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Room-temperature ionic liquids (ILs) are salts, that are characteristically liquid at room temperatures and own remarkable properties, for example negligible vapour pressure, non-flammability, good thermal stability, and wide electrochemical window. Due to the large number and versatility of cation-anion pair combinations, the potential applicability of ILs is limitless. To improve the industrial efficiency of ILs, where it is used as an electrolyte, catalytic environment or as a thin layer of lubricant, ILs are often combined with various solid supports. Such nanoconfined behaviour of the ionic liquids was extensively studied through numerous experiments; however, a lack of a theoretical, fundamental picture is still noticeable. The reason for that can be originated in the complexity of the investigated model systems, with all conformational fluctuations and spatial reorientation. An ideal and consistent method that gives a correct interpretation of the experimental data and accurately predicts the atomic-level behaviour of nanoconfined ILs is molecular dynamic (MD) simulations. Never the less, employing of MD techniques on nanoconfined systems can be challenging. The first step, during the work on PhD, was to develop a complete and transferable methodology for the simulations of the nanoconfined ILs systems. The geometry of the simulated model system was designed to characterize a prototypical setup employed in the novel, experimentally designed Supported Ionic Liquid Phase catalysis (SILP). While there are currently numerous attempts to characterize thick films of molecular liquids on solid support, using molecular modelling techniques, this study stands out by its technical rigor – the approach used in this thesis is unique in that it is systematically tested against available experiments on liquids in the bulk, solid-liquid, and liquid-vacuum interfaces. In that sense, I believe this project has significantly raised the standards of molecular modelling of ILs and established a prototypical protocol for the determination of the correct parametrization of ILs. Using this model, I was able to relate the conformational molecular features with the structural properties of the liquid throughout the film from the solid to the vacuum interface. Most significantly, these features are further associated with the non-homogenous and anisotropic dynamic properties of the film, which is the first analysis of this type in the literature of ILs. The somewhat surprising emergent result is the identification of multiple time scales governing molecular transport. Consequently, the optimal parametrization was then used to predict novel physical properties on the family of thick imidazolium based IL films ([CnMim][NTf2] (n=2,4,6,8,10)) including the spatial organization of the ions at the solid-liquid and/or liquid-gas interfaces as well as correct mobility of ions between and on those interfaces. The densities together with mobilities in-plane and normal to the interfaces were calculated based on statistical physics techniques to account for the loss of symmetry in the film. Interestingly, strong correlations between the IL’s stratification and diffusive transport were found several nanometres deep into IL films. Also, compared to changes in distribution of anions, which are small, the associated remodelling of density profiles becomes more and more pronounced with the size of cations. Moreover, similar interfacial restructuring is also seen with increasing temperature, as evidenced by the associated drop in surface tension. Furthermore, a line of study focused on thin layers has been comprehensively investigated. What is of importance to interfacial science both from a fundamental as well as an application point of view is to understand the structural ordering of mono- and bi-layers of the IL depending on how they are prepared from a drop in wetting simulations. To understand the relation between the emergent film structure, adsorption and establishment of the film, I performed extensive simulations in which a cylinder of [C2Mim][NTf2] is allowed to spread on a hydroxylated alumina surface, as a function of temperature and cylinder size. In all cases a monolayer is obtained on the surface, however, its structure is found to be very much sensitive to temperature. Interestingly, a transition from an ordered to a disordered structure is found between 300K and 350K, as evidenced by the change in the structure factor of both, cations and anions, which form, in principle intercalated lattices. The stability of the pattern is not only sensitive to temperature, but also to the surface density. Namely, disorder is introduced in the monolayer prior to the nucleation of a bilayer, the latter first appearing as islands on the monolayer at the critical density. This behaviour of IL also points to potentially interesting phase behaviour of fluids, which has been predicted theoretically to change upon confinement. Besides changes in thermodynamic conditions, considerable reorganization can be investigated by creating mixtures with three different combinations of altered cations (PFBMIm+) and anions (PF6-), which provided an important tool to regulate SILP catalysis. Namely, strong anti-correlations between the cation stratification and positioning of a particular catalyst within the film were found in the simulations. Specifically, the calculation of the potential of mean force (PMF) between the catalyst and the film shows that the minima in the potential coincide with the minima in cation density. Hence, the evaluation of PMFs, as well as stratification of density and transport coefficients is crucial for future upscaling.

This article contains data on structural characterization of the [C2Mim][NTf2] in bulk and in nano-confined environment obtained using MD simulations. These data supplement those presented in the paper "Insights from Molecular Dynamics Simulations on Structural Organization and Diffusive Dynamics of an Ionic Liquid at Solid and Vacuum Interfaces" [1], where force fields with three different charge methods and three charge scaling factors were used for the analysis of the IL in the bulk, at the interface with the vacuum and the IL film in the contact with a hydroxylated alumina surface. Here, we present details on the construction of the model systems in an extended detailed methods section. Furthermore, for best parametrization, structural and dynamic properties of IL in different environment are studied with certain features presented herein.

Our model3 enables us to reproduce the experimentally observed X-ray reflectivity, surface tension and diffusion coefficients with reasonable accuracy. Structuring at both solid- liquid and vacuum-liquid interface are also verfiyed with new experimental data, namley the cis conformation of the anion at the solid- liquid intreface. Similarly, the cation tail is pointing towards the vacuum. We have adressed the influence of the model system size and delineated the importance of rigorous sampling.

In the last decades it has become a common practice to use ionic liquid films in the context of catalysis. A particular advantage of these systems is their low vapour pressure and powerful solvation. Understanding the solvent effects both in the context of interface wetting and chemical reactions is vitally important for the technological applications of ILs, however, the understanding of these processes is still not satisfactory. To address this problem, we employ atomistic molecular dynamics (MD) simulations and investigate the behavior of the archetypical imidazolium-based IL [C2Mim][NTf2] at interfaces (i.e. a hydroxylated sapphire surface and vacuum). We establish a refined additive force field model for [C2Mim][NTf2], which reproduces the experimentally observed x-ray reflectivity, surface tension and diffusion coefficients with reasonable accuracy. Based on our validated new force field, we are able to investigate the structuring of the IL and the changes of its transport properties as a function of the distance from the interface of choice.

The Water-Gas shift reaction (WGSR) results in the conversion of carbon monoxide and water into hydrogen and carbon dioxide, usually in the presence of a catalytic material. This is a very important process in the industry [1], and finding and understanding catalytic systems which maximize the efficiency of the reaction is of great value.In this work we focus on a Ruthenium based class of catalysts, which show great performance in the supported ionic liquid phase (SILP) [2]. The problem of unresolved mechanism is tackled alongside the monomer-dimer equilibrium and potential active species. We utilize a wide varietyof techniques from quantum chemistry, ranging from optimizations and vibrational analysis to nudged elastic band searches, to characterize this system. All of the calculations are done within the density functional theory framework using the augmented def2 basis sets which were shown to work well for these kinds of systems [3]. The goal of this study is to describe the reaction mechanism involving the species that show highest activities in SILP systems, in both the qualitative and the quantitative manner. Also the equilibrium between different monomeric and dimeric species and the effect of the solvent are estimated. These findings can later be applied within different theoretical frameworks to modelthe modern SILP reactors on multiple scales.

Room Temperature Ionic Liquids (RTILs) have found a vast range of applicability in research and development.1 For applications in heterogeneous and transport systems, as well as porous environments, knowledge of the wettability of RTILs is required.2 Using extensive molecular dynamics (MD) simulations, we have investigated the surface-wetting properties of a model RTIL [C2Mim][NTf2] by employing cylindrically shaped nanodroplets with 2 different radii3(with the longitudinal axis oriented along the x direction). Analysis of our MD simulations allows, for example, the evaluation of the contact angle between the RTIL and the sapphire surface. Additional important properties that are accessible in this way include spreading velocity, film thickness, precursor film and surface tension, all of which are analyzed and described in appreciable detail.

Calcium carbonate crystals with different morphologies are interesting model for studying the additive-controlled processes which are important for pharmaceutical industry and for understanding the crystallization in biological systems [1]. Calcite is the most stable calcium carbonate polymorph that crystallizes with notable variety of habits under different environmental conditions. The addition of inorganic ions such as Mg2+ and Li+ can exert profound effect on the calcite morphology [2]. In previous experimental studies it has been shown that increasing amounts of lithium enhance the formation of (001) calcite form [3]. Atomistic simulation of predicted calcite morphology shows that the crystals, with incorporated lithium ions are tabular, comprising basal (001) and (104) side faces [4]. Such crystals could be used as a good model for determination of adsorption mechanisms of organic molecules on the (001) calcite surface. The aim of this study was to define the factors that favor the formation of plate-like calcite in a number of model systems. For this purpose the hydrodynamic parameters (a mode of mixing of the reaction components) and the concentration of the lithium ions, in the range from, c = 0.0 to 1.0 mol dm−3, were extensively studied. Precipitated calcite samples were studied by FTIR/ATR spectroscopy, thermogravimetry and PXRD method. The SEM and AFM microscopy were used for identification and surface analysis of (001) face. In addition, the chemical composition of the precipitate has been determined by the ion chromatography. The results indicated that the plate-like calcite is preferably precipitated when the ultrasound was applied, as well as after the addition of lithium ions at concentrations higher than, c = 0.3 mol dm−3. Precipitation of the plate-like calcite is also observed in the systems in which the magnetic and mechanical stirring and higher concentrations of lithium ions in the solution were applied.

We investigated three archetypal ILs consisting of an imidazolium based cation ([C4Mim] together with prototypical anion specie ([NTf2]-).

Understanding the molecular-level behavior of ionic liquids (ILs) at IL−solid interfaces is of fundamental importance with respect to their application in, for example, electrochemical systems and electronic devices. We employed atomistic molecular dynamics (MD) simulations to investigate the behavior of the archetypical imidazolium-based IL, namely [C4Mim][NTf2] and [C6Mim][NTf2] ([C2Mim][NTf2] in the previous work)i, at the neutral sapphire interface. Our strategy enables us to compare experimental and theoretically calculated reflectivities in a direct manner, thereby critically assessing the applicability of two force-field variants.

Each year the number of scientists who are interested in ILs are increasing due their remarkable chemical and physical properties, and many of them are already commercially available. The molecular structure at liquid-solid interface remains unclear despite the fact that is one of the key properties which determine the performance and technological applications involving ILs. We investigate three differenet methods to derivate charges (full value and 90% scaled), and influence of that charges on static and dynamic properties.

Antimicrobial resistance is a problem that occurs when the antibiotic loses the ability to control or inhibit the growth of bacteria. The bacteria continue to multiply in spite of therapeutic drug concentrations. Studies have shown that antimicrobial resistance is increasing, and it is necessary to create a new mode of action against pathogens. The aim of this thesis was to find a minimum inhibitory concentration (MIC) for certain strains of bacteria that were treated with diluted antimicrobial peptides. The selected group of bacteria causes most infections in immunocompromised patients and in hospital settings. Antimicrobial peptides used in the experimental part of this thesis have different backgrounds. MAPL6A is the computer-modified peptide cell-penetrating peptide. DAP is a hybrid peptide made as seqential dimer of weakly active natural amphibian peptide. One amino acid substitution was introduced into sequential dimmer, because the Mutator algorithm (http://split4.pmfst.hr/mutator/) suggested that it will increase its selectivity against Gram- negatives. The hospital laboratory measurements were performed on resistant and sensitive strains. Eight strains have been tested of which five are Gram-negative and three are Gram-positive. MIC values are less than 10 micrometers for almost all strains. Strains with MIC value greater of 10 μM are: E. coli ATCC (12μM) and MRSA (25μM) for DAP and K. pneumoniae for MAPL6A (12μM). As the most important value of MIC, we highlight 3 μM (DAP) for multiresistant A. baumannii and P.areuginosa. A. baumannii is considered to be the most difficult to destroy in hospitals.The results encourage additional work in order to find the best possible peptide (or combinations of peptide antibiotics with other antibiotics) to deal with the one of the most pressing problems in the hospitals, the emergence of pan-resistant bacterial pathogens.

Primijećeno je da pri temperaturi faznog prijelaza čista materija ne doživljava fazni prijelaz već egzistira, neko vrijeme, kao stara faza, iako je stabilno stanje materije u toj točki faznog dijagrama nova faza. Ta stanja nazivamo metastabilna. U ovom, radu razmatraju se kriteriji metastabilnosti sistema. Poseban osvrt je na stanja pregrijane i pothlađene kapljevine, te pothlađeni para.