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Nuclear Magnetic Resonance - Science method

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Questions related to Nuclear Magnetic Resonance
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The elutrap apparatus I need is for electroeluting the RNA from large preparatory polyacrylamide gel for NMR application. The Elutrap is discontinued kindly please let me know if there is an alternative available for india market .
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Hello, may I ask if you have found an alternative available or Elutrap BT Membranes? I am also looking for a substitute and BT Membranes at the same time.
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The reviewer asked me "NMR: An external standard should be referred for calibration?" But I did not add external standard (TMS or TSP.) when I made it, may I use heavy water (sample dissolved in heavy water) to locate the residual peak of heavy water solvent (4.71)?
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It is not clear from the question what the reviewer is demanding. What kind of calibration? Probably calibration of the chemical shift. This is a very tricky thing and a lot of discussion has been on this problem. An external standard for this purpose always performs inferior compared to an internal one and external referencing is not recommended any longer, therefore. See, for example, Rosenau et al. Angewandte Chemie 2018 (doi: 10.1002/anie.201802620). My personal recommendation is to make a clear and unambiguous statement on the referencing procedure. It is not sufficient to state "the solvent/water signal was used as reference", it is better to write "for chemical shift calibration, the water signal was set to 4.71 ppm" or something like that. This is clear, understandable and unambiguous and will assure for 100% reproducibility.
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In the structural characterization of polysaccharides, the reviewer asked me a question about nuclear magnetism
“NMR: an external standard should be referred for calibration.?”
what is the meaning of external standard ?
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Dear Wu Chuan,
the chemical shift of the residual D2O (actually HDO) does depend on the pH of the sample. You may guess that this pH does not vary if poly-saccharides are dissolved (which will likely be true, if the molecules so not have chemical modifications)....
I hope this helps
Kind regards
Alfred
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can you help me with the calculation of amine group chitosan as meq? I made deacetylation reaction by NMR I calculated as 94%.
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Dear Meltem,
I guess that you already know this literature:
Good luck
Alfred
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There are some papers using HPLC & NMR for separation and determination, respectively. But I am looking for some other techniques, easy to apply and more available?
Many thanks in advance.
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Thank you for your answers.
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was reading an older textbook (Duddeck) they describe H,C correlated COSY, interpreted as C connected to H. Is this essentially interpreted the same as HSQC and HETCOR?
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For interpretation purposes there is no difference. The difference is in the acquisition process. Depending on the device and software used in spectra processing(MestreNova) , in HSQC it is possible to distinguish the CH2 carbons. Important to highlight that both H-C cosy or HSQC, the observed correlation is C-H.
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In most of the textbooks on NMR, we come across the fact that under the 1.4 Tesla external magnetic field, the precession frequency of 1H (proton) is 60 MHz. Can anyone tell why it's always mentioned as 1.4 T instead of 1 T?
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Ganguly
1.4 Tesla is the maximum field strength achievable in a conventional configuration (natural magnet-at the time) which was known in the early stage of NMR development (before the manufacture of superconducting magnets).
Good luck
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I'm a beginner in NMR analysis. I want to know how to read the NMR from my attached file.
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Daptomycin is a type protein. You can see the file. Hope it help you.
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My compounds are not completely soluble in the DMSO-d6, CDCl3, MeOD. I also tried combination of solvents, also I tried 0.1% HCl and heating. Because of the less solubility of compound, the NMR peaks are not as intense as the solvent peaks and I found after heating the compound it is capturing the moisture and showing a sharp peak.
Please help me out to produce the publishable NMR data.
Thank you in advance
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Dinesh, you may want to try Toluene (Benzene) or D2O....
Good luck
Alfred
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I am looking for a good reference for 1-13C NMR peaks for Beta-hmb (beta-hydroxy beta-methylbutyrate), and alpha-HIC (alpha-hydroxyisocaprate). I have not been able to find a single experimental instance of 1 carbon Beta-HMB, or aplha-HIC; however, this experimental data is important for proving a hypothesis in a paper I am working on.
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Dear Donovan,
as you have enough material for a 13C 1D it must be easy to acquire 2D 1H-13C correlated HSQC and HMBC by which a structure determination of the compounds you mention should be simple....
Kind regards
Alfred
P.S beta-hydroxy beta-methylbutyrate may also run under beta-hydroxy isovaleric acid?
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Hi everyone, I am trying to assess the drug loading of a small molecule on PEG. I don't find anything in literature. How can I measure (for dosing purposes) how much of the small molecule is actually attached to PEG? I have read that someone did it with NMR integration but I don't see how since I don't know the exact number of hydrogens in the PEG. Does someone have an idea?
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For a tightly binding small molecule you could diffusion filter the spectrum. Bound drug should have a significantly different diffusion constant compared to free.
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I used a 2 M trifluoroacetic acid solution and hydrolyzed the EPS at 100°C for 2 h. How can I distinguish this method hydrolyzed the samples completely? I don't have access to NMR
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James E Hanson Thank you very much for your valuable help
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Is there an effective way to detect oil/lubricant residuals dissolved in an organic solvent. Both qualitative and quantitative measurements are fine. I am looking for more of a bench top method, quick and easy. I know NMR or HPLC are good for detection.
Is it possible to use UV/VIS spectrophotometer or contact angle measurement??
Any other idea would be highly appreciated.
Thanks
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Hi,
We are looking for the best method to characterize aliphatic sulfur compounds which are decomposed in a few minutes after dissolving in NMR solvents?
Thanks,
Rohit
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Dear Sir,
If your compound has low molecular weight and has volatile nature, you can detect the compounds by simple GC-MS or headspace GC-MS.
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Hello Researcher,
I would like to ask a question about crude (1H) NMR product yield calculation?
When we assign product integration and internal standard integration for percentage yield calculation does solvent (DMF. EtOAc and DMSO) which is used for reaction and workup affects percentage yield? Should I need to give a high vacuum before the crude 1H NMR?
Thanks in advance.
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When re-reading your question I see the phrase "....does solvent (DMF. EtOAc and DMSO) which is used for reaction and workup affects percentage yield...".
Based on this I conclude that your question actually is NOT a NMR question, but a synthesis question. With my very limited synthesis understanding it is clear that different solvents will induce different reaction kinetics related to differences in yield....
I hope this helps
Alfred
P.S. Thanks John for pointing out the 13C satellite problem! This sometimes is important to remember!
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I am working on seaweed polysaccharides and I conduct proton and C13 NMR analysis for the characterization of these polymers. So is there any good software that can interpret the NMR signals/peaks? Or atleast any experts who can help with this?
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I see so many of these questions! Is there software that will solve the answer to complex NMR data? The answer is "no". There is software that will process NMR data, software that will attempt(!) to confirm a simple chemical structure, and software that will aid assignment.
Fundamentally, especially for something as complex as polysaccharides, there is no alternative to an expert.
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Is there any rule to apply in the deconvolution of a MAS V51 NMR curve (in my case, the central transition -1/2 <-> 1/2)? Like limitation of the number of peaks, baseline selection, etc.?
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Hello,
There are a lot of rules! So many that I would recommend using dedicated freeware to do it:
Baseline_corrector for baseline correction if the acquisition was performed with a single pulse acquisition and wide spectral width:
And DMfit for deconvolution:
Nice tutorials exist for both freeware!
Good luck
Maxime
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Hello,
I have used two polymer called PCL and PLGA in 50:50 ratio to make electrospun nanofiber. Are they going be present still in 50:50 ratio in the nanofiber? Is it possible to determine by NMR?
Thank you
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Dear Jakia Khanom, first you should decide on the type of NMR to be used, there a broad informative differences between solid and solution states NMR tools. Solid state NMR is more suited since it reflects the actual phase repartion of the polymers forming the blend. Please have a look at the following documents. My Regards
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I've been collecting a solids HETCOR experiment on a VNMRS (phx 1.6mm probe). When dropping the data into a 3D party program, the F1 dimension isn't scaled to the peaks in the HETCOR. Has anyone ever dealt with this before?
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This almost looks like a factor two problem. Does the 3rd party not account for a split evolution time or is the ppm scale in the indirect dimension based on the 1H frequency?
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I am working with some molecules having benzotrifluoride and fluorobenzene. In the C13 NMR, some couplings are seen. If you have any good paper on the Carbon-Fluorine coupling and coupling constant, please share it with me. It will be appreciated.
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This is always the first place I look
If you go to fluorobenzene (13C) you will see there is coupling to all the carbon positions.
Note these are spectra are quite old and consequently at a very low frequency so on a modern instrument (at higher field) some of the smaller couplings may be not be resolved.
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I'm working on metal-organic coordination complexes, I got a wavy and large NMR shifts for some of complexes which I anticipated as paramagnetic.
Can you explain the relation between paramagnetic nature and large shifting in NMR ?
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Dear Manel Taferguennit in this context, please have a look at the following instructive presentation:
Paramagnetic NMR
The presentation is freely available on the internet. It might also be worth reading the answers given to the following closely related question which has been asked earlier on RG:
Why do unpaired electrons make NMR measurements difficult?
(6 answers)
Good luck with your work!
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Hello experts,
I am using MestReNova software for NMR data processing and plotting, but I am unable to find out an option by which I can show the integration and peak values in the stacked spectrum. stacked spectrum only showing peak, neither peaks values nor integration values. please help me out.
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Hi Rejeev,
I had the same problem and as far as I know, there is no solution to have integrals and peak values in stacked form.
Here is how I fixed the issue: I just processed both spectra in different pages and then I adjusted the height and copied and pasted one spectrum to the other page. For zooming in and out both spectra at the same time, you just need to select all first. I know it might be too late for you, but it can help others.
Bests,
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I am conducting long NMR experiments at 30°C on samples that contain some volatile compounds and chloroform-d as lock solvent. In order to avoid the loss of the analytes and the solvent, I would like to flame-seal the NMR tube. I managed to do so by using a torch lighter. However I found in some bibliographical sources that, the tube must be placed under vacuum.
My question is : Is it mandatory to place the NMR tube under vacuum when sealing it by flame ?
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Dear Salem Baroudi I fully agree with Jean-François Gal in that serum caps or normal plastic caps are most likely not suitable for your purposes. If your samples are highly volatile but not really air-sensitive, I would suggest to use NMR tubes with a stable screw cap. If the samples are also air-sensitive, J Young NMR tubes with an inlet for vacuum / inert gas (as suggested by Lewis Copsey) are certainly the best choice.
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Looking for a high-reliability lab that can run plant samples for metabolomic analysis using untargeted approaches byeither NMR or LC-MS with follow up with data analysis (PCA/PLSDA).
If possible ideally also annotate discriminatory compounds
any suggestions?
Already came across a few amongst which creative-proteomics/metabolomics in USA although many focus more on biomedical sciences (BioAnalytix Inc, Charles River Laboratories, or KBI Biopharma).
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The Metabolomics Innovation Centre (Canada) - www.metabolomicscentre.ca
Over 50 targeted assays (with absolute quantitation) and 6 global/ untargeted assays. Both NMR and MS based services are available, including assays specifically for plants studies. All prices/ assays are available online. Fell free to contact me directly.
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I have learned that there are different methods to study Hydrogen diffusion in metals, like pulsed field gradient (PFG) NMR, and quasi-elastic neutron scattering.
QENS has the advantage of giving the spatial and temporal information.
Are the both methods very effective for all the materials (here restricted in metals and alloys)?
What's the difference between them?
Are there any limits for these two methods? for examples, the covered length scale? or time scale?
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Has anyone isolated and characterized simple straight chain fatty acid sugar esters from plants? Kindly share your experiences.
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  • I would like to ask if anyone has done NMR multiplet fitting, how to export the original data of the peaks (red solid line) after fitting like me, but every time I export the data is the original data of the NMR peak itself (black line) )
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jMRUI software can help. You can insert the raw data and after fitting you can export the fitted data easily.
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I have synthesized a polymer of PAMAM and I see some traces of ethylenediamine (used for the modification) in the NMR. I want to know is there any method I can purify my polymer to get rid of the ethylenediamine? As purification of this polymer is difficult. Both the ethylenediamine and polymer are soluble in the same solvent.
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Dear Anuja Kulkarni, please have a look at the following document, hope it will be usefull. My Regards
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Der NMR colleagues,
  • How can one discriminate NH2 from NH3+ reliably by use of solid-state NMR. The difference in 15N chemical shift due to protonation is often smaller compared to changes induced by different crystal-environments.
  • Due to technical limitations (spinning speed < 15 kHz) we do not have the possibility to acquired 1H data (not knowing whether this would help!).
  • I measured buildup-curves [I5Nsingal(cross-polarization time)] of 15N magnetization, but the results were not very convincing.
Big thanks for any idea!
Alfred
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Dear Dr. Ross,
This is indeed a difficult task. My college Gerhard Althoff-Ospelt proposes a 15N HETCORE. Here, the combination of 15N and 1H chemical shift could give rise to the protonation state. Which kind of equipment do you have? A 7mm probe would be advantageous with respect to sensitivity but a 4mm probe would also be suitable.
Another solution would off course be fast spinning and 1H detection.
Many Greetings
Kristof Grohe
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A sample of water and xerogel was prepared and used. The sample was put in the NMR machine. Then, the sample was inserted in the dryer and then again in the NMR machine several times. The same happened for the second sample which had water, xerogel, and NaCl.
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Does anyone know where I can find some NMR data on the Mannich reaction product from formaldehyde, acetylacetone and piperidine?
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You should see one signal for the two methylgroups near 2 ppm, a triplet or dxd for the methine, a doublet for the methylene and the other 10 protons of the piperidine looking quite similar to free piperidine.
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Dear colleagues,
Do you know any software (free would be the best!) to plot first-order simulated NMR spectra (including chemical shift, coupling constants, splitting pattern and integration)?
After NMR calculations with Gaussian 16 (NMR=(GIAO, SPINSPIN)) I obtained my chemical shifts and coupling constants. Unfortunately, Gaussview, as well as Multiwfn are able to plot only chemical shifts without taking account of spin-spin couplings.
I found WebMo seems able to carry out this kind of plot but not sure it is available for free and would prefer a program working stand-alone on my own computer. I also know NMRPlot, implemented with ENSO package for XTB is able to do this, but not sure it could read Gaussian 16 output.
Thank you by advance!
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Dear Corentin, I guess you know this researchgate post from some time back: https://www.researchgate.net/post/Best_way_to_visualise_Gaussian_NMR_output
Kind regards
Alfred
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I have a mixture of some unknown chemicals. e.g. Isophthalic acid, terephthalic acid, adipic acid or neopentyl glycol, 1, 6-Hexanediol, ethylene glycol etc.
In these mixture 1 component is measure while the other two are in very small quantity which I am not able to detect in NMR.
Can I find the small quantity via GC-MS? if yes, how to develop the method for the detection?
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Thank you Isam Eldin Hussein Sir and Madhukar Sir for your comments.
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I have the NMR and IR of an organic unknown. The percentage of C, H, and O, is 71.1, 5.22, and 23.68, separately. And what are its 2,4-Dinitrophenylhydrazone derivative and Semicarbazone derivatives?
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is that 4,4'-Dimethoxybenzil?
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Hello,
Solvent suppression or in general selective suppression of NMR signals is well established and known in 1D 1H experiments. But how to perform multiple signal suppression (more than one NMR signal) in 2D experiments ? for example perform a COSY with the suppression of two specific NMR signals.
Thank you.
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Thank you Gentelmen for those valuable answers.
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I am working on a NMR data but I could not open the file format in MNova 14. It is showing unknown fid file format repeatedly. I tried to find out the solution but I could not sort it out. Please leave your valuable suggestions to get me out of this problem.
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Hi,
I faced the same problem and solved it. You need to download the mestrenova lite with NMR lite plug-in in it. Here is the download site: https://mestrelab.com/download/mnova/nmr-lite/
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Hello to you all,
In my lab we are trying to find a substitution for producing amorphous water to our current method (using 50 % glycerol and freezing with liquid nitrogen).
When researching the matter, I couldn't find any physical method that produces any substantial amounts of well-vitrified water.
The closest thing would be high pressure freezing used in EM, but it seems that the degree of crystallisation is still quite high here, at least in areas of the sample.
We are using the glassed sample for dynamic nuclear polarisation experiments. The less well-vitrified our sample is, the less NMR signal we get due to the nonuniform distribution of the radicals needed for signal amplification
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To potentially save someone some work in the future: I found a differing method in the paper by B. Lama et al.: "Expeditious dissolution dynamic nuclear polarization without glassing agents", 2016, NMR in Biomedicine
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In our group, the monofunctional benzoxazine monomer containing both bulky group and reactive group was synthesized, and then copolymerized with main-chain benzoxazine resin to form a series of copolymers. We proposed that increasing free volume and cross-linking density simultaneously in the resin could induce the formation of specific multi-structural networks (relatively dense near reactive group and relatively loose near bulky group). We did not find the evidence of the presence of multi-structural network based on the homogeneous morphologies from FESEM results. Nevertheless, the assumed mechanism could be discussed based on the results of true density and cross-linking density (DMA) results of the copolymers.
Now we just wonder whether solid NMR is available to characterize the formation or presence of the multi structural network.
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We have done positron annihilation lifetime spectroscopy (PALS) measurements to characterize the free volume and network structure of samples.
Normally, conventional techniques like XRD, FTIR, TGA, DSC and DMA are used to infer changes in the cross-linking network structure of polymers (Zeng, M., Radiat. Phys. Chem. 2010, 79, 966). However, DMA cannot provide direct information about the changes in the free volume and network structure. Spectroscopic techniques such as ESR, NMR and fluorescence measurements have been used to measure directly the free volume in polymers (Scarlata S.F., Polym. Commun., 1986, 27, 41). However, PALS can provide direct information about the changes in the free volume (subnanolevel) and network structure which are not possible by other techniques (MacQueen, R. C., Prog. Org. Coat. 1996, 28, 97). The advantage of PALS over NMR technique is that PALS uses a smaller probe, allowing detection of the smallest voids (subnanolevel) in a polymer (MacQueen, R. C., Prog. Org. Coat. 1996, 28, 97). Hence, PALS method is chosen to characterize the free volume and network structure of samples.
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I performed a Gaussian calculation and get the data of NATURAL LOCALIZED MOLECULAR ORBITAL (NLMO) ANALYSIS.
I'm wondering if it would be possible to get the sum of the contribution of ''Pi NLMO'' to each Cartesian NMR shielding tensor.
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hello, using IOP's can be helpful.
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What keyword should I use to get all the NLMO that contributions to Atom in different portions(ex: Sigma-zz) using Gaussian and NBO7.0?
I calculated the NLMO by using the keyword ''NMR=GIAO pop=NCSall IOp(6/65=-1)'' in NBO3.0.
But, it does not work for NBO7.0.
Thanks!!!
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hello, using IOP's can be helpful.
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Hello,
I have samples that contain analytes with relatively low concentration (in the order of tens of ppm) in various solvents (aqueous and organic solvents). As the 1H NMR solvents signals are very strong they hinder the observation of the analytes signals (which are present in relatively low quantities), hence, I would like to perform 1H multiple solvent suppression experiments. How should I proceed ? Which pulse program to choose ? (I work on a BRUKER Avance neo spectrometer).
Thank you in advance.
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I am not sure about this video, but it may be helpful,
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If I were to look at the same Li salt in a series of solvents would I expect to observe a trend in which the 7Li NMR signal shifts up field (becomes more shielded) as the Gutmann donor number of the solvent is increased? What other important characteristics of the solvents should I consider when analyzing the results of said experiment? 
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Hi, Watkins, many thanks for your response. I read your suggested papers. I am also confused about the chemical shift of 7Li-NMR. In my opinion, by combining some literature, the 7Li-NMR signal shifts upfield with the increased DN of the solvents, just like the 23Na-NMR trends. However, the explanation of the shift of 7Li-NMR signal is complex because the shift has a relationship with both anions and solvents. The anion competes with solvents to interact with cation (Li+ for example), by forming contact ion pair (CIP) of anion-cation interaction and complete solvated Li+ (cation in solvents cage) of solvent-cation interaction. The papers indicate that the strong solvent-Li+ effect shields the 7Li-nucleus, moving the signal to the upfield. It is generally considered that a solvent with high DN has a strong interaction with Li+. However, some cases are still not clear to me.
1. What’s the effect of an anion when it penetrates into the shell of cation by replacing solvent(s)? Erlich et al. (Journal of the American Chemical Society 1971, 93 (22), 5620-5623) indicated that ClO4−, I−, and BPh4−deshield the cation when they penetrate into the shell of Na+, moving Na signal to downfield. However, Yan et al. (Angew. Chem. Int. Ed. 2018, 57, 14055 –14059) suspected NO3− possess electron-donating to Li+, moving Li signal to upfield. We can also see the opposite trends of Na+ shifts for NaClO4 in different solvents (CH3CN, CH3NO2) with concentrations (Journal of Physical Chemistry 1975, 79 (1), 80-85). It seems ClO4−has inconsistent effects in different solvents, which is confusing.
2. For 23Na NMR shifts with various solvents, Johnson et al. gave an opposed result (Figure S1 in Nature Chem. 2014, 6, 1091–1099).
For a carbonated electrolyte with LiPF6salt, carbonyl oxygen devotes electrons to Li+, forming a solvated structure and moving 7Li NMR signal to upfield. However, 17O NMR signal also shifts to upfield (J. Phys. Chem. Lett. 2013, 4, 1664−1668), meaning the shielding effect (electron cloud density) of O-nucleus is reinforced, which is also confusing.
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Can anyone suggest me how to distinguish between two -NH proton in NMR . my ligand structure consists of two -NH protons. From NMR it was observed one -NH peak resonated at 11.27ppm and another at 10.59ppm. Both the NH protons lie side by side and both of them are attached to carbonyl group on either side. Now I have to ascertain which NH proton posses 11.27 ppm value and 10.59 ppm. Structure is given below. Should I go for D2O exchange NMR.plz help.
O=C-NH-NH-C=O
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The molecule is completely symmetrical so both NH should give same peak; they are chemically identical.
is there another proton on the carbonyl carbon? Your carbonyl carbon only has 3 bonds.
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I have been making labeling medium for NMR work where I add the following:
K2HPO4 12 g/L
KH2PO4 9 g/L
15NH4Cl 3 g/L
NaCl 2.5 g/L
ISOGRO®-13C,15N, Powder 1 g/L
13C-Glucose 4 g/L
MgSO4 0.5 g/L
H2O 1 L (pH adjusted to ~7.4 with NaOH)
When I adjust the pH to 7.4 I observe a huge precipitation. What is precipitating?
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Certainly it's the Magnesium that precipitates as Mg(OH)2.
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Efficacy of NMR spectra software
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Dear Sengottuvelan,
As many people said already Bruker TopSpin is free of charge.
You just have to register (for free) and apply for a license for academia (if you are in academia ;) )
MestraNova is easy to learn and has a good user-interface. It is good for daily NMR-use. For example, you measured a 1H 1D, 13C 1D COSY and HSQC or so. Such data are convenient to analyze with MNova. If you have 3D spectra MNova is not suited. And if you have large spectra or many spectra that you want to analyze simultaneously than I would choose TopSpin.
About other software I cannot comment, because I have no experience.
Many Greetings,
Kristof
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It should be possible to detect the RF signals from the NMR response of ground targets .
But does any one know any algorithm to actually do it?
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Dear Sayandeep
Your questions(YouTube snip) made me think!
you find a figure on absorption of electromagnetic waves in earths atmosphere which shows that anything with a wavelength longer than 100m is blocked. This corresponds to a frequency of 3 MHz. But in this figure it is not clear what happens to REAL low frequencies.
In the paper you find in figure 3 an attenuation of only 10 dB/1000km in the few-kHz range...
Low-frequency attenuation is important, because the larmor frequency of Hydrogen (as present in water) in the earth magnetic field is about 2 kHz (all other elements have much lower frequencies). This is the frequency needed for "imaging" of water (if possible et all).
You have to find the "real" number of transmission/attenuation through the atmosphere in the few-kHz range before you can think about whether MRI of water from a satellite might be possible from a atmosphere-physics (far not yet technical!) perspective.
Kind regards
Alfred
P.S. Again: all this said by a REAL non-expert in the field!
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Dear Scientists,
Hoping all you are fine.
I need to know if someone can recommend me how to know if Al extracted from a zeolite is extraframework or of the framework? (Other technique than NMR of Al)
In Colombia it is complicated to perform NMR of solids and we need to know that data.
Open also to collaborations.
Thanks a lot,
With kind regards,
Julián Sánchez.
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Thanks al, for the response please help me I need Complication Neonatal framework
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I have tried to quaternise P4VP and the mass residue increases from 0 to 12% at 750oC. I have tried to quaternise by chloroacetamide and confirmed it through FTIR and NMR
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Dear all, what is the counter ion of the quaternized polymer ? Possibly, it is not excluded even at high temperature. Thus it counts for residual mass increase. My Regards
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I need a site where I can see 19F, 1H, 13C spectra of organic compounds.
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Shubham Gupta hi! Spectral Database for Organic Compounds (SDBS), Reaxys.
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Hi everyone, I hope you can help me answer my questions:
1- what is the benefit of terminal hydrogen in nanosheets?
2- I need simple information help me to understand B3LYP, LaNl2DZ, GGA and BSSE in easy way
3- I need simple information help me to understand NLO, UV, IR,NMR, E(thermal), ZPE and Cv and their importance in hydrogen storage
Thank you..
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Perhaps opening up or channeling thermal oscillations to some energy-intensive thermal oscillation (or containment of phonon) can raise Cv (const. volume-specific heat). But why one needs to purposefully increase it? Well, then more thermal energy would be required to cause its temperature change, so thermal fluctuation would be smoothed out, or the material itself can be used as a heat storage medium without excessive cooling or heating. Coupled with the high thermal conductivity of 2D and 1D allotropes of carbon, this means the thermal storage media within itself would not undergo much thermal-gradient induced stress. So thus you have a twofold advantage.
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The protein is in phosphate buffer pH 8 and when i try to decrease to ph7 it aggregates.
Is a virus envelope protein with 42 Kda and it is fusogenic. I want to do some NMR experiments with this protein, and i can decrease pH in low concentrations like 5 uM. But when i concentrate to 300 uM it aggregates.
Thank you all!
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Hello everyone!
Our group is trying to synthesize PIM-1 and bought some TFTPN from different companies. However, the TFTPN from different companies showed different colors-from white to yellow. The companies told us that they are the same good and provided us with the NMR spectrum. I am confused about how could the same compound has two colors. Did you encounter the same issue before or have any idea?
Thanks!
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Dear Yuewen Jia, whatever the color is, it should be purified by sublimation prior to its use. My Regards
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I searched the related questions, some people answered that the nitro group will make this carbon missing in the NMR. But I would like to know the principle how does the nitro group affect?
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It is very likely that the C attached to the nitro group has a (very) long relaxation time (as do all C atoms without a H attached).
If you repeat the experiment with a longer wait between pulses you will give the C time to relax (but it will of course increase the experimental time).
This C will also not benefit from NOE as only C with H attached will show this effect (caused by the decoupling).
There may also be some coupling of this C to the quadrupolar 14N which due to the small electric field gradient typical in nitro nitrogens and consequently may not completely decouple itself.
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Hello community,
I would like to have an efficient drying protocol of deuterated NMR solvents. Which drying agent to use ? How much do I have to use ? Do I have to wait for a certain time (24h or less) ?
Thank you in advance.
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Baroudi
You can add molecular sieves directly to the deuterated solvent and cap. Leave at least 24 hrs and prepare your NMR sample under a dry inert atmosphere.
Good luck
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Done
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As far as I know you can still upload a PDB file for NMR data, but PDB_extract will convert the format if needed. Upload one model file with all the 20 models in the ensemble superimposed.
The optional files in extract are crystallographic. You don't need to upload optional files.
Start a session at wwPDB and see how far you get, it is reasonably intuitive. If you are stuck, there is a means of communicating with wwPDB staff who are the ideal people to give you advice
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I have functionalised some low viscosity alginate with adipic dihydrazide. I have already carried out FTIR on the polymer, which shows that my synthesis has been successful in modifying the alginate with the ADH. I am now trying to conduct NMR on it to find the degree of functionalisation. However, I cannot get the alginate-ADH to dissolve properly in any of the standard NMR solvents (DMSO, DMF, water). Deuterated water has been the most successful so far, but the alginate will only dissolve at 0.25 wt%, which is too low to get a good spectrum. At the standard 2 wt% it forms a gel, which means I can't do NMR on it. Does anyone have any idea what is causing this problem or what I can do to solve it? Thanks in advance!
These are the papers I used for the synthesis protocol:
They do not mention any solubility issues when it comes to conducting NMR.
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Prepare a 2% gel, then heat it sharply to a transparent solution, and then cool it sharply to a temperature at which you can do NMR. Polymer solutions take a long time to come to an equilibrium state. You may need to find the best heating and cooling times.
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Hello, I want to analyze the metabolic profile of cell lines by using NMR and LC-MS. After doing the NMR on the sample, I want to know whether I can use the same sample for LC-MS?Thanks
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Dear Saman,
In what solvent do you do your cellular extract (deuterated MeOD/D2O)?
Presence of exchangeable OD's will complicate the MS analytics substantially, because any exchangeable OH will be present as a OH/OD mixture...MS experts are normally not happy with this situation.
If you do the extract with MeOH/H2O I would split the sample prior of adding D2O lock. Normally a small aliquot of a NMR sample is adequate for LC-MS anyways.
I hope this helps
Alfred
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In a synthesis, I am trying to react a cationic Re complex (with BF4 as counter anion) with tetrabutylammonium chloride. This gives me a Re-Cl complex and nBu4NBF4 (tetrabutylamonium tetrafluoroborate) in the reaction mixture. For workup, I am washing with pentane and diethylether and extracting the ReCl complex in benzene. But the NMR shows signals for tetrabutylammonium cation. Could anyone suggest me how to clean up the reaction?
P.S.: The Re compound is air and water sensitive. Prepared in glove box.
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Is  your compound stable to alumina or silica? You could run it through a quick plug, which should grab the TBAOH because it is ionic. Recrystallizing from MeOH, EtOH, oriPrOH would work too if your compound can be crystallized from those solvents. TBAOH would be somewhat soluble in those solvents. Good luck!
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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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In Vietnam, there is not any place to test the solid-state CP-MAS C13 NMR spectra at the current time. If you know, please recommend in the details (contact person, reference price, and so on). Thank in advance!
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Dear Prof. Dr. Nada,
Thanks for your participation in this discussion. I would like to share an outstanding article about the solid-state CP--MAS 13C NMR spectra as the following article:
Upcoming, I will contact to the group (Saint Petersburg State University: Saint Petersburg, Russia) to see how.
Best regards.
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It is known that direction of the ring current in an aromatic molecule is such as to generate a magnetic field that opposes the external field inside the ring (a 'diatropic' current), while the ring current in an antiaromatic molecule flows in the reverse direction ('paratropic'). What is the reason behind this?
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When a external field is applied over a molecule, it was shown that it creates an induced magnetic fields and as a response to that, the electrons move around the molecule as explained classically by the Faraday's Law (this is similar to the effect of magnetic fields on a coil in classical physics).
We must also notice that due to quantum mechanical effects, the current can flow on two different ways: (the classical one) the diatropic, or the paratropic. There is an advanced review with useful information.
doi: 10.1002/wcms.1270
There is another one who explain how to obtain the magnetically induced current densities:
doi:10.1016/j.chemphys.2008.10.040
I hope this information works.
Kind Regards.
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Can anyone please explain which type of structure is preferred for a ligand-Receptor docking study? When both the NMR based and X ray crystallography based structures both are available in PDB?
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X-ray-based structures are preferred because of their higher resolutions
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Hi I am relatively new at using Gaussian. I ran an NMR calculation in gaussian09 but when I try to view this it doesn't look anything like the example in the documentation. It doesn't show any splittings or couplings even though I used the SpinSpin module. Also I have fewer plot properties visible. Have I missed something out of my input file? Sorry if this is a silly question and thanks in advance.
Edit:
I seem to be having issues adding attachments. This is the beginning section on my input file.
%NProcShared=4
%Chk=NOOO.chk
#n B3LYP/6-31G(d) NMR = (giao,spinspin)
NOOO-Pbca NMR
Edit:
Sorry I wasn't clear, I was already using GaussView. I've now used another computer to upload pictures and you can see in the NMR I've done its a series of lines rather than a spectra with the splitting patterns and there aren't many properties available to alter.
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You can use Multiwfn (http://sobereva.com/multiwfn) to simulate NMR spectrum based on output file of NMR task of Gaussian, it is easy to use, flexible and has rich capabilities. See Section 4.11.10 of Multiwfn manual on examples of plotting NMR spectrum for various cases.
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I want to make Poly(N-Isopropylacrylamide) amine terminated, using Free Radical Polymerization (i use AIBN as initiator and DMF as solvent, reaction temperature is 70˚C) and 2-aminoethanethiol as chain transfer agent.
After polymerization, i concentrate the reaction mixture and precipitate in ether, then filter and vacuum dry to obtain white powder.
I have tried several times but the NMR spectra shows no peak of amino terminated.
Is there any tips or suggestion to make AESH correctly reacted and make sure that my product has amine terminated group at the end of polymer chain?
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Hello, Bernard, do you find the reason for your problem I have the same so please shear problem solution
thank you in advanec
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NMR spectra for natural compounds
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Please go through these attachments and I hope this will helps you. 
1. Charisiadis, P., Kontogianni, V., Tsiafoulis, C., Tzakos, A., Siskos, M., & Gerothanassis, I. (2014). 1H-NMR as a Structural and Analytical Tool of Intra- and Intermolecular Hydrogen Bonds of Phenol-Containing Natural Products and Model Compounds. Molecules, 19(9), 13643–13682. doi:10.3390/molecules190913643
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I am trying to use CB(8) and various gels as a part of my PhD project, and wish to do some NMR on it to confirm inclusion within it. But as it is quite insoluble in many solvents or they become a gel in other solvents, I do not know the best way to go about it. Any suggestions would be appreciated!
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What feature the spectra and, or methods can you use to confirm inclusion?
The rate of overall molecular motion determines how much H-H dipolar coupling contributes to the H--1 and/or C-13 NMR line widths.
For solids, you would need to use solid-state NMR methods.
For gels, the answer depends on the viscosity of the sample. H-1 NMR may be possible. The lower the viscosity the more narrow the line widths. If the inclusion complexes are stable above room temperature, increasing the probe temperature could be helpful.
Finally, is there a dynamic equilibrium between inclusion and non-inclusion species? If you are unlucky, the exchange rate could render the relevant lindwidths to be very broad.
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I intend to characterize a synthesized polymeric particle, and I've been wondering if the CP-MAS version can provide any additional information about the involved chemical bonds and the material's inherent properties. If it does, is the method of interpretation any different?
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Dear Iman Azamian,
2) The method of interpretation is same same. You could refer my article which have mentioned the solid state-NMR spectra of anionite lignocellulosic materials as the following link: pubs.acs.org/doi/10.1021/acsomega.0c01984
Best regards.
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Hello,
It's a Sparky beginner. I wanted to make a nice picture with protein assignment but for all assigned residues I have the name format as ex. L166N-HN and I want to avoid "N-HN". I have found in Sparky manual that:
Display format for assignment labels
The assignment format specifies how to display assignment labels on contoured spectra. The default format is "%a1-%a2" for a 2-D spectrum. The "%a1" means display the full atom name for the w1 assignment. The full atom name includes the group. Then the "-" is just put into the label. Then "%a2" means display the atom name for the w2 assignment. The "%a2" will not display the group if it is the same as the group displayed in the preceding "%a1" part. To force the groups to be displayed use "%A1-%A2". In general, "%a" means display the atom name and leave off the group name if the preceding % format displayed the group, whereas "%A" means always show the full atom name. To show just the group names use "%G1-%G2". To show just the group name for the w2 axis use "%G2".
So I've changed the assignment format for %G2, but nothing changed in my spectrum, although peak list changed. I also tried to save the new peak list and upload it again, but then I have problems with unreadable lines..
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type "pl" and change it to whatever you want under the "user".
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Dear all,
I have a question concerning a 2D-1H/1H-NOESY NMR of a two-compound mixture.
The compounds in question are two atropoisomers which are present in a roughly 2:1 ratio (the phenomenon of atropisomerism is known for these compounds:
- Kingo, U. et al., Chemistry Letters 1999, 28 (1), 63-64
- Göstl, R. et al., Chemistry – A European Journal 2012, 18 (45), 14282-14285
- Uchida, K. et al., Journal of Molecular Structure: THEOCHEM 2002, 579(1), 115-120
- Goldberg, A. et al., The Journal of Physical Chemistry A 2003, 107 (25), 4982-4988).
Having examined the corresponding 1H, 13C, COSY, HSQC and HMBC- spectra I could elucidate the connectivites of the major compound present (in CD2Cl2 @ 280 K, concentration roughly 50 mM). To ascertain which of the two possible atropoisomers is the major compound at hand I have recorded a 2D-NOESY spectrum and the result is shown in the attachment. What you see there are the crosspeaks between the aliphatic protons (namely the allylic protons of a 1,2-cyclopentene moiety and the methylene of two attached 2-ethyl-hetar-1-yl systems in 1,2-position of the cyclopentene).
Now the strange thing I noticed are the crosspeaks e.g. between the dublett at 7.81 ppm to the multipletts at 3.05 and 2.90 ppm since HSQC clearly tells me that these latter two multipletts clearly correspond to the minor species. Along those lines, the crosspeaks between the three multipletts at around 7.55 to 7.65 ppm to the multiplett at 3.25 ppm should also not be possible since the former downfield multipletts clearly belong to the minor species (as elucidated by heteronuclear coupling).
The question I have is now the following:
Has anyone of you experienced similar artifacts in 2D-NOESY spectra?
Best regards and I'm looking forward to your ideas
EDIT: Could it be that the mixing time was too long and that this is why I see correlations between the isomers?
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If there is slow exchange between the two isomers it is possible to see cross peaks between the isomers. First you should look for cross peaks between the same atoms on both isomers. You can also make it easier to distinguish between NOESY peaks and exchange peaks if you run ROESY instead of NOESY. In ROESY experiments Oberhauser and exchange peaks will always have opposite phase. Also cooling down the sample will reduce exchange related signals.
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I am looking for a laboratory that specializes in separation, analysation (analyse by NMR) and interpretation of alkaloids, please can anyone helpe me?
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Doctor Tatou Touahria , if you were from Baghdad, I would guide you to a number of research centers that provide analytical equipment for research purposes, but it became clear to me that you are from Algeria.
My greetings
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Hello,
I synthesized alginate methacrylate and performed an NMR spectrum. I'm not an expert in organic chemistry and I would like to be sure how to calculate the degree of methacrylation.
Thank you very much for your help
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We can not calculate the degree of methacrylation by using NMR spectra. In this case, the role of NMR spectra only conform that the chemical reaction has occured or not through looking up the feature peak of chemical bonds (For example: C=O, C=C, and so on). If your samples exist the solid state, you can calulate the degree of methacrylation by using the increase level of dry mass and titration method of functional groups.
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I have done NMR of a catecholate type siderophore, and I have expected to be a Bacillibactin, but I don't understand what the peak represent and how to derive a structure from that graph and peaks.
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Dear Aftab Ali ,
Concerning siderophore, they might be quite big molecules and not the simplest to elucidate through NMR analysis. Nevertheless, from a experimental point of view, I could suggest you to take a look on these different articles:
As you can notice, many methods are used in NMR for the elucidation of structure (1D: 1H, 13C, 15N, 2D: COSY, HMBC, HSQC, H2BC... and NOESY) as the structures are complex.
From the point of view of theory, and, if you are familiar with calculations, It is also possible to "predict" NMR spectra via ENSO (developed by Grimme's group) and ENSO utility:
To compare with experiment, I could suggest you to take a look at this excellent article :
Hope this could help you in knowing your structure !
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I have a freshly synthesized formyl-CoA but not sure if it really is. Some published articles introduce that they used ToF Mass spectroscopy. But as a matter of money and time, for me it will be difficult to use it.
What other techniques can I use to identify this big molecule formyl-CoA?
Can I use NMR?
A little explanation of how it's possible will be hugely appreciated.
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Dear Jo
You can use the electrospray ionization-ion mobility spectrometry apparatus for detection of the big molecules.
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I prepared an in-cell E. coli NMR sample according to the protocol mentioned in :
However, I was not able to lock the sample with 10%D2O. Any help would be highly appreciated. Thank you.
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One thing you could do is pre-lock on a mock sample of bacteria in the conditions your real sample will be. just grow some cells (the ones to produce your protein or even DH5alpha, doesn't matter) in some rich medium, spin them down gently and resuspend them in the final medium (incl D2O) as your good sample will also be. Fill an NMR tube (shigemi without plunger) by gently spinning down the cell suspension in the tube, yielding a cell pellet,. Make sure you have enough cells for the pellet to occupy the whole coil volume, and leave some medium from the supernatant above the cell pellet (that will replace the plunger). use that sample to lock and shim before inserting your real deal sample (prepared the same way). that should give you enough flexibility to play around with parameters before inserting your precious sample.
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I suspect I have some dissolved methane (and maybe propane) in my aqueous solutions. Please see attached spectrum (for both spectra: number of scans is 256; same receiver gain; same method; water suppression was poorer for my experimental sample). In green is my experimental sample and in red a control one with only pure water (red shows a few peaks which can only be some sort of contamination). If it was a liquid or solid species, I would buy a commercial standard and spike my NMR tube after acquiring the spectrum to see if a new peak(s) appears or the one I saw previously grows (confirming it's the same species).
Is this possible with gases? Should I simply add such gas in the headspace of the NMR tube, shake the contents for a while, and re-analyze?
On top of this, I'm of course performing all sorts of negative controls to make sure these putative gases don't come from a contamination and were indeed synthesised during my experiments (which is what I'm looking for).
Thank you,
Eloi
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There should be no problem to "spike" the solution with additional gas (bubbling it through the solution or fill the space above the liquid and shake), we did this often with hydrogen or hydrocarbons. If you suspect methane as product, you can identify it by recording 13C since its shift is very characteristic (below 0 ppm). If the concentration is very low, you may use indirect detection.
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I did some reaction of polymer synthesis in which triethylamine was used. I have NMR of the resultant polymer in which I am expecting that triethylamine is converted into diethylamine. Is it possible? Please share some references. Thanks in advance.
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