Color Me Crazy

Courtesy of zazzle.com

In the coming week, with St. Patrick's day right around the corner, everything will start to turn green. From candy, to beverages, to shirts galore! But green isn't the only artificial color in the world around us. In fact, nearly everything around us is colored using dyes of some sort! Before we can dive into the structure of dyes, lets first discuss the phenomenon of color in a more general sense. 

Courtesy of wikipedia.com

Visible light is a form of electromagnetic radiation (waves that have both an electric and magnetic component) which has a wavelength in the range of about 380nm to about 740nm. Light above and below these wavelengths has the same properties as visible light, but as humans we lack the ability to see it. Other animals, such as bees, however, can see these different wavelengths. For a little more detail on how light perception and vision works, check out the previous blogpost here. The specific color of light is dependent on the wavelength its wavelength, 700nm corresponds to red, 380nm corresponds to violet, and all the other colors fall between the two. Scientists typically remember this range using the  acronym ROYGBIV for Red, Orange, Yellow, Green, Blue, Indigo, Violet. White light is a combination of all these visible wavelengths. 



The perception of color is where things get a little tricky. When the human eye perceives a particular color, it can mean one of two things, either the incident light is only of that specific wavelength, or it is the entire visible spectrum of wavelength minus the complimentary color of the one that is observed. For instance, when you see a LASER that's red, the reason the light you see looks red is because the LASER is sending out a frequency of light around 700nm. Conversely, if you see a red shirt it's because molecules in the shirt are absorbing blue-green wavelengths and reflecting all the rest of the visible spectrum. Let's look at this idea in a little more detail. 

Courtesy of stainsfile.info

Electrons within a molecule are said to occupy energy levels known as ground states. Above these ground states are a number of excited states which the electrons may transition to. The electrons can only reach there excited states, however, by absorbing very specific wavelengths of light. The unique wavelengh(s) absorbed by a given molecule are dependent on its structure. Below there are a few examples given. 

When white light hits a molecule (1), the electrons absorb certain wavelengths and are promoted to their excited states(2). The remaining light is then reflected at the observer who sees the remaining wavelengths that were not absorbed (3) (see figure above). 

So when you don your green in the coming weekend, or take a sip of an artificially flavored drink, take a second to think of all those excited electrons jumping up and down, and relish in the intricate processes that bring us the beautiful world of color!

More on the history of dyes and organic chemistry:

• http://stoltz.caltech.edu/litmtg/2002/trend-lit-8_22_02.pdf

References:

• http://stainsfile.info/StainsFile/dyes/dyecolor.htm
• http://www.rsc.org/Membership/Networking/InterestGroups/OrganicDivision/organic-chemistry-case-studies/organic-chemistry-colour-dyes.asp
• http://chemistry.umeche.maine.edu/~amar/spring2010/OrganicDyes.pdf
• http://monographs.iarc.fr/ENG/Monographs/vol99/mono99-7.pdf

The 99.99%: Part 2

Ever noticed that your hands feel cold after using a hand sanitizer such as Purell? This is caused by the evaporation of alcohol from your skin, which pulls body heat from your hands to convert liquids from the sanitizer into their gaseous form. In this second installment of the 99.99% we'll be discussing another major component found in today's cleaners and disinfectants: alcohols. Similar to phenolics, alcohols have several modes of action which lead to their disinfectant capabilities. 

In the field of chemistry, alcohols are organic (carbon-containing) molecules in which a hydroxyl group (-OH) is bound to a carbon. In nomenclature, the suffix -ol (i.e. ethanol, methanol, etc.) is used to denote an alcohol containing molecule. In fact, phenolics (or phenols) (the compounds described in The 99.99%: Part 1) are examples of alcohols. For the purposes of disinfection, however, only ethanol, methanol, and isopropanol are primarily used. 

Courtesy of http://www.innovateus.net

As for their mechanism of action, alcohols work in three ways: dehydration of cells, membrane disruption, and protein denaturation. Dehydration is a process in which an organism loses water. Typically, this process is caused by osmotic pressure differences between the interior and exterior of the specimen. Within the cytosol of a cell, which is primarily water, the concentrations of various compounds are highly regulated by a myriad of mechanisms. In addition, the cell wall of many organisms is permeable to water, meaning that water can move freely across it. When a cell is surrounded by a solution of higher concentration of certain compounds, called a hypertonic solution, water begins to diffuse out of the cell in an effort to equalize the concentration of the compound across the membrane (see above). As water leaves the cell, the cell membrane becomes shrunken and the concentrations of vital compounds within the cell become greatly disrupted, eventually leading to cell death. For the purposes of disinfection, a 70% alcohol solution is typically used. 

Similar to phenolics, alcohols also have a denaturation effect on proteins. As mentioned previously, protein folding is a complicated factor which is dependent on a wide range of cellular factors. One of these factors, is hydrogen bonding, a type of bonding between a polar hydrogen with an electronegative atom; typically nitrogen, oxygen or fluorine. Hydrogen bonding affects both the secondary and tertiary structures of proteins helping provide their distinctive three-dimensional shape. Due to their polar hydroxyl groups, alcohols can also participate in hydrogen bonding. Once the alcohols are within the cell, they disrupt the native hydrogen bonding, leading to the denaturation (inactivation) of proteins, disrupted cellular function and cell death.

Alcohols also take the place of water within the cell membrane. In doing so, the alcohol molecules break down the orderly arrangement of the phospholipids, making the membrane more liquid like and more permeable to certain compounds. Additionally, alcohols affect the shape and function of proteins within the cell membrane in the same way they affect proteins within the cell.

All combined, these affects make alcohols a powerful antiseptic agent, effective against a broad range of bacteria, viruses, and fungi. So next time you lather up, think of all those alcohol molecules swooping in to save the day!

References:

• http://www.ou.edu/research/electron/bmz5364/prepare.html
• http://peer.tamu.edu/curriculum_modules/cell_biology/module_2/hazards2.htm
• http://www.microrao.com/micronotes/sterilization.pdf
• http://www.elmhurst.edu/~chm/vchembook/568denaturation.html
• http://www.cliffsnotes.com/study_guide/Chemical-Methods-of-Control.topicArticleId-8524,articleId-8429.html

Nemo's Wrath

Courtesy of heavy.com

In honor of Blizzard Nemo, today's post will talk about the science and chemistry of snowflakes! It is said that no two snowflakes are alike, but how could this be possible? How do these intricate ice crystals come to form and what controls the various shapes they make.

Courtesy of blog.needsupply.com

Before we delve deeper, it's important to briefly review the various states of matter and how they interchange. There are four basic types of matter observable in everyday life: solid, liquid, gas, and supercritical fluid. The distinction between these types of matter is mainly based on their qualitative properties. At low temperatures, individual molecules don't have a lot of energy, and as such, they tend to stick together due to intermolcular forces. The molecules pack together in an order arrangement giving the material a high density and rigid shape, making them very difficult to compress. As the molecules warm up, they eventually gain enough energy to break some of the intermolecular bond which hold them in place. The molecules then begin to diffuse into their container, leading to an increase in disorder of the system. This is the liquid state. The particles are still close to one another but now have the ability to move freely. When the temperature gets high enough, the molecules gain enough energy to escape from their intermolecular forces and entirely seperate from one another. In this state, the gaseous state, particles have complete freedom of motion and individual molecules are very spread apart and moving very fast. Because they are mostly space, gases completely fill their containers and can be easily compressed. The fourth state of matter is supercritical fluid, a state with both gas and liquid properties. This state arises at high temperatures and pressures when molecules have too much energy to be compressed into a liquid at any pressure.

Courtesy of chem.ufl.edu

High up in the clouds, when the temperature drops below 32° F (0°C) water droplets (liquid) begin to freeze around dust particles. It is from these small crystals that snowflakes then form! While snowflake formation is a highly dynamic process that depends on temperature, humidity, air currents, etc. there are several general guidelines regarding what types of crystals form at different heights and temperatures. Generally, in high clouds, six-sided hexagonal crystals form, while at mid range heights flat six-sided crystals dominate. At colder temperatures, sharper tipped snowflakes with more intricate branching patterns also tend to form. The short video below gives a great overview of the whole process.

Who knew that fluffy white stuff could be so amazing!

References:

• http://chemistry.about.com/od/moleculescompounds/a/snowflake.htm
• http://www.chem.purdue.edu/gchelp/atoms/states.html

The 99.99%: Part 1

With the flu season in full swing, people are more germ conscious than ever. From Lysol, to Clorox,  to Purell, the shelves are full of consumer products claiming to kill 99.99% of bacteria and/or viruses, but how do they manage to kill germs without hurting our hands or stripping the varnish off our tabletops. 


While many cleaning products accomplish the same goal, most are made up of a unique blend of active ingredients responsible for their potency. These bacteria killing chemicals can be broken down in to a number of more general categories: phenolics, quarternary ammonium centers, alcohols, and halogen based compounds. In this first segment, we'll discuss phenolics.

 Phenolics are molecules which contain a phenol group (an aromatic six carbon ring with a hydroxyl (OH)).  This anti-bacterial, first used as an antiseptic in the 1860s, acts by damaging cell membranes and denaturing enzymes within bacterial cells. On a molecular level, phenolics work by inserting into the phospholipid bilayer of cells, acidifying the cell membrane, and denaturing proteins within the cell. 

The hydrogen atom of the hydroxyl group in phenol is weakly acidic, but can lose it's proton around biological pH (~7). At the surface of the plasma membrane, phenols can exchange protons with molecules and proteins, changing the relative distribution of charge across the cell membrane. While this may seem minor, even small changes in the charge surrounding the cell membrane can cause charge sensitive membranes, responsible for the transport of compounds across the cell membrane to shut down: nothing in and nothing out. 

While phenol compounds contain a polar alcohol (R-OH) group, the phenyl ring make them largely nonpolar. This characteristic allows phenols to insert themselves into the phospholipid bilayer of the cell membrane. As these molecules begin to build up within the cell membrane, they can begin to displace phospholipids, compromising the integrity of the cell membrane. Once within the membrane, phenolics which have lost their hydrogen atom also have the ability to shuttle cations across the cell membrane, leading to further membrane permeability and loss of the cell's content. 

Lastly, once within the cell, phenolics can denature (inactivate) proteins. The cell's cytoplasm is mostly made up of water, a polar substance. Normally, proteins fold in such a way to expose a maximum number of its polar side chains to the surrounding polar environments while hiding its nonpolar side chains internally. When nonpolar phenolic molecules begin to interact with a protein it will change its shape to expose some of its nonpolar portions. This change in conformation leads to inactivation of the protein (denaturation), due to the fact that protein form and function are interdependent.

In terms of disinfectants, phenolics are only one component that makes up the laundry list of ingredients in household cleaners. As you can see, however, the way these molecules interact with bacteria, viruses, and fungi can be quite complicated! Tune in soon for the next antiseptic in the series!

Related Video:

• http://www.youtube.com/watch?v=obDsnyMBZMY

References:

• http://www.madsci.org/posts/archives/mar99/921165350.Mi.r.html
• http://www.cliffsnotes.com/study_guide/Chemical-Methods-of-Control.topicArticleId-8524,articleId-8429.html
• http://books.google.com/books?id=iwiJwnrq6a8C&pg=SA10-PA13&lpg=SA10-PA13&dq=phenolics+inactivate+proteins&source=bl&ots=Agoq5Kp9a4&sig=0WUHpss8Mp2Q6FsWzpQq4Y5oHXU&hl=en&sa=X&ei=BbgOUdD7O_SB0QGq1IHwDw&ved=0CHwQ6AEwCA#v=onepage&q=phenolics%20inactivate%20proteins&f=false
• http://books.google.com/books?id=y5-VzA5CxvsC&pg=PA170&lpg=PA170&dq=mechanism+of+phenolic+membrane+disruption&source=bl&ots=ZY93r4K4X5&sig=OzUFOL1Mvbz5NrW3Oqr9siOiVvY&hl=en&sa=X&ei=HrwOUYjYGMqw0AG1woHYAg&ved=0CEwQ6AEwAw#v=onepage&q=mechanism%20of%20phenolic%20membrane%20disruption&f=false
• http://ecosystems.wcp.muohio.edu/studentresearch/ns1fall02/cummins/morning/resistance/articles/Mechanisms%20of%20Action%20of%20Disinfectants.pdf
• https://facultystaff.richmond.edu/~lrunyenj/bio384/lecturenotes/ch7.pdf

It’s a bird! It’s a plane! It’s Superglue!

Courtesy of Ifoundouttoday.com

Things break, that’s just how the world works. While materials like wood or metal can be mended with rivets, nails, or screws, other materials are not repaired so easily. Enter: superglue. When things like mugs shatter, pots break, plastic pieces snap, superglue is here to save the day! If you’ve ever accidently got some on your fingers and stuck them together, you know just how powerful this adhesive can be. But what makes this substance so sticky, and how can such small amounts of it be so strong?

Superglue isn’t your everyday Elmer’s. Firstly, many traditional glues, such as Elmer’s, work through what is known as solvent evaporation. In this process, a polymer (a long repeating chain of chemical units known as monomers) such as polyvinylacetate, is first suspended in a water solution (this solution is what you purchase in the store). When the solution is applied to a material and exposed to air, the water from the solution begins to evaporate. Eventually, all of the water evaporates, leaving behind a layer of flexible polymer. Superglue, however, goes through a process known as curing, in which a chemical reaction actually takes place!

The main component in superglue is a chemical called cyanoacrylate. When exposed to air, water droplets in the air initiate a process known as anionic polymerization.  First, a water droplet attacks the carbon-carbon double bond in cyanoacrylate, pushing a pair of electrons onto one of the carbons. Now, this carbon has more electrons than it needs, and therefore has a negative charge (electrons have a negative charge), and is referred to as an anion. To get rid of this negative charge, this carbon then attacks a nearby molecule of cyanoacrylate, causing a new negative charge to form. This process continues until all of the molecules of methyl cyanoacrylate have reacted, creating a network of long chains of polycyanoacrylate. It is this multitude of bonds that gives superglue its super strength!

Ten Facts about Super Glue: http://www.supergluecorp.com/blog/2010/05/17/10-fun-facts-about-super-glue/

References:

• chm233.asu.edu/notes/halides/
• http://home.howstuffworks.com/question695.htm
• http://books.google.com/books?id=OZ6CbJlsJM8C&pg=PA1131&lpg=PA1131&dq=chemistry+of+superglue&source=bl&ots=Qp4NViO9bD&sig=OdYbttoZuBTnBY9t06CKfsmpItI&hl=en&sa=X&ei=-ob8UJboAuGT0QGAioCgBg&ved=0CE8Q6AEwAw#v=onepage&q=chemistry%20of%20superglue&f=true

Boom Goes the Dynamite

Happy New Year Everyone! I apologize for the wait, but we’re back again, and with the New Year come new resolutions, so expect consistent updates! In celebration of the New Year, today I’ll be discussing fireworks. They light up the sky on special occasions creating colors and shapes to amaze, but what is it that produces this brilliance? From sparklers to aerial fireworks, it’s a wide world of bright lights!

From sparklers to aerials, all fireworks are made up of the same few components: an oxidizing agent, a reducing agent, a coloring agent and binders. In order to burn the mixture and create the various colors and patterns, fireworks need a fuel source: the oxidizer. Oxidizers, usually composed of nitrates (NO3-), chlorates (ClO3-) or perchlorates  (ClO4-) release oxygen by reacting and exchanging electrons with metal ions (an example of this is shown below).

                                                4KNO3     ------->    2K2O + 2N2 + 5O2

Of these oxidizers, nitrates are the least reactive but also the most controllable. As such, nitrates are used as the major component of black powder, the compound responsible for thrusting the firework high into the sky. The less stable chlorates, react more intensely, producing an explosion upon reaction rather than a consistent burn. Although chlorates are used in fireworks, they are relatively unstable, giving them limited use. Their most stable counterparts, however, perchlorates, are more stable and produce more oxygen, making them ideal to produce the brilliant explosions found in fireworks. 

The oxygen released from the oxidizing agents then quickly reacts with the reducing agents, typically either sulfur and carbon (charcoal). These reactions produce hot and rapidly expanding gases, either sulfur dioxide or carbon dioxide respectively, adding to the explosive force of the reaction.  It is the heat and force generated from this reaction that produces the loud explosions and bright colors characteristic of fireworks.

The colors of fireworks are created by heating metal salts such as strontium carbonate, barium chloride, and copper(I) chloride, each of which produces a unique color. Energy from the combustion of the reducing agents excites electrons within the metal atoms into a higher energy state. The electron then falls back to its ground state, emitting a characteristic wavelength of light with a specific color. Depending on the salt used, a wide range of colors can be produced!

Red	strontium salts, lithium salts lithium carbonate, Li2CO3 = red strontium carbonate, SrCO3 = bright red
Orange	calcium salts calcium chloride, CaCl2 calcium sulfate, CaSO4·xH2O, where x = 0,2,3,5
Gold	incandescence of iron (with carbon), charcoal, or lampblack
Yellow	sodium compounds sodium nitrate, NaNO3 cryolite, Na3AlF6
Electric White	white-hot metal, such as magnesium or aluminum barium oxide, BaO
Green	barium compounds + chlorine producer barium chloride, BaCl+ = bright green
Blue	copper compounds + chlorine producer copper acetoarsenite (Paris Green), Cu3As2O3Cu(C2H3O2)2 = blue copper (I) chloride, CuCl = turquoise blue
Purple	mixture of strontium (red) and copper (blue) compounds
Silver	burning aluminum, titanium, or magnesium powder or flakes

                                                                                                                                                 courtesy of about.com

The anatomy of a firework is relatively simple. A fuse runs out of the firework allowing an observer to ignite the ignition charge from a safe distance. Once lit, the fuse, composed of a fast action and time delay fuse, quickly ignites the lift-off mixture. As mentioned before, the power needed to thrust the firework into the air is provided by black powder, a combination of sulfur, charcoal (carbon) and potassium nitrate.  As the firework rockets into the sky and reaches its apex, the time delay fuse ignites a burst charge, similar in composition to black powder, which creates a large explosion. This explosion propels small clay like balls, known as stars, flying. These stars contain the oxidizing-reducing-metal salt combination that produces the colorful patterns we all enjoy! Who knew that so much went into lighting up the night sky! 

How fireworks are made!

References:

• http://library.thinkquest.org/15384/chem/index.htm
• http://chemistry.about.com/od/fireworkspyrotechnics/a/fireworkcolors.htm
• http://science.howstuffworks.com/innovation/everyday-innovations/fireworks.htm
• http://scifun.chem.wisc.edu/chemweek/fireworks/fireworks.htm

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