hypervalent_iodine

And that is why, as it stands, it is not overly useful as a ubiquitous drawing tool for chemical structures. It does not show enough information. The only comparisons I made were drawn from examples that you yourself put forward. I never said you were a crackpot, nor did I in any way imply that you were lacking intelligence based on your idea. I apologise if that's how it came across. I actually quite like these sorts of things and learning new processes. That being said, I believe in the power of constructive criticism when I see it is needed. I have not tried attacking you or telling you to give up on your idea, merely offered criticisms as to where your current model is lacking and where you may want to improve. If you don't want to hear them, then I have to ask what your point in coming here was?

I never said they were. I would in fact completely agree that they are quite the opposite of interested in chemical structure or reaction mechanisms. However, to say that it is not necessary to go beyond empirical formula is a little presumptuous.

I completely understand the reason behind why would want to attempt this. As you say though, the investment in learning a new language that is only suited for a small subset of cases is simply not worth it (outside of its use as a medium with which to exercise the brain, that is). Developing ideas like this, I'll agree is fun and mentally rewarding, so there's certainly no faulting you there. Also, something I noticed just now in the drawing of your Heme-A structure; The way you've drawn it makes it look as though the porphyrin nitrogens are not contained within the ring, but are a substituent of an all-carbon ring.

Generally, the chemistry involved in metabolic pathways or biochemical reactions only applies to a small section of the compound as a whole (such as the terminating ends of an amino acid chain, binding pockets of proteins, etc.). As such, it is not necessary to continually draw out the entire compound every time you wish to represent it, merely the parts of it that are involved. I can really only see this being useful for compounds that have no stereochemistry whatsoever, and only if you include double and triple bond information as well as charges and hetero-atom bound hydrogens. Outside of that it fails to provide an adequate amount of detail. For the case of amino acids, the only real way I can see around the stereochemistry issue is if you predefine the chain as having all L or all D configuration. I also think that having to learn different symbols for every single element, which I am assuming would have to be the case and please correct me if not, is terribly inconvenient and not particularly easy to do.

Hydrogen atoms must be included when they are bound to heteroatoms as it can be ambiguous otherwise. Particularly where they are bound to atoms able to form hypervalent bonds. Speaking of which, does your model make room for charged species? With practice, drawing the compound to mentioned in your post neatly by hand is actually quite easy. Even ignoring that, there are a lot of software packages out there that you can use to draw structures, which obviously circumvents the issue of messy hand drawings.

Stereochemistry and double/triple bonds, etc. are still very important pieces of information, no matter how big your structure is. Perhaps this new system of yours will be useful for you, but only in the same capacity as if I were to learn a secret language with which to fill out my lab book. It's all well and good for me, since I know what's going on, but it fails miserably in being able to clearly and easily communicate the information to others (another rather important aspect of science). There are other ways of drawing extremely large compounds such as proteins (ribbon structures, etc.); when you are trying to convey chemical information however, the system we use is suited perfectly. You aren't improving on the pre-existing methods. All you've done is made is made them more complicated and less informative. The system we use currently, while perhaps more spatially demanding and time consuming, are intuitive and easy to learn. At first glance, yours does not appear to possess this quality. Even if it did, I still fail to see the point of having to learn an entirely new language for representing chemical structures when it (as aforementioned) a.) it doesn't give adequate information and b.) we already have an easy to use system that works and works well. I would have to disagree. Cyclohexane is by no means the same as a phenyl group. "Extra bond lines", in this case (and every case), are therefore far from being irrelevant. In all, I can appreciate the idea behind the task, even if I don't agree with it. I suppose if nothing else, it's a better and more respectable way to pass the time than say, reading Twilight.

Well unfortunately for you, stereochemistry and bond order are two extremely important pieces of information that you need to convey in your drawings. So again, I do not see the point. Why fix what 'aint broke, ya' know?

Why would I need to or want to do that? Additionally, how does your method exhibit stereochemical information? I also do not see any representation of double bonds.

Like this: For the record, writing in 'CH3', etc. is actually not required, you can simply leave it off. For citation's sake, I should mention that I got this from wikipedia.

Correct, which is why it's not used unless necessary. Chemistry already has simplified ways of drawing things that convey all the information you might require, so I'm still not sure what purpose this serves.

Things I love the most at this point in my life/career: Epiphanies. The joy of having chemicals finally do what I tell them to after 3 months of nothing. Old books. Having a student actually understand and appreciate what you're teaching them. The smell of rain on bitumen.

Not having much experience in programming or script writing, I'm going to have ask what may be an obvious question; what is the point of representing chemical notation like that when we already have a fairly efficient system of drawing and representing compounds? As I say, I may be missing something here, but this seems slightly pointless and unnecessarily complicated.

Personally, I would go with the sand route. You should also be fine if you use a hard-hydrogenated oil like cottonseed. That being said, I would have thought that silicone oil would work alright. I had a look at Vogel, which said that a silicone bath can be heated up to 250oC; 180oC shouldn't be too much of an issue so long as you keep an eye on the temperature (i.e. keep either an internal or external thermometer).

Not every reaction is an SN1, SN2, E1 or E2 reaction; unless you are learning about those reactions specifically, they probably won't be labeled as such. What reactions are you referring to?

It really depends on your course requirements as to what you need to remember. As a general rule, it is nice to try and remember them. Different metals are more suited for different purposes, so perhaps it might even be worth your while learning reasons behind why certain metals are used for certain reactions.

As mississippi said, the best way to identify compounds is to use NMR. IR really doesn't cut it in terms of structural elucidation/confirmation, unless your compound is well characterised and you can reference the fingerprint region to a library. Given that you can't really buy an NMR machine (practically speaking), it might be worth your while taking a trip to the chemistry department of your university (if I'm not mistaken, you still attend university, yes?) and ask whoever is in control of the NMR equipment if they could help you run a few samples. I'm not sure if this will work given that this is private research, but there's no harm in asking and it's probably your best option. There are of course a million different chemical tests to help you identify structures (NMR hasn't always existed, after all), however these are usually only diagnostic for certain functional groups. If you're doing this for biological application, purity is of utmost importance and while chemical tests certainly have their benefits, they aren't going to tell you if you have byproducts in your samples. As above, you will need to get NMR data. Yes, however (as I mentioned above) this won't necessarily tell you that you don't also have something else in your compound. You may generate byproducts that have the same functional groups you are testing for, but in a different position. The standard way to purify compounds is by silica gel chromatography (aka flash column chromatography). Depending on your compounds, there are also simpler ways to purify them similar to what you are describing. For example, if you are converting an azide to an amine you can remove any starting material and purify your amine simply by doing an acid base work up. I'm assuming C. elegans? Anyway, I hope that answers your immediate questions. Feel free to come back with any more specific questions related to your compounds P.S. A simple FT-IR like that would probably be a sufficient in terms of getting data for simple organic compounds. To be honest though, and as I said before, IR is not really going to be that useful to you if your compounds aren't already known or if there hasn't already been IR data recorded for it in the literature.

It is only moot so far as the question in the OP goes. All in all, something can can sustain itself on nylon is pretty impressive as a biological entity, though I myself am not terribly familiar with this particular example. Not really. It is a fact that there are organisms that survive off CO2 and that CO2 is, for all intents and purposes, an inorganic substrate. The same may be said with the other examples John Cuthber listed. Hyperthermophillic bacteria (specifically, lithotrophs) are known for this, as in this article. (Note that to read the full article you'll need access or a credit card. The abstract should be sufficient for this purpose). Also of note is this wiki article on lithotrophs.

The Ziegler-Natta catalyst(s) would likely promote facial bias during the addition of monomers, hence giving you syndiotactic or isotactic polymer chains. Essentially what that means is that there is a component of the catalyst that sterically blocks one face of the growing chain, which means that a monomer unit can only be added to the other face. This means that you preferentially get one stereoisomer forming over the other. I'm not terribly familiar with anionic polymerisation, but I imagine it would be the same. The anion itself will be flat, so I presume that there is something else in the reaction that is promoting facial bias. If you're interested, it might be worth your while to look up the concepts of prochirality and how various things can effect the chiral outcome of a reaction. This wiki article gives a brief overview of it, though an organic chemistry text book will probably give you a better insight. Alternatively, I can always go through it with you PS. Sorry for the delay, I know I said I'd do this on Saturday but I got a little caught up with other things and then forgot about it.

I thought it might be another term for NMR, but I wasn't sure as I've not seen it called that before. And back in the 80's people used to use lanthanides to spread out chemical shifts. With the advent of 2D spectra and things like NOESY, it's become more or less obsolete.

In third year I sold my molecular cell biology and biochemistry text book. I regret now only because I realise they were somewhat useful to me. As for my other texts: I have kept all of my organic chemistry texts and my inorganic text. I also still have 2 genetics texts books, an organic chem text from the 60's that I found and a 2nd edition copy of Linus Pauling's, 'The Nature of the Chemical Bond', which I bought in a second hand book store in NZ. The latter two I keep because they amusing/interesting to read if you have the time and patience and the former two I kept because I still consult them every now and then. My organic chem text books I find to be an extremely useful tool that I read through quite regularly and if I could afford to buy more, I almost definitely would. I have the largest one in my office in a pile of other books on my desk. It gets used quite a lot by myself and others in the group. In addition to my text books I also have three binders with all of my notes from undergrad chemistry, which I also read from time to time. There are of course libraries and the internet, all of which are arguably easier than owning giant and expensive books. I prefer having them handy and actually owning the copies myself, partly because I am absolutely terrible at remembering to return library books (my record for library fines in one semester is in excess of $200) and partly because the library is all the way over there and I'm here

Could you clarify what MRS stands for? I am not familiar with the acronym.

I would be cautious of adding acetone to a solution containing H2O2 as you may end up with acetone peroxides, which are incredibly nasty and explosive.

The question is very much related to genetics. I only suggested it be moved since I doubt it will be answered in this forum, given that the majority of people who read the chemistry sub-forums are chemistry orientated rather than biology. And you'll notice I didn't simply ask for it to be moved, I did inquire further of the OP if they could clarify/if they had any specific questions related to organic chemistry that I could perhaps answer. You can ask a mod to move it if you would like it moved. I wasn't being rude and I am still happy to answer your question, I'm just not terribly sure what your question is.

Tripolation just provided you a link to Amazon listings, so how about you start there. As a side note, if perchance you were hoping that a member here would provide you with a link to download a free copy then I'm afraid you are out of luck as it is against the T&C's, which I am sure you read upon becoming a member.