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 6h ago

Someone told me that methanol is a product of Ritalin metabolism. Is this true?

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28 Upvotes

r/OrganicChemistry 18h ago

Synthesis Pathway

1 Upvotes

Hello there,

I synthesized C-Amidoxime like that

C-Ami electrode fabrication. Carbon felt (Alfa Aesar, 99.0%) was cut into 1 cm2

circular shapes as electrode substrates. Polyacrylonitrile (Sigma-Aldrich,

molecular weight∼150,000), activated carbon was suspended into

N,N -dimethylformamide (DMF) solvent at a mass ratio of 1:1:30. The solution

was stirred overnight to form a uniform slurry. The carbon felt substrate was then

dip-coated with the slurry and air-dried on a hotplate (70◦ C). Then the coated

electrode was put into a water bath (25 ml) stabilized at 70◦ C. 80 mg ml−1

hydroxylamine hydrochloride (Sigma-Aldrich, 99%) and 60 mg ml−1 sodium

carbonate were added into the water bath quickly and the reaction was allowed to

proceed for 90 min (ref. 27). After the reaction, the electrode was washed with

deionized water and air-dried in a furnace (80◦ C) for use.

After that my C-Ami captures metal from metal salts.

Can anyone give me the chemica structural pathway how this happens?

And in that what is the role of sodium carbonate?


r/OrganicChemistry 1d ago

Discussion Enolates, thermodyn/kinetic product

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15 Upvotes

I'm having a hard time understanding why this is the kinetic product of this reaction. My point of view is that the tertiary carbocation should be more stable than the secondary (lower activation energy), which would result in the product with the DB on the left side being the kinetic product. I am apperently wrong. Can someone explain to me where my error lies?


r/OrganicChemistry 2d ago

Is this a valid resonance structure?

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81 Upvotes

r/OrganicChemistry 2d ago

I see a good benzylic leaving group. Why don’t you see things like benzalkonium chlorides undergo SN2?

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37 Upvotes

r/OrganicChemistry 2d ago

Detection of air pollutants from vegetal matrix with proteomics-MS setup

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1 Upvotes

r/OrganicChemistry 3d ago

Discussion What is the total number of stereoisomers in this molecule?

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26 Upvotes

r/OrganicChemistry 3d ago

advice Why is the ether a methylbenzene but the amine is benzyl?

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19 Upvotes

The amine group is called "N-Ethylbenzylamine", while the ether group is called "Ethoxymethylbenzene". Why can't the ether group be called "Ethoxybenzyl"?

I get so confused to the naming of benzene, how it turns to phenyl or benzyl, and how I should apply it when naming organic compounds.

EDIT: Is there a general rule on how aromatic hydrocarbons nomenclature differ from each functional groups?


r/OrganicChemistry 3d ago

Can someone explain to me why I got this wrong?

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109 Upvotes

I put B since the first one looked correct but the second one was pointing from a sigma bond which my professor told us cannot be broken to create resonance structures. Thank you for the help

Edit: The correct answer is D. The first one is wrong because the arrow should go to the bond between the carbon and nitrogen rather than to the carbon. As you cannot move lone pairs from one atom to another for resonance. So the arrow should be pointing to the half way point of the bond between the carbon and nitrogen which would move the lone pair off the nitrogen and create a pi bond between those two atoms. The second structure is wrong as you cannot break a sigma bond in resonance.


r/OrganicChemistry 3d ago

mechanism Are these mechanisms correct? Reaction schemes included

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16 Upvotes

I'm unsure about the electron pushing on the last step in part B. Would that make an alcohol waste product? Also unsure if deprotonation by TFA is valid in part C.


r/OrganicChemistry 3d ago

How to conjugate Histidine (or Imidazole gruops in general) to carboxylic acids?

1 Upvotes

I want to conjugate a species of carboxylic acid to a Histidine amino acid, and I will protect the NH2 group to hopefully get the Imidazole Nitrogens to attack. Is this feasible?


r/OrganicChemistry 3d ago

Compound with no pos and cos but only aaos making it optically inactive?

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0 Upvotes

r/OrganicChemistry 3d ago

Who are the current famous/top physical organic chemists in the world? What are they exactly working on?

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1 Upvotes

r/OrganicChemistry 4d ago

Discussion Is this synthetic route + mechanism feasible/any alternative suggestions?

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54 Upvotes

r/OrganicChemistry 5d ago

I saw this structure today and wondered. Which nitrogen is the most basic?

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137 Upvotes

r/OrganicChemistry 5d ago

is organic chemistry tutor's members only contents worth it

8 Upvotes

I already use his free video and find them helpful. I noticed there are much longer versions of some topic available through his channel membership.

For people who have actually watched the longer versions: do they provide substantially more useful explanations and practice than the free video, or is the difference mostly extra examples?

I'm trying to decide whether the membership is worth paying for specifically for physics. (maybe I'll use it in the future for ap chemistry too)


r/OrganicChemistry 7d ago

Why doesn’t water dissolve hexane through induced dipole interaction?

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418 Upvotes

r/OrganicChemistry 6d ago

Stretching decelerates ring-opening metathesis at cis-olefins in stressed molecular bows

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4 Upvotes

r/OrganicChemistry 7d ago

H-NMR spectrum: meta coupling + second order deformation?

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10 Upvotes

Hi,

I tend to ask long questions so this time I will try to be brief.

Here's a H-NMR spectrum took in 100% DMSO-d6. This is an unknown compound and I try to figure out its overall structure.

Given that the coupling constant of the peak 1 and 2 is really small (2.9 Hz) my hypothesis is that I am looking at a trisubstituted aromatic ring that allows a meta coupling.

I first thought that peak 2 was in fact 2 distinct signals, 2 doublets, but integration rules the thing out.That plus the fact it features exactly the same 2.9 Hz meta coupling than the peak 1.

So my conclusion is :

- peak 1 would be normally a singlet, but is linked by meta coupling to peak 2 so at the end we get a doublet

- peak 2 is a doublet of doublets with a weird and strong second order "roof effect" that give the doublet to the right more intensity

- peak 3 is ortho coupling with peak 2 and should be a plain doublet, but experiences and a even more intense "roof effect"

The look of peak 3 baffles me. Especially the little peak encircled to the right. Maybe it comes from another compound. And the intensity of the "roof effect" makes me doubt.

Anyway, do you the trisubstituted aromatic ring with meta coupling makes sense?

What do you think about peak 3?

If I play with solvents maybe I would be able to spread apart peak 3 and peak 2 and get rid of proximity interference?

Thanks!


r/OrganicChemistry 7d ago

Has anyone actually found Darling's Molecular Model easy to use?

3 Upvotes

I bought the kit because everyone recommended it. But once I got my hands of it, the roughness of the plastics molecules surprised me! It took me 20 minutes and a red pair of hands just to get the old molecule out of a bonding stick. Am I supposed to use the kit more so the plastics soften up? I'm worried about my hands by then. Look forward to hearing your experiences! Thank you.


r/OrganicChemistry 9d ago

Discussion What is this kind of strain called?

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33 Upvotes

R prefers to sit pseudoaxial in this half chair due to a steric interaction with R1 when placed pseudoequatorially.

What is this steric interaction called?

I've been calling it 1,2-allylic strain but I guess you could call it 1,3-pseudoallylic strain given the planarity about the N. Are either of these correct? What would you call it?


r/OrganicChemistry 10d ago

People say avagadro’s number is big. Is it big enough that there’s a single naturally occurring molecule of benzene like this?

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327 Upvotes

r/OrganicChemistry 9d ago

advice Starting my Master thesis in a month's time.What should I be doing to maximise this year and opportunities?

5 Upvotes

I'm starting my Master thesis in a month's time on click chemistry.

What would I be doing to get the best out of myself for the lab?

Also, I'd like to know how you'd recommend that I read literature.

What would you do differently or better if you started your master thesis again?


r/OrganicChemistry 9d ago

Purification of DDQ?

2 Upvotes

For those of you who regularly use DDQ in organic synthesis, do I really need to purify ddq (and quinones alike) before using them in a reaction?

Thanks!