Everyday Chirality

Bean There Done That

It has been a long and wet spring, but I am happy to report, we saw the sun for brief moments the last day or two.  Though the weather has not been good for morale, it has been good for the water bill and the back yard garden.  Along with knee-high grass, the kohlrabi, lettuce, and carrots are off to a good start.  After a disappointing failure last year at growing beans, I gave it another try. I am happy to report that at this moment they are thriving.

In the background, you will see a second stalk.  This is my second attempt to train it onto the trellis.  I hooked it on yesterday, but I hooked it on the left side of the pole.  When I came out today, it had pushed itself off trying to curl to the left.  At first, I mumbled, "Silly beanstalk, turn right" forgetting that right turns are not the forte' of creatures in my care.  So today, I trained it to the right side of the bar.  I guarantee it will be wrapping its way up the trellis tonight.

Here is a time lapse video of beans growing.  Notice the same spiral turn as it searches for the next link of the fence:

Now that might seem strange to non-gardeners. Why will it only turn left?  Well, beanstalks, like many things in nature are what chemists call chiral.

The Right Way:

Chirality is a trait of objects often referred to as "Handedness."  This comes from looking at your hands.  You have a right and left hand.  They are mirror images of each other, but you could never make them match up or superimpose on each other.  Superimpose  is not easy to grasp, but I liken it to ghosts in cartoons that enter someone else.  The ghost left hand has to enter the person's left hand to move it.  Well the ghost left hand can never overlap with the right hand or the thumb would be sticking out the wrong side or be upside down.  You can try this.  Put your palms together...your hands are mirror images.  Put your right hand on top of your left hand so that your four fingers are aligned... thumbs on opposite sides. Your hands are chiral!

The structures above are mirror images (wedges are out and dashes back), but will never be able to perfectly overlap, (a thumb will always be hanging off the side). Try lining up any two groups, the other two will be reversed.  This is common in many biological molecules. It comes from a change in ONE ATOM! Four different groups around ONE ATOM can determine whether a molecule smells like spearmint or caraway!  If you want to see the structure of this molecule, check out the post on terpenes.  (S)-carvone is caraway, (R)-carvone is spearmint.  All due to a single atom like above.
Living things are oozing with chirality.

Chemists use terms like D and L, R and S, or P and M to assign whether molecules turn to the right or left respectively.  That discussion is for another day... but in practical application it is mind-boggling how nature works.  Almost all amino acids in your body (the molecules that make up proteins) are only one type of chirality, which we call L. Statistics would say that we should have a 50/50 mixture of L and D, but that is not the case. Somewhere in the world's history, an L-molecule was formed and cascaded through all life on the planet. All DNA helices twist the same way (we call it R or P). This is the same as the beanstalk!

Here is a picture off of Wikipedia:

http://en.wikipedia.org/wiki/File:ADN_animation.gif

My Steak is Chiral?

All the proteins in your steak are made of chiral molecules.  When you go to grill it, you find even more chirality. Engineers use chirality to their advantage to make sure you use proper adapters for flammable gasses. Screws, nuts, and bolts are all chiral.  The old adage, "Righty-tighty, Lefty-losey" only exists because someone chose it by convention. To read about the history, click HERE. Some flammable gas regulators are threaded "lefty-tighty, righty-losey" to prevent you from accidents. No washing machine hoses on the propane tank! You may want to revisit the post Time for Grillin'!

Imagine if you had to buy light-bulbs based on whether you had sockets that turned left or right, someone had to choose that you can screw them in clockwise.

That reminds me of a joke.  How many professors does it take to screw in a lightbulb?  None, they call it "research on chirality" and ask the students to do it. 

All that aside, I am trying to get the comment board fired up this month.  If you run in to some unexpected chirality, post it below.  Let's see what we can find together. 

1. Beanstalks

2. My shoes

3. The cap on my Leinie's Summer Shandy

4. The rest is up to you...

A Little Shakespearean Musing on a Rainy Day...

To know or not to know; that is the question:
Whether 'tis nobler in the lab to suffer the slings and arrows of Organic Chemistry,
Or take arms against a sea of molecules, and by functional groups, react them?

To precipitate: to separate; no more;
And by separate to say to end the thousand column fractions the reaction is heir to.
'tis a purification devoutly to be wished.

To precipitate, to separate,
To separate again: Aye there's the rub,
For in that desired fraction what enantiomers may come?

The structure above is that of pleiadiene, first synthesized by V. Boekelheide and G. Vick in 1956 (1).  It reminds me of the skull that Hamlet finds so endearing.  Interestingly "pleiad means a group of seven illustrious or brilliant persons"(2), just scholarly enough for Shakespeare, me thinks.

(1) V. Boekelheide and G. K. Vick J. Am. Chem. Soc. 1956, 78, 653-658.
(2) A. Nickon and E. F. Silversmith Organic Chemistry The Name Game; Pergamon Press: New York, 1987; pp172-173.

Happy _______ Day!

Put a little constant in your year...

Happy Pi Day to those of you who follow such things.

 It is a great day indeed.  I have been told that any pie-related calories that are consumed in honor of the unit-less ratio between circumference and diameter (3.14159 and so on) are not added to your hips.  So on this 3/14 have some Tres Leches or "Three Milks"from Cafe Latte'.  I know it is not technically pie, but life does not follow rules like mathematics.

On this day, I would like to call attention to other days that are or should be celebrated.


Days that are celebrated (by some people):

Mole Day (10/23)!
No, not the little furry creatures that are in your lawn. Mole day celebrates the number of particles (atoms, molecules, etc.) in one mole of a substance, otherwise known as Avogadro's number (6.022 x 10^23).  Yes, it is a little strange that it is on the exponent and not June 2nd, but it is a good excuse for a late-autumn celebration. It conveniently is in the middle of National Chemistry Week by the American Chemical Society.

Square Root Day (Varies):

Square root day is like the passing of a close comet, though not as periodic.  It comes from when the month and day are the square root of the year.  This was last celebrated on 3/3/09 and will be celebrated again on 4/4/16.

Days that should be celebrated:

Gas Constant Day (8/31): 

This value roughly represents the work per mole of a substance per degree.  So this is a bit of a stretch because unlike PI or e it changes based on what units you are using.  This might be a good thing, since there could be multiple celebrations each year.  I choose 8.3141 J/molxK mostly because it is my mom's birthday.  If you want you can choose 1/9 to be in kcal/molxK and so on. 

e Day (2/7):

This day would just be irrational, but it is used in calculating compound interest and other important exponential trends.  Here is a good description of it's application.

2-Day (Now):

What better day to celebrate than the day you are living right now.  Let this be the best day you have had in the last 24 hours!  If it happens to be one of the above days, even better.  If not, find something to celebrate, even if it is as simple as seeing the sun, talking to a friend, or just one more chance  to experience a day on Earth (or near Earth, sorry astronauts). 


If you have other good ideas for days to celebrate, leave them in the comments section!

Keep Smiling!

Be Awesome...

You may have seen the video of the kid dressed as a president giving the country a pep-talk. If not, you can see it here.  It is cute, funny, and you can help but smile when his take home advice, to put it simply, is "Be Awesome."

Recently I came across a short article about Amoxicillin and in it was a quote from Alexander Flemming, the discoverer of Penicillin, the parent molecule to Amoxicillin.

“When I woke up just after dawn on September 28, 1928, I certainly didn’t plan to revolutionize all medicine by discovering the world’s first antibiotic, or bacteria killer. . . but I suppose that was exactly what I did.”
 
I often think about the fact that it took Michelangelo roughly four years to paint the Sistine Chapel.  The mastery, artistry, and effort to accomplish such a thing is outstanding and we have been able to bask in its beauty for centuries.  A chemist might spend as much time running reactions and making bonds to produce a drug or molecule.  The difference is, we never get to see the product.  To have a pill of Amoxicillin in your hand is to be in the presence of a billion little Sistine Chapels that have the benefit of being beautiful and purposeful in stopping bacteria.

Wonder in Discovery:

Now, some might claim that Amoxicillin is a derivative of penicillin, and penicillin was made by a fungus not a human. There is only ONE Sistine Chapel, and it was made solely by a human.  Maybe it is not a fair comparison, but it should still lead to wonder and awe, even if we can never lay back and take in the vision of these molecules.  Then again, the dyes and pigments on the ceiling of the Sistine Chapel are chemicals too.  Today researchers can design pigments to turn off an on with electrical current. We can sit back and read about the Sistine Chapel on our Kindle or Nook. All this because some pioneers designed molecules that took years to make and test bond by bond (brush stroke by brush stroke) until they were a modern masterpiece.

What will be the next game-changing discovery?  Will it be from slightly tweaking what was made before?  Will it be the culmination of a life long search? Or, will it be the unexpected that was noticed by the prepared individual?

August Kekule' (who described the structure of benzene) stated in 1858, "One cannot explore new countries in express trains, nor will the study of even the best textbooks qualify a man to become a discoverer. Whoever is content to follow well-laid promenades until he reaches some pleasant eminence frequented by tourists, may, by striking into the thickets, gather some forgotten flower; or if cryptograms, mosses and lichens satisfy him he may even bring home a well-filled vasculum; but anything essentially new he will not find."

He goes on to say that you must walk in the footsteps of those who went before you and upon understanding how they made it to that place, be ready for the opportunity to, "perceive where the foot of a further pioneer may find solid ground."

-From a translation printed in the Journal of Chemical Education 1958, 35, 21-23.

As Dr. Niel deGrasse Tyson suggests, we don't even know what field that stepping stone will come from:

You might be the next pioneer, if you are ready.

"Luck is what happens when preparation meets opportunity." -Seneca

Ripe for a Revisit

I was skimming Scientific American the other day and came across this video regarding ripening fruit with powdered ethylene.
 
You will have to click on the link to view the video since it would not embed on the page, sorry.

Now, as I discussed on one of the original posts for this blog, ethylene is a gas  and a natural plant hormone used for ripening fruit.  I was a bit thrown off by the  video calling it "powdered ethylene" since compressing this gas to a solid would not be a trivial feat without being very cold or under immense pressure. Last week's post discussed that propane must be at -44 °F to even become a liquid, and ethylene is even smaller than that with two carbon atoms and four hydrogen atoms C2H4.

I did a little digging and found that the group traps the ethylene gas in a solid material made from starch.  This porous material allows the ethylene to work its way out of the solid matrix slowly and eventually fill the space surrounding it (like the shipping container with the fruit). Here is a link to the article.

It is still an interesting idea.  The material can be measured easily as a powder and it gives a slow release of ethylene in transit. This way that the food arrives ripe at a grocery store rather than having to be forcibly ripened on site.  I just wish they were a little more clear that it is not solid ethylene.

I don't know if it will catch on, but there is nothing like a ripe Mexican tomato in the depths of Minnesota January.

Time for Grillin'

Brr, it's cold out there!

Here is what my car thermometer the other morning in Northern Minnesota:

Yes, that says -10 degrees Fahrenheit.  I left this cold place for the balmy +1 °F that day. After I left, they dropped to around -30 °F.  Other than bolstering the bragging rights of Minnesotans, this cold reminded me about a fun trick my friend Mike sent me back around when I started the blog.  He is a much more seasoned and frequent social media type. He blogs for Massachusetts General Hospital,  you can check him out on twitter at @MDMorrison82

His trick was about checking the level of the a propane tank with warm water.  If you pour a glass of warm water down the side, the propane will conduct the heat away and you can find the level by feeling where the metal becomes cold.  Pretty cool!  Here is an example.

There are some other ways, such as little thermostats you can buy at the store or the traditional shake method, but the warm water is quick and easy. You could always take the straightforward route and buy a pressure gauge to put between the tank and your grill, but that may just be too logical. Here is a good summary of methods available online.

Can I Grill?

The pressing question is, can you still grill at -10 °F?  If you ignore the time to heat the metal, not freeze your hands to the utensils and to get food to a proper temperature, you may still be able to grill!   It might be a challenge to get that propane to ignite, but there should still be pressure in the tank.  People in most other parts of the country would never consider such things, but there is a point in Minnesota, where all grilling will likely cease.


Propane is a small hydrocarbon.  Essentially three carbon atoms and eight hydrogen atoms C3H8. Since it is so small and has little polarity, it has a very very low freezing and boiling point.  The measured boiling point of propane is -44 °F, that means at or below that temperature at atmospheric pressure, propane is happily a liquid.  Part of the reason propane is in tanks, is that it is pressurized to a liquid and vaporizes to a gas once pressure is released (hence it is a gas when it comes out of the burners).  Temperatures below -44 °F will result in the propane not having enough energy to become a gas and therefore no pressure at the burner.  Now, almost anywhere else, this would never be an issue, but as we know in the Great North Woods, -44 degrees is definitely possible.

Looks like International falls may be out of luck for two months of the year!

Embarrass, MN has it even worse!

How can I cook in the winter?

Various camping burners actually run the gas line through the heating zone to vaporize the gas before it gets to the burner.  This is because you are typically burning a fuel that needs much higher temperatures to build up pressure.  Back when I did a lot of camping, I bought this MSR Dragonfly stove, and it was a pretty nice setup. It is lightweight and since the pump is on the bottle, you can avoid spills. One that a troop I worked with had the Coleman 533. This has the burner attached to the bottle, but is a robust little stove. You can see the brass pipe running across the top to heat the fuel in the picture below.
 

Don't worry hunny, it's OK...

So if you "forgot" to put the grill away last fall, just tell your spouse that you were waiting for the proper time to test the physical properties of hydrocarbons by checking the boiling point of propane. The warm water trick probably will not work if the water freezes almost instantly at -10 °F though.

For a bit of extra information, the boiling point of butane, having only ONE MORE carbon atom and two more hydrogen atoms C4H10, jumps dramatically to about +30 °F, making lighting that cigarette even more troublesome in the winter.  Perhaps it would be a good New Year's resolution to quit anyway.

3D Musings

I was listening to a news blurb about 3D Televisions recently, and I began musing about the three dimensional world.  Most of us have a general understanding of dimensions from high school geometry.  Zero dimension is a point, one dimension is a line, two dimensions constitute a plane, and three dimensions has depth x, y, z if you are using a Cartesian coordinate system. 

If I asked you how many dimensions we live in, you might say 3 or maybe 4 if you want to be spry.  Perhaps you are a follower of string theory, wherefore you will give some unbelievable number. As stated on Season 1, Episode 1 of  The Big Bang Theory

Leonard: At least I didn’t have to invent 26 dimensions just to make the math come out.
Sheldon: I didn’t have to invent them. They’re there.
Leonard: In what universe?
Sheldon: In all of them. That’s the point.

Technically we live in a 3D world. Though, I am starting to think we are in a 3D world but confined to a primarily 2D plane that happens to have topography.  Yes the Earth is roughly a sphere, but human experience is basically a plane.  Regarding the other type of planes, we do go up-and down, but we always return to our pseudo-3D existence. This lead me to muse (hence the title of this post) about what things actually experience true three dimensions.

Minute Physics tells us how we know one of them.

But that is about it. Molecules will expand in 3D by diffusion. I am not sure where limit lies.  There must be some relationship between size and mass of an object for when it falls prey to the effects of gravity. Perhaps astronauts can fall into this category also, free motion in any of the space around them. Those of us who are earth-bound are gravitationally confined to this flat life.  Our cells are attached to us.  The enzymes and organelles in our cells are confined by microtubules. It is the molecules that swirl and spin and flitter about that get to experience three dimensions. 

It is one of the great challenges of chemists and chemistry students to be able to think of structures devoid of dimensional limitations.  We think in this pseudo-3D fashion and often are constrained to a 2D piece of paper for exams and notes.  Computer modelling has been a big advancement in helping to understand this 3D nature of molecules. 

Here is a model of the simple sugar glucose.  Imagine all the ways you could draw this in 2D when rotating it in 3D!

Many people are working on showing how molecules interact in 3D as a method for finding new drugs and understanding life processes. Here is a video I found on YouTube of a drug binding with a protein.  I couldn't find a reference to tell you more about it, but it is a good depiction of what pharmaceutical companies and scientists are now doing to understand the minutest interactions within the body.

Long before we had this understanding, Albert Einstein thought about this problem.  I don't know what his particular thought experiment was specifically.  In my words, he observed that small particles that should be confined to our pseudo-3D world like dust and pollen would move.  This suggested there were even smaller particles out there interacting with them.  Again, I will turn to Minute Physics to demonstrate.

So, as you go for a walk, climb a tree, or take a flight this month, think about the fact that you are living in a limited three dimensional world.  Even the lightest snowflake must fall to the ground.

If I had you convinced that molecules have it easy, remember that even they (except maybe helium) are confined to our atmosphere and don't get to just float off into space. So much for 3D.  Maybe that is why we dream of 26 dimensions.

One final note, here are how 3D TVs work!

http://www.popsci.com/gadgets/article/2010-01/its-about-time-3-d-comes-home

http://www.wired.com/gadgetlab/2009/10/3d-tv-explainer/