Interpreting infrared spectra!

Brief overview:

The infrared spectrum of an organic compound provides useful clues about the compound’s molecular structure. When infrared radiation is applied to a compound, certain groups (e.g., alkyl, ketones, amines) can be identified. This is possible because the covalent bonds within these groups absorb characteristic wavelengths of infrared radiation; the wavenumber (cm-1) unit used in the IR spectrum below is simply the reciprocal of wavelength (increasing wavelength decreases wavenumber). When these groups absorb IR radiation, it causes their atoms to vibrate and thus their covalent bonds to stretch and/or bend.

Analyzing this spectrum:

From the graph and the table below it, the three most prominent absorption peaks (and therefore the three lowest transmittance percentages) are at wavenumbers 3358, 2974, and 1050 cm-1. Only alcohols (3200-3550 cm-1) and amines (3300-3500 cm-1) would significantly absorb at 3358 cm-1; furthermore, alcohols display strong, broad peaks while peaks from amines are of medium intensity: considering the 3358 absorption is relatively broad (for example, compared to the sharper, more concise peak just to the right at 2974 cm-1) and strong (only 12% transmittance), this peak is likely from the hydroxyl group (-OH) of an alcohol.

C—H bonds produce peaks from 2800-3300 cm-1. More specifically, C—H bonds with sp3-hybridized C atoms produce peaks from 2800-3000 cm-1. Hydrocarbon bonds attached to these C atoms are weaker and less rigid than those attached to sp2- or sp-hybridized C atoms. These more flexible bonds require less frequency, and thus less energy, to vibrate; it is for this reason that these weaker bonds absorb at the lower end of the wavenumber range (wavenumber = 1/wavelength; frequency = speed of light / wavelength; lower wavelength = lower frequency). Because the graph shows a considerable peak at 2974 cm-1, it suggests our compound includes C—H bonds in which the C is sp3-hybridized.

Stretching of the C—O bond of ethers, alcohols, and esters produces peaks within the 1020-1275 cm-1 range; our 7% transmittance peak at 1050 cm-1 may therefore be from this bond.

While infrared spectrometry is an extremely useful tool in identifying a substance, it is one of many available tools, and we would be hard-pressed to determine a chemical’s identity on this information alone. However, if our spectrum above was accompanied by a boiling point, a melting point, molecular weight, solubility information, or other spectroscopic data, it would be MUCH easier to identify this unknown as ethyl alcohol, aka ethanol!

Posted 7/14/2018

Updated 7/22/18

Reward your cat and repel your mosquitoes: Use catnip to kill two birds with one lactone - Sunday, July 8, 2018

Catnip has long been hailed as an exhilarating treat for furry felines, but are you aware of the plant’s deterrent effect on mosquitoes?

This plant, known more formally as Nepeta cataria, is also effective at warding off beetles (Arthur, Fontenot, & Campbell, 2011) and flies (Zhu et al., 2009).

What cats find so alluring and bugs find so distasteful in catnip is its primary component: nepetalactone (Simmons, Gobble, & Chickos, 2016): this organic compound contains a cyclic ester and thus is classified as a lactone. More specifically, it is the (4aS,7S,7aR) diastereomer that is most abundant, not the (4aS,7S,7aS) form (Simmons et al., 2016); for readers unfamiliar with organic chemistry, the numbers refer to carbon atoms in the structure (i.e. 4a, 7, and 7a), and the capital letters denote how the structure is oriented at those carbon atoms.

In addition to its effectiveness, the absence of any significant health risks is another factor supporting Nepeta cataria’s potential as a botanical boon. Zhu et al. (2009) reported over 96% repellency rates against stable flies (Stomoxys calcitrans) at a 20 mg dose and a rate of 86% against houseflies (Musca domestica) at only a 2 mg dose. To put these dosages in perspective, this study also conducted catnip toxicity tests for various routes of administration, finding that the acute oral LD50 (how high of an oral dose is needed to kill 50% of animals in the laboratory) was 3160 mg/kg of body weight for female rats and 2710 mg/kg of body weight for male rats (Zhu et al., 2009). Assuming the more toxic figure of 2710 mg/kg, a 160-pound (72.6-kg) man would have a 50% chance of dying if he orally ingested 196677.708 mg (0.43 lbs) of catnip in a single dose; this is over 9800 times the effective 20 mg dose. The study reported even less toxicity (and therefore a higher LD50 value) in acute dermal exposure.

Fortunately for us and unfortunately for mosquitos, catnip oil evaporates and disperses at a rate similar to DEET: Simmons et al. (2016) reported that the vapor pressure of nepetalactone, an indication of its evaporation rate, was comparable to that of DEET. This finding, coupled with the plant’s safety, has promising implications for catnip’s practicality as a DEET substitute. To this end, science and engineering company DuPont teamed up with Entomol Products in 2015 to offer a plant-based insect repellant capitalizing on catnip’s capability to cause critters to keep away.


Arthur, F. H., Fontenot, E. A., & Campbell, J. F. (2011). Evaluation of Catmint Oil and Hydrogenated Catmint Oil as Repellents for the Flour Beetles, Tribolium castaneum and Tribolium confusum . Journal of Insect Science, 11, 128.

Simmons, D., Gobble, C., & Chickos, J. (2016). Vapor pressure and enthalpy of vaporization of oil of catnip by correlation gas chromatography. The Journal of Chemical Thermodynamics, 92, 126-131.

Zhu, J. J., Zeng, X.-P., Berkebile, D., Du, H.-J., Tong, Y., Qian, K. (2009). Efficacy and safety of catnip (Nepeta cataria) as a novel filth fly repellent. Medical and Veterinary Entomology, 23, 209-216.

Posted 7/9/2018

Jellyfishing on the National Mall - Monday, July 2, 2018 - Washington, DC

In what was forecast as the hottest day of the year to date, the Smithsonian’s Department of Invertebrate Zoology was given the opportunity to present and discuss its research on the intriguing and mesmerizing world of jellyfish! Thanks to the Smithsonian Congress of Scholars (SCOS), a research tent was created at the 17th Annual Smithsonian Staff Picnic (see photographs under Experience tab) for this very purpose, to disseminate scientific ideas and add to the collective wisdom of staff and the public alike: an apt testament to “the increase and diffusion of knowledge” sought by Smithsonian founder James Smithson.

On this scorching day, our jellyfish team comprised several devoted zoologists, students, and interns: Allen Collins, Cheryl Lewis Ames, Anna Klompen, Christine Martin, Allison Becker, Abby Jackson, and myself. Together we hauled our animals and equipment onto the Mall and established two stations: one, a cart full of preserved specimens, and the other, a table featuring our living jellyfish.

Allen and Cheryl presided over the specimen cart (in the shade!) for most of the three-hour event, showing off the beautiful and often perplexing variety within the phylum Cnidaria. From the striking fluorescent tentacles of the flower hat jelly to the image-forming eyes of the box jellyfish, our cart’s collection offered a brief glimpse into the impressive biodiversity that we get to study and appreciate more and more every day at the Smithsonian, almost always indoors.

Our humble but distinct banner reading “The Lives of Jellyfish,” handmade by Christine, effectively drew the attention of passersby. With this banner situated next to the other tables’ more information-laden posters, I was reminded of two things: one, my own tendency to oversaturate presentations, and two, the effectiveness that simplicity and conciseness can have, especially in the world of science! The live animal table was fortunately stationed under the research tent, which cooled us down the same degree that a single ice cube might cool down a swimming pool. But any respite from the sun was most welcome as we positioned ice packs around our aquarium, attempting to limit sudden temperature fluctuations and mitigate any harm to our jellies.

Much was discussed with those who stopped by our two stations. Anna engaged other scientists with her expertise on Cassiopea, often answering the very common question “why do they sit on the bottom and pulse like that?” Christine has been the primary caretaker of our jellies recently, and as such she was able to offer valuable explanations on the life cycles, living conditions, and feeding habits of both Cassiopea and Aurelia, the two genera of living jellyfish that we displayed. Allison, Abby, and I focused on describing our DNA research with the jellies, from extracting DNA to interpreting the resulting sequences. And in addition to explaining our own scientific ventures, we got to learn about what other scientists are doing; concentrating predominantly on Cnidarians day in and day out, it is invigorating to be reminded just how massive the scope of research at the Smithsonian is.

Posted 7/5/2018

All blog entries written by Daniel Jackson