Monthly Archives: May 2018

The Mental Health Problem in Grad School


DVUpoV6W4AEOvkZMental health problems in graduate students have existed for ages. The constant and ever-increasing competition both in and out of the academic realm puts an extra toll on young students who already must deal with harsh economic conditions, an uncertain future, and the general unrecognition from society, not to mention sometimes a bullying environment from advisors. Back in the old days, struggling students were said to be ‘cracking under pressure‘, only for the heightening of thriving students who, in comparison, were deemed superior.

The story of Jason Altom is an extreme example of how a highly competitive environment may transform into an abusive one. Jason took his life in 1998 by ingesting potassium cyanide during his final years at Harvard. He was 26. The molecule he was trying to synthesize was completed the following year, and the corresponding report in JACS listed him as a co-author. It was also dedicated to his memory in the acknowledgements section. He was also not the first in the lab to take his life but his suicide note, as reported by The Crimson, suggested some policy changes like having not one but three supervisors per student.

Research institutions outside the top highest in the world, have also a lot of pressure put on students and young researchers even if the stakes are not Nobel-Prize-high. At the same time there are more graduate students now than ever before; the high demand for higher qualifications without the proper emotional development led to a critical mass of frustrated students who become bitter against the same activity they were first drawn to.

Getting a PhD, a real one, is tremendously hard, no question about it, but it shouldn’t be something you lose your mind for. Nothing should. One of my dearest mentors, Prof. Raymundo Cea-Olivares whom I’ve quoted many times before in this blog, often said that any human activity is hard, especially if you try to push its limits, yet PhD students are six-times more prone to suffer some kind of mental issue than a person the same age in the general population. To me, getting a PhD -or doing research for that matter- means you are trying to solve a question nobody else has been able to answer with methods you first need to master before even knowing whether they’re entirely suitable or not. A recurring theme in troubled students is not fully understanding what they are doing or why things are not going out the way they’re supposed to, which only increases the ‘impostor syndrome’ we all feel at some point or another. By definition, you are only an impostor if you’re working unethically, faking or stealing data, otherwise you’re welcome to my lab always; in fact, I prefer to deal with colleagues suffering from impostor syndrome than Dunning-Kruger‘s any day of the week.  Here is the bottom line: superior or inferior its a relative term that only exists when you compare yourself to others. Don’t. Ever. The amount of time you devote to comparing yourself to others or indulging in self pity is wasted time you could well be using in doing something for yourself, whether it is studying, working or living.

If I should say something to struggling students is this: You are better than you think. That’s it. Seriously. You got into grad school and more importantly you will come out of it.

Nature has recently curated a collection of articles and essays addressing the mental-health problem in academia. Also, Prof. Christopher J. Cramer has a popular video on the matter, and somewhat tangentially so does Dr. Neil deGrasse Tyson. There are many other resources at your local university to help you cope with your PhD-derived anxiety, because remember: You are not alone.

 

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Mg²⁺ Needs a 5th Coordination in Chlorophylls – New paper in IJQC


Photosynthesis, the basis of life on Earth, is based on the capacity a living organism has of capturing solar energy and transform it into chemical energy through the synthesis of macromolecules like carbohydrates. Despite the fact that most of the molecular processes present in most photosynthetic organisms (plants, algae and even some bacteria) are well described, the mechanism of energy transference from the light harvesting molecules to the reaction centers are not entirely known. Therefore, in our lab we have set ourselves to study the possibility of some excitonic transference mechanisms between pigments (chlorophyll and its corresponding derivatives). It is widely known that the photophysical properties of chlorophylls and their derivatives stem from the electronic structure of the porphyrin and it is modulated by the presence of Mg but its not this ion the one that undergoes the main electronic transitions; also, we know that Mg almost never lies in the same plane as the porphyrin macrocycle because it bears a fifth coordination whether to another pigment or to a protein that keeps it in place (Figure 1).

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Figure 1 The UV-Vis spectra of BCHl-a changes with the coordination state

During our calculations of the electronic structure of the pigments (Bacteriochlorophyll-a, BChl-a) present in the Fenna-Matthews-Olson complex of sulfur dependent bacteria we found that the Mg²⁺ ion at the center of one of these pigments could in fact create an intermolecular interaction with the C=C double bond in the phytol fragment which lied beneath the porphyrin ring.

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Figure 2 Mg points ‘downwards’ upon optimization, hinting to the interaction under study

 

This would be the first time that a dihapto coordination is suggested to occur in any chlorophyll and that on itself is interesting enough but we took it further and calculated the photophysical implications of having this fifth intramolecular dihapto coordination as opposed to a protein or none for that matter. Figure 3 shows that the calculated UV-Vis spectra (calculated with Time Dependent DFT at the CAM-B3LYP functional and the cc-pVDZ, 6-31G(d,p) and 6-31+G(d,p) basis sets). A red shift is observed for the planar configuration, respect to the five coordinated species (regardless of whether it is to histidine or to the C=C double bond in the phytyl moiety).

 

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Figure 3 CAMB3LYP UV-VIS spectra. Basis set left to right cc-PVDZ, 6-31G(d,p) and 6-31+G(d,p)

Before calculating the UV-Vis spectra, we had to unambiguously define the presence of this observed interaction. To that end we calculated to a first approximation the C-Mg Wiberg bond indexes at the CAM-B3LYP/cc-pVDZ level of theory. Both values were C(1)-Mg 0.022 and C(2)-Mg 0.032, which are indicative of weak interactions; but to take it even further we performed a non-covalent interactions analysis (NCI) under the Atoms in Molecules formalism, calculated at the M062X density which yielded the presence of the expected critical points for the η²Mg-(C=C) interaction. As a control calculation we performed the same calculation for Magnoscene just to unambiguously assign these kind of interactions (Fig 4, bottom).

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Figure 4 (a), (b) NCI analysis for Mg-(C=C) interaction compared to Magnesocene (c)

This research is now available at the International Journal of Quantum Chemistry. A big shoutout and kudos to Gustavo “Gus” Mondragón for his work in this project during his masters; many more things come to him and our group in this and other research ventures.

I’m done with Computational Studies


I’ve lately reviewed a ton of papers whose titles begin with some version of “Computational studies of…“, “Theoretical studies of…” or even more subtly just subtitled “A theoretical/computational study” and even when I gotta confess this is probably something I’ve done once or twice myself, it got me thinking about the place and role of computational chemistry within chemistry itself.

As opposed to physicists, chemists are pressed to defend a utilitarian view of their work and possibly because of that view some computational chemists sometimes lose sight of their real contribution to a study, which is far from just performing a routine electronic structure calculation. I personally don’t like it when an experimental colleague comes asking for ‘some calculations’ without a clear question to be answered by them; Computational Chemistry is not an auxiliary science but a branch of physical chemistry in its own right, one that provides all the insight experiments -chemical or physical- sometimes cannot.

I’m no authority on authoring research papers but I encourage my students to think about the titles of their manuscripts in terms of what the manuscript most heavily relies on; whether it’s the phenomenon, the methodology or the object of the study, that should be further stressed on the title. Papers titled “Computational studies of…” usually are followed by ‘the object of study’ possibly overlooking the phenomenon observed throughout such studies. It is therefore a disservice to the science contained within the manuscript, just like experimental papers gain little from titles such as “Synthesis and Characterization of…“. It all comes down to finding a suitable narrative for our work, something that I constantly remind my students. It’s not about losing rigor or finding a way to oversell our results but instead to actually drive a point home. What did you do why and how. Anna Clemens, a professional scientific writer has a fantastic post on her blog about it and does it far better than I ever could. Also, when ranting on Twitter, the book Houston, we have a narrative was recommended to me, I will surely put it my to-read list.

While I’m on the topic of narratives in science, I’m sure Dr. Stuart Cantrill from Nature Chemistry wouldn’t mind if I share with you his deconstruction of an abstract. Let’s play a game and give this abstract a title in the comments section based on the information vested in it.DcJCrr_W0AQCNQZ

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