mgperson2002

For anyone interested: There's now an OChemdle game up on the site, with a tournament starting Oct 1. https://organicchemmaster.com/chemdle/signup

For anyone looking for an organic chemistry game of the wordle family style, I'm currently working on OChemdle: https://organicchemmaster.com/chemdle

Pinch in and pinch out gestures (using two fingers) are now supported for zoom in and zoom out effects of the molecule. A good example on which to test the new support is https://organicchemmaster.com/MolGen/Molecules/remdesivir?Options=AtomAbbrev Write up of the update is at: http://molecularpathwaygenerator.blogspot.com/2021/09/introduction-of-pinch-zoom-controls-for.html

Hi again all. Another quick update. Two new reactions are now supported by the framework of the application: The Benzoin condensation reaction which can be viewed here: https://www.organicchemmaster.com/Molgen/Reaction/benzaldehyde/benzoin?options=Calc,Reac and here: https://www.organicchemmaster.com/Reaction/Rule/031 As well as the Dieckmann condensation reaction which can be viewed here: https://tinyurl.com/5cet2mpv and here: https://tinyurl.com/4tam8kwa In each of the two reactions the first link provides the parameters for a synthesis pathway search (going from molecule A to molecule B) which utilizes that reaction and the second link provides a description of the reaction and a sandbox tool to predict the product of the reaction with a given reactant molecule. I am still looking to create a large team to build this app out to be as useful as possible to both students and chemists. Thanks.

A quick update. Hopefully some of the panning issues will be resolved by a new "auto zoom out" feature that will detect if the molecule exceeds the boundaries of the workspace upon its loading. https://www.organicchemmaster.com/MolGen/Molecules/remdesivir?options=AtomAbbrev Remdesivir, among other more complex molecules, will be more easily seen. Thanks again for the feedback. My goal is to one day work with a large team to build this app out to be as useful as it can be to chemistry students and chemists.

Right, so definitely not all functionality is available yet on smartphone, but the subset of the functionality necessary for designing and editting a molecule IS there on the smartphone. If there is any confusion about HOW to specifically edit the molecule, there ARE tutorials available (the question icon in the upper right of the workspace). If you are able to, would appreciate any feedback on the tutorial itself. The approach of also adding the pop-up window on the smart phone CERTAINLY is something to be considered. It would definitely introduce all the atom details and click and change to edit modality to the smaller screens. One pretty import consideration, though, is that a small screen often does not have the pixel real estate to both include a reasonably sized workpsace AND the aforementioned pop-up window. My goal for small screen design was to prioritize plenty of screen real estate for the workspace view and editting of the molecule while still offering full editting functionality. Adding the pop-up window was a secondary consideration. That said, I am certainly amenable to suggestions for how that pop up window might work. I'm hesistant to put that pop up window in a place where the user would have to scroll to find it, because I'd like to keep the entire experience of molecule editting contained within the screen size. I'm also a bit hesitant to put in the same pop up style of view/editting, because that would require the user to switch back and forth between viewing the entire molecule AND viewing specific info on one atom. If you have a suggestion for how to maintain the simplicity and practicality of viewing the entire molecule at once while still viewing the detail of an individual atom and being able to edit that atom on a small screen, I am all ears! As for your interface suggestions, LMB instead of hover to select atom: This is interesting. I am open to more feedback of if the volume of users prefer this method. LMB to change bond: Also open to volume of feedback on this. In my mind I wanted to make the editting of the bond type (single, double, triple) or the orientation of the bond (dashed/wedge) to be simple enough to be done WITHOUT the popup window. LMB to pan: This is actually what currently happens. Using the two finger zoom in zoom out as opposed to using the + and - buttons is certainly possible. I am interested in your suggested of select all/select none as well. This could certainly be a future feature to implement. Finally, re: panning molecule view and the scroll top/bottom, do you mean how the molecule workspace is layed out on a small screen? Do you have any other suggestions or preferences for accomplishing this? Keep the feedback coming. Goal is to make this eventually the ultimate o-chem tool, lofty a goal as that is.

Thanks again. For now, zoom out has been powered enough to fit the entire Remdesivir molecule in the workspace: https://www.organicchemmaster.com/MolGen/Molecules/remdesivir?options=AtomAbbrev. To further work on is the auto zoom feature which will zoom out to an appropriate level once the molecule is first drawn and the rotate feature. Yes I have a smartphone. Yes I use the website from the smartphone. Yes I am aware there is no hover event exactly as is found in desktop web browsers. The functionality of designing and editting a molecule can actually all be done without the hover event other than creating ions. Though should there be enough interest in implementing the hover features on small screens that can be developed as well. The left click to change wedge-dash notation SHOULD be working correctly on smartphone; what do you mean exactly by "touch display"? There is a chance that it might pick up your finger at a wider sensitivity level than you are expecting. For that I'd suggest zooming in more. If you'd like, you could post a screenshot here and indicate where on the screen you are touching and I can attempt to recreate the issue. Of note, clicking on an atom to change the wedge/dash is actually best thought of as changing the chirality of that atom (of course only relevant in stereocenters) and THEN seeing the change in the visualization of that molecule. In programming terms this means changing the model and having that trigger a change in the view.

Thanks @Sensei. Yup do need to work on updating zoom out as Remdesivir is a larger molecule than previously supported. Write up for process of modeling and next steps can be seen here: http://molecularpathwaygenerator.blogspot.com/2020/11/covid-19-ii-remdesivir.html

One more update: After a few months the site is now capable of modeling Remdesivir. https://www.organicchemmaster.com/MolGen/Molecules/remdesivir?options=AtomAbbrev. Also working on modeling some relevant syntehsis pathways. Very fortunate the vaccines are now being distributed.

A quick update that the site now supports the modeling for the (somewhat controversial) treatment drug of chloroquine https://www.organicchemmaster.com/MolGen/Molecules/chloroquine?options=AtomAbbrev for the novel corona virus. Hopefully planning to model the synthesis pathway soon as well. Of course, if we learn more in the near future maybe that will have to switch over to Remdesivir...

Hmm, it seems like williamhakespeare's comment was a copy from an earlier reply hypervalent_iodine. But I appreciate whatever feedback there is! I did finish adding support for the intermediate molecules and reactions used in the Daraprim (pyrimethamine) pathway that was discovered by Australian high school students in 2016: https://www.abc.net.au/news/2016-11-30/daraprim-nsw-students-create-drug-martin-shkreli-sold/8078892 . The pathway synthesis search engine is now capable of "rediscovering" the pathway: https://www.organicchemmaster.com/Molgen/Reaction/1-chloro-4-(2-cyanoethyl)benzene/5-(4-chlorophenyl)-6-ethylpyrimidine-2,4-diamine?options=Calc%2CReac&fbclid=IwAR0qwO493DIEOi-mOy5G7BDn3aZxvSUtMESRlh9bnB602zI_E-llRgAfERE The blog for this update is again at: http://molecularpathwaygenerator.blogspot.com/ Still absolutely a lot of work to be done, and still absolutely welcoming all feedback. Thanks again, Matt Person

Thanks for the reply @Avidmind. Again, I am DEFINITELY looking to work very closely with an organic chemist (team of organic chemists) for examples like this to actually draw on their knowledge/experience and incorporate that into the reaction modeling. An update of the progress of the project. I have gone ahead and added support for the user to use the click and select approach for designing a molecule as opposed to the drag and drop approach while in large screen (desktop/non-mobile) mode: http://molecularpathwaygenerator.blogspot.com/2019/10/introduction-of-click-to-select-and.html. The hope is to allow the user an interface more similar to a familar ChemDoodle/JSME style. One further update is that I am currently in the process of modeling the molecule pyrimethamine (Daraprim) and the reactions/intermediate steps involved in one of its traditional syntheses. If enough work could be done on the project that one day power could be taken away from people like Martin Shkreli capitalizing on lack of competition for a certain drug, the project would be highly worthwhile. Finally, I actually am finding myself currently in Australia for the next few days. I will be in Canberra tomorrow (dec 12) and travelling from Canberra to Sydney Friday (dec 13) where I will remain for the weekend. I would absolutely be interested in discussing the project in person with anyone who is available and interested at that time. Thanks again. Matt Person

Hi again all. A further update after the addition of some more features. I have added full support for esters in the interface. As such, I was able to go ahead and expand the LiAlH4 reduction rules to INCLUDE reduction of an ester as was previously mentioned missing by @hypervalent_iodine. An example of such a reduction reaction can be viewed here: https://www.organicchemmaster.com/Molgen/Reaction/methyl ethanoate/ethan-1-ol?options=Calc,Reac. Also mentioned was the lack of support for heteroatoms. I have gone ahead and introduced support for nitrogen heteroatoms in particular for this update, with the motivating goal being to support all 5 DNA/RNA bases as well as the medicine allopurinol. A tutorial for how heteroatoms can be added to a molecule can be found here: https://www.organicchemmaster.com/MolGen/Tutorial/HeteroatomMolecule. I am particularly interested in feedback on this approach for adding heteroatoms. Future updates will include other heteroatoms as well. Also of note, the support of allopurinol required, in turn, the support of heterocyclic molecules. Once again, there is still absolutely MUCH more work to be done, and I do sincerely appreciate all feedback. The project blog again can be viewed at : http://molecularpathwaygenerator.blogspot.com/ Thanks all

Hi all. An update for those who are following. I have gone ahead and done a re-haul of the interface and specialized/optimized many parts of it for a mobile or small-screen device. Eventually the goal will also be to create an app for ios and android, but for now the site www.organicchemmaster.com will render as it has before on a desktop/large screen device (specifically with screen width of greater than 992px) and will now render in a special mobile optimized mode for a device with a smaller screen. @hypervalent_iodine I did take to mind your suggestion that the draw tool be more intuitive/similar to JSME or ChemDoodle for the mobile version. As such I switched away from a drag and drop approach for adding carbon chains/atoms and towards a click to select and click to add approach. It is my hope to add the bond-line/ zig zag style as an option as well in the near future. @Sensei I did add support for free-radical chlorination. Your search for a pathway from ethane to chloroethane will now be successful. The reaction specifics can be viewed at https://www.organicchemmaster.com/Reaction/Rule/027. There is of course still much more work to be done. The latest updates can be viewed on the project blog at : http://molecularpathwaygenerator.blogspot.com/ Thanks to all who have responded.

Appreciated re: your comment of a different design tool for the student than the main one. Will fully take that into consideration. You actually can currently do this. If you click on the molecule name under molecule properties, then enter a different IUPAC name, the molecule structure will change to that name. The basic molecule tutorial describes this: https://www.organicchemmaster.com/MolGen/Tutorial/BasicMolecule . Apologies if I wasn't clear in this case! As long as the IUPAC name is obtainable the structure can be drawn, so this feature can eventually be used for SMILES and CAS numbers. Full enantioselectivity of reactions is indeed something that is planned to be modeled. Currently full stereochemistry support is implemented in the molecule modeling/naming. Some of the named reactions are stereospecific in modeling already, such as this glycolysis step. The thoughts are to include stereospecificity in the rules of a rule based reaction. I had not yet considered convergent syntheses, but I see how those would be valuable. I have some rough ideas for how this might be accomplished using the search engine. That is indeed fair. The process I most reasonably see this project/application taking is FIRST being useful as an educational tool. Then utilizing the knowledge gained and the improvement of the reaction modeling framework (the code backend) to translate that framework to be useful for researcher. You are absolutely right that the second goal will require a much larger team and many more resources and it is indeed more than I can chew. This is the main reason I am actually hoping to build a much larger team, eventually. I KNOW how hard this will be. But I want to see it happen. The first step is indeed to pitch primarily to students. My current thoughts to aid in discovery of a new drug are currently both using the reaction predictor (clicking on the reaction edit pencil will allow you to predict applying that reaction to a given molecule, might change this to a double click anywhere in the row) and including a feature to specially mark a molecule that is either previously unknown, or has other interesting values that is included in a synthesis pathway result. I am absolutely open to more thoughts. I'll take the "I'm a small team" part as a compliment Now it's a free to use web-based service as again, I am looking to gather interest and find others interested in working on the project. Absolutely a tool that is useful for researchers specifically would not follow this model.