CYP2C9 is one of our major drug metabolising enzymes and belongs to the cytochrome P450 (CYP) super family. The aim of this thesis was to gain an understanding of the quantitative structure–activity relationships (QSAR) of CYP2C9 substrates and inhibitors. This information will be useful in predicting drug metabolism and the potential for drug–drug interactions. To achieve this, a well characterised data set of structurally diverse, competitive CYP2C9 inhibitors was identified in our laboratory. Several computational methodologies, many based on GRID molecular interaction fields, were applied or developed in order to handle issues such as compound alignment and bioactive conformer selection. First, a traditional 3D QSAR was carried out in GOLPE, generating a predictive model. In this model the selection of a bioactive conformer and alignment was based on docking in a homology model of CYP2C9. Secondly, we introduced the concept of alignment independent descriptors from ALMOND. These descriptors were used to generate quantitatively and qualitatively predictive models. We subsequently derived conformation independent descriptors from molecular interaction fields calculated in FlexGRID. This enabled the derivation of 3D QSAR models without taking into account the selection of an alignment or a bioactive conformer. A subsequent programming effort enabled the conversion of this model back to 3D aligned pharmacophores. Similar alignment independent descriptors were also used in the development of the software MetaSite® that predicts the site of metabolism for CYP2C9 ligands. Finally, as crystal information on this isoform emerged, the performance of molecular dynamics simulations and homology models and the flexibility of the protein were evaluated using statistical analyses. These modelling efforts have resulted in detailed knowledge of the structural characteristics in ligand interactions with the cytochrome P450 2C9 isoform.

The aqueous solvation of metal ions is one of the long-standing and complex problems in chemistry, with implications for and applications in a broad range of biochemical and electrochemical systems, where water is the all-pervasive medium. This thesis describes computer simulations of Al3+(aq), Fe2+(aq), Fe3+(aq) and Cu2+(aq). Various aspects of the solvation of these polyvalent metal ions in water are addressed, at different levels of theory, using Car-Parrinello molecular dynamics, classical molecular dynamics and quantum-mechanical cluster calculations. Polyvalent metal ions are particularly interesting because of their large influence on the solvent structure, dynamics and thermodynamics, as well as on the properties of the individual solvent molecules. Polyvalent metal ions in aqueous solution also constitute a challenging subject for computer simulations since a sophisticated interaction model is needed to incorporate the large many-body effects. All the ion-water coordination figures in this thesis are octahedral, except in the Cu2+(aq) solution, where the ion is penta-coordinated with four equatorial neighbours in a plane and one axial neighbour located ~0.45 Å further out from the ion. The equatorial ion-water bonds have covalent character, while the axial water molecule is only electrostatically bound. For all the ions, the OD stretching frequencies of the first-shell water molecules are much more downshifted than in liquid water. In the case of Cu2+(aq), however, only the OD frequencies of the equatorial water molecules are downshifted with respect to bulk water whereas the OD frequencies of the axial water molecule are slightly upshifted. Various limitations of the Car-Parrinello molecular dynamics simulations have been explored and compared, such as finite system-size effects and shortcomings in the electronic structure calculations. The Car-Parrinello simulations are found to give reasonable descriptions of the polyvalent metal ions in aqueous solution.

Bilayers formed by molecules that possess long alkyl hydrophobic tails are ubiquitous in the natural world manifesting both in biological systems as well as in chemistry. The lipid bilayer is an integral feature of cell membranes of living systems with functions that are of critical importance to the life of the cell. Long chain amphiphilic surfactant molecules can be introduced within the interlamellar region of layered inorganic host lattices to form anchored alkyl chainbilayerswithinthegalleries.Theintercalatedbilayerbearsastriking resemblance to lipid bilayers. However, unlike lipid bilayers where individual molecules can undergo lateral diffusion and also flip-flop between layers the anchored bilayer is characterized by the total absence of translational mobility. The degrees of freedom of the alkyl chains of the anchored bilayer are restricted to changes in conformation. This thesis describes a detailed investigation of the anchored bilayer formed by the intercalation of the anionic surfactant dodecyl sulphate (DDS) in a layered solid, Mg-Al Layered Double Hydroxide(Mg-AlLDH) using both experimental measurements and Molecular Dynamics (MD) simulations (Chapter 2). The thesis is organized as two parts. The first (Chapters 2 -4) deals with the anchored bilayer in the condensed phase -the conditions for the formation of the bilayer arrangement of the intercalated surfactant chains and the conformation and dynamics of the alkyl chains of the surfactant in the galleries of the layered solid. The surfactant intercalated Mg-AlLDH-DDS may be delaminated in nonpolar solvents to give colloidal dispersions of individual Mg-Al LDH sheets with the DDS surfactant chains remaining tethered to the inorganic sheets(Scheme 1).The second part of thesis(Chapters 5 -9)describe studies on the dispersions of the Mg-AlLDH-DDS in toluene. A summary of the results of the of the investigations of the anchored bilayer, formed by the intercalation of DDS ions in Mg-Al LDH, in the condensed and the dispersed phases is presented in the concluding chapter(Chapter10). Layered Double Hydroxides(LDH) are insulating lamellar solids of the general chemical formula[M’(1-x) Mx(OH)2], where M’ is a divalent metal ion and M a trivalent ion. Their structure may be derived from that of Brucite, Mg(OH)2, by isomorphous substitution of apart of the Mg2+ by trivalent ions like Al3+ with electrical neutrality maintained by interlamellar exchangeable ions. The studies reported in this thesis are on an Mg-Al LDH,Mg(1−x)Alx(OH)2, x ranging from 0.17 to 0.37. Dodecyl sulphate surfactant ions have been ion-exchange intercalated in Mg-AlLDH (Chapter 3). By varying the Mg-Al ratio, differing packing densities of the surfactant chains in the interlamellar space of the Mg-Al LDH-DDS are realized. At high packing densities the alkyl chains of the intercalated dodecyl sulphate ions anchored on opposing Mg-Al LDH sheets are arranged as bilayers while at lower packing densities the surfactant chains form a monolayer with the chains oriented flat in the galleries. This composition driven monolayer to bilayer transformation in the surfactant intercalated Mg-AlLDH-DDS is also reproduced by MD simulations. The simulations also indicate that there are profound differences in the factors that decide the arrangement of the surfactant chains. In the bilayer arrangement it is dispersive van der Waals interactions between the chains in opposing layers that is responsible for the cohesive energy of the solid whereas at lower packing densities, where a monolayer arrangement is favored, Coulomb interactions between the positively charged Mg-Al LDH sheets and the negatively charged head-group of the DDS anion dominate. The conformation and dynamics of the alkyl chains of the intercalated surfactant chains in both the monolayer and bilayer arrangements as well as the effect of packing density on these parameters is reported in Chapter 4. The conformation was studied using spectroscopic techniques, infra-red, Raman and 13C Nuclear Magnetic Resonance (NMR) while the dynamics by Variable Contact Time Cross Polarization Magic Angle Spinning(VCT -CPMAS) and2DWidelineSeparation(2DWiSe)NMR techniques. The results showed the expected trends; the concentration of gauche defects and the dynamics of the chains increase with decreasing packing density. There is, however a sharp increase in the gauche concentration and conformational mobilities of the intercalated surfactant chains associated with the bilayer to monolayer transformation. The results of the MD simulations, too, reflect these trends. The second part of thesis describes the delamination of the intercalated anchored bilayer (Mg-AlLDH-DDS) in non-polar solvents. Delamination results in a colloidal dispersion Of the anchored bilayer, isolated Mg-AlLDH sheets with the DDS chains tethered to them, as neutral nanosheets of nanometer thickness and micron size. With increasing concentration of the anchored bilayers in the solvent a gel state is realized. The sol to gel transformation of the dispersions of the anchored bilayer in toluene has been investi-gated. Frequency dependent rheology measurements (Chapter6) were used to investigate the visco-elastic properties of the dispersions and Small Angle X-ray Scattering (SAXS) measurements(Chapter 7) to understand the structure and shape of the nanosheets. The rheology experiments showed that the dispersions irrespective of their concentrations showed shear thinning. The SAXS results indicate a tactoid structure of the dispersions as well as in the gel phase. At higher concentrations, the X-ray scattering curves indicated that the layers stack loosely with an interlamellar space of ~ 39 Å , a value much larger than the interlayer lattice spacing of solid Mg-AlLDH-DDS( ~ 27 Å). The nature of interactions between solvent molecules and the anchored DDS chains were probed by 1Hand 2H NMR measurements(Chapter8). A clear association between the toluene molecules and the alkyl chains of the anchored surfactant was observed. 2D NOESY experiments established that there are toluene molecules in close proximity that interact with the methyl tail of the anchored surfactant. NMR measurements were also able to distinguish two types of solvent molecules based on their widely differing mobilities. MD simulations(Chapter9)of the dispersed anchored bilayer are able to reproduce the essential features of the experimental observations including the formation of a loosely bound lamellar structure. It also provides an explanation on how the spectroscopic observation of motional heterogeneity gives rise to the viscoelastic properties of the dispersed anchored bilayer.

The overall objective of this PhD thesis research is to understand and control phase separation in mixed perfluorinated fatty acid-phospholipid surfactant systems that have applications as pulmonary surfactant (PS) mixtures, with an ultimate view of controlling film composition, morphology and mechanical properties. In this context the interaction between perfluorooctadecanoic acid (C18F), 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC), the major component of native PS extract, and 1,2-dipalmitoyl-sn-glycero-3-phosphoglycerol (DPPG) has been explored in Langmuir monolayers and Langmuir–Blodgett (LB) films using a combination of atomic force microscopy (AFM), fluorescence microscopy (FM) and Brewster angle microscopy (BAM) measurements. Thermodynamic and morphological studies of binary and ternary mixed films made of C18F, DPPC and DPPG indicated that both the phospholipids and C18F were miscible over a wide range of compositions. The mixed phospholipid-C18F films contained multimolecular aggregates that were highly enriched in the phospholipids. Furthermore, it was found that the magnitude of the DPPC-C18F interaction could be modulated by altering the concentration of sodium ions in the underlying subphase. Using a highly simplified lung mimic fluid (pH 7.4, 150mM NaCl), DPPC and C18F became fully immiscible. Moreover, the performance characteristics of the mixed films demonstrated the usefulness of C18F as an additive for PS formulations. The effectiveness of a PS protein mimicking peptide was evaluated against DPPC to allow comparison with previous measurements of DPPC-C18F mixed system. The mixing thermodynamics of the peptide and DPPC in Langmuir monolayer implied a repulsive interaction between the film components. The hysteresis response of the mixed monolayer films indicated that the lipid-protein mixture improved the re-spreading of DPPC films. Moreover, molecular-level organization of the mixed films explored by both FM and BAM confirmed the formation of liquid-expanded DPPC domains in the presence of minute amount of the peptide. In order to obtain a thorough understanding of the effect of the deposition process and surfactant tail polarities on the interfacial behavior of perfluorocarbon-hydrocarbon mixed monolayer films, both BAM and AFM measurements of arachidic acid (C20) with perfluorotetradecanoic acid (C14F) and palmitic acid (C16) with C18F mixed monolayer were performed. These measurements revealed that film morphology was minimally perturbed upon its deposition onto solid substrates. Coarse grained molecular dynamics (MD) simulations of films comprised of DPPC molecules with tails of various polarities suggested that the phase separation between the monolayer components could be controlled by varying surfactant tail polarities.

Computational approaches play an important role in today's materials science owing to the remarkable advances in modern supercomputing architecture and algorithms. Ab initio simulations solely based on a quantum description of matter are now very able to tackle materials problems in which the system contains up to a few thousands atoms. This dissertation aims to address the modern electronic structure calculation methods applied to a range of various materials such as liquid and amorphous phase materials, nanostructures, and small organic molecules. Our simulations were performed within the density functional theory framework, emphasizing the use of real-space ab initio pseudopotentials. On the first part of our study, we performed liquid and amorphous phase simulations by employing a molecular dynamics technique accelerated by a Chebyshev-subspace filtering algorithm. We applied this technique to find l- and a- SiO₂ structural properties that were in a good agreement with experiments. On the second part, we studied nanostructured semiconducting oxide materials, i.e., SnO₂ and TiO₂, focusing on the electronic structures and optical properties. Lastly, we developed an efficient simulation method for non-contact atomic force microscopy. This fast and simple method was found to be a very powerful tool for predicting AFM images for many surface and molecular systems. / text

No description available.

Recent experimental studies indicate that polymeric structures with a well-adjusted balance of amphiphilic parts may translocate through self-assembled phospholipid bilayers and enhance the passive trans-membrane transport of smaller molecules. Using a coarse grained lattice Monte Carlo model with explicit solvent we investigate self-assembled lipid bilayers interacting with a linear polymer chain under variation of the hydrophobicity of the chain. Here, we focus on the relationship between the chain's hydrophobicity and its translocation behavior through the membrane as well as induced membrane perturbations. We show, that there is an adsorption transition of the polymer at the bilayer interface, where effectively the solvent phase and the tail phase of the bilayer are equally repulsive for the polymer. Close to this adsorption threshold of the polymer both the translocation probability of the polymer as well as the permeability of the membrane with respect to solvent are enhanced significantly. The frequency of polymer translocation events can be understood quantitatively assuming a simple diffusion along a one-dimensional free energy profile, which is controlled by the effective lipophilicity of the chain and the tail-packing in the bilayer's core. / Dieser Beitrag ist mit Zustimmung des Rechteinhabers aufgrund einer (DFG-geförderten) Allianz- bzw. Nationallizenz frei zugänglich.

This doctoral study consists of three parts. In the first part, structural and electronic properties of Al_kTi_lNi_m (k+l+m=2,3) microclusters have been investigated by performing density functional theory (DFT) calculations within the B3LYP [which comprises the Becke-88 exchange functional and the correlation functional of Lee, Yang, and Parr] and the effective core potential (ECP) level. Dimers and trimers of the elements aluminum, titanium, and nickel, and their binary and ternary combinations have been studied in their ground states. The optimum geometries, possible dissociation channels, vibrational properties, and electronic structure of the clusters under study have been obtained. In the second part, after an empirical potential energy function (PEF) has been parametrized for the AlTiNi ternary system, stable (minimum-energy) structures of Al_kTi_lNi_m (k+l+m=4) microclusters have been determined by molecular dynamics (MD) simulations. The energetics of the microclusters in 1K and 300 K have been discussed. By performing, again, DFT calculations (within the B3LYP and ECP level), the possible dissociation channels and electronic properties of the obtained clusters have been calculated. In the last part, using the empirical PEF parametrized previously for the AlTiNi ternary system, minimum-energy structures of Al_nTi_nNi_n (n= 1-16) ternary alloy nanoparticles have been determined by performing MD simulations. The structural and energetic features of the obtained nanoparticles have been investigated.

Στην παρούσα εργασία μελετήθηκε η ανάπτυξη και η επακόλουθη συμπεριφορά κατά τη θέρμανση υμενίων μεταλλικού νικελίου και χρωμίου σε μονοκρυσταλλικό οξείδιο του νικελίου, NiO(100). Οι αποθέσεις έγιναν κοντά στη θερμοκρασία δωματίου σε περιβάλλον υπερυψηλού κενού 2 x 10-10 mbar χρησιμοποιώντας πηγές θερμικής εξάχνωσης, ενώ η χημική κατάσταση των επιφανειών προσδιορίστηκε με την χρήση φασματοσκοπίας φωτοηλεκτρονίων ακτίνων-Χ (XPS) και στην περίπτωση της απόθεσης Cr επιπλέον με φασματοσκοπία σκέδασης ιόντων (ISS). Οι φασματοσκοπικές μετρήσεις έγιναν με το υπόστρωμα σε θερμοκρασίες από 550 Κ έως 680 Κ, ώστε να αυξηθεί η αγωγιμότητα και να αποφευχθεί η διαφορική φόρτιση της επιφάνειας του κρυστάλλου. Η θέρμανση μέχρι 2 μονοστρώματα (ML) νικελίου αποτεθειμένου σε NiO(100) είχε πρόσφατα βρεθεί ότι οδηγεί σε σταδιακή εξαφάνιση του Ni0, φαινόμενο που αποδόθηκε σε οξείδωσή του με οξυγόνα από το υπόστρωμα. Καθώς η ποσότητα αυτή είναι σημαντικά μεγαλύτερη από τις τυχόν διαθέσιμες ποσότητες επιφανειακού οξυγόνου (π.χ. προσροφημένα υδροξύλια) και δεν υπάρχουν ενδείξεις για την παρουσία μη στοιχειομετρικού οξυγόνου στο εσωτερικό του μονοκρυστάλλου NiO(100), επιδιώχθηκε η διερεύνηση της προέλευσης των οξυγόνων που συμμετείχαν στην οξείδωση. Προς τούτο έγιναν διαδοχικές αποθέσεις Ni0 1,6 ML, 3,8 ML και 7,5 ML, ενώ μετά από κάθε απόθεση και πριν από την επόμενη το δείγμα θερμάνθηκε μέχρι τους 940 Κ, όπου στις δύο πρώτες περιπτώσεις επήλθε πλήρης οξείδωση του Ni0 ενώ στην τρίτη η οξείδωση δεν ολοκληρώθηκε στα χρονικά περιθώρια του πειράματος. Μια κατ’ αρχήν μοντελοποίηση της κινητικής της οξείδωσης υποδεικνύει προέλευση του διαθέσιμου οξυγόνου από πηγή σταθερής συγκέντρωσης στο εσωτερικό του κρυστάλλου. Η μοντελοποίηση των εντάσεων των φωτοκορυφών XPS με βάση σωματιδιακά υμένια νικελίου σταθερού μέσου πάχους που καλύπτουν κλάσμα της επιφάνειας, οδηγεί στο συμπέρασμα ότι η θέρμανση αρχικά οδηγεί σε γρήγορη συσσωμάτωση του νικελίου, ενώ στην συνέχεια τα μεγάλα σωματίδια Ni0 που σχηματίζονται καλύπτονται αρχικά από NiO και στην συνέχεια η οξείδωση προχωρά προς τον μεταλλικό τους πυρήνα. Καθώς από το πείραμα δεν προκύπτει άλλη πληροφορία για την προέλευση των οξυγόνων, διεξάχθηκαν προσομοιώσεις Μοριακής Δυναμικής προκειμένου να διερευνηθεί η δυνατότητα του τέλειου μονοκρυστάλλου να παρέχει πλεγματικά οξυγόνα στην επιφάνεια. Οι προσομοιώσεις έγιναν στο ισόθερμο κανονικό στατιστικό σύνολο χρησιμοποιώντας τη μέθοδο του Nose πάνω σε μονοκρύσταλλο από 1728 ιόντα με εφαρμογή περιοδικών οριακών συνθηκών. Η ολοκλήρωση των εξισώσεων κίνησης έγινε με τον αλγόριθμο του Verlet, με χρονικό βήμα 2x10-15 s και χρησιμοποιήθηκε δυναμικό του τύπου σκληρών ιόντων, ενώ οι συνεισφορές Coulomb υπολογίστηκαν με την μέθοδο του Ewald. Πραγματοποιήθηκαν προσομοιώσεις για αποθέσεις με 8 ιόντα νικελίου (0,06ML), 16 ιόντα νικελίου (0,11ML) και 32 ιόντα νικελίου (0,22ML) σε θερμοκρασία 0,37Tm, με καταγραφή της συνάρτησης τοπικής πυκνότητας κατανομής των ιόντων οξυγόνου ανά 2000 βήματα. Οι προσομοιώσεις δείχνουν ότι ο τέλειος μονοκρύσταλλος μπορεί να σχηματίσει μεγάλο αριθμό οπών ιόντων οξυγόνου της τάξης του 10%, γεγονός που επιτρέπει την ερμηνεία του πειράματος, όπου περίπου 8ML Ni0 οξειδώθηκαν με οξυγόνα από το υπόστρωμα, χωρίς την ανάγκη υπόθεσης της παρουσίας άλλης πηγής μη στοιχειομετρικού οξυγόνου στο εσωτερικό του μονοκρυστάλλου. Για την μελέτη της αλληλεπίδρασης του Cr με το NiO(100), η οποία δεν είχε μελετηθεί συστηματικά μέχρι τώρα σε κλίμακα νανομετρικών υμενίων, έγιναν 4 πειράματα απόθεσης, που κατέληξαν σε 1,10 nm , 0,12 nm, 0,05 nm και 0,30 nm Cr0. Η απόθεση μεταλλικού χρωμίου σε θερμοκρασία δωματίου οδήγησε σε πλήρη κάλυψη της επιφάνειας του NiO(100), ενώ θέρμανση στους 550 Κ προκάλεσε συσσωμάτωση του χρωμίου και οξείδωσή του με παράλληλη αναγωγή του νικελίου του υποστρώματος. Περαιτέρω θερμάνσεις σε υψηλότερες θερμοκρασίες προκάλεσαν την εκ νέου οξείδωση του νικελίου. Η μοντελοποίηση των εντάσεων των φωτοκορυφών XPS με βάση σωματιδιακά υμένια χρωμίου και νικελίου δείχνει ότι το χρώμιο οξειδώνεται από κάτω προς τα πάνω και τελικά καλύπτει το μεταλλικό νικέλιο, χωρίς να αποκλείεται η ενδιάμεση ανάμειξη των δύο μετάλλων. Η μοντελοποίηση της οξείδωσης του ανηγμένου νικελίου σε μεγαλύτερη θερμοκρασία, δείχνει ότι ακολουθείται γενικά η ίδια πορεία , όπως και για απόθεση καθαρού Νi, με το οξείδιο του χρωμίου αρχικά να καλύπτει το σχηματιζόμενο NiO. Κατά την παρατεταμένη θέρμανση της διεπιφάνειας στους 940 Κ, η απόκλιση των πειραματικών σημείων από τις προβλέψεις του μοντέλου υποδεικνύει διεπιφανειακή ανάμειξη των υμενίων NiO και Cr2O3 και πιθανό σχηματισμό σπινελίου NiCr2O4, όπως αναφέρεται και στην βιβλιογραφία. Τα αποτελέσματα της φασματοσκοπίας ISS επιβεβαιώνουν σε ποιοτικό επίπεδο την ερμηνεία που αποδίδουν τα μοντέλα στις μετρήσεις XPS. / Deposition and annealing of Ni and Cr on a NiO(100) single crystal was studied using X-ray photoelectron spectroscopy (XPS) and Molecular Dynamics Simulations (MD) for the case of Ni and using XPS and Ion Scattering Spectroscopy (ISS) for the case of Cr. Depositions were carried out near room temperature in ultra high vacuum with base pressure of 2 x 10-10 mbar using Ni and Cr thermal evaporation sources . Both XP and IS spectra were taken while the sample was kept at an elevated temperature between 550K and 680K in order to avoid differential substrate charging. Annealing of up to 2 monolayers (ML) Ni deposited on NiO(100) has been reported to result in the gradual elimination of metallic Ni, attributed to oxidation via the substrate. Since the necessary quantity of oxygen is far greater than any possibly available surface oxygen (e.g. adsorbed hydroxyl species) and there is no evidence of non stoichiometric oxygen within the NiO(100) single crystal, it was decided to investigate the origin of the oxygen species involved. To that purpose, three successive depositions of Ni0 on NiO(100) were conducted, 1.6 ML 3.8 ML and 7.5 ML. After each deposition and before the next one, the sample was annealed up to 940 K resulting in the complete oxidation of the deposited Nio , with the exception of the final deposition of 7.5 ML whereby the oxidation was not completed within the time frame of the experiment. Simple kinetic modelling of the oxidation is consistent with oxygen originating from a constant concentration source within the substrate. Modelling of the XPS photoelectron intensities based on particulate films covering part of the substrate surface indicates that annealing leads initially to sintering and then to oxidation of the Ni0 particles, whereby they are covered by NiO as oxidation proceeds toward the metallic core. Since the experiment cannot provide any more information with respect to the origin of the oxygen, MD simulations where performed in order to investigate the ability of the perfect crystal to provide lattice oxygen to its surface. The Molecular Dynamics simulations were carried out in the constant temperature canonical ensemble using the Nose scheme, with a slab geometry consisting of 1728 ions and applying periodic boundary conditions. The equations of motion were integrated by means of Verlet’s algorithm and with a time step of 2 x10-15 s, whereas a rigid ion potential was adopted for the atomic interactions and the Coulombic contributions were evaluated with the use of the Ewald summation. Results are presented for depositions of 8 Ni (0.06ML), 16 Ni (0.11ML) and 32 Ni (0.22ML) ad-cations. The evolution of these systems was followed for up to 300000 time steps at a temperature corresponding to 0.37Tm , while the oxygen ions local density distribution function was recorded every 2000 time steps during each simulation run. The simulations show that the perfect crystal can successively form up to 10% of oxygen vacancies in each layer, which can explain the experimental results whereby 8ML of Ni0 where oxidized, without affecting the equivalent concentration of the available oxygen in the substrate and without having to assume any non stoichiometric oxygen inside the NiO(100) single crystal. In order to study the interaction of Cr with NiO(100), which has not been studied systematically so far in the nanometric film thickness range, four quantities of Cr0 , 10 nm, 0,12nm, 0,05 nm and 0,30 nm , were deposited. Deposition at room temperature resulted in complete coverage of the NiO(100) surface, while annealing at 550 K caused sintering and oxidation of Cr as well as reduction of NiO to Ni0 while farther annealing at higher temperatures caused the re-oxidation of the reduced Ni. Modelling of the XPS photoelectron intensities based on particulate films, indicated that Cr0 particles are oxidized from the bottom and finally cover the Ni0 film produced by reduction of the NiO(100) substrate, however the possibility that metallic Cr mixes with metallic Ni forming surface alloy during the process cannot be excluded. The XPS-based modelling of the oxidation process of the reduced Ni at higher temperatures shows that these particles are initially covered by NiO while the oxidation proceeds toward the metallic core, just as in the case of pure deposited Ni. Upon extensive annealing of the interface at 940 K, the deviation of the experimental results from the predictions of the model suggests that mixing of Cr2O3 and NiO occurs at the interface and possibly a NiCr2O4 spinel is formed, as reported in the literature. The ISS results qualitatively support the interpretation of the XPS results provided by the models.

L'eau est partout et joue un rôle déterminant dans une multitude deprocessus. Cependant, on la trouve souvent au sein de minusculescellules, pores, ou canaux. En de tels cas, les proprietés“macroscopiques” de l'eau sont modifiées par les restrictions spatialeset les interactions entre les molécules d'eau et le matériau confinant.Elucider les propriétés de l'eau en confinement est crucial, et unecompréhension générale peut seulement être obtenue à traversl'utilisation de modèles. Alors que l'eau confinée dans des matériauxdurs tels que les nanotubes de carbone est bien documentée, nous n'avonspas trouvé de modèle général pour l'étude de l'eau confinée a desmatériaux mous, et ce en dépit de décénies de recherches sur de nombreuxmodèles spécifiques à une biomolécule ou un polymère en particulier.Dans cette thèse, nous présentons un modèle numérique d'eau confinéedans des géométries molles, générées par auto-assemblage. Nouscomprenons la manière dont les interactions réciproques entre l'eau etla matrice confinante déterminent la structure des assemblages et lespropriétés de transport de l'eau. Nous avons choisi un modèle desurfactant ioniques, matériaux très versatiles qui sont capables des'auto-assembler en diverses géométries confinantes.Nous nous concentrons sur l'effet des interfaces sur la formation de lananostructure et sur les propriétés de transport à l'échelle de lananoseconde. Nous nous distancons de l'approche traditionnelle auproblème du transport de l'eau dans des nanomatériaux. Nous montrons quel'hypothèse habituelle du transport diffusif est invalide car la matriceconfinante piège les molécules d'eau à l'interface. Nous proposons deremplacer cette hypothèse par celle du transport sous-diffusif, et nousmettons en évidence le rôle de l'échelle de taille et des propriétéstopologiques du confinement. Nous montrons que cette approche expliquedes résultats expérimentaux pour léau confinée dans des matériaux desynthèse, et qu'elle est compatible avec les développements récents liésà l'eau biologique. / Water is omnipresent and plays a decisive role in a myriad of processes.However, it is often found hidden in tiny cells, pores, or channels. Insuch cases, the usual “bulk” features of water are modified by thelimited available space and the interactions of individual moleculeswith the confining material. Elucidating the properties of water in suchconfined states is critical and general understanding can only beachieved through models. While water confined in model hard materialssuch as carbon nanotubes is well documented, we found that there existno general model to study water confined in soft materials, althoughthis has been an active research topic for decades and despite thenumerous models specific to one biomolecule or polymer that have beendeveloped. In this thesis, we present a numerical model of waterconfined in soft self-assembled environments, and we provide anunderstanding of how the interplay between water and the confiningmatrix affects the structure of the assemblies and transport propertiesof water. Our model confining matrix is composed of ionic surfactants.This versatile model is able to self-assemble to a wide variety ofconfining geometries.We focus on the role of interfaces in shaping the nanometer scalestructure, and nanosecond scale transport properties. This work is adeparture from the traditional approach to the problem of transport ofwater confined in soft nanomaterials. We show that the usual hypothesisof diffusive water transport does not hold due to trapping of moleculesat the interface with the confining matrix. Instead, we support apicture where transport is sub-diffusive, and we highlight the role ofthe length-scale of the confinement and of its topological features. Wefind that this rationale explains experimental results for waterconfined in synthetic materials, and that it is compatible with recentadvances in the understanding of biological water.