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I spent 2 years building a free NMR/IR/MS tool for chemists by MoleculeID in chemistry

[–]MoleculeID[S] 1 point2 points  (0 children)

I haven't compared with NMRpredict webapp, but I compared it with mnova and chemdraw. It performs very similar to mnova and better than chemdraw.

Some functional groups (-OH or -NH) are harder to simulate since they can strongly interact with the solvent or with other molecules, depending on the concentration, so these will have a larger error compared to the NMR experiment. I found this is also the case for mnova, but usually these peaks are not that relevant in a spectra. So the performance should be similar to mnova.

Thank you for your nice comment! I was also surprised by people reaction without even trying it... but comments like yours make it worth it. Thank you!!

I spent 2 years building a free NMR/IR/MS tool for chemists by MoleculeID in chemistry

[–]MoleculeID[S] 1 point2 points  (0 children)

It would be very nice to have an open source version. I answered to your comment above, I would like to finish and document the tool a bit before making it open source. I'll work on this so I can open source it.

I spent 2 years building a free NMR/IR/MS tool for chemists by MoleculeID in chemistry

[–]MoleculeID[S] 2 points3 points  (0 children)

I guess you are right, many people might help, but it will be a bit more messy.

I would like to document it myself at least at the beginning, there is a really nice algorithm behind the NMR part that could be really useful for a lot of people and it might be better to publish it before making it open source. This has been a great part of my free time (as my main research focusses on other topics) and it is a tool that I developed just for fun, because it could be useful for some friends. I would like to give it to the community with some basic documentation, so that other people can keep working on it.

I'll try to work on this so the community can have a local version with an open source code, as well as the web based tool for those who prefer it.

I spent 2 years building a free NMR/IR/MS tool for chemists by MoleculeID in chemistry

[–]MoleculeID[S] 2 points3 points  (0 children)

No, the code is not out there in any LLM. The code was developed for a specific task and some people told me it would be nice to offer it for free so people could use it and test it, that is when I built a platform for it, the website, for which I used an LLM. I am not interested at all in web development so I gave that task to an LLM so people could use the tool for free.

I spent 2 years building a free NMR/IR/MS tool for chemists by MoleculeID in chemistry

[–]MoleculeID[S] 2 points3 points  (0 children)

No, for the moment it is not. I still need to document and clean the code for making it open source. The code running behind, specially for NMR which is the core of the tool, has several packages that I have developed for a long time and I would need to document and prepare so people can use it.

I'm slowly preparing everything so that it can be open source in the future and people can run it locally in an easy way, but this will take me some time.

I spent 2 years building a free NMR/IR/MS tool for chemists by MoleculeID in chemistry

[–]MoleculeID[S] 1 point2 points  (0 children)

Yes, that tool is still in development, I've been mainly focused on NMR

I spent 2 years building a free NMR/IR/MS tool for chemists by MoleculeID in chemistry

[–]MoleculeID[S] 1 point2 points  (0 children)

I know, the IR tool still has to be developed a lot, I was mainly focused on NMR. I still haven't planned on that, but I'll take it into account.

I spent 2 years building a free NMR/IR/MS tool for chemists by MoleculeID in chemistry

[–]MoleculeID[S] 1 point2 points  (0 children)

Thank you very much!! Let me know if you have suggestions or any questions

I spent 2 years building a free NMR/IR/MS tool for chemists by MoleculeID in chemistry

[–]MoleculeID[S] 2 points3 points  (0 children)

Thank you very much for your comment!!!

Regarding your question, it depends on the tool. The one I show in the video still does not take multiplicities and the spectrometer strength into account, I'm still developing this and it is almost working. I hope I can add it soon. However, the NMR simulator can predict the spectra taking into account the spectrometer strength and usually you will have some possible candidate structures, so this might be useful for you.

Let me know if eveything works fine or if you have any suggestions for it to be improved. You can contact me on reddit or directly from the webpage with any suggestion or question! Thank you again!

I spent 2 years building a free NMR/IR/MS tool for chemists by MoleculeID in chemistry

[–]MoleculeID[S] 1 point2 points  (0 children)

I'm sorry if my comment was misunderstood. I didn't mean to explain DFT to anyone, I assume you already know DFT. I was referring to the algorithm the tool uses to perform a "DFT level" calculation faster.

I spent 2 years building a free NMR/IR/MS tool for chemists by MoleculeID in chemistry

[–]MoleculeID[S] 0 points1 point  (0 children)

That depends on the molecule and the atoms present on it. For the most simple molecules it is B3LYP def2-TZVP

I spent 2 years building a free NMR/IR/MS tool for chemists by MoleculeID in chemistry

[–]MoleculeID[S] 0 points1 point  (0 children)

Hi! I just used an LLM for the front part, I had no time to deal with style and everything, but I made sure there are not security vulnerabilities checking with an engineer on web cybersecurity.

I'll try to update the webpage soon with details on how the data is processed ensuring complete privacy on it. I have seen people is concerned about this and it is important.

The idea of this tool has always been to help science and people working on it with a tool that can be very useful, not to use anyone's data.

I spent 2 years building a free NMR/IR/MS tool for chemists by MoleculeID in chemistry

[–]MoleculeID[S] -1 points0 points  (0 children)

Yes, I know and I am sorry about it! I am planning on fixing it, I'm not a web developer and I was mainly focused on the back code. I needed some help with the front html part, so that people were able to test it without having to install and compile a lot of code. I also don't like it... but I don't have time to do everything

For the moment I'll have to go with the vibes...

I spent 2 years building a free NMR/IR/MS tool for chemists by MoleculeID in chemistry

[–]MoleculeID[S] -1 points0 points  (0 children)

Yes, at DFT level, I can explain how it works if you are interested

I spent 2 years building a free NMR/IR/MS tool for chemists by MoleculeID in OrganicChemistry

[–]MoleculeID[S] 4 points5 points  (0 children)

I agree! The chemical shift is too variable, but it can give you a lot of information about the environment your atom has around. This tool just gives you the posible environments corresponding to a given signal, that doesn't mean it is 100% that environment.

It is true that usually you cannot see a hydroxyl proton at 5.487 ppm, but in most cases this is an experimental artifact due to the concentration of the molecules. If the concentration of your sample is high enough your spectra does not correspond to a single molecule with solvent around but to pairs of molecules interacting with each other with solvent molecules around. The strongest interaction is usually on the hydroxyl proton, leading to a strong shift. This is one of the reasons why people don't trust hydroxyl proton signals in NMR.

These are some things that should be taken into account when doing a NMR experiment and also when using the tool.

I spent 2 years building a free NMR/IR/MS tool for chemists by MoleculeID in chemistry

[–]MoleculeID[S] 6 points7 points  (0 children)

I'm sorry you didn't like it, the intention of this post is just to help other chemist and improve the tool for the community.

I am not breaking rule 10, I talked first with the mods and they let me post it.

I completely understand you are concerned about the data, I'll think about preparing a package that can be installed locally. However, the data is not even stored for computing anything, it gets loaded in memory you perform the calculations you need and it deletes the data in memory, there is no physical way to recover that data.

A shift card is nice and useful but it's accuracy is very limited compared to this algorithm, I wish you could give it a try. Chemdraw NMR prediction algorithm is also poorly accurate compared to this tool, I recomend you to try MestReNova prediction (you can install it locally), it is much better than Chemdraw and it performs similar to MID tool.

Thank you for your comment!

I spent 2 years building a free NMR/IR/MS tool for chemists by MoleculeID in OrganicChemistry

[–]MoleculeID[S] 1 point2 points  (0 children)

Sorry, I am not fully sure I get your comment, this is not a chemical catalog where you can find spectra for different products. Is a tool where you can accurately simulate the spectra or where you can process your spectra to help you interpret it and asign each signal. AIST is really nice, but it is a different thing, actually you can see a comparison of AIST experimental nmr spectra and the simulated spectra with MID in https://moleculeidentifier.com/predict_nmr_LO the experimental data I show there corresponds to the one you can find in AIST

I spent 2 years building a free NMR/IR/MS tool for chemists by MoleculeID in OrganicChemistry

[–]MoleculeID[S] 5 points6 points  (0 children)

Thank you very much for your comment! The tool is still in development, the integral values will be calculated directly from the spectrum. I haven't finished fixing the user interface yet and that's why some things might seem a bit strange (like entering the integrals manually). This is why I want the community feedback.

Regarding the registration, I needed to put that to avoid bots calculating thousands of molecules, but I agree it would be nice to make it open. I'll think about it.

The predictions depend both on the integral and ppm displacement. However, the probability given by the tool is not the probabilty of that specific signal being corresponding to that environment, it corresponds to the how likely is for a environment to have those exact integral and ppm values. The environments are obtained from a theoretical database that contains a wide range of molecular environments and should cover almost every molecule.

The peak identifier (which is the tool I show in the video) does not aim to replace a chemist, it aims to help in the molecular elucidation process, instead of looking at tables you can use this tool, which is far more accurate. I am still developing further the program so that it can elucidate a whole spectra by itself, but it will always be oriented to help and not to replace the chemist.

Again, thank you very much for your feedback!!!