Nuclear Magnetic Resonance - Science method

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.

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

Dear Meltem,

I guess that you already know this literature:

Good luck

Alfred

Thank you for your answers.

Haitham Saad Al-mashriqi

Afroza Begum

Jun Uzawa

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.

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

Daptomycin is a type protein. You can see the file. Hope it help you.

Dinesh, you may want to try Toluene (Benzene) or D2O....

Good luck

Alfred

Dear Donovan,

as you have enough material for a 13C 1D it must be easy to acquire 2D 1H-13C correlated HSQC and HMBC by which a structure determination of the compounds you mention should be simple....

Kind regards

Alfred

P.S beta-hydroxy beta-methylbutyrate may also run under beta-hydroxy isovaleric acid?

For a tightly binding small molecule you could diffusion filter the spectrum. Bound drug should have a significantly different diffusion constant compared to free.

James E Hanson Thank you very much for your valuable help

The following link is also very useful: https://www.googleadservices.com/pagead/aclk?sa=L&ai=DChcSEwj3zfWbsen3AhUYp3cKHRSqDcIYABAAGgJlZg&ae=2&ohost=www.google.com&cid=CAESbOD2KZ40kaCxmGfg3ASL3Jzer14yFfMtRQpRN7fxEU9NOMowXRZT-1uO8b3T1HHdtrtl8rw9Afav-wg959rbQPDwAksU-qmO-K5w97g0ejz124AzSUR7ji_XNGiOHYsai6JRszlD0zYt_Q-GFw&sig=AOD64_0Ss0AIrwAyKttE-v5aARo_n6GVaw&q&adurl&ved=2ahUKEwiTpu2bsen3AhV3iv0HHZ5wALI4ChDRDHoECAAQAQ

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.

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!

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.

Hello,

There are a lot of rules! So many that I would recommend using dedicated freeware to do it:

Baseline_corrector for baseline correction if the acquisition was performed with a single pulse acquisition and wide spectral width:

And DMfit for deconvolution:

Nice tutorials exist for both freeware!

Good luck

Maxime

Dear Jakia Khanom, first you should decide on the type of NMR to be used, there a broad informative differences between solid and solution states NMR tools. Solid state NMR is more suited since it reflects the actual phase repartion of the polymers forming the blend. Please have a look at the following documents. My Regards

This almost looks like a factor two problem. Does the 3rd party not account for a split evolution time or is the ppm scale in the indirect dimension based on the 1H frequency?

This is always the first place I look

If you go to fluorobenzene (13C) you will see there is coupling to all the carbon positions.

Note these are spectra are quite old and consequently at a very low frequency so on a modern instrument (at higher field) some of the smaller couplings may be not be resolved.

Dear Manel Taferguennit in this context, please have a look at the following instructive presentation:

The presentation is freely available on the internet. It might also be worth reading the answers given to the following closely related question which has been asked earlier on RG:

(6 answers)

Good luck with your work!

Hi Rejeev,

I had the same problem and as far as I know, there is no solution to have integrals and peak values in stacked form.

Here is how I fixed the issue: I just processed both spectra in different pages and then I adjusted the height and copied and pasted one spectrum to the other page. For zooming in and out both spectra at the same time, you just need to select all first. I know it might be too late for you, but it can help others.

Bests,

Dear Salem Baroudi I fully agree with Jean-François Gal in that serum caps or normal plastic caps are most likely not suitable for your purposes. If your samples are highly volatile but not really air-sensitive, I would suggest to use NMR tubes with a stable screw cap. If the samples are also air-sensitive, J Young NMR tubes with an inlet for vacuum / inert gas (as suggested by Lewis Copsey) are certainly the best choice.

The Metabolomics Innovation Centre (Canada) - www.metabolomicscentre.ca

Over 50 targeted assays (with absolute quantitation) and 6 global/ untargeted assays. Both NMR and MS based services are available, including assays specifically for plants studies. All prices/ assays are available online. Fell free to contact me directly.

You can read:

and:

also: http://wrap.warwick.ac.uk/110787/

I hope this helps!

jMRUI software can help. You can insert the raw data and after fitting you can export the fitted data easily.

Dear Anuja Kulkarni, please have a look at the following document, hope it will be usefull. My Regards

Dear Dr. Ross,

This is indeed a difficult task. My college Gerhard Althoff-Ospelt proposes a 15N HETCORE. Here, the combination of 15N and 1H chemical shift could give rise to the protonation state. Which kind of equipment do you have? A 7mm probe would be advantageous with respect to sensitivity but a 4mm probe would also be suitable.

Another solution would off course be fast spinning and 1H detection.

Many Greetings

Kristof Grohe

These publications maybe of interest.

You should see one signal for the two methylgroups near 2 ppm, a triplet or dxd for the methine, a doublet for the methylene and the other 10 protons of the piperidine looking quite similar to free piperidine.

Dear Corentin, I guess you know this researchgate post from some time back: https://www.researchgate.net/post/Best_way_to_visualise_Gaussian_NMR_output

Kind regards

Alfred

Thank you Isam Eldin Hussein Sir and Madhukar Sir for your comments.

is that 4,4'-Dimethoxybenzil?

Thank you Gentelmen for those valuable answers.

Hi,

I faced the same problem and solved it. You need to download the mestrenova lite with NMR lite plug-in in it. Here is the download site: https://mestrelab.com/download/mnova/nmr-lite/

To potentially save someone some work in the future: I found a differing method in the paper by B. Lama et al.: "Expeditious dissolution dynamic nuclear polarization without glassing agents", 2016, NMR in Biomedicine

hello, using IOP's can be helpful.

hello, using IOP's can be helpful.

I am not sure about this video, but it may be helpful,

https://www.youtube.com/watch?v=8rtpCgMm4cE

Hi, Watkins, many thanks for your response. I read your suggested papers. I am also confused about the chemical shift of 7Li-NMR. In my opinion, by combining some literature, the 7Li-NMR signal shifts upfield with the increased DN of the solvents, just like the 23Na-NMR trends. However, the explanation of the shift of 7Li-NMR signal is complex because the shift has a relationship with both anions and solvents. The anion competes with solvents to interact with cation (Li+ for example), by forming contact ion pair (CIP) of anion-cation interaction and complete solvated Li+ (cation in solvents cage) of solvent-cation interaction. The papers indicate that the strong solvent-Li+ effect shields the 7Li-nucleus, moving the signal to the upfield. It is generally considered that a solvent with high DN has a strong interaction with Li+. However, some cases are still not clear to me.

1. What’s the effect of an anion when it penetrates into the shell of cation by replacing solvent(s)? Erlich et al. (Journal of the American Chemical Society 1971, 93 (22), 5620-5623) indicated that ClO4−, I−, and BPh4−deshield the cation when they penetrate into the shell of Na+, moving Na signal to downfield. However, Yan et al. (Angew. Chem. Int. Ed. 2018, 57, 14055 –14059) suspected NO3− possess electron-donating to Li+, moving Li signal to upfield. We can also see the opposite trends of Na+ shifts for NaClO4 in different solvents (CH3CN, CH3NO2) with concentrations (Journal of Physical Chemistry 1975, 79 (1), 80-85). It seems ClO4−has inconsistent effects in different solvents, which is confusing.

2. For 23Na NMR shifts with various solvents, Johnson et al. gave an opposed result (Figure S1 in Nature Chem. 2014, 6, 1091–1099).

For a carbonated electrolyte with LiPF6salt, carbonyl oxygen devotes electrons to Li+, forming a solvated structure and moving 7Li NMR signal to upfield. However, 17O NMR signal also shifts to upfield (J. Phys. Chem. Lett. 2013, 4, 1664−1668), meaning the shielding effect (electron cloud density) of O-nucleus is reinforced, which is also confusing.

The molecule is completely symmetrical so both NH should give same peak; they are chemically identical.

is there another proton on the carbonyl carbon? Your carbonyl carbon only has 3 bonds.

Certainly it's the Magnesium that precipitates as Mg(OH)2.

Dear Sengottuvelan,

As many people said already Bruker TopSpin is free of charge.

You just have to register (for free) and apply for a license for academia (if you are in academia ;) )

MestraNova is easy to learn and has a good user-interface. It is good for daily NMR-use. For example, you measured a 1H 1D, 13C 1D COSY and HSQC or so. Such data are convenient to analyze with MNova. If you have 3D spectra MNova is not suited. And if you have large spectra or many spectra that you want to analyze simultaneously than I would choose TopSpin.

About other software I cannot comment, because I have no experience.

Many Greetings,

Kristof

Dear Sayandeep

Your questions(YouTube snip) made me think!

.....on the web-page https://gisgeography.com/atmospheric-window/

you find a figure on absorption of electromagnetic waves in earths atmosphere which shows that anything with a wavelength longer than 100m is blocked. This corresponds to a frequency of 3 MHz. But in this figure it is not clear what happens to REAL low frequencies.

In the paper you find in figure 3 an attenuation of only 10 dB/1000km in the few-kHz range...

Low-frequency attenuation is important, because the larmor frequency of Hydrogen (as present in water) in the earth magnetic field is about 2 kHz (all other elements have much lower frequencies). This is the frequency needed for "imaging" of water (if possible et all).

You have to find the "real" number of transmission/attenuation through the atmosphere in the few-kHz range before you can think about whether MRI of water from a satellite might be possible from a atmosphere-physics (far not yet technical!) perspective.

Kind regards

Alfred

P.S. Again: all this said by a REAL non-expert in the field!

Thanks al, for the response please help me I need Complication Neonatal framework

Dear all, what is the counter ion of the quaternized polymer ? Possibly, it is not excluded even at high temperature. Thus it counts for residual mass increase. My Regards

Shubham Gupta hi! Spectral Database for Organic Compounds (SDBS), Reaxys.

Perhaps opening up or channeling thermal oscillations to some energy-intensive thermal oscillation (or containment of phonon) can raise Cv (const. volume-specific heat). But why one needs to purposefully increase it? Well, then more thermal energy would be required to cause its temperature change, so thermal fluctuation would be smoothed out, or the material itself can be used as a heat storage medium without excessive cooling or heating. Coupled with the high thermal conductivity of 2D and 1D allotropes of carbon, this means the thermal storage media within itself would not undergo much thermal-gradient induced stress. So thus you have a twofold advantage.

See the following link: https://www.pharmtech.com/view/excipient-selection-protein-stabilization

Dear Yuewen Jia, whatever the color is, it should be purified by sublimation prior to its use. My Regards

It is very likely that the C attached to the nitro group has a (very) long relaxation time (as do all C atoms without a H attached).

If you repeat the experiment with a longer wait between pulses you will give the C time to relax (but it will of course increase the experimental time).

This C will also not benefit from NOE as only C with H attached will show this effect (caused by the decoupling).

There may also be some coupling of this C to the quadrupolar 14N which due to the small electric field gradient typical in nitro nitrogens and consequently may not completely decouple itself.

Baroudi

You can add molecular sieves directly to the deuterated solvent and cap. Leave at least 24 hrs and prepare your NMR sample under a dry inert atmosphere.

Good luck

As far as I know you can still upload a PDB file for NMR data, but PDB_extract will convert the format if needed. Upload one model file with all the 20 models in the ensemble superimposed.

The optional files in extract are crystallographic. You don't need to upload optional files.

Start a session at wwPDB and see how far you get, it is reasonably intuitive. If you are stuck, there is a means of communicating with wwPDB staff who are the ideal people to give you advice

Kavya Ganabady

Prepare a 2% gel, then heat it sharply to a transparent solution, and then cool it sharply to a temperature at which you can do NMR. Polymer solutions take a long time to come to an equilibrium state. You may need to find the best heating and cooling times.

Dear Saman,

In what solvent do you do your cellular extract (deuterated MeOD/D2O)?

Presence of exchangeable OD's will complicate the MS analytics substantially, because any exchangeable OH will be present as a OH/OD mixture...MS experts are normally not happy with this situation.

If you do the extract with MeOH/H2O I would split the sample prior of adding D2O lock. Normally a small aliquot of a NMR sample is adequate for LC-MS anyways.

I hope this helps

Alfred

Is  your compound stable to alumina or silica? You could run it through a quick plug, which should grab the TBAOH because it is ionic. Recrystallizing from MeOH, EtOH, oriPrOH would work too if your compound can be crystallized from those solvents. TBAOH would be somewhat soluble in those solvents. Good luck!

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.

Dear Prof. Dr. Nada,

Thanks for your participation in this discussion. I would like to share an outstanding article about the solid-state CP--MAS 13C NMR spectra as the following article:

Upcoming, I will contact to the group (Saint Petersburg State University: Saint Petersburg, Russia) to see how.

Best regards.

When a external field is applied over a molecule, it was shown that it creates an induced magnetic fields and as a response to that, the electrons move around the molecule as explained classically by the Faraday's Law (this is similar to the effect of magnetic fields on a coil in classical physics).

We must also notice that due to quantum mechanical effects, the current can flow on two different ways: (the classical one) the diatropic, or the paratropic. There is an advanced review with useful information.

doi: 10.1002/wcms.1270

There is another one who explain how to obtain the magnetically induced current densities:

doi:10.1016/j.chemphys.2008.10.040

I hope this information works.

Kind Regards.

X-ray-based structures are preferred because of their higher resolutions

You can use Multiwfn (http://sobereva.com/multiwfn) to simulate NMR spectrum based on output file of NMR task of Gaussian, it is easy to use, flexible and has rich capabilities. See Section 4.11.10 of Multiwfn manual on examples of plotting NMR spectrum for various cases.

Bernard Timothy

Hello, Bernard, do you find the reason for your problem I have the same so please shear problem solution

thank you in advanec

Please go through these attachments and I hope this will helps you. 

1. Charisiadis, P., Kontogianni, V., Tsiafoulis, C., Tzakos, A., Siskos, M., & Gerothanassis, I. (2014). 1H-NMR as a Structural and Analytical Tool of Intra- and Intermolecular Hydrogen Bonds of Phenol-Containing Natural Products and Model Compounds. Molecules, 19(9), 13643–13682. doi:10.3390/molecules190913643

2.

What feature the spectra and, or methods can you use to confirm inclusion?

The rate of overall molecular motion determines how much H-H dipolar coupling contributes to the H--1 and/or C-13 NMR line widths.

For solids, you would need to use solid-state NMR methods.

For gels, the answer depends on the viscosity of the sample. H-1 NMR may be possible. The lower the viscosity the more narrow the line widths. If the inclusion complexes are stable above room temperature, increasing the probe temperature could be helpful.

Finally, is there a dynamic equilibrium between inclusion and non-inclusion species? If you are unlucky, the exchange rate could render the relevant lindwidths to be very broad.

Dear Iman Azamian,

1) Regarding to the principles of CP-MAS NMR, please refer to the earlier question in RG: https://www.researchgate.net/post/What-is-the-principle-of-solid-state-MAS-NMR-and-what-is-the-difference-between-the-solid-and-liquid-nmr

2) The method of interpretation is same same. You could refer my article which have mentioned the solid state-NMR spectra of anionite lignocellulosic materials as the following link: pubs.acs.org/doi/10.1021/acsomega.0c01984

Best regards.

type "pl" and change it to whatever you want under the "user".

If there is slow exchange between the two isomers it is possible to see cross peaks between the isomers. First you should look for cross peaks between the same atoms on both isomers. You can also make it easier to distinguish between NOESY peaks and exchange peaks if you run ROESY instead of NOESY. In ROESY experiments Oberhauser and exchange peaks will always have opposite phase. Also cooling down the sample will reduce exchange related signals.

Doctor Tatou Touahria , if you were from Baghdad, I would guide you to a number of research centers that provide analytical equipment for research purposes, but it became clear to me that you are from Algeria.

My greetings

We can not calculate the degree of methacrylation by using NMR spectra. In this case, the role of NMR spectra only conform that the chemical reaction has occured or not through looking up the feature peak of chemical bonds (For example: C=O, C=C, and so on). If your samples exist the solid state, you can calulate the degree of methacrylation by using the increase level of dry mass and titration method of functional groups.

Dear Aftab Ali ,

Concerning siderophore, they might be quite big molecules and not the simplest to elucidate through NMR analysis. Nevertheless, from a experimental point of view, I could suggest you to take a look on these different articles:

As you can notice, many methods are used in NMR for the elucidation of structure (1D: 1H, 13C, 15N, 2D: COSY, HMBC, HSQC, H2BC... and NOESY) as the structures are complex.

From the point of view of theory, and, if you are familiar with calculations, It is also possible to "predict" NMR spectra via ENSO (developed by Grimme's group) and ENSO utility:

To compare with experiment, I could suggest you to take a look at this excellent article :

Hope this could help you in knowing your structure !

Dear Jo

You can use the electrospray ionization-ion mobility spectrometry apparatus for detection of the big molecules.

One thing you could do is pre-lock on a mock sample of bacteria in the conditions your real sample will be. just grow some cells (the ones to produce your protein or even DH5alpha, doesn't matter) in some rich medium, spin them down gently and resuspend them in the final medium (incl D2O) as your good sample will also be. Fill an NMR tube (shigemi without plunger) by gently spinning down the cell suspension in the tube, yielding a cell pellet,. Make sure you have enough cells for the pellet to occupy the whole coil volume, and leave some medium from the supernatant above the cell pellet (that will replace the plunger). use that sample to lock and shim before inserting your real deal sample (prepared the same way). that should give you enough flexibility to play around with parameters before inserting your precious sample.

There should be no problem to "spike" the solution with additional gas (bubbling it through the solution or fill the space above the liquid and shake), we did this often with hydrogen or hydrocarbons. If you suspect methane as product, you can identify it by recording 13C since its shift is very characteristic (below 0 ppm). If the concentration is very low, you may use indirect detection.

Raja Summe Ullah

Yes, it is possible. check von Braun degradation.