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First Principles Studies on Chemical and Electronic Structures of Adsorbates
KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512). (Department of Theoretical Chemistry)
2009 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

In this thesis, we focus on theoretical study of adsorbates on metal and oxide surfaces that are important for surface chemistry and catalysis. Based on first principles calculations, the adsorption ofCO, NO, NO2, C4H6S2, C22H27SH and other molecules or radicals on nobel metal surfaces (gold and silver) are investigated. Also, NO oxidation on oxygen pre-covered Au(111)surface and CO oxidation on water-oxygen covered Au(111)surface aretheoretically studied. A new mechanism of water-enhanced COoxidation is proposed. As for oxide surfaces, we first investigatethe geometric, electronic and magnetic structures of FeO ultrathin film on Pt(111) surface. The experimentally observed scanning tunneling microscopy images are well reproduced for the first timewith our model. The adsorption and dissociation of water on rutileTiO2(110) surface are investigated by quantum molecular dynamics.By theoretical X-ray photoemission spectroscopy (XPS) calculations,the surface species are properly assigned. The same strategy has applied to the study of the phase transition of water covered reconstructed anatase TiO2(001) surface, from which two different phases are theoretically identified. The structure of graphene oxideis also studied by comparing experimental and theoretical XPS spectra. Based on the novel structures identified, a new cutmechanism of graphene oxide is proposed.

Place, publisher, year, edition, pages
Stockholm: KTH , 2009. , xii, 57 p.
Series
Trita-BIO-Report, ISSN 1654-2312 ; 2009:8
National Category
Inorganic Chemistry Other Physics Topics Condensed Matter Physics
Identifiers
URN: urn:nbn:se:kth:diva-10215ISBN: 978-91-7415-278-4 (print)OAI: oai:DiVA.org:kth-10215DiVA: diva2:211397
Public defence
2009-05-06, FA 32 AlbaNova, Roslagsvägen, Stockholm, 10:00 (English)
Opponent
Supervisors
Note
QC 20100819Available from: 2009-05-06 Created: 2009-04-14 Last updated: 2011-11-23Bibliographically approved
List of papers
1. A first-principles study of NO adsorption and oxidation on Au(111) surface
Open this publication in new window or tab >>A first-principles study of NO adsorption and oxidation on Au(111) surface
2008 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 129, no 13, 134708- p.Article in journal (Refereed) Published
Abstract [en]

Density functional theory and slab models are employed to study NO molecule adsorption and reaction on clean and atomic oxygen precovered Au(111) surfaces. While clean Au(111) surface is catalytically inert and can only weakly adsorb NO, an atomic oxygen precovered Au(111) surface is found to be very active to NO. On the clean surface, NO prefers to bond at the onefold on-top surface site with a tilted geometry. On 0.33 ML (monolayer) oxygen precovered surface NO reacts with chemisorbed oxygen to form chemisorbed NO2 by conquering a small energy barrier about 0.18 eV, and the desorption energy of NO 2 is 0.64 eV. On 1.0 ML oxygen coverage surface, no barrier is found while NO reacts with precovered oxygen. The desorption energy of NO2 is 0.03 eV. The desorption of NO2 is the rate determining step on both surfaces and the overall reaction barriers are 0.64 and 0.03 eV, respectively. The activation energies depend on the initial coverage of oxygen, which compare favorably with experiments on Au surface with different oxygen coverages.

Keyword
DENSITY-FUNCTIONAL THEORY; INITIO MOLECULAR-DYNAMICS; CO OXIDATION; CARBON-MONOXIDE; ADSORBED OXYGEN; ATOMIC OXYGEN; NITRIC-OXIDE; GOLD; PT(111); CATALYSIS
National Category
Chemical Sciences
Identifiers
urn:nbn:se:kth:diva-10320 (URN)10.1063/1.2985668 (DOI)000259876700047 ()2-s2.0-53449087247 (Scopus ID)
Note

QC 20100818

Available from: 2009-05-06 Created: 2009-05-06 Last updated: 2017-12-13Bibliographically approved
2. Density Functional Study on the Mechanism of CO Oxidation with Activated Water on O/Au(111) Surface
Open this publication in new window or tab >>Density Functional Study on the Mechanism of CO Oxidation with Activated Water on O/Au(111) Surface
2009 (English)In: Chinese Science Bulletin, ISSN 1001-6538, E-ISSN 1861-9541, Vol. 54, no 11, 1973-1977 p.Article in journal (Refereed) Published
Abstract [en]

With density functional theory, the mechanism of water-enhanced CO oxidation on oxygen pre-covered Au (111) surface is theoretically studied. First, water is activated by the pre-covered oxygen atom and dissociates to OHads group. Then, OHads reacts with COads to form chemisorbed HOCOads. Finally, with the aid of water, HOCO ads dissociates to CO2. The whole process can be described as 1/2H2O ads + H2Oads + 1/2O ads + COads → H3Oads + CO 2, gas. One CO2 is formed with only 1/2 pre-covered oxygen atom. That is why more CO2 is observed when water is present on oxygen pre-covered Au (111) surface. Activation energy of each elementary step is low enough to allow the reaction to proceed at low temperature

Keyword
Au(111) surface; CO oxidation; Density functional theory; Reaction mechanism; Water activated
National Category
Chemical Sciences
Identifiers
urn:nbn:se:kth:diva-10321 (URN)10.1007/s11434-009-0057-y (DOI)000266582000025 ()2-s2.0-67049086580 (Scopus ID)
Note

QC 20100819

Available from: 2009-05-06 Created: 2009-05-06 Last updated: 2017-12-13Bibliographically approved
3. Electronic structure of [121]tetramantane-6-thiol on gold and silver surfaces
Open this publication in new window or tab >>Electronic structure of [121]tetramantane-6-thiol on gold and silver surfaces
Show others...
2009 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 130, no 054705Article in journal (Refereed) Published
Abstract [en]

The mechanism for electron photoemission of [121]tetramantane and its functionalized compound [121]tetramantane-6-thiol adsorbed on different noble metal surfaces has been investigated by density functional theory calculations. It is found that good chemical bonding between molecules and metal surfaces is a helpful but not a necessary condition for electron photoemission. A lower work function and weaker hybridization between the molecule and the metal could lead to much more efficient electron photoemission. It is observed that, neglecting final state effect, a simple ground state picture cannot result in negative electron affinity for the systems under investigation. Calculations have shown that by exciting an electron in the lowest unoccupied molecular orbital, the highest singly occupied molecular orbital of the molecule can be shifted above the vacuum level, resulting in negative electron affinity and emission of the accumulated electrons.

Keyword
adsorption; bonds (chemical); density functional theory; gold; ground states; orbital calculations; organic compounds; photoemission; silver
National Category
Chemical Sciences
Identifiers
urn:nbn:se:kth:diva-10322 (URN)10.1063/1.3072334 (DOI)000263167100039 ()2-s2.0-59949095835 (Scopus ID)
Note

QC 20100819

Available from: 2009-05-06 Created: 2009-05-06 Last updated: 2017-12-13Bibliographically approved
4. First-Principles Study on Different BDT-gold Contact Structures
Open this publication in new window or tab >>First-Principles Study on Different BDT-gold Contact Structures
(English)Manuscript (Other academic)
Abstract [en]

Density functional theory calculations have been carried out for a benzene-1,4-dithiol (BDT)molecule adsorbed on a perfect Au (111) surface, a gold nanowire of 1 nm in diameter and alsosurface supported gold cluster (point). It is indicated that a BDT molecule prefers to adsorbon irregular surface sites. The Simulated S K-edge x-ray absorption spectra (XAS) and ultra-violet photoemission spectra (UPS) are presented. The predicted XAS spectra show that x-rayspectroscopy could be a powerful method to study the structure of molecule-metal contact.

National Category
Chemical Sciences
Identifiers
urn:nbn:se:kth:diva-10323 (URN)
Note
QC 20100819Available from: 2009-05-06 Created: 2009-05-06 Last updated: 2010-08-19Bibliographically approved
5. First Principles Study on the Geometric and Electronic Structures of the FeO/Pt(111) Surface
Open this publication in new window or tab >>First Principles Study on the Geometric and Electronic Structures of the FeO/Pt(111) Surface
2009 (English)In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 113, no 19, 8302-8305 p.Article in journal (Refereed) Published
Abstract [en]

The geometric, electronic, and magnetic properties of the FeO monolayer on a Pt(111) surface are investigated by first principles calculations. Generally, antiferromagnetic (AFM) structures are more stable than that of the ferromagnetic one. On the basis of a specific AFM structure, the long puzzling scanning tunneling microscopy (STM) experimental observations can be well explained. In this AFM model, the Fe-O layer distance at the fee region is larger than the hcp region, in contrast to previous theoretical results. The STM images at the field-emission regime are explained by local surface potential.

Keyword
initio molecular-dynamics, scanning-tunneling-microscopy, augmented-wave method, ultrathin films, nickel-oxide, monolayer, pt(111), transition, nial(110), mechanism
National Category
Chemical Sciences
Identifiers
urn:nbn:se:kth:diva-10324 (URN)10.1021/jp810751j (DOI)000265895500048 ()2-s2.0-67049171543 (Scopus ID)
Note

QC 20100819. Updated from submitted to published, 20120315. Previous title: First principles study of the geometric and electronic structure of FeO/Pt(111) surface

Available from: 2009-05-06 Created: 2009-05-06 Last updated: 2017-12-13Bibliographically approved
6. Quantum molecular dynamics study of water onTiO2(110) surface
Open this publication in new window or tab >>Quantum molecular dynamics study of water onTiO2(110) surface
Show others...
2009 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 129, no 064703Article in journal (Refereed) Published
Abstract [en]

The adsorption of water on perfect TiO2(110) surface is studied by quantum molecular dynamics simulation adopting a periodic model formed by five water molecules on a (5 x 1) surface unit cell of a five layer slab of TiO2. The total simulation time is 3.2 ps. At about 1.3 ps, one water molecule dissociates with the help of other adsorbed waters and surface bridging oxygens. During the remaining 1.9 ps, the waters and OH groups vibrate, but no more dissociation or recombination is observed. By comparing recent experimental O1s photoemission (x-ray photoelectron spectroscopy) spectra of H2O/TiO2(110) to the computed spectrum of the adsorbate in the configurations supplied by the molecular dynamics simulation, the observed peaks can be attributed to different oxygen species. The proposed assignment of the main spectral features supports the occurrence of partial water dissociation (similar to 20%) also on a perfect TiO2 surface.

Keyword
adsorption; rutile; h2o; dissociation; tio2; pseudopotentials; 1st-principles; transition; simulation; metals
National Category
Chemical Sciences
Identifiers
urn:nbn:se:kth:diva-10325 (URN)10.1063/1.2955452 (DOI)000258490600055 ()2-s2.0-49749121868 (Scopus ID)
Note
QC 20100819Available from: 2009-05-06 Created: 2009-05-06 Last updated: 2017-12-13Bibliographically approved
7. Interaction of biomolecular systems with titanium-based materials: computational investigations
Open this publication in new window or tab >>Interaction of biomolecular systems with titanium-based materials: computational investigations
2009 (English)In: Theoretical Chemistry accounts, ISSN 1432-881X, E-ISSN 1432-2234, Vol. 123, no 3-4, 299-309 p.Article in journal (Refereed) Published
Abstract [en]

Ab initio calculations and molecular dynamics simulations were performed to investigate the adsorption mode of various oligopeptides on titanium dioxide surfaces and to characterize their conformational behavior upon adsorption. The models were progressively improved obtaining a description compatible with the experimental observations.

Keyword
Peptides; Titanium dioxide; Adsorption
National Category
Chemical Sciences
Identifiers
urn:nbn:se:kth:diva-10326 (URN)10.1007/s00214-009-0513-4 (DOI)000266928400014 ()2-s2.0-67449127109 (Scopus ID)
Note
QC 20100819Available from: 2009-05-06 Created: 2009-05-06 Last updated: 2017-12-13Bibliographically approved
8. Theoretical study on phase transition of watercovered anatase TiO2 (001) surface
Open this publication in new window or tab >>Theoretical study on phase transition of watercovered anatase TiO2 (001) surface
(English)Manuscript (Other academic)
Abstract [en]

With the (4x1) ADM structural model proposed by Lazzeri and Selloni, the behavior of wateron reconstructed anatase TiO2 (001) surface is studied by quantum molecular dynamics simulationsand an interpretation of the x-ray photoemission spectra, recently collected for such systems, with different water coverage, is provided. The spectrum of the low coverage phase is assigned to oxygencore ionization of only acceptor hydrogen bonded hydroxyl species, while the spectrum of the highcoverage phase is due to contributions from both donor and acceptor hydrogen bonded hydrox-yls. The experimental spectral evolution with temperature and dosing is also well interpreted bytheoretical simulations.

National Category
Chemical Sciences
Identifiers
urn:nbn:se:kth:diva-10327 (URN)
Note
QC 20100819Available from: 2009-05-06 Created: 2009-05-06 Last updated: 2010-08-19Bibliographically approved
9. Theoretical Study of X-ray PhotoemissionSpectra of Graphene Oxide
Open this publication in new window or tab >>Theoretical Study of X-ray PhotoemissionSpectra of Graphene Oxide
(English)Manuscript (Other academic)
Abstract [en]

Chemical structure of graphene oxide is complicated by the presence of many different oxidation species. We report here a density functional theory study on binding energy of carbon 1s at different oxidation environments on a graphene oxide sheet. It is shown that the calculated results can be wellused to interpret experimental X-ray photoemission spectra of different research groups and provide united spectral assignments. New species that are important for understanding cut mechanisms of graphene oxide have been identified.

National Category
Chemical Sciences
Identifiers
urn:nbn:se:kth:diva-10328 (URN)
Note
QC 20100819Available from: 2009-05-06 Created: 2009-05-06 Last updated: 2010-08-19Bibliographically approved
10. How Graphene is Cut upon Oxidation?
Open this publication in new window or tab >>How Graphene is Cut upon Oxidation?
2009 (English)In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 131, no 18, 6320-6321 p.Article in journal (Refereed) Published
Abstract [en]

Our first principles calculations reveal that an oxidative cut of graphene is realized by forming epoxy and then carbonyl pairs. Direct formation of a carbonyl pair to tear graphene up from an edge position is not favorable in energy. This atomic picture is valuable for developing effective means of graphene manipulation. The proposed epoxy pairs may be related to some long puzzling experimental observations on graphene oxide.

Keyword
graphite oxides; films
National Category
Other Basic Medicine
Identifiers
urn:nbn:se:kth:diva-10331 (URN)10.1021/ja8094729 (DOI)000265939200006 ()2-s2.0-69949159680 (Scopus ID)
Note

QC 20100819

Available from: 2009-05-06 Created: 2009-05-06 Last updated: 2017-12-13Bibliographically approved

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