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Theoretical Characterization of Functional Molecular Materials
KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
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 [en]
first-principles, soft X-ray spectroscopy, endohedral fullerene, fullerene derivatives, self-assembled monolayers
National Category
Theoretical Chemistry
Research subject
SRA - Molecular Bioscience
Identifiers
URN: urn:nbn:se:kth:diva-94540ISBN: 978-91-7501-367-1 (print)OAI: oai:DiVA.org:kth-94540DiVA: diva2:525965
Public defence
2012-06-08, FD5, AlbaNova University Center, Roslagstullsbacken 21, Stockholm, 10:00 (English)
Opponent
Supervisors
Note

QC 20120523

Available from: 2012-05-23 Created: 2012-05-09 Last updated: 2014-02-04Bibliographically approved
List of papers
1. The equilibrium geometry of A@C60: A test case for conventional density functional theory
Open this publication in new window or tab >>The equilibrium geometry of A@C60: A test case for conventional density functional theory
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2014 (English)In: Chemical Physics Letters, ISSN 0009-2614, E-ISSN 1873-4448, Vol. 591, 312-316 p.Article in journal (Refereed) Published
Abstract [en]

Potential energy surfaces (PESs) along the reaction pathway towards the center of CC bond between two six membered rings for ten different endohedral fullerenes A@C60 (A = H, C, O, S, N, P, He, Ne, Ar, Kr) have been studied by density functional theory (DFT) and Hartree-Fock (HF) method. The results show that no suitable method can consistently describe the interaction between atom A and carbon cage. The dispersion corrected DFT methods fail to describe the equilibrium geometry and PES of the complexes with light atoms. Nevertheless, the inclusion of the dispersion stabilizes the system as reflected by interaction energies (IEs) between atom A and C60.

Keyword
Carbon cages, Endohedral fullerene, Equilibrium geometries, Hartree-Fock methods, Interaction energies, Light atoms, Reaction pathways, Six-membered rings
National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:kth:diva-95373 (URN)10.1016/j.cplett.2013.11.050 (DOI)000329210200063 ()2-s2.0-84890827107 (Scopus ID)
Note

QC 20140204. Updated from submitted to published. Previous title: "The equilibrium geometry of A@C60: a difficult case for conventional dentisy functional theory"

Available from: 2012-05-23 Created: 2012-05-23 Last updated: 2017-12-07Bibliographically approved
2. Theoretical study of core excitation spectroscopy of fullerene-based solarcell acceptors
Open this publication in new window or tab >>Theoretical study of core excitation spectroscopy of fullerene-based solarcell acceptors
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(English)Article in journal (Other academic) Submitted
National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:kth:diva-95380 (URN)
Note
QS 2012Available from: 2012-05-23 Created: 2012-05-23 Last updated: 2012-05-23Bibliographically approved
3. Effects of Protonation, Hydrogen Bonding, and Photodamaging on X-ray Spectroscopy of the Amine Terminal Group in Aminothiolate Monolayers
Open this publication in new window or tab >>Effects of Protonation, Hydrogen Bonding, and Photodamaging on X-ray Spectroscopy of the Amine Terminal Group in Aminothiolate Monolayers
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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.

National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:kth:diva-95381 (URN)10.1021/jp302716w (DOI)000305356200035 ()2-s2.0-84862297554 (Scopus ID)
Note
QP 2012. QC 20120716Available from: 2012-05-23 Created: 2012-05-23 Last updated: 2017-12-07Bibliographically approved
4. Energy landscape inside the cage of neutral and charged N@C60
Open this publication in new window or tab >>Energy landscape inside the cage of neutral and charged N@C60
2011 (English)In: Chemical Physics Letters, ISSN 0009-2614, E-ISSN 1873-4448, Vol. 517, no 4-6, 199-203 p.Article in journal (Refereed) Published
Abstract [en]

Potential energy surfaces along different escaping paths of the nitrogen atom inside the neutral and charged endohedral fullerene N@C60 have been constructed at the density functional theory level. It is found that the dispersion force plays an important role in determining the equilibrium geometry of the neutral system. The most energetic favorable escaping path is towards the center of C = C/C–C bond connecting two neighboring rings for all three systems. The rate determining potential energy surface shows a very small dependence on the charging state. The presented theoretical results should be useful for the practical applications of N@C60 in quantum computing and information.

National Category
Theoretical Chemistry
Research subject
SRA - E-Science (SeRC)
Identifiers
urn:nbn:se:kth:diva-72961 (URN)10.1016/j.cplett.2011.10.045 (DOI)000299018200016 ()2-s2.0-82455199136 (Scopus ID)
Funder
Swedish e‐Science Research Center
Note
QC 20120202Available from: 2012-02-01 Created: 2012-02-01 Last updated: 2017-12-08Bibliographically approved

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