Discovery of conical intersection mediated photochemistry with growing string methods

Cody Aldaz, Joshua A. Kammeraad and Paul M. Zimmerman (2018)

Highlighted by Jan Jensen

Photochemistry is becoming an increasing important synthetic tool but is significantly harder to study computationally than thermal chemistry. Zimmerman and co-workers have developed a new tool that promises to help change that.

The method uses a growing string method (usually used to find TSs) to locate minimum energy conical intersections (MECI), the lowest energy point where the excited state PES intersects the ground state PES. Ground state geometry optimisation starting from the MECI structures are then used to identify the products of the photochemical reaction. Crucially, the method doesn't just find the MECI closest to the reactant structure, but considers several search directions.

One has to define a driving coordinate but this can be automatically determined by generating several possible products, e.g. using Zimmerman's ZStruct method. As far as I know the molecule is not in thermal equilibrium on the excited state PES, so I am not sure one can use the relative energies of the MECIs to predict a product distribution.  Still, an important step forward.



This work is licensed under a Creative Commons Attribution 4.0 International License.

Electron-Driven Proton Transfer Along H2O Wires Enables Photorelaxation of πσ* States in Chromophore−Water Clusters

More than just shifting state energies, polar solvents may actively participate in the photochemistry of excited molecules

Szabla, R.; Šponer, J.; Góra, R. W. J. Phys. Chem. Lett. 2015, 6, 1467-1471.

Highlighted by Mario Barbatti

For decades, it has been well known that solvents, especially polar ones, have a large impact on the photodynamics of chromophores. Phenomenological models, such as the Lim Proximity effect (1), for instance, have been developed to describe how the energy shift caused by the solvent molecules determines radiative and non-radiative rates.

These early approaches focused mostly on the description of the shape of the potential energy surfaces and on the relative shift between them. From that tradition, we learned, for example, the important heuristic rule telling that, in comparison to the gas phase, water stabilizes the ππ* state of the chromophore, while it destabilizes the nπ* state. Those models, however, did not consider that new electronic states arising from the chromophore-solvent interaction could play a major role in the fate of the excited system.

From the photochemical point of view, the solvent was understood as an important but passive factor. Many simulations relied on this important-but-passive hypothesis, to restrict, for instance, the quantum-mechanical region in QM/MM modelling to the chromophore only, saving precious computational time.

In the last years, however, the important-but-passive hypothesis has been challenged by a number case studies (2). Diverse computational simulations have shown that the solvent may indeed play an active role in photochemistry. (I have myself contributed to the field by showing a case where a water-to-chromophore electron transfer could create a conical intersection (3).)

The paper by Szabla, Šponer, and Góra (4) belongs to this new tradition, the important-and-active hypothesis.

Using surface hopping simulations based on ADC(2) excited states, they investigated the ultrafast dynamics of 2-aminooxazole (AMOX) microsolvated by water. They found out that an important radiationless pathway for the AMOX-(H₂O)₅ cluster involves an electron-driven proton transfer along water wires. This process occurs in an electronic state characterized by an electron transfer from an n orbital at the chromophore to a σ* orbital in one of the water molecules (Fig. 1).

Fig. 1 - Electron-driven proton transfer along water wires.

Szabla, Šponer, and Góra note that similar deactivation mechanism has been observed before in simulations of other heterocyclic chromophores. This means that it may be a common pattern in the photochemistry of these compounds.

Although this is is matter for speculation, all these examples imply that we cannot restrict ourselves to credit polar solvents a passive role only. Any new investigation, either experimental or theoretical, has now to take into account the possibility that the solvent may actively be contributing to the photochemistry.

In particular, for the next generation of excited-state QM/MM simulations, the message (and the cost) is clear: quantum-mechanical microsolvation is simply mandatory.

References
(1) Lim, E. C. Proximity effect in molecular photophysics: dynamical consequences of pseudo-Jahn-Teller interaction. J. Phys. Chem. 1986, 90, 6770-6777. doi: 10.1021/j100284a012

(2) Liu, X.; Sobolewski, A. L.; Borrelli, R.; Domcke, W. Computational investigation of the photoinduced homolytic dissociation of water in the pyridine-water complex. Phys. Chem. Chem. Phys. 2013, 15, 5957-5966. doi: 10.1039/C3CP44585B

(3) Barbatti, M. Photorelaxation Induced by Water–Chromophore Electron Transfer. J. Am. Chem. Soc. 2014, 136, 10246-10249. doi: 10.1021/ja505387c

(4) Szabla, R.; Šponer, J.; Góra, R. W. Electron-Driven Proton Transfer Along H₂O Wires Enables Photorelaxation of πσ* States in Chromophore–Water Clusters. J. Phys. Chem. Lett. 2015, 6, 1467-1471. doi: 10.1021/acs.jpclett.5b00261

How Electronic Dynamics with Pauli Exclusion Produces Fermi-Dirac Statistics.

Triet S. Nguyen, Ravindra Nanguneri, and John Parkhill, arxiv:14115324v1 (2014)
Contributed by Alán Aspuru-Guzik

A very interesting preprint by John Parkhill from the University of Notredame and his group provides a solution for a long-standing theoretical problem: Many of the quantum master equations that treat electron-phonon interactions fail to reach a Fermi-Dirac distribution at long times. For example, Ehrenfest dynamics is one of the usual suspects for this behavior. By employing a combination of time-dependent perturbation theory and the extended normal ordering theory of Kutzelnigg and Mukherjee, Parkhill and his co-workers arrive to a novel master equation.

The results from this work show that the Pauli principle "blocks" electron relaxation and slows it down, and in addition it leads to a time-dependent relaxation rate. The plot below shows the correct asymptotic relaxation of a double excitation in a model system and the plot in the right shows a time-dependent relaxation rate.

The paper says that "A paper using these new formulas in a useful all-electron dynamics code is

an immediate follow up.". The contributor is looking forward to it.

Ultrafast X-ray Auger probing of photoexcited molecular dynamics

McFarland, B. K.; Farrell, J. P.; Miyabe, S.; Tarantelli, F.; Aguilar, A.; Berrah, N.; Bostedt, C.; Bozek, J. D.; Bucksbaum, P. H.; Castagna, J. C.; Coffee, R. N.; Cryan, J. P.; Fang, L.; Feifel, R.; Gaffney, K. J.; Glownia, J. M.; Martinez, T. J.; Mucke, M.; Murphy, B.; Natan, A.; Osipov, T.; Petrović, V. S.; Schorb, S.; Schultz, T.; Spector, L. S.; Swiggers, M.; Tenney, I.; Wang, S.; White, J. L.; White, W.; Gühr, M. Nat Commun 2014, 5, doi:10.1038/ncomms5235.
Highlighted by Mario Barbatti

The deconvolution of nuclear and electronic ultrafast motions poses a great challenge for spectroscopic approaches and nonadiabatic dynamics simulations has been a valuable tool to help with this task.

But are dynamics simulations providing reliable information?

Take, for instance, thymine. The ultrafast dynamics of this molecule has been under debate for a decade. 

Thymine has the longest excited-state lifetime among the five canonical nucleobases in the gas phase. According to Ref. (1), after 267-nm excitation, thymine shows a double-exponential deactivation with 105-fs and 5.12-ps time constants. 

The long time constant, which has been assigned to the excited-state lifetime of thymine, was attributed at first to a trapping of the population in the S₁ (nπ*) state after a quick relaxation from the initially excited S₂ (ππ*) state (2) (see Fig. 1). 

As a second possibility, an independent study proposed that the deactivation occurred solely on the ππ* state, without any major influence of the nπ* state (3). In this case, the trapping site would be located at another region of the S₁ surface at a minimum with ππ* character. 

Either way, from one of those S₁ minima, thymine would take a few picoseconds to find the seam of conical intersections to the ground state, explaining its longer lifetime. 

Fig. 1 - After photoexcitation, how does thymine returns to the ground state?

This interpretation has been disputed since different sets of dynamics simulations at CASSCF level predicted that the S₂ (ππ*) → S₁ (nπ*) relaxation time itself occurs on a few picoseconds (4,5). Hence both, elongated S₂ (ππ*) → S₁ (nπ*) relaxation and then S₁ (nπ*) trapping, would contribute to the long time constant.

This entangled story has gained another chapter with a curious twist (6): based on ultrafast X-ray Auger probe spectroscopy and simulations (ADC(2), CK-CIS), McFarland and co-authors found strong evidences that thymine excitation at 266 nm should populate the S₁ (nπ*) state within only 200 fs, just like in the first proposal.

It makes possible that the S₂ (ππ*) trapping was, after all, an artifact of dynamics simulations limited to CASSCF surfaces.

References

(1) Canuel, C.; Mons, M.; Piuzzi, F.; Tardivel, B.; Dimicoli, I.; Elhanine, M. J. Chem. Phys. 2005, 122, 074316-074316. doi:10.1063/1.1850469
(2) Perun, S.; Sobolewski, A. L.; Domcke, W. J. Phys. Chem. A 2006, 110, 13238-13244. doi:10.1021/jp0633897
(3) Merchán, M.; González-Luque, R.; Climent, T.; Serrano-Andrés, L.; Rodriuguez, E.; Reguero, M.; Pelaez, D. J. Phys. Chem. B 2006, 110, 26471-26476. doi:10.1021/jp066874a
(4) Hudock, H. R.; Levine, B. G.; Thompson, A. L.; Satzger, H.; Townsend, D.; Gador, N.; Ullrich, S.; Stolow, A.; Martínez, T. J. J. Phys. Chem. A 2007, 111, 8500-8508. doi:10.1021/jp0723665
(5) Szymczak, J. J.; Barbatti, M.; Soo Hoo, J. T.; Adkins, J. A.; Windus, T. L.; Nachtigallová, D.; Lischka, H. J. Phys. Chem. A 2009, 113, 12686-12693.doi:10.1021/jp905085x
(6) McFarland, B. K.; Farrell, J. P.; Miyabe, S.; Tarantelli, F.; Aguilar, A.; Berrah, N.; Bostedt, C.; Bozek, J. D.; Bucksbaum, P. H.; Castagna, J. C.; Coffee, R. N.; Cryan, J. P.; Fang, L.; Feifel, R.; Gaffney, K. J.; Glownia, J. M.; Martinez, T. J.; Mucke, M.; Murphy, B.; Natan, A.; Osipov, T.; Petrović, V. S.; Schorb, S.; Schultz, T.; Spector, L. S.; Swiggers, M.; Tenney, I.; Wang, S.; White, J. L.; White, W.; Gühr, M. Nat Commun 2014, 5, doi:10.1038/ncomms5235.

Using Orbital Symmetry to Minimize Charge Recombination in Dye-Sensitized Solar Cells

Maggio, E., Martsinovich, N. and Troisi, A. (2013), Angew. Chem. Int. Ed., 52: 973–975.
Contributed by Gemma Solomon 

Orbital symmetry can be used in dye design to retard charge recombination in dye-sensitized solar cells. 

Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim

Finding the balance between competing processes is a central challenge in optimizing the performance of dye-sensitized solar cells. One aspect of this problem is the dichotomy between the requirement for fast charge injection between the dye and a semiconductor surface (for photo-induced charge separation) and slow charge recombination between the two. There are a range of strategies available for optimizing one or other of these processes; but clever chemical design is required in order to optimize the two together. Minimizing unwanted charge recombination involves beating the Coulomb interaction, and this is a formidable opponent indeed.

In their recent paper Maggio, Martsinovich and Troisi have proposed an elegant solution: use orbital symmetry to retard charge recombination. Building on the ideas from studies of electron transfer, they show that it is possible to design dyes where the charge injection is symmetry allowed, while charge recombination is symmetry forbidden. In terms of molecular orbitals, charge recombination involves injection into the HOMO of the dye from the semiconductor, while charge injection involves the LUMO of the dye injecting into the surface. Depending on the symmetry of the dye, and the position at which it is substituted, the authors show that it is possible to have the LUMO interacting strongly with the surface (delocalizing into the binding arm) while the HOMO remains isolated, as illustrated above.

This represents a new strategy for dye design and an exciting prediction from computational chemistry. It will be interesting to see how dyes using this strategy perform in devices and should remind us all that we have a powerful tool for molecular design with symmetry at our disposal.   

Computational Design and Selection of Optimal Organic Photovoltaic Materials

Noel M. O’Boyle, Casey M. Campbell and Geoffrey R. Hutchison Journal of Physical Chemistry C 2011, 115, 16200 (Paywall)

Quantum chemistry for high throughput screening
In this work over 90,000 pi-conjugated copolymer were computationally screened for new and efficient organic photo-voltaics. Not being an expert in organic photo-voltaics I highlight this paper as a very interesting example of what I believe is an important emerging trend in the use of quantum chemistry: efficient high through-put screening of molecules for desirable properties.  Computers and software have now reached a point where this is computationally feasible to perform computations on thousands of molecules and the challenge is now to make it practically possible, i.e. to find the right combinations of methods and automate their use.

How does one construct 90,000 geometries?  Cheminformatics meets quantum chemistry
OpenBabel is used to construct the 3D structure of each polymer, starting from its SMILES string, and to find the lowest energy conformation using a weighted rotor-search and the MMFF94 force field.  This lowest energy conformation is then minimized with PM6 and used to compute energies and oscillator strengths of the 15 lowest- energy electronic transitions with ZINDO/S, which forms the basis for estimating the energy conversion efficiency (see the paper for more details).  The required CPU time is  8-10 minutes per polymer on a single core.  To put that number in perspective: using 100 cores, 100,000 polymers can be screened in roughly a week.

Starting from 131 different monomers, all possible (19,701) dimers are made and these dimers are then used to construct the corresponding 58,707 tetramers. (A brief description on how exactly this was scripted would have been a welcome addition to the supplementary materials).  The energy conversion efficiency was computed for all these dimer and tetramers.  These results were used to calibrate a genetic search algorithm that was used to identify hexamers and octamers with high energy conversion efficiency without doing an exhaustive search.

Promising candidates and new strategies
The current state-of-the-art is ca 8% energy conversion efficiency.  This study found 621 polymers (mostly hexamers and octamers) with greater than 9%  and 2 with greater than 11 % energy conversion efficiency.  (As the authors point out these polymers still need to be filtered for solubility, crystal packing, and other factors.)  Just as interestingly new design strategies emerged:

"Our analysis of component monomers, dimers, and the copolymer sequence demonstrates important design rules for copolymer photovoltaics. Most importantly, the conventional picture of combining a strong donor and strong acceptor into an alternating copolymer is found to frequently yield poor energy- level alignment. Instead, our top hexamers and octamers reflect a decreased optical band gap due to high coupling between the two-component monomers, not solely due to particular HOMO or LUMO energies of the monomers themselves."

This work is licensed under a Creative Commons Attribution 3.0 Unported License. 

Roaming-mediated isomerization in the photodissociation of nitrobenzene

M. L. Hause, N. Herath, R. Zhu, M. C. Lin, A. G. Suits Nature Chemistry 2011, 3, 932 (Paywall)
Contributed by Steven Bachrach.

Reposted from Computational Organic Chemistry with permission

The roaming mechanism has gained some traction as a recognizable model.^1,2 This mechanism involves typically the near complete dissociation of a molecule into two radical fragments. But before they can completely separate they form a loose complex on a flat potential energy surface. The two fragments can then wander about each other (the “roaming” part of the mechanism), eventually finding an alternative exit channel. The first example was the dissociation of formaldehyde which forms the complex H + CHO.³ The hydrogen atom roams over to the other side of the HCO fragment and then abstracts the second hydrogen atom to form H₂ and CO – with the unusual signature of a hot H₂ molecule and CO in low rotational/vibrational states.

The photodissociation of nitrobenzene is now suggested to also follow a roaming pathway.⁴ Bimodal distribution is found for the NO product channel. There is a slow component with low J and a fast component with high J. This suggests two different operating mechanisms for dissociation.

G2M(CC1)/UB3LYP/6-311+G(3df,2p) computations provide the two mechanisms. Near dissociation to phenyl radical and NO₂ can lead to a roaming process that eventually leads to recombination to form phenyl nitrite, which can then dissociate to the slow NO product. The fast NO product is suggested to come from rearrangement of nitrobenzene to phenylnitrite on the triplet surface, again eventually leading to loss of NO, but with high rotational excitation.


References
(1) Herath, N.; Suits, A. G., "Roaming Radical Reactions," J. Phys. Chem. Lett. 2011, 2, 642-647, DOI: 10.1021/jz101731q

(2) Bowman, J. M.; Suits, A. G., "Roaming reactions: The third way," Phys. Today 2011, 64, 33-37, DOI: 10.1063/PT.3.1330

(3) Townsend, D.; Lahankar, S. A.; Lee, S. K.; Chambreau, S. D.; Suits, A. G.; Zhang, X.; Rheinecker, J.; Harding, L. B.; Bowman, J. M., "The Roaming Atom: Straying from the Reaction Path in Formaldehyde Decomposition," Science 2004, 306, 1158-1161, DOI: 10.1126/science.1104386.

(4) Hause, M. L.; Herath, N.; Zhu, R.; Lin, M. C.; Suits, A. G., "Roaming-mediated isomerization in the photodissociation of nitrobenzene," Nat. Chem 2011, 3, 932-937, DOI: 10.1038/nchem.1194


This work is licensed under a Creative Commons Attribution-NoDerivs 3.0 Unported License.