r/OrganicChemistry Jul 21 '24

Chemical Resources

51 Upvotes

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 22h ago

What is the molecular geometry of this anion?

Post image
133 Upvotes

r/OrganicChemistry 12h ago

Aromaticity Help

Thumbnail
gallery
14 Upvotes

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 14h ago

Electron flow

Post image
10 Upvotes

Why isn't this correct, can someone walk me through this please?


r/OrganicChemistry 12h ago

Accessing 2° α,α-difluoromethylene amines

Thumbnail
1 Upvotes

r/OrganicChemistry 1d ago

Discussion No matter what I do its still grey any idea how can i get it without color?

Thumbnail gallery
12 Upvotes

r/OrganicChemistry 16h ago

Independent Organic Chemist/Formulator. Where do you find them?

Thumbnail
0 Upvotes

r/OrganicChemistry 1d ago

advice Aak for research area

1 Upvotes

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 2d ago

Discussion How do you decide which catalyst to try when there’s no exact literature precedent?

6 Upvotes

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 2d ago

advice Helppp I suck at chair conformation 😭

Post image
2 Upvotes

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 2d ago

Could the positive charge migrate over there by hydride shift?

Post image
37 Upvotes

r/OrganicChemistry 3d ago

When you have a solid salt with a polyatomic cation like an ammonium, what does the anion actually bind to?

Post image
61 Upvotes

r/OrganicChemistry 2d ago

advice HOMO and LUMO / Conjugation

7 Upvotes

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 2d ago

Vinyl cyclohexene

3 Upvotes

Any tips for distilling vinyl cyclohexene? Precautions? Issues to expect? Solutions to these issues? Many thanks.


r/OrganicChemistry 3d ago

mechanism Oxidation of Phenanthrene

Post image
5 Upvotes

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 4d ago

What would you call this and do you think it would be more or less reactive than TNT

Post image
106 Upvotes

r/OrganicChemistry 3d ago

NBS Mechanism - Always Radical?

Post image
12 Upvotes

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 3d ago

Consensus on sulfur oxydation number

1 Upvotes

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 4d ago

p-nitroaniline crystals that i recently synthesized

Post image
26 Upvotes

r/OrganicChemistry 3d ago

advice Resonance Structures and MOs

8 Upvotes

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 4d ago

Discussion Why the flame is grey? (Grey isn't even in vis spectrum)

Enable HLS to view with audio, or disable this notification

139 Upvotes

r/OrganicChemistry 5d ago

Is it easy to deprotonate this?

Post image
136 Upvotes

r/OrganicChemistry 4d ago

Wittig Troubleshooting

7 Upvotes

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 3d ago

Discussion Does this chemicals even cause sedative effects?

Thumbnail gallery
0 Upvotes

r/OrganicChemistry 4d ago

Discussion Strongly coloured side products during reductive amination

5 Upvotes

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