Browsing by Author "Krejčí, Ondřej"

Now showing 1 - 7 of 7
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    Advancing scanning probe microscopy simulations : A decade of development in probe-particle models
    (Elsevier Science B.V., 2024-12) Oinonen, Niko; Yakutovich, Aliaksandr V.; Gallardo, Aurelio; Ondráček, Martin; Hapala, Prokop; Krejčí, Ondřej; Department of Applied Physics; Surfaces and Interfaces at the Nanoscale; Computational Electronic Structure Theory; Swiss Federal Laboratories for Materials Science and Technology; Fundacion IMDEA Nanociencia; Czech Academy of Sciences
    The Probe-Particle Model combine theories designed for the simulation of scanning probe microscopy experiments, employing non-reactive, flexible tip apices to achieve sub-molecular resolution. In the article we present the latest version of the Probe-Particle Model implemented in the open-source ppafm package, highlighting substantial advancements in accuracy, computational performance, and user-friendliness. To demonstrate this we provide a comprehensive review of approaches for simulating non-contact Atomic Force Microscopy. They vary in complexity from simple Lennard-Jones potential to the latest full density-based model. We compared those approaches with ab initio calculated references, showcasing their respective merits. All parts of the ppafm package have undergone acceleration by 1-2 orders of magnitude using OpenMP and OpenCL technologies. The updated package includes an interactive graphical user interface and seamless integration into the Python ecosystem via pip, facilitating advanced scripting and interoperability with other software. This adaptability positions ppafm as an ideal tool for high-throughput applications, including the training of machine learning models for the automatic recovery of atomic structures from nc-AFM measurements. We envision significant potential for this application in future single-molecule analysis, synthesis, and advancements in surface science in general. Additionally, we discuss simulations of other sub-molecular scanning-probe imaging techniques, such as bond-resolved scanning tunneling microscopy and kelvin probe force microscopy, all built on the robust foundation of the Probe-Particle Model. Altogether this demonstrates the broad impact of the model across diverse domains of on-surface science and molecular chemistry.
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    Differences in Molecular Adsorption Emanating from the (2 × 1) Reconstruction of Calcite(104)
    (AMERICAN CHEMICAL SOCIETY, 2023-02-23) Heggemann, Jonas; Ranawat, Yashasvi S.; Krejčí, Ondřej; Foster, Adam S.; Rahe, Philipp; Department of Applied Physics; Surfaces and Interfaces at the Nanoscale; Computational Electronic Structure Theory; Osnabrück University
    Calcite, in the natural environment the most stable polymorph of calcium carbonate (CaCO3), not only is an abundant mineral in the Earth’s crust but also forms a central constituent in the biominerals of living organisms. Intensive studies of calcite(104), the surface supporting virtually all processes, have been performed, and the interaction with a plethora of adsorbed species has been studied. Surprisingly, there is still serious ambiguity regarding the properties of the calcite(104) surface: effects such as a row-pairing or a (2 × 1) reconstruction have been reported, yet so far without physicochemical explanation. Here, we unravel the microscopic geometry of calcite(104) using high-resolution atomic force microscopy (AFM) data acquired at 5 K combined with density functional theory (DFT) and AFM image calculations. A (2 × 1) reconstruction of a pg-symmetric surface is found to be the thermodynamically most stable form. Most importantly, a decisive impact of the (2 × 1) reconstruction on adsorbed species is revealed for carbon monoxide.
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    Electrostatic Discovery Atomic Force Microscopy
    (AMERICAN CHEMICAL SOCIETY, 2022-01-25) Oinonen, Niko; Xu, Chen; Alldritt, Benjamin; Canova, Filippo Federici; Urtev, Fedor; Cai, Shuning; Krejčí, Ondřej; Kannala, Juho; Liljeroth, Peter; Foster, Adam S.; Hapala, Hapala; Department of Applied Physics; Department of Computer Science; Surfaces and Interfaces at the Nanoscale; Atomic Scale Physics; Professorship Kannala Juho; Computer Science Professors; Computer Science - Artificial Intelligence and Machine Learning (AIML); Computer Science - Visual Computing (VisualComputing); Aalto University
    While offering high resolution atomic and electronic structure, scanning probe microscopy techniques have found greater challenges in providing reliable electrostatic characterization on the same scale. In this work, we offer electrostatic discovery atomic force microscopy, a machine learning based method which provides immediate maps of the electrostatic potential directly from atomic force microscopy images with functionalized tips. We apply this to characterize the electrostatic properties of a variety of molecular systems and compare directly to reference simulations, demonstrating good agreement. This approach offers reliable atomic scale electrostatic maps on any system with minimal computational overhead.
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    Integrating Bayesian Inference with Scanning Probe Experiments for Robust Identification of Surface Adsorbate Configurations
    (WILEY-VCH VERLAG, 2021-08-09) Järvi, Jari; Alldritt, Benjamin; Krejčí, Ondřej; Todorović, Milica; Liljeroth, Peter; Rinke, Patrick; Department of Applied Physics; Computational Electronic Structure Theory; Atomic Scale Physics; Surfaces and Interfaces at the Nanoscale
    Controlling the properties of organic/inorganic materials requires detailed knowledge of their molecular adsorption geometries. This is often unattainable, even with current state‐of‐the‐art tools. Visualizing the structure of complex non‐planar adsorbates with atomic force microscopy (AFM) is challenging, and identifying it computationally is intractable with conventional structure search. In this fresh approach, cross‐disciplinary tools are integrated for a robust and automated identification of 3D adsorbate configurations. Bayesian optimization is employed with first‐principles simulations for accurate and unbiased structure inference of multiple adsorbates. The corresponding AFM simulations then allow fingerprinting adsorbate structures that appear in AFM experimental images. In the instance of bulky (1S)‐camphor adsorbed on the Cu(111) surface, three matching AFM image contrasts are found, which allow correlating experimental image features to distinct cases of molecular adsorption.
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    On-Surface Synthesis of a π-Extended Diaza[8]circulene
    (AMERICAN CHEMICAL SOCIETY, 2020-05-15) Nakamura, Kimihiro; Li, Qiang Qiang; Krejčí, Ondřej; Foster, Adam S.; Sun, Kewei; Kawai, Shigeki; Ito, Shingo; Department of Applied Physics; Surfaces and Interfaces at the Nanoscale; Nanyang Technological University; National Institute for Materials Science
    Heterocyclic [8]circulenes are an important class of polycyclic aromatic hydrocarbon molecules because of their unique structural properties and promising applications. However, the synthesis of heterocyclic [8]circulenes is still limited and thus is an important synthetic challenge. Here we describe the first example of a π-extended diaza[8]circulene surrounded by and fused with six hexagons and two pentagons, which was successfully synthesized only by a combined in-solution and on-surface synthetic strategy. State-of-the-art scanning tunneling microscopy with a CO-functionalized tip and density functional theory calculations revealed its planar conformation and unique electronic structure.
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    On-surface synthesis of disilabenzene-bridged covalent organic frameworks
    (Nature Publishing Group, 2023-01) Sun, Kewei; Silveira, Orlando J.; Ma, Yujing; Hasegawa, Yuri; Matsumoto, Michio; Kera, Satoshi; Krejčí, Ondřej; Foster, Adam S.; Kawai, Shigeki; Department of Applied Physics; Surfaces and Interfaces at the Nanoscale; Computational Electronic Structure Theory; National Institute for Materials Science; National Institutes of Natural Sciences, Institute for Molecular Science; University of Tsukuba
    Substituting carbon with silicon in organic molecules and materials has long been an attractive way to modify their electronic structure and properties. Silicon-doped graphene-based materials are known to exhibit exotic properties, yet conjugated organic materials with atomically precise Si substitution have remained difficult to prepare. Here we present the on-surface synthesis of one- and two-dimensional covalent organic frameworks whose backbones contain 1,4-disilabenzene (C4Si2) linkers. Silicon atoms were first deposited on a Au(111) surface, forming a AuSix film on annealing. The subsequent deposition and annealing of a bromo-substituted polyaromatic hydrocarbon precursor (triphenylene or pyrene) on this surface led to the formation of the C4Si2-bridged networks, which were characterized by a combination of high-resolution scanning tunnelling microscopy and photoelectron spectroscopy supported by density functional theory calculations. Each Si in a hexagonal C4Si2 ring was found to be covalently linked to one terminal Br atom. For the linear structure obtained with the pyrene-based precursor, the C4Si2 rings were converted into C4Si pentagonal siloles by further annealing.
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    Synthesis and Local Probe Gating of a Monolayer Metal-Organic Framework
    (WILEY-VCH VERLAG, 2021-05-26) Yan, Linghao; Silveira, Orlando J.; Alldritt, Benjamin; Krejčí, Ondřej; Foster, Adam S.; Liljeroth, Peter; Department of Applied Physics; Atomic Scale Physics; Surfaces and Interfaces at the Nanoscale
    Achieving large-area uniform 2D metal-organic frameworks (MOFs) and controlling their electronic properties on inert surfaces is a big step toward future applications in electronic devices. Here a 2D monolayer Cu-dicyanoanthracene MOF with long-range order is successfully fabricated on an epitaxial graphene surface. Its structural and electronic properties are studied by low-temperature scanning tunneling microscopy and spectroscopy complemented by density-functional theory calculations. Access to multiple molecular charge states in the 2D MOF is demonstrated using tip-induced local electric fields. It is expected that a similar strategy could be applied to fabricate and characterize 2D MOFs with exotic, engineered electronic states.