arXiv subjects

Timo Jacob

Publications and source records attributed to Timo Jacob.

17 recordsLinked to original sources

arXiv2026

Computationally guided modifications of CviUPO to improve catalytic activity

Unspecific peroxygenases (UPOs) are promising biocatalysts that selectively oxyfunctionalize saturated hydrocarbons using only hydrogen peroxide as a co-substrate. Peroxide-induced enzyme inactivation makes targeted enzyme engineering essential to mitigate this effect and also enhance catalytic performance. To meet this need, systematic approaches are used, including extensive database studies for rational enzyme design, as well as computational enzyme engineering. In this study, we followed the latter strategy and explored the possibility for computationally-guided modification of UPOs. Specifically, our focus was on uncovering the influence of active site amino acids on the catalytic activity of the enzyme CviUPO. Two mutations were introduced close to the active center, and the changes in the energy barriers leading to the activated complex were investigated in detail by Quantum Mechanics/Molecular Mechanics Nudged Elastic Band simulations. Our studies revealed that a change of the glutamic acid, assisting the catalytic cycle, by the shorter aspartic acid, leads to an increased reaction barrier, probably decreasing the catalytic activity of the enzyme. Exchanging the heme-anchoring cysteine group by a histidine exhibited promising behavior as the energy barriers decreased significantly. However, it is possible that the histidine modification also alters the reaction behavior of the peroxygenase, turning it into a peroxidase, an aspect that so far could not be confirmed beyond doubt. Simulations alone cannot conclusively determine whether substrate specificity and reactivity are maintained in the modifications tested. Nevertheless, our results highlight the importance of spin states and active pocket hydration for the catalytic reaction and demonstrate why a synergistic approach of theoretical predictions and experimental verifications is required for efficient enzyme engineering.

physics.bio-ph↗

arXiv2026

Polarizable Embedding QM/MM for Periodic Systems

A general polarizable embedded (PE) quantum mechanics/molecular mechanics scheme for periodic systems is presented, describing mutual polarization of the two subsystems. The QM system, described with density functional theory (DFT), is coupled to a single center multipole expansion (SCME) model, characterising H$_2$O molecules in the MM region. In SCME the H$_2$O molecules are ascribed anisotropic dipole and quadrupole polarizabilities and permanent multipoles up to and including the hexadecapole. Our embedding scheme illustrates a smooth and efficient convergence pattern of the periodic interaction potential by introducing a single and clustered multipole expansion points in the far-field. By choosing the near- and far-field expansion of the potential carefully the PE-QM/MM calculation matches the level of accuracy of a the QM calculation. In the short range, the electrostatic interaction between the QM and MM subsystems is damped with a real-space and pair-wise isotropic damping functions - resulting in a screened interaction and preventing over-polarization. In molecular dynamics simulations the two subsystems are separated with the elastic scattering assisted flexible inner region [Kirchhoff et. al. JCTC, 2021, 17, 9, 5863] - ensuring a smooth transition in the radial distribution at the boundary between the two subsystems.

physics.chem-ph↗

arXiv2025

Phenylalanine modification in plasma-driven biocatalysis revealed by solvent accessibility and reactive dynamics in combination with protein mass spectrometry

Biocatalysis is an emerging field that provides an environmentally friendly alternative to conventional catalysis, but still it faces some challenges. One of the major difficulties for biocatalysts that require reactive species like H2O2 as co-substrates lies in the concentration of these reactive species. On the one hand, they are used as reactants, but on the other hand, they inactivate the enzymes at high concentrations. When utilizing non-thermal plasma to deliver H2O2 for biocatalysis, it is essential to understand the potential interactions between plasma-generated species (PGS) and enzymes. This is particularly important because, alongside \ch{H2O2}, other reactive species such as hydroxyl radicals, atomic oxygen, superoxide, and nitric oxide are also produced. The investigation of the localized reactivity of the solvent accessible surface area (SASA) of an enzyme, with certain species, is an important tool for predicting these interactions. In combination with reactive molecular dynamics (MD) simulations this enabled us to identify amino acid residues that are likely targets for modifications by the PGS. A subset of the theoretical predictions made in the present study were confirmed experimentally by mass spectrometry, underlining the utility of the SASA and MD based screening approach to direct time-consuming experiments and assist their interpretation.

physics.bio-ph↗

arXiv2025

Roadmap on Advancements of the FHI-aims Software Package

Electronic-structure theory is the foundation of the description of materials including multiscale modeling of their properties and functions. Obviously, without sufficient accuracy at the base, reliable predictions are unlikely at any level that follows. The software package FHI-aims has proven to be a game changer for accurate free-energy calculations because of its scalability, numerical precision, and its efficient handling of density functional theory (DFT) with hybrid functionals and van der Waals interactions. It treats molecules, clusters, and extended systems (solids and liquids) on an equal footing. Besides DFT, FHI-aims also includes quantum-chemistry methods, descriptions for excited states and vibrations, and calculations of various types of transport. Recent advancements address the integration of FHI-aims into an increasing number of workflows and various artificial intelligence (AI) methods. This Roadmap describes the state-of-the-art of FHI-aims and advancements that are currently ongoing or planned.

cond-mat.mtrl-sci↗

arXiv2025

Atomic-Scale Investigation of an Asymmetric SrTiO$_{3}$ Grain Boundary

Grain boundaries (GBs) in oxide perovskites significantly influence their functional properties. This study examines the atomic-scale structure and composition of a faceted asymmetric grain boundary in strontium titanate (SrTiO$_3$) using scanning transmission electron microscopy (STEM), atom probe tomography (APT), and density functional theory (DFT). STEM and APT reveal an atomically sharp boundary with asymmetric and symmetric facets, marked by strong Sr depletion over a width of less than 1 nm. STEM-EELS shows Ti concentration variations of up to 20% between facets, while APT constrains this variation to less than 10%. DFT$+U$ calculations of a symmetric ${\Sigma}$5 facet confirm that Sr depletion minimizes boundary energy while maintaining Ti content. The variation in Ti suggests cation mobility that enables local energy minimization. Differences in facet surface energies likely drive Ti redistribution, offering strategies for GB structure control. This combined experimental-theoretical approach provides key insights into the structure and energy landscape of GBs in SrTiO$_3$, aiding in the prediction of their impact on ionic and electronic transport.

cond-mat.mtrl-sci↗

arXiv2024

C-Pol: Point charge perturbation scheme for mapping tensor moment surfaces

We present an efficient moment-based perturbation scheme for evaluating polarizability tensors of small molecules at a fraction of the computational cost of conventional energy-based approaches. Rather than applying explicit electric fields, the method perturbs the molecular charge density using strategically arranged external point charges, as in QM/MM simulations, and extracts polarizability tensors from finite differences of multipole moments extrapolated to the zero-perturbation limit. C-Pol is implemented as a backend-agnostic Python package requiring only that the host quantum chemistry code support external point-charge potentials. We demonstrate interfaces with three codes spanning complementary numerical approaches: GPAW (real-space grids), NWChem, and PySCF (atom-centered basis sets with complete basis set extrapolation). Validation against Gaussian 16 energy-based reference calculations across molecules representing all 19 commonly occurring point groups yields agreement within 3%, with the largest deviations confined to tensor components that are numerically small and contribute negligibly to the electrostatic potential. Finite-difference polarizabilities computed via C-Pol are further shown to agree with analytic coupled-perturbed Hartree-Fock values to within 0.02 a.u. across all tested basis sets, at comparable computational cost for medium-sized systems and with more favorable scaling for larger ones. The package provides a practical and transferable route to high-quality multipole polarizability data for force field development, polarizable embedding, and machine-learning training sets.

physics.chem-ph↗

arXiv2024

Structural Influence on Exciton Formation and the Critical Role of Dark Excitons in Polymeric Carbon Nitrides

Polymeric carbon nitrides (PCNs) exhibit intriguing optical properties and exceptional performance in (photo)catalysis, optoelectronics, and energy storage. Nevertheless, the intricate phenomena involving light absorption extending to the visible range, long-lived excitons, photo-charging, and photochemical processes observed in PCN derivatives remain poorly understood. Our theoretical investigation elucidates the origin of distinct dark and bright excitons, their stability and lifetimes, and their correlation with the microstructural attributes of PCNs. Furthermore, we identify the decisive role of dark excitons in catalytic reactivity, which underlies the differences in the photocatalytic performance of different PCN derivatives.

cond-mat.mtrl-sci↗

arXiv2024

Unraveling the Optical Signatures of Polymeric Carbon Nitrides: Insights into Stacking-Induced Excitonic Transitions

Two-dimensional (2D) materials have attracted considerable attention due to their unique physicochemical properties and significant potential in energy-related applications. Polymeric carbon nitrides (PCNs) with 2D stacked architecture show promise as photocatalysts for solar-to-fuel conversion and as versatile 2D semiconductors. However, the lack of a clear definition of the exact structural model of these materials limits our fundamental understanding of their unique properties. Here, we investigate the structure-induced optical properties of PCNs through \textit{ab initio} calculations. Our study on the electronic and optical properties of PCNs highlights the significant influence of structure on their behavior, especially near band edges. The analysis reveals that the degree of condensation and corrugation influences the electron/hole localization and the energy levels of $\pi$ electrons, which are crucial for the optical behavior. In addition, the microstructures of 2D configurations lead to divergent optical properties in 3D configurations, with characteristic peaks identified at 350 nm and interlayer interactions ranging from 400 to 500 nm, depending on the specific microstructures. Through observations over 2D and 3D structures, we elucidate exciton photophysical processes in PCN materials. This highlights the substantial differences in optical properties between actual 2D and 3D structures, while also demonstrating the potential for carrier and energy transport mechanisms to occur perpendicular to the plane. Finally, our results provide deep insights into the understanding of previously hidden microstructural, electronic, and optical properties of PCNs, paving the way for further performance and property enhancements in this class of materials.

cond-mat.mtrl-sci↗

arXiv2023

In-Silico Characterization of Nanoparticle Catalysts

Nanoparticles (NPs) make for intriguing heterogeneous catalysts due to their large active surface area and excellent and often size-dependent catalytic properties that emerge from a multitude of chemically different surface reaction sites. NP catalysts are, in principle, also highly tunable: even small changes to the NP size or surface facet composition, doping with heteroatoms, or changes of the supporting material can significantly alter their physicochemical properties. Because synthesis of size- and shape-controlled NP catalysts is challenging, the ability to computationally predict the most favorable NP structures for a catalytic reaction of interest is an in-demand skill that can help accelerate and streamline the material optimization process. Fundamentally, simulations of NP model systems present unique challenges to computational scientists. Not only must considerable methodological hurdles be overcome in performing calculations with hundreds to thousands of atoms while retaining appropriate accuracy to be able to probe the desired properties. Also, the data generated by simulations of NPs are typically more complex than data from simulations of, for example, single crystal surface models, and therefore often requires different data analysis strategies. To this end, the present work aims to review analytical methods and data analysis strategies that have proven useful in extracting thermodynamic trends from NP simulations.

physics.chem-ph↗

arXiv2023

On the challenge of obtaining an accurate solvation energy estimate in simulations of electrocatalysis

The effect of solvent on the free energy of reaction intermediates adsorbed on electrocatalyst surfaces can significantly change the thermochemical overpotential, but accurate calculations of this are challenging. Here, we present computational estimates of the solvation energy for reaction intermediates in oxygen reduction reaction (ORR) on a B-doped graphene (BG) model system where the overpotential is found to reduce by up to 0.6 V due to solvation. BG is experimentally reported to be an active ORR catalyst but recent computational estimates using state-of-the-art hybrid density functionals in the absence of solvation effects have indicated low activity. To test whether the inclusion of explicit solvation can bring the calculated activity estimates closer to the experimental reports, up to 4 layers of water molecules are included in the simulations reported here. The calculations are based on classical molecular dynamics and local minimization of energy using atomic forces evaluated from electron density functional theory. Data sets are obtained from regular and coarse-grained dynamics, as well as local minimization of structures resampled from dynamics simulations. The results differ greatly depending on the method used and the solvation energy estimates and are deemed untrustworthy. It is concluded that a significantly larger number of water molecules is required to obtain converged results for the solvation energy. As the present system includes up to 139 atoms, it already strains the limits of computational feasibility, so this points to the need for a hybrid simulation approach where efficient simulations of much larger number of solvent molecules is carried out using a lower level of theory while retaining the higher level of theory for the reacting molecules as well as their near neighbors and the catalyst.

physics.chem-ph↗

arXiv2022

Structure and optical properties of polymeric carbon nitrides from atomistic simulations

Detailed understanding of the structural and photophysical properties of polymeric carbon nitride (PCN) materials is of critical importance to derive future material optimization strategies towards more desirable optical properties and more photocatalytically active materials. However, the wide range of structural motifs found in synthesized PCNs complicates atomistic simulations that rely on well defined models. Performing hybrid DFT studies, we systematically investigate formation energy trends and optical properties of PCNs as a function of dimensionality, going from molecular oligomers over periodic sheet models to stacked crystals. Thermochemical calculations that take into account vibrational enthalpy and entropy contributions predict that a mixture of structural motifs including the melon string structure, poly(heptazine imide), and g-C3N4 motifs is stable under typical synthetic conditions. The degree of lateral condensation as well as stacking can reduce the bandgap while out-of-plane corrugation of the material increases both stability and the optical gap. The key result of this work is that already small domains of strongly condensed PCN are calculated to give rise to favorable optical properties. This result reconciles conflicting literature reports indicating that the thermodynamically favorable melon motif has a too large bandgap compared to experiments, while the g-C3N4 structure, for which bandgap calculations are in better agreement with experiments, does not agree with measured chemical compositions of PCNs. Finally, we postulate a new computational model for carbon nitride materials that encompasses the most important structural motifs and shows a bandgap of ca. 2.9 eV.

cond-mat.mtrl-sci↗

arXiv2022

Simulations of the Electrochemical Oxidation of Pt Nanoparticles of Various Shapes

The activity and stability of a platinum nanoparticle (NP) is not only affected by its size but additionally depends on its shape. To this end, simulations can identify structure-property relationships to make a priori decisions on the most promising structures. While activity is routinely probed by electronic structure calculations on simplified surface models, modeling the stability of NP model systems in electrochemical reactions is challenging due to the long timescale of relevant processes such as oxidation beyond the point of reversibility. In this work, a routine for simulating electrocatalyst stability is presented. The procedure is referred to as GREG after its main ingredients - a grand-canonical simulation approach using reactive force fields to model electrochemical reactions as a function of the galvanic cell potential. The GREG routine is applied to study the oxidation of 3 nm octahedral, cubic, dodecahedral, cuboctahedral, spherical, and tetrahexahedral platinum NPs. The oxidation process is analyzed using adsorption isobars as well as interaction energy heat maps that provide the basis for constructing electrochemical phase diagrams. Onset potentials for surface oxidation increase in the sequence cube ~= dodecahedron <= octahedron <= tetrahexahdron < sphere < cuboctahedron, establishing a relationship between oxidation behavior and surface facet structure. The electrochemical results are rationalized using structural and electronic analysis.

physics.chem-ph↗

arXiv2021

Assessment of the Accuracy of Density Functionals for Calculating Oxygen Reduction Reaction on Nitrogen Doped Graphene

Experimental studies of the oxygen reduction reaction (ORR) at nitrogen doped graphene electrodes have reported a remarkably low overpotential, on the order of 0.5 V, similar to Pt based electrodes. Theoretical calculations using density functional theory have lent support for this claim. However, other measurements have indicated that transition metal impurities are actually responsible for the ORR activity, thereby raising questions about the reliability of both the experiments and the calculations. In order to assess the accuracy of the theoretical calculations, various generalized gradient approximation (GGA), meta-GGA and hybrid functionals are employed here and calibrated against high-level wave function based coupled cluster calculations (CCSD(T)) of the overpotential as well as self-interaction corrected density functional calculations and published quantum Monte Carlo calculations of O adatom binding to graphene. The PBE0 and HSE06 hybrid functionals are found to give more accurate results than the GGA and meta-GGA functionals, as would be expected, and for low dopant concentration, 3.1%, the overpotential is calculated to be 1.0 V. The GGA and meta-GGA functionals give a lower estimate by as much as 0.4 V. When the dopant concentration is doubled, the overpotential calculated with hybrid functionals drops, while it increases in GGA functional calculations. The opposite trends result from different potential determining steps, the *OOH species being of central importance in the hybrid functional calculations while the reduction of *O determines the overpotential obtained in GGA and meta-GGA calculations. The results presented here are mainly based on calculations of periodic representations of the system, but a comparison is also made with molecular flake models which are found to give erratic results.

cond-mat.mtrl-sci↗

arXiv2021

The modular Atom Probe Concept

Atomic probe tomography (APT), based on the work of Erwin Mueller, is able to generate three-dimensional chemical maps in atomic resolution. The required instruments for APT have evolved over the last 20 years from an experimental to an established method of materials analysis. Here, we describe the realization of a new instrument concept that allows the direct attachment of APT to a dual beam SEM microscope with the main achievement of fast and direct sample transfer. New operational modes are enabled regarding sample geometry, alignment of tips and microelectrode. The instrument is optimized to handle cryo-samples at all stages of preparation and storage. The instrument comes with its own software for evaluation and reconstruction. The performance in terms of mass resolution, aperture angle, and detection efficiency is demonstrated with a few application examples.

physics.ins-det↗

arXiv2021

Elastic Collision Based Dynamic Partitioning Scheme for Hybrid Simulations

The scattering-adapted flexible inner region ensemble separator (SAFIRES) is a partitioning scheme designed to divide a simulation cell into two regions to be treated with different computational methodologies. SAFIRES prevents particles from crossing between regions and resolves boundary events through elastic collisions of the particles mediated by the boundary, conserving energy and momenta. A multiple-time-step propagation algorithm is introduced where the time step is scaled automatically to identify the moment a collision occurs. If the length of the time step is kept constant, the new propagator reduces to a regular algorithm for Langevin dynamics, and to the velocity Verlet algorithm for classical dynamics if the friction coefficient is set to zero. SAFIRES constitutes the exact limit of the premise behind boundary-based methods such as FIRES, BEST, and BCC which take advantage of the indistinguishability of molecules on opposite sides of the separator. It gives correct average ensemble statistics despite the introduction of an ensemble separator. SAFIRES is tested in simulations where the molecules on the two sides are treated in the same way, for a Lennard-Jones (LJ) liquid and a LJ liquid in contact with a surface, as well as for liquid modelling simulations using the TIP4P force field. Simulations using SAFIRES are shown to reproduce the unconstrained reference simulations without significant deviations.

physics.chem-ph↗

arXiv2021

Surface states influence in the conductance spectra of Co adsorbed on Cu(111)

We calculate the conductance spectra of a Co atom adsorbed on Cu(111), considering the Co $3d$ orbitals within a correlated multiple configurations model interacting through the substrate band with the Co $4s$ orbital, which is treated in a mean-field like approximation. By symmetry, only the $d_{z^2}$ orbital couples with the $s$ orbital through the Cu bands, and the interference between both conduction channels introduces a zero-bias anomaly in the conductance spectra. We find that, while the Kondo resonance is mainly determined by the interaction of the Co $d$ orbitals with the bulk states of the Cu(111) surface, a proper description of the contribution given by the coupling with the localized surface states to the Anderson widths is crucial to describe the interference line shape. We find that the coupling of the Co $4s$ orbital with the Shockley surface states is responsible of two main features observed in the measured conductance spectra, the dip shape around the Fermi energy and the resonance structure at the surface state low band edge.

cond-mat.mes-hall↗

arXiv2021

Thermodynamic Description of Interfaces applying the 2PT method on ReaxFF Molecular Dynamics simulations

The interface between liquid water and the Pt(111) metal surface is characterized structurally and thermodynamically via reactive molecular dynamics (MD) simulations within the ReaxFF framework. The formation of a distinct buckled adsorbate layer and subsequent wetting layers is tracked via the course of the waters density as well as the distribution of the H2O molecules with increasing distance to the metal surface. Hereby, also the Two Phase Thermodynamics method (2PT) has been utilized for studying the course of entropy as well as the translational, rotational and vibrational entropic contributions throughout the Pt(111)/H2O interface. A significant reduction of the entropy compared to the bulk value is observed in the adsorbate layer ($S$ = 31.05$\pm$2.48\,J/molK ) along with a density of 3.26$\pm$0.06g/cm$^{3}$. The O-O interlayer distribution allows direct tracing of the water ordering and a quantified comparison to the ideal hexagonal adlayer. While the adsorbate layer at the Pt surface shows the occurrence of hexagonal motifs, this near-order is already weakened in the wetting layers. Bulk behavior is reached at 15$\mathrm{\mathring{A}}$ distance from the Pt(111) metal. Introducing an electric field of 0.1 V/$\mathrm{\mathring{A}}$ prolongs the ordering effect of the metal surface into the liquid water.

physics.chem-ph↗