Conformations of amino acids characterized by theoretical spectroscopy

Abstract: Amino acids are the basic building blocks of proteins. The determinationof their structures plays an important role in correctly describing the functionsof the proteins. This thesis is devoted to theoretical studies on the potentialenergy surface of amino acids, in particular the infrared and soft X-ray spectralfingerprints of their most stable conformers.The stable structures of amino acids can be explored by different methods.We have used a full space systematic search strategy to determine the potentialenergy surface of deprotonated arginine and revealed several new conformers.With that, the calculated thermodynamic parameters are finally in good agreementwith their experimental counterparts. We have also proposed a molecularfragment based step-by-step strategy to search for the most stable conformers oflarge biomolecules. The high efficiency and good accuracy of this strategy havebeen firmly illustrated by the modeling of several polypeptides.Infrared (IR) spectroscopy has become one of the most applied techniques tocharacterize the structures of gas-phase amino acids. A direct comparison betweenexperimental and calculated infrared spectra provides an efficient way to describethe conformation exchanges of the amino acids. It is found that the conformersof an amino acid are not always necessary to reach the thermal equilibrium undercertain experimental conditions. The local minima could be responsible for theappearance of the measured spectra. This important point has been highlightedby the calculations of deprotonated tyrosine and cysteine, as well as the arginine.The near-edge X-ray absorption fine structure (NEXAFS) spectra and X-rayphotoelectron spectra (XPS) have also been simulated for neutral, deprotonatedand protonated arginine. The influences of intra-, and intermolecular hydrogenbonds on the electronic structure of the arginine have been carefully examined. Itis suggested that the XPS is capable of distinguishing the canonical and zwitterinicisomers of arginine, and works much better than any other tools available.