In dieser Arbeit werden Algorithmen für die Berechnung elektronischer Korrelations- und Anregungsenergien mittels der Coupled-Cluster Methode auf adaptiven Gittern entwickelt und implementiert. Die jeweiligen Funktionen und Operatoren werden adaptiv durch Multiskalenanalyse dargestellt, was eine Basissatz unabängige Beschreibung mit kontrollierter numerischer Genauigkeit ermöglicht. Gleichungen für die Coupled-Cluster Methode werden in einem verallgemeinerten Rahmen, unabhängig von virtuellen Orbitalen und globalen Basissätzen, neu formuliert. Hierzu werden die amplitudengewichteten Anregungen in virtuelle Orbitale ersetzt durch Anregungen in n-Elektronenfunktionen, welche durch Gleichungen im n-Elektronen Ortsraum bestimmt sind. Die erhaltenen Gleichungen können, analog zur Basissatz abh¨angigen Form, mit leicht angepasster Interpretation diagrammatisch dargestellt werden. Aufgrund des singulären Coulomb Potentials werden die Arbeitsgleichungen mit einem explizit korrelierten Ansatz regularisiert. Coupled-Cluster singles mit genäherten doubles (CC2) und ähnliche Modelle werden, für geschlossenschalige Systeme und in regularisierter Form, in die MADNESS Bibliothek (eine allgemeine Bibliothek zur Darstellung von Funktionen und Operatoren mittels Multiskalenanalyse) implementiert. Mit der vorgestellten Methode können elektronische CC2 Paarkorrelationsenergien und Anregungsenergien mit bestimmter numerischer Genauigkeit unabhängig von globalen Basissätzen berechnet werden, was anhand von kleinen Molekülen verifiziert wird / In this work algorithms for the computation of electronic correlation and excitation energies with the Coupled-Cluster method on adaptive grids are developed and implemented. The corresponding functions and operators are adaptively represented with multiresolution analysis allowing a basis-set independent description with controlled numerical accuracy. Equations for the coupled-cluster model are reformulated in a generalized framework independent of virtual orbitals and global basis-sets. For this, the amplitude weighted excitations into virtuals are replaced by excitations into n-electron functions which are determined by projected equations in the n-electron position space. The resulting equations can be represented diagrammatically analogous to basis-set dependent approaches with slightly adjusted rules of interpretation. Due to the singular Coulomb potential, the working equations are regularized with an explicitly correlated ansatz. Coupled-cluster singles with approximate doubles (CC2) and similar models are implemented for closed-shell systems and in regularized form into the MADNESS library (a general library for the representation of functions and operators with multiresolution analysis). With the presented approach electronic CC2 pair-correlation energies and excitation energies can be computed with definite numerical accuracy and without dependence on global basis sets, which is verified on small molecules.

This thesis presents computational studies of problems in the organic and polymer chemistry. The state-of-the art quantum chemical methods are used to gain further insight into the origin and the nature of the reactions in three different organic and polymer systems. The research questions are conceptually approached by identifying the key aspects. Then an appropriate strategy for the quantum chemical modeling is developed. In the scope of the polymer chemistry, the novel synthesis technique of nanostructured materials, the so-called twin polymerization, is investigated. Using three model systems of increasing complexity the influence of the anion (trifluoroacetate) in the reaction system is investigated. The effect of the solvent polarity as well as the effect of the entropic contributions are also considered. The rearrangement reaction of the volatile cyanotritylcarbenes is another topic. These carbenes readily rearrange to ethene main products, however also small amount of the unexpected heptafulvenes is formed. This unprecedented heptafulvene formation is modeled in detail and the energetics is systematically evaluated to identify most reasonable rearrangement pathways of the probable multiple alternative routes. Computational investigation of other tritylcarbenes with varying spectator substituents results in sophisticated data base for experimental investigations. At last, some controversial observations in experimental studies concerning the kinetics of the electrophilic alkylation of the barbiturate anion are studied. To interpret the kinetic measurements, different alkylation pathways are analyzed with respect to their energetics. Further, the influence of microsolvation is demonstrated.

Catalysis is a key area of chemistry. Through catalysis it is possible to achieve better synthetic routes, exploit molecules normally considered to be inactive and also attain novel chemical transformations. The development of new catalysts is crucial to furthering chemistry as a field. Computational chemistry, arising from applying the equations of quantum and classical mechanics to solving chemical problems, offers an essential route to investigating the underlying atomistic detail of catalysis. In this thesis calculations have been applied towards studying a number of different catalytic processes. The processing of renewable chemical sources via homogeneous reactions, specifically cardanol from cashew nuts, is discussed. All routes examined for monoreduction of a diene model by [Ru(H)(iPrOH)(Cl)(C₆H₆)] and [Ru(H)(iPrOH)(C₆H₆)]⁺ are energetically costly and would allow for total reduction of the diene if they were operating. While this accounts for the need of high temperatures, further work is required to elucidate the true mechanism of this small but surprisingly complex system. Gold-mediated protodecarboxylation was examined in tandem with experiment to find the subtle steric and electronic effects that dictate CO₂ extrusion from gold N-heterocyclic carbene activated benzene-derived carboxylic acids. The origin of a switch in the rate limiting step from decarboxylation to protodeauration with less activated substrates was also clearly demonstrated. Studies of gold systems are closed with examinations of 1,2-difluorobenzene C–H activation and CO₂ insertion by [Au(IPr)(OH)]. Calculations highlight that the proposed mechanism for oxazole-derived substrates cannot be extended to 1,2-difluorobenzene and instead a digold complex offers more congruent predicted kinetics. The lens of quantum chemistry was turned upon palladium-mediated methoxycarbonylation reactions. An extensive study was undertaken to attempt to understand the bidentate diphosphine ligand dependency on forming either methylpropanoate (MePro) or copolymers. Mechanisms currently suggested in literature are shown to be incongruous with the formation of MePro by Pd(OAc)₂ and bulky diphosphines. A possible alternative route is proposed in this thesis. Four mechanisms for methoxycarbonylation with Pd(2-PyPPh₂)ₙ are detailed. The most accessible route is found to be congruent with experimental reports of selectivity, acid dependency and slight steric modifications. A modification of 2-PyPPh₂ to 2-(4-NMe₂-6-Me)PyPPh₂ is shown to improve both selectivity and turnover, the latter by four orders of magnitude (highest transition state from 22.9 kcal/mol to 16.7 kcal/mol ∆G), and this new second generation in silico designed ligand is studied for its applicability to wider substrate scope and different solvents. The final chapter of this thesis is a mixed quantum mechanics and molecular mechanics (QM/MM) examination of an enzymatic reaction, discussing the need for certain conditions and the role of particular amino acid residues in an S[sub]N2 hydrolysis reaction.

Ce mémoire s’inscrit dans le cadre des recherches sur les molécules ultra-froides, en forte expansion depuis plusieurs années. Contrairement aux atomes, les molécules ne peuvent que très difficilement être refroidies par laser. Il est donc nécessaire d’explorer des méthodes alternatives pour parvenir à la création de gaz moléculaires ultra-froids. Ce travail théorique s’est focalisé sur une classe particulière de molécules diatomiques hétéronucléaires, présentant un moment dipolaire électrique ou magnétique intrinsèque à l’origine de leurs interactions mutuelles anisotropes.Sur la base de la connaissance précise de la spectroscopie des molécules KRb et KCs (présentant un moment dipolaire électrique intrinsèque notable), combinée à des résultats théoriques, nous avons modélisé le refroidissement de leurs degrés de liberté internes au moyen du passage adiabatique Raman stimulé (STIRAP), processus laser conduisant les molécules dans leur état fondamental absolu. Plusieurs schémas STIRAP ont été discutés et comparés entre eux du point de vue de leur efficacité.Nous avons ensuite étudié la molécule RbCa, dont la spectroscopie est encore inconnue. Cette espèce est caractérisée par la présence conjointe d’un moment dipolaire électrique et magnétique permanent, qui présente un fort intérêt pour les possibilités de contrôle des interactions anisotropes qu’ils engendrent. Nous avons déterminé la structure électronique de RbCa par deux méthodes différentes de chimie quantique, permettant ainsi de qualifier la précision des résultats. Nous avons aussi proposé un schéma de transitions laser conduisant à la formation de molécules froides de RbCa à partir des atomes séparés.La manipulation et le piégeage de molécules repose sur la connaissance de leur réponse à un champ électromagnétique externe, caractérisée par leur polarisabilité dipolaire dynamique. Les calculs de chimie quantique entrepris plus haut nous ayant permis d’accéder à des états moléculaires très excités, nous avons déterminé cette quantité pour toute une série de molécules diatomiques (dimères alcalins, RbCa, RbSr,…). Nous avons ainsi pu déterminer les paramètres optimaux pour le piégeage laser de ces molécules. / This thesis deals with ultracold molecules research, which interest has been growing for several years. Unlike atoms, laser-cooling molecules is very difficult. Alternative methods are necessary to be searched for in order to create ultracold molecular gases. This theoretical work focuses on a particular type of heteronuclear diatomic molecules, possessing an intrinsic electric or magnetic dipole moment, from which originates their mutual anisotropic interactions.Based on the precise knowledge of KRb and KCs molecules (possessing a significant intrinsic electric dipole moment) spectroscopy, combined with theoretical results, the cooling of their internal degrees of freedom using Stimulated Raman Adiabatic Passage (STIRAP), a laser process bringing molecules towards their absolute ground state, has been modelled. Several STIRAP schemes have been investigated and compared regarding their efficiency. The RbCa molecule has then been studied, which spectroscopy is still unknown. The ability of controlling the anisotropic interactions induced by the simultaneous presence of an electric and magnetic dipole moment provided by this species is a clear advantage. The electronic structure of RbCa has been computed with two methods, thus allowing to estimate the reliability of the results. A scheme of laser transitions bringing to the formation of cold RbCa molecules from separate atoms has been proposed.Manipulating and trapping molecules relies on the precise knowledge of their response to an external electromagnetic field, characterised by their dynamic dipolar polarisability. The quantum chemistry calculations mentioned earlier allowed us to compute high-lying excited states, dynamic polarisability has then been computed for a whole set of diatomic molecules (alkali dimers, RbCa, RbSr, …). The optimal parameters for trapping those molecules has then been determined.

Simulações de sais de carbonato fundidos pelo método de Dinâmica Molecular (MD) foram efetuadas com o modelo polarizável de cargas flutuantes (FC). O modelo de cargas flutuantes implementa os efeitos de polarização pelo método de Lagrangiano estendido, onde as variáveis extras são as próprias cargas parciais do íon poliatômico. O modelo FC foi parametrizado por meio de cálculos ab inito, aplicado ao ânion carbonato. Cálculos de Química Quântica ab initio foram utilizados para corroborar o modelo proposto para o ânion carbonato. Os sistemas investigados consistem em misturas de carbonatos alcalinos fundidos, Li2CO3/K2CO3, os quais são utilizados como eletrólitos em células a combustível. As simulações MD foram utilizadas para verificar o efeito da polarização dos ânions sobre a estrutura e dinâmica do líquido. Estudamos o efeito da inclusão de polarização sobre a condutividade do eletrólito. / Simulations of molten carbonate salts by the method of Molecular Dynamics (MD) have been performed with the fluctuanting charge (FC) model. The FC model implements the effect of polarization by using method of extended Lagrangian, where the extra variables are the partial charges of the poliatomic ion. The FC model was parametrized by ab inito calculations os a single carbonate anion. Quantum Chemistry calculations bave been used to corroborate the model for the carbonate anion. The investigated systems consist of alkaline carbonate mixtures, Li2CO3/K2CO3, which are used as electrolytes in fuel cells. MD simulations have been used to verify polarization effects on structure and dynamics of the liquid. We study the effect of including anion polarization on the condutivity of the electrolyte.

La present tesi, tot i que emmarcada dins de la teoria de les Mesures Semblança Molecular Quántica (MQSM), es deriva en tres àmbits clarament definits:- La creació de Contorns Moleculars de IsoDensitat Electrònica (MIDCOs, de l'anglès Molecular IsoDensity COntours) a partir de densitats electròniques ajustades.- El desenvolupament d'un mètode de sobreposició molecular, alternatiu a la regla de la màxima semblança.- Relacions Quantitatives Estructura-Activitat (QSAR, de l'anglès Quantitative Structure-Activity Relationships).L'objectiu en el camp dels MIDCOs és l'aplicació de funcions densitat ajustades, ideades inicialment per a abaratir els càlculs de MQSM, per a l'obtenció de MIDCOs. Així, es realitza un estudi gràfic comparatiu entre diferents funcions densitat ajustades a diferents bases amb densitats obtingudes de càlculs duts a terme a nivells ab initio. D'aquesta manera, l'analogia visual entre les funcions ajustades i les ab initio obtinguda en el ventall de representacions de densitat obtingudes, i juntament amb els valors de les mesures de semblança obtinguts prèviament, totalment comparables, fonamenta l'ús d'aquestes funcions ajustades. Més enllà del propòsit inicial, es van realitzar dos estudis complementaris a la simple representació de densitats, i són l'anàlisi de curvatura i l'extensió a macromolècules. La primera observació correspon a comprovar no només la semblança dels MIDCOs, sinó la coherència del seu comportament a nivell de curvatura, podent-se així observar punts d'inflexió en la representació de densitats i veure gràficament aquelles zones on la densitat és còncava o convexa. Aquest primer estudi revela que tant les densitats ajustades com les calculades a nivell ab initio es comporten de manera totalment anàloga. En la segona part d'aquest treball es va poder estendre el mètode a molècules més grans, de fins uns 2500 àtoms.Finalment, s'aplica part de la filosofia del MEDLA. Sabent que la densitat electrònica decau ràpidament al allunyar-se dels nuclis, el càlcul d'aquesta pot ser obviat a distàncies grans d'aquests. D'aquesta manera es va proposar particionar l'espai, i calcular tan sols les funcions ajustades de cada àtom tan sols en una regió petita, envoltant l'àtom en qüestió. Duent a terme aquest procés, es disminueix el temps de càlcul i el procés esdevé lineal amb nombre d'àtoms presents en la molècula tractada.En el tema dedicat a la sobreposició molecular es tracta la creació d'un algorisme, així com la seva implementació en forma de programa, batejat Topo-Geometrical Superposition Algorithm (TGSA), d'un mètode que proporcionés aquells alineaments que coincideixen amb la intuïció química. El resultat és un programa informàtic, codificat en Fortran 90, el qual alinea les molècules per parelles considerant tan sols nombres i distàncies atòmiques. La total absència de paràmetres teòrics permet desenvolupar un mètode de sobreposició molecular general, que proporcioni una sobreposició intuïtiva, i també de forma rellevant, de manera ràpida i amb poca intervenció de l'usuari. L'ús màxim del TGSA s'ha dedicat a calcular semblances per al seu ús posterior en QSAR, les quals majoritàriament no corresponen al valor que s'obtindria d'emprar la regla de la màxima semblança, sobretot si hi ha àtoms pesats en joc.Finalment, en l'últim tema, dedicat a la Semblança Quàntica en el marc del QSAR, es tracten tres aspectes diferents:- Ús de matrius de semblança. Aquí intervé l'anomenada matriu de semblança, calculada a partir de les semblances per parelles d'entre un conjunt de molècules. Aquesta matriu és emprada posteriorment, degudament tractada, com a font de descriptors moleculars per a estudis QSAR. Dins d'aquest àmbit s'han fet diversos estudis de correlació d'interès farmacològic, toxicològic, així com de diverses propietats físiques.- Aplicació de l'energia d'interacció electró-electró, assimilat com a una forma d'autosemblança. Aquesta modesta contribució consisteix breument en prendre el valor d'aquesta magnitud, i per analogia amb la notació de l'autosemblança molecular quàntica, assimilar-la com a cas particular de d'aquesta mesura. Aquesta energia d'interacció s'obté fàcilment a partir de programari mecanoquàntic, i esdevé ideal per a fer un primer estudi preliminar de correlació, on s'utilitza aquesta magnitud com a únic descriptor. - Càlcul d'autosemblances, on la densitat ha estat modificada per a augmentar el paper d'un substituent. Treballs previs amb densitats de fragments, tot i donar molt bons resultats, manquen de cert rigor conceptual en aïllar un fragment, suposadament responsable de l'activitat molecular, de la totalitat de l'estructura molecular, tot i que les densitats associades a aquest fragment ja difereixen degut a pertànyer a esquelets amb diferents substitucions. Un procediment per a omplir aquest buit que deixa la simple separació del fragment, considerant així la totalitat de la molècula (calcular-ne l'autosemblança), però evitant al mateix temps valors d'autosemblança no desitjats provocats per àtoms pesats, és l'ús de densitats de Forats de fermi, els quals es troben definits al voltant del fragment d'interès. Aquest procediment modifica la densitat de manera que es troba majoritàriament concentrada a la regió d'interès, però alhora permet obtenir una funció densitat, la qual es comporta matemàticament igual que la densitat electrònica regular, podent-se així incorporar dins del marc de la semblança molecular. Les autosemblances calculades amb aquesta metodologia han portat a bones correlacions amb àcids aromàtics substituïts, podent així donar una explicació al seu comportament.Des d'un altre punt de vista, també s'han fet contribucions conceptuals. S'ha implementat una nova mesura de semblança, la d'energia cinètica, la qual consisteix en prendre la recentment desenvolupada funció densitat d'energia cinètica, la qual al comportar-se matemàticament igual a les densitats electròniques regulars, s'ha incorporat en el marc de la semblança. A partir d'aquesta mesura s'han obtingut models QSAR satisfactoris per diferents conjunts moleculars. Dins de l'aspecte del tractament de les matrius de semblança s'ha implementat l'anomenada transformació estocàstica com a alternativa a l'ús de l'índex Carbó. Aquesta transformació de la matriu de semblança permet obtenir una nova matriu no simètrica, la qual pot ser posteriorment tractada per a construir models QSAR. / The present work, even embraced by the Molecular Quantum Similarity Measures (MQSM) theory, is divided into three clearly defined frameworks:- Creation of Molecular IsoDensity Contours (MIDCOs) from fitted electronic densities.- Development of an alternative superposition method to replace the maximal similarity rule.- Quantitative Structure-Activity Relationships (QSAR).The objective in field of MIDCOs is the application of fitted density functions, initially developed to reduce the computational costs of calculating MQSM, in order to obtain MIDCOs. So, a graphical comparison is carried out using different fittings to different basis sets, derived from calculations carried out at ab initio level. In this way, the visual analogy between the density representations, along with the values of previously calculated similarity measures, which in turn are fully comparable, reinforces the usage of such fitted densities.Apart from the initial idea, two further studies were done to complement the simple density representations, these are the curvature analysis and the extension to macromolecules. The first step corresponds not only to verify the visual similarity between MIDCOs, but to ensure their coherence in their behaviour at curvature level, allowing to observe inflexion points in the representations and those regions where the density itself presents a convex or concave shape. This first study reveals that both fitted and ab initio densities behave in the same way. In the second study, the method was extended to larger molecules, up to 2500 atoms.Finally, some of the MEDLA philosophy is applied. Knowing that electronic density rapidly decays as it is measured further from nuclei, its calculation at large distances from the nearest nucleus can be avoided. In this way, a partition of the space was proposed, and the fitted density basis set is only calculated for each atom only in its vicinity. Using this procedure, the calculation time is reduced and the whole process becomes linear with the number of atoms of the studied molecule.In the chapter devoted to molecular superposition, the creation of an algorithm, along with its practical implementation, called Topo-Geometrical Superposition Algorithm (TGSA), able to direct those alignments that coincide with chemical intuition. The result is an informatics program, codified in Fortran 90, which aligns the molecules by pairs, considering only atomic numbers and coordinates. The complete absence of theoretical parameters allows developing a general superposition method, which provides an intuitive superposition, and it is also relevant, in a fast way without much user-supplied information. Major usage of TGSA has been devoted to provide an alignment to later compute similarity measures, which in turn do not customarily coincide with those values obtained from the maximal similarity rule, most if heavy atoms are present.Finally, in the last studied subject, devoted to the Quantum Similarity in the QSAR field, three different scopes are treated:1) Usage of similarity matrices. Here, the so-called similarity matrix, calculated from pairwise similarities in a molecular set, is latterly, and properly manipulated, used a source of molecular descriptors for QSAR studies. With in this framework, several correlation studies have been carried out, involving relevant pharmacological properties, as well as toxicity and physical properties.2) Application of the electron-electron repulsion energy. This simple contribution consists briefly of taking the value of this magnitude, and by analogy with the self-similarity notation, it is assimilated as a particular case of this measure. This interaction energy is easily obtainable from mecanoquantic software and becomes ideal in order to make a preliminary correlation study, where this magnitude is used as a single descriptor.3) Calculation of self-similarities, where the density has been modified to account a particular substituent. Previous studies using density fragments, even they provide valuable results, lack of conceptual rigour when isolating a fragment, supposed to be responsible for a particular molecular response, even those densities associated to a particular fragment are already different due to they belong to a common skeleton with different substitutions. A procedure able to fill the gap between usage of density fragments , which avoid the heavy atom effect, and the whole molecular density, which allows to compute a self-similarity, is proposed. It consists of using Fermi Hole density functions, where the holes are defined and averaged around a particular fragment. This procedure medifies the density in a way that is basically collapsed in this molecular bay, but allowing at the same time obtaining a a density function that behaves mathematically in the same way as a regular electronic density; hence it is included in the similarity framework. Those self-similarities computed using this procedure provide good correlations with substituted aromatic acids, allowing to provide an explanation for their acidic behaviour.From another point of view, conceptual contributions have been developed. A new similarity measure, Kinetic Energy-based, has been implemented, which consists of taking the recently developed Kinetic Energy density function, which has been incorporated into the similarity framework due to it mathematically behaves like a regular density function. Satisfactory QSAR models, derived from this new measure, have been obtained for several molecular systems. Within the similarity matrices field, it has been implemented a new scaling, called stochastic transformation, as an alternative to Carbó Index. This transformation of the matrix allows obtaining a new non-symmetric matrix, which can be later used as a source of descriptors to build QSAR model.

Proteins have an indispensable role in the cell. They carry out a wide variety of structural, catalytic and signaling functions in all known biological systems. To perform their biological functions, proteins establish interactions with other bioorganic molecules including other proteins. Therefore, protein-protein interactions is one of the central topics in molecular biology. My thesis is devoted to three different topics in the field of protein-protein interactions. The first one focuses on solvent contribution to protein interfaces as it is an important component of protein complexes. The second topic discloses the structural and functional potential of fluorine's unique properties, which are attractive for protein design and engineering not feasible within the scope of canonical amino acids. The last part of this thesis is a study of the impact of charged amino acid residues within the hydrophobic interface of a coiled-coil system, which is one of the well-established model systems for protein-protein interactions studies. I. The majority of proteins interact in vivo in solution, thus studies of solvent impact on protein-protein interactions could be crucial for understanding many processes in the cell. However, though solvent is known to be very important for protein-protein interactions in terms of structure, dynamics and energetics, its effects are often disregarded in computational studies because a detailed solvent description requires complex and computationally demanding approaches. As a consequence, many protein residues, which establish water-mediated interactions, are neither considered in an interface definition. In the previous work carried out in our group the protein interfaces database (SCOWLP) has been developed. This database takes into account interfacial solvent and based on this classifies all interfacial protein residues of the PDB into three classes based on their interacting properties: dry (direct interaction), dual (direct and water-mediated interactions), and wet spots (residues interacting only through one water molecule). To define an interaction SCOWLP considers a donor–acceptor distance for hydrogen bonds of 3.2 Å, for salt bridges of 4 Å, and for van der Waals contacts the sum of the van der Waals radii of the interacting atoms. In previous studies of the group, statistical analysis of a non-redundant protein structure dataset showed that 40.1% of the interfacial residues participate in water-mediated interactions, and that 14.5% of the total residues in interfaces are wet spots. Moreover, wet spots have been shown to display similar characteristics to residues contacting water molecules in cores or cavities of proteins. The goals of this part of the thesis were: 1. to characterize the impact of solvent in protein-protein interactions 2. to elucidate possible effects of solvent inclusion into the correlated mutations approach for protein contacts prediction To study solvent impact on protein interfaces a molecular dynamics (MD) approach has been used. This part of the work is elaborated in section 2.1 of this thesis. We have characterized properties of water-mediated protein interactions at residue and solvent level. For this purpose, an MD analysis of 17 representative complexes from SH3 and immunoglobulin protein families has been performed. We have shown that the interfacial residues interacting through a single water molecule (wet spots) are energetically and dynamically very similar to other interfacial residues. At the same time, water molecules mediating protein interactions have been found to be significantly less mobile than surface solvent in terms of residence time. Calculated free energies indicate that these water molecules should significantly affect formation and stability of a protein-protein complex. The results obtained in this part of the work also suggest that water molecules in protein interfaces contribute to the conservation of protein interactions by allowing more sequence variability in the interacting partners, which has important implications for the use of the correlated mutations concept in protein interactions studies. This concept is based on the assumption that interacting protein residues co-evolve, so that a mutation in one of the interacting counterparts is compensated by a mutation in the other. The study presented in section 2.2 has been carried out to prove that an explicit introduction of solvent into the correlated mutations concept indeed yields qualitative improvement of existing approaches. For this, we have used the data on interfacial solvent obtained from the SCOWLP database (the whole PDB) to construct a “wet” similarity matrix. This matrix has been used for prediction of protein contacts together with a well-established “dry” matrix. We have analyzed two datasets containing 50 domains and 10 domain pairs, and have compared the results obtained by using several combinations of both “dry” and “wet” matrices. We have found that for predictions for both intra- and interdomain contacts the introduction of a combination of a “dry” and a “wet” similarity matrix improves the predictions in comparison to the “dry” one alone. Our analysis opens up the idea that the consideration of water may have an impact on the improvement of the contact predictions obtained by correlated mutations approaches. There are two principally novel aspects in this study in the context of the used correlated mutations methodology : i) the first introduction of solvent explicitly into the correlated mutations approach; ii) the use of the definition of protein-protein interfaces, which is essentially different from many other works in the field because of taking into account physico-chemical properties of amino acids and not being exclusively based on distance cut-offs. II. The second part of the thesis is focused on properties of fluorinated amino acids in protein environments. In general, non-canonical amino acids with newly designed side-chain functionalities are powerful tools that can be used to improve structural, catalytic, kinetic and thermodynamic properties of peptides and proteins, which otherwise are not feasible within the use of canonical amino acids. In this context fluorinated amino acids have increasingly gained in importance in protein chemistry because of fluorine's unique properties: high electronegativity and a small atomic size. Despite the wide use of fluorine in drug design, properties of fluorine in protein environments have not been yet extensively studied. The aims of this part of the dissertation were: 1. to analyze the basic properties of fluorinated amino acids such as electrostatic and geometric characteristics, hydrogen bonding abilities, hydration properties and conformational preferences (section 3.1) 2. to describe the behavior of fluorinated amino acids in systems emulating protein environments (section 3.2, section 3.3) First, to characterize fluorinated amino acids side chains we have used fluorinated ethane derivatives as their simplified models and applied a quantum mechanics approach. Properties such as charge distribution, dipole moments, volumes and size of the fluoromethylated groups within the model have been characterized. Hydrogen bonding properties of these groups have been compared with the groups typically presented in natural protein environments. We have shown that hydrogen and fluorine atoms within these fluoromethylated groups are weak hydrogen bond donors and acceptors. Nevertheless they should not be disregarded for applications in protein engineering. Then, we have implemented four fluorinated L-amino acids for the AMBER force field and characterized their conformational and hydration properties at the MD level. We have found that hydrophobicity of fluorinated side chains grows with the number of fluorine atoms and could be explained in terms of high electronegativity of fluorine atoms and spacial demand of fluorinated side-chains. These data on hydration agrees with the results obtained in the experimental work performed by our collaborators. We have rationally engineered systems that allow us to study fluorine properties and extract results that could be extrapolated to proteins. For this, we have emulated protein environments by introducing fluorinated amino acids into a parallel coiled-coil and enzyme-ligand chymotrypsin systems. The results on fluorination effect on coiled-coil dimerization and substrate affinities in the chymotrypsin active site obtained by MD, molecular docking and free energy calculations are in strong agreement with experimental data obtained by our collaborators. In particular, we have shown that fluorine content and position of fluorination can considerably change the polarity and steric properties of an amino acid side chain and, thus, can influence the properties that a fluorinated amino acid reveals within a native protein environment. III. Coiled-coils typically consist of two to five right-handed α-helices that wrap around each other to form a left-handed superhelix. The interface of two α-helices is usually represented by hydrophobic residues. However, the analysis of protein databases revealed that in natural occurring proteins up to 20% of these positions are populated by polar and charged residues. The impact of these residues on stability of coiled-coil system is not clear. MD simulations together with free energy calculations have been utilized to estimate favourable interaction partners for uncommon amino acids within the hydrophobic core of coiled-coils (Chapter 4). Based on these data, the best hits among binding partners for one strand of a coiled-coil bearing a charged amino acid in a central hydrophobic core position have been selected. Computational data have been in agreement with the results obtained by our collaborators, who applied phage display technology and CD spectroscopy. This combination of theoretical and experimental approaches allowed to get a deeper insight into the stability of the coiled-coil system. To conclude, this thesis widens existing concepts of protein structural biology in three areas of its current importance. We expand on the role of solvent in protein interfaces, which contributes to the knowledge of physico-chemical properties underlying protein-protein interactions. We develop a deeper insight into the understanding of the fluorine's impact upon its introduction into protein environments, which may assist in exploiting the full potential of fluorine's unique properties for applications in the field of protein engineering and drug design. Finally we investigate the mechanisms underlying coiled-coil system folding. The results presented in the thesis are of definite importance for possible applications (e.g. introduction of solvent explicitly into the scoring function) into protein folding, docking and rational design methods. The dissertation consists of four chapters: ● Chapter 1 contains an introduction to the topic of protein-protein interactions including basic concepts and an overview of the present state of research in the field. ● Chapter 2 focuses on the studies of the role of solvent in protein interfaces. ● Chapter 3 is devoted to the work on fluorinated amino acids in protein environments. ● Chapter 4 describes the study of coiled-coils folding properties. The experimental parts presented in Chapters 3 and 4 of this thesis have been performed by our collaborators at FU Berlin. Sections 2.1, 2.2, 3.1, 3.2 and Chapter 4 have been submitted/published in peer-reviewed international journals. Their organization follows a standard research article structure: Abstract, Introduction, Methodology, Results and discussion, and Conclusions. Section 3.3, though not published yet, is also organized in the same way. The literature references are summed up together at the end of the thesis to avoid redundancy within different chapters.

Στην εργασία αυτή μελετάμε μια σειρά από αντιπροσωπευτικά νανοφασικά συστήματα πυριτίου, στο πλαίσιο κοινών ιδιοτήτων και αρχών που θα βοηθήσουν σε μελλοντικές εφαρμογές σχεδιασμού μοριακών υλικών βασισμένων σε αυτά τα συστήματα. Οι κατηγορίες των συστημάτων με τα οποία ασχολούμαστε είναι (α) υδρογονωμένα και μη-υδρογονωμένα νανοσυσσωματώματα και νανοκρυσταλλικά συστήματα πυριτίου με ή χωρίς ενσωματωμένα μέταλλα μετάπτωσης, που αποτελούν χαρακτηριστικά μοντέλα ενδοεπιφάνειας μετάλλου−ημιαγωγού, (β) υπέρλεπτα υδρογονωμένα νανοσύρματα πυριτίου και (γ) οργανομεταλλικά πολλαπλών στρώσεων (multidecker-sandwiches) πυριτίου−άνθρακα. Εκτός από τη μελέτη των δομικών, ηλεκτρονικών, οπτικών, δονητικών και μαγνητικών ιδιοτήτων των συστημάτων, εστιάζουμε στην αναζήτηση μηχανισμών σταθεροποίησης και την εύρεση και καθορισμό κανόνων που μπορούν να λειτουργήσουν ως «εργαλεία μοριακού σχεδιασμού» με τη γενικότερη δυνατή ισχύ. Τα συσσωματώματα πυριτίου σταθεροποιούνται μέσου των μετάλλων μετάπτωσης σε δομές κλωβού και χαρακτηρίζονται συχνά από υψηλή συμμετρία και μεγάλα ενεργειακά χάσματα, ιδιότητες επιθυμητές για εφαρμογές στην οπτοηλεκτρονική και νανοηλεκτρονική. Στη μελέτη των νανοσυρμάτων πυριτίου συγκρίνουμε την σταθερότητα μεταξύ νανοσυρμάτων με διαφορετικές επιφανειακές δομές ενώ διατυπώνουμε κανόνα «μαγικότητας» νανοσυρμάτων με τον οποίο ερμηνεύουμε την σταθερότητά τους και την συνδέουμε με την ελαστικότητα και την κατανομή υδρογόνου στην επιφάνεια τους. Τέλος, βασιζόμενοι στην ισολοβική αρχή the boron connection, σχεδιάζουμε και μελετάμε μια νέα κατηγορία νανοδομών τύπου multidecker sandwiches οργανοπυριτίου. Στη διάρκεια εκπόνησης αυτής της διατριβής δημοσιεύτηκαν συνολικά 19 εργασίες σε διεθνή περιοδικά και σε πρακτικά συνεδρίων. / In this work we study a series of representative nanoscale systems based on silicon, in the context of common properties and principles which will assist in future applications in designing molecular materials based on these systems. The categories of the systems which we work on are (a) hydrogenated and non-hydrogenated silicon nanoclusters and nanocrystallic systems with or without embedded transition metals, which constitute models of metal−semiconductor interfaces, (b) ultrathin hydrogenated silicon nanowires and (c) organometallic silicon−carbon multidecker-sandwiches. In addition to the study of structural, electronic, optical, vibrational and magnetic properties of these systems, we focus on a search for stabilizing mechanisms and in finding and defining rules that can function as “molecular designing tools” with the broadest possible validity. The silicon nanoclusters are stabilized to cage-like structures by the insertion of transition metals and are characterized by high symmetry and large energy gaps, desirable properties for applications in optoelectronics and nanoelectronics. In the study of silicon nanowires we compare the stability between nanowires with different surface structures while we formulate “magicity” rules for nanowires with which we interpret their stability and associate it with their elasticity and the distribution of the surface hydrogen. Finally, based on the isolobal principle the boron connection, we design and study a new class of organometallic multidecker-sandwich type nanostructures. During the elaboration of this dissertation we published overall 19 papers in international scientific journals and conferences’ proceedings.

Les descriptions des interactions faibles et notamment de la dispersion représentent un problème majeur pour la théorie de la fonctionnelle de la densité. En effet, le caractère fortement local des fonctionnelles rend problématique la description des interactions à longue-portée. Aussi, plusieurs stratégies sont envisagées: des corrections des fonctionnelles existantes ou une introduction de méthodes post-Hartree-Fock par séparation de portée. Des résultats dans les deux cas sont exposés. Tout d'abord, la méthodologie hybride est appliquée à des dimères de métaux de transition (Cr2, Mn2 et Zn2). Ensuite, le calcul de coefficients de corrections pour la dispersion dans un cadre relativiste est présenté. Enfin, les interactions faibles peuvent également résulter de l'interaction d'une molécule avec un champ magnétique. Dans ce cadre, une modélisation de la modification de la densité électronique dans les systèmes aromatiques sous l'influence d'un champ magnétique extérieur est présentée. / In quantum chemistry description of weak interactions, and particularly dispersion forces, are major problems for density functional theory. The strongly local character of functional does not allow to describe properly the long range interactions. Thus, two different strategies have been considered. Correcting the available functional or introduce post-Hartree-Fock methods by mean of range separation.Results in the two cases are discussed. First, the range separated hybrid methodology is applied to transition metal dimers (Cr2, Mn2 and Zn2). Then, correction coefficients for dispersion are calculated within the relativistic framework. Within this relativistic framework, a modelling of the electronic density in aromatic system under the influence of an external magnetic field is also presented.

Simulações de sais de carbonato fundidos pelo método de Dinâmica Molecular (MD) foram efetuadas com o modelo polarizável de cargas flutuantes (FC). O modelo de cargas flutuantes implementa os efeitos de polarização pelo método de Lagrangiano estendido, onde as variáveis extras são as próprias cargas parciais do íon poliatômico. O modelo FC foi parametrizado por meio de cálculos ab inito, aplicado ao ânion carbonato. Cálculos de Química Quântica ab initio foram utilizados para corroborar o modelo proposto para o ânion carbonato. Os sistemas investigados consistem em misturas de carbonatos alcalinos fundidos, Li2CO3/K2CO3, os quais são utilizados como eletrólitos em células a combustível. As simulações MD foram utilizadas para verificar o efeito da polarização dos ânions sobre a estrutura e dinâmica do líquido. Estudamos o efeito da inclusão de polarização sobre a condutividade do eletrólito. / Simulations of molten carbonate salts by the method of Molecular Dynamics (MD) have been performed with the fluctuanting charge (FC) model. The FC model implements the effect of polarization by using method of extended Lagrangian, where the extra variables are the partial charges of the poliatomic ion. The FC model was parametrized by ab inito calculations os a single carbonate anion. Quantum Chemistry calculations bave been used to corroborate the model for the carbonate anion. The investigated systems consist of alkaline carbonate mixtures, Li2CO3/K2CO3, which are used as electrolytes in fuel cells. MD simulations have been used to verify polarization effects on structure and dynamics of the liquid. We study the effect of including anion polarization on the condutivity of the electrolyte.