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First Principles Studies of Carbon Based Molecular Materials
KTH, School of Biotechnology (BIO), Theoretical Chemistry.
2008 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

The aim of this thesis was to investigate carbon based molecular materials at first principles levels. Special attention has been paid to simulations of X-ray spectroscopies, including near edge X-ray absorption fine structure (NEXAFS), X-ray photoelectron, and X-ray emission spectroscopy, which can provide detailed information about core, occupied and unoccupied molecular orbitals of the systems under investigation. Theoretical calculations have helped to assign fine spectral structures in high resolution NEXAFS spectra of five azabenzenes (pyridine, pyrazine, pyrimidine, pyridazine and s-triazine), and to identify different local chemical environments among them. With the help of NEXAFS, the characters of important chemical bonds that might be responsible for the unique magnetic properties of the tetracyanoethylene compound has been revealed. Calculations have demonstrated that X-ray spectroscopies are powerful tools for isomer identification and structure determination of fullerenes and endohedral metallofullerenes. A joint experimental and theoretical study on metallofullerene Gd@C82 has firmly determined its equilibrium structure, in which the gadolinium atom lies above the hexagon on the C2 axis. It is found that the gadolinium atom could oscillate around its equilibrium position and that its oscillation amplitude increases with increasing temperature.

In this thesis, several new computational schemes for large-scale systems have been proposed. Parallel implementation of a central insertion scheme (CIS) has been realized, which allows to effectively calculate electronic structures of very large systems, up to 150,000 electrons, at hybrid density functional theory levels. In comparison with traditional computational methods, CIS provides results with the same high accuracy but requires only a fraction of computational time. One of its applications is to calculate electronic structures of nanodiamond clusters varying from 0.76 nm (29 carbons) to 7.3 nm (20,959 carbons) in diameter, which enabled to resolve the long-standing debate about the validity of the quantum confinement model for nanodiamonds. Electronic structures and X-ray spectroscopies of a series of single-walled carbon nanotubes (SWCNTs) with different diameters and lengths have been calculated, which have made it possible to interpret the existing experimental results.

Place, publisher, year, edition, pages
Stockholm: KTH , 2008. , x, 63 p.
Series
Trita-BIO-Report, ISSN 1654-2312 ; 2008:10
Keyword [en]
first principles simulations, carbon based molecular materials, X-ray spectroscopies
National Category
Theoretical Chemistry
Identifiers
URN: urn:nbn:se:kth:diva-4724ISBN: 978-91-7178-963-1 (print)OAI: oai:DiVA.org:kth-4724DiVA: diva2:13642
Public defence
2008-05-23, FB42, AlbaNova, Roslagstullsbaken 21, Stockholm, 10:00
Opponent
Supervisors
Note
QC 20100727Available from: 2008-05-06 Created: 2008-05-06 Last updated: 2010-07-27Bibliographically approved
List of papers
1. An efficient first-principle approach for electronic structures calculations of nanomaterials
Open this publication in new window or tab >>An efficient first-principle approach for electronic structures calculations of nanomaterials
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2008 (English)In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 29, no 3, 434-444 p.Article in journal (Refereed) Published
Abstract [en]

An efficient parallel implementation has been realized for a recently proposed central insertion scheme (Jiang, Liu, Lu, Luo. J Chem Phys 2006,124,214711; J Chem Phys 2006,125, 149902) that allows to calculate electronic structures of nanomaterials at various density functional theory levels. It has adopted the sparse-matrix format for Fock/Kohn-Sham and overlap matrices, as well as a combination of implicitly restarted Arnoldi methods (IRAM) and spectral transformation for computing selected eigenvalues/eigenvectors. A systematic error analysis and control for the proposed method has been provided based on a strict mathematical basis. The efficiency and applicability of the new implementation have been demonstrated by calculations of electronic structures of two different nanomaterials consisting of one hundred thousand electrons.

Keyword
nanomaterials; density functional theory; electronic structures; carbon nanotubes; diamondoids
National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:kth:diva-6984 (URN)10.1002/jcc.20799 (DOI)000252864500011 ()2-s2.0-38349153574 (Scopus ID)
Note
QC 20100726Available from: 2007-04-17 Created: 2007-04-17 Last updated: 2010-07-30Bibliographically approved
2. The C 1s and N 1s near edge x-ray absorption fine structure spectra of five azabenzenes in the gas phase
Open this publication in new window or tab >>The C 1s and N 1s near edge x-ray absorption fine structure spectra of five azabenzenes in the gas phase
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2008 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 128, no 4, 044316-1-044316-12 p.Article in journal (Refereed) Published
Abstract [en]

Near edge x-ray absorption fine structure spectra have been measured and interpreted by means of density functional theory for five different azabenzenes (pyridine, pyridazine, pyrimidine, pyrazine, and s-triazine) in the gas phase. The experimental and theoretical spectra at the N 1s and C 1s edges show a strong resonance assigned to the transition of the 1s electron in the respective N or C atoms to the lowest unoccupied molecular orbital with pi* symmetry. As opposed to the N 1s edge, at the C 1s edge this resonance is split due to the different environments of the core hole atom in the molecule. The shift in atomic core-level energy due to a specific chemical environment is explained with the higher electronegativity of the N atom compared to the C atom. The remaining resonances below the ionization potential (IP) are assigned to transitions to valence/Rydberg orbitals with mixed pi*/sigma* character. Upon N addition, a reduction of intensity is observed in the Rydberg region at both edges as compared to the intensity in the continuum. Above the IP one or more resonances are seen and ascribed here to transitions to sigma* orbitals. Calculating the experimental and theoretical Delta(pi) term values at both edges, we observe that they are almost the same within +/- 1 eV as expected for isoelectronic bonded pairs. The term values of the pi* and sigma* resonances are discussed in terms of the total Z number of the atoms participating in the bond.

Keyword
Density functional theory; Ionization potential; Molecular orbitals; Resonance; Rydberg states; X ray absorption near edge structure spectroscopy; Gas phases; Pyrimidine; Rydberg orbitals
National Category
Natural Sciences
Identifiers
urn:nbn:se:kth:diva-8340 (URN)10.1063/1.2822985 (DOI)000252821200039 ()2-s2.0-38849108213 (Scopus ID)
Note
QC 20100726Available from: 2008-05-06 Created: 2008-05-06 Last updated: 2010-09-16Bibliographically approved
3. Near-edge x-ray absorption studies of Na-doped tetracyanoethylene films: A model system for the V(TCNE)x room-temperature molecular magnet
Open this publication in new window or tab >>Near-edge x-ray absorption studies of Na-doped tetracyanoethylene films: A model system for the V(TCNE)x room-temperature molecular magnet
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2008 (English)In: Physical Review B. Condensed Matter and Materials Physics, ISSN 1098-0121, E-ISSN 1550-235X, Vol. 77, no 5, 054420-1-054420-8 p.Article in journal (Refereed) Published
Abstract [en]

V(TCNE)(x), with TCNE=tetracyanoethylene and x similar to 2, is an organic-based molecular magnet with potential to be used in spintronic devices. With the aim of shedding light on the unoccupied frontier electronic structure of V(TCNE)(x) we have studied pristine TCNE and sodium-intercalated TCNE by near edge x-ray absorption fine structure (NEXAFS) spectroscopy as well as with theoretical calculations. Sodium-intercalated TCNE was used as a model system of the more complex V(TCNE)(x) and both experimental and theoretical results of the model compound have been used to interpret the NEXAFS spectra of V(TCNE)(x). By comparing the experimental and theoretical C K-edge of pristine TCNE, the contributions from the various carbon species (cyano and vinyl) could be disentangled. Upon fully sodium intercalation, TCNE is n doped with one electron per molecule and the features in the C and N K-edge spectra of pristine TCNE undergo strong modification caused by partially filling the TCNE lowest unoccupied molecular orbital (LUMO). When comparing the C and N K-edge NEXAFS spectra of fully sodium-doped TCNE with V(TCNE)(x), the spectra are similar except for broadening of the features which originates from structural disorder of the V(TCNE)(x) films. The combined results from the model system and V(TCNE)(x) suggest that the lowest unoccupied molecular orbital with density on the nitrogen atoms in V(TCNE)(x) has no significant hybridization with vanadium and is similar to the so-called singly occupied molecular orbital of the TCNE anion. This suggests that the LUMO of V(TCNE)(x) is TCNE- or vanadiumlike, in contrast to the frontier occupied electronic structure where the highest occupied molecular orbital is a hybridization between V(3d) and cyano carbons. The completely different nature of the unoccupied and occupied frontier electronic structure of the material will most likely affect both charge injection and transport properties of a spintronic device featuring V(TCNE)(x).

Keyword
ELECTRONIC-STRUCTURE; SPINTRONICS; MILLENNIUM
National Category
Natural Sciences
Identifiers
urn:nbn:se:kth:diva-8341 (URN)10.1103/PhysRevB.77.054420 (DOI)000253764000062 ()2-s2.0-40749158753 (Scopus ID)
Note
QC 20100726Available from: 2008-05-06 Created: 2008-05-06 Last updated: 2010-07-26Bibliographically approved
4. Spectral identification of fullerene C82 isomers
Open this publication in new window or tab >>Spectral identification of fullerene C82 isomers
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2007 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 127, no 16, 164314-1-164314-8 p.Article in journal (Refereed) Published
Abstract [en]

Ultraviolet photoelectron spectra (UPS) of C-82 isomers have been calculated using hybrid density functional theory in combination with the Gelius model [Proceedings of the International Conference on Electron spectroscopy, edited by D. A. Shirley (North-Holland, Amsterdam, 1972), p. 311; J. Electron Spectrosc. Relat. Phenom. 5, 985 (1974)]. The calculated UPS spectra are found to be isomer dependent and in good agreement with the experimental counterparts. Near-edge x-ray absorption fine structure (NEXAFS), x-ray photoelectron spectroscopy (XPS), x-ray emission spectroscopy, and the resonant inelastic x-ray scattering (RIXS) spectra of three important isomers [3(C-2), 6(C-s), and 9(C-2v)] have also been simulated. Strong isomer dependence has also been found for NEXAFS, XPS, and RIXS spectra.

Keyword
Computer simulation; Density functional theory; Isomers; Ultraviolet photoelectron spectroscopy; X ray absorption near edge structure spectroscopy; X ray scattering; Gelius model; Resonant inelastic x-ray scattering (RIXS); X ray emission spectroscopy
National Category
Natural Sciences
Identifiers
urn:nbn:se:kth:diva-8342 (URN)10.1063/1.2800028 (DOI)000250589400035 ()2-s2.0-36049002760 (Scopus ID)
Note
QC 20100726Available from: 2008-05-06 Created: 2008-05-06 Last updated: 2010-07-26Bibliographically approved
5. The structural determination of endohedral metallofullerene Gd@C-82 by XANES
Open this publication in new window or tab >>The structural determination of endohedral metallofullerene Gd@C-82 by XANES
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2008 (English)In: Chemical Communications, ISSN 1359-7345, E-ISSN 1364-548X, no 4, 474-476 p.Article in journal (Refereed) Published
Abstract [en]

Although the Gd ion in Gd@C-82 has been shown to lie above the C-C bond on the C-2 axis as an anomalous structure from the MEM/Rietveld analysis, the present XANES study reveals that it lies above the hexagon on the C-2 axis as a normal structure, and Gd oscillates around its equilibrium position with an amplitude increasing with temperature increase.

Keyword
ABSORPTION FINE-STRUCTURE; POWDER DIFFRACTION; CAGE; CLUSTER; LA; DIMETALLOFULLERENE; SC-2-AT-C-84; EU-AT-C-82; MOTION; C-82
National Category
Chemical Sciences
Identifiers
urn:nbn:se:kth:diva-14216 (URN)10.1039/b714603e (DOI)000252254500015 ()2-s2.0-38049145955 (Scopus ID)
Note
QC 20100726Available from: 2010-07-26 Created: 2010-07-26 Last updated: 2010-07-26Bibliographically approved
6. A density functional theory study of shake-up satellites in photoemission of carbon fullerenes and nanotubes
Open this publication in new window or tab >>A density functional theory study of shake-up satellites in photoemission of carbon fullerenes and nanotubes
2008 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 128, no 23, 234704-1-234704-7 p.Article in journal (Refereed) Published
Abstract [en]

Carbon 1s shake-up spectra of fullerenes C-60, C-70, and C-82 and single-walled carbon nanotubes (SWCNTs) of (5,5), (6,5), and (7,6) have been investigated by using equivalent core hole Kohn-Sham density functional theory approach, in which only one-electron transition between molecular orbitals within core-hole potential is considered. The calculated spectra are generally in good agreement with results of equivalent core-hole time-dependent density functional theory calculations and available experiments, and reliable assignments for the complicated shake-up spectra of such large systems are provided. Calculations have also been performed for endohedral metallofullerene Gd@C-82 to demonstrate the possible use of shake-up processes to identify the charge transfer between the metal ion and the carbon cage. It is found that the exciton binding energy of all systems under investigation is around 0.5 eV.

Keyword
Binding energy; Carbon; Carbon nanotubes; Charge transfer; Chemical bonds; Emission spectroscopy; Fullerenes; Gadolinium; Ion exchange; Metal ions; Metals; Molecular orbitals; Nanopores; Nanostructures; Nanotubes; Probability density function; Quantum chemistry; Single-walled carbon nanotubes (SWCN)
National Category
Natural Sciences
Identifiers
urn:nbn:se:kth:diva-8344 (URN)10.1063/1.2943676 (DOI)000256936700031 ()2-s2.0-47249130886 (Scopus ID)
Note
QC 20100726. Uppdaterad från submitted till published (20100726). Tidigare titel: Shake-up satellites in photoemission of carbon fullerenes and nanotubes: a DFT studyAvailable from: 2008-05-06 Created: 2008-05-06 Last updated: 2010-07-26Bibliographically approved
7. Energy gaps, electronic structures, and x-ray spectroscopies of finite semiconductor single-walled carbon nanotubes
Open this publication in new window or tab >>Energy gaps, electronic structures, and x-ray spectroscopies of finite semiconductor single-walled carbon nanotubes
2008 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 128, no 8, 084707-1-084707-8 p.Article in journal (Refereed) Published
Abstract [en]

We report hybrid density functional theory calculations for electronic structures of hydrogen-terminated finite single-walled carbon nanotubes (6,5) and (8,3) up to 100 nm in length. Gap states that are mainly arisen from the hydrogen-terminated edges have been found in (8,3) tubes, but their contributions to the density of states become invisible when the tube is longer than 10 nm. The electronic structures of (6,5) and (8,3) tubes are found to be converged around 20 nm. The calculated band-gap energies of 100 nm long nanotubes are in good agreement with experimental results. The valence band structures of (6,5), (8,3), as well as (5,5) tubes are also investigated by means of ultraviolet photoelectron spectra (UPS), x-ray emission spectroscopy (XES), and the resonant inelastic x-ray scattering (RIXS) spectra theoretically. The UPS, XES and RIXS spectra become converged already at 10 nm. The length-dependent oscillation behavior is found in the RIXS spectra of (5,5) tubes, indicating that the RIXS spectra may be used to determine the size and length of metallic nanotubes. Furthermore, the chiral dependence observed in the simulated RIXS spectra suggests that RIXS spectra could be a useful technique for the determination of chirality of carbon nanotubes.

Keyword
Electronic structure; Energy gap; Semiconductor materials; Ultraviolet photoelectron spectroscopy; Valence bands; X ray photoelectron spectroscopy; Gap states; Hydrogen-terminated edges; Metallic nanotubes; Valence band structures
National Category
Natural Sciences
Identifiers
urn:nbn:se:kth:diva-14218 (URN)10.1063/1.2839294 (DOI)000254047200046 ()2-s2.0-40149088031 (Scopus ID)
Note
QC 20100726Available from: 2010-07-26 Created: 2010-07-26 Last updated: 2010-07-26Bibliographically approved
8. Chirality and diameter dependent x-ray absorption of single walled carbon nanotubes
Open this publication in new window or tab >>Chirality and diameter dependent x-ray absorption of single walled carbon nanotubes
2009 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 131, no 3, 034704-1-034704-7 p.Article in journal (Refereed) Published
Abstract [en]

The lack of good understanding on the electronic structure of individual carbon nanotubes severely limited the applications of carbon nanotubes. By employing density functional theory in combination with the equivalent core hole approximation, we are able to provide near edge x-ray absorption fine structure (NEXAFS) spectra of all possible single walled carbon nanotubes (SWCNTs) with diameters below 1.45 nm. It is shown that the pi(*) absorption edges in NEXAFS spectra of SWCNTs are converged already at the length of 3 nm, while a good description of the full spectra can only be obtained after 7 nm. A recent high resolution experimental spectrum of a bundle of SWCNTs with diameters 1.37 +/- 0.08 nm has been successfully assigned by the calculations. Noticeable chirality and diameter dependence have been identified for the simulated NEXAFS spectra. The collection of calculated spectra serves as a useful reference for experimental identification of individual carbon nanotubes.

Keyword
carbon nanotubes, chirality, density functional theory, electronic structure, XANES
National Category
Natural Sciences
Identifiers
urn:nbn:se:kth:diva-14221 (URN)10.1063/1.3181809 (DOI)000268206800050 ()2-s2.0-67651156155 (Scopus ID)
Note
QC 20100726. Uppdaterad från submitted till published 20100726.Available from: 2010-07-26 Created: 2010-07-26 Last updated: 2010-07-26Bibliographically approved
9. A magic structural factor in hydrogen-terminated nanodiamond clusters
Open this publication in new window or tab >>A magic structural factor in hydrogen-terminated nanodiamond clusters
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(English)In: Physical Review Letters, ISSN 0031-9007Article in journal (Other academic) Submitted
National Category
Natural Sciences
Identifiers
urn:nbn:se:kth:diva-8347 (URN)
Note
QS 20120327Available from: 2008-05-06 Created: 2008-05-06 Last updated: 2012-03-27Bibliographically approved

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