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Understanding the Structure and Reaction of Single Molecules on Metal surfaces from First Principles
KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
2011 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

The study of surface adsorption and reaction is not only interesting from a scientific point of view, but also important in many application fields such as energy, environment, catalysis, corrosion, electronic device, and sensor. Theoretical calculations are essential in these studies.

In this thesis, first principles studies for the structure and reaction of some important single molecules on the surface are presented. Dehydrogenation of single trans-2-butene molecule on a Pd(110) surface is the first example. The adsorption configurations of both reactant and produce are assigned and the whole dehydrogenation pathway is revealed. Our calculations show that the reactant, i.e. trans-2-butene molecule, undergoes a rotation before dehydrogenation occurs, which is an important detail that cannot be observed directly in scanning tunneling microscopy (STM) experiments. The dissociation and rotation processes of single oxygen molecule on a Pt(111) surface have been a subject of extensive studies in the past. A new intermediate state with a peculiar configuration is identified. The puzzled adsorption site is well explained. The calculated energy barriers agree well with experimental results for both dissociation and rotation processes.

Another aspect addressed in this thesis is the mechanism of molecular electronic switches induced by molecular structural changes. By carefully examining the tautomerization process of a naphthalocyanine molecule, an intermediate state is located on the potential surface of the tautomerization. Our calculations indicate that the experimentally observed switching involves four-states, rather than the two-state as proposed by the experimentalists. In a joint experimental and theoretical study the dehydrogenation, tautomerization, and mechanical switching processes of a single melamine molecule on a Cu(100) surface have been comprehensively examined. A new dual-functional molecular device with integrated rectifying and switching functions is made for the first time. In collaborating with another experimental group, we have simulated the switching process of a single 1,1,2,3,4,5-hexaphenylsilole molecule on a Cu(111) surface. The role of the orientation of the molecule is carefully examined and a new switching mechanism is proposed.

Switching processes are strongly associated with the inelastic electron tunneling. We have proposed a statistical model that allows explaining the non-integer exponent in the power-law relationship between the switching rate and tunneling current. In this model, the importance of the randomness in inelastic electron excitations and the lifetime of the immediate state are emphasized. It has shown that the inelastic electron tunneling is a collection of various n-electron processes with different statistical weight.

Place, publisher, year, edition, pages
Stockholm: KTH Royal Institute of Technology , 2011. , xii, 72 p.
Series
Trita-BIO-Report, ISSN 1654-2312 ; 2011:16
National Category
Theoretical Chemistry
Identifiers
URN: urn:nbn:se:kth:diva-33565ISBN: 978-91-7415-978-3OAI: oai:DiVA.org:kth-33565DiVA: diva2:416112
Public defence
2011-06-10, FA32, AlbaNova University Center, Roslagstullsbacken 21, Stockholm, 10:00 (English)
Opponent
Supervisors
Note
QC 20110524Available from: 2011-05-24 Created: 2011-05-10 Last updated: 2011-05-24Bibliographically approved
List of papers
1. First-principles calculations of adsorption and dehydrogenation of trans-2-butene molecule on Pd(110) surface
Open this publication in new window or tab >>First-principles calculations of adsorption and dehydrogenation of trans-2-butene molecule on Pd(110) surface
2009 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 131, no 15Article in journal (Refereed) Published
Abstract [en]

Adsorption and dehydrogenation processes of trans-2-butene molecule on the Pd(110) surface have been studied by density functional theory calculations. Different adsorption configurations of the reactant, the dehydrogenated product, and the most favorable reaction pathway have been determined. The calculated energy barrier agrees well with the value deduced from experiments. It is found that the reactant molecule must undergo a rotation before the C-H bond cleavage, and surface Pd atoms are involved in the dehydrogenation reaction through the formation of the Pd-C-H three-membered metallacycle. Our calculations have not only provided reliable interpretation for various experimental observations but also shed more light on the dynamics of the reaction processes.

Keyword
scanning tunneling microscope, total-energy calculations, wave, basis-set, ab-initio, 1, 3-butadiene, selectivity
Identifiers
urn:nbn:se:kth:diva-18902 (URN)10.1063/1.3234419 (DOI)000271219000039 ()2-s2.0-70449377193 (ScopusID)
Note
QC 20100525Available from: 2010-08-05 Created: 2010-08-05 Last updated: 2011-05-24Bibliographically approved
2. A first principles study on the dissociation and rotation processes of a single O2 molecule on the Pt(111) surface
Open this publication in new window or tab >>A first principles study on the dissociation and rotation processes of a single O2 molecule on the Pt(111) surface
2011 (English)In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 115, no 14, 6864-6869 p.Article in journal (Refereed) Published
Abstract [en]

Through density functional theory calculations, a detailed description on the dissociation and rotation processes of a single oxygen molecule adsorbed on the Pt(111) surface has been provided. Both dissociation and rotation reaction pathways have been identified, and some interesting phenomena related to the scanning tunneling microscopy experiments are finally explained. It is found that the prior occupation of oxygen atom on the metastable hcp-hollow site after O2 dissociation is originated from the particular structure of the intermediate state, and the low energy barrier of the O2 rotation can be attributed to an effective pathway. The experimentally observed noninteger power-law dependence of the rotation rate as a function of the current has been accurately determined by a newly developed statistical model for the inelastic electron tunneling. By considering the randomness of multielectron inelastic tunneling processes, it is found that the noninteger exponent comes from a statistical contribution of various n-electron events.

Place, publisher, year, edition, pages
American Chemical Society, 2011
Keyword
scanning tunneling microscope, density-functional theory, total-energy calculations, wave basis-set, atom-transfer, oxygen dissociation, adsorption, mechanism, switch, spectroscopy
National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:kth:diva-33362 (URN)10.1021/jp200687t (DOI)000289215400090 ()2-s2.0-79953766611 (ScopusID)
Funder
Swedish Research Council
Available from: 2011-05-04 Created: 2011-05-04 Last updated: 2011-09-08Bibliographically approved
3. Mechanism for tautomerization induced conductance switching of naphthalocyanin molecule
Open this publication in new window or tab >>Mechanism for tautomerization induced conductance switching of naphthalocyanin molecule
2009 (English)In: Applied Physics Letters, ISSN 0003-6951, E-ISSN 1077-3118, Vol. 95, no 18Article in journal (Refereed) Published
Abstract [en]

Reaction mechanism for tautomerization process of a single naphthalocyanin molecule has been studied using density functional theory. It is found that tautomerization of the naphthalocyanin molecule is not a concerted reaction, but a step-wise process in that one hydrogen atom transfers after another. A stable intermediate state and the possible transition state of the reaction processes have been located. The occurrence of the intermediate state suggests that the tautomerization induced conductance switching involves four conductance states with different conductances, and the earlier proposed two-state system model is not valid.

Keyword
density functional theory, isomerisation, organic compounds, scanning tunneling microscope, total-energy calculations, wave, basis-set, conformational-changes, single molecules, atom-transfer
Identifiers
urn:nbn:se:kth:diva-18948 (URN)10.1063/1.3224186 (DOI)000271666800036 ()2-s2.0-71049191107 (ScopusID)
Note
QC 20100525Available from: 2010-08-05 Created: 2010-08-05 Last updated: 2011-05-24Bibliographically approved
4. Design and control of electron transport properties of single molecules
Open this publication in new window or tab >>Design and control of electron transport properties of single molecules
Show others...
2009 (English)In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 106, no 36, 15259-15263 p.Article in journal (Refereed) Published
Abstract [en]

We demonstrate in this joint experimental and theoretical study how one can alter electron transport behavior of a single melamine molecule adsorbed on a Cu (100) surface by performing a sequence of elegantly devised and well-controlled single molecular chemical processes. It is found that with a dehydrogenation reaction, the melamine molecule becomes firmly bonded onto the Cu surface and acts as a normal conductor controlled by elastic electron tunneling. A current-induced hydrogen tautomerization process results in an asymmetric melamine tautomer, which in turn leads to a significant rectifying effect. Furthermore, by switching on inelastic multielectron scattering processes, mechanical oscillations of an N-H bond between two configurations of the asymmetric tautomer can be triggered with tuneable frequency. Collectively, this designed molecule exhibits rectifying and switching functions simultaneously over a wide range of external voltage.

Keyword
hydrogen tautomerization, melamine molecules, rectifying effect, switching property, negative differential-resistance, scanning tunneling microscope, total-energy calculations, wave basis-set, conformational-changes, azobenzene, dissociation, efficiency, melamine, device
Identifiers
urn:nbn:se:kth:diva-18741 (URN)10.1073/pnas.0903131106 (DOI)000269632400033 ()2-s2.0-70349304456 (ScopusID)
Note
QC 20100525Available from: 2010-08-05 Created: 2010-08-05 Last updated: 2011-05-24Bibliographically approved
5. Single molecule's conductance depending on its orientation
Open this publication in new window or tab >>Single molecule's conductance depending on its orientation
Show others...
2009 (English)In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 113, no 1, 26-30 p.Article in journal (Refereed) Published
Abstract [en]

Single molecules of 1,1,2,3,4,5-hexaphenylsilole adsorbed on Cu(111) have been investigated using low-temperature scanning tunneling microscopy, scanning tunneling spectroscopy, and quantum chemistry calculations. Two adsorption states have been identified, showing distinctive tunneling conductance. The molecules can switch their states under tip influence. Theoretical calculations indicate that the two states are associated with molecules adsorbed at two 90°-rotated orientations, and the tunneling conductance is attributed to molecular orbitals that spatially bridge tip-to-substrate gap. Our findings demonstrate a decisive dependence of single-molecule conductance on the molecular orientation with respect to electrodes.

Keyword
transport-properties, junction conductance, electron-transport, surface, atom, 2, 3, 4, 5-tetraphenylsiloles, conductivity, gold
National Category
Chemical Sciences
Identifiers
urn:nbn:se:kth:diva-33364 (URN)10.1021/jp8089215 (DOI)000262168000006 ()2-s2.0-65249167503 (ScopusID)
Available from: 2011-05-04 Created: 2011-05-04 Last updated: 2011-10-10Bibliographically approved

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