Redox reactions are crucial to biological processes that protect organisms against oxidative stress. Metalloenzymes, such as cytochrome c peroxidases which reduce excess hydrogen peroxide into water in the periplasm of multiple bacterial organisms, play a key role in detoxification mechanisms. While accurate computational tools can be used to simulate ground state redox potentials in biomolecules, adapting such approaches to properly describe redox reactions in transition metal complexes, particularly in hemes in heterogeneous protein environments, remains a significant challenge. Here we present the results of polarizable hybrid QM/MM studies of the reduction potentials of two heme sites in the cytochrome c peroxidase of Nitrosomonas europaea. The simulated redox potential of the catalytic site Low Potential (LP) is in good agreement with the experiment, while for the High Potential (HP) heme the computational estimate significantly overestimate the experimental value. We have found that environment polarization shifts the computed value of the redox potential of the catalytic LP heme by 1.3 V, while it does not affect that of the non-catalytic High Potential (HP) heme. We demonstrate that it is necessary to account for mutual polarization of heme site and the protein environment when describing redox processes, particularly those that involve more charged heme sites. We have explored the role of various factors such as heme geometries, axial ligands, propionate side chains, and electrostatic field of the protein in tuning the redox potentials of hemes in NeCcP. The fluctuations in computed vertical ionization and electron attachment energies are predominantly affected by fluctuations in the electrostatic field of the environment but not by fluctuations in heme geometries. We attribute the difference in computed LP and HP heme reduction potentials of 0.05 V and 1.15 V, respectively, to different axial ligands and electrostatic interactions of the hemes with the protein environment. / 2023-06-30T00:00:00Z

The size and conformational complexity of proteins and other large systems represent major challenges for today's methods of quantum chemistry.This thesis is centered around the development of new computational tools to gain molecular-level insight into electronic transitions in such systems. To meet this challenge, we focus on the polarizable embedding (PE) model, which takes advantage of the fact that many electronic transitions are localized to a smaller part of the entire system.This motivates a partitioning of the large system into two regions that are treated at different levels of theory:The smaller part directly involved in the electronic process is described using accurate quantum-chemical methods, while the effects of the rest of the system, the environment, are incorporated into the Hamiltonian of the quantum region in an effective manner. This thesis presents extensions of the PE model with theaim of expanding its range of applicability to describe electronic transitions in large molecular systemsin the optical and X-ray regions. The developments cover both improvements with regardto the quantum region as well as the embedding potential representing the environment.Regarding the former, a damped linear response formulation has been implemented to allow for calculations of absorption spectra of large molecular systems acrossthe entire frequency range. A special feature of this development is its abilityto address core excitations that are otherwise not easily accessible.Another important development presented in this thesis is the coupling of the PE model to a multi-configuration self-consistent-field description of the quantum region and its further combination with response theory. In essence, this extends the PE model to the study of electronic transitions in large systems that are prone to static correlation --- a situation that is frequently encountered in biological systems. In addition to the direct environmental effects on the electronic structure of the quantum region, another important component of the description of electronic transitions in large molecular systems is an accurate account of the indirect effects of the environment, i.e., the geometrical distortions in the quantum region imposed by the environment. In thisthesis we have taken the first step toward the inclusion of geometry distortions in the PE frameworkby formulating and implementing molecular gradients for the quantum region. To identify critical points related to the environment description, we perform a theoretical analysis of the PE model starting from a full quantum-mechanicaltreatment of a composite system. Based on this, we present strategies for an accurate yet efficient construction of the embedding potentialcovering both the calculation of ground state and transition properties. The accurate representation of the environment makes it possible to reduce the size of the quantum region without compromising the overall accuracy of the final results. This further enables use of highly accurate quantum-chemical methods despite their unfavorable scaling with the size of the system. Finally, some examples of applications will be presented to demonstrate how the PE model may be applied as a tool to gain insight into and rationalize the factors influencing electronic transitions in large molecular systems of increasing complexity. / <p>The dissertation was awarded the best PhD thesis prize 2016 by the Danish Academy of Natural Sciences.</p><p></p><p>QC 20170209</p>

Dans cette thèse, les propriétés optiques de biomolécules importantes ont été étudiées en utilisant une approche théorique et, dans un cas, aussi expérimentale. La Théorie de la fonctionnelle de la densité (DFT) et la timedependent-DFT (TD-DFT) sont les principales méthodes de chimie quantique utilisées dans cette thèse. Plusieurs spectroscopies ont été étudiées (au niveau théorique et, dans certains cas, également au niveau expérimental) : absorption électronique linéaire (absorption à un photon, OPA) et non-linéaire (absorption à deux ou trois photons, TPA et 3PA), dichroïsme circulaire électronique (DCE) et spectroscopie de fluorescence. Les effets de l’environnement, particulièrement importants dans des systèmes biologiques, ont été pris en compte, pour les propriétés de l’état fondamental et des états excités en utilisant une méthode multi-échelles QM/MM appelée Polarizable Embedding (PE). L’échantillonnage des conformations a été pris en compte avec des simulations de dynamique moléculaire (MD) qui sont basées sur la mécanique classique. Deux thématiques ont été étudiées dans cette thèse : le cholestérol et le design in silico de ses analogues fluorescents ainsi que la caractérisation des coudes de type β dans différentes conformations grâce à la simulation des spectres DCE. La simulation de plus d’une spectroscopie a été importante dans l’étude des états excités du cholestérol dans des solutions organiques. Le design in silico a suggéré un nouveau stérol-polyénique (P-stérol) qui montre despropriétés optiques améliorées pour le mécanisme d’excitation à trois photons par rapport au déhydroergostérol (DHE), une sonde du cholestérol déjà très utilisée. Ce nouveau P-stérol a été suggéré pour la synthèse. L’étude des spectres de DCE des coudes β en différentes conformations a mené une double conclusion : même si deux allures de DCE pour les conformations des coudes β étudiées (4) ont été trouvées (dans la majorité des cas), la spectroscopie de DCE doit toujours être associée à d’autres techniques spectroscopiques dans la caractérisation en solution des coudes β. / In this thesis, the optical properties of important biomolecules were studied using a theoretical approach and, in one case, also an experimental one. Density Functional Theory (DFT) and time-dependent-DFT (TD-DFT), were the principal quantum chemical methods adopted in this thesis.Various spectroscopies were studied (theoretically and, in some cases, also experimentally) : linear (one-photon, OPA) and non-linear (two- and three-photon, TPA and 3PA) electronic absorption, electronic circular dichroism (ECD) and fluorescence spectroscopy. The environment effects, which are particularly important in biological systems, were taken into account, for both ground and excited states properties, using a multiscale QM/MM method called Polarizable Embedding (PE). The sampling of conformations was addressed by Molecular Dynamic (MD) simulations based on classical mechanics. Two topics were studied in this thesis: cholesterol and the in-silico design of its fluorescent analogues, and the characterization of β-turns in different conformations by simulations of their ECD spectra in aqueous solutions. The simulation of more than one spectroscopy resulted to be important when studying the electronic excited states of cholesterol in organic solutions. The in-silico design study suggested a novel polyene-sterol (P-sterol) which shows improved optical properties for the three-photon excitation mechanism with respect to dehydroergosterol (DHE), an already widely used cholesterol probe. This new P-sterol was thus suggested for synthesis. The achievement from the study of ECD spectra for different β-turn conformations is two-fold: even if two ECD patterns for the β-turn conformations studied (4) were found (in most of cases), ECD spectroscopy should be always associated with other spectroscopic techniques when trying to characterize the β-turn conformations in solutions.