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

(note: to see image captions, place mouse on image!)

Happy late update!  My week became something along the lines of “fucked” and so unfortunately, I am writing this during my D&D session.

So, today I shall be teaching a lesson on ionic bonding.  It is the most commonly known style of bonding and probably the most important style of bonding to baby-chem students who are studying solubility and other various aspects of compounds in solution.  (Both topics that I shall talk on at some point in time.)

Ionic bonds typically couple a metal from the right side of the periodic table to a non-metal to the left side of the periodic table.*  Since the right-side elements (such as Na, Li and K) typically have outer shells with either one or two electrons, they are much more capable of ionizing down to their cationic state.  Due to this property, a much more electronegative element (such as Cl, O or Br) can come right along and pluck off the “loosely” held electrons for themselves. (It should be noted that non-metals are usually greedy little bitches.  If someone lost an electron, it likely went to them.)

Now, this leaves us with a cation and an anion, which, as anyone who has ever played with a magnet would know, attract each other.  Thusly, we have an ionic bond.  It’s easiest to understand the ionic bond as occurring when opposite attract, but technically there is another force at play–energy. (It should also be noted that usually, energy plays a huge role in anything chemistry related).

I really gotta get a tablet...

I really gotta get a tablet...

Let’s use table salt as an example, seeing as it is the most commonly demonstrated ionic compound.  Energetically, it is more favorable for Na to lose its valence electron to Cl.  On the flip side, it is also favorable for Cl to pick up the extra electron.  Once this electron trade is done, both Na and Cl have fully filled valence electron shells. (Remember, all atoms are looking for a full eight electrons to fill their shells.  Except for H and He of course.)  Thusly, the bonding of the two atoms into a molecule produces a decrease in energy that is thermodynamically favorable.**

Since the bond is mainly a connection due to the polarized atoms, the Na region of the molecule is partially positive (little delta +) and the Cl region of the molecule, obviously, is partially negative (little delta -).  This effect makes ionic compounds break down easily in water, which is also ionic (with the H being + and the O being -).  With the ionic compound broken into its cation and anion, it is quite easy to add another compound (ionic or no) and induce a chemical reaction.  This is one of the prime reasons that ionic bonding is important to solubility rules.***

*It should be noted now that many of the common anions that baby-chemistry typically memorizes can also participate in ionic bonding and will often do so.  (Such as NO3-, which commonly bonds with Na to create an incredibly un-reactive compound that once drove me incredibly mad.  Due to its inert nature, it also is a commonly used salt-bridge in electro-voltaic cells–we use this for oxidation-reduction reactions and one will likely encounter them in all introductory chemistry levels.)

Hopefully this has made the idea of Ionic bonding a little bit clearer!

Happy Chemistry,

The Alchemist Kitten

**This concept is easily explained by the Gibbs Free Energy Equation.  It is an incredibly important topic to cover, and I shall do so once I talk of…

***Solubility rules, which is what I plan to teach on next, since I have covered-albeit briefly-ionization in water.

Fondest greetings to you all on this fine Tuesday!  I hope that your Labor Day weekend was relaxing and fulfilling.  Unfortunately, its back to the old grind for most of us and in lieu of a lecture, I bring you something more interesting—a brief history of our knowledge of DNA!

So, without further adieu, lets take a step back in time and discover the initial unearthing of the “molecule of life”…

Any high-school biology class will tell you about Gregor Mendel’s description of a predictable pattern of inheritance through his pea plants.  Four years later, in 1869, Friedrich Miescher isolated nucleic acids from white blood cells taken out of pus on surgical bandages (ew!).  Little did these two men know that their findings were intimately related—we wouldn’t make this connection until the mid-1900’s.

I’m not here to talk about Mendel or Miescher, however.  They are topics for another post at another time.  Today, our subjects are Oswald Avery, Colin MacLeod and Maclyn McCarty and their groundbreaking experiment from 1944.

Rough-Left, Smooth-Right

Rough-Left, Smooth-Right

The Avery-MacLeod-McCarty experiment took two strands of the bacteria pneumococci (one non-virulent and one virulent) and injected them into mice in order to determine that DNA was the key component in information transfer.  It was already known that the smooth strain (virulent) could transform the rough strain (non-virulent) into itself via a “transformation principle” (see Frederick Griffith’s work).

Ah the joys of clean experimentation...

Ah the joys of clean experimentation...

As seen in the image, the heat-killed smooth strain transformed the rough strain into its own type using a “transformation principle” that had, up until this point, remained an unknown substance.  Avery et. al. went on to extract the “transformation principle” from the cells and apply tests to identify the substance.

First, they heat killed the bacteria and extracted its components with a saline-solution (since the “transformation principle” was saline-soluble.)  Next, they removed excess proteins and polysaccharides via precipitate using chloroform or enzymes respectively.  Finally, through alcohol fractionation (a subject I will touch on at a later date), the single strands of DNA were removed from the remaining solution into long whispy strands.

Since testing proved that proteases and lipases had no effect on the substance, Avery et. al. was able to rule out proteins and lipids as the substance in question.  They found that the “principle” precipitated in alcohols, unlike carbohydrates.  Finally, through the use of ribonuclease and the Dische-diphenylamine test, it was deduced that the substance must contain dioxyribose nucleic acids.

Hurray!  We’ve discovered that DNA is the substance that carries genetic information, right? Wrong!

Unfortunately, it was a commonly believed principle in those days that proteins, not nucleic acids, were the “molecule of life”.  You might be feeling a double-take here, but bear with me.  Proteins use twenty-two amino acids to build themselves into incredibly complex polypeptides.  Nucleic acids only have five base pairs (remember RNA’s uracil!) and had been deemed with no viable purpose as of yet.  So, with logic us towards the more complex molecule as the substance that carries genetic information, nucleic acids were looked over as something irrelevant.  Yet again, however, it was proved that the most complex solution can be found in the simplest answers.

Not only were Avery, MacLeod and McCarty challenging common belief, they were doing so well!  Biochemically, theAvery Oswald experiments and procedures used on the pneumococci bacterium were incredibly sound and the techniques were clean.  Common contemporaries were baffled at the results and some even threw the report out the window as “rubbish”.  Due to this disbelief, the Nobel Prize that year went to another chemist in what is now believed to be one of the darkest marks on the Nobel Prize’s history.

Eventually, Alfred Hershey and Martha Chase confirmed DNA’s role as a genetic carrier with their (much less biochemically sound in my honest opinion*) T2-Phage experiment.  Right on thier heels was Watson and Crick, who through the use of Rosalind Franklin’s x-ray diffractions, discovered DNA’s trademark double-helix structure and thus cemented DNA into the public eye as the “molecule of life”.

This is where I shall stop our historical journey today and bring us back to the present.  When I was first presented with the knowledge that DNA had been found several years earlier than Hershey-Chase and Watson-Crick, I was shocked!  The scientific community was a place where I felt any and all ideas were given the time deserved.  (Granted, they should be well researched and well documented, as Avery et. al.’s was.)  In the end, I suppose that even the most well-thought out, well organized research can be ignored if too premature.  Nevertheless, this blog post today was to bring Avery-MacLeod-McCarty’s work to the light again and remind the community who it was who discovered DNA’s actual purpose.

Cheers!

The Alchemical Kitten

*I wish to expand upon the unsound T2 experiment in comparison to the pneumococci experiment and will do so at another time.  However, this post was for history only.  A commentary will come in due time.

You guys have my sincerest apologies for my lack-of-update on Thursday!  I completely forgot!  However, as a treat, I decided to explain one of the more complicated concepts from general chemistry…

That’s right!  Today we’re going to talk about the seemingly complex topic of electronegativity.  A lot of general chemistry and baby/AP chemistry students struggle with this concept and how it applies to reactions and molecules.  For now, I’ll cover the general basics and trends of the subject.

First, let’s define electronegativity.

An atom is considered “electronegative” depending on its ability to attract electrons towards itself.  In this sense, electronegativity is a chemical property of a particular element.  Unfortunately, like most subjects in chemistry, this simple explanation, though sufficient, doesn’t completely grasp the entire subject.  For now, we will stick with this simple definition for our purposes today.

Since electronegativity is a chemical property, we should be able to map its trend across the periodic table.  Indeed we can.  Let’s think about some atoms for a moment and deduce whether they would prefer to have electrons or not.

Lithium—Li has three electrons in two valence shells.  Two electrons are on the inner shell closest to the nucleus and the last one is on the next shell alone and unpaired.  With this idea in our heads, lets ponder whether Li would want another electron or not.  The outer shell of Li requires seven more electrons to make the atom “happy”.  Finding seven electrons could be quite an impossible feat, and thusly Li tends to lose that electron rather than keep it.  This means that according to our definition of electronegativity, Li has low eNeg.

Oxygen—O has eight electrons in two valence shells.  Unlike Li, O’s outer shell electrons fill six of the eight electrons needed to fill up the second shell.  Again, let’s consider O ability to pick up electrons.  Those six outer electrons are not going to go away easily and thusly it is much more energetically favorable for O to pick up two extra electrons than to give away six.  Therefore, O has a high eNeg.

From looking at Li and O, we can define a trend of increasing eNeg going from left to right across the periodic table.  We’re not done yet, however!  Does the trend go up or down on the table?

Well, to describe this, we must think about atom size.  Let’s compare two right-side elements, say, F and I, both having a similar eNeg.  Comparatively, F is incredibly small—I having 44 more electrons than F—and therefore I’s outer seven electrons are much further away from the positive nucleus than F’s.  Due to this distance from the nucleus, I is less capable of attracting electrons than F.

So, our trend must increase in eNeg from left to right and from bottom to top! (A good way to remember this is “Up and to the Right”.)

Paint ftw!  I've got to get a tablet...

Paint ftw! I've got to get a tablet...

Hopefully, this little explanation helps you all understand the basic idea of eNeg and how to identify which atoms are more electronegative than others.

Happy Chemistry!

The Alchemist Kitten

As I was working on my History of Science and Religion project (The Evolution of Evolution) and having visited the Sam Noble museum, I suppose it is time for me to talk about creation.  How was the world created?  How did humans come to be?  Why are we here?

These questions are why both religion and science surfaced.

So, what of the big bang?  The LHC and other large physics centers have brought us within seconds of the creation of the universe.  I have to wonder what those men and women must think they will find when they close the gaps and reach the moment at the beginning of time as we know it.  Will we find what Christians call “God”?  Or will we find something more abstract—something more profound and deeply moving?

Is that why the fear of science has built in recent years from religion?  What happens if science finds a truth that once-and-for-all debunks the idea that a god could exist and create our world?  Would morality die?  I hardly think that humanity would go insane with the knowledge that “God is dead”, so to speak.  Still, the question remains, how will people react?

My best example of what might happen comes from a recent video game from Bethesda, Fallout 3.  Laugh if you may, but Fallout provides a fine example of a world in which God is non-existent.  An atomic war did a fine job of ridding the world of God–and subsequently many beings’ morality.  However, as the “Lone Wanderer”, you emerge into the Capitol Wasteland and encounter an almost primitive religion that worships the very atomic technology that tore the world to pieces in the first place.

In the little community of Megaton, built up around an active atomic bomb that had yet to detonate after about two-hundred years, the Lone Wanderer encounters a small faction of townspeople who worship the radiation from the bomb itself as a source of life and salvation.  The Sons of Atom can be found scattered throughout the wasteland, their features becoming more and more ghoulish due to their love of radiation.  Though I shan’t spoil any of the actual story for those of you who have yet to play (who hasn’t?), it must be mentioned that these Sons of Atom go so far as to irradiate pure water in order to gain enlightenment.

On an Earth where pure water is nigh extinct, this seems just a little ludicrous.  *heave sigh* This is dogma for you.

So, we find that despite the ruin of the world, people still find a need to worship.  That poses the question: If we find that God doesn’t exist, will people still need to worship an entity?  If so, what?  Will we have the “Apostles of the LHC”?

What will that do to humanity?

I shall leave you all to ponder that deep message.  As Three-Dog would say,

That’s all, Children!

TheAlchemicalKitten

Woo!  I meant to get this blog up and going for months now, but my summer was hot and blurry after finals and I just never got around to actually publishing anything.  Now that I’ve found myself relatively stable in my new semester, I figured I ought to get to posting.  Below is an journal entry from my History of Science and Religion class (HSCI 3443 for you OU students interested.)

I find myself incredibly disappointed in the fact that I missed your lecture on Friday.  Alas, the need to see some of my closest friends overcame the need for intellectual stimulation.  That, and I had a need for Inspiration’s “Paris” tea.            Sadly, of all days for me to be absent, was the day you covered alchemy!  Seeing as my internet pseudonym is “The Alchemist Kitten”, I fear that I must have missed some history pertinent to my studies.

However, as a modern day alchemist, I can happily say that some of the ancient forms of alchemy are coming to fruition in our own laboratories.  For example, the old theory and now adage that one could turn a common metal into gold; this reaction is typically called chrysopoeia.  This revolution is closer to our hands than commonly thought.  If one has, say, iron, with its 26 protons, 29 neutrons and (at its neutral state, not its +2 and +3 ions) 26 electrons and gives the atom 53 protons and the equivalent neutrons and electrons to bring the state to neutral, the iron would become gold.  With our current technology, we are inching ever closer to that age old goal.

Another grand thing that current science is bringing us towards is the “panacea”, or the elixir of life.  Stem-cell research has reared its head on current debates as a way of extending life and preserving youth.  I just recently read an account of a clinic in Korea that claims that it can take one’s fat cells, convert them into stem-cells, and insert them into one’s face to preserve its youthful splendor.  How accurate that article was and how true the clinic’s claims is another topic for another day.  Nevertheless, stem-cells are a bright and vibrant hope for those who suffer from HIV, cancer and other diseases that wreak havoc on our bodies.

Unlike chrysopoeia, in which most chemists and physicists find themselves (relatively) unhindered in their splicing of nuclei and tampering with particles, the doctors and biochemists who look deeper into what life truly is often hit a giant roadblock of morality and/or those who wish to impose their own morality.  It is unfortunate that this is so, for perhaps a way to ease the pains of others has been lost in the picket line of religious zealots.  Having dealt with the fear and pain brought about by cancer first and second hand, I cannot come to fathom why someone would oppose the good things in which exploring said “panaceas” could bring us.

Nevertheless, scientists have brought forth many of the alchemical theories from centuries ago and made them reality, or at least a semblance of.

Hopefully, this made a semblance of sense, seeing as I just copy/pasted.  Enjoy!

Cheers,

The Alchemist Kitten