Tools to study molecules in high electric fields

This thesis describes the application of the quantum mechanics/molecular mechanics (QM/MM) Car-Parrinello methodology to two systems of high biological interest: (a) The potassium channel KcsA from Streptomyces lividans and (b) The DNA repair enzyme EndoIV of E.Coli. bacteria. The two studies provide new insights into key biological mechanisms such as the ion selectivity of cell membranes and the DNA repair system. Special emphasize was put on the importance of polarization effects in these systems. Most classical simulations performed today are based on non-polarizable force fields which only include electronic polarization implicitly. This thesis work shows that non-polarizable potential functions do not describe accurately the permeation in ion channels in all cases. Indeed, most current biomolecular packages were developed for the study of globular proteins and have only recently been applied to the study of ion channels. The importance of ion/protein induced polarization effects in the KcsA channel was demonstrated using different computational approaches: first, the fluctuations in the electronic density were studied (Chapter 3). Second, the quantum mechanical electrostatic potential inside the channel was compared to the corresponding result of popular MM force fields (Chapter 4). Third, the coordination geometry of the K+ and Na+ ions inside the channel was investigated (Chapter 5). It was found that the binding geometry of Na+ observed in classical simulations differs significantly from the results of ab initio simulations. In Chapter 6, the protonation state of the Glu71 and Asp80 residues is investigated. While errors due to a neglect of induced polarization effects amount to typically ∼0.1e/per atom, errors in the attribution of a protonation state cause an error of 1e. Thus a correct description of protonation states of the Glu71 and Asp80 residues is crucial. These residues located in the vicinity of the conductive pore in the KcsA K+ channel were found to share dynamically a proton, which may directly influence ion conduction. The proton exchange was found to be faster (sub-picosecond) than the ion translocation (nanosecond). It is important to stress that this mechanism could not have been seen by a classical study. The influence of Glu-71 on the ionic conduction was subsequently confirmed by structural and electrophysiological experiments (Cordero-Morales, Cuello et al. 2006; Cordero-Morales, Cuello et al. 2006), which indicate that Glu71 acts as a voltage sensor regulating the gating of the channel. Chapter 7 deals with an investigation of the catalytic efficiency of the DNA repair enzyme Endonuclease IV. The enzyme catalyses the hydrolysis of DNA at the phosphodiester bond of apurinic/apyrimidinic (AP) sites. The computer model highlighted the importance of electrostatic interactions in the stabilization of the phosphorane transition state. A revised catalytic mechanism is proposed for the phosphohydrolysis which involves a proton transfer. Our results also suggest that the reaction rate is not controlled by the chemical step, which is in agreement with experimental results.

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

Investigations of the non-adiabatic photophysics of Cu(I)-phenanthroline complexes

Gloria Capano

Cu(I)-phenanthrolines are an important class of metal-organic molecules that exhibits much promise for solar energy harvesting and solar-driven catalysis applications. Although many experimental studies have been performed calling for high-level simulations to elucidate their photophysics, a complete picture is still missing. This is the goal of the present thesis. On the ultrafast (femtosecond) timescale we studied the non-adiabatic relaxation of a prototypical Cu(I)-phenanthroline, [Cu(dmp)2]+, by performing excited state simulations using two approaches: quantum dynamics and trajectory surface hopping. These simulations help to identify several mechanisms, internal conversion, pseudo Jahn-Teller distortion, intersystem crossing, occurring in the subpicosecond time scale. Surprisingly, we have found that intersystem crossing does not take place between the lowest singlet and triplet excited states, as previously proposed, but between the lowest singlet and higher triplet states. Moreover, we observed the initial stages (< 100 fs) of the solvent reorganization due to the electronic density changes in the excited state. This leads to an energy stabilization of the excited states that is associated with an increase of the non-radiative decay rate. The quantum dynamics simulations allowed us to provide indications for performing additional spectroscopy measurements by using the recently developed X-ray Free Electron Lasers (X-FELs). This technology can monitor both electronic and structural changes with an unprecedented time resolution of tens of femtoseconds and, therefore, is capable of revealing the aforementioned processes. In addition, we questioned the feasibility of such experiments and calculated the signal strengths for XAS and XES transient spectra. Finally, we analyzed the luminescence quenching, which has been observed for all Cu(I)-phenanthroline complexes when they are dissolved in strongly donating solvents. By performing Molecular Dynamics calculations we showed that, in contrast with the previously accepted model based on the formation of an exciplex (a species formed by two molecules, one in the excited state and one in the ground state), no stable exciplex is formed and that quenching is due to electrostatic solute-solvent interactions. In addition, we investigated how the geometry configuration can affect the luminescence lifetime in these molecules. We found a correlation between rigidity of the copper complex - inhibition of the pseudo Jahn-Teller distortion - and lifetime of the emission. The more the metal complex retains the ground state structure (large substituents), the longer its lifetime. This effect is attributed to a higher energy gap (excited state minus ground state energy) due to the reduction of relaxation. Our research reveals important insights into the relaxation mechanism and the complex interplay between geometry and electronic structure in Cu(I)-phenanthroline. These results can be exploited for guiding the synthesis of complexes with the desired physical properties.

EPFL2016

Search for long-lasting electronic coherence using on-the-fly ab initio semiclassical dynamics

Nikolay Golubev, Alan Scheidegger, Jiri Vanicek

Using a combination of high-level ab initio electronic structure methods with efficient on-the-fly semiclassical evaluation of nuclear dynamics, we performed a massive scan of small polyatomic molecules searching for a long-lasting oscillatory dynamics of the electron density triggered by the outer-valence ionization. We observed that in most of the studied molecules, either the sudden removal of an electron from the system does not lead to the appearance of the electronic coherence or the created coherences become damped by the nuclear rearrangement on a time scale of a few femtoseconds. However, we report several so far unexplored molecules with the electronic coherences lasting up to 10 fs, which can be good candidates for experimental studies. In addition, we present the full-dimensional simulations of the electronic coherences coupled to nuclear motion in several molecules which were studied previously only in the fixed nuclei approximation.& nbsp;(c) 2022 Author(s). All article content, except where otherwise noted, is licensed under a Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).