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NEXAFS spectroscopies of blocked alanine in water solution from first-principles simulations
KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).ORCID iD: 0000-0002-6706-651X
KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).ORCID iD: 0000-0002-1763-9383
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(English)Manuscript (preprint) (Other academic)
National Category
Theoretical Chemistry
URN: urn:nbn:se:kth:diva-32061OAI: diva2:408371
QS 2011Available from: 2011-04-04 Created: 2011-04-04 Last updated: 2011-11-22Bibliographically approved
In thesis
1. Structure and spectroscopy of bio- and nano-materials from first-principles simulations
Open this publication in new window or tab >>Structure and spectroscopy of bio- and nano-materials from first-principles simulations
2011 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

This thesis is devoted to first-principles simulations of bio- and nano-materials,focusing on various soft x-ray spectra, ground-state energies and structures of isolated largemolecules, bulk materials, and small molecules in ambient solutions.

K-edge near-edge x-ray absorption fine structure (NEXAFS) spectra, x-ray emission spectra, andresonant inelastic x-ray scattering spectra of DNA duplexes have been studied by means oftheoretical calculations at the density functional theory level. By comparing a sequence of DNAduplexes with increasing length, we have found that the stacking effect of base pairs has verysmall influence on all kinds of spectra, and suggested that the spectra of a general DNA can bewell 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 modelswith increasing sizes to represent the infinite crystals of nucleobases and nucleosides, infinitegraphene sheet, as well as a short peptide in water solution. And the equivalent core holeapproximation has been extensively adopted, which provides an efficient access to these largesystems. We have investigated the influence of external perturbations on the nitrogen NEXAFSspectra of guanine, cytosine, and guanosine crystals, and clarified early discrepancies betweenexperimental and calculated spectra. The effects of size, stacking, edge, and defects to theabsorption spectra of graphene have been systematically analyzed, and the debate on theinterpretation of the new feature has been resolved. We have illustrated the influence of watersolvent 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 isshown that the conformation of a peptide within the cage does not corresponds to its lowest-energyconformation in vacuum, due to the Zn-O bond formed between the peptide and the cage, and theconfinement effect of the cage.

Special emphasis has been paid on a linear-scaling method, the generalized energy basedfragmentation energy (GEBF) approach. We have derived the GEBF energy equation at the Hartree-Focklevel with the Born approximation of the electrostatic potential. Numerical calculations for amodel system have explained the accuracy of the GEBF equation and provides a starting point forfurther refinements. We have also presented an automatic and efficient implementation of the GEBFapproach which is applicable for general large molecules.

Place, publisher, year, edition, pages
Stockholm: KTH Royal Institute of Technology, 2011. xvi, 74 p.
Trita-BIO-Report, ISSN 1654-2312 ; 2011:05
soft x-ray spectroscopy, bio- and nano-materials, first-principles simulation, host-guest interaction, generalized energy-based fragmentation
National Category
Theoretical Chemistry Physical Chemistry
Research subject
SRA - Molecular Bioscience
urn:nbn:se:kth:diva-31944 (URN)978-91-7415-928-8 (ISBN)
Public defence
2011-04-28, FA31, AlbaNova University Center, Roslagstullsbacken 21, Stockholm, 14:00 (English)
QC 20110404Available from: 2011-04-04 Created: 2011-03-30 Last updated: 2011-04-13Bibliographically approved

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Hua, WeijieAi, Yue-JieÅgren, Hans
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