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Nuclear Magnetic Resonance - Science method

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Hi solid-state NMR experts,
What happens to the 1H resonances when a proton exchange starts to take place at the surface of metal oxides? Let's say we have multiple highly resolved 1H resonances in the MAS spectrum of an evacuated metal oxide material. There are basic and acidic hydroxyl functions (terminal, bridging and triply bridging).
If this material is exposed to humidity and rehydroxylation starts to occur, a proton exchange with the acidic OH groups (?) is expected to occur under ambient conditions, isn't it? If yes, what would be the possible effect(s) on the 1H MAS spectrum?
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Thank you for your answer. Unfortunately, due to circumstance I cannot do any more experiments now (otherwise I was thinking of using D2O already).
What I have observed is that I have got splitting of some of the acidic sites into a 2:1 doublet or an asymmetric but very well-resolved triplet.
I have re-admitted air into the sample rotor step-by-step and measured a few times. The (sharpening and) splitting has come progressively with more exposure to air and has passed through a max. splitting. The magnitude of splitting is 60 to 70 Hz. We're talking about isolated OH groups (no or little H bonding involved), I've very sharp lines for solid-state NMR.
For instance, an initially 2.73 ppm resonances gradually splits into 2.85, 2.72 and 2.60 ppm. There is slight shift of position.
The basic OH group at very high-field does not undergo splitting, supporting the assumption of proton exchange at the acidic OH sites.
But I cannot understand why such a splitting occurs if it is simply the protons being exchange between H2O in the immediate surrounding and the OH at the surface.
The sample is gamma-alumina. My first theory was actually something completely different: namely, the asymmetric triplet is caused by a residual dipole-dipole interaction between 1H and 27Al (1/2 vs 1/2, 1/2 vs 3/2, 1/2 vs 5/2). But the way the splitting occurs (i.e. increases by increasing humidity exposure) makes me a bit skeptical about this theory.
So based on the above details, what would you assume?
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I am coding a solid-state NMR pulse sequence on SIMPON (attached file) but I get this error (error: acq overflow in fid points) that I don't know what it means. Does anyone knows what it means?
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Forgot to attach the code....
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I am in need to perform variable temperature NMR for my sample. Kindly let me know any universities which makes the services available for externals.
Thanks
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Both VT-HT and VT-LT are available at SAIF, IIT-M for external users
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It is not possible to quantitatively assess the hole concentration by using the
((Tc)/(Tc_maxc) = {1 − 82.6(p − 0.16)^2 In other words, the argument of determination of holes concentration] is scientifically incorrect by above formula. the correct determination of holes concentration is from nuclear magnetic resonance (NMR) and angle-resolved photo emission spectroscopy (ARPES) experiments that multi-layered cuprate superconductors have non-uniform hole concentrations in each CuO2 plane.
Is the above statement true? Give answer in the light of above comment please.
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Thanks for your answer please explain for superconductor composites
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Hi guys, I am preparing a presentation on diffusion NMR, where I introduce great names on NMR, such as Hahn, Purcell and Stejskal. I can`t seem to find much information on Dr. John E. Turner Jr (from the Stejskal-Tanner equation).
Does anyone know of his fate and birth year?
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Auto correct change tanner to turner --'
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Compounds isolated from plant are to be characterized using NMR, FTIR and MS.
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Luc is perfectly right. I REALLY depends very much on what you want to do. To add two which is widely used for quantitative NMR based (plant) metabonimcs: https://www.chenomx.com/ or https://spin.ccic.osu.edu/index.php/colmar
... but is definitely is NOT the one if you are after de-novo structure determination of yet unknown natural products (here ACD with all its packages may help, as Luc already pointed out).
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I have to acquire NMR spectra of marine sediment so I have very high concentrations of salt. I'm using a cryoprobe on a Bruker 600MHz spectrometer and I'm getting very high 90° pulse durations (˜25us) from pulsecal and I'm worried that they could damage the probe.
I have tried diluting the sample to two times the initial volume and the pulse duration goes down a bit (˜18us) but it's still way higher than the suggested 8us.
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Dear Lorenzo,
I am VERY much wondering why HSQC is a problem.
  • What I do to estimate what NMR time it takes in a 2D HSQC I do the following:
  • First acquire a 1D 1H
  • write this spectrum to a 2nd process number (e.g. wrp 2)
  • Divide the spectrum in procno 2 by 100 (dc 0.01, mulc) to accomodate for 13C natural abundance
  • superimpose this spectrum with the noise of the original 1D 1H spectrum.
Doing so you can estimate how many more scans it will take to have a signal substantially higher than noise.
  • If you need to multiply the down-scaled spectrum by 8 and it took 32 scans for the 1D 1H you will need (at least) (8*8)*32*2 scans in total in the 2D.
  • For a HSQC with 256 t1 increments this means NS has to be at least 16.
All this is of course ONLY true for small molecules where relaxation can be neglected.
In our experience matching and tuning is NOT highly affected on 13C by high salt....
Goog luck
Alfred
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Dear ResearchGate Community,
I hope this message finds you all well. My name is Michael G. , and I am a Ph.D. student. We are currently synthesizing the lipid NBD-DPPE and are facing some challenges concerning its purification, NMR sample preparation, and in need of NMR data.
  1. Purification: We're looking for effective methods to purify NBD-DPPE. Any advice regarding techniques, tips, or even literature recommendations would be greatly appreciated. In particular, we'd like to know details regarding column chromatography (mobile-phase, stationary phase, etc)
  2. NMR Sample Preparation: We would also appreciate guidance on preparing the NBD-DPPE lipid sample for NMR analysis, including the most suitable solvent system and ideal concentration. We understand that lipids can sometimes present specific challenges in NMR analysis due to their hydrophobic nature and tendency to aggregate, and so any advice on this matter would be highly valuable.
  3. NMR Data: Lastly, if anyone has NMR data of NBD-DPPE lipid and would be willing to share, this would immensely help us in validating our results and ensuring the accuracy of our product.
Thank you very much for your time and consideration. I look forward to any advice or suggestions the ResearchGate community may have to offer.
Best regards,
Michael G. Ph.D. Student.
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I can't help you with your purification or reference spectra, but we do occasionally work with comparable lipids and they tend to dissolve relatively well in methanol/chloroform mixtures.
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4 protons peak may be CH2 near a heteroatom .
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I don't think your question is specific enough. Where is this extra peak located for instance. What is your NMR solvent? And if you are doing a basic ester hydrolysis, what do you mean with "hydrolysis in acid NMR"?
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How can we employ NMR spectroscopy to determine the molecular weight of polyethylene glycol (PEG)? Is it feasible to use NMR to quantify the number of monomers within the PEG chain?
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you should convert the alcoholic endgroups into esters by reaction with (non proton bearing) derivatisation reagents like trichloroacetic anhydrid or trichloroacetyl isocyanate. See: Polymer Bulletin 1991 , 27, 201-204
Best regards and good luck
Gerhard
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I checked NMR of commercial PGA NMR and i getting two peaks between 4.9 to 4.8.
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You should only be getting one peak. What is the ratio of the peaks?
Could the other peak be residual glycolide?
Does the CHCl3 peak look normal, or could the two peaks be caused by poor shimming?
Can you run a 13C spectrum to verify that you actually have two peaks?
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It is known that sample conductivity affects pulse durations in 1H NMR experiments. But how does the concentration of NaCl in a sample affects pulse durations in sodium-23 (23Na) NMR experiments? Is it the same effect as with protons?
It would be helpful if some references can be given. Thank you.
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Thank you Gregory J Rees!
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Is it possible that the peak intensities of an MTSL-labeled protein+ligand be higher than the peak intensities of the unlabeled protein+ligand in 2D NMR? And what would that mean if it happened?
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Dear Paul,
William gave an excellent explanation...nonetheless three questions:
* Are ALL peaks in 2D (presumably 1H-15N HSQC?) affected or only a subset (in line with Williams explanation).
* How do 1D 1H (e.g. watergate) with long interscan delays (>10s) of the two samples compare?
* Have you deterined the 90° pulses for both samples? Absence or presence of salt (coming or not comping with the protein constructs) may be another explanation.
Alfred
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How can we detect the molecular weight of PEG in NMR? Is it possible to detect the number of monomers in that?
Thanks
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it depends on the MW. If you can see the resonances of terminal units ( usually in polymers they have a slightly different Chemical shift) you can try to make the calculation of MW from the ratio of their integral with respect to that of the CH2 units of the polymer , Otherwise a DOSY 2D experiment may give an estimate of the molecular Diffusion from which you can derive the MW by the Stokers Einstein equation.
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I analyzed my polymer sample after polymerization by NMR and GPC. The Mn that I obtained by GPC didn't match with my conversion rate obtained by NMR.
For exemple, for a PEGMA RAFT polymerization I have an average Mn at 20852 and I calculated a conversion rate at 62%. My monomer molecular weight was 500 so, normally I have to have a molecular weight around 31000 for a conversion at 62 (62*500=31000). What is the problem?
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Hi Mathilde. This is perfectly normal. The molecular weight obtained by SEC is not actually molecular weight. The SEC instrument 'sees' the hydrodynamic volume of your polymer and reports the molecular weight relative to the hydrodynamic volume of standards that were used to calibrate the instrument. So you will always get different results when you compare molecular weights obtained from NMR and SEC. Hope this helps.
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Does phosphorus proton coupling exist in solid phosphorus NMR?
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For a 1H-31P bond there will be a J-coupling, however as others have noted it will typically not be irectly observable due to the more dominant dipolar coupling (through-space).
It might be possible to measure the coupling using spin-echo based methods as shown in https://doi.org/10.1016/j.crci.2009.05.001
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how to convert .jdf NMR file to Topspin compatible format?
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It is helpful to execute this command while another data set is open. Otherwise there are problems with stoing the converted data set. if the jdf file is digitally filtered data use PHC1 of ~ 6900
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Any software for this purpose?
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You can use POKY for that (https://poky.clas.ucdenver.edu).
Poky menu -> Universal NMR Formats -> NEF chemical shifts to Sparky resonance list
Once a resonance list file is generated, it can be loaded in the project from the resonances list tab or from the resonance window (rl).
Then, you can repopulate assigned peaks using Transfer-and-Simulate tool (ta).
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Hello
I wanted a thesis topic in the field of food grade nanostructured lipid carrier (NLC) to work with NMR, XRD and DSC. Can you make suggestions?
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You can address the Effect of Solid Lipid Nanoparticle Incorporation on the Lipid Digestion Kinetics and Bioaccessibility of Encapsulated Bioactive Compounds in Food Grade Nanostructured Lipid Carriers: A NMR, XRD, and DSC Study.
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To determine the NMR yield of fluorine containing product, I need to calculate %yield from 19F NMR spectra using trifluoromethylbenzene as reference standard.
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Dear Nuruzzaman,
If the Educt has also a 19F you do not need a reference, because the ratio of the 19F signals of educt and product is the yield. NMR signals directly represent molar ratios. For 19F you may have to take care for the excitation profile of the pulse you are using. I normally place the carrier in the middle between the educt and product signal (doing so, both have the same offset effect)...
I hope this is of help!
Alfred
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Dear community,
I am currently running some solvent suppression experiment on water samples. I first run a one scan 1H experiment to get the ''O1P'' and then implement it in the solvent suppression experiment (''zgpurge'' pulse program). However the water signal appears distorted, it is asymmetrical and most likely unphased (other signals appear completly fine), which results in an inefficient solvent suppression experiment. I tried to overcome the problem by performing a 3D shimming, and adjusting the phasing parameters (Autophase during the lock and calibrated the autophase offset) but the problem persisted.
What could be the origin of the problem ?
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I suspect this issue is related to the gradients. I would decrease the gradient strength and, or the delay after the gradient(s) to see if the resonance shape near the baseline becomes more symmetrical.
Residual vibrations caused by eddy currents contain anharmonic vibrations. The discrete FT requires the decay of all time-domain signals to be pure exponentials. But residual eddy current vibrations contain components that decay with with nonharmonic, nonperiodic modulation. The DFT can not accurately model these anharmonic signals. The problem isn’t the eddy currents, it’s that the DFT mathematically processes the anharmonic components as if they were harmonics.
The result is often an artifact in the wings of the frequency domain water-signal baseline similar to the one in your figure. Details about the impact of nonharmonic, nonperiodic water signal components can be found here: “High dynamic-range magnetic resonance spectroscopy (MRS) time-domain signal analysis.” Hutton, W. C.; Bretthorst, G. L.; Garbow, J. R.; Ackerman, J. J., Magn Reson Med, (2009) 62, pp 1026-35.
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When I do an NMR of plain DMSO-d6 I have observed a small hump around 1.2-1.3ppm. It looks like a broad signal and am not sure as to what this signal could be assigned to. I have tried with new NMR solvent, NMR tube and also clean dry used NMR tube. All these have shown the same result. However, 13C signals correspond to DMSO-d6 only and nothing else. Was wondering if any one of the experts have any explanation to this observation, can be very helpful to me. TIA
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Did you notice any hump at 0.8ppm?
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In a ligand-protein binding 2D NMR study, what does it mean when there is no chemical shifts but there's a decrease in peak intensities and an increase in linewidths?
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Jani Rahkila one of them is 975 g/mol and the other one is 328 g/mol.
No, I don't have access to the NMR machine at the moment.
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If the intensity of a peak is lower and/or the linewidth is higher, does it mean the specificity/affinity of the ligand is higher for that residue?
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Dear Paul,
essentially all explained by the McConnel equation https://groups.chem.ubc.ca/straus/Nlecture3.pdf
Alfred
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I've done 15N hmqc to determine the interaction between ligand-protein.
There was no chemical shifts in amino acids after adding the ligand. However, the peak heights of almost every residue were decreased in a dose dependent manner.
Could someone tell me what it means please?
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I'm not sure if this answer applies to 15N HMQC experiments, but in the past when we did 2-D NMR experiments to measure ligand binding to a protein by measuring chemical shift changes of peaks, a loss of multiple peak intensities was taken to mean that the ligand was binding in a non-specific manner, such as an aggregator or denaturant. Such compounds were discarded.
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To start of I am designing an HVAC system where for a laboratory application utilizing Nuclear Magnetic Resonance operating at 300 MHz.
I am well aware of the helium cooling within nitrogen shell and the liquified gases refilling. However, I'd like to know if it emits heat while operation, if there is an extraordinary environment required for operation by the device.
Thank you in advance.
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The magnet itself does not produce a significant amount of heat, but the console cabinet with all the electronics does.
Your local Bruker office (https://www.bruker.com/en/services/support/office.india-middle-east-africa.egypt-gizeh.html?technology=magnetic-resonance) can provide you a site-planning guide (or you can find one via google) with all the information you need.
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I have synthesized a Schiff base compound but everytime I do NMR I found an aldehyde peak of intensity 0.20 or 0.25 like that. I have tried column, recrystallization, solvent wash but couldn't get the clean NMR of the final product.
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Robin is correct. The Schiff base is always an equilibrium and must be reduced (e.g., cyanoborohydrin) to create a permanent imine. You have to use an aprotic solvent (e.g., acetonitrile) to trap the Schiff base. There is also a byproduct urea that forms that is 1 Da off in mass.
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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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Without knowing the specific structures of the two chemicals in question, it is impossible to predict the exact positions of the 13C NMR peaks. The position of 13C NMR peaks depends on the unique chemical environment surrounding each carbon atom in the molecule, which is determined by the arrangement of other atoms, the type of functional groups present, and the hybridization of the carbon atom.
However, as a general guide, here are some typical 13C NMR chemical shift ranges for various types of carbon atoms in organic compounds:
  • Alkanes: 0-50 ppm
  • Alkenes: 100-140 ppm
  • Aromatics: 110-160 ppm
  • Alkynes: 60-90 ppm
  • Carboxylic acids: 160-180 ppm
  • Esters: 160-180 ppm
  • Ketones: 190-220 ppm
  • Amides: 160-180 ppm
It should be noted that these are only general trends and chemical shifts may vary depending on the specific compound and the context of the carbon atom in question. A detailed interpretation of 13C NMR spectra requires careful analysis of the entire spectrum, as well as knowledge of the specific chemical structures being analyzed.
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Hello everyone,
for my research project, I am doing synthesis with polymer (PEG) and I confirm the formation of the product via NMR. But for me, I don't really trust NMR and it cannot confirm me the formation of my product based on:
- esterification of PEG-OH with acid compound (step 1)
- imine formation (schiff base reaction-step 2)
So I tried to do FT-IR to see the peaks of COO and C=N in my second product. And it is still unclear for me. My spectrum are really strange.
For the formation of imine (step 2) I see the shift in NMR, characteristic to the formation of CH=N (literature) but for me I need more data to confirm it.
Furthermore, I have some additional peaks (not supposed to be here) with high content of protons. So I think my product is not pure....
So I have 3 questions:
1) in FT-IR, how can I confirm the conjugation of OH and COOH (ester) in my synthesis 1
2) in FT-IR, how can I confirm the C=N bond (synthesis 2)
2) For impurities in NMR, what are the options to remove it ?
Thanks in advance
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1)answer 1: first time, please obtained FT-IR of the monomer (which monomer of your obtained polymer), and then In FT-IR, the presence of a peak around 1700-1750 cm-1 can indicate the formation of an ester bond. This peak corresponds to the carbonyl stretching vibration of the C=O bond in the ester group. Additionally, you can also look for a peak around 1100-1050-1100-1300 cm-1, which corresponds to the C-O-C stretching vibration in the ester group.
2)n FT-IR, the presence of a peak around 1600-1700 cm-1 can indicate the formation of a C=N bond, carbonyl bond. This peak corresponds to the stretching vibration of the C=N bond in the imine group. Additionally, you can also look for a peak around 3300-3500 cm-1 screeching and Overton of this, 1400- 1500- 1450 cm-1, which corresponds to the N-H stretching vibration in the imine group.
  1. To remove impurities in NMR, you have a few options:
  • You can try re-dissolving your sample in a different solvent to see if the impurities are solvent-dependent.
  • You can try using a different purification method, such as column chromatography or recrystallization. or other solvent and please check your compound is dry.
  • If the impurities are water-soluble, you can try washing your sample with water to remove them. please dry your sample
  • cheek resolved and precipitate 3 times.
  • If you can not answer about purification
  • please check your monomer or the first material you used that
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Hi, everyone. I am doing CO2 reduction experiments and I wanted to use NMR to detect the liquid products formed. My media is organic (CH3CN). I have seen some similar works by Prof. Kubiak, et al. that use 1H-NMR to detect the liquid products (particularly, formic acid) in CD3CN but the NMR sample requires the addition of Verkade's base. I am not so familiar with this compound. Does anyone know why (1) the peak of formic acid is not visible (supposedly around 8.02 ppm) if you do not add this base, and (2) what happens between the base and formic acid that causes a peak at 8.50 ppm to occur? Thank you so much!
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Verkade base is one of the strongest base; after protonation, it forms a conjugate acid with pKa value of ~33. That means it can deprotonate even a weakest acid and hence the signal disappears. This includes for your both the questions 1 and 2. Conjugate acid is = [HP......]+ [pKa = 33]
Best
Balakrishna
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Is it possible to convert a fid file of NMR to any of the following formats - PDB/mmCIF/XML/UCSF
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UCSF is the spectrum format in frequency domain. You can process with TopSpin to generate a 2rr/3rrr file, and you just convert using POKY.
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I am running an MD simulation on a protein-protein complex.
After seeing a similar question on research gate, I checked the amino acids rtp file in my force fields folder, and as expected from this error, the HD1 atom was not present in the HSE entry. The atom HD2 is however present in that entry. So I figured replacing the HD1 atoms in my PDB file with HD2 should solve the error.
And it did. For the time being.
To reaffirm, I made changes in Histidine's hydrogen atoms in the PDB file. When I went ahead with the energy minimization step, I got an error that said there's an Infinite Force on an atom. It turns out that the atom was "HD2" of some Histidine in the PDB file.
I saw online that the reason behind this error was due to atom overlap. Hence, just for seeing if that was the case for me, I changed the coordinates of that atom a little bit (this was just for checking, I can't do this for the actual work). When I ran the EM step again, I got the same error, but for a HD2 of a different Histidine molecule. So yes, overlapping of the atoms is the reason for this particular error. I cannot solve it by changing coordinates of all the HD2 atoms of the Histidines. So it all boils down to the main fatal error that I mentioned.
How do I approach this?
1. Changing the atom name (as in HD1 -> HD2 is not working due to the subsequent error)
2. I do not know if I should add the atom HD1 in the HSE entry in the rtp file (I tried this and got several warnings).
3. I cannot (or should I?) use -ignh because mine is not an NMR structure. I have modelled my proteins on Modeller and refined them online.
Any suggestions/solutions will help me a lot. Thank you in advance!
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Hi, a crude measure is to use -ignh during pdb2gmx, it will rebuild all the H-atoms based on the force field you are using. Most of the time, it is a reasonable choice (though not always), as the H-atoms are mostly absent in crystallographic structure (as it is difficult to resolve h-atom positions).
Histidine is unique in the sense that its side chain offers multiple h-bonds at physiological pH. The better procedure is to check which heavy atom of His side chain is forming H-bond in the protein (either it is delta or epsilon), and rename your His residues accordingly (HIS, HIE, HID, please check your FF how these residues are named there).
"2. I do not know if I should add the atom HD1 in the HSE entry in the rtp file (I tried this and got several warnings)." > Try not to mess with rtp entry at this stage (as you are very new), and if you like to play around, just make a backup of FF directory and do as you like.
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Hi,
i am starting my master thesis And I am doing polymer synthesis following by precipitation method (dissolution in solvent, non solvent precipitation, centrifugation) repeated 2-3 times. I have some impurities in my NMR analysis.
So I want to know if precipitation method in cold ethyl ether is enough to purify a polymer chain ? if yes, it the best procedure to do a good purification through This method?
Example: addition drop by drop is important ? Stirring fast also ?
Is it better than soxhlet extraction ?
Another suestion regarding the purity of final product. Is GPC can confirm the formation of product ? How can I confirm clearly that the reaction work and the product is formed (in complement with NMR) ?
thanks
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Hello Saya Bird,
the purification depends on the polymer and the side products/impurities, which you want to remove.
Additional purification methods might be following:
Dialysis; I used this to remove some salts, which could leave the polymer solution through the membrane of the dialysis tube, whereas the polymer remained in the tube.
Fractionated precipitation: I used this to separate blockcopolymers from homopolymers or different moecular weight fractions of the same polymer from each other. You add a non solvent to a polymer solution and the less soluble polymer (depending on their chemistry in the case of block copolymer) or the polymer with the higher molecular weight (in the case of different molecular weights) precipitates first as a polymer gel.
There are also methods, that require more elaborate equipment, like preparative GPC or separation by LCCC.
If your separation does not remove the impurities, maybe add the solvent slower (drop by drop, as you mentioned) and use another solvent (or non-solvent). Maybe you polymer precipitates so easily, that the impurities are trapped in your solid polymer. If the polymer precipitates slower the impurities may stay dissolved (similar to the case of fractionated precipitation).
The confirmation of your product also depends on the polymer. Maybe some groups on your monomer were changed by the polymerization, which could be detected by IR-spectroscopy.
For the chracterization of polyurethanes (as an example), remaining isocyanate groups can be titrated.
If you use a new method to obtain a known polymer, you can also compare it's properties with literature values (i.e. the glass transition temperature via DSC) to get a hint if the reaction might have worked.
There are plenty of complex and simple methods to characterize a polymer, but it depends on your polymer if you can use them.
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A reaction of A and B, gives C. the NMR of reaction mixture contain all peaks of A,B,C. I need to calculate yield or percentage conversion of B to C. A has no role . Yield of C need to calculate with respect to B. all have distinguish peaks. On integration, specific peak of C has 1.00 while B has 0.35. both contain 2 hydrogens each. Can I say yield of C is 1/1.35 *100= 74% ? Or is there any other methods to calculate the yield ?
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Carlos F. Marcos
- ERETIC2 and QUANTAS are both software approaches based on the PULCON method of Wider et al. (J Am Chem Soc. 2006 Mar 1;128(8):2571-6. doi: 10.1021/ja055336t). Note that the original ERETIC (Akoka et al.) is a hardware-based approach and may not be suitable. QUANTAS reference: Magn Reson Chem. 2010 Oct;48(10):753-62. doi: 10.1002/mrc.2647. PMID: 20803488.
There is no reason why these approaches can't be used in a benchtop NMR.
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Hello
I wanted a thesis topic in the field of food grade nanostructured lipid carrier (NLC) to work with NMR, XRD and DSC. Can you make suggestions?
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tes
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Hello everybody,
I am getting output from ORCA program for NMR chemical shifts in the form of Anisotropic and Isotropic shielding in ppm units for both reference and standard(TMS). So, how can I compare these values with experimental chemical shifts of sample? I am attaching here my ORCA output file also.
Thank you.
Shravan B Rathod
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I have been studying a dynamic protein and have selectively labelled a cysteine for 19F NMR. This cysteine has two peaks corresponding to a major and minor conformation. On a 500-MHz spectrometer, the relative populations are roughly 4:1. After I switched to a 700-MHz spectrometer, the relative populations are now roughly 2:1. I have confirmed that this is not a one-time fluke. Can a higher operating frequency enhance the minor population with respect to the major population?
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Dear William,
Here is a good website explaining the T1 dependence with magnetic field and including references.
It focuses on 1H, but gives a good general idea.
Best,
Maxime
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Is there an alternative to gNMR for iterative NMR simulation?
Many years ago, I used gNMR to simulate complex spin systems, but it seems gNMR is no longer supported. Do you know of an alternative to the gNMR?
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Solution = iNMR
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Hello Everyone,
I did an initial test with F19NMR but my peaks in -CF3 part were overlapped.
My sample was a combination of 4 standard solutions of C4F7COOH, C6F11COOH, C8F15COOH and C10F19COOH which was 100uL plus 100 uL of deuterum MeOH and 800 uL of normal MeOH. I applied 400 NeoNMR which has a specific prob for NMR.
My conclusion is that I have to apply higher frequency like 600MHz or 900 MHZ.
Please let me know if you have any ideas to get a clear signal with this method.
I appreciate any assistance.
Faranak
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Since the molecular weights of the components of your mixture are significantly different, you may try 19F DOSY to distinguish the 19F signals of CF3 groups. See, for example, https://pubs.rsc.org/en/content/articlelanding/2016/cc/c6cc02917e
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I need to use 27Al NMR for liquid sample and i whant to know if quartz NMR tube have lower backgroud than NMR glass tube.
If someone know how to reduce the bacground noise let me know.
Thanks
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To complement Clemens answer, I would like to mention backward linear prediction, which is a standard procedure in almost all NMR processing software packages. It helped me a lot for measuring 11B NMR spectra using standard (non-quartz) NMR tubes.
Good luck,
Vladimir
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Is it possible to suggest a title (Biophysics of food) that includes all three NMR SAXS DSC devices?
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In my suggestion the title may be " Characterization of Food materials for their quality"
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Hi all,
Attached below is the proton nmr spectra of biodiesel. The integration value of peak at 5.2 ppm is set to 1. and corresponding all other integration values are obtained. Is that right .
From there. I'm calculating the yield of biodiesel by using integration values at 3.6 and 2.3 ppm.
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Dear Alisha,
to answer the question I (we) need to know the reaction-scheme.
Was it a trans-esterification of glycerol-esters? If this is the case I'd guess that the signal at 3.6 is the O-CH3 of the product (which you have divide by 3, as described above) and the signal at 5.2 might be one hydrogen of the glycerol in the educt. And I(O-CH3)/3/I(educt) would be the molar ratio of product/educt (which is not the necessarily the yield!). But this might be wrong if my "hand-wavy" assignment is wrong.
Alfred
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I can find the NMR information of purplad&aldehyde adduct in . However, it is very hard to find the mass spectrum characterization of the purpald&formaldehyde in literature. Who has the relevant publication? Thanks!
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Do you have a Scifinder or reaxys access? They both have very good structure and substructure search masks, so if there is a mass spectrum in a good journal, they should hopefully find it.
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I have prepared some derivatives of the Copper 8-Hydroxyquinoline complex. It has very low solubility in the DMSO, DMF, and CDCl3. In such a scenario, having a paramagnetic Cu2+ in the structure, How to record an NMR spectrum of the Copper 8-Hydroxyquinoline complex and its derivatives?
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Dear Prasad,
Cu2+ usually increase T1 relaxation but not really T2 relaxation (which would be bad). This means you can reduce the D1 delay to reduce measurementtime. Otherwise it should be fine to record 1H experiments, but no garantee. to determine the T1 relaxation and teherefore the d1 delay time you can use the parameterset 1HsatrecT1. after recording you can click on "Applications->Dynamics->Prepare for Dynamics Center" and than again at the same button Saying "Dynamics Center" and the result should pop up. If you have installed the free of charge Bruker Dynamics Center on yur computer.
Many Greetings,
Kristof
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Hello scientific community,
Although I have a very specific question related to a very specific equipment, I hope that I will find some answers and/or orientations.
I am actually trying to operate a Bruker Prodigy Cryoprobe, but I am facing some technical issues related to the failure of the cooldown process. I cannot achieve it as the system tells that the cooldown is too slow. What could be the reason for this? Are you using this kind of equipment Flawlessly? What is your experience with this kind of cryoprobe? are they reliable, and robust ?
Thank you in advance.
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Dear Ahmad,
Thank you for your detailed answer, I eventually managed to solve the problem with the aid of Bruker technician. The problem was due to an insufficient cooling because of a bad vaccum in the liquid nitrogen transfer line, I just had to redo it.
Many thanks.
Salem
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If i take a crude nmr of my reaction mixture containing one reactant and product without adding any internal standard , is it possible to calculate yield of product integrating distinguish peaks of reactant and product?
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It depends what level of accuracy you require. In simple terms, identify a signal from your product and one from your reactant, integrate and normalise these for the number of protons that they represent and these numbers will give you the molar ratios of the product and reactant. There is no need for an internal standard in this case.
There are caveats. This method assumes that your reactant only produces product and that there are no by-products. If there are by products then you could also integrate signals from these. Alternatively, use a reference signal such as ERETIC2 or QUANTAS and this will allow you to quantify independently.
If you require accurate results, then you need to follow William C Hutton's comments about signal-to-noise, etc. - particularly relaxation delays!
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HI, I've started ti learn using JMRUI to analyse NMR spectroscopy signals. I completely don't know how to use AMARES quantitation or any other type of quantitation. I have to determine the concentration of metabolites in the spectrum derived from the human brain. I have watched tutorials on youtube, but during them, there are used some databases .sv type to make quantitation and I don't where can I find something like that?
I really beg for help
Best regards,
Aleksandra
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The time domain quantification of metabolite signals was conducted using AMARES algorithm with custom prior knowledge.Metabolite concentrations were reported for tCr (creatine plus phosphocreatine), NAA (N-acetyl-aspartate), tCho (phosphocholine and glycerophosphocholine), Ins (myoinositol) and Glx (glutamate and glutamine). The AMARES prior knowledge model consisted of peaks for NAA, choline (Cho), creatine (Cr), glutamate + glutamine (Glx) and myoinositol (Ins). The amplitudes of NAA, Cho, Cr, Glx, and Ins peak were estimated by the algorithm. The relative phases of NAA, Cho, Cr, Glx, and Ins peak were fixed at 0. The linewidth of NAA was estimated by the algorithm, and the linewidths of the remaining peaks were set to be equal to that of NAA. The frequencies of NAA, Cho, Cr, Glx, and Ins peak were estimated by AMARES. All peak shapes were fixed at Lorentzian.
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I need a solvent to be able to take NMR test from my samples PET-PBT blend. I will really appreciate if you can help me. I already tried DMSO, Chloroform, Water, and Ethanol.
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you can use CF3COOD/CDCl3 (2/1 v/v)
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I have two small characteristic peaks in the NMR spectrum showing negative integration values. I would appreciate it if you could share your opinion.
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Dear David Stephenson, Thank you for the tips. They worked.
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Can use D2O peak at 4.7 ppm to align 1H 1D NMR Spectra?
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The problem has been solved. Thank you for your professional reply
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Usually, it provides a singlet at 5.37 ppm in 1H NMR spectroscopy. But i got one NMR with two singlets at 5.21 and 5.44 ppm. Did they belong to CH2of benzoyl benzoate, or could it be something else??? Please shed light on this issue. Thanks
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Thanks a lot for your precious suggestions.
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I am trying to prepare Indigo using Baeyer–Drewson method. However, the NMR spectrum in DMSO shows the presence of a side product along with Indigo. How can i purify the material
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Nitika Grover hope this helps.
US5116997A - Purification of indigo - Google Patents
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I am working in a HVAC project that includes a NMR 300, I found out that it cools down by liquid helium or liquid nitrogen so i want to know the amount or the range of heat rejected to the surrounding
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Dear Omar,
Interesting question....I never thought about it. If once the cool-down is done (only done once while installation of the machine) the calculation for "regular operation" can probably done like this:
Latent Heat of Evaporation of N2 is 200 kJ/kg. If we assume a loss of 100 l per week (actually it is lower for a 300 MHz machine) we end up if I calculated correctly about "30 W" of "cooling power" 200.000[kJ/kg]*0.8[kg/l]*100[l/week]/(24[h]*7[days]*3600[s])..I'll guess the He contribution can be neglected, but the electronics of the console adds a few hundred watts.
So at the end for a decent air-conditioning no problem!
I hope I calculated half-way correctly
Alfred
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Can plz anyone help me to calculate J-coupling constant for the given NMR spectra?
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Dear Lubna Afroz a conclusive analysis and answer to your question can only be given if the splitting pattern of your signals is clearly perceptible. This is not the case with your illustration. Swapnamoy Ganguly , I do not agree with your analysis for two reasons: (1) you cannot be sure that the signals are "triplets" or "quartets" (I doubt about that) and hence the calculation is questionable; (2) coupling constants larger than 20 Hz are very rare, not to say unlikely for organic compounds.
Moreover, applying a line broadenig factor of 1 Hz is not really helpful for most proton spectra, and the integral labels look very strange to me (as there are four regions of relative intensity 2 but only three peaks groups of appropriate size). Please check everything.
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I need to perform NMR of my sample. Please suggest the minimum amount to sample to do NMR.
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As John mentioned, it depends. Mostly because molar concentrations of the active nuclei matter in spectroscopy, not the w/w or w/v. So, 0.1 mg/ml may be pretty ok for 1H NMR of a small molecule, but not the large one and not (natural abundance) 13C NMR.
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Hello,
I am trying to analyze the stability of DYBP (2,5-Dimethyl-2,5-di(tert butyl peroxy)hexyne-3). It is 85% and comes dissolved in mineral oil. What technique would work the best apart from NMR? Would GC-MS or HPLC with reverse phase work?
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A stable derivative of the compound is made using a chemical like TMS or equivalent which then will not undergo further decomposition during the chromatography step (eg. ). Alternatively, you could quantify the increasing degradation products and infer the remaining amount of parent compound.
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What is the equation for determination of DPn or molecular weight of polybutylene succinate (the polymer was prepared by polycondensation of diol and diacid) from NMR spectroscopy?
TIA
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Dear Fatima,
without a clear terminal (or close-to-terminal as Clemens mentioned) signal with a defined number of atoms per polymer contributing to the NMR signal it is not possible!
The integral of a NMR signal is given by
(molar concentration of a polymer)*(number of atoms in this polymer)
Thus half of the molar concentration of the polymer with twice the number of monomers unit (double MW) will lead to the same integral.
An estimate of MW may be obtained by measuring diffusion (DOSY technique) coefficient D. But you will need (several) reference polymers of same type/chemistry and known MWs for calibration
...or you find something useful in literature.
A rough estimate of the MW may be "guessed" if you only have one MW reference by a polymer-scaling law - to my remembering D(MW)~MW^(3/5) for unstructured polymers. But please check this!
If you have MW references there are more simple (SEC, gel-filtration) chromatography methods.
Good luck
Alfred
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In a 19F-NMR spectrum, the chemical shifts are usually negative. Therefore, does "upfield" become leftward movement towards zero, or does it still refer to rightward movement, but now becoming more negative?
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Wolfgang's answer is absolutely correct in every respect. That said, I still struggle with alternatives to upfield and downfield. Try putting the alternatives into a descriptive sentence. You can't very well say that a signal is "higher" than another signal as this could refer to its intensity. You could say that it is "higher frequency" than another signal but the chemical shift scale is dimensionless (it is normally described in "ppm") so this perhaps isn't truly valid either unless your scale is in Hz. I've been told that "to higher ppm" or "to lower ppm" is valid but it is ungainly and counter-intuitive as people tend to thing of higher being to the right and lower to the left (which is the opposite of the delta ppm scale). Perhaps we should go back to tau where TMS comes at 10ppm... (only joking).
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I have a COF solid powder, and I want to get its NMR, I need a good solvent to dissolve the COF. DMSO or THF are suitable solvents for dissolving COFs?
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Der Mashid,
not any COF is soluble. Solid-state NMR might be an option. For soluble ones also mixtures of ACN with water or acidified water was reported...
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Generally we use such polymer to make the MIP of a template where non-covalent bond is formed rather than the covalent bond which are difficult to breakdown. So without doing NMR how can we the type of bond formation between the template and polymer.
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Yes there are, if you are lucky then may be you will find exactly the answer on the possible reactions you are dealing with. Please have a look at the following links. My Regards
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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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generally if it happens in DMSO-d6, one can heat the sample with heating gun or else after adding D2O some compounds will get dissolved.
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While performing DOSY, I noticed something strange that I can't explain:
I performed 2 DOSYs of 2 polymers with exactly the same parameters (pulse sequence, small and big delta, temperature, same solvent (CDCl3)). What puzzles me is that the diffusion coefficient for the residual CHCl3 in the 2D DOSY plots of Mestre (same processing) is extremely different in both spectra (1.6e-04 and 5.4e-05). I am not very experienced with DOSY, but shouldn't these Ds for CHCl3 at least be in the same range?
I am not concerned with finding exact and correct diffusion coefficients, but rather performing mixture analysis, yet this result seems strange and makes the impression that the processing is not very reliable.
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Hallo,
It's not a big difference if the polymers are different or the concentration is different. What is the standard deviation of these coefficients you mention? The polymer signals may have a good decay and with enough increments for the fitting, this may not be the case for CDCl3. Do you have a good decay for the CDCl3 signal?
You could repeat the experiments with the shortest possible d20, the diffusion coefficient of the components in the sample should be "equal" to your first measurement.
If you are using an edited pulse sequence, mestrenova will not be able to calculate the diffusion time (big delta) properly and this results in an error.
Any difficulty look for our group in Regensburg, we can help.
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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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I'm a beginner in NMR analysis. I want to know how to read the NMR from my attached file.
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I greatly appreciate all the suggestions. Thank you.
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In this paper Authors didn't provide NMR data. Many publications sited this publication about this Emblicanin A and B content but none of them provide NMR data. Thank you.
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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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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.