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NMR Structure Elucidation - Science topic

NMR Structure Elucidation is the use of NMR to assist in the determination of chemical/molecular structure.
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I recently analysed NMR data for one of my pure compounds and there was a singlet peak (1H NMR) integrating for 18H. My supervisor has said that no natural product comes with a t-butyl moiety and my compound may be a contaminant or plasticizer. Is it because having two t-butyl groups would be bulky and is biosynthetically not probable?
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Apparently 2,4-di-tert-butylphenol is produced by dozens of different organisms. I am still in two minds as to whether this is true, or the result of either environmental contamination or bad lab technique. The more I read on this topic the more it seems it is indeed a natural product. It could be easily resolved by conducting an experiment where 13C-glucose is used as the sole carbon source...
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For example in case of NMR spectrum n-Propanol in CDCl3 why don't we get the signal of ( -OH) functional group in the absolute right position of the spectra instead the peak appears after the (-CH2) Group as a triplet. What is the possible reason for that?
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With aliphatic alcohols you only get exchange of the hydroxyl protons if there is something to exchange with - normally if water is present.
In CDCl3 the solvent breaks up hydrogen-bonding interactions (that would be present in pure propanol) so the chemical shift of the -OH protons is reduced and will appear between the CH3 and CH2 chemical shifts.
The same thing happens in ethanol and is a classical example of these effects and as such is explained in "Physical Chemistry" by W.J.Moore.
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Usually the proton NMR ,the aromatic,NH2peak appears downfield between 4-6. Is it possible to observe it at even more down field?.Is there a possibility for merger of aromatic NH2 and aromatic ring hydrogens?
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NH peak observed upfield region with variable position (5 to 8.6 delta ppm ) where as -OH peaks observed in down field region about 14.5 delta ppm in proton NMR
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When trying to identify an organophosphorus compound, one of the ways to proceed is to compare the phosphorus chemical shift of the compound of interest with those of a standard. However, this comparison is meaningful only when operating in the same conditions. When using deuterated water as a solvent, pH is one of the parameters that must be taken into account. So does pH really influences the 31P chemical shift ? and if so, how strong is this influence ?
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It does, however it depends on the class of examinated organophosphorous compound. For most of 1-aminoalkylphosphonic acids (1-APAs) and hydroxyphosphonic acids (HAPAs) pH significantly influences the 31P NMR shift.
NMR-titration is not in my interest so I cannot give you exact pH values, however I have few examples just to give you overview:
1) 1-APAs 31P NMR chemical shift may change for about 5ppm.
My example is 1-(methyloctylamino)ethylphosphonic acid: 14ppm in acidic solutions (6M HCl); 10ppm in alkaline solutions (as disodium salt with NaOH).
Another example is 1-amino-1-methylethylphosphonic acid: 22ppm in acidic solutions (4M HCl); 17ppm in alkaline solutions (as disodium salt with NaOH).
2) APAs 31P NMR chemical shifts may change for about 5ppm. My example is 1-hydroxycyclohexylphosphonic acid: 27ppm in acidic solutions (4M HCl); 22ppm in alkaline solutions (3M NaOH).
For other classes of organophosphorous compounds pH-dependent changes in chemical shift may be as high as 10ppm. I may suggest few articles where this issue is discussed:
b) J. Chem. Soc., Dalton Trans., 1999, 1603–1607
c) Fresenius Z Anal Chem (1984) 317:697-698
To identify compounds by 31P NMR I also compare multiplets (on 31P NMR spectra without decoupling) and coupling constants (as they are less sensitive to pH changes).
Best regards,
Anna Brol
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How  we can predict or determine apparent  molecular mass for globular proteins using pulse field gradient -Stimulated Echo NMR experiments. I am looking forward to characterize the presence of different oligomeric forms of protein using Translational Diffusion Coefficient as a parameter   Can anyone suggest the references in which  similar studies have been discussed
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Molecular weight prediction with no dependence on solvent viscosity. A quantitative pulse field gradient diffusion NMR approach. Polymer Chemistry, 7(26), 4326–4329. https://doi.org/10.1039/C6PY00691D
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Dear eminants,
goo morning,
I have isolated a plant compound and characterized usingLC/MS and NMR but the structure elucidation is very much difficult to us. Will you please help in this regard. If accepted, I will send you LCMS and NMR data to you.
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Dear Ravi, If you are still searching for the solution, you can inbox me the inquiry.
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What is the minimum amount of sample required for different kinds of NMR analysis (1H, 13C, 2D NMR etc.)? Does the amount will be vary for different NMR instruments depending on the strength (like 500 mhz, 600 mhz etc)?
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An excellent question, really, but I am at a loss to answer it, though I should be qualified enough. One thing is a routine, fast acquisition with a standard 5 mm tube of a solution of relatively small molecule which is the dominant substance in the sample. Then it might be maybe a microgram for 1H and a milligram for 13C on a standard high field instrument. But it all depends on a long list of conditions and desiderata:
1) You should ask about molar concentration (molality), refered to the specific nuclei that you need to observe; total amount of sample is meaningless. For example, if you are looking for impurities in, say, aspirin, it is a completely different question than looking at the aspirin molecule itself.
2) Can you afford higher concentration in a smaller volume? 3 mm tubes, or even microfluidic probe with nanoliter volumes (they have better molar sensitivity).
3) Field strength, as you mention. It goes (very roughly) with square of field strength, and it may depend on instrument make and its current state of maintenance. In general, its a big deal when you switch from 200 MHz to 800, not really too much when the jump is from 500 to 600
4) How much time can you give it? Sensitivity goes inversely with the square root of the accumulation time, roughly. So, considering 1 minute overhead, the difference between 1 minute and 1 hour measurements is really huge.
5) Do you have access to a cryo-probe?
6) What do you mean by "different kinds of NMR analysis"; does it include 2D's, 3D's, MAS, DOSY, HR relaxation time measurements, reaction kinetics, ...
An exhaustive and competent answer would take a review of a considerable size, I think. If you narrow down the question, I am sure that you will start getting a lot of answers.
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Dear researchers,
Currently we are working on ssDNA aptamers against various diseases in humans. We would like to get supports from the NMR data through collabarations. drop a message if anyone interested.
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Hi,
Although I am not good at NMR technology, I suggest you might try to work with Creative-Biostructure, whose NMR platform has the state-of-the-art NMR instruments.
All the best!
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Can anyone tell me how to search AIST database with proton/carbon NMR chemical shifts? Before I tried, but in the long run failed to get the suggested chemical structure. Your cooperation would highly be acknowledged.
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Whether you are asking a person or using a program, you need to give some information about the structure, you cannot just put in the numbers and expect to get an answer.
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Can anyone give me a step by step guide to predict a compound structure using NMR results.After the NMR analysis of our samples, we always been provided with PDF file or Image file of a spectrum. with that how can we predict the structure of a molecule. And is it sufficient to have the H and C NMR to find out the structure or we need the 2D NMR.
Valuble suggestions are welcome. I am basically a microbiologist. I do not have any chemistry background. Moreover, I still search for a chemist for collaboration.
Hope some one will guide me to the right path.
Thanks in advance,
Dr. Siva
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Dear Sivasankar,
You should read a book which teaches you how to determine the structure by NMR. You don't need to read the physical basics of NMR. Here I attached a book which I think can be helpful for you. Actually, I can't give you a step by step guide because then there are much to write! 
About your second question, it depends on your structure that whether you need 2D NMR or not. The normal structures can be determined by H NMR and C NMR. But for complicated structures such as natural products or for the compounds with a special stereochemistry, you might need 2D experiments.
Cheers,
Ashkan
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Dear plz confirm NMR spectra of enclosed structure with NMR spectra Whether is it correct or not if not then kindly predict correct spectra if possible
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This is unlikely. The molecule shows a -OCH3 on one of the rings. There is no singlet to be seen between 3 and 4 ppm.  The aromatic signals do not really add up to 12 when one excludes the Chloroform signal.
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Suppose R1CHOHR2 is a chemical reaction in which hydrogen is replacing by fluorine. Where is the chemical shift of R1CHOFR2 in F19 NMR.
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Dear Prof. Anthony,
Thank you Prof. for your positive reply.  Yes, It is very informative. But in my case, R1 and R2 is not alkane group. I am getting peak In this region. but I think they are obtaining by an addition of fluorine to carbon as I sent you the possible structure. I will send you the detail of F19 NMR processing.
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Hello,
I synthesized (HO)2P(O)CH2CH2P(O)(OH)2 and made NMR analysis. 1H and 31P are very good. 13C gives me a strange pattern, though.
There is a publication about the Methylester, they also observed this pattern but gave no further description. (http://dx.doi.org/10.1016/j.tetlet.2016.06.079)
An unsymmetrical bisphosphonate gave two well defined doubletts of a doublett. Thats easy to explain.
But in this case (see attachment) I can not explain how the signals are achieved.
Has any one an explanation?
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Even if it is a bit late, an additional remark on this interesting topic: in carbon NMR you observe a molecule that has three NMR active nuclei (one 13C, two inequivalent 31P because of lacking symmetry in the observed species, as has been pointed out by ETK Haupt). So it is not an AA'XX' but an ABX spin system (X carbon, A and B phosphorus) which may show in its X part up to six lines. Five were observed, two may coincide, so there is nothing wrong. If you consult some old-fashioned text books on NMR, you will find these phenomena discussed, but, unfortunately, most modern texts leave them out. So I frequently get asked about such "oddities" in the carbon NMR spectra of "symmetric" phosphorus compounds, but there is nothing special at all...
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I have optimized  benzene  and biphenyl rings separately. how to combine benzene into the 4th position of biphenyl ring.
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in gauss view:
1) open both of your molecules in separate windows, copy benzene by edit-->copy
2) in the window of biphenyl ring, past your molecule by Edit-->past--> append molecule
3) to set the position correctly you should use keyboard and mouse
holding (shift+alt) will move only that molecule which you click.
holding (Alt) and moving mouse will rotate only that molecule which you click.
4) move and rotate your molecule using keyboard shortcuts and place your molecule at your desired location make/remove bond by builder--> modify bond and then clean the structure (Edit --->clean)
5) now you can optimize. after which you get the desired structure
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I need help regarding the DOSY NMR, I have a sample mixture which consists of two components confirmed by 1H NMR and ESI-MS analysis. The two components has a molecular weight difference of nearly 2500 g/mol . But after doing the DOSY NMR It is showing the single diffusion coefficient value for both the components rather than two diffusion coefficient values.What parameters need to be changed in order get the better resolution of diffusion coefficients in DOSY NMR. Any kind of help will be appreciated. Thanks
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Hello,
you may have some success by experimenting with different solvents or mixtures thereof. The next issue of Magn. Reson. Chem. will contain a paper touching this subject:
Resolving DOSY spectra of isomers by methanol-d4 solvent effects (pages 759–762)
Indrek Reile, Ruud L. E. G. Aspers, Martin C. Feiters, Floris P. J. T. Rutjes and Marco Tessari. DOI: 10.1002/mrc.4587
Maybe that helps. Best wishes,
Ludger Ernst
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I would like know about metal effects on nmr spectra. 
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I don't know about these specific compounds, but Pregosin's book is an excellent general text on NMR of organometallics:
Pregosin, P. S. (2012). NMR in Organometallic Chemistry. Weinheim, Germany, Wiley-VCH.
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For 1H and 13C NMR data analysis, I am using Bruker Topspin 3.5. Is there any preliminary actions I should do on the raw spectrum (background substraction, corrections, etc) before analysing the data? . Thanks all for the support.
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In many cases also apodization and baseline correction are useful tools.
However,  all these operations may introduce several changes in the peaks intensity which should be considered if you are interested in the evaluation of the integrals values.
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I have got 2 pure compounds both 0.8mg. One is a white powder-like substance while the other is clear and gooey-like. I had isolated them using HPLC and wanted to know if they can be analysed by NMR even though their masses are quite low. Both are able to dissolve in MeOH.
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Dear Mr. Sinclair,
if your compounds are uniform it should be possible to do some NMR experiments on them using a sensitive spectrometer, e. g. one with a cryo probehead. You could obtain one-dimensional 1H-NMR spectra without problems and also, by indirect detection, two-dimensional heteronuclear correlated spectra like 1H,13C-HSQC or -HMBC spectra. If possible, one should not use (deuterated) methanol as the solvent because one would lose information on the presence of exchangeable protons (OH, NH, SH).
Best wishes.
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Dear colleagues, I need to know, is it  impossible, difficult or not important? Did you know anyone ever tried this? Thank you!
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I did use a disorder prediction software and it shows that the C-term of P2X7 is actually intrinsically disordered. And the recent publication on P2X7 structure does not includes the C-term as well. Might be due to the reason where it is impossible to crystal?  
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Hi everyone! I would like to know if there are any quidelines or literature on how to set up and run a quantitative 1H-NMR experiment on a 400MHz Bruker NMR. What commands do I use and how do I process the results?
Thank you!!
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Enter the Manuals section in topspin (or type "docs" in the command line). In the "Analysis and Simulation" section, you will find a manual  (or rather a presentation) called "Quantitative NMR".  I have, in any case, attached the file to this answer.
In principle, you just have to set up a normal 1H spectrum. You add an internal standard (some known amount of substance), and can then calculate the contents of the analyte either on your own from the integrals or use the "nmrq"-command to do that for you (which is the better way to do this).
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What is the minimum quantity of a compound required for solid state proton and carbon NMR spectra
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 For 13Carbon around 25-30 mg and solid state even more. not more than 100 mg.....
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In aluminoborate glasses, [3]B - [4]Al interactions are preferred over [4]Al - [4]Al or [4]B - [4]B interactions due to tetrahedral avoidance rule. Can anyone comment on the comparison between [3]B - [4]B and [3]B - [4]Al interactions in aluminoborate glasses? Which one of the two is thermodynamically more stable/favorable? Any reference from literature?
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Thanks for the detailed response, Elizabeth.
-Ashutosh
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..
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Okay thanks, 
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Dear all,
I am observing a peak at 0.08 ppm in the 1H NMR spectra CD2Cl2 (I attach a copy of the 1H NMR spectra).
Does anyone had observed this before? Does anyone know what compound gives a signal at 0.08 ppm in the 1H NMR spectra CD2Cl2?
Many thanks for your help
Best regards
Vicente
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There are multiple different silanes or siloxanes that give signals in this range. It could be TMS but one often sees "joint grease" there or other compounds that can be leached out of for example rubber seals in disposable syringes.
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I expected occurrence of two isomers populated at 3% and 97%, but it seems i used diluted sample. can u advise which concn. is suitable for 1D and 2D NMR measurement. I noticed in HNMR and CNMR that the amplitude is very low. iN NOESY and HMQC, i noticed the intensity of cross peaks is fairly good. 
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I noticed that two carbons have integration of 50, while the other carbons have integration between 110-130. Can i conclude existence of two isomers. Regarding H-NMR, peaks integration are almost identical. 
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Because of the nuclear overhauser effect, primary, secondary, tertiary, and quatenary carbons all have different integral for the same number of carbon atoms.
secondly, due to the low abundance of the C13 isotope, the integral of the same type of carbon has limited accuracy. 
You will probably be better off finding the isomers in the 1H NMR. You only mention the integration, but the coupling could also provide evidence of isomers if the splitting is more complicated than expected (i.e. you get a multiplet instead of triplet, or doublet etc.)  This is a very general statement and must be seen in the context of your compound.
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Dear All, Can anyone kindly assist in the interpretation of the attached file containing 13C NMR of a newly isolated compound.  I need the assistance of an expert in NMR interpretation and structural elucidation of the file attached to this post.
I would gladly welcome your kind assistance. Thanks. You could also contact me via siroplc@gmail.com
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Thank you all for your concern and interest to assist me.
@Uday and John, kindly see the scanned copy of the 1H NMR.
@Clemens and Widyo, I sincerely appreciate your contributions. Thank you so much.
I would be more grateful if anyone could assist me with the structural elucidation.
Kindly let me know if any other information is required.
Thank you.
SIR Okoduwa,
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Dear one and all,
I am working on a metabolite of an organism. I am trying to deduce the structure of that metabolite using spectral analysis. I got the chemical shifts around 60-65 ppm for the methylene moieties connected to the nitrogen atom. And 68-73 ppm chemical shifts for the methylene moieties connetced to carbonyl moiety. The compound is containing an iodine atom as well. In general, the methylene mioeties can not have such higher chemical shifts. Why am I getting such results? Whether, it is due to presence of iodine moiety?
How far the chemical shifts in a NMR spectrum are influenced by presence of iodine moieties in a carbonyl compound? Whether the chemical shifts for the methylene moieties connected to nitrogen atom and/or carbonyl carbons can go around 60-70 ppm in a NMR spectrum.
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Thank you so much Sir.
Regards,
A K Dubey
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Hi there,
I need some opinion. I've conducted my research project using bioassay- guided method. Out of three sample crude extract I've used, only two of them showed an activity. I've further fractionated the two of it using packed column. Unfortunately, none of the fraction showed any activity. What I can conclude is that the activity happens because of the synergistic interaction between phytochemical present in crude. Do I still need to isolate those compound? Or should I just proceed to identify what compound contain in each fraction using NMR perhaps? For the information, I did screening those fraction using TLC and in each fraction, there were one or two spots developed under UV 365 nm.
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Thank you for all the opinion. I'll try to check back my extraction method. =)... there must be some point that I missed out.
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I have isolated Triterpenoids olean type. For structure elucidation I am working on NMR spectral data My peaks for 12-ene in oleanolic acid is different compared to  the reported chemical shift. My nmr solvent is chloroform whereas I could fine the data in Pyridine. So how solvent changes the chemical shifts for only 12-ene rest are same?
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Dear Dr Aisha, the value of 160 for carbon in 13 position is compatible with the chemical shift of a quaternary carbon in beta position to a carbonyl function conjugated with an alfa-beta unsaturation, but 112 ppm for carbon in 12 position is a low value, it should be around 130 ppm.
Carbonyls may have longher relaxation delay. If you are sure that the signal at 160 ppm cannot be due to a different carbon than C-13, you may re-run the 13C-NMR accumulating more transient in respect of the previous experiment (may be the double of the scansions) and setting a major delay for d1 (may be 2 or 3 sec). With these condition an eventual carbonyl signal should be visualized.
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Dear All
Pertaining on the title, I would like to know, how do you double check the result to ensure all compound identified is correct. Here I attached the lc-ms result for perusal. I don't have authentic standard to check it. Can I just use Nmr or FTIR to double check the structure and compound. please advise
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Usually high-resolution mass-spectra data is fairly reliable and can be used for identification. If you want to confirm the identity of the detected compounds, then using standards is the most straightforward method (you will have a combination of HRMS and retention time data, which is pretty unique). 
IR would be useful for identification of functional groups, and of course NMR is the best tool to determine the structure. However, for taking the IR or NMR spectra you will have to isolate each component is sufficient amount and purity, which is (usually) not practical.
In any case, having LC-HRMS data is a good starting point; perhaps you may need to confirm the presence of only few compounds of interest. If, for example, it is critical to confirm the presence of only one, let's say, unusual compound, I would make efforts to isolate it and collect all possible data, including NMR, IR, etc.
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My protein has two tryptophans. The indole resonance of one disappears while unfolding and then reappears when the protein completely unfolds. What could be the possible reasons?  
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Exchange with the solvent is certainly one option. But I would also check if it is not just shifting somewhere else. What pulse sequence are you using. If the sequence includes a 3919 part make the interpulse delay quite a bit shorter to make sure the resonance did not fall into the next null. 
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i am in need of reference NMR data for physcion 1-O-β-gentiobioside. I searched it but could not find. i want to know the change in chemical shift values in proton and carbon  NMR data when the glucose is attached to 1 and 8 position of an aglycon, Physcion.
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A direct comparison with an original sample is the best solution. However the following papers may be also of help for the structure elucidation of glycosidic anthraquinones.
Francis et al, Magn. Reson. Chem. 36, 769-772 (1998)
Holzschuh et al, Planta Medica (1982), 46(3):159-161
Ko, S.K. Arch Pharm Res (2000) 23: 159. doi:10.1007/BF02975506
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I synthesized iron oxide NPs capped with a branched polyethyleneimine. 
But I dont know how many amines are included on iron oxide NPs
and  actually I also dont know polyethyleneimine cover the iron oxide NPs
Though I used IR spectrometer to check functional group on surface of iron oxide NPs, I couldn't confirm amine functional group. I think the reason is the color of iron oxide NPs is black.
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why not try SEM or XPS to first confirm the anchoring of amine functional group?
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There have been instances where I observed a new spot in TLC plate and have isolated it via Column Chromatography.But it could not be characterized even after obtaining data for 1H, 13C and DEPT 135.
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Combine it with other methods too. Mass Spectrum can be analyzed also, to provide valuable information on your new compound.
Make sure to anticipate what you synthesize, also the biproducts. If you have any clues prior to an NMR analysis, it will be much easier. Simulated spectras can be generated for possible compounds and this may lead to your final conclusion.
Otherwise, if the compound is somewhat medium sized or small, it should be possible to identify it using your mentioned methods, 1H, 13C and DEPT 135.
Although you probably know, there are a few more NMR methods you can also apply which may help, especially 2D, such as COSY/HETCOR,
Hope it helps,
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I am trying to find a way to analyse migration of certain type of organic molecules into polymer tubing. This organic molecule contains basically carbon/hydrogen/oxygen. I've tried to use IR microscopy to detect the molecule in the tubing cross-section, however, the peaks were barely discernible on top of the polymers, given that most peaks overlap, and the quantity of this molecule is very low. I am thinking about using the isotope labeling for the molecule, substituting hydrogen with deuterium. The IR microscopy is one option, since C-D, O-D will all have different peak locations from the C-H, O-H. Considering the low quantity of the molecule, are there more straightforward/sensitive/nondestructive ways to detect D element itself? SEM/EDX is not feasible to light elements, what are other options?  
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I dont think deuterium labeling will be of much help- since the exchange rate with hydrogen is very high - so you will lose your labeling fast.
Can you prepare your samples with C13 or N15?  if so - the detection will be straightforward 
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One of my isolated compounds didn't match with any structure on Scifinder data base. Do i have to try other data bases or not? If it is yes which database that I should look through?
Thanks in advance 
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 Science Finder is the best database to know the novelty of your compound (s).
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Respected Researchers, I have isolated Astaxanthin compound and it is in semi-solid phase. Just i have isolated bands by Pre-TLC. Anybody can suggest me how to prepare and send my sample for NMR analysis?
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Dear Eswar,
If you are still looking for the answer, please check this link. I believe that this will be of great help.
Regards
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Running a reduction with excess of PhSiH3. In the NMR of my aliphatic product I find a big ugly bulge in aromatic area. It can only be some oligomers or polymers of arylsilanes bound with Si-O or Si-C* bonds. The reaction was quenched by HF in methanol and product isolated by column chromatography (the impurity doesn't show up in TLC), so the sneaky polymer is not so easy kill.
Does anyone have a clue how to destroy or get rid of this thing? My product is rather stable, so, harsh methods can be used.
* At the reaction conditions I can also see the formation of Ph2SiH2 from PhSiH3, so, the formation of new Si-C bonds is definitely possible
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Since your product is perfectly soluble in hexane, the using of fractional ditillation as David J. Pérez  mentioned is quite good. I agree with him.
Best wishes
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I get the fragments of Pulegone, Menthofuran, Sabinene hydrate, Dihydro carvone from GC/MS. So, how can I decide the chemical structure of fragments? Is there any reference paper regarding the fragment structure of those terpenoids?
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Dear Somnath,
Since, you already have mass spectrum of each of your compound of interest. You may directly match your recorded spectra with available libraries if installed in your mass spectrometer.  I am sure that the  resultant hits (library) will be very much correct as these compounds are already known.
If you are willing to understand in detail about mass spectral fragmentation technique specific to type of functional groups, you should consult textbooks like Spectrometric Identification of Organic Compounds by Robert M. Silverstein, Francis X. Webster, David J. Kiemle, David L. Bryce etc.
Otherwise, attachment named terpene by Mr. Raj is also useful in order to understand this concept.
Good Luck
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The use of a combination of natural product/herb and medicine is still difficult to establish the effects produced by them.
Can anyone share about the step in investigating the combination effect of plant and a single compound drug in inhibiting enzyme?
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The Chou and Talalay method is widely used. See the following papers:
(1) Chou, T.; Talalay, P. Quantitative Dose-Effect Relationships : The Combined Effects of Multiple Drug or Enzyme Inhibitors. Adv. Enzym. Regul. 1984, 22.
(2) Chou, T. C. Drug Combination Studies and Their Synergy Quantification Using the Chou-Talalay Method. Cancer Res. 2010, 70 (2), 440–446.
(3) Chou, T.; Kurin, E.; Mučaji, P.; Nagy, M.; Hidalgo, M.; Sánchez-Moreno, C.; de Pascual-Teresa, S.; Iacopini, P.; Baldi, M.; Storchi, P.; Sebastiani, L.; Chou, T.; Wang, S.; Wang, D.; Liu, Z. Theoretical Basis, Experimental Design, and Computerized Simulation of Synergism and Antagonism in Drug Combination Studies. J. Food Compos. Anal. 2010, 67 (3), 621–681.
(4) Chou, T. C. Frequently Asked Questions in Drug Combinations and the Mass-Action Law-Based Answers. Synergy 2014, 1 (1), 3–21.
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I am wondering, if it is possible to have multiplate and doublet of doublet anomeric protons in polyphenol glycosides? If possible then in what case? Usually, alpha- and beta- configurations of sugar attachments are determined through J-couplingvalue but J value is absent in multiplate anomers whereas there are two J values present for doublet of doublet anomer. So how can we determine the alpha- or beta- configuration of sugar. 
I am looking forward its answer with literature references. 
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I just want to mention one detail for you, Prakash. If you are not certain about if there is a mixture of anomers or not, just run a quality analytical HPLC (C-18?) of your glycoside. That should answer your doubts easily.
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Hi, I am performing a cyana str. calculation using automated noe assignments. 
The following is my CALC.cya file.
peaks := 13Cnoe,15Nnoe          # NOESY peak lists
prot := new                                 # names of chemical shift lists
constraints := new.aco               # additional (non-NOE) constraints
tolerance := 0.028,0.028,0.32    # chemical shift tolerances
calibration :=                              # NOE calibration parameters
structures := 200,20                   # number of initial, final structures
steps := 10000                           # number of torsion angle dynamics steps
rmsdrange := 10..80                  # residue range for RMSD calculation
randomseed := 434726              # random number generator seed
noeassign peaks=$peaks prot=$prot autoaco
=======
The problem here is that I have acquired the 13C and 15N edited noesy spectra with slightly different mixing times which is 100 and 120ms respectively. Now how do I ask cyana (OR perform peak calibration) to set slightly upper distance limit to 15N noesy? 
Your response is highly appreciated. Thank you for your time.
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You can use automatic option (empty) and dref for the first run.
And then, the outcomes (final.upl) can be adjusted manually.
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I am working on Natural products and we search for Novel products and check its NMR prediction online.Before, our university had an access to nmrdata.com but now we don't have an access. I ma not so skilled so that i can directly draw a structure from 13C NMR. as,i have no idea without NMR database.So, please anyone can help me to tell me any website on which i can check my NMR data for free.Thanks.
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Dear Syed Shams ul Hassan,
You could try at the nmrdb.org website:
The predictor looks legitimate, but I have never used it, for such things I usually use ChemAxon MarvinSketch NMR predictor. It is a chemical structure drawing program, which you can use for free with an academic license.
To obtain it, please visit:
You can first request an evaluation license and next - apply for the 2-year academic research license if you like the program.
You could also try using the NMR predictor from CambridgeSoft ChemDraw or MestreNova - these packages offer very accurate and reliable predictions, but you need to pay for the license.
Finally, remember that what NMR predictor tells you is only some kind of a qualitative guideline, and usually you shouldn't expect perfect matching between the predicted and real spectra.
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My compounds are aromatic. The peaks and integration of aromatic region is accordingly, still some extra peaks mainly from 0.7 to 3 ppm, are observed.  the peaks from 2 to 3 are usually singlet. The compounds are purified by c.c using DCM or ethyl acetate/n-Hexane. Can you please share your experience??????? Thank You.
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From my experience, many peaks are coming from solvent traces or other impurities (e.g. grease used with glass material). In the case of solvent traces, I don't think that your peaks are related to ethyl acetate or n-hexane, as you should find multiplets.
Simply, you should do first a blank experiment (solvents without compound) to identify the source of impurities.
Alternatively, I recommend to do additional NMR experiments (1D 13C and/or 2D-HSQC) to assign these peaks and check whether it is related to your compounds.
With additional information, I think that we will be able to solve the problem.
Hope it helps.
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NMR spectra for metabolomics
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There is no online tool that helps you guessing an unknown compound from NMR data. 13CNMR suits best for that (that is why there is NMRdata.com) but 1HNMR is quite complicated.  The best advice is that you learn how to do structure elucidation based on 1D and 2D data. My advice:  try the methodology explained in the Crews et al. book.
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Is it possible to assign a noesy spectrum with sparky/nmrfam. If not what other softwares are good for a reliable noesy spectra assignment.
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Hallo,
With Sparky it is possible to assign a noesy Spectrum. Programs like ccpnmr and cara are also able to do this. All these programs are free. I would prefer ccpnmr.
greetings,
Kristof
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which is position of the peak in NMR and how many peak would be there?
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19F NMR (400 MHz, CDCl3): δ -100.9 (1F, s, CF) ppm
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I am willing to analyze this molecule (3,3',4,4'-benzophenone-tetracarboxylic dianhydride, also known as 4,4′-Carbonyldiphthalic anhydride) by NMR spectroscopy (1H).
I cannot find any scientific reference about this analysis, although my guess was CDCl3, but maybe there is a better solvent, such as d6-DMSO ?
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Both CDCl3 and d6-DMSO seems viable, and both can be easily dried prior to use. You  may find that two different solvents may give you slightly different 1H NMR spec as well.
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Could anyone please explain how and when 195Pt satellites can disappear from 13C NMR spectra in 2JPt-P-C or 3JPt-P-C-C heterocoupled systems? Thanks.
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Imre, one reason they can disappear is when 195 Pt relaxation becomes too fast due to CSA. 195 Pt satellites can be present in spectra at lower field, broaden at intermediate fields and disappear at high fields.
Clemens
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I've got the C9 formula of a lignin sample, and calculated the percentages of each proton type from the 1H NMR spectra. Now how should I calculate the proton numbers per C9 formula? I need the specific calculation method, or the related references.
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your welcome :)
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Hi everyone! I'm currently on my way for structural elucidation and I'm having a hard time getting a useful HMBC data. I'm using a Varian 500 MHz and VNMRJ 3.2 as software to operate the machine. I'm just using the default settings for gHMBCAD because I think they are already optimized(Jnxh=8 Hz etc.). Most of the time, the data that I usually obtained includes several peaks at around from 1- 5 ppm(mostly in the aliphatic region) but lacks signals for aromatic and carbonyl groups.  My sample weighs usually at around 1-3 mgs. Usual operations such as finding lock signals, shims seems to be fine, temperature etc. Do you have any thoughts about my problems. I run it mostly more than 12 hours. Thanks in advance.
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I presume you have been using VNMRJ for quite some time and I further presume you are familiar with ChemPack Pulse Sequences. The following are my suggestions, assuming that there are no hardware related issues; (1). Ensure that the probe file is complete with all the mandatory values, (2). Check the performance with Varian supplied Application Sample - "2-ethyl-1-indanone" - by running a proper 1H NMR Spectrum followed by choosing the menu option - "Convert Current Parameters To Do --> .... -> .... -> ....." and choosing "gHMBCAD", (3). Choose the default value settings and record the experiment, (4). Process the data and observe how the 2D spectrum looks like. The outcome will give an insight and have the doubts cleared that the system, probe and software are working fine. Now, you can repeat the experiment with your sample. As an alternative to HMBC, you can also record CIGAR which is also part of VNMRJ Pulse Sequence Library. Few tips; (1). Ensure that the probe is properly tuned for 1H and 13C, (2). Always record the 2D experiments under VT regulated condition. If your sample is not sensitive to temperature then my preferred VT setting is 30 Deg C.
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I have searched through Dictionary of Natural Products and found a reported compound. The structure of my compound was found to be identical with the reported one. However, there are some slight difference in signals for proton NMR which might be due to the use of different solvent. I am using deuterated chloroform while the reported compound was measured using DMSO-d6. Three NH-functional groups were observed with my compound exhibiting signals at 6.39, 8.15, and 10.14 ppm as opposed to the reported signals at 8.14, 10.55 and 10.79 ppm in 1H NMR spectrum. Thus, I would like to figure out the novelty of my compound. Is the use of different solvent for NMR analysis the cause of such difference in signals? 
I would greatly appreciate any opinion or suggestions about my question from any professionals and researchers in the field. Thanks in advance
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The chemical shift differences for the NH protons are entirely consistent with the solvent change. DMSO is a much stronger H-bonding solvent than chloroform, causing significant shifts to higher frequency for NH and OH protons. The one NH shift of 10.14 ppm in CDCl3 suggests a possible intramolecular H-bond involving that proton. You could check to see if your structure is  consistent with a bond like that.
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This cyclic peptide has poor solubility in many solvents, such as methanol, acetonitrile, CHCl3, DMSO, DMF, and water.
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I think IR and eventually solid state (CP-MAS) 13C NMR could be a good start.
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I have extracted oil from a shell and I assume that it is product A is dark brown in colour. I then distilled product A and obtained a colourless product B. I want to combine A and B so that I can find a drug which can be used for cancer. Is it possible? If no, please can you explain why?
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Thank you sir i will work it out.
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I isolated a compound from a plant, sent it to NMR and got some results but I have no idea how to read the spectrum or detect the compound and structure elucidation. Any help is appreciated.
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I think better start with reading all paper about your species that you are working with,, (or review article)
and list all secondary metabolites from that paper
usually you might find similar or even same compound from that published article
good luck!
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I got some active principle say it as an antibiotic. In order to know the exact molecule what are all the validations and methods I should employ to find its structure. Kindly brief each and possible references. Though FTIR , NMR and MALDI can help I wanted to know any thing else is still available new?
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Before going to NMR you need MW, UV spectrum, mechanism of action, a panel of antibacterial activities also comprising strains resitent to known classes of antibiotics, to check in literature for already known compounds ( about 20,000 are the microbial products).
Also stability of the molecule at 3 pH is useful.
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Thanks
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Do you want to send a protein sample or your amino acid sequence? If you want to do it experimentally, you can start with CD spectroscopy to get an idea of the secondary structures. Ultimately you would choose some crystallization method to really see the 3D structure. There is many groups and I am sure that your lab is affiliated with someone, otherwise I can't see why this wouldn't be done commercially, although I don't have an example.
If it is just about the sequence, Ahmed is right, there is plenty tools from simple secondary structure prediction to complex threading algorithms. Besides the ones mentioned by Ahmed, you can also find an overview of available tools on wikipedia. http://en.wikipedia.org/wiki/List_of_protein_structure_prediction_software
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see above
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It could also be that poor digital resolution is limiting the ability to truly define the peak maxima. Try zero-filling 2x or 4x more points to be sure that you are measuring the true maxima in the spectral lines, and you can also use deconvolution methods to determine the true peak maxima if there is overlap.
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I need to know the best solvent for solution NMR spectroscopy of cellulose.
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Gudluck
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While I run H nmr for an isolated cpd using CD3OD as a solvent, the CH3O group which should appear at 3.8 ppm is lost. It only could be detected through HSQC cross peak.
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What I meant was that if the CH3O moiety would have been replaced by a CD3O moiety as you suggested, the carbon signal would not be a singlet, but look similar to the carbon signal from CD3OD i.e. it should have 7 peaks, about 21 Hz from each other.
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Though it's common to measure 13C NMR for 2-mercaptoethanol, I would like to measure 1H NMR spectra.
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2-Mercaptoethanol, 1H NMR (200 MHz, CDCl3, δ, ppm): 3.71 (dt, HO-CH2), 2.70 (dt, HSCH2), 2.18 (s, OH), 1.38 (t, SH).
13C NMR (300 MHz, CDCl3, δ, ppm): 63.41 (HO-CH2), 26.71 (HS-CH2).
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I am trying to record the 2D-NMR of a peptide in DPC. Currently I am having some problems to get the proton NMR signal itself after addition of DPC into the water solution of peptide. Though the proton NMR of peptide in 10% D2O water is very clean. After addition of DPC (generally people start titration with target lipid until observe any micelle effect or chemical shift of peptide H-NMR signal) the H-NMR signal disappears. Does anybody have an idea on how to solve this? Peptide precipitates in SDS micelle.
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There are probably two possibilities:
1. The peptide aggregates in DPC, causing the formation of large mixed peptide micelles that are invisible to NMR. If this is the case, the whole 1H spectrum should have disappeared including the residual DPC peaks. DLS can also give you conformation that large mixed micelles are present. This is not uncommon with cationic peptides that do not adopt secondary structure upon membrane binding (see for example
If this is the problem, try adding the detergent to the peptide above the CMC immediately. Free detergent below the CMC may be the cause of the aggregation.
If this doesn't work,there isn't an easy answer to this problem except to try another detergent.
2. The peptide binds the micelle in the intermediate time-scale which leads to broadening of the peaks. In this case, the peptide should have a broadened signal but the residual DPC peaks should be sharp (most of the DPC molecules should not be participating in exchange). You may have to add some protonated DPC to see the peaks. If this is the problem you can try the following to shift the on/of rate to move the timescale into either a slower or faster region to get a better spectrum:
1. Change the temperature
2. Add more DPC (keep above CMC)
3. Go to a different field spectrometer (since the relevant timescale depends on the magnetic field)
4. Add NaCl
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In NMR based structural determination we label N15 or P31 and determine the structure with various methods e.g. NOSY. How would we do that in checking protein ligand interaction?
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Express your protein in minimal media containing 15N-ammonium chloride as a nitrogen source. Similarly to using 13C-enriched D-glucose as carbon source. That's how it's done in our lab. Usually the % labeled amines is quite high although the protein yield in minimal media is typically low compared to complex media.
Protein-ligand interactions on the other hand are relatively simple to do with NMR. A 15N-1H HSQC is already very informative if you can assign the resonances to the corresponding amino acids. For assignment you naturally require several more multidimensional spectra than HSQC. Of course, using conventional 1D and 2D small-molecule spectra, you can follow the ligand resonances in the presence of unlabeled protein and so-forth figure out which parts of the ligand are responsible for interaction.
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Some isolated compounds are somehow difficult to detect their masses by electron bombardment MS
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If you have a gc-ms and don't have acess to an api-ms try chemical ionization, it might solve your problem.
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I have been trying to alkylate one of my early transition metal-dichloride complexes. The alkylating reagent is benzyl magnesium chloride (as a 2M THF solution). In spite of all my attempts, I am unable to get rid of the free benzyl magnesium chloride peak at 2.75 ppm in my 1H NMR (C6D6 solvent). How does one commonly remove such impurities? Crystallization does not help!
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Add a few drops of 1,4-dioxane. It shifts the schlenk equilibrium to give Bn2Mg and MgCl2 which are very insoluble and then after removing all solvents under reduced pressure, your product can be extracted with aromatic or hydrocarbon solvent, depending on solubility.
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Is their any relation between the J-coupling constant and the geometry of molecules? I have a molecule: 1,3-Oxazepine 4,7-dione derivatives and it has chiral center. I would like to determine if it has R or S configuration and was wondering if I could do so by using the J-coupling constant? If so, how?
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If you have only one chiral center in your molecule, then you cannot distinguish R/S absolute configurations by simple NMR spectroscopy, since two enantiomers will have identical spectra. J-coupling can only allow you to assign the relative configuration (cis/trans or E/Z) to diastereomers, i.e. when you have two or more chiral centers.
If you want to assign the R/S absolute configuration to your compounds you will have to use chiroptical spectroscopies like circular dichroism, or perform NMR with chiral shift reagents.