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Effects of Protonation, Hydrogen Bonding, and Photodamaging on X-ray Spectroscopy of the Amine Terminal Group in Aminothiolate Monolayers
KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
Shandong Normal University, Shandong, Peoples R China.
BAM Fed Inst Mat Res & Testing, Berlin, Germany .
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2012 (English)In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 116, no 23, 12649-12654 p.Article in journal (Refereed) Published
Abstract [en]

The amine head group, NH2, in aminothiolate monolayers can often generate unexpectedly rich structures in its N K-edge X-ray photoelectron spectra (XPS) and near-edge X-ray absorption fine structure (NEXAFS) spectra that are difficult to assign. We have carried out density functional theory (DFT) calculations to study the XPS and NEXAFS of amine head group in four different aminothiolate monolayers, namely aliphatic 11-aminoundecane-1-thiol (AUDT), aromatic 4-aminobenzenethiol (ABT) and araliphatic 4-aminophenylbutane-1-thiol (APBT) and 3-(4”-amino-1,1’:4’,1”-terphenyl-4-yl)propane-1-thiol (ATPT), with the focus on structure changes caused by protonation, hydrogen bonding and X-ray damaging. Spectra of all possible saturated and unsaturated species, as well as X-ray damage products, such as imine, nitrile, azo species and cumulative double bonds, have been thoroughly examined. It is found that extra spectral structures observed in the experimental XPS spectra are not resulted from protonation, but from the formation of a primary ammonium. The X-ray excitation can induce cross linking between two neighboring molecules to form different complexes that contribute to the π features in NEXAFS spectra.

Place, publisher, year, edition, pages
2012. Vol. 116, no 23, 12649-12654 p.
National Category
Theoretical Chemistry
Identifiers
URN: urn:nbn:se:kth:diva-95381DOI: 10.1021/jp302716wISI: 000305356200035Scopus ID: 2-s2.0-84862297554OAI: oai:DiVA.org:kth-95381DiVA: diva2:528000
Note
QP 2012. QC 20120716Available from: 2012-05-23 Created: 2012-05-23 Last updated: 2017-12-07Bibliographically approved
In thesis
1. Theoretical Characterization of Functional Molecular Materials
Open this publication in new window or tab >>Theoretical Characterization of Functional Molecular Materials
2012 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Nowadays, material, energy and information technologies are three pillar industries. The materials that have close relation with our life have also been the foundation for the development of energy and information technologies. As the new member of the material family, functional molecular materials have become increasingly important for many applications, for which the design and characterization by the theoretical modeling have played the vital role. In this thesis, three different categories of functional molecular materials, the endohedral fullerenes, the fullerene derivatives and the self-assembled monolayers (SAMs), have been studied by means of first principles methods.

The non-metal endohedral fullerene N@C60 is a special endohedral fullerene that is believed to be relevant to the construction of future quantum computer. The energy landscape inside the N@C60 has been carefully explored by density functional theory (DFT) calculations. The most energy favorable potential energysurfaces (PESs) for the N atom to move within the cavity have been identified. The effect of the charging on the PESs has also been examined. It is found that the inclusion of dispersion force is essential in determining the equilibriumstructure of N@C60. Furthermore, the performance of several commonly useddensity functionals with or without dispersion correction has been verified for ten different endohedral fullerenes A@C60 with the atom A being either reactive nonmetal or nobel gases elements. It shows that the inclusion of the dispersion forcedoes provide better description for the binding energy (BE), however, none ofthem could correctly describe the energy landscape inside all the ten endohedral fullerenes exclusively. It thus calls for the further improvement of current density functionals for weak interacting systems.

Soft X-ray spectroscopy is a powerful tool for studying the chemical and electronic structures of functional molecular materials. Theoretical calculations have been proven to be extremely useful for providing correct assignments for spectraof large systems. In this thesis, we have performed first principles simulations forthe near-edge X-ray absorption fine structure (NEXAFS) and X-ray photoelectron spectra (XPS) of fullerene derivatives and aminothiolates SAMs. Our calculatedspectra can accurately reproduce experimental results available for all the systemsunder investigations, and identify the species or structures that are responsible for those unexpected spectral features observed in experiments. We have suggested a modified building block (MBB) approach that allows to calculate NEXAFS spectraof a large number of fullerene derivatives with very small computational cost, and resolved the long standing puzzle around the experimental XPS and NEXAFS spectra of SAMs with aminothiolates.

Place, publisher, year, edition, pages
Stockholm: KTH Royal Institute of Technology, 2012. xviii, 49 p.
Series
TRITA-BIO-Report, ISSN 1654-2312 ; 2012:16
Keyword
first-principles, soft X-ray spectroscopy, endohedral fullerene, fullerene derivatives, self-assembled monolayers
National Category
Theoretical Chemistry
Research subject
SRA - Molecular Bioscience
Identifiers
urn:nbn:se:kth:diva-94540 (URN)978-91-7501-367-1 (ISBN)
Public defence
2012-06-08, FD5, AlbaNova University Center, Roslagstullsbacken 21, Stockholm, 10:00 (English)
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Supervisors
Note

QC 20120523

Available from: 2012-05-23 Created: 2012-05-09 Last updated: 2014-02-04Bibliographically approved

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