Teilbibliothek Naturwissenschaften: Chemie

Publications

Teilbibliothek Naturwissenschaften: Chemie
Image: Jan-Peter Kasper (University of Jena)

Peer reviewed publications

Books and book chapters

  • Markus Kitzler and Stefanie Gräfe (Eds.),
    Ultrafast Dynamics Driven by Intense Light Pulses.External link
    Springer Series on Atomic, Optical, and Plasma Physics, 978-3-319-20173-3 (2016).
  • Dirk Bender, Leticia González and Stefanie Gräfe,
    Short Introduction to Atomic and Molecular Configuration.
    in: Handbook of Biophotonics, J. Popp, V. V. Tuchin, A. Chiou, S. Heinemann (Eds.), Wiley-VCH Weinheim, Vol. 1(Basics and Techniques), 39-86 (2011).

Other publications

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Highlighted authors are members of the research group.

  1. Modeling high-order harmonic generation in quantum dots using a real-space tight-binding approach

    Authors
    M. Thümmler, A. Croy, U. Peschel, S. Gräfe
    Year of publication
    Published in:
    The Journal of Chemical Physics : JCP
    Recently, the size-dependence of high-order harmonic generation (HHG) in quantum dots (QDs) has been investigated experimentally. In particular, for longer driving wavelengths and quantum dots smaller than 3 nm, HHG was strongly suppressed; however, there is no computational model capable of describing the strong-field response of such systems. In this work, we introduce a computationally efficient three-dimensional real-space tight-binding model specifically designed for the simulation of HHG in confined systems. The model parameters are meticulously derived from density functional theory calculations for the semiconductor bulk, followed by a process of Wannierization. Our findings demonstrate that the proposed model accurately captures the observed dependency of the HHG yield on the quantum dot size. In addition, we simulate the HHG yield for elliptically polarized pulses for different QD-sizes and driving wavelengths up to 5 μm. The proposed model fills the theoretical void in simulating HHG within medium-sized nanostructures, which cannot be described by methods applied for periodic solids, or small molecules or atoms.
    University Bibliography Jena:
    fsu_mods_00034842External link

  2. Semiconductor Bloch equations in Wannier gauge with well-behaved dephasing

    Authors
    M. Thümmler, T. Lettau, A. Croy, U. Peschel, S. Gräfe
    Year of publication
    Published in:
    Computer physics communications: an international journal devoted to computational physics and computer programs in physics
    The semiconductor Bloch equations (SBEs) with a dephasing operator for the microscopic polarizations are a well established approach to simulate high-harmonic spectra in solids. We discuss the impact of the dephasing operator on the stability of the numerical integration of the SBEs in the Wannier gauge. It is shown that the commonly used phenomenological approach to apply dephasing is ill-defined in the presence of band crossings and leads to artifacts in the carrier distribution. They are caused by rapid changes of the dephasing operator matrix elements in the Wannier gauge, which render the convergence of the simulation in the stationary basis infeasible. In the comoving basis, also called Houston basis, these rapid changes can be resolved, but only at the cost of a largely increased computation time. As a remedy, we propose a modification of the dephasing operator with reduced magnitude in energetically close subspaces. This approach removes the artifacts in the carrier distribution and significantly speeds up the calculations, while affecting the high-harmonic spectrum only marginally. To foster further development, we provide our parallelized source code.
    University Bibliography Jena:
    fsu_mods_00029532External link

  3. Efficient Machine Learning Prediction of Solvent-Dependent 1H NMR Chemical Shifts in Zinc Complexes

    Authors
    J. Pillay, M. Ringleb, A. Croy, S. Zechel, U. Schubert, S. Gräfe
    Year of publication
    Published in:
    Journal of computational chemistry : organic, inorganic, physical, biological
    Accurate prediction of NMR chemical shifts in transition metal complexes remains challenging due to the wide range of coordination environments and complex electronic structures of these systems. In this work, we present a machine learning approach (ML) for rapid and accurate prediction of formula presented NMR shifts in zinc complexes across multiple solvent environments. We systematically selected a diverse set of zinc complexes from the transition metal quantum mechanics (tmQM) database using K-means clustering on SOAP descriptors, and performed DFT NMR calculations across five solvents to generate training data. We combine smooth overlap of atomic positions (SOAP) descriptors with tree-based ensemble methods to predict proton chemical shifts. Among several ML algorithms evaluated, LightGBM achieved the best performance on held-out test complexes (MAE = 0.016 ppm, RMSE = 0.028 ppm, formula presented  = 0.99), demonstrating excellent generalization to unseen molecular structures. External validation against experimental NMR data across multiple solvents revealed strong predictive performance ( formula presented  = 0.90, MAE = 0.56 ppm), with exceptional accuracy in methanol ( formula presented  = 0.96) and acetonitrile ( formula presented  = 0.91). Notably, the model demonstrated robust transferability to acetonitrile despite this solvent not being included in the training set. This approach provides a computationally efficient alternative to expensive quantum chemical calculations for predicting formula presented NMR shifts in transition metal complexes, offering prediction times that are orders of magnitude faster while maintaining accuracy comparable to DFT methods, potentially accelerating the characterization and design of organometallic compounds.
    University Bibliography Jena:
    fsu_mods_00035714External link

  4. Unraveling Charging and Discharging Processes in Organic Radical-Based Electrodes : A Hierarchical Molecular and Quantum Mechanical Approach

    Authors
    C. Zens, G. Shillito, C. Friebe, S. Kupfer
    Year of publication
    Published in:
    ChemSusChem :: chemistry & sustainability, energy & materials
    Organic batteries represent a promising class of energy storage materials, due to their mechanical flexibility and sustainability. Typically, stable radicals, lacking intrinsic conductivity, are utilized as redox-active materials. A recently introduced strategy to overcome this shortcoming is to incorporate stable radicals, i.e., (2,2,6,6-tetramethylpiperidin-1-yl)oxyl (TEMPO), into a polythiophene backbone. Thereby, an electrode material was obtained which does not require conductive additives. The current computational study aims to elucidate the functionality of this material by drawing in-depth structure–property relationships utilizing a hierarchical molecular and quantum mechanical approach. Initially, structural properties of the electrode material's macroenvironment—containing the functionalized polythiophene, electrolyte, and solvent—were assessed in various charging states by molecular dynamics simulations. Subsequently, electronic properties were investigated by time-dependent density functional theory for 564 microenvironments. Via this computational setup, the electronic communication within the material was assessed along intrastrand and interstrand CT processes involving the respective TEMPO and polythiophene units. Thereby, our hierarchical computational approach reveals that the intrinsic conductivity and charge storage capacity of the electrode material stems from efficient intrastrand TEMPO-polythiophene CT processes along short and rigid amid linkers. These insights help to tailor improved conductive organic electrode materials with higher charging and discharging rate capabilities.
    University Bibliography Jena:
    fsu_mods_00034972External link

  5. A donor–acceptor photosensitizer-catalyst dyad for light-driven nicotinamide hydrogenation

    Authors
    A. Tombrink, M. Semwal, T. Maisuradze, A. Mengele, D. Straub, A. Kuehne, S. Rau, S. Kupfer, B. Dietzek-Ivanšić, B. Esser
    Year of publication
    Published in:
    Chemical science
    Using light energy to drive chemical transformations is of great relevance, with photosynthesis in nature as a grand example. In artificial light-driven catalysis, part of nature's complex supramolecular architecture can be mimicked through the so-called covalently linked photosensitizer-catalyst (PS-CAT) dyads. We herein report a dyad using an organic donor–acceptor PS, with dipyridophenazine as the acceptor and tert-butylcarbazole as the donor (2 t BuCzDPPZ), that contains a coordination site for a rhodium(iii)Cp* center as the catalyst. The organic PS shows a charge-transfer transition upon visible-light irradiation and has redox properties similar to typically used ruthenium-based PSs. The resulting PS-CAT dyad 2 t BuCzDPPZRhCp* shows – with methoxy-substituted 1,3-dimethyl-2-phenyl-2,3-dihydro-1H-benzo[d]imidazole (BIH-OMe) as the sacrificial electron donor – photocatalytic activity in light-driven NAD ⁺ reduction with a TON of 3.2 (after 4 h). Femtosecond transient absorption and resonance Raman spectroscopy, as well as time-dependent density functional theory (TDDFT) calculations, shed light on the photophysical properties of the PS and PS-CAT dyad and reveal a high dependency of the photoluminescence quantum yield and excited state properties on solvent polarity – in line with its donor–acceptor structure. This work presents a new design concept for PS-CAT dyads in artificial light-driven catalysis and provides important insight into the interplay between solvation dynamics of organic donor–acceptor systems and their photophysics, paving the way for future design strategies.
    University Bibliography Jena:
    fsu_mods_00034669External link

  6. Synthesis and Characterization of a β-Thio-δ-Diimine (BTDDI) and the Related Bimetallic Dimethylaluminium(III) Compound

    Authors
    J. Kowalke, T. Rathsack, T. Rüffer, S. Kupfer, R. Kretschmer
    Year of publication
    Status
    Review pending
    Published in:
    Zeitschrift für anorganische und allgemeine Chemie : ZAAC = Journal of inorganic and general chemistry
    Thionation of the β-oxo-δ-diimine (BODDI) 3 with P ₂ S ₅ ·2Py affords the ditopic β-thio-δ-diimine (BTDDI) 4. Based on ¹ H NMR spectroscopy and single-crystal X-ray diffraction, 4 is best described as a bis(β-enamine)-thione in both solution and the solid state. Furthermore, 4 features a thermochromic behavior in solution (c > 2 mmol l −¹ ) and as a solid. Reaction with trimethyl aluminium readily affords the bimetallic dimethylaluminium BTDDI complex 5. In contrast to its oxygen relative, 5 is only weakly emissive and the emission is significantly red-shifted. Scalar-relativistic time-dependent density functional theory calculations suggest that introduction of the sulfur atom promotes an intersystem crossing pathway (∼1 ns) to low-lying and non-emissive triplet states, which competes with fluorescence (∼5 ns).
    University Bibliography Jena:
    fsu_mods_00035653External link

  7. Zandpack: A general tool for time-dependent transportsimulation of nanoelectronics

    Authors
    A. Bach Lorentzen, A. Croy, A. Jauho, M. Brandbyge
    Year of publication
    Published in:
    Computer physics communications: an international journal devoted to computational physics and computer programs in physics
    The auxiliary mode approach to time-dependent open quantum system calculations is implemented and refined to yield a feasible computational approach to simulate nanostructures far from equilibrium. It is done by a careful diagonalization of the electrode level-width function, and provides an efficient approach which can simulate large, open systems at the level of time-dependent density functional theory. The approach, as given in this work, is implemented in the new open-source code Zandpack. The framework is applied to three systems perturbed by the same THz electromagnetic field pulse-form: 1) A Hubbard model for hydrogen on graphene is used to calculate spin-currents, mutual information, spin-transitions, and a pump-probe setup. 2) An armchair graphene nanoribbon (AGNR) probed by a metal tip showing electrons excited from the valence band of the AGNR into the tip via electron-electron interactions. 3) A gold break-junction is modeled with various gap distances, and displays behavior that is more different from the adiabatic case as the gap widens. In the examples 2 and 3, we develop and use a general linearization scheme for time-dependent open system calculations, which utilizes the DFTB+or SIESTAcodes. Program summary Program Title: Zandpack CPC Library link to program files: (to be added by Technical Editor) Developer's repository link: https://github.com/AleksBL Licensing provisions: MPL-2.0 Programming language: Python Nature of problem: Simulating the evolution of electrons in a device region connected to electrodes that are experiencing a time-dependent and strong bias, while at the same time describing the evolving device electrons accurately at the mean-field level. The electronic structure of the electrodes must also be described accurately in terms of the energy-dependence of its level-width function. This on a practical level requires fitting a set of known functions to a sum of Lorentzians. This fit then fixes the parameters of a coupled system of ODEs, in which the electronic density and Hamiltonian appears. Lastly, this system of ODEs has to be solved numerically. Solution method: A user-friendly routine for fitting the electrode level-width functions is implemented. It can either take input from TBtrans or custom user input and convert it to a sum of Lorentzians. We employ the auxiliary mode expansion (AME) method following Popescu and Croy [New J. Phys. 18, 093,944 (2016)] with a modified version of the diagonalization technique, combined with an effective account for the electrode level-width functions. The code can obtain the initial steady state, and propagate this initial steady state after application of a user-defined voltage bias-pulse applied to the electrodes using an explicit Runge-Kutta solver. Throughout this propagation, a user-defined density-dependence is needed, e.g. by interfacing to an external LCAO-DFT code. Such an interface is available for SIESTA and DFTB+, but can also be written by the user. Additional comments including restrictions and unusual features: The AME method does not have any restrictions on how fast oscillations can be, meaning it is valid for slow (e.g. THz fields) as well as fast (e.g. optical fields) perturbations. Simulations with normal-superconducting-normal type setups are also possible. In the current implementation, phonons cannot be included in the calculation, but the method does in theory allow for such [Y. Zhang, C. Y. Yam, G. Chen, J. Chem. Phys. 138 (16) (2013)].
    University Bibliography Jena:
    fsu_mods_00034615External link

  8. eminus — Pythonic electronic structure theory

    Authors
    W. Schulze, S. Schwalbe, K. Trepte, S. Gräfe
    Year of publication
    Published in:
    SoftwareX
    In current electronic structure research endeavors such as warm dense matter or machine learning applications, efficient development necessitates non-monolithic software, providing an extendable and flexible interface. The open-source idea offers the advantage of having a source code base that can be reviewed and modified by the community. However, practical implementations can often diverge significantly from their theoretical counterpart. Leveraging the efforts of recent theoretical formulations and the features of Python, we try to mitigate these problems. We present eminus, an education- and development-friendly electronic structure package designed for convenient and customizable workflows, yet built with intelligible and modular implementations.
    University Bibliography Jena:
    fsu_mods_00019240External link

  9. Towards simultaneous imaging of ultrafast nuclear and electronic dynamics in small molecules

    Authors
    S. Mhatre, Z. Dube, A. Staudte, S. Gräfe, M. Kübel
    Year of publication
    Published in:
    Scientific Reports
    When a chemical bond is broken, the molecular structure undergoes a transformation. An ideal experiment should probe the change in the electronic and nuclear structure simultaneously. Here, we present a method for the simultaneous time-resolved imaging of nuclear and electron dynamics by combining Coulomb explosion imaging with strong-field photoelectron momentum imaging. We study the dissociative photoionization of H₂ and N₂O using time-resolved photoion-photoelectron coincidence spectroscopy. The measured delay-dependent kinetic energy release clearly reveals the ultrafast nuclear dynamics. The transient changes in the electronic structure of the dissociating molecular ion are studied by solving the three-dimensional Schrödinger equation in the fixed-nuclei approximation. A detailed comparison of the numerical results to those from a simple imaging model is conducted. The numerical results reflect the evolution in the electron density in the molecular ion as its bond is first stretched and then breaks apart. While these details remain unresolved in the H₂ experiment, we demonstrate the sensitivity of the photoelectron signal to the site of electron localization following bond cleavage for the case of N₂O. Our work shows opportunities and challenges on the track towards capturing simple gas-phase chemical dynamics in complete molecular movies.
    University Bibliography Jena:
    fsu_mods_00023458External link

  10. Nonradiative transitions in molecular devices for energy conversion and storage

    Author
    C. Zens
    Year of publication
    University Bibliography Jena:
    fsu_mods_00026685External link

  11. Probing Metal Tip-Induced Bond Weakening of a Reactive Alkyne Center Aligned via a Rigid Triphenylmethane-Based Tripod on Au(111) by TERS and DFT

    Authors
    G. Li, S. Mennicken, L. Zhu, S. Ehtesabi, T. Reichenauer, S. Kupfer, D. Schäfer, S. Mehrparvar, G. Haberhauer, Y. Zhang, S. Gräfe, S. Schlücker, Z. Dong
    Year of publication
    Published in:
    Journal of Raman spectroscopy
    The chemical reactivity of molecules can be controlled by a variety of effects, ranging from chemical reagents to purely physical stimuli. Metal tips employed in scanning probe microscopy are an elegant tool to manipulate reactive centers in single molecules. However, to achieve excellent control over distance and orientation, it is crucial to immobilize the reactive center and align it along the direction of the tip. Here, we aligned a reactive alkyne center via a rigid triphenylmethane-based tripod for upright adsorption on Au(111) for inducing bond weakening in the alkyne moiety by approaching a silver tip. Single-molecule ultrahigh vacuum low-temperature tip-enhanced Raman scattering was employed for probing tip-induced bond weakening in the gap distance range from 550 to 250 pm. Both the ≡C–H stretching at ~3330 cm−¹ and the dominant –C≡C– stretching peak at ~2130 cm−¹ exhibit a shift to smaller wavenumbers due to tip-induced bond weakening and an exponential increase in Raman intensity originating from the increased local electric field in the nanogap. To rationalize the underlying physical contributions and chemical effects of tip-induced bond weakening, density functional theory calculations for gap distances in the range 800 to 100 pm were performed. The computational results confirmed the presence of different gap distance regimes including the onset of Pauli repulsion for short distances; for the latter, the calculations additionally predict structural distortions of the terminal alkyne induced by the nearby metal tip. These findings allow us to set a lower limit for the tip–tripod gap distance in studies requiring an intact upright configuration of the alkyne-tripod, for example, electric field-induced chemistry.
    University Bibliography Jena:
    fsu_mods_00029568External link

  12. Evaluating the contribution of electromagnetic nearfield gradients in TERS

    Authors
    A. Khodadadi, K. Fiederling, S. Kupfer, S. Gräfe
    Year of publication
    Published in:
    Optics communications : a journal devoted to the rapid publication of contributions in the field of optics and interaction of light with matter
    University Bibliography Jena:
    fsu_mods_00025747External link
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