Electronic Structure Calculations of Amino Acids Under the Influence of Electric Fields

By the use of highly intense X-ray pulses, with durations in the scale of tenths of fs, high resolutiondiffraction images of the structures of individual macro-molecules can be obtained. To generatea self-consistent 3D-image of the structures the diffraction images of thousands of copies of thesame molecules have to be compounded. The composition relies on advanced algorithms with longcomputational times and is not always successful or even possible. Simulations of proteins in electricfields have proven that pre-orientation of molecules could yield results otherwise unobtainable.When a molecule enters the electric field it will experience an increasing field strength, i.e. a timedependent electric field, and the change in the field strength will be a function of the moleculestranslational velocity. Proteins are compounded by amino-acids. If amino-acids structures arealtered it could indicate that the structures of proteins would be altered as well. The initial objectof this project was to determine if there exists any critical molecular velocities at which the structuresof amino-acids significantly are altered. If the structures are altered the diffraction imageswill be of other structures than of those intended. The project was based on computer simulations.When approximating the plates of a capacitor as two point charges it was found that the timelapsewould be too long for the simulations intended. Instead it was asked at which field strengthsthe amino-acids would start to lose their essential structures. The amino-acids were simulated inconstant electric fields on a computer at Uppsala University. It was found that the amino-acidscould start to lose their structures in fields intended for pre-orientation of proteins. It was alsofound that the field strengths required for a change in the intramolecular forces depended on thesize of the amino-acid as well as the direction of the field in relation to the amino-acids orientation