Structure and spectroscopy of bio- and nano-materials from first-principles simulations

This thesis is devoted to first-principles simulations of bioand nano-materials, focusing on various soft x-ray spectra, ground-state energies and structures of isolated large molecules, bulk materials, and small molecules in ambient solutions. K-edge near-edge x-ray absorption fine structure (NEXAFS) spectra, x-ray emission spectra, and resonant inelastic x-ray scattering spectra of DNA duplexes have been studied by means of theoretical calculations at the density functional theory level. By comparing a sequence of DNA duplexes with increasing length, we have found that the stacking effect of base pairs has very small influence on all kinds of spectra, and suggested that the spectra of a general DNA can be well reproduced by linear combinations of composed base pairs weighted by their ratio. The NEXAFS spectra study has been extended to other realistic systems. We have used cluster models with increasing sizes to represent the infinite crystals of nucleobases and nucleosides, infinite graphene sheet, as well as a short peptide in water solution. And the equivalent core hole approximation has been extensively adopted, which provides an efficient access to these large systems. We have investigated the influence of external perturbations on the nitrogen NEXAFS spectra of guanine, cytosine, and guanosine crystals, and clarified early discrepancies between experimental and calculated spectra. The effects of size, stacking, edge, and defects to the absorption spectra of graphene have been systematically analyzed, and the debate on the interpretation of the new feature has been resolved. We have illustrated the influence of water solvent to a blocked alanine molecule by using the snapshots generated from molecular dynamics. Multi-scale computational study on four short peptides in a self-assembled cage is presented. It is shown that the conformation of a peptide within the cage does not corresponds to its lowest-energy conformation in vacuum, due to the Zn-O bond formed between the peptide and the cage, and the confinement effect of the cage. Special emphasis has been paid on a linear-scaling method, the generalized energy based fragmentation energy (GEBF) approach. We have derived the GEBF energy equation at the Hartree-Fock level with the Born approximation of the electrostatic potential. Numerical calculations for a model system have explained the accuracy of the GEBF equation and provides a starting point for further refinements. We have also presented an automatic and efficient implementation of the GEBF approach which is applicable for general large molecules.