<div>Computational Chemistry has proven to be an effective means of solving chemical problems. The two main tools of Computational Chemistry - quantum mechanics and molecular mechanics, have provided viable avenues to probe such chemical problems at an electronic or molecular level, with varying levels of accuracy and speed. In this work, attempts have been made to combine the speed of molecular mechanics and the accuracy of quantum mechanics to work across multiples scales of time and length, effectively resulting in simulations of large chemical systems without compromising the accuracy.</div><div><br></div><div>The primary tool utilized for methods development and application in this work is the Effective Fragment Potential (EFP) method. The EFP method is a computational technique for studying non-covalent interactions in complex systems. EFP is an accurate \textit{ab initio} force field, with accuracy comparable to many Density Functional Theory (DFT) methods, at significantly lower computational cost. EFP decomposes intermolecular interactions into contributions from four terms: electrostatics, polarization, exchange-repulsion and dispersion.</div><div><br></div><div>In the first chapter, the possibility of applying EFP method to study large radical-water clusters is probed. An approximate theoretical model in which the transition dipole moments of excitations are computed using the information from the ground state orbitals is implemented.</div><div><br></div><div>A major challenge to broaden the scope of EFP is to overcome its limitation in describing only small and rigid molecules such as water, acetone, etc. In the second chapter, the extension of EFP method to large covalently bound biomolecules and polymers such as proteins, lipids etc., is described. Using this new method, referred to as BioEFP/mEFP, it is shown that the effect of polarization is non-negligible and must be accounted for when modeling photochemical and electron-transfer processes in photoactive proteins.</div><div><br></div><div>Another area of interest is the development of novel drug-target binding models, in which a chemically active part of the ligand is modified via functional group modification, while the rest of the system remains intact. In the third chapter, the development and application of a drug-target binding model is explained.<br></div><div><br></div><div><div>Lastly, in the fourth and final chapter, we show the derivation for working equations corresponding to the coupling gradient term describing the dispersion interactions between quantum mechanical and effective fragment potential regions.</div><div><br></div><div>The primary focus of this work is to explore and expand the boundaries of multiscale QM/MM simulations applied to chemical and biomolecular systems. We believe that the work described here leads to exciting pathways in the future in terms of modeling novel systems and processes such as heterogeneous catalysis, QSAR, crystal structure prediction, etc.</div></div>

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Corrosion of metallic materials is a natural process, and our study shows that even in an alkaline environment severe corrosion may occur on a carbon steel surface. While corrosion cannot be stopped it can be retarded. Many of the traditional anti-corrosion approaches such as the chromate process are effective but hazardous to the environment and human health. Mefp-1, a protein derived from blue mussel byssus, is well known for its extraordinary adhesion and film forming properties. Moreover, it has been reported that Mefp-1 confers a certain corrosion protection for stainless steel. All these facts indicate that this protein may be developed into corrosion inhibitors with ‘green’, ‘effective’ and ‘smart’ properties. In this study, a range of surface-sensitive techniques have been used to investigate adsorption kinetics, film forming and film compaction mechanisms of Mefp-1. In situ atomic force microscopy (AFM) enables the protein adsorption on substrates to be visualized, whereas the ex situ AFM facilitates the characterization of micro- and nano-structures of the protein films. In situ Peak Force AFM can be used to determine nano-mechanical properties of the surface layers. The quartz crystal microbalance with dissipation monitoring (QCM-D) was used to reveal the build-up of the Mefp-1 film on substrates and measure the viscoelastic properties of the adsorbed film. Analytical techniques and theoretical calculations were applied to gain insights into the formation and compaction processes such as oxidation and complexation of pre-formed Mefp-1 films. The electron probe micro analyzer (EPMA) and X-ray photoelectron spectroscopy (XPS) were utilized to obtain the chemical composition of the surface layer. Electrochemical impedance spectroscopy (EIS) measurements were performed to evaluate the corrosion inhibition efficiency of different forms of Mefp-1 on carbon steel substrates. The results demonstrate that Mefp-1 adsorbs on carbon steel surfaces across a broad pH interval, and it forms a continuous film covering the substrate providing a certain extent of corrosion protection. At a higher pH, the adsorption is faster and the formed film is more compact. At neutral pH, results on the iron substrate suggest an initially fast adsorption, with the molecules oriented preferentially parallel to the surface, followed by a structural change within the film leading to molecules extending towards solution. Both oxidation and complexation of the Mefp-1 can lead to the compaction of the protein films. Addition of Fe3+ induces a transition from an extended and soft protein layer to a denser and stiffer one by enhancing the formation of tri-Fe3+/catechol complexes in the surface film, leading to water removal and film compaction. Exposure to a NaIO4 solution results in the cross-linking of Mefp-1, which also results in a significant compaction of the pre-formed protein film. Mefp-1 is an effective corrosion inhibitor for carbon steel when added to an acidic solution, and the inhibition efficiency increases with time. As a film-forming corrosion inhibitor, the pre-formed Mefp-1 film provides a certain level of corrosion protection for short term applications, and the protection efficiency can be significantly enhanced by the film compaction processes. For the long term applications, a thin film composed of Mefp-1 and ceria nanoparticles was developed. The deposited Mefp-1/ceria composite film contains micro-sized aggregates of Mefp-1/Fe3+ complexes and CeO2 particles. The Mefp-1/ceria film may promote the further oxidation of ferrous oxides, and the corrosion resistance increases with time. Moreover, phosphate ions react with Fe ions released from the surface and form deposits preferentially at the surface defect sites. The deposits incorporate into the Mefp-1/ceria composite film and heal the surface defects, which result in a significantly improved corrosion inhibition effect for the Mefp-1/ceria composite film in both initial and prolonged exposure situations / <p>QC 20130610</p>

This thesis describes technical and scientific aspects of new types of composite films/coatings for corrosion protection of carbon steel, composite films with nanometer thickness consisting of mussel adhesive protein (Mefp‐1) and ceria nanoparticles, and polymeric composite coatings with micrometre thickness consisting of conducting polymer and ceria nanoparticles in a UV‐curing polyester acrylate (PEA) resin. The influence of microstructure on corrosion behaviour was studied for a Fe‐Cr‐V‐N alloy containing micro‐sized nitrides with different chemical composition spread in martensitic alloy matrix. The Volta potential mapping suggested higher relative nobility for the nitride particles than the alloy matrix, and the nitrides with higher amounts of nitrogen and vanadium exhibited higher nobility. Potentiodynamic polarization measurements in a 0.1 M NaCl solution at neutral pH and ambient temperature showed passivity breakdown with initiation of localized corrosion which started in the boundary region surrounding the nitride particles, especially the ones enriched in Cr and Mo. Mefp‐1/ceria nanocomposite films were formed on silica and metal substrates by layer‐by‐layer immersion deposition. The film formation process was studied in situ using a Quartz Crystal Microbalance with Dissipation (QCM‐D). The film grows linearly with increasing number of immersions. Increasing Mefp‐1 concentration or using Mefp‐1 with larger size leads to more Mefp‐1 being deposited. Peak Force Quantitative Nanomechanical Mapping (Peak Force QNM) of the composite films in air indicated that the elastic modulus of the film increased when the film deposited had a higher Mefp‐1 concentration. It was also noted that the nature of the outermost layer can affect bulk morphology and surface mechanical properties of the film. The QCM‐D study of Mefp‐1 on an iron substrate showed that Mefp‐1 adsorbs at a high rate and changes its conformation with increasing adsorption time. The QCM‐D and in situ Peak Force QNM measurements showed that the addition of Fe3+ ions causes a transition in the single Mefp‐1 layer from an extended and soft layer to a denser and stiffer layer. In situ ATR‐FTIR and Confocal Raman Microscopy (CRM) analyses revealed complex formation between Fe3+ and catechol groups in Mefp‐1. Moreover, optical microscopy, SEM and AFM characterization of the Mefp‐1/ceria composite film formed on carbon steel showed micron‐size aggregates rich in Mefp‐1 and ceria, and a nanostructure of well dispersed ceria particles in the film. The CRM analysis confirmed the presence of Mefp‐1/Fe complexes in the film. Electrochemical impedance microscopy and potentiodynamic polarization measurements showed that the Mefp‐1/ceria composite film can provide corrosion protection for carbon steel, and that the protection efficiency increases with exposure time. Composite coatings of 10 μm thickness composed of a UV‐curing PEA resin and a small amount of conductive polymer and ceria nanoparticles were coated on carbon steel. The conductive polymer (PAni) was synthesized with phosphoric acid (PA) as the dopant by chemical oxidative polymerization. The ATR‐FTIR and SEM analyses confirmed that the added particles were well dispersed in the coatings. Electrochemical measurements during long exposure in 0.1 M NaCl solution, including open circuit potential (OCP) and EIS, were performed to investigate the protective performance of the coatings. The results showed that adding ceria nanoparticles can improve the barrier properties of the coating, and adding PAni‐PA can lead to active protection of the coating. Adding PAni‐PA and ceria nanoparticles simultaneously in the coating can improve the protection and stability of the composite coating, providing excellent corrosion protection for carbon steel. / <p>QC 20131024</p>