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Natural Product Chemistry - Science topic

Synthesis and Isolation of Natural Products
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Hello dear colleagues, I would like to open discussion about the bioinformatic methods that can be used in the field of natural products, which methods do you know ? where can they be used ? under which conditions ? and what are their benefits ?
I think this topic will be a good opportunity to share our knowledge and help each other discover new methods. Thank you very much.
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Bioinformatics combines computer programming, big data, and biology to help scientists understand and identify patterns in biological data. It is particularly useful in studying genomes and DNA sequencing, as it allows scientists to organize large amounts of data.Apr 28, 2021
What is Bioinformatics? | Northeastern University
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I am a PhD student and am currently working on metabolite profiles of some marine invertebrates.
While analysing some raw data generated from LC-MS, HRMS, NMR and FTIR, I was told by some researchers that these raw data, once submitted to a journal as supporting files, cannot be used further for any other analysis. For each analysis I need to generate the raw data again, otherwise it will be treated as a case of self-plagiarism.
I can see that my raw data has a potential of producing three distinct publications. I can analyse different parts of my raw data differently to present distinct conclusions.
But generating all the raw data again from these analyses, and that too for each publication, does not look sustainable to me. And clubbing all three publications in one also does not seem to be a good option here.
So I would like to know your views on this matter as a researcher and also as an Editor/Reviewer. Also, please share your similar experiences and solutions to it.
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It depends. Much data, for example fisheries records, are published for a given purpose - for example to manage a fishery. Many years after that data was published, it may provide other researchers with other information - for example on understanding "shifting baselines". There are many very good pieces of research using historic datasets. My herbarium vouchers are a form of "data". They are lodged in public Herbaria across Australia. The Herbarium staff make the vouchers, and the associated environmental data, available to researchers around the world. They do not limit the number of times any particular voucher may be used to provide a datapoint in someone's research. Those of us who contribute these data rarely hear about their reuse unless we subscribe to platforms like Bionomia. Over a career collecting environmental data I have much that I may never explore fully. I use platforms like the Atlas of Living Australia's BioCollect platform to host my old datasets. It is possible that one day someone may use the hypersaline lake diatom and physico-chemical data from Australia to develop a "diatom metric" index of water quality for these understudied habitats... or for gnammas, or coastal lagoons...
IAs you know what analyses you plan to subject the dataset to, maybe you would be better served in clubbing a group of papers together that look at the different things you have extracted from the dataset, and then provide the entire group to one journal to publish as a "set".
But I would not like for you to have the opinion that data may only be used once then needs be discarded. What a waste of effort. Well conserved datasets, with excellent metadata relating to the methodologies and data collection, can be valuable into the future, in ways we have no current understandings about.
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1- ONLINE SEARCH?
2- DATA BASE?
3- OTHER WAYS??
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Dear Ahmed,
this is clearly an important technical question of broad general interest. Of course, an initial online search on the general internet is always a good idea. In my experience, the best source of information in all areas of chemistry is the SciFinder. However, to my knowledge an institutional subscription to SciFinder is rather expensive, so that many universities / institutions do not have access to this platform. Thus you need to check first if there is access to SciFinder available at your institution. If not, you can certainly ask a colleague abroad to carry out a SciFinder search for you.
Good luck with your work and best wishes!
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Where can I find alagebrium I want to use it in my research ?
And astaxanthin also and is it expensive?
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Hello.
Take alagebrium for example, you can search it on google scholar (or others) and get some articles about it. I picked up one as below.
Am J Transl Res. 2019; 11(3): 1569–1580.; PMCID: PMC6456531
In this article, they mentioned that "......AGEs inhibitor ALT-711 (20 μg/mL; MedChemExpress, China) was added......". So you can turn to "MedChemExpress" to see if the price and distance are ideal or not. If not, turn to other papers.
It has to be mentioned that, you can go to https://scifinder.cas.org/scifinder. Using substance identifier will easily lead you to what you want, though I had not bought through this way.
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The contribution of natural products (NPs) to modern drug discovery can not be denied. More interestingly, the application of in silico (computer-based approaches) has even given more success to the search of NP-based starting molecules in the search for novel, potent and cheaper drug candidates. However, these in silico based methods also face some challenges. Obviously, most of the challenges are usually not discussed in scientific publications; in several cases rendering the use of in silico based approaches to investigate NPs (even in combination with experimental validation techniques) difficult to identify and propose new NP drug-base molecules. In this discussion, I would be happy if we can highlight some of these challenges. The idea is to give newcomers in this area of research an idea of what they can come across or should be expecting.
Peace
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See this article:
Applications of Virtual Screening in Bioprospecting: Facts, Shifts, and Perspectives to Explore the Chemo-Structural Diversity of Natural Products
10.3389/fchem.2021.662688
Here, we discuss some biases and limitations of computational methods applied in the screening of natural products.
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If you read the labels on food, you'll see the words "natural flavoring" or "artificial flavoring". The initial impression may be that the first must be good, while the second must be bad but if we look at what natural & artificial really mean in practice, most natural & artificial flavors are exactly the same chemical compounds, differing only by their source and both natural & artificial chemicals are or will be purified in a lab.
Is natural really better or safer or more tasty than artificial?
In some cases, natural flavoring may be more dangerous than artificial flavoring (e.g., natural flavor extracted from almonds can contain toxic cyanide but the artificial flavor has the taste but does not have cyanide).
Few years ago, my students prepared natural & artificial strawberry jams in a practical course. The taste of the artificial was judged to be better unanimously by the technician, my students & me.
Few years ago, a colleague's students made real strawberry ice cream & artificially- flavored strawberry ice cream. I tasted both & the second was more delicious, for me.
These two observations puzzled me. I know something about flavoring but I am not a full-fledged expert so I am asking to learn: Are natural flavorings really better & safer than the artificial counterparts? Is the public health at risk upon consuming foods & drinks with artificial flavors?
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The term natural flavor or natural flavoring means the essential oil, oleoresin, essence or extractive, protein hydrolysate, distillate, or any product of roasting, heating, or enzymolysis, which contains the flavoring constituents derived from a spice, etc. Artificial flavors, on the other hand, are made from anything else that doesn't fall under the "natural" umbrella. Interestingly, both types of flavors are made in the lab by scientists called "flavorists," who blend various chemicals together. The flavorist creating an artificial flavoring must use the same chemicals in his formulation as would be used to make a natural flavoring, however. Otherwise, the flavoring will not have the desired flavor. Although "natural" sure sounds better than "artificial," ingredients that come from nature aren't always safer than those that are artificially made. There are many deadly toxins that are produced in nature. In addition, artificial flavorings are simpler in composition and potentially safer because only safety-tested components are utilized. Besides health effects, natural flavors also may have more negative environmental impacts than artificial flavors. An example of massoia lactone, which is used for a creamy, coconut, spicy flavor. Harvesting it from the massoia tree in Malaysia kills the tree because harvesters have to remove the bark. In other cases collecting natural flavors involves clear-cutting and carbon emissions, which doesn't happen when flavors are created in the lab.
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I have precipitated saponins and it was soluble in water. A brown precipitate was obtained when barium hydroxide added. Is it saponins again? or Polyphenols? How can I choose mobile phase for further separation?
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"The use of the aqueous solution of barium hydroxide octahydrate, in contact with the saponins, liberates ions Ba+2, which form a complex with the pairs of free electrons of the glycoside hydroxyls (OH-). Washing with calcium chloride removes the excess hydroxide that was not complexed with the saponins. Subsequently, after the addition of the aqueous solution of potassium dichromate, which reacts by precipitating the barium chromate, a pale-yellow precipitate will form (Vogel 1981). This yellowish coloration can undergo oxi-reduction of the chromate, resulting in green coloring (Baccan 2011). For this reason, the readings of post-coloration sections should be carried out immediately, in order to identify the areas that possess yellow coloring."
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Tyrosine kinase (TK) are essential components in humans and their role has been manifested in many diseases. Normally we used to synthesise the TK inhibitors. So I want to know is there any plant source of tyrosine kinase inhibitor?
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Sengupta A, Ghosh S, and Bhattacharjee S. Allium vegetables in cancer pevention: An overview. Asian Pacific Journal of Cancer Prevention 2004; 5: 237-245.
Yuk T H, Kang J H, Lee S R, Yuk S W, Lee K G, Song B Y, Kim C H, Kim D W, Kim D, Lee T K, and Lee C H. Inhibitory effect of Carthamus tinctorius L. seed extracts on bone resorption mediated by tyrosine kinase, COX-2 (cyclooxygenase) and PG (prostaglandin) E2. The American Journal of Chinese Medicine 2002; 30(1): 95-108.
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Dear colleagues, do you have any idea about the advances on phytochemistry especially the use of informatics for chemical studies, and biological activities molecular interactions modelisations, and is there any other applications of informatics on this field. Thank you
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Informatics study on natural products chemistry is possible but you should know about phytochemicals , then individual separation .Then apply the informatics to study the bioactivity.
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Other than parsley leaf oil.
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Cold-pressed Nigella Sativa oil appears to have menthatriene in significant amounts. I have been reading more focused on thymoquinone and found this incidentally this morning. I hope it is helpful. https://www.hindawi.com/journals/ecam/2016/6273817/
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I was having the issue that a series of compounds degradate by the mild acidity of chloroform when we perform NMR experiments. I think that these compounds could be terpenoids (dollabellane type). And I wonder if other kind of molecules could degradate or are unestable in chloroform?
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Its advisable to keep your samples dry in fume cupboard once you are not running in NMR machine. Keeping them in chloroform for a long time may cause degradation.
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Can you please suggest specific spray reagents for TLC visualization of, 
1. Falvonoids?
2. Terpenoids?
3. Phenolics?
Thank you
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Please refer the attached file:
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I am a student in ethnobotany in France and I am particularly interested in the contraceptive properties of plants to compare with hormonal chemical actual methods.
Do you know researches which deal with this subject, or do you have any information from your own researches or your own culture ?
Ideally, I am looking for the latin name of the plants, the way it is used and any ethnobotanic and medical details.
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Greetings
I'm doing an increasing polarity successive extraction on tree leaves with n-hexane, methanol, and hot water successively. The n-hexane extract gave dark green coloration, while the methanol extract gave dark green-brownish color. However, the last phase of extraction with hot water gave clear water with foam on the top, so I suspect that there is no extract left in the leave. Is this normal to happen?
Thank you in advance for your answers
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This is normal because the hexane extract extracted the pigments (which can sometimes be chlorophyll a) and other nonpolar compound and the methenol extract extracted almost all of the polar compounds with the rest of the pigments vegetable (chlorophyll b, c and xanthophylls) containing in the material on the other hand the extract with water has extracted only the strongly polar compounds remaining in the residue, the foam of these compounds allows us to say that it was saponins.The question I'm going to ask you is why you are extracting with hot water instead of cold water and what type of extraction technique have you adopted?
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Dear All,
I am studying about antimicrobial activity of protein based edible films. I am dissolving protein extracts in water at 4% concentration with 1.6 g glycerol, then adjusting pH 12, and heating 95 oC for 1 hour. After cooling to room temperature, 1 mL essential oil and 0.25 g Tween 80 is added to solution, and then, homogenized at 14.000 rpm for 3 min. When air bubles cleared from solution with a vacum pump, it is pouring into petri dishes for drying at 38 oC overnight. Dried films hold into a desicator with 58% relative humidity. Then, films are cut 10 mm diameter circular shape, and placed on Nutrient agar inoculated with microorganisms. After just 2 or 3 min, films are melting and becoming fluidized. Water solubility of films are approximately 40% of dry weight basis.
I attached a figure for illustration more detaily.
How can I fix this problem? How can I make antimicrobial activity analysis of films?
Please help. 
Thanks.
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Hi Furkan,
did you try to increase the amount of glycerol? instead of 40%,@ you can use 50%.
and why you use pH 12 and heating processes together?
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I have 3 extracts, methanolic, ethyl acetate, and hexane. Should I evaporate it and storage in dry condition ? Or just storage them in their original condition in refrigerator ?
The bacteria is Streptomyces spp.
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You can save the abstracts as required
You can store the extracts dissolved with these solvents in the refrigerator for a short period ranging from a week to ten days away from light to avoid oxidation
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Dear scientist fellows, 
We would like to investigate the effect of various enzyme cocktails on the hydrolysis of a range of biomass and then quantify sugars by HPLC. However we are concerned with microbial contamination. Therefore we are looking for a robust method to prevent any microbial contamination while having minimum effect on the hydrolysis itself. For example, we would like to avoid to autoclave our biomass as it is expected to have strong effect on the polysaccharides. 
Our biomass is not sterile (harvested in nature), but has been dried (40°C) and grinded (coffee grinder) and then store at 5°C. 
We are thinking of using microbial inhibitor such as Lactrol, Pen Strep, or others. But we don't know which one to use. We are seeking on your advice on that matter ! 
Thanks,
Arthur 
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There are several contamination interferences and preventative means that NREL (https://www.nrel.gov/docs/fy15osti/63351.pdf ) have highlighted for enzymatic saccharification of lignocellulosic biomass, please read section 5. Interferences, point 5.9 and 5.10 in attached file. Hope this is of help. Cheers.
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I am working on a lauraceaous plant. I extracted the leaves of the plant sequetially with petether, chloroform and methanol. I did CC of all extracts. in methanol extract, I was not able to isolate any promising fraction which could lead to a compound. So I tried to fractionate the methanol extract by other solvent (like ethyl acetate and butanol etc.) to reduce the complexity of extract. But when I dissolved the methanol extract in water more than 50% of extract was insoluble in water.
I want to know that what could be done with this water insoluble fraction. Can I isolate polysacchrides from this? Please suggest the methods for isolation of polysaccharides...
Bandana
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I am working on phyto-chemical analysis of Cassia angustifolia extracts. GC-MS conditions were used from published literature. I got GC-MS results in the form of graph and a list of 900 compounds. None of the compounds mentioned in the list can be found in literature. Even the most common compounds like kaempferol etc are not present in my extract. What can be the reason for this?
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If you aren't so sure about the Calibration of your machine, try to run same experiments but this time using know verified compounds. Then compare the RTs.
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Can anybody explain the IUPAC for the given structure ?
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Сhemical nomenclature to the studio!
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Can anyone suggest a suitable solvent system in TLC for n-hexane extracts to get better fractions for HPLC analyses?
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Hexane, petroleum ether or benzene with ethyl acetate in a ratio starting from 20: 1 increasing ethyl acetate. Sometimes you can use chloroform
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Is saponin isolation using methanol extraction and precipitation with acetone a good method? Is there any possibility for protein precipitation? or any other?
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It OK as Robin and Devang has said.
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Hello researchers,
I would like to know the various techniques/methods which are used to characterize the crystals of a known substance (xylitol) and to check the purity as well as to quantify the impurities present in a crystalline compound such as xylitol (a sugar alcohol).
Eagerly waiting for the replies..
Dr. Sidana
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Arushdeep.. X-ray diffraction, XRD, is the major tool for the examination of crystalline solids. Powder XRD may furnish the preliminary data on the crystallinity. The more precise technique is the XRD examination of a single crystal of your material. You may get after using the supplied software, the bond lengths and the exact distribution of atoms within the crystal. Good luck
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I am working on Natural product Chemistry and I am interested to test my natural products against HIV/AIDS. The best and easy choice would be to do some in vitro testing first. That's why I am interested to get some info. Looking forward to get your kind response please.
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Thank you so much Nordirali and Imadeddin for your help.
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My ammine part is only dissolved in DMSO and Aldehyde is dissolved in acetone, chloroform, methanol and others. What solvent should I use to form my desired imine? Can I use DMSO? WIll that may make any problem?
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May be you can useful from the following article
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Natural indigo dye produced from different sources contains many impurities in it.What is the best method to purify it ?
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My thesis's subject is determination of flavonoids; catechin and quercetin from sea buckthorn leaves with HPLC-DAD. I have extracted the leaves with ethyl acetate 5x12,5ml, and I have now extract about 40ml. I think next step before determination with HPLC is acid hydrolysis, because flavonoids have glucosides and I gues those should dorp out of measurement.
But I have a problem, how should I do the acid hydrolysis? Should I use 4M HCl or weaker, about 2-6M, and should I use reflux 2h at temperature 40C with stirring?
For now I have tried to do this acid hydrolysis like this: 9,5ml ethyl acetate extract + 0,5ml 4M HCl and heated for 5min in waterbath 75°C. The end concentration of sample is 0,6M (I mean extract + HCl). I have found this advice from here page on 47-48
But this doesn't work so well. Am I doing something wrong? I haven't found any good or spefisic advice. So would you guys help me?
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can anyone tell me the Rf value of standard D-quinovose??? I have searched alot but did not find it.
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I use ethylacetate:hexane solvent system, and is giving me tailing separations. My aim is to isolate flavonoids from the n-butanol fraction. Regards
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We use the following systems for the butanol fraction to identify flavonoids using TLC:
1. Chloroform: methanol: acetic acid: water in a ratio of 7:3:0.5:0.5 (v/v/v/v)
2. n-butanol: acetic acid: water in a ratio of 4: 1: 2 and 4: 1: 5(v/v/v). PS^ after cooking the system is left to saturate, then the non-displaced water must be removed
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I am trying to isolate the constituents (polar and non polar organic compounds) from all parts including the edible part of dried herbal plant? Which is the best solvent to use? Or we have to extract polar and non polar organic compounds separately.
Thank you very much for your time and assistance.
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Use a polar and non-polar solvent. For non-polar compounds, hexane, benzene, petroleum ether, etc. For polar compounds, ethanol 40% and 70% can be used. It depends on what class of compounds you are studying. Methanol and 96% ethanol extracts all secondary and primary metabolites from plants.
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I tried running column chromatography of my flavonoid extract using chloroform. I tried wet packing using chloroform and and while i was washing the column with chloroform, i noticed that the flowing stopped and the silica gel inside the column was cracking even though there was sufficient solvent on the top. has it got anything to do with temperature? The room temperature was 32 degrees.
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First dry the silica gel with the system and try before filling the column with silica gel.
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Hi there, sometimes we have trouble dissolving 1 % (w/v) birchwood xylan for use as a substrate for xylanases. Any suggestions?
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Thank you for your help.
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The compound Drosophilin A is known to have antibacterial and antifungal activity (Anchel et al. 1955; Anchel 1952; Kavanagh et al. 1952). Its methylated analog, Drosophilin A methyl ether, also a fungal metabolite (Teunissen 1999), has no reported -as far as i know- any biological activity.
  • DA IUPAC Standard InChIKey: XIWJLPHQDBDOAN-UHFFFAOYSA-N
  • DAME IUPAC Standard InChIKey: HICARXIPJINIRA-UHFFFAOYSA-N
Chemical structures from NIST Chemistry WebBook, SRD 69
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There is report that the lignicolous basidiomycete Phellinus badius deposits up to 30,000 mg of the halogenated metabolite drosophlilin A methyl ether ( DAME, tetrachloro-1,4 dimethoxybenzene ) per kilogram of decayed hearthwood in the mesquite Proscpis julifora.. DAME occurs as clusters of glassy crystals up 1 mm long within the decayed heartwood. For more details consult The Science of Nature 102(3-4): 18 DOI: 10.1007/s00114-015-1268-5
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Is fractionation by simply shaking with solvents of increasing polarity successively sufficient or is it needed to always have 2 immiscible solvents?
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1). n- Hexane removes all non polar compounds
2). chloroform removes all pigments such as chlorophyll etc
3). ethyl acetate is where all biological active compounds are excepted such as flavonoids, anthraquinones, anthocyanine ,benzo pyrans etc
4). n-butanol extracts all other hydrocarbons
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I am trying to find a way to functionalize purified genomic DNA.
That is, I need a way to add reactive handles (amines, carboxylic acids... any conventional chemical group, really) on a linear, natural DNA, with an efficiency high enough to graft it to activated surfaces, incorporate it into polymers etc. So, something like 1 reactive handle every 102-103 bp would be a minimum. The downstream applications are chemistry rather than molecular biology, so I am interested in reactions that would be applicable to fairly concentrated samples (above 1mg/mL) and large volumes, which rules out enzymatic reactions.
I have tried to use the primary amines of bases (A & G) for reaction with epoxides or aldehydes, but I could not access these despite DNA denaturation. I also considered shearing the DNA to access reactive terminal phosphates, for EDC/Imidazole functionalization, but cutting the DNA is detrimental for downstream applications.
On a side note, because the DNA is fairly concentrated, reactions cannot be performed in acidic conditions because DNA would precipitate.
Any ideas? Thanks!
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I do not think you can do this kind of functionalizition effficiently by pure chemistry, you need to do it by enzyme biologically. Those NH2 groups on A G C are not really primary amines because they are not on saturated alkane, they are not very reactive, they are like NH2 on aniline. You need much harsh condition for those NH2 groups to react with epoxides or aldehydes , even so, it will not very efficient.
But you can introduce H2NCH2CH=CH-dU on the end of DNA by enzyme with H2NCH2CH=CH-dUTP, I do not know how, I am not a molecular biologist, I only know it can be done this way.
Good look!
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What is the best method of extracting oil from the honey of stingless bee?
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if we extract the propolis powder using oil eg corn oil, olive oil...what the best way to separate back from oil to get the crude extract?thanks
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I am searching for a useful alternative for NIST/EPA/NIH Mass Spectral Library.
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Thanks Bojidarka, but i can't open files with .MS and .ELU format. I found another open source alternative: https://www.openchrom.net/home
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I am working on isolation, purification and characterization of biomolecules from leaf extracts. I have methanolic extract of leaf and I want to remove the chlorophyll from it first.
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you can remove chlorophyll by the following step:-
1. dry out the methanolic/ethanolic extract and then dissolved it in a sterile milliq or distilled water.
2. after dissolving with water some of the particles will not dissolve. So, to dissolve it you add hexane(analytical grade) double the amount of water and mix it and pour it in a separation funnel.
3. two layer will form the upper layer is hexane layer which will contain chlorophyll and it will turn dark green and the lower layer is aqueous layer. collect the aqueous layer in a separate beaker and hexane layer in a separate beaker.
4. to remove more traces of chlorophyll from aqueous layer than you have to add the equal amount of chloroform and follow the step 3
finally you will get the chlorophyll free aqueous fraction which will have 80% of secondary metabolite which are polar and semi polar.
hope this will help you. best of luck.
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Natural Products Chemistry
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By using C1V1=C2V2
Here your C1 is 40mg/ml and C2 is 30mg/ml. Suppose you want to make 10ml of your 30mg/ml plant extract. Therefore, your V2 is 10ml. Now you need to know how much volume from stock solution you need to take to make 10ml of your working concentration.
So just put all the values in the equation.
40mg/ml × V1= 30mg/ml × 10ml
V1 = 7.5 ml
So take 7.5ml from your stock and add 2.5ml of your solvent in which your extract was dissolved.
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HPLC is the most commonly used method to identify the isolated compounds in phytochemistry. So how can we choose the solvent for an unknown fraction. Which solvent is best for a particular class of isolated phytocompounds
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Greetings and Regards;
Thank you for your answer, but for the extraction of the Soxhlet method, or another method, I want to examine the stool from sting water from the aqueduct, in which there are copesterin and a few stool sterols.
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i search for standard method to study antifungal effect of plant extracts on plant pathogenic fungi
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Plant pathogenic fungi will behave any other fungi. So there are no special culture conditions for plant pathogenic fungi. You can follow the usual procedure followed for studying the antifungal activity of extracts. NCCLS broth dilution methods are considered to be standard for studying anti-bacterial or anti-fungal activity. If you want to publish in an international journal your work, you must follow NCCLS method.
Wish you all the best.
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Suggest methos of total saponin estimation from Aloe vera. Also suggest the extration method and parameter of HPLC.
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I am working on saponines analysis and according my experience the HILIC mode of UPLC is a convenient tool to assess the triterpenoid saponines content in extracts. The detection technique is also problem on account of no UV activity of these compounds - ELSD and especially MS in negative mpde are decisions.
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Lately I became interested in silico modelling used as natural products biological activity screening. Although I have no idea where to start. I need tutorial/some basic informations or maybe contact to someone who can help me get into the topic.
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Dear Daniel,
I have listed some names of softwares to predict the pharmacokinetic properties like Mol wt, C log p, HBD.HBA, TPSA, NRB, GI absorption, BBB penetrability, skin penetrability, metabolizing enzymes involved and safety like mutagenicity, carcinogenicity, irritancy, reproductive effect, cardiac toxicity, skin sensitization, rat acute toxicity, environmental toxicity, possible adverse effects - 
Datawarrior,online
swissADME predictor,online
ossiris property explorer.online
GUSAR antitarget predictor, Rat acute toxicity (LD50) online and
to predict the pharmacodynamics properties(molecular docking studies)
PASS online 
swissDOCK online
swiss target predictor online
molinspiration tool online
MVD
glide/schrodinger and so on.
I wish you al the best.
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I am embarking on an exploratory research project on secondary metabolites of marine organisms particularly on sea stars and brittle stars. What natural products should I consider first? Im looking for a list of natural products and various methods I can use to identify and quantify them. I am planning to do zoochemical analyses, in vitro antioxidant activity, and cytotoxicity.
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Natural Product Chemistry, Isolation of Flavanoids, phytochemistry
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you can isolate hesperidin easily by adding acetic acid to orange peel methanolic extract after defatting
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I am in need of a specific name for the Phakellia sp. sample I am currently studying on since I am not an expert on marine species. Here's a photo.
Any answer will be appreciated. Thank you.
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Hi Abigail! While I'm not an expert on sponges I can send you a link of a study by UPD on the shallow water marine sponges found in Cebu. One of the species listed is Phakellia cavernosa. Hope it helps!
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I have done analysis of liquid hydrocarbon (linear chain paraffin)with D2887 method (SimDis) and the data are in the form of percentage yield vs IBP. How to calculate the fraction of individual componenent i.e. C10,C11,C12 etc.
% off               Temp deg C
IBP: 0.5%       131
        5%          145
        10%         170
.............................
FBP :99.%       471
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The API Technical Data Book, most recent major edition is 2005 or so.  It has the best means of converting distillation curves to/from TBP from which molar weight  % vs boiling point curve can be discerned by mass or volume percent.   Then use that curve to compare to various BP's for different hydrocarbon types and isomers.  A more time consuming and expensive procedure involves a GC-MS( at least two runs on a full range crude with different heat up rates) to make the same curve by carbon number and isomer type. An old package called ZBsaic did this pretty well but needed some calibration when  the crude type changed significantly. 
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My 80% MeOH aq extraction of a plant leaves followed by vacuum evaporation and N2 purge resulted thick wax. As most literature express gallic acid equiv (GAE) of total phenolic content (TPC) based on its dry matter, I wonder if there is alternative to express TPC not in terms of dry matter.
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Do you mean the reference? I used gallic acid for total phenolic content reference
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10 g of the powder was put into a conical flask and then 50 ml of 20% aqueous ethanol was added. The sample was heated with continuous stirring at 55˚c over a hot waterbath for 4 hours. This mixture was filtered and the remaining residue re extracted with another 100 ml, 20% ethanol. Both the extract combined and reduced up to 40 ml over water bath at 90˚c. The concentrate obtained was transferred into a 250 ml separating funnel and 10 ml of diethyl ether was added and shaken vigorously. In separating funnel ,two separate layers was observed out of which aqueous layer was recovered and the ether layer was discarded. The process of purification was repeated. To the aqueous extract 30 ml of n-butanol was added. The combined extracts were washed twice with 10 ml of 5% aqueous sodium chloride. The remaining solution was heated in a water bath. After evaporation the sample obtained were dried in oven to a constant weight and the saponin percentage was calculated.This is the procedure that I used.
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 hai,,
i have read the procedure u adopted. at the end u used the aqs. Nacl. in fact This step is not necessary. If the saponin u are looking is in glycoside form it will enter into this aqs. NaCl. if only the saponin aglycon it will not enter into water and remain in the organic layer. 
a mistake in procedure is observed. n-butanol addition is not necessary as this is highly polar than ethanol. 
for conformation of saponin availability in water and butanol layers, simply perform liebermann bucchard test.l this is the 1 drop of extract solution in test tube add conc. sulphuric acid without shaking and from the side walls of test tube. at the junction of two layers agreen color appears indicates the presence of saponin.
now the correct extraction procedure is use of alcohol or hydro alcohol solvent. heat at 50 degre C, filter. ensure the removal of solvent from the filtrate. redissolve in water in separatin funnel. add hexane. remove hexane layer repeat 2-3 times. now the water layer evaporate to dryness. this contains saponins will answer the above test. 
another simple test is foam test. take extract put in 25 ml measuring cylinder. add water 10ml. shake well to get foam on above the solution for 1ml ht. and should remain same for 15mins. 
all the best
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I've been reading some articles about the acetyl bromide method to quantify the lignin content, but I have some problems with cell wall (CW) isolation by organics solvents. Moreira-Vilar et al (2014, goo.gl/v9wI6R) show an easy way to prepared the CW, but I would like to use the method acetyl bromide adapted for small samples sizes (dry bath and ELISA, etc) despite it is not the same form that they established. So, What should be my concern about mixing these procedures?
Thank you for your attention!
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Hi, Marcia. The procedures to prepare the samples for acetyl bromide lignin determination aims to remove interference (compounds that absorve in the same wave-length). Therefore, by changing the washing protocols you must be sure that all potential interfering compounds are removed. As lignin is insoluble (at least most of it) the protocols usually involve washing the samples with successive solvents Includin ionic solutions, and surfactants). To establish our protocol we followed the absorbance in 280 nm in solution after each washing step. The washing was repeated until the absorbance remain stable, so we change the solvent. Using Soxhlet, the principium is the same, but the solvent mixture remains the same and the recycle is kept until the absorbance desapear. The procedure is simpler, but In this case, part of the lignin is solubiliized, and is computed as soluble lignin. If you give me more details about your samples specificities I would be happy to help you better. Best Regards.
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Does anyone know how to produce and purify NO3? I would like to use NO3 as a point source to study the degradation of some volatile organic plumes in a 20m wind tunnel by NO3. So, I would like to isolate the NO3 from any other compound that may affect the results such as N2O5, O3, O2, NO. The production of the radical I believe is as follows: N2O5<--->NO2+NO3
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Thank you very much Stefano. This is very useful and thanak yiu for the references as well.
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I want to make an extraction for measurement of Trigonelline in the seed fenugreek. I couldn’t find a good method for that. I want to know more details for making extraction. But usually the authors didn’t mention to details in publications. I'd appreciate any feedback.
Many thanks
Aliyeh
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Ultrasound assisted extraction method (UAEM)
The UAEM was performed using a CPX 500 model of Cole Parmer, USA (500 W, 20 kHz) having a standard Horn probe with threaded end and replaceable tip (¾”, 125mm L × 19 mm Dia.). The dried aerial parts (20 g) of N. leucophylla were extracted with solvents of different polarity. The same plant material was extracted three times with 150, 75 and 75 mL of solvent for 30, 15 and 15 min, respectively. The extraction was carried out at 55±1 ˚C with the controlled temperature sensitive probe. Every time, the liquid extract was filtered twice using Whatman filter paper no. 1. Finally, it was evaporated to dryness with the help of rotary vacuum evaporator at 45 ˚C. The percentage yield of the extracts was noted and these were stored at low temperature for further studies.
Soxhlet extraction method
Dried aerial parts (80 g in methanol, 85 g in chloroform and hexane) were extracted for 36 h at the boiling point of solvent (300 mL) used. After the extraction, same steps were followed as described above to obtain the dried plant extract.
Maceration method
In this method, the plant material (20 g) was extracted three times in a row using 150, 75 and 75 mL of solvent at room temperature (30±3 ˚C) in the dark. In each case, the extraction time was 32 h. After this, a similar procedure was followed as illustrated in the previous methods to get the final material.
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 I want to know the main tests that are required to assess the risks of any new substance for those are working in natural product 
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First you must identify the source of the compound. You must study the toxicity of the source from which you extracted the natural compound and evaluate the risk. These first steps are to protect you physically from the compound (personal protection items). You can also evaluate which chemical groups are in the compound by test for flavonoids, tannins, CN, amines (you will find tests on the web). But if you want to evaluate toxicity, genotoxicity, if the compound is mutagenic, you should study the compounds on different cell lines (toxicity), Ames test, karyotype (genotoxicity).
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Both 1H and C13 NMR values of my sample can be assigned to a known molecule except at one place. From reference values and theoretical point of view, a methine proton (CH) near to a methylene proton (CH2) should give a triplet but I am getting a singlet. Why does this happen? Is there an explanation to this? 
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is CH2_ engaged in H bonding pl.check
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It is slightly soluble in water and is very soluble in dilute alkalies, but is unstable. Does that mean that if I dissolve it first in a base and than mix it really fast with water or other components of my vitamin the decomposition of riboflavin will stop?
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I just  completed a small experiment to test the solubility of (-)-Riboflavin that our lab purchased from Sigma.  The product data sheet was no help so I took some suggestions from this feed and using 1:1 serial dilutions I was able to dissolve riboflavin at ~1mM final concentration in 10 mM Tris-Cl, pH 7.5 with 5% acetonitrile with no observable precipitate after centrifugation.  Hope this helps others as well.
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Whenever the Friedel-Craft alkylation of benzene is bringing about with 1 equiv. of t-But chloride, so a large amount of para-di-tert-butylbenzene is forming, along with the mono-substitution product. Why doesn't all the benzene react to give tert-butylbenzene (a mono-substitution product), any one can suggest a convenient reason.
Thanksgivings.
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After the first alkylation, the product is more nucleophilic than the original benzene reactant, so the t-butyl benzene is now more reactive. The t-butyl group is also "directs" the second t-butyl group to the para position.
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Editor of Journal of Functional Foods has suggested me to include all three compounds in my manuscript
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The natural product curcumin contains three compounds and each of these can have cis-trans geometrical isomers, see attached link; http://www.fao.org/fileadmin/templates/agns/pdf/jecfa/cta/61/Curcumin.pdf
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Please provide reference/ protocol for the extraction of metabolites from the mycelia of penicillium after the filtration step ?
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Yes Sir
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Especially in the extraction and determination of seaweed antioxidants, i have tried with the Pertoleum ether, chloroform, dichloromethane, ethanol and aqueous. i m getting effective antioxidant results for the ethanoilc extracts namely for TPA, TFA, TAA, DPPH, ABTS than other solvents. Could somebody tell me the reason behind the efficacy and role of ethanol in the extraction then any the other above mentioned solvents?
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Dear Thanigaivel,
the reason of your results is that ethanol known as polar solvent for extraction which gives the advantage of extraction polar phytochemicals especially polyphenols. the latter ones are knowing as the most potent antioxidants. there many methods for extracting natural products and each method gives different results especially on the chemical composition which play an important role on the biological effects of these extracts.
the other mentioned solvents are used for extracting specific phytochemical classes with different polarity, for example, petroleum ether is knowing for the extraction of nonpolar constituents, chloroform is knowing for extracting terpenoids  and some nonpolar polyphenols (aglycones). for water which is knowing as the polar solvent for extraction, the aqueous extract will contain all the constituents which play an role in the decrease and the increase of some biological activities basing on the phytochemical classes.
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i am interested to do work on volatile but i need procedure how can i extract volatile compound from sucrose
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I think sucrose is not volatile..
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Hi,
Can celite be used in place of hyflo super cel for filtration of pant extract?
Shall be grateful for a prompt  response.
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surely you can but be cautious  if tjhe filtrate is to be used for food or drug no escape of filtering material is admissible. use protecting filament of smaller pore  size than that of your particle size.
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If I am preparing a herbal formulation with extract and I want the dissolution studies of the same, is it possible to estimate percentage cumulative release (because for estimation of this we need claimed amount of drug and the extract contain number of phtoconstituents) ?  
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Well, that might be a tricky issue. I´d say it depends how many different substance are in your extract, what are their absorption spectra, are they release at the same time and rate and what did you formulate them with. Also, the important questions is what equipment you have available. If you have an HPLC with an diode array detector, this might be relatively straightforward.
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I have a plant with interesting anti-diabetic activities (in vivo experiments) and i want to investigate the effect of some phytochemical constituents of this plant on diabetic enzymes (enzyme inhibition) 
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Dear Thamere, here you have some that we are working on: Amylase, glucosidase, dipeptidyl peptidase-4
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Blue stain with Erlich reagent on mushroom stalk or cap indicate d presence of psilocin or psilocybin but what does green indicates? 
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Thank you Sir Matthew Bernart for your valuable suggestions. 
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We have done a clinical study on herbal tooth paste. We wanted to know if there were any nicotine or nicotine related contents in the samples as there were few papers which raised concerns about presence of nicotine related compounds in herbal based tooth pastes. We got sample analysis done in IIT mumbai. They gave the results but refused to interpret the data. If any one who is interested in giving authentic interpretation we would gladly welcome an duly acknowledge. 
Thanks and regards
Dr. Rajesh.H
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Hi, in addition of the comments above, I think you can predict your compound by using some on line data base, as example you can try the attached link, I think there are many other free MS on line data bases, best regards
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i want to calculate flavonoid and phenolic content of my crude fungus extract in mg/g of dry mass), is their any easiest way to calculate.
mycelia dry weight = 2.40 gm
total extract 237 mg
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Hello,
I am sorry but your question seems to be incomplete. 
Are you looking for the experimental procedure for TP/TF? 
Or you have the procedure and need calculation for it in terms of Wt/Wt?
If you only need procedure, you can get it in any publish article. If your talking about calculation then you have to provide calibration curve for the assay and corresponding value of the sample extract you are using.
Regards,
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i would like to use Flash chromatography.
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Do you know what impurities you have? That will, in part, determine the solvent system and media to use.
Start with thin layer chromatography. More polar solvents cause compounds to elute more rapidly (move further on silica TLC, run faster on a column). Try alumina and silica.  C18 may work too, methanol/water with a little formic or acetic acid to keep the phenols protonated. For C18, the methanol causes the compounds to elute faster.
In the link below, toluene/ethyl acetate was used for purification from silica: https://www.researchgate.net/publication/259133594_Isolation_of_green_coffee_chlorogenic_acids_using_activated_carbon
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which solvent is preferred
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It depends on the species you want to study.
Defatting may eliminate several low polarity constituents and make more easy the fractionation procedure but you must be sure to not eliminate components of interest. Ethyl acetate may extract well medium polarity compounds while ethanol is a more wide extraction solvent. You may also use a multi solvent extraction starting with low polarity solvent as hexane and then use more polar solvent on the base of the elutropic scale. In any cases the choice of the extraction method depends on the nature of the materials you want to study and compounds you want to obtain on the basis of their chemical nature.
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i'm making a hot aqueous crude extract of C. sinensis leaves to see the fungistatic effect on C. albicans. Can someone explain the process of making a crude extract with hot aqueous method? i have read some publication but i don't really get it.
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The suggested procedures are quite correct. But I would suggest to add a step. Once you have filtered the solution obtained by infusion / decotion you should prior perform a lyophilization to obtain dry crude extract which may be weighted. Then you may re-dissolve in a known volume of water until no suspended materials occour. In this way you may have some additional data i.e. efficiency of the extraction method. Then is possible to perform activity tests on more standardized conditions.
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I have dissolved my essential oil in DMSO for some activity. now i want to remove DMSO to obtain solvent free sample.
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I ran into that issue myself. I submitted a compound for NMR in DMSO-D6 and needed the compound back. Essential oils are usually somewhat volatile.
There are two things to try:
  1. If your essential oil isn't soluble in water, just extract the oil using water, and your compound dissolved in dichloromethane, ethyl acetate, hexanes, depending on which organic solvent dissolves your compound. A couple of water washes will remove the DMSO. This is probably the easiest method.
  2. Use a small C18 column, essentially solid phase extraction. One can use a small open column, but I used a small flash column. Details here: http://www.isco.com/WebProductFiles/Applications/101/Application_Notes/AN97_Removal%20of%20Non%20volatile%20Solvents.pdf If your compound(s) don't elute in methanol, the column can be washed with methanol, and the compounds eluted with ethyl acetate or dichloromethane if using silica-based C18. I find this method works better for more polar compounds that are water soluble, yet retain on C18.
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I did a spike and recovery analysis where I spiked a sample with a known concentration of alkaloid , dried the sample and extracted the alkaloids.
My results show that the concentration of spiked sample alkaloids are lower than spiked sample.
What does this mean in terms of method validation?
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Hi, I do agree with those comments above; It could be the method of extraction was not OK, so the recovery will be lower; Have you evaluated the stability of your compound in the selected solvent. Ia attach new guideline for validation studies., best regards
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I need to list all known constituents (not only active compounds) of a group of herbs I am researching. Is there a quicker way than conducting a literature review on each herb?
A colleague recommended Reaxys, but Im new to it and its not as straightforward as I thought,
Any other ideas?
Thanks
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I am working on the effect of a natural compound (quorum quencher) against P.aeruginosa.For the E.coli bioluminescent assay, I want to extract AHL from P.aeruginosa. The method I followed was, the cells and cell debris were removed by centrifuging at 6000xg for 20mins at 4'C. The supernatant was filtered(0.22 micron) and lyophilized. And then it was dissolved in DMSO. 
1. The lyophilized powder is not getting dissolved in DMSO
2. The E.coli reporter strain did not show luminescence.
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Hi:
I have worked with the other QS signal type (AI-2), and detection using Vibrio harveyi worked fine if you filter sterilize only, not lyophilized. Then I put the supernatant in 96-well plates, together with the reporter and measured luminiscence. For the quencher analysis, put supernatant, your compound and the reporter, but at first, test if your reporter is correct. Yet, I don't know the protocol for AHL and I am talking only by experience
Does the reporter work properly with an AHL-positive control? 
Maybe it will work, good luck! 
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I would like to analyze the ceramide content in cells after addition of NBD-ceramide.
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Hi Maiku. Do you mean you want to see the NBD-ceramide by TLC or unlabelled endogenous ceramide?  For either, collect the cells in PBS, add 5 volumes of chloroform:methanol 2:1 and vortex vigorously several times. You should have 2 phases with cell debris at the interphase. Centrifuge to quickly clarify the 2 phases or allow to sit several hours.  Both ceramide and NBD-ceramide are in the lower phase- dry this down and run a portion on silica TLC plates in the solvent chloroform:methanol:water, 90:15:1.  
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What is the procedure to quantify the chlorophyll content from  microalgal  WATER extracts using OD???
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sure sir... currently i am following APHA protocol but that requires the solvent to be acetone not water
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please give answer with paper proof
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Dear Subhaswaraj Pattnaik,
For phenylethyl alcohol, see Table 7 in page 6798 (Chemical composition of methanolic extraction of L. pumila var. alata.) of the attached publication. Regarding benzyl hydrazine, no report was found in my search. However, hydrazin 1,2-dimethyl was found in the methanolic extraction of L. pumila var. alata.
hoping this will be helpful,
Rafik
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When I made the analysis GC-MS of an essential oil, I found as majority product the 1-Chloromethyl-1-(3,5-dimethylcyclohexyloxy)-1-silacyclohexane is that possible and logic the presence of sila (metal Si)
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I strongly suspect that the library search has given a wrong identification. However, it is possible that the chemical class is correct. In such case it may derive from the siloxanes of the column stationary phase
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when we extract rosmarinic acid using Ethyl acetate the spec obtained is 3-6%. How to increase the purity to 34-60%? Any solutions?
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I'd try an ion exchange column. I've been successful purifying acidic plant extracts with a SAX (strong anion exchange) column, and this looks like a good candidate for this purification.
The basic procedure is to dissolve the extract in methanol containing some ammonium hydroxide, filter if needed (to remove neutral or basic non-polar compounds that aren't dissolved), load on the column, wash with methanol (plain methanol), then elute with acidic water (acetic or formic acid). Depending on the column, it may need to be conditioned prior to use with an appropriate ion (acetate, in my case). The columns I used were packed containing a chloride counter-ion and the weak organic acids couldn't displace this ion.
See the flowing links for more details and hints: