About this picture...

Getting Help
CHEM 1810 (Lab)UVA Home

Chemical Principles Laboratory (CHEM 181L)

Molecule of the Week Archive

Identify this molecule and expalin how it and the cranberries people eat over Thanksgiving may just save their lives someday.

Moleculae of the Week


From Christopher Yang: The molecule of the week is quercetin which belongs to a class of compounds called flavonoids which have a similar molecular structure to that of flavone. Quercetin is found in many fruits (cranberries contain a relatively high amount of quercetin compared to other fruits), vegetables, and even some drinks like tea. This molecule has sparked interest recently in the scientific community because it has been found to have many therapeutic effects when consumed. Although much research still has to be done, scientists are suggesting that it can help people afflicted with artherosclerosis, high chloesterol, schizophrenia, asthma, cancer, chronic fatigue syndrome, gout, etc. This is surprising because the nature of each of these illnesses are very different from each other yet quercetin seems to have a therapeutic effect for all of them. It is foreseeable that quercetin could be used to create a widely used drug in the near future.

References: Quercetin. (accessed Dec 1, 2013).

Neto, C. C. Cranberry and Its Phytochemicals: A Review of In Vitro Anticancer Studies. J. Nutr., 137, 1865-1935, 2007.


Explain how the structure of the drug shown below, aka AZD8329, was determined using H1-NMR and density functional theory (DFT) calculations.

Moleculae of the Week


From Sarah Koch: A team of international scientists, led by Lyond Emseley and Graeme M. Day, used solid-state NMR to determine the 3D structure of AZD8329. The innovative process included three steps. First, the scientists used computational analysis to find the possible crystal structures of the molecule. Then, they used density functional theory chemical shift calculations to create plots of the 1H NMR shifts that would result from each crystal structure. Next, they ran NMR spectroscopy on the molecule and compared this experimental data to the various possible 1H NMR shifts obtained using density functional theory chemical shift calculations to find the correct crystal structure.

References: Kemsely, Jyllian. "Solving Powder Structures." Chemical and Engineering News. 11 Nov 2013. Accessed 17 Nov 2013.


Identify these three "sick" molecules and discuss what they have in common.

Molecule of the Week


From Caleb Ziamba: The first molecule is 2-(2-chlorobenzylidene)malononitrile and it is the primary ingredient in tear gas, also known as CS gas. Tear gas is used for riot control due to this chemical, which reacts with the moisture in the eyes, nose, mouth and throat to cause burning sensations. The result is the victims closing their eyes, excessive tear production (from which the gas derives its name), coughing, mucus pouring out from the nose, and in severe cases vomiting.

The second molecule is diphenylchloroarsenic, or sneezing gas, was used as a chemical weapon in WW1 trench warfare. It induced vomiting and was able to penetrate the gas masks of the time, causing irritation and forcing removal of the mask.

The third molecule is another sneezing gas, 10-chloro-5,10-dihydrophenarsazinine, also known as adamsite. Although its effects are similar to the other compounds, adamsite has a brief incubation period of 5 minutes before the effects are experienced. All three of these compounds contain Cl and benzene rings, which together may be one cause of the effects they induce. They may be considered "sick" molecules due to both its use as a chemical weapon and for it causing vomiting in its victims.


In 1997—is this the year you were born?!—I published a paper with Suzanne Harris and Kay Carter describing the bonding in the dimethylthiophene complex Cp*(PMe3)Rh[C,S-2,5-Me2(SC4H2)]. Track down the paper and describe the molecular orbital interactions involved in the HOMO.


From Caroline Kerr: The HOMO of the dimethylthiopene complex is an antibonding orbital formed from the interactions between the dz2 orbital of the metal fragment and the HOMO of the thiopene fragment. The dz2 orbital of the metal is a nonbonding orbital and the HOMO of the thiopene fragment is a pi bonding orbital with much of the electron density centered around the sulfur and the α carbon of the thiopene fragment. The interactions between the two orbitals occur between the upper lobe of the thiopene pi orbital and the torus of the metal's dz2 orbital, and between the lower portion of the pi orbital and the lower lobe of the dz2 orbital. The HOMO of the dimethylthiopene complex is the antibonding molecular orbital from these interactions. It has significant sulfur pi character from the HOMO of the thiopene fragment, which is a pi orbital concentrated around the sulfur atom.

Reference: Palmer, M., Carter, K., & Harris, S. (1997). Structure, bonding, and reactivity in transition-metal-inserted thiophene complexes. Organometallics, 16, 2448-2459.


Identify this drug and give me your best advice as to whether you think I should continue taking it after 4 months of daily use.

Molecule of the Week


From Claire Schacht: This drug is Diclofenac and it is a nonsteroidal anti-inflammatory drug taken to relieve a wide range of inflammatory disorders, one being arthritis. I would not recommend that this drug be taken long-term, or longer than 4 months, because it can cause other medical problems. While there is a range of various side effects this drug can have, the most common is gastrointestinal problems. Specifically, if taken for a long period of time, the drug can erode areas of the gastrointestinal tract and cause peptic ulcers or peptic ulcer disease.

References: Retrieved October 23,2013 from http://www.drugs.com/diclofenac.html

Retrieved October 23, 2013 from http://en.wikipedia.org/wiki/Diclofenac

Explain why these thermoacoustic speakers are cool but not cool.


From Rawan Abdelrahman: Thermoacoustic speakers are a recent technological development in the world of speakers. Unlike traditional speakers, which were comprised of a cone, magnetic field and a coil through which an AC current was passed (this caused the cone to move, push air and thereby create pressure waves), thermoacoustic speakers are built upon the theories of thermoacoustics, which involve heating a material to produce sound. Electrified nanotubes of carbon (utilized because of their conductive properties) are positioned on a lattice of silicon and are rapidly warmed up and cooled down: this temperature fluctuation produces sound waves. Because heat is being used to produce the sound waves, the speakers are therefore warm instead of being cold. Since the speakers lack actual vibrating parts, they have greater durability than traditional speakers. Recent research by Chinese scientists has also discovered that these thermoacoustic speakers do not just work on land but that they are also capable of being used underwater (at frequencies of 1Hz- 100KHz).

References: Atherton, K. D. Thermoacoustic headphones make sound with hot nanotubes. (Accessed Oct 15, 2013)

Berger, M. Nanotechnology loudspeakers keep on rocking- even underwater. (Accessed Oct 17, 2013)


Explain why the microbeads shown below are not as good for the Great Lakes as they might be for your face.



From Madina Kamilova: Microbeads are polyethylene microplastic particles, typically less than 1 mm in size, that are usually used in skin cleansing products as exfoliators. When they are washed down the drain along with the cream/soap, they end up in marine waters and act as debris and pollutants just like any other piece of plastic. These microbeads are often eaten by organisms in the lakes and can be digested; therefore, they are a safety hazard for marine biology.

Reference: Hogue, C. (2013). Microplastic Beads Pollute Great Lakes. Chemical & Engineering News, 91(37), 23-25.

Identify this molecule and explain why it comes as a breath of fresh air to many people.

Molecule of the Week


From Mason Brannon: Although the above molecules scientific name is 4-(2-(tert-butylamino)-1-hydroxyethyl)-2-(hydroxymethyl)phenol, it is known to the many people suffering from asthma and other respiratory problems as Albuterol . Albuterol, which belongs to a family of medicines known as adrenergic bronchodilators, is used to treat patients with a wide variety of respiratory issues, most commonly asthma, but also including bronchitis and emphysema. Essentially, Albuterol works by opening up the bronchi in order for air to pass by. If used in excess, Paradoxical bronchospasm can occur which actually is an extreme form of wheezing. It is known as "paradoxical" because in excess, a drug that traditionally reduces wheezing and opens bronchi will collapse the bronchi and induce potentially life threatening wheezing. Albuterol originates as a solid white crystal, however, in order to be administered directly to the affected area (the bronchi and respiratory system), it is sometimes combined with sulfate or dissolved into a solution that can then be inhaled. Interestingly, this molecule is also used in inhalation form with patients with Hyperkalemia, which is a condition in which someone has too much potassium in the blood. Albuterol saves the lives asthma patients everyday and it's fascinating to discover that this relatively simple chemical structure can play such an important role in the treatment of respiratory diseases.

References: The Mayo Clinic, Albuterol (Inhalation Route). http://www.mayoclinic.com/health/drug-information/DR603121 (accessed Sep 22, 2013).


In 1982, Joel S. Miller of the University of Utah was part of a team that uncovered a single compound containing all five of the major types of chemical bonds (see image below). What is the compound, what are the different bond types, and which parts of the compound form them?

Molecule of the Week


From Madeleine Stone: The compound K2Pt(CN)4Br0.33H2O in its solid state has the five major types of chemical bonds. These bonds include covalent bonds, coordinate covalent bonds, ionic bonds, metallic bonds, and hydrogen bonds. The covalent bonds include O-H (single) and C-N (triple) bonds. The coordinate covalent bonds include the Pt-CN bond. The ionic bonds include K-Br and K-Pt(CN)4. The metallic bonds include the bonds between Pt atoms. Hydrogen bonding is between the H2O molecules and Br- as well as CN .

Masuo, Steven T., Joel S. Miller, Elizabeth Gebert, and Arthur H. Reis. (1982). One-dimensional K2Pt(CN)4BrO 3•H20. A Structure Containing Five Different Types of Bonding. Journal of Chemical Education, 59.5. Retrieved from http://pubs.acs.org/doi/pdf/10.1021/ed059p361.

Identify HFO-1234yf and explain why it is so "cool" compared to other similar molecules.


From Sarah Wyckoff: HFO-1234yf is also known as 2,3,3,3-Tetrafluoropropene, and its molecular formula is CH2=CFCF32. According to Wikipedia, HFO-1234yf is “cool” because it can be used as a cooling agent in air conditioners—particularly those in automobiles. It is “cooler” than other similar molecules, like R-134a, because it has a lower environmental impact and is considered greener. It has an “atmospheric lifetime that is about 400 times shorter than R-134a. HFO-1234yf degrades to trifluoroacetic acid which has been found to make an insignificant contribution to the formation tropospheric ozone (aka smog).

Environmental Protection Agency. (2012, June). Air Quality: Revision to Definition of Volatile Organic Compounds – Exclusion of trans-1,3,3,3- tetrafluoropropene.

Wikimedia Foundation. (2013, July 10). 2,3,3,3-Tetrafluoropropene.


Discuss the link between this Madagascar frog and the molecules shown.



From Lekha Pandya: These molecules (L-R) are Gephyromantolide A, 8-Methyl-2-nonanol, and (S)-Phoracantholide J. These are airborne chemicals that Mantellidae frogs (a family found on the island of Madagascar) use to communicate. 8-Methyl-2-nonanol, and (S)-Phoracantholide J are pheromones produced in the femoral glands of these frogs, and these pheromones then waft through the air. Other frogs are able to detect this, and will hop toward the source of these signals. Because each species produces these pheromones in a different ratio, the odors are important in helping with species recognition. The third chemical, Gephyromantolide A, is another natural product that was recently discovered. It is thought to also function in airborne communication, but its exact role has not yet been determined.

Everts, Sarah. "First Airborne Frog Pheromone." Chemical and Engineering News 6 Feb. 2012: n. pag. American Chemical Society, 6 Feb. 2012. Web. 6 Dec. 2012.


These toxic molecules, produced by seaweed, damage some of the most fragile coral in the oceans. Identify the class of molecules they belong to and the unlikely sea critter that gobbles them up.



From Gloria Marino: Corals in the genus acropora are highly prone to damage from a certain toxic seaweed, chlorodesmis fastigiata, better known as turtleweed. This seaweed produces two toxic terpenes, as shown in the picture above. Terpenes can be either hydrocarbons or have ketones and aldehydes. They can also be found in cleaning products and certain topical medications. When this toxic seaweed comes in contact with the coral, the coral releases an odor that attracts goby fish. These fish eat up the seaweed and thereby reduce the damage that it would cause. After eating it, the goby become toxic and are thereby more protected against predators. In this way, gobies exhibit a symbiotic relationship with coral. Fun fact: these gobies are only 3 cm long but are responsible for protecting the main structural component of most coral reefs!

Dixson, D.; Hay, M Corals Chemically Cue Mutualistic Fishes to Remove Competing Seaweeds. Science. 9 November, 2102. (Accessed November 26, 2012).

Everts, S. The Coral-Seaweed Battleground. Chemical and Engineering News. (Accessed November 26, 2012).

Kashani, J. Terpene Toxicity. Medscape Reference. (Accessed November 26, 2012).


This molecule and others like it are at the center of a recent lawsuit. Identify the molecule and discuss the merits of the lawsuit.


From Ellen Hightower: The molecule shown is glucuronolactone, which is a naturally occurring chemical that is found in connective tissues. It is often used in energy drinks as a means of detoxifying the body. Glucuronolactone has been shown to interfere with the synthesis of toxic by-products linked to heavy exercise or fatigue.

The recent lawsuit regarding glucuronolactone concerns an FDA statement that 13 deaths may have been caused by the consumption of 5-Hour Energy, a popular energy drink. 5-Hour Energy contains high amounts of caffeine, taurine, glucuronolactone, and malic acid, among other ingredients. In addition, 30 out of 90 cases regarding the effects of 5-Hour Energy have stated that the drink caused serious or life-threatening conditions, such as miscarriages or heart problems.

CNN Health. FDA investigates deaths preliminarily linked to energy shots. (accessed Nov 22, 2012).

The Merck Index. D-Glucuronolactone. (accessed Nov 22, 2012).

Newsmax. 5-Hour Energy Cited in 13 Deaths; Caffeine in Energy Drinks Blamed. (accessed Nov 22, 2012).

The Use of Taurine and D-Glucurono-gamma-lactone As Constituents of the So-Called "Energy" Drinks. EFSA Journal [Online] 2009, 935, 1-31. (accessed Nov 22, 2012).

Wikipedia. Glucuronolactone. (accessed Nov 22, 2012).


Identify this molecule and discuss its importance to dogbane beetles and milkweed bugs.

Molecule of the Week


From William Martin: While ouabain is actually lethal to many animals (including humans!) in anything but minute doses (if small enough, it can help with heart function), it is a very interesting subject when it comes to dogbane beetles and milkweed bugs. To ward off insects and other animals that may eat their leaves for lunch, plants such as milkweed (in addition to foxglove and oleander) produce heart-stopping and brain-freezing compounds called cardenolides, which are toxins. Ouabain is one of these cardenolides produced by these plants, and it is meant to act as a defense mechanism against these leaf-eating insects. In response to this, a wide variety of insects, including dogbane beetles and milkweed bugs, have evolved and developed a resistance to this poison, allowing them to continue eating these plants that produce such cardenolides. A research team found that these poison-leaf-eating insects developed a few mutations on a specific protein, which in turn blocks any ingested cardenolides (like ouabain) from binding, and therefore having any effect. Additionally, the same research team discovered that instead of inheriting this mutation from a common ancestor, diverse species of insects have evolved this poison protection mechanism in parallel.

Source: Chemical & Engineering News. Volume 90 Issue 41, p. 48. Issue date: October 8, 2012.


The most recent article of C&ENews has an article about hexabromocyclododecane. Identify the article, determine what this molecule is traditionally used for, and discuss the controversary surrounding it as well as alternatives. Don't forget to properly cite your source(s).


From Katie Brodie: A Chemical and Engineering News article from October 29, 2012 titled "Ablazed Over Furniture Fires" talks about the presence of flame retardant chemicals in furniture and their risks to health. Almost all furniture has some sort of flame retardant found usually in the polyurethane foam of the furniture's innards. One particular chemical, hexabromocyclododencane that is used as a flame retardant in furniture, is under fire (no pun intended) by the EPA for the health risks it carries. Hexabromocyclododecane comes from a class of flame-retardants known as pentabromodiphenyl ethers. Some scientists insist that brominated flame-retardants, such as hexabromocyclododecane, can act as endocrine disrupters or have neurological and other health effects. It has even been found to accumulate in the tissues and has been detected in the blood of adults and children. Children are at the most risk to have chronic health problems resulting from exposure to these fire retardants. Not only is it argued that these flame-retardants are toxic, it is also thought that are not as effective as they are advertised to be. The scientists studying their toxicity and use have a goal of removing these flame-retardants from furnitures.

Schulz, W. Ablazed Over Furniture Fires. Chemical and Engineering News. 2012.


Identify this molecule and decide whether the benefits of it are worth the risks. Make sure your sources are scientific.



Maha Hassan: N,N-diethyl-3-methylbenzamide, also known as DEET, is the most common active ingredient in insect repellents. Compared to other synthetic and botanical repellents, DEET protects considerably longer against insects. However, negative effects can occur, usually as a result from the overuse of DEET or high concentrations. Additionally, DEET does irritate mucous membranes, and at high concentrations, can dissolve plastic. With this information, DEET's benefits outweigh its risks, if used properly. A repellent with a low concentration of DEET should be used conservatively, and should be washed off from clothes and skin when it is no longer needed.

Citations Richard J. Pollack, Ph.D., Anthony E. Kiszewski, D.Sc., and Andrew Spielman, Sc.D. N. Repelling Mosquitoes. England Journal of Medicine. 2002, 347:2-3 (accessed Oct 29, 2012)

Deb, Utsab; Ahmed, Fakhruddin; Singh, Seema; Mendki, M. J.; Vijayaraghavan, R. Comparative effects of insect repellent N,N-diethylbenzamide, N,N-diethylphenylacetamide, and N,N-diethyl-3- methylbenzamide aerosols on the breathing pattern and respiratory variables in mice. Inhalation Technology 2010 pp 469-478. (accessed Oct 29, 2012)


This molecule changed the course of history. Identify it, describe it's infamy, and discuss the general features of the class of compounds it belong to.



Michael Zhang: The molecule of the week is coniine, which is found in the plant Hemlock. As many of us know, Socrates was sentenced to death for "corrupting the minds of the youth" for refusing to retract his principles and retract his claim that only wise people acknowledge their own ignorance. He basically critiqued the government and high officials and was termed the "gadfly" of Athens. The punishment was drinking a solution containing hemlock. It's a poisonous neurotoxin that causes respiratory paralysis, and belongs to a group of compounds called alkaloids, compounds that contain nitrogen. Many other alkaloids are toxic to animals. These compounds can also be synthesized into medications.

Wikipedia. Coniine. (accessed October 16, 2012) Wikipedia. Alkaloid. (accessed October 16, 2012)


This molecule has a distinctive flavor and odor. Identify it and explain why, although it's completely edible, it's not possible to eat an entire teaspoonful of it at one time.



From Sarah Tait: The molecule of the week is cinnamaldehyde. A popular game called the "cinnamon challenge" requires a person to eat an entire teaspoon of tablespoon without water. Though it sounds simple enough, it's actually impossible to do. The cinnamon powder blocks the salivary glands, preventing them from releasing any saliva into the mouth. When the salivary glands are functioning, saliva helps to lubricate food and allow it to easily pass into the esophagus and down into the stomach. Without saliva or water, the cinnamon just sits in the mouth and causes choking and coughing. Choking and coughing, in turn, can allow some cinnamon powder into the lungs. Any fine powder that coats the lungs can lead to infection and pulmonary edema. Finally, while taking the cinnamon challenge some have had such a strong coughing reaction to the cinnamon that a lung collapses. Though cinnamon itself is not bad for the body, attempting to swallow a teaspoon of cinnamon without water is not only impossible, it's dangerous.

ABC News: Medical Unit. 'Cinnamon Challenge' Sparks Health Concerns. (accessed Oct 9, 2012).

CBS News. Popular "Cinnamon Challenge" Has Potential to be Deadly. (accessed Oct 9, 2012).

Today Moms. Poison Centers Warn About Cinnamon Challenge. (accessed Oct 9, 2012).


Research the new guidelines for labeling sunscreens and comment on whether you think this new system is better for consumers. If you use web sources, make sure they are legitimate and as unbiased as possible. Click here for a guide to help you decide.


From Madeleine Fleshman: The Food and Drug Administration has released a series of updates concerning labeling on sunscreens. They encourage consumers to be aware of the changes and completely read the labels so they can understand the differences and which sunscreen best protects them.
Some of the main changes:

  • All sunscreens must undergo new testing for effectiveness in skin protection
  • Sunscreens no longer can list an SPF higher than 50 since there is no evidence that an SPF higher than 50 is any more effective. Labels now say SPF 50+.
  • Sunscreens that prevent against all types of sun damage (ultraviolet A (UVA) and ultraviolet B (UVB) radiation) will be labeled “Broad Spectrum”
  • Sunscreens that are not Broad Spectrum or have an SPF 2-14 will have warnings on the label.
  • Waterproof sunscreens must indicate how long they remain effective (40 or 80mins).

"FDA Sheds Light on Sunscreens." U.S. Food and Drug Administration. U.S. Department of Health & Human Services, 9 Aug. 2012. Web. 30 Sept. 2012.


This molecule is often added to dog foods. Identify it and decide whether you would buy foods for your pup that contain it. Be sure to include properly formated references.



From Allie Ivener: The molecule is L-methionine.I would definitely feed my dog food with l-methionine in it. Methionine is one of the 10 essential amino acids to have in a diet and it is not produced in the body. It is added to a dog's food to enhance its diet. One study showed that a lack of methionine in a dog's diet led to severe weight loss and loss of appetite. Additionally, methionine is known to treat liver disorders, to help the liver process fats, and to improve wound healing. It also provides sulfur to help prevent disease of the skin, hair, and nails. Mainly, methionine is involved in controlling the acidity of urine. It helps to regulate the formation of ammonia and the ammonia content in urine. Based on those benefits, I would feed my dog food with this molecule in it.

Dodman, N. Methionine. (accessed 9/26/2012). Nutrition Requirements of Dogs and Cats; The National Academy of Sciences: Washington, D.C. 2006.

MP NOTE: Some studies have show negative side effects when given in too high of levels.

Dagada, R.; Advances in Aging Research: Why Methionine Restriction is an Attractive Life-Extension Strategy. Examiner, July 14, 2009; (accessed Sept 22, 2012).


Not a bad molecule to have during these hot, muggy days. Research it and let me know what it's used for.
Be sure to include properly formated references.



From Thamanna Nishath: The molecule of the week is Quinine; it comes from a plant named Cinchona succirubra (1). It is used to treat malaria (2).

  1. "Quinine Bark." Rainforest-Database. N.p., n.d. Web. 19 Sept. 2012.
  2. "Quinine." Quinine. U.S. National Library of Medicine, 1 Feb. 2011. Web. 19 Sept. 2012.

Watch The Icy Finger of Death and then send me via email a brief description of the chemical principle at work and at least two other common examples which make use of the principle.



From Bryan Cochran: The chemical principle behind the 'brinicle' is that adding an impurity to a substance will raise its boiling point and lower its freezing point. Salt in this case is the impurity. The super salty brine water has a lower freezing point and is much colder than the surrounding ocean water so the ocean water freezes on contact.

Another example of this is adding salt to water when boiling it for pasta. By adding the salt, the boiling temperature is raised just slightly and better cooks the pasta.

Another example of this principle can be seen in winter time when salt trucks dump salt out on the roads. The salt lowers the freezing point of the snow/water and makes it harder for ice to form on the roads.

Identify the common name for this molecule, discuss its natural origins, and identify the elict drug it's used to make.

Moleculae of the Week


From Ben Learner: The molecule is 5-allylbenzo[d][1,3]dioxole, also known as safrole, which is an oil extracted from sassafras plants. In plants, it functions as a natural pesticide. Safrole is also used to manufacture the drug MDMA, widely known as ecstasy. Safrole has been found to be a carcinogen in rats. [Funny that the structure looks like a rat! MP]

Citation "Safrol." Report on Carcinogens (1981). Web. 30 Nov. 2011.

From Thomas Scheevel: There are multiple routes for synthesiszing ecstasy, but one stood out as particularly easy—just required the addition of HBr followed by methylamine to safrole. By some quick checks and estimations I made, it seems like this could be used to make over a thousand tabs of ecstasy for under $200!


Reading the label of my Powerade Ion4, I came across the following ingredient: glycerol ester of rosin. Identify this Molecule of the Week and tell me what it's doing in my drink. Convince me that your source is trustworthy (and not just a paid advertisement)


From John Neseman: According to several sources, glycerol esters of resin acids of wood rosins or glycerol ester of rosin is used as an additive in beverages and chewing gum. Rosin is collected from the stumps of the longleaf pine (Pinus palustris), purified, and mixed with other ingredients to form a thickening agent called ester gum. This ester gum is usually used to stabilize food such as ice cream and chewing gum, and is not suitable for beverages. However, when it is combined with glycerol it becomes a useful stabilizer for beverages. The wood acid composition of rosin can vary a lot however the main one is abietic acid and the rest are a complex mixture of isometric ditrepenoid monocarboxylic acids with an empirical formula of C20H30O2. The main use of glycerol ester of rosin is used to help the flavoring oils mix with the carbonated water, or just normal water, in many commercial drinks. As oils do not mix well with water the addition of glycerol ester of rosin lets the flavoring oils remain in suspension when blended with water instead of remaining separated. There is not much evidence that wood rosin can be detrimental to the health of consumers. Even so, the FDA prevents a concentration of 100 parts of wood rosin per million, thus there is only a trace amount of wood rosin in a typical comercial drink.

Dr G.J.A. Speijers, GLYCEROL ESTER OF WOOD ROSIN (food and beverage grade) at RIVM; Bilthoven, Netherlands. (accessed Nov 17, 2011)

Code of Federal Regulations: Sec. 172.735 Glycerol ester of rosin. (accessed Nov 17, 2011)

JECFA; Glycerol Ester of Wood Rosin. (accessed Nov 17, 2011)


Identify the following two molecules and discuss why they're important to honey bees.

MOleculae of the Week


From Alex Reed: The top molecule is (E)-9-hydroxydec-2-enoic acid, also known as 9-HDA. 9-HDA is part of a "pheromone cycle" for bees, in which worker bees convert 9-ODA, sent by the queen, into 9-HDA and send 9-HDA back to the queen. 9-ODA is produced in the mandibular glands of the queen bee. These pheromones are used for communication between the queen bee and worker bees. The 9-ODA produced by the queen after the queen receives 9-HDA from the workers is involved in "caste maintenance."

The second molecule is (E)-10-hydroxydec-2-enoic acid, also known as 10-HDA. This molecule is secreted by young honeybees and maintains the freshness of the royal jelly. It is capable of fighting gram-positive bacteria, viruses, and fungus. As a result, this molecule prevents illness in the beehive by keeping the food source safe. Interestingly, 10-HDA is also valuable in medicine because of its ability to fight pathogens. It stimulates the production of antibodies and is frequently included in nutritional supplements

Kodai, T.; Nakatani, T.; Noda, N. The Absolute Configurations of Hydroxy Fatty Acids from the Royal Jelly of Honeybees (Apis mellifera). AOCS. 2010, 46, 263-270.

Royal Jelly. Guarantee 10-HAD. (accessed Nov 12, 2011). .


Watch this award-winning 'Dance Your Ph.D.' video and then dig a little deeper to understand the differences between the structures of alpha- and beta-titanium. In what ways are they different? And, why does this lead to the different properties the dance demonstrates?

From Laura Baker: Alpha titanium has a hexagonal close packed (hcp) lattice structure while beta titanium has a body centered cubic (bcc) lattice structure. In the hcp lattice structure, there are three layers of atoms. In the bottom layer and top layer, six titanium atoms are arranged in a hexagon shape with one atom in the center. In the middle layer, there are three titanium atoms that are situated in the gaps. In the bcc lattice structure, the titanium atoms are at eight corners of a cube and then there is one central titanium atom. This is the high temperature form of the titanium metal. The beta phase forms when the temperature is above 883 °C. The bcc structure does not allow the atoms to pack together as closely as the hcp structure; it is more loosely packed. The packing factor of the bcc structure is .68, while the packing factor of the hcp structure is .74. This information is in agreement with the video, which says that the alpha phase is stiffer than the beta phase of titanium. Stiffness is important in bone transplant considerations because bones have to be both flexible and strong.

NDT Resource Center. Primary Metallic Crystalline Structures. (accessed Oct 23, 2011).


Molecule of the Week


From Duanpeng (Roy) Ma: Nicotine is a well-known component of cigarettes, and nicotine addiction has been cited as one of the primary reasons why quitting cigarette smoking is difficult for many smokers. Many of the products that are sold as nicotine substitutes or smoking cessation aids, such as Fluoxetine Hydrochloride (also known as Prozac), and electronic cigarettes, have not been FDA approved. These products often have been known to have their own harmful side effects, and the companies that produce them often provide inaccurate information regarding the components of their product and health hazards involved in consumption.These non-FDA approved products are likely not safer for consumption than nicotine, because their adverse effects are still being researched, and they do often do not follow strict FDA regulations.

Trehy, M. L.; Ye, W.; Hadwiger, M. E.; Moore, T. W.; Allgire, J. F.; Woodruff, J. T.; Ahadi, S. S.; Black, J. C.; Westenberger, B. J. J. Liq. Chromatogr. Relat. Technol. 2011, 34, 1442-1458

Di, X.; Zhao, B.; Zhongguo Yancao Xuebao. 2011, 17, 71-77


Molecule of the Week

From Laura Baker: This molecule is called Bisphenol A, or BPA. It is used in polycarbonate plastics and epoxy resins. BPA can be dangerous at high levels because it acts as an endocrine disruptor and can mimic the body's hormones. This can cause large imbalances that lead to health problems, especially in early development. Research shows that BPA might contribute to cardiovascular disease, decreases in fertility, and some cancers.

Polypropylene, Polyethylene Terephthalate (PET), and High Density Polyethylene (HDPE) are all plastics that can be used as replacements for BPA. Polypropylene is a widely spreading alternative because it can be used to create re-usable containers. HDPE is not known to leach any suspected carcinogenic or hormone disrupting chemicals. PET is safe for one time use, but refilling a PET bottle might increase the possibility of chemicals leaching into the water. The plastic alternatives are not known to pose any major health risks, but more research is needed. Two additional alternatives for BPA bottles are aluminum and stainless steel. Stainless steel would be the best alternative, since it is known to be safe and it does not require a lining, unlike aluminum. An alternative for the BPA-containing sealants of canned foods and drinks is a lining made from the oil and resin extracted from plants.

Bounce Energy. The Dangers of BPA. (accessed Oct. 2, 2011).

National Institute of Environmental Health Sciences. Bisphenol A (BPA). (accessed Oct. 2, 2011).

Oregon Environmental Council. Safer Alternatives to Bisphenol A (BPA). (accessed Oct. 2, 2011).

Live Science. Are BPA-Free Plastics Really Safe? (accessed Oct. 2, 2011).


IMolecule of the Week

From Emily Tonks: The first molecule is oxybenzone and the second is known as an avobenzone. Both compounds can be used as sunscreen. Oxybenzone is the more effective sunscreen, however, because it protects against two types of UV light, UVB and UVA II, while the avobenzone only protects against UVA I radiation. Avobenzone's region of absorbtion also includes some rays of visible light which are not malignant to the integumentary system. The oxybenzone has also been proven safe for application to the human skin, while avobenzones are only just beginning to be marketed as sunscreens, and there are some concerns about their photostability.

Roscher, N.M.; Lindemann, M.K.O.; Kong, S.B.; Cho, C.G.; Jiang, P. J. Photochem. Photobiol. A: Chem,1994, 80, 417-421.

Juan, S.R.; Santiago, N.; Francisco, M.O.; Ricardo, M.; Adaya, G.S. 3-Dialkylaminophenyl 2-Alkoxycarbonylbenzoic Compounds. European Patent Office. 2010.


Molecule of the Week

From Triet Nguyen: This molecule belongs to a group of compounds called iso-alpha-acids that contribute to the bitter taste of beer, infamously known as skunking. As the beer ages, the iso-alpha-acids degrade and release a long-lasting, volatile aftertaste. This means that fresher beer is more likely to have a desirable bitter taste without the harsh aftertaste. In order to keep degradation of iso-alpha-acids low, the beer's pH level should be kept constant with its temperature as low as possible. Therefore, you should get fresh beer and store it on a cold place immediately so that it doesn't skunk.

Intelmann, D.; Haseleu, G.; Dunkel, A.; Lagemann, A.; Stephan, A.; Hofmann, T. J. Agric. Food Chem., 2011, 59 (5), pp 1939–1953.


Molecule of the Week


Vitamin D promotes calcium absorption in the gut, thus helping the body maintaining calcium and phosphate concentrations. Some have also suggested that vitamin D is essential for preventing various types of cancer, high blood pressure, cardiovascular disease, and immune system abnormalities, but no real strong evidence exists.

Adults need about 600 International Units (IU) of vitamin D per day. Most of this can be obtained through exposure to the sun; three 10-15 minute sessions of full sun exposure per week is sufficient. Experts also recommend eating natural sources of vitamin D (e.g. dairy products, egg yolks, fatty fish, lean meats).

Office of Dietary Supplements, National Institutes of Health's Dietary Supplement Fact Sheet: Vitamin D. (accessed Sep 12, 2011).

Congratulations to Arslan Zahid, winner of this week's chocolate!


Nylon 6,6

Nylon 6,6 is produce from the following reaction:


Congratulations to Sarah Heuer, winner of this week's chocolate!


Molecules of the Week


The two molecules play on the naming conventions for substituted benzenes. When bezene has substituents in the 1 & 2 positions, the prefix othro is attached to the name; 1 & 3, the prefix meta is attached; and 1 & 4, the prefix para is attached. Thus, the molecule on the left is "paradocs" and the one on the right is "metafour" :-)
Molecule of the Week

2,4,6-trinitrotoluene, or TNT, is the yellow-colored solid with the following spectral data:

     Molecular formula: C7H5N3O6

     IR: strong peaks at 1350 and 1530 cm-1

     1H-NMR: singlet @ δ ~1 ppm (3H)
                   singlet @ δ ~7 ppm (2H)

Note: The spectral data does not uniquely identify this as TNT; an alternative assignment is 3,4,5-trinitrotoluene. Do you think this particular compound is also yellow?


Molecule of the Week


The molecule is pacitaxel, or commonly know as taxol. It is a mitotic inhibitor used to treat patients with lung, ovarian, breast, and head and neck cancer. It was originally isolated from the bark of the Pacific yew tree, but, becuase of environmental impact, synthethic routes have been discovered. Currently, all paclitaxel production uses plant cell fermentation technology. The process starts from a specific Taxus cell line (related to the yew tree) propagated in aqueous medium in large fermentation tanks. Paclitaxel is then extracted directly, purified by chromatography and isolated by crystallization.


IR spectroscopy is the best tool to quickly distinguish between morphine and herione. Morphine will have a broad OH stretch around 3300 wavenumbers; heroine will not exhibit this stretch. Additionally, herione will have the distinct C=O stretch of a carboxylic acid around 1710 wavenumbers.

In early 2009, the FDA approved a new zero-calorie sweetner developed by Coca-Cola and the agribusiness giant Cargill. You may have recently seen commercials for it; it's marketed as Truvia. Truvia is composed of erythritol and a component from a small herb plant called stevia. Some research has been done on the safety of erythritol but relatively little is known about the strevia component. Identify this second component in Truvia and discuss whether you think it is safe for consumption based on current research. The research you cite must be peer-reviewed (i.e. from a scientific journal and not a website. Be careful what you believe because Coca-Cola sponsored much of the research out there.)


Rebiana (rebaudioside A), or stevia, is the second component of Truvia®. There are a number of recent articles reporting both positive effects (e.g. reduces high blood pressure) and negative ones (e.g. cytotoxic in large doses). The general concensus of the class—based on currently available research—is that this sweetner is safe for human consumption. Drink on...if you believe your classmates!

There are a couple of candidates for the chemical with the longest name in most shampoos: methylchloroisothiazolinone (left) and guar hydroxyproplytrimonium chloride (not pictured and much more complicated!). Methylchloroisothiazolinone is added to shampoo as a preservative and anti-bacterial/anti-fungal. It is added to other comsmetic products for these same properties. The guar compound primarily acts as a conditioner to reduce tangling.

Congratulations to Dianne Cheon, winner of this week's chocolate!



In 1973, Walter Morris published a paper containing high-resolution infrared (IR) specta of 99 fragrance and flavor compounds. Cuminaldehyde, eugenol, and carvone— components of the essential oils we'll explore later in the semester—were included. The reference is below. (Note that the title of the article is not included in the reference.)

Morris, W. W. J. Assoc. Off. Anal. Chem. 1973, 56, 1037-1064.

Congratulations to Mackenzie Long, winner of this week's chocolate!


Avobenzone is an oil soluble substance used in sunscreens. Its absorption max is at 357 nm, but is it considered a broad spectrum UV protectant because of its ability to absorb a wide range of UV light. Unfortunately, it degrades rather quickly. And, avobenzone binds with iron, causing it to stain skin and clothes. What's in your sunscreen?

Congratulations to Noaa Spiekermann, winner of this week's chocolate!



One of the Journal of the American Chemical Society articles we looked at this week in class was authored by William Jones. In a 1997 article I published with Prof. Jones, I predicted the structure of (C5Me5)Rh(PMe3)(η2-C,S-C4H2S) using computational chemistry which he later confirmed in the laboratory. The structure of the molecule is shown on the left and the complete and accruate citation to the article is:

Blonski, C.; Myers, A.W.; Palmer, M.; Harris, S.; Jones, W.D. Organometallics. 1997, 16, 3819-3827.

Congratulations to Jonathan Torre, winner of this week's chocolate!



Fluticasone priopionate (pictured) is mixed with salmeterol xinafoate (C25H37NO4) to make Advair, which is commonly prescribed for asthma.

Congratulations to Hyeon Jin Lee, the first to identify this week's mystery molecule!




Though it has many unique properties and uses, theobromine is most well known for its mild stimulant effects and the slightly bitter taste it imparts on chocolate.

Congratulations to Anne Knisely & Dylan Holt, the first to identify this week's mystery molecule!

© 2004-2013 Michael Palmer