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Alrighty, so even though this is going to be several days late, *hides in shame*, I finally found some downtime to type up some of the most fundamental rules to naming organic compounds.  To be honest, the entire idea of nomenclature wouldn’t be so bad, since IUPAC (International Union of Pure and Applied Chemistry) did a mighty fine job-ish of coming up with a good systematic way to name compounds.  Unfortunately, as it is with everything in chemistry, it is never that easy.  To put it the way Professor Glatzhofer did: “The first three pages of the IUPAC text, which is about three times your text book, is all you’ll ever really need to know about nomenclature.  The rest is the exceptions.”  Gee, thanks.

Yes, so not only does the IUPAC naming system have its own little twists and turns on the rules, we also have common names.  Obviously, these are the names that we used for compounds before IUPAC came along and created a giant rule book.  Nevertheless, the simpler compounds are rather easy to name and follow a comfortable step-by-step process.  Yay! (Right?)

The Carbon Chain–First and foremost, we must identify what the base chain of the compound is.  Usually, this can be a 12 membered carbon.relatively easy as it just entails counting up how many carbons we’ve got.  Of course, it will get difficult when the chain branches into several units.  Just remember, the longest chain may NOT be the one that looks like a straight (if zig-zaggedy) line across the page.  Quite often, if the chain is branched, the longest chain will follow a branch.  Also, you can only number two ways: left to right and right to left.  For now, just number it left to right.  Now, how many carbons do you have?  The nomenclature goes as follows: methane, ethane, propane, butane, pentane, hexane, heptane, octane, nonane, decane and so forth.

A derivative of this compound will become very useful to you in the future!There are two exceptions to this:  Is there a ring in your compound?  If yes, then you must use the ring as your base compound.  If there is more than one ring, use the largest one.  The naming follows the above pattern, just with a cyclo- prefix.  Does your compound contain a double or triple bond?  Then drop the -ane and add -ene or -yne respectively.  Are there branches of C chains coming off your main chain?  Then count the number of carbons and name it, then remove -ane and add -yl (i.e. methyl, ethyl, butyl…)

Easy, yes?  Great.  It gets better!

Simple Substituents on the Chain–Now of course, we would all love if everything was just a saturated carbon chain.  It never works out as such since substituents are the atoms we rely on to react organic compounds!  Let’s just do alcohols and halides for time’s sake, though I do plan to go into much further detail at some point in time (ketones, aldehydes, carboxylic acids, esters, ethers etc).  However, today is supposed to be a breif overview.  The rest will require their own topic…

Of course, an alcohol is an organic compound that contains an -OH group.  You, dear reader, will probably be quite familiar with ethanol, since that is the culprit in alcoholic beverages.  As you just saw, to name an alcohol, you drop the -ane, (-ene, or -yne) and add an -ol.  Simple, yes?

Halides are a bit different, as their nomenclature involves a prefix instead of a suffix.  We typically call them alkyl-halides and they are quite simple to name.  If there is a chlorine on your chain, you’d name it chloro-name (or boro, floro or iodo).

Putting it together–Alright, now you didn’t think you could just slap some -ol’s and boro-‘s on the name of your chain and get away with it scott-clean, did you?  Of course not, chemistry is never that nice.  You counted the number of substituents on your carbon chain for a reason, remember?

Now, in order to give someone who is reading the name of your compound enough information to actually draw/identify the Name that Molecule!compound, we must number its substituents.  Here it gets a tad tricky.  You want to number your carbon chain in the direction in which you get the smallest numbers. Ex: If I had this compound, the first thing I would do is count the number of carbons; the base chain is pentane.  Then, I would identify the fact that there is a chlorine group on the carbon chain, so I need to number as such that Cl gets the lowest number possible.  As it turns out, it is in the middle of the carbon and should be numbered as 3.  So, to put this together, the compound is named 3-Chloropentane.

If there is an alcohol somewhere on the compound, it gets numbering priority and you should number your base chain in the direThis one is trickier!ction that gives the OH group the smallest number.  So!  If we have this compound, we should first note that the carbon chain branches!  Lucky for you, however, the branches are the equivalent.  The only difference is that one methyl group comes out of the plane of the page, where as one goes into the plane of the page. So, when counting, we get 4 carbons, so our main chain is butane.  We have two functional groups here, an OH and a CH3 group.  The OH group has numbering priority so we must number such that OH gets the lowest number possible.  That gives us 2.  So we have 2-butanol so far.  Now, we must add the methyl group in.  It is on the same carbon as the OH group; therefore, we get 2-methyl-2-butanol!

Lets do one last example, one that takes into account what happens if we have two of one substituent.Name this Compound! Obviously, we only have one carbon, so this is a methyl compound.  Now, we have two Chlorines and and two Flourines.  I said that things need to go alphabetically, right?  Well, what happens when we have two functional groups that start with the same letter? (Dichloro and Difluoro)  Well, we remove the di- and we alphabetize that way. So, here we have dichloro-difluoromethane.

So, how was that for a brief overview of nomenclature?  Not very brief, eh?  Well, I hoped you all enjoyed this and you have a better understanding of the basic ways in which we name organic compounds.

Happy Chemistry!

The Alchemist Kitten

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Unfortunately, life has been kicking my ass. With my new position as “lackey” in a micro-biology lab and the giant biochem test last week, i’ve been a tad bit swamped. However, I did get a rather pleasing comment this week and decided since I do have a bit of down time, I ought to comment on it.

Mohab R wrote “…if we have , Chlorine And Florine … what’s higher in eNeg ? and Why ? What’s the rule controlling that ? ”

Its rather simple, actually. It does have almost everything to do with atom size.  Chemistry is a subject that relies heavily on the student assuming that things just work.  I went through most of my baby-chem/AP chem years just knowing that electronegativity trends ran left and up and never really questioned why, as long as I could get the damned problems right.  However, eventually we all need to learn the rules and I’m glad you asked!

Chlorine, as you’ll learn, Mohab (et all), is a rather non-picky molecule in comparison to its other column mates.  It will preferentially react in organic chemistry to make several isomers, where as its brethren, Bromine, will not.  Flourine, unlike Chlorine, is like the whore of column 17.  She’ll react with just about anything and with explosive results I must add.  A prime example will come when you study Organic and you’ll find that though Cl and Br will react and bond to organic molecules and are incredibly useful when it comes to the plethora of reactions that you’ll inevitably memorize, I and F will not (for different reasons, mind you–F’s being that is damn reactive and is nigh uncontrollable in laboratory settings.  I is just so damn slow that its not worth the time usually).  It all boils down to, whether you like it or not, molecule size.

Remember, the only electrons that truly matter when determining electronegativity (or almost anything else in chemistry for that matter: bonding, ionizing etc) are the valence shell electrons.  The other shells play absolutely no role in determining eNeg except for this:  the more shells you have on a molecule, the bigger and bulkier it is.  If you’ll notice when you determine orbital shells, that F has an electron hybridization of (1s2, 2s2, 2p5), where as Cl has a hybridization of (1s2, 2s2, 2p6, 3s2, 3p).  There’s a vast difference, you’ll notice.  Cl has two shells (1 with 2 e’s, 1 with 8 e’s) separating its nucleus from its valence electrons, thus making it harder for the protons in the middle to keep a good hold on the 7 e’s, as well as attract more.  (This is in comparison to Flourine, not the rest of the periodic table, in which Cl trumps most other elements in electronegativity).  F, on the other hand, has only one shell separating its protons and its electrons and this shell, you’ll remember, is made of only 2 e’s.  (The first valence shell is made of only 2 electrons, the subsequent ones are made of 8).  Thusly, F has a much much stronger hold on its valence electrons and can easily attract the final electron needed to fill its shell.

Hopefully, this explains why F is considered the most electronegative element and makes the differences between the halogens’ electronegativity a bit more apparent.

Thank you, Mohab, for your great question!

The Alchemist Kitten

This past weekend, I had a rather full discussion with my boyfriend, Justin, about the rather gray line between chemistry and its adjacent fields (such as biology).  Recently, I acquired a job working in the medical buildings with a microbiology lab and have found myself at a loss of words in awe at how beautifully my education and past lab experiences will fit smoothly into my upcoming ones.  As we come flying hard and fast out of high school, our minds bewildered with the idea of adulthood, we often only glance at the possibilities before us with bemusement before diving headlong into majors, minors and the livelyhood that comes with the title “college student”.

Now that I sit happily in my last few semesters, I feel that “the earth is getting rather large in the window”, as my mom likes to quote to me from my favorite movie.  Today marks the last week of my time as a student working with an あるばと, or part-time job.  Next week, I shall blast forward into what will hopefully be the rest of my life.  That being as it may, I was considering how closely related all the mechanisms of science really are.

Membrane pump like this!  It should move too!Take, as Justin and I did, chemistry in relation to biology.  Truely, the focus is rather similar.  Some chemists (and especially biochemists, whom I feel stand directly on the line between the two fields and wave their hands like only a mad chemist could) study on the mechanisms that cause life to function.  An example could be: what chemical mechanism drives that ion pump in the cell’s membrane?  Some biologists, on the other hand, could look at that same ion pump and wonder what effect it has on the organism as a whole.

As chemists, we work with the building blocks of everything on earth.  The keys I’m typing with, the board my professor isHoly Shit!  Yep, that's Chemistry for you.  Big Booms.  Always. writing on, the chalk, my lab partner next to me.  All of these are made up of the chemicals that we, via definition, focus on.  I find this staggering.  There is so much I could do and see, learn and discover but only so many years in which to do so.  It is rather unfortunate and yet at least I know I shall always be employed!  Of course, my field is narrowed by a driven need to improve the human race and my love for medicinal chemistry.  (The internship I had a few years ago solidified that for me!)

I just find it phenomenal that each and every object about us all is made of tiny particles fluctuating with tiny bonds through minuscule electrons.

Anyways!  Since that was my second rant in a row, I promise to have a lesson of some sort ready for later this week.  Tune back in on Thursday for some good, ol’e fashioned, IUPAC organic nomenclature.  That’ll be fun, right?

Happy Chemistry,

The Alchemist Kitten

Greetings, fellow chemistry aficionados.

Kitty is tired...*sigh*First of all, I want to extend a sincere apology for my lack of updates over the past few weeks.  Last week was a “test-block” for me–in which all of my classes decided to dump tests on me within a 3 day radius.  Needless to say, I was rather swamped.  Following that, mother nature, aided via stress and supplemental hormones, decided to strike me this week.  So, I sit here today on this beautiful Autumn Friday, I figure I ought to give you all a glimpse into the Kitten’s mind.  Lots of things have been flowing there recently and I plan just to let them out.

This semester has me taking the organic laboratory over again because OU, great school as it is, has required me to take their lab–apparently, SMU’s lab was not sufficient.  Initially, I had no problem with this, fully intending to make the most of a nice lab and previous knowledge of the experiments to be run.  Unfortunately, I’ve been sorely dissapointed.

Not only does the organic chemistry lab lack in luster, it lacks in teaching ability as well.  Besides spending two 3-and-a-half hour periods in the lab with a TA (whom I actually love and who is just as fed up as I am), I have to take time on Tuesdays to return to school at 5pm in order to sit through a lecture class.  Right, not so bad, really?  Wrong.  Though I hear that the lab professor isn’t half-bad when actually teaching Organic, he has only half-a-clue of what’s going on in the actual labs.

How so?  Our first real lab included distilling two compounds from each other using a Hickman still.  Ah, no biggie.  Distillations are easy, I thought, rather naively I might add.  The two compounds, had relative boiling temperatures of 90C and 120C respectively and thusly one can heat the compounds up to about 90, let it reflux until a reasonable amount of distillate forms, collect, then continue to heat up to 120 to collect the next sample.  Well, lo and behold, here I sit with my hotplate at 90C and nothing is happening.  Okay, I think. Maybe I should let it go for ten minutes or so.  It will boil.

Nope.  Never refluxed at 90C.  So, shrugging my shoulders, I cranked my hotplate up to 120C.  Again, I waited ten minutes.  No reflux.  Sighing with disdain, I crank the plate up even further and finally, the compounds begin to reflux at 150C.  Please, dear readers, note that I was using toluene, which should be on FIRE at this point in time.  (Okay, maybe not fire, but it should be burnt and crispy at this temperature.)  Incredibly frustrated as I was, I collected my distillates and submitted them.

My spectra came back the following lab period and specifically read two unknown chemicals that were NOT what we were supposed to be using.  So, not only did this lab fail incredibly, the manual or the prep-man in the chem stock room royally fucked up.  I am frustrated with this lab.  Very, very frustrated.

But, what can you do?  Unfortunately, I have no control over anything that happens in the lab (thankfully, that will change one Damn, I've never been so proud of ethanol!day).  I, like many of my fellow chemists in the lab, have to persevere through this bullshit for the rest of the semester.  Thankfully, not all is lost, as I have found that if I tweak the labs to make them more like SMU’s effective labs, I tend to get better results.  A prime example is my partner, Russ, and I’s perfect 95% Ethanol distillation and purification.  We’re quite proud of that moonshine! xP

This weekend looks to be full as I need to analyze and complete two long labs that I have done recently.  I’ll post more about my incredible disappointment with this lab as time moves on.  Hopefully, these complaints will bring clarity to my own work and perhaps to yours.

Cheers!

The Alchemist Kitten

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