It is not without regret that I write this last post.  True, many of my readers probably found themselves lost in translation, a testament to the fact that I can’t quite lose the chemistry jargon.  Explaining physical chemistry demands a lot from a tyro researcher.  This learning experience is healthy, I’m sure—the perfect practice for grad school interviews and poster presentations.  But what inspired me and I will miss most about this summer was the lab environment.  Students and professors worked beside one another.  Everybody sported interest in other lab groups’ projects and enjoyed discussing research as much as the best liquid nitrogen ice cream flavors or that week’s upcoming Friday lunch outing.  I found this constant conversation refreshing.  Within my own lab, we all asked about each others’ projects and methods to the point that we could substitute for them one day if they needed the help.  Working in the lab was thoroughly enjoyable and I’d be lucky to recreate the experience in future research.

Looking back, I realize my abstract and blog posts do not quite match up.  It turns out that the molecules I studied had all been synthesized by or during this summer.  With that done, I was ready to begin the physical studies.  Fluorescence assays and I got uncomfortably close, let’s just say, for the first month or so of my research.  I found that the most effective probe of solvent acidity had a t-butyl group on the carbonyl end and no further enhancements at the amino site.  This probe’s range was the largest by at best a factor of 3/2 relative to the next best probe of solvent acidity—the same molecule except for the amino group restricted to a planar conformation within a ring.  This result makes sense based on our original hypothesis that twisted compounds would respond best to changes in solvent acidity.

Recent research consisted of working an onslaught of new and modified synthetic organic procedures.  My goal in this side project was to make a fluorescent probe in order to determine the solvent acidity of isopropanol-water mixtures in future experiments.  Few laboratories have worked with this class of compounds, (1,2,4,5-tetrazines,) in the past 150 years; in fact, only 200 separate articles seem to document their use.  Even fewer articles document their synthesis, many of which use more brute methods because their main goal is photophysical study rather than synthesis.  With so little to go on, my work here moved slowly.  I tried a variety of reactions: I used different precursor compounds to make one reagent, increased the pressure and reaction time, and varied the compound ratios.  As of now, my best bet seems to be the synthesis of an ester as one relatively safe and high-yield reactant.  From here, the synthetic route includes only reactions documented in introductory orgo books, a promising sign.

I look forward to mentoring new students in our lab as they scramble about setting up these reactions.  My place lies back at the fluorimeter.  Having identified the most suitable probes and establishing that their fluorescent properties do in fact correlate positively to increasingly protic solvent mixtures, I am ready to move on and test the probes on an actual molecule: cyclodextrin.  This project will compose my honors thesis.  It is time to put those painful exams on kinetics back in action.  I cross my fingers that these results have enough meat to publish.

Thanks to anyone who’s followed me this far.  Best of luck to you in your own research and in pursuit of any interest the world may inspire in you.  Peace.

These two weeks flew by in a whirlwind of literature.  Due to the problem of aggregation of the probes in mostly aqueous environments and an inconsistency in calibrating probes that stems from the intrinsic differences between chemically distinct solvents, my lab has been using an isopropanol/water gradient to test the probes.  This choice in solvent should prove that the probes yield the same results, within error, for different solvent systems, and also make up for the differences in refractive index and density between the different solvents.  The new same-solvent system seems, for the latter reason, most promising for calibrating the probes.

The issue with this, however, is that we have no literature values for the solvent acidity of isopropanol/water mixtures.  My solution is to obtain the same probe used to determine the solvent acidity of the previously used alcohols.  This molecule would be 3,6-diethyl-1,2,4,5-tetrazine.  Sadly, the only premade tetrazine available online seems to be a ridiculously gouged Chinese product at $500/gram.  I would much prefer to synthesize the molecule with reagents already stocked in lab.  I have been searching the literature on how to synthesize the compound and found hits from as recent as May 2011 to as long ago—the original synthesis—as 1921.  I even dredged up a 1970 synthesis from a German journal kept in Swem’s offsite storage.

Currently, I am trying out some of the syntheses and concurrently glancing over the literature to see if any of the reactions could be improved.  They all seem rather circuitous and some potentially risky because of the reactant, hydrazine, which is essentially rocket fuel.  I just tried one reaction but changed a side group on my reactant, which seems to have completely changed the nature of the reaction.  Instead of the 2.51g bright yellow solid expected, I found a lovely grapefruit colored solution.  I am still at the drawing board, hoping to synthesize my tetrazine probe before the summer is out.

Lately I’ve come to believe that the astonishing discoveries in life come not to the lucky brash experimenters, but rather to the conscientious workers who choose the path of diligent repetition and patience.  Careful work creates a framework off of which we base our interpretations of anomalous data.  At least, I sure hope this is true.  In my case, the anomalous data has tended to reveal hiccups in the experimental setup.  A few lucky times, however, I have been able to interpret the outlying data points in a way not previously studied in chemistry literature.

As I previously explained, I study how organic solvents of differing acidities affect the fluorescence of six organic probes.  It takes about half a day to run through all the solvents with one probe.  This involves filling a cuvette with solvent, blanking the machine, injecting a sample of the probe, reading the absorption and emission intensity, washing it out and then repeating with the next solvent.  In the end, I manipulate the data to get peaks of fluorescence intensity.  By comparing the peaks generated with different solvents, I can judge the effectiveness of a probe.

Each peak can be measured in a variety of ways.  I use two methods: maximum peak height and integral area, which is harder to calculate but also better describes an asymmetric peak.  I then plot emission versus solvent acidity, or hydrogen-bonding capacity.  This should yield a straight line with a slope of between about three and ten.  A higher slope is desirable because this means that the probe’s fluorescence changes more dramatically in response to changing solvent acidity.  The larger range is characteristic of more sensitive probes.

Lately, however, some of my plots have given two intersecting linear fits.  This appears to be due to an effect called aggregation, which my lab group found primarily from Moyano et al. in “New Insights on the Behavior of PRODAN in Homogeneous Media and in Large Unilamellar Vesicles”.  Because Prodan (and Prodan-based probes) is based off of a bulky hydrophobic fused benzene structure, it tends to form complexes of itself in more polar solvents such as water, much like oil tends to clump into little droplets and separate in water.  The probe that aggregates into self-contained complexes fluoresces at a higher energy than the free probe because it cannot be as easily stabilized by the solvent.  However, this discovery requires a reworking of our previous plots.  Because the aggregation is exaggerated for more polar solvents, my previous studies are no longer normalized and need to be reinterpreted.  I need to first determine whether aggregation occurs with all six probes under conditions in which one would use the probe experimentally.  We may even be able to use this new phenomenon to help characterize polarity or other parameters.  This is somewhat exciting because nobody in the literature has studied aggregation as an analytical tool before.

To sum up after the chemistry jargon: I found a hitch in my studies—my samples do not make a homogeneous solution after equilibration.  But on the bright side, I have a new branch of studies to possibly explore.  In any case, I am learning how to interpret unexpected plots and to tweak my trials to include this new factor.