arXiv subjects

Reinhard J. Maurer

Publications and source records attributed to Reinhard J. Maurer.

At least 37 records · Page 2Linked to original sources

arXiv2024

Nonadiabatic Quantum Dynamics of Molecules Scattering from Metal Surfaces

Nonadiabatic coupling between electrons and molecular motion at metal surfaces leads to energy dissipation and dynamical steering effects during chemical surface dynamics. We present a theoretical approach to the scattering of molecules from metal surfaces that incorporates all nonadiabatic and quantum nuclear effects due to the coupling of the molecular degrees of freedom to the electrons in the metal. This is achieved with the hierarchical equations of motion (HEOM) approach combined with a matrix product state representation in twin space. The method is applied to the scattering of nitric oxide from Au(111), for which strongly nonadiabatic energy loss during scattering has been experimentally observed, thus presenting a significant theoretical challenge. Since the HEOM approach treats the molecule-surface coupling exactly, it captures the interplay between nonadiabatic and quantum nuclear effects. Finally, the data obtained by the HEOM approach is used as a rigorous benchmark to assess various mixed quantum-classical methods, from which we derive insights into the mechanisms of energy dissipation and the suitable working regimes of each method.

physics.chem-ph↗

arXiv2024

One-step synthesis of graphene containing topological defects

Chemical vapour deposition enables large-domain growth of ideal graphene, yet many applications of graphene require the controlled inclusion of specific defects. We present a one-step chemical vapour deposition procedure aimed at retaining the precursor topology when incorporated into the grown carbonaceous film. When azupyrene, the molecular analogue of the Stone-Wales defect in graphene, is used as a precursor, carbonaceous monolayers with a range of morphologies are produced as a function of the copper substrate growth temperature. The higher the substrate temperature during deposition, the closer the resulting monolayer is to ideal graphene. Analysis, with a set of complementary materials characterisation techniques, reveals morphological changes closely correlated with changes in the atomic adsorption heights, network topology, and concentration of 5-/7-membered carbon rings. The engineered defective carbon monolayers can be transferred to different substrates, potentially enabling applications in nanoelectronics, sensorics, and catalysis.

cond-mat.mtrl-sci↗

arXiv2024

Equivariant Representation of Configuration-Dependent Friction Tensors in Langevin Heatbaths

Dynamics of coarse-grained particle systems derived via the Mori-Zwanzig projection formalism commonly take the form of a (generalized) Langevin equation with configuration-dependent friction and diffusion tensors. In this article, we introduce a class of equivariant representations of tensor-valued functions based on the Atomic Cluster Expansion (ACE) framework that allows for efficient learning of such configuration-dependent friction and diffusion tensors from data. Besides satisfying the correct equivariance properties with respect to the Euclidean group E(3), the resulting heat bath models satisfy a fluctuation-dissipation relation. Moreover, our models can be extended to include additional symmetries, such as momentum conservation, to preserve the hydrodynamic properties of the particle system. We demonstrate the capabilities of the model by constructing a model of configuration-dependent tensorial electronic friction calculated from first principles that arises during reactive molecular dynamics at metal surfaces.

cond-mat.mtrl-sci↗

arXiv2024

Integrated workflows and interfaces for data-driven semi-empirical electronic structure calculations

Modern software engineering of electronic structure codes has seen a paradigm shift from monolithic workflows towards object-based modularity. Software objectivity allows for greater flexibility in the application of electronic structure calculations, with particular benefits when integrated with approaches for data-driven analysis. Here, we discuss different approaches to create "deep" modular interfaces that connect big-data workflows and electronic structure codes, and explore the diversity of use cases that they can enable. We present two such interface approaches for the semi-empirical electronic structure package, DFTB+. In one case, DFTB+ is applied as a library and provides data to an external workflow; and in another, DFTB+ receives data via external bindings and processes the information subsequently within an internal workflow. We provide a general framework to enable data exchange workflows for embedding new machine-learning-based Hamiltonians within DFTB+, or to enabling deep integration of DFTB+ in multiscale embedding workflows. These modular interfaces demonstrate opportunities in emergent software and workflows to accelerate scientific discovery by harnessing existing software capabilities.

cond-mat.mtrl-sci↗

arXiv2024

Benchmarking of machine learning interatomic potentials for reactive hydrogen dynamics at metal surfaces

Simulations of chemical reaction probabilities in gas surface dynamics require the calculation of ensemble averages over many tens of thousands of reaction events to predict dynamical observables that can be compared to experiments. At the same time, the energy landscapes need to be accurately mapped, as small errors in barriers can lead to large deviations in reaction probabilities. This brings a particularly interesting challenge for machine learning interatomic potentials, which are becoming well-established tools to accelerate molecular dynamics simulations. We compare state-of-the-art machine learning interatomic potentials with a particular focus on their inference performance on CPUs and suitability for high throughput simulation of reactive chemistry at surfaces. The considered models include polarizable atom interaction neural networks (PaiNN), recursively embedded atom neural networks (REANN), the MACE equivariant graph neural network, and atomic cluster expansion potentials (ACE). The models are applied to a dataset on reactive molecular hydrogen scattering on low-index surface facets of copper. All models are assessed for their accuracy, time-to-solution, and ability to simulate reactive sticking probabilities as a function of the rovibrational initial state and kinetic incidence energy of the molecule. REANN and MACE models provide the best balance between accuracy and time-to-solution and can be considered the current state-of-the-art in gas-surface dynamics. PaiNN models require many features for the best accuracy, which causes significant losses in computational efficiency. ACE models provide the fastest time-to-solution, however, models trained on the existing dataset were not able to achieve sufficiently accurate predictions in all cases.

physics.chem-ph↗

arXiv2024

Predicting long timescale kinetics under variable experimental conditions with Kinetica.jl

Predicting the degradation processes of molecules over long timescales is a key aspect of industrial materials design. However, it is made computationally challenging by the need to construct large networks of chemical reactions that are relevant to the experimental conditions that kinetic models must mirror, with every reaction requiring accurate kinetic data. Here we showcase Kinetica.jl, a new software package for constructing large-scale chemical reaction networks in a fully-automated fashion by exploring chemical reaction space with a kinetics-driven algorithm; coupled to efficient machine-learning models of activation energies for sampled elementary reactions, we show how this approach readily enables generation and kinetic characterization of networks containing $\sim10^{3}$ chemical species and $10^{4}$ - $10^{5}$ reactions. Symbolic-numeric modelling of the generated reaction networks is used to allow for flexible, efficient computation of kinetic profiles under experimentally-realizable conditions such as continuously-variable temperature regimes, enabling direct connection between bottom-up reaction networks and experimental observations. Highly efficient propagation of long-timescale kinetic profiles is required for automated reaction network refinement and is enabled here by a new discrete kinetic approximation. The resulting Kinetica.jl simulation package therefore enables automated generation, characterization, and long-timescale modelling of complex chemical reaction systems. We demonstrate this for hydrocarbon pyrolysis simulated over timescales of seconds, using transient temperature profiles representing those of tubular flow reactor experiments.

physics.chem-ph↗

arXiv2024

First-principles Nonadiabatic Dynamics of Molecules at Metal Surfaces with Vibrationally Coupled Electron Transfer

Accurate description of nonadiabatic dynamics of molecules at metal surfaces involving electron transfer has been a longstanding challenge for theory. Here, we tackle this problem by first constructing high-dimensional neural network diabatic potentials including state crossings determined by constrained density functional theory, then applying mixed quantum-classical surface hopping simulations to evolve coupled electron-nuclear motion. Our approach accurately describes the nonadiabatic effects in CO scattering from Au(111) without empirical parameters and yields results agreeing well with experiments under various conditions for this benchmark system. We find that both adiabatic and nonadiabatic energy loss channels have important contributions to the vibrational relaxation of highly vibrationally excited CO(vi = 17), whereas relaxation of low vibrationally excited states of CO(vi = 2) is weak and dominated by nonadiabatic energy loss. The presented approach paves the way for accurate first-principles simulations of electron transfer mediated nonadiabatic dynamics at metal surfaces.

cond-mat.mtrl-sci↗

arXiv2023

The electrostatic potential of atomic nanostructures on a metal surface

The discrete and charge-separated nature of matter - electrons and nuclei - results in local electrostatic fields that are ubiquitous in nanoscale structures and are determined by their shape, material, and environment. Such fields are relevant in catalysis, nanoelectronics and quantum nanoscience, and their control will become even more important as the devices in question reach few-nanometres dimensions. Surface-averaging techniques provide only limited experimental access to these potentials at and around individual nanostructures. Here, we use scanning quantum dot microscopy to investigate how electric potentials evolve as nanostructures are built up atom by atom. We image the potential over adatoms, chains, and clusters of Ag and Au atoms on Ag(111) and quantify their surface dipole moments. By focusing on the total charge density, these data establish a new benchmark for ab initio calculations. Indeed, our density functional theory calculations not only show an impressive agreement with experiment, but also allow a deeper analysis of the mechanisms behind the dipole formation, their dependence on fundamental atomic properties and on the atomic configuration of the nanostructures. This allows us to formulate an intuitive picture of the basic mechanisms behind dipole formation, which enables better design choices for future nanoscale systems such as single atom catalysts.

cond-mat.mtrl-sci↗

arXiv2023

Machine learning interatomic potentials for reactive hydrogen dynamics at metal surfaces based on iterative refinement of reaction probabilities

Reactive chemistry of molecular hydrogen at surfaces, notably dissociative sticking and hydrogen evolution, plays a crucial role in energy storage and fuel cells. Theoretical studies can help to decipher underlying mechanisms and reaction design, but studying dynamics at surfaces is computationally challenging due to the complex electronic structure at interfaces and the high sensitivity of dynamics to reaction barriers. In addition, ab initio molecular dynamics, based on density functional theory, is too computationally demanding to accurately predict reactive sticking or desorption probabilities as it requires averaging over tens of thousands of initial conditions. High-dimensional machine learning-based interatomic potentials are starting to be more commonly used in gas-surface dynamics, yet, robust approaches to generate reliable training data and to assess how model uncertainty affects the prediction of dynamic observables are not well established. Here, we employ ensemble learning to adaptively generate training data while assessing model performance with full uncertainty quantification for reaction probabilities of hydrogen scattering on different copper facets. We use this approach to investigate the performance of two message-passing neural networks, SchNet and PaiNN. Ensemble-based uncertainty quantification and iterative refinement allow us to expose the shortcomings of the invariant pairwise-distance-based feature representation in the SchNet model for gas-surface dynamics.

physics.chem-ph↗

arXiv2023

libMBD: A general-purpose package for scalable quantum many-body dispersion calculations

Many-body dispersion (MBD) is a powerful framework to treat van der Waals (vdW) dispersion interactions in density-functional theory and related atomistic modeling methods. Several independent implementations of MBD with varying degree of functionality exist across a number of electronic structure codes, which both limits the current users of those codes and complicates dissemination of new variants of MBD. Here, we develop and document libMBD, a library implementation of MBD that is functionally complete, efficient, easy to integrate with any electronic structure code, and already integrated in FHI-aims, DFTB+, VASP, Q-Chem, CASTEP, and Quantum ESPRESSO. libMBD is written in modern Fortran with bindings to C and Python, uses MPI/ScaLAPACK for parallelization, and implements MBD for both finite and periodic systems, with analytical gradients with respect to all input parameters. The computational cost has asymptotic cubic scaling with system size, and evaluation of gradients only changes the prefactor of the scaling law, with libMBD exhibiting strong scaling up to 256 processor cores. Other MBD properties beyond energy and gradients can be calculated with libMBD, such as the charge-density polarization, first-order Coulomb correction, the dielectric function, or the order-by-order expansion of the energy in the dipole interaction. Calculations on supramolecular complexes with MBD-corrected electronic structure methods and a meta-review of previous applications of MBD demonstrate the broad applicability of the libMBD package to treat vdW interactions.

physics.chem-ph↗

arXiv2023

Assessing mixed quantum-classical molecular dynamics methods for nonadiabatic dynamics of molecules on metal surfaces

Mixed-quantum classical (MQC) methods for simulating the dynamics of molecules at metal surfaces have the potential to accurately and efficiently provide mechanistic insight into reactive processes. Here, we introduce simple two-dimensional models for the scattering of diatomic molecules at metal surfaces based on recently published electronic structure data. We apply several MQC methods to investigate their ability to capture how nonadiabatic effects influence molecule-metal energy transfer during the scattering process. Specifically, we compare molecular dynamics with electronic friction, Ehrenfest dynamics, Independent Electron Surface Hopping, and the Broadened Classical Master Equation approach. In the case of Independent Electron Surface Hopping, we implement a simple decoherence correction approach and assess its impact on vibrationally-inelastic scattering. Our results show that simple, low-dimensional models can be used to qualitatively capture experimentally observed vibrational energy transfer and provide insight into the relative performance of different MQC schemes. We observe that all approaches predict similar kinetic energy dependence, but return different vibrational energy distributions. Finally, by varying the molecule-metal coupling, we can assess the coupling regime in which some MQC methods become unsuitable.

physics.chem-ph↗

arXiv2023

Stability of Single Metal Atoms on Defective and Doped Diamond Surfaces

Polycrystalline boron-doped diamond (BDD) is widely used as a working electrode material in electrochemistry, and its properties, such as its stability, make it an appealing support material for nanostructures for electrocatalytic applications. Recent experiments have shown that electrodeposition can lead to the creation of stable small nanoclusters and even single metal adatoms on BDD surfaces. We investigate the adsorption energy and kinetic stability of single metal atoms adsorbed onto an atomistic model of BDD surfaces using density functional theory. The surface model is constructed using hybrid quantum/molecular mechanics embedding techniques and is based on an oxygen-terminated diamond (110) surface. We use the hybrid quantum mechanics/molecular mechanics method to assess the ability of different density-functional approximations to predict the adsorption structure, energy and the barrier for diffusion on pristine and defective surfaces. We find that surface defects (vacancies and surface dopants) strongly anchor metal adatoms on vacancy sites. We further investigate the thermal stability of metal adatoms, which reveals high barriers associated with lateral diffusion away from the vacancy site. The result provides an explanation for the high stability of experimentally imaged single metal adatoms on BDD and a starting point to investigate the early stages of nucleation during metal surface deposition.

cond-mat.mtrl-sci↗

arXiv2023

Characterizing Molecule-Metal Surface Chemistry with Ab-Initio Simulation of X-ray Absorption and Photoemission Spectra

X-ray photoemission and x-ray absorption spectroscopy are important techniques to characterize chemical bonding at surfaces and are often used to identify the strength and nature of adsorbate-substrate interactions. In this study, we judge the ability of x-ray spectroscopic techniques to identify different regimes of chemical bonding at metal-organic interfaces. To achieve this, we sample different interaction strength regimes in a comprehensive and systematic way by comparing two topological isomers, azulene and naphthalene, adsorbed on three metal substrates with varying reactivity, namely the (111) facets of Ag, Cu, and Pt. Using density functional theory, we simulate core-level binding energies and x-ray absorption spectra of the molecular carbon species. The simulated spectra reveal three distinct characteristics based on the molecule-specific spectral features which we attribute to types of surface chemical bonding with varying strength. We find that weak physisorption only leads to minor changes compared to the gas-phase spectra, weak chemisorption leads to charge transfer and significant spectral changes, while strong chemisorption leads to a loss of the molecule-specific features in the spectra. The classification we provide is aimed at assisting interpretation of experimental x-ray spectra for complex metal-organic interfaces.

cond-mat.mtrl-sci↗

arXiv2023

High-throughput property-driven generative design of functional organic molecules

The design of molecules and materials with tailored properties is challenging, as candidate molecules must satisfy multiple competing requirements that are often difficult to measure or compute. While molecular structures, produced through generative deep learning, will satisfy those patterns, they often only possess specific target properties by chance and not by design, which makes molecular discovery via this route inefficient. In this work, we predict molecules with (pareto)-optimal properties by combining a generative deep learning model that predicts three dimensional conformations of molecules with a supervised deep learning model that takes these as inputs and predicts their electronic structure. Optimization of (multiple) molecular properties is achieved by screening newly generated molecules for desirable electronic properties and reusing hit molecules to retrain the generative model with a bias. The approach is demonstrated to find optimal molecules for organic electronics applications. Our method is generally applicable and eliminates the need for quantum chemical calculations during predictions, making it suitable for high-throughput screening in materials and catalyst design.

physics.chem-ph↗

arXiv2023

Efficient implementation and performance analysis of the independent electron surface hopping method for dynamics at metal surfaces

Independent electron surface hopping (IESH) is a computational algorithm for simulating the mixed quantum-classical molecular dynamics of adsorbate atoms and molecules interacting with metal surfaces. It is capable of modelling the nonadiabatic effects of electron-hole pair excitations on molecular dynamics. Here we present a transparent, reliable, and efficient implementation of IESH, demonstrating its ability to predict scattering and desorption probabilities across a variety of systems, ranging from model Hamiltonians to full dimensional atomistic systems. We further show how the algorithm can be modified to account for the application of an external bias potential, comparing its accuracy to results obtained using the hierarchical quantum master equation. Our results show that IESH is a practical method for modelling coupled electron-nuclear dynamics at metal surfaces, especially for highly energetic scattering events.

physics.chem-ph↗

arXiv2022

Direct experimental evidence for substrate adatom incorporation into a molecular overlayer

While the phenomenon of metal substrate adatom incorporation into molecular overlayers is generally believed to occur in several systems, the experimental evidence for this relies on the interpretation of scanning tunnelling microscopy (STM) images, which can be ambiguous and provides no quantitative structural information. We show that surface X-ray diffraction (SXRD) uniquely provides unambiguous identification of these metal adatoms. We present the results of a detailed structural study of the Au(111)-F4TCNQ system, combining surface characterisation by STM, low energy electron diffraction and soft X-ray photoelectron spectroscopy with quantitative experimental structural information from normal incidence X-ray standing waves (NIXSW) and SXRD, together with dispersion corrected density functional theory (DFT) calculations. Excellent agreement is found between the NIXSW data and the DFT calculations regarding the height and conformation of the adsorbed molecule, which has a twisted geometry rather than the previously supposed inverted bowl shape. SXRD measurements provide unequivocal evidence for the presence and location of Au adatoms, while the DFT calculations show this reconstruction to be strongly energetically favoured.

cond-mat.mtrl-sci↗

arXiv2022

NQCDynamics.jl: A Julia Package for Nonadiabatic Quantum Classical Molecular Dynamics in the Condensed Phase

Accurate and efficient methods to simulate nonadiabatic and quantum nuclear effects in high-dimensional and dissipative systems are crucial for the prediction of chemical dynamics in condensed phase. To facilitate effective development, code sharing and uptake of newly developed dynamics methods, it is important that software implementations can be easily accessed and built upon. Using the Julia programming language, we have developed the NQCDynamics.jl package which provides a framework for established and emerging methods for performing semiclassical and mixed quantum-classical dynamics in condensed phase. The code provides several interfaces to existing atomistic simulation frameworks, electronic structure codes, and machine learning representations. In addition to the existing methods, the package provides infrastructure for developing and deploying new dynamics methods which we hope will benefit reproducibility and code sharing in the field of condensed phase quantum dynamics. Herein, we present our code design choices and the specific Julia programming features from which they benefit. We further demonstrate the capabilities of the package on two examples of chemical dynamics in condensed phase: the population dynamics of the spin-boson model as described by a wide variety of semi-classical and mixed quantum-classical nonadiabatic methods and the reactive scattering of H2 on Ag(111) using the Molecular Dynamics with Electronic Friction method. Together, they exemplify the broad scope of the package to study effective model Hamiltonians and realistic atomistic systems.

physics.chem-ph↗

arXiv2022

Thermodynamic Driving Forces for Substrate Atom Extraction by Adsorption of Strong Electron Acceptor Molecules

A quantitative structural investigation is reported, aimed at resolving the issue of whether substrate adatoms are incorporated into the monolayers formed by strong molecular electron acceptors deposited onto metallic electrodes. A combination of normal-incidence X-ray standing waves, low energy electron diffraction, scanning tunnelling microscopy and X-ray photoelectron spectroscopy measurements demonstrate that the systems TCNQ and F4TCNQ on Ag(100) lie at the boundary between these two possibilities and thus represent ideal model systems with which to study this effect. A room-temperature commensurate phase of adsorbed TCNQ is found not to involve Ag adatoms, but to adopt an inverted bowl configuration, long predicted but not previously identified experimentally. By contrast, a similar phase of adsorbed F4TCNQ does lead to Ag adatom incorporation in the overlayer, the cyano endgroups of the molecule being twisted relative to the planar quinoid ring. Density functional theory (DFT) calculations show that this behaviour is consistent with the adsorption energetics. Annealing of the commensurate TCNQ overlayer phase leads to an incommensurate phase that does appear to incorporate Ag adatoms. Our results indicate that the inclusion (or exclusion) of metal atoms into the organic monolayers is the result of both thermodynamic and kinetic factors.

cond-mat.mtrl-sci↗