Computational studies for the description of electronic and optical properties for photocatalysis in Metal Organic Frameworks

Metal-organic frameworks(MOFs) are promising materials for photocatalytic applications. MOFs modular and porosity structure provides a platform to assemble photo-active and catalytic-sites building block units that can offer unique photo-physics. This feature is of great interest for H2 evolution photocatalytic applications. However, MOFs current photocatalysts do not meet the industrial need for their implementation as a technology due to performance limitations. Thus, elucidating and predicting the optical properties of MOFs will have wide implications in the development of MOF-based photocatalysts. Computational studies can be of great aid for the discovery of MOFs photocatalyst. Yet, this is a challenging task for computational chemistry given the complexity of the photophysical properties, the inorganic-organic nature, the number of atoms, and the unit cell size of MOFs. The principal goal of this thesis is the study MOFs photophysical properties for predicting their feasibility for photocatalytic applications. Density functional theory (DFT) and linear-response time-dependent DFT (LR-TDDFT) formalisms are used for the description of the light absorption, charge separation, and charge transfer properties of MOFs. We first address the dependence of the ligand in the UV/Vis optical absorption of porphyrin-based MOFs. The characterization of the excited states of the porphyrin ligands in MOFs requires an appropriate approximation for the description in periodic crystal MOFs. The selection of proper functionals and approximations within DFT/TDDFT calculations is necessary to overcome the erroneous description of properties like excitonic effects, optical transitions, and gap-renormalization. Later, we continue with the study of the charge separation in a porphyrin ruthenium-based MOF. We describe the importance of missing coordinated solvents anions in the metal node for the stability and charge transfer mechanism in the material. Within this study, we computed electron-hole interacting energy indicating a low electron-hole recombination rate. We next introduce a computational strategy to describing the long-lived electron-hole pairs and the long-rage charge transfer in MOFs. This description can be depicted by computing charge transfer numbers and the effective mass of carriers, respectively. This methodology can correctly predict the charge separation and the effective mass of 15 representative MOF structures promising for photocatalysis in agreement with the literature. Finally, we present an experimental and theoretical combined study investigation towards optimal photocatalytic hydrogen evolution reaction (HER) in MOFs. Isostructural pyrene-based MOFs with different transition metals allowed us a proper comparison. This study highlights the interplay between tunning electronic properties and crystal morphology on the photocatalytic HER performance of the MOFs. These results presented in this thesis can be exploited and transfer to the study of other MOFs for HER photocatalysis.

Capturing Non-local Effects in Kohn-Sham Density Functional Theory

Andrey Laktionov

Density Functional Theory (DFT) and its time-dependent extension (TDDFT) have become two of the most popular approaches for computer simulations of the electronic structure and response properties of quantum systems. A reasonable compromise between accuracy and computational cost allows to apply DFT to a wide range of systems from small molecules to biological complexes. Despite the in principle exact nature of DFT and TDDFT, practical calculations require the use of approximate DFT exchange-correlation (XC) functionals and TDDFT kernels and the accuracy of the obtained results is determined by the accuracy of the chosen XC description. These approximations inevitably introduce some limitations in the use of DFT-based methods.The inability of the local spin density approximation, generalized gradient approximations (GGA) and even some hybrid functionals to properly describe charge transfer (CT) excitations and predict intermolecular interaction energies of weakly bound complexes are two major drawbacks of current XC descriptions. This thesis is therefore devoted to the improvement of XC functionals for the special cases of weak interactions and charge-transfer excitations. Many original strategies have been suggested to cure DFT calculations from these failures. In particular, the Dispersion-Corrected Atom-Centered Potentials (DCACP) approach provides an accurate description of dispersion forces within generalized gradient approximations for the exchange-correlation functional. The DCACP method has been extensively used for the last seven years and has shown an excellent performance for a large class of applications. However, one of the drawbacks of the current implementation of DCACP is that the correct R-6 asymptotics of dispersion interaction is not reproduced. A first goal of this thesis was to enable DCACP to recover the R-6 asymptotic limit. To this end, we have designed a new 2-channel version of DCACP and carried out test calculations on both small molecules and large macromolecular complexes. The obtained results demonstrate the excellent performance and transferability of the DCACP approach. Moreover, for large macromolecular complexes, in which the binding energy is dominated by dispersion, [pi]-stacking, or hydrogen bonding, 2-channels DCACP were found to be the best method overall for correcting the popular BLYP functional. Our study clearly shows that account of R-6 asymptotics is crucial for the description of large complexes and that 2-channels DCACP are fully able to capture these effects. On the contrary, an account of R-6 asymptotics is of little importance for small molecules since the remaining errors of the underlying GGA functional are dominating. With the aim of deepening our understanding of the DCACP concept and the reasons for its excellent performance, we explored the properties of the two DCACP parameters and were able to establish some systematic trends. It turned out that variational tuning of the DCACP can be done in an analytical manner that enables the easy generation of DCACP potentials for the full periodic table. Furthermore, since DCACP have little but crucial impact on the electronic density, dispersion energies can be obtained from non-self-consistent electron densities. These empirical findings suggest that the high transferability of DCACP is due to their atom-centered form and the intrinsically weak nature of dispersion interactions. [...]

EPFL2014

Development of Site-Specific Mg2+-RNA Force Field Parameters: A Dream or Reality? Guidelines from Combined Molecular Dynamics and Quantum Mechanics Simulations

Lorenzo Casalino, Giulia Palermo, Ursula Röthlisberger

The vital contribution of Mg2+ ions to RNA biology is challenging to dissect at the experimental level. This calls for the integrative support of atomistic simulations, which at the classical level are plagued by limited accuracy. Indeed, force fields intrinsically neglect nontrivial electronic effects that Mg2+ exerts on its surrounding ligands in varying RNA coordination environments. Here, we present a combined computational study based on classical molecular dynamics (MD) and Density Functional Theory (DFT) calculations, aimed at characterizing (i) the performance of five Mg2+ force field (FF) models in RNA systems and (ii) how charge transfer and polarization affect the binding of Mg2+ ions in different coordination motifs. As a result, a total of similar to 2.5 mu s MD simulations (100/200 ns for each run) for two prototypical Mg2+-dependent ribozymes showed remarkable differences in terms of populations of inner-sphere coordination site types. Most importantly, complementary DFT calculations unveiled that differences in charge transfer and polarization among recurrent Mg2+-RNA coordination motifs are surprisingly small. In particular, the charge of the Mg2+ ions substantially remains constant through different coordination sites, suggesting that the common philosophy of developing site-specific Mg2+ ion parameters is not in line with the physical origin of the Mg2+-RNA MD simulations inaccuracies. Overall, this study constitutes a guideline for an adept use of current Mg2+ models and provides novel insights for the rational development of next-generation Mg2+ FFs to be employed for atomistic simulations of RNA.

2017

Development of a non-adiabatic ab initio molecular dynamics method and its application to photodynamical processes

Enrico Marko Tapavicza

Photoprocesses are ubiquitous in nature, science, and engineering. The understanding as well as the optimization of photochemical and photophysical properties of molecular systems requires computational tools that are able to describe the dynamical evolution of the system in electronically excited states. Ab Initio Molecular Dynamics (AIMD) based on Density Functional Theory (DFT) has become an established tool for elucidating mechanisms of chemical reactions that occur in the electronic ground state. However, to describe photoprocesses by AIMD, an underlying electronic-structure method that is able to treat excited states is necessary. This complicates the description of these processes because in the past this implied the use of computationally expensive wavefunction-based methods, which in addition are not straightforward to use. Time-Dependent Density Functional Theory (TDDFT) provides an in principle exact description of electronically excited states, although in practice, approximations have to be introduced. Compared to wavefunction-based methods, TDDFT is computationally less demanding and is relatively straightforward and easy to use. Recently, TDDFT nuclear gradients have become available and allow to carry out AIMD in excited states. In this thesis a TDDFT-based AIMD method that is able to account for non-adiabatic effects is developed and implemented. The non-adiabatic couplings are computed by means of a Kohn-Sham orbital based reconstruction of the many-electron wavefunction for ground and excited states. The non-adiabatic scheme is based on the fewest switches trajectory surface hopping (SH) method introduced by Tully. The method is applied to describe decay processes, such as fragmentation or isomerization, that occur upon photoexcitation of the molecules protonated formaldimine and oxirane. In the case of protonated formaldimine, the results of the TDDFT-SH method are in good agreement with SH simulations based on the state-averaged complete active space (SA-CASSCF) method, both with respect to the observed reaction mechanisms and the excited state life times. In the case of oxirane, the TDDFT-SH simulations confirm the main experimental results and provide an additional refinement of the postulated reaction mechanism. The accuracy of TDDFT is investigated with respect to different issues that are especially important for the proper description of photoprocesses. These aspects include the accuracy of non-adiabatic coupling (NAC) vectors, the description of S1-S0 conical intersections, and the description of locally excited states in systems where charge transfer (CT) states are present, that are affected by the well-known CT failure of TDDFT. Concerning the NAC vectors, a qualitative agreement with SA-CASSCF is found, although magnitudes are underestimated by TDDFT/PBE. Regarding the description of conical intersections to the ground state, we find as expected that TDDFT in the adiabatic approximation (ALDA) is not able to predict an intersection that is strictly conical. However, we find that TDDFT is able to approximate a conical intersection that has a similar shape as the one predicted by SA-CASSCF. For an electron donor-bridge-acceptor molecule it is shown that the CT failure of TDDFT can also considerably affect properties of non-CT states. The use of TDDFT using conventional exchange-correlation functionals is thus not recommended for the description of such systems. Using the second-order approximate coupled cluster (CC2) method in conjunction with a high quality basis set, an accurate and balanced description of both locally excited and CT states can be made. The use of CC2 with large basis sets for AIMD simulations is however still computationally unaffordable for larger systems. TDDFT is still in its infancy and several attempts to cure some of its defiencies have already been made. These attempts mainly concern improvements of the approximations of the exchange-correlation functionals and associated TDDFT kernels. The TDDFT-SH method that has been developed in this thesis can in principle be applied in combination with any approximation for the exchange correlation functional, provided that nuclear gradients for this approximation are available and the computational cost remains acceptable. In this way, the method developed here is able to directly profit from the ongoing improvements in the active research field of exchange-correlation functionals and kernels.