Characterization and prediction of peptide structures on inorganic surfaces

Interfaces between peptides and metallic surfaces are the subject of great interest for possible use in technological and medicinal applications, mainly since organic systems present an extensive range of functionalities, are abundant, cheap, and exhibit low toxicity. Exemplary applications are biosensors that may be sensitive to specific metabolites or harmful compounds. However, these hybrid interfaces pose a challenge to computational modelling, particularly regarding predicting the most relevant configurations at the surface, which determines the electronic properties of the system as a whole. From a theoretical point of view, predicting the most stable interface configuration requires searching through the enormous structure space of flexible biomolecules with respect to the surface for different configurations and performing computational calculations of their properties. However, it is impossible to investigate those parts separately due to complex interactions during adsorption. In order to capture these complex interactions, one has to employ accurate theoretical methods, which are very computationally expensive. In this thesis, we provide a comprehensive description of the complex nature of the interaction of selected amino acids with metallic surfaces using state-of-the-art dimensionality reduction techniques and accurate ab initio theoretical methods and creation of tools tailored for the high-throughput investigations of interface systems. The theoretical methods used in the thesis are described in the first part of the thesis. The second section looks into the conformational space changes of Arginine (Arg) and its protonated counterpart after adsorption on three noble metallic surfaces. Arg is an excellent testbed because it is tiny enough to be treated using density functional theory, which is considered the best compromise between accuracy and computational efficiency. At the same time, Arg is complex enough due to a highly flexible side-chain that allows for hundreds of different configurations in the gas phase alone. The examination of adsorption behavior requires creating a database by performing a large number of geometry optimizations of various conformations and orientations. The investigation of that database includes creating a low-dimensional representation of the conformational spaces using recent dimensionality reduction techniques, followed by examining various bonding and charge transfer patterns and how they affect the available conformational spaces.The third section of the thesis is concerned with developing tools for the automated structure search of interface systems and the modelling of self-assembly patterns formed after adsorption. Different geometry optimization algorithms and a flexible method of preconditioning the quasi-Newton optimization algorithms are implemented in the GenSec package that was developed. Together, these enable a more straightforward interface with a wide range of quantum chemistry packages for sampling the conformational spaces of flexible molecules in 1D (ions), 2D (surfaces), and 3D (cavities and molecules) systems. Structure search of the conformational space of a flexible molecule using GenSec provided satisfactory results for di-L-alanine adsorbed on Cu(110) surface.