Decorate Your Terpene Tree

Decorate Your Terpene Tree

Many of my favorite natural products seem to come to the forefront of my mind this time of year.  Molecules such as pinene (pine), thymol (thyme), carvone (caraway), carvacrol (oregano), menthol (mint) play an important role in making the season what it is.  

                                                        pinene       carvone        thymol          carvacrol         menthol

 

Each of these molecules is a type of terpene.  They are all produced with the biological form if the molecule isoprene is polymerized (I have discussed polymers before).  Technically terpenes are all dimers, made of two of these molecules. The molecule reacts with itself and then in some form of cascade reaction, ends up in the approximate shape of the molecules above.  Notice how they all have ten carbons!  They all come from the same basic building blocks. The natural starting material is thought to be geranyl pyrophosphate.  This molecule can cyclize many ways to produce reactive intermediates.  The pyrophosphate is essentially a natural "trigger" which activates the molecule to cyclize.  

Below are a few known and proposed synthetic routes.  My new personal favorite terpene (and personally proposed) mechanism is the last one.  It generates a constituent of black pepper and a molecule found in Norway spruce.  It is also might have some special significance to some folks I know in the Pacific Northwest.

Color Code:  

green = isoprene units

red = terpene connection

blue = new bond formed to generate shape

black = "decorations" usually from water molecules

Depending on what organism makes the molecule, it controls this reaction to generate the shape it wants.  This critter then uses enzymes to "decorate" the product with other functional groups. I believe this is actually called postsynthetic modification.  I prefer to call it decorating your terpene with functional groups.  This produces everything from pheromones, many decicious oils we use in cooking, and even that great smell of pine in the room.

I liken this to the many houses with Christmas trees.  Everyone picks their tree shape.  Some are wide, some are tall, and some have a few missing branches.  Many houses have similar shaped trees, but every home puts on different ornaments to make it truly their own.

To all of those out there decorating actual Christmas trees, Merry Christmas!

P.s. I relied a great deal on Wikipedia today for the links.  They are a non-profit organization that has become a main source for much of the electronic information out there.  It appears from the last few days of searching that are currently fundraising, please support them if you wish.

Also, here are some primary literature sources that I have been reading.  Only a few are public access, so it might be difficult to get to for some folks.

"Turpenoids: Lower"

Croteau, R.; Satterwhite, D. M.; Wheeler, C. J.; Felton, N. M. "Biosynthesis of monoterpenes. Stereochemistry of the enzymatic cyclizations of geranyl pyrophosphate to (+)-alpha-pinene and (-)-beta-pinene." J. Biol. Chem. 1989, 264, 2075-80.

Gambliel, G. and Croteau, R. "Pinene cyclases I and II. Two enzymes from sage (Salvia officinalis) which catalyze stereospecific cyclizations of geranyl pyrophosphate to monoterpene olefins of opposite configuration." J. Biol. Chem. 1984, 259, 740-748.

http://www.sciencedirect.com/science/article/pii/S003194220600344X 

 

The North Wind Is Blowing

Last week was a wake-up call that I live in Minnesota.

 Winter is a fact of life and with it comes many considerations like "What shovel should I buy?" and "How long can I wait to put up Christmas lights?" Today though, I would like to address the other two considerations that nag us every year:

1. What sidewalk salt should I use?
2. What antifreeze should I use?

What's it made of?

Salts:  So, we throw around the word "salt" a lot.  Sea salt, table salt, salt of the earth, but really there are many types of salts.  Salt is a word that describes an ionic compound.  Now, this in itself may be another term, but ionic compound just stands for a thing that is made up of parts with charges.  These can be atoms or molecules themselves.  One of the parts has extra electrons and is negatively charged.  This is the anion. The other is missing some electrons and is positively charged.  This is called a cation. 

I have made a diagram to help YUMMY:

The key thing about a salt is that when put in water it will dissociate or separate into the two charged parts.  Here is another description using dogs to demonstrate (super cute).

Table salt is made of sodium (Na) and chloride (Cl), but that is one of many salts.  The salt used by the DOT is typically calcium chloride  CaCl2.  Since calcium has two positive charges it needs two negatively charged chloride ions to be neutral.  Sea salt is just salts from the ocean.  It has all kinds of cations and anions in it.  Sometimes magnesium (Mg) as a cation and sometimes bromine (Br) as anions.  A great deal of it is still sodium chloride, but it is not as pure as the table salt in your shaker.

Antifreeze: Now we will discuss why salt stops water from freezing or melts ice in a bit, but the term antifreeze has little to do with the process that the salts are doing.  Antifreeze is really just a different molecule altogether that can be used to prevent water from freezing, but often is just used by itself to be a liquid that will not freeze at low temperature.  The molecules most often employed are ethylene glycol and propylene glycol.  Glycol is a term for molecules that have neighboring alcohol groups on them otherwise known as 1,2-diols (see below).  The presence of these groups on small molecules (ethylene and propylene) mean that the freezing point is very low and the substance can dissolve in water very well.

How does it work?

Salt: Salts work to break up ice or prevent water from freezing by a process called Freezing Point Depression.  That seems like a logical name.  In essence, each ion dissolved in water helps to disrupt the ability of the water to freeze at its normal temperature.  The more ions, the lower the freezing point.  One sodium chloride provides two ions, a whole handful of sodium chloride provides many ions, and water no longer freezes at 32 degrees F, but rather closer to -6 degrees F (0 C -> -20 C).  Calcium chloride, if you remember, has three ions and does an even better job.  Here is a link to a bunch of other possible salts and their properties.  One fun trick with kids is to make an ice cube stick to a string, or my favorite, Homemade Ice Cream!

Antifreeze: The not-freezing ability of antifreeze is mostly due to its interactions between molecules.  It is not water, so has fewer interactions and therefore takes longer to freeze.  Pure ethylene glycol freezes at about 9 degrees F and propylene glycol at -54 degrees F. Both are lower than water, and therefore keep flowing even in relatively cold weather.  (I should also note here that they boil at 387 F and 370 F respectively, way higher than water. Maybe I will revisit this next summer.)

So, Which should I Use? 

Salt: Here's where it depends. You just need more ions, so technically you can pick any salt.  You may need more sodium chloride than calcium chloride since there are fewer ions, but it also costs less. There are also "pet friendly" salts that use amine salts, but again, these are more expensive and often less effective because their ions are bigger and bigger. A 6.5 pound bottle of pet-friendly salt is about the same cost as a 20 pound bag of a "chloride" salt.  Though typically prevent paws from drying and cracking, you could also just wipe down paws.  The ASPCA has some tips.
  

The one thing you might want to consider is vegetation and concrete.  Some salts can take a toll on both.  Here is a link that describes some considerations. Bigger ions are typically better, so Magnesium or Calcium chlorides are a little less corrosive to the driveway.

Antifreeze: 
Well, both work relatively well.  Most often you mix them with water, but the key factor to take into consideration is whether you have pets and kids around that might get into the pure antifreeze if unattended.  Though both can be toxic, ethylene glycol should be avoided if you are not attentive to your children or pets.  Ethylene glycol can be more dangerous to animals and kids because it has the added problem of tasting semi-sweet.  Dogs that get into a pool of it have a tendency to drink it all up, exposing themselves to a larger dose.  Propylene glycol is the safer alternative.  As it turns out, that one extra carbon changes the biochemical pathway for degradation. Ethylene glycol is processed by the body to glyoxylic acid and oxalic acid, both of which can harm the kidneys and other organs.

Instead of making a molecule called oxalic acid, propylene glycol degrades into lactic acid and pyruvic acid.  These two molecules are part of normal metabolism.  As a result, unless consumed in really high doses, propylene glycol is only mildly toxic.  Combining this with its good antifreeze properties, I think it might be a better choice for the money.  Because of this lower toxicity, it is also a main component of aircraft deicers and is in the electronic cigarettes that help people quit smoking.  Sometimes when deicing you might smell a sickly sweet smell in the cabin, that is a bit of the proplyene glycol getting pulled into the air handler.  Nothing to worry about!

Just ONE Carbon?

Yes indeed! One carbon can make the whole difference between being a toxic substance and one that can be productive.  In fact, there are several cases where it is not even an additional carbon, just the orientation of one carbon in the environment that can make something be a useful molecule (drug, flavor, scent) or something that can be harmful or stink.  Maybe that is a good metaphor for all of us when we are caught in snowstorm traffic or see someone with a plowed-in car.  It could be especially useful for those in public office these days. 

If It Were ONLY That Simple

Sorry for the gap in posts, as the semester has ramped up, my time for this activity has been siphoned toward other tasks.  In an effort to make up for this fact, I turned to the internet for a good quote. In a letter to George Washington on May 16, 1792, Thomas Jefferson wrote, "Delay is Preferable to Error." 

** Side-Note**  I thought this quote would be a good excuse for this delay in posting.  I wanted it to be just right. In finding this quote nearly everywhere on the internet, I have yet to figure out the context.  People seemed to have quoted it in law briefs, blogs, and nearly every quote site out there, but I don't know.  Construction of the White House (not known by that name at the time) was started.  Perhaps it was telling him to check-over the blueprints one more time to spare change-orders with the contractor, but that is just my guess.  I am curious. SO, if anyone of you has some insight, please submit it in the comments.

Back to the blog:

"Plastics," says Mr. McGuire. "There is a great future in Plastics."  Even in 1967 that was great advice.  It is like saying, "it's the economy stupid" and then not talking about the innumerable minutia that drive the economy.    Assuming one person, business, or theory is the perfect way to fix an economy is like saying the only plastic is Bakelite!  Oh, but we have come so far from that wonder material of art deco fame. We have plastics that glow, plastics that blow, plastics that flow, and even plastics that mow.  That said, maybe Bakelite is a good place to start, it only gets more exciting from there.

Good Enough to Eat Off Of...

Bakelite is one of those materials that seems so innocuous, but it changed the world as we know it.  It was developed by Leo Bakeland in 1907 and was one of the first easily moldable thermoset plastics.  This is a great article describing the history. It was the first molecule named by the American Chemical Society as a national chemical landmark in 1993.   Now, the essence of this discovery is that one could shape it into nearly any shape and when it was done reacting, it was "chemical resistant" (did not dissolve with solvents or react with many types of chemicals) and a good electrical insulator. Prior to its invention, almost all transmission lines used glass or ceramic insulators.  One bad hail storm and... smash!

Here is an excerpt from the book Napoleon's Buttons: (Napoleons Buttons By Le Couteur, Penny M./ Burreson, Jay (Google Affiliate Ad))



It also allowed for other objects to be made of different shapes and sizes. This made the perfect material for knife handles, rotary telephones, and most importantly jewelry!

Bakelite gets its properties from reacting phenols (benzene rings attached to oxygen and hydrogen) with formaldehyde.  This links the molecules together in long chains or polymers "many-units" a term often used synonymously with "plastic," but it is a bit more nuanced.  By linking these molecules with different properties, you get a connected network of very stable molecules, with a flexible linker.


This concept, linking molecules of one type with molecules that have different physical properties is something used even to this day.  Combining properties of some molecules with others (an approach currently being used to develop the next generation of solar cells, solar cells, and light emitting diodes as well as new filters) gives access to a multitude of properties that are not available to either of the molecules independently.

There current polymers have yet to gain the same properties as the current state-of-the-art materials in some fields.  If Bakelite was any indication of the possibilities unleashed once that point is reached, we are in for a treat in the next 50 years.  For polymers (and perhaps even the economy), there is still much work to be done, but once we get it figured out we have a bright future ahead.

Now You See It; Now You Don't!

The phrase, "Science is Magic" is one that needs to show itself to the door.  This Target ad puts it right out there in an effort to get you to buy Graphic Tees and Converse One Star Tennies! Despite this, I personally love the fact that target is selling stuff with science.  I much prefer that to them selling things with teen celebrities.  The Van De Graff generator in the ad is a nice addition, especially since I have had friends get married under the largest VDG in the world at the Museum of Science in Boston. The problem is that despite science being MAGICAL, it is not MAGIC. It is not illusion, science is testable and provable.  It is true that often science will be surprising, make you think, change your worldview, and so much more.  When it does this, it feels like watching magic. Those are the best parts of science,
and today's post will touch on one of those topics.

It's All Smoke and Mirrors:

We have all seen some variation of the magic trick where the assistant drops into a covered box from the top but is really going behind a mirror.  When the sheet is removed, POOF, no person, because the mirror is showing you a different part of the stage.  Though we don't see the assistant, they are still there. Something, in this case the mirror, is covering them up and obscuring them from view.  I found directions to make your own magic mirror box online, or this magic kit (right) probably even comes with its own mirror box.  I bring this up, because as we look around this fall we are seeing the magical side of nature, the changing color of leaves.  But wait! See those colorful leaves changing outside?  That is your mirror of science.  The orange is always there, but the green fades away!

Leaves are the energy factories of the tree.  Sunlight hits the leaves and starts a chain reaction that ends with the production of glucose.  We know this process as photosynthesis:

"Photosynthesis" By: TMBG

The biochemical process is relatively complex, but the important note is that visible light enters the leaf and promotes an electron to a higher energy.  This is not the easiest process, light hits things all of the time and does not always move electrons.  Humans have designed materials that are capable of this process, solar cells.  The most efficient human-made solar cells have about 40% efficiency.  It is hard to compare that to plants, because solar cells do not make corn, but some people have tried to quantify the process and found that solar cells can be more than 10 times as efficient as plants.  That said, solar cells don't come the size of a seed and grow themselves into a power plant (no pun intended) either!  

In order for the plant to use light to promote an electron, a specialized molecule has developed called chlorophyll. There are many variations on chlorophyll, but they all have a porphyrin center that cradles a magnesium ion.  

 

Depending on what other groups are around the porphyrin, the chlorophyll absorbs light of varying wavelengths.  The wavelength of light determines its color, and anything not absorbed is reflected. Chlorophyll does not absorb well in the 500-600 nanometer (nm) range.  As a result, plants are green! Because of its complexity, the second the tree starts to limit the nutrient supply to the leaves, chlorophyll is one of the first molecules to degrade.  What is left behind are carotenoids and flavenoids, which make up the yellow, oranges and reds of the fall foliage. Carotenoids are what give pumpkins, squash, and tomatoes their color as well. 

These molecules are always there, they just don't get to show off until the chlorophyll degrades. It is MAGICAL!  Eventually, they too degrade, which is why leaves turn brown before too long. Want to see this at home?  Here is a way to separate all of the molecules with items you can find around the house as well as a few leaves from the yard (Leaf Chromatography).  If you want to jump to the result before you try, here is a video from YouTube:

If you are looking outside the next several weeks, you will see that chlorophyll degrade.  Now you see it, in a month you don't! That's way better than magic any day.

Other Materials:

While I was making this post, I stumbled upon a few other good articles.  Enjoy:

Is Fall really fall, or more like Shove?

Is Science Magic?

Mr. Wizard Clock Reaction - Truly Magical (1st Section of the Episode)

Ripe for Discussion

I have been picking tomatoes out of the garden a little before they are ripe this year.  This is in part because the second they ripen, the chipmunks find them.  The other reason is that I am more likely to cook with them if they are ready for consumption in the kitchen. Picking them a little early lets them last longer on the counter. 

As I was harvesting recently, it occurred to me that fruit ripening might be a good topic for Try Some Science (TSS).  I am by no means the first to expound upon this online.  The topic has been approached to prove the old adage, "One bad apple spoils the whole bunch" (here is an article from Cell as well). Ripening has also been discussed on other “sciency” blogs, blogs, articles, and articles.  The Osmonds even tried to refute the idea in the 70's (definitely check out this song). All of this is perfect, since the semester is about to start, and time is fleeting. Therefore, I will use this post as a quick summary and resource to help guide your own investigation into how a little science can save you some dough (or at least some bananas).

On a global scale, controlling the ripening of fruit is the backbone of any industry dependent on produce.  In the depths of a Minnesota winter, one can still find a banana in the grocery store.  We can assume it was not imported from Wisconsin!  In fact, over $1.6 Billion, yes billion, worth of fresh bananas were imported to the U.S. in 2011. Therefore, it had to be harvested at the proper time in Costa Rica or Ecuador so that it could be shipped, clear customs, travel to Minnesota and get distributed to each grocery store without rotting.  Some fruits do this better than others, and controlling that process can make the difference between making millions or losing millions of dollars and fruit.  If you look at the origins of your produce (read labels), you can almost watch the harvest move further and further into the southern hemisphere as we get deeper and deeper into winter.

Let’s Talk:

The foundation for a ripe and fruitful life is communication, whether it is with your spouse or between a bunch of apples. From bacteria to bananas, there is a complex network of signaling that lets parts of a cell talk to other parts, cells talk to other cells, and organisms talk to other organisms. For instance, some bacterial will not become toxic until they sense a big enough population, this quorum sensing is a little scary and my be a good future TSS Topic. For fruit, the topic of today, the right mixture of signals starts a series of chemical signals which tell the fruit it should stop getting bigger and turn all of its filler to sugar. 

In many fruits, this means taking starch and chopping it up into little bits, typically sucrose.  Starch is a type of carbohydrate made of long chains of individual sugar molecules, kind of like a beaded string.  It is relatively flavorless (think raw potato).  Sucrose, on the other hand,  is only two of those sugars so it is tiny in comparison.  It interacts with the sweet spot on our taste buds and "lights up" our brain.  A ripe apple is full of sucrose.  Chop sucrose up and you get the old favorites glucose (table sugar) and fructose (corn syrup).  I know fructose is controversial, so just ignore I wrote it. I can come back to that another time on TSS. If you want to prepare, here is a good link.  

 
We all probably have some trigger that induces changes. For me, the smell of a campfire sets off a series of chemical reactions that lowers my blood pressure and makes me hungry for s'mores. For some, the taste of a good cannoli might bring you back to sitting with friends in Boston's North End. For fruit, ethylene does the job. This small molecule only contains two carbon atoms and four hydrogen atoms. Few organic molecules can be made that are smaller. It exists as a gas under normal conditions, and this makes sense.  If you are a fruit and want to "talk" to your neighbors, it is hard to get up and walk to them, so you give off a gas that can spread all around you.  When other fruits "sense" the gas, it triggers the chemical processes for ripening in them as well.  It is astounding that this tiny thing can be such a powerful trigger.  You can see this for yourself (or your kids) with this simple experiment you can do at home.

                                                  .

So, how do we control this gaseous love letter between fruits?  It depends if you want to manipulate it for ripening or against ripening. If you are trying to keep the apples on your counter or in your fridge from over ripening, there are now some products like these vegetable bags (left) that are porous enough to let the ethylene diffuse out and not build up in the bags.  This approach can buy you some time.  If you want to quickly ripen your tomatoes or have a pear that you just must eat, place them in a paper bag with another ripening fruit.  This will concentrate the gas and help them ripen sooner. Happy medium, just don't put them all in a closed container, you are just asking for trouble. Maybe the best bet is to be patient.

There are some other options.  On a large scale, sometimes fruit will be shipped with potassium permanganate.  This chemical reacts with ethylene to oxidize it (add oxygen), and lower the concentration in the air.  This assumes that the ethylene will have to diffuse to the chemical.  It is logistically difficult, since you might have to wrap each fruit individually.  I did find this cute product the BluApple which is a permanganate packet in a plastic apple.   It is still subject to the diffusion problem above; so I wonder if it would be truly effective.  I do, however, admire the wittiness of the product.  Maybe they should change their slogan to "One good apple, saves the bushel"? Either way, they have an excellent FAQ page that is very thorough on the chemistry (they even do the half-reactions).  Please just put your marketing shields up.  One of the best methods is keeping fruits cold.  Colder temps slow down most metabolic processes, including ripening. One big problem is that most people keep things cold in a refrigerator, a closed container, where the ethylene can also build up. Good timing and cooled shipping is one of the most effective ways we get strawberries from California in September.

There are many things that can communicate the ripening of fruit.  Since this blog is Try some science, I will not go into the complex signaling pathways, but many people study the biochemistry of fruits to determine what  pathways can be manipulated to control the rates of ripening.  The Minnesota apple harvest is early this year in part because of the nutty winter last year.  Warm late winter and a late spring frost nearly wiped out many of the orchards.  If apple picking is a fall tradition, you might want to start early.  I just juiced a liter of grapes from my trellis, at least two weeks earlier than last year.  Now I just need to communicate to the racoons that they are not welcome to the feast.

Final Note:


Speaking of nutty, I hope you all enjoy the beginning of fall.  Just remember, if you place a bunch of fruits in a confined space, even a few bad apples can spoil the whole thing.  So please vote a little permanganate in this year or we might all go bananas!

Capitol Building by Peter Griffin

Orange You Glad?

One of the best ways to get some science in your life is to always ask, "What's in that?"  From food to fragrance and soap to nuts, asking this question will reveal a lot about what you come in contact with each and every day.

Today's topic:

Orange Cleaners - A Lesson On Origin

By no means am I a chemo-phobe.  I believe every chemical has its place.  Some of them have a place in my food, and others have a place written in a textbook never to come in contact with man, beast, or plant. Understanding the origin, properties, and destination of each chemical helps to make that decision easier.  Not knowing these things can leave you the target of clever marketers and late night infomercials that want you to believe that origin is the difference between good and bad, safe and dangerous.

Here's a great YouTube example...

"It's all natural and made from pure orange oil!" 

Let's dissect that statement for a moment.   

All Natural:

All Natural sounds great.  Something made from nature must be good for you.  It has a soothing ring like Organic (not in the chemical sense) and Sustainable.  It may make you think of a butterfly landing on a delicate orange blossom bathed in the Florida sun. That warm feeling, however, should be chilled by the fact that some of the most toxic substances in the world are All Natural.  Uranium, lead, and arsenic are a few naturally occurring elements.  The family of compounds that makes poison ivy itchy, urshiols, is from nature.  Spider and snake venom are all natural.  In contrast, some of the most useful substances are also from nature.  One of the most effective cancer drugs, taxol, was isolated from the pacific yew tree.  The best smelling fragrances, such as linalool from lavender, are made by nature.  The snake venom I mentioned above might also be beneficial someday.  Yes, oil from oranges can make a good wood-cleaner, but Try Some Science (TSS) is about understanding, not just following warm feelings.  Origin is important, but it doesn't inherently make it good...or bad.

Made from pure orange oil:

Oranges are plants; pure plant extracts are good.  Cleaning with something pure from a plant should be good for us.  We should all clean with turpentine.  If that late night infomercial was selling turpentine, you might be a little hesitant to run to the phone and grab your wallet.  I can see it now, "But wait, call now and you can get two bottles of turpentine, It's all natural and made from pine trees!" Yes, the solvent of Adam Sandler lore is made from pine trees.  It is harvested from some varieties or extracted in the production of paper (this might be a good future TSS topic), but it is a natural product.  Your grandpa may have used it to thin paint or degrease the carburetor, but isn't that essentially what the orange stuff is claiming?  Alright, you know they are different, it isn't just marketing, nobody would use turpentine on their furniture.  Or would they (note pine essential oil)?

Lets Compare:

They are very similar molecules.  Both are hydrocarbons (molecules containing only hydrogen and carbon atoms) and even have the same molecular formula C10H16, which means they have ten carbon and sixteen hydrogen atoms.  They melt and boil at nearly the same temperature and have similar solubility.  If you rub one on a cabinet, water is sure to slide off because they repel each other like oil and water (because they are oil and water!).

Much of this similarity is because they belong to a family of molecules called terpenes.  Terpenes are versatile building blocks for many natural products.  The details of these are too great for this post, but I might revisit that in the future.

Should I use it or not?

Sure! Use it if you want to keep things clean and smelling like oranges.  Keep in mind that it is not orange juice,  raw peel, pulp, or seeds; it is a highly purified and refined flammable oil that happens to come from the skin of oranges.  It does what it is advertised to do because it is an organic (this time in the chemical sense) molecule that contains only carbon and hydrogen and therefore has properties similar to that type of molecule.  Treat it like you would treat turpentine, another flammable oil, and you will be using some science and some common sense.

There are a lot of companies out there marketing these products, this blog is here to help you become an educated consumer. I don't want to advocate for one thing or another, just to help you in your own decision making process.

Take Home Message:

For now, let's say we tried some science and really got to know what was in our All Natural cleaning polish.

Orange you glad you asked?

Welcome!

Welcome to my newest adventure, Try Some Science, a site that wants you to connect science to your daily life.  I am an assistant professor of organic chemistry.  I make it a daily goal to make what is perceived as one of the most challenging subjects for undergraduate students a topic that they can not only learn, but one that they recognize is relevant to their day-to-day interaction with others and the world around them.

I hope this blog can introduce you to something you may not have known or may never have tried, while learning a little science along the way.  Most of the content should be of general appeal, but I have a few personal favorites that might be of local interest along the way.  Thank you for taking the time to check the site out, and enjoy.

Sincerely,
Eric