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Author Topic: Chemical Irregularities: Sci 222  (Read 1439 times)

Offline Letonna

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Chemical Irregularities: Sci 222
« on: February 12, 2015, 04:13:58 PM »
Sci 221

An Introduction, Fascination, Peculiarity, and Investigation, with Respect to, and with Regards to Chemical Irregularities and Intrigues.
Lecture 1: Bismuth

   Bismuth is one of my favorite elements. Its such an oddball given it’s atomic number and place on the periodic table. Periodically speaking, it’s in a bad neighborhood. All it’s neighbors are nasty elements like lead, polonium, and mercury, all toxic and or radioactive. However, Bismuth is the heaviest element on the periodic table that isn’t toxic. Why is that?

Bismuth is actually technically radioactive. But hold a geiger counter up to a little lump of it and you won't hear much. This is because bismuth has a half life that is currently longer than the age of our universe. This means that in the billions of years our universe has existed, most bismuth is still here, and hasn’t decayed yet.

It’s because of Bismuth’s lack of toxicity that allows us to put it to use in the form of pharmaceuticals. Many of you have probably used an over the counter drug called Pepto-Bismol(other brands are available). This organic bismuth ether quells upset digestive tracks by both acting as an antacid, slowing bacterial action and acting as an anti-inflammatory. Most interestingly, is antibacterial action. Bismuth is also used in certain eye drops, as well as medications to control excessive smell of released gas and feces.

Bismuth subsalicylate, active ingredient in peptobismol

Bibrocathol, active ingredient in an antibacterial eye drop called Noviform

Bacteria can be very picky of their environments. Many heavy metals can act as enzyme inhibitors or disrupt the coiling of your DNA. In harmful bacteria in our guts, bismuth slows down cell processes. It’s not entirely certain exactly what mechanism of action is causing this, but it’s most likely one of the previously stated possibilities in regards to heavy metals.

Finally, what I find unique to the element, and perhaps the most easy to see, is it’s famous oxides. If you've ever been in a mineral shop, you've likely seen a bismuth crystal. You’ll know it by it’s sharp 90 degree angles, cuboid structures and rainbow colored oxides. The rainbow colors are actually caused by different amounts of oxidation thickness on the surface, and the reflection of light caused by said thickness.

Next week, this course will explore antibiotics, and what makes them so unique.

Offline Delfos

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Re: Chemical Irregularities: Sci 222
« Reply #1 on: February 12, 2015, 04:58:09 PM »
So I thought about looking up extraction because this metal seems like a nice alternative to lead for some industrial purposes, apparently by a large difference China is the biggest extractor and it's usually what in wikipedia called "byproduct" of tungsten (or lead, copper, tin and molybdenium), which kinda explains why it's not very used in Europe or maybe even America in Industry. The Chinese mine the hell out of tungsten for metal coating against the western counterparts that use carbon cementation, it's likely why they also encounter Bismuth, and why we don't even bother to apply it. The biggest industry to use it is pharma and other chemicals like cosmetics, not surprising from what Letonna said.

The US gov has been trying to use Bismuth as replacement of lead, but weirdly the wiki article mentions: "Some manufacturers use bismuth as a substitute in equipment for potable water systems such as valves to meet "lead-free" mandates in the U.S. (starts in 2014).". That is scary... :anguish: the lead part of course.

Offline Letonna

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Re: Chemical Irregularities: Sci 222
« Reply #2 on: February 16, 2015, 02:25:48 AM »
Sci 221

Lecture 2

Antibiotics, The little Enzyme Inhibitor that could.

The common structure of penicillin like drugs

Antibiotics are enzyme inhibitors, but in General, most prescription drugs you get are enzyme inhibitors. Not all of course, but generally, that’s the case. But what is an enzyme inhibitor, and what does it have to do with antibiotics?

Firstly, and enzyme is a massive molecule that helps along, or “catalyzes” a specific chemical reaction. It’s not used up in the reaction, but rather speeds it up, and can be reused many times. An enzyme, if you remember from basic biology, is very similar to a protein(in fact they are proteins) but just behave a little differently than your run of the mill protein. An enzyme inhibitor, simply stating, is a chemical that stops the enzyme from working. It binds to the enzyme, often times destroying it, or putting in need of repair for an extended time.

Everything in life uses Enzymes, and their subsequent inhibitors. In fact, all of us drink a very common enzyme inhibitor every morning. Caffeine. Caffeine inhibits the cATPase enzyme found in your small intestine that stops the breakdown of a high energy chemical called cyclic-adenosinetriphosphate, giving you that energy buzz.

A common cup of coffee

But we’re talking about antibiotics right? Not coffee. But we aren’t ready quite yet for the meat and potatoes. First, we must also address what makes something an antibiotic. It must be something that impress the cell in such a way that it can not reproduce, carry out metabolic functions, or continue on homeostasis. Most antibiotics inhibit an enzyme that is essential to any one of these functions. If you’ll recall last weeks lecture, you’ll remember some bismuth drugs were antibiotic.

Let’s start with the most famous antibiotic, penicillin. Besides the famous story of how it was discovered, it’s one of the most widely prescribed drugs (along with it’s cousins). But what does it do? Why are penicillin drugs so unique? They fascinate me because they inhibit the cell in such an ingenious way, making the cell essentially kill itself.

Penicillin inhibits a special enzyme only formed when the cell is replicating. The enzyme is responsible for cutting the cell in two. See, bacteria(and many archaea(but you’ll learn about those in biology)) have these thick cell walls, impervious to many forms of chemical attack. They work great, but the problem arises of how to divide when the time comes. A special enzyme complex cuts and reforms the cell wall, allowing for a fluid growth. Penicillin inhibits one of these enzymes, so bacteria make defective cells walls, quickly losing their armor, being exposed to the outside world and dying. Penicillin has many cousins, but they all function similarly.

Other examples are the Flouroquinolone class of antibiotics, which inhibit an enzyme crucial in DNA separation and halts cell division. Lincosamides inhibit RNA transcription. Sulfonamides block Amino acid formations. The list goes on and on. The key point is we have developed the technology to wipe out a whole population of organisms in our bodies by simply inhibiting one other chemical, without doing any harm to us(except for the common side effect of diarrhea). 

Next week we will look at polymers, and the weird concept of linking together two identical chemicals and how they revolutionized manufacturing and laxatives.
« Last Edit: February 17, 2015, 07:29:41 PM by Letonna »

Offline Letonna

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Re: Chemical Irregularities: Sci 222
« Reply #3 on: March 09, 2015, 11:07:48 PM »
When Carbon Bonds to Metals: Organometallic compounds

A typical organoarsenic compound

I love organometallic compounds. I find they are so exciting. There’s so much potential in learning about them. I would even argue a lot of research is being put into them to find easier ways to perform reactions.

But I’m getting ahead of myself. What is an Organometallic compound? Well, simply speaking, it’s when a metal bonds to at least one metal ion covalently. If your high school chemistry ever said carbon only bonds to other commonly covalent elements, well they’re wrong.

The most famous, and maybe the more boring ones are the Grignard Reagents. This is when a carbon compound is covalently bonded to magnesium. They are used in a lot of different processes, from moving an oxygen around, to polymerizing to making a resonance structure.

However, I’m going to talk about some weird chemicals involving arsenic, tin, and lead.

Firstly, lead. Most of you may own a car, and most of you probably put gas in that car and drive it around. Assuming you buy the gas here and not Algeria or Myanmar, then you’ve probably seen signs that say “unleaded gas” or “lead free.” This is because we used to put lead in gasoline.

The structure of Tetraethyl lead

There’s an interesting little story to why this was. In the early part of the 20th century, when vehicles were becoming more and more abundant, it was discovered that adding certain chemicals to gasoline could not only increase fuel efficiency, but also help in antiknocking and as an octane booster. In the 1920’s, It was discovered that Tetraethyl lead was great at all these.

A typical gas pump; modern day

Tetraethyl Lead is exactly that. It’s 4 ethyl groups covalently bonded to a lead atom. Also at this time we discovered that ethanol was a good additive as well, and worked just as well. However, the patent holders of tetraethyl lead ran a massive campaign to encourage to use of leaded gas, and it worked. If you know anything about lead, then you probably know why we stopped using it. Something about lead being in the air and destroying catalytic converters, or so the story goes.

The common structures of antimicrobial arsenic medications

Now, for arsenic. Arsenic is a fun element really. If it wasn’t so toxic and had such a nasty reputation, I feel a lot of interesting chemistry could be done with it. We used to use arsenic for a lot of different applications. Paint, dye, medicines, alloys. Of course we don’t do any of that anymore. What a lot of people may not know, is there’s this bizarre chemical that we used to use as an antibiotic some time ago.

Organoarsenic medications have an interesting back story, one fitting of my other class, The Darker Side of Science. When Europe, primarily Britain was colonizing Africa, there arose a problem of African diseases affecting livestock on a detrimental scale. This made colonization hard for European settlers, used to eating foods revolving around the use of cattle, sheep, and general european farm animals.

In 1905, two British scientists reported that an organoarsenic compound discovered a few years before was very effective at treating trypanosomiasis in livestock and humans.  It was very difficult to store however, and unless an exact dose was given, the patient risked losing limbs or even life. After further development, the drug was put to the test in the German East Africa. The results weren’t promising, as 2% of all patients reported blindness, but it did help reduce the disease.

[Fun Fact: Colonial medicine was so crucial to European expansion, that in 1922, the German chemical company Bayer offered the British Government the formula to it’s new antimicrobial compound Bayer-205 in exchange for the return of colonies Germany lost after WWI]

Eventually, a new drug (with less side effects, including death) was developed using arsenic, called Salvarsan, or Compound 606. It was a drug that was not only effective at trypanosomiasis, but also effective at treating patients with syphilis. The drug was very volatile, and still had many side effects like nausea(you got to give them credit, they were giving people mercury salts before this) but was regardless effective. It remained in use until the 1940, when penicillin was developed.

Organoarsenic compounds are still of interest, because arsenic is a metal that bonds relatively easy to carbon. In some ways it behaves like it’s cousin nitrogen, forming bonds in 3,4, and 5 configurations. It was even thought that a bacteria using arsenic in it’s DNA was found, but that was disproven.

Finally, organomercury compounds. Mercury is one of those elements that has a good and bad side. I personally think besides it’s ability to bond with carbon, it’s chemistry is on the dull side. It’s organo compounds are used in applications where it’s toxicity is useful, like as a pesticide, fungicide, and preservative.

Merbromin structure

Most people over 30 probably remember using a product called Merbromin. It’s aa brominated aromatic structure covalently bonded to a mercury, used as a topical antiseptic. It’s falling out of favor in more civilized nations, but is still in use in a lot of developing parts of the world, where a cheap, easy to make antiseptic is an integral part of a budding health care system.

Merbromin anticeptic

Nitromersol, another aromatic mercuric compound, was used for vaginal contraception, diaper rash, and as a preservative for vaccines. Alkylated mercury compounds are used a fungicides and pesticides.

Structure of Nitromersol

You may have noticed an interesting trend in this lecture. The metals I picked to talk about all have a bad rap about them. This was intentional. I wanted to show that even in the stereotypical bad reaches of the periodic table, lie some interesting gems. A good chemist knows that stereotypes about elements are often skin deep. An element is toxic, how can we refine that property? How can we turn something that is bad all the time, and instead make it bad at one specific thing(like a bacteria, or pest)? An element bonds a specific way, how can that be useful?