hypervalent_iodine

EtOAc is the devil. When I worked with sugar based compounds last year, I spent most of my time trying to get rid of the stuff. Working with sugars meant I also couldn't heat my product above 30 degrees C, lest I make toffee. Most of my products took a few days under high vac before they would even think about crystallizing out.

I would have drawn it like this:

I personally think that drawing the carbonyl is easier in a lot of cases than is writing CO. Plus, it makes drawing ring structures a bit easier (for me at least). Groups such as Et, CO₂Et, Ph, etc. I tend to write, depending on what I'm doing. If I'm drawing a mechanism, I draw out the pertinent bits of the molecule that I might otherwise write in short hand. If it's for a paper, I do short hand for protecting groups and typical reagents only.

As for the phenyl group problem: I personally don't like the circle in the middle business and I will always draw the bonds. It's a matter of preference I suppose. Another way to represent a phenyl group is with the symbol, Ø. It obviously doesn't to the case above. It's more if the phenyl group is a substituent.

What's wrong with dry ice? It's by far the safest option that I can think of.

What do you need the crystals for? Often, compounds will exist as liquids at room temperature. It's just how it is really. If you were expecting crystals and you aren't getting them it may be that you have solvent contaminating your product. Some solvents can be quite tricky to get out. My advice would be to pump it down as much as you can on a rotary evaporator (you may need to put in a water bath at about 45 degrees C) and then put it under a high vacuum or lyophiliser.

A simple proton NMR should tell you if solvents are the problem. Otherwise, your product may just have a low melting point. Nothing wrong with that, unless of course you wanted to get an X-ray crystal structure.

Edit to add: your product may be hydroscopic (I've not looked into it for your exact case). If you leave it under high vac for a while, you may see condensation on your gooseneck connector. A quick treatment with a heat gun will get rid of that. Keeping water out will probably involve a super seal on your flask, parafilm and a fridge. Or transfer it to a dry, glass vial and parafilm around the lid before putting it in the fridge.

Nabilesmail,

As this is a homework question, I will not give you the answers. I can assist in understanding the concepts, so if you could perhaps tell me what it is you aren't getting specifically, I (or the others on the site) could assist?

We have to wear gloves all of the time when handling chemicals here. Most people I've encountered aren't complacent enough to suppose that gloves are a be all and end all in terms of protection - with the exception of first years perhaps.

Also, they let first years in chemistry labs there? My goodness. That's unheard of here! I had so much trouble finding a spot in a lab for the summer following my first year that I ended up in a biology lab doing PCR for weeks on end.

Tisk tisk. Whatever would occupational health and safety say of that!?

right, hydrochloric. sorry. i got the two confused, but they are both halogens so i guess thats where the confusion came from. thats my mistake.

Fantastic. And a 100% safe mistake to make!

It is often the case that text books either gloss over complicated processes either because the mechanisms are not fully understood or because the target audience for the books themselves is not at a level at which a complicated explanation is necessary. For undergraduate, asking a student to just accept that this thing does that is quite common place, because of time restraints or because it is simply to complicated for their level of education. University level text books will generally assume no more than a high-school equivalent knowledge (sometimes, they won't even assume that), so no, the things you mentioned are not things you should already know. If you have questions like that, the best place to search for answers is by reading scientific literature. You can search topics on Google scholar if you do not already have access to a scientific journal search engine. Pubmed is another site that may provide a wealth of knowledge (although not all of it is accessible).

Or, you could always ask specific questions here. There are a lot of biologists, chemists (such as myself), physicists, etc. who would be more than willing to help understand

I have my reservations about him.

I mean, if you look at his wiki article and scroll to the 2nd last paragraph (end of the Woodward-Hoffman rules), there is a clear implication that he was somehow involved in Woodward's death. Scandal!

Can I just ask about something that seems to have been missed here.?

"It won't. We haven't even discovered any extra-terrestrial life out there yet. And if this is the case, then I'm sure God would understand as He is fair and merciful. "

I'd just like to ask on behalf of the people in Japan, New Zealand, etc etc ad nauseam. Are you sure about the "fair and merciful" bit?

Well gosh, let's not stop at current events.

farmboy, I'm not sure I quite understand what you're attempting to say, so please forgive any misinterpretations. I don't think the definition of homosexuality vs. heterosexuality is so-much the issue here. Or at least, the issue does not appear to have been raised within the context of this thread (until now). Can I ask what it is about my previous post that you do not agree with? It wasn't made particularly clear to me where there was disagreement on your part, judging by your post.

This thread has something of a surfer tone to it. You're making chemistry sound deceivingly casual.

Ah, I see it. I had considered that something along those lines may be implicated, but then I couldn't be bothered to model it in my head.

At a guess, I would say it is to do with stereoelectronics. The cyclopentane with the t-Bu group on it will be feeding more electron density towards the migratory carbon than will the cyclopentene, which would of course stabilise the transition states to a higher degree during the migration. Perhaps I am wrong on that assumption though.

I agree with Ringer. You do not ever need to memorise the periodic table. The stuff they teach in the beginner chemistry course where I am includes:

States of matter

What is an atom? (protons, neutrons and electrons)

Orbitals

How to calculate valence electrons

How to read the periodic table (I.e. Where the transition metals are, electronegative trends, etc.)

The concept of a mole and other stoicheometric relationships

Different types of compounds (fatty acids, carbohydrates, etc)

Ionic bonding

Covalent bonding

Hydrogen bonding

Van der Waals forces

London dispersion forces

The concept of pH

Density

Pauli exclusion principle

Aufbau principle

That other principle related to the above two and whose name escapes me

That's all I recall from tutoring it a while back. They may have also learnt things pertaining to VESPR and Lewis diagrams, hybridization, transition metals, electrochemistry, equilibrium calculations, more complicated pH stuff, acid dissociation, phase diagrams and the associated maths, ideal gas laws, Gibbs free energy, entropy, enthalpy, molecular geometry, crystal field theory, solubility, reaction rate kinetics, quantum numbers and basic organic chem. I would focus on that top list before hazarding a go at the rest though.

Anyway, I think that's most of it off the top of my head. Apologies if I missed something.

dichlorine methane on plastic... it melted a hole in my fridge

It will do that.

Even more horrible is DCM and contact lenses. The vapours will react with the polymers in the lenses and cause them to adhere to your eyes.

Are you given the structure of a carbohydrate and asked to determine stereochemistry in terms of ® and (S) or are you also being asked to determine if it is a D or L sugar and what the name of it is, etc.?

Thanks for the reply's, all help is appreciated!

 

Well, i do know the creature exists in fact there are two which are said to secrete the same chemical. As for the chemical, well i don't even know if it is a chemical but to my best knowledge and some research it seems to be the work of a chemical secreted by this organism.

 

I might have access to a lab, although i don't know all the equipment they have(although i know some of it worked there for 3 years), i have a decent biology and chemistry background, nothing that could probably help me but , i'm motivated. Some of this can be done at home while the chemical part in the lab.

 

I want a little help with a breakdown of the experiment step by step of how i should go about it. I already have a rough idea in my head but its only an idea, lol. I know the biggest problem is isolating the chemical and finding out what it is, but i might get lucky and it might only secrete a few chemicals, couldn't i sent a chemical to a lab for analysis, it might already exist? I have an idea to help it secrete the chemical i want, the chemical is said to be secreted due to the immune system of the host.

 

I feel life you guys may be making this a little more complicated then it is, but maybe your right, i don't know it's an experiment after all, can never know until you try it.

 

Thanks Chris

I don't know about farmboy, but Horza and myself are both PhD level synthetic, organic chemists. I tend to think that we have more than just a bit of an idea with what's involved in structural elucidation. It really isn't an easy task, even for those who have a PhD and have completed post-doc projects in the area. If you don't even know if this 'thing' it secrets is a relatively simple chemical or a protein my first question would be, how will you even know it's what you want (presuming you somehow manage to isolate it)? Isolating compounds can be a painful process as it is, even when you know exactly what you are looking for - which you apparently do not. Chances are, your organism secrets hundreds or more chemicals, all of which you would have to sift through and test individually to find exactly what you are after. Could you send to a lab to get tested? Probably not. I wouldn't think that any labs capable of such a thing would be willing cooperate with single individuals not associated with a research group, industry, etc. I could be wrong on that though.

Doing this sort of thing 'at home' is not sufficient if you intend to market your end product. You need a controlled laboratory environment for every step of the process if you don't intend to have your results thrown out and discarded entirely. This takes me back to the point on having access to equipment. If you do not have access to NMR, HPLC, IR, mass spec, etc. etc., you will not be able to do this.

As for your organism. You need to ask yourself a few questions. How hard is to to obtain your organism? How much maintenance is required and what sort of equipment do you have to have to be able to cultivate them? We cannot answer these questions without knowing what the organism is, as every organism requires a different environment for optimal growth. You should find specifics in the literature though.

I am not saying these things to simply dampen your spirits and nor am I making this sound harder than it is. In fact, that you would think we are doing that tells me you do not have the experience needed to attempt this. In any case, we are trying to be a bit realistic about your idea. It could be a fantastic idea, I don't know, but it is unfeasible for someone with little experience in the field and for someone with no access to the right equipment.

Finally, if I may ask you, are you trying to find the active chemical/protein/whatever responsible for the claims that hookworms can eliminate the affects of allergies? Because that's what this sounds like.

I think it's called Helminthic therapy...

 

Ok, so you are farmboy both agree that chemical interactions are not as complex as language but you don't see any way to learn "chemical intuition" about why/how reactions occur in certain ways except to develop it through processes of reading and practicing different reactions? That sounds exactly like learning a language where you can explain long lists of formalized rules but using them to construct a coherent sentence or fluidly read a paragraph would be awkward and take a long time.

I in fact said nothing about it being akin to learning a language or otherwise, merely that I agreed with farmboy on the point of developing chemical intuition being far more advantageous than memorising reactions.

I don't think that would be all that beneficial to be honest dude, and I don't really think that learning nomenclature like a language would be all that wise either unfortunately (thoughit is good to see people thinking outsude the box). Whilst it might seem very complicated to begin with, learning the 'language' of chemistry is not anywhere near as tough as learning a new regular language. More importantly learning the words that represent the different molecules is actually not all that important, it is the chemical features that these words indicate that is the important part. Once you understand the basic chemistry of the different atoms you will be able to know intuitively how the molecules are put together. You will probably start off learning how some of the basic functional groups tend to react under different conditions, but just memorising reactions in that fashion won't be very useful in the long run unlike say learning french. With chemistry you will need to understand why the functional groups act the way they do, and once you have done that there is no need to just memorise you will just know how a reaction is likely to proceed.

 

And with regards to the periodic table of functional groups, that wouldn't really work in my opinion. The periodic table contains all the elements arranged in order of increasing mass, but actually for chemists it tells us a hell of a lot more than that. There are trends and patterns of behaviour amongst the elements, and the periodic table allows us to make guesses about how elements will behave just from looking at their position.

While your bit about learning the structures of functional groups, etc. over their names may be true, it certainly will not be helpful in an exam type situation and even less helpful when you are trying to communicate to your colleagues (or when they are trying to communicate with you).

I 100% agree with you when you said that learning why reactions occur they way they do is much more useful than simply memorising a reaction. There are simply too many reactions in organic chemistry for anyone to be able to memorise them all. Understanding why reactions occur the way that they do allows you develop a certain type of chemical intuition, which is an invaluable trait to have to a synthetic organic chemist such as myself.

The SO2 will smell somewhat like fireworks or a just-struck match. SO3 is stronger in its smell than SO2 and is often described as having a suffocating smell. You really would not want to smell them though, considering the risks. SO2 is toxic via ingestion and SO3 will react with water in the air and in your body to make sulphuric acid, which is quite harmful if you swallow it or inhale it.

As for the colour. The FeSO₄.7H₂O will have a bright blue-green colour. The Fe₂O_3, which is Iron (III) oxide (aka rust) will be a red-brown colour.

Do you have access to a research laboratory? If not, this is all going to be very hard for you to do in a practical sense.

Ignoring that and ignoring the biological aspects, identifying the compounds it secrets will be extremely difficult if not impossible for you to do without a strong background in structure elucidation and organic chemistry as well as access to an NMR and mass spec machine (at the very least). Determining the absolute structure of a compound is often made to look easier than it actually is. It requires a great deal of precise training and prerequisite knowledge to understand the techniques and interpret the data outputs correctly. When you have no clue as to the compound you are looking at, the task is harder again.

If you are looking for a specific compound with suspected bioactive profiles and your aim is to isolate, characterise and market it, make sure the next 10 or 20 years are free for you to do work. Truth be told, without the resources, funding and access, achieving this is impractical and most likely not work. If you are not doing this simply for your own benefit, your task will be much simpler though will still prove somewhat unfeasible should you not have the necessary equipment or chemical/biological knowledge at your disposal.

Hmm. I might have a look-see throughweb of science when I get home. Potentially, the compound may not have been isolated and characterised.

Honestly. I go away to do science for a week, and people start topics that I can answer, but that have already been answered. (I'm looking at you, Horza).

I literally just presented a lecture on this subject 2 days ago.

Dan, you mentioned chiral solvents. They are expensive and useless and deuterated NMR solvents would be even more expensive. As Horza said, the use of chiral NMR solvents isn't particularly useful for the large and complex molecules we like to try and make. In terms of their use as an asymmetric synthetic promoter, they are probably one of the most daft agents out there. It costs more money to obtain something that is enantiomerically pure than not, as I mentioned. Solvents being used in large quantities compared to the rest of the components of your reaction makes the whole concept ridiculously unfeasible. In my research for the lecture I presented on Wednesday, I was in fact only able to come up with one paper that used a chiral solvent in their reaction. The thing I found really laughable was that it didn't even work on its own. To give an ee of above 80%, the reaction needed a catalytic amount of enantiomerically pure proline.

There is another reason why we use racemates. Horza eluded to the fact that we often do not know which stereoisomer we want. Depending on what your product is designed to do, this may mean that we don't know which stereoisomer confers bioactivity or 'gives the best result' (most natural products we synthesis are studied because of their medicinal properties - it's how we gratuitous chemists get money to do science). Even if we did have an inclination as to which stereoisomer we wanted, we have to be able to present a full activity profile of the compound we are making - and that includes all possible stereoisomers. If we can't do that, it doesn't bode particularly well for in the case where we want to push it through the rigour of the drug design and development process.

If you wanted to synthesise a single enantiomer of something, then there are many ways you might choose so as to achieve this. For most practical purposes, asymmetric synthesis will necessitate the use of some enantiomerically pure, chiral component. These may be:

- chiral solvents

As I said, these are mostly useless due the cost and need for a high excess of solvent - having said that, chiral solvating agents are a reasonably good alternative, though not often used.

- chiral reagents

Many of these fall into the latter category of catalysts. The only true reagent under this category is a LiAlH₄ ester of darvon alcohol to mediate a enantioselevtive reduction. Nice concept, but it doesn't really work terribly well.

- chiral adjuvants/auxiliaries

Historically useful, though mostly superseded by recent developments in chiral catalysts - however they remain the only viable route for a number of synthetic transformations. It's based on a similar concept to kinetic resolution - add a temporary chiral moiety to a prochiral compound. The diastereomeric relationship invoked by this conjugation leads to transition states/intermediates/end products of differing energies and will thus favour the formation of one isomer over the other. It of course relies on the group being orthogonal and easily put on/taken off and that upon its removal, stereogenicity is retained. Recyclability is also nice.

- chiral catalysts

These are the method of choice, where possible. They are cheap by virtue of the fact that they are used in small amounts and are regenerated. An example of this is in Sharpless' epoxidation and dihydroxylation reactions.

The assignment of absolute stereochemistry is achieved only through X-ray crystallography (NMR, etc. cannot do this). The problem of this is that it needs, well, crystals. This isn't always possible. Before the development of X-ray crystallography, the determination of stereochemistry was all relative. You should look at the work of Fischer for a better idea of this. What he did was a combination of sheer brilliance and pot-luck. He was able to assign the relative configurations of 3, 4, 5 and 6 membered sugars starting from glycerol through a series of chemical transformations and observations. By a process of sheer luck, he also assigned their absolute configurations, as was found some time after in one of the first published demonstrations of the use of X-rays in this manner.

A lot of the time, indeed most of the time, we tend to operate with relative designations. This is okay, provided we use reactions with predictable and well-tested models. Often, the correlations made on asymmetric protocol are speculative and empirical (you should take a look at Horeau's method for determining stereochemistry of secondary alcohols - you can't get much more empirical), with no definitive mechanism. The problem then comes with the ever-present 'exception to the rule', though you can usually discern this via NMR, given that you know the absolute configuration of the rest of your product.

To your last post: Certainly, this would be your first port of call. TLC is by no means a fantastic analytical tool (good, but not fantastic). It's helpful if you want a rough guesstimate as to the progress of your reaction or the location of various compounds following column chromatography. Where it falls down though is in the case that a compound you want and some by-product has a similar RF. In combination with what mississippi was saying, this can be a real nightmare. NMR will generally tell you that something is up, particularly if the concentration of one is greater than another (your integrations will look crazy).

Anyway, I feel that I am rambling and should probably stop.