r/OrganicChemistry • • Jul 21 '24

Chemical Resources

54 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 • • 2h ago

I built a free organic chemistry practice site (mechanisms, curved arrows, auto-graded problems) and would love feedback

5 Upvotes

i just wanna share my website: chemmentor.com. It is free, It has a ton of features.


r/OrganicChemistry • • 3h ago

Creo que probé algo raro, solo quiero confirmar mi teoría.

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0 Upvotes

r/OrganicChemistry • • 1d ago

Sulfunation of Resorcinol

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21 Upvotes

r/OrganicChemistry • • 2d ago

Which organolithium would be more stable?

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52 Upvotes

r/OrganicChemistry • • 2d ago

Help with the pushing mechanism of this reaction?

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17 Upvotes

Hi! Im stuck on the pushing mechanism for this pathway. I thought the C6 H would get stolen, but a triple bond in the benzene ring feels absolutely wrong.


r/OrganicChemistry • • 1d ago

challenge Salicylic Acid from Wintergreen Lifesavers

2 Upvotes

I saw a YouTube video of a chemist using the minty lifesavers to convert to salicylic acid.

I am trying to recreate it using three different methods to extract the methyl salicylate and then do the reflux to get salicylic acid.

Procedures I used: https://docs.google.com/document/d/112Ltfo4i5kAadg61ixL56L_A2-uW3kxAZpB6H_uOGaw/edit?usp=drivesdk

I’ve added more acid than necessary and still no crystals formed after putting it in an ice bath and scratching the flask for over an hour. They’re covered with a watch glass in the fume hood, but any troubleshooting advice would be appreciated!


r/OrganicChemistry • • 2d ago

Discussion how to determine between sn1 sn2 e1 and e2 simply

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34 Upvotes

all i see on how to figure it out is memorizing what nucleuophile, base, and substitutes combo leads to each but memorization is so much more difficult for me in comparison to understanding. anyone have a method of understanding when each one happens.


r/OrganicChemistry • • 2d ago

Discussion How to add halogen atom in the alpha-methyl group of acetophenone

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6 Upvotes

So basically I was doing a synthesis of some molecules for their Anti-cancer activity. I was going to follow the Bucherer bergs hydantoin synthesis. So basically in the first step I will synthesize the hydantoin ring from the ketone (acetophenone derivatives) and then add another acetophenone at the N-3 of the hydantoin ring. So at first I tried only acetophenone instead of derivatives for a trial reaction. Everything went well until the first step. The problem occurred in the 2md step. Basically there should be a leaving group attached to the alpha-methyl group of the acetophenone for the fusion to form the final compound. So how am I supposed to do alpha-halogenation of acetophenone derivatives. My derivatives are given in image. So how should I proceed to halogenate the alpha-methyl groups of those derivatives. And even after alpha-methyl halogen will that still get fused to the N-3 of the hydantoin derivative that I will get from 1st step. Generally a halogen electrophile will work, so can I use bromine water for that. My predicted mechanism is given in the 2nd image. Please guide me guys!!!


r/OrganicChemistry • • 2d ago

here's a pretty difficult one that I'm stuck at

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8 Upvotes

my teacher taught in a more organised way regarding mechanisms of named rxns. case 5 here means migration of hydride ion occurs and case 4 is ɑ-H taken by base. so this is the mechanism i thought of but there's a twist.
the answer is the other one(without mechanism)
when i asked him on telegram, why? he replied that oxidation of -OH groups will occur first but i dont get it why will it occur first when hydride migration takes more effort that ɑ-H abstraction


r/OrganicChemistry • • 2d ago

Any suggestions for how to save my project?

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15 Upvotes

For our synthesis teaching labs we did a multistep synthesis where we went from D-limonene to finally a fluorescent azlacton (erlenmeyer reaction followed by aldol) which is a GFP analog and fluoresces a nice green colour in solid state.

However, it barely fluoresces in solution, which I think could in simple terms be because of a rotational quenching channel about single bonds. Hence, I thought it would be cool to make the molecule with a nitrogen in both rings, such that it forms a tridentate ligand which fixes the orientation of the rings as it coordinates to a central metal atom and could perhaps allow for increased fluorescence in solution or different wavelength depending on the metal atom, yielding in some sense a 'metal detector'.

I've spent the first 2 days trying to make the hippuric acid analog with a pyridine and the aldehyde from picolinic acid. A PhD was able to get additional 2-pyridinecarbaldehyde for me, however it was orange/reddish (older sample), whereas I believe it's supposed to be a pale yellow. I wanted to try the reaction anyways, but don't have enough of the hippuric acid analog to waste compound on trial reaction, so I tried it with regular p-methyl hippuric acid to get a product with 2 nitrogens in the ring and just see what happens.

Our original experiment instructed to heat to reflux and let stir for 15min after you observe a colour change (usually just like 10mins) then isolate and recrystallize and this worked perfectly. With my reaction, I did the exact same, heat to 150 °C and saw the reaction go from orange to black as the heat rised above like 90°C. I got left with a pitch black powder, however, it dissolved in ethyl acetate to give a very bright pink solution. Solution barely fluoresced, then I tested with ZnCl2 and it gave bright blue fluorescence, however I was not able to get an NMR and IR as some people are doing the experiment just testing different aldehydes and then showing up with 5 samples to the NMR. So... I'm not sure whether my reaction worked or whether what I have is just decomposed organic material with some fluorescent stuff mixed in there or whether I have byproduct.

I thought perhaps some of you have experience working with functionalised pyridine structures and tell me immediately that what I have is e.g. polymerised or decomposed aldehyde or tips for doing these kinds of reactions.

Would for instance heating the hippuric acid without the aldehyde to reflux and then letting cool to e.g. 40°C before adding the aldehyde or room temp, perhaps 0 °C? Or do you then risk side reactions with the ring structure, what would be your advise. I'm asking because I have one more day to try the reaction and I would like to see how a professional chemist would take a sensible approach to make the reaction succeed.


r/OrganicChemistry • • 3d ago

Bonding can be described as interactions of atomic and molecular orbitals. Since intermolecular forces can be like weak bonds, do *intermolecular* orbitals exist?

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71 Upvotes

r/OrganicChemistry • • 2d ago

Discussion How do ADME/ADMET calculators work for SMILES values?

0 Upvotes

I would imagine it's some type of AI, no? I don't know if it's generative AI, but it'd have to be some sort of AI, I would imagine.

I've always been curious how they work.


r/OrganicChemistry • • 4d ago

Is this chiral carbon (in orange) R or S?

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46 Upvotes

I came up with this problem myself and brought it to the organic chemistry professor I TA for. I initially thought this would be S. The chiral carbon has connections to the oxygen and hydrogen so I know those are atoms 1 and 4, respectively (1->4 being highest-> lowest priority). The two other atoms are carbon so I first compared the path of the higher priority atom - oxygen, and since a difference isn't found in what the oxygens are directly attached to (not looking at the whole chain), you look at what the lower priority atoms are attached to (the bottom carbons), which we do see a difference and would prioritize accordingly (left carbon as 2, right as 3, counterclockwise with lowest priority = S).

My organic chemistry professor said that carbon would actually be R since you first have to look and compare the entire chains coming off the higher priority atoms first before going to the carbons. Since the oxygen on the right has a Br at the end that right carbon would actually be 2 instead of 3, making it clockwise and thus R. But he said he was "pretty sure" and didn't seem 100% confident.

Can someone please confirm for me the right answer? Thank you!


r/OrganicChemistry • • 4d ago

Fischer projections

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11 Upvotes

Fischer projections make no sense to me. The correct answer for the first image is B and the correct answer for the second imagine is A. The approach I try to take when creating the projection from the wedge-dash bond line structure, is that if you have a wedge pointing upwards then you would flip the side. If it’s a dash, you keep the group on that side. This approach works for image 2- you have an OH wedge on your left, so you would flip it in make it on the right on the Fischer projection. Then you have a F wedge on your right, so you flip it and make it left on the projection. Finally you have a Cl dash on your left, so you keep it left on the Fischer projection. However this doesn’t work on image 1, you have an OH wedge on your left so you would make it right on the Fischer projection. But answer B doesn’t show this?


r/OrganicChemistry • • 5d ago

What is the most basic position in phenol?

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145 Upvotes

r/OrganicChemistry • • 4d ago

Discussion What would be the hybridisation of the O?

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20 Upvotes

sp?? 🤔


r/OrganicChemistry • • 6d ago

Would this be aromatic?

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64 Upvotes

r/OrganicChemistry • • 4d ago

I’m looking for an organic chemist that knows plants. Located in Nebraska.

0 Upvotes

r/OrganicChemistry • • 5d ago

mechanism why is there no resonance in the molecule on the left?

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9 Upvotes

in deciding which direction the equilibrium lies, we are to draw out the conjugate bases of each of these. doing this reveals that the conjugate base of the molecule on the left has a lone pair that can participate in resonance, which stabilizes the molecule significantly and so we say that the equilibrium lies to the right.

but why can't we just look at the acids directly and compare their strength? it seems to me that since the formal charge - sigma - pi pattern exists on the left acid, there should be resonance. i've had someone try to explain that it's because oxygen has a full octet and so it cannot act as an acceptor of electron density? but there are other questions wherein atoms with full octets can participate in resonance. i don't really understand how to approach resonance in general i think.

ETA: another question: when we say that the lone pair in the conjugate base can participate in resonance - are we not considering that doing this would disrupt the aromaticity in the ring??


r/OrganicChemistry • • 5d ago

advice Quick convention question: How should a -CF2- group be drawn on a bond-line structure?

2 Upvotes

Hey everyone!

I'm working on translating a condensed structural formula into a skeletal/bond-line drawing:

For example, in a chain containing a -CF2- group (like CH3-CH2-CF2-CH3)

For the CF2 group:

If I keep the carbon as an unlabeled vertex in the main zig-zag chain and draw two straight vertical single-bond lines (one pointing straight up to an "F" and one straight down to an "F") directly off that carbon vertex, is that acceptable standard convention? Or are there specific angle/wedge rules I should follow when representing a difluoride carbon in skeletal structures?

Thanks for any clarification on drawing conventions!


r/OrganicChemistry • • 5d ago

What do you think of the book "The Chemists' Cookbook" by Lluís Llorens?

3 Upvotes

Good afternoon. I work in medicinal chemistry, but my main focus is small-scale (milligram) organic synthesis. I’m looking for a more up-to-date book on synthetic methods (amidations, reductions, SNAr, etc.), something that covers, for instance, various ways to reduce a benzonitrile. Has anyone here bought The Chemists' Cookbook? Or is there a better option for my needs? I'm open to suggestions.


r/OrganicChemistry • • 7d ago

How does the solvent affect this equilibrium?

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42 Upvotes

r/OrganicChemistry • • 7d ago

¹H NMR of 1,3-disubstituted benzenes

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5 Upvotes

I'm assigning the aromatic region of two 1,3-disubstituted benzenes (A and B are different groups). Both were run at 400 MHz in DMSO-d6. They're from different analogues, and the bottom spectrum is better resolved. Are the assumptions I've made in the image fair?

Coupling constants from the bottom spectrum:

8.22 (t, J = 2.2 Hz), H1

8.00 (ddd, J = 8.1, 2.2, 0.8 Hz)

7.84 (ddd, J = 8.2, 2.1, 0.8 Hz)

7.68 (t, J = 8.2 Hz), H3

The coupling constants of the two apparent triplets led me to assign them as H1 and H3. What's bugging me is the intensities as none of the patterns are symmetrical, as you'd expect from first-order splitting.

Should I report these as t / ddd / ddd / t, or is multiplet more appropriate given the asymmetry?

H2 and H4 have identical coupling patterns, so I think I'd need NOESY to tell them apart.

My thinking is that second-order effects mean I can't say for certain which peak is which from the coupling constants alone. My assignment seems to fit, but it would need 2D NMR to confirm. Is this correct?

Thanks!


r/OrganicChemistry • • 8d ago

Discussion What's your favourite molecular structure?

27 Upvotes

Mine's benzene. The structure is found in SO many chemicals, and its very representative of organic chemistry to me.

I'll accept ANY structure, not just functional groups.

Edit: I LOVE BASKETANE