arXiv subjects

Jan Čechal

Publications and source records attributed to Jan Čechal.

17 recordsLinked to original sources

arXiv2026

Oxygen-Pressure-Limited Recovery of the Hematite α-Fe$_2$O$_3$(0001) Surface from a Reduced Fe$_3$O$_4$(111)-Like Layer

The oxidation kinetics of hematite α-Fe$_2$O$_3$(0001) surfaces are vital for its applications in catalysis, environmental remediation, and industrial processes. Despite prior studies, the roles of temperature, oxygen partial pressure, and oxygen chemical potential in controlling nucleation and growth kinetics are not fully understood. Using real-time Low Energy Electron Microscopy/Diffraction (LEEM/LEED), we systematically investigate the oxidation of a reduced Fe$_3$O$_4$(111)-like surface layer to hematite under controlled conditions. We show that complete recovery of the hematite surface termination is closely linked to the nucleation and lateral growth of a two-dimensional honeycomb (H) phase. While higher temperatures accelerate nucleation, they slow lateral growth at constant oxygen pressure, indicating that oxygen supply limits the oxidation rate. Below an oxygen partial pressure threshold (~2$\times$10$^{-6}$ mbar), growth dramatically slows, underscoring the critical role of oxygen availability. Below a certain oxygen pressure threshold, the growth time rapidly increases. Our study elucidates the interplay between thermodynamics and kinetics in hematite surface oxidation, informing strategies to optimize surface properties for catalytic and industrial processes.

cond-mat.mtrl-sci↗

arXiv2026

Essential Principles and Practices in X-ray Photoelectron Spectroscopy

X-ray photoelectron spectroscopy (XPS) is a widely used technique for chemical analysis of solid surfaces, sensitive to the chemical environments of atoms via core-level binding energy shifts. While modern instruments allow experimental data to be acquired with ease, their evaluation and interpretation remain challenging for newcomers to the field, as a profound knowledge of the method is required for correct analysis. Here we present a concise yet comprehensive overview of the fundamental principles and methodologies of XPS, covering photoemission processes, chemical shifts, charge referencing, peak fitting, and quantification strategies. This overview aims to bridge the gap between data collection and reliable analysis, providing essential knowledge for correct interpretation. By clarifying key concepts and common practices, this work supports improved accuracy in surface chemical characterization using XPS.

cond-mat.mtrl-sci↗

arXiv2026

Structural flexibility dictates reactivity of single-atom catalysts

Unravelling the origins of single-atom catalyst reactivity is a central challenge in heterogeneous catalysis research. A key question is whether the activity arises solely from atomic isolation or from distinct structural and electronic configurations of the single atoms. Here, we use precisely defined Fe-N$_3$ and Fe-N$_4$ model catalyst sites synthesized on an inert support to quantify the effect of coordination geometry on chemical reactivity. Both the Fe-N$_3$ and Fe-N$_4$ models have the same electronic configuration (high-spin Fe$^{2+}$ with S=2), and even their d-orbital occupancies and positions with respect to Fermi level are almost identical. Despite this electronic similarity, the adsorption energy of CO differs by more than 0.6 eV between the Fe-N$_3$ and Fe-N$_4$ sites, as indicated by density functional theory computations and confirmed by atomically-resolved scanning tunneling microscopy experiments. We trace this reactivity difference to the structural flexibility of the Fe-N$_3$ sites, which allows strengthening of the Fe 3d$_{xz/yz}$-CO 2$π$* back-bonding by lifting the Fe atom from the -N$_3$ plane. These results demonstrate that coordination geometry plays a crucial role in defining the reactivity of single-atom catalysts, and that such effects cannot be predicted by analysis of the sites' electronic structures alone.

cond-mat.mtrl-sci↗

arXiv2026

Unveiling Davydov-Split Excitons in a Template-Engineered Molecular-Graphene Heterostructure

The realization of high-fidelity organic-inorganic quantum emulators is frequently hindered by the interfacial imperfections introduced during device fabrication. Here, we demonstrate a robust nanofabrication protocol that restores the atomic-scale purity of epitaxial graphene on SiC to UHV-equivalent levels, as confirmed by Low-Energy Electron Diffraction, and Microscopy. This pristine interface enables the emergence of macroscopic excitonic coherence in epitaxial overlayers of 2,3,6,7,10,11-hexamethoxytriphenylene (HMTP), a model molecular system characterized by intense electron-phonon coupling. Through a combination of high-sensitivity Fourier Transform Photo-current Spectroscopy, photoluminescence, and dynamic Raman mapping, we resolve a complex vibronic manifold governed by Davydov splitting. We show that the $P6_3/m$ crystalline symmetry of the HMTP overlayer lifts the degeneracy of the HOMO-LUMO transition, creating discrete bright and dark excitonic branches. Using an analytical tight-binding model parameterized by ARPES-derived intermolecular coupling and Raman vibrational modes validated by molecular dynamics simulations, we quantify the polarization energy, the Huang-Rhys factor, and Herzberg-Teller corrections to the Franck-Condon model. Our results reveal that the dark-state branch dominates the radiative channel, following a polaron-mediated relaxation pathway consistent with Kasha's rule. By reconciling macroscopic device architecture with UHV-level surface science, this work establishes a scalable platform for the study of dark-exciton dynamics and the development of solid-state molecular quantum memories.

cond-mat.mes-hall↗

arXiv2026

Fe-DCA Metal-Organic Frameworks on the Bi2Se3(0001) Topological Insulator Surface

The formation of two-dimensional metal-organic frameworks (MOFs) on an inert surface of a topological insulator (TI) is a pathway to engineer quantum materials with exotic properties. MOFs featuring ferromagnetically coupled metal atoms are theoretically predicted to induce an exchange gap in the TI surface band structure, potentially leading to a quantum anomalous Hall effect. However, achieving ordered MOFs on TI surfaces remains challenging due to the limited knowledge of self-assembly on these substrates. In this paper, we demonstrate self-assembly of Fe atoms and dicyanoanthracene (DCA) molecules into 2D MOFs on the Bi2Se3(0001) surface at room temperature, investigated via a combination of low-energy electron microscopy and diffraction (LEEM/LEED), scanning tunneling microscopy (STM), and ab initio calculations based on density functional theory (DFT). Two competing Fe-DCA phases form. The first phase corresponds to a close-packed Fe1DCA3 structure. In contrast, the second phase exhibits a larger unit cell with no match to either known or DFT-calculated systems, indicating a more complex bonding environment. These findings advance the understanding of the growth of MOFs on a strong topological insulator surface and provide insights for designing MOFs/TI interfaces with tailored electronic and magnetic properties.

cond-mat.mtrl-sci↗

arXiv2026

Interfacial Coupling Controls Molecular Epitaxy of HMTP on Graphene/SiC

Epitaxial growth critically influences structural and electronic properties of organic semiconductors. Graphene serves as a prominent van der Waals template for molecular self-assembly; however, graphene on SiC is intrinsically heterogeneous, with decoupled monolayer graphene coexisting with residuals of a covalently bound buffer layer, which may affect molecular ordering. Here, we track the ordering of the molecular donor, 2,3,6,7,10,11-hexamethoxytriphenylene (HMTP), from the first layer to thin films, combining low-energy electron microscopy and diffraction with X-ray diffraction. HMTP forms highly ordered epitaxial layers on single-layer graphene, whereas growth on the buffer layer initiates as amorphous and evolves into polycrystalline films with weak orientation with respect to the substrate. Crucially, hydrogen intercalation decouples the buffer layer, converting it into quasi-freestanding monolayer graphene and restoring epitaxial growth. These findings demonstrate that interfacial coupling governs molecular epitaxy on graphene/SiC, and interface engineering via hydrogen intercalation provides a scalable route to control organic thin-film crystallinity on graphene.

cond-mat.mtrl-sci↗

arXiv2025

Molecular Arrangements in the First Monolayer of Cu-Phthalocyanine on In$_2$O$_3$(111)

Well-ordered organic molecular layers on oxide surfaces are key for organic electronics. Using a combination of scanning tunneling microscopy (STM) and non-contact atomic force microscopy (nc-AFM) we probe the structures of copper phthalocyanine (CuPc) on In$_2$O$_3$, a model for a prototypical transparent conductive oxide (TCO). These scanning-probe images allow the direct determination of the adsorption site and distortions of the molecules, which are corroborated by DFT calculations. Isolated CuPc molecules adsorb in a flat, slightly tilted geometry in three symmetry-equivalent configurations on the stoichiometric In$_2$O$_3$(111) surface. Increasing the coverage leads to densely-packed 1D chains oriented along $\langle1\bar{1}0\rangle$ directions, which dissolve into a highly ordered (2$\times$2) superstructure upon increasing the CuPc density to 3/4 per surface unit cell. At a coverage of one CuPc per surface unit cell, a densely packed (1$\times$1) superstructure fully covers the surface. The molecules still assume the same site and orientation as before, but they partially overlap to accommodate the high packing density, leading to a bending of the molecules. These results are compared to the behavior of CoPc on In$_2$O$_3$(111). In summary, we demonstrate that a uniform first layer of metal-phthalocyanine molecules can be realized on the In$_2$O$_3$(111) surface when using the proper metal atom in the molecule.

cond-mat.mtrl-sci↗

arXiv2025

Low-energy electron microscopy as a tool for analysis of self-assembled molecular layers on surfaces

Low-energy electron microscopy (LEEM) is a surface science method that works primarily in the UHV environment. It provides information complementary to the other established techniques: it extends the limited view of scanning probe microscopies from nanometers to micrometers and measurement time down to tens of milliseconds, enabling to visualize the changes during sample treatment, e.g., annealing, deposition, and gas or light exposure. From the point of structural analysis, it allows the measurement of diffraction patterns from an area of diameter below 200 nm and imaging of phase distribution on the surfaces either through dark-filed imaging or LEEM-I(V) fingerprinting. The advanced modes provide local angle-resolved photoelectron spectra and surface potential distribution. In this review, we aim to describe the utilization of LEEM to study self-assembled molecular structures on solid surfaces. We present the LEEM instrumentation and analysis of measured data in a tutorial way to provide the necessary background knowledge to enter the field. In the second part, we summarize the knowledge obtained by LEEM for several selected systems, which points to the strength of LEEM in understanding the self-assembled molecular systems and its synergy with other surface science techniques.

cond-mat.mes-hall↗

arXiv2024

Robust Dipolar Layers between Organic Semiconductors and Silver for Energy-Level Alignment

The interface between a metal electrode and an organic semiconductor (OS) layer has a defining role in the properties of the resulting device. To obtain a desired performance, interlayers are introduced to modify the adhesion and growth of OS and enhance the efficiency of charge transport through the interface. However, the employed interlayers face common challenges, including a lack of electric dipoles to tune the mutual position of energy levels, being too thick for efficient electronic transport, or being prone to intermixing with subsequently deposited OS layers. Here, we show that monolayers of 1,3,5-tris(4 carboxyphenyl)benzene (BTB) with fully deprotonated carboxyl groups on silver substrates form a compact layer resistant to intermixing while mediating energy level alignment and showing a large insensitivity to substrate termination. Employing a combination of surface-sensitive techniques, i.e., low-energy electron microscopy and diffraction, X-ray photoelectron spectroscopy, and scanning tunneling microscopy, we have comprehensively characterized the compact layer and proven its robustness against mixing with the subsequently deposited organic semiconductor layer. DFT calculations show that the robustness arises from a strong interaction of carboxylate groups with the Ag surface, and thus, the BTB in the first layer is energetically favored. Synchrotron radiation photoelectron spectroscopy shows that this layer displays considerable electrical dipoles that can be utilized for work function engineering and electronic alignment of molecular frontier orbitals with respect to the substrate Fermi level. Our work thus provides a widely applicable molecular interlayer and general insights necessary for engineering of charge injection layers for efficient organic electronics.

cond-mat.mtrl-sci↗

arXiv2023

Water Structures Reveal Local Hydrophobicity on the In2O3(111) Surface

Clean oxide surfaces are generally hydrophilic. Water molecules anchor at undercoordinated surface metal atoms that act as Lewis-acid sites, and they are stabilized by H bonds to undercoordinated surface oxygens. The large unit cell of In2O3(111) provides surface atoms in various configurations, which leads to chemical heterogeneity and a local deviation from this general rule. Experiments (TPD, XPS, ncAFM) agree quantitatively with DFT calculations and show a series of distinct phases. The first three water molecules dissociate at one specific area of the unit cell and desorb above room temperature. The next three adsorb as molecules in the adjacent region. Three more water molecules rearrange this structure and an additional nine pile up above the OH groups. Despite offering undercoordinated In and O sites, the rest of the unit cell is unfavorable for adsorption and remains water-free. The first water layer thus shows ordering into nanoscopic 3D water clusters separated by hydrophobic pockets.

cond-mat.mtrl-sci↗

arXiv2023

Hematite $α-Fe_{2}O_{3}(0001)$ in top and side view: resolving long-standing controversies about its surface structure

Hematite $α-Fe_{2}O_{3}(0001)$ is the most-investigated iron oxide model system in photo and electrocatalytic research. The rich chemistry of Fe and O allows for many bulk and surface transformations, but their control is challenging. This has led to controversies regarding the structure of the topmost layers. This comprehensive study combines surface methods (nc-AFM, STM, LEED, and XPS) complemented by structural and chemical analysis of the near-surface bulk (HRTEM and EELS). The results show that a compact 2D layer constitutes the topmost surface of $α-Fe_{2}O_{3}(0001)$; it is locally corrugated due to the mismatch with the bulk. Assessing the influence of naturally-occurring impurities shows that these can force the formation of surface phases that are not stable on pure samples. Impurities can also cause the formation of ill-defined inclusions in the subsurface and modify the oxidation phase diagram of hematite. The results provide a significant step forward in determining the hematite surface structure that is crucial for accurately modeling catalytic reactions. Combining surface and cross-sectional imaging provided the full view that is essential for understanding the evolution of the near-surface region of oxide surfaces under oxidative conditions.

cond-mat.mtrl-sci↗

arXiv2022

Tunable Energy Level Alignment in the Multilayers of Carboxylic Acids on Silver

The precise energy level alignment between a metal electrode and an organic semiconductor is required to reduce contact resistance and enhance the efficiency of organic-semiconductor-based devices. One of the ways is to include interlayers that mediate the energy level alignment, i.e., charge injection layers (CILs). Here we introduce the monolayer thick CILs based on the aromatic carboxylic acids that can induce the energy level shift in the subsequent layers by up to 0.8 eV. By gradual chemical transformation of the as-deposited molecules, we achieve a highly tunable energy level shift in the range of 0.5 eV. We reveal that the position of both the work function and energy-level position in the CIL increases linearly with the density of induced dipoles. The energy level position of subsequent layers changes in the same way as the CIL. Our results thus connect the energy alignment quantities, i.e., energy level positions of both CIL and subsequent layers and sample work function. The high tunability would allow precise tuning of the active layers deposited on the CIL, which marks the path towards efficient charge injection layers on metal electrodes.

cond-mat.mtrl-sci↗

arXiv2022

The Role of Phase Stabilization and Surface Orientation in 4,4'-Biphenyl-Dicarboxylic Acid Self-Assembly and Transformation on Silver Substrates

Molecular functionalization of nanoparticles and metallic substrates can be used to tune their properties for specific applications. However, polycrystalline substrates and nanoparticles exhibit surface planes with distinct crystallographic orientations. Therefore, the development of reliable strategies for molecular functionalization requires knowledge of the role of the surface plane orientation in the growth kinetics, structure, and properties of the molecular layer. Here, we apply a multiscale analysis to investigate the self-assembly of 4,4'-biphenyl-dicarboxylic acid (BDA) on Ag(111) and critically discuss the difference to Ag(100). Whereas the structural motifs for intact and fully deprotonated BDA are similar on both surfaces, the intermediate phases comprising partially deprotonated BDA differ in the structure and chemical composition. A real-time view of the phase transformations enables us to present a generalized picture of the phase transformations between the self-assembled molecular phases on the surfaces and underline important features such as the phase stabilization of the chemical composition and the mechanism of the related burst transformation. The influence of the substrate orientation on the structure of molecular layers and phase transformations provides the necessary background for developing functionalization strategies of the substrates displaying multiple surface planes and kinetic models for the growth near thermodynamic equilibrium.

cond-mat.mtrl-sci↗

arXiv2022

Fabrication and micro-Raman spectroscopy of arrays of copper phthalocyanine molecular-magnet microdisks

Phthalocyanines as organic semiconductors and molecular magnets provide plenty of industrial or high-tech applications from dyes and pigments up to gas sensors, molecular electronics, spintronics and quantum computing. Copper phthalocyanine (CuPc) belongs among the most used phthalocyanines, typically in the form of powder or films but self-grown nanowires are also known. Here we describe an opposite, i.e., top-down approach based on fabrication of ordered arrays of CuPc microstructures (microdisks) using electron beam lithography and other steps. Among critical points of this approach belongs a choice of a proper resist and a solvent. Fabricated CuPc microdisks have a diameter of 5 $μ$m and heights from 7 up to 70 nm. Micro-Raman spectroscopy of the films and microdisks reveals a crystalline $β$ phase associated with a paramagnetic form. Additional measurements with an increasing laser power show a significant shift ($Δω$ ~ 7.1 cm$^{-1}$ ) and broadening of a peak at 1532 rel$\cdot$cm$^{-1}$ corresponding to the phonon B1g mode. The observed smooth changes exclude a phase transition and confirm the thermally stable polymorph. Our versatile fabrication technique using the common lithographic resist brings new possibilities for the fabrication of various micro/nanostructures such as micromagnets, heterostructures or organic electronic devices.

physics.app-ph↗

arXiv2020

Single-layer graphene on epitaxial FeRh thin films

Graphene is a 2D material that displays excellent electronic transport properties with prospective applications in many fields. Inducing and controlling magnetism in the graphene layer, for instance by proximity of magnetic materials, may enable its utilization in spintronic devices. This paper presents fabrication and detailed characterization of single-layer graphene formed on the surface of epitaxial FeRh thin films. The magnetic state of the FeRh surface can be controlled by temperature, magnetic field or strain due to interconnected order parameters. Characterization of graphene layers by X-ray Photoemission and X-ray Absorption Spectroscopy, Low-Energy Ion Scattering, Scanning Tunneling Microscopy, and Low-Energy Electron Microscopy shows that graphene is single-layer, polycrystalline and covers more than 97% of the substrate. Graphene displays several preferential orientations on the FeRh(001) surface with unit vectors of graphene rotated by 30°, 15°, 11°, and 19° with respect to FeRh substrate unit vectors. In addition, the graphene layer is capable to protect the films from oxidation when exposed to air for several months. Therefore, it can be also used as a protective layer during fabrication of magnetic elements or as an atomically thin spacer, which enables incorporation of switchable magnetic layers within stacks of 2D materials in advanced devices.

cond-mat.mtrl-sci↗

arXiv2019

Step-edge assisted large scale FeSe monolayer growth on epitaxial Bi2Se3 thin films

The interest in Fe-chalcogenide unconventional superconductors is intense after the critical temperature of FeSe was reported enhanced by more than one order of magnitude in the monolayer limit at the interface to an insulating oxide substrate. In heterostructures comprising interfaces of FeSe with topological insulators, additional interesting physical phenomena is predicted to arise e.g. in form of {\it topological superconductivity}. So far superconductive properties of Fe-chalcogenide monolayers were mostly studied by local scanning tunneling spectroscopy experiments, which can detect pseudo-gaps in the density of states as an indicator for Cooper pairing. Direct macroscopic transport properties which can prove or falsify a superconducting phase were rarely reported due to the difficulty to grow films with homogeneous material properties. Here we report on a promising growth method to fabricate continuous carpets of monolayer thick FeSe on molecular beam epitaxy grown Bi$_2$Se$_3$ topological insulator thin films. In contrast to previous works using atomically flat cleaved bulk Bi$_2$Se$_3$ crystal surfaces we observe a strong influence of the high step-edge density (terrace width about 10~nm) on MBE-grown Bi$_2$Se$_3$ substrates, which significantly promotes the growth of coalescing FeSe domains with small tetragonal crystal distortion without compromising the underlying Bi$_2$Se$_3$ crystal structure.

cond-mat.mtrl-sci↗

arXiv2018

Identification of two-dimensional $FeO_2$ termination of hematite $α-Fe_2O_3(0001)$ surface

Iron oxides are among the most abundant compounds on Earth and have consequently been studied and used extensively in industrial processes. Despite these efforts, concrete understanding of some of their surface phase structures has remained elusive, in particular the oxidized $α-Fe_2O_3(0001)$ hematite surface. We detail an optimized recipe to produce this phase over the entire hematite surface and study the geometrical parameters and composition of its complex structure by means of atomically resolved microscopy, electron diffraction and surface-sensitive spectroscopies. We conclude that the oxidized $α-Fe_2O_3(0001)$ surface is terminated by a two-dimensional iron oxide with structure, lattice parameters, and orientation different from the bulk substrate. Using total-energy density functional theory for simulation of a large-scale atomic model, we identify the structure of the surface layer as antiferromagnetic, conductive $1T-FeO_2$ attached on half-metal terminated bulk. The model succeeds in reproducing the characteristic modulations observed in the atomically resolved images and electron diffraction patterns.

cond-mat.mtrl-sci↗