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| 2. |
- Baran, Jakub D., et al.
(författare)
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A Case of Unusually Large Density of States Changes For Physisorption - TetraPhenyl-Porphyrins on Cu(111)
- 2015
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- Conformational changes caused by surface adsorption can dramatically affect a molecule’s properties. The conformational flexibility of the porphyrin family of molecules has been exploited particularly well in a number of contexts, including prototypical molecular switches. Despite this level of study, however, the exact mechanisms underpinning conformational switching are often unclear. We show that the conformation of the tetra(4-bromophenyl) porphyrin (Br4TPP) on Cu(111) depends critically on the precise adsorption site of the molecule, and that, remarkably, large conformational changes are driven entirely by van der Waals (vdW) interactions between the molecule and the substrate surface. A combination of scanning probe microscopy, low temperature single molecule manipulation, dispersion-corrected density functional theory (DFT) and molecular dynamics (MD) simulations shows that van der Waals forces dominate the adsorption of TPP molecules, causing significant distortions of the molecular architecture so that the porphyrin can adopt one of two low energy conformations. In addition, scanning probe manipulation has been used to translate and switch the Br4TPP molecule between conformations via an intermediary, ‘hybrid’ structure. We have used the generalized gradient approximation (GGA) parameterization by Perdew—Burke—Ernzerhof (PBE), and the sparse-matter optBP86b-vdW20 (vdW-DFT) exchange and correlation functional to account for the missing dispersion forces. In order to check for the presence of chemical bonding we have analyzed the molecule-surface complexes using electron localization function (ELF) and Bader charges. We find that vdW-forces alone are capable of causing large shifts in the molecular density of states, despite the complete absence of chemical interactions.
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| 3. |
- Baran, Jakub D., et al.
(författare)
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DFT Computation Of Metal-Phthalocyanines Bonded To Ag(111)
- 2007
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Konferensbidrag (refereegranskat)abstract
- To study the adsorption of metal-phthalocyanines (MPc (M=Co; Sn; Pb) on the Ag(111) surface we have performed electronic structure calculations using a cluster representation of the surface within the framework of density functional theory (DFT) [1]. Our calculations use the generalized gradient approximation (GGA) parameterization by Pedrew-Burke-Ernzerhof (PBE) for the exchange-correlation energy [2]. We have investigated bonding on three surface adsorption sites (hcp-hollow; fcc-hollow and on-top). SnPc was found to adsorb weakly to the surface (0.15 to 0.25 eV); and to prefer hollow bonding rather than on-top bonding. The distance between the Sn atom and the top layer Ag-surface atoms (hcp-hollow and fcc-hollow) is consistent with experimental data obtained by normal incidence X-ray standing wave spectroscopy (NIXSW) [3;4]. CoPc is much more strongly bound to the Ag(111) surface and was found to prefer the on-top site. The calculated binding energy is 1.2 eV and the distance between the Co atom and the top layer Ag atoms is 3 (which also matched the experimental data well). For PbPc; successful adsorption was only obtained on the hcp-hollow site with a binding energy of 0.5 eV. For each of these systems we have found good agreement in binding geometries with experimental data.
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| 4. |
- Baran, Jakub D., et al.
(författare)
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Interactions of Metal-phthalocyanines MPc (M=Co; Sn; Pb) with Silver Surface Ag(111) : A Density Functional Study
- 2008
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Konferensbidrag (refereegranskat)abstract
- Deposited and/or self-assembled on metal electrodes; metal-phthalocyanine are attractive candidates for novel molecular sensors; memory; and light-harvesting components. The knowledge of the their molecular geometry and electronic structure are crucial points in order to understand their interactions with surfaces. To study the adsorption of metal-phthalocyanines (MPc (M=Co; Sn; Pb) bonded parallel on the Ag(111) surface we have performed electronic structure calculations using a cluster representation (55 and 169 silver atoms) of the surface within the framework of density functional theory (DFT) [1]. Our calculations use the generalized gradient approximation (GGA) parameterization by Pedrew-Burke-Ernzerhof (PBE) for the exchange-correlation energy [2] and multipole accelerated resolution of identity method [3]. We have investigated bonding on three surface adsorption sites (hcp-hollow; fcc-hollow and on-top). For each of these systems we have found good agreement in binding geometries with experimental data obtained by normal incidence X-ray standing wave spectroscopy (NIXSW) [4;5]. Binding energies and geometries for all systems are given. We propose flat chemisorption of respective MPcs on Ag(111).
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| 5. |
- Baran, Jakub D., et al.
(författare)
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Theoretical and Experimental Study of Metal-phthalocyanines on Ag(111).
- 2009
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Konferensbidrag (refereegranskat)abstract
- Metal-phthalocyanines deposited and/or self-assembled on metal surface are considered as candidates for novel molecular sensors; molecular memories and photovoltaic cells. To study the adsorption of three metal-phthalocyanines (MPc (M=Co; Sn; Pb) on Ag(111) we performed density functional theory DFT calculations using the generalized gradient approximation (GGA) parameterization by Pedrew-Burke-Ernzerhof (PBE) for the exchange-correlation energy [1;2]. Three initial adsorption site were considered (hcp-hollow; fcc-hollow and on-top). Our results show that the most favourite adsorption site is hcp-hollow for SnPc and PbPc and on-top for CoPc. All calculated structures are compared with experimental data obtained by normal incidence X-ray standing wave spectroscopy (NIXSW) [3;4] Good agreement in binding geometries with experiment was found. To understand the hybridization of MPc s molecular orbitals with silver orbitals we have compared selected partial density of states PDOS for a free and adsorbed MPcs. SnPc and PbPc hybridize mostly with surface by central metal atom; however the effect from the aromatic rings is not negligible. Adsorption of CoPc on the silver surface results in a transfer of electron density from the surface to the central Co atom. After adsorption; the magnetic moment of CoPc is completely quenched which is in agreement with similar studies on adsorption on Au(111) [5]. Binding energies for all of systems are reported showing chemisorptive nature of the molecule-metal surface interaction
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| 6. |
- Jarvis, Samuel P., et al.
(författare)
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Measuring the mechanical properties of molecular conformers
- 2015
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 6
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Tidskriftsartikel (refereegranskat)abstract
- Scanning probe-actuated single molecule manipulation has proven to be an exceptionally powerful tool for the systematic atomic-scale interrogation of molecular adsorbates. To date, however, the extent to which molecular conformation affects the force required to push or pull a single molecule has not been explored. Here we probe the mechanochemical response of two tetra(4-bromophenyl)porphyrin conformers using non-contact atomic force microscopy where we find a large difference between the lateral forces required for manipulation. Remarkably, despite sharing very similar adsorption characteristics, variations in the potential energy surface are capable of prohibiting probe-induced positioning of one conformer, while simultaneously permitting manipulation of the alternative conformational form. Our results are interpreted in the context of dispersion-corrected density functional theory calculations which reveal significant differences in the diffusion barriers for each conformer. These results demonstrate that conformational variation significantly modifies the mechanical response of even simple porpyhrins, potentially affecting many other flexible molecules
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| 7. |
- Jarvis, Samuel P., et al.
(författare)
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Physisorption Controls the Conformation and Density of States of an Adsorbed Porphyrin
- 2015
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Ingår i: The Journal of Physical Chemistry C. - : American Chemical Society (ACS). - 1932-7447 .- 1932-7455. ; 119:50, s. 27982-27994
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Tidskriftsartikel (refereegranskat)abstract
- Conformational changes caused by adsorption can dramatically affect a molecule's properties. Despite extensive study, however, the exact mechanisms underpinning conformational switching are often unclear. Here we show that the conformation of a prototypical flexible molecule, the free-base tetra(4-bromophenyl) porphyrin, adsorbed on Cu(111), depends critically on its precise adsorption site and that, remarkably, large conformational changes are dominated by van der Waals interactions between the molecule and the substrate surface. A combination of scanning probe microscopy, single-molecule manipulation, DFT with dispersion density functional theory, and molecular dynamics simulations show that van der Waals forces drive significant distortions of the molecular architecture so that the porphyrin can adopt one of two low-energy conformations. We find that adsorption driven by van der Waals forces alone is capable of causing large shifts in the molecular density of states, despite the apparent absence of chemical interactions. These findings highlight the essential role that van der Waals forces play in determining key molecular properties.
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| 8. |
- Muthukumar, Kaliappan, et al.
(författare)
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Cerium Endohedral fullerenes (Ce@C82 and Ce2@C80) Theoretical Interpretations for Experimental observation
- 2008
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Konferensbidrag (refereegranskat)abstract
- Many questions remain unanswered for the endohedral fullerenes. Owing to the improvement in separation of isomers and in theoretical studies (DFT and ab-initio) evolving as imperative tool for characterization; these can be addressed.1;2 Understanding of the position and binding configuration of the metal atom inside the cage is crucial as it controls the structural and electronic properties of the molecule.3 Theoretical calculations proved to be efficient in explaining many controversies in the field of lanthanoid endohedral fullerenes.2-5 Fig; Ce2@C80; Ce2@C78) DFT optimized structures of Ce2@C80 D3d and Ce2@C78 D3h Here in this study we use DFT to characterize Ce doped metallofullerenes and report some surprising theoretical findings on the binding of cerium inside various carbon cages; (C60; C78; C80; C82). We observe that the presence of an additional Ce atom puts restrictions on the binding in the C80 cage6; but this does not happen in the C78 cage. We explain the reason behind this by analyzing the electronic structure. Further various spectra (RESPES; IETS; STM/STS) have been simulated for Ce@C82 and Ce2@C80 which we compare and discuss with experiments
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| 9. |
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| 10. |
- Muthukumar, Kaliappan, et al.
(författare)
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Surprising Findings for Ce Doped Fullerenes and Understanding of Experiments through Theoretical Modelling A DFT Approach
- 2008
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- Endohedral fullerenes; which have one metal atom encapsulated; are relatively well studied compared to species that have two elements inside the cage.1-5 Cerium; the most reactive elements of the rare earth group can be encapsulated into fullerene (C78; C80; C82) cages;1 which works as a n-dopant and in the incarcerated form it can be used as quantum bits in quantum computing2. Understanding of the position and binding pattern of the metal atom inside the cage is important as it controls the structural and electronic properties of the molecule. We found that Ce in Ce@C82 has a specific and unique binding site in C82-C2v and has a C2v symmetric structure; which is explained by the specific charge pattern of this binding site and the symmetry of the MO s that comply well with the Ce d orbital bonding.6 This six-membered ring binding site is also favored by La in La@C82. Each of the six-membered rings of C80-Ih fulfills this symmetry criterion and therefore a similar kind of binding site is expected for Ce in Ce2@C80. But; we observe a novel binding site for Ce in presence of an additional cerium atom; while La preserve its usual binding pattern in La2@C80 as in La@C82.7 We here discuss and analyze the reason for the preference of novel binding site of Ce atoms in C80-Ih by explaining the competitive binding nature of Ce-Ce and Ce-C. Surprisingly; Ce in Ce2@C78 unlike Ce2@C80 has its binding pattern as in Ce@C60 and in Ce@C82 (binding to a six-membered ring). We explain this variation in binding together with the nature of the charge transfer between the Ce atoms and the cage (C82 and C80). In addition; we explain experimental observations for Ce@C82 and Ce2@C80 from RESPES; IETS; STM/STS spectra by comparison with simulated properties
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