hypervalent_iodine

Your professor / instinct regarding the reaction is more or less correct. However, I think your professor may be a little wrong saying the product is the same as with the aldehyde, as the two would react ever so slightly differently. The main thing you'll need to think about here is how the silyl enol ether will feed into the traditional Bayliss Hillman mechanism and where the nucelophile is more likely to attack. Looking at the general mechanism for the Bayliss Hillman (image taken from here because I couldn't be assed drawing it): In this mechanism, you see that the stabilised nucleophillic anion on what was the reacting alkene attacks in at the most electropositive centre of the incoming aldehyde - i.e. the carbon in the carbonyl bond. The tertiary amine is then eliminated by either an intramolecular proton abstraction or base mediated proton abstraction. If we then feed a silyl enol ether into this, we see that the most electrophilic centre is more or less the same (the carbon bound to the oxygen), but there would be a slight difference in the way the reaction proceeds after the initial attack. I drew this for you, which should make some sense (hopefully): There is a potential issue with condensation of the silyl ether with your amine, but I don't think it will be a problem since the resulting product from that would be very high energy and unstable. Also, this is a super cool reaction; you could make all sorts of wacky conjugated dienes with it. I mentioned it to a friend who has a bit of a love hate relationship with the Bayliss Hillman reaction and he's decided he's going to give it a shot over summer as a bit of something to do. I'll let you know how he goes with it Another thought I've had is that *maybe* the anion that forms after attack of the EWG nucleophile onto the enol is that you get an intramolecular reaction whereby the charge attacks the Si, causing the bond between the Si and the O to break. This would then undergo the same reaction as in the aldehyde version, with the exception of the Si being substituted alpha to the alcohol. Don't know how likely it is, but it's an idea.

Most universities that I know of allow you to take in model kits to exam. I doubt they'd be so lenient with computers. Additionally, it can sometimes be easier to visualise things in 3D with the structure in your hand than on a computer screen. As I said above, it's really a case of each to their own.

Well, there's a little more to it than that; that's the crux of it though, I suppose.

A few things you need to know to work out % yield: How to convert from grams to moles. Do you know how to do this and by association, do you know how to calculate molar mass of t-amyl chloride? You will need to know how many grams of the t-amyl alcohol you had to be able to work out the number of moles of it; do you know how convert volume to mass? Hint: It has to do with density. Once you work out how many moles of starting material (the alcohol) you have, you will need to work out how many moles of the chloride you would expect to get if 100% of the alcohol reacted. Working out the stoicheometry should be fairly straight forward; how many molecules of the alcohol do you need to make one molecule of your product? If it's 1 molecule of starting material for every molecule of product, that means (assuming 100% conversion) for every 1 mole of starting material you should, in theory, get 1 mole of product. Theoretical yield is described as the mass of starting material you get assuming 100% conversion. Percent yield, which you need to calculate, is simply a an expression we use to describe what percentage of that you actually get after doing the experiment. Let's say, for instance, I have a reaction in which my theoretical yield is 1 gram. After doing the experiment, I only get 0.6 grams. My percent yield is found simply by dividing what I got by what I expected: 0.6 g / 1 g x 100% = 60%. In regards to your second question, the important thing to note is what silver nitrate does when it reacts with an alkyl halide. Without giving too much away, you may find this bit from wiki useful. The precipitate you are seeing should tell you that some sort of reaction has taken place. No precipitate = no reaction. To understand why this is, you will need to look a little closer at how an SN1 reaction occurs (i.e. the mechanism) compared to an SN2 reaction. Before I start giving away the answer, can you tell me what you know about SN1 vs. SN2 reactions? Also, would you be able to list what the alkyl halides you used were and which ones you saw give a precipitate? To get you started, think about the following reactions: Of these, which do you think will most likely undergo an SN1 type of reaction, which will undergo SN2 and why?

... what?

Just to clarify a bit for our non-chemist friend, the OH at the bottom right of the page is incorrectly drawn because of the charge present. It can be fixed either by removing the charge that they've drawn (as per the above quote), since the -OH is neutral by itself, or by removing the hydrogen (as I mentioned), which would make the oxygen appropriately negatively charged. I suspect that the person drawing this was trying to represent all the appropriate charges present at physiological pH, which would be the reason they've bothered including them at all. In any case, it's still drawn wrong. Either the charge needs to go or the hydrogen does, I suppose it depends what they were really trying to show.

Looks like a small oligopeptide chain. It's comprised of 4 amino acids, from left to right: asparagine, isoleucine, cysteine and lysine. Whether or not this particular peptide has a specific biological function, I don't know. I can find out for you, however (if you would like). You should tell your friend that if they were trying to draw this structure as it exists at physiological pH that they've actually drawn two parts of the structure incorrectly. The terminal -COOH with the negative charge shouldn't have the hydrogen on it (the oxygen won't be charged if it's bound to a H like that) and the amine on the lysine side chain should be NH3+. If it were me, I'd tell them that their structure is wrong but refuse to tell them why. I'm facetious like that, though. Also, NH2 isn't ammonia, NH3 is and it's a compound in its own right. The NH2 group on the asparagine side chain is actually incorporated as part of what's called an amide functional group. Technical details, though; and I'm sure nothing your history major really cares for

This depends somewhat on context. Shen, could you perhaps elaborate some more?

It really depends on how good you are at visualising things in 3D. I myself never really needed one thoughout undergrad, though I know of lecturers, etc. who still struggle without the assistance of models. Essentially, if you feel that you can imagine things in 3D and manipulate images in your head without the need of a physical model, then a molecular model kit is somewhat unnecessary. If not, then definitely get one. You don't really need anything particularly intricate or expensive, either. They all do more or less the same thing regardless of price.

1. Schrodinger's hat 2. insane_alien 3. DrRocket 4. CaptainPanic 5. timo 6. lemur (I chose lemur for the last category based on the assumption that since he's last posted here, he's started writing in paragraphs. I had a look at a few of his most recent posts and saw that they were either two paragraphs or two sentences, which I guess is indication of progress )

I think analytical chemists either just like being difficult or invented a new set of units to give themselves something to do that doesn't involve making up a heap of serial dilutions . Analytical chem is literally the only area I've ever had to use those types of calculations. In terms of toxicity, there is data on toxicity levels for things like arsenic and whatnot in ppm, etc. It's also used to show concentrations of volatile/gaseous substances in the air. You'll often find things like the concentration at which we can detect smells, etc. expressed this way. That's not to say that ppm, etc. is not completely daft. I really and truly think that it is, or is at the very less, incredibly deceptive. For some reason, chemists are afraid of having to look at numbers in which they have to use scientific notation. Don't ask me to explain it, because I really don't understand it myself. I'm hoping it's one of those grand conspiracies that will get bestowed upon me when I finish my PhD, but I won't be holding my breath.

It is counter-intuitive give the name, but that is how it is measured.

Shouldn't be necessary if you have it stirring.

Yes, you will quite often find diethyl ether referred to simply as ether.

Easiest way to check would be to look up the solubility of your compound in each of these. I would say you only need one solvent, although there's no harm in trying the mix if you have ample product. The worst thing I can see happening is that your compound doesn't dissolve in it at all or the impurities dissolve along with it, which are both easily fixed. To do the recrystallisation itself, I would normally put a small amount of solvent in a flask containing my product and heat it to near boiling with a heat gun. It's much more efficient than pre-boiling the solvent on a hot plate. After that, if I see any precipitate persisting in the solution, I'll vacuum filter the solution through a fine, sintered funnel into an RBF. If not, then I just remove the solvent on the rot evap and dry it under high vacuum.

It's safer and it also precludes the possibility of dropping an open reaction vessel into the oil bath, which I can assure you is not fun to have to deal with.

As per your other thread and as you have noted, we can't simply give you the answers. Tell us what you have done, even if it's nothing, and what you are having trouble with and we'll go from there for you Starting with the first question, is there anything specifically you don't get? Do you know what units ppb or ppm are in? As a side note, I saw this comment in the other thread: This isn't how you calculate ppb.

It's okay, I think I solved my own problem. Aren't we all?

This was my quote from the previous page: It would not be useful in what I do as my area requires explicit detail in all aspects of molecular structure. That is not a criticism, simply a statement. Might I ask what area you work in?

Again, not directed at you. Please read more thoroughly before replying to me. In response to you criticism of my post: you have misinterpreted me. It was an anecdote of my experience coming into undergrad intending to do biochemistry only to realise that it was not as I had expected it to be. I don't how much clearer I can make this for you.

I think you are misinterpreting what I am saying and I haven't really disagreed with anything you have said. My original post regarding biochemistry was this: I never said that biochemists were overly concerned with molecular structure as a whole. When I said 'small section of the compound', I really had the amino acid residues within protein binding pockets in mind. To my knowledge, binding residues are well within the confines of biochemistry. Small polypetide chains, I'll admit, are more suited for biological chemistry or organic chemistry. In any case, I've agreed with everything you've said and I'm a little tired of the off-topic ramblings. Whatever stress you're under, taking it out with people over the internet is probably better placed elsewhere. This is not the place for it. I answered your thread all subsequent posts with no ill-intentions and nor will I in future. I have only re-asked questions where I didn't feel your reply was sufficient and have since agreed to move on from the topic in question. If you would like to re-visit it, then by all means go ahead. I perhaps come off condescending as a consequence of my rather black and white style of writing rather than as a result of my own feelings towards you. I come here to help people, not to belittle them. In future it might be better for you to assume that when I say I'm not meaning to offend you, that I am really not meaning to offend you. In the interest of continuing this thread, I am going to restate a question you didn't answer before: Other than amino acid sequences, what other types chemical structures do you envisage your Dscript being able to be used for? Also, you didn't clarify my point from earlier about the way you drew your Heme A.

I wasn't directing that particular comment at you, sorry for the confusion.

Again, I agree with you. Biochemistry is, however, far form a complete science and there are still a number of processes that are yet to be chemically described. I wasn't really criticising biochemistry so much as I was confirming your point. I'm not interested in arguing with you and no where have I insulted you. Again, I apologise if that is how you are interpreting what I am saying. All I am doing is offering you feedback and asking questions out of my own, idle curiosity. I had assumed that was the intention of you posting here. Additionally, I would appreciate if you offered me the same courtesy I have extended to you thus far and respond to me civilly, without hostility and without putting words in my mouth. Greg: I didn't read your edit until after I had posted. Protein structure is obviously not something you would want to model exactly with chemical nomenclature. I was more referring to the biochemical reactions themselves.

Quite alright. It's often quite difficult to perceive the true intentions of words said over the internet. Not at all. You seem an intelligent person and it would be wrong of me to assume otherwise. I'm just curious as to where you could really apply a style of drawing in which such information is omitted. I keep coming back to it because you haven't really given me an explanation for it. Then you lose vital information. That is my point. I fail to see how your Dscript is more stereochemically accurate than empirical formula. In chemistry, empirical formulas are rarely used as means of communication because it provides insufficient structural information. Your method is certainly better in that respect. In any case and in the interest of keeping this thread friendly, I'm willing to move on as per your request. Questions: Is this intended to communicate chemical information to others or is it simply an efficient note taking/study tool? Other than amino acid sequences, what other types chemical structures do you envisage your Dscript being able to be used for?

I agree. I was most disappointed to do biochemistry at uni here in QLD to find that it in fact only vaguely resembles chemistry in the widest definition of the discipline. That's not to say that the actual chemistry behind the process is not important and not studied though, which is more or less what I was talking about.