Category Archives: Photochemistry

Population Analysis in the Excited State with Gaussian


To calculate what the bonding properties of a molecule are in a particular excited state we can run any population analysis following the root of interest. This straightforward procedure takes two consecutive calculations since you don’t necessarily know before hand which excited state is the one of interest.

The regular Time Dependent Density Functional Theory (TD-DFT) calculation input with Gaussian 16 looks as follows (G09 works pretty much the same), let us assume we’ve already optimized the geometry of a given molecule:

%OldChk=filename.chk
%nprocshared=16
%chk=filename_ES.chk

#p TD(NStates=10,singlets) wb97xd/cc-pvtz geom=check guess=read

Title Card Required

0 1
--blank line--

This input file retrieves the geometry and wavefunction from a previous calculation from filename.chk and doesn’t write anything new into it (that is what %OldChk=filename.chk means) and creates a new checkpoint where the excited states are calculated (%chk=filename_ES.chk)

In the output you search for the transition which peeks your interest; most often than not you’ll be interested in the one with the highest oscillator strength, f. The oscillator strength is a dimensionless number that represents the ratio of the observed, integrated, absorption coefficient to that calculated for a single electron in a three-dimensional harmonic potential [Harris & Bertolucci, Symmetry and Spectroscopy]; in other words, it is related to the probability of that transition to occur, and therefore it takes values from 0.0 to 1.0 (for single photon absorption processes.)

The output of this calculation looks as follows, the value of f for every excitation is reported together with its energy and the orbital transitions which comprise it.

 Excitation energies and oscillator strengths:

 Excited State   1:      Singlet-A      3.1085 eV  398.86 nm  f=0.0043  <S**2>=0.000
      56 -> 59        -0.11230
      58 -> 59         0.69339
 This state for optimization and/or second-order correction.
 Total Energy, E(TD-HF/TD-DFT) =  -1187.56377917
 Copying the excited state density for this state as the 1-particle RhoCI density.

 Excited State   2:      Singlet-A      4.0827 eV  303.68 nm  f=0.0016  <S**2>=0.000
      52 -> 59         0.46689
      52 -> 64        -0.20488
      53 -> 59         0.19693
      54 -> 59         0.40414
      54 -> 64        -0.16261
...
... 
Excited State   8:      Singlet-A      5.2345 eV  236.86 nm  f=0.8063  <S**2>=0.000
      52 -> 60         0.17162
      53 -> 59         0.47226
      53 -> 60        -0.11771
      54 -> 59        -0.27658
      54 -> 60        -0.22006
      55 -> 59         0.20496
      56 -> 59         0.15029

Now we’ve selected excited state #8 because it has the largest value of f from the lot, we use the following input to read in the geometry from the old checkpoint file and we generate a new one in case we need it for something else. The input file for doing all this looks as follows (I’ve selected as usual the Natural Bond Orbital population analysis):

%oldchk=a_ES.chk
%nprocshared=16
%chk=a_nbo.chk

#p TD(Read,Root=8) wb97xd/cc-pvtz geom=check density=current guess=read pop=NBORead

Title Card Required

0 1

$NBO BOAO BNDIDX E2PERT $END

--blank line--

The flags at the bottom request the calculation of Wiberg Bond Indexes (BNDIDX) as well as Bond Order in the Atomic Orbital basis (BOAO) and a second order perturbation theory for the electronic delocalization (E2PERT). Now we can compare the population analysis between ground and the 8th excited state; check figure 1 and notice the differences in Wiberg’s bond order for this complex made of two molecules and one Na+ cation.

Figure 1. Natural Population Analysis comparison for a supramolecular arrangement. Numbers next in brackets correspond to the sum of charges for each molecule. Notice the significant change in charges for each molecule when going from the ground to the 8th excited state.

In this example we can observe that in the ground state we have a neutral and a negative molecule together with a Na+ cation, but when we analyze the population in the 8th excited state both molecules acquire a similar charge, ca. 0.46e, which means that some of the electron density has been transferred from the negative one to the neutral molecule, forming an Electron Donor-Acceptor complex (EDA) in the excited state.

This procedure can be extended to any other kind of population analysis and their derived combination, e.g. one could calculate their condensed fukui functions in the Nth excited state; but beware! These calculations yield vertical excitations, should the excited state of interest have a minimum we can first optimize the ES geometry and then perform the population analysis on said geometry; just add the opt keyword to perform both jobs in one go, but bear in mind that the NBO population analysis is performed before and after the optimization process so look for the tables and values closer to the end of the output file.

In the case of open shell systems the procedure is the same but one should be extremely careful in searching for the total population analysis since the output file contains this table for the alpha and beta populations separately as well as the added values for the total number of electrons.

Photosynthesis in the near-IR. A New paper in JCTC


Photosynthetic organisms are so widespread around the globe they have adapted to various solar lighting conditions to thrive. The bacteria Blastochloris viridis absorbs light in the near infrared region of the electromagnetic spectrum, in fact, it holds the record for the longest wavelength (~1015 nm) absorbing organism whose Light Harvesting complex 1 (LHC1) has been elucidated. Despite their adaptation to a wide number of light conditions, photosynthetic organism can only make use of so many pigments or chromophores; the LHC1 (Figure 1) in B. viridis in fact is made up of Bacteriochlorophyll-b (BChl-b) molecules, one of the most abundant photosynthetic pigments on Earth, whose main absorption in solution (MeOH) is observed at 795 nm.

Figure 1. B. viridis LHC1 (PDB 6ET5)

So, how can B. viridis use BChl-b molecules to absorb near IR radiation and how does it achieve this remarkable red-shifting effect? The LHC1 structure was solved in 2018 by Qian et al. through Cryo-EM at a 2.9 Å resolution; it is comprised of 17 protein subunits surrounding the so called photosynthetic pigments special pair. Each of these subunits is made up of three α-helix structures surrounding two BChl-b and one dihydroneurosporene (DHN) molecule for a total of 34 of these photosynthetic pigments inside the LHC and 17 DHN molecules interacting between the protein structures and the
main BChl-b pigments.

It was Dr. Jacinto Sandoval and Gustavo “Gus” Mondragón who brought this facts to our attention during their survey of potential candidates for calculating exotic exciton transfer mechanisms in photosynthetic organisms, part of Gustavo’s PhD thesis. To them, it was clear from the start that some sort of cooperative effect between pigments was operating and possibly leading to the red-shifted absorption, therefore a careful dissection of all possible pigments combinations was carried out and their UV-Vis spectra were calculated at the CAMB3LYP/cc-pVDZ on PBE0/6-31G(d) optimized geometries, leading to the systems shown below in figure 2.

Figure 2. Two and Three containing pigments systems under study

System B7 reproduced the red-shifted absorption at 1026 nm, but since the original structure was fitted from the Cryo-EM with a 2.9 Å resolution, “Gus” suggested reaching out to the group of Prof. Andrés Gerardo Cisneros and Dr. Jorge Nochebuena at UT Dallas for carrying out QM/MM calculations; this optimization included the proteins surrounding the pigments in the MM layer and the interacting residues (Hys coordinated to Mg2+ ions in BChl-b) along the chromophores were incorporated into the QM layer, however the thus obtained minima for the B7 system lost the main absorption in the near-IR region, therefore, Dr. Nochebuena suggested running an MD simulation (45 ns) and took a random sampling of ten structures (Figure 3).

Figure 3. Structure sampling of the MD structures based on k-means
clustering analysis.

All structures in the sampling reproduced the red-shifted absorption (~1000 nm) successfully proving that cooperative and dynamic effects allow B. viridis to perform photosynthesis with low energy radiation (Figure 4). Therefore, close intermolecular interactions along with thermal/dynamical fluctuations allow for a regular pigment such as BChl-b to form near-IR absorbing photosystems for organisms to thrive in low conditions of solar light.

Figure 4. Calculated spectra of representative structure 7 vs the experimental spectrum. (a) Calculated spectrum (on green) including the DHN
molecule fragment. (b) Calculated spectrum (blue) excluding the DHN molecule fragment.

If you want to read further details, this work is now published in the Journal of Chemical Theory and Computation of the American Chemical Society. I’ll talk about this and other ventures in photosynthesis next week at the WATOC conference in Vancouver, swing by to talk CompChem!

Virtual Winter School on Computational Chemistry 2022


I’m very excited and honored to participate in this year’s Virtual Winter School on #CompChem. This event started back in 2015 and this year the list of participants includes Nobel Laureate and legend Roald Hoffmann. The topics will range from drug design to quantum chemistry on quantum computers. Additionally, two workshops will be given for ADF and Gaussian.

Aside from the teaching sessions there will also be some virtual social gatherings that promise to be a lot of fun. So don’t miss it next 21—25 of February 2022. Register here.

I will teach the tools to model Exciton Energy Transfer processes, a handy set of skills to work on the fields of photophysics, photosynthesis, or photochemistry of materials. We’ll review the concepts of excitons and the basic mechanisms by which they are originated and transferred.

Thanks to Henrique Castro from Rio de Janeiro for inviting me to be a part of this event which is a direct heir from the first electronic conferences organized by Profs. Bacharach and Rzepa. Here is the program.

Geometry Optimizations for Excited States


Electronic excitations are calculated vertically according to the Frank—Condon principle, this means that the geometry does not change upon the excitation and we merely calculate the energy required to reach the next electronic state. But for some instances, say calculating not only the absorption spectra but also the emission, it is important to know what the geometry minimum of this final state looks like, or if it even exists at all (Figure 1). Optimizing the geometry of a given excited state requires the prior calculation of the vertical excitations whether via a multireference method, quantum Monte Carlo, or the Time Dependent Density Functional Theory, TD-DFT, which due to its lower computational cost is the most widespread method.

Most single-reference treatments, ab initio or density based, yield good agreement with experiments for lower states, but not so much for the higher excitations or process that involve the excitation of two electrons. Of course, an appropriate selection of the method ensures the accuracy of the obtained results, and the more states are considered, the better their description although it becomes more computationally demanding in turn.

Figure 1. The vertical excitation does not match the minimum on the excited state

In Gaussian 09 and 16, the argument to the ROOT keyword selects a given excited state to be optimized. In the following example, five excited states are calculated and the optimization is requested upon the second excited state. If no ROOT is specified, then the optimization would be carried out by default on the first excited state (Where L.O.T. stands for Level of Theory).

#p opt TD=(nstates=5,root=2) L.O.T.

Gaussian16 includes now the calculation of analytic second derivatives which allows for the calculation of vibrational frequencies for IR and Raman spectra, as well as transition state optimization and IRC calculations in excited states opening thus an entire avenue for the computation of photochemistry.

If you already computed the excited states and just want to optimize one of them from a previous calculation, you can read the previous results with the following input :

#p opt TD=(Read,Root=N) L.O.T. Density=Current Guess=Read Geom=AllCheck

Common problems. The following error message is commonly observed in excited state calculations whether in TD-DFT, CIS or other methods:

No map to state XX, you need to solve for more vectors in order to follow this state.

This message usually means you need to increase the number of excited states to be calculated for a proper description of the one you’re interested in. Increase the number N for nstates=N in the route section at higher computational cost. A rule of thumb is to request at least 2 more states than the state of interest. This message can also reflect the fact that during the optimization the energy ordering changes between states, and can also mean that the ground state wave function is unstable, i.e., the energy of the excited state becomes lower than that of the ground state, in this case a single determinant approach is unviable and CAS should be used if the size of the molecule allows it. Excited state optimizations are tricky this way, in some cases the optimization may cross from one PES to another making it hard to know if the resulting geometry corresponds to the state of interest or another. Gaussian recommends changing the step size of the optimization from the default 0.3 Bohr radius to 0.1, but obviously this will make the calculation take longer.

Opt=(MaxStep=10)

If the minimum on the excited state potential energy surface (PES) doesn’t exist, then the excited state is not bound; take for example the first excited state of the H2 molecule which doesn’t show a minimum, and therefore the optimized geometry would correspond to both H atoms moving away from each other indefinitely (Figure 2). Nevertheless, a failed optimization doesn’t necessarily means the minimum does not exist and further analysis is required, for instance, checking the gradient is converging to zero while the forces do not.

Figure 2. An unbound excited state with no minima ensures the dissociation of the system along the reaction coordinate

Orbital Contributions to Excited States


This is a guest post by our very own Gustavo “Gus” Mondragón whose work centers around the study of excited states chemistry of photosynthetic pigments.

When you’re calculating excited states (no matter the method you’re using, TD-DFT, CI-S(D), EOM-CCS(D)) the analysis of the orbital contributions to electronic transitions poses a challenge. In this post, I’m gonna guide you through the CI-singles excited states calculation and the analysis of the electronic transitions.

I’ll use adenine molecule for this post. After doing the corresponding geometry optimization by the method of your choice, you can do the excited states calculation. For this, I’ll use two methods: CI-Singles and TD-DFT.

The route section for the CI-Singles calculation looks as follows:

%chk=adenine.chk
%nprocshared=8
%mem=1Gb

#p CIS(NStates=10,singlets)/6-31G(d,p) geom=check guess=read scrf=(cpcm,solvent=water)

adenine excited states with CI-Singles method

0 1
--blank line--

I use the same geometry from the optimization step, and I request only for 10 singlet excited states. The CPCP implicit solvation model (solvent=water) is requested. If you want to do TD-DFT, the route section should look as follows:

%chk=adenine.chk
%nprocshared=8
%mem=1Gb

#p FUNCTIONAL/6-31G(d,p) TD(NStates=10,singlets) geom=check guess=read scrf=(cpcm,solvent=water)

adenine excited states with CI-Singles method

0 1
--blank line--

Where FUNCTIONAL is the DFT exchange-correlation functional of your choice. Here I strictly not recommend using B3LYP, but CAM-B3LYP is a noble choice to start.

Both calculations give to us the excited states information: excitation energy, oscillator strength (as f value), excitation wavelength and multiplicity:

Excitation energies and oscillator strengths:

 Excited State   1:      Singlet-A      6.3258 eV  196.00 nm  f=0.4830  <S**2>=0.000
      11 -> 39        -0.00130
      11 -> 42        -0.00129
      11 -> 43         0.00104
      11 -> 44        -0.00256
      11 -> 48         0.00129
      11 -> 49         0.00307
      11 -> 52        -0.00181
      11 -> 53         0.00100
      11 -> 57        -0.00167
      11 -> 59         0.00152
      11 -> 65         0.00177

The data below corresponds to all the electron transitions involved in this excited state. I have to cut all the electron transitions because there are a lot of them for all excited states. If you have done excited states calculations before, you realize that the HOMO-LUMO transition is always an important one, but not the only one to be considered. Here is when we calculate the Natural Transition Orbitals (NTO), by these orbitals we can analyze the electron transitions.

For the example, I’ll show you first the HOMO-LUMO transition in the first excited state of adenine. It appears in the long list as follows:

35 -> 36         0.65024

The 0.65024 value corresponds to the transition amplitude, but it doesn’t mean anything for excited state analysis. We must calculate the NTOs of an excited state from a new Gaussian input file, requesting from the checkpoint file we used to calculate excited states. The file looks as follows:

%Oldchk=adenine.chk
%chk=adNTO1.chk
%nproc=8
%mem=1Gb

#p SP geom=allcheck guess=(read,only) density=(Check,Transition=1) pop=(minimal,NTO,SaveNTO)

I want to say some important things right here for this last file. See that no level of theory is needed, all the calculation data is requested from the checkpoint file “adenine.chk”, and saved into the new checkpoint file “adNTO1.chk”, we must use the previous calculated density and specify the transition of interest, it means the excited state we want to analyze. As we don’t need to specify charge, multiplicity or even the comment line, this file finishes really fast.

After doing this last calculation, we use the new checkpoint file “adNTO1.chk” and we format it:

formchk -3 adNTO1.chk adNTO1.fchk

If we open this formatted checkpoint file with GaussView, chemcraft or the visualizer you want, we will see something interesting by watching he MOs diagram, as follows:

We can realize that frontier orbitals shows the same value of 0.88135, which means the real transition contribution to the first excited state. As these orbitals are contributing the most, we can plot them by using the cubegen routine:

cubegen 0 mo=homo adNTO1.fchk adHOMO.cub 0 h

This last command line is for plotting the equivalent as the HOMO orbital. If we want to plot he LUMO, just change the “homo” keyword for “lumo”, it doesn’t matter if it is written with capital letters or not.

You must realize that the Natural Transition Orbitals are quite different from Molecular Orbitals. For visual comparisson, I’ve printed also the molecular orbitals, given from the optimization and from excited states calculations, without calculating NTOs:

These are the molecular frontier orbitals, plotted with Chimera with 0.02 as the isovalue for both phase spaces:

The frontier NTOs look qualitatively the same, but that’s not necessarily always the case:

If we analyze these NTOs on a hole-electron model, the HOMO refers to the hole space and the LUMO refers to the electron space.

Maybe both orbitals look the same, but both frontier orbitals are quite different between them, and these last orbitals are the ones implied on first excited state of adenine. The electron transition will be reported as follows:

If I can do a graphic summary for this topic, it will be the next one:

NTOs analysis is useful no matter if you calculate excited states by using CIS(D), EOM-CCS(D), TD-DFT, CASSCF, or any of the excited states method of your election. These NTOs are useful for population analysis in excited states, but these calculations require another software, MultiWFN is an open-source code that allows you to do this analysis, and another one is called TheoDORE, which we’ll cover in a later post.

Gustavo “Gus” Mondragón M.Sc. – Thesis Defense


We celebrate the successful thesis defense of Gustavo “Gus” Mondragón who has now completed his Masters degree and is now on to getting a PhD in our group. Gustavo has worked on the search for multiexcitonic states and their involvement in the excitonic transference between photosynthetic pigments, specifically between bacteriochlorophyll-d molecules (BChl-d) from the bchQRU chlorosome whose whole structure is shown in the gallery below. To this end, Gustavo has studied and implemented the Restricted Active Space method with double spin flip (RAS-2SF) with the use of QChem5.0, a method that has required the use and understanding of states with high multiplicities. Additionally, Gustavo has investigated the influence of the environment within the chlorosome by performing ONIOM calculations for the spectroscopic properties of a BChl-d dimer, finding albeit qualitatively a batochromic effect, probably an expected result but nonetheless an impressive feat for the level of theory selected.

There’s still a lot of work to do in this line of research and although we’re eager to publish our results in this excitonic transference mechanism we want to be completely sure that we’re taking every possibility into consideration so we don’t incur into any inconsistencies.

Gustavo cultivates many research interests from excited states of these pigments to biochemical processes that require the use of various tools; I’m sure his permanence in our lab will bring lots of interesting results. Congratulations, Gus! Thank you for your hard work.

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).

TOC_final

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.

fig3

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).

 

Fig6

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).

Fig4.jpg

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.

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!

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!

Maru Sandoval M.Sc. – Our First Graduate Thesis


It is with great pride that I’d like to announce that for the first time we have a Masters Student graduated from this Comp.Chem. lab: María Eugenia “Maru” Sandoval-Salinas has finished her graduate studies and just last Friday defended her thesis admirably earning not only the degree of Masters of Science in Chemistry but doing so with the highest honors given by the National Autonomous University of Mexico.

Maru’s thesis is for many reasons a landmark in this lab not only because it is the first graduate thesis published from our lab but also the first document on our work about the study of Photosynthesis, a long sought after endeavor now closer to publication. It must also be said that Maru came to this lab when she was an undergraduate student five years ago when I just recently joined UNAM as a researcher fresh out of a postdoc stay. After getting her B.Sc. degree and publishing an article in JCTC (DOI: 10.1021/ct4004178) she now is about to publish more papers that I’m sure will be as highly ranked as the previous one. Thus, Maru was a pioneer in our lab giving it a vote of confidence when we had little to nothing to show for; thanks to her hard work and confidence, along with that of the students who have followed her, we managed to succeed as a consolidated research group in the field of computational chemistry.

More specifically, her thesis centered around finding a mechanism for the excitonic transference between pigments (bacteriochlorophyl-a, BChl-a) in the Fenna-Matthews-Olson (FMO) complex, a protein trimer with seven BChl-a molecules in each monomer, located between the antenna complex and the reaction center in green sulfur bacteria. Among the possible mechanisms explored were Förster’s theory, a modification to Marcus’ theory and finally we explored the possibility of Singlet Fission occurring between adjacent molecules with the help of Dr. David Casanova from the Basque Country University where Maru took a short research stay last autumn. Since nature doesn’t conform to any specific mechanism -specially in a complex arrangement such as the FMO- then it could be possible that a combination of the above might also occur but lets just wait for the papers to be published to discuss it. Calculations were performed through the TD-DFT and the C-DFT formalisms using G09 and Q-Chem; comparing experimental data in CH3OH (SMD implicit calculations with the SVWN5 functional) were undertaken previously for selection of the level of theory.

Now, after two original theses written and successfully defended, an article published in JCTC and more in process, at least five posters, a couple of oral presentations and countless hours at her desk, Maru will go pursuit a PhD abroad where I’m sure she will exceed anyone’s expectations with her work, drive, dedication and scientific curiosity. Thank you, Maru, for all your hard work and trust when this lab needed it the most, we wish you the best for you earn it. You will surely be missed.

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