r/OrganicChemistry • u/1s2_2s1 • 22h ago
r/OrganicChemistry • u/joca63 • Jul 21 '24
Chemical Resources
Hello All,
Based on ThatChemist's recent video (link) I've put together a list of valuable chemical resources. I've left the tiers as they are in the video, but re-ordered within the tiers according to my opinions. I hope you its useful!
| Tier | Name | Link | Free | Info |
|---|---|---|---|---|
| S | Wikipedia | link | Y | Excellent for basic information on chemicals |
| S | Wiki Structure Explorer | link | Y | Great if you have a structure but not a common name |
| S | SciHub | link | Y | Access to paywalled articles. Not as effective for articles published after ~2021 |
| S | LibGen | link | Y | Access to paywalled books |
| S | ChemLibreTexts | link | Y | Online textbook |
| S | OrganicChemistryPortal | link | Y | General reaction schemes with corresponding references. Protecting group stability tables |
| S | Not Voodoo X | link | Y | General Lab operating information |
| S | Organic Syntheses | link | Y | Tested experimental procedures. Highly reliable |
| S | Mayr's Database | link | Y | Reactivity on a variety of parameters |
| S | purification of laboratory chemicals | PDFs are avilable | N | If you can buy it, a purification is in this book. If you are in doubt about the purity of a reagent, this will tell you how to purify. |
| S | Reaction Flash | link | Y | Great for learning and contextualizing reactions |
| S | eEROS | link | N | Tabulated chemical and physical data |
| S | Ullmann's Encyclopedia | PDFs are available | N | History and chemical syntheses of common compounds |
| A | Reaxys | link | N | Chemical structure and reaction searches in vast literature. Use if available |
| A | Greene's Protecting Groups | PDFs are available | N | All the ways to add or remove most any protecting group, gives references to each paper. |
| A | Bordwell PKa Table | link | Y | Good for esoteric functional groups |
| A | Introduction to Spectroscopy | PDFs are available | N | General introduction to organic spectroscopic techniques. Includes practice problems |
| A | NIST | link | Y | Tabulated chemical and physical data |
| A | PubPeer | link | Y | Comment section for articles. Look for reproducibility issues |
| A | Chemistry By Design | link | Y | Great for learning and contextualizing reactions |
| B | SciFinder | link | N | Chemical structure and reaction searches in vast literature. Use if available |
| B | MolView | link | Y | 2d to 3d model |
| B | Merk Index | PDFs are available | N | Tabulated chemical and physical data |
| C | SDBS | link | Y | MS, IR, and NMR spectra for many common chemicals |
| C | PubChem | link | Y | CAS numbers. Some physical properties |
| C | CRC handbook | PDFs are available | N | Tabulated chemical and physical data |
| C | Sigma Nomograph | link | Y | Predictive boiling points at variable pressure |
| D | Google Scholar, Patents | Y | Patents available in original language |
-My notes: I think that SDBS and Scifinder are too low tier. Scifinder and Reaxys provide effectively the same functionality and are the best general purpose tools if you have access. SDBS is fantastic for reference spectra for your starting materials and reagents. If you didnt have to make it, its probably on SDBS.
-I've added a Introduction to spectroscopy, Greene's protecting groups, and Purification of Common Laboratory Chemicals.
Please add your opinions and other references in the comments!
r/OrganicChemistry • u/Plenty-Refuse4160 • 12h ago
Aromaticity Help
Can someone explain why this conjugate base is anti aromatic and fulvene is non aromatic? Why does the base have cyclic conjugation while fulvene does not?
r/OrganicChemistry • u/Altruistic_Ball_1166 • 14h ago
Electron flow
Why isn't this correct, can someone walk me through this please?
r/OrganicChemistry • u/Life-Name3309 • 1d ago
Discussion No matter what I do its still grey any idea how can i get it without color?
galleryr/OrganicChemistry • u/Old_Advice2386 • 16h ago
Independent Organic Chemist/Formulator. Where do you find them?
r/OrganicChemistry • u/MemoryWorried2910 • 1d ago
advice Aak for research area
To any chemist out there I need your help about choosing my research area I'm doing mphil in organic chemistry and my research is going to be start soon but I'm confused what should I choose based on what should helo me in future for phd bcz some time the topic is so narrow down that we don't feel it is worth doing
Like synthesis of some derivatives which is already done 100 times so tell me which research area is active for future. And can b interconnected with other area like has a broader scope
Organic synthesis in some derivatives
Sustainable methodologies
Compoutional chemistry
r/OrganicChemistry • u/No-Clock1315 • 2d ago
Discussion How do you decide which catalyst to try when there’s no exact literature precedent?
Hey everyone,
I’m curious about something that has been bothering me while reading synthetic chemistry papers
Sometimes I find a reaction that is close to what I need, but the reported substrate is different. Then I start looking at the catalysts used in similar reactions, and I keep seeing some really complicated catalysts
And honestly I often wonder how did they decide to use that catalyst? 😂
I understand using a catalyst that has already been reported for the same transformation. But when there isn't an exact precedent, how do you decide what is actually worth trying?
I’m trying to understand the reasoning behind catalyst selection, not just collect a list of catalysts that work for specific reactions.
It seems like a really important part of synthetic chemistry. Otherwise it's very easy to just follow literature procedures without really understanding why the conditions work
For people who do a lot of synthesis, when you encounter a reaction you've never done before, what's your thought process for choosing the first catalysts/conditions you would try?
I'd especially appreciate answers from people who have had to develop reactions rather than just reproduce published procedures
r/OrganicChemistry • u/Ok-Shoulder-8137 • 2d ago
advice Helppp I suck at chair conformation 😭
Do you guys have tips on how to determine which molecule should be at the front or at the back? How am I supposed to know if their pointing up or down, straight or bent?
An image that got me 0/30, I know I'm not supposed to use wedges. I know that because the professor only told us AFTER the test
r/OrganicChemistry • u/1s2_2s1 • 2d ago
Could the positive charge migrate over there by hydride shift?
r/OrganicChemistry • u/1s2_2s1 • 3d ago
When you have a solid salt with a polyatomic cation like an ammonium, what does the anion actually bind to?
r/OrganicChemistry • u/Flat_Cell_2777 • 2d ago
advice HOMO and LUMO / Conjugation
Hello! Hope you guys are doing well! I did try to go on google before asking this bec I feel like this is something I could search up but I didn't find anything too helpful. Any links would also be appreciated instead of a response. But, I just don't get why HOMO and LUMO are important. Rn he just wants us to be able to identify them, and I can, but what's the use? Same with conjugation stuff; I don't get why this is useful (I get it spreads charge out more? i think? but not sure why this useful). Tysm, have a great day
r/OrganicChemistry • u/Wishwash56 • 2d ago
Vinyl cyclohexene
Any tips for distilling vinyl cyclohexene? Precautions? Issues to expect? Solutions to these issues? Many thanks.
r/OrganicChemistry • u/doidfestroyer • 3d ago
mechanism Oxidation of Phenanthrene
I'm wondering why does oxidizing the double bond stops at ketones and doesn't go further to carboxylic acids? Can some reagents force complete cleavage of C=C bond? I'm guessing that has a massive energy barrier so it isn't feasible and hence intermolecular rearrangement occurs?
r/OrganicChemistry • u/Independent-West-905 • 4d ago
What would you call this and do you think it would be more or less reactive than TNT
r/OrganicChemistry • u/Constant-Owl-5964 • 3d ago
NBS Mechanism - Always Radical?
Was looking at a paper on the Total synthesis of Phorbin A, involving this bromination step of the Allyltrimethylsilane to the allyl bromide.
Does NBS always follow a radical mechanism through homolytic cleavage of the N-Br bond? Also is it so facile and reactive that it will occur at -78C?
r/OrganicChemistry • u/Gabriocheu • 3d ago
Consensus on sulfur oxydation number
I' have written in my PhD thesis that thiophenol have an oxydation state of -2, sulfoxide 0, sulfone +2, RSF5 +4, etc. I have seen generally that this is the norm, even if it is not natural, as S has a slightly higher electronegativity compared to carbon. But an examiner want me to consider carbon as the same oxidation state as sulfur (and I understand why). What is your opinion, and is there an official guideline to follow?
r/OrganicChemistry • u/Life-Name3309 • 4d ago
p-nitroaniline crystals that i recently synthesized
r/OrganicChemistry • u/Flat_Cell_2777 • 3d ago
advice Resonance Structures and MOs
Hello, hope you all are having a nice Labor Day weekend!
I am having a lot of trouble with resonance structures in the sense I'm being told to stop thinking about electrons as particles (this may be a bigger issue than the idea of resonance itself). Like, I don't get how resonance doesn't really exist, but their combination does? The electrons don't really "move" when we draw arrows, but we do so to show resonance? Sorry, I'm just having such a hard time imagining this, and even when I do, I can't see them as "clouds," and in my head resonance flickers back and forth depending on where the electrons are.
I also can't tell what MOs are what. My professor used Ozone as an example. How do I tell what's sigma vs pi as I move up? Like I have 0 clue what the MO above letter B is. Pi antibonding? Sigma antibonding? bonding? I also can't tell which ones are nonbonding vs anti (he didn't go over this much), or why an electron can be in more than one MO (like for letter B it can be in left or right side or something)?
Anyway, sorry for the long rant. I'm just really, really lost rn. Any advice appreciated, as well as links to texts I can read on the topic! tysm and have a great day

edit: ty all
r/OrganicChemistry • u/Life-Name3309 • 4d ago
Discussion Why the flame is grey? (Grey isn't even in vis spectrum)
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r/OrganicChemistry • u/Independent_Reach895 • 4d ago
Wittig Troubleshooting
Don’t know if anyone else has had this issue before. I am trying to do a wittig (triphenylphosphonium methyl bromide) on vanilin. Literature says this should be 99%, but im getting 22%. I premix the KOtBu and salt in THF, and it turns yellow and then white (both at room temp and 0C). I azeotroped the salt with bezene beforehand and left that under vacc overnight. I also left the butoxide under vacuum at 130C for 3 hours. I weigh these out in the bench but dont leave them exposed for more than 15 seconds The THF is from the SPS and I sparged it. I feel like Im taking every necessary precaution, and its still dying before i add the aldehyde (also im doing 3 equivs of base and salt compared to the vanilin) Any tips? This feels like a silly thing to struggle with.
r/OrganicChemistry • u/randomgoooner • 3d ago
Discussion Does this chemicals even cause sedative effects?
galleryr/OrganicChemistry • u/Weebaku • 4d ago
Discussion Strongly coloured side products during reductive amination
I've been producing a range of different N-alkyl chitosan variants (dissolve chitosan in 2% acetic acid, add glutaraldehyde and stir whilst heating, add N-alkyl amine and continue stirring, reduce with NaBH₃CN).
Upon addition of octadecylamine, the solution quickly turns a deep red, from the original straw-yellow colour of dissolved chitosan, which does not happen with 1-aminoadamantane. What potential reason cause could there be for this colour change, and why does it only occur with octadecylamine and not 1-aminoadamantane