1
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Van den Bossche M. Three-Center Tight-Binding Together with Multipolar Auxiliary Functions. J Chem Theory Comput 2024; 20:2538-2550. [PMID: 38483273 DOI: 10.1021/acs.jctc.4c00018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
We present an ab initio tight-binding method that allows to improve on the effective potential and minimal basis approximations employed in semiempirical calculations. Three-center expansions are used to evaluate the zeroth-order Hamiltonian matrix elements and repulsive energy terms in the spirit of the Horsfield method. Self-consistency is handled by expanding atomic orbital products in an auxiliary basis following the work of Giese and York, combined with a two-center expansion of the exchange-correlation kernels. Together with nonminimal main basis sets (double-ζ plus polarization), we show that the resulting method trades a modest amount of accuracy for a significant gain in speed, compared to that of numerical atomic orbital density functional theory, in calculations on small molecules, bulk compounds, and metal nanoclusters.
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2
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Zamalloa-Serrano JM, Gómez-Fernández JM, Sánchez-Sánchez C, López MF, Martínez JI, Martín-Gago JÁ, Palacio I. Transition mechanism of the coverage-dependent polymorphism of self-assembled melamine nanostructures on Au(111). Phys Chem Chem Phys 2024; 26:3941-3949. [PMID: 38241018 DOI: 10.1039/d3cp05960j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Molecular self-assembled films have recently attracted increasing attention within the field of nanotechnology as they offer a route to obtain new materials. However, careful selection of the molecular precursors and substrates, as well as exhaustive control of the system evolution is required to obtain the best possible outcome. The three-fold rotational symmetry of melamine molecules and their capability to form hydrogen bonds make them suitable candidates to synthesize this type of self-assembled network. In this work, we have studied the polymorphism of melamine nanostructures on Au(111) at room temperature. We find two coverage-dependent phases: a honeycomb structure (α-phase) for submonolayer coverage and a close-packed structure (β-phase) for full monolayer coverage. A combined scanning tunnel microscopy and density functional theory based-calculations study of the transition regime where both phases coexist allows describing the mechanism underlying this coverage driven phase transition in terms of the changes in the molecular lateral tension.
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Affiliation(s)
| | - José María Gómez-Fernández
- Institute of Material Science of Madrid (ICMM-CSIC), C/Sor Juana Inés de la Cruz 3, 28049 Madrid, Spain.
| | - Carlos Sánchez-Sánchez
- Institute of Material Science of Madrid (ICMM-CSIC), C/Sor Juana Inés de la Cruz 3, 28049 Madrid, Spain.
| | - María Francisca López
- Institute of Material Science of Madrid (ICMM-CSIC), C/Sor Juana Inés de la Cruz 3, 28049 Madrid, Spain.
| | - José Ignacio Martínez
- Institute of Material Science of Madrid (ICMM-CSIC), C/Sor Juana Inés de la Cruz 3, 28049 Madrid, Spain.
| | - José Ángel Martín-Gago
- Institute of Material Science of Madrid (ICMM-CSIC), C/Sor Juana Inés de la Cruz 3, 28049 Madrid, Spain.
| | - Irene Palacio
- Institute of Material Science of Madrid (ICMM-CSIC), C/Sor Juana Inés de la Cruz 3, 28049 Madrid, Spain.
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3
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Fan Y, Tao S, Pitié S, Liu C, Zhao C, Seydou M, Dappe YJ, Low PJ, Nichols RJ, Yang L. Destructive quantum interference in meta-oligo(phenyleneethynylene) molecular wires with gold-graphene heterojunctions. NANOSCALE 2023; 16:195-204. [PMID: 38050747 DOI: 10.1039/d3nr04012g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/06/2023]
Abstract
Quantum interference (QI) is well recognised as a significant contributing factor to the magnitude of molecular conductance values in both single-molecule and large area junctions. Numerous structure-property relationship studies have shown that para-connected oligo(phenyleneethynylene) (OPE) based molecular wires exemplify the impact of constructive quantum interference (CQI), whilst destructive quantum interference (DQI) effects are responsible for the orders of magnitude lower conductance of analogous meta-contacted OPE derivatives, despite the somewhat shorter effective tunnelling distance. Since molecular conductance is related to the value of the transmission function, evaluated at the electrode Fermi energy, T(EF), which in turn is influenced by the presence and relative energy of (anti)resonances, it follows that the relative single-molecule conductance of para- and meta-contacted OPE-type molecules is tuned both by the anchor group and the nature of the electrode materials used in the construction of molecular junctions (gold|molecule|gold vs. gold|molecule|graphene). It is shown here that whilst amine-contacted junctions show little influence of the electrode material on molecular conductance due to the similar electrode-molecule coupling through this anchor group to both types of electrodes, the weaker coupling between thiomethyl and ethynyl anchors and the graphene substrate electrode results in a relative enhancement of the DQI effect. This work highlights an additional parameter space to explore QI effects and establishes a new working model based on the electrode materials and anchor groups in modulating QI effects beyond the chemical structure of the molecular backbone.
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Affiliation(s)
- Yinqi Fan
- Department of Chemistry, Xi'an-Jiaotong Liverpool University, Suzhou, 215123, China.
- Department of Chemistry, University of Liverpool, Liverpool, L69 7ZD, UK
| | - Shuhui Tao
- Department of Chemistry, Xi'an-Jiaotong Liverpool University, Suzhou, 215123, China.
- NUS (Chongqing) Research Institute, Chongqing, China
| | - Sylvain Pitié
- Applied Quantum Chemistry Group, E4, IC2MP, UMR 7285 Poitiers University CNRS, 86073 Poitiers, France
| | - Chenguang Liu
- Department of Electrical and Electronic Engineering, Xi'an-Jiaotong Liverpool University, Suzhou, 215123, China
| | - Chun Zhao
- Department of Electrical and Electronic Engineering, Xi'an-Jiaotong Liverpool University, Suzhou, 215123, China
| | | | - Yannick J Dappe
- SPEC, CEA, CNRS, Université Paris-Saclay, CEA Saclay, 91191 Gif-sur-Yvette Cedex, France
| | - Paul J Low
- School of Molecular Sciences, University of Western Australia, 35 Stirling Highway, 6009 Crawley, Australia
| | - Richard J Nichols
- Department of Chemistry, University of Liverpool, Liverpool, L69 7ZD, UK
| | - Li Yang
- Department of Chemistry, Xi'an-Jiaotong Liverpool University, Suzhou, 215123, China.
- Department of Chemistry, University of Liverpool, Liverpool, L69 7ZD, UK
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4
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Snegir S, Dappe YJ, Sysoiev D, Huhn T, Scheer E. Nonuniform STM Contrast of Self-Assembled Tri- n-octyl-triazatriangulenium Tetrafluoroborate on HOPG. ACS OMEGA 2023; 8:38766-38772. [PMID: 37867726 PMCID: PMC10586247 DOI: 10.1021/acsomega.3c06454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 09/21/2023] [Indexed: 10/24/2023]
Abstract
We have assembled 4,8,12-tri-n-octyl-4,8,12-triazatrianguleniumtetrafluoroborate (TATA-BF4) on highly oriented pyrolytic graphite (HOPG) and have studied the structure and tunneling properties of this self-assembled monolayer (SAM) using scanning tunneling microscopy (STM) under ambient conditions. We show that the triazatriangulenium cations TATA+ form hexagonally packed structures driven by the interaction between the aromatic core and the HOPG lattice, as evidenced by density functional theory (DFT) modeling. According to the DFT results, the three alkyl chains of the platform tend to follow the main crystallographic directions of HOPG, leading to a different STM appearance. The STM contrast of the SAM shows that the monolayer is formed by two types of species, namely, TATA+ with BF4- counterions on top and without them. The cationic TATA+ platform gives rise to a seemingly higher appearance than neutral TATA-BF4, in contrast to observations made on metallic substrates. The variation of the STM tunneling parameters does not change the relative difference of contrast, revealing the stability of both species on HOPG. DFT calculations show that TATA-BF4 on HOPG has sufficient binding energy to resist dissociation into TATA+ and BF4-, which might occur under the action of the electric field in the tunneling gap during STM scanning.
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Affiliation(s)
- Sergii Snegir
- Department
of Physics, University of Konstanz, Universitätsstraße 10, Konstanz 78464, Germany
| | - Yannick J. Dappe
- SPEC,
CEA, CNRS, Université Paris-Saclay, CEA Saclay, Gif-sur-Yvette Cédex 91191, France
| | - Dmytro Sysoiev
- Department
of Chemistry, University of Konstanz, Universitätsstraße 10, Konstanz 78464, Germany
| | - Thomas Huhn
- Department
of Chemistry, University of Konstanz, Universitätsstraße 10, Konstanz 78464, Germany
| | - Elke Scheer
- Department
of Physics, University of Konstanz, Universitätsstraße 10, Konstanz 78464, Germany
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5
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Negre CFA, Lopez-Bezanilla A, Zhang Y, Akrobotu PD, Mniszewski SM, Tretiak S, Dub PA. Toward a QUBO-Based Density Matrix Electronic Structure Method. J Chem Theory Comput 2022; 18:4177-4185. [PMID: 35658437 DOI: 10.1021/acs.jctc.2c00090] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Density matrix electronic structure theory is used in many quantum chemistry methods to "alleviate" the computational cost that arises from directly using wave functions. Although density matrix based methods are computationally more efficient than wave function based methods, significant computational effort is involved. Because the Schrödinger equation needs to be solved as an eigenvalue problem, the time-to-solution scales cubically with the system size in mean-field type approaches such as Hartree-Fock and density functional theory and is solved as many times in order to reach charge or field self-consistency. We hereby propose and study a method to compute the density matrix by using a quadratic unconstrained binary optimization (QUBO) solver. This method could be useful to solve the problem with quantum computers and, more specifically, quantum annealers. Our proposed approach is based on a direct construction of the density matrix using a QUBO eigensolver. We explore the main parameters of the algorithm focusing on precision and efficiency. We show that, while direct construction of the density matrix using a QUBO formulation is possible, the efficiency and precision have room for improvement. Moreover, calculations performed with quantum annealing on D-Wave's new Advantage quantum computer are compared with results obtained with classical simulated annealing, further highlighting some problems of the proposed method. We also suggest alternative methods that could lead to a more efficient QUBO-based density matrix construction.
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Affiliation(s)
| | | | | | - Prosper D Akrobotu
- Department of Mathematical Sciences, University of Texas at Dallas, Richardson, Texas 75080, United States
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6
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Gao T, He C, Liu C, Fan Y, Zhao C, Zhao C, Su W, Dappe YJ, Yang L. Oligothiophene molecular wires at graphene-based molecular junctions. Phys Chem Chem Phys 2021; 23:21163-21171. [PMID: 34528653 DOI: 10.1039/d1cp03050g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The use of graphene as a new type of electrode at molecular junctions has led to a renewal of molecular electronics. Indeed, the symmetry breaking induced by the graphene electrode yields different electronic behaviors at the molecular junction and in particular enhanced conductance for longer molecules. In this respect, several studies involving different molecular backbones and anchoring groups have been performed. Here in the same line, we consider oligopthiophene based hybrid gold-graphene junctions and we measure their electrical properties using the STM-I(s) method in order to determine their attenuation factor and the effect of specific anchoring groups. The results are supported by density functional theory (DFT) calculations, and exhibit a similar behavior to what is observed at alkane-based junctions.
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Affiliation(s)
- Tingwei Gao
- Department of Chemistry, Xi'an-Jiaotong Liverpool University, Suzhou, 215123, China. .,Department of Chemistry, University of Liverpool, Liverpool, L69 7ZD, UK
| | - Chunhui He
- Department of Chemistry, Xi'an-Jiaotong Liverpool University, Suzhou, 215123, China. .,Department of Chemistry, University of Liverpool, Liverpool, L69 7ZD, UK
| | - Chenguang Liu
- Department of Chemistry, Xi'an-Jiaotong Liverpool University, Suzhou, 215123, China.
| | - Yinqi Fan
- Department of Chemistry, Xi'an-Jiaotong Liverpool University, Suzhou, 215123, China. .,Department of Chemistry, University of Liverpool, Liverpool, L69 7ZD, UK
| | - Cezhou Zhao
- Department of Electrical and Electronic Engineering, Xi'an-Jiaotong Liverpool University, Suzhou, 215123, China
| | - Chun Zhao
- Department of Electrical and Electronic Engineering, Xi'an-Jiaotong Liverpool University, Suzhou, 215123, China
| | - Weitao Su
- College of Materials and Environmental Engineering, Hangzhou Dianzi University, Hangzhou, 310018, China
| | - Yannick J Dappe
- SPEC, CEA, CNRS, Université Paris-Saclay, CEA Saclay, Gif-sur-Yvette Cedex 91191, France
| | - Li Yang
- Department of Chemistry, Xi'an-Jiaotong Liverpool University, Suzhou, 215123, China. .,Department of Chemistry, University of Liverpool, Liverpool, L69 7ZD, UK
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7
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Snegir S, Dappe YJ, Sysoiev D, Pluchery O, Huhn T, Scheer E. Where do the counterions go? Tip-induced dissociation of self-assembled triazatriangulenium-based molecules on Au(111). Phys Chem Chem Phys 2021; 23:9930-9937. [PMID: 33861285 DOI: 10.1039/d1cp00221j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Chemical coupling of functional molecules on top of the so-called platform molecules allows the formation of functional self-assembled monolayers (SAMs). An often-used example of such a platform is triazatriangulenium (TATA), which features an extended aromatic core providing good electronic contact to the underlying metal surface. Here, we present a study of the SAM formation of a TATA platform on Au(111) employing scanning tunneling microscopy (STM) under ambient atmospheric conditions. In solution, the TATA platform is stabilized by BF4 counterions, while after deposition on a gold substrate, the localization of the BF4 counterions remains unknown. We used 1,2,4-trichlorobenzene as a solvent of TATA-BF4 to induce SAM formation on a heated (∼50 °C) Au substrate. We show by STM how to detect and distinguish TATA-BF4 from TATA platforms, which lost their BF4 counterions. Finally, we observe a change of the counterion position on the SAM during the STM scanning, which we explain by an electric-field-induced decrease of the electrostatic interaction in TATA-BF4 on the surface. We applied DFT calculations to reveal the influence of the gold lattice and the electric field of the STM tip on the stability of TATA-BF4 physisorbed on the surface.
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Affiliation(s)
- S Snegir
- Department of Physics, University of Konstanz, Universitätsstraße 10, 78464 Konstanz, Germany.
| | - Y J Dappe
- SPEC, CEA, CNRS, Université Paris-Saclay, CEA Saclay, 91191 Gif-sur-Yvette Cedex, France
| | - D Sysoiev
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78464 Konstanz, Germany
| | - O Pluchery
- Sorbonne Université, CNRS, Institut des NanoSciences de Paris (INSP), 4 place Jussieu, 75005 Paris, France
| | - T Huhn
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78464 Konstanz, Germany
| | - E Scheer
- Department of Physics, University of Konstanz, Universitätsstraße 10, 78464 Konstanz, Germany.
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8
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Soler-Polo D, Mendieta-Moreno JI, Trabada DG, Mendieta J, Ortega J. Proton Transfer in Guanine-Cytosine Base Pairs in B-DNA. J Chem Theory Comput 2019; 15:6984-6991. [DOI: 10.1021/acs.jctc.9b00757] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Diego Soler-Polo
- Departamento de Física Teórica de la Materia Condensada and Condensed Matter Physics Center (IFIMAC), Facultad de Ciencias, Universidad Autónoma de Madrid, E-28049 Madrid, Spain
| | - Jesús I. Mendieta-Moreno
- Departamento de Física Teórica de la Materia Condensada and Condensed Matter Physics Center (IFIMAC), Facultad de Ciencias, Universidad Autónoma de Madrid, E-28049 Madrid, Spain
| | - Daniel G. Trabada
- Departamento de Física Teórica de la Materia Condensada and Condensed Matter Physics Center (IFIMAC), Facultad de Ciencias, Universidad Autónoma de Madrid, E-28049 Madrid, Spain
| | - Jesús Mendieta
- Departamento de Biotecnología, Universidad Francisco de Vitoria, E-28223 Pozuelo de Alarcón, Madrid, Spain
| | - José Ortega
- Departamento de Física Teórica de la Materia Condensada and Condensed Matter Physics Center (IFIMAC), Facultad de Ciencias, Universidad Autónoma de Madrid, E-28049 Madrid, Spain
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9
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Artaud A, Magaud L, Ratter K, Gilles B, Guisset V, David P, Martinez JI, Martin-Gago JA, Chapelier C, Coraux J. Size-Selective Carbon Clusters as Obstacles to Graphene Growth on a Metal. NANO LETTERS 2018; 18:4812-4820. [PMID: 29975539 DOI: 10.1021/acs.nanolett.8b01379] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Chemical vapor deposition (CVD) on metals is so far the best suited method to produce high-quality, large-area graphene. We discovered an unprecedentedly large family of small size-selective carbon clusters that form together with graphene during CVD. Using scanning tunneling microscopy (STM) and density functional theory (DFT), we unambiguously determine their atomic structure. For that purpose, we use grids based on a graphene moiré and a dilute atomic lattice that unambiguously reveal the binding geometry of the clusters. We find that the observed clusters bind in metastable configurations on the substrate, while the thermodynamically stable configurations are not observed. We argue that the clusters are formed under kinetic control and establish that the evolution of the smallest clusters is blocked. They are hence products of surface reactions in competition with graphene growth, rather than intermediary species to the formation of extended graphene, as often assumed in the literature. We expect such obstacles to the synthesis of perfect graphene to be ubiquitous on a variety of metallic surfaces.
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Affiliation(s)
- Alexandre Artaud
- Univ. Grenoble Alpes, CEA, INAC, PHELIQS , 38000 Grenoble , France
- Univ. Grenoble Alpes, CNRS, Grenoble INP, Institut NEEL , 38000 Grenoble , France
| | - Laurence Magaud
- Univ. Grenoble Alpes, CNRS, Grenoble INP, Institut NEEL , 38000 Grenoble , France
| | - Kitti Ratter
- Univ. Grenoble Alpes, CNRS, Grenoble INP, Institut NEEL , 38000 Grenoble , France
- Univ. Grenoble Alpes, CNRS, Grenoble INP, SIMAP , 38000 Grenoble , France
| | - Bruno Gilles
- Univ. Grenoble Alpes, CNRS, Grenoble INP, Institut NEEL , 38000 Grenoble , France
- Univ. Grenoble Alpes, CNRS, Grenoble INP, SIMAP , 38000 Grenoble , France
| | - Valérie Guisset
- Univ. Grenoble Alpes, CNRS, Grenoble INP, Institut NEEL , 38000 Grenoble , France
| | - Philippe David
- Univ. Grenoble Alpes, CNRS, Grenoble INP, Institut NEEL , 38000 Grenoble , France
| | - Jose Ignacio Martinez
- Materials Science Factory , Instituto de Ciencia de Materiales de Madrid-CSIC , C/Sor Juana Inés de la Cruz 3 , Madrid 28049 , Spain
| | - Jose Angel Martin-Gago
- Materials Science Factory , Instituto de Ciencia de Materiales de Madrid-CSIC , C/Sor Juana Inés de la Cruz 3 , Madrid 28049 , Spain
| | - Claude Chapelier
- Univ. Grenoble Alpes, CEA, INAC, PHELIQS , 38000 Grenoble , France
| | - Johann Coraux
- Univ. Grenoble Alpes, CNRS, Grenoble INP, Institut NEEL , 38000 Grenoble , France
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10
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Zobač V, Lewis JP, Jelínek P. Non-adiabatic molecular dynamic simulations of opening reaction of molecular junctions. NANOTECHNOLOGY 2016; 27:285202. [PMID: 27255903 DOI: 10.1088/0957-4484/27/28/285202] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
We report non-adiabatic molecular dynamic simulations of the ring opening reaction of diarylethene (DAE) derivative molecules, both free standing and embedded between gold electrodes. Simulations are performed by the surface hopping method employing density functional theory. Typically, the free-standing molecules exhibit large quantum yields to open and close; however the process is quenched for the molecules embedded between electrodes. Our simulations reveal the importance of the DAE side chemical groups, which explain the efficiency of the quenching process. Namely, delocalization of the LUMO state contributes to electronic coupling between the molecule and electrodes, suppressing or enhancing the reaction process. The simulations indicate that a proper choice of the chemical side group, which provides the strong localization of the LUMO state, can substantially diminish the quenching mechanism. Additionally, we analyze a strong dependency of the quantum yield of the opening reaction coming from the mechanical strength of the molecules.
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Affiliation(s)
- Vladmír Zobač
- Institute of Physic, Academy of Sciences of the Czech Republic, Cukrovarnická 10, CZ-16200, Prague, Czech Republic. Department of Physical Electronics, Faculty of Nuclear Sciences and Physical Engineering, Czech Technical University in Prague, Břehová 10, CZ-11519, Prague, Czech Republic
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11
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Rangan S, Ruggieri C, Bartynski R, Martínez JI, Flores F, Ortega J. Densely-packed ZnTPPs Monolayer on the Rutile TiO 2(110)-(1×1) Surface: Adsorption Behavior and Energy Level Alignment. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2016; 120:4430-4437. [PMID: 26998188 PMCID: PMC4793616 DOI: 10.1021/acs.jpcc.5b12736] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The adsorption of a densely packed Zinc(II) tetraphenylporphyrin monolayer on a rutile TiO2(110)-(1×1) surface has been studied using a combination of experimental and theoretical methods, aimed at analyzing the relation between adsorption behavior and barrier height formation. The adsorption configuration of ZnTPP was determined from scanning tunnel microscopy (STM) imaging, density functional theory (DFT) calculations and STM image simulation. The corresponding energy alignment was experimentally determined from X-ray and UV-photoemission spectroscopies and inverse photoemission spectroscopy. These results were found in good agreement with an appropriately corrected DFT model, pointing to the importance of local bonding and intermolecular interactions in the establishment of barrier heights.
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Affiliation(s)
- Sylvie Rangan
- Dept. Physics and Astronomy, and Laboratory for Surface Modification, Rutgers, The State University of New Jersey, Piscataway, NJ 08854-8019 (USA)
| | - Charles Ruggieri
- Dept. Physics and Astronomy, and Laboratory for Surface Modification, Rutgers, The State University of New Jersey, Piscataway, NJ 08854-8019 (USA)
| | - Robert Bartynski
- Dept. Physics and Astronomy, and Laboratory for Surface Modification, Rutgers, The State University of New Jersey, Piscataway, NJ 08854-8019 (USA)
| | - José Ignacio Martínez
- Dept. Surfaces, Coatings and Molecular Astrophysics, Institute of Materials Science of Madrid (ICMM-CSIC), Sor Juana Inés de la Cruz 3, E-28049 Madrid (Spain)
| | - Fernando Flores
- Dept. Física Teórica de la Materia Condensada and Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, ES-28049 Madrid (Spain)
| | - José Ortega
- Dept. Física Teórica de la Materia Condensada and Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, ES-28049 Madrid (Spain)
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12
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Mendieta-Moreno JI, Walker RC, Lewis JP, Gómez-Puertas P, Mendieta J, Ortega J. fireball/amber: An Efficient Local-Orbital DFT QM/MM Method for Biomolecular Systems. J Chem Theory Comput 2015; 10:2185-93. [PMID: 26580543 DOI: 10.1021/ct500033w] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In recent years, quantum mechanics/molecular mechanics (QM/MM) methods have become an important computational tool for the study of chemical reactions and other processes in biomolecular systems. In the QM/MM technique, the active region is described by means of QM calculations, while the remainder of the system is described using a MM approach. Because of the complexity of biomolecules and the desire to achieve converged sampling, it is important that the QM method presents a good balance between accuracy and computational efficiency. Here, we report on the implementation of a QM/MM technique that combines a DFT approach specially designed for the study of complex systems using first-principles molecular dynamics simulations (fireball) with the amber force fields and simulation programs. We also present examples of the application of this QM/MM approach to three representative biomolecular systems: the analysis of the effect of electrostatic embedding in the behavior of a salt bridge between an aspartic acid and a lysine residue, a study of the intermediate states for the triosephosphate isomerase catalyzed conversion of dihydroxyacetone phosphate into glyceraldehyde 3-phosphate, and the detailed description, using DFT QM/MM molecular dynamics, of the cleavage of a phosphodiester bond in RNA catalyzed by the enzyme RNase A.
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Affiliation(s)
- Jesús I Mendieta-Moreno
- Departamento de Física Teórica de la Materia Condensada and Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid , ES-28049 Madrid, Spain.,Molecular Modelling Group, Center of Molecular Biology "Severo Ochoa" (CSIC- UAM) , ES-28049 Madrid, Spain.,Biomol-Informatics SL, Campus UAM, ES-28049 Madrid, Spain
| | - Ross C Walker
- San Diego Supercomputer Center and Department of Chemistry and Biochemistry, University of California-San Diego, La Jolla, California 92093, United States
| | - James P Lewis
- Department of Physics, West Virginia University , Morgantown, West Virginia 26506-6315, United States
| | - Paulino Gómez-Puertas
- Molecular Modelling Group, Center of Molecular Biology "Severo Ochoa" (CSIC- UAM) , ES-28049 Madrid, Spain
| | - Jesús Mendieta
- Molecular Modelling Group, Center of Molecular Biology "Severo Ochoa" (CSIC- UAM) , ES-28049 Madrid, Spain.,Biomol-Informatics SL, Campus UAM, ES-28049 Madrid, Spain
| | - José Ortega
- Departamento de Física Teórica de la Materia Condensada and Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid , ES-28049 Madrid, Spain
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13
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Mendieta-Moreno JI, Marcos-Alcalde I, Trabada DG, Gómez-Puertas P, Ortega J, Mendieta J. A Practical Quantum Mechanics Molecular Mechanics Method for the Dynamical Study of Reactions in Biomolecules. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2015; 100:67-88. [PMID: 26415841 DOI: 10.1016/bs.apcsb.2015.06.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Quantum mechanics/molecular mechanics (QM/MM) methods are excellent tools for the modeling of biomolecular reactions. Recently, we have implemented a new QM/MM method (Fireball/Amber), which combines an efficient density functional theory method (Fireball) and a well-recognized molecular dynamics package (Amber), offering an excellent balance between accuracy and sampling capabilities. Here, we present a detailed explanation of the Fireball method and Fireball/Amber implementation. We also discuss how this tool can be used to analyze reactions in biomolecules using steered molecular dynamics simulations. The potential of this approach is shown by the analysis of a reaction catalyzed by the enzyme triose-phosphate isomerase (TIM). The conformational space and energetic landscape for this reaction are analyzed without a priori assumptions about the protonation states of the different residues during the reaction. The results offer a detailed description of the reaction and reveal some new features of the catalytic mechanism. In particular, we find a new reaction mechanism that is characterized by the intramolecular proton transfer from O1 to O2 and the simultaneous proton transfer from Glu 165 to C2.
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Affiliation(s)
- Jesús I Mendieta-Moreno
- Departamento de Física Teórica de la Materia Condensada and Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, Madrid, Spain; Molecular Modelling Group, Center of Molecular Biology "Severo Ochoa" (CSIC-UAM), Madrid, Spain
| | - Iñigo Marcos-Alcalde
- Molecular Modelling Group, Center of Molecular Biology "Severo Ochoa" (CSIC-UAM), Madrid, Spain
| | - Daniel G Trabada
- Departamento de Física Teórica de la Materia Condensada and Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, Madrid, Spain
| | - Paulino Gómez-Puertas
- Molecular Modelling Group, Center of Molecular Biology "Severo Ochoa" (CSIC-UAM), Madrid, Spain
| | - José Ortega
- Departamento de Física Teórica de la Materia Condensada and Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, Madrid, Spain.
| | - Jesús Mendieta
- Molecular Modelling Group, Center of Molecular Biology "Severo Ochoa" (CSIC-UAM), Madrid, Spain; Biomol-Informatics SL, Campus UAM, Madrid, Spain
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14
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Zobač V, Lewis JP, Abad E, Mendieta-Moreno JI, Hapala P, Jelínek P, Ortega J. Photo-induced reactions from efficient molecular dynamics with electronic transitions using the FIREBALL local-orbital density functional theory formalism. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2015; 27:175002. [PMID: 25791682 DOI: 10.1088/0953-8984/27/17/175002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The computational simulation of photo-induced processes in large molecular systems is a very challenging problem. Firstly, to properly simulate photo-induced reactions the potential energy surfaces corresponding to excited states must be appropriately accessed; secondly, understanding the mechanisms of these processes requires the exploration of complex configurational spaces and the localization of conical intersections; finally, photo-induced reactions are probability events, that require the simulation of hundreds of trajectories to obtain the statistical information for the analysis of the reaction profiles. Here, we present a detailed description of our implementation of a molecular dynamics with electronic transitions algorithm within the local-orbital density functional theory code FIREBALL, suitable for the computational study of these problems. As an example of the application of this approach, we also report results on the [2 + 2] cycloaddition of ethylene with maleic anhydride and on the [2 + 2] photo-induced polymerization reaction of two C60 molecules. We identify different deactivation channels of the initial electron excitation, depending on the time of the electronic transition from LUMO to HOMO, and the character of the HOMO after the transition.
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Affiliation(s)
- Vladimír Zobač
- Institute of Physic, Academy of Sciences of the Czech Republic, Cukrovarnická 10, CZ-16200 Prague, Czech Republic. Department of Physical Electronics, Faculty of Nuclear Sciences and Physical Engineering, Czech Technical University in Prague, Czech Republic
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15
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Neukirch AJ, Park J, Zobac V, Wang H, Jelinek P, Prezhdo OV, Zhou HC, Lewis JP. Calculated photo-isomerization efficiencies of functionalized azobenzene derivatives in solar energy materials: azo-functional organic linkers for porous coordinated polymers. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2015; 27:134208. [PMID: 25767112 DOI: 10.1088/0953-8984/27/13/134208] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Recently, we used a local orbital density functional theory code called FIREBALL, to study the photoisomerization process in azobenzene derivatives for solar energy materials. Azobenzene functional groups undergo photoisomerization upon light irradiation or application of heat. Zhou et al (2012 J. Am. Chem. Soc. 134 99-102) showed that these azobenzenes can then be introduced into metal-organic frameworks via an organic linker in order to create a reversible switch for CO2 adsorption. In this manuscript, we examined how the addition of organic linkers (isophthalic acid) changes the relaxation times, isomerization mechanism, and quantum yield for both the cis↔trans pathways. We then tuned these properties by substituting functional groups, finding an increase in quantum yield as well as improved optical properties.
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Affiliation(s)
- Amanda J Neukirch
- Department of Physics and Astronomy, University of Rochester, Rochester, NY 14627, USA
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16
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Bazarnik M, Jurczyszyn L, Czajka R, Morgenstern K. Mechanism of a molecular photo-switch adsorbed on Si(100). Phys Chem Chem Phys 2015; 17:5366-71. [DOI: 10.1039/c4cp04353g] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We present a combined scanning tunneling microscopy and density functional theory study of a compact molecular photoswitch on a Si(100) surface.
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Affiliation(s)
- Maciej Bazarnik
- Institute of Physics
- Poznan University of Technology
- 60-965 Poznan
- Poland
- Insitute of Applied Physics and Interdisciplinary Nanoscience Center Hamburg
| | - Leszek Jurczyszyn
- Institute of Experimental Physics
- University of Wroclaw
- 50-204 Wroclaw
- Poland
| | - Ryszard Czajka
- Institute of Physics
- Poznan University of Technology
- 60-965 Poznan
- Poland
| | - Karina Morgenstern
- Chair of Physical Chemistry I
- Ruhr-Universität Bochum
- D-44801 Bochum
- Germany
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17
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Fang YW, Ding HC, Tong WY, Zhu WJ, Shen X, Gong SJ, Wan XG, Duan CG. First-principles studies of multiferroic and magnetoelectric materials. Sci Bull (Beijing) 2015. [DOI: 10.1007/s11434-014-0628-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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18
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Racis A, Jurczyszyn L, Bazarnik M, Koczorowski W, Wykrota A, Czajka R, Radny MW. Self-organisation of inorganic elements on Si(001) mediated by pre-adsorbed organic molecules. Phys Chem Chem Phys 2015; 17:23783-94. [DOI: 10.1039/c5cp02894a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
A combined theoretical and experimental study on the adsorption of an isolated benzonitrile molecule on the Si(001) surface, followed by the adsorption of Al (group III), Pb (carbon group) and Ag (transition metal) is presented.
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Affiliation(s)
- A. Racis
- Institute of Experimental Physics
- University of Wrocław
- 50-204 Wrocław
- Poland
| | - L. Jurczyszyn
- Institute of Experimental Physics
- University of Wrocław
- 50-204 Wrocław
- Poland
| | - M. Bazarnik
- Institute of Physics
- Poznań University of Technology
- 60-965 Poznań
- Poland
- Department of Physics
| | - W. Koczorowski
- Institute of Physics
- Poznań University of Technology
- 60-965 Poznań
- Poland
| | - A. Wykrota
- Institute of Physics
- Poznań University of Technology
- 60-965 Poznań
- Poland
| | - R. Czajka
- Institute of Physics
- Poznań University of Technology
- 60-965 Poznań
- Poland
| | - M. W. Radny
- Institute of Physics
- Poznań University of Technology
- 60-965 Poznań
- Poland
- School of Mathematical and Physical Sciences
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19
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Viciano-Chumillas M, Li D, Smogunov A, Latil S, Dappe YJ, Barreteau C, Mallah T, Silly F. Tailoring the structure of two-dimensional self-assembled nanoarchitectures based on ni(ii) -salen building blocks. Chemistry 2014; 20:13566-75. [PMID: 25225027 DOI: 10.1002/chem.201403169] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2014] [Revised: 06/16/2014] [Indexed: 11/09/2022]
Abstract
The synthesis of a series of Ni(II) -salen-based complexes with the general formula of [Ni(H2 L)] (H4 L=R(2) -N,N'-bis[R(1) -5-(4'-benzoic acid)salicylidene]; H4 L1: R(2) =2,3-diamino-2,3-dimethylbutane and R(1) =H; H4 L2: R(2) =1,2-diaminoethane and R(1) =tert-butyl and H4 L3: R(2) =1,2-diaminobenzene and R(1) =tert-butyl) is presented. Their electronic structure and self-assembly was studied. The organic ligands of the salen complexes are functionalized with peripheral carboxylic groups for driving molecular self-assembly through hydrogen bonding. In addition, other substituents, that is, tert-butyl and diamine bridges (2,3-diamino-2,3-dimethylbutane, 1,2-diaminobenzene or 1,2-diaminoethane), were used to tune the two-dimensional (2D) packing of these building blocks. Density functional theory (DFT) calculations reveal that the spatial distribution of the LUMOs is affected by these substituents, in contrast with the HOMOs, which remain unchanged. Scanning tunneling microscopy (STM) shows that the three complexes self-assemble into three different 2D nanoarchitectures at the solid-liquid interface on graphite. Two structures are porous and one is close-packed. These structures are stabilized by hydrogen bonds in one dimension, while the 2D interaction is governed by van der Waals forces and is tuned by the nature of the substituents, as confirmed by theoretical calculations. As expected, the total dipolar moment is minimized.
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Affiliation(s)
- Marta Viciano-Chumillas
- Institute of Chemistry and Molecular Materials of Orsay, University of Paris Sud 11, 91405 Orsay (France)
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20
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Beltrán J, Flores F, Ortega J. The role of charge transfer in the energy level alignment at the pentacene/C60 interface. Phys Chem Chem Phys 2014; 16:4268-74. [PMID: 24452709 DOI: 10.1039/c3cp55004d] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Understanding the mechanism of energy level alignment at organic-organic interfaces is a crucial line of research to optimize applications in organic electronics. We address this problem for the C60-pentacene interface by performing local-orbital Density Functional Theory (DFT) calculations, including the effect of the charging energies on the energy gap of both organic materials. The results are analyzed within the induced density of interface states (IDIS) model. We find that the induced interface potential is in the range of 0.06-0.10 eV, in good agreement with the experimental evidence, and that such potential is mainly induced by the small, but non-negligible, charge transfer between the two compounds and the multipolar contribution associated with pentacene. We also suggest that an appropriate external intercompound potential could create an insulator-metal transition at the interface.
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Affiliation(s)
- J Beltrán
- Depto. de Física Teórica de la Materia Condensada and Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, 28049-Madrid, Spain.
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21
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Dappe YJ, González C, Cuevas JC. Carbon tips for all-carbon single-molecule electronics. NANOSCALE 2014; 6:6953-6958. [PMID: 24838986 DOI: 10.1039/c4nr00516c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
We present here an exhaustive ab initio study of the use of carbon-based tips as electrodes in single-molecule junctions. Motivated by recent experiments, we show that carbon tips can be combined with other carbon nanostructures, such as graphene, to form all-carbon molecular junctions with molecules like benzene or C60. Our results show that the use of carbon tips can lead to relatively conductive molecular junctions. However, contrary to junctions formed with standard metals, the conductance traces recorded during the formation of the all-carbon single-molecule junctions do not exhibit clear conductance plateaus, which can be attributed to the inability of the hydrogenated carbon tips to form chemical bonds with the organic molecules. Additionally, we explore here the use of carbon tips for scanning tunneling microscopy and show that they are well suited for obtaining sample images with atomic resolution.
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Affiliation(s)
- Y J Dappe
- Service de Physique de l'Etat Condensé (CNRS URA2464), IRAMIS, CEA Saclay, 91191 Gif-Sur-Yvette, France.
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22
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Wang L, Wang H, Liu F, Zheng A, Zhang J, Sun Q, Lewis JP, Zhu L, Meng X, Xiao FS. Selective catalytic production of 5-hydroxymethylfurfural from glucose by adjusting catalyst wettability. CHEMSUSCHEM 2014; 7:402-406. [PMID: 24399510 DOI: 10.1002/cssc.201301076] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Revised: 10/27/2013] [Indexed: 06/03/2023]
Abstract
The development of highly-efficient catalysts for conversion of glucose and fructose to 5-hydroxymethylfurfural (HMF) is of great importance. In this work, theoretical simulations form the basis for rational design and synthesis of a superhydrophobic mesoporous acid, that can completely prevent HMF hydration, giving HMF as sole product from full conversion of fructose. Interestingly, the combined superhydrophobic solid acid and superhydrophilic solid base catalysts are very efficient for one-pot conversion of glucose to HMF, giving a yield as high as 95.4 %. The excellent catalytic data in the conversion of glucose to HMF is attributed to the unique wettabilities of the solid acid and base catalysts.
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Affiliation(s)
- Liang Wang
- Key Laboratory of Applied Chemistry of Zhejiang Province, Zhejiang University, Hangzhou 310028 (PR China)
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23
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Greene-Diniz G, Jones SLT, Fagas G, Haverty M, Lacambra CM, Shankar S, Greer JC. Divacancies in carbon nanotubes and their influence on electron scattering. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2014; 26:045303. [PMID: 24592478 DOI: 10.1088/0953-8984/26/4/045303] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
First-principles calculations are applied to study the formation energies of various divacancy defects in armchair and zigzag carbon nanotubes of varying diameter, and the transport properties for the corresponding structures. Our explicit ab initio calculations confirm that the lateral 585 divacancy is the most stable defect in small diameter tubes, with the 555 777 divacancy becoming more stable in armchair tubes larger than (30, 30). Evaluating the electron transmission as a function of diameter and chirality for a range of defects, the strongest scattering is found for the 555 777 divacancy configuration, which is observable in electrical spectroscopy experiments. Finally, validation of an approximation relating contributions from independent scattering sites enables the study of the characteristic localization length in large diameter tubes. Despite the fixed number of channels, localization lengths increase with increasing diameter and can exceed 100 nm for typical defect densities.
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24
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Neukirch AJ, Shamberger LC, Abad E, Haycock BJ, Wang H, Ortega J, Prezhdo OV, Lewis JP. Nonadiabatic Ensemble Simulations of cis-Stilbene and cis-Azobenzene Photoisomerization. J Chem Theory Comput 2013; 10:14-23. [PMID: 26579888 DOI: 10.1021/ct4009816] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Amanda J. Neukirch
- Department of Physics
and Astronomy, University of Rochester, Rochester, New York 14627, United States
- Department of Physics and Astronomy, West Virginia University, Morgantown, West Virginia 26506-6315, United States
| | - Logan C. Shamberger
- Department of Physics and Astronomy, West Virginia University, Morgantown, West Virginia 26506-6315, United States
| | - Enrique Abad
- Computational Biochemistry Group, Institute of Theoretical Chemistry, University of Stuttgart, 70569 Stuttgart, Germany
| | - Barry J. Haycock
- Department of Physics and Astronomy, West Virginia University, Morgantown, West Virginia 26506-6315, United States
| | - Hong Wang
- Department of Physics and Astronomy, West Virginia University, Morgantown, West Virginia 26506-6315, United States
| | - José Ortega
- Departmento de Física Teórica de la Materia Condensada and Conensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, Madrid 28049, Spain
| | - Oleg V. Prezhdo
- Department of Physics
and Astronomy, University of Rochester, Rochester, New York 14627, United States
- Department of Chemistry, University of Rochester, Rochester, New York 14627, United States
| | - James P. Lewis
- Department of Physics and Astronomy, West Virginia University, Morgantown, West Virginia 26506-6315, United States
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25
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Martínez JI, Abad E, Beltrán JI, Flores F, Ortega J. Barrier height formation in organic blends/metal interfaces: Case of tetrathiafulvalene-tetracyanoquinodimethane/Au(111). J Chem Phys 2013; 139:214706. [DOI: 10.1063/1.4836635] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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26
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Abad E, Zenn RK, Kästner J. Reaction Mechanism of Monoamine Oxidase from QM/MM Calculations. J Phys Chem B 2013; 117:14238-46. [DOI: 10.1021/jp4061522] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Enrique Abad
- Computational Biochemistry
Group, Institute of Theoretical Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Roland K. Zenn
- Computational Biochemistry
Group, Institute of Theoretical Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Johannes Kästner
- Computational Biochemistry
Group, Institute of Theoretical Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
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27
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Abad E, Lewis JP, Zobač V, Hapala P, Jelínek P, Ortega J. Calculation of non-adiabatic coupling vectors in a local-orbital basis set. J Chem Phys 2013; 138:154106. [DOI: 10.1063/1.4801511] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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28
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Gómez-Carrillo SC, Bolcatto PG. Exploring the T-Θ phase diagram of S adsorbed on Au(111) substrate on the Θ = 0.5 ML line. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2013; 25:045005. [PMID: 23232454 DOI: 10.1088/0953-8984/25/4/045005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Theoretical results for the adsorption of half of a monolayer of S on Au(111) are presented. The simulations were made using a density functional theory (DFT) tight binding approach combined with classical molecular dynamics at 800, 500, 300, 150 and 1 K. By considering a minimal (2 × √3) unit cell, two stable adsorbed phases are found: a dimeric one and another forming a rhomboidal structure depending on the preparation of the sample at high temperatures. Optimized calculations at T = 0 K indicate that the stability of the dimeric phase is due to the increase of the binding energies between sulfur atoms. Enforcing previous results (Gómez-Carrillo et al 2011 Phys. Chem. Chem. Phys. 13 461) it is verified that at high temperatures (T > 300 K) sulfur atoms have a high mobility which allows migration among different adsorption sites. The mobility decreases with the temperature and, as in the previous work, a thermal barrier of 25-30 meV is found. On enlarging the unit cell new agglomerates are found, in good agreement with experimental data.
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Affiliation(s)
- S C Gómez-Carrillo
- Departamento de Física, Facultad de Ingeniería Química, Universidad Nacional del Litoral, Santiago del Estero 2829 S3000AOM Santa Fe, Argentina.
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29
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Computing the Properties of Materials from First Principles with SIESTA. STRUCTURE AND BONDING 2012. [DOI: 10.1007/b97943] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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30
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Pieczyrak B, Abad E, Flores F, Ortega J. Charging energy and barrier height of pentacene on Au(111): A local-orbital hybrid-functional density functional theory approach. J Chem Phys 2011; 135:084702. [DOI: 10.1063/1.3626522] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
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31
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Sanati M, Albers RC, Lookman T, Saxena A. First-principles study of stability of the bcc and ω phases of a low Al concentration Nb1-xAlx alloy. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2011; 23:295501. [PMID: 21727310 DOI: 10.1088/0953-8984/23/29/295501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The phase stability and site occupancy of bcc (body centered cubic) Nb(5)Al and slightly rearranged atomic structures have been examined by means of first-principles calculations. In order to use first-principles methods, a periodic cell is required and we used ordered Nb(5)Al compounds as a tractable example of a low Al concentration Nb(1 - x)Al(x) alloy (in this case, for about 17 at.% Al). The instability against an ω-structure atomic displacement was also studied, since this structure is detrimental to ductility. Mulliken population analysis was used to provide an understanding of the hybridization between the atoms and the electronic origin of the site occupancy and instability of the underlying bcc structures. By making calculations for several different configurations of the Nb-Al system we estimated the strengths of the Nb-Nb and Nb-Al bonds. It is shown that the stability of the underlying bcc phases is directly related to Nb-Nb and Nb-Al first-nearest-neighbor interactions. The first-principles calculations were extended to finite temperature by including various contributions to the free energy. In particular, the vibrational free energy was calculated within the quasiharmonic approximation, and it is shown that the contribution of the low energy modes to the lattice entropy helps to stabilize ordered bcc phases against ω-type phase transformations. Semi-quasi-random structures were employed to study the stability of the ordered and disordered bcc phases. Our study showed, in agreement with experiment, that the ω, ordered, and disordered phases can coexist in a nonequilibrium state at finite temperature.
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Affiliation(s)
- M Sanati
- Physics Department, Texas Tech University, Lubbock, TX 79409, USA
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32
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Frauenheim T, Porezag D, Elstner M, Jungnickel G, Elsner J, Haugk M, Sieck A, Seifert G. An ab initio two-center tight-binding approach to simulations of complex materials properties. ACTA ACUST UNITED AC 2011. [DOI: 10.1557/proc-491-91] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
ABSTRACTWe describe theab initioconstruction of two-center tight-binding (TB) hamiltonians, which at a properly chosen input density upon non-selfconsistent solution of the related Kohn-Sham equations transform the energy within density-functional theory (DFT) into a tight-bindinglike expression. In cases, where the electron density of the interacting many-atom structure in good approximation may be represented as a sum of atomic-like densities, the method has been shown to operate highly transferable, being particularly successful in determining the properties of low-energy silicon clusters, in predicting the structure and vibrational signatures of fullerene oligomers, amorphous carbons and carbon nitrides and in simulating elementary growth reactions on diamond surfaces. The uncertainties within the standard non-SCF DF-TB-variant, however, increase if the chemical bonding is controlled by a delicate charge balance between different atomic constituents, as e.g. in organic molecules and in polar semiconductors. Therefore, we extend the standard TB-approach to the operation in a selfconsistent-charge mode(SCC-DFTB)in order to improve total energies, forces, and transferability in the presence of considerable long-range Coulomb interactions. By using a variational technique, we derive a transparent and readily calculable expression for the iterative modification of Hamiltonian matrix elements and show, that the final energy is a second order approximation to the total energy in density-functional theory,see M. Elstner et al., this Symposium.First successful applications to surface studies of GaAs and dislocation modeling in GaN will be presented.
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33
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Ashraf MK, Bruque NA, Tan JL, Beran GJO, Lake RK. Conductance switching in diarylethenes bridging carbon nanotubes. J Chem Phys 2011; 134:024524. [DOI: 10.1063/1.3528118] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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34
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Gómez-Carrillo SC, Bolcatto PG. Coexistence of √3 × √3 and quasi-linear phases of sulfur adsorbed (Θ = 1/3) on a gold (111) substrate. Phys Chem Chem Phys 2011; 13:461-6. [DOI: 10.1039/c0cp00534g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Kamiński W, Rozsíval V, Jelínek P. Theoretical study of electronic and transport properties of PPy-Pt(111) and PPy-C(111):H interfaces. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2010; 22:045003. [PMID: 21386305 DOI: 10.1088/0953-8984/22/4/045003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
We present a first-principles study of promising hybrid organic-inorganic interface systems consisting of a polypyrrole (PPy) chain sandwiched between metallic Pt(111) or hydrogen-terminated diamond C(111):H electrodes. We combine ab initio density-functional-theory total energy calculations, Green's function approach and the complex band-structure method in order to determine electronic and transport properties of those organic-semiconductor/metal (semiconductor) interfaces. We analyze one- and multi-bond nanocontact formation including structural modification (H desorption) as well as PPy length dependence. For selected ground state configurations of the considered interface systems we study their energetics and structural properties. Through the analysis of the local density of states, in particular isosurfaces of the charge density, the mechanism of the charge transfer and the charge neutrality levels are determined. The voltage dependence of the electrical conductance and the I-V characteristics are compared to the transport properties based on the complex band-structure method. The obtained results support recent experiments, where PPy nanowires are formed via electrochemical synthesis and placed between platinum or diamond microelectrodes.
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Affiliation(s)
- Wojciech Kamiński
- Institute of Experimental Physics, University of Wrocław, Wrocław, Poland.
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36
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Navrotsky A. Thermodynamics of solid electrolytes and related oxide ceramics based on the fluorite structure. ACTA ACUST UNITED AC 2010. [DOI: 10.1039/c0jm01521k] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Flores F, Ortega J, Vázquez H. Modelling energy level alignment at organic interfaces and density functional theory. Phys Chem Chem Phys 2009; 11:8658-75. [PMID: 20449007 DOI: 10.1039/b902492c] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A review of our theoretical understanding of the band alignment at organic interfaces is presented with particular emphasis on the metal/organic (MO) case. The unified IDIS (induced density of interface states) and the ICT (integer charge transfer) models are reviewed and shown to describe qualitatively and semiquantitatively the barrier height formation at those interfaces. The IDIS model, governed by the organic CNL (charge neutrality level) and the interface screening includes: (a) charge transfer across the interface; (b) the "pillow" (or Pauli) effect associated with the compression of the metal wavefunction tails; and (c) the molecular dipoles. We argue that the ICT-model can be described as a limiting case of the unified IDIS-model for weak interface screening. For a fully quantitative understanding of the band alignment at organic interfaces, use of DFT (density functional theory) or quantum chemistry methods is highly desirable. In this Perspective review, we concentrate our discussion on DFT and show that conventional LDA or GGA calculations are limited by the "energy gap problem of the organic materials", because the LDA (or GGA) Kohn-Sham energy levels have to be corrected by the self-interaction energy of the corresponding wavefunction, to provide the appropriate molecule transport energy gap. Image potential and polarization effects at MO interfaces tend to cancel these self-interaction corrections; in particular, we show that for organic molecules lying flat on Cu and Ag, these cancellations are so strong that we can rely on conventional DFT to calculate their interface properties. For Au, however, the cancellations are weaker making it necessary to go beyond conventional DFT. We discuss several alternatives beyond conventional LDA or GGA. The most accurate approach is the well-known GW-technique, but its use is limited by its high demanding computer time. In a very simple approach one can combine conventional DFT with a "scissor" operator which incorporates self-interaction corrections and polarization effects in the organic energy levels. Hybrid potentials combined with conventional DFT represent, probably, the best alternative for having a simple and accurate approach for analyzing organic interfaces. The problem then is to find an appropriate one for both the metal and the organic material in a plane-wave formulation; we show, however, how to overcome this difficulty using a local-orbital basis formulation. As examples of these alternatives, we present some DFT-calculations for several organic interfaces, using either the scissor operator or a hybrid potential, which can be interpreted in terms of the unified IDIS-model.
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Affiliation(s)
- F Flores
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, 28049, Spain.
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38
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Romero MA, Gómez-Carrillo SC, Bolcatto PG, Goldberg EC. Spin fluctuation effects on the conductance through a single Pd atom contact. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2009; 21:215602. [PMID: 21825551 DOI: 10.1088/0953-8984/21/21/215602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
A controversy about the conductance through single atoms still exists. There are many experiments where values lower than the quantum unity G(0) = 2e(2)/h have been found associated to Kondo regimes with high Kondo temperatures. Specifically in the Pd single atom contact, conductance values close to G(0)/2 at room temperature have been reported. In this work we propose a theoretical analysis of a break junction of Pd where the charge fluctuation in the single atom contact is limited to the most probable one: [Formula: see text]. The projected density of states and the characteristics of the electron transport are calculated by using a realistic description of the interacting system. A Kondo regime is found where the conductance values and their dependence on temperature are in good agreement with the experimental trends observed in the conduction of single molecule transistors based on transition metal coordination complexes.
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Affiliation(s)
- M A Romero
- Instituto de Desarrollo Tecnológico para la Industria Química (INTEC), Universidad Nacional del Litoral, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Güemes 3450 CC 91, 3000 Santa Fe, Argentina
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Pieczyrak B, González C, Jelínek P, Pérez R, Ortega J, Flores F. Mechanical and electrical properties of stretched clean and H-contaminated Pd-nanowires. NANOTECHNOLOGY 2008; 19:335711. [PMID: 21730637 DOI: 10.1088/0957-4484/19/33/335711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
We analyze theoretically the formation of stretched Pd-nanowires and their interaction with hydrogen. In our approach, we simulate the nanowire stretching process using a first-principles molecular-dynamics method to obtain realistic atomic geometries of the contact in its final stages before the nanowire breaks. The electrical conductance of the nanowire is also calculated at each point of the deformation path. For the clean Pd-nanowire in the last stages of the deformation process we find that the nanowire develops, first, a one-atom-neck and, at the end, a dimer whose bond is finally broken. For these atomic configurations, the calculated electrical conductances are in good agreement with the experimental evidence. The interaction with hydrogen is analyzed adsorbing one or two H atoms on the Pd-nanowire for different configurations along the stretching process. In the case of one H atom we obtain geometries with conductances in the range 0.8-1.4G(0), while for two H atoms we find conductance plateaus with values ∼0.5G(0) and ∼1.0G(0). These results are in excellent agreement with the experimental evidence for nanocontact breaking in an H(2) atmosphere and indicate that the conductance peak around 0.5G(0) observed experimentally is associated with nanowires where two H atoms have been adsorbed.
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Affiliation(s)
- B Pieczyrak
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049, Spain. Institute of Experimental Physics, University of Wroclaw, plac Maksa Borna 9, 50-204 Wroclaw, Poland
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40
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Wang H, Stalnaker J, Chevreau H, Lewis JP. Potential of mean force calculations using ab initio tight-binding molecular dynamics: Application to N–NO2 bond dissociation in DMNA and HMX. Chem Phys Lett 2008. [DOI: 10.1016/j.cplett.2008.03.064] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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41
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Gusso M. Study on the maximum accuracy of the pseudopotential density functional method with localized atomic orbitals versus plane-wave basis sets. J Chem Phys 2008; 128:044102. [DOI: 10.1063/1.2821023] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Snijders PC, Moon EJ, González C, Rogge S, Ortega J, Flores F, Weitering HH. Controlled self-organization of atom vacancies in monatomic gallium layers. PHYSICAL REVIEW LETTERS 2007; 99:116102. [PMID: 17930452 DOI: 10.1103/physrevlett.99.116102] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2007] [Indexed: 05/25/2023]
Abstract
Ga adsorption on the Si(112) surface results in the formation of pseudomorphic Ga atom chains. Compressive strain in these atom chains is relieved via creation of adatom vacancies and their self-organization into meandering vacancy lines. The average spacing between these line defects can be controlled, within limits, by adjusting the chemical potential mu of the Ga adatoms. We derive a lattice model that quantitatively connects density functional theory (DFT) calculations for perfectly ordered structures with the fluctuating disorder seen in experiment and the experimental control parameter mu. This hybrid approach of lattice modeling and DFT can be applied to other examples of line defects in heteroepitaxy.
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Affiliation(s)
- P C Snijders
- Kavli Institute of NanoScience Delft, Delft University of Technology, 2628 CJ Delft, The Netherlands.
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Takahashi R, Wang H, Lewis JP. Electronic Structures and Conductivity in Peptide Nanotubes. J Phys Chem B 2007; 111:9093-8. [PMID: 17625821 DOI: 10.1021/jp0708446] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Self-assembling cyclic D,L-peptide nanotubes are electronically insulating and possess wide band gaps (E(g) > 4 eV). Our ab initio electronic structure calculations indicate that the presence of aromatic rings in the side chain of peptide nanotubes significantly reduces the band gap. We investigate the conductivity of the modified peptide nanotubes through calculations of the electron tunneling probability. The electron tunneling probability through a molecule depends on the length of the molecule, L, as e-beta(E)L, where the tunneling beta(E)-factor is strongly energy-dependent. We have calculated beta(E) in three types of peptide nanotubes that have different sequences of amino acid residue, (L-Gln, D-Ala)(4), (L-Gln, D-Leu)(4) and (L-Gln, D-Phe)(4), using the complex band structure approach. We find large beta values near midgap, making these peptide nanotubes a poor tunneling conductor.
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Affiliation(s)
- R Takahashi
- Department of Physics and Astronomy, Brigham Young University, Provo, Utah 84602, USA
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Bartlett RJ, Mcclellan J, Greer JC, Monaghan S. Quantum mechanics at the core of multi-scale simulations. ACTA ACUST UNITED AC 2006. [DOI: 10.1007/s10820-006-9018-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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45
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He J, Sankey O, Lee M, Tao N, Li X, Lindsay S. Measuring single molecule conductance with break junctions. Faraday Discuss 2006; 131:145-54; discussion 205-20. [PMID: 16512369 DOI: 10.1039/b508434m] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Single-molecule conductance measurements made under potential control provide a critical link between chemical and molecular electronic data. These measurements are made possible by the STM break-junction method introduced recently, but questions remain about its reliability. Here we report the use of a logarithmic current-to-voltage converter to examine a wide range of currents in an STM break junction study of octanedithiol, clearly showing both the gold-quantum wire regime and the single molecule conductance regime. We find two sets of molecular currents that we tentatively ascribe to different bonding geometries of the molecules in the break junction.
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Affiliation(s)
- Jin He
- Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
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Biel B, García-Vidal FJ, Rubio A, Flores F. Anderson localization in carbon nanotubes: defect density and temperature effects. PHYSICAL REVIEW LETTERS 2005; 95:266801. [PMID: 16486382 DOI: 10.1103/physrevlett.95.266801] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2005] [Indexed: 05/06/2023]
Abstract
The role of irradiation induced defects and temperature in the conducting properties of single-walled (10, 10) carbon nanotubes has been analyzed by means of a first-principles approach. We find that divacancies modify strongly the energy dependence of the differential conductance, reducing also the number of contributing channels from two (ideal) to one. A small number of divacancies (5-9) brings up strong Anderson localization effects and a seemly universal curve for the resistance as a function of the number of defects. It is also shown that low temperatures, about 15-65 K, are enough to smooth out the fluctuations of the conductance without destroying the exponential dependence of the resistivity as a function of the tube length.
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Affiliation(s)
- Blanca Biel
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, Spain
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47
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Bruque N, Pandey RR, Lake RK, Wang H, Lewis JP. Electronic transport through a CNT-Pseudopeptide-CNT hybrid material. MOLECULAR SIMULATION 2005. [DOI: 10.1080/08927020500323879] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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48
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Gómez-Navarro C, de Pablo PJ, Gómez-Herrero J, Biel B, Garcia-Vidal FJ, Rubio A, Flores F. Tuning the conductance of single-walled carbon nanotubes by ion irradiation in the Anderson localization regime. NATURE MATERIALS 2005; 4:534-9. [PMID: 15965479 DOI: 10.1038/nmat1414] [Citation(s) in RCA: 124] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2005] [Accepted: 05/10/2005] [Indexed: 05/03/2023]
Abstract
Carbon nanotubes are a good realization of one-dimensional crystals where basic science and potential nanodevice applications merge. Defects are known to modify the electrical resistance of carbon nanotubes; they can be present in as-grown carbon nanotubes, but controlling their density externally opens a path towards the tuning of the electronic characteristics of the nanotube. In this work, consecutive Ar+ irradiation doses are applied to single-walled nanotubes (SWNTs) producing a uniform density of defects. After each dose, the room-temperature resistance versus SWNT length (R(L)) along the nanotube is measured. Our data show an exponential dependence of R(L) indicating that the system is within the strong Anderson localization regime. Theoretical simulations demonstrate that mainly di-vacancies contribute to the resistance increase induced by irradiation, and that just a 0.03% of di-vacancies produces an increase of three orders of magnitude in the resistance of a SWNT of 400 nm length.
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Affiliation(s)
- C Gómez-Navarro
- Departamento de Física de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain
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González C, Snijders PC, Ortega J, Pérez R, Flores F, Rogge S, Weitering HH. Formation of atom wires on vicinal silicon. PHYSICAL REVIEW LETTERS 2004; 93:126106. [PMID: 15447286 DOI: 10.1103/physrevlett.93.126106] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2004] [Indexed: 05/24/2023]
Abstract
The feasibility of creating atomic wires on vicinal silicon surfaces via pseudomorphic step-edge decoration has been analyzed for the case of Ga on Si(112). Scanning tunneling microscopy and density functional theory calculations indicate the formation of Ga zigzag chains intersected by quasiperiodic vacancy lines or "misfit dislocations." This structure strikes a balance between the system's drive towards chemical passivation and its need for strain relaxation in the atom chains. Spatially fluctuating disorder, intrinsic to the reconstruction, originates from the two symmetry-degenerate orientations of the zigzag chains on vicinal Si.
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Affiliation(s)
- C González
- Facultad de Ciencias, Departamento de Fisica Teorica de la Materia Condensada, Universidad Autonoma de Madrid, Madrid 28049, Spain
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