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Fang CM, Mohammodi V, Nihtianov S, Sluiter MHF. Stability, geometry and electronic properties of BH n (n = 0 to 3) radicals on the Si{0 0 1}3 × 1:H surface from first-principles. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2020; 32:235201. [PMID: 31962296 DOI: 10.1088/1361-648x/ab6e43] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
A new generation of radiation detectors relies on the crystalline Si and amorphous B (c-Si/a-B) junctions that are prepared through chemical vapor deposition of diborane (B2H6) on Si at low temperature (~400 °C). The Si wafer surface is dominated by the Si{0 0 1}3 × 1 domains that consist of two different Si species at low temperature. Here we investigate the geometry, stability and electronic properties of the hydrogen passivated Si{0 0 1}3 × 1 surfaces with deposited BH n (n = 0 to 3) radicals using parameter-free first-principles approaches. Ab initio molecular dynamics simulations using the density functional theory (DFT) including van der Waals interaction reveal that in the initial stage the BH3 molecules/radicals deposit on the Si(-H), forming (-Si)BH4 radicals which then decompose into (-Si)BH2 with release of H2 molecules. Structural optimizations provide strong local relaxation and reconstructions at the deposited Si surface. Electronic structure calculations reveal the formation of various defect states in the forbidden gap. This indicates limitations of the presently used rigid electron-counting and band-filling models. The attained information enhances our understanding of the initial stage of the PureB process and the electric properties of the products.
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Affiliation(s)
- C M Fang
- BCAST, Brunel University London, Kingston Lane, Uxbridge, Middlesex, UB8 2AD, United Kingdom
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2
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Structure, Properties, and Reactivity of Porphyrins on Surfaces and Nanostructures with Periodic DFT Calculations. APPLIED SCIENCES-BASEL 2020. [DOI: 10.3390/app10030740] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Porphyrins are fascinating molecules with applications spanning various scientific fields. In this review we present the use of periodic density functional theory (PDFT) calculations to study the structure, electronic properties, and reactivity of porphyrins on ordered two dimensional surfaces and in the formation of nanostructures. The focus of the review is to describe the application of PDFT calculations for bridging the gaps in experimental studies on porphyrin nanostructures and self-assembly on 2D surfaces. A survey of different DFT functionals used to study the porphyrin-based system as well as their advantages and disadvantages in studying these systems is presented.
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Diller K, Papageorgiou AC, Klappenberger F, Allegretti F, Barth JV, Auwärter W. In vacuo interfacial tetrapyrrole metallation. Chem Soc Rev 2016; 45:1629-56. [PMID: 26781034 DOI: 10.1039/c5cs00207a] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The metallation of tetrapyrroles at well-defined surfaces under ultra-high vacuum conditions represents an unconventional synthesis approach to achieve tetrapyrrole-based metal-organic complexes and architectures. Different protocols, pioneered over the last decade, and now widely applied in several fields, provide an elegant route to metallo-tetrapyrrole systems often elusive to conventional procedures and give access and exquisite insight into on-surface tetrapyrrole chemistry. As highlighted by the functionality of metallo-porphyrins in biological or other environments and by the eminent role of metallo-phthalocyanines in synthetic materials, the control on the metal centres incorporated into the macrocycle is of utmost importance to achieve tailored properties in tetrapyrrole-based nanosystems. In the on-surface scenario, precise metallation pathways were developed, including reactions of tetrapyrroles with metals supplied by physical vapour deposition, chemical vapour deposition or the tip of a scanning tunnelling microscope, and self-metallation by atoms of an underlying support. Herein, we provide a comprehensive overview of in vacuo tetrapyrrole metallation, addressing two-dimensional as well as three-dimensional systems. Furthermore, we comparatively assess the available library of on-surface metallation protocols and elaborate on the state-of-the-art methodology.
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Affiliation(s)
- Katharina Diller
- Physik-Department E20, Technische Universität München (TUM), James-Franck-Str. 1, 85748 Garching, Germany. and Institute of Condensed Matter Physics (ICMP), École Polytechnique Fédérale de Lausanne (EPFL), Station 3, CH-1015 Lausanne, Switzerland.
| | - Anthoula C Papageorgiou
- Physik-Department E20, Technische Universität München (TUM), James-Franck-Str. 1, 85748 Garching, Germany.
| | - Florian Klappenberger
- Physik-Department E20, Technische Universität München (TUM), James-Franck-Str. 1, 85748 Garching, Germany.
| | - Francesco Allegretti
- Physik-Department E20, Technische Universität München (TUM), James-Franck-Str. 1, 85748 Garching, Germany.
| | - Johannes V Barth
- Physik-Department E20, Technische Universität München (TUM), James-Franck-Str. 1, 85748 Garching, Germany.
| | - Willi Auwärter
- Physik-Department E20, Technische Universität München (TUM), James-Franck-Str. 1, 85748 Garching, Germany.
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Müller M, Diller K, Maurer RJ, Reuter K. Interfacial charge rearrangement and intermolecular interactions: Density-functional theory study of free-base porphine adsorbed on Ag(111) and Cu(111). J Chem Phys 2016; 144:024701. [PMID: 26772581 DOI: 10.1063/1.4938259] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We employ dispersion-corrected density-functional theory to study the adsorption of tetrapyrrole 2H-porphine (2H-P) at Cu(111) and Ag(111). Various contributions to adsorbate-substrate and adsorbate-adsorbate interactions are systematically extracted to analyze the self-assembly behavior of this basic building block to porphyrin-based metal-organic nanostructures. This analysis reveals a surprising importance of substrate-mediated van der Waals interactions between 2H-P molecules, in contrast to negligible direct dispersive interactions. The resulting net repulsive interactions rationalize the experimentally observed tendency for single molecule adsorption.
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Affiliation(s)
- Moritz Müller
- Department Chemie, Technische Universität München, D-85747 Garching, Germany
| | - Katharina Diller
- Department Chemie, Technische Universität München, D-85747 Garching, Germany
| | - Reinhard J Maurer
- Department Chemie, Technische Universität München, D-85747 Garching, Germany
| | - Karsten Reuter
- Department Chemie, Technische Universität München, D-85747 Garching, Germany
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Pawlak R, Ouyang W, Filippov AE, Kalikhman-Razvozov L, Kawai S, Glatzel T, Gnecco E, Baratoff A, Zheng Q, Hod O, Urbakh M, Meyer E. Single-Molecule Tribology: Force Microscopy Manipulation of a Porphyrin Derivative on a Copper Surface. ACS NANO 2016; 10:713-722. [PMID: 26571003 DOI: 10.1021/acsnano.5b05761] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The low-temperature mechanical response of a single porphyrin molecule attached to the apex of an atomic force microscope (AFM) tip during vertical and lateral manipulations is studied. We find that approach-retraction cycles as well as surface scanning with the terminated tip result in atomic-scale friction patterns induced by the internal reorientations of the molecule. With a joint experimental and computational effort, we identify the dicyanophenyl side groups of the molecule interacting with the surface as the dominant factor determining the observed frictional behavior. To this end, we developed a generalized Prandtl-Tomlinson model parametrized using density functional theory calculations that includes the internal degrees of freedom of the side group with respect to the core and its interactions with the underlying surface. We demonstrate that the friction pattern results from the variations of the bond length and bond angles between the dicyanophenyl side group and the porphyrin backbone as well as those of the CN group facing the surface during the lateral and vertical motion of the AFM tip.
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Affiliation(s)
- Rémy Pawlak
- Department of Physics, University of Basel , Klingelbergstrasse 82, Basel 4056, Switzerland
| | - Wengen Ouyang
- Center for Nano and Micro Mechanics, Tsinghua University , Beijing 100084, China
| | - Alexander E Filippov
- Donetsk Institute for Physics and Engineering, National Academy of Sciences of Ukraine , Donetsk 83114, Ukraine
| | | | - Shigeki Kawai
- Department of Physics, University of Basel , Klingelbergstrasse 82, Basel 4056, Switzerland
| | - Thilo Glatzel
- Department of Physics, University of Basel , Klingelbergstrasse 82, Basel 4056, Switzerland
| | - Enrico Gnecco
- Otto Schott Institute of Materials Research (OSIM), Friedrich Schiller University Jena , Jena 07743, Germany
| | - Alexis Baratoff
- Department of Physics, University of Basel , Klingelbergstrasse 82, Basel 4056, Switzerland
| | - Quanshui Zheng
- Center for Nano and Micro Mechanics, Tsinghua University , Beijing 100084, China
| | | | | | - Ernst Meyer
- Department of Physics, University of Basel , Klingelbergstrasse 82, Basel 4056, Switzerland
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Stephan R, Hanf MC, Sonnet P. Opening the way to molecular cycloaddition of large molecules on supported silicene. J Chem Phys 2015; 143:154706. [DOI: 10.1063/1.4933369] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
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Boukari K, Duverger E, Sonnet P. Molecular chemisorption on passivated and defective boron doped silicon surfaces: a "forced" dative bond. Phys Chem Chem Phys 2014; 16:24866-73. [PMID: 25318974 DOI: 10.1039/c4cp03347g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We investigate the adsorption mechanism of a single trans 4-pyridylazobenzene molecule (denoted by PAB) on a doped boron Si(111)√3×√3R30° surface (denoted by SiB) with or without boron-defects, by means of density functional theory calculations. The semiempirical approach proposed by Grimme allows us to take the dispersion correction into account. The role of the van der Waals correction in the adsorption geometries and energies is presented. In particular, two adsorption configurations are electronically studied. In the first one, the molecule is parallel to the surface and interacts with the SiB surface via the -N=N- bond. In the presence of a boron-defect, a Si-N chemical bond between the molecule and the surface is then formed, while electrostatic or/and van der Waals interactions are observed in the defectless surface. In the second adsorption configuration, the molecule presents different orientations with respect to the surface and interacts via the nitrogen atom of the pyridyl part of the PAB molecule. If the molecule is perpendicular to the perfect SiB surface, the lone-pair electrons associated with the heterocyclic nitrogen atom fill the empty dangling bond of a silicon adatom via a dative bond. Finally, in the presence of one boron-defect, the possibility of a "forced" dative bond, corresponding to a chemical bond formation between the PAB molecule and the silicon electron occupied dangling bond, is emphasized.
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Affiliation(s)
- Khaoula Boukari
- Institut de Science des Matériaux de Mulhouse (IS2M), CNRS UMR 7361, Université de Haute Alsace, 3b rue Alfred Werner, 68093 Mulhouse cedex, France.
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Boukari K, Duverger E, Stephan R, Hanf MC, Sonnet P. C60 molecules grown on a Si-supported nanoporous supramolecular network: a DFT study. Phys Chem Chem Phys 2014; 16:14722-9. [PMID: 24920165 DOI: 10.1039/c4cp01677g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
C60 fullerene assemblies on surfaces have attracted considerable attention because of their remarkable electronic properties. Now because of the competition between the molecules-substrate and the molecule-molecule interactions, an ordered C60 array is rather difficult to obtain on silicon surfaces. Here we present density functional theory simulations on C60 molecules deposited on a TBB (1,3,5-tri(1'-bromophenyl)benzene) monolayer lying on the Si(111)-boron surface (denoted SiB). The C60 molecules are located in the nanopores formed by the TBB network. Adsorption energy calculations show that the SiB surface governs the C60 vertical position, whereas the TBB network imposes the C60 lateral position, and stabilizes the molecule as well. The low charge density between the C60 and the SiB substrate on one hand, and on the other hand between the C60 and the TBB molecules, indicates that no covalent bond is formed between the C60 and its environment. However, according to charge density differences, a drastic charge reorganisation takes place between the Si adatoms and the C60 molecule, but also between the C60 and the surrounding TBB molecules. Finally, calculations show that a C60 array sandwiched between two TBB molecular layers is stable, which opens up the way to the growth of 3D supramolecular networks.
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Affiliation(s)
- Khaoula Boukari
- IS2M UMR CNRS 7361 - UHA, 15 rue Jean Starcky, 68057 Mulhouse, France
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Boukari K, Duverger E, Stauffer L, Sonnet P. A new assisted molecular cycloaddition on boron doped silicon surfaces: a predictive DFT-D study. Phys Chem Chem Phys 2014; 16:12164-71. [PMID: 24817040 DOI: 10.1039/c4cp00839a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
In the framework of the Density Functional Theory (DFT-D), we investigate the phthalocyanine (H2Pc) molecule adsorption on SiC(0001)3 × 3 and Si(111)√3 × √3R30°-B (SiB) surfaces, and particularly compare the involved molecular adsorptions. In the H2Pc-SiC(0001)3 × 3 system, the molecular adsorption can be ascribed to a [10+2] cycloaddition. The H2Pc-SiB system is considered in three cases: defectless SiB surface (denoted SiB-0D) and SiB surfaces presenting one or two boron defects (denoted SiB-1D and SiB-2D respectively). The SiB-0D surface is passivated by a charge transfer from the Si adatoms to the boron atoms and therefore no chemical bond between the molecule and the substrate is observed. A similar molecular adsorption as already evidenced in the H2Pc-SiC(0001)3 × 3 system is involved in the SiB-2D case. In the case of the SiB-1D surface, two Si-N bonds (Si1-N1 and Si2-N2) are observed. One of them, Si1-N1, is nearly similar to that found in the H2Pc-SiB-2D system, but the Si2-N2 bond is unexpected. The Bader charge analysis suggests that, in the presence of the H2Pc molecule, the boron atoms behave like an electron reservoir whose availability varies following the involved molecular adsorption process. In the SiB-1D case, charges are transferred from the substrate to the molecule, allowing the Si2-N2 bond formation. Such a kind of molecular adsorption, not yet observed, could be designed by "assisted pseudo cycloaddition".
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Affiliation(s)
- Khaoula Boukari
- Institut de Science des Matériaux de Mulhouse (IS2M), Université de Haute Alsace, CNRS UMR 7361, 3b rue Alfred Werner, 68093 Mulhouse cedex, France.
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