Chemistry of Antibiotics: Cell Wall Synthesis

Introduction

In this post we will continue our exploration of the chemistry of antibiotics with a look at drugs that interrupt wall synthesis and how bacteria develop resistance to these drugs.

The target of these antibiotics is crucial because it explains how antibiotics can attack bacteria without affecting human cells. Bacterial cells, unlike animal cells, have cell walls. Therefore, a drug that attacks cell walls will not be able to impact human cells. Bacterial cell walls are essentially a peptidoglycan layer that is composed of units of peptides (proteins) and glycans (sugars). This layer is the primary and most important component of the cell wall.

β-lactam Antibiotics

The most common class of antibiotics that interferes with cell wall synthesis are the β-lactam antibiotics, which

include penicillin. These types of antibiotics function by impeding the synthesis of the peptidoglycan of the bacterial cell wall. There are multiple ways to inhibit the synthesis of the peptidoglycan layer but the most common is by means of destroying the enzymes that do so. If the antibiotic does not function by destroying synthetic enzymes, it could also destroy the enzymes that convert the polymers into a layer of the cell wall. β-lactam antibiotics inhibit cell wall synthesis by preventing the assembly of the peptidoglycan layer. This is done when the antibiotic competes with the polymer at the site of binding.

This video gives a general overview of how peptidoglycans are inhibited by the mechanisms of a beta-lactam antibiotic:

 The Chemistry of Penicillin

 

Penicillin is one of the most common β-lactam antibiotics, and is characterized by three structural requirements: one fused β-lactam structure, a free carboxylic acid group, and one or more substituted amino acid side chains. Penicillin’s structure prevents the cross linking of peptide chains – weaker cell walls will allow water to flow into the cell freely and the cell will swell and burst, causing cell death. If you change the side R-group chain on the penicillin, the penicillin can possess different properties, such as acidity or penicillinase resistance.

The β-lactam ring in the penicillin reacts with an enzyme that is used for building the cell wall called DD-transpeptidase. Resemblances between a segment of the penicillin structure and the backbone of a peptide chain of the bacterial cell wall have been used to explain the mechanism of beta-lactam antibiotics.

Bacteria Fighting Back

Bacteria have a number of ways to evolve and beat our human antibiotics. One method that bacteria employ in order to fight drugs that interrupt cell wall synthesis, is changing the structure of their cell walls. One instance of this is mutation of pathogenic bacteria. Bacteria that colonize the mucosal pathways, such as nostrils, lips and eyelids, must undergo changes in order to avoid the antimicrobials of the host. In particular, they must avoid lysozyme, an enzyme that destroys the cell walls of bacteria. The activity of lysozyme is similar to β-lactam antibiotics since they both attack the cell walls of bacteria. Since the muramidase activity of lysozyme leads to hydrolysis of the β-1,4 glycosidic bond between the C-1 carbon of N-acetyl muramic acid (MurNAc) and the C-4 carbon of N-acetylglucosamine (GlcNAc), that is the bond that the bacteria have to change in order to survive.Streptococcus pneumoniae and bacillus anthracis, two lysozyme resistant bacteria, have peptidoglycan cell walls that are N-deacetylated, which means that the composition and structure of the sugar component of the cell wall is changed. It was shown that N-acetylating them caused them to be more susceptible to lysozyme. Therefore, it was concluded that N-deacetylating the caused lysozyme resistance. This shows that through changes in structure, bacteria can evade agents that inhibit their cell wall synthesis. When this happens, we too must evolve and change our tactics. This is why new drugs always need to be developed. Bacteria develop resistance, and we must develop new antibiotics.

Want to know more about different classes of antibiotics that inhibit cell wall synthesis? Check out thislink to learn about glycopeptide antibiotics. Of course that’s not enough to satisfy the hunger of your mind, so here is a website that goes further in-depth regarding the processes of cell wall synthesis.

Local Anesthetics: The Caine Family

As seen in the previous post, local anesthetics generally work to prevent only a small area of the body from experiencing pain by inhibiting the flow of sodium ions (preventing action potential thus preventing nerve activity) through sodium channels embedded in the cell membrane of neurons. More specifically, the local anesthetic will bind to a receptor inside the sodium channels and antagonize it, therefore closing the sodium channels thus creating the halt in the influx of ions through the channels as seen in the diagram below.

 .

Many local anesthetics commonly bind to the N-methyl-D-aspartate (NMDA) receptor (an image of how the anesthetic might bind to a receptor through the polar attractions between the receptor and anesthetics is shown here), such as the constituents of the Caine family: a category of local anesthetic compounds that share similar qualities (i.e. similar receptors and mechanism of actions) and end in the suffix “caine”. The following will consist of descriptions of three different local anesthetics, particularly from the Caine family, to demonstrate the functional and molecular diversity in the compounds of local anesthesia.

Cocaine:

Cocaine, otherwise known as benzoylmethylecgonine, can be used as a type of local anesthetic, but for the past several decades it has reached the headlines for different reasons. Cocaine was used historically as an eye and nose anesthetic, used to block nerve signals during surgery, but side effects of cocaine exposure during surgery include intense vasoconstriction and cardiovascular toxicity. It is a powerful nervous system stimulant, and above all, it is extremely addictive. Repeated use of the drug can cause strokes, cardiovascular disease, and several hundred other afflictions such as gingivitis, lupus, and an increased chance for heart attacks. Cocaine can be administered in many different ways, most commonly through insufflation, injection, and in the case of crack cocaine, inhalation. Cocaine is a controlled substance around the world due to its addictive properties and terrible side effects of constant use.

How To Use It:

Most users of pure cocaine are drug addicts, but cocaine hydrochloride is still used as a topical anesthetic. It is applied through the mouth, or the nose using a cotton swab to numb the area. It should not be used in the eye or injected, and rarely, addictive behavior will be expressed by the patient. Use the medication as specified by a healthcare professional, and do not use more frequently or longer than specified.

Molecular Structure:

Cocaine usually contains pure C17H21NO4 from the leaves of the coca plant.]

2D structure                                              3D structure

Properties:

• The molecular weight of cocaine is 303.35 g/mol.
• The molecular formula is C17H21NO4
• The systematic name is Methyl (1R,2R,3S,5S)-3-(benzoyloxy)-8-methyl-8-azabicyclo[3.2.1]octane-2-carboxylate
• Approximately 35.9 million Americans aged 12 and older have tried cocaine at least once in their lifetime, according to a national survey, and about 2.1 million Americans are regular users

Novocain (Procaine):

First synthesized in 1905, novocain (the trade name of procaine) is an ester-type local anesthetic that is able to induce a loss of sensation when injected, as opposed to oral intake which has been stated to wield therapeutic values. The first synthetic local anesthetics to be produced, novocain was primarily utilized for oral surgeries in dentistry however due to ester-type anesthetics having generally a high potential of causing allergic reactions, it eventually became obsolete and eventually replaced by a more effective anesthetic known as lidocaine. Ester-type anesthetics are more prone causing allergic reactions compared to Amide-type anesthetics because when they metabolize in the body, they form a compound known as para-aminobenzoic acid (PABA). PABA has a documented history of causing allergic reactions that range from urticaria to anaphylaxis. Generally, the adverse side effects of using novocain include heartburn, migraines, nausea, and can induce a serious condition known as systemic lupus erythematosus (SLE), therefore it is highly advised that intake is performed by a healthcare professional. However, novocain also retains the property and advantage of constricting blood vessels, reducing bleeding unlike many other local anesthetics.

How To Use It:

The common and primary method of intake of novocain for its anesthetic properties is through injection in solution state. However, if novocain is present in capsule or tablet form, oral ingestion can also performed though its properties and effects will be greatly mitigated and may induce therapeutic rather than anesthetic conditions.  An informative video of how novocain is administered in oral surgeries of dentistry can be found  below.

Molecular Structure:

Novocain contains pure C13H20N2O2.

2D structure                            3D structure

Properties:

• The molecular weight of novocain is 236.31 g/mol.
• The molecular formula is C13H20N2O2.
• The systematic name is 2-(diethylamino)ethyl 4-aminobenzoate
• The melting point of novocain is approximately 61 °C while its pKa value at 15 °C is 8.05

 

Tetracaine:

Tetracaine is a type of local anesthetic and it is used as a numbing medication. It is generally used for surface and spinal anesthesia and it works by blocking the nerve signals in your body. There most used type of tetracaine medication is cream and ointment. It’s primary use is to reduce pain or discomfort caused by minor skin irritations, cold sores or fever blisters, sunburn or other minor burns, insect bites or stings, and many other sources of minor pain on a surface of the body. The reason why this medication is given is to lessen the pain caused by the insertion of a medical instrument such as a scope or a tube. Although in most situations tetracaine is used on the skin, it can also be used on the eye. This eye medication is in the form of drops and it is used to decrease the feeling in your eyes right before going through surgery or perhaps a test or procedure involving the eyes.

How To Use It:

The eye drops medication should be issued by the clinic and after going through the procedure, the patient must refrain from touching his or her eye until the medication is no longer in effect and in some cases, an eye patch is required. The Tetracaine topical gel is applied by very small amounts only necessary to cover the area and should not be used more than four times a day unless the doctor specifies otherwise.

Molecular Structure:

Tetracaine contains more than 98 percent of .C15H24N2O2  calculated on the dried basis..

2D structure                                                      3D structure

Properties:

• The molecular weight of tetracaine is 264.36 g/mol.
• The molecular formula is C15H24N2O2.
• The systematic name is 2-(dimethylamino)ethyl 4-(butylamino)benzoate.
• The boiling point of tetracaine is between 362.4 degrees Celsius and 416.4 degrees Celsius at the standard 1 ATM.

Chemicals of Europa

As we mentioned at the end of our previous blog post, there are certain chemicals we know Europa would need to have in order for there to be life.

Detection Of Chemicals

At first it may seem strange to be talking about the chemicals of Europa at all. To date, no probes have skimmed the atmosphere of Europa, let alone landed and taken samples for chemical analysis. Yet here you are about to read about the chemicals that are present. This is made possible by of one of the most basic tenets of quantum mechanics, namely the idea that electrons have quantized energy levels. This means that electrons can only exist in certain regions of an atom, with a specific energy inherent to that region. In order to move from one of these energy levels to another an electron must either emit or absorb a photon whose energy is the difference between the energy levels. The energy, and also color of a particular photon is determined by its frequency. Therefore, if you look at the light emitted by a heated substance, you will see distinct bands of colors indicating the electron transitions occurring. What makes this useful for identifying chemicals is that the energy levels that are available to the electrons and the transitions that occur are completely dependent upon the element or compound. Moreover, each unique compound has its own emission and absorption spectra, the features of which can be detected even amongst a whole moon full of chemicals nearly 400 million miles away. This method has discovered the presence of two important chemicals on Europa: oxygen and hydrogen peroxide.

The Importance of Oxygen and Hydrogen Peroxide

The reason that scientists think that finding evidence of hydrogen peroxide and oxygen on Europa is important is because they are among the best oxidation agents known to exist. Oxidation agents are essential to every form of life that we know exists. They are most important because of their role in redox, or oxidation-reduction, reactions. In a redox reaction one compound takes electrons from another.  The compound that gains the electrons becomes reduced, and the compound that loses the electrons is oxidized. Examples of redox reactions include everything from the rusting of iron (where iron is oxidized and oxygen is reduced) to the reaction between glucose and oxygen.

Respiration- Both Simple and Complex

Perhaps the most important redox reactions for living organisms are those involved in respiration. Just like all compounds, organic compounds, such as the proteins and carbohydrates that make up organisms, have energy stored in the bonds that hold it together. Taken as a whole, respiration works a lot like combustion, in which a hydrocarbon is oxidized and energy is realized in the form of heat. However, if fires were constantly starting in our mitochondria, we would have some significant problems. Fortunately, the process is broken into many steps, each of which releases a relatively small amount of energy. In complex multicellular life on Earth, this process is done through a series of increasingly powerful oxidizing agents known as the electron transport chain. The electron transport chain transfers electrons from the organic compound being brought down through a series of complex compounds until it ends up being captured by oxygen, the final electron acceptor.

Water

Perhaps the most important substance for life to exist is liquid water. In the first blog post, we talked about how and why scientists suspect that there is liquid water on Europa. Now we are going to talk about why water in particular is so important.

Polarity

Anyone who knows anything about electronegativity can tell you that water is a polar molecule. The oxygen atom takes on a partial negative charge (denoted 𝛿-) and each of the hydrogen atoms takes on a partial positive charge (denoted 𝛿+). These partial charges allow water to dissolve countless polar and ionic solids, hence why it is referred to as the universal solvent. Most biological reactions will only happen if all of the reactants are in the aqueous state. There is a tendency for polar compounds to dissolve other polar compounds and for non-polar compounds to dissolve other non-polar compounds, and this allows for the easy storage of water. Non-polar molecules like lipids are used to form membranes in cells that are capable of retaining water.

Water’s efficacy as a solvent is part of why it is so vital to life on Earth. All (known) living organisms contain liquid water in their bodies. Water is used to transport nutrients and other vital substances (e.g. glucose) to the areas of our body in need. Other compounds, such as salts are also transported via water. In most animals, blood forms the primary method of active nutrient transfer in the body, and blood’s ability to transport the nutrients depends on water’s solubility.

Hydrogen Bonding

Because water contains hydrogen atoms bonded to oxygen atoms, it contains in what is called “hydrogen bonds”, the strongest type of intermolecular force. This leads to a series of interesting and important properties of water. For one, each water molecule is strongly attracted to the other water molecules around it, making it hard for water molecules to break away and evaporate into the vapor phase. This gives water a relatively high boiling point (100°C) for such a small molecule. This means that it would take very serious changes in the environment to cause a phase change for large amounts of water. Hydrogen bonding is also responsible for water’s unusual property of having it’s solid phase (ice) be less dense than its liquid phase (water). The optimal bond lengths for the hydrogen bonds are actually greater than the distances water molecules usually are from each other causing them to expand as they freeze. This allows for the phenomenon of underwater oceans to exist because the less dense ice essentially floats on top of the water.  The ice basically thermally insulates the rest of the water from the surrounding freezing conditions. In Europa’s case, the ice acts as an insulating blanket, trapping the internal heat generated by Europa’s movement around Jupiter. This insulated layers allow for the possibility of a liquid ocean existing.

Future

Future missions to explore Europa, like NASA’s proposed Europa Clipper aim to analyze the surface of Europa. The mission would launch a satellite to orbit Europa, performing repeated close flybys of the moon’s surface. Various scientific instruments would be used to analyze the surface and trace atmospheric composition of Europa. High-resolution cameras would also enable exquisitely detailed surface imaging of Europa’s icy outer layer. Additionally, there exists the possibility for radar to be included on the satellite, which would allow NASA to determine the depth of Europa’s surface ice.

Multigraphs in Chemistry

Today we are going to talk about multigraphs and apply them to chemistry.  A multigraph is just a graph in which multiple edges and loops are allowed.  Multiple edges are the name for having more than one edge between two vertices, and loops are edges both of whose ends are at the same vertex.  It turns out we can once again represent Lewis structures like this.  A lone pair is a loop, a double bond is two edges, and a triple bond is three edges.

Above is a multigraph, courtesy of the great Wikipedia:  http://upload.wikimedia.org/wikipedia/commons/thumb/c/c9/Multi-pseudograph.svg/220px-Multi-pseudograph.svg.png.

Note that you have the red multiple edges and the blue loops.

So what are the properties of a mutigraph we are concerned with?  Once again we have vertices, edges, and degree.  The vertices are the gray dots in the above diagram, and the edges are the black, red, and blue in the diagram.  Degree is defined to be the number of edges adjacent to a vertex, where loops are counted twice, one for each end.  In this way the sum of all degrees is still twice the number of vertices.

This is nice.  For starters we can represent any Lewis structure much more completely with this convention.  Graph theoretic properties once again have interesting meanings.  Every edge still represents an electron pair.  The degree of a vertex still represents the number of electrons in its valence shell after bonding, where loops are counted twice for a vertex.  Formal charge has an interesting representation now.  It is the difference between the number of electrons present on the individual atom and the degree in the accompanying graph.

Pictures might be an excellent aid, but it’s better to construct lewis structures yourself!  Draw the Lewis dot structure of your favorite compound, say glucose.  Go on now.  Do it on paper.  Start by making a graph with the atoms as vertices.  Now, turn the lone pairs into loops, so for every lone pair, drawn an edge from that lone pair’s atom to itself.  Finally, draw an edge between two atoms with a single bond, draw two between two with a double bond, and draw three between two with a triple bond.  There you go.

Now, once again these multigraphs can be applied to calculate the formula of certain compounds!  Let’s start with hydrocarbons because they are simple.  Say we have an acyclic hydrocarbon with 5 carbons and 8 hydrogens.  What bonds can it have?

Note that this is an alkane so there are no cycles.  There are also no lone pairs because carbon is not very electronegative and instead makes 4 bonds.  The carbons in total have degree 20 because they need to be adjacent to 4 edges (electron pairs).  Since 8 of these are taken up by carbon-carbon sigma bonds (there are 4, because of our tree with 4 edges, but each is counted twice for each of the carbons), and 8 by C-H bonds, C-C pi bonds are counted a total of 4 times, which means that there are 2 of them.  So either there is a triple bond or two double bounds.

Let’s do another example.  What does carbon monoxide look like?  First, we can draw the simple graph for it, which is a carbon connected to an oxygen.  The edges in the simple graph represent the sigma bonds that do not hold lone pairs, and onto them we will draw the extra multiple edges which represent pi bonds.  Clearly 5 edges need to be drawn in some capacity, since we need 10 total valence electrons.  4 are for the carbon, and 6 for the oxygen.  The only way to do this is to make two extra pi bonds between C and O and then give each of C,O a lone pair.  So we have a graph on two vertices connected by a triple edge, each of which has a loop attached to it.

So we have seen that the idea of interpreting Lewis structures as simple graphs can be extended to interpreting them as multiple graphs.  Once again, this allows us to mathematically capture the structure of many compounds and rationalize their structures to some extent using degree arguments.  Once again, there is still nothing about the actual shape of the molecules involved here, but that is covered very nicely in our previous posts on Group Theory.  Stay tuned for next time!

The Chemistry of War: Non Lethal Weapons Tear Gas

an entry by Mika Thomas, Helen Sakharova, Ko Cheng Chan

Figure 1: A Us soldier wearing a gas mask while traveling through a field filled with tear gas during a training drill

The human body is wonderfully capable of quickly responding to its environment.  Different substances trigger different reaction in the human body.  Tear gas, or a lachrymator, is a substance that interacts violently with the mucosal membranes such as the eyes, mouth, nose and lungs.  Tear gas is actually not a gas, but a colloid, more specifically, an aerosol.  The chemical structure of tear gas is what causes it to affect us differently than other substances.

    Pepper spray also applies to the definition of a tear gas however, unlike CN gas, it is considered an inflammatory agent.  Pepper spray causes painful swelling of capillaries in the eyes and caused temporary blindness.   Pepper spray is relatively simple compared to CN and CS gases.  As the name would suggest, it is derived from peppers.  Peppers contain a group of chemicals called capsaicin.  Pepper spray is also referred to as OC spray, Oleoresin Capsicum spray.  A capsaicin is a colorless irritating phenolic amide C18H27NO3  and is responsible for giving peppers their pungent spicy flavor.  Capsaicins’ molecular structure enable them to bind directly with proteins found in the membranes of pain sensing neurons.   This causes a victim to feel an intense burning sensation, excess salivation, excess mucous production, and even vomiting.  Therefore, pepper spray should be used wisely.   The difference between sweet peppers and the infamously painful ghost pepper is the concentration of capsaicin that they both contain.

This concept of concentration also plays strongly into the potency of pepper sprays and tear gases.  Different states have different laws on the limit of capsaicin that can be used for personal protection.  Even so, for almost all pepper sprays, a 1 second blast can render a person incapacitated for fifteen minutes to an hour. Different brands of pepper spray contain different amounts of solvents such as alcohols, and water.   The more dilute the concentration of capsaicin, the less potent the spray will be.  Like other forms of tear gas, pepper spray is canned under extremely high pressures and this results in an average can of pepper spray having a shooting range of about 10 feet.  More application differences between CN gas and pepper spray can be read about here.

Figure 2 : an image of a molecule of capsaicin.  The black balls represent carbon atoms, the white balls represent hydrogen atoms, the blue ball represents an atom of nitrogen and the red balls represent oxygen atoms.

    Tear gas is qualified as a nonlethal weapon, but there are serious risks involved.  Tear gases qualify as a type of chemical warfare and are prohibited in war by many international warfare treaties.  However, tear gases are allowed to be used by branches of the military for training.  Tear gases are use used normally for domestic riot control or personal protection.    CN (chloroacetophenone) gas, CS (chlorobenzylidenemalononitrile)) gas and bromoacetone are the types of tear gases used by law enforcement.  A familiar form of CN gas is Mace, a popular trademark brand of CN gas sold for personal protection.

    CS gas is normally composed of a white powder mixed in a dispersal agent like methylene chloride. At standard temperature and pressure, CS forms a white crystal with a low vapour pressure and poor solubility.  CS crystals are converted into microparticulate clouds by pyrotechnic devices.  CS gas may seem to be a continuous solution or a gas, but it is also a colloid.

Figure 3: An image of a Us soldier wearing a gas mask to avoid the painful, yet temporary effects of CS gas. CS gas appears to be a white gas, but it is composed of small particles of white solid.

    As a result, CS gas is usually stored in cans at high pressures. A can of CS contains a gas and skin irritating solvents. When this can is used, highly pressurized gas escapes a can and the gas carries ultra-fine particles of CS.  The powdered CS becomes attached to the mucous membranes of organisms. The physical effects of CS gas is felt almost immediately.  A person’s breathing rate slows and excessive use of CS gas can lead to death. The poor solubility of CS makes it that it can exist on a mucous membrane for a long period of time if not physically removed.  Luckily, wind and fresh air can removed CS particles from the skin.  Gas masks work by protecting ones mucous membranes.

    Because it has been dubbed a nonlethal weapon there is fear that authoritative forces use it too liberally.    Tear gas is technically a “less-than-lethal” weapon because it can, in some cases, lead to death.  There is controversy over allowing authoritative forces to use tear gas.  Often, law enforcers must be exposed to tear gas themselves before they gain the right to use it.  While the memory f the pain of peppery spray might stop a young officer from using it too much, an older officer might not remember the pain and use it too often.  CN gas is excruciatingly painful and is often used on protesters as shown below.  The use of tear gas has raised social controversy that has even inspired for scientific research to be conducted on tear gases.  

Different OLED Variants

In a market where consumers demand innovation and novelty products with each passing quarter, some ideas flop while others soar to unimaginable amounts of profit. The technology industry is commanded by the need to satisfy the ever changing needs of the techno-savvy community. Right now, exploration into OLED’s has taken the big name corporations by storm, as they consider the plethora of different paths they can take with such an applicable concept. Whether it be in the lighting, cellular phone, or television, OLED’s are sure to make it into the homes of Americans soon. Yes, OLEDS are the next big thing.

AMOLED

Although not prominently advertised as OLED displays, there are multiple variants of OLEDs that have been in the market for many years. One of those is AMOLED, the active-matrix organic light emitting diode, often seen specifically in the smartphones that several Americans have today.  It is also present in televisions and its market is perfect for affordable and efficient devices.

The AMOLED holds the active matrix, which generates the light the thin-film transistor (TFT) array is electrically activated.  In an AMOLED, the TFT serves as a series of switches that controls the current flowing to each pixel.  As its name suggests, TFT is a field-effect transistor that deposits thin films on an active semiconductive layer onto a substrate usually made of glass. Commonly made from silicon, the characteristics of a silicon-TFT are dependent on the crystal structure of the silicon.  As previously mentioned the TFT layer can be composed of indium tin dioxide to create a transparent semiconductor for use in displays such as OLED and AMOLED.  The TFT array plays a significant role in AMOLED function due to its duality.  The continuous current to a pixel is controlled simultaneously by two TFTs.  One TFT starts the charging of the storage capacitor while the other provides a voltage that maintains a constant current.  This process allows for a lower required current to run, making the AMOLED more ideal in smartphone use.

The integration of TFTs is fundamental to the function of AMOLED displays.  The two main TFT technologies in commercial use are polycrystalline silicon (poly-Si) and amorphous silicon (a-Si).  Amorphous silicon does not contain the normal long range order of a tetrahedrally bounded silicon atom.  Thus, it can be passivated by hydrogen which allows a-Si to be deposited in low temperatures.  On the other hand, polycrystalline silicon is composed of a homogenous crystalline framework.  The entire layer is continuous and deposited easily onto a semiconductor wafer.  In the end, both methods allow the active-matrix backplanes to be fabricated in low temperatures for flexible AMOLED displays.  Further information on TFT displays can be found here.

Figure 1: Different variants of TFT layers used for various applications

 

AMOLED displays and phones were most commonly developed by Samsung and Motorola.  Like all technologies, there are various variations within the AMOLED family as well.  Samsung has incorporated the AMOLED displays into their Galaxy S range quite extensively, as the powerful Samsung Galaxy Note 3 was fitted with a Super AMOLED screen.  The Super AMOLED Plus was later introduced with the Samsung Galaxy S II.  It is an improvement from the Super AMOLED screen by replacing the PenTile 2 subpixel RGBG matrix with the three subpixel RGB RGB matrix. Upgrading from a two subpixel RGBG matrix with the three subpixel RGB RGB matrix allows for a crisper image, and cleaner, smoother looking text.  This replacement made the screen much brighter and energy efficient than its predecessor while giving a clearer picture due to the increase in subpixels.  The HD Super AMOLED would then follow in the Samsung Galaxy Note.  Although the Galaxy S III uses a 2 subpixel RGBG matrix HD Super AMOLED, the screen was upgraded for the Galaxy Note II by using a 3 subpixel RBG matrix.  The Samsung Galaxy Round also uses the AMOLED screen, as a part of the curved phone fad that has started to hit the market.  This screen, the Super Flexible AMOLED capacitive touchscreen is paramount curved handsets, since it is able to be made transparent and flexible, which is required for a phone that wants to achieve wider viewing angles through bending screens.

Figure 2: Samsung Galaxy phones using an AMOLED display

 

PMOLED

       OLEDs can also be made using passive-matrix addressing schemes.  PMOLEDs are fundamentally the opposite from an AMOLED.  They were used in early displays and are not commonly seen anymore.  They function by controlling each line of pixels sequentially without the use of a capacitor.  The lack of a capacitor makes PMOLEDs different from AMOLEDs in that they do not use a TFT layer to keep the pixels constantly on.  This results in most of the pixels being off for the majority of the time.  To adjust for this, more voltage is required for brightness.  Although this principle makes PMOLEDs easy to manufacture, the quality and lifetime of PMOLEDs are severely lower than AMOLEDs.  The fact that they require more voltage for each line of pixels also restricts the size of PMOLED displays.

 

Figure 3: Transparent TDK PMOLED screens

Conclusion

       Although PMOLED displays were a good foray for many companies when the OLED market was still in its infancy, it is now clear that they are less desirable than AMOLED displays.  By using the technology similar to old CRT displays, PMOLED pixels were controlled by switching on a row and a column.  The intersection of the row and column was then lit up.  Although they were easy to build, the restrictions in size severely limited PMOLED applications.  They also consumed power at a higher rate.  On the other hand, AMOLEDs used a unique principle where each pixel is controlled individually.  This allows for larger displays and power efficiency at the cost of ease of production.  Thus, as the full capabilities of PMOLED and AMOLEDs were discovered, each fit into their own niche market.  PMOLEDs are now integrated more in small MP3 players while AMOLEDs dominate the smartphone market.

Evonik’s ULTRASIL Tires increase fuel efficiency

Company Profile:

Evonik Industries is one the world’s lead specialty chemical companies. One of the main goals of the company is to provide product that solve problems and provide a maximum benefit to customers and society. Recently, they have developed a more fuel efficient tire that does not compromise on performance through the implementation of a silica-silane system, known as ULTRASIL.

ULTRASIL:

The greenhouse effect is a natural process in which radiant heat from the sun is captured in the lower half of the atmosphere, directly resulting in higher temperatures and thus global warming. In order to reduce this greenhouse effect, most companies are working towards minimizing carbon dioxide emissions from transportation. Carbon emissions from combustion of energy fuels has accounted for 81.5% of total greenhouse gas emissions over the last several years, and global warming is quickly becoming a major problem throughout the world. Transportation contributes to this on a large scale, and it is responsible for 31% of the CO₂ emissions from the United States. However, Evonik’s silica-silane system (ULTRASIL) is a unique approach to this problem. ULTRASIL is created in several different forms and is applicable in many different situations, however its primary purpose is to serve as a coating for tires. This advanced tire technology can reduce the rolling resistance of tires, increase traction in wet conditions, and reduce carbon dioxide emissions. In general, tires have been targeted as quick way to reduce carbon dioxide emissions, as simple changes in size and shape can increase fuel efficiency by up to 15%.

ULTRASIL is able to reduce rolling resistance between tires and wet or icy road conditions due to the presence of intermolecular forces (IMFs), which can determine whether a solid will be hydrophobic (resists water) or hydrophilic (attracts water). This is an important concept to the concept of ULTRASIL because it is produced with hydrophobicity in mind. Being hydrophobic, water will adhere to the ULTRASIL coated tires, resulting in increased traction between the tires and the road. The major types of intermolecular forces that impact hydrophobicity include dipole-dipole forces, hydrogen bonding, ionic interactions, and London dispersion forces.

Dipole-dipole forces, hydrogen bonding, and ionic interactions are all known to be hydrophilic interactions. The larger presence of these forces in a molecule, the more the solid will attract water molecules. Dipole moments in a molecule are dictated by the polarity of a molecule. Polarity is the sum of all of the bond polarities in a molecule, resulting in dipole moments. The dipole moment is measured in a vector as the sum of the individual vector movements. For example, CO₂, a linear and non-polar molecule, has no dipole moment. Hydrogen bonds are the interactions of a hydrogen atom with a nitrogen, oxygen, or fluorine atom. They are a much more powerful force than dipole-dipole forces, resulting in a larger increase on the hydrophilicity of the molecule. Similarly, the presence of ionic bonds (interactions between positive and negative ions) can have the same effect.

London dispersion forces, the weakest of the intermolecular forces, are the sole forces that can raise the hydrophobicity of a molecule. This force, also called an induced dipole-dipole force, is a temporary attractive force that results when the electrons in two adjacent positions occupy positions that make the atoms form temporary dipoles. These forces occur in all molecules. In the production of ULTRASIL, Evonik has created a silica-silane system, where the hydrophobic regions of the molecule dominate, causing adhesive forces to arise and increase the tension between tires and wet/icy road conditions. More information about intermolecular forces can be found here, or

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Also, the chemical structures of the silica helps contribute to its unique properties. Silicon dioxide can exhibit one of the largest varieties of crystal structures among the compounds commonly available and used. These many different crystalline forms allow silica to be used in a broad range of applications, including ULTRASIL. Precipitated silica, which is key to this product’s functionality, is a specially prepared form that has an amorphous structure, similar to silica gel or glass, both of which are predominantly silicon dioxide, or silica. As already discussed, adding these silicon dioxide granules to the surface of rubber tires has many beneficial effects on vehicle performance, but binding this hydrophilic molecular solid to the long, continuous, and hydrophobic polymer chains that make up vulcanized rubber can be difficult. It is up to sulfur, linking the polymers of vulcanized rubber to make it more resistant to temperature extremes, to act as a coupling agent for silica, since the hydrocarbon polymers will not bond to it by themselves.

From what we know, however, ULTRASIL production takes a rather different approach to solving the problem of coupling silica to rubber: the silica-silane system. By treating the original rubber  material with various organosilanes, a surface that silica particles can easily bond to is created, making it possible to form the desired composite with more cross-links to the silica granules and a higher overall thermal stability than without the treatment. Organosilanes usually have both a nonpolar and polar end and can not only bond with vulcanized rubber, but also with the silicon dioxide particles, through dehydration synthesis of their hydroxyl groups with the hydroxyl groups that cover the surface of the silica particles.

While many of the specific details of the ULTRASIL manufacturing process are trade secrets of Evonik, the company does share the basic concept of how it obtains the very pure amorphous silica needed for its products: precipitation from solution. Precipitated silica is widely used in industrial processes around the world, and Evonik Industries is its largest producer. Just like in ULTRASIL, these fine silica grains are often used in rubber products like tires and shoe soles for benefits similar to those of Evonik’s products. Generally, an aqueous silicate salt is reacted with an inorganic acid (like H₂SO₄) to form insoluble silica in the following reaction:

Na₂SiO_3(aq) + H₂SO_4(aq) → SiO_2(s) + Na₂SO_4(aq) + H₂O_(l)

    After the silica precipitate has been dried, it still contains no more than 88% silicon dioxide according to Evonik, with most of the rest being water. The ensuing treatment to purify the product varies depending on the desired size and quality of the particles obtained, but eventually a fine powder consisting of 99% silica can be obtained. The precipitated silica used in the ULTRASIL product line consists of miniscule, porous granules often of nanoparticle size to allow a high surface area to volume ratio, with the 7000 GR variant having a surface area of 170 m² per gram. It is this kind of fine silica that allows for the reinforced rubber of the emerging “Green Tire” that advances in silica rubber have created.

Further Reading:

If you are interested in the chemistry behind Evonik’s ULTASIL, there is a lot of in depth reading available in scientific journals. A thorough account of this technology and the chemistry that drives it can be found

• In this study by Brinke, Debnath, Reuvkamp, and Noordermeer
• And this article by Park and Cho

The Chemistry of Cannabis: Detection of Cannabis Farms

*This blog post is purely for educational purposes. We do not support the production, distribution, or consumption of Cannabis.

Welcome back! So, since you’ve clearly been overwhelmed by the amazingness of the information in our blog posts, we think you deserve a refresher. In previous blog posts, we have discussed the effects thatCannabis has on the brain, and the different forms through which Cannabis can enter the body and results in these effects. In this blog post, we’ll discuss new and innovative ways that law enforcement is using to detect Cannabis farms.

Scratch ‘N Sniff™

(yes, you read that right)

A charity organization based in London, England has come up with an innovative way to help police officers locate Cannabis farms. The organization has created Scratch ‘N Sniff™ cards. These Scratch ‘N Sniff™ cards that mimic the scent of Cannabis in its growing stage, and are being distributed to English citizens so that they can to familiarize themselves with the smell of growing Cannabis and can notify the police if they detect the scent. So far, the organization has issued more than 200,000 scratch and sniff cards to hotspots in England, and, there has been a 28% increase in information from the public on Cannabis farms.

Now, how do these Scratch ‘N Sniff™ cards work? The ideas of chemistry can be applied to the Scratch ‘N Sniff™ technology through the ideas associated with entropy. Entropy is the number of ways a system can be arranged. In this case, aroma molecules that are microencapsulated are at a state of low entropy, since they are enclosed in minute capsules. The manufacturing process of scratch and sniff cards utilizes this entropy idea. The diagram shown below illustrates the process. In general, the process includes taking the aroma-generating chemical and encapsulating it in gelatin or plastic spheres that are a few microns in diameter, and this traps the odor. A certain chemical catalyst is used to bring about the reaction which finalizes the encapsulation of the odor. In other words, the catalyst is the metaphorical “kick in the pants,” or the thing that bring about the reaction. This  reaction requires a “kick in the pants” because it will not happen on its own; this type of reaction prevents particles from diffusing, as they would “like” to, and in order to get particles to do something they don’t want to, you have to bribe them with energy.

When these capsules are given another metaphorical “kick in the pants,” or an activation energy, they are released and they dissipate and spread the scent. Even though the particles want to diffuse, a “kick in the pants” is required to give them enough energy to break through the capsule. This energy required to get this reaction going comes in the form of kinetic energy from a person, when he/she scratches the card, applying friction to the capsules. The aroma molecules are then released, and since they have more volume to diffuse into, they achieve a higher state of entropy.

This idea of  Scratch ‘N Sniff™ technology, then, can support the notion that the entropy of the universe is always increasing. Spontaneous reactions, which have a negative free energy value, are constantly occurring in the universe. The Scratch ‘N Sniff™ system is one primary example of this chemical theory. Since this technology embodies the principles underlying entropy, then it also applies to The Second Law of Thermodynamics. This law states that “In an isolated system, natural processes are spontaneous when they lead to an increase in disorder, or entropy.”

Thermal Cameras

Authorities are beginning to use thermal cameras to detectCannabis farms. Often, Cannabis growers employ heat lamps when growing indoors. Further modifications to the growing area typically include the addition of ventilation and irrigation systems. Thermal cameras are being used to detect growers who hideCannabis around other plants, rendering them invisible to the naked eye. However, the grower must make some changes to the soil, which allow these cameras to detect hidden plants. The soil is turned over and the vegetation around the plant is trimmed off to allow for better absorption of water and nutrients. As a result the soil also absorbs heat at a higher rate than the other surrounding plants. Consequently, they stand out in thermal scans.

Just like any other camera you use, thermal cameras detect light. However, they differ from conventional cameras in that they detect different wavelengths of light. Thermal cameras detect infrared light as opposed to visible light. Because the lamps generate heat, the system emits infrared radiation. At the atomic level, the heat is simply the movement of particles. When the particles collide with each other, they can affect each other and induce a dipole oscillation. Due to this volatile distribution of charge, electric and magnetic waves are emitted as photons within a certain range of frequencies. Finally, the hotter an object is, the shorter the wavelength it emits. Thus, thermal cameras display hotter areas closer to white and darker areas closer to black. Also, if an object is hot enough it can emit thermal radiation that is visible to the human eye, a simple example being fire.

Well, that’s all folks!

Essentials of Fragrance Chemistry

By Matthew Tittensor, Nicholas Lang, and Sohum Sanghvi

Two more common hygiene products are perfume and cologne.  We know that these sprays smell nice and permeate throughout a room, but what is it that gives them their scent and more importantly why does it disperse?  In today’s blog post we will get into this by discussing the organic structures of esters, specific scents, commercial uses for esters, and the process of diffusion.

           An ester follows the format follows the format of the image to the right, with the R group being any hydrocarbon.  This is written a RCO2R’.  The alcohol component makes up the basis of the alkyl component and R’OH’s root name and is based on the longest chain with an OH attached to it. Meanwhile, RCO2H is the carboxylic acid, from which the –oate in the name is derived from.  The full name for an ester is an alkyl alkanoate. Now that the nomenclature is out of the way, what do esters smell like and would they be used in perfumes?

Esters often have a pleasant fruity aroma as can be seen in the chart to the right.  However, that does not necessarily make them ideal for perfumes.  Most simple esters give off these pleasant smells, but problems arise because they are not prepared to handle the sweat that a human body releases.  This sweat hydrolyzes the simple ester and can replace this seemingly nice smell with a harsh one.  A common example is that butyric acid smells like rancid butter, but ethyl butyrate, an ester it can be derived from, smells like pineapples.  This is one reason that simple esters are not utilized in the perfume industry.  However, perfumeries get around this by often including many esters in their products as well as essential oils to prevent the hydrolysis of the esters.  Esters serve a role in the food and beverage industry as well.

           Would you rather eat a delicious food that smells rancid or a mediocre food that smells delicious, if you did not know how each one tasted?  This is a problem that major manufacturers come to face when they make their products.  These companies utilize a combination of esters and essential oils as well to produce a scent that is please to both smell and taste.  It is not so simple as getting one pleasant odor and taste either, as the human has over 9000 taste receptors on its tongue and smell plays a large role in perception of taste.  To create an ideal, it takes a lot of testing and a wide variety of organic and synthesized compounds to be used.

           Diffusion is the movement of molecules from an area that contains a higher concentration to one with a lower concentration of the molecule.  These molecules are already in constant motion and move in random directions due to the random collisions that they experience with each other and other particles.  The net movement is always towards the lower concentrated expanse as more collisions occur on a more highly concentrated zone, making it more likely for the molecule to be pushed over to the other area.  Dynamic Equilibrium only comes to exist after the concentration gradient, difference in molecule distribution, is removed.  This applies to perfumes and colognes as they emanate from their more highly concentrated location on the wrist or neck to the areas surrounding the wearer.  This creates a nice scent around the user and fulfills the purpose of removing or covering up body odors.

We have taken a look at the concept of esters, specific scents, commercial uses for esters, and basics about the process of diffusion. Using the right ester is vital for obtaining the scent that is wanted, and diffusion is important for making sure the scent remains on the user and covers the body odors. In our next blog post, we will continue our discussion on fragrances and continue to unveil interesting chemistry behind perfumes and colognes.

Balls from Fury: Buckminsterfullerene (C60)

  There’s a molecule out there that can hit a stainless steel plate at 15,000 mph and just bounce back. It’s the state molecule of Texas, if that says anything. And you probably already know what it looks like. If you said the molecule is a buckyball, you’re correct. Buckyballs, specifically C60, look almost exactly like a regulation soccer ball, in order to produce extremely stable sp2 bonds throughout all 60 of the

carbons. Buckminsterfullerene, the more technical name for buckyball, was based on the domes of world famous architect Buckminster Fuller. The purported structure of C60 upon its discovery looked remarkably like many of his domes (well, more like B80but that’s another story).

Buckminsterfullerene has a density of 1.65 g/cm3. In its solid form it takes on the appearance of rather dark, needle-shaped crystals. It won’t stay that way for long, for it sublimes at around 800 K. Being that it’s made up of all carbons, it’s a nonpolar substance; it won’t dissolve in water, and it’ll barely dissolve in other nonpolar substances like benzene. When stimulated with life, it prefers to act as an electron acceptor, in the same manner as an electron-deprived alkene. Unless it’s in solution, it doesn’t prefer to be reduced, with each individual reduction from C60 to C606- being negative and approaching the penultimate -2.549 V at the final reduction at 213 K. It does prefer being oxidized, however, at very low temperatures, though past C60+ the products tend to be rather unstable. And here’s a kicker–buckyballs are the largest known molecule to exhibit wave-particle duality (at least in a diffraction grating). It’s a wonder we’ve even discovered a molecule with these properties; in fact, mostly everything about this molecule is still a wonder.

 One of the Best Accidents?

 C60 became nothing short of a chemist’s dream come true upon its discovery in 1985. Yet, it was discovered purely by accident by H.W. Kroto, J. R. Heath, S. C. O’Brien, R. F. Curl & R. E. Smalley at RICE University in Houston, Texas. The understanding of how long chains of carbon were formed in interstellar space was sought. Lasers shot at a rotating disk of graphite in concentrated helium, and… well, the researchers ended up being inevitably shocked. Sure, they found molecules containing 40 or more carbons, but most prominent was the presence of 60 carbons (followed by 70). Conventional structures did not seem to work in having a molecule of 60 carbons be stable, so they sought alternatives. One structure they noted is as follows: “the C60 molecule which results when a carbon atom is placed at each vertex of this structure has all valences satisfied by two single bonds and one double bond, has many resonance structures, and appears to be aromatic.” Even by this alone was the structure hinted at. They hypothesized that “fragments are torn from the surface as pieces of the planar graphite fused six-membered ring structure. … When these hot ring clusters are left in contact with high-density helium, the clusters equilibrate by two- and three-body collisions towards the most stable species, which appears to be a unique cluster containing 60 atoms.” They even specified the diameter of the molecule, 7 angstroms, which was enough to stick an atom inside. The rest of the chemistry world found this discovery to be nothing short of awesome, and Kroto, Curl, and Smalley were awarded the 1996 Nobel Prize in Chemistry for this.

The only issue in the discovery was that the initial method of production failed to produce substantial quantities of buckyballs. 5 years later, a technique using the evaporation of graphite electrodes in a light atmosphere of helium emerged, allowing for the mass production of buckyballs. Or, as discovered later on, one could just sublime the buckyballs out of graphite.

Possibly the Only Ball Safe for Human Consumption

    In these previous 29 years of existence buckyballs have found potential uses in this world. For instance, doping a buckyball with potassium results in a superconductor that is functional at temperatures of 18 K, which a high temperature for a superconductor. Moreover, there’s evidence to show that buckyballs can bind to the insides of the protein HIV protease, effectively inhibiting their function and not allowing the HIV virus to replicate. And they may be even useful antioxidants. Buckyballs have a tendency to act as an electron reservoir; they can give free radicals (molecules specifically desiring an electron to become stable) the extra needed electron in order to stop them from taking electrons from other molecules inside the body. Plus, C60 is known to not be toxic to human cells, and it has the ability to go inside of cells rather easily. In fact, there’s olive oil with buckyballs dissolved in it at a concentration of 45 mg/50 mL on the market.

You Might Want to Duck

 

Even when leaving the confines of Earth, buckyballs were from its discovery speculated to exist in interstellar space, specifically because it has the ability to form in some of the mostadverse conditions known to exist. One theory about its formation is that UV irradiation takes PAHs (polycyclic aromatic hydrocarbons) and converts them to graphene and then into buckyballs. This is seemingly more efficient than an alternate explanation, one in which carbon atoms clump together in the hot, dense center region of stars.

The first place that buckyballs were found in (along with hydrogen) were planetary nebulae. Three nebulae with dying stars like ours contained these buckyballs; what makes this remarkable is that these stars were in our own galaxy. (Even more so, there was a nearby star containing buckyballs in a mass of nearly 15 times larger than that of our own moon). Nebulae are emitted by dying stars; in the middle of all the layers of gas being shed there is a white dwarf holding it all together. There is a stage where the white dwarf spits out a lot of carbon. Even more astounding was the hydrogen it was found with: researchers had previously assumed that the presence of hydrogen would cause it to form the chains and rings originally sought after. And that was just in the gaseous form: in 2012 it was found in solid form. What that means is not yet clear, but it can imply that it might have been a building block of life.

You’re probably sitting there shaking your head. So what if a molecule’s been found in space? It probably isn’t of much importance, is it? All these claims are surely false. Wrong. Buckyballs have been found in meteorites. Meteors, being the huge hunks of rock they are, have the ability to house materials not seen and never before seen on a planet. When they become meteorites and slam into Earth, not only does the resulting collision cause adverse climate changes (which no organism really likes, as evidenced by mass extinctions usually brought along with them) but it can also spread those materials all over Earth.

As stated at the beginning, a buckyball can hit a stainless steel plate at 15,000 mph and just bounce back, and it can also house atoms or even molecules inside. For instance, there was anasteroid impact marking the end of the Permian period, which took out nearly all life on Earth. The meteorite has been found to contain buckyballs housing helium-3 and helium-4, with helium-3 now being present in the atmosphere.

“Buckyballs are carbon molecules in the shape of a cage and they are very tough and hard to destroy,” said Kris Sellgren, a professor of astronomy at The Ohio State University in Columbus, OH.  She noted that although life forms, let alone a single molecule of DNA, absolutely dwarf a buckyball, “single atoms or small molecules can become trapped and can survive inside the cage while the buckyball safely travels through the harsh conditions of space.”

“Buckyballs with extraterrestrial gases trapped inside them, for example, have previously been found in meteorites that have slammed into Earth. Spotting buckyballs in interstellar space also reveals that relatively big molecules can persist and maybe even form in the diffuse, unforgiving voids between the stars.” These are something your regular soccer balls can’t handle.