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.
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.
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).
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.
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!
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.
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.
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.
I have written about extracting information from excited state calculations but an important consideration when analyzing the results is the proper use of the keyword density.
This keyword let’s Gaussian know which density is to be used in calculating some results. An important property to be calculated when dealing with excited states is the change in dipole moment between the ground state and any given state. The Transition Dipole Moment is an important quantity that allows us to predict whether any given electronic transition will be allowed or not. A change in the dipole moment (i.e. non-zero) of a molecule during an electronic transition helps us characterize said transition.
Say you perform a TD-DFT calculation without the density keyword, the default will provide results on the lowest excited state from all the requested states, which may or may not be the state of interest to the transition of interest; you may be interested in the dipole moment of all your excited states.
Three separate calculations would be required to calculate the change of dipole moment upon an electronic transition:
1) A regular DFT for the ground state as a reference
2) TD-DFT, to calculate the electronic transitions; request as many states as you need/want, analyze it and from there you can see which transition is the most important.
3) Request the density of the Nth state of interest to be recovered from the checkpoint file with the following route section:
# TD(Read,Root=N) LOT Density=Current Guess=Read Geom=AllCheck
replace N for the Nth state which caught your eye in step number 2) and LOT for the Level of Theory you’ve been using in the previous steps. That should give you the dipole moment for the structure of the Nth excited state and you can compare it with the one in the ground state calculated in 1). Again, if density=current is not used, only properties of N=1 will be printed.
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:
#p CIS(NStates=10,singlets)/6-31G(d,p) geom=check guess=read scrf=(cpcm,solvent=water)
adenine excited states with CI-Singles method
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:
#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
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:
#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.
The canonical molecular orbital depiction of an electronic transition is often a messy business in terms of a ‘chemical‘ interpretation of ‘which electrons‘ go from ‘which occupied orbitals‘ to ‘which virtual orbitals‘.
Natural Transition Orbitals provide a more intuitive picture of the orbitals, whether mixed or not, involved in any hole-particle excitation. This transformation is particularly useful when working with the excited states of molecules with extensively delocalized chromophores or multiple chromophoric sites. The elegance of the NTO method relies on its simplicity: separate unitary transformations are performed on the occupied and on the virtual set of orbitals in order to get a localized picture of the transition density matrix.
 R. L. Martin, J. Chem. Phys., 2003, DOI:10.1063/1.1558471.
After running a TD-DFT calculation with the keyword TD(Nstates=n) (where n = number of states to be requested) we need to take that result and launch a new calculation for the NTOs but lets take it one step at a time. As an example here’s phenylalanine which was already optimized to a minimum at the B3LYP/6-31G(d,p) level of theory. If we take that geometry and launch a new calculation with the TD(Nstates=40) in the route section we obtain the UV-Vis spectra and the output looks like this (only the first three states are shown):
Excitation energies and oscillator strengths: Excited State 1: Singlet-A 5.3875 eV 230.13 nm f=0.0015 <S**2>=0.000 42 -> 46 0.17123 42 -> 47 0.12277 43 -> 46 -0.40383 44 -> 45 0.50838 44 -> 47 0.11008 This state for optimization and/or second-order correction. Total Energy, E(TD-HF/TD-KS) = -554.614073682 Copying the excited state density for this state as the 1-particle RhoCI density. Excited State 2: Singlet-A 5.5137 eV 224.86 nm f=0.0138 <S**2>=0.000 41 -> 45 -0.20800 41 -> 47 0.24015 42 -> 45 0.32656 42 -> 46 0.10906 42 -> 47 -0.24401 43 -> 45 0.20598 43 -> 47 -0.14839 44 -> 45 -0.15344 44 -> 47 0.34182 Excited State 3: Singlet-A 5.9254 eV 209.24 nm f=0.0042 <S**2>=0.000 41 -> 45 0.11844 41 -> 47 -0.12539 42 -> 45 -0.10401 42 -> 47 0.16068 43 -> 45 -0.27532 43 -> 46 -0.11640 43 -> 47 0.16780 44 -> 45 -0.18555 44 -> 46 -0.29184 44 -> 47 0.43124
The oscillator strength is listed on each Excited State as “f” and it is a measure of the probability of that excitation to occur. If we look at the third one for this phenylalanine we see f=0.0042, a very low probability, but aside from that the following list shows what orbital transitions compose that excitation and with what energy, so the first line indicates a transition from orbital 41 (HOMO-3) to orbital 45 (LUMO); there are 10 such transitions composing that excitation, visualizing them all with canonical orbitals is not an intuitive picture, so lets try the NTO approach, we’re going to take excitation #10 for phenylalanine as an example just because it has a higher oscillation strength:
%chk=Excited State 10: Singlet-A 7.1048 eV 174.51 nm f=0.3651 <S**2>=0.000 41 -> 45 0.35347 41 -> 47 0.34685 42 -> 45 0.10215 42 -> 46 0.17248 42 -> 47 0.13523 43 -> 45 -0.26596 43 -> 47 -0.22995 44 -> 46 0.23277
Each set of NTOs for each transition must be calculated separately. First, copy you filename.chk file from the TD-DFT result to a new one and name it after the Nth state of interest as shown below (state 10 in this case). NOTE: In the route section, replace N with the number of the excitation of interest according to the results in filename.log. Run separately for each transition your interested in:
#chk=state10.chk #p B3LYP/6-31G(d,p) Geom=AllCheck Guess=(Read,Only) Density=(Check,Transition=N) Pop=(Minimal,NTO,SaveNTO) 0 1 --blank line--
By requesting SaveNTO, the canonical orbitals in the state10.chk file are replaced with the NTOs for the 10th excitation, this makes it easier to plot since most visualizers just plot whatever set of orbitals they read in the chk file but if they find the canonical MOs then one would need to do some re-processing of them. This is much more straightforward.
Now we format our chk files into fchk with the formchk utility:
formchk -3 filename.chk filename.fchk
formchk -3 state10.chk state10.fchk
If we open filename.fchk (the file where the original TD-DFT calculation is located) with GaussView we can plot all orbitals involved in excited state number ten, those would be seven orbitals from 41 (HOMO-3) to 47 (LUMO+2) as shown in figure 1.
If we now open state10.fchk we see that the numbers at the side of the orbitals are not their energy but their occupation number particular to this state of interest, so we only need to plot those with highest occupations, in our example those are orbitals 44 and 45 (HOMO and LUMO) which have occupations = 0.81186; you may include 43 and 46 (HOMO-1 and LUMO+1, respectively) for a much more complete description (occupations = 0.18223) but we’re still dealing with 4 orbitals instead of 7.
The NTO transition 44 -> 45 is far easier to conceptualize than all the 10 combinations given in the canonical basis from the direct TD-DFT calculation. TD-DFT provides us with the correct transitions, NTOs just paint us a picture more readily available to the chemist mindset.
NOTE: for G09 revC and above, the %OldChk option is available, I haven’t personally tried it but using it to specify where the excitations are located and then write the NTOs of interest into a new chk file in the following way, thus eliminating the need of copying the original chk file for each state:
NTOs are based on the Natural Hybrid orbitals vision by Löwdin and others, and it is said to be so straightforward that it has been re-discovered from time to time. Be that as it may, the NTO visualization provides a much clearer vision of the excitations occurring during a TD calculation.
Thanks for reading, stay home and stay safe during these harsh days everyone. Please share, rate and comment this and other posts.
Last week at the congress of the Mexican Society of Chemistry I presented some of our results in the study of photosynthesis. Below I embeded the talk. Unfortunately for the wider audience of this blog, the talk is in Spanish (if anyone out there is willing to make subtitles for it I’ll hire you on the spot!)
The slides are also in Spanish although they should be easier to follow for non-Spanish speakers and they are uploaded in SlideShare at this link.
A big thank you to Maria Eugenia “Maru” Sandoval for all the hard work and time invested in this project!
Thanks for clicking!
As we approach to the end of another year, and with that the time where my office becomes covered with post-it notes so as to find my way back into work after the holidays, we celebrate another paper published! This time at the Journal of Physical Chemistry A as a follow up to this other paper published last year on JPC-C. Back then we reported the development of a selective sensor for Hg(II); this sensor consisted on 1-amino-8-naphthol-3,6-disulphonic acid (H-Acid) covalently bound to a modified silica SBA-15 surface. H-Acid is fluorescent and we took advantage of the fact that, when in the presence of Hg(II) in aqueous media, its fluorescence is quenched but not with other ions, even with closely related ions such as Zn(II) and Cd(II). In this new report we delve into the electronic reasons behind the quenching process by calculating the most important electronic transitions with the framework laid by the Time Dependent Density Functional Theory (TD-DFT) at the PBE0/cc-pVQZ level of theory (we also included an electron core potential on the heavy metal atoms in order to decrease the time of each calculation). One of the things I personally liked about this work is the combination of different techniques that were used to assess the photochemical phenomenon at hand; some of those techniques included calculation of various bond orders (Mayer, Fuzzy, Wiberg, delocalization indexes), time dependent DFT and charge transfer delocalizations. Although we calculated all these various different descriptors to account for changes in the electronic structure of the ligand which lead to the fluorescence quenching, only delocalization indexes as calculated with QTAIM were used to draw conclusion, while the rest are collected in the SI section.
Thanks a lot to my good friend and collaborator Dr. Pezhman Zarabadi-Poor for all his work, interest and insight into the rationalization of this phenomenon. This is our second paper published together. By the way, if any of you readers is aware of a way to finance a postdoc stay for Pezhman here at our lab, please send us a message because right now funding is scarce and we’d love to keep bringing you many more interesting papers.
For our research group this was the fourth paper published during 2014. We can only hope (and work hard) to have at least five next year without compromising their quality. I’m setting the goal to be 6 papers; we’ll see in a year if we delivered or not.
I’d like to also take this opportunity to thank all the readers of this little blog of mine for your visits and your live demonstrations of appreciation at various local and global meetings such as the ACS meeting in San Francisco and WATOC14 in Chile, it means a lot to me to know that the things I write are read; if I were to make any New Year’s resolutions it would be to reply quicker to questions posted because if you took the time to write I should take the time to reply.
I wish you all the best for 2015 in and out of the lab!
Having a new paper out is always fun and this week we got the wonderful news from the Journal of Physical Chemistry C that a paper I co authored with Prof. Alireza Badiei at the University of Tehran in Iran and his student, who actually got us all in touch, Dr. Pezhman Zarabadi-Poor, was accepted for publication.
The paper is titled “Selective Optical Sensing of Hg(II) in Aqueous Media by H-Acid/SBA-15: A Combined Experimental and Theoretical Study“; in it we explored the fluorescence quenching mechanism for a Hg(II) complex which forms the basis of a novel selective mercury detector. Geometry optimizations were carried out at the PBE0/6-31++G** PCM level of theory (along with the aug-cc-pVDZ-PP basis set and corresponding ECP for Hg), also the electronic spectrum of both the free acid and the Hg(II) complex was calculated.
(Frontier orbitals were depicted using Chemcraft)
We can observe that HOMO and LUMO+1 are mainly located on the naphtalene ring allowing for the S0 -> S1 transition and back, which accounts for the molecular fluorescence. Other internal conversion processes were also assessed and discussed in the paper which accounts for the quenching effect. In short, we have obtained a full quantum description of the mechanism by which coordination of the free acid to Hg(II) alters the ligand’s electronic structure converting its emisive lowest-lying excited state to a dark state, i.e., quenching! Pretty cool stuff!
Once again thanks to both Dr. Zarabadi-Poor and Prof. Badiei for thinking about me for collaborating with them in this joint endeavor which hopefully wont be our last. A PDF copy of the article is available by direct request through this post.
Thanks for reading, sharing, rating and commenting.