify my compound ?
to get rid of Cesium Carbonate, BINAP and Pd2dba3 ?
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Thanks a lot @Vladimir Khlebnikov
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How do I remove succinimide from a water soluble product without column chromatography? Any tips for extractions etc.?
Cheers,
Andreas
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The question is if product is insoluble in DMF/ DMSO, how to remove Succinimide from the reaction mass.
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How to remove N- methyl morpholine from the coupling reaction for getting a pure compound?
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I am wondering if anyone has any insight as to the reactivity of malonyl dichloride in the presence of pyridine and mono-boc-protected phenylenediamine? I start the synthesis with the boc-protected amine and pyridine in a dry THF solution. a diluted solution of malonyl dichloride is then added drop-wise ca. 1 drop/sec over 40 min. As soon as I start adding the malonyl dichloride, the solution starts turning pink. If the solution is left over 2 days at RT, it turns blue. I tried to adjust the temp (-20degC), time (30 min and monitor by TLC), but, somehow, it keeps turning pink/dark red.
If the reaction is replicated with dimethyl malonyl dichloride, no pink solution is observed, and the reaction proceeds towards products, with high yields.
Does anyone have experience with malonyl dichloride?
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The difference between malonyl and 2,2-dimethylmalonyl dichlorides is that the former possesses hydrogens in the alfa position to the carbonyl group. What often happens with acyl chlorides of this sort in the presence of bases is the formation of ketenes by abstraction of HCl by the base. The stronger the base, the greater the extent. ketenes are capable of acylation, but prone to the formation of other products. Phenylenediamine, even with Boc-protection is not an easy compound either. You judgement was quite correct when you were adding the dichloride dropwise at -20oC. Pyridine as a base is a good choice, too. It is likely that you generated a good yield of the desired malonyl diamide, but some colored impurities are hardly avoidable when you have an acyl chloride as reactive as the one you use. If these impurities are critical or the yield is too low, you may wish to react malonyl dichloride with N-hydroxysuccinimide. Once bis(N-oxysuccinimidyl) malonate, a much milder acylation agent, is formed in situ, it can be reacted with mono-Boc phenylenediamine. Good luck with your chemistry!
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In the structure of many drugs, there is a carboxylic group
What is the significance of this group? Why should it exist in the structure of a drug?
Do you know any article or book or reference about this subject?
Thanks a lot
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Nalidixic acid - A NSAID grs of drugs or pain killer .REF : en.wikipedia.org ( Image Source ) .
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Is there any free website or software for checking physical/chemical properties of organic compounds or published papers by structure search?
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Dear Malar vizhi J.M functional groups in 2-bromo-4,5-dimethoxycinnamic acid are principally all substituents other than hydrogen atoms. First you have the bromo substituents, which can be substituted by other moieties. Other functional groups are the two methoxy (–OMe) groups and the carboxylic acid (–COOH) functional group. Finally, the -CH=CH- double bond can also be seen as a functional group as you can do derivative chemistry with it (such as adding Br2). I hope this answers your question. Good luck with your work and best wishes, Frank Edelmann
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In my job I work with bent-core molecules, which have many aromatic rings with ester and biphenyl groups. And I use a benzylic group as a protecting group for one aromatic OH.
In the literature, the deprotection of this group to an OH takes place overnight. However, I require heating up to 50 °C or leaving the reaction for at least 3 days.
Why could this be?
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1. You must use high hydrogen pressure on a large scale of starting material (2g or more) for rapid hydrogenolysis.
2. Try working with a wet 50% Pd/C, dry Pd/C often fails.
3. An alternative method is to use lewis acids (FeCl3, TiCl4)
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Dear RG Community,
quinalizarin is a dye that used to be very common. Unfortunately, it is hardly used today and, as far as I know, can only be purchased in small quantities at very high prices from Sigma Aldrich:
A BASF synthesis route (according to Bohn) uses the hydroxylation of alizarin with oleum. However, we could not find a detailed synthesis protocol for this.
We would like to use quinalizarin for educational purposes of our students to detect Mg2+ and Al3+ as lake pigments. Of course, we are aware of other methods and reagents, but would like to try this particular option.
My question is therefore, if someone knows a source of purchase quinalizarin or if a group still has stocks from which they could help us with a small amount.
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Dear Florian and Chen Jingwen unfortunately Alfa Chemistry does not sell quinalizarin either. When you check their website for the term "quinalizarin" you receive a message saying that the product is currently not available (please see attached screenshot).
With best wishes, Frank Edelmann
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Could anyone provide a details on separating allene from alkynes in the mixture of allene and alkyne?
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Dear Sarah Rabbitt the boiling points of propiolic acid and pyruvic acid are 21 deg. apart. Thus it should be possible to separate the two acids by careful distillation though a Vigreux column. In case that this issue is still of interest to you, I think you should not hesitate to ask this as a separate technical question on RG. Good luck with your work!
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I extracted the essential oil and I found that my major compound represent 95 % of the mixture and only less than 5 % as minor constituents ( 20 constituents).
I'm I allowed to take my major constituent as starting material to perform chemical reactions?
Do the minor constituents representing only 5 % will not disturb the obtention of the desired compound?
I would like to insert some functional groups to increase bioactivity.
Any help in this regard will be appreciated.
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Dear Alexander Sinko, well done ! 95% !!!, as dear Dr Erdal mentioned , I advise you to be careful to remained 5% ( 20 components), you can use Column Chromatography or Solvent extraction........
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What kind of functional groups do we need to insert by the synthesis in organic chemistry to have anti-cancer activity in perspective?
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Consider two small molecule anti-cancer drugs, Enasidenib and Ivosidenib, which are IDH1/2 inhibitors approved for AML treatment. The fluoride moieties are a prominent feature. If you remove them from the molecules, their PK will be completely messed up; in fact, without the fluorines, they will most likely vanish like the clappers once they reach the liver, due to rapid metabolic degradation. Another distinguishing feature is the predominance of six-member aromatic rings and amide/amine linkages. A drug must be reasonably soluble in water and capable of being transported through the bloodstream to be effective when taken orally. Because amines are weak bases, they are frequently converted to salts with some acid, and thus some oral drugs contain amine salts. One reason for their presence is that they provide the drug with some water solubility. Scientists have taken a cue from nature by utilising the versatility of the amide group. The amide chemical group reigns supreme in medicinal chemistry. The group features in almost all of the bestselling drugs. Because amides have the right amount of stability and polarity, they can interact with biological receptors and enzymes. Because drug design is so nuanced and cancers are so variable, determining which functional groups should be inserted into a drug to boost anticancer activity is best left to experience, modeling software, and repeated tests.
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I want to start from phenol to synthesize this compound, but I dont know about the detailed mechanisms and conditions.
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Dear Jialiang,
many thanks for sharing this very interesting technical question with other RG members. I did a SciFinder search for this compound and found that it is not known from the previous chemical literature. However, the analogous compound is known in which the ethyl group in para-position of the phenyl ring on the left side is replaced by a methyl group. This compound has been reported in the following article:
Chemoselectivity in the Cu-catalyzed O-arylation of phenols and aliphatic alcohols
Fortunately this paper has been posted by the authors a public full text on RG. Thus you can freely download it as pdf file and print it out if required. The synthetic route is outlined in the attached reaction equation. You just need to replace the starting material 4-iodotoluene by 4-iodoethylbenzene.
Good luck with your reserach work and best wishes, Frank Edelmann
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I have a dowex column in H+ form and I want to exchange it with tetrabutylammonium form. What concentration of tetrabutylammonium hydroxide do I need to prepare to pass through the dowex column? What other steps do I need to take?
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Hey. Its been so long, I can't remember if I got the result that I needed or not.
You could call the company that manufactures the Dowex columns and ask for assistance. They might be able to guide you in the right direction. Good luck.
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I've been trying to prepare polyimine based polymer in DCM/DMF/TOL solvent system.
First I let aromatic di-aldehyde reacted with di-amine with long carbon chains (4-6 carbons), as soft segments. After some time, I introduced aromatic di-amine, the hard segments, as chain extender, then the solvent became very turbid, showing that the solubility is not good.
Later I found the turbid solution can only be solubilized by AcOH.
The hard segment is very important to my project and I can't replace it, and the weight% is quite low already.
I was thinking if I could prepare the polymer all over but in pure HOAc, or high weight% of HOAc?
All my solvents are non-aqueous, or only trace of water coming from the formation of imine.
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Dear Bryan,
thank you for posting this interesting question on RG. As an inorganic chemist I'm not a specialist in polymer chemistry enough to give you a qualified answer. In this context I keep wondering about two things: Why are you expecting a soluble polymer when you use aromatic units as hard segments? And why do you want to work in nasty acetic acid when "normal" organic solvents will also work? To the best of my knowledge the formation of low-molecular weight Schiff bases from aldehydes and amines is often catalyzed by small amounts of acetic acid. Thus I assume that a few drops / ml of acetic acid will do in your case too. For some potentially useful information please have a look at the following relevant articles in which the formation of polyimines in various organic solvents has been studied:
Tuning the physical properties of malleable and recyclable polyimine thermosets: the effect of solvent and monomer concentration
and
Synthesis of imine bond containing insoluble polymeric ligand and its transition metal complexes, structural characterization and catalytic activity on esterification reaction
The first article is freely available as public full text on RG, while the second one is not. However, five of the authors have RG profiles, so that you can easily request the full text from one of them directly via RG (provided that it is of interest to you).
In any case I wish you good luck with your research work!
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I am performing an esterification reaction using "A with -acid chloride + B with alcohol" to get "A - Ester - B". This reaction uses Pyridine to trap HCl gas as Pyridinium Hydrochloride, so that we can easily remove the impurities. Other than Pyridine, is there any reagents I can use which are non-toxic.
(I already reject Triethyl amine, and DMAP).
Any advise in this regard is highly valued.
Thanks.
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Try with triethylamune.
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I am trying to do quaternization of acridine dye at 100 deg. Celsius under solvent free conditions and in a nitrogen atmosphere. After I added the DMS, it started to boil at 100 deg. Celsius and formed droplets on RBF walls and the reaction did not complete. The actual boiling point for DMS is 180 deg. Celsius.
I don't understand what is happening in the reaction? I have worried about the purity of the DMS. Although I added excess of DMS, the reaction is not completing. Please help me to solve this issue.
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You can check the amine value while adding DMS at different times. Once amine value becomes zero or less than 5, you can stop the reaction or addition of DMS.
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In literature, it is reported that barbituric acid is soluble in water, however, it appears to have solubility issues and as such it does not dissolve completely in water or alcohol.
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Barbituric acid slighltly soluble in water. So, you can wash the reaction mixture with NaHCO3 solution after completion. it may remove the unreacted barbituric acid.
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How can/should we distinguish between a Biochemical and a Chemical Reaction.
As per one explanation:-
Chemical reactions are discrete reactions with catalyst involved in the process where as in biochemical reactions there are a series of reactions involved with the product of one acting as the substrate for another and this complex process of interchanges taking place with the involvement of enzymes.
For a more specific example if we are conducting photosynthesis in vitro then it will be considered as a biochemical reaction rather than a chemical reaction.
But the dilemma stems from the fact that, even chemical reactions go through complex series of steps, like any organic synthesis reaction. In this case also there is the involvement of catalysts like enzymes. Thus, can we consider it as a biochemical reaction! But mostly we only attribute it to be a chemical reaction which is indeed the case.
So, what is the proper difference or point of distinction between a biochemical and a chemical reaction. How can we exactly relate that one reaction is a biochemical and the other is chemical!
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Dear @Mrutyunjaya Panda All biochemical reactions are chemical reactions. I agree with Dr @Frank T. Edelmann in that in principle, there is no major difference. The same reaction can occur 'in vivo' and 'ex vivo'. You can also access a similar discussion at the following link:
Best wishes, AKC
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In reaction of isocyanate or isothiocyanate with compound containing aromatic amino and hydrazine group, how to improve reaction selectivity toward hydrazine group only?
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Dear Mohamed H. Aboutaleb many thanks for your interesting question. Unfortunately the question is a bit too general in nature to give you a qualified answer. In this point I fully agree with Vladimir Khlebnikov in that it would be helpful if you could specify you aromatic amine / hydrazine precursor in some more detail. If I knew a structural formula I could easily do a SciFinder search for you to find out if reactions with isocyanates or isothiocyanate have already been reported.
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Trying to improve a process I have been given. The chloro analogue is far more readily available and I would prefer to use that to couple with my acetylene.
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The palladium(II) complex is an effective catalyst for the coupling reactions of aryl Chloroaromatics.
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I want to remove the solvents from my product in acid and base medium. If I use the rota evaporator it means the pump gets affected. Is there any solution for this problem?
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The best method of removing solvents like chloroform, THF, dichloromethane without using a rotary evaporator is simple distillation on water bath.
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The simple polymer tests in that image incited these questions to me-
  • Why would red-hot copper wire burns with Green flame when polyvinyl chloride (PVC) is burnt on it but orange flame in case of polystyrene (PS) and polyethylene terephthalate (PET)? Is the HCl generated from burning PVC generates Cu(II) compounds upon reacting with copper in case of PVC, but not in case of PS or PET? But doesn't Hydrogen have higher reduction potential than Copper (EMF series), and copper may anyways oxidize in air at high temperature to provide a green-blue flame?
  • Why acetone reacts with PS but not PET? Acetone's (propanone) central C atom is not as much electropositive as methanal (formaldehyde), but still it can undergo nucleophilic addition. But while one alkyl group (ortho-para substituent) enhances electrophilic substitution reaction tendency in case of benzene ring of styrene in PS, two carboxylic groups in terephthalate causes benzene ring to be deactivated for electrophilic substitution in PET. Is this reasoning okay or is there anything wrong with it?
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One side is looking at density - whether it sinks or floats in liquids of different densities - water, alcohol, etc. Geologists do this with minerals - but they use bromoform (2.6 g/mL)!
the other side is using chemistry and solubility - flame tests to show presence of chlorine in PVC, what solvents different polymers dissolve in.
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I just made a small molecular compound comprising of both amine and hydroximic acid groups, after I quenched and neutralized the reaction, I directly freeze-dried the mixture and then dissolved the solid in acetonitrile and water (1:1) solvent for HPLC. The mixture just separated into two layers after the full dissolution. I think it is a little odd as the ACN is miscible with water and I cannot do HPLC if the mixture has two layers, so what should I do.
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1.You can change solvent methanol Water
2.also use buffer.
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Hi everyone,
I am a teacher of Heterocycles Synthesis,
Is there a home practice that you recommend for undergraduate students? A simulator would also be useful
Due to the pandemic, students only have materials that they can buy in the market.
Regards,
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Dear Reyna Martha Gallegos Alvarado here is another interesting heterocycle synthesis experiment designed for undergraduate students.
One-pot green synthesis of dihydropyran heterocycles
"This experiment aims provide the students with the knowledge about the One-Pot synthesis of dihydropyrans."
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I have produced oleum by adding sulfur trioxide, SO3, to sulfuric acid. It mostly contains disulfuric acid (also called pyrosulfuric acid) but i think this method is not suitable for laboratory purpose so is there any feasible procedure for the synthesis of oleum for laboratory purpose?
Suggestions will be highly appreciable.
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Dear Daniyal Ahmed just in case that this question is still of interest to you: The article cited below contains a detailed description of how to make oleum in the laboratory:
Preparation of Sulfur Trioxide and Oleum
Personally I would suggest to buy oleum from commercial sources as it is an industrial product manufactured on a large scale.
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Can anyone recommend some any software/models available that can predict substance reactivities and the reaction yield under a specific set of reaction conditions process and proposing pathways to synthesize target molecules from a complex mixture?
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Dear Talal Ashraf there are two potentially useful article on this topic available as public full texts right here on RG:
1. Predicting Feasible Organic Reaction Pathways Using Heuristically Aided Quantum Chemistry
2. Neural networks for the prediction organic chemistry reactions
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SPPS of a 16 aa peptide was performed on a 0.15 mmol scale. Resin gained a minimal amount of weight: starting weight of 224 mg and a final weight of 280.I believe my peptide failed to elongate but im not sure why.
Rink amide MBHA resin was swollen, deprotected by 20% Piperidine/DMF prior to addition of an Fmoc protected Diaminobenzoic acid linker (Fmoc-Dbz; Peptide Intl). After coupling of Fmoc-Dbz for 40 min, a Kaiser test indicates a 99.8% coupling yield. I proceeded with the synthesis and ended with a standard Dbz --> Nbz derivitization (acylation of Dbz with p-nitrochloroformate, followed by base-catalyzed cyclization; Dawson 2008).
Ive performed many synthesis and have never failed to elongate. I will attempt to cleave the product soon and analyze by LCMS but I need to wait through the holiday. Does anyone have any experience with this sort of failed synthesis?
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Hi i agree with Saraniya Bharathi Based individual amino acid combination - the peptide validated as "Easy" "Hard" to synthesis.
You may synthesized many peptides but this was failed due to sequence difficult - if you provide sequence means i will validate it and give you clear reply.
Some Points :
1. You used Rink amide resin - so here there was no problem found
2. After first amino acid coupling - amino acids solvation effect and coupling deficiency issues synthesis goes to wrong direction .
3. Each amino acids have different internal properties - Neutral and Hydrophobic amino acids create trouble - so before planning to synthesis - you write protocol for each "Hard" amino acid.
If sequence easy means no issues - if "difficult sequences" means should be careful and modify your procedure in difficult red-zone area of the sequence.
Hope some of my publications have details about this - may helpful for your research.
All The Best For Your Research and Success
- Dr.R.Selvam - Custom Peptide Synthesis Expert
Grey Matter Research Foundation.
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I found only one procedure where they use CaH2, is CaH2 safe to be used with BF3?
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Unlike other halides of boron BF3 doesn't undergo hydrolysis. BF3-2H2O is a very stable compound. So BF3 etherate is also hygroscopic and you need to dry it before using it with any sensitive reagent. I dried it using CaH2 and distilled under reduced pressure. It's better to filter off CaH2 and the solid residue if you don't want to distill under vacuum. I also came across someone using P2O5.
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I tried several routs suggested in literature to perform coupling reaction between acid and amine at the Au surface using EDC-NHS in water but was not successful. Could you please suggest any better way to do this?
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I think you can use DCC for better result 📷
For other approachable method you can go to those link where you can find various method of successful bioconjugation
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Is there any effective method to reduce oxidation effect of nitrous acid (HNO2)
as it is converting my diazo compound into tars while diazotizing it,affecting the results of my final product.
Below attachment is my diazo compound.
Suggestions will be highly appreciated.
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Lignosulfonate is an insoluble biopolymer in the organic solvents. How we can dissolve this polymer in an organic solvent?
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and who told you that LS are not soluble in organic solvents. Try it first.
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How can I remove excess amine from these reaction products? I did the reaction which may formed mono and di adduct and also present some excess amine.
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You can prepare a mono adduct of amide from the reaction between lactone and ethylenediamine by heating one mole of lactone with half mole of ethylene diamine in ethanolic solution.
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Is there any possibility of nucleophilic aromatic substitution of hydroxyl group directly without the presence of sulfonic group etc ???
kindly suggest me??
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There no possibility of nucleophilic aromatic substitution of hydroxyl group without the presence of sulfonic group as OH is not a better leaving group.
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I am using chlorosulfonic acid in chloroform (inert, 2 hr, RT) to para-sulfonate benzyl groups on a dibenzyl ether. The work up is extraction with water. The reaction, however, does not seem to work. Are there other reaction conditions and/or work up to try for aromatic sulfonation reaction?
I have tried an alternative, stirring with sulfuric acid for a few days, however, I cannot obtain pure product without large amounts of inorganic salts.
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agree with Kurt Wachholder
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According to the fact that we couldn't use huge sonicators and run the same lab based experiment for industrial productions because of its acute or chronic health effects, I wonder what is the best replacement for sonication to obtain a homogenous mixture of polymers and nanosheets in industries?
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Dear all, what is the role of sonication in your case? Is it for mixing/dispersion or for reaction assisting. If it is for the later option you can use microwaves. My Regards
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Etherification was carried out between aromatic -OH group and alkyl chloride in the presence of ethanolic KOH. The precursor is a bulky dye compound that consists of an aromatic -OH group and an ester group.
When the reaction stopped, I tried to remove the excess KOH by extraction. The product can only extracted by ethyl acetate (cannot be extracted by DCM, CHCl3, diethyl ether, toluene). However, strong acetic acid smell was detected in the extracted layer after the solvent was evaporated.
I tried to directly recrystallized the product in ethanol after the reaction, no crystal was formed but an oily layer emerged beneath the ethanol.
Is there any suggestion to remove these KOH and unwanted inorganic by-product after etherification?
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To remove the KOH from ethanolic etherification without using extraction method , neutralize the reaction mixture obtained after reflection by treating with 2N HCl to PH=7 , organic layer separates out.Extract organic layer with chloroform or dichloromethane. Removal of Organic layer under vacuum will give ether.
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In the last step of the synthesis of 1,2,4-triazole from acids hydrazides and isothiocyanates, 1 M HCl must be added to get the final product precipitated, by mistake I used concentrated HCl, the IR spectrum says that the product is the acid from which I synthesized the acid hydrazide (one of the starting material)! is it possible that 1,2,4-triazoles get hydrolyzed in such strong acidic media?
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1,2,4-triazoles is stable compd. for action of acids and alkalies.At high temperature above 200 deg. it may loose nitrogen in the form of N2.
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I'm working on gelatin modification. To do this, the amine group was protected by BOC and the carboxylic group was activated by EDAC and NHS to form a stable amide bonds with another amino-content small molecule.
Now I need to remove the protecting group. As in the reference, they use the conc. HCl (0.5 % v/v to sample) at 4 degree Celsius to deprotect the BOC. But this spend about 2 weeks to reach the full deprotection.
I hope to fasten this process, I have found some papers such as using conc. HCl (0. 01% v/v) at 40 degree celsius take about 16 hours and HCl (4M)/dioxane at 0 degree celsius take around 30 mins for deprotection. Will these methods also break the amide bond of gelatin and the additional group that I'm grafting to the backbone? Anyone has experienced in this kind of reaction, please help !!!!
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You may try 0.1 N HCl in hexafluoroisopropanol or trifluoroethanol.
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Hi, can anybody suggest me a single step ortho carboxylation of methoxybenzene derivatives. What are the best sets of reagents
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In addition to the answers afforded by Frank T. Edelmann and Abdelkader BOUAZIZ , I suggest another synthetic way. This includes the formylation of anisole using Vilsmeier–Haack reaction and the product is then oxidized to form the target product.
All the best
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I am working on research. I would like to connect a conjugated aldehyde (like citral) to another ketone compound at the carbon alpha to the latter's carbonyl group. I tried to use Mukaiyama aldol reaction. I generated an enol silane from this ketone compound and then reacted with a conjugated aldehyde, but it failed. I guess that the relatively high stability of the conjugation system from conjugated aldehyde may be a reason. Can anyone suggest me another way to do the job?
I intend to do double alkylation at that carbon position and I would like to preserve an -OH or C=O group at the beta position with respect to the C=O group on the reactant conjugated aldehyde.
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Dear Alan
Can you please attached the proposed synthetic scheme to clarify your question and point my answer?
Regards
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Hello All,
I tried to protect the free thiol group using 4-methoxybenzyl chloride via SN2 reaction, but I was not able to do so. I am wondering if you have any suggestions on how to proceed this reaction or on any alternative pathway to protect the S-H group? Thanks :)
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To protect thiol group convert it into thioether by reacting it with alkyl halide in acetone in presence of anhydrous base as potasiummcarbonate
… Read more
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Does the ester bond in my compound breaks If I proceeded a Sonogashira coupling reaction to react my compound (R-O-CO-Ar-Br) with the alkyne derivative?
The reaction condition I'm using:
Bis(triphenylphosphine)palladium(II); DME; TEA; CuI; 200 C; 24h
Thanks!!
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You might have cleavage of the ester depending on the base you use, but most bases traditionally employed in Sonogashira couplings should be safe.
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I am trying to synthesize a compound which has both carboxylic acid and amine. During the purification, when I do the pH adjustment it forms a zwitterion and goes into the aqueous layer. Is there a way to desalt such compounds?
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Crystallization of a zwitterion at the isoelectric point is tricky and often inefficient. If you only need a small amount of product and high yield is not the goal, AND you have a good estimate of pI, this can be the quickest way to get what you need. If you are doing this preparatively and/or if the compound does not crystallize well from your original mixture, ion exchange resins will probably be the most effective tools. (If you are trying to recover your product from a complex mixture, you will need to do IEX chromatography; please provide more details.)
When amino acid zwitterions are being synthesized, cation exchange resins such as Dowex 50, Amberlite IRC120 and others offer a very simple and efficient method for recovering products. The following process is frequently used following acid treatment, such as amino acid amide hydrolysis in HCl(aq):
RCH(NH[R'C=O])CO2H + xs HCl(aq) --> RCH(CO2H)NH3+ . Cl- + R'CO2H
The hydrolysis mixture consists of RCH(CO2H)NH3+ . Cl-, R'CO2H, water and excess HCl (e.g. R'=CH3 for an amino acid acetamide, where acetic acid is a volatile byproduct).
1) Evaporate excess volatile acid (rotary evaporation will remove water and HCl gas.) Purging HCl gas in a stream of N2(g) beforehand (fume hood) will reduce bumping during evaporation. Vent the vacuum pump exhaust to fume hood.
2) Dissolve the acid evaporation residue in a small volume of water
3) Calculate the number of millimoles of the zwitterionic substance you intend to isolate and pack a short column with 2-5 times this number of milli-equivalents of appropriately-washed NH4-form ion exchange resin (preparation usually done by washing with strong acid solution followed by water to give neutral eluate, then aqueous ammonia treatment to convert RSO3H groups to RSO3- .NH4+, and finally thorough washing with deionized water to give neutral filtrate.)
4) Slowly apply the solution of evaporated hydrolysis mixture residue onto the column, then wash the column with pure water until the eluate is free of Cl- (AgNO3 test) and the pH is neutral (or not lower than the pH of your DI water). At this point, the acidified zwitterion should be completely bound to the resin [RCH(CO2H)NH3+ . resin-SO3-]. (Check the column application eluate to be sure nothing has leaked through. TLC with ninhydrin detection works well for amino acids). You may also check dried drops of eluate with ninhydrin to be sure that displaced NH4+ ion is no longer eluting from the column.
Elute the washed column with aqueous NH4OH, using approximately twice the number of millimoles as meq of resin (e.g a column containing 50 mL of 0.8 meq/mL resin would be eluted with 2 x 50 x 0.8 = 80 mmol of NH4OH(aq), say 40 mL of 2 M). If the product has not completely eluted from the column by this time, more water should be used before you add more ammonia. Very hydrophobic amino acids may elute better if some methanol or ethanol is added to the water.
5) Evaporate the ammonia eluate. As with the HCl solution in step 1, this solution may behave better during rotary evaporation if you first bubble a stream of N2 gas into the eluate to purge excess NH3 (fume hood), followed by vacuum evaporation, only heating once all free ammonia is gone. Nearly all ammonium carboxylate salts (RCO2- . NH4+) decompose upon evaporation with heating to carboxylic acids, so this step is basically:
[RCH(CO2-)NH2 .NH4+](aq) --> RCH(CO2-)NH3+(s) + NH3(g)
i.e. once ammonia gas leaves, this residue is theoretically pure zwitterion.
6) At this point the purification method of choice is usually recrystallization, commonly from water-alcohol mixtures.
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I have synthesized a carbazole-linked donor-acceptor molecule. The 3 position of carbazole is still free. Can I introduce aldehyde group there?
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Formylation: Vilsmeier-Hack Reaction -> Formylation at C3
it is conspicious, that the presenec of an electron- withdrawing substituent at nitrogen directs electrophilic substituition to C2
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What is the most feasible method to synthesise benzoxazole from aminophenol?
i had tried with carboxylic acid derivative in the presence of PPA as a solvent,
but i am looking for some more feasible procedures and methods??
Suggestions would be appreciated.
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Synthesis of benzoxazole can be achieved by heating o-aminophenol with carboxylic acid in presence of polyphosphoric acid. In another method o-amino phenol is heated with HC(OCH3)3 in presence of HCl.
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Hello there, need some ideas and conditions for pyrrolidone cleavage with formation of double bond (C=C) , for now i know that in strong acid conditions (HCl) this group is stable and cleavage do not occurs. Anyone have experience in cleavage this type compounds or seen some papers about this?
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interesting answers
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Role of solvent.
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Dear Gagandeep Kaur,
Polarity of solvent can also have a big influence on the products obtained in organic photochemistry. For example, in the case of photoinduced hydrogen transfer. Two mechanisms are possible : a one-step mechanism where the electron and the proton are transferred in the same time and a two-steps mechanism where electron in transferred first and proton follows. These two mechanisms cannot be distinguished in terms of energy, they are both exergonic. But, for a one-step process, the electron transfer is endergonic where as in the case of a two-steps process, the electron transfer is exergonic. As you could see in our publications (10.1039/C9NJ03061A, 10.1002/chem.200903045), different products can be obtained with different solvent (cage effect discussion is made in the former). $\Delta G^{0}_{el}$, electron transfer exergonicity, is available from the Rehm-Weller equation, as a function of polarity of solvent. For a less thermodynamic point of view and a more kinetic point of view, I suggest you to see this last publication in Science for concerted proton-electron transfer :
10.1126/science.aaw4675.
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Tin in HCl
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The best reagent for the reduction of NO2 group to NH2 group is heterogeneous catalytic reduction using H2/Pt in acetic acid.
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Hi,
I synthesize stannane compound using bromo octylthiophene, n-BuLi and Bu3SnCl. The reaction seems to go well in lithiation step (checking by TLC), but after adding Bu3SnCl,nothing change. I have check NMR for final product but it's octyl thiophene. I doubt that I have problem with my Bu3SnCl because I have opened it for one year.
Could you share your experience if the problem comes from Bu3SnCl and how to treat it to reuse?
Thank you!
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There is a common precautions to consider when it comes to storing conditions and storage time for the chemicals to preserve their initial structure. Such substances can be decomposed with the effect of light and heat. Also if you open them without the right provision ,the material can be subjected to air. Such substances can react with oxygen and water moisture.
You have to keep such materials sealed under the proper storage conditions till their use.
The other thing is that their recovery can be very difficult to you.
So, i would advice you to use fresh chemicals for your experiment.
For sure the cause of the failure of the experiment is the expired Bu3SnCl .
Best wishes
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Chloride salts of following organic bases are commercially available. How can I get their anhydrous hydroxide form?
N,N-dimethylamine, N,N,N-trimethylamine, Guanidine, N-mrthylguanidine and N,N-dimethylguanidine
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I am starting to synthesis my first batch of MOF materials and after a literature review, I often found that the amount of the metal precursor is always higher than that of the organic ligand as required stoichiometrically. Is there any reason behind this?
For example: For the synthesis of Cu3HHTP2 MOF, the stochimetric ratio Cu:HHTP is 3:2 and in literature I found the real ratio used is 2:1 (powder synthesis) and even 10:1 (thin film synthesis).
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In general:
MOFs are "bulk" materials, usually contain more than one ion-pairs and not "isolated" ions/ion pairs unlike in a real solution. That means, on the nanometer scale the particles considerably fewer ions on the surface than the total number. And so, the ligand exchange is restricted to the surface. Additionally, not all the surface ligands can be exchanged.
An example (because I am not an expert of Cu3HHTP2, but I assume that it is general): rutile builds up tetragonal unit cells, where the unit cell dimensions are a = b = 0.458 nm, and c = 0.295 nm. The Ti2+ ions are surrounded by 6 oxygen atoms, forming an octahedron, and the unit cell contains more than one TiO2. Not to say anything about the intercalated other ions.
That means, > 1 nm particle sizes contain fewer replaceable, in the case of rutile the unit cell contains (as average, as Axel wrote) 5 TiO2 while on the surface (of the unit cell) only 8 (of 10) Oxygen is active. In theory on a ~1x1x1 nm particle, while the number of constituting TiO2 is 30, the number of surface O is only 20 (of 60). And usually, the nanoparticles are larger than 1 nm.
Of course, in (theoretical) two-dimensional cases the numbers are different.
Additionally, multidentate ligands further reduce potential substitution sites. So, the mentioned 2:1
Finally, Balakrishna's comment is an inappropriately undervalued comment.
Regarding your example.
There are many missing data, and I assume they are also hidden for you. For the solid synthesis, you mentioned 2:1 ratio. In solid syntheses, there is a size limit, which is generally higher than 1 nm. After that a) I have doubts and the 2D structure might be true only; b) using a 2:1 molar ratio seems to be too low.
Due to solubility issues in solution and lack of yield, isolation method, etc., the 10:1 can be reasonable.
Please, also note that thin films are not necessarily 2D structures, and the reactions are rarely so ideal as they are described in publications - as you are getting more experienced you will see the difference between a publication and real life. Many tricks remain hidden in publications, independently from the journal rank.
So, firstly try to reproduce the published method (=do strictly what is written even if you are not in agreement with the authors!), then, based on your experiments and comparison with the written matters, try to find explanations and understand the authors' synthetic method. This way usually works well. Thinking a lot of unknown things, then to conclude finally to repeat the published method is many times a waste of time.
Good luck,
Laszlo
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I was previously using one of the strong base NaOH in order to convert it into sodium naphtholate (as my compound's physical appearance is in flakes form)
then at the coupling stage with diazonium chloride,
which i assume that my diazonium chloride is reacting at that NaO group (after converting 2-naphthol into sodium naptholate) on the compound.
So, how can i couple my diazonium chloride at the 1st/Alpha/Para Position of the following compound???
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Thankyou Dear Grant Simpson For Sharing This Valuable Information.
I am sure this will be helpful.
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Dear all,
Recently I started collaborating with a chemistry group to synthesize a sugar derivative with isobutyric acid sticking out. The synthesis went well, however the final product has a huge amount of lithium acetate (10:1 Li ac:sugar).
This makes my enzymatic work impossible.
Does anyone know any method by which we could remove LiAc from the solution?
NB:
the compound is soluble in both water and ethanol
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Try using a zeolite resin. It works for removing Sodium in water OR you can try 'reverse osmosis'. Follow was Waters or other water suppliers use.
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When HOCl is added to propene, the product is 1-chloro 2-propanol. However, when the same HOCl adds to allyl alcohol, the expected product is 3-chloropropan-1, 2-diol. But actually, 2-chloropropan-1,3-diol is formed. Why? What is the mechanism of this reaction?
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Could be explained by radical mechanism and allylic resonance. Hydroxyl radical attacks the double bond. Secondary carbon is more stable as a radical so the chlorine attacks carbon no 2.
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Suggestions Required On How Can I Make Below Compound Reactive ?
Basically,I Want To Couple This Compound With The Other (Which Is Highly Reactive).
I Have Tried Converting In Sodium Salt And Dispersing It By Some Dispersants And Solvents But That Doesn't Providing Me The Desirable Results.
Comments And Suggestions Will Be Highly Appreciated.
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I don't think you really need such a strong base as n-BuLi to deprotonate the methylene group in this substrate; bases like NaH of t-BuOK would be sufficient (even K2CO3 in aprotic solvents is used successfully for alkylation of malonates). In this particular case perhaps the electrophile is not reactive enough.
Also, let's not forget that we have an amide NH in a molecule, which is also pretty acidic, perhaps more acidic than methylene. Chances are that you may need to use more than one equivalent of the base. And of course for good results the reaction media should be anhydrous.
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I'm studying the polymerization in solution between a ketone and a secondary amine in function of the pH of the solution. I need some references to study the equilibrium constants of the first hydrolytic step and the second polymerization reaction, in particular I'd like to understand how much intermediate I can aspect and how its presence in solution can affect the reversibility of the reaction.
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https://www.ncbi.nlm.nih.gov › articles › PMC6419043
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I got 2,6-dibromopyrazin and i want to synthesise pyrazine-2,6-dicarbonitrile.
I already tried with CuCN/NaCN in DMF (Reflux, on), according to a literature procedure for pyridine-2,6-dicarbonitrile (DOI: 10.1039/C4DT00341A) and also with Pd(PPh3)4/Zn(CN)2 in DMF (reflux, on).
Does anyone have another suggestion for me, how to synthesis pyrazine-2,6-dicarbonitrile?
Thanks in advance!
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Refer to our publication," synthesis of phthalonitriles using a palladium catalyst".
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Hey all,
I wanted to gather expert input on the stability of dimethylformamide under basic conditions at reflux:
I want to reproduce the results of Michael G. Bell et al. in his patent
"Preparation of 3-phenylisoxazole derivatives for treatment of dyslipidemia
By Bell, Michael Gregory et alFrom PCT Int. Appl., 2007092751, 16 Aug 2007 "
They claim that the condensation reaction of 2-fluorobenzaldehyde with mercaptoacetic acid in refluxing DMF with KOH as base proceeds smoothly and with a yield of 78%.
EDIT: The product of said reaction is benzo[b]thiophene-2-carboxylic acid.
On the other hand it's been reported that KOH as a strong base readily catalyzes the decomposition of DMF to dimethylamine and potassium formate (presumably), as can be read in the EROS article ( ).
Now I want to ask you guys whether you've worked under these conditions before and whether you've experienced a disastrous decomposition of solvent or a pleasant reaction with pure products :)
Best regards
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I deed reaction of benzyl alcohol derivative with 2-fluro toluene using KOH as a base and DMF as a solvent at 80-120°C. Reaction time was 5-12 hr. It was yielding 65-80% desired product. Reaction was almost clean on TLC observed under UV but reaction mass was thickened and darkened with time. What I am assuming is that DMF degradation is happening but with a lower rate than the desired reaction.
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I want to know if there is any particular behavior observed in mixed organic acid anhydrides.
For example, would acetic-benzoic anhydride acylate or benzoylate salicylic acid? How about acetic-hexanoic anhydride?
Maybe these properties are pKa dependent or volatility and steric property related?
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Hi, I saw this in Apay's link. The answer to your question is that it depends on the reaction mode. If it's a standard Lewis acid catalysed reaction then the most stable Lewis acid base complex is formed (even although its a kinetic process of course). If you read through George Olah's work you'll find your answer and many others. He was one on my chemistry idols when I was working on acylations!
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I am synthesizing the compound 1 by using chan-lam reaction as the figure showing. However, the conversion yield of ortho fluoroboronic acid (less than 20% on LC/MS) is much lower than the para fluoroboronic, which is very strange since the boronic acid is a nucleophile reagent and the F is ortho/para activated substituent and smaller than H in size.
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Hi;
Steric hindrance (the reaction site is blocked by F and B(OH)2 groups forming part of the molecule).
Best regards
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can anyone please suggest me how to sulfonate aromatic benzene ring in para position and instead of ortho position ?
On Which factor this position alteration depends?
Kindly please suggest me???
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Hi;
Substituted rings are divided into two groups based on the type of the substituent that the ring carries:
•Activated rings: the substituents on the ring are groups that donate electrons. •Deactivated rings: the substituents on the ring are groups that withdraw electrons.
Examples of activating groups in the relative order from the most activating group to the least activating: -NH2, -NR2 > -OH, -OR> -NHCOR> -CH3 and other alkyl groups
with R as alkyl groups (CnH2n+1)
Examples of deactivating groups in the relative order from the most deactivating to the least deactivating: -NO2, -CF3> -COR, -CN, -CO2R, -SO3H > Halogens
The activating group directs the reaction to the ortho or para position, which means the electrophile substitute the hydrogen that is on carbon 2 or carbon 4. The deactivating group directs the reaction to the meta position, which means the electrophile substitute the hydrogen that is on carbon 3 with the exception of the halogens that is a deactivating group but directs the ortho or para substitution. Best regards
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i have  boc protected amine which i want to alkylate using alkyl halide..which base should i use..please suggest .
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Sodium Hydide in DMF at RT works like a charm.
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Dear All,
Can we detect a non-fluorescent organic compound (with some aromatic rings) by TLC under UV light?
For example, a compound has absorption peak at 450nm but fluorescence intensity at longer wavelength is insignificant, so can we monitor it under UV lamp?
Thank you.
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For UV TLC plates the compound fluorescence is not a requirement because the UV plate is fluorescent and the absorption of the UV light shadows the plate fluorescence. If your compound has UV absorption in the range of 250-370 nm you can see black spots under the UV lamp. Because your compound contains aromatic groups you have good chances to see it. Please, also note that there are two commercially available UV active TLC sheets: 254 nm and 366 nm. My experience is that the 254 is better. Please, also note that the quantitation on the TLC by UV is not always obvious (because of the spot-spreading) unlike the charring or other visualization methods.
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I'm working up a Lawesson reaction. I tried the chromatography on silical gel, but there was always a spot at the starting point on TLC (UV 254 nm). The H-MNR and ESI-MS only showed signals of the product but the yield is over 100%.
What are the possible impurities of the reaction and how can I remove them to get the pure product?
Thank you.
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4-Methoxybenzenecarbothioic acid will be the by-product of the Lawesson's reagent after the functional conversion of the carbonyl group (C=O) to the thiocarbonyl group (C=S). That might be the spot you are seeing at the baseline of your TLC and this by-product is also UV active which is in agreement with your observation.
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does there is any chemical mechanism or procedure through which we can increase the intensity of color and also its frequency (lowering wavelength)???
kindly suggest?
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Dear David Oulton Sir,
Thankyou Once Again For Your Valuable Opinion.
Regards,
Daniyal
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how to produce an intensely coloured molecule with a conjugated azo linked (single/double/ single/ double bonded) structure, and avoid missing conjugated azo link in a structure.
Any suggestions??
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Hi Ahed,
All aromatic azo compounds are completely conjugated.For example from aniline prepare diazonium salt then couple it with phenol you will get the required azo compound for procedure use book ( practical organic chemistry by Vogel) in this book you will see many other azo compound preparation procedures. Good luck
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I synthesized a very polar ligand. KCl was formed as side product.
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Try to use AgClO4. Both AgCl and KClO4 are badly soluble in water and polar solvents
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I am trying to make a benzoxazole compound.
Is it possible to carry out the condensation with acetic acid?
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There are a few patents as mentioned below which talks of similar methods. The feasibility part is for you to decide.
EP0031296B1
CN102070627A
US3641044A
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o-amino phenol condensation with thiopene2,5 di-carboxylic acid?
can I carry out condensation in polar solvents?
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Do esterification/acid halide conversion (with equimolar ratio) of carboxylic acid first followed by careful addition to amine. Works well for amide preparation without affecting alcohol functional group.
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I'm working on the project in which p-toluenesulfonyl chloride (TsCl) is the main material to synthesis the mono-tosyl substituted. The TsCl in my lab is produce in China and has been opened nearly 8 months, I have purify it by recrystallize in Chloroform/Hexane or CCl4 but the results still not good (poor yield of substitution) so I wonder about it's purity, is it was being degraded?
Is there any analytical method to test the purity of TsCl?
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You can check by NMR, elemental analysis, LC-MS or GC-MS.
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Dear colleagues,
kindly share me your experience to convert phthalic anhydride into phthalic hydrazide
Thanks in advance
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I think it is difficult to prepare the monohydrazide as the compound will have a tendency to form phthalylhydrazide (2,3-dihydrophthalazine-1,4-dione) on heating. I am not sure whether it will work or not, one can try the following procedure : Stirring of phthalic anhydride in large excess (say 10 times or more but without solvent) of hydrazine hydrate at room temperature (or at lower temperature) for a long time. It is expected to obtai the monohydrazide carboxylic acid salt of hyazine. Careful neutralization with with dil HCl under cold condition will generate the free acid and hydrazine will be removed as salt. Thus the monohydrazide will be precipitated. Filter it to collect the solid (excess of HCl to be avoided as it would make the hydrazide soluble as a salt). It is to be dried under vacuum without heating (heating can convert it to phthalylhydrazide again).
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I perform reaction between compound 1 (liberates HCl upon hydrolysis) and in situ synthesized imine compound 2 at 65 centigrade
The hydrolysis step is essential for CPD1 to work, but the liberated HCl in the aqueous media hydrolyze the imine CPD2
How to do capture HCl from the media to protect the imine from hydrolysis whereas the reaction is one pot reaction, i.e., all materials are charged together in the same vial?