Browsing by Author "Krejci, Ondrej"

Now showing 1 - 7 of 7
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    Automated structure discovery in atomic force microscopy
    (AMER ASSOC ADVANCEMENT SCIENCE, 2020-02-26) Alldritt, Benjamin; Hapala, Hapala; Oinonen, Niko; Urtev, Fedor; Krejci, Ondrej; Federici Canova, Filippo; Kannala, Juho; Schulz, Fabian; Liljeroth, Peter; Foster, Adam; Department of Applied Physics; Department of Computer Science; Atomic Scale Physics; Surfaces and Interfaces at the Nanoscale; Professorship Kannala Juho
    Atomic force microscopy (AFM) with molecule-functionalized tips has emerged as the primary experimental tech- nique for probing the atomic structure of organic molecules on surfaces. Most experiments have been limited to nearly planar aromatic molecules due to difficulties with interpretation of highly distorted AFM images originat- ing from nonplanar molecules. Here, we develop a deep learning infrastructure that matches a set of AFM images with a unique descriptor characterizing the molecular configuration, allowing us to predict the molecular struc- ture directly. We apply this methodology to resolve several distinct adsorption configurations of 1S-camphor on Cu(111) based on low-temperature AFM measurements. This approach will open the door to applying high-resolution AFM to a large variety of systems, for which routine atomic and chemical structural resolution on the level of individual objects/molecules would be a major breakthrough.
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    Biphenylene network: A nonbenzenoid carbon allotrope
    (AMER ASSOC ADVANCEMENT SCIENCE, 2021-05-21) Fan, Qitang; Yan, Linghao; Trip, Matthias R.; Krejci, Ondrej; Dimosthenous, Stavrina; Kachel, Stefan R.; Chen, Mengyi; Foster, Adam; Liljeroth, Peter; Gottfried, J. Michael; Department of Applied Physics; Atomic Scale Physics; Surfaces and Interfaces at the Nanoscale; Phillips-Universität Marburg; University of Marburg
    The quest for planar sp2-hybridized carbon allotropes other than graphene, such as graphenylene and biphenylene networks, has stimulated substantial research efforts because of the materials’ predicted mechanical, electronic, and transport properties. However, their syntheses remain challenging given the lack of reliable protocols for generating nonhexagonal rings during the in-plane tiling of carbon atoms. We report the bottom-up growth of an ultraflat biphenylene network with periodically arranged four-, six-, and eight-membered rings of sp2-hybridized carbon atoms through an on-surface interpolymer dehydrofluorination (HF-zipping) reaction. The characterization of this biphenylene network by scanning probe methods reveals that it is metallic rather than a dielectric. We expect the interpolymer HF-zipping method to complement the toolbox for the synthesis of other nonbenzenoid carbon allotropes.
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    Diacetylene Linked Anthracene Oligomers Synthesized by One-Shot Homocoupling of Trimethylsilyl on Cu(111)
    (2018-08-07) Kawai, Shigeki; Krejci, Ondrej; Foster, Adam; Pawlak, Rémy; Xu, Feng; Peng, Lifen; Orita, Akihiro; Meyer, Ernst; Department of Applied Physics; Surfaces and Interfaces at the Nanoscale; National Institute for Materials Science; University of Basel; Okayama University of Science
    On-surface chemical reaction has become a very powerful technique to conjugate small precursor molecules and several reactions have been proposed with the aim to fabricate functional nanostructures on surfaces. Here we present an unforeseen adsorption mode of 9,10-bis-((trimethylsilyl)ethynyl)anthracene on a Cu(111)surface and the resulting one-shot desilylative homocoupling of of the adsorbate by annealing at 400 K. With a combination of high-resolution atomic force microscopy and density functional theory calculations, we found that the triple bonds and silicon atoms of the monomer chemically interact with the copper surface. After the oligomerization, we discovered that the anthracene units are linked to each other via buta-1,3-diynediyl fragments while keeping the surface clean. Furthermore, the force measurement revealed the chemical nature at the center of anthracene unit.
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    Gaussian Process Regression for Pre- dicting Charges and Dipoles for Infrared Spectroscopy
    (2023-09-15) Brata, Barnik; Krejci, Ondrej; Perustieteiden korkeakoulu; Korpi-Lagg, Maarit
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    Molecular structure reconstruction from atomic force microscopy data using machine learning
    (2018-10-10) Määttä, Petri; Krejci, Ondrej; Perustieteiden korkeakoulu; Tuomisto, Filip
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    Synthesis of Regioisomeric Graphene Nanoribbon Junctions via Heteroprecursors
    (AMERICAN CHEMICAL SOCIETY, 2019-07-18) Sun, Kewei; Krejci, Ondrej; Foster, Adam S.; Okuda, Yasuhiro; Orita, Akihiro; Kawai, Shigeki; Department of Applied Physics; Surfaces and Interfaces at the Nanoscale; National Institute for Materials Science; Okayama University of Science
    Graphene nanoribbons are one of the most promising materials for nanoscale electronics. While various structures have successfully been synthesized by on-surface reactions, curved connections remain less investigated, yet they could prove highly useful in the development of copolymerization technology. Here, we present the synthesis of three different regioisomeric junctions on Au (111) by using 10,10'-dibromo-9,9'-bianthryl and 1,3,6,8-tetrabromopyrene. The chemical structures and the electronic properties of junctions were studied with a combination of scanning tunneling microscopy with a CO terminated tip, scanning tunneling spectroscopy, and density functional theory calculations. We found that two identical nanoribbon-junction interface electronic states appear within the band gaps of connected graphene nanoribbons.
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    Three-dimensional graphene nanoribbons as a framework for molecular assembly and local probe chemistry
    (AMER ASSOC ADVANCEMENT SCIENCE, 2020-02-28) Kawai, Shigeki; Krejci, Ondrej; Nishiuchi, Tomohiko; Sahara, Keisuke; Kodama, Takuya; Pawlak, Rémy; Meyer, Ernst; Kubo, Takashi; Foster, Adam; Department of Applied Physics; Surfaces and Interfaces at the Nanoscale; National Institute for Materials Science; Osaka University; University of Basel; Osaka Prefecture University
    Recent advances in state-of-the-art probe microscopy allow us to conduct single molecular chemistry via tip- induced reactions and direct imaging of the inner structure of the products. Here, we synthesize three-dimensional graphene nanoribbons by on-surface chemical reaction and take advantage of tip-induced assembly to demon- strate their capability as a playground for local probe chemistry. We show that the radical caused by tip-induced debromination can be reversibly terminated by either a bromine atom or a fullerene molecule. The experimental results combined with theoretical calculations pave the way for sequential reactions, particularly addition reac- tions, by a local probe at the single-molecule level decoupled from the surface.