Science method

NMR Spectroscopy - Science method

A forum to address questions regarding nuclear magnetic resonance spectroscopy, most commonly known as NMR spectroscopy.
Questions related to NMR Spectroscopy
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Hi everyone, I have synthesized 3-amino functionalized cage molecule by treating the benzophenoneimine bonded cage with excess aqueous HCl. The identity of the molecule was confirmed by NMR spectroscopy but I am now suspicious from the fact that amine groups can be in the form of -NH3Cl or just -NH2 because I could not achieve to crystallize the same molecule reported in the literature. Do you have any idea about how to distinguish whether the amino groups are in its protonated form or not.
Best regards.
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Der Ferit,
if you have a a-protic solvent (with narrow enough NMR signal of the NH2/NH3+) you should be able to discriminate this by the integral of the signal. Optionally you may want to use a multiplicity edited (or along f1 undecoupled/refocussed) version of 1H/15N HSQC - if you have enough material!
Good luck
Alfred
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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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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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The determination of the MW of polymers without a easily identifiable endgroup is difficult by NMR. You polymer can have hydroxy or carboxylic acid endgroup. The neighboring CH2 will not be sufficiently different from the other CH2 to allow quantification. It is much easier if the polymer has distinct endgroups such as methyl or vinyl. The the MW can be calculated from the integral ratio of main chain versus endgroup. It might be possible by quantitative 13C NMR where a carboxylic acid is different from a ester. The CH2OH end might also be identifiable.
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Detection of mono/di/polysulphide linkages in the vulcanized rubber using solution as well as solid state NMR 
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It is a China made low-field NMR Company, which has the special products for crosslinking density measurement.
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Hello All,
I would like to know how to find Spin Orbit Coupling (SOC) from NMR spectroscopy in organics materials.
Any Ideas?
Thank you for your time and help.
Best Regards,
Dani
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Dear Dr Dani S. Assi,
I think these articles (in attached) may actually help you.
Best wishes,
Sabri
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Required for protein structure characterization
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Hi Sunny,
This is quite a big question. Do you mean how to build a structure from the data? You can use TALOS to predict the backbone torsion angles from the chemical shifts. Coupled with sufficient distance restraints from e.g. NOEs and residual dipolar couplings it becomes possible to then calculate a structure. CYANA is used for the final model building.
Hope this is helpful!
Best wishes,
James
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I have prepared a Co(III)corrole, and the NMR in DCCl3 shows broad signals between 7.30 and 9 ppm. I've read that Co(III)corroles are paramagnetic with S = 1. So I attempted to add MeCN to coordinate the Co ion. It didn't change anything. Then excess triethylammine and although the broad signals move slightly, and some fine signals appear at ~10 ppm, there is still no big change. I thought that maybe I had aggregation, so I greatly diluted the same sample, and although I obtained much weaker signals, they were still broad.
I also prepared the analogous Al(III)corrole, and the NMR is similarly broad, with signals in the same region. That one threw me off.
Does anyone know what could be happening?
Thank you very much!
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Add 5% of NH3 H2O into your NMR sample will solve the problem. Here is the ref:
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The deuterated solvent e.g. CDCl3 when used in NMR spectroscopy shows signal , is it because of the residual proton or there are some other factors?
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It is mostly the residual protons that you see. The solvent is typically deuterated to 99 - 99.9 % the rest is 1H. In Chloroform the residual signal is a signlet. In other solvents such as DMSO or Aceton it will shown up as 5 lines due to the coupling of one 1H in CD2H with the two deuterons.
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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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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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We acquired MR spectroscopy signals from phantoms with certain metabolites in our Lab(at 37 centigrade), using a Bruker 9.4T MR machine. We compared the peaks of metabolite with the literature[In Vivo NMR Spectroscopy, de Graaf], and they are not the same. The differences are in the range of 0 to 5 Hz.
We reacquired signals with different temperatures and with a calibrated pH meter. Shifts change more or less linearly with temperature but are different from the literature.
I was wondering if any Lab did the same measurement? I could not found a study with phantom measurement in 9.4T.
I attached a picture illustrating the issue in the Cr+NAA phantom.
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Stan Sykora thanks for your answer. I would add hardware imperfections as well. Apparently, we have to live with this. I definitely bring your greetings, I bet he will understand :))
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How  we can predict or determine apparent  molecular mass for globular proteins using pulse field gradient -Stimulated Echo NMR experiments. I am looking forward to characterize the presence of different oligomeric forms of protein using Translational Diffusion Coefficient as a parameter   Can anyone suggest the references in which  similar studies have been discussed
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Molecular weight prediction with no dependence on solvent viscosity. A quantitative pulse field gradient diffusion NMR approach. Polymer Chemistry, 7(26), 4326–4329. https://doi.org/10.1039/C6PY00691D
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Along with regular 1H and 13C NMR data, DOSY NMR data also help in important role in determining the diffusion coefficient of supramolecular noncovalent architecture formation. But else we can get from DOSY NMR data?
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DOSY is a simple experiment to implement but there are a few pitfalls. Chloroform is not an ideal solvent, the BRUKER DOSY manual from the early 2000s almost describes a methodology before computers, there are some important acquisition and processing parameters that should be correctly set. When I first started out, I found I got highly variable results simply by running the same experiment with different acquisition parameters (as suggested by the manual) - or taking the same data set and processing it with different parameters. It is important to nullify these systematic errors by choosing parameters that will accurately report over the range of diffusion coefficients that you are used to. I have used DOSY to study various aspects of carbohydrates, polymers, molecular interactions, DNA folding, protein size and oligomeric state....
I've also looked at the physical properties of ionic liquids by DOSY. While I don't have published experience, for synthetic chemists, it gives an idea about purity, confirms spurious peaks as coming from solvent(s) etc. However, as separation is by size in the diffusion dimension, a hydrogenation product may have essentially the same diffusion coefficient as the starting molecule.
I don't like using research gate as a means of personal promotion, but my paper from 2017 in Polymer Chemistry was written as a practical guide to DOSY rather than an experimental paper/review. It describes ten important points for running DOSY and few published papers score even half marks. In other words, trying to follow a published paper in the field is futile as half of the information to run the experiment is missing. Back to polymers - you need to use sets of DOSY parameters that can accurately analyse a mixture of monomers and high molecular weight polymers in one sample. This is an ultimate challenge so if the guidelines are applied to 'normal' samples then it should improve your protocols.
I'm happy to discuss further any specifics, provide papers etc.
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I'm working in the field of plants, isolation, and structure determination of biologically active natural compounds.
I need NMR of proton, carbon-13, 2D,...
Any suggestions in this regard; free book, course, or support is valuable.
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Dear Alexander Sinko thank you for your interesting technical question. Ideally, the person at your institution who runs the NMR spectrometer will give you a personal instruction or perhaps offers a course. It's not a matter of half an hour to learn NMR spectroscopy, especially when it comes to characterizing complicated biologically active natural compounds.
On the general internet you can easily find a variety of free courses and tutorials when you search for "Introduction to NMR spectroscopy", including YouTube videos.
For example, please have a look at the following useful links:
INTRODUCTION TO NMR SPECTROSCOPY
This rather comprehensive introduction can be freely downloaded as pdf file.
Introduction to Nuclear Magnetic Resonance
Basic Introduction to NMR Spectroscopy
and many others.
Good luck and please stay safe and healthy! 👍
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Dear All!
Is there a software in which I will make NMR prediction of compounds in deuterated acetontrile, acetone or methanol ? In mestrenova I can make only predictions in chloroform, dmso or water.
Thank you so much for your help!
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Mrs/Miss Haraźna,
Do you know the reliability of these so called predictions of NMR spectra?
There is a plenty of software for prediction of mass spectra as well. However, a comparative analysis with experiment shows a dramatic lack of accuracy between theory and experiment.
Such software are very useful to only educational purpose. Because of, all important and really observed both NMR and mass spectrometric phenomena are unable to be accounted. Thus, the so-call predicted spectra produce very illustratively the fundamental basick knowledge.
An additional comment on: RG represent forum for exchange of knowledge at a highly specialized professional level. Very frequently, many participants are unable to distinguish between highly specialized technical information and low specialized information of general or popular character. The latter one is typical for the public press. Owing to the fact that the comments on RG are inaccessible to the mass reader or to the communities as whole, this means that RG does not represent forum for distribution of knowledge at a general public level.
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I have two peptides. Some residues are D and some are L in peptides. How to get aminoacid residue specific information using NMR spectroscopy
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By Pure NMR this will be difficult. If You want to proceed the NMR way You will probably need to use chiral shift reagents.
Otherwise it might be easier to follow an approach using enantioselective chromatography
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I am working with some organic compounds synthesized by me and some purchased. I have taken NMR spectra. How to interpret that NMR spectrum of my compounds? Is there any books or reference websites available for it. Kindly give suggestions.
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Dear Sara Shams,
Thank you for your response.
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I have 20% (w/w) formaldehyde-d2 in water. I want to calculate the isotopic purity using NMR. But I am getting 3 to 4 peaks corresponding to different polymers of methylene glycol. How to find the isotopic purity of formaldehyde-d2? NMR is a suitable method or is there any other method which I can use?
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As you have found in water formaldehyde will hydrate and form oligomers. Not only that but the deuterium will even distribute itself with the water and the oligomers. So use a solvent other than water.
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I am doing NMR spectroscopy and now we are studying relaxation times. From them you can find out about the correlation time. I would be glad if someone could explain how correlation times are related to molecule mobility. And it would also be great if someone could recommend literature or articles where it is clearly written about it. I would also like to clarify the very concept of correlation time more.
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In gromacs gmx order computes the order parameter per atom for carbon tails. For atom i the vector i-1, i+1 is used together with an axis. then we use this S mol = 1/2(3cos^2 (θ ) − 1),.
So to compute the molecular order parameter for atom for example C3. We need to have indexes for atom C2 and C4 (because we write a vector and check the angle).
But what we should do, when we have the last atom in the tail. For example, I have oleic acid and I want to compute the order parameter for C18? How to do this? I can make an index for C17, but I haven't C19 (because this atom doesn't exist in oleic acid), so how can I write a vector? Maybe I should make an index for H atom at the end of the tail???
I ask you because I want to compare results from the simulation of my membrane POPC to these from 1 H– 13 C solid-
state nuclear magnetic resonance (NMR) spectroscopy and there they check C-H bond (so they don't use vector Ci-1 Ci+1 for Ci), so they are able to check this parameter for the last carbon of the tail.
And I also have a question.
why in NMR they use CH vector and then in GROMACS they use vector Ci-1 - Ci+1? And they have similar results I don't get it.
Thank you in advance for your help.
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Use the cpptraj tool in AMBER or some lib such as mdtraj for python.
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NMR spectroscopy
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Yes there are. These are basically comparable to liquid state NMR experiments. The main difference being in the fact the "concentration" of the observe species is often much lower than in the condensed state. High pressure tubes allows the gas to be concentrated. There is a book about it:https://pubs.rsc.org/en/content/ebook/978-1-78262-161-4
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problems and solution in proton nmr spectroscopy
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Ok, I think I can help.
Could you please provide me your email id.
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Many studies showed the ability of NMR spectroscopy to distinguish Tuberculosis (TB) Patient.
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Whilst NMR may identify some systemic changes in biofluids as a response to the Covid-19 virus, it is unlikely to progress specific mechanistic understanding. Thus a combination of NMR and MS would be a better approach.
From literature around SARs an MERs, it seems that both cytokine response and lipid transport would be important. There are several metabolic profiling laboratories that are investigating the metabolic response using these technologies including Rutgers and the Australian National Phenome Centre
If multiple centres undertake similar research, there would be substantial merit in creating a broader international database
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I want to know whether electron lone pair situated above hetero atoms will effect the chemical shift position(s) of proton(s) and carbon(s) if they positioned in such way, directly above in a rigid system. It is true that, in the case of heteroatoms in the same molecule will affect the neighbouring atoms. But, what will happen if another different molecule positioned over the hetero atom of the former molecule in a rigid system? Can be see the spatial interaction leading to change in chemical shift if molecule A is positioned over B?
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For the heteroatom on one molecule to affect the chemical shift on another molecule, the two molecules would need to be tightly bound, or at least spend significant time in a single relative orientation. This is not normally observed but it is possible to observe. Chiral solvating agents such as TFAE create an anisotropic environment that will interact with different enantiomers of other molecules to change their chemical shifts. This is an extreme case and relies on having a large excess of the solvating agent to maximise the chance of collisions and binding. In normal situations, we seldom observe this behaviour (seldom, but not never!)
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Ayurvedic herbo-mineral formulations are very complex in nature. Even their methodof preparations is also very complex. So in such cases the modern advanced analytical tests are employed to understnad their structure. But is it possible to know the complex structures of the formulations with adopting tests like X ray diffraction, Spectroscopy, FTIR, Scanning electron microscopy etc.
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Yes it is possible, Chromatographic techniques follwed by spectroscopic techniques as you mentioned can answer your question.
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What organic compound has highest chemical shift (more than 13 ppm) at proton-NMR and has high purity? Not active hydrogen (such as COOH or OH of NH....)
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Dear Ting, carboxylic acids with the structure R-COOH have the highest chemical shift: in the range 10-13 ppm.
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Actually I am looking at the oxidation state of a transition metal in the extended structure(3D), but I got one experimental paper wherein they are telling that they have confirmed the oxidation state of Mn to be +1 using Solid-state 55 Mn NMR spectroscopy. How much we can rely on it. please help
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Hello,
NMR gives local structural information, so one, in practice, could calculate the oxidation state from the structure.
Also, Mn has a number of paramagnetic oxidation states, which you are unlikely to observe by NMR. so if the authors present a 55Mn spectra, then it is likely to be a diamagnetic oxidation state of 55Mn.
Beyond that, without seeing the paper, I do not want to comment too much.
Best wishes, Greg
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Hi researchers!
I am an engineering student aiming to develop a portable and relatively inexpensive method to detect sub-standard drugs. As far as I know, the current accurate method for this characterization is NMR Spectroscopy but it is not really portable.
Going through drug metrics, found the Partition Coefficient and I wish to know if it could be used as a trait to compare a sample of drug with its existing, known to be genuine specimen and determine if it is sub-standard or not.
Please share your views and pardon me for my lack of knowledge as I am new to medicinal chemistry.
Thanks
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You must compare the characteristics trait to some unknown sample
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Hi researchers!
I am an engineering student aiming to develop a portable and relatively inexpensive method to detect sub-standard drugs. As far as I know, the current accurate method for this characterization is NMR Spectroscopy but it is not really portable.
Going through drug metrics, found the Partition Coefficient and I wish to know if it could be used as a trait to compare a sample of drug with its existing, known to be genuine specimen and determine its effectiveness.
Please share your views and pardon me for my lack of knowledge as I am new to medicinal chemistry.
Thanks
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The method you propose has a number of potential problems.
First, you need to establish an equilibrium between your sample dissolved in two different phases and then assess the partition coefficient. That means choosing the phases, a considerable amount of sample handling (weighing, dissolution, shaking, ...) that might take its time, and finally the assessment method for the concentrations. Moreover, you would need to carefully research the robustness of the method with respect to spurious or intentional contaminations (how pure must be the sample), temperature effects, etc.
Second, after the assay, you get just one number and that is by far not enough to discriminate between maybe hundreds or thousands of potential candidates. You could complement this with other physico-chemical measurement (refraction index, melting point, absorbance at any selected wavelength, ...) but still, the "discriminating power" might remain low.
The advantage of spectroscopic methods such as NMR, MS or IR is that they "output" the intensities of many peaks (tens to hundreds) and thus offer an incomparably richer information content.
If you need something affordable and portable, you might consider one of those portable NIR (near infrared) devices.
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What is the best choice to normalize serum samples to be analysed by metabolomic approach using NMR-spectroscopy?
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Data normalization in NMR-based metabolomics can be rather challenging. Have a look at the attached papers for important pitfalls and strategies to avoid them.
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Can any one please tell me , How to determine the purity of deuterated solvents by NMR Spectroscopy ?
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1H NMR with internal standards of known concentration can give you information such as degree of deuteration and amounts of impurities. Alternatively, degree of deuteration can also be obtained by 13C NMR using isotope effects. For a description of that method, see: Anal Chim Acta. 2016, 927, 89-98.
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Dear researchers,
Currently we are working on ssDNA aptamers against various diseases in humans. We would like to get supports from the NMR data through collabarations. drop a message if anyone interested.
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Hi,
Although I am not good at NMR technology, I suggest you might try to work with Creative-Biostructure, whose NMR platform has the state-of-the-art NMR instruments.
All the best!
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Hi guys,
I want to perform some MD simulations of a protein that has been resolved by NMR spectroscopy (thus it has multiple structure models). Should I start with an average structure or should I randomly choose one of the model instead? Do you know how to calculate that structure using Gromacs? Any advice would be welcome.
Regards,
Xabi
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Dear Xavier,
Kindly, I will suggest that you be a little more specific when you ask your questions, to avoid getting answers that do not indicate what you really want to solve.
In relation to your "new question", I recommend the gmx cluster of Gromacs tools, to solve your problem. You can save using vmd a frame of your protein in .gro and all the frames together in .trr format (surely you already knew it, I put it in case this is useful for another person), what saves you steps, for your choice of the conformation most representative of the most populated clusters. You can choose, of course, one conformation of each cluster.
Regards
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I have a peak around 1.2  in H-NMR and an associated peak around 27.5  in C-NMR. Does anyone know where this peak is coming from?The solvent we used to run the NMR was CDCl3. These two peaks are associated to each other but I can't find what material they are coming from.
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Maybe hexane, maybe not... it is extremely difficult to answer a question with such rudimentary information. Remember that you should get from hexane or similar saturated hydrocarbons not only one single signal but, in the case of n-hexane, an additional one at about 0.9 ppm. There is also an update to the JOC publication mentioned by M.A.M.: Organometallics vol 29 (2010) pp 2176-2179, this is very helpful.
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I'm just starting to learn a little bit about NMR. I want to know if the result or peaks obtained with NMR is compared with the existing database like XRD to identify the molecular, structure or type of compound?
Is it very specific like XRD and HPLC or is it not that strict and followed a range identification like FTIR spectroscopy?
I'm sorry if my English is confusing...
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I agree with the previous comment and would also underline the primary importance of NMR tecniques in Natural Product Chemistry. In this context you may compare the experimental data with those in literature when you analyze a known compound but you must interpret the obtained data if the compound was not previously described.
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Hi everybody,
I am looking for free NMR simulators (software or web) using AI which allow working different conformers. I know some, as for example: nmrdb.org , but they do not distinguish between conformers.
Thank you very much!
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Hi Amjad,
Thank you very much for the clarification. I agree with you. It is evident you have a strong background in NMR, your comments are really appreciated.
I will continue adding comments based on my own experience to this topic in the future. New contributions are also welcome.
Let’s keep the debate alive!
Regards,
Ignacio.
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I need to measure Concentration of a compound in cell extract. How can i do it. thanking you
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Hi
Mahadeo's answer is basically correct but if you are looking to quantify just a single compound 1D spectroscopy is probably easier. First you need to identify the resonances of this compound. If you know what you are looking for you can spike a sample with this compound and look for the signals that change in intensity compared to a spectrum before the addition of the material. If you can identify one or more resoances with minimum overlap with others you can either use external referencing methods i.e. Eretic2 or add an internal reference such as TSP, DSS or others to the sample.
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I need to measure Concentration of a compound in cell extract. How can i do it. thanking you
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NMR is qualitative AND quantitative technique. If you have Bruker spectrometer look at Eretic2 manual (in TopSpin -> Help -> Manuals (docs) -> Eretic2)
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H chemical shiifht and their multiplicities
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In general the proton spectrum of a saccharide moiety may give little informations since the majority of the signals result overlapped. In some cases the signal of the anomeric proton (chemical shift and coupling constant) may be of help in the assignation of a glycosidic substituent and the configuration of the glycosidic bond. In any case the carbon spectra are the most useful to distinguish the different saccharidic moieties since any saccharide show a different pattern of singals (which is different also for the alpha and beta anomer for the same compound).
A detailed collection of 13C data for both the free saccharides (pentoses and hexoses, comprising xylose and arabinose) and several of their glycosides is reported in the following book:
Breitmaier, E., Voelter, W. 1990. Carbon-13 NMR spectroscopy, New York, VCH, 1990. ISBN: 0-89573-493-1
A comparison of the experimental data with those reported in this reference may be of help to distinguish the two saccharides.
It is obvious that the two saccharides could be also identified by 2D-NMR experiments due to their different stereochemistry. The 1H-1H NOESY pulse sequence (using an appropiate mixing time) should give good results if the proton signals are sufficiently separated one from the another.
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Hi,
I performed an in-situ 1H-NMR study of the reaction between benzaldehyde and n-butylamine to form an imine some time ago, but I am currently struggling to explain some of the behaviours of the observed peaks.
Although I have been able to identify all of the peaks belonging to the reactants and products (and possibly the intermediate), I can't seem to find any clear literature/background theory that explains the following behaviours:
-Peak movement: the peaks belonging to the n-butylamine reactant shift to higher δ over time, towards their corresponding δ in the imine product. At first I thought this was due to the butylamine's conversion to the imine, but I don't see this behaviour with the benzaldehyde (these peaks only decrease in intensity whilst the imine product peaks increase). I was wondering if the movement of the peaks could be explained by the butylamine's involvement in the reaction mechanism, but I haven't been able to find any decent literature to support/explain this.
-Broad (+ moving) peak. I also observe a broad (δ 3.45-3.8) peak that shifts to higher δ over time whilst decreasing in intensity. Again, I am unsure of the interpretations of moving peaks over time and I am also unsure about the potential explanations for broad 1H-NMR peaks - I believe one explanation is hydrogen exchange occurring on the same time scale as the NMR acquisition time.
If anybody has any potential suggestions for these in-situ behaviours, or any useful literature/background theory, I would be really grateful. 
Thanks
Jonathan
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Yes, hydrogen-bonding, some covalent bondings could potentially cause shift in the peaks on NMR timescale. Physical changes, i.e. temperature, viscosity, pH etc. could also play a role in peak movement in 1H NMR. 
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I need help regarding the DOSY NMR, I have a sample mixture which consists of two components confirmed by 1H NMR and ESI-MS analysis. The two components has a molecular weight difference of nearly 2500 g/mol . But after doing the DOSY NMR It is showing the single diffusion coefficient value for both the components rather than two diffusion coefficient values.What parameters need to be changed in order get the better resolution of diffusion coefficients in DOSY NMR. Any kind of help will be appreciated. Thanks
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Hello,
you may have some success by experimenting with different solvents or mixtures thereof. The next issue of Magn. Reson. Chem. will contain a paper touching this subject:
Resolving DOSY spectra of isomers by methanol-d4 solvent effects (pages 759–762)
Indrek Reile, Ruud L. E. G. Aspers, Martin C. Feiters, Floris P. J. T. Rutjes and Marco Tessari. DOI: 10.1002/mrc.4587
Maybe that helps. Best wishes,
Ludger Ernst
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One the important factor for hydrocarbon is the role of water during the reaction. Water is generally considered deleterious in solid-acid chemistry. First, water is a competitive base that strongly adsorbs at the acid site, thereby inhibiting proton availability for hydrocarbon reagents. 
One the method to track the hydrocarbon mechanism on the catalyst is to seal in the environment without any water. 
One the sealing method is using ampule glass and then inserting into the NMR rotor.
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I would not recommend manufacturing your own glass ampoule for MAS experiments: Considering the mechanical stress the sample experiences upon fast rotation, a glass ampoule that does not fit the rotor extremely well will inevitably break.
There are commercial solutions to this problem, with precisely fitted glass inserts for MAS rotors. These glass inserts can either be flame-sealed, like a "normal" liquids NMR tube, with a torch. Alternatively, they can be sealed by using a drop of superglue to seal the constriction.
Among others, Wilmad Lab Glass offers  Pyrex glass rotor inserts, I have included a link to their products.
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For 1H and 13C NMR data analysis, I am using Bruker Topspin 3.5. Is there any preliminary actions I should do on the raw spectrum (background substraction, corrections, etc) before analysing the data? . Thanks all for the support.
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In many cases also apodization and baseline correction are useful tools.
However,  all these operations may introduce several changes in the peaks intensity which should be considered if you are interested in the evaluation of the integrals values.
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Dear All,
I want to know the MW of polyethylene glycol. Please suggest me how to calculate the molecular weight from proton NMR.
Thanking you.
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The method I mentioned earlier works only if you can resolve/identify/integrate the end group -CH2OH; this may require high-field NMR. Some articles suggest using the end --CH2O(this may also require high field NMR, and dry sample/solvent). There is also a paper that suggests using a shift reagent. Quantitative 13C has also been shown to be useful for analyzing PEG.  I am attaching some references and spectra.
P.S. The TFA-d is move the OH resonance away from the OCH2's so its integral is not included; it should also remove any possible contribution of moisture. Some people also use dry DMSO-d6 as solvent which hydrogen-bonds with OH.
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I am looking to verify the extent of epoxidation of fatty acid esters; more specifically the unreacted fraction. Could I conceptually use 2D-tocsy spectra to quantify the total protons next to the ester group vs epoxy cross peaks? Would that be (approximately) quantitative? I have only modest experience with 2D techniques, any tips would be welcome.
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Hallo Rafael Dera,
nomally 2D-spectra are processed with sine or qsine function. After this the integral is not proportional to the concentration. If you use exponential function with line-broadering you get worse 2D-spectra. The 2D-spectra are normally not measured under quantitative conditions, too short D1 time. The TOCSY cross signal is also dependent on the coupling constant to the proton. The epoxide will have a differnet coupling constant to its next proton. The easiest way is always a 1D-1H-spectrum with Long relaxation- delay. For crude estimations it will work but not for quantitative results . If the coupling constant is nealy the same I think it will be not better than +/-10%. But you can try to measure both spectra and see the difference.
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Does anybody know, during 13C NMR scan, changing scan width i.e. focusing on specific region (I am trying to find C=O bonds in esters and carboxylic acids) will increase resolution or not? Which is one better scanning whole region or specific region at high scan numbers? I have observed that scanning 0-200 ppm at 5000 scan numbers takes about 5h, but scanning 150-250 ppm at 5000 takes more time. So which one is better is there any publications on this
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If you are struggling with sensitivity the proton detected experiments are the way to go.  Juraj's suggestion to use HMBC is definitely the best one for you.  For an ester or carboxylic acid, I wouldn't expect the carbon shift to be greater than 180ppm for most normal structures.  If your chemical shift range goes to 200ppm you will see all esters and carboxylic acids.  You may need to go to 240ppm for some ketones or thioketones
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Hi everyone! I would like to know if there are any quidelines or literature on how to set up and run a quantitative 1H-NMR experiment on a 400MHz Bruker NMR. What commands do I use and how do I process the results?
Thank you!!
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Enter the Manuals section in topspin (or type "docs" in the command line). In the "Analysis and Simulation" section, you will find a manual  (or rather a presentation) called "Quantitative NMR".  I have, in any case, attached the file to this answer.
In principle, you just have to set up a normal 1H spectrum. You add an internal standard (some known amount of substance), and can then calculate the contents of the analyte either on your own from the integrals or use the "nmrq"-command to do that for you (which is the better way to do this).
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I want to give numbering to carbons in NMR signals according to IUPAC. The position of methyl on benzoate should be 11' or it will be consider entire different Please see the attached structure, IUPAC name and numbering I have assigned. Is is correct?
Thanks in advance.
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I looked all over the place (I get a little OCD when I don't know something I think I knew) and for what I can tell, the primary substituyent is the carbonyl, therefore all the carbons (in this case just one) following that substituyent should be numbered acording to the main structure, benzoate, so I would think the methyl side of the ester would carry the number 8 since it's part of what the original numbering determines the main structure. The numbering sugests the amine portion is a subsection of the acid which forms the ester, the methyl group is not part of that subsection, it's part of the ester which is denoted with the numbers without the ' therefore I'm pretty sure it would carry the number 8.
PS: I like the drawing part more to be perfectly honest...lol, I always rather see the molecule than to read it's name. 
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The 13C NMR for dimethylsulfoxide shows a signal at 39.7ppm, but we observed additional signals with low intensities.Why?
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The broad signal at ~3.3 ppm in the proton spectrum is due to traces of moisture (water).
May you give additional details about the additional signals in carbon spectrum?  I.e. chemical shifts,  multiplicity...
Are they symmetrical in respect to the septuplet at ~39 ppm?
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Regarding charaterization
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This will strongly depend on the instrument available. With a 300 MHz you will need ca 5 - 10 mg's for 13C and 0.1 - 0.5 mg for 1H. If you have an 800 Mhz with cryogenically cooled probe you will be able to collect 13C with ca 0.1 mg and 1H with less than 1 microgram. It will also depend on the time you want to allocate to the data collection.
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I have synthesised [Ru-(OMe)2TPACl2] but not sure off till because it is not giving me nmr spectra but mass m/z = 522 which correspond to this value. So I thought that I have synthesised [Ru-(OMe)2TPACl2]Cl rather than [Ru-(OMe)2TPACl2] or mix. of Ru(II)/ Ru(III). so can anyone has some idea regarding the separation of Ru(II)/ Ru(III) two species. If there are some reports please share here that would be really helpful for me.
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Hi again,
I still would suggest that for the refluxing step exchanging EtOH to tBuOH would be a worthwhile experiment, as for the NMR part -> if 1H spectra has broad/irreadable peaks 13C might give more information to whether You have one or multiple species because hydrogen atoms are affected by the environment (such as motions and sterics) to much higher degree than carbon nuclei. This would also give You insight if the main reason for the broad peaks are paramagnetics or not.
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How can I get a particular protein in milligram quantity for analyzing using NMR spectrometer? also, would like to know the option of purchasing it from anyone in India.
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There are some places that will do custom protein expression with 13C and 15N labeling for NMR samples. But I do not know if there is such a lab in India. One example is: http://www.nexomics.com/Protein%20Production.html
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Is it possible to observe NMR peak of carboxylic acids proton when D20 is being used as a solvent?
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Only when the carboxylic acid proton is involved in a relatively strong hydrogen bond that do not permit its exchange with deuterium
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Hi..I have a schiff base containing 2-hydroxy naphthalene ring, where C1 has imine bond. NMR and IR shows the presence of OH group.
But LCMS is not giving the expected mass.It is giving M-18. Is it possible to have water loss from such a system?if yes;please help me with reference..Thanks
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I too agree with Nitesh Patel. This can happen in MS due to source fragmentation.
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i have the full set nmr result for my compound included 1H, 13C, dept, cosy, hsqc & hmbc. However, some of my carbon peak (all quaternary C) didnt appeared. One of the proton showed correlation with one of the carbon in HMBC but there is no signal in that region. I did sent my compound for mass spectometry, unexpected target mass correspond to the molecular weight of my compound. Could you please give me some advice(s) regarding on how to improve my result or any analysis test to further confirm the structure? My compound is a small molecule...Thanks in advance. 
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Quaternary carbons have long relaxation times. They can often not yet be seen when all other signals are present. Make sure the carbon spectrum was acquired with a sufficiently long relaxation delay. Carbons next to nitrogen can be broadened to such an extent that they are difficult to recognize.  If the chemical shift in the HMBC makes sense with the proposed structure then you need to optimize the conditions for the 13C spectrum to be able to see it. If it does not make sense it could be an artefact.
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If we carried out 27Al NMR characterization of sample in DMSO and another 27Al NMR in Solid state then the chemical shift of Al is Changes? Or it is apeared at same position for both the spectra?
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It is probably slightly different. Most NMR signals have a chemical shift that is solvent dependent, and the difference between dmso and solid state is presumably much greater than the difference between dmso and D2O. That said, I doubt there would be a huge shift unless the coordination environment of the Al is substantially different in the solid state than in dmso solution--dmso is Lewis basic enough to be a good ligand, and would likely coordinate strongly to trivalent aluminum species, and could potentially displace weakly bound ligands (like bromide or triflate)...
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I feel it's impossible to confirm if correlation of two protons separated by 0.02 ppm in NOESY. Any suggestion to solve this problem??
Also, i appreciate if you could explain (or sending me references) helping to understand how to interpret NOESY cross peaks. I like to understand what is positive and negative peaks, out of phase and in phase peaks, color coding of peaks (red/blue, black/red), number of circular peaks, determining coupling constants .....etc
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Dear Muhammad,
The second part of your question you can easily look up in many NMR textbooks. Tim Claridges book would be one example. "High-Resolution NMR Techniques in Organic Chemistry"  and there are many more.
As for  the first part it is unlikely that you will be able to do this in a 2D NOESY experiment This would require an experiment with very high resolution. It would take a very long time to acquire. A possible solution would be a 1D selective NOESY or NOEDIFF This can be acquired with the resolution of a standrad 1D experiment. It requires selective excitation or saturation. You will have the best chance by running this at the highest field available. At 400 your signals will only 8 Hz apart. If you can get access to a 800 you now have 16 Hz to work with. Still very challenging.  The other possible solution would be a 13C edited NOESY. If the separation between the signals is larger in 13C than in 1H then running a  HSQC-NOESY might give your the answer.
Clemens
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We have try to characterized some plant derived compounds by spectroscopic analysis. By comparing the 1H NMR data of the compounds with reported data the compounds were identified. We have compare our results with the attached paper. 
So now how can I calculate my free induction decay (FID) of 1H NMR?
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It is indeed very odd and unusual to plot the FID, since based on what your goal is, there is nothing the FID can tell you which is the FT spectrum can't (other than some unimportant details)
Anyway, most processing software can display the FID, including Bruker TopSpin, MestreNova. ACD Labs. SpinWorks. 
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Dear all,
I am observing a peak at 0.08 ppm in the 1H NMR spectra CD2Cl2 (I attach a copy of the 1H NMR spectra).
Does anyone had observed this before? Does anyone know what compound gives a signal at 0.08 ppm in the 1H NMR spectra CD2Cl2?
Many thanks for your help
Best regards
Vicente
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There are multiple different silanes or siloxanes that give signals in this range. It could be TMS but one often sees "joint grease" there or other compounds that can be leached out of for example rubber seals in disposable syringes.
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I expected occurrence of two isomers populated at 3% and 97%, but it seems i used diluted sample. can u advise which concn. is suitable for 1D and 2D NMR measurement. I noticed in HNMR and CNMR that the amplitude is very low. iN NOESY and HMQC, i noticed the intensity of cross peaks is fairly good. 
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Dear All,
Please can anyone assist me with the 13C NMR shift for 
1: 11,13-dihydrovernolidalin
2: Vernolide. 
I would sincerely appreciate your kind expert assistance. Thank you. siroplc@gmail.com
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Dear Stanley,
on the basis of the provided spectra I think that the hypothesis of the presence of 11,13-dihydrovernodalin is improbable. Theoretically you should have 6 quaternary carbons, 6 methilenes, 6 methines and one only methyl, but from the DEPT experiments are visible 6 quaternary carbons, 9 methilenes, 6 methins and 3 (at least 2) methyls.
There should be present 3 methilenes on sp2 carbons between 120 and 130 ppm but from DEPT experiments only one is visible.
I cannot exclude that you have a mixture of (at least) two compounds (the decoupled 13C spectrum presents all the signals splitted, may be also due to some setting problems), and none of them is 11,13-dihydrovernodalin, maybe more than one unsaturation of vernodalin is in saturated form. In any case, more experimental details are necessary to make a solid based hypotesis, i.e. a 13C-NMR without splitting of resonances, an HSQC experiment, two HMBC (one with JnC-H = 8 Hz one with 4 Hz), a TOCSY and an ESI-MS in both negative and positive ionization modes.
Anyway, time is required for the interpretation of the data.
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I noticed that two carbons have integration of 50, while the other carbons have integration between 110-130. Can i conclude existence of two isomers. Regarding H-NMR, peaks integration are almost identical. 
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Because of the nuclear overhauser effect, primary, secondary, tertiary, and quatenary carbons all have different integral for the same number of carbon atoms.
secondly, due to the low abundance of the C13 isotope, the integral of the same type of carbon has limited accuracy. 
You will probably be better off finding the isomers in the 1H NMR. You only mention the integration, but the coupling could also provide evidence of isomers if the splitting is more complicated than expected (i.e. you get a multiplet instead of triplet, or doublet etc.)  This is a very general statement and must be seen in the context of your compound.
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Can anyone please suggest me that where C-13 NMR spectrum of the compound butyrylcholine iodide is available online ? I tried to search it on SDBS database but couldn't able to find it. Does anyone have the image of the same spectrum? Kindly, let me know from your side.
Thanking you,
Regards,
AKD
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On SciFinder there is a 13C nmr spectrum of butyrylcholine iodide when you search for the compound and look up the spectra.
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I do an 1H-RMN spectra and I see two differents J in my doublets, the first one is 12.8Hz and the second one 9.8 Hz. How I can assign to the cis- or trans- isomer? Is there any database where I can look for?
Thank you for your time
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The J-coupling for trans is larger than that of  cis-isomer. IR will help you to see if it is cis or trans.
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New to crystallography...I want to compare ligand binding in a crystal structure to one generated using NMR. I have tried the pdbsum and the pisa servers but the hydrogen bonds that are identified differ from the ones identified in the publication of the NMR structure, perhaps because they used the NMR program MOLMOL for analysis? Although I can use pdbsum or pisa to identify the ligand bonding mechanism in the crystal structure...I'm not sure whether it would be correct to compare this with those identified in the publication of NMR structure since I know that using these servers the bonds identified in the NMR structure also differ..so I can't be sure if any difference identified would be a true difference or just a difference in analysis method. Or perhaps these servers aren't suitable for analysis of NMR structures? Any advice much appreciated!
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You can manually identify hydrogen bonds in NMR structures as they usually come with hydrogens in PDB file. If H - O distances are less than 2.0 while N - O distances are less than 3.0, they may be right. Also, NMR structures differ from X-ray structures because 1) NMR is usually used to determine proteins in solution while X-ray structures are from crystallized sample, 2) NMR structure determination is just different from X-ray. It is not like what you get what you see. It is pure computational energy minimization by slow simulated annealing steps using distance information obtained from NOESY spectra. So, they can be different.
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please give the specific answer.
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If by unpaired 'unpaired electrons' you mean paramagnetic species, then:
Paramagnetic species drastically reduces the relaxation times, which can be helpful in the T1 relaxation case, but when T2 is reduced a lot, your lines become exceedingly broad and hardly observable. 
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I have managed to derive some data out of LCMS analyses that needed a lot of tweaking to be cleaned up.  The analyses was done on different days and contain an enormous amount of background noise which needed to be eliminated first.  Of course this contributed alignment problems etc. and to obtain a good PCA discrimination. At the moment this data is in a .csf file format. Several software packages  is available at a price but because this is at an experimental phase I need to make use of free available software such as R, which also needs a steep learning curve before it can be successfully implemented.
My question is if any other credible free software is available that can easily be used without going through to much of a learning curve time.  
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Ian, which methods are you looking for? PCA, PLS, PCR or any other?
I have a couple of suggestions:
1. If you can store your data in Excel or in a text file format (tab-delimited .txt or .csv) you could try ConsumerCheck to do some quick explorative analysis. It is a free open source data analysis tool with a GUI and quite intuitive to use. It comes with binaries for Windows and Mac. https://consumercheck.co/ 
2. You could use The Unscrambler on a trial license. As with Simca (mentioned above), it is easy to use and has plenty of methods implemented. Simca and Unscrambler are competing software.
Good luck finding the "right" software!
Oliver
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Have run the reaction of POCl3 with a carboxylic acid in the presence of a catalytic amount of DMF. I know I have the acid chloride, but (besides H3PO4 and remaining POCl3) I also see a very minor amount of a compound in the 31P spectrum. It has two doublets at -8 and -15 ppm (J= 35 Hz). Could any colleague please provide me with a clue about the ID of this compound and the corresponding literature to back up the ID proposal? Thanks in advance!
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As there is no 1H coupling on these signals the experiment is easy to setup. Read in a proton COSY. Change the nucleus to 31P and adjust O1 and SW. Set the pulses and go.  The structures you propose do not have an element that would lead to a 35 Hz splitting of the 31P signal. So I still think that you are looking at a molecule with two 31P.
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As the two isomer are veri similar, only difference in in H NMR signals i was wondering if in coul be for same steric hindrance effect
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I see two differences in the two spectra.
1. The chemical shifts are different, In the right hand spectrum the chemical shifts are also closer to each other. This leads to a stronger roofing effect as the two signals are coupled to each oter.
2. The line width of the two spectra is different. This can be shimming or an effect of some dynamics in the molecule. If the spectra for the left molecule get sharper at higher temperatures then there is indeed some slow dynamics going on.
A bit more information about the molecules and conditions would help.
Clemens
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In many research, there are nmr spectrum of many polymers by CDCl3 or DMSO-d6. But I can't understand how to do that especially PDMS. PDMS is viscous material before solidify in oven, and solid film is not soluble to the nmr solvents. Is there any special method to measure nmr spectum?
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Solid State NMR Spectroscopy might be help you 
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Hexacarbonylcobalt-alkyne complex was the key intermediate in Nicholas reaction. The NMR characterization of these kind of organometalic compounds has been reported by hundreds of papers. When I was trying to character one of these compounds on bruker 400 MHz instrument  for 1H NMR, the shim process became quite problematic, a warning: "the signal to noise is too low" was come out after an autoshim process. Though I have tried to add more compound or used a mannual shim program, the peaks were still so wide that cannot be treated as a reliable spectrum. Can anyone help me on this sort of things?
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Hi, I think Pedro got the right answer and you have paramagnetic species in your sample. The other option would be convection in the sample that can also affect topshim. Try "topshim convcomp". This compensates for convection. If this still does not help it is most likely the paramagnetism.
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Dear Colleagues and Professors,
I am working on the synthesis of block copolymer using ATRP polymerization.
I need a help about how i can monitor the conversion rate of these blocks using NMR spectroscopy.
If you can provide an equation or detailed strategy, it would be appreciated.
Thank you for your help.
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If you have a non-reactive internal standard, you can integrate the amounts of starting materials from the blocks to see how fast they disappear and get their ratio of incorporation. If you polymer crashes out or gives broad NMR signals you can't use the product signals to quantify things. 
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Some of my clients need a NMR and I am thinking of suggesting oxford  60MHz spectrometer for them, but so far I am not yet convince about the feature. So I need someone who has used it before to tell me more about the equipment Hardware and Software. Thanks!!!
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Mr. Sunday,
Can provide a NMR spectrum of this 60 MHz instrument online?
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In some cases hydroxy protons give delta value above 10. So is there any fundamental related to this?
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due to an intramolecular hydrogen bond
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I am really confused because every author in the litterature use his own method , sometimes from some neighbouring protons integrals and sometimes using all the protons surrounding the bromine atom (or other functional entities)
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Thank you all @ Aaron Bloomfield , @ John Hollerton @ Bojidarka B. Ivanova
Your answers were very helpful !
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I am getting negative chemical shifts in ppm for H-NMR analysis. Besides, most of the peaks are overlapping. Appreciate if anyone can answer my question.
Attached here with the H-NMR result.
Thank you.
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Yes, negative 1H NMR shifts do exist, for example the inner Nitrogen-bound Protons of porphyrins usually have negative chemical shifts (ranging from -1.5 - -4.5 ppm) due to the strong shielding effect of the macrocyclic aromatic ring current on Protons inside the macrocycle (as opposed to Protons outside the macrocycle).
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It can be explained only from Gyromagnetic values or any other reason?
Please suggest??
Thank you in Advance!
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Thank you Dr. Özgür Alver.
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I need that my protein after expression contains C-terminal His-tag and cleavage site before this His-tag (Tev protease / Thrombin ) without any addition signal sequenses and tags on the N-terminal.
Protein is need for NMR experiment. Sequence of protein: FKDPNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKK LGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAYRAKG
Another one question; whether there can be a problem with expression such short protein?
Thank you for the all suggestion!
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Yes other things being equal, you can expect less mass from a smaller protein.  One reason for that is that initiation is a stochiometric mechanism -- whatever fixed amount of protein gets to initiate is going to have less mass, the smaller the protein is.  
Except other things are not equal.  There isn't a reliable way to predict this short of trying.  But there are some rules of thumb -- avoid proteins phylogenetically far away from e. coli;  Avoid proteins with advanced structures, like disulfide bonds or subdomains.  Avoid small proteins is just one of the rules. 
My intuition would be to express this as MBP fusion.  It means that you're making a lot of mass (52kDa that you'll throw away later).  But it's the best way to get your initiation rate to the highest point