Can't Sleep, Thesis Will Eat Me

I know I have been remiss in writing here lately, and I greatly appreciate the number of comments/questions. Too bad it has taken me so long to get back. I shall blame it on writing my thesis. After spending an entire day writing (or staring at a blinking cursor, trying to write-depending on how good my day is) I just don't seem to want to write more on my blog. Although, this is much more fun. 

But with all of the writing I have been doing, I have had the luck of getting a paper published. It is one I have been working on for more time than I care, but the scientific community has agreed to publish it (who am I to argue?) so here is a link to my paper , just to prove that I am a real scientist with actual real credentials. 

I intend to write something here soon, but please don't let my slow response keep you from reading, or asking questions. 

Chemistry is awesome!

Operation Thesis Continues

I am still working away at my thesis. It really means that I am having trouble coming up with ideas for blogs on my own. So please ask me some questions. I am desperate for new ideas to write about. I have a few thoughts, but maybe some feedback with let me know whether there would be any interest:

1) vaccines-what they are and how they work

2) fluorescence-because of that whole mountain dew myth

3) what is a flame? This might really be my attempt at answering Alan Alda's "what is a flame?" challenge. 

And I am out. Please ask your questions. And also vote on whether or not you would like to see a post about any of the above topics.

 

Ask a Chemist: Operation Thesis

It never fails that when I am away for a bit, that is when I get numerous questions. I apologise for my delay in replies. 

Please keep your questions coming. 

I have begun writing my thesis. The completion of this masterpiece is under the label: Operation Thesis. Along the way I shall be happy to share what I learn. Also, I am looking for the distraction.

Happy (Belated) Canada Day!

This past weekend was Canada Day. And tomorrow, for Americans, is Independence Day. Common to both of these holidays is celebrations that demonstrate the best use of gunpowder. What I mean to say is FIREWORKS! Without chemistry there would be no fireworks so to share a little about the chemistry of fireworks let me introduce you to a video from the American Chemical Society. Chemistry of Fireworks.

Enjoy!

Chemisty of Stain Removal

I am just returning home from the 95th Canadian Society for Chemistry conference, which was hosted in Calgary, Alberta this year. One of the great things about going to Calgary for me (aside from visiting the zoo) is that my sister lives there. Instead of staying in one of the over-priced hotels near the conference centre, I was able to stay in one of the over-priced downtown apartments near the conference centre. This was great! And sure, the accommodation may not have had the most comfortable bed, it did come with free internet, home cooked meals, and a couple of cats to snuggle with. Oh, and family that I love. In this time though, my sister found that having a free-loading chemist as a house guest isn't all that bad. Not only will she leave her fabulous shoes for you to wear, she can apply her knowledge to help you remove a baked-in oil stain from one of your favourite sweaters.

The stain: in an expensive and great lululemon zip-up hoodie, an oil stain that was very visible was set in the pockets. The sweater had been machine washed and dried. Its distraught owner was quite sure nothing further could be done for the sweater. It was to fall victim to this villainous stain. 

Our heros: a chemist, canola oil, and dishsoap. The canola oil was rubbed into the stained areas. Then dishsoap was poured on top and also rubbed in. The sweater was then thrown back into the washing machine.

The outcome: one stain-free sweater, good as new.

That's right, we used oil to remove oil. Magic right? Not so. Here's the chemistry: because the oil had been washed and dried, it was now trapped in the fibers of the fabric and therefore  not accessible to soap when further washing would take place. This is because water and oil, as the saying goes, don't mix. This creates a barrier between the oil in the fibers and the soap. In order to get the oil out then, we need to find a medium that it does mix with. This is where the chemistry phrase "like dissolves like" comes in. Oils are soluble in other oils. Any oil will do: canola, olive, WD40, take your pick. By rubbing the oil onto the stain, it is able to dissolve the oil that is set into the fabric fibers. Once it has, you pour on the dishsoap, and the soap does what soap is designed to do, and form what are called "micelles" around the oil particles that can now be washed away in water. The result is a stain-free fabric. 

I talk a little bit more about some of the factors involved in my blog about water. The terms hydrophobic, hydrophilic all play a role in this chemistry. Oil is hydrophobic: water-hating. Soap is what is called "amphiphilic", meaning that one part of it likes water, while the other part doesn't. When placed in water it will arrange itself in the small spheres (micelles) with the hydrophilic (water-loving) part facing out into the water, the hydrophobic part facing in. Because oil is also hydrophobic, it ends up on the inside of these micelles, away from the water.    

So there you have, practical chemistry to save your clothing from destruction!

 

Starbucks is Serving What?!

I dedicate this particular post my sister. 

Basically what I gather is that some person found out that their red or pink food dye that makes their Starbucks frappuccino a delicious-looking pink came from insects and this caused some vegans to get upset since apparently bugs count in the abstinence of eating animal products. You can step on them, you just can't eat them. Whatever, that's not really what I care about. What I care about is the chemistry, so let's talk about this red dye:

It is carmine. Carmine is the aluminum salt of carminic acid (shown above). Carmine is also know as natural red 4. Where does the "natural" come from? "Natural" means that it has been isolated from nature, meaning not synthesised in a lab by chemists like me, otherwise it would be referred to as "synthetic" or "artificial". In this case, carminic acid (and similar compounds) are isolated from the scales of insects. There are various methods to prepare this compound, and the more pure, the deeper the colour. 

This is the red in lipsticks, paints, inks, and food products. There have been instances of allergic reaction to this compound-as with most other chemicals, both natural and artificial. 

So if natural is not what you want in your food (FYI you can add this naturally derived chemical to juice and still label your product as having not artificial colours) and you would prefer not to have bug extract in your food, what is left for you is synthetic dyes. 

Synthetic dyes are ones that are made in labs by chemists like me. I like the idea of Starbucks having to switch to synthetics-it means I will be employable. (Ok, I am being a little facetious there.) Synthetic isn't bad either. Food dyes, cosmetic dyes are treated like any other consumer product and have to meet certain legislated standards, not unlike what I described for pharmaceuticals. But the draw back of going synthetic means that there will be some chemicals that have been derived from oil that are used in the process. It is all a trade off.  This particular compound, carminic acid, was first synthesised in 1991 in the lab of John Tyman: Journal of the Chemical Society-Chemical Communications, 1991, 18, 1319-1320.

While many dyes and pigments are derived from plants, not all are. This is a case where insects are used. Tyrian purple, also known as royal purple, was obtain from a kind of shellfish.

Pharmaceuticals-How Are They Produced?

I thought I would talk a little about pharmaceuticals. Chances are you take some, know someone who takes them, and have all complained about their prices. This past semester, I took a pharmaceutical chemistry class taught by scientists from Gilead, and I must say it was very enlightening. I thought I would share some of the lessons I learned and some of the key problems that face those charged with making these chemicals that many people depend on.

Let's start with a poignant news story. What would you do if you were suddenly unable to get a hold of a medication that you require? When a company decides to stop producing a compound, what can be done? Is that right or wrong? How should medications be priced? These are questions that are very difficult to answer.

To understand a little bit about the complexity of the issues with the pharmaceutical industry I think it is first important to understand how these medications are produced. I know I found it eye opening. Guess how long it takes to produce a drug? 0-5 yrs? 5-10 yrs? 10-15 yrs? 15-20 yrs? If you guessed 15-20 yrs, then you would be correct. It takes 20 years and (as of 2008) $1.7 billion to develop a SINGLE drug. 

The timeline:

Discovery/Preclinical Trials

Time: 1-3 years

In this time, the company will begin by identifying a medical need, such as anti-HIV medications, and then study that disease to determine where drugs can target the disease and the possible interactions of the drug. This is where potential contenders for a drug are determined. This amounts to some 30 000 chemical compounds will be screened! These preclinical trials will involve pharmacodynamics and pharmacokinetics.

Pharmacodynamics: studies how a drug interacts with a target-this is the impact of the drug on the body. Is the drug going to do what is was intended to do? Is it going to do something else? 

Pharmacokinetics: this is how a drug is transported to the target-this is really looking at the impact of the body on the drug. This looks at four things: absorption, distribution, metabolism, and excretion. Remember, your body is one self contained complex chemical reactor. I think one excellent example of the importance of studying this effect is the notorious thalidomide. There are two versions of thalidomide: R and S. One is an anti-emetic (R) while the other causes birth defects (S). Yes it is possible to separate the two and give a person only the version that DOES NOT cause birth defects; however, once in the body, the drug is inter-converted to the other form (a process called racemisation).

Any potential drug will be screened for toxicity using two species: one rodent and one non-rodent. They will be tested for single and repeated dosing. They will be tested by various delivery methods. (Side note: a 14-day rat trial costs $250 000.)

During this time, chemists will be answering the questions of: can the drug be made? How many steps (hint: more steps, more costly, more trouble)? What are the yields (not all chemical conversions give 100% yield-actually very few give 100%)? Is chemical manufacturing possible, feasible, and affordable? 

After all of this, about 100-200 of the 30 000 compounds will make it on to the next step. 

Safety Review

Time: about 30 days 

This is where the pharmaceutical company is trying to get approval from human clinical trials. All of the information gleaned in the preclinical trials must be presented to the regulatory bodies, including the synthetic routes for production. This is also the time that a company will take out a patent on a compound (a process in the tens of thousands of dollars for each one). 

Clinical Trial: Phases 1, 2, 3:

Time: 2-10 years

This is where the human trials begin. 

Phase 1: 

- 10-100 volunteers

- months to 1 year

- involves "proof of concept" and determines whether the drug is adequate, safe, tolerable. 

- 50-70% of the compounds (that made it to clinical trial) will be abandoned. 

Phase 2:

- 50-500 patients 

- 2 years

- 60% of the compounds (that made it to phase 2) will be abandoned

Phase 3:

- 500-2000 patients

- 3-5 years

- only 4-10% of compounds will succeed

Approval:

Time: up to 7 years

This is the stage where regulatory bodies determine if a drug is safe enough and effective enough to sell to the population. 

Now if you have been keeping track, we are about 15 years from when the patent was filed to the point that the drug can be sold. A patent is only good for 20 years; therefore, a company only has about 5 years to recover the cost of the production. This also means that drugs that are currently hitting the market were just getting out of preclinical trials in 1996.

During this time, optimisation is ongoing to make the manufacturing process safer, cheaper, and more efficient. However, if the process is changed too much, it may mean that a company will need to refile their drug for approval. 

There is lots of interesting chemistry in pharmaceutical production. I think I will leave that for another entry, but if you have found this interesting, please check out these course notes for reference material.  

Beautiful Chemistry

Okay, I need a moment to rant a little and reiterate what the purpose of my blog is. Chemistry is a beautiful science. Molecules, atoms, bonding-it is filled with all the lovely simplicities and complexities that give rise to our universe. I have just written about water and how crucial it is to life. Look at the immense diversity of life on this planet and realise that it is a simple molecule of two hydrogens and one oxygen that makes it possible. Even more amazing is my personal favourite molecule DNA. This simple, and I mean ridiculously simple especially when compared to the proteins that actually make up the human body, molecule is what encodes the amazing diversity that we see everyday. And yet this amazing and beautiful science is marred with fear-mongering and hate. 

I really can't stand this "chemical-free" culture that has arisen because it is a complete lie! Everything is a chemical. Life is chemical, water is chemical, the earth is chemical. Chemicals are diverse. Some are good, some are bad. Just like human beings. Some are nice, some are mean, some are okay on their own but terrible when they get together. Chemicals are not evil. Because chemicals are what makes up matter, you can't ever have anything that is chemical-free. It is blatant false advertising (can we get litigious about this?) and creates a culture of hate. The most damning chemicals in the world are nature-made poisons, a little strychnine anyone? Did you know that while asprin (acetyl salicylic acid) is man-made it is actually better for you than its natural counterpart, salicylic acid isolated from willow bark. This is because the acetyl group that chemists put on the the salicylic acid mitigates many of the harsh side effects that salicylic acid has. 

So what is the solution to help rail against those that would denigrate chemistry and chemicals? Well that is what I see the purpose of my blog as. Ask me your chemistry questions and I will answer them as non-technical as possible. I wish to spread the knowledge that I have gained in the 10 years that I have been studying chemistry and share it with the world to show the world there is nothing to be scared of and the chemistry is a big part of their lives, whether they know it or not. I encourage other scientists to do the same. We can't sit back and shake our heads, laughing or getting angry at the numerous people falling victim to this smear campaign. We need to take arms (metaphorically) and share our knowledge, making chemistry fun and interesting. Giving people the knowledge they need to combat the misinformation they are given on a daily basis. It is part of being an ethical scientist that we share what we learn, not just with other scientists, but with non-scientists as well.

Combat the fear-mongering with knowledge and education. chemical free nonsense 

Water Water Everywhere

If there was one molecule that I could spend weeks writing about, it would be water. It isn't a complicated structure, like strychnine. It isn't a huge money making pharmaceutical like Lipitor. This is the molecule that is required for life, and yet there isn't a single atom of carbon-the element that forms the backbone of life-in it. The presence of water is the single most important indicator for the possibility of life on other planets. You can live weeks without food, you can only live days without water. What is so important about this simple molecule that some of us are able to take for granted? Let's talk about its chemistry.

Water, aqua, eau, dihydrogen monoxide, whatever your word for it is, is made up of two hydrogen atoms bonded covalently to a single oxygen atom. A covalent bond is one where the two atoms share electrons between them. This is different from an ionic bond, where electrons are transferred from one atom to another to create ions, one positive ion and one negative ion, and these ions are then attracted to each other via that whole "opposites attract" thing, known in the science world as electrostatic forces. Table salt, or sodium chloride, is an example of a compound held together by an ionic bond rather than a covalent bond. That was a lot of jargon, so to simplify things, you can think of an ionic bond like two atoms dating, or living together. Each atom is currently content with the arrangement, but if things should go awry they can easily separate themselves and go on their merry way. Conversely, covalent bonds are atom marriages. Much bigger commitment, everything is shared between the two, and breaking up is much more difficult. So back to water. Water has a polygamous marriage happening, with the two hydrogen atoms. Also, not all atom marriages involve a 50-50 sharing of assets (electrons). Some atoms tend to be a little needier (or greedier) and will hoard more of the assets (electrons). Oxygen is one such atom. Oxygen is what we call an electronegative atom. To be specific, it is the second most electronegative atom on the periodic table (fluorine is the most electronegative). This makes oxygen a big electron hog. This results in the two electrons that make up the oxygen-hydrogen bond spending most of their time on the oxygen end of the bond. The result is that the hydrogen end of the molecule has a partial positive charge (a full positive charge would mean that we now have an ionic species-we don't.) and the oxygen end has a partial negative charge. This polarity of the bonds is crucial! When you have many water molecules together, they each have this polar bond (partial positive on one end and partial negative on the other). The molecules will then order themselves such that the positive end of one molecule lines up with the negative end of another molecule, in a fashion similar to ionic bonds. Now these bonds are much weaker than covalent or ionic bonds, but are still extremely important in dictating the properties of water. These bonds are called hydrogen bonds. 

Hydrogen bonds are what makes water highly cohesive and gives it a high surface tension. The surface tension is what allows insects like water striders to walk on its surface, and also what it hurts so much to do a bellyflop into a pool. This is also why water has such a high boiling point (100 C) where as similar molecules, like H2S, are gases at 25 C. Hydrogen bonds are also what makes ice float. In liquid water, there remains a lot of disorder, with these hydrogen bonds continually breaking and reforming. As the water changes state from liquid to gas, the amount of order increases. The molecules are frozen in such a way to maximise the bonds. This makes the solid state much less dense than the liquid state, and thus the ice floats on top of the river, pond, sea. Imagine trying to go ice-fishing if this wasn't the case.

The polarity of the water molecule is also key to life. Humans are over 60% water by mass. All living cells have a significant water content. Cells are made up of, and defined by, a phospholipid bylayer called the cell membrane. Phospholipids are made up of a head group that likes water (hydrophilic) and a tail group that doesn't (hydrophobic). When these phospholipids are mixed with water they arrange themselves in a two-layered sheet with the the tails on the inside of the sheet away from the water and the heads remain on the outside edge mixing with the water, forming a spherical species called a vesicle, that has water on the inside and the outside, but not within the wall.  As these vesicles evolved into more complex structures we got life that eventually evolved into the multicellular beings that we are. Crazy to think that it was the properties of water that dictated that evolution, eh?

References:

Pratt, C. W.; Cornely, K. Essential Biochemistry 2004, John Wiley & Sons, Inc. Hoboken, NJ.