Question about structure of carbonyl

[Genecks]

Say I have a carbonyl, such as a ketone with two R groups and the double bonded oxygen to the center carbon.

 

 

Is there another name for the oxygen pi bonded to the center carbon?

 

I call it "d.b. oxygen" for "double bonded oxygen," but I'm looking for a more appropriate name.

Edited February 23, 2011 by Genecks

[mississippichem]

I've always called it the carbonyl oxygen. Are you looking for a formal IUPAC name or something?

Edited February 16, 2011 by mississippichem

[Genecks]

Typically I'm looking for a formal (IUPAC) name rather than a decent informal name. "Carbonyl oxygen" seems like an informal name to me. I am, however, ok with decent informal names if people have a good one and don't know of a formal name.

 

I am going through reaction mechanisms at the moment. As I do such, I attempt to reduce each step into a three word phrase, such as "CarbO atk H+" for the first step in acetal formation w/ MeOH. CarbO in this case, inspired you by mississippichem, stands for carbonyl oxygen.

 

p.s.

 

I'm aware it's electron flow rather than atomic attack.

Edited February 16, 2011 by Genecks

[mississippichem]

More formally you would number that oxygen for that compound by nomenclature conventions and call it O1 or O2 etc. But carbonyl oxygen is a decent informal name.

[Horza2002]

If your looking in a molecule that only has one carbonyl (be it an aldehyde, ketone, ester, aminde, etc) you normally just refer to it as the carbonyl group. However, if you have more than one group in your molecule (as it typical in undergraduate organic exam questions normally asking you to pick between the reacive of a cetome over and ester type), I would then be specific about which carbonyl your talking about (i.e. the methanol attacks the ketone and not the ester).

 

In several PhD thesis I have read, it is simply refered to as a carbonyl group, so I'm sure that is an accept way to talk about them.

[hypervalent_iodine]

Typically I'm looking for a formal (IUPAC) name rather than a decent informal name. "Carbonyl oxygen" seems like an informal name to me. I am, however, ok with decent informal names if people have a good one and don't know of a formal name.

 

I am going through reaction mechanisms at the moment. As I do such, I attempt to reduce each step into a three word phrase, such as "CarbO atk H+" for the first step in acetal formation w/ MeOH. CarbO in this case, inspired you by mississippichem, stands for carbonyl oxygen.

 

p.s.

 

I'm aware it's electron flow rather than atomic attack.

 

 

 

As the other two have said, carbonyl oxygen is an acceptable term. You could, obviously, generate a more specific name with a more detailed structure. However, since you are dealing with generalised structures, generalised terms are fine.

 

Also, be careful with your abbreviations. You don't need to make things overly complicated or else you mightn't understand it when you go back to it later. It is much easier, in my opinion, to actually draw the mechanism out with 'curly arrows' than it is to write it (unless you need to make specific notes regarding chemo/regio/stereo selectivity than you can show diagrammatically). That's what I teach to my first and second years, anyway. It seems to work better from a teaching perspective for people to be able to visualise what's going on through the aid of clear diagrams as opposed to paragraphs of text.

 

 

[mississippichem]

It is much easier, in my opinion, to actually draw the mechanism out with 'curly arrows' than it is to write it (unless you need to make specific notes regarding chemo/regio/stereo selectivity than you can show diagrammatically). That's what I teach to my first and second years, anyway. It seems to work better from a teaching perspective for people to be able to visualise what's going on through the aid of clear diagrams as opposed to paragraphs of text.

 

Yes, as Hypervalent Iodine has stated. I strongly encourage that a student use the "curly arrow" notation for reactions. If one can follow the electrons, then they can follow the reaction.

 

I like to tell students to use curly arrows because, even if you can't remember an exact mechanism, you can play with curly arrows until you find something that looks remotely like the mechanism you forgot. It has saved me on exams before. I used to never be able to remember the oxymercuration-demercuration mechanism.

[Horza2002]

It is much much MUCH better to learn the currly arrow mechanism than using abbreviations. If you want to do a degree in chemistry, at some point you are going to have to learn to do curlly arrow mechanism at some point so I'd learn it now, while its easy, before you have to think about all the other things as well.

 

I have also had the moment in exams, not being able to remember the mechanism and just playing around with the arrows until I got something that worked.

[Genecks]

The arrows mean little to me unless there is a reason for them or I can explain what they arrows are doing. At least, this is how I learn the reactions I've been learning.

 

The notes also provide me with quick re-integration of previously learned material.

 

Thanks for the replies.

 

- Genecks

Edited February 23, 2011 by Genecks

[Mr Skeptic]

The arrows mean little to me unless there is a reason for them or I can explain what they arrows are doing.

 

They symbolize what the electrons are doing. Keeping track of the electrons, of course, is pretty much all of chemistry.

[Genecks]

Error: Cannot compute.

 

Yes, it's keeping track of the electrons. But I'm not learning about energy fields, I think.

 

Keeping track of the arrows depends on keeping track of charges on aspects of atoms in the structure. There can be positive and negative charges throughout said structures. Also, there are some stability issues that can help determine what a particular molecule/atom/shift will do.

 

I often use (delta + or delta -) and then use those aspects to attempt to figure out where to start the arrow and point it. It also depends on the conditions of the substances being reacted.

 

I really can't seem to get into the act of pure memorization of these things.

 

Anyway, with the orgo II class I'm in at the moment, all we're really doing is memorization of reactions. Not learning anything else, such as nomenclature, sterics... etc... just straight up mechanisms and maybe some stereochemistry.

 

In one organic professor, I suspected I'd have to learn maybe 30 mechanisms with him. With this professor I'm with now, she's giving us well over 30 mechanisms. Slightly entertaining, though.

 

It's appears to all focused around functional group analysis. It's like learning the truth without the language of truth: Insight without explanation for insight.

Edited February 23, 2011 by Genecks

[Horza2002]

Curly arrows are one of the corner stones of organic chemistry (along with tetravalent carbons and a few other little gems). The curly arrows, will are talking about orbital overlap, don;t require you to know about the orbtial overlap (for a basic understanding anyway). If you have already worked out where the delta negative is and where the delta positive is, then all you need to do is put an arrow between the two and your sorted.

 

Curly arrows are normally only reserved for organic mechanisms since metal ions are a little more tricky and often to react in that way.

 

In one organic professor, I suspected I'd have to learn maybe 30 mechanisms with him. With this professor I'm with now, she's giving us well over 30 mechanisms. Slightly entertaining, though.

 

That Is exactly the reason we have all recommended that you learn the basics of using curly arrows so you don't have to memorises thirty mechanisms (and beleive me, by the end of your degree when you've had close to 100 mechanism to study, you won't be able to memorise them). Once you understand the basics of how to use curly arrows, you'll see that most of the mechanisms are very similar anyway.

[hypervalent_iodine]

Geneks, I spend a lot of time tutoring first years in O. Chem here at my university. I can promise you that everything is so much easier and so much clearer if you can understand and draw curly arrows. Memorizing mechanisms, in my opinion, is pretty damn useless if you have no idea where the electons are going and why. It's the equivalent of memorizing the answer to a calculus question without actually knowing how to do calculus. I cannot stress enough how important it is for you to take some time out and read through a text book (McMurry and Clayden are good) and get a feel for curly arrows, what they mean and how to use them. If you can apply it to what you're learning in your class, it will do you a world of good. Memorizing reactions will not help you learn organic chemistry and what it's about.

[mississippichem]

I'm also a chemistry tutor, and let me tell you; there are too many reactions out there for you to memorize. You are much better off learning the best method to figure out reactions; pushing curly arrows. In my undergraduate organic classes the teachers required that we show curly arrow notation on some reactions.

 

Now that I'm about to graduate, they've got me working on some more difficult stuff like combinatorial synthesis, or organometallic catalytic cycles. I can't imagine being able to understand these things or especially be able to write them down without curly arrows. Biochem as well; I never could memorize the Edman Degradation so I use my chemical sense and push arrows around. Hey, it really works.

 

It's up to you. I imagine you can learn reactions however you like, but all the chemistry people here recommend curly arrows.

Edited February 23, 2011 by mississippichem

[Genecks]

...Curly arrows are normally only reserved for organic mechanisms since metal ions are a little more tricky and often to react in that way...

 

Definitely, as I'm annoyed by the way a Simmons-Smith reagent works with a cyclohexene. I've boiled it down to just having a cyclohexene react with a C-Zn bond, thus the pi bond attacks C and the Zn-C sigma bond attacks the alkene's corner carbon. So, all I need are the alkene and C-Zn sigma bond to abstract from. I can figure as much that the carbon is electropositive due to dipole moments, but to figure out that the Zn-C sigma bond is doing the attacking? Well, I don't see that; but not the point of this thread.

 

Maybe all of you are on about something that I don't know about. But for the most part, I do use arrows when drawing out the mechanisms. And I don't believe I'm using pure photographic memorization without understanding of the material. However, I do believe I'm memorizing particular things and abstracting from them (this is at least my view from a cognition background).

 

As I quip to professors and other, "You can't abstract from something unless you have something memorized." They've told me in rebuttal that the problems some students have is that they will literally attempt to memorize one thing (the mechanism and those particular reagents, the specific molecules themselves in their chemical formula, in the reactions) and think it will be on the exam/quiz.

 

But yeah, memorization needs to occur to a degree.

 

At least, I started doing incredibly better in first semester organic when I noticed the professor knew little to nothing about cognition, thus I decided to start to "memorize" particular things, and I did a ton better. Not only that, but there are aspects of the motor cortex that tie into memory and the visual cortex. As such, it can often become an unconscious act to start recalling reaction mechanisms, I believe.

 

The act is very similar to studying anatomy, during which wrote memorization can help increase retain learned knowledge.

 

p.s.

 

I looked over some reactions recently. I suspect in a way thinking about orbital, which orbitals are vacant, and particular aspects of orbitals can help a person exhaust what is going on in a reaction. But when I have something, say a water group on an organic molecule, I've got to have known that the water molecule is going to leave.

Edited February 23, 2011 by Genecks

[hypervalent_iodine]

I don't agree so much with your little quip. Sure, there's an element of memorising at some point in the learning process, but that should only be for fundamental type processes. A more appropriate quote might have been, 'you can't abstract something unless you have something understood" . Memorising something is not the same as understanding something. For o. chem, curly arrows are a very simple way of achieving this. The more time you spend drawing them out, the more you can get a feel for how electrons move around and why. Simply, once you've got down why reactions occur, there is very little memory work necessary. As we have all said in one way or another, there are simply too many reactions in o. chem to memorise. There are of course aspects that are not so intuitive and things that you will need to learn. Generally though, it all comes back to one fundamental process or another.

 

Anatomy has no instinctual logic behind it - it is all memory work. Organic chemistry, as I and others have stated, is a fairly intuitive branch of science once you have a grasp on the basics. And although I sound like a broken record by saying this, memorising reactions will serve you no good (in the long run) whatsoever.

 

Finally, thinking about orbitals is definitely useful in a lot of cases - most notably in pericyclic chemistry and inorganic. However, you don't often have to consider vacant orbitals in much depth when looking at a reaction mechanism. With respect to the water as a leaving group - yes, to an extent, but there is a reason for why it is a good leaving group.