Eye Spy

Every day we awaken to the world around us, opening our eyes to see what the day may bring. But have you ever thought about how we’re able to see all that the world around us has to offer. How is it that the light reflecting off of objects is translated in our brains to produce the images we see in our head?

Although it may seem rather complex, vision can be broken down into several major steps. First, light enter the pupil, is focused by the lens, and then hits the retina, a surface covered in light-sensitive detectors. These detectors, known as rods and cones, convert the light into electrical impulses which are then transmitted to the brain via brain nerves. It is from this array of impulses that the brain then creates a picture, enabling us to see.

Isomerization of Retinal

The chemistry of vision lies in the photoreceptor cells lining the retina. Within the retina, there are 7 million cones cells, which provide color information and sharpness, while there are 120 million rods cells which are responsible for detecting white light and providing most of our night vision. Just under the surface of rod cells lie pigment discs which contain proteins bound to the molecule 11-cis-retinal. Upon absorption of light, 11-cis-retinal isomerizes into all-trans-retinal. 

Courtesy of chemistry.wustl.edu

When retinal changes shape, it causes a change in the shape of the protein it sits within, called opsin. Together, 11-cis-retinal and opsin are known as rhodopsin.  Upon isomerization to all-trans-retinal, the complex is known as bathorhodopsin. In order to fit properly in the protein, the retinal molecule has to twist into an unfavorable shape. Due to this instability, bathorhodopsin rapidly changes its shape and expels the retinal molecule from it. 

Just before the molecule leaves the protein (now called metarhodopsin II), the protein complexes with another protein, transducing, which then activates the enzyme photodiesterase. Photodiesterase leads to the hydrolysis of cyclic GMP, a molecule required to open Na⁺ channels in the cells membrane. With closed Na⁺ channels, the cell develops a difference in charge across it’s cell membrane, producing an electrical signal, which can then be sent to the brain and create vision!

Courtesy of RSC Publishing

In cone cells, the process is mostly the same. There are three different cone cells within the body, responsible for perceiving red, blue, and green. Each of these different cells contains a different protein bound to 11-cis-retinal. Given the number and type of cone cells activated by incoming light, the brain is able to decipher what images we are looking at. 

Just think, all of this is happening millions of times every second! The body is certainly an amazing thing!

Cool Videos about the Chemistry of Vision:

1. http://www.youtube.com/watch?v=r6v21W8zRIw
2. http://www.youtube.com/watch?v=Fm45A4yjmvo

References:

1. http://chemwiki.ucdavis.edu/Biological_Chemistry/Photoreceptors/Chemistry_of_Vision
2. http://www.chemistry.wustl.edu/~edudev/LabTutorials/Vision/Vision.html

OLEDs: Brightening the World of Tomorrow

In today’s technological world, electronic devices continue to get smaller and thinner, including televisions. From the older days of rear projection TVs to today’s plethora of plasma, LCD (liquid crystal display), LED (light-emitting diodes), who knew it could be so difficult to buy a TV! One of the more recent developments in this area is the use of devices known as OLEDs, which stands for Organic Light Emitting Diodes. These newer devices can provide brighter, crisper displays than the more conventional systems while consuming less power. In other words, you can have your cake and eat it too!

Courtesy of howstuffworks.com

Internally, although somewhat complicated, OLED’s are similar to batteries (so hopefully you had a chance to read last week’s post).  The entire device is made up of a substrate, an anode, a conductive layer, an emissive layer, and a cathode. The substrate is simply the backing which supports the device and is typically made out of glass, plastic or foil. The anode, which is transparent, is the site where reduction occurs, a process in which electrons are removed from the conductive layer, creating “positive holes”. The conductive layer is made up of organic molecules which help transfer the formed positive holes from the anode to the emissive layer. Similar to the conductive layer, the emissive layer is also made up of organic molecules which, in contrast to the conductive layer, transport electrons from the cathode into the conductive layer. The cathode completes the system and is responsible for places electrons back into the system. But how does this process create the light we see?

When an OLED is attached to a power supply, electrons begin to flow from the cathode towards the anode, passing through the emissive layer. Simultaneously, electrons are removed from the conductive layer at the anode, sending positive holes back towards the cathode. When the electrons and positive holes meet in the middle at the interface of the emissive and conductive layers, energy is released in the form of light.

The particular color of light emitted depends on the organic molecule used in the emissive layer (some examples are shown below). The intensity of the light emitted can also easily be increased or decreased by changing the amount of current applied to the system. The more current, the brighter the light!

Courtesy of howstuffworks.com

Today there are a few different types of OLEDs which vary slightly in their construction, each of which is suited for a particular use. These categories include passive-matrix OLEDs (phones and MP3 players), Active-matrix OLEDs (computer monitors and TVs), transparent OLEDs (heads-up displays), top-emitting OLEDs (smart cards), foldable OLEDs (smart clothing), white OLEDs (commercial lighting). Some of constructions of these different OLED types are shown in adjacent image.

While OLED’s are thinner, lighter, brighter, more flexible, and consume less power, the manufacturing process of them remains expensive, limiting their use. As the technology of OLED’s continues to advance, this technology will become increasingly prevalent, from phones, to TVs, even to car lighting!

References:

• http://www.konicaminolta.com/about/research/oled/about/index.html
• http://electronics.howstuffworks.com/oled.htm
• http://en.wikipedia.org/wiki/OLED

Tools of the Trade: Chromatography

So…where were we? Oh yeah, Chrom-a, chrom-a, ah ah, Chromatography! (Yeah, I just made a Lady Gaga reference) When most chemicals are made, the crude reaction mixture typically contains some unwanted side products, unreacted starting material as well as many other chemicals involved in the reaction such as catalysts. In order to be used, these chemicals will have to be separated and purified from this crude mixture. This is where chromatography comes into play. Chromatography simply is a fancy-pants chemistry term for the act of separating a complex chemical mixture into its individual components, typically based on the polarity of the chemicals.

The polarity of a molecule is somewhat analogous to that of a regular metal magnet. Certain elements, like fluorine and oxygen, are greedy and do not like to share their electrons with other atoms (this is what chemists refer to as electronegativity). This means that the electrons in covalent bonds (bonds made by two atoms sharing electrons) tend to lie on the more electronegative atom. The uneven sharing causes a slight negative charge on the more electronegative atom (one pole of the “magnet”) and a slight positive charge on the other atom (the other pole of the “magnet”). In a broad sense, polar molecules tend to stick to other polar molecules and likewise for nonpolar molecules. This phenomenon is why oil (very nonpolar) and vinegar (polar) do not mix together.

Schematic of a Gas Chromatograph

All chromatography consists of a stationary phase and a mobile phase. The molecules that we are trying to separate stick to the stationary phase. Since each molecule has a specific polarity, they interact differently with the stationary phase. The variations in interactions cause different molecules in the mixture to move at different speeds through the system, which causes them to separate. The mobile phase serves to move all the molecules through the system.

 In the case of the gas chromatograph (GC), which was mentioned in my earlier post on mass spectroscopy, the mobile phase is a gas such as nitrogen, and the stationary phase is a tiny tube, called a column, lined with a thin polymer film. The GCMS instrument is extremely useful because the GC separates the mixture into individual components that can then be analyzed by the mass spectrometer. If the complex solution were put directly into the MS without separation, we would not be able to definitively determine what compounds were in the sample.

Source:

http://en.wikipedia.org/wiki/Chromatography

Feel the Electricity

Courtesy of nynewsdaily.com

Cell phones, flashlights, smoke detectors, cars, and iPods are all enabled by a technology which we take for granted in today’s age: batteries.  We use them every day, but what is it that makes batteries able to power the devices which illuminate the dark, send messages across the globe, and alert us of unseen dangers?

While batteries come in a wide variety of sizes and shapes, they all work by the same basic principle, known as an electrochemical process. Originally discovered in 1799 by the Italian physicist Count Alessandro Volta, the chemical reaction taking place involves the flow of electrons between two materials immersed in an electrolyte. More formally, these three parts are referred to as the anode (-), the cathode (+), and the electrolyte. These symbols may appear familiar to you if you’ve replaced a battery recently! 

Courtesy of http://media.tumblr.com/tumblr_loecuzgfyS1qf00w4.gif

In the battery, the anode and cathode, known as electrodes, are separated by a barrier which allows electric charge to flow between the two electrodes but prevents the two metal pieces from coming into contact. The medium through which the electrical charge travels is the electrolyte, a solution or paste filled with charged particles. Each type of battery contains a specific electrolyte.

When a battery is placed in a device, wires within the device now connect the anode and the cathode, making a complete circuit for electrons to flow between the two electrodes. At the anode, the metal surface loses electrons to form ions (charged atoms or molecules) which combine with other ions from the electrolyte, in a process known as oxidation (an example is given below in Equation 1).

                                                       Zn(s) -->  Zn²⁺(aq) + 2e^-                                           Eq. 1

The liberated electrons then decide to leave the negative and crowded party at the anode and make their way to the much more upbeat and positive shin-dig going on at the cathode. It is here that ions from the electrolyte combine with the released electrons in a process known as reduction (an example is given below in Equation 2).

                 2MnO₂ + 2e^- + 2NH₄Cl  --> Mn₂O₃ + 2NH₃ + H₂O + 2Cl^-                 Eq. 2

Courtesy of Lonestarlearning.com

A friendly pneumonic to remember these principles is "LEO the lion goes GER" for Loss of Electrons is Oxidation and Gain of Electrons is Reduction. The electrons produced from reduction and oxidation are the same ones that power your devices! 

Batteries eventually run out of power because there are a limited number of ions in the electrolyte solution. Once the ions are depleted, the reduction-oxidation reactions which cause the electrons to flow, can no longer occur. Rechargeable batteries work by running a current of electrons into the battery, reversing the cathode and anodes, and releasing ions back into the solution. Below are some of the common battery types and the materials that make them up.

Battery Type	Cathode	Anode	Electrolyte
Zinc-Carbon	Manganese Dioxide (MnO2)	Zinc	Ammonium Chloride (NH4Cl) or Zinc Chloride (ZnCl2)
Alkaline	Manganese Dioxide (MnO2)	Zinc Powder	Potassium Hydroxide (KOH/H2O)
Lithium-Ion	Lithium Cobalt Oxide (LiCoO2)	Carbon (C)	Lithium Hexaflurorphosphate (LiPF6)
Lead-Acid	Lead Dioxide (PbO)	Lead (Pb)	Sulfuric Acid (H2SO4/H2O)

The Fisker Karma, an electric car
(courtesy of Road & Track)

So next-time you put some new batteries into a device or charge your cell phone, think of all those electrons speeding through the wires as ions are formed and destroyed in the tug of war between cathode and anode. Who knew batteries could be so interesting!

References:

1. http://electronics.howstuffworks.com/everyday-tech/battery.htm
2. http://www.qrg.northwestern.edu/projects/vss/docs/power/2-how-do-batteries-work.html
3. http://en.wikipedia.org/wiki/Battery_(electricity)
4. http://www.tumblr.com/tagged/how+do+zinc+carbon+batteries+work

Tools of the Trade: Mass Spectrometry

So, you’re watching an episode of CSI Miami and after a series of bad puns, Horatio and the gang come across a mystery substance that they need identified. They then put a sample into a Magic Chemical Identifying Machine™. Two beeps and a boop later, they know exactly what the mystery chemical is. For once, this is not all Hollywood magic. The Magic Chemical Identifying Machine™ is actually two distinct machines linked together: a gas chromatograph and a mass spectrometer.

Today, we’ll focus on the mass spectrometer device (stay tuned for the chromatography post!). A mass spectrometer is an extremely sensitive device that can tell you the mass of charged particles called ions. Gaseous molecules enter the mass spectrometer, but they are neutral and unable to be detected. So how exactly does the mass spec. make neutral molecules into analyzable ions? With a handy-dandy electron beam of course! When the electrons from the electron beam hit the molecule, an additional electron is stripped from the molecule, which results in a +1 charge on the molecule.

Schematic of a typical mass spectrometer

The typical mass spectrometer uses an array of electrodes called a quadrupole. These electrodes are capable of generating very precise electric fields. The computer attached to the mass spectrometer makes the quadrupole rapidly sweep through different electric fields. At any moment in time, only one exact ion mass is capable of moving straight through the machine. All other masses are deflected harmlessly onto the walls of the device. When an ion hits the analyzer in the mass spectrometer, the small current produced is measured as a signal. By matching the time of impact with the electric field that would cause the impact (and using some clever physics), the computer is able to determine the mass of the ion.

But, wait a minute, how can this information be used to identify specific molecules? Recall the +1 ion generated by the handy-dandy electron beam (I’m quite sure that is the technical term). For most molecules, this “molecular ion” is very unstable. The unstable ion usually fragments into smaller, more stable ions. One might think that fragmentation is a bad thing, but in fact most molecules generate a “fingerprint” of fragment ions. By cross-referencing the fingerprint of the unknown with that of known compounds, we can identify the unknown compound. Now that Horatio knows what the unknown compound is, he can catch the killer and wrap up the case with a perfect one-liner.

Source: 

http://en.wikipedia.org/wiki/Mass_spectrometry

PTFE: Keeping Pans Slippery since 1961

From plastic bottles, to rubber tires, to the DNA in your cells, our world is full of compounds known as polymers. Polymers are a unique class of materials which are made up long chains of repeating structural units called monomers and are a subset of a larger family of molecules known as macromolecules. Last week when discussing sugars, I mentioned polysaccharides, which are in fact polymers chains of monomer sugar units!

Courtesy of wikipedia.com

If you’ve ever seen a cooking infomercial or been in the cooking section of a store, you’ve probably heard something called Teflon®. While Teflon® is the registered named used by DuPont™, the chemical itself is specifically called polytetrafluoroethylene. Breaking the name into its individual parts can help make sense of its structure: poly (many), tetra (four), fluoro (fluorine), ethylene (two carbons), and commonly its name is abbreviated PTFE.

A glitter/water mix rolling across a PTFE coated surface 
Courtesy of article.wn.com

Consisting of entirely carbon and fluorine (see above image), PTFE is a high molecular weight compound which is white solid at room temperature. As a material, PTFE is hydrophobic, meaning it is not wetted by water or water containing substances. From a qualitative point of view, this means that water simply rolls off of PTFE coatings without sticking (see right insert); giving the material its unique ability to keep pots and pans clean! For this reason, Teflon® is also commonly used as a lubricant in industrial equipment.

Courtesy of wikipedia.com

Like many scientific advances, PTFE was actually discovered by accident. While attempting to make new refrigerants, a scientist named Roy Plunkett noticed that the tetrafluoroethylene gas tank he was using would stop flowing before the gauge on the bottle read empty. After filling the bottle several times and noting this, he finally decided to saw open the bottle and see what was happening. Within it he discovered a waxy white material which was extremely slippery which had been created due to the high pressures in the bottle and the bottles iron metal which was acting as a catalyst for the chemical reaction. The technology was not applied to pan coatings for another 20 years when “The Happy Pan” hit the US market in 1961.

Greedy Fluorine

While it may seem scary that this compound which coats our pots and pans contains fluorine, a compound unfamiliar to many consumers, in reality, fluorine is what gives this material many of its unique and beneficial properties.  The carbon-fluorine bonds are polar meaning that the electrons which form the bond are not evenly distributed between carbon and fluorine.  As an element fluorine is extremely greedy with electrons, and as such it pulls the bonding electrons away from the carbon, bringing the two atoms closer together and forming the strong bond.  In fact, the carbon-fluorine bond is the strongest bond known in organic chemistry!

Due to this strength, carbon-fluorine compounds are generally unreactive, making it a great coating for pots and pans. If pans are heated above 500°F, the coating can begin to break down and pose some health effects. For reference, meat is typically fried around 400°F and most household oils will begin to smoke long before reaching the 500°F benchmark, so there’s no need to be alarmed!

Sources: 

1. http://en.wikipedia.org/wiki/Polymer
2. http://en.wikipedia.org/wiki/Polytetrafluoroethylene
3. http://www2.dupont.com/Teflon/en_US/index.html

Galactose, and Fructose, and Glucose...Oh My!

Courtesy of partycheap.com

Happy Halloween everyone! Given the holiday, this week’s topic will be the chemistry of candy. (We all love our candy!) From Snickers and M&M’s to caramel and Skittles; one of the key ingredients present in all of these is sugar. We know we love it, but what does this magical little molecule look like?

Courtesy of envirodad.com

Sugar is actually a general term used to refer to vast class sweet-flavored compounds utilized in food. Chemically, sugars are a member of the carbohydrate family. This means that they consist only of carbon, hydrogen, and oxygen, typically with a 1:1 ratio of carbon to H₂O (C_n(H₂O)_n hence the term carbohydrate). Different types of sugars can be extracted from various sources. The most familiar type of sugar (table sugar) is sucrose, a compound formed from the two simple sugars glucose and fructose.

Sugars are classified as monosaccharides (“simple sugars”) which are made up of a single carbohydrate unit, disaccharides that are made up of two carbohydrate units, or oligosaccharides that are composed of many carbohydrate units.  The most common monosaccharide is glucose, a molecule used as the primary energy source for cells in our body! Fructose and galactose are two other common monosaccharides. In addition to sucrose, other common disaccharides are maltose (made of two glucose molecules), which originates from grains, and lactose (made from galactose and glucose), which is found in milk.

Although small, the differences in these disaccharides can lead to big biological effects. In order for the body to use the sugar in the foods you consume, it first must be break down disaccharides into its simple sugar units such as glucose.  If you or someone you know is lactose intolerant, that means that you/they lack an enzyme in their body known as lactase, which is responsible for breaking lactose into galactose and glucose. This phenomenon also explains why humans lack the ability to survive on grass like other animals. Humans lack enzymes known as cellulases that break down the special type of bond formed between glucose molecules in cellulose, known as a β-linkages. We are unable to get energy from cellulose because we cannot break it down into glucose units. Unfortunately, plants are roughly 33% cellulose by weight, meaning that most of the usable energy in plants goes to waste!

So this Halloween, after you’ve collected all of your goodies, take a look at the ingredients and see what sugars are in your candy!  Hey, I did say that glucose was a primary energy source, so eat up!

Candy Links:

• http://www.youtube.com/watch?v=VY8q0hN6KwA
• http://www.yale.edu/ynhti/curriculum/units/2009/3/09.03.05.x.html
• http://www.exploratorium.edu/cooking/candy/candy-links.html

Sources:

1. http://en.wikipedia.org/wiki/Sugar
2. http://butane.chem.uiuc.edu/pshapley/GenChem2/B10/1.html
3. http://www.humanbodydetectives.com/blog/2011/10/sugar-sugar-chemistry/

Chemistry: One Big Family

Among the sciences, chemistry is uniquely situated at the crossroads between physics and the more applied sciences such as biology. Because of this relationship, chemistry is sometimes referred to as "the central science." Simply put, chemistry is concerned with understanding the interactions between atom (chemical reactions), structure, and composition of matter (or “stuff” in non-technical terms). Given chemistry’s central role, chemists work on a wide variety of projects. In a broad sense, chemistry can be divided into 4 subdisciplines: biological, inorganic, organic, and physical.

                                                                                                  Biological

An enzyme with molecules bound

As you might guess, biologitcal chemistry (or biochemistry) is concerned with the chemistry of life. Biochemists, such as this year’s Nobel Prize winners in chemistry, study the structure of large biomolecules like DNA, proteins, sugars, and fats. Progress in this field has lead to the development and utilization of modern medical science.

                                             

         Inorganic

Inorganic chemists play a vital
role in aluminum recycling.

Inorganic chemistry is broadly defined as the chemistry of metals. Inorganic chemists study the structure and physical properties of metallic compounds and apply that knowledge to fields ranging from semiconductors (the “guts” of all modern electronics) to industrial scale catalysts that make chemical reactions faster and more efficient. 

                                                               




 
                                                                 Organic

Structure of Linezolid: A man-made antibiotic

Organic chemistry revolves around the chemistry of carbon (not related to “organic” food!). Organic chemists specialize in creating complex molecules from smaller, simpler precursors. Everything from plastic cups to cardboard to our own bodies is made of carbon, and so organic chemists have their hands in quite a few cookie jars.





 
                                                 Physical

MRI machines use techniques
developed by physical chemists to
take images of our bodies.

No, this is not the kind of chemistry that you want to have with the cute girl who sits behind you in fifth period English. Physical chemistry is the interface between chemistry and physics. Physical chemists are concerned with applying and studying chemistry at the atomic and subatomic level. In the course of their work, they use advanced equipment such as super computers, high-powered magnets, and lasers (pew! pew!).

In reality, most work in chemistry can't be separated into just one of these categories, and so the majority of projects involve a great deal of collaboration between chemists with differing specialties.


Image sources:
http://www.rcsb.org/pdb/explore/explore.do?structureId=1PFK
http://academyoffood.blogspot.com/2012/09/you-can-tell-coke-from-pepsi-but-can.html
http://en.wikipedia.org/wiki/Linezolid
http://www.diagnosisms.com/2012/04/30/mri-for-multiple-sclerosis/