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The Evolution of Photosynthesis


Recently, the journal ACS Central Science asked me to write a viewpoint for their First Reactions section about a research article by Prof. Alán Aspuru-Guzik from Harvard University on the evolution of the Fenna-Matthews-Olson (FMO) complex. It was a very rewarding experience to write this piece since we are very close to having our own work on FMO published as well (stay tuned!). The FMO complex remains a great research opportunity for understanding photosynthesis and thus the origin of life itself.

In said article, Aspuru-Guzik’s team climbed their way up a computationally generated phylogenetic tree for the FMO from different green sulfur bacteria by creating small successive mutations on the protein at a time while also calculating their photochemical properties. The idea is pretty simple and brilliant: perform a series of “educated guesses” on the structure of FMO’s ancestors (there are no fossil records of FMO so this ‘educated guesses’ are the next best thing) and find at what point the photochemistry goes awry. In the end the question is which led the way? did the photochemistry led the way of the evolution of FMO or did the evolution of FMO led to improved photochemistry?

Since both the article and viewpoint are both published as open access by the ACS, I wont take too much space here re-writing the whole thing and will instead exhort you to read them both.

Thanks for doing so!

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Photosynthesis and Singlet Fission – #WATOC2017 PO1-296


If you work in the field of photovoltaics or polyacene photochemistry, then you are probably aware of the Singlet Fission (SF) phenomenon. SF can be broadly described as the process where an excited singlet state decays to a couple of degenerate coupled triplet states (via a multiexcitonic state) with roughly half the energy of the original singlet state, which in principle could be centered in two neighboring molecules; this generates two holes with a single photon, i.e. twice the current albeit at half the voltage (Fig 1).

Imagen1

Jablonski’s Diagram for SF

It could also be viewed as the inverse process to triplet-triplet annihilation. An important requirement for SF is that the two triplets to which the singlet decays must be coupled in a 1(TT) state, otherwise the process is spin-forbidden. Unfortunately (from a computational perspective) this also means that the 3(TT) and 5(TT) states are present and should be taken into account, and when it comes to chlorophyll derivatives the task quickly scales.

SF has been observed in polyacenes but so far the only photosynthetic pigments that have proven to exhibit SF are some carotene derivatives; so what about chlorophyll derivatives? For a -very- long time now, we have explored the possibility of finding a naturally-occurring, chlorophyll-based, photosynthetic system in which SF could be possible.

But first things first; The methodology: It was soon enough clear, from María Eugenia Sandoval’s MSc thesis, that TD-DFT wasn’t going to be enough to capture the whole description of the coupled states which give rise to SF. It was then that we started our collaboration with SF expert, Prof. David Casanova from the Basque Country University at Donostia, who suggested the use of Restricted Active Space – Spin Flip in order to account properly for the spin change during decay of the singlet excited state. A set of optimized bacteriochlorophyll-a molecules (BChl-a) were oriented ad-hoc so their Qy transition dipole moments were either parallel or perpendicular; the rate to which SF could be in principle present yielded that both molecules should be in a parallel Qy dipole moments configuration. When translated to a naturally-occurring system we sought in two systems: The Fenna-Matthews-Olson complex (FMO) containing 7 BChl-a molecules and a chlorosome from a mutant photosynthetic bacteria made up of 600 Bchl-d molecules (Fig 2). The FMO complex is a trimeric pigment-protein complex which lies between the antennae complex and the reaction center in green sulfur dependent photosynthetic bacteria such as P. aestuarii or C. tepidium, serving thus as a molecular wire in which is known that the excitonic transfer occurs with quantum coherence, i.e. virtually no energy loss which led us to believe SF could be an operating mechanism. So far it seems it is not present. However, for a crystallographic BChl-d dimer present in the chlorosome it could actually occur even when in competition with fluorescence.

FMO

FMO Complex. Trimer (left), monomer (center), pigments (right)

Imagen2

BChQRU chlorosome. 600 Bchl-d molecules

I will keep on blogging more -numerical and computational- details about these results and hopefully about its publication but for now I will wrap this post by giving credit where credit is due: This whole project has been tackled by our former lab member María Eugenia “Maru” Sandoval and Gustavo Mondragón. Finally, after much struggle, we are presenting our results at WATOC 2017 next week on Monday 28th at poster session 01 (PO1-296), so please stop by to say hi and comment on our work so we can improve it and bring it home!

A New Graduate Student


With pleasure I announce that last week our very own Gustavo “Gus” Mondragón became the fifth undergraduate student from my lab to defend his BSc thesis and it has to be said that he did it admirably so.

Gus has been working with us for about a year now and during this time he not only worked on his thesis calculating excited states for bacteriochlorophyl pigments but also helped us finishing some series of calculations on calix[n]arene complexes of Arsenic (V) acids, which granted him the possibility to apear as a co-author of the manuscript recently published in JIPH. Back in that study he calculated the interaction energies between a family of calix macrocycles and arsenic acid derivatives in order to develop a suitable extracting agent.

For his BSc thesis, Gus reproduced the UV-Vis absorption spectra of bacteriochlorophyll-a pigments found in the Fenna-Matthews-Olson complex of photosynthetic purple bacteria using Time Dependent Density Functional Theory (TD-DFT) with various levels of theory, with PBEPBE yielding the best results among the tried set. These calculations were performed at the crystallographic conformation and at the optimized structure, also, in vacuo results were compared to those in implicit solvent (SMD, MeOH). He will now move towards his masters where he will further continue our research on photosynthesis.

Thank you, Gustavo, for your hard work and your sense of humor. Congratulations on this step and may many more successes come your way.

 

Internal Symposium at CCIQS – 2016 edition


Having a symposium right after the winter holidays is a great way to get back in touch with colleagues and students; we get to hear how their work is progressing and more importantly I get forced to become focused once again after a few weeks of just not paying much attention to anything related to work.

This year our group has happily gained some additions and sadly seen some others leave in search of a better future. María Eugenia “Maru” Sandoval gave a talk on the work she did on Singlet Fission (SF) in the Fenna-Matthews-Olson (FMO) complex during a three month stay at the Basque Country University in Spain under the supervision of Dr. David Casanova. Aside her calculations regarding Förster theory and a modification to Marcus’ equation, Singlet Fission was explored by her as a possible mechanism in which the Photosynthetic complex FMO might transfer solar energy from the antennae to the reaction center; one that might explain the high efficiency of it.

SF is a fascinating phenomenon: So you get an excited state S1 for a molecule1 that has been struck with a suitable photon; this excited state can either radiate back to the ground state (S0) but if there were two degenerate and coupled triplets whose energies are similar to half the S1 energy then the excited state might decay into [TT]1, hence singlet fission. In some cases (e.g. polyacene crystals) one of these triplets might be located in an adjacent molecule, this creates a hole in a second molecule due to the same single photon! This means creating twice the current albeit at half the voltage in photovoltaic materials. Maru has explored the possibility of SF occurring in natural systems and we think we might be on to something; she will defend her masters thesis any day now and we should see a publication later on this year. After that, she is pondering a few interesting options for her PhD.

On the poster session, our lab was represented by Marycarmen Reséndiz, Gustavo Mondragón and Guillermo Caballero. Durbis Pazos just now joined our group so he didn’t have to present a poster but nevertheless showed up gladly to support his colleagues. Gustavo will work on other aspects regarding the photochemistry of the FMO complex while Marycarmen is working on calculating the electronic interactions of chemically modified nucleotides when incorporated into DNA strands. Guillermo had a poster on his calculations for another reaction mechanism that caught his eye while still working with the experimentalists. I’m pleased to say that Guillermo is close to being published and also close to leaving us in order to get a PhD in a prestigious university that shall remain unnamed.

Thank you guys for keeping up the good work and maintaining the quality of the research we do, here is to a year full of success both in and out of the lab! Any success this lab has is due to you.

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